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Pybus OG, Harvey PH.. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc R Soc London B Biol Sci 267: 2267-2272
Proceedings of the Royal Society B
Abstract
Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.
... In order to detect significant decreases in diversification rates, γ statistic was calculated for the two local trees (Pybus and Harvey, 2000). The γ statistic measures the relative distribution of internal nodes of a given phylogeny between the tree root and the extant tips by comparing it to the expectation under a constant rate pure-birth model. ...
... The γ statistic measures the relative distribution of internal nodes of a given phylogeny between the tree root and the extant tips by comparing it to the expectation under a constant rate pure-birth model. Pybus and Harvey (2000) proposed the use of Monte Carlo constant rate (MCCR) test to account for incomplete sampling by adjusting the critical value of γ. In this analysis, the γ statistics of the two local phylogenies and the respective adjusted critical values were calculated with the R packages, "phytools" and "laser" (Revell, 2012;Rabosky, 2006). ...
... Such results indicated that there was no significant decrease in diversification rates over time, and that the diversification processes underlying the local phylogenies were not with a constant rate null hypothesis (see Section 3.3 above). However, although the γ statistic has been commonly used to detect decreases in diversification rates, its ability will be seriously compromised when it comes to detecting increases because the statistic could not distinguish accelerated diversification from past extinction events, which could bias the distribution of internal nodes toward the present tips, an effect known as "the pull of the present" (Pybus and Harvey, 2000;Fordyce, 2010;Rabosky, 2006). As a result, there might be potential increases in the diversification rates of the local trees (i.e., significant deviations from the constant rate null model) which could not be detected by the γ statistic. ...
Tropical rainforests harbour exceptionally high species diversity of beetles (order Coleoptera) and are often regarded as diversification hotspots. Traditionally, two hypotheses have been proposed to explain the tropical hyper-biodiversity. The "cradle" model predicts that the rainforests have undergone relatively recent and rapid accumulation of species. The "museum" model expects that the preservation of ancient lineages that diversified in the distant past plays the major role in generating the observed species richness. By focusing on two tropical regions, Malaysia and Panama, this project utilised both qualitative and quantitative analyses to detect historical diversification rate changes. The evolutionary dynamics at the two tropical regions showed mixed characteristics of cradle and museum models, suggesting both explanations could account for the empirical beetle diversity at the two sites. Furthermore, the project proposed a more systematic approach for understanding diversification rate shift events by associating evolution with abiotic and biotic factors. The phylogenetic results produced by the project will also contribute to our progression towards a more comprehensive picture of Coleoptera evolution.
The paper was originally written as a bachelor's final year research project dissertation under the supervision of Prof Alfried Vogler and Dr Thomas Creedy at the Natural History Museum, London. Since the article here has not yet been peer-reviewed, any comment or even criticism will be very much appreciated.
... If geographically structured ecological opportunity governs the propensity for lineages to speciate, then temporal changes in opportunity should be reflected in alterations to the speciation rate. A correlation between ecological opportunity and changing speciation rate is most frequently inferred when diversification slows towards the present, as commonly seen in molecular phylogenies (Phillimore & Price, 2008;Price, 2008;Pybus & Harvey, 2000;Rabosky & Lovette, 2008a, 2008b. Contemporary declines in speciation rate can be interpreted as a clade experiencing limits to diversity, with lineage proliferation slowing as there are fewer ecological roles for species to fill (Rabosky & Lovette, 2008a;Schluter, 2000;Walker & Valentine, 1984). ...
... Contemporary declines in speciation rate can be interpreted as a clade experiencing limits to diversity, with lineage proliferation slowing as there are fewer ecological roles for species to fill (Rabosky & Lovette, 2008a;Schluter, 2000;Walker & Valentine, 1984). Such slowdowns are commonly detected in molecular phylogenies by nodes being disproportionately shifted towards the root relative to the expectation under a pure-birth model of evolution (γ statistic of Price, 2008;Pybus & Harvey, 2000;Weir, 2006), or by calculating the proportional difference in diversification rate between the first and second half of a clade's phylogenetic history (ρ, Pigot et al., 2010). Such metrics provide continuous approximations of clade dynamics, with likelihood-based approaches facilitating differentiation with, for example, continuous rate models (Etienne et al., 2016). ...
... I compared the degree of sympatry for families defined using all constituent species ranges (maximum and mean number of overlapping ranges, Figure 1C) against two aspects of family evolutionary history: temporal change in speciation rate and overall species richness. I quantified whether clades show deviation from constant diversification using two metrics: the γ statistic (Pybus & Harvey, 2000) calculated using the R package 'ape' (Paradis & Schliep, 2018), and the ρ statistic (Pigot et al., 2010). ρ is calculated by comparing the diversification history in the first (r 1 ) and second (r 2 ) half of the phylogenetic data (ρ = (r 2 − r 1 )/(r 1 + r 2 ), Pigot et al., 2010), where r = (log(n 2 ) − log(n 1 ))/t (Magallόn & Sanderson, 2001). ...
Aim
Whether species co-occur with closely related taxa has long been thought to influence both the rate of species formation and maximum clade diversity. However, it is unclear whether these processes act concordantly across entire clades and between taxa with disparate dispersal and life history strategies. Quantifying these patterns will yield a better understanding of the factors regulating biodiversity. I investigate whether allopatry promotes lineage diversification leading to greater clade richness. I also test whether slowdowns in diversification and family richness are correlated with increased sympatry.
Location
Global.
Taxon
Birds, mammals, and amphibians.
Methods
Posterior distributions of speciation rate estimates were compared between different definitions of lineage allopatry. Temporal changes in speciation rate were compared against family diversity as well as the mean and maximum number of overlapping familial ranges.
Results
More diverse families accumulate more overlapping ranges, but this process is nonrandom with predominantly nonsister taxa overlapping. Sister species in allopatry have higher speciation rates, with rates generally suppressed when allopatry is defined using all confamilial taxa, suggesting that the effect changes over the course of a radiation. Slowdowns in diversification are uncorrelated with the maximum and mean number of regionally sympatric species, therefore appearing to be either an idiosyncratic feature of certain clades or at least not related to spatial packing of confamilial species.
Main conclusions
Allopatry of sister species is correlated with rapid diversification at 1–3 Ma timescales. At the family level, maximal clade diversity is achieved through increased sympatry of member species, that is, packing of related species within a single geographic area.
... We further tested for a significant departure from the null hypothesis of a constant rate of diversification using the constant-rate (CR) test [58], as implemented in the package APE. The statistic γ indicates whether internal nodes are closer to the root or to the tips of the tree than expected under a CR model (γ = 0). ...
... A significant p-value for a negative value of γ indicates a decrease in the diversification rate over time, and a positive value of γ indicates that nodes are closer to the tips and implies an acceleration of the accumulation of lineages. A CR model of diversification can be rejected at the 95% level of significance if γ < −1.645 [58]. Since we obtained a nearly complete sampling of species, the CR test was appropriate, without having to perform a Monte Carlo simulation to account for missing lineages. ...
The ancestral area of Kurixalus on the East Asian islands is under dispute, and two hypotheses exist, namely that distribution occurred only on the Asian mainland (scenario of dispersal) and that wide distribution occurred on both the Asian mainland and the East Asian islands (scenario of vicariance). In this study, we conducted biogeographic analyses and estimated the lineage divergence times based on the most complete sampling of species, to achieve a more comprehensive understanding on the origin of Kurixalus on the East Asian islands. Our results revealed that the process of jump dispersal (founder-event speciation) is the crucial process, resulting in the distribution of Kurixalus on the East Asian islands, and supported the model of the Asian mainland origin: that Kurixalus on the East Asian islands originated from the Asian mainland through two long-distance colonization events (jump dispersal), via the model of vicariance of a widespread ancestor on both the Asian mainland and the East Asian islands. Our results indicated that choices of historical biogeography models can have large impacts on biogeographic inference, and the procedure of model selection is very important in biogeographic analysis. The diversification rate of Kurixaus has slightly decreased over time, although the constant-rate model cannot be rejected.
... To analyse shifts in diversification rates, we used the ultrametric trees constructed based on reduced data sets containing singular unique sequence per species/entity. Significant departures from the constant diversification rate model were tested following the rationale of Pybus and Harvey (2000). Their γ statistic compares the relative positions of nodes in phylogeny to those expected under a constant diversification rate model, under which the statistic follows a standard normal distribution. ...
... Analysing diversification events with their shifts by using the γ statistics may be biased towards negative values if the phylogeny does not comprise all the species of a given group. In order to solve this problem, Pybus and Harvey (2000) developed the Monte Carlo constant rates test (MCCR). Their test accounts for taxonomic sample size and undersampling in the phylogeny (Fordyce, 2010) to recover estimates of whether the observed negative values are indeed significantly negative. ...
Understanding the dynamics of speciation and extinction events is one of the most interesting subjects in evolutionary biology that relates to all life forms, even the smallest ones. Tardigrades are microscopic invertebrates that attracted public and scientific attention mostly due to their ability to enter into the diapause stage called cryptobiosis and in such stage resist extremely harsh environmental conditions. However, although recent research solved a considerable number of phylogenetic uncertainties and further uncovered physiological mechanisms of cryptobiosis, not much attention is given to the evolutionary forces shaping tardigrade diversity. Here, we investigated the effect of reproductive mode on diversification rates in tardigrades using three groups: macrobiotids, echiniscids and milnesids, which represent low, moderate and high levels of parthenogenesis, respectively. Our results showed a decreasing tempo of diversification events for each of the studied groups without any differences that could be ascribed to reproductive mode. We discussed the observed lack of effect in tardigrades acknowledging deficiencies in available data sets and encouraging further studies to understand whether our results can be considered reliable.
... These lineage-through-time (LTT) plots were drawn for each of the individual beast runs, the combined MCC tree, and two subtrees representing the trajectories of the freshwater lineages, and the marine lineages, separately. For each tree, we also estimated the gamma statistics (Pybus & Harvey, 2000), and assessed its significance by comparing the observed value against a distribution of values from 1000 random trees with 74 tips, generated under a Yule model with the empirical speciation rate estimated in ape. ...
... and freshwater (γ = 0.7702, p = .4412) lineages gave also a nonsignificant positive γ(Pybus & Harvey, 2000). ...
The salinity barrier that separates marine and freshwater biomes is probably the most important division in biodiversity on Earth. Those organisms that successfully performed this transition had access to new ecosystems while undergoing changes in selective pressure, which often led to major shifts in diversification rates. While these transitions have been extensively investigated in animals, the tempo, mode, and outcome of crossing the salinity barrier have been scarcely studied in other eukaryotes. Here, we reconstructed the evolutionary history of the species complex Cyphoderia ampulla (Euglyphida: Cercozoa: Rhizaria) based on DNA sequences from the nuclear SSU rRNA gene and the mitochondrial cytochrome oxidase subunit I gene, obtained from publicly available environmental DNA data (GeneBank, EukBank) and isolated organisms. A tree calibrated with euglyphid fossils showed that four independent transitions towards freshwater systems occurred from the Mid Miocene onwards, coincident with important fluctuations in sea level. Ancestral trait reconstructions indicated that the whole family Cyphoderiidae had a marine origin and suggest that ancestors of the freshwater forms were euryhaline and lived in environments with fluctuating salinity. Diversification rates did not show any obvious increase concomitant with ecological transitions, but morphometric analyses indicated that species increased in size and homogenized their morphology after colonizing the new environments. This suggests adaptation to changes in selective pressure exerted by life in freshwater sediments.
... The temporal pattern of lineage diversification was visually assessed with a semi log-scaled Lineage-through-time (LTT) plot in the R package phytools (Revell, 2012) using the pruned time-calibrated tree (see above), as well as 500 simulated LTTs assuming a pure-birth process of the same duration and resulting in the same total number of species. The γ statistic (Pybus & Harvey, 2000) was simultaneously calculated, which can detect whether the net diversification rate deviated over time from a pure birth model (standard normal distribution with a mean of 0). We conducted a Monte Carlo constant rates test (MCCR test; Pybus & Harvey, 2000) implemented in the R package LASER (Rabosky, 2006), to account for incomplete sampling (Fordyce, 2010). ...
... The γ statistic (Pybus & Harvey, 2000) was simultaneously calculated, which can detect whether the net diversification rate deviated over time from a pure birth model (standard normal distribution with a mean of 0). We conducted a Monte Carlo constant rates test (MCCR test; Pybus & Harvey, 2000) implemented in the R package LASER (Rabosky, 2006), to account for incomplete sampling (Fordyce, 2010). The test mimicked incomplete sampling by randomly pruning taxa from phylogenies, which were simulated to the full size of the group (i.e., about 100 described species according to Krishna et al. (2013)). ...
Late Cenozoic climate change led to the progressive aridification of Australia over the past 15 million years. This gradual biome turnover fundamentally changed Australia's ecosystems, opening new niches and prompting diversification of plants and animals. One example is the Australian Amitermes Group (AAG), consisting of the Australian Amitermes and affiliated genera. Although it represents the most speciose and diverse higher termite group in Australia, little is known about its evolutionary history. We used ancestral range reconstruction and diversification analyses to illuminate 1) the origin and phylogenetic relationships of the AAG, 2) biogeographical processes leading to the current continent-wide distribution, and 3) timing and pattern of diversification in the context of late Cenozoic climate change. By estimating the first time-calibrated phylogeny, we show that the AAG is a monophyletic group, whose ancestor arrived ~11-10 million years ago from Southeast Asia. Ancestral range reconstruction indicates that Australia's monsoon region was the launching point for a continental radiation that has been shaped by range expansions and within-area speciation rather than vicariance. We found that multiple arid species diversified from mesic and tropical ancestors in the Plio-Pleistocene, but also observed diversification in the opposite direction. Finally, we show that two pulses of rapid diversification coincided with past climate change during the late Miocene and early Pliocene. Consistent with rapid diversification, species accumulation then slowed, likely caused by progressive niche saturation. This study provides a stepping stone for predicting the future response of Australia's termite fauna in the face of human-mediated climate change.
... This sort of program could, for example, be implemented as part of an application to visualise parts of a tree that drive values of summary statistics the most. Tree statistics including tree length, the Gamma statistic (Pybus & Harvey, 2000), Sackin Index and Colless Imbalance Index (Fischer et al., 2023). ...
There is an increasing number of libraries devoted to parsing, manipulating and visualising phylogenetic trees in JavaScript. Many of these libraries bundle tree manipulation with visualisation, but have limited ability to manipulate trees and lack detailed documentation. As the number of web‐based phylogenetic tools and the size of phylogenetics datasets increases, there is a need for a library that parses, writes and manipulates phylogenetic trees that is interoperable with other phylogenetic and data visualisation libraries. Here we introduce PhyloJS, a light zero‐dependency TypeScript and JavaScript library for reading, writing and manipulating phylogenetic trees. PhyloJS allows for modification of and data‐extraction from trees to integrate with other phylogenetics and data visualisation libraries. It can swiftly handle large trees, up to at least 10⁶ tips in size, making it ideal for developing the next generation of more complex web‐based phylogenetics applications handling ever larger datasets. The PhyloJS source code is available on GitHub (https://github.com/clockor2/phylojs) and can be installed via npm with the command npm install phylojs. Extensive documentation is available at https://clockor2.github.io/phylojs/.
... Likewise, Moran's local indicator of phylogenetic association (LIPA; Moran, 1950) recovered mixed local correlation (Fig. 2). The lineage through time (ltt), which is a function to compute gamma statistics and plot the extant versus extinct species, as suggested by Pybus and Harvey (2000), recovered a high gamma value (0.63) but was not significant (p=0.53; Fig. S6-S7). ...
... On one hand, phylogenies are inferred to uncover past evolutionary trajectories and understand the relatedness and differences among organisms. On the other hand, phylogenies provide the basis for downstream phylogenetic analyses such as studying trait evolution (see, e.g., the review by [1]), ancestral state reconstruction (see, e.g., [2] for an overview and [3] for a more recent study), estimation of diversification rates and testing of macroevolutionary models (e.g., [4][5][6]), and quantifying biodiversity (e.g., [7][8][9]). To provide meaningful results, these downstream analyses rely on accurate phylogenies representing the evolutionary relationships among the organisms studied. ...
Many questions in evolutionary biology require the specification of a phylogeny for downstream phylogenetic analyses. However, with the increasingly widespread availability of genomic data, phylogenetic studies are often confronted with conflicting signal in the form of genomic heterogeneity and incongruence between gene trees and the species tree. This raises the question of determining what data and phylogeny should be used in downstream analyses, and to what extent the choice of phylogeny (e.g., gene trees versus species trees) impacts the analyses and their outcomes. In this paper, we study this question in the realm of phylogenetic diversity indices, which provide ways to prioritize species for conservation based on their relative evolutionary isolation on a phylogeny, and are thus one example of downstream phylogenetic analyses. We use the Fair Proportion (FP) index, also known as the evolutionary distinctiveness score, and explore the variability in species rankings based on gene trees as compared to the species tree for several empirical data sets. Our results indicate that prioritization rankings among species vary greatly depending on the underlying phylogeny, suggesting that the choice of phylogeny is a major influence in assessing phylogenetic diversity in a conservation setting. While we use phylogenetic diversity conservation as an example, we suspect that other types of downstream phylogenetic analyses such as ancestral state reconstruction are similarly affected by genomic heterogeneity and incongruence. Our aim is thus to raise awareness of this issue and inspire new research on which evolutionary information (species trees, gene trees, or a combination of both) should form the basis for analyses in these settings.
... The birth-death family of models has proven useful for estimating diversification rates ("Extinction Rates Can Be Estimated from Molecular Phylogenies," 1994; "The Reconstructed Evolutionary Process," 1994; Höhna et al., 2015) and choosing biologically motivated priors in Bayesian analyses (Rannala & Yang, 1996;Velasco, 2008). However, analyses of divergence times (Pybus & Harvey, 2000) and tree shape (Mooers & Heard, 1997;Tracy A. Heath et al. 2008;Jones, 2011) have shown that empirical phylogenies differ from those expected under a constant rate birth-death process. To more accurately explain the observed patterns, these statistical models have undergone several extensions to account for a wide range of biological processes and systematic sampling challenges. ...
Gene-flow processes such as hybridization and introgression play important roles in shaping diversity across the tree of life. Recent studies extending birth-death models have made it possible to investigate patterns of reticulation in a macroevolutionary context. These models allow for different macroevolutionary patterns of gene flow events that can either add, maintain, or remove lineages—with the gene flow itself possibly being dependent on the relatedness between species—thus creating complex diversification scenarios. Further, many reticulate phylogenetic inference methods assume specific reticulation structures or phylogenies belonging to certain network classes. However, the distributions of phylogenetic networks under reticulate birth-death processes are poorly characterized, and it is unknown whether they violate common methodological assumptions. We use simulation techniques to explore phylogenetic network space under a birth-death-hybridization process where the hybridization rate can have a linear dependence on genetic distance. Specifically, we measured the number of lineages through time and role of hybridization in diversification along with the proportion of phylogenetic networks that belong to commonly used network classes (e.g., tree-child, tree-based, or level-1 networks). We find that the growth of phylogenetic networks and class membership are largely affected by assumptions about macroevolutionary patterns of gene flow. In accordance with previous studies, a lower proportion of networks belonged to these classes based on type and density of reticulate events. However, under a birth-death-hybridization process, these factors form an antagonistic relationship; the type of reticulation events that cause high membership proportions also lead to the highest reticulation density, consequently lowering the overall proportion of phylogenies in some classes. Further, we observed that genetic distance–dependent gene flow and incomplete sampling increase the proportion of class membership, primarily due to having fewer reticulate events. Our results can inform studies if their biological expectations of gene flow are associated with evolutionary histories that satisfy the assumptions of current methodology and aid in finding phylogenetic classes that are relevant for methods development.
... We constructed a lineage-throughtime (LTT) plot and evaluated the fit of the LTT curve to a model of diversification with constant rate through a Monte Carlo Constant Rate (MCCR) test using the phytools package (Revell, 2012). This test estimates the g statistic for incompletely sampled phylogenies by contrasting the distribution of inter-node distances between the root and its time-calibrated midpoint to the distribution of distances between this midpoint and the tips (Pybus and Harvey, 2000). Negative values of g indicate that inter-node distances between the root and midpoint are shorter at early history than those from midpoint to the tips, suggesting that most branching events occurred in early history of Achelata. ...
Slipper (Scyllaridae) and spiny (Palinuridae) lobsters show a complex life cycle with a planktonic larval phase, named phyllosoma. This unique larval form within Achelata (Decapoda) is characterized by a transparent dorsoventrally compressed body and a pair of antennae. This conspicuous morphology has been attributed to adaptive specialization of planktonic life. Early studies suggest that phyllosoma morphology has remained constant over the evolutionary history of Achelata, while recent evidence points out large morphological changes and that diversification of phyllosoma larvae is a consequence of radiation and specialization processes to exploit different habitats. Given the ecological and evolutive significance of phyllosoma, we used shape variation of the first phyllosoma stage (phyllosoma I) and a time-calibrated phylogeny of extant Achelata to study how diversification of phyllosoma I shape occurred along with the evolutionary history of Achelata. Our results show a conserved phyllosoma I with a pear-shaped cephalic shield and large antennae in spiny lobsters and older groups of slipper lobsters, yet highly specialized phyllosoma I with wide rounded cephalic shield and short antennae in younger groups of slipper lobsters. Analyses revealed two bursts of lineage diversification in mid and late history without a slowdown in recent times. Both bursts preceded large bursts of morphological disparity. These results joined with the allopatric distribution of species and convergence of phyllosoma I shapes between largely divergent groups suggest that diversification involves nonadaptive radiation processes. However, the correlation of a major direction of shape with the maximum distribution depth of adults and the occurrence of the second burst of diversification post-extinction of competitors within Achelata presuppose some ecological opportunities that might have promoted lineage and morphological diversification, fitting to the characteristic components of adaptive radiations. Therefore, we conclude that diversification of Achelata presents a main signature of nonadaptive radiation with some components of adaptive radiation.
... Likewise, Moran's local indicator of phylogenetic association (LIPA; Moran, 1950) recovered mixed local correlation (Fig. 2). The lineage through time (ltt), which is a function to compute gamma statistics and plot the extant versus extinct species, as suggested by Pybus and Harvey (2000), recovered a high gamma value (0.63) but was not significant (p=0.53; Fig. S6-S7). ...
... This was done using tree statistics that measure balance and imbalance of a phylogeny. In [23], they state that Gamma ( γ ) statistic was defined in [24]. Let 2 3 , , , n g g g be the inter-node distances of the reconstructed phylogeny with n taxa, the γ -statistic is defined as: ...
... To assess lineage diversification rates, we plotted a 'lineage through time' (LTT) via the function 'LTT' plot to define the relative time ratio required for the Chaetothyriales to give rise to the present lineages. The gamma statistic was calculated according to Pybus and Harvey (2000). ...
Dark septate endophytes (DSE) are pigmented fungi that colonize plant roots. They represent a morpho-functional status composed of many species belonging to the phylum Ascomycota, distributed in different orders. The order Chaetothyriales has representatives with diverse lifestyles, among which the rock-inhabiting one has been proposed to be the ancestral ecological character state. However, all taxa have the phenotypic characteristic of being highly melanized. This trait has been considered relevant in most Chaetothyriales because it allows them to tolerate extreme or toxic environmental conditions. In the present study, aiming to reconstruct the evolutionary history of this order, we analyzed the contribution of the DSE habit to the diversification of the Chaetothyriales. We also report the distribution of the DSE habit among the main families and/or clades within the order. Our results suggest that DSE had a key position in the evolution of the order Chaetothyriales, both as an ancestral ecological character and as a character from which other specialized forms such as Domatium probably derived.
... Assuming low (n = 5) and high (n = 50) numbers of missing species, respectively, net diversification rates were computed for a low extinction rate (ε = 0) and a high extinction rate (ε = 0.9). The gamma statistic, which assumes complete sampling, was calculated using the gamStat (γ) function in 'ape', to see if the diversification rate was constant through time (Pybus and Harvey, 2000). A Monte Carlo Constant Rates (MCCR) test was also used to assess the influence of incomplete sampling on the observed gamma rate using the function mccrTest, assuming 20 different clade sizes (Table 6). ...
The tropical forests of the Western Ghats (WG) of India are considered ‘refugia’ harbouring highly diverse and endemic taxa but these refugia are under immense anthropogenic pressure. Most phylogenetic studies have explained diversity patterns across the WG using vertebrates, however, the processes impacting the highly endemic invertebrate fauna are still poorly understood. Here we investigate the evolutionary history of an ancient and widespread arachnid lineage (Pseudoscorpiones: Chthoniidae: Tyrannochthoniini) in the WG through a variety of biogeographical and diversification analyses, including sequence data from three markers for 45 terminals from the WG and 22 from Africa, East and Southeast Asia, Australasia and the Neotropics. Our results show that WG Tyrannochthoniini are rendered paraphyletic by African taxa, a result consistent with continental drift. WG Tyrannochthoniini are further split into two major clades, a southern WG clade and an African-central WG clade, due to vicariance along a major biogeographical barrier, the Palghat Gap. Central WG pseudoscorpions diverged from their African relatives at the Jurassic-Cretaceous boundary, coinciding with the separation of India from Africa. Despite ancient vicariance, six dispersal events occurred across the Palghat Gap, beginning in the Early Cretaceous as India was rafting towards Southeast Asia and ending by the early Miocene, implying that the Palghat Gap became impermeable to dispersal for these humid-adapted organisms during Miocene aridification. Although the ancestor of WG Tyrannochthoniini originated in lowland WG forests, three dispersal events into high montane Shola forests occurred most likely as a result of Late Cretaceous orogenesis and Neogene uplift, allowing lineages to occupy niches at higher elevations. An exponentially declining diversification rate, typical of older lineages, supports the ‘museum’ model of diversification for WG Tyrannochthoniini. Our study sheds light on the historical biogeography of relictual soil-arthropods in the WG and emphasises the role of WG forest refugia in preserving ancient invertebrate biodiversity.
... Firstly, the γ statistic test for departure from a constant rate (CR) pure birth model (Pybus and Harvey, 2000) was conducted with both CR test and Monte Carlo CR (MCCR) test as implemented in LASER. A γ value ≤ 1.645 (p < 0.05) was interpreted as supporting the rejection of the purebirth model under a one-tailed test, providing support for the alternative hypothesis of a slowdown in diversification as predicted with an explosive early pattern. ...
Evolutionary slowdowns in diversification have been inferred in various plant and animal lineages. Investigation based on diversification models integrated with environmental factors and key characters could provide critical insights into this diversification trend. We evaluate diversification rates in the Cirrhopetalum alliance (Bulbophyllum, Orchidaceae subfam. Epidendroideae) using a time-calibrated phylogeny and assess the role of Crassulacean acid metabolism (CAM) as a hypothesised key innovation promoting the spectacular diversity of orchids, especially those with an epiphytic habit. An explosive early speciation in the Cirrhopetalum alliance is evident, with the origin of CAM providing a short-term advantage under the low atmospheric CO2 concentrations (pCO2) associated with cooling and aridification in the late Miocene. A subsequent slowdown of diversification in the Cirrhopetalum alliance is possibly explained by a failure to keep pace with pCO2 dynamics. We further demonstrate that extinction rates in strong CAM lineages are ten times higher than those of C3 lineages, with CAM not as evolutionarily labile as previously assumed. These results challenge the role of CAM as a “key innovation” in the diversification of epiphytic orchids.
... The pattern of lineage diversification for the Pomacentridae is that of a highly steady lineage through time plot (S4 Fig in S1 File), with non-significant difference from a constant rate model when accounting for sampling fraction and without sampling fraction (p = 0.73 and p = 0.11, respectively) using the gamma statistic of Pybus and Harvey [71]. The results of MuHiSSE models of trait effects on diversification show that both size and ecotype are significantly associated with diversification rate across the phylogeny (Figs 6 and 7). ...
The damselfishes (family Pomacentridae) inhabit near-shore communities in tropical and temperature oceans as one of the major lineages in coral reef fish assemblages. Our understanding of their evolutionary ecology, morphology and function has often been advanced by increasingly detailed and accurate molecular phylogenies. Here we present the next stage of multi-locus, molecular phylogenetics for the group based on analysis of 12 nuclear and mitochondrial gene sequences from 345 of the 422 damselfishes. The resulting well-resolved phylogeny helps to address several important questions about higher-level damselfish relationships, their evolutionary history and patterns of divergence. A time-calibrated phylogenetic tree yields a root age for the family of 55.5 mya, refines the age of origin for a number of diverse genera, and shows that ecological changes during the Eocene-Oligocene transition provided opportunities for damselfish diversification. We explored the idea that body size extremes have evolved repeatedly among the Pomacentridae, and demonstrate that large and small body sizes have evolved independently at least 40 times and with asymmetric rates of transition among size classes. We tested the hypothesis that transitions among dietary ecotypes (benthic herbivory, pelagic planktivory and intermediate omnivory) are asymmetric, with higher transition rates from intermediate omnivory to either planktivory or herbivory. Using multistate hidden-state speciation and extinction models, we found that both body size and dietary ecotype are significantly associated with patterns of diversification across the damselfishes, and that the highest rates of net diversification are associated with medium body size and pelagic planktivory. We also conclude that the pattern of evolutionary diversification in feeding ecology, with frequent and asymmetrical transitions between feeding ecotypes, is largely restricted to the subfamily Pomacentrinae in the Indo-West Pacific. Trait diversification patterns for damselfishes across a fully resolved phylogeny challenge many recent general conclusions about the evolution of reef fishes.
... We first tested deviation from a constant-rate pure-birth diversification process using the γ-statistic of Pybus and Harvey (2000), while controlling for incomplete taxon sampling via the Monte Carlo constant rates (MCCR) test with 5,000 simulations using PHYTOOLS. Our assumed sampling fraction is based on having sampled 188 out of 840 described species of coleoids (Hoving et al., 2014). ...
Coleoids are the most diverse group of cephalopod mollusks. While their origin is date during the Mesozoic, the diversification pattern is unknown. However, two hypotheses have been proposed. The first suggests an increasing diversification rate after the Cretaceous-Paleogene extinction event (K-Pg) as consequence of empty habitats left by the ammonites and belemnites. The second hypothesis proposes a mid-Cenozoic increase in diversification rate related to distributional changes during ice ages and biotic interactions. To test these hypotheses, we estimated a lineage through time (LTT) and the gamma-statistic along with model-based diversification rates. These analyses were conducted on a dated molecular phylogeny for coleoids that we reconstructed using five molecular markers (cytochrome b, 16S rRNA, cytochrome oxidase I, rhodopsin, and PAX-6). Our divergence time estimation suggests that coleoids originated in the Mesozoic Era (Middle Triassic) and that both main clades (Decapodiformes and Octopodiformes) diverged in the Cretaceous/Jurassic Period. The LTT, gamma statistic, and diversification rates inferred with the Bayesian Analysis of Macro-evolutionary Mixtures (BAMM), indicate an acceleration in diversification rate over time since the origin of coleoids. Additionally, BAMM allowed us to detect abrupt increases in diversification rate before and after the K-Pg boundary. Our results partially support both hypotheses as all analyses indicate that the coleoid diversification rate was increasing during the Cenozoic. However, our results also indicate increasing diversification rates before the K-Pg boundary. We propose that the radiation of coleoids has been shaped by an acceleration in diversification rate over time, including exceptional episodes of abrupt increases before and after the K-Pg boundary.
... introduction of mutants) of the evolutionary simulation algorithm can generate variation between model realizations I run 20 replicates of each assembled competitive consumer community. Furthermore, to corroborate some of the mechanistic explanations of some of the effects seen on the distance metrics presented above I use the γ-statistics 64 www.nature.com/scientificreports/ Springer Nature journal content, brought to you courtesy of Springer Nature Customer Service Center GmbH ("Springer Nature"). ...
It is well known that ecological and evolutionary processes act in concert while shaping biological communities. Diversification can, for example, arise through ecological opportunity and adaptive radiations and competition play an essential role in such diversification. Eco-evolutionary components of competition are thus important for our understanding of community assembly. Such understanding in turn facilitates interpretation of trait- and phylogenetic community patterns in the light of the processes that shape them. Here, I investigate the link between competition, diversification, and trait- and phylogenetic- community patterns using a trait-based model of adaptive radiations. I evaluate the paradigm that competition is an ecological process that drives large trait- and phylogenetic community distances through limiting similarity. Contrary to the common view, I identify low or in some cases counterintuitive relationships between competition and mean phylogenetic distances due to diversification late in evolutionary time and peripheral parts of niche space when competition is weak. Community patterns as a function of competition also change as diversification progresses as the relationship between competition and trait similarity among species can flip from positive to negative with time. The results thus provide novel perspectives on community assembly and emphasize the importance of acknowledging eco-evolutionary processes when interpreting community data.
... pure birth) using 1,000 simulations in "phytools" (Revell, 2012). We calculated the γ-statistic in order to detect acceleration or deceleration in the rate of cladogenesis (Pybus & Harvey, 2000). This statistic measures the density of ordered inter-node distance on a phylogeny, to determine if they are evenly distributed (γ = 0, pure birth), clustered early (γ < 0; early burst) or clustered late (γ > 0; late burst or high early extinction). ...
Aim
We investigated evolutionary relationships and biogeographical patterns within the genus Boeckella to evaluate (1) whether its current widespread distribution in the Southern Hemisphere is due to recent long-distance dispersal or long-term diversification; and (2) the age and origin of sub-Antarctic and Antarctic Boeckella species, with particular focus on the most widely distributed species: Boeckella poppei.
Location
South America, sub-Antarctic islands, maritime Antarctica, continental Antarctica and Australasia.
Methods
To reconstruct phylogenetic patterns of Boeckella, we used molecular sequence data collected from 12 regions and applied Bayesian and Maximum Likelihood analyses using multiple loci. We also estimated divergence times and reconstructed ancestral ranges using two different models of species evolution.
Results
Phylogenetic analyses and divergence time estimates suggested that Boeckella originated on the Gondwanan supercontinent and initially split into two main clades during the late Cretaceous (ca. 80 Ma). The first clade diversified in Australasia, and the second clade is currently distributed in South America, various sub-Antarctic islands and Antarctica. Dispersal from South America to the Kerguelen and Crozet archipelagos occurred during the Eocene/Oligocene (B. vallentini) and in the late Pliocene (B. brevicaudata), while South Georgia and the maritime Antarctic were likely colonized during the late Pleistocene (B. poppei).
Main conclusions
Boeckella has a Gondwanan origin, with further diversifications after the physical separation of the continental landmasses. Extant populations of Boeckella from the Scotia Arc islands and Antarctic Peninsula originated from South America during the Pleistocene, suggesting that original Antarctic Gondwanan lineages did not survive repeated glacial cycles during the Quaternary ice ages. A continuous decline in the species accumulation rate is apparent within the genus as the early Eocene, suggesting that Boeckella diversification may have decreased due to progressive cooling throughout the Cenozoic era.
... As a first approach, we calculated the γ-statistic and its significance for the pteropodid tree using the package phytools for R (Revell 2012). The γ-statistics is a measure of diversification-rate trends along the phylogeny: positive values are associated with increasing rates, while negative values reflect higher rates at the clade origin with a subsequent decrease (Pybus and Harvey 2000). ...
Pteropodidae constitutes one of the most diverse bat families. These bats have evolved a phytophagous diet, likely lost laryngeal echolocation capability, and attained the largest body sizes among bats. Previous phylogenetic studies suggested that the family might have experienced an explosive diversification at its origin. Here, we readdress this hypothesis using a macroevolutionary approach based on Bayesian statistics (BAMM), a sampling of 139 pteropodid species, and divergence date estimates obtained in a comprehensive phylogenetic study of Chiroptera with multiple fossil calibration points. We evaluated the effect of missing data and of a reduced outgroup by repeating the analyses across simulated complete phylogenies and across a comprehensive Yinpterochiroptera phylogeny, respectively. Additionally, we performed an alternative analysis to detect diversification-rate shifts through time, the birth-death-shift method. In contrast with a previous study, we found strong statistical signals of rapid diversification at the origin of Pteropodidae. BAMM also detected diversification-rate shifts (increases) at the origin of Pteropus, as well as at crown Hipposideridae and Rhinolophidae. The birth-death-shift method detected a shift at approximately 25 million years ago, the estimated crown ages of both Pteropodidae and Hipposideridae. Our results point to a complex dynamics in the evolution of bat families, likely related to key innovations, demographic factors, and environmental opportunity enhanced by global-scale climatic and geographic changes.
... We used the R package Phytools [69] to generate a lineage-through-time (LTT) plot for maples and to perform the Monte Carlo constant-rates (MCCR) test of Pybus & Harvey (2000). Rates of diversification through time were estimated with the R package TESS [71]. ...
Acer (Sapindaceae) is an exceptional study system for understanding the evolutionary history, divergence, and assembly of broad-leaved deciduous forests at higher latitudes. Maples stand out due to their high diversity, disjunct distribution pattern across the northern continents, and rich fossil record dating back to the Paleocene. Using a genome-wide supermatrix combining plastomes and nuclear sequences (~585 kb) for 110 Acer taxa, we built a robust time-calibrated hypothesis investigating the evolution of maples, inferring ancestral ranges, reconstructing diversification rates over time, and exploring the impact of mass-extinction on lineage accumulation. Contrary to fossil evidence, our results indicate Acer first originated in the (north)eastern Palearctic region , which acted as a source for recurring outward migration. Warm conditions favored rapid Eocene-onward divergence, but ranges and diversity declined extensively as a result of the Plio-Pleistocene glacial cycles. These signals in genome-wide sequence data corroborate paleobotanical evidence for other major woody north-temperate groups, highlighting the significant (disparate) impact of climatic changes on the evolution, composition , and distribution of the vegetation in the northern hemisphere.
... The tempo of increase in species richness was visualized by a lineage through time (LTT) plot. We also estimated the γ-statistic (Pybus & Harvey, 2000) as a quantitative measure of deviation from a constant-diversification model. In addition, we produced a regional line- ...
Aim: Historical processes that shaped current diversity patterns of seaweeds remain poorly understood. Using Dictyotales, a globally distributed order of brown seaweeds as a model, we test if historical biogeographical and diversification patterns are comparable across clades. Dictyotales contain some 22 genera, three of which, Dictyota, Lobophora and Padina, are exceptionally diverse. Specifically, we test whether the evolutionary processes that produced the latitudinal diversity patterns in these clades are in line with the tropical conservatism, out-of-the-tropics or diversification rate hypotheses.
Location: Global coastal benthic marine environments.
Taxon: Dictyotales (Phaeophyceae).
Methods: Species diversity was inferred using DNA-based species delineation, ad- dressing cryptic diversity and circumventing taxonomic problems. A six-gene time-calibrated phylogeny, distribution data of 3,755 specimens and probabilistic modelling of geographical range evolution were used to infer historical biogeographical patterns. The phylogeny was tested against different trait-dependent models to compare diversification rates for different geographical units as well as different thermal affinities.
Results: Our results indicate that Dictyotales originated in the Middle Jurassic and reach a current peak of species diversity in the Central Indo-Pacific. Ancestral range estimation points to a southern hemisphere origin of Dictyotales corresponding to the tropical southern Tethys Sea. Our results demonstrate that diversification rates were generally higher in tropical regions, but increased diversification rates in different clades are driven by different processes. Our results suggest that three major clades underwent a major diversification burst in the early Cenozoic, with Dictyota and Padina expanding their distribution into temperate regions while Lobophora retained a predominantly tropical niche.
Main conclusions: Our results are consistent with both the tropical conservatism hypothesis, in which clades originate and remain in the tropics (Lobophora), and the out-of-the-tropics scenario, where taxa originate and expand towards the temperate regions while preserving their presence in the tropics (Dictyota, Padina).
The imprint left by niche evolution on the variation of biological diversity across spatial and environmental gradients is still debated among ecologists. Furthermore, understanding to what extent dispersal limitation may reinforce or blur such imprint is still a gap in the ecological knowledge. In this article we introduce a simulation approach coupled to approximate Bayesian computation (ABC) that parameterizes both the adaptation rate of species' niche positions over the evolution of a monophyletic lineage and the intensity of dispersal limitation associated with the variation of species alpha diversity among assemblages distributed across spatial and environmental gradients. The analytical tool was implemented in the R package 'mcfly' (www.r‐project.org). We evaluated the statistical performance of the analytical framework using simulated datasets, which confirmed the suitability of the analysis to estimate adaptation rate parameter but showed to be less precise in relation to the dispersal limitation parameter. Also, we found that increased dispersal limitation levels improved the parameterization of the adaptation rate of species' niche positions in simulated datasets. Further, we evaluated the role played by niche evolution and dispersal limitation on species alpha diversity variation of Phyllostomidae bats across the Neotropics. The framework proposed here shed light on the links between niche evolution, dispersal limitation and gradients of biological diversity, and thereby improved our understanding of evolutionary imprints on current biological diversity patterns.
Ecomorphs result from divergent natural selection, leading to species-rich adaptive radiations. Identifying ecomorphs and the resulting adaptive radiations in frogs is challenging due to conserved morphology and high species diversity. In this study, we demonstrate the ecological and climate specializations that have driven the diversification of shrub frogs of the genus Pseudophilautus in Sri Lanka, a tropical continental island. We use a time-calibrated phylogeny, morphometric analyses, and climate-niche evolution, and identify five ecomorphological categories, including Tree-shrub, Rock-boulder, Leaf-litter, Habitat Generalists, and Canopy forms, and describe their evolution. Body size is the primary factor separating species, and specific body features correlate with habitat type. Ecomorphs likely evolved multiple times in disparate lineages, and in different regions and altitudes, during cold climatic periods owing to monsoon cycles resulting from the Himalayan-Tibetan orogeny. The common ancestor was a medium-sized, wet-adapted, tree-shrub habitat specialist which originated in the late Oligocene. Extreme size classes (diminutive leaf litter forms and large canopy forms) evolved recently and suggest that morphological disparity arose late in diversification, possibly aided by favorable climates. This work will facilitate understanding of adaptive radiations in frogs, which possibly will help uncover the prevalence of subtle adaptive radiations in frogs, just as in tailed-vertebrates.
The assumption of an ecological limit to the number of species in a given region is frequently invoked in evolutionary studies, yet its empirical basis is remarkably meager. We explore this assumption by integrating data on geographical distributions and phylogenetic relationships of nearly six thousand terrestrial vertebrate species. In particular, we test whether sympatry with closely-related species leads to decreasing speciation rates. We introduce the concept of clade density, which is the sum of the areas of overlap between a given species and other members of its higher taxon, weighted by their phylogenetic distance. Our results showed that, regardless of the chosen taxon and uncertainty in the phylogenetic relationships between the studied species, there is no significant relationship between clade density and speciation rate. We argue that the mechanistic foundation of diversity-dependent diversification is fragile, and that a better understanding of the mechanisms driving regional species pools is sorely needed.
North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.
Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic 'fuses' leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today's mammals. Molecular data and the fossil record can give conflicting views of the evolutionary past. For instance, empirical palaeontological evidence by itself tends to favour the 'explosive model' of diversification for extant placental mammals 1 , in which the orders with living representatives both originated and rapidly diversified soon after the Cretaceous/Tertiary (K/T) mass extinction event that eliminated non-avian dinosaurs and many other, mostly marine 2 , taxa 65.5 million years (Myr) ago 1,3,4. By contrast, molecular data consistently push most origins of the same orders back into the Late Cretaceous period 5-9 , leading to alternative scenarios in which placental line-ages persist at low diversity for some period of time after their initial origins ('phylogenetic fuses'; see ref. 10) before undergoing evolutionary explosions 1,11. Principal among these scenarios is the 'long-fuse model' 1 , which postulates an extended lag between the Cretaceous origins of the orders and the first split among their living representatives (crown groups) immediately after the K/T boundary 8. Some older molecular studies advocate a 'short-fuse model' of diversification 1 , where even the basal crown-group divergences within some of the larger placental orders occur well within the Cretaceous period 5-7. A partial molecular phylogeny emphasizing divergences among placental orders suggested that over 20 lineages with extant descendants (henceforth, 'extant lineages') survived the K/T boundary 8. However, the total number of extant lineages that pre-date the extinction event and whether or not they radiated immediately after it remain unknown. The fossil record alone does not provide direct answers to these questions. It does reveal a strong pulse of diversification in stem eutherians immediately after the K/T boundary 4,12 , but few of the known Palaeocene taxa can be placed securely within the crown groups of extant orders comprising Placentalia 4. The latter only rise to prominence in fossils known from the Early Eocene epoch onwards (,50 Myr ago) after a major faunal reorganization 4,13,14. The geographical patchiness of the record complicates interpretations of this near-absence of Palaeocene crown-group fossils 14-16 : were these clades radiating throughout the Palaeocene epoch in parts of the world where the fossil record is less well known; had they not yet originated; or did they have very long fuses, remaining at low diversity until the major turnover at the start of the Eocene epoch? The pattern of diversification rates through time, to which little attention has been paid so far, might hold the key to answering these questions. If the Cretaceous fauna inhibited mammalian diversification , as is commonly assumed 1 , and all mammalian lineages were able to radiate after their extinction, then there should be a significant increase in the net per-lineage rate of extant mammalian diversification , r (the difference between the per-lineage speciation and extinction rates), immediately after the K/T mass extinction. This hypothesis, along with the explosive, long-and short-fuse models, can be tested using densely sampled phylogenies of extant species, which contain information about the history of their diversification rates 17-20. Using modern supertree algorithms 21,22 , we construct the first virtually complete species-level phylogeny of extant mammals from over 2,500 partial estimates, and estimate divergence times (with confidence intervals) throughout it using a 66-gene alignment in conjunction with 30 cladistically robust fossil calibration points. Our analyses of the supertree indicate that the principal splits underlying the diversification of the extant lineages occurred (1) from 100-85 Myr ago with the origins of the extant orders, and (2) in or after the Early Eocene (agreeing with the upturn in their diversity known from the fossil record 4,13,14), but not immediately after the K/T boundary, where diversification rates are unchanged. Our findings-that more extant placental lineages survived the K/T boundary than previously recognized and that fewer arose immediately after it than previously suspected-extend the phylogenetic fuses of many extant orders and indicate that the end-Cretaceous mass extinction event had, at best, a minor role in driving the diversification of the present-day mam-malian lineages. A supertree with divergence times for extant mammals The supertree contains 4,510 of the 4,554 extant species recorded in ref. 23, making it 99.0% complete at the species level (Fig. 1; see also
Endeavours in species discovery, particularly the characterisation of cryptic species, have been greatly aided by the application of DNA molecular sequence data to phylogenetic reconstruction and inference of evolutionary and biogeographic processes. However, the extent of cryptic and undescribed diversity remains unclear in tropical freshwaters, where biodiversity is declining at alarming rates. To investigate how data on previously undiscovered biodiversity impacts inferences of biogeography and diversification dynamics, we generated a densely sampled species-level family tree of Afrotropical Mochokidae catfishes (220 valid species) that was ca. 70% complete. This was achieved through extensive continental sampling specifically targeting the genus Chiloglanis a specialist of the relatively unexplored fast-flowing lotic habitat. Applying multiple species-delimitation methods, we report exceptional levels of species discovery for a vertebrate genus, conservatively delimiting a staggering ca. 50 putative new Chiloglanis species, resulting in a near 80% increase in species richness for the genus. Biogeographic reconstructions of the family identified the Congo Basin as a critical region in the generation of mochokid diversity, and further revealed complex scenarios for the build-up of continental assemblages of the two most species rich mochokid genera, Synodontis and Chiloglanis. While Syndontis showed most divergence events within freshwater ecoregions consistent with largely in situ diversification, Chiloglanis showed much less aggregation of freshwater ecoregions, suggesting dispersal as a key diversification process in this older group. Despite the significant increase in mochokid diversity identified here, diversification rates were best supported by a constant rate model consistent with patterns in many other tropical continental radiations. While our findings highlight fast-flowing lotic freshwaters as potential hotspots for undescribed and cryptic species diversity, a third of all freshwater fishes are currently threatened with extinction, signifying an urgent need to increase exploration of tropical freshwaters to better characterise and conserve its biodiversity.
This study uses phylogenetic relationships of the species-rich section
Astragalus (Incani), to follow up on recent evidence pointing to rapid and
recent plant diversification patterns in the west of Iran. Section Incani is
introduced for its taxonomic complication resulting from overlapping
morphological characters, but few studies have been done on this section;
hence, we also lack a robust time-calibrated chronogram to address
hypotheses (e.g., biogeography and diversification rates) that have implicit
time assumptions. Two loci (rpl32-trnL(UAG) and nrDNA ITS) were amplified
and sequenced for 87 taxa across Incani for phylogenetic reconstruction and
a chronogram in BEAST. Incani is identified as the sister clade to all
remaining sections with high support, and within the clade Incani, two
strongly supported groups are seen: (1) Clade I includes nine species
restricted to eastern Iran and Central Asia, and (2) clade II includes a
bulk of the species from west and northwestern Iran, Turkey and southern
Europe. Divergence time estimates suggest Incani diverged from remaining
sections 3 Mya during the late Pliocene. The crown date for Incani is
estimated at 1.5 Mya (Pleistocene). Biogeography showed significant
improvement in the likelihood score when the ‘‘jump dispersal” parameter was
added. An eastern origin (Central Asia) is implicated as important ancestral
area in all deeper nodes. BAMM analyses indicate that the best configuration
included one significant shift in diversification rates within Incani: near
the crown of Incani (1.5-2 Mya) including clade II. Issues with conducting
diversification analyses more generally are examined in the context of
scale, taxon sampling, and larger sets of phylogenetic trees.
The genus Onosma is a homogeneous taxon with high morphological variation and
due to the similarities among the Onosma taxa, there are many problems in
their identification. Hence, systematically and taxonomically, it is
considered a difficult genus. In the present study, we included a large
number of Onosma species throughout their distribution range. Using nuclear
(ITS) and two plastids (rpl32-trnL(UAG) and trnH-psbA) markers, we analyzed
the evolutionary history, divergence time and diversification patterns of
Onosma across the tropical, subtropical and temperate regions. Divergence
time estimates suggest the early radiation of Onosma s.l. happened at the
Oligocene-Miocene boundary. BAMM analyses indicate that the best
configuration included one significant shift in diversification rates within
Onosma: on the branch leading to the clade comprised of species of confined
to Iran.
Aridity conditions and expansion of arid biomes in South America are closely linked to the onset of Andean orogeny since at least 30 Mya. Among arid-associated taxa, spiders belonging to the genus Petrichus are found along the Andes mountains and across the diagonal of open formations of the Chaco and Cerrado domains. In this contribution, we asked whether Petrichus originated prior to the central Andean uplift and what historical processes have promoted their diversification. We time-calibrated the phylogenetic tree of Philodromidae and estimated the divergence times of Petrichus. Considering phylogenetic uncertainty, we assessed biogeographical hypotheses of the historical events associated with the diversification of these spiders in South America. Petrichus originated along the Pacific coastal deserts in the Central Andes during the Early Miocene. The species likely dispersed from the western to the eastern side of the Andes coincidently with the central Andean uplift. The diversification of these spiders is coeval with the expansion of open grassland formations during the Late Miocene and Early Pliocene. Multiple dispersal events occurred from the Monte desert to southern South America and eastward to Chaco between ∼8 and 2.5 Mya. The Andes might have played a role as a corridor favoring geographical range expansions and colonization of new environments. In addition, we also suggest that Philodromidae might have an Oligocene origin or earlier. Future analyses based on further evidence and larger taxon sampling should be carried out to corroborate our findings.
The astonishing diversity of plants and insects and their entangled interactions are cornerstones in terrestrial ecosystems. Co‐occurring with the species diversity is the diversity of plant secondary metabolites (PSMs). So far, their estimated number is of more than 200,000 compounds, which are not directly involved in plant growth and development but play important roles in helping plants handle their environment including the mediation of plant‐insect interactions. Here, we use plant volatile organic compounds (VOCs), a key olfactory communication channel that mediates plant‐insect interactions, as a showcase of PSMs. In spite of the cumulative knowledge on the functional, ecological, and microevolutionary roles of VOCs, we still lack a macroevolutionary understanding of how they evolved with plant‐insect interactions and contributed to species diversity throughout the long coevolutionary history of plants and insects. We first review the literature to summarise the current state‐of‐the‐art research on this topic. We then present various relevant types of phylogenetic methods suitable to answer macroevolutionary questions on plant VOCs and suggest future directions of employing phylogenetic approaches in studying plant VOCs and plant‐insect interactions. Overall, we found that current studies in this field are still very limited in their macroevolutionary perspective. Nevertheless, with the fast‐growing development of metabolome analysis techniques and phylogenetic methods, it is becoming increasingly feasible to integrate the advances of these two areas. We highlight promising approaches to generate new testable hypotheses and gain mechanistic understanding on the macroevolutionary roles of chemical communication in plant‐insect interactions. This article is protected by copyright. All rights reserved.
The Dasylirion genus is highly represented in the arid and semi-arid regions of Mexico and USA, playing important ecological and economical roles. Inferring the evolutionary patterns of this group will eventually facilitate understanding biological phenomena and outlining conservation and usage strategies. We performed a molecular phylogenetic analysis based on two chloroplast DNA regions: maturase-K gene ( matK ) and the large subunit of ribulose-1,5-bisphosphate carboxylase gene ( rbcL ). We constructed a phylogenetic tree by maximum likelihood with GTR as the sequence substitution model and a relaxed clock, inferred diversification patterns by lineage through time and explored the diversification rates of Dasylirion by the Yule model. The study included 11 species of the genus, which represent 50% of all its known species. We used two calibration points to date the tree, one based on fossil records of Acorus gramineus , and the other on the estimated stem age of the Yucca genus. The combined sequences of the two partial genes comprised 1455 bp and 18 polymorphic sites. We estimated an average substitution rate of 0.0005 nucleotide per million years for the concatenated DNA sequences. The molecular dating analysis estimated that the Dasylirion genus appeared more than 5.46 million years ago, with a rate of diversification of 0.0466 net speciation events per million years. The estimated age represents a lower bound, since not all Dasylirion species are included. These findings are consistent with other origin and diversification hypotheses for arid-land Asparagaceae in the Mexican highlands as a result of geomorphological events in North America.
Phylogenetic trees describe relationships between extant species, but beyond that their shape and their relative branch lengths can provide information on broader evolutionary processes of speciation and extinction. However, currently many of the most widely used macro-evolutionary models make predictions about the shapes of phylogenetic trees that differ considerably from what is observed in empirical phylogenies. Here, we propose a flexible and biologically plausible macroevolutionary model for phylogenetic trees where times to speciation or extinction events are drawn from a Coxian phase-type (PH) distribution. First, we show that different choices of parameters in our model lead to a range of tree balances as measured by Aldous’ $$\beta $$ β statistic. In particular, we demonstrate that it is possible to find parameters that correspond well to empirical tree balance. Next, we provide a natural extension of the $$\beta $$ β statistic to sets of trees. This extension produces less biased estimates of $$\beta $$ β compared to using the median $$\beta $$ β values from individual trees. Furthermore, we derive a likelihood expression for the probability of observing an edge-weighted tree under a model with speciation but no extinction. Finally, we illustrate the application of our model by performing both absolute and relative goodness-of-fit tests for two large empirical phylogenies (squamates and angiosperms) that compare models with Coxian PH distributed times to speciation with models that assume exponential or Weibull distributed waiting times. In our numerical analysis, we found that, in most cases, models assuming a Coxian PH distribution provided the best fit.
Studying the relationship between diversification and functional trait evolution among broadly co‐occurring clades can shed light on interactions between ecology and evolutionary history. However, evidence from many studies is compromised because of their focus on overly broad geographic or narrow phylogenetic scales. We addressed these limitations by studying 46 independent, biogeographically delimited clades of songbirds that dispersed from the Eastern Hemisphere into the Americas and assessed (1) whether diversification has varied through time and/or among clades within this assemblage, (2) the extent of heterogeneity in clade‐specific morphological trait disparity and (3) whether morphological disparity among these clades is consistent with a uniform diversification model. We found equivalent support for constant rates birth–death and density‐dependent speciation processes, with notable outliers having significantly fewer or more species than expected given their age. We also found substantial variation in morphological disparity among these clades, but that variation was broadly consistent with uniform evolutionary rates, despite the existence of diversification outliers. These findings indicate relatively continuous, ongoing morphological diversification, arguing against conceptual models of adaptive radiation in these continental clades. Additionally, they suggest surprisingly consistent diversification among the majority of these clades, despite tremendous variance in colonization history, habitat valences and trophic specializations that exist among continental clades of birds. Diversification trends vary between songbird clades in the Americas, but morphological evolution appears surprisingly uniform.
Unravelling why species richness shows such dramatic spatial variation is an ongoing challenge. Common to many theories is that increasing species richness (e.g. with latitude) requires a compensatory trade‐off on an axis of species' ecology. Spatial variation in species richness may also affect genetic diversity if large numbers of coexisting, related species result in smaller population sizes.
Here, we test whether increasing species richness results in differential occupation of morphospace by the constituent species, or decreases species' genetic diversity. We test for two potential mechanisms of morphological accommodation: denser packing in ecomorphological space, and expansion of the space. We then test whether species differ in their nucleotide diversity depending on allopatry or sympatry with relatives, indicative of potential genetic consequences of coexistence that would reduce genetic diversity in sympatry. We ask these questions in a spatially explicit framework, using a global database of avian functional trait measurements in combination with >120,000 sequences downloaded from GenBank.
We find that higher species richness within families is not systematically correlated with either packing in morphological space or overdispersion but, at the Class level, we find a general positive relationship between packing and species richness, but that points sampled in the tropics have comparatively greater packing than temperate ones relative to their species richness. We find limited evidence that geographical co‐occurrence with closely related species or tropical distributions decreases nucleotide diversity of nuclear genes; however, this requires further analysis.
Our results suggest that avian families can accumulate species regionally with minimal tradeoffs or cost, implying that external biotic factors do not limit species richness.
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Late Cenozoic climate change led to the progressive aridification of Australia over the past 15 million years. This gradual biome turnover fundamentally changed Australia's ecosystems, opening new niches and prompting diversification of plants and animals. One example are termites of the Australian Amitermes group (AAG), consisting of the Australian Amitermes and affiliated genera. Although the most speciose and diverse higher termite group in Australia, little is known about its evolutionary history. We used ancestral range reconstruction and diversification analyses to illuminate 1) phylogenetic relationships of the AAG, 2) biogeographical processes leading to the current continent‐wide distribution and 3) timing and pattern of diversification in the context of late Cenozoic climate change. By estimating the largest time‐calibrated phylogeny for this group to date, we demonstrate monophyly of the AAG and confirm that their ancestor arrived in Australia ~11–10 million years ago (Mya) from Southeast Asia. Ancestral range reconstruction indicates that Australia's monsoon region was the launching point for a continental radiation shaped by dispersal and within‐biome speciation rather than vicariance. We found that multiple arid‐zone species diversified from mesic and tropical ancestors in the Plio‐Pleistocene, but also observed diversification in the opposite direction. Finally, we show that diversification steadily increased from ~8 to 9 Mya during the ‘Hill Gap' and accelerated from ~4 Mya in concert with major ecological change during the Pliocene. Consistent with rapid diversification, species accumulation then slowed down into the present, likely caused by progressive niche saturation. This study provides a stepping stone for predicting future responses of Australia's termite fauna in the face of human‐mediated climate change.
With more than six million square kilometers, Amazonia hosts the largest tract of lowland tropical rainforest in the world and a large portion of the global terrestrial diversity. However, the temporal and spatial origins of this diversity remain poorly understood and need to be better comprehended to identify the processes responsible for this tremendous diversification. Amphibians are a particularly adequate group for investigating patterns of biogeographical history within Amazonia because they extensively diversified within the region and present important disparities in habitat use and dispersal abilities across groups. We first investigated the historical biogeography of the terra-firme genus Allobates and identified western Amazonia as an important source of diversification between 14 and 10 million years ago (Mya). This spatio-temporal pattern was coinciding with the existence of the Pebas system, a mega-wetland system that occupied most of western Amazonia during this period, that was unsuitable for terra-firme species. The Pebas system discharge was likely followed by an extension of terra-firme forests that likely fostered Allobates diversification. Our results also suggested that western Amazonia rivers might have subsequently (after 10 Mya) promoted diversification, by acting as semi-permeable barriers allowing speciation by dispersal and isolation. Secondly, we investigated the biogeographical history of the Pristimantis conspicillatus group which, instead, presented a continuous diversification throughout Neogene. This group displays a striking spatial pattern of diversification with four ancient clades that have diversified concomitantly in distinct areas in Amazonia and the Atlantic Forest, with much fewer dispersal events between areas than in Allobates. These differences suggest that amphibian species display differences in dispersal abilities that can be related to their life history traits. Finally, we compared the biogeographic histories of six frog clades, including the two aforementioned ones, that share comparable crown ages and span the Amazonian frog diversity in terms of life history traits, taxonomy, habitat use and reproduction modes. We identified western Amazonia as the principal source of diversification for Amazonian amphibians, although it acted as such only after 10 Mya for the groups that have adapted to various types of habitats; and only between 10 and 5 Mya for the ecologically conservative groups. This suggest that species with lower habitat availability reach niche filling more rapidly than ecologically adaptive species, resulting in shorter diversification phases. Our results also suggest that riverine barrier effect seems to have affected solely conservative groups particularly when the river course is stable over time. While these results were obtained by considering only a fraction of Amazonian diversity, they provide interesting insights on the influence of niche conservatism upon Amazonian evolutive trajectories, which will hopefully foster further and more ample research in this direction.
Background
An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates.
Results
We simulate phylogenies and molecular sequences under three different realistic rate variation models—one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used “relaxed clock” molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML.
Conclusions
We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.
Grasslands are predicted to experience a major biodiversity change by the year 2100. A better understanding of how grasslands have responded to past environmental changes will help predict the outcome of current and future environmental changes. Here, we explore the relationship between past atmospheric CO 2 and temperature fluctuations and the shifts in diversification rate of Poaceae (grasses) and Asteraceae (daisies), two exceptionally species-rich grassland families (~11,000 and~23,000 species, respectively). To this end, we develop a Bayesian approach that simultaneously estimates diversification rates through time from time-calibrated phylogenies and correlations between environmental variables and diversification rates. Additionally, we present a statistical approach that incorporates the information of the distribution of missing species in the phylogeny. We find strong evidence supporting a simultaneous increase in diversification rates for grasses and daisies after the most significant reduction of atmospheric CO 2 in the Cenozoic (~34 Mya). The fluctuations of paleo-temperatures, however, appear not to have had a significant relationship with the diversification of these grassland families. Overall, our results shed new light on our understanding of the origin of grasslands in the context of past environmental changes.
How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolution. Here, we use a near complete phylogenomic-scale phylogeny and a comprehensive morphological dataset comprising more than a thousand specimens to assess the role of biotic and abiotic processes in the diversification of monitor lizards (Varanidae). This charismatic group of lizards shows striking variation in species richness among its clades and multiple instances of endemic radiation in Indo-Australasia (i.e., the Indo-Australian Archipelago and Australia), one of Earth's most biogeographically complex regions. We found heterogeneity in diversification dynamics across the family. Idiosyncratic biotic and geographic conditions appear to have driven diversification and morphological evolution in three endemic Indo-Australasian radiations. Furthermore, incumbency effects partially explain patterns in the biotic exchange between Australia and New Guinea. Our results offer insight into the dynamic history of Indo-Australasia, the evolutionary significance of competition, and the long-term consequences of incumbency effects.
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Neotropical cichlids include over 550 species from Central and South America and the Caribbean and are increasingly recognized as models for studying evolutionary diversification. Cichlinae’s great morphological, ecological, and behavioral diversity is concentrated in the tribes Geophagini, Heroini, and Cichlasomatini. Feeding and swimming morphology broadly fit two gradients of ecomorphological differentiation: An “elongation axis” follows a ram–suction feeding gradient of deep-bodied fishes with diverse diets at one end and mostly predatory shallow-bodied taxa at the other end. Body and fin configurations correspond with habitats spanning open substrate to structured areas. A second gradient of morphology spans suction feeders and biters with benthic-feeding or complex three-dimensional habitats. Several body configurations reflect specializations to live in rapids. Rates of Cichlinae ecomorphological disparity and lineage diversification often showed early, rapid acceleration followed by a slowdown. Early divergence in South America was likely dominated by the radiation of Geophagini. Rapid geophagin diversification into new niches may have precluded divergence in other South American cichlids, particularly Heroini and Cichlasomatini. Further lineage and morphological divergence in Heroini increased after colonization of Central America. Cichlinae appear to have repeatedly radiated by taking advantage of ecological opportunity in novel environments across the Neotropics, resulting in widespread convergence.
Adaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genus Niphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe. There are relatively few known extant adaptive radiations in Europe that predate the Pleistocene. Here, Borko et al. characterize the diversity and diversification of the subterranean amphipod genus Niphargus, showing evidence for a large adaptive radiation associated with massif uplift 15 million years ago.
Heterogeneity in species diversity is driven by the dynamics of speciation and extinction, potentially influenced by organismal and environmental factors. Here, we explore macroevolutionary trends on a phylogeny of golden orbweavers (spider family Nephilidae). Our initial inference detects heterogeneity in speciation and extinction, with accelerated extinction rates in the extremely sexually size dimorphic Nephila and accelerated speciation in Herennia, a lineage defined by highly derived, arboricolous webs, and pronounced island endemism. We evaluate potential drivers of this heterogeneity that relate to organisms and their environment. Primarily, we test two continuous organismal factors for correlation with diversification in nephilids: phenotypic extremeness (female and male body length, and sexual size dimorphism as their ratio) and dispersal propensity (through range sizes as a proxy). We predict a bell-shaped relationship between factor values and speciation, with intermediate phenotypes exhibiting highest diversification rates. Analyses using SSE-class models fail to support our two predictions, suggesting that phenotypic extremeness and dispersal propensity cannot explain patterns of nephilid diversification. Furthermore, two environmental factors (tropical versus subtropical and island versus continental species distribution) indicate only marginal support for higher speciation in the tropics. Although our results may be affected by methodological limitations imposed by a relatively small phylogeny, it seems that the tested organismal and environmental factors play little to no role in nephilid diversification. In the phylogeny of golden orbweavers, the recent hypothesis of universal diversification dynamics may be the simplest explanation of macroevolutionary patterns.
Aim
We explore the biogeographic history of the Gondwanan lineage Triaenonychidae, a dispersal‐limited arachnid taxon that underwent a recent taxonomic revision based on phylogenomic data. We explicitly test hypotheses related to a biogeographical pattern of ‘common vicariance, rare dispersal’, predicted for dispersal‐limited taxa.
Location
Continental landmasses of former temperate Gondwanan terranes (southern South America, southern Africa, Madagascar, Australia, New Zealand, and New Caledonia).
Taxon
Triaenonychidae, Opiliones, Arachnida.
Methods
Utilizing a recently published phylogenomic data set based on ultra‐conserved elements, we conduct Bayesian divergence dating analyses, ancestral area estimation in a likelihood model testing framework, and analyses of macroevolutionary dynamics. Results are correlated with geological history and palaeoclimate reconstructions to infer biogeographic history and distribution.
Results
We find that divergence dates of ancestral Triaenonychidae pre‐date continental breakup of Gondwana and could be attributed to palaeoclimatic differentiation across Gondwana. There is evidence for two separate expansion routes that span eastern and western Gondwana corresponding to northern warmer climate and southern cooler climate lineages. Many divergences across intercontinental lineages coincide with the timing of continental fragmentation, supporting vicariance as a dominant force. However, some lineages are supported as obvious examples of rare long‐distance dispersal. Biogeographic results support the predicted pattern of common vicariance and rare dispersal for these dispersal‐limited organisms.
Main conclusions
Vicariance due to continental fragmentation was important in the early diversification of Triaenonychidae. Their unique combination and degrees of dispersal ability and microhabitat preference resulted in complex phylogenetic patterns of geographic distribution not typically seen in other animal taxa. Examining biogeographic patterns across recent studies of arachnid taxa with varying dispersal ability, it is clear that biological characteristics play an important role in the relative importance of dispersal and vicariance (dispersal–vicariance continuum) for any given taxon and can be useful in forming testable a priori hypotheses.
Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations’ ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.
The ‘Out of India’ hypothesis is often invoked to explain patterns of distribution among Southeast Asian taxa. According to this hypothesis, Southeast Asian taxa originated in Gondwana, diverged from their Gondwanan relatives when the Indian subcontinent rifted from Gondwana in the Late Jurassic, and colonized Southeast Asia when it collided with Eurasia in the early Cenozoic. A growing body of evidence suggests these events were far more complex than previously understood, however. The first quantitative reconstruction of the biogeography of Asian forest scorpions (Scorpionidae Latreille, 1802: Heterometrinae Simon, 1879) is presented here. Divergence time estimation, ancestral range estimation, and diversification analyses are used to determine the origins, dispersal and diversification patterns of these scorpions, providing a timeline for their biogeographical history that can be summarized into four major events. (1) Heterometrinae diverged from other Scorpionidae on the African continent after the Indian subcontinent became separated in the Cretaceous. (2) Environmental stresses during the Cretaceous–Tertiary (KT) mass extinction caused range contraction, restricting one clade of Heterometrinae to refugia in southern India (the Western Ghats) and Sri Lanka (the Central Highlands). (3) Heterometrinae dispersed to Southeast Asia three times during India’s collision with Eurasia, the first dispersal event occurring as the Indian subcontinent brushed up against the western side of Sumatra, and the other two events occurring as India moved closer to Eurasia. (4) Indian Heterometrinae, confined to southern India and Sri Lanka during the KT mass extinction, recolonized the Deccan Plateau and northern India, diversifying into new, more arid habitats after environmental conditions stabilized. These hypotheses, which are congruent with the geological literature and biogeographical analyses of other taxa from South and Southeast Asia, contribute to an improved understanding of the dispersal and diversification patterns of taxa in this biodiverse and geologically complex region.
Diversity does not drive speciation
The role of the environment in the origin of new species has long been debated. Harvey et al. examined the evolutionary history and species diversity of suboscine birds in the tropics (see the Perspective by Morlon). Contrary to expectations that the tropics have higher rates of speciation, the authors observed that higher and more constant speciation rates occur in harsh environments relative to the tropics. Thus, for this group of birds, diversification in temperate to Arctic regions followed by the movement and retention of species in the tropics results in their higher local levels of species diversity.
Science , this issue p. 1343 ; see also p. 1268
A fundamental goal of ecology is to reveal generalities in the myriad types of interactions among species, such as competition, mutualism and predation. Another goal is to explain the enormous differences in species richness among groups of organisms. Here, we show how these two goals are intertwined: we find that different types of species interactions have predictable impacts on rates of species diversification, which underlie richness patterns. On the basis of a systematic review, we show that interactions with positive fitness effects for individuals of a clade (e.g. insect pollination for plants) generally increase that clade's diversification rates. Conversely, we find that interactions with negative fitness effects (e.g. predation for prey, competition) generally decrease diversification rates. The sampled clades incorporate all animals and land plants, encompassing 90% of all described species across life. Overall, we show that different types of local-scale species interactions can predictably impact large-scale patterns of diversification and richness.
Inferences about macroevolutionary process have traditionally depended solely on the fossil record, but such inferences can be strengthened by also considering the shapes of the phylogenetic trees that link extant taxa. The realization that phylogenies reflect macroevolutionary processes has fed to a growing literature of theoretical and comparative studies of tree shape. Two aspects of tree shape are particularly important: tree balance and the distribution of branch lengths. We examine and evaluate recent developments in and connections between these two aspects, and suggest directions for future research. Studies of tree shape promise useful and powerful tests of macroevolutionary hypotheses. With appropriate further research, tree shape may help us detect mass extinctions and adaptive radiations, measure continuous variation in speciation and extinction rates, and associate changes in these rates with ecological or biogeographical causes. The usefulness of tree shape extends well beyond the study of macroevolution. We discuss applications to other areas of biology, including coevolution, phylogenetic inference, population biology, and developmental biology.
Although several decades of study have revealed the ubiquity of variation of evolutionary rates among sites, reliable methods for studying rate variation were not developed until very recently. Early methods fit theoretical distributions to the numbers of changes at sites inferred by parsimony and substantially underestimate the rate variation. Recent analyses show that failure to account for rate variation can have drastic effects, leading to biased dating of speciation events, biased estimation of the transition:transversion rate ratio, and incorrect reconstruction of phylogenies.
The analysis of the tempo and mode of evolution has a strong tradition in paleontology. Recent advances in molecular phylogenetic reconstruction make it possible to complement this work by using data from extant species.
This paper presents an estimate of the phylogeny of all 203 species of primate. The composite tree is derived by applying a parsimony algorithm to over a hundred previous estimates, and is well resolved, containing 160 nodes. The ages of over half the clades in the tree have been estimated from information in the literature. Bootstrapping has been used to indicate the degree of certainty associated with each clade. The tree will be a useful framework for comparative biologists and shows which areas of primate phylogeny are still only sketchily known.
We apply new statistical methods to a recent estimate of the phylogeny of all living primate species to test a range of models of cladogenesis. Null models in which probabilities of speciation and extinction do not differ among contemporaneous lineages are not consistent with the phylogeny. We present evidence that the net rate of cladogenesis (speciation rate minus extinction rate) increased in the lineage leading to the Cercopithecidae (Old World monkeys), and that there have been further increases in some lineages within that family. Such increases suggest the occurrence of clade selection, although we have not identified the selected trait or traits. There is no evidence that the net rate of cladogenesis is a function either of how many primate lineages are already present or of time. Intriguingly, three other clades--Strepsirhini, Platyrrhini and Hominoidea--appear to have had very similar rates of clade growth, in spite of their great biological differences.
Phylogenies reconstructed from contemporary taxa do not contain information about lineages that have gone extinct. We derive probability models for such phylogenies, allowing real data to be compared with specified null models of evolution, and lineage birth and death rates to be estimated.
Computer simulations are developed and employed to examine the expected temporal distributions of nodes under a null model of stochastic lineage bifurcation and extinction. These Markovian models of phylogenetic process were constructed so as to permit direct comparisons against empirical phylogenetic trees generated from molecular or other information available solely from extant species. For replicate simulated phylads with n extant species, cumulative distribution functions (cdf's) of branching times were calculated, and compared (using the Kolmogorov-Smirnov test statistic D) to those from three published empirical trees. Molecular phylogenies for columbine plants and avian cranes showed statistically significant departures from the null expectations, in directions indicating recent and ancient species' radiations, respectively, whereas a molecular phylogeny for the Drosophila virilis species group showed no apparent historical clustering of branching events. Effects of outgroup choice and phylogenetic frame of reference were investigated for the columbines and found to have a predictable influence on the types of conclusions to be drawn from such analyses. To enable other investigators to statistically test for nonrandomness in temporal cladogenetic pattern in empirical trees generated from data on extant species, we present tables of mean cdf's and associated probabilities under the null model for expected branching times in phylads of varying size. The approaches developed in this report complement and extend those of other recent methods for employing null models to assess the statistical significance of pattern in evolutionary trees.
An improved Bayesian method is presented for estimating phylogenetic trees using DNA sequence data. The birth-death process with species sampling is used to specify the prior distribution of phylogenies and ancestral speciation times, and the posterior probabilities of phylogenies are used to estimate the maximum posterior probability (MAP) tree. Monte Carlo integration is used to integrate over the ancestral speciation times for particular trees. A Markov Chain Monte Carlo method is used to generate the set of trees with the highest posterior probabilities. Methods are described for an empirical Bayesian analysis, in which estimates of the speciation and extinction rates are used in calculating the posterior probabilities, and a hierarchical Bayesian analysis, in which these parameters are removed from the model by an additional integration. The Markov Chain Monte Carlo method avoids the requirement of our earlier method for calculating MAP trees to sum over all possible topologies (which limited the number of taxa in an analysis to about five). The methods are applied to analyze DNA sequences for nine species of primates, and the MAP tree, which is identical to a maximum-likelihood estimate of topology, has a probability of approximately 95%.
A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.
Shrews of the genus Sorex are characterized by a Holarctic distribution, and relationships among extant taxa have never been fully resolved. Phylogenies have been proposed based on morphological, karyological, and biochemical comparisons, but these analyses often produced controversial and contradictory results. Phylogenetic analyses of partial mitochondrial cytochrome b gene sequences (1011 bp) were used to examine the relationships among 27 Sorex species. The molecular data suggest that Sorex comprises two major monophyletic lineages, one restricted mostly to the New World and one with a primarily Palearctic distribution. Furthermore, several sister-species relationships are revealed by the analysis. Based on the split between the Soricinae and Crocidurinae subfamilies, we used a 95% confidence interval for both the calibration of a molecular clock and the subsequent calculation of major diversification events within the genus Sorex. Our analysis does not support an unambiguous acceleration of the molecular clock in shrews, the estimated rate being similar to other estimates of mammalian mitochondrial clocks. In addition, the data presented here indicate that estimates from the fossil record greatly underestimate divergence dates among Sorex taxa.
The molecular clock hypothesis remains an important conceptual and analytical tool in evolutionary biology despite the repeated observation that the clock hypothesis does not perfectly explain observed DNA sequence variation. We introduce a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process. Events of substitution rate change are placed onto a phylogenetic tree according to a Poisson process. When an event of substitution rate change occurs, the current rate of substitution is modified by a gamma-distributed random variable. Parameters of the model can be estimated using Bayesian inference. We use Markov chain Monte Carlo integration to evaluate the posterior probability distribution because the posterior probability involves high dimensional integrals and summations. Specifically, we use the Metropolis-Hastings-Green algorithm with 11 different move types to evaluate the posterior distribution. We demonstrate the method by analyzing a complete mtDNA sequence data set from 23 mammals. The model presented here has several potential advantages over other models that have been proposed to relax the clock because it is parametric and does not assume that rates change only at speciation events. This model should prove useful for estimating divergence times when substitution rates vary across lineages.
As progress in cell developmental biology carries on at a breakneck speed, new techniques constantly arise to plug the gaps left by traditional strategies. Cellular Interactions in Development provides detailed discussion and protocols of some of these new techniques, which allow the manipulation of developing organisms such as Drosophila or plants, when and where cells interact with each other to influence their development. The book looks at the really exciting innovations of the identification and functional test of molecules which control these cellular behaviours. The book also describes a number of new ways of hunting for these important proteins involved in cellular communication. A fully comprehensive manual which will prove indispensable to researchers in the fields of cell, developmental, and molecular biology.
One tool in the study of the forces that determine species diversity is the null, or simple, model. The fit of predictions to observations, good or bad, leads to a useful paradigm or to knowledge of forces not accounted for, respectively. It is shown how simple models of speciation and extinction lead directly to predictions of the structure of phylogenetic trees. These predictions include both essential attributes of phylogenetic trees: lengths, in the form of internode distances; and topology, in the form of internode links. These models also lead directly to statistical tests which can be used to compare predictions with phylogenetic trees that are estimated from data. Two different models and eight data sets are considered. A model without species extinction consistently yielded predictions closer to observations than did a model that included extinction. It is proposed that it may be useful to think of the diversification of recently formed monophyletic groups as a random speciation process without extinction.
Phylogenies that are reconstructed without fossil material often contain approximate dates for lineage splitting. For example, particular nodes on molecular phylogenies may be dated by known geographic events that caused lineages to split, thereby calibrating a molecular clock that is used to date other nodes. On the one hand, such phylogenies contain no information about lineages that have become extinct. On the other hand, they do provide a potentially useful testing ground for ideas about evolutionary processes. Here we first ask what such reconstructed phylogenies should be expected to look like under a birth-death process in which the birth and death parameters of lineages remain constant through time. We show that it is possible to estimate both the birth and death rates of lineages from the reconstructed phylogenies, even though they contain no explicit information about extinct lineages. We also show how such phylogenies can reveal mass extinctions and how their characteristic footprint can be distinguished from similar ones produced by density-dependent cladogenesis.
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.
If all species in a clade are equally likely to speciate or become extinct, then highly symmetric and highly asymmetric phylogenetic trees are unlikely to result. Variation between species in speciation and extinction rates can cause excessive asymmetry. We developed six non-parametric statistical tests that test for nonrandom patterns of branching in any bifurcating tree. The tests are demonstrated by applying them to two published phylogenies for genera of beetles. Comparison of the power of the six statistics under a simple model of biased speciation suggests which of them may be most useful for detecting nonrandom tree shapes.
Shrews of the genus Sorex are characterized by a Holarctic distribution, and relationships among extant taxa have never been fully resolved. Phylogenies have been proposed based on morphological, karyological, and biochemical comparisons, but these analyses often produced controversial and contradictory results. Phylogenetic analyses of partial mitochondrial cytochrome b gene sequences (1011 bp) were used to examine the relationships among 27 Sorex species. The molecular data suggest that Sorex comprises two major monophyletic lineages, one restricted mostly to the New World and one with a primarily Palearctic distribution. Furthermore, several sister-species relationships are revealed by the analysis. Based on the split between the Soricinae and Crocidurinae subfamilies, we used a 95% confidence interval for both the calibration of a molecular clock and the subsequent calculation of major diversification events within the genus Sorex. Our analysis does not support an unambiguous acceleration of the molecular clock in shrews, the estimated rate being similar to other estimates of mammalian mitochondrial clocks. In addition, the data presented here indicate that estimates from the fossil record greatly underestimate divergence dates among Sorex taxa.
The 27 species of Dendroica wood-warblers represent North America's most spectacular avian adaptive radiation. Dendroica species exhibit high levels of local sympatry and differ in plumage and song, but the group contrasts with other well–know avian adaptive radiations such as the Hawaiian honeycreepers and Galapagos finches in that Dendroica species have differentiated modestly in morphometric traits related to foraging. Instead, sympatric Dendroica tend to partition resources behaviourally and they have become a widely cited example of competitive exclusion. We explore the temporal structure of Dendroica diversification via a phylogeny based on 3639 nucleotides of protein–coding mitochondrial DNA (mtDNA). The taxa sampled include 60 individuals representing 24 Dendroica species and a variety of other paruline warbler and outgroup species. Mitochondrial divergences among Dendroica species were generally large (mean pairwise interspecific distances, 10.0%) and many species were rooted in a basal polytomy.
The prevalence of long terminal branches indicates that these species have evolved efficient isolating mechanisms that hav prevented mtDNA introgression despite the many opportunities for hybridization resulting from local sympatry. Comparison with a null model of random bifurcation–extinction demonstrate that cladogenesis in Dendroica has been clustered non–randomly with respect to time, with a significant burst of speciation occurring early in the histor of the genus, possibly as long ago as the Late Miocene or Early Pliocene periods. Although this non–random clustering of speciatio is consistent with the pattern expected of an adaptive radiation, the age of the Dendroica radiation suggests it is an ‘ancient species flock’ in which most extant species represent lineages that have long been evolutionaril independent.
One tool in the study of the forces that determine species diversity is the null, or simple, model. The fit of predictions to observations, good or bad, leads to a useful paradigm or to knowledge of forces not accounted for, respectively. It is shown how simple models of speciation and extinction lead directly to predictions of the structure of phylogenetic trees. These predictions include both essential attributes of phylogenetic trees: lengths, in the form of internode distances; and topology, in the form of internode links. These models also lead directly to statistical tests which can be used to compare predictions with phylogenetic trees that are estimated from data. Two different models and eight data sets are considered. A model without species extinction consistently yielded predictions closer to observations than did a model that included extinction. It is proposed that it may be useful to think of the diversification of recently formed monophyletic groups as a random speciation process without extinction.
Developed a quantitative null model based on a randomly branching Markovian process to test the stochasticity of patterns of diversity as represented by phylogenesis of contemporary organisms. -from Authors
If all species in a clade are equally likely to speciate or become extinct, then highly symmetric and highly asymmetric phylogenetic trees are unlikely to result. Variation between species in speciation and extinction rates can cause excessive asymmetry. We developed six non-parametric statistical tests that test for nonrandom patterns of branching in any bifurcating tree. The tests are demonstrated by applying them to two published phylogenies for genera of beetles. Comparison of the power of the six statistics under a simple model of biased speciation suggests which of them may be most useful for detecting nonrandom tree shapes.
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.
A new method for estimating divergence times when evolutionary rates are variable across lineages is proposed. The method, called nonparametric rate smoothing (NPRS), relies on minimization of ancestor-descendant local rate changes and is motivated by the likelihood that evolutionary rates are autocorrelated in time. Fossil information pertaining to minimum and/or maximum ages of nodes in a phylogeny is incorporated into the algorithms by constrained optimization techniques. The accuracy of NPRS was examined by comparison to a clock-based maxi-mum-likelihood method in computer simulations. NPRS provides more accurate estimates of divergence times when (1) sequence lengths are sufficiently long, (2) rates are truly nonclocklike, and (3) rates are moderately to highly autocorrelated in time. The algorithms were applied to estimate divergence times in seed plants based on data from the chloroplast rbcL gene. Both constrained and unconstrained NPRS methods tended to produce divergence time estimates more consistent with paleobotanical evidence than did clock-based estimates.
Species lists change for a variety of reasons, including new information and preferences for different species concepts. Uncertainty over species numbers is potentially damaging to tests of proposed correlates of species richness, particularly if taxonomic changes are biased toward some clades over others. We investigate the effects of this error and bias by testing the same suite of macroevolutionary hypotheses in seven different arrangements of primate taxonomy. This is the first time that the effects of the ‘species problem’ have been systematically investigated in this way. Primates are an excellent model system for examining the effects of taxonomic uncertainty: species numbers have doubled in the past two decades, with the fastest growth in the Neotropics. We found that different variables were significantly associated with species richness in each taxonomic arrangement. However, there were no significant differences among taxonomies in the regression slopes for any predictor variable. We found no tendency for significant correlations to occur in taxonomies with more species, suggesting that the results cannot be explained by a lack of power in the smaller taxonomies. The findings are discussed with reference to the wider implications for testing macroevolutionary hypotheses.
Few issues in evolutionary biology have received as much attention over the years or have generated as much controversy as those involving evolutionary rates. One unresolved issue is whether or not shifts in speclation and/or extinction rates are closely tied to the origin of 'key' innovations in evolution. This discussion has long been dominated by 'time-based' methods using data from the fossil record. Recently, however, attention has shifted to 'tree-based' methods, in which time, if It plays any role at all, is incorporated secondarily, usually based on molecular data. Tests of hypotheses about key innovations do require Information about phylogenetic relationships, and some of these tests can be implemented without any information about time. However, every effort should be made to obtain information about time, which greatly increases the power of such tests.
A new method to estimate the diversification rate of a lineage from a phylogeny of recent species is presented. This uses survival models to analyse the ages of the species as derived from the phylogeny. Survival models can analyse missing data where the exact date of death is unknown (censoring). This approach allows us to include missing data (species not included in a detailed phylogenetic study) in the analysis, provided a minimum age is known for these species. Three models are presented, with emphasis on temporal variation in diversification rates. The maximum likelihood method and Akaike information criteria are used to derive estimators and tests of hypotheses. A simulation study demonstrates that the method is able to detect a temporal variation in diversification rate only when it is present, avoiding type I and type II errors. A lineage with ten species may be sufficient to detect a temporal variation in diversification rate even with 50 per cent of missing data. An application is presented with data from a phylogeny of birds of the genus Ramphocelus.
Studies of shifts in diversification rates and adaptive radiations are difficult when there are no fossils because past events cannot be inferred. The phylogenies of recent species, however, allow one to infer the patterns of past diversifications. I present a new method for estimating the diversification rate of a lineage, provided that a phylogeny of recent species, constructed, for instance, with molecular data, is available. This method was inspired by survival models and takes into account species that are not included in detailed phylogenetic data, provided that approximate dates of origin of these species are known. Likelihood ratio tests and Akaike Information Criterion make it possible to test for differences in diversification among lineages or groups of lineages and, thus, to evaluate adaptive radiation hypotheses. The present modeling approach can easily be extended to include temporal variations in diversification rates. A simulation study showed that the method is statistically consistent, avoiding Type I and Type II errors, and that it is robust to periodic or random fluctuations in the speciation rate. An example is presented with a composite phylogeny of primates.
The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.
Pleistocene glaciations have been suggested as major events influencing speciation rates in vertebrates. Avian paleontological studies suggest that most extant species evolved in the Pleistocene Epoch and that species' durations decreased through the Pleistocene because of heightened speciation rates. Molecular systematic studies provide another data base for testing these predictions. In particular, rates of diversification can be determined from molecular phylogenetic trees. For example, an increasing rate of speciation (but constant extinction) requires shorter intervals between successive speciation events on a phylogenetic tree. Examination of the cumulative distribution of reconstructed speciation events in mtDNA phylogenies of 11 avian genera, however, reveals longer intervals between successive speciation events as the present time is approached, suggesting a decrease in net diversification rate through the Pleistocene Epoch. Thus, molecular systematic studies do not indicate a pulse of Pleistocene diversification in passerine birds but suggest, instead, that diversification rates were lower in the Pleistocene than for the preceding period. Documented habitat shifts likely led to the decreased rate of diversification, although from molecular evidence we cannot discern whether speciation rates decreased or extinction rates increased.
Molecular phylogenies can be used to reject null models of the way we think evolution occurred, including patterns of lineage extinction. They can also be used to provide maximum likelihood estimates of parameters associated with lineage birth and death rates. We illustrate: (i) how molecular phylogenies provide information about the extent to which particular clades are likely to be under threat from extinction; (ii) how cursory analyses of molecular phylogenies can lead to incorrect conclusions about the evolutionary processes that have been at work; and (iii) how different evolutionary processes leave distinctive marks on the structure of reconstructed phylogenies.
Birth-Death (Bi-De) is an application for the Apple Macintosh which simulates the growth of phylogenetic trees using various models of lineage birth and death. The trees produced are intended to be analogous to those reconstructed from molecular sequence data. The user may define a constant birth rate and death rate or a function describing how these rates vary by time or population size. Instantaneous mass extinctions can also be simulated. The package allows the tree produced to be used as a template for the simulated evolution of molecular sequence data under a range of different transition models.
Motivation:
Phylogenetic trees constructed from molecular sequences contain information about the evolutionary or population dynamical processes that created them. Here we describe a computer package (End-Epi) that uses graphical methods to allow researchers to make inferences about these processes from their data. Statistical analyses can be performed to test the consistency of the data with various competing hypotheses.
Availability:
End-Epi can be obtained by WWW from http://evolve.zoo.ox.ac.uk/ and by anonymous FTP from ftp://evolve.zoo.ox.ac.uk/packages/End-Epi10.hqx. This file contains the compiled application, the manual and a test tree.
The evolutionary success of flowering plants has been attributed to key innovations that originated at the base of that clade.
Maximum likelihood methods were used to assess whether branching rate increases were correlated with the origin of these traits.
Four hypotheses for the basal relationships of angiosperms were examined by methods that are robust to uncertainty about the
timing of internal branch points. Recent hypotheses based on molecular evidence, or on a combination of molecular and morphological
characters, imply that large increases in branching rate did not occur until after the putative key innovations of angiosperms
had evolved.
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Reconstructing shifts in diversi¢cation rates on phylogenetic trees Testing the stochasticity of patterns of organismal diversity: an improved null model Estimating the rate of evolution of the rate of molecular evolution
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End-Epi: an application for inferring phylogenetic and population dyna-mical processes from molecular sequences Stochastic models of phylogeny and the evolution of diversity
- A Rambaut
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- P H Harvey
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Recognising the forest for the trees: testing temporal patterns of cladogenesis using a null model of stochastic diversi¢cation Among-site rate variation and its impact on phylogenetic analyses Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method
- K Wollenberg
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End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences
- A Purvis
- S Nee
- P H Harvey