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A Bayesian approach for evaluating the impact of historical events on rates of diversification
Abstract
Evolutionary biologists often wish to explore the impact of a particular historical event (e.g., the origin of a novel morphological trait, an episode of biogeographic dispersal, or the onset of an ecological association) on rates of diversification (speciation minus extinction). We describe a Bayesian approach for evaluating the correlation between such events and differential rates of diversification that relies on cross-validation predictive densities. This approach exploits estimates of the marginal posterior probability for the rate of diversification (in the unaffected part of the tree) and the marginal probability for the timing of the event to generate a predictive distribution of species diversity that would be expected had the event not occurred. The realized species diversity can then be compared to this predictive diversity distribution to assess whether rates of diversification associated with the event are significantly higher or lower than expected. Although simple, this Bayesian approach provides a robust inference framework that accommodates various sources of uncertainty, including error associated with estimates of divergence times, diversification-rate parameters, and event history. Furthermore, the proposed approach is relatively flexible, allowing exploration of various types of events (including changes in discrete morphological traits, episodes of biogeographic movement, etc.) under both hypothesis-testing and data-exploration inference scenarios. Importantly, the cross-validation predictive densities approach facilitates evaluation of both replicated and unique historical events. We demonstrate this approach with empirical examples concerning the impact of morphological and biogeographic events on rates of diversification in Adoxaceae and Lupinus, respectively.
... However, the mechanisms underlying this association remains elusive for many taxa. For instance, for plant clade Dipsacales, it was found that some increases in species diversification rates were associated with dispersal to new geographic areas [40,41]. Similarly, in Caribbean Anole lizards, it was found that diversification increases occurred after a lineage colonized an island above a certain island size [30,50]. ...
... This recent tendency to identify dispersals as drivers of biological diversification have increased with time (Figure 1). This tendency is related with the growing recognition of dispersal not only as a process able to generate congruent distributional patterns [11,49,61,72], but also as a driver of species diversification [41]. It seems that the traditional and senseless dispute about whether vicariance or dispersal explains biotic distribution is a thing of the past [34,49]. ...
... It is evident that dispersal and vicariance events can be associated, either in a narrative or quantitative way, with shifts in species diversification. The link can be inferred directly in some cases [4,41]; however, again the mechanisms operating behind these events are unknown. Although it is necessary to identify these evolutionary or ecological mechanisms, it is still not clear how these mechanisms can be disentangled. ...
... The implied shift in diversification rate along the stem lineage of /Primula was further corroborated by BAYESRATE [54] analyses, which reveal that the shift is owing to lower extinction rates (but similar speciation rates) in the heterostylous clade (/Primula) relative to the non-heterostylous grade (/Soldanella þ /Androsace), leading to higher net-diversification rates in the heterostylous clade (figure 3 and table 1; electronic supplementary material, figure S2 and table S3). The net effects of extinction-rate differences owing to the evolution of heterostyly in /Primula were further confirmed using crossvalidation predictive diversity densities (CVPDD) [55]. These results indicate that /Primula contains significantly more species than would be expected if the group had diversified under the background (non-heterostylous) diversification rate of /Soldanella and /Androsace (electronic supplementary material, figure S3). ...
... This method accommodates uncertainty in the inferred phylogeny, divergence times, speciation and extinction-rate parameters, and incorporated missing species by specifying the proportion of species sampled. The cross-validated posterior diversity densities approach [55] implemented in R was also used to test shifts in diversification. This approach does not require inference of extinction rates, which are notoriously difficult to estimate [56]. ...
The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower-pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evolution profoundly affects angiosperm diversification. However, consequences for speciation and extinction dynamics remain poorly understood. Here, we investigate trajectories of species diversification focusing on heterostyly, a remarkable floral syndrome where outcrossing is enforced via cross-compatible floral morphs differing in placement of their respective sexual organs. Heterostyly evolved at least 20 times independently in angiosperms. Using Darwin's model for heterostyly, the primrose family, we show that heterostyly accelerates species diversification via decreasing extinction rates rather than increasing speciation rates, probably owing to avoidance of the negative genetic effects of selfing. However, impact of heterostyly appears to differ over short and long evolutionary time-scales: the accelerating effect of heterostyly on lineage diversification is manifest only over long evolutionary time-scales, whereas recent losses of heterostyly may prompt ephemeral bursts of speciation. Our results suggest that temporal or clade-specific conditions may ultimately determine the net effects of specific traits on patterns of species diversification.
... Two contrasting evolutionary mechanisms might be invoked to explain how taxa respond to global temperature variation: "key innovations" involving intrinsic biotic factors, such as morphological or behavioral changes, can enable lineages to overcome abiotic stressors and enable novel niche invasions (Larridon et al., 2021;Moore and Donoghue, 2007). By contrast, "key opportunities" involve pre-existing adaptations that enable lineage survival in a changing abiotic environment, including climatic variation through time and biogeographical events (Moore and Donoghue, 2009;Donoghue and Sanderson, 2015). The essential difference between these is that a key innovation narrative implies agency on the part of species adapting to changing situations, whereas key opportunity narratives invoke species that are "in the right place at the right time" with traits preadapted for changing conditions. ...
Aim
Tropical rainforests harbour the richest biodiversity among terrestrial ecosystems, but few studies have addressed underlying processes of species diversification in these ecosystems. We use the pantropical and early divergent flowering plant family Annonaceae as a model system to investigate how abiotic factors such as climate and biogeographic events contribute to the diversification process and lead to its high diversity across a long evolutionary history.
Location
Tropics and subtropics
Taxon
Annonaceae
Methods
A super-matrix was constructed for 835 taxa (34% of Annonaceae species), based on eight chloroplast regions. To understand the patterns of diversification, we reconstructed climatic niche evolution and historical biogeographical events, and tested their association with diversification rates.
Results
The analysis of temperature-dependent models in Annonaceae lineages provides strong support for the significant influence of global temperature on net diversification and accumulation of species diversity. The pattern of lineage accumulation in the initial radiation is better aligned with the “museum model,” followed by later accumulation consistent with the “recent cradle model” from the late Oligocene to the present. The increase in the diversification rate of the family (around 25 Ma) lags behind the accumulation of niche divergences (around 15 Ma). Biogeographic events are related to only two of the five diversification rate shifts detected. While no direct relationship to shifts in the diversification rate was uncovered, shifts in niche evolution appear to be associated with increasingly seasonal environments.
Main Conclusions
Global temperature plays a crucial role in driving recent rapid diversification in the Annonaceae. Our study challenges the prevailing assumption of the “museum model” alone and proposes instead a transition from the “museum model” to the “recent cradle model” during the diversification history of the family. However, our findings do not support the direct correlation of any particular climatic niche shifts or historical biogeographical events with shifts in diversification rate. Instead, Annonaceae diversification can lead to later niche divergence as a result of increasing interspecific competition arising from species accumulation. The evolutionary direction of niche shifts furthermore provides insight into the future expansion of Annonaceae into temperate regions. Our results highlight the complexity of the diversification process in taxa with long evolutionary histories, indicating that identifying isolated driving factors is simplistic and inadequate for explaining the observed patterns. Further comprehensive analyses of range evolution are necessary to delve deeper into the interplay among key opportunities, key innovation, and species diversification.
... According to our molecular dating, current Ulex lineages, including most polyploids, diverged < 1 Mya (Figs 5, 6), as also supported by the low level of sequence variation among the plastid DNA regions analysed in this study and elsewhere (Ainouche et al., 2003). In addition, these divergence times may still be over-estimated given that the Lupinus/Genisteae divergence used as a secondary calibration in the dating of our phylogenetic tree might be more recent (Moore & Donoghue, 2009;Drummond et al., 2012). All evidence therefore points towards a recent diversification of Ulex spp. ...
Hybridization and polyploidy are key evolutionary forces in plant diversification, and their co-occurrence in the context of allopolyploid speciation is often associated with increased ability to colonize new environments and invasiveness. In the genus Ulex (Fabaceae), the European gorse (Ulex europaeus subsp. europaeus) is the only invasive and the only polyploid that has recently spread in different eco-geographical regions across the world. Understanding what confers such ecological advantages to this species, compared to its diploid and polyploid congeners, first requires clarification of the ecogeographical and evolutionary context of its formation. To achieve this, the geographical distributions of all Ulex spp. were estimated from species occurrence records, and phylogenetic analyses including all Ulex spp. were performed based on four nuclear (ITS and ETS nrDNA) and plastid (rps12 intron and trnK-matK) regions. The resulting trees were dated using a secondary calibration. Patterns of DNA sequence variation and dated phylogenetic trees were then interpreted in light of previous knowledge of chromosome numbers in Ulex to infer past events of polyploid speciation in the genus. We show that: (1) most current Ulex spp. radiated in the Iberian Peninsula during the past 1–2 Myr; (2) the history of Ulex was punctuated by multiple whole-genome duplication events; and (3) U. europaeus subsp. europaeus is the only gorse taxon that was formed by hybridization of two well-differentiated lineages (which separated c. 5 Mya) with wide climatic ranges (currently represented by Ulex minor and Ulex europaeus subsp. latebracteatus), possibly contributing to the invasive nature and wider climatic range of U. europaeus subsp. europaeus. These findings provide a much-needed evolutionary framework in which to explore the adaptive consequences of genome mergers and duplication in Ulex.
... However, even the very best of the competing models may nevertheless be woefully inadequate in an absolute sense. Accordingly, TESS implements methods to assess the absolute fit of a candidate diversification model to a given study tree using posterior-predictive simulation (Gelman et al., 1996;Bollback, 2002;Moore and Donoghue, 2009;Brown, 2014). The basic premise of this approach is as follows: if the diversification model under consideration provides an adequate description of the process that gave rise to our study tree, then we should be able to use that model to generate new phylogenies that are in some sense 'similar' to our study tree. ...
Many fundamental questions in evolutionary biology entail estimating rates of lineage diversification (speciation–extinction). We develop a flexible Bayesian framework for specifying an effectively infinite array of diversification models—where rates are constant, vary continuously, or change episodically through time—and implement numerical methods to estimate parameters of these models from molecular phylogenies, even when species sampling is incomplete. Additionally we provide robust methods for comparing the relative and absolute fit of competing branching-process models to a given tree, thereby providing rigorous tests of biological hypotheses regarding patterns and processes of lineage diversification.
... This genus is an excellent case study due to its broad distribution in the Americas at different elevational ranges. Exploring the diversification of specific groups is a key step to understand the origin of the diversity in species-rich regions as a whole (Moore & Donoghue, 2009). We rely on molecular dating of a densely sampled phylogenetic tree using secondary calibrations, historical biogeography with the dispersal-extinction-cladogenesis (DEC) model and distinct diversification approaches to address the following issues. ...
Evolutionary and ecological processes that influenced the assembly of the New World flora are best understood through investigation of spatio-temporal processes of specific lineages, but some groups still lack a historical overview. Here, we produced a well-sampled dated tree, reconstructed ancestral ranges and performed diversification analyses for Sisyrinchium (Iridaceae) to elucidate its evolution in the Americas. Eight molecular markers and samples representing its full geographical range and morphological diversity were used to estimate divergence times with a Bayesian relaxed clock with secondary calibrations. Ancestral range reconstruction under likelihood methods and diversification analyses were performed. Sisyrinchium originated in a broad range including the Andes and Mesoamerica in the Mid-Miocene. Diversification at high elevations occurred in the early diverging lineages, which feature the highest extinction rates. Increase in diversification rate was detected during the Pliocene/Pleistocene after the colonization of lower elevations. Later sympatric speciation in south-eastern Brazil was followed by movements to other regions, including a long-dispersal event to North America. Higher extinction rates were followed by movements to lower elevations, with periods of accelerated Andean orogeny and global temperature decrease. Our results indicate that palaeoclimate and changes in elevational range influenced diversification in Sisyrinchium.
... Besides, plant morphology, taxonomical values of the phytochemical amentoflavone isolated from Viburnum leaves and branchlets [19], as well as anatomical characteristics of fruits, cork, assimilating parenchyma, and leaf epidermal cells [20,21], were also assessed. More recently, assessments of Viburnum diversification have been made at a molecular level [3,4,8,22,23]. Clement et al. [24] proposed a Viburnum phyloge-netic classification and provided formal phylogenetic definitions for 30 clades. ...
The genus Viburnum (Adoxaceae, Dipsacales) is of scientific interest due to the chemical components and diverse biological activities found across species of the genus, which includes more than 230 species of evergreen, semievergreen, or deciduous shrubs and small trees. Although frequently used as an ornament, the Viburnum species show biological properties with health-promoting effects. Fruits, flowers, and barks of certain species are used for pharmaceutical purposes or as cooking ingredients, hence containing biochemical compounds with health-promoting activity such are carotenoids, polyphenols, and flavonoids. However, its taxonomical determination is difficult, due to its wide distribution and frequent hybridizations; therefore, an objective classification would allow us to understand its biological activity based on its phytochemical components. More than sixty phytochemical compounds have been reported, where vibsanin-type diterpenes and their derivatives are the most prevalent. Leaves and twigs of V. dilatatum contain the largest number of phytochemicals among the genus. Through preclinical evidence, this study provides insight regarding antioxidant, antibacterial, anti-inflammatory, cytotoxic, and anticancer activities of genus Viburnum.
... Structure cluster analysis use allelic and genotype data from multiple loci, such as SSR loci, to construct a cluster model. Structure 2.0 program was based on Bayesian probability theory, adopt Markov-Monte Carlo simulation algorithm, and used mixed model when running the program to reveal the unknown population genetic relationship and potential population Structure from all population levels 38 . The expected number of classification (K value) of the detected group was set at runtime, which can be used to divide all individuals and reflect Table 1. ...
The present study aimed to systematically evaluate the genetic diversity of Chinese domestic duck breeds and ensure the most effective allocation and usage of conservation funds. We first performed an analysis of DNA genetic distance in 21 duck breeds by measuring short tandem repeats. Then, we calculated the extinction probability, contribution rate, and marginal diversity for each breed. The results showed that the extinction rate of the Zhongshan duck, Guangxi duck, and Ji’an duck were the highest at 0.67, 0.59, and 0.59, respectively, and that of the Linwu duck, Jinding duck, and Gaoyou duck were the lowest at 0.15, 0.18, and 0.19, respectively. The current diversity of populations was 7.72 and the expected diversity in five hundred years is 5.14 ± 1.15. The marginal diversity of the Chinese Muscovy duck was the largest (−2.20), accounting for 42.61% of the expected diversity, followed by the Guangxi duck (−0.49, 9.44%), whereas the Jinding duck was the smallest (−0.12; 2.32%). The protection potency of the Chinese Muscovy duck was the largest (0.61), followed by Guangxi duck (0.29), whereas the Jinding duck was the smallest (0.02). This study provides a reference for determining the conservation priority of Chinese domestic duck breeds or genetic resources.
... Surprisingly, PHRAPL did not recover this scenario within a set of top-ranking delimitation models (ΔAIC range 0-2), with the best-fitting single-species model having a ΔAIC of 6.83 (Additional file 9: Table S1). This program extensively relies on "testing" species delimitation models that were initially suggested by the data, thus falling in danger of finding effects that are spurious because random noise is being modeled as structure [41,42]. In addition, PHRAPL requires estimation of gene trees prior to analysis; so uncertainties in gene tree estimation are not appropriately accounted for, affecting the statistical performance of this method [43]. ...
We report two host-specific lineages of scab mites of the genus Caparinia, parasitizing European and African hedgehogs. Based on morphology, these mite lineages are closely related sister groups. The morphological differences, however, are subtle and do not provide clear-cut evidence for the existence of separate species. CO1 divergence between these lineages was 7.4–7.8%, well above the CO1 barcoding gaps or thresholds commonly used to separate species, whereas divergence of five nuclear genes was very low, 0.06–0.53%, suggesting that these lineages could belong to a single species with gene flow between them. Thus, there is a conflict between the mitochondrial (CO1) gene and nuclear genes (i.e mito-nuclear discordance). We attribute this conflict to the ‘gray zone’ where species delimitation is ambiguous due to substantial gene flow. We also report another ‘gray zone’ species, Psoroptes ovis (a species of veterinary importance), whose within-species CO1 distances reached 6.0%. We provide a detailed morphological description and figures of C. ictonyctis stat. res. from the African hedgehog, using light and SEM microscopy and give morphometric data for this species and its sister species, Caparinia tripilis from Europe. For all known species of Caparinia, we document their host associations and give a key to species of the world based on results of our morphological and molecular analyses and a nearly exhaustive study of museum specimens.
... Surprisingly, PHRAPL did not recover this scenario within a set of top-ranking delimitation models (ΔAIC range 0-2), with the best-fitting single-species model having a ΔAIC of 6.83 (Additional file 9: Table S1). This program extensively relies on "testing" species delimitation models that were initially suggested by the data, thus falling in danger of finding effects that are spurious because random noise is being modeled as structure [41,42]. In addition, PHRAPL requires estimation of gene trees prior to analysis; so uncertainties in gene tree estimation are not appropriately accounted for, affecting the statistical performance of this method [43]. ...
Background: The cox1-barcoding approach is currently extensively used for high-throughput species delimitation and discovery. However, this method has several limitations, particularly when organisms have large effective population sizes. Paradoxically, most common, abundant, and widely distributed species may be misclassified by
this technique.
Results: We conducted species delimitation analyses for two host-specific lineages of scab mites of the genus Caparinia, having small population sizes. Cox1 divergence between these lineages was high (7.4–7.8%) while that of nuclear genes was low (0.06–0.53%). This system was contrasted with the medically important American house dust mite, Dermatophagoides farinae, a globally distributed species with very large population size. This species has two distinct, sympatric cox1 lineages with 4.2% divergence. We tested several species delimitation algorithms PTP, GMYC, ABGD, BPP, STACEY and PHRAPL, which inferred different species boundaries for these entities. Notably, STACEY recovered the Caparinia lineages as two species and D. farinae as a single species. BPP agreed with these
results when the prior on ancestral effective population sizes was set to expected values, although delimitation of Caparinia was still equivocal. No other cox1 species delimitation algorithms inferred D. farinae as a single species, despite the fact that the nuclear CPW2 gene shows some evidence for introgression between the cox1 groups. This indicates that the cox1-barcoding approach may result in excessive species splitting.
Conclusions: Our research highlights the importance of using nuclear genes and demographic characteristics to infer species boundaries rather than relying on a single-gene barcoding approach, particularly for putative species having large effective population sizes.
... Phylogeny-based statistical methods have been developed to detect shifts in diversification rate through time, such as tree-wide shifts in diversification rate associated with episodes of mass extinction or adaptive radiation (Stadler, 2010(Stadler, , 2011Morlon et al., 2011;Höhna et al., 2015;May et al., 2016), or diversity-dependent decreases in diversification rate associated with ecological limits on speciation (Rabosky and Lovette, 2008;Morlon et al., 2010;Höhna, 2014;Leventhal et al., 2014). Other methods seek to identify correlations between rates of diversification and some other variable, such as the evolution of discrete or continuous traits (Maddison et al., 2007;FitzJohn, 2010) or episodes of biogeographic or climatic change (Moore and Donoghue, 2009;Goldberg et al., 2011). Here, we focus on a third class of methods that seek to detect shifts in diversification rate along lineages of a phylogenetic tree (Moore et al., 2004;Chan and Moore, 2005;Rabosky et al., 2007;Alfaro et al., 2009;Rabosky, 2014). ...
Evolutionary biologists have long been fascinated by the extreme differences in species numbers across branches of the Tree
of Life. This has motivated the development of statistical methods for detecting shifts in the rate of lineage diversification
across the branches of phylogenic trees. One of the most frequently used methods, MEDUSA, explores a set of diversification-rate models, where each model assigns branches of the phylogeny to a set of diversification-rate
categories. Each model is first fit to the data, and the Akaike Information Criterion (AIC) is then used to identify the optimal
diversification model. Surprisingly, the statistical behavior of this popular method is uncharacterized, which is a concern
in light of: (1) the poor performance of the AIC as a means of choosing among models in other phylogenetic contexts; (2) the
ad hoc algorithm used to visit diversification models, and; (3) errors that we reveal in the likelihood function used to fit diversification
models to the phylogenetic data. Here, we perform an extensive simulation study demonstrating that MEDUSA (1) has a high false-discovery rate (on average, spurious diversification-rate shifts are identified ≈30% of the time), and
(2) provides biased estimates of diversification-rate parameters. Understanding the statistical behavior of MEDUSA is critical both to empirical researchers—in order to clarify whether these methods can make reliable inferences from empirical
datasets—and to theoretical biologists—in order to clarify the specific problems that need to be solved in order to develop
more reliable approaches for detecting shifts in the rate of lineage diversification.
... We inferred one significant mass-extinction event at 23 Ma (with very strong support) and two potential mass-extinction events (with positive but lower support).Chan & Moore 2005;Alfaro et al. 2009;Rabosky 2014). The second class of statistical phylogenetic methods is intended to detect significant correlations between diversification rate and some other variable, such as the evolution of discrete or continuous traits(Paradis 2005;Maddison, Midford & Otto 2007;FitzJohn, Maddison & Otto 2009;FitzJohn 2010) or episodes of biogeographic or climatic change(Moore & Donoghue 2009;Goldberg, Lancaster & Ree 2011;Condamine, Rolland & Morlon 2013). The final class of statistical phylogenetic methodsto which the CoMET model belongsis intended to detect shifts in diversification rate through time, such as treewide increases in diversification rate associated with episodes of adaptive radiation(Paradis , 1997(Paradis , , 1998Rabosky & Lovette 2008;Stadler , 2010Stadler , , 2011aMorlon et al. 2016), timedependent decreases in diversification rate associated with the species age(Rabosky 2006;Morlon, Potts & Plotkin 2010;Morlon, Parsons & Plotkin 2011;Paradis 2011;Lambert, Alexander & Stadler 2014), or diversity-dependent decreases in diversification rate associated with ecological limits on speciationH€ ohna 2014) ...
The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass‐extinction events on molecular phylogenies, even in the presence of tree‐wide diversification‐rate variation and in the absence of additional information from the fossil record.
Our approach is based on an episodic stochastic‐branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree‐wide shifts in speciation rate; (ii) instantaneous tree‐wide shifts in extinction rate and (iii) instantaneous tree‐wide mass‐extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event‐specific rate parameters. The magnitude of each event is drawn from an event‐specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible‐jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree‐wide diversification‐rate variation and mass‐extinction events by specifying a biologically informed prior on the magnitude of mass‐extinction events and empirical hyperpriors on the diversification‐rate parameters.
We demonstrate via simulation that this method has substantial power to detect the number of mass‐extinction events and provides unbiased estimates of the timing of mass‐extinction events, while exhibiting an appropriate (i.e. <5%) false‐discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction ≈23 Ma.
This new approach – the CPP on Mass‐Extinction Times ( CoMET ) model – provides an effective tool for detecting the impact of mass‐extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.
... The main difficulty would be obtaining a comprehensive sample of the large number of species that occur in remote localities (Thomas, 2010). If species representative of major Begonia clades were sequenced, new Bayesian analytical approaches could be applied, where diversification rates are estimated with incomplete species-level samples (Moore & Donoghue, 2009;Silvestro et al., 2011;Wertheim & Sanderson, 2011;Drummond et al., in press). The second barrier to this approach is the scarcity of fossil Begonia material (Stults & Axsmith, 2011) for calibrating a dated phylogeny. ...
Begonia L. is one of the largest plant genera, comprising over 1500 species. Weak species
cohesion, and the rapid evolution of reproductive barriers in allopatry, are two processes that
have been postulated to explain the generation of such hyper-diversity of taxa within a single
genus of plants. The aim of this thesis is to investigate whether these factors are likely to have
been important contributors to the diversity of species found in Central American Begonia.
Species cohesion was analysed in the widespread Central American species Begonia
heracleifolia and B. nelumbiifolia. Interpopulation seed flow was estimated with seven plastid
microsatellites. Breeding system estimates and measures of genetic differentiation at nine
nuclear microsatellites were used to infer levels of interpopulation pollen flow. Controlled
crosses were employed to assess the strength of reproductive barriers both between populations
within species, and between species differing in ecology. The potential for gene flow between
species in the wild was assessed in natural hybrid zones using molecular markers. Finally a
quantitative trait locus (QTL) approach was employed to investigate the genetic basis of
reproductive traits that differ between species. No plastid polymorphisms were found in B.
nelumbiifolia, suggesting it has been through a recent population bottleneck. In contrast, B.
heracleifolia possessed many plastid haplotypes that were strongly differentiated between
populations (G’ST = 0.829). Nuclear microsatellites showed high genetic differentiation within
species, and both species were self-compatible and self-fertilize at a moderate rate (B.
heracleifolia F’ST = 0.506, FIS = 0.249; B. nelumbiifolia F’ST = 0.439, FIS = 0.380). F1s between
ecologically similar B. heracleifolia and B. sericoneura were partly fertile (2-5% seed set), and
F1s and early generation backcrosses were found in a hybrid swarm. F1s between B.
heracleifolia and the ecologically contrasting B. nelumbiifolia were pollen sterile, and 3 hybrid
swarms showed no evidence of hybrids beyond the F1 generation. Seven QTL were found for
reproductive traits, including: sex ratio, pollen sterility and stamen number. The population
biology of Begonia, with limited seed and pollen dispersal, small population sizes and frequent
self-fertilization predisposes them to genetic isolation, increasing the chances that reproductive
barriers evolve. These characteristics may underlie the large number of endemics in Begonia.
... Further assessments may look at the disease agents as dynamic organisms that evolve, change, and adapt (14). Recently, Bayesian approaches, for example, have provided a new area for development through the assessment of genetic relations and evolution accounting by the effect of time, space, and relevant epidemiological variables (15,16). ...
Epidemiological methods are applied in veterinary science to investigate the dynamics, frequency, and determinants of diseases in populations of veterinary interest. This information is subsequently used to manipulate such determinants, with the ultimate objective of preventing, mitigating, or eliminating the impact of disease in susceptible populations (1). Because, for a given population-health problem, there are typically a number of alternative interventions available, economics, the science of making choices (2), is inherently related to veterinary epidemiology.
... According to our molecular dating, current Ulex lineages, including most polyploids, diverged < 1 Mya (Figs 5, 6), as also supported by the low level of sequence variation among the plastid DNA regions analysed in this study and elsewhere (Ainouche et al., 2003). In addition, these divergence times may still be over-estimated given that the Lupinus/Genisteae divergence used as a secondary calibration in the dating of our phylogenetic tree might be more recent (Moore & Donoghue, 2009;Drummond et al., 2012). All evidence therefore points towards a recent diversification of Ulex spp. ...
... Our genus-level approach could not demonstrate that these traits significantly increased species richness, perhaps due to limited statistical power (N = 27 southern hemisphere genera), but suggests those traits as candidates for species-level comparative analyses of single traits (e.g. (Maddison et al. 2007;Moore and Donoghue 2009), which are statistically more powerful but need this prior insight for choosing meaningful candidates. ...
Species selection occurs when species traits influence speciation or extinction. But it is often difficult to demonstrate a net effect of traits on diversification, for example due to balancing effects of extinction and speciation. We tested if, since conifers lost their former status of dominant land plants to angiosperm trees, their extant diversity shows a signature of traits conferring resistance to extinction. We compared extant species richness across conifer genera in relation to phenotypic and ecological traits predicted to affect speciation and/or extinction, in two geographic regions that experienced distinct regimes of extinction and species turnover (the northern vs. southern hemispheres). Species richness had low phylogenetic signal across conifer genera, and species-rich genera were not older than species-poor ones, indicating intrinsic differences in diversification. High-altitude genera, which are ecologically more dissimilar to angiosperm trees, were more species-rich, suggesting that distinctiveness from angiosperm competitors facilitated conifer diversification. This effect seems more due to increased speciation than to reduced extinction, because it was unique to northern hemisphere genera, where rates of extinction and species turnover have been higher than in the south. We found no strong evidence that resistance to extinction was the main mechanism of species selection in conifers. Instead, having a marginal ecological niche relative to angiosperm competitors facilitated diversification in conifers, likely due to increased speciation. Resistance to extinction may nonetheless have been important in certain ancient lineages, and we discuss suggestive results for traits that may explain the endurance of such lineages.
... Other approaches, pre-dating the SSE framework, also explicitly require replication. This includes sister-clade contrasts and tests that reconstruct separately the locations on the tree of character state changes and diversification shifts (Ree 2005;Moore and Donoghue 2009). These methods have their own inherent problems, notably how sister clades are chosen (Maddison 2006;Kafer and Mousset 2014) and how ancestral states are reconstructed. ...
Species richness varies widely across the tree of life, and there is great
interest in identifying ecological, geographic, and other factors that affect
rates of species proliferation. Recent methods for explicitly modeling the
relationships among character states, speciation rates, and extinction rates on
phylogenetic trees- BiSSE, QuaSSE, GeoSSE, and related models - have been
widely used to test hypotheses about character state-dependent diversification
rates. Here, we document the disconcerting ease with which neutral traits are
inferred to have statistically significant associations with speciation rate.
We first demonstrate this unfortunate effect for a known model assumption
violation: shifts in speciation rate associated with a character not included
in the model. We further show that for many empirical phylogenies, characters
simulated in the absence of state-dependent diversification exhibit an even
higher Type I error rate, indicating that the method is susceptible to
additional, unknown model inadequacies. For traits that evolve slowly, the root
cause appears to be a statistical framework that does not require replicated
shifts in character state and diversification. However, spurious associations
between character state and speciation rate arise even for traits that lack
phylogenetic signal, suggesting that phylogenetic pseudoreplication alone
cannot fully explain the problem. The surprising severity of this phenomenon
suggests that many trait-diversification relationships reported in the
literature may not be real. More generally, we highlight the need for
diagnosing and understanding the consequences of model inadequacy in
phylogenetic comparative methods.
... Analyses identifying the timing and primary drivers of diversification within particular clades can help evaluate these ideas, and delineate factors important for the process of speciation. New analytical methods have been developed for identifying particular nodes on a phylogeny where shifts in diversification rate have occurred (Chan and Moore, 2005;Rabosky et al., 2007;Moore and Donoghue, 2009;Alfaro et al., 2009) and for testing alternative models of diversification rate change (Rabosky, 2006a,b;Rabosky and Lovette, 2008a). ...
Understanding how and why lineages diversify is central to understanding the origins of biological diversity. The avian family Falconidae (caracaras, forest-falcons, falcons) has an uneven distribution of species among multiple well-supported clades, and provides a useful system for testing hypotheses about diversification rate and correlation with environmental changes. We analyzed ten independent loci for 1 to 7 individuals from each of the 64 currently recognized Falconidae species, together with two fossil falconid temporal calibrations, to assess phylogeny, absolute divergence times and potential shifts in diversification rate. Our analyses supported similar diversification ages in the Early to Middle Miocene for the three traditional subfamilies, Herpetotherinae, Polyborinae and Falconinae. We estimated that divergences within the subfamily Falconinae began about 16 mya and divergences within the most species-rich genus, Falco, including about 60% of all Falconidae species, began about 7.5 mya. We found evidence for a significant increase in diversification rate at the basal phylogenetic node for the genus Falco, and the timing for this rate shift correlates generally with expansion of C4 grasslands beginning around the Miocene/Pliocene transition. Concomitantly, Falco lineages that are distributed primarily in grassland or savannah habitats, as opposed to woodlands, and exhibit migratory, as opposed to sedentary, behavior experienced a higher diversification rate.
... For example, within the Lentago clade, V. nudum and V. cassinoides produce buds in which what appear to be the bud scales instead generally expand into normal vegetative leaves. In contrast, the related V. lentago produces bud scales that typically fall off as the shoot expands, though in this case various degrees of evolved within Sambucus ( Eriksson and Donoghue, 1997 ;Moore and Donoghue, 2009 ). ...
• Premise of the study: Despite recent progress, significant uncertainties remain concerning relationships among early‐branching lineages within Viburnum (Adoxaceae), prohibiting a new classification and hindering studies of character evolution and the increasing use of Viburnum in addressing a wide range of ecological and evolutionary questions. We hoped to resolve these issues by sequencing whole plastid genomes for representative species and combining these with molecular data previously obtained from an expanded taxon sample.
• Methods: We performed paired‐end Illumina sequencing of plastid genomes of 22 Viburnum species and combined these data with a 10‐gene data set to infer phylogenetic relationships for 113 species. We used the results to devise a comprehensive phylogenetic classification and to analyze the evolution of eight morphological characters that vary among early‐branching lineages.
• Key results: With greatly increased levels of confidence in most of the early branches, we propose a phylogenetic classification of Viburnum , providing formal phylogenetic definitions for 30 clades, including 13 with names recognized under the International Code of Nomenclature for Algae, Fungi, and Plants, eight with previously proposed informal names, and nine newly proposed names for major branches. Our parsimony reconstructions of bud structure, leaf margins, inflorescence form, ruminate endosperm, extrafloral nectaries, glandular trichomes, palisade anatomy, and pollen exine showed varying levels of homoplasy, but collectively provided morphological support for some, though not all, of the major clades.
• Conclusions: Our study demonstrates the value of next‐generation plastid sequencing, the ease of creating a formal phylogenetic classification, and the utility of such a system in describing patterns of character evolution.
... Thus transitions between aquatic and terrestrial habitats may play an important role in determining diversity patterns in hydrophilids. Indeed, the largest terrestrial clade (Sphaeridiinae+Rygmodinae) contains approximately 35% of all hydrophilid species, suggesting that a shift between aquatic and terrestrial habitats may have been a key event [sensu 30,31] that promoted an increase in diversification rates. However, investigations of aquatic-terrestrial habitat shifts across major lineages of insects and the role of these habitat transitions in determining diversity patterns remain understudied. ...
Explaining the disparity of species richness across the tree of life is one of the great challenges in evolutionary biology. Some lineages are exceptionally species rich, while others are relatively species poor. One explanation for heterogeneity among clade richness is that older clades are more species rich because they have had more time to accrue diversity than younger clades. Alternatively, disparity in species richness may be due to among-lineage diversification rate variation. Here we investigate diversification in water scavenger beetles (Hydrophilidae), which vary in species richness among major lineages by as much as 20 fold. Using a time-calibrated phylogeny and comparative methods, we test for a relationship between clade age and species richness and for shifts in diversification rate in hydrophilids. We detected a single diversification rate increase in Megasternini, a relatively young and species rich clade whose diversity might be explained by the stunning diversity of ecological niches occupied by this clade. We find that Amphiopini, an old clade, is significantly more species poor than expected, possibly due to its restricted geographic range. The remaining lineages show a correlation between species richness and clade age, suggesting that both clade age and variation in diversification rates explain the disparity in species richness in hydrophilids. We find little evidence that transitions between aquatic, semiaquatic, and terrestrial habitats are linked to shifts in diversification rates.
... The term "key innovation" refers to a character that is considered to be critically linked to the origin of a higher taxon or niche, lineage diversification, or adaptive radiation (reviewed by Hunter, 1998;Yoder et al., 2010). The connection of key innovations to these phenomena of biological diversifications has been, and continues to be, the subject of extensive theoretical discussion and numerous empirical or comparative phylogenetic studies (Cracraft, 1990;Slowinski and Guyer, 1993;Bond and Opell, 1998;Ree, 2005;Alfaro et al., 2009a;Moore and Donoghue, 2009;Drummond et al., 2012;Erkens et al., 2012). However, relatively little attention has been paid to the role of key innovations in phenotypic or morphological diversification. ...
Much research and discussion have focused on the effects of key innovations on lineage diversification, whereas little has been done to investigate their role in morphological evolution using phylogenetic approaches. Here we present the first comprehensive molecular phylogeny of the Harpactorini (Insecta: Reduviidae), the largest assassin bug tribe, sampling 229 terminal taxa and using five gene segments (28S D2, D3–D5, 16S, COI, and Deformed). Employing comparative phylogenetic methods, we demonstrate the correlation of a putative key innovation, the sticky trap predation strategy, with accelerated rates of morphological evolution of the predatory fore leg in assassin bugs. We show that bugs exhibiting sticky trap predation have evolved more slender and longer fore femora than non-sticky bugs. Using phylogenetically independent contrast analyses, we document correlated evolution between femoral thickness and length. We argue that the novel sticky trap predation strategy may allow sticky bugs to alleviate functional constraints on the fore femur and thus to attain a higher rate of evolution than other Harpactorini or Reduviidae. We discuss the possibility that sticky bugs represent a case of adaptive radiation. We also test historical supra-generic groups within the Harpactorini, and show that most of them are not monophyletic. We confirm the paraphyly of Harpactorini with respect to Rhaphidosomini.
... The genus Lupinus (Genisteae, Papilionoideae; c. 275 species) has emerged as a model system for testing species diversification rate shifts and understanding rapid species radiations in plants, and has already been the focus of four separate attempts to estimate diversification rates and locate rate shifts using different approaches based on a phylogeny that includes up to 122 species (46% taxon sampling) (Drummond et al., 2012;Hughes and Eastwood, 2006;Moore and Donoghue, 2009;Silvestro et al., 2011). Here these studies are extended by implementing a new BayesRate analysis of four tree partitions delimited on the basis of three diversification rate shifts found by a previous MEDUSA analysis (Drummond et al., 2012). ...
Whatever criteria are used to measure evolutionary success – species numbers, geographic range, ecological abundance, ecological and life history diversity, background diversification rates, or the presence of rapidly evolving clades – the legume family is one of the most successful lineages of flowering plants. Despite this, we still know rather little about the dynamics of lineage and species diversification across the family through the Cenozoic, or about the underlying drivers of diversification. There have been few attempts to estimate net species diversification rates or underlying speciation and extinction rates for legume clades, to test whether among-lineage variation in diversification rates deviates from null expectations, or to locate species diversification rate shifts on specific branches of the legume phylogenetic tree. In this study, time-calibrated phylogenetic trees for a set of species-rich legume clades – Calliandra, Indigofereae, Lupinus, Mimosa and Robinieae – and for the legume family as a whole, are used to explore how we might approach these questions. These clades are analysed using recently developed maximum likelihood and Bayesian methods to detect species diversification rate shifts and test for among-lineage variation in speciation, extinction and net diversification rates. Possible explanations for rate shifts in terms of extrinsic factors and/or intrinsic trait evolution are discussed. In addition, several methodological issues and limitations associated with these analyses are highlighted emphasizing the potential to improve our understanding of the evolutionary dynamics of legume diversification by using much more densely sampled phylogenetic trees that integrate information across broad taxonomic, geographical and temporal levels.
... Molecular phylogenies and the relaxed molecular clocks provide a framework for analyzing species diversification patterns and processes (Harvey & al., 1994;Nee, 2006;Moore & Donoghue, 2009). Statistical methods for inferring rates of speciation and extinction from time-calibrated phylogenies have seen dramatic developments over the past decade, and the trend shows no signs of abating (e.g.,Rabosky, 2006;Rabosky & al., 2007;Alfaro & al., 2009;Wertheim & Sanderson, 2010;Silvestro & al., 2011). ...
Biogeography is a multidisciplinary science concerned with how and why organisms are distributed as they are on Earth. It links fields such as systematics, ecology, paleontology, and climatology, and occupies a central position in evolutionary biology, being fundamental to the study of processes such as speciation and adaptive radiation. Here we provide a brief overview of some particularly dynamic areas of inquiry and offer some perspectives on future directions for the field. We hope that some historical debates, such as those over the importance of dispersal, or the validity of molecular dating, are finally being put to rest. Over the last decade, biogeography has become increasingly integrative, and has benefited from advances in statistical methods for inferring geographic range dynamics in a phylogenetic context, molecular estimation of lineage divergence times, and modeling lineage birth and death. These are enabling greater insights into patterns of organismal diversification in time and space. In the next decade, analytical challenges are emerging on several fronts. For example, phylogenies are increasing in size and taxonomic breadth and new sequencing technologies enabling phylogenetic and phylogeographic data sets are increasingly genomic in depth. In addition, geographic occurrence data are accumulating in online repositories, yet tools for data mining and synthetic analysis are lacking for comparative multi-lineage studies. Biogeography is thus entering an era characterized by phylogenomic data sets, increasingly comprehensive sampling of clades, and interdisciplinary synthesis. We anticipate continued progress in our understanding of biodiversity patterns at regional and global scales, but this will likely require greater collaboration with specialists in bioinformatics and computational science. Finally, it is clear that biogeography has an increasingly important role to play in the discovery and conservation of biodiversity. Lessons learned from biogeographic studies of islands are being applied to better understand extinction dynamics as continental ecosystems become more fragmented, and phylogeography and ecological niche modeling offer innovative paths toward the discovery of previously unknown species distributions and priority areas for conservation. The future of biogeography is bright and filled with exciting challenges and opportunities.
... What is important is to have comprehensive taxonomic sampling and to be able to include phylogenetic uncertainty into the statistical analyses. For example, Moore & Donoghue (2009) have taken into account the uncertainty in tree topology and divergence times to conclude that single-seeded fruits in Viburnum are associated with higher rates of diversification than other species of the family Adoxaceae. In contrast to trees reconstructed from DNA sequences, 'opinion-based' phylogenies provide no estimation of branch lengths and little information regarding phylogenetic uncertainty. ...
Ten years after DNA barcoding was initially suggested as a tool to identify species, millions of barcode sequences from more than one hundred thousand species are available in public databases. While several papers have reviewed the methods and potential applications of DNA barcoding, most have focused on species identification and discovery, and relatively few have addressed applications of DNA barcoding data to ecology. These data, and the associated information on the evolutionary histories of taxa that they can provide, offer great opportunities for ecologists to investigate questions that were previously difficult or impossible to address. We present an overview of potential uses of DNA barcoding relevant in the age of ecoinformatics, including applications in community ecology, species invasion, macroevolution, trait evolution, food webs and trophic interactions, metacommunities, and spatial ecology. We also outline some of the challenges and potential advances in DNA barcoding that lie ahead. This article is protected by copyright. All rights reserved.
... Punctual extinction or decreasing extinction rates might produce a similar pattern (Antonelli and Sanmartín, 2011b;Crisp and Cook, 2011;Stadler, 2013) that might not be associated to an increase in speciation in Hypericum in the páramos. These hypotheses need to be tested and compared to the influence of morphological, physiological, and spatiotemporal patterns to reveal causal cohesive motives underlying the observed extraordinary species richness (de Aguiar et al., 2009;Moore and Donoghue, 2009;Crisp et al., 2011;Stadler, 2011). ...
The páramos, high-elevation Andean grasslands ranging from ca. 2800 m to the snow line, harbor one of the fastest evolving biomes worldwide since their appearance in the northern Andes 3–5 million years (Ma) ago. Hypericum (St. John's wort), with over 65% of its Neotropical species, has a center of diversity in these high Mountain ecosystems. Using nuclear rDNA internal transcribed spacer (ITS) sequences of a broad sample of New World Hypericum species we investigate phylogenetic patterns, estimate divergence times, and provide the first insights into diversification rates within the genus in the Neotropics. Two lineages appear to have independently dispersed into South America around 3.5 Ma ago, one of which has radiated in the páramos (Brathys). We find strong support for the polyphyly of section Trigynobrathys, several species of which group within Brathys, while others are found in temperate lowland South America (Trigynobrathys s.str.). All páramo species of Hypericum group in one clade. Within these páramo Hypericum species enormous phenotypic evolution has taken place (life forms from arborescent to prostrate shrubs) evidently in a short time frame. We hypothesize multiple mechanisms to be responsible for the low differentiation in the ITS region contrary to the high morphological diversity found in Hypericum in the páramos. Amongst these may be ongoing hybridization and incomplete lineage sorting, as well as the putative adaptive radiation, which can explain the contrast between phenotypic diversity and the close phylogenetic relationships.
... Rapid radiations with increased rates of diversification, due to increased speciation rates and/or decreased rates of extinction, are generally considered to be influenced by intrinsic traits (so-called key innovations) or extrinsic events (so-called key opportunities) (Hodges, 1997;Moore and Donoghue, 2009;Vamosi and Vamosi, 2011). The emergence of morphological, physiological or behavioural novelties has been linked particularly to subsequent diversification [e.g. ...
Background and AimsTribe Arabideae are the most species-rich monophyletic lineage in Brassicaceae. More than 500 species are distributed in the majority of mountain and alpine regions worldwide. This study provides the first comprehensive phylogenetic analysis for the species assemblage and tests for association of trait and characters, providing the first explanations for the enormous species radiation since the mid Miocene.Methods
Phylogenetic analyses of DNA sequence variation of nuclear encoded loci and plastid DNA are used to unravel a reliable phylogenetic tree. Trait and ancestral area reconstructions were performed and lineage-specific diversification rates were calculated to explain various radiations in the last 15 Myr in space and time.Key ResultsA well-resolved phylogenetic tree demonstrates the paraphyly of the genus Arabis and a new systematic concept is established. Initially, multiple radiations involved a split between lowland annuals and mountain/alpine perennial sister species. Subsequently, increased speciation rates occur in the perennial lineages. The centre of origin of tribe Arabideae is most likely the Irano-Turanian region from which the various clades colonized the temperate mountain and alpine regions of the world.Conclusions
Mid Miocene early diversification started with increased speciation rates due to the emergence of various annual lineages. Subsequent radiations were mostly driven by diversification within perennial species during the Pliocene, but increased speciation rates also occurred during that epoch. Taxonomic concepts in Arabis are still in need of a major taxonomic revision to define monophyletic groups.
... At the other extreme, a single to few migration events could be followed by high in situ diversification . Furthermore, rates of diversification can be influenced by intrinsic morphological characteristics associated with particular species (i.e., " key innovations " such as plant elaiosomes; Forest et al. 2007), some extrinsic geological or environmental feature associated with the biogeographic region (e.g., episode of vicariance or the onset of an ecological association; Moore and Donoghue 2009), or some combination of both (e.g., adaptive radiation of morphotypes following colonization of a novel habitat; Baldwin and Sanderson 1998; Losos et al. 1998; Schluter 2000; Wagner et al. 2012). By estimating diversification rates using timecalibrated phylogenies, the likelihoods of diversification models with different rates for each biogeographic region, each taxonomic group, or a combination of both can be compared. ...
Broad-scale patterns of species diversity have received much attention in the literature, yet the mechanisms behind their formation may not explain species richness disparities across small spatial scales. Few taxa display high species diversity on either side of Wallace's Line and our understanding of the processes causing this biogeographical pattern remains limited, particularly in plant lineages. To understand the evolution of this biogeographical pattern, a time-calibrated molecular phylogeny of Livistoninae palms (Arecaceae) was used to infer the colonization history of the Sahul tectonic plate region and to test for disparities in diversification rates across taxa and across each side of Wallace's Line. Our analyses allowed us to examine how timing, migration history, and shifts in diversification rates have contributed to shape the biogeographical pattern observed in Livistoninae. We inferred that each of the three genera found in Sahul crossed Wallace's Line only once and relatively recently. In addition, at least two of the three dispersing genera underwent an elevation in their diversification rate leading to high species richness on each side of Wallacea. The correspondence of our results with Southeast Asian geologic and climatic history show how palms emerge as excellent models for understanding the historical formation of fine-scale biogeographic patterns in a phylogenetic framework.
... More recently, comparisons of absolute rates of diversification are used to relax the requirement that the clades being compared be the same age (Maddison et al. 2007, Magallón & Sanderson 2001, Moore & Donoghue 2009, Ree 2005. Ree (2005), for example, used a Bayesian phylogenetic approach to identify a significantly elevated rate of species diversification in the plant genus Aquilegia. ...
Adaptive radiation is a response to natural selection and ecological opportunity involving diversification of species and associated adaptations. Although evolutionary biologists have long speculated that adaptive radiation is responsible for most of life's diversity, persistent confusion and disagreement over some of its most fundamental questions have prevented it from assuming a central role in explaining the evolution of biological diversity. Today, answers to many of these questions are emerging from a new wave of integrative research that combines phylogenetic trees with a variety of other data and perspectives. In this review, I discuss how modern phylogenetic analyses are central to (a) defining and diagnosing adaptive radiation, (b)identifying the factors underlying the occurrence and scope of adaptive radiation, (c)diagnosing predictable patterns of ecological diversification during adaptive radiation, and (d) reconstructing the history of adaptive radiations.
Around 90 species of the genus Medicago , including important forage species (e.g., alfalfa), are widely distributed across Asia, Europe, and Africa. The evolutionary processes that allow its widespread radiation remain largely unknown. In this study, we constructed well-solved phylogenies for the genus based on a majority of known species using both genome-scale nuclear and plastome data. We demonstrated that spiral pods, which arose in the late Miocene in the ancient Mediterranean region, were likely a key innovation in this group and contributed its widespread radiation by decreasing extinction rates and facilitating long-distance dispersal so that species could occupy new niches. With repeated niche shifts, we showed that perennials evolved from annuals multiple times. We further revealed extensive hybridizations within the group that may have increased the ability of species to adapt during the colonization of novel habitats. These results provide an exceptional example of a widespread radiation of a globally important group driven by trait innovation and hybridization that are accompanied by niche expansion and life history shifts.
Premise:
Phylogenetic relationships within major angiosperm clades are increasingly well resolved, but largely informed by plastid data. Areas of poor resolution persist within the Dipsacales, including placement of Heptacodium and Zabelia, and relationships within the Caprifolieae and Linnaeeae, hindering our interpretation of morphological evolution. Here, we sampled a significant number of nuclear loci using a Hyb-Seq approach and used these data to infer the Dipsacales phylogeny and estimate divergence times.
Methods:
Sampling all major clades within the Dipsacales, we applied the Angiosperms353 probe set to 96 species. Data were filtered based on locus completeness and taxon recovery per locus, and trees were inferred using RAxML and ASTRAL. Plastid loci were assembled from off-target reads, and 10 fossils were used to calibrate dated trees.
Results:
Varying numbers of targeted loci and off-target plastomes were recovered from most taxa. Nuclear and plastid data confidently place Heptacodium with Caprifolieae, implying homoplasy in calyx morphology, ovary development, and fruit type. Placement of Zabelia, and relationships within the Caprifolieae and Linnaeeae, remain uncertain. Dipsacales diversification began earlier than suggested by previous angiosperm-wide dating analyses, but many major splitting events date to the Eocene.
Conclusions:
The Angiosperms353 probe set facilitated the assembly of a large, single-copy nuclear dataset for the Dipsacales. Nevertheless, many relationships remain unresolved, and resolution was poor for woody clades with low rates of molecular evolution. We favor expanding the Angiosperms353 probe set to include more variable loci and loci of special interest, such as developmental genes, within particular clades.
The Modern Synthesis (or “Neo‐Darwinism”), which arose out of the reconciliation of Darwin's theory of natural selection and Mendel's research on genetics, remains the foundation of evolutionary theory. However, since its inception, it has been a lightning rod for criticism, which has ranged from minor quibbles to complete dismissal. Among the most famous of the critics was Stephen Jay Gould, who, in 1980, proclaimed that the Modern Synthesis was “effectively dead.” Gould and others claimed that the action of natural selection on random mutations was insufficient on its own to explain patterns of macroevolutionary diversity and divergence, and that new processes were required to explain findings from the fossil record. In 1982, Charlesworth, Lande, and Slatkin published a response to this critique in Evolution, in which they argued that Neo‐Darwinism was indeed sufficient to explain macroevolutionary patterns. In this Perspective for the 75th Anniversary of the Society for the Study of Evolution, we review Charlesworth et al. (1982) in its historical context and provide modern support for their arguments. We emphasize the importance of microevolutionary processes in the study of macroevolutionary patterns. Ultimately, we conclude that punctuated equilibrium did not represent a major revolution in evolutionary biology – although debate on this point stimulated significant research and furthered the field – and that Neo‐Darwinism is alive and well.
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Chirostoma humbodtianum (Valenciennes, 1835), es una especie de pez blanco, endémica de México, habita de manera discontinua en sistemas lénticos desde el Estado de México hasta Nayarit, a lo largo de las cuencas del Río Lerma-Santiago. Esta especie tiene importancia biológica, económica y social ya que desde la época precolombina ha sido consumida por los habitantes de la región. Hoy en día, se han observado declives poblacionales aunados a fragmentación del hábitat, sobreexplotación, introducción de especies exóticas y contaminación de los lagos en el Valle de México. El objetivo del presente trabajo fue evaluar dos poblaciones silvestres (Tiacaque, Edo. México (T) y Tepuxtepec, Michoacán (Tx)) y realizar la fertilización in vitro de las mismas poblaciones que se encuentran en cautiverio en la Planta Experimental de Producción Acuícola (PExPA), con la finalidad de determinar la existencia de barreras reproductivas en la F1, su diversidad genética y morfológica, así como comparar la diversidad con las poblaciones silvestres y el lote reproductor; para orientar su manejo acuícola y contrarrestar la sobrexplotación
de la especie.
Se llevaron a cabo fertilizaciones in vitro a través de la extracción de gametos femeninos y
masculinos de organismos presentes de dos poblaciones en cautiverio en PExPA UAM-I.
(Tiacaque y Tepuxtepec). Se le dio seguimiento a la F1 durante el desarrollo temprano desde el momento de la activación del huevo hasta el periodo juvenil. Se cuantificó la sobrevivencia. El análisis morfológico, consistió en el registro del tamaño corporal (LT, LNC) y el peso de los peces (P). Los análisis genéticos consistieron en la evaluación, por medio de análisis de diversidad y estructura genética y análisis de parentesco, de una muestra de cada una de las poblaciones silvestres, los juveniles y reproductores con ocho loci microsatelitales nucleares.
La mayor sobrevivencia se presentó en la cruza de T ♀ X Tx ♂ con 17.47%, mientras que la
cruza de Tx♀ X T♂ fue de solo 3%. La población silvestre de Tepuxtepec presentó mayor número de heterocigotos (Tx; HE= 0.759), mientras que la F1 (PT) obtuvo el menor número de heterocigos en todas las poblaciones analizadas HE= 0.414. Todas las poblaciones mostraron un número significativo, positivo y alto en el coeficiente de endogamia (FIS). Se observó una fuerte estructura genética con tres pozas génicas diferenciadas (K=3), en donde las poblaciones silvestres T y Tx presentan cada una su propia poza génica, mientras que los individuos en cautiverio (reproductores y F1) comparten una misma poza génica con flujo génico entre ellas. La fuerte estructura poblacional y la pérdida de heterocigotos sugiere una tendencia hacia la adaptación al entorno cautivo, un proceso de efecto fundador y por lo tanto una pérdida de diversidad genética; mientras que en las poblaciones silvestres, la pérdida de variación genética puede ser debido a la fragmentación del hábitat, a eventos de cuello de botella, deriva génica y un bajo tamaño efectivo poblacional, relacionado con la historia evolutiva de la especie. Se sugiere, considerar estos resultados para orientar la eficiencia en las prácticas del manejo de la especie tanto en cautiverio como en las poblaciones silvestres.
Phylogeny, molecular sequences, fossils, biogeography, and biome occupancy are all lines of evidence that reflect the singular evolutionary history of a clade, but they are most often studied separately, by first inferring a fossil-dated molecular phylogeny, then mapping on ancestral ranges and biomes inferred from extant species. Here we jointly model the evolution of biogeographic ranges, biome affinities, and molecular sequences, while incorporating fossils to estimate a dated phylogeny for all of the 163 extant species of the woody plant clade Viburnum (Adoxaceae) that we currently recognize in our ongoing worldwide monographic treatment of the group. Our analyses indicate that while the major Viburnum lineages evolved in the Eocene, the majority of extant species originated since the Miocene. Viburnum radiated first in Asia, in warm, broad-leaved evergreen (lucidophyllous) forests. Within Asia we infer several early shifts into more tropical forests, and multiple shifts into forests that experience prolonged freezing. From Asia we infer two early movements into the New World. These two lineages probably first occupied warm temperate forests and adapted later to spreading cold climates. One of these lineages (Porphyrotinus) occupied cloud forests and moved south through the mountains of the Neotropics. Several other movements into North America took place more recently, facilitated by prior adaptations to freezing in the Old World. We also infer four disjunctions between Asia and Europe: the Tinus lineage is the oldest and probably occupied warm forests when it spread, while the other three were more recent and in cold-adapted lineages. These results variously contradict published accounts, especially the view that Viburnum radiated initially in cold forests and, accordingly, maintained vessel elements with scalariform perforations. We explored how the location and biome assignments of fossils affected our inference of ancestral areas and biome states. Our results are sensitive to, but not entirely dependent upon, the inclusion of fossil biome data. It will be critical to take advantage of all available lines of evidence to decipher events in the distant past. The joint estimation approach developed here provides cautious hope even when fossil evidence is limited.
Evolutionary innovation contributes to the spectacular diversity of species and phenotypes across the tree of life. ‘Key innovations’ are widely operationalized within evolutionary biology as traits that facilitate increased diversification rates, such that lineages bearing the traits ultimately contain more species than closely related lineages lacking the focal trait. In this article, I briefly review the inference, analysis and interpretation of evolutionary innovation on phylogenetic trees. I argue that differential rates of lineage diversification should not be used as the basis for key innovation tests, despite the statistical tractability of such approaches. Under traditional interpretations of the macroevolutionary ‘adaptive zone’, we should not necessarily expect key innovations to confer faster diversification rates upon lineages that possess them relative to their extant sister clades. I suggest that a key innovation is a trait that allows a lineage to interact with the environment in a fundamentally different way and which, as a result, increases the total diversification—but not necessarily the diversification rate—of the parent clade. Considered alone, branching patterns in phylogenetic trees are poorly suited to the inference of evolutionary innovation due to their inherently low information content with respect to the processes that produce them. However, phylogenies may be important for identifying transformational shifts in ecological and morphological space that are characteristic of innovation at the macroevolutionary scale.
This article is part of the themed issue ‘Process and pattern in innovations from cells to societies’.
Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks (GRNs, used here in a broad sense incorporating not just the genetic circuitry per se but the factors controlling the timing and location of gene expression and repression), the non-linear relation between magnitude of genetic change and the phenotypic results, the evolutionary potential of co-opting existing GRNs, and developmental responsiveness to nongenetic signals (i.e. epigenetics and plasticity), all requiring modification of standard microevolutionary models, and rendering difficult any simple definition of evolutionary novelty. The developmental factors underlying macroevolution create anisotropic probabilities—i.e., an uneven density distribution—of evolutionary change around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. From this standpoint, “punctuated equilibrium” and “phyletic gradualism” simply represent two cells in a matrix of evolutionary models of phenotypic change, and the origin of trends and evolutionary novelty are not simply functions of ecological opportunity. Over long timescales, contingency becomes especially important, and can be viewed in terms of macroevolutionary lags (the temporal separation between the origin of a trait or clade and subsequent diversification); such lags can arise by several mechanisms: as geological or phylogenetic artifacts, or when diversifications require synergistic interactions among traits, or between traits and external events. The temporal and spatial patterns of the origins of evolutionary novelties are a challenge to macroevolutionary theory; individual events can be described retrospectively, but a general model relating development, genetics, and ecology is needed. An accompanying paper (Jablonski in Evol Biol 2017) reviews diversity dynamics and the sorting of variation, with some general conclusions.
In entomogamous plants, the presence and function of floral secretory structures, whose main role is to attract pollinators, is strictly associated with the pollination ecology and hence the reproductive success of the plant. The aims of the present paper were to analyse the micromorphology and anatomy of flower nectaries and stigmas in Viburnum opulus and V. lantana and to determine the function and microstructure of inflorescence trichomes in both taxa using light and scanning electron microscopy as well as histochemical assays. It was found that stigmas were formed by papillae, which contained lipids, polysaccharides, tannins, and pigments. Stigmatic secretion proceeded via cuticular pores. Floral nectaries formed a thick layer around the styles, and nectar was secreted through numerous nectarostomata. There were no traces of vascular bundles penetrating the nectary tissue. In turn, numerous tannin deposits were observed in the cells of the glandular parenchyma. Pedicels, hypanthia, and bracts had mainly peltate and capitate glandular trichomes as well as stellate non-glandular trichomes (in V. lantana). The trichomes were shown to contain lipids, mucilage, and tannins. Many similarities in the flower and nectaries microstructure and considerable heterogeneity were observed in the examined Viburnum species. Knowledge of the microstructural characteristics of flowers, nectaries, and trichomes may be important for the phylogenesis and taxonomy of the genus Viburnum and the family Adoxaceae. Additionally, floral and nectaries features are helpful in assessment of the relatedness between taxa and provide better understanding of the floral biology and pollination ecology.
A cytological study was carried out on 16 taxa belonging to seven clades of Viburnum (Adoxaceae). Chromosome numbers of these 16 taxa were counted and karyotypes of 12 taxa were analyzed. Chromosome numbers of four species and karyotypes of nine taxa are new records. Three chromosome numbers 2n = 16, 18 and 32 of these 16 taxa were discovered, of which the corresponding basic chromosome number was x = 8 or 9. Most taxa showed relatively symmetrical karyotypes, while the well-known V. macrocephalum form. keteleeri, which has a long cultivation history and is culturally important in China, presented the most asymmetrical karyotype. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis of V. cylindricum and V. punctatum supports the recognized clades Coriacea and Punctata that were previously subsections of Megalotinus. The chromosomal pattern with few polyploids suggests that structural changes of karyotype at the diploid level may be the main trend in chromosomal evolution in Viburnum.
Paleontologists and biologists are often interested in the tempo of evolution: how fast or slow does evolution proceed? There are many separate components of evolution – the development and extinction of lineages, molecular change, and morphological transformation are three of the most general – and these may or may not be related to each other. Therefore, it is instructive to look at each of these separately (if possible), in order to gain a more nuanced understanding of evolutionary change. This chapter will focus specifically on morphological evolution: changes in size, shape, and discrete anatomical features and how rates of change can be calculated. Such calculations have a rich legacy in the macroevolution literature (e.g., Westoll 1949; Derstler 1982; Forey 1988; Cloutier 1991; Ruta et al. 2006; Brusatte et al. 2008a).
We used a near-complete phylogeny for the angiosperm clade Viburnum to assess lineage diversification rates, and to examine possible morphological and ecological factors driving radiations. Maximum-likelihood and Bayesian approaches identified shifts in diversification rate and possible links to character evolution. We inferred the ancestral environment for Viburnum and changes in diversification dynamics associated with subsequent biome shifts. Viburnum probably diversified in tropical forests of Southeast Asia in the Eocene, with three subsequent radiations in temperate clades during the Miocene. Four traits (purple fruits, extrafloral nectaries, bud scales and toothed leaves) were statistically associated with higher rates of diversification. However, we argue that these traits are unlikely to be driving diversification directly. Instead, two radiations were associated with the occupation of mountainous regions and a third with repeated shifts between colder and warmer temperate forests. Early-branching depauperate lineages imply that the rare lowland tropical species are 'dying embers' of once more diverse lineages; net diversification rates in Viburnum likely decreased in these tropical environments after the Oligocene. We suggest that 'taxon pulse' dynamics might characterize other temperate plant lineages.
© 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.
Fabre, P.-H., Galewski, T., Tilak, M.-k. & Douzery, E.J.P. (2012) Diversification of South American spiny rats (Echimyidae): a multigene phylogenetic approach. —Zoologica Scripta, 00, 000–000.
We investigated the phylogenetic relationships of 14 Echimyidae (spiny rats), one Myocastoridae (nutrias) and one Capromyidae (hutias) genera based on three newly sequenced nuclear genes (APOB, GHR and RBP3) and five previously published markers (the nuclear RAG1 and vWF, and the mitochondrial cytochrome b, 12S rRNA and 16S rRNA). We recovered a well-supported phylogeny within the Echimyidae, although the evolutionary relationships among arboreal echimyid taxa remain unresolved. Molecular divergence times estimated using a Bayesian relaxed molecular clock suggest a Middle Miocene origin for most of the extant echimyid genera. Echimyidae seems to constitute an example of evolutionary radiation with high species diversity, yet they exhibit only narrow skull morphological changes, and the arboreal and terrestrial taxa are shown to retain numerous plesiomorphic features. The most recent common ancestor of spiny rats is inferred to be a ground-dwelling taxon that has subsequently diverged into fossorial, semiaquatic and arboreal habitats. The arboreal clade polytomy and ancestral character estimations suggest that the colonization of the arboreal niche constituted the keystone event of the echimyid radiation. However, biogeographical patterns suggest a strong influence of allopatric speciation in addition to ecology-driven diversification among South American spiny rats.
Testing whether a certain biological trait significantly affects clade diversification is central to macroevolutionary research. To this end, many scientists use constant-rate estimators (CR estimators) of diversification. However, it has never been examined whether these estimators report meaningful relationships between traits and diversification even when the diversification itself decelerates over time. In this study, I simulate trait-driven diversification concurrently with diversification slowdowns. Then, I test whether CR estimators manage to uncover the simulated relationships. Results suggest that CR estimators are robust against violation of rate constancy and successfully detect trait-dependent diversification in spite of diversification declines. Interestingly, correct results were recovered whether clade age correlated with clade diversity or not. Further comparison of CR estimators with QuaSSE suggested that QuaSSE performs better under constant diversification, but tends to report spuriously significant outcomes when diversification decelerates (=elevated Type I error). Given that diversification slowdowns have been recently reported for a wide range of taxa, these findings may be of particular relevance for future diversification studies.
This study marks a significant increase in the number of species and genetic loci used in reconstructing the phylogeny of Viburnum. In particular, we expanded sampling of the morphologically heterogeneous section Megalotinus of Southeast Asia, which to date has been represented by only one species. Our results provide increased support for the monophyly of most of the previously named clades and for relationships within them. However, the four subsections of Megalotinus are placed with confidence in widely separate places in the phylogeny, and their disparate relationships are supported by morphological characters including branching patterns, inflorescence types, and trichomes. These findings, along with the phylogenetic placement of several additional Southeast Asian species, are critical in assessing the ancestral condition of Viburnum inflorescence architecture and endocarp shape. Our results also highlight a new biogeographic possibility, namely that Viburnum may have originated and initially diversified in montane subtropical forests in Southeast Asia and later moved into northern temperate forests, which most of them are associated with today. This study provides a clear-cut example of the importance of including in phylogenetic studies rare and difficult-to-obtain species from outside the main centers of diversity and of the value of dismantling nonmonophyletic taxonomic groups.
With increases in both the size and scope of phylogenetic trees, we are afforded a renewed opportunity to address long-standing comparative questions, such as whether particular fruit characters account for much of the variation in diversity among flowering plant clades. Studies to date have reported conflicting results, largely as a consequence of taxonomic scale and a reliance on potentially conservative statistical measures. Here we examine a larger and older angiosperm clade, the Campanulidae, and infer the rates of character transitions among the major fruit types, emphasizing the evolution of the achene fruits that are most frequently observed within the group. Our analyses imply that campanulids likely originated bearing capsules, and that all subsequent fruit diversity was derived from various modifications of this dry fruit type. We also found that the preponderance of lineages bearing achenes is a consequence of not only being a fruit type that is somewhat irreversible once it evolves, but one that also seems to have a positive association with diversification rates. Although these results imply the achene fruit type is a significant correlate of diversity patterns observed across campanulids, we conclude that it remains difficult to confidently and directly view this character state as the actual cause of increased diversification rates.
Aim We use parametric biogeographical reconstruction based on an extensive DNA sequence dataset to characterize the spatio‐temporal pattern of colonization of the Old World monarch flycatchers (Monarchidae). We then use this framework to examine the role of dispersal and colonization in their evolutionary diversification and to compare plumages between island and continental Terpsiphone species.
Location Africa, Asia and the Indian Ocean.
Methods We generate a DNA sequence dataset of 2300 bp comprising one nuclear and three mitochondrial markers for 89% (17/19) of the Old World Monarchidae species and 70% of the Terpsiphone subspecies. By applying maximum likelihood and Bayesian phylogenetic methods and implementing a Bayesian molecular clock to provide a temporal framework, we reveal the evolutionary history of the group. Furthermore, we employ both L agrange and Bayes ‐ L agrange analyses to assess ancestral areas at each node of the phylogeny. By combining the ancestral area reconstruction with information on plumage traits we are able to compare patterns of plumage evolution on islands and continents.
Results We provide the first comprehensive molecular phylogenetic reconstruction for the Old World Monarchidae. Our phylogenetic results reveal a relatively recent diversification associated with several dispersal events within this group. Moreover, ancestral area analyses reveal an Asian origin of the Indian Ocean and African clades. Ancestral state reconstruction analyses of plumage characters provide an interpretation of the plumage differentiation on islands and continents. Ancestral plumage traits are inferred to be close to those of the Asian paradise‐flycatcher ( Terpsiphone paradisi ), and island species display a high degree of plumage autapomorphy compared with continental species.
Main conclusions Terpsiphone paradisi is polyphyletic and comprises populations that have retained the ancestral plumage of the widespread Terpsiphone genus. The genus appears to have colonized south‐west Asia, the Indian Ocean and Africa from eastern Asia. The phylogeny and divergence time estimates indicate multiple simultaneous colonizations of the western Old World by Terpsiphone . These results reinforce a hypothesis of range expansions of a Terpsiphone paradisi ‐like ancestor into eastern Asia and the western Old World.
Background and AimsThe genome size of an organism is determined by its capacity to tolerate genome expansion, given the species' life strategy and the limits of a particular environment, and the ability for retrotransposon suppression and/or removal. In some giant-genomed bulb geophytes, this tolerance is explained by their ability to pre-divide cells in the dormant stages or by the selective advantage of larger cells in the rapid growth of their fleshy body. In this study, a test shows that the tendency for genome size expansion is a more universal feature of geophytes, and is a subject in need of more general consideration.Methods
Differences in monoploid genome sizes were compared using standardized phylogenetically independent contrasts in 47 sister pairs of geophytic and non-geophytic taxa sampled across all the angiosperms. The genome sizes of 96 species were adopted from the literature and 53 species were newly measured using flow cytometry with propidium iodide staining.Key ResultsThe geophytes showed increased genome sizes compared with their non-geophytic relatives, regardless of the storage organ type and regardless of whether or not vernal geophytes, polyploids or annuals were included in the analyses.Conclusions
The universal tendency of geophytes to possess a higher genome size suggests the presence of a universal mechanism allowing for genome expansion. It is assumed that this is primarily due to the nutrient and energetic independence of geophytes perhaps allowing continuous synthesis of DNA, which is known to proceed in the extreme cases of vernal geophytes even in dormant stages. This independence may also be assumed as a reason for allowing large genomes in some parasitic plants, as well as the nutrient limitation of small genomes of carnivorous plants.
Freshwater habitats make up only ∼0.01% of available aquatic habitat and yet harbor 40% of all fish species, whereas marine habitats comprise >99% of available aquatic habitat and have only 60% of fish species. One possible explanation for this pattern is that diversification rates are higher in freshwater habitats than in marine habitats. We investigated diversification in marine and freshwater lineages in the New World silverside fish clade Menidiinae (Teleostei, Atherinopsidae). Using a time-calibrated phylogeny and a state-dependent speciation-extinction framework, we determined the frequency and timing of habitat transitions in Menidiinae and tested for differences in diversification parameters between marine and freshwater lineages. We found that Menidiinae is an ancestrally marine lineage that independently colonized freshwater habitats four times followed by three reversals to the marine environment. Our state-dependent diversification analyses showed that freshwater lineages have higher speciation and extinction rates than marine lineages. Net diversification rates were higher (but not significant) in freshwater than marine environments. The marine lineage-through time (LTT) plot shows constant accumulation, suggesting that ecological limits to clade growth have not slowed diversification in marine lineages. Freshwater lineages exhibited an upturn near the recent in their LTT plot, which is consistent with our estimates of high background extinction rates. All sequence data are currently being archived on Genbank and phylogenetic trees archived on Treebase.
Recent innovations in phylogenetic comparative methods (PCMs) have spurred a renaissance of research into the causes and consequences of large-scale patterns of biodiversity. In this paper, we review these advances. We also highlight the potential of comparative methods to integrate across fields and focus on three examples where such integration might be particularly valuable: quantitative genetics, community ecology, and paleobiology. We argue that PCMs will continue to be a key set of tools in evolutionary biology, shedding new light on how evolutionary processes have shaped patterns of biodiversity through deep time.
Over the course of the last decades computers have evolved from a useful tool for rapidly calculating large amounts of equations to an indispensable part of everyday life. Today, cars will not run if a chip is faulty, and communication not only by phone and email, but also by conventional mail depends on computer codes. Computer generated or edited sounds and images dominate advertising, and their influence on education and especially entertainment is rapidly growing.
Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a hierarchical Bayes method for inferring the ancestral states on a tree. The method integrates over uncertainty in the tree, branch lengths, and substitution model parameters by using Markov chain Monte Carlo. Wecompare the hierarchical Bayes inferences of ancestral states with inferences of ancestral states made under the assumption that a specific tree is correct. We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analys
We review accuracy estimation methods and compare the two most common methods: crossvalidation and bootstrap. Recent experimental results on arti cial data and theoretical results in restricted settings have shown that for selecting a good classi er from a set of classiers (model selection), ten-fold cross-validation may be better than the more expensive leaveone-out cross-validation. We report on a largescale experiment|over half a million runs of C4.5 and a Naive-Bayes algorithm|to estimate the e ects of di erent parameters on these algorithms on real-world datasets. For crossvalidation, we vary the number of folds and whether the folds are strati ed or not � for bootstrap, we vary the number of bootstrap samples. Our results indicate that for real-word datasets similar to ours, the best method to use for model selection is ten-fold strati ed cross validation, even if computation power allows using more folds. 1
Improved knowledge of Dipsacales phylogeny provides a solid framework for studies of character evolution. Although the polarity of many characters can now be confidently established, for others it remains unclear. This results largely from uncertainty about the broader relationships of Dipsacales and is especially problematic for characters that differentiate the two basal lineages, Adoxaceae and Caprifoliaceae. Within Caprifoliaceae, changes in stamen number became decoupled from corolla evolution, a reduction from five to four stamens, coinciding with the origin of the Linnina clade. Subsequently, there was a reduction to two stamens within Morinaceae and to three, two, and one within Valerianaceae. In contrast, within Adoxaceae, stamen number covaries with the number of corolla lobes, although the number of stamens was effectively doubled within Adoxina by the division of each stamen. Fleshy fruits may have evolved separately in Adoxaceae and in Caprifolieae. These vary in the number of seeds and in the presence or absence of an endocarp and show repeated patterns in the evolution of color, perhaps underlain by shifts in the timing of developmental events. In Caprifoliaceae, dry fruits include bicarpellate septicidal capsules in Diervilleae and initially tricarpellate, single-seeded achenes in Linnina. Achene fruits exhibit a variety of independently evolved dispersal mechanisms, especially involving modifications of the calyx lobes or bracts subtending the ovary. Within Linnina, a distinctive epicalyx surrounding the ovary appears to have originated through the fusion of supernumerary bracts. It is possible that the epicalyx evolved twice, once in the ancestor of the Morinaceae and again in the Triplostegia-Dipsacaceae clade. Within the Dipsacaceae, modifications of the epicalyx parallel those of the ovary and calyx within Valerianaceae, suggesting a transference of function involving homeoheterotopy. Evolutionary adjust-ments of the epicalyx, calyx, and ovary wall in relation to protection and dispersal may have established an evolutionarily stable configuration.
The program MRBAYES performs Bayesian inference of
phylogeny using a variant of Markov chain Monte Carlo.
Availability: MRBAYES, including the source code, documentation,
sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
Contact: johnh{at}brahms.biology.rochester.edu
Quantification in historical biogeography has usually been based on the search for a single branching relationship among areas
of endemism. Unlike organisms, however, areas rarely have a unique hierarchical history. Dispersal barriers appear and disappear
and may have different effects on different species. As a result, the biota of an area may consist of several components with
separate histories, each of which may be reticulate rather than branching. In an attempt to address these problems, I present
a new biogeographic method, dispersal–vicariance analysis, which reconstructs the ancestral distributions in a given phylogeny
without any prior assumptions about the form of area relationships. A three-dimensional step matrix based on a simple biogeographic
model is used in the reconstruction. Speciation is assumed to subdivide the ranges of widespread species into vicariant components;
the optimal ancestral distributions are those that minimize the number of implied dispersal and extinction events. Exact algorithms
that find the optimal reconstruction(s) are described. In addition to their use in taxon biogeography, the inferred distribution
histories of individual groups serve as a basis for the study of general patterns in historical biogeography, particularly
if the relative age of the nodes in the source cladograms is known.
Many evolutionary studies use comparisons across species to detect evidence of natural selection and to examine the rate of character evolution. Statistical analyses in these studies are usually performed by means of a species phylogeny to accommodate the effects of shared evolutionary history. The phylogeny is usually treated as known without error; this assumption is problematic because inferred phylogenies are subject to both stochastic and systematic errors. We describe methods for accommodating phylogenetic uncertainty in evolutionary studies by means of Bayesian inference. The methods are computationally intensive but general enough to be applied in most comparative evolutionary studies.
Differential rates of nucleotide substitutions among taxa are a common observation in molecular phylogenetic studies, yet links between rates of DNA evolution and traits or behaviors of organisms have proved elusive. Likelihood ratio testing is used here for the first time to evaluate specific hypotheses that account for the induction of shifts in rates of DNA evolution. A molecular phylogenetic investigation of mutualist (lichen-forming fungi and fungi associated with liverworts) and nonmutualist fungi revealed four independent transitions to mutualism. We demonstrate a highly significant association between mutualism and increased rates of nucleotide substitutions in nuclear ribosomal DNA, and we demonstrate that a transition to mutualism preceded the rate acceleration of nuclear ribosomal DNA in these lineages. Our results suggest that the increased rate of evolution after the adoption of a mutualist lifestyle is generalized across the genome of these mutualist fungi.
The molecular clock, i.e., constancy of the rate of evolution over time, is commonly assumed in estimating divergence dates. However, this assumption is often violated and has drastic effects on date estimation. Recently, a number of attempts have been made to relax the clock assumption. One approach is to use maximum likelihood, which assigns rates to branches and allows the estimation of both rates and times. An alternative is the Bayes approach, which models the change of the rate over time. A number of models of rate change have been proposed. We have extended and evaluated models of rate evolution, i.e., the lognormal and its recent variant, along with the gamma, the exponential, and the Ornstein-Uhlenbeck processes. These models were first applied to a small hominoid data set, where an empirical Bayes approach was used to estimate the hyperparameters that measure the amount of rate variation. Estimation of divergence times was sensitive to these hyperparameters, especially when the assumed model is close to the clock assumption. The rate and date estimates varied little from model to model, although the posterior Bayes factor indicated the Ornstein-Uhlenbeck process outperformed the other models. To demonstrate the importance of allowing for rate change across lineages, this general approach was used to analyze a larger data set consisting of the 18S ribosomal RNA gene of 39 metazoan species. We obtained date estimates consistent with paleontological records, the deepest split within the group being about 560 million years ago. Estimates of the rates were in accordance with the Cambrian explosion hypothesis and suggested some more recent lineage-specific bursts of evolution.
Prolific cladogenesis, adaptive radiation, species selection, key innovations, and mass extinctions are a few examples of biological phenomena that lead to differential diversification among lineages. Central to the study of differential diversification rates is the ability to distinguish chance variation from that which requires deterministic explanation. To detect diversification rate variation among lineages, we propose a number of methods that incorporate information on the topological distribution of species diversity from all internal nodes of a phylogenetic tree. These whole-tree methods (M(Pi), M(Sigma), and M(R)) are explicitly connected to a null model of random diversification--the equal-rates Markov (ERM) random branching model--and an alternative model of differential diversification: M(Pi) is based on the product of individual nodal ERM probabilities; M(Sigma) is based on the sum of individual nodal ERM probabilities, and M(R) is based on a transformation of ERM probabilities that corresponds to a formalized system that orders trees by their relative symmetry. These methods have been implemented in a freely available computer program, SYMMETREE, to detect clades with variable diversification rates, thereby allowing the study of biological processes correlated with and possibly causal to shifts in diversification rate. Application of these methods to several published phylogenies demonstrates their ability to contend with relatively large, incompletely resolved trees. These topology-based methods do not require estimates of relative branch lengths, which should facilitate the analysis of phylogenies, such as supertrees, for which such data are unreliable or unavailable.
Many questions in evolutionary biology are best addressed by comparing traits in different species. Often such studies involve mapping characters on phylogenetic trees. Mapping characters on trees allows the nature, number, and timing of the transformations to be identified. The parsimony method is the only method available for mapping morphological characters on phylogenies. Although the parsimony method often makes reasonable reconstructions of the history of a character, it has a number of limitations. These limitations include the inability to consider more than a single change along a branch on a tree and the uncoupling of evolutionary time from amount of character change. We extended a method described by Nielsen (2002, Syst. Biol. 51:729-739) to the mapping of morphological characters under continuous-time Markov models and demonstrate here the utility of the method for mapping characters on trees and for identifying character correlation.
MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
Availability: http://morphbank.ebc.uu.se/mrbayes
Contact: fredrik.ronquist@ebc.uu.se
*
To whom correspondence should be addressed.
Multicellular animals, or Metazoa, appear in the fossil records between 575 and 509 million years ago (MYA). At odds with paleontological evidence, molecular estimates of basal metazoan divergences have been consistently older than 700 MYA. However, those date estimates were based on the molecular clock hypothesis, which is almost always violated. To relax this hypothesis, we have implemented a Bayesian approach to describe the change of evolutionary rate over time. Analysis of 22 genes from the nuclear and the mitochondrial genomes under the molecular clock assumption produced old date estimates, similar to those from previous studies. However, by allowing rates to vary in time and by taking small species-sampling fractions into account, we obtained much younger estimates, broadly consistent with the fossil records. In particular, the date of protostome-deuterostome divergence was on average 582 +/- 112 MYA. These results were found to be robust to specification of the model of rate change. The clock assumption thus had a dramatic effect on date estimation. However, our results appeared sensitive to the prior model of cladogenesis, although the oldest estimates (791 +/- 246 MYA) were obtained under a suboptimal model. Bayes posterior estimates of evolutionary rates indicated at least one major burst of molecular evolution at the end of the Precambrian when protostomes and deuterostomes diverged. We stress the importance of assumptions about rates on date estimation and suggest that the large discrepancies between the molecular and fossil dates of metazoan divergences might partly be due to biases in molecular date estimation.
Unlabelled:
SymmeTREE implements several tests of differential diversification rates that exploit information on the topological distribution of species diversity throughout entire trees to address two general questions: (1) Has a given tree experienced significant variation in diversification rates among its branches? and (2) If so, along which branches have significant shifts in diversification rate occurred? These explicitly model-based methods are robust to uncertainty in estimates of branch length/duration and can accommodate incompletely resolved trees and other forms of phylogenetic uncertainty.
Availability:
http://www.phylodiversity.net/bmoore/software.html
Contact:
brian.moore@yale.edu.
Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny.
SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution.
Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.
Species radiations provide unique insights into evolutionary processes underlying species diversification and patterns of biodiversity. To compare plant diversification over a similar time period to the recent cichlid fish radiations, which are an order of magnitude faster than documented bird, arthropod, and plant radiations, we focus on the high-altitude flora of the Andes, which is the most species-rich of any tropical mountains. Because of the recent uplift of the northern Andes, the upland environments where much of this rich endemic flora is found have been available for colonization only since the late Pliocene or Pleistocene, 2–4 million years (Myr) ago. Using DNA sequence data we identify a monophyletic group within the genus Lupinus representing 81 species endemic to the Andes. The age of this clade is estimated to be 1.18–1.76 Myr, implying a diversification rate of 2.49–3.72 species per Myr. This exceeds previous estimates for plants, providing the most spectacular example of explosive plant species diversification documented to date. Furthermore, it suggests that the high cichlid diversification rates are not unique. Lack of key innovations associated with the Andean Lupinus clade suggests that diversification was driven by ecological opportunities afforded by the emergence of island-like habitats after Andean uplift. Data from other genera indicate that lupines are one of a set of similarly rapid Andean plant radiations, continental in scale and island-like in stimulus, suggesting that the high-elevation Andean flora provides a system that rivals other groups, including cichlids, for understanding rapid species diversification.
• leguminosae
• Lupinus
• phylogeny
• species diversification
We extend our recently developed Markov chain Monte Carlo algorithm for Bayesian estimation of species divergence times to allow variable evolutionary rates among lineages. The method can use heterogeneous data from multiple gene loci and accommodate multiple fossil calibrations. Uncertainties in fossil calibrations are described using flexible statistical distributions. The prior for divergence times for nodes lacking fossil calibrations is specified by use of a birth-death process with species sampling. The prior for lineage-specific substitution rates is specified using either a model with autocorrelated rates among adjacent lineages (based on a geometric Brownian motion model of rate drift) or a model with independent rates among lineages specified by a log-normal probability distribution. We develop an infinite-sites theory, which predicts that when the amount of sequence data approaches infinity, the width of the posterior credibility interval and the posterior mean of divergence times form a perfect linear relationship, with the slope indicating uncertainties in time estimates that cannot be reduced by sequence data alone. Simulations are used to study the influence of among-lineage rate variation and the number of loci sampled on the uncertainty of divergence time estimates. The analysis suggests that posterior time estimates typically involve considerable uncertainties even with an infinite amount of sequence data, and that the reliability and precision of fossil calibrations are critically important to divergence time estimation. We apply our new algorithms to two empirical data sets and compare the results with those obtained in previous Bayesian and likelihood analyses. The results demonstrate the utility of our new algorithms.
Determining whether speciation and extinction rates depend on the state of a particular character has been of long-standing interest to evolutionary biologists. To assess the effect of a character on diversification rates using likelihood methods requires that we be able to calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect. Here we describe how to calculate this probability for a phylogenetic tree and a two-state (binary) character under a simple model of evolution (the "BiSSE" model, binary-state speciation and extinction). The model involves six parameters, specifying two speciation rates (rate when the lineage is in state 0; rate when in state 1), two extinction rates (when in state 0; when in state 1), and two rates of character state change (from 0 to 1, and from 1 to 0). Using these probability calculations, we can do maximum likelihood inference to estimate the model's parameters and perform hypothesis tests (e.g., is the rate of speciation elevated for one character state over the other?). We demonstrate the application of the method using simulated data with known parameter values.
The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented.
BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license.
BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.
Molecular techniques provide ancestral phylogenies of extant taxa with estimated branching times. Here we studied the pattern of ancestral phylogeny of extant taxa produced by branching (or cladogenesis) and extinction of taxa, assuming branching processes with time-dependent rates. (1) If the branching rate b and extinction rate c are constant, the semilog plot of the number of ancestral lineages over time is not a straight line but is curvilinear, with increasing slope toward the end, implying that ancestral phylogeny shows apparent increase in the branching rate near the present. The estimate of b and c based on nonlinear fitting is examined by computer simulation. The estimate of branching rate can be usable for a large phylogeny if b is greater than c, but the estimate of extinction rate c is unreliable because of large bias and variance. (2) Gradual decrease in the slope of the semilog plot of the number of ancestral lineages over time, as was observed in a phylogeny of bird families based on DNA hybridization data, can be explained equally well by either the decreasing branching rate or the increasing extinction rate. Infinitely many pairs of branching and extinction rates as functions of time can produce the same ancestral phylogeny. (3) An explosive branching event in the past would appear as a quick increase in the number of ancestral lineages. In contrast, mass extinction occurring in a brief period, if not accompanied by an increase in branching rate, does not produce any rapid change in the number of ancestral lineages at the time. (4) The condition in which the number of ancestral lineages of extant species changes in parallel with the actual number of species in the past is derived.
At a time when historical biogeography appears to be again expanding its scope after a period of focusing primarily on discerning area relationships using cladograms, new inference methods are needed to bring more kinds of data to bear on questions about the geographic history of lineages. Here we describe a likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time. Unlike existing methods for estimating ancestral areas, such as dispersal-vicariance analysis, this approach incorporates information on the timing of both lineage divergences and the availability of connections between areas (dispersal routes). Monte Carlo methods are used to estimate branch-specific transition probabilities for geographic ranges, enabling the likelihood of the data (observed species distributions) to be evaluated for a given phylogeny and parameterized paleogeographic model. We demonstrate how the method can be used to address two biogeographic questions: What were the ancestral geographic ranges on a phylogenetic tree? How were those ancestral ranges affected by speciation and inherited by the daughter lineages at cladogenesis events? For illustration we use hypothetical examples and an analysis of a Northern Hemisphere plant clade (Cercis), comparing and contrasting inferences to those obtained from dispersal-vicariance analysis. Although the particular model we implement is somewhat simplistic, the framework itself is flexible and could readily be modified to incorporate additional sources of information and also be extended to address other aspects of historical biogeography.
Phylogenetic evidence for biological traits that increase the net diversification rate of lineages (key innovations) is most commonly drawn from comparisons of clade size. This can work well for ancient, unreversed traits and for correlating multiple trait origins with higher diversification rates, but it is less suitable for unique events, recently evolved innovations, and traits that exhibit homoplasy. Here I present a new method for detecting the phylogenetic signature of key innovations that tests whether the evolutionary history of the candidate trait is associated with shorter waiting times between cladogenesis events. The method employs stochastic models of character evolution and cladogenesis and integrates well into a Bayesian framework in which uncertainty in historical inferences (such as phylogenetic relationships) is allowed. Applied to a well-known example in plants, nectar spurs in columbines, the method gives much stronger support to the key innovation hypothesis than previous tests.
Extending work of D. B. Rubin [ibid. 12, 1151-1172 (1984; Zbl 0555.62010)] this paper explores a Bayesian counterpart of the classical p-value, namely, a tail-area probability of a “test statistic” under a null hypothesis. The Bayesian formulation, using posterior predictive replications of the data, allows a “test statistic” to depend on both data and unknown (nuisance) parameters and thus permits a direct measure of the discrepancy between sample and population quantities. The tail- area probability for a “test statistic” is then found under the joint posterior distribution of replicate data and the (nuisance) parameters, both conditional on the null hypothesis. This posterior predictive p- value can also be viewed as the posterior mean of a classical p-value, averaging over the posterior distribution of (nuisance) parameters under the null hypothesis, and thus it provides one general method for dealing with nuisance parameters. Two classical examples, including the Behrens-Fisher problem, are used to illustrate the posterior predictive p-value and some of its interesting properties, which also reveal a new (Bayesian) interpretation for some classical p-values. An application to multiple-imputation inference is also presented. A frequency evaluation shows that, in general, if the replication is defined by new (nuisance) parameters and new data, then the Type I frequentist error of an α-level posterior predictive test is often close to but less than α and will never exceed 2α.
Molecular techniques provide ancestral phylogenies of extant taxa with estimated branching times. Here we studied the pattern of ancestral phylogeny of extant taxa produced by branching (or cladogenesis) and extinction of taxa, assuming branching processes with time-dependent rates. (1) If the branching rate b and extinction rate c are constant, the semilog plot of the number of ancestral lineages over time is not a straight line but is curvilinear, with increasing slope toward the end, implying that ancestral phylogeny shows apparent increase in the branching rate near the present. The estimate of b and c based on nonlinear fitting is examined by computer simulation. The estimate of branching rate can be usable for a large phylogeny if b is greater than c, but the estimate of extinction rate c is unreliable because of large bias and variance. (2) Gradual decrease in the slope of the semilog plot of the number of ancestral lineages over time, as was observed in a phylogeny of bird families based on DNA hybridization data, can be explained equally well by either the decreasing branching rate or the increasing extinction rate. Infinitely many pairs of branching and extinction rates as functions of time can produce the same ancestral phylogeny. (3) An explosive branching event in the past would appear as a quick increase in the number of ancestral lineages. In contrast, mass extinction occurring in a brief period, if not accompanied by an increase in branching rate, does not produce any rapid change in the number of ancestral lineages at the time. (4) The condition in which the number of ancestral lineages of extant species changes in parallel with the actual number of species in the past is derived.
Quantification in historical biogeography has usually been based on the search for a single branching relationship among areas of endemism. Unlike organisms, however, areas rarely have a unique hierarchical history. Dispersal barriers appear and disappear and may have different effects on different species. As a result, the biota of an area may consist of several components with separate histories, each of which may be reticulate rather than branching. In an attempt to address these problems, I present a new biogeographic method, dispersal-vicariance analysis, which reconstructs the ancestral distributions in a given phylogeny without any prior assumptions about the form of area relationships. A three-dimensional step matrix based on a simple biogeographic model is used in the reconstruction. Speciation is assumed to subdivide the ranges of widespread species into vicariant components; the optimal ancestral distributions are those that minimize the number of implied dispersal and extinction events. Exact algorithms that find the optimal reconstruction(s) are described. In addition to their use in taxon biogeography, the inferred distribution histories of individual groups serve as a basis for the study of general patterns in historical biogeography, particularly if the relative age of the nodes in the source cladograms is known.
The present distribution and ecology of New Zealand plants is discussed from a historical viewpoint.It is suggested that during the Miocene a southern extension of the New Zealand archipelago supported a cool temperste flora, which gave rise to the present mountain flora after the onset of orogeny and climatic cooling in the Pliocene.As there was scarcely any simultaneous development of a distinctive flora adapted to the dry conditions which prevail to the east of the mountain axis, Cockayne§ opinion that extremely arid Pleistocene climates evoked certain characteristic life forms—notably the divaricating juvenile form of some trees—is considered to be substantially incorrect. That these life forms are adapted to still–existing conditions seems more probable.The broader features of present distribution are explllined in terms of Pleistocene glaciation and subsequent climatic amelioration.From the evidence of endemism and discontinuous distribution, it is concluded that Otago and Southland,Nelson and Marlborough, Auckland,the subantarctic regions and the Chatham Islands are areas where much of the present flora survived during the glaciation,whereas the middle portion of the South Island and the south of the North Island were characterised by extinction.Adjustment of the vegetation to post Pleistocene conditions is still incomplete, and complicated by the effect of continuing climatic fluctuations
Abstract The extraordinary contemporary species richness and ecological predominance of flowering plants (angiosperms) are even more remarkable when considering the relatively recent onset of their evolutionary diversification. We examine the evolutionary diversification of angiosperms and the observed differential distribution of species in angiosperm clades by estimating the rate of diversification for angiosperms as a whole and for a large set of angiosperm clades. We also identify angiosperm clades with a standing diversity that is either much higher or lower than expected, given the estimated background diversification rate. Recognition of angiosperm clades, the phylogenetic relationships among them, and their taxonomic composition are based on an empirical compilation of primary phylogenetic studies. By making an integrative and critical use of the paleobotanical record, we obtain reasonably secure approximations for the age of a large set of angiosperm clades. Diversification was modeled as a stochastic, time-homogeneous birth-and-death process that depends on the diversification rate (r) and the relative extinction rate (∈). A statistical analysis of the birth and death process was then used to obtain 95% confidence intervals for the expected number of species through time in a clade that diversifies at a rate equal to that of angiosperms as a whole. Confidence intervals were obtained for stem group and for crown group ages in the absence of extinction (∈= 0.0) and under a high relative extinction rate (∈= 0.9). The standing diversity of angiosperm clades was then compared to expected species diversity according to the background rate of diversification, and, depending on their placement with respect to the calculated confidence intervals, exceedingly species-rich or exceedingly species-poor clades were identified. The rate of diversification for angiosperms as a whole ranges from 0.077 (∈= 0.9) to 0.089 (∈= 0.0) net speciation events per million years. Ten clades fall above the confidence intervals of expected species diversity, and 13 clades were found to be unexpectedly species poor. The phylogenetic distribution of clades with an exceedingly high number of species suggests that traits that confer high rates of diversification evolved independently in different instances and do not characterize the angiosperms as a whole.
— Information on the history of cospeciation and host switching for a group of host and parasite species is contained in the DNA sequences sampled from each. Here, we develop a Bayesian framework for the analysis of cospeciation. We suggest a simple model of host switching by a parasite on a host phylogeny in which host switching events are assumed to occur at a constant rate over the entire evolutionary history of associated hosts and parasites. The posterior probability density of the parameters of the model of host switching are evaluated numerically using Markov chain Monte Carlo. In particular, the method generates the probability density of the number of host switches and of the host switching rate. Moreover, the method provides information on the probability that an event of host switching is associated with a particular pair of branches. A Bayesian approach has several advantages over other methods for the analysis of cospeciation. In particular, it does not assume that the host or parasite phylogenies are known without error; many alternative phylogenies are sampled in proportion to their probability of being correct.
Phylogenetic trees imply that flowers with a single plane of symmetry (zygomorphic flowers) have evolved several times independently from radially symmetrical (actinomorphic) ancestors within the Asteridae. However, there also appear to have been reversals to actinomorphy. A few evolutionarily derived actinomorphic flowers resemble mutants caused by loss-of-function mutations in genes such as CYCLOIDEA. However, a majority of the shifts from zygomorphy to actinomorphy appear to have entailed a reduction in petal number and flower size, implying a mechanism other than loss of CYCLOIDEA function. Within the Asteridae there appear to be three common forms of zygomorphy. An explanation for the virtual absence of other forms rests on the near universality of the basic orientation of the flower in the Asteridae.
Improvements in our understanding of green plant phylogeny are casting new light on the connection between character evolution and diversification. The repeated discovery of paraphyly has helped disentangle what once appeared to be phylogenetically coincident character
changes, but this has also highlighted the existence of sequences of character change, no one element of which can cleanly be identified as the ‘‘key innovation’’ responsible for shifting diversification rate. In effect, the cause becomes distributed across a nested series of nodes in the tree. Many of the most conspicuous plant ‘‘innovations’’ (such as macrophyllous leaves) are underlain by earlier, more subtle shifts in development (such as overtopping growth), which appear to have enabled the exploration of a greater range of morphological designs. Often it appears that these underlying changes have been brought about at the level of cell interactions within meristems, highlighting the need for developmental models and experiments focused at this level. The standard practice of attempting to identify correlations between recurrent character change (such as the tree growth habit) and clade diversity is complicated by the observation that the ‘‘same’’ trait may be constructed quite differently in different lineages (e.g., different forms of cambial activity), with some solutions imposing more architectural limitations than others. These thoughts highlight the need for a more nuanced view, which has implications for comparativemethods. They also bear on issues central to Stephen Jay Gould’s vision of macroevolution, including exaptation and evolutionary recurrence in relation to constraint and the repeatability of evolution.
Information on the history of cospeciation and host switching for a group of host and parasite species is contained in the DNA sequences sampled from each. Here, we develop a Bayesian framework for the analysis of cospeciation. We suggest a simple model of host switching by a parasite on a host phylogeny in which host switching events are assumed to occur at a constant rate over the entire evolutionary history of associated hosts and parasites. The posterior probability density of the parameters of the model of host switching are evaluated numerically using Markov chain Monte Carlo. In particular, the method generates the probability density of the number of host switches and of the host switching rate. Moreover, the method provides information on the probability that an event of host switching is associated with a particular pair of branches. A Bayesian approach has several advantages over other methods for the analysis of cospeciation. In particular, it does not assume that the host or parasite phylogenies are known without error; many alternative phylogenies are sampled in proportion to their probability of being correct.
The extraordinary contemporary species richness and ecological predominance of flowering plants (angiosperms) are even more remarkable when considering the relatively recent onset of their evolutionary diversification. We examine the evolutionary diversification of angiosperms and the observed differential distribution of species in angiosperm clades by estimating the rate of diversification for angiosperms as a whole and for a large set of angiosperm clades. We also identify angiosperm clades with a standing diversity that is either much higher or lower than expected, given the estimated background diversification rate. Recognition of angiosperm clades, the phylogenetic relationships among them, and their taxonomic composition are based on an empirical compilation of primary phylogenetic studies. By making an integrative and critical use of the paleobotanical record, we obtain reasonably secure approximations for the age of a large set of angiosperm clades. Diversification was modeled as a stochastic, time-homogeneous birth-and-death process that depends on the diversification rate (r) and the relative extinction rate (epsilon). A statistical analysis of the birth and death process was then used to obtain 95% confidence intervals for the expected number of species through time in a clade that diversifies at a rate equal to that of angiosperms as a whole. Confidence intervals were obtained for stem group and for crown group ages in the absence of extinction (e = 0.0) and under a high relative extinction rate (epsilon = 0.9). The standing diversity of angiosperm clades was then compared to expected species diversity according to the background rate of diversification, and, depending on their placement with respect to the calculated confidence intervals, exceedingly species-rich or exceedingly species-poor clades were identified. The rate of diversification for angiosperms as a whole ranges from 0.077 (epsilon = 0.9) to 0.089 (epsilon = 0.0) net speciation events per million years. Ten clades fall above the confidence intervals of expected species diversity, and 13 clades were found to be unexpectedly species poor. The phylogenetic distribution of clades with an exceedingly high number of species suggests that traits that confer high rates of diversification evolved independently in different instances and do not characterize the angiosperms as a whole.
Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows
for rapid analysis of large data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic methods use currently
available stochastic models of sequence evolution. However, as with other model-based approaches, the results of Bayesian
inference are conditional on the assumed model of evolution: inadequate models (models that poorly fit the data) may result
in erroneous inferences. In this article, I present a Bayesian phylogenetic method that evaluates the adequacy of evolutionary
models using posterior predictive distributions. By evaluating a model's posterior predictive performance, an adequate model
can be selected for a Bayesian phylogenetic study. Although I present a single test statistic that assesses the overall (global)
performance of a phylogenetic model, a variety of test statistics can be tailored to evaluate specific features (local performance)
of evolutionary models to identify sources failure. The method presented here, unlike the likelihood-ratio test and parametric
bootstrap, accounts for uncertainty in the phylogeny and model parameters.
Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a hierarchical Bayes method for inferring the ancestral states on a tree. The method integrates over uncertainty in the tree, branch lengths, and substitution model parameters by using Markov chain Monte Carlo. We compare the hierarchical Bayes inferences of ancestral states with inferences of ancestral states made under the assumption that a specific tree is correct. We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis.
Mapping of mutations on a phylogeny has been a commonly used analytical tool in phylogenetics and molecular evolution. However,
the common approaches for mapping mutations based on parsimony have lacked a solid statistical foundation. Here, I present
a Bayesian method for mapping mutations on a phylogeny. I illustrate some of the common problems associated with using parsimony
and suggest instead that inferences in molecular evolution can be made on the basis of the posterior distribution of the mappings
of mutations. A method for simulating a mapping from the posterior distribution of mappings is also presented, and the utility
of the method is illustrated on two previously published data sets. Applications include a method for testing for variation
in the substitution rate along the sequence and a method for testing whether the dN/dS ratio varies among lineages in the phylogeny.
Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny from the distribution of traits observed in contemporary organisms. Because phylogenies are normally inferences from data, it is desirable to account for the uncertainty in estimates of the tree and its branch lengths when making inferences about ancestral states or other comparative parameters. Here we present a general Bayesian approach for testing comparative hypotheses across statistically justified samples of phylogenies, focusing on the specific issue of reconstructing ancestral states. The method uses Markov chain Monte Carlo techniques for sampling phylogenetic trees and for investigating the parameters of a statistical model of trait evolution. We describe how to combine information about the uncertainty of the phylogeny with uncertainty in the estimate of the ancestral state. Our approach does not constrain the sample of trees only to those that contain the ancestral node or nodes of interest, and we show how to reconstruct ancestral states of uncertain nodes using a most-recent-common-ancestor approach. We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods (BayesMultiState) is available from the authors.
Testing whether some species traits have a significant effect on diversification rates is central in the assessment of macroevolutionary theories. However, we still lack a powerful method to tackle this objective. I present a new method for the statistical analysis of diversification with species traits. The required data are observations of the traits on recent species, the phylogenetic tree of these species, and reconstructions of ancestral values of the traits. Several traits, either continuous or discrete, and in some cases their interactions, can be analyzed simultaneously. The parameters are estimated by the method of maximum likelihood. The statistical significance of the effects in a model can be tested with likelihood ratio tests. A simulation study showed that past random extinction events do not affect the Type I error rate of the tests, whereas statistical power is decreased, though some power is still kept if the effect of the simulated trait on speciation is strong. The use of the method is illustrated by the analysis of published data on primates. The analysis of these data showed that the apparent overall positive relationship between body mass and species diversity is actually an artifact due to a clade-specific effect. Within each clade the effect of body mass on speciation rate was in fact negative. The present method allows to take both effects (clade and body mass) into account simultaneously.
Phylogenetic evidence for biological traits that increase the net diversification rate of lineages (key innovations) is most commonly drawn from comparisons of clade size. This can work well for ancient, unreversed traits and for correlating multiple trait origins with higher diversification rates, but it is less suitable for unique events, recently evolved innovations, and traits that exhibit homoplasy. Here I present a new method for detecting the phylogenetic signature of key innovations that tests whether the evolutionary history of the candidate trait is associated with shorter waiting times between cladogenesis events. The method employs stochastic models of character evolution and cladogenesis and integrates well into a Bayesian framework in which uncertainty in historical inferences (such as phylogenetic relationships) is allowed. Applied to a well-known example in plants, nectar spurs in columbines, the method gives much stronger support to the key innovation hypothesis than previous tests.
At a time when historical biogeography appears to be again expanding its scope after a period of focusing primarily on discerning area relationships using cladograms, new inference methods are needed to bring more kinds of data to bear on questions about the geographic history of lineages. Here we describe a likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time. Unlike existing methods for estimating ancestral areas, such as dispersal-vicariance analysis, this approach incorporates information on the timing of both lineage divergences and the availability of connections between areas (dispersal routes). Monte Carlo methods are used to estimate branch-specific transition probabilities for geographic ranges, enabling the likelihood of the data (observed species distributions) to be evaluated for a given phylogeny and parameterized paleogeographic model. We demonstrate how the method can be used to address two biogeographic questions: What were the ancestral geographic ranges on a phylogenetic tree? How were those ancestral ranges affected by speciation and inherited by the daughter lineages at cladogenesis events? For illustration we use hypothetical examples and an analysis of a Northern Hemisphere plant clade (Cercis), comparing and contrasting inferences to those obtained from dispersal-vicariance analysis. Although the particular model we implement is somewhat simplistic, the framework itself is flexible and could readily be modified to incorporate additional sources of information and also be extended to address other aspects of historical biogeography.
We describe a Bayesian method for investigating correlated evolution of discrete binary traits on phylogenetic trees. The method fits a continuous-time Markov model to a pair of traits, seeking the best fitting models that describe their joint evolution on a phylogeny. We employ the methodology of reversible-jump (RJ) Markov chain Monte Carlo to search among the large number of possible models, some of which conform to independent evolution of the two traits, others to correlated evolution. The RJ Markov chain visits these models in proportion to their posterior probabilities, thereby directly estimating the support for the hypothesis of correlated evolution. In addition, the RJ Markov chain simultaneously estimates the posterior distributions of the rate parameters of the model of trait evolution. These posterior distributions can be used to test among alternative evolutionary scenarios to explain the observed data. All results are integrated over a sample of phylogenetic trees to account for phylogenetic uncertainty. We implement the method in a program called RJ Discrete and illustrate it by analyzing the question of whether mating system and advertisement of estrus by females have coevolved in the Old World monkeys and great apes.
Studies of character evolution often assume that a phylogeny's shape is determined independently of the characters, which then evolve as mere passengers along the tree's branches. However, if the characters help shape the tree, but this is not considered, biased inferences can result. Simulations of asymmetrical speciation (i.e., one character state conferring a higher rate of speciation than another) result in data that are interpreted to show a higher rate of change toward the diversification-enhancing state, even though the rates to and from this state were in fact equal. Conversely, simulations of asymmetrical character change yield data that could be misinterpreted as showing asymmetrical rates of speciation. Studies of biased diversification and biased character change need to be unified by joint models and estimation methods, although how successfully the two processes can be teased apart remains to be seen.
We explore patterns of diversification in the plant clades Adoxaceae and Valerianaceae (within Dipsacales), evaluating correlations between biogeographic change (i.e., movements into new areas), morphological change (e.g., the origin of putative key innovations associated with vegetative and reproductive characters), and shifts in rates of diversification. Our findings indicate that rates of diversification in these plants tend to be less tightly correlated with the evolution of morphological innovations but instead exhibit a pronounced correlation with movement into new geographic areas, particularly the dispersal of lineages into new mountainous regions. The interdependence among apparent novelties (arising from their nested phylogenetic distribution) and the correlation between morphological and biogeographic change suggests a complex history of diversification in Dipsacales. Overall, these findings highlight the importance of incorporating biogeographic history in studies of diversification rates and in the study of geographic gradients in species richness. Furthermore, these results argue against a simple deterministic relationship between dispersal and diversification: like other factors that may influence the probability of speciation and/or extinction, the impact of dispersal on diversification rates depends on being in the right place at the right time.