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Calyceraceae: Unexpected Diversification Pattern in the Southern Andes
Abstract
Calyceraceae comprises 46 species mostly endemic to the Andes and Patagonia in Southern South America, and it is the sister family of Asteraceae, one of the largest Angiosperm families.
With a robust phylogeny and with an exceptionally good sampling fraction, we performed macroevolution and biogeographic analyses to understand paleodiversity dynamics through time and space, and its potential drivers. We address the impact of the Andean uplift, global temperature, life forms, and biogeography on Calyceraceae diversification through a time-calibrated phylogeny.
Calyceraceae diversification was homogeneous through time and followed a low speciation rate for the last 24 Mya, with no lineage differing much in their diversification dynamics. In accordance with the homogeneous speciation rate, we found that neither the Andean uplift, nor the evolution of global average temperature, nor the different life forms have affected its diversification. The Southern Andes is the centre of origin of the family and major clades within it, and most dispersal events occurred from the Andes to Patagonia. Most Calyceraceae species seem to have originated, evolved, and dispersed within the Argentinean Arid Diagonal, indicating that niche conservatism could have played an important role in the evolution of Calyceraceae. Differences in macroevolution dynamics could explain the asymmetry of species richness in the two sister families Asteraceae-Calyceraceae.
... ; https://doi.org/10. 1101/2023 rbcL. The study by Cooper et al. (2012b), which estimated the crown age of Lepidoziaceae at 116 Ma, used nine fossil calibrations and a data set comprising only three molecular markers from 212 liverwort species (64 Lepidoziaceae). ...
... Neotropical endemic taxa either have origins in the Neotropics itself, e.g., the angiosperm family Calyceraceae (Brignone et al., 2023), or from elsewhere, e.g., the fern family Cyatheaceae (Korall and Pryer, 2014). Our study shows that Micropterygioideae are among the lineages that the Neotropical region holds in its collection of taxa with circum-Antarctic links. ...
... ; https://doi.org/10.1101/2023 ...
Lepidoziaceae are the third-largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of 13 genetic markers, sampled from 147 species. Based on our phylogenetic estimate, we used statistical dispersal-vicariance analysis to reconstruct the biogeographic history of the family. We inferred a crown age of 197 Ma (95% credible interval 157-240 Ma) for the family in the Australian region, with most major lineages also originating in the same region. Micropterygioideae are placed as the sister lineage to Lembidioideae, with these two groups diverging from each other about 132 Ma in the South American-Australian region. Our results suggest a circum-Antarctic link between Micropterygioideae and the rest of the family, along with extinction of the lineage in the region. Crown Micropterygioideae were inferred to have arisen 45 million years ago in South America, before the continent separated from Antarctica. Our study reveals the influence of past geological events on the evolution and distribution of a widespread and diverse family of liverworts.
Lepidoziaceae are the third-largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of 13 genetic markers, sampled from 147 species. Based on our phylogenetic estimate, we used statistical dispersal-vicariance analysis to reconstruct the biogeographic history of the family. We inferred a crown age of 197 Ma (95% credible interval 157–240 Ma) for the family in the Australian region, with most major lineages also originating in the same region. Micropterygioideae are placed as the sister group to Lembidioideae, with these two lineages diverging from each other about 132 Ma in the South American–Australian region. With South America and Australia being connected through Antarctica at the time, our results suggest a circum-Antarctic link between Micropterygioideae and the rest of the family. Crown Micropterygioideae were inferred to have arisen 45 Ma in South America before the continent separated from Antarctica. Extinction from southern temperate regions might explain the present-day restriction of Micropterygioideae to the Neotropics. Our study reveals the influence of past geological events, such as continental drift, on the evolution and distribution of a widespread and diverse family of liverworts.
One of the central goals of macroevolution is to understand palaeodiversity dynamics through time and space, and its potential drivers. Estimating palaeodiversity dynamics has been historically addressed with the fossil record because it directly reflects the past variations of biodiversity. Unfortunately, some groups or regions lack a good fossil record, and dated phylogenies can be useful to estimate deep-time diversification dynamics. Recent methodological developments have unlocked the possibility to investigate palaeodiversity dynamics with dated phylogenies by using birth-death models with non-homogeneous rates through time and across clades. One of them, which models rate heterogeneity as a local clock, seems particularly promising to detect clades whose diversity has declined through time. However, empirical applications of the method have been hampered by its lack of automation as leading the analysis by hand was costly and error-prone.
Here we propose an automation with additional features accounting for recent developments and we implement it in the R package RPANDA. We also test the approach with simulations focusing on its ability to detect shifts of diversification and to infer palaeodiversity dynamics. Finally, we illustrate the automation by investigating the palaeodiversity dynamics of Cetacea, Vangidae, Parnassiinae, and Cycadales.
Simulations showed that we accurately detected shifts of diversification although false shift detections were higher for complex diversification models. The median global error of palaeodiversity dynamics estimated with the automated model is low showing that the method can capture diversity declines. We detected shifts of diversification for three of the four empirical examples considered (Cetacea, Parnassiinae and Cycadales). These heterogeneities of diversification rates unveil a waxing-and-waning pattern due to a phase of negative net diversification rate embedded in the trees after isolating recent radiations.
Our work allows to easily apply non-homogeneous models of diversification in which rates can vary through time and across clades to reconstruct palaeodiversity dynamics. By doing so, we detected palaeodiversity declines among three of the four groups tested, highlighting that such periods of negative net diversification might be common. We discuss the extent to which this approach might provide reliable estimates of extinction rates and we provide guidelines for users.
There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras. Here, the authors use full-plastome phylogenomics and multiclade comparative models to reconstruct the tempo and drivers of six European Alpine angiosperm lineages before and during the Pleistocene. They find that geographic divergence and bedrock shifts drive speciation events, while diversification rates remained steady.
The Andes are the world's most biodiverse mountain chain, encompassing a complex array of ecosystems from tropical rainforests to alpine habitats. We provide a synthesis of Andean vascular plant diversity by estimating a list of all species with publicly available records, which we integrate with a phylogenetic dataset of 14 501 Neotropical plant species in 194 clades. We find that (i) the Andean flora comprises at least 28 691 georeferenced species documented to date, (ii) Northern Andean mid-elevation cloud forests are the most species-rich Andean ecosystems, (iii) the Andes are a key source and sink of Neotropical plant diversity, and (iv) the Andes, Amazonia, and other Neotropical biomes have had a considerable amount of biotic interchange through time.
Mountainous areas host a disproportionately large fraction of Earth's biodiversity, suggesting a causal relationship between mountain building and biological diversification. Mountain clade radiations are generally associated with changes in environment, climate, and the increase in heterogeneity therein during mountain building. However, examining the causal relationship between mountain building and diversification is a complex challenge, because isolating the effects of surface uplift from other abiotic (climate) or biotic variables is not straightforward. In this study, we investigate the relative contributions of abiotic climate-driven (temperature) and geology-driven (elevation) drivers on evolutionary rates of ancient groups of organisms in the South American Andes. We present regional curves of Andean elevation based on a recent compilation of paleo-elevational data back to the Late Cretaceous, and analyse the diversification history of six Andean frog and lizard families that originated equally far back in time. For two clades (Aromobatidae and Leptodactylidae), we find that they diversified most rapidly during the early phase of mountain building (Late Cretaceous - Paleogene), when the first high-elevation habitats emerged in South America. The diversification of one clade (Centrolenidae) is correlated with Cenozoic temperature variations, with higher speciation rates during warm periods. The last three clades (Dendrobatidae, Hemiphractidae and Liolaemidae) are best explained by environment-independent diversification, although for Liolaemidae, an almost equally strong positive correlation was found between speciation and Andean elevation since the late Eocene. Our findings imply that throughout the long-lived history of surface uplift in the Andes, mountain building drove the diversification of different clades at different times, while not directly affecting other clades. Our study illustrates the importance of paleogeographic reconstructions that capture the complexity and heterogeneity of mountain building in our understanding of the effects that a changing environment plays in shaping biodiversity patterns observed today.
Carex subgenus Psyllophorae is an engaging study group due to its early diversification compared to most Carex lineages, and its remarkable disjunct distribution in four continents corresponding to three independent sections: sect. Psyllophorae in Western Palearctic, sect. Schoenoxiphium in Afrotropical region, and sect. Junciformes in South America (SA) and SW Pacific. The latter section is mainly distributed in Patagonia and the Andes, where it is one of the few Carex groups with a significant in situ diversification. We assess the role of historical geo-climatic events in the evolutionary history of the group, particularly intercontinental colonization events and diversification processes, with an emphasis on SA. We performed an integrative study using phylogenetic (four DNA regions), divergence times, diversification rates, biogeographic reconstruction, and bioclimatic niche evolution analyses. The crown age of subg. Psyllophorae (early Miocene) supports this lineage as one of the oldest within Carex. The diversification rate probably decreased over time in the whole subgenus. Geography seems to have played a primary role in the diversification of subg. Psyllophorae. Inferred divergence times imply a diversification scenario away from primary Gondwanan vicariance hypotheses and suggest long-distance dispersal-mediated allopatric diversification. Section Junciformes remained in Northern Patagonia since its divergence until Plio-Pleistocene glaciations. Andean orogeny appears to have acted as a northward corridor, which contrasts with the general pattern of North-to-South migration for temperate-adapted organisms. A striking niche conservatism characterizes the evolution of this section. Colonization of the SW Pacific took place on a single long-distance dispersal event from SA. The little ecological changes involved in the trans-Pacific disjunction imply the preadaptation of the group prior to the colonization of the SW Pacific. The high species number of the section results from simple accumulation of morphological changes (disparification), rather than shifts in ecological niche related to increased diversification rates (radiation).
Mountain building in the Andes, the longest continental mountain range on Earth, started in the Late Cretaceous but was highly diachronous. Reconstructing the timing of surface uplift for each of the different Andean regions is of crucial importance for our understanding of continental-scale moisture transport and atmospheric circulation, the origin and evolution of the Amazon River and Rainforest, and ultimately, the origin and evolution of species on the world most biodiverse continent. Here, I present (1) a compilation of estimates of paleoelevation for 36 geomorphological domains of the Andes from the literature, and (2) a paleoelevation reconstruction of the Andes since 80 Ma. In the northern Andes, uplift started in the Late Cretaceous (~70 Ma) in the Western and Central Cordilleras of Ecuador, while the northwestern corner of the continent was still covered by shallow seas. Mountain building migrated progressively northwards, with the Perija Range and Santander Massif uplifting since the Oligocene and the Eastern Cordillera, Garzon Massif and Mérida Andes since the Miocene. In the central Andes, uplift migrated from west to east, whereby the main phase of uplift in the Western Cordillera took place during the Late Cretaceous-Paleocene, in the western Puna plateau during the Paleocene, in the eastern Puna plateau during the early-mid Miocene, and in the Altiplano and Eastern Cordillera during the mid-late Miocene. In the southern Patagonian Andes, significant elevation was already in place at 80 Ma and in western Patagonia, modern elevations were reached in the early Eocene. A second pulse of uplift and eastward migration of the orogenic front occurred during the early-mid Miocene. The reconstruction developed here is made available as a series of raster files, so that it can be used as input for a variety of studies in the solid Earth, climate, and biological sciences, thereby being a stepping stone on the path towards a better understanding of the coevolution of the solid Earth, landscapes, climate, and life in South America.
Calyceraceae is a small South American family sister to Asteraceae. Previous phylogenetic analyses revealed that Calyceraceae genera are para‐ or polyphyletic. Fruit and inflorescence characters used historically as diagnostic in Calyceraceae taxonomy have proven unreliable in defining natural groups. Surprisingly, flower morphology does not appear in diagnoses of Calyceraceae genera, and its diversity and evolution has remained unstudied before now. Based on phylogenetic analyses using six molecular markers and an almost complete sampling of the family (43 of 46 species), we propose a taxonomic re‐arrangement of Calyceraceae. In the search for diagnostic morphological characters, we studied flower structure diversity and optimized 12 discrete characters by maximum parsimony and maximum likelihood to reconstruct floral evolution in the family. Calyceraceae species are arranged in eight genera (three monotypic, five with 6 to 13 species). Two genera are new (Anachoretes, Asynthema), one is reinstated (Leucocera), with the remaining five emended (Acicarpha, Boopis, Calycera, Gamocarpha, Moschopsis). Flower morphology is notably diverse but provides only a few diagnostic features. Many floral attributes likely reflect selection for pollination or fruit dispersal rather than phylogenetic affinity. In the context of this taxonomic revision, we include a key to genera, new and emended diagnoses, and new combinations.
Biodiversity is not evenly distributed among related groups, raising questions about the factors contributing to such disparities. The sunflower family (Asteraceae, >26,000 species) is among the largest and most diverse plant families, but its species diversity is concentrated in a few subfamilies, providing an opportunity to study the factors affecting biodiversity. Phylotranscriptomic analyses here of 244 transcriptomes and genomes produced a phylogeny with strong support for the monophyly of Asteraceae and the monophyly of most subfamilies and tribes. This phylogeny provides a reference for detecting changes in diversification rates and possible factors affecting Asteraceae diversity, which include global climate shifts, whole‐genome duplications (WGDs), and morphological evolution. The origin of Asteraceae was estimated at ~83 Mya, with most subfamilies having diverged before the Cretaceous–Paleocene boundary. Phylotranscriptomic analyses supported the existence of 41 WGDs in Asteraceae. Changes to herbaceousness and capitulescence with multiple flower‐like capitula, often with distinct florets and scaly pappus/receptacular bracts, are associated with multiple upshifts in diversification rate. WGDs might have contributed to the survival of early Asteraceae by providing new genetic materials to support morphological transitions. The resulting competitive advantage for adapting to different niches would have increased biodiversity in Asteraceae.
Much of our understanding of Earth's past climate comes from the measurement of oxygen and carbon isotope variations in deep-sea benthic foraminifera. Yet, long intervals in existing records lack the temporal resolution and age control needed to thoroughly categorize climate states of the Cenozoic era and to study their dynamics. Here, we present a new, highly resolved, astronomically dated, continuous composite of benthic foraminifer isotope records developed in our laboratories. Four climate states-Hothouse, Warmhouse, Coolhouse, Icehouse-are identified on the basis of their distinctive response to astronomical forcing depending on greenhouse gas concentrations and polar ice sheet volume. Statistical analysis of the nonlinear behavior encoded in our record reveals the key role that polar ice volume plays in the predictability of Cenozoic climate dynamics.
Aim
Plant life‐forms characterize key morphological strategies that enable large‐scale comparisons of plant communities. This study applies Raunkiær's plant life‐form concept that was developed for temperate climate to a subtropical island flora, in parts, dominated by summer aridity. We quantify how plant life‐form patterns as well as patterns of important plant functional traits (PFTs) relate to important climate and topographic characteristics.
Location
La Palma, Canary Islands.
Taxon
Flora of La Palma.
Methods
We assigned each native plant species a plant life‐form, that is, phanerophyte, chamaephyte, hemicryptophyte, geophyte and therophyte, as well as PFTs (succulence and N‐fixer). We used stacked species distribution models to assess occurrence probability for each species using the Atlantis database (500 m × 500 m grid). We related richness and percentage values for each plant life‐form and PFT to climate and topography.
Results
Plant life‐forms and PFTs showed a clear pattern within geographic but also climate space, while topography had a minor effect. Phanerophytes mainly contributed to the flora in humid areas. Chamaephytes and hemicryptophytes most strongly contributed to the summit scrub flora and, to some degree, also to the arid coastal regions. Geophytes and therophytes were mainly found in dry coastal regions. N‐fixers contributed mainly to warm‐arid and cool‐arid regions, while succulent species were mainly found in arid coastal regions.
Main conclusions
Raunkiær's plant life‐form concept can be comprehensively transferred to a subtropical island flora by adapting to local unfavourable growing conditions, that is, aridity. Using the strong environmental gradients offered by our study island, we identify substantial climate‐driven variation in patterns of plant life‐forms and PFTs that might be used for large‐scale comparisons in macroecological studies. The growth strategies reflected in Raunkiær's plant life‐forms suggest differences in species establishment and coexistence dynamics within different parts of the island's climate space.
Asterids are one of the most successful angiosperm lineages, exhibiting extensive morphological diversity and including a number of important crops. Despite their biological prominence and value to humans, the deep asterid phylogeny has not been fully resolved, and the evolutionary landscape underlying their radiation remains unknown. To resolve the asterid phylogeny, we sequenced 213 transcriptomes/genomes and combined them with other datasets, representing all accepted orders and nearly all families of asterids. We show fully supported monophyly of asterids, Berberidopsidales as sister to asterids, monophyly of all orders except Icacinales, Aquifoliales and Bruniales, and monophyly of all families except Icacinaceae and Ehretiaceae. Novel taxon placements benefited from the expanded sampling with living collections from botanical gardens, resolving hitherto uncertain relationships. The remaining ambiguous placements here are likely due to limited sampling and could be addressed in the future with relevant additional taxa. Using our well-resolved phylogeny as reference, divergence time estimates support an Aptian (Early Cretaceous) origin of asterids and the origin of all orders before the K-Pg boundary. Ancestral state reconstruction at the family level suggests that the asterid ancestor was a woody terrestrial plant with simple leaves, bisexual and actinomorphic flowers with free petals and free anthers, a superior ovary with a style, and drupaceous fruits. WGD analyses provide strong evidence for 33 WGDs in asterids and one in Berberidopsidales, including four supra-familial and seven familial/sub-familial WGDs. Our results advance the understanding of asterid phylogeny and provide numerous novel evolutionary insights into their diversification and morphological evolution.
With ca. 300 species of herbs, shrubs and subshrubs adapted to saline or alkaline soils, the evolution of the genus Atriplex is key to understand the development of semi‐arid environments worldwide. Previous phylogenetic analyses of Atriplex, including only a few species from South America, especially in comparison with North American species represented, proposed a North American origin for the South American Atriplex, through more than one dispersal event. Since South America is one of the four centres of Atriplex diversity, with a high number of endemic species, a wider and more representative sampling of this region is essential to understand the origin and evolution of the genus Atriplex in the Americas. We performed a phylogenetic analysis with estimated clade ages and an ancestral range estimation focused on the American species of Atriplex, to identify South American lineages, their relationships with other lineages of the genus (and particularly with North American ones), and to unravel their biogeographical history in the Americas. Phylogenetic analyses were conducted with sequence data from ITS, ETS and atpB‐rbcL spacer markers, using maximum parsimony, Bayesian inference and maximum likelihood approaches. The DEC+J model implemented in BioGeoBEARS was applied in order to infer ancestral ranges. The Americas were colonized by Atriplex in two independent dispersal events: (1) the C4 Atriplex from Eurasia or Australia, and (2) the C3 Atriplex (represented only by the extant A. chilensis) from Eurasia. The C4 American lineage of Atriplex originated roughly 10.4 Ma (95% HPD = 13.31–7.62 Myr) in South America, where two lineages underwent in situ diversification and evolved sympatrically. North America was colonized by Atriplex from South America; later, one lineage moved from North America to South America. Most of the extant species have arisen in the last 3–4 Myr, in Pliocene–Pleistocene. We detected some South American taxa differing in position between both nuclear and atpB‐rbcL spacer partitions, which could be explained by chloroplast capture.
Diversification rates vary over time, yet the factors driving these variations remain unclear. Temporal declines in speciation rates have often been interpreted as the effect of ecological limits, competition, and diversity dependence, emphasising the role of biotic factors. Abiotic factors, such as climate change, are also supposed to have affected diversification rates over geological time scales, yet direct tests of these presumed effects have mainly been limited to few clades well represented in the fossil record. If warmer climatic periods have sustained faster speciation, this could explain slowdowns in speciation during the Cenozoic climate cooling. Here, we apply state‐of‐the art diversity‐dependent and temperature‐dependent phylogenetic models of diversification to 218 tetrapod families, along with constant rate and time‐dependent models. We confirm the prevalence of diversification slowdowns, and find as much support for temperature‐dependent than diversity‐dependent models. These results call for a better integration of these two processes in studies of diversification dynamics.
The sunflower family, Asteraceae, comprises 10% of all flowering plant species and displays an incredible diversity of form. Asteraceae are clearly monophyletic, yet resolving phylogenetic relationships within the family has proven difficult, hindering our ability to understand its origin and diversification. Recent molecular clock dating has suggested a Cretaceous origin, but the lack of deep sampling of many genes and representative taxa from across the family has impeded the resolution of migration routes and diversifications that led to its global distribution and tremendous diversity. Here we use genomic data from 256 terminals to estimate evolutionary relationships, timing of diversification(s), and biogeographic patterns. Our study places the origin of Asteraceae at ∼83 MYA in the late Cretaceous and reveals that the family underwent a series of explosive radiations during the Eocene which were accompanied by accelerations in diversification rates. The lineages that gave rise to nearly 95% of extant species originated and began diversifying during the middle Eocene, coincident with the ensuing marked cooling during this period. Phylogenetic and biogeographic analyses support a South American origin of the family with subsequent dispersals into North America and then to Asia and Africa, later followed by multiple worldwide dispersals in many directions. The rapid mid-Eocene diversification is aligned with the biogeographic range shift to Africa where many of the modern-day tribes appear to have originated. Our robust phylogeny provides a framework for future studies aimed at understanding the role of the macroevolutionary patterns and processes that generated the enormous species diversity of Asteraceae.
Understanding how and why diversification rates vary through time and space and across species groups is key to understanding the emergence of today’s biodiversity. Phylogenetic approaches aimed at identifying variations in diversification rates during the evolutionary history of clades have focused on exceptional shifts subtending evolutionary radiations. While such shifts have undoubtedly affected the history of life, identifying smaller but more frequent changes is important as well. We developed ClaDS—a new Bayesian approach for estimating branch-specific diversification rates on a phylogeny that relies on a model with changes in diversification rates at each speciation event. We show, using Monte Carlo simulations, that the approach performs well at inferring both small and large changes in diversification. Applying our approach to bird phylogenies covering the entire avian radiation, we find that diversification rates are remarkably heterogeneous within evolutionarily restricted species groups. Some groups such as Accipitridae (hawks and allies) cover almost the full range of speciation rates found across the entire bird radiation. As much as 76% of the variation in branch-specific rates across this radiation is due to intraclade variation, suggesting that a large part of the variation in diversification rates is due to many small, rather than few large, shifts.
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.
Testing hypotheses on the drivers of clade evolution and trait diversification provides insight into many aspects of evolutionary biology. Often, studies investigate only the intrinsic biological properties of organisms as the causes of diversity, however extrinsic properties of a clade's environment, particularly geological history, may also offer compelling explanations. The Andes are a young mountain chain known to have shaped many aspects of climate and diversity of South America. The Liolaemidae are a radiation of South American reptiles with over 300 species found across all biomes and with similar numbers of egg‐laying and live‐bearing species. Using the most complete dated phylogeny of the family, we tested the role of Andean uplift in the biogeography, diversification patterns, and parity mode of the Liolaemidae. We find that the Andes has promoted lineage diversification and acted as a species pump into surrounding biomes. We also find strong support for the role of Andean uplift in boosting the species diversity of these lizards via allopatric fragmentation. Finally, we find repeated shifts in parity mode associated with changing thermal niches, with live‐bearing favored in cold climates and egg‐laying favoured in warm climates. Importantly, we find evidence for possible reversals to oviparity, an evolutionary transition believed to be extremely rare.
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The Andes are an important biogeographic region in South America extending for about 8000 km from Venezuela to Argentina. They are – along with the Patagonian steppes – the main distribution area of ca. 18 polyploid species of Silene sect. Physolychnis. Using nuclear ITS and plastid psbE-petG and matK sequences, flow cytometric ploidy level estimations and chromosome counts, and including 13 South American species, we explored the origin and diversification of this group. Our data suggest a single, late Pliocene or early Pleistocene migration of the North American S. verecunda lineage to South America, which was followed by dispersal and diversification of this tetraploid lineage in the Andes, other Argentinian mountain ranges and the Patagonian steppes. Later in the Pleistocene South American populations hybridized with the S. uralensis lineage, which led to allopolyploidisation and origin of decaploid S. chilensis and S. echegarayi occurring at high elevations. Additionally, we show that the morphological differentiation in leaf shape correlated with divergent habitats (high elevation Andes vs. lower elevation Patagonian steppes) is also supported phylogenetically, especially in the ITS tree. Lastly, the species boundaries among the narrow-leaved Patagonian steppe species are poorly resolved and need more thorough taxonomic revision.
The most important Cenozoic marine transgression in Patagonia occurred during the late Oligocene–early Miocene when marine waters of Pacific and Atlantic origin flooded most of southern South America including the present Patagonian Andes between ~41° and 47° S. The age, correlation, and tectonic setting of the different marine formations deposited during this period are debated. However, recent studies based principally on U–Pb geochronology and Sr isotope stratigraphy, indicate that all of these units had accumulated during the late Oligocene–early Miocene. The marine transgression flooded a vast part of southern South America and, according to paleontological data, probably allowed for the first time in the history of this area a transient connection between the Pacific and Atlantic oceans. Marine deposition started in the late Oligocene–earliest Miocene (~26–23 Ma) and was probably caused by a regional event of extension related to major plate reorganization in the Southeast Pacific. Progressive extension and crustal thinning allowed a generalized marine flooding of Patagonia that reached its maximum extension at ~20 Ma. It was followed by a phase of compressive tectonics that started around 19–16 Ma and led to the growth of the Patagonian Andes. The youngest (~19–15 Ma) marine deposits that accumulated in the eastern Andean Cordillera and the extra-Andean regions are coeval with fluvial synorogenic deposits and probably had accumulated under a compressive regime.
Mountain ranges harbour exceptionally high biodiversity, which is now under threat from rapid environmental change. However, despite decades of effort, the limited availability of data and analytical tools has prevented a robust and truly global characterization of elevational biodiversity gradients and their evolutionary origins1,2. This has hampered a general understanding of the processes involved in the assembly and maintenance of montane communities2,3,4. Here we show that a worldwide mid-elevation peak in bird richness is driven by wide-ranging species and disappears when we use a subsampling procedure that ensures even species representation in space and facilitates evolutionary interpretation. Instead, richness corrected for range size declines linearly with increasing elevation. We find that the more depauperate assemblages at higher elevations are characterized by higher rates of diversification across all mountain regions, rejecting the idea that lower recent diversification rates are the general cause of less diverse biota. Across all elevations, assemblages on mountains with high rates of past temperature change exhibit more rapid diversification, highlighting the importance of climatic fluctuations in driving the evolutionary dynamics of mountain biodiversity. While different geomorphological and climatic attributes of mountain regions have been pivotal in determining the remarkable richness gradients observed today, our results underscore the role of ongoing and often very recent diversification processes in maintaining the unique and highly adapted biodiversity of higher elevations.
Phylogenetic studies of geographic range evolution are increasingly using statistical model selection methods to choose among variants of the dispersal-extinction-cladogenesis (DEC) model, especially between DEC and DEC+J, a variant that emphasizes “jump dispersal,” or founder-event speciation, as a type of cladogenetic range inheritance scenario. Unfortunately, DEC+J is a poor model of founder-event speciation, and statistical comparisons of its likelihood with DEC are inappropriate. DEC and DEC+J share a conceptual flaw: cladogenetic events of range inheritance at ancestral nodes, unlike anagenetic events of dispersal and local extinction along branches, are not modelled as being probabilistic with respect to time. Ignoring this probability factor artificially inflates the contribution of cladogenetic events to the likelihood, and leads to underestimates of anagenetic, time-dependent range evolution. The flaw is exacerbated in DEC+J because not only is jump dispersal allowed, expanding the set of cladogenetic events, its probability relative to non-jump events is assigned a free parameter, j, that when maximized precludes the possibility of non-jump events at ancestral nodes. DEC+J thus parameterizes the mode of speciation, but like DEC, it does not parameterize the rate of speciation. This inconsistency has undesirable consequences, such as a greater tendency towards degenerate inferences in which the data are explained entirely by cladogenetic events (at which point branch lengths become irrelevant, with estimated anagenetic rates of 0). Inferences with DEC+J can in some cases depart dramatically from intuition, e.g. when highly unparsimonious numbers of jump dispersal events are required solely because j is maximized. Statistical comparison with DEC is inappropriate because a higher DEC+J likelihood does not reflect a more close approximation of the “true” model of range evolution, which surely must include time-dependent processes; instead, it is simply due to more weight being allocated (via j) to jump dispersal events whose time-dependent probabilities are ignored. In testing hypotheses about the geographic mode of speciation, jump dispersal can and should instead be modelled using existing frameworks for state-dependent lineage diversification in continuous time, taking appropriate cautions against Type I errors associated with such methods. For simple inference of ancestral ranges on a fixed phylogeny, a DEC-based model may be defensible if statistical model selection is not used to justify the choice, and it is understood that inferences about cladogenetic range inheritance lack any relation to time, normally a fundamental axis of evolutionary models.
Geologic events promoting the aridization of southern South America contributed to lineage divergences and species differentiation through geographic (allopatric divergence) and biotic and abiotic factors (ecological divergence). For the genus Anarthrophyllum, which is distributed in arid and semi-arid regions of Patagonia, we assessed how these factors affected species diversification and reconstructed its possible biogeographic history in South American arid environments. Sequences were obtained from two molecular markers: the ITS nuclear region and the trnS-trnG plastid region. Using Parsimony, Maximum likelihood and Bayesian inference individual gene trees were reconstructed, and a species tree was obtained using multi-species coalescent analysis. Divergence times among species were estimated using secondary calibrations. Flexible Bayesian models and stochastic character mapping were used to elucidate ancestral geographic distributions and the evolution of the floral and vegetative phenotypes in the genus. Gene trees and species tree analyses strongly support Anarthrophyllum as monophyletic; all analyses consistently retrieved three well-supported main clades: High Andean Clade, Patagonian Clade 1, and Patagonian Clade 2. Main diversification events occurred concomitant with the Andean uplift and steppe aridization; the Andean mountain range possibly acted as a species barrier for the High Andean Clade. Vegetative traits showed adaptations to harsh climates in some clades, while pollinator-related floral features were associated with independent diversification in bee- and bird-pollinated clades within both Patagonian Clades. In conclusion, evolutionary and biogeographic history of Anarthrophyllum resulted from the action of ecological, historical, and geographic factors that acted either alternatively or simultaneously.
Calyceraceae is a small family with six traditionally recognized genera and 47 species from southern South America. Most species grow along the Andes (of both Argentina and Chile) and in arid regions of the Patagonian steppe. This family belongs to the well-supported MGCA clade within Asterales, which includes Menyanthaceae + Goodeniaceae + Calyceraceae + Asteraceae. Calyceraceae is monophyletic and sister to Asteraceae, one of the five largest families of angiosperms. Although Calyceraceae is clearly distinct as a family, its genera are not, and taxonomic revisionary effort has confirmed the lack of sharp boundaries among genera. We performed a phylogenetic analysis of Calyceraceae with a broad taxon sampling (41 of 47 species), and with sequence data from multiple regions from the nuclear (ITS) and plastid genomes (ycg6-psbM, psbM-trnD, trnS-trnG, trnH-psbA, trnD-trnT) using maximum parsimony and Bayesian approaches. We aimed at identifying monophylectic groups, their putative morphological synapomorphies and their geographical distribution; we also estimated divergence times and examined chromosomes numbers in an evolutionary context. We obtained well-resolved and strongly supported phylogenies that show Calyceraceae to be divided into two major clades with geographically structured subclades within each. Our results indicate that an early split within Calyceraceae occurred about 27.4 Ma, probably related to differential changes in chromosome numbers, which allowed the two lineages to evolve in sympatry. We found that major natural subgroups diverged 15–12 Ma, following the Early-Miocene South Andes construction stage. Finally, the diversification of the extant species is probably associated to Andean orogeny and climate changes in the last 5–4 Myr. We recovered Acicarpha as monophyletic, while the remaining traditionally recognized genera of Calyceraceae are para- or polyphyletic. Most species of Moschopis are included in the Glutinose group, but M. monocephala is more closely related to some Calycera species. Calycera is divided into two clades: the Calycera group and the Pilose group. All species of Nastanthus are placed in a well-supported main group with species of Gamocarpha and Boopis. Gamocarpha could be monophyletic after exclusion of G. dentata and G. angustifolia, but is nested within Nastanthus and Boopis species. Boopis is clearly polyphyletic with its species distributed in all main groups.
Aim
The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long‐distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood ( ML ) methods and newly developed biogeographical stochastic mapping ( BSM ) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present‐day distribution.
Location
Worldwide.
Methods
Building on a recently inferred megaphylogeny of Solanaceae, we conducted ML model fitting of a range of biogeographical models with the program ‘BioGeo BEARS ’. We used the parameters from the best fitting model to estimate ancestral range probabilities and conduct stochastic mapping, from which we estimated the number and type of biogeographical events.
Results
Our best model supported South America as the ancestral area for the Solanaceae and its major clades. The BSM analyses showed that dispersal events, particularly range expansions, are the principal mode by which members of the family have spread beyond South America.
Main conclusions
For Solanaceae, South America is not only the family's current centre of diversity but also its ancestral range, and dispersal was the principal driver of range evolution. The most common dispersal patterns involved range expansions from South America into North and Central America, while dispersal in the reverse direction was less common. This directionality may be due to the early build‐up of species richness in South America, resulting in large pool of potential migrants. These results demonstrate the utility of BSM not only for estimating ancestral ranges but also in inferring the frequency, direction and timing of biogeographical events in a statistically rigorous framework.
Biodiversity results from multiple evolutionary mechanisms, including genetic variation and natural selection. Whole genome duplications (WGDs), or polyploidizations, provide opportunities for large-scale genetic modifications. Many evolutionarily successful lineages, including angiosperms and vertebrates, are ancient polyploids, suggesting that WGDs are a driving force in evolution. However, this hypothesis is challenged by the observed lower speciation and higher extinction rates of recently formed polyploids than diploids. Asteraceae includes about ten percent of angiosperm species, is thus undoubtedly one of the most successful lineages and paleopolyploidization was suggested early in this family using a small number of datasets. Here, we used genes from 64 new transcriptome datasets and others to reconstruct a robust Asteraceae phylogeny, covering 73 species from 18 tribes in six subfamilies. We estimated their divergence times and further identified multiple potential ancient WGDs within several tribes and shared by the Heliantheae alliance, core Asteraceae (Asteroideae-Mutisioideae), and also with the sister family Calyceraceae. For two of the WGD events, there were subsequent great increases in biodiversity; the older one proceeded the divergence of at least 10 subfamilies within 10 My, with great variation in morphology and physiology, while the other was followed by extremely high species richness in the Heliantheae alliance clade. Our results provide different evidence for several WGDs in Asteraceae, and reveal distinct association among WGD events, dramatic changes in environment and species radiations, providing a possible scenario for polyploids to overcome the disadvantages of WGDs and to evolve into lineages with high biodiversity.
Dated molecular phylogenetic trees show that the Andean uplift had a major impact on South American biodiversity. For many Andean groups, accelerated diversification (radiation) has been documented. However, not all Andean lineages appear to have diversified following the model of rapid radiation, particularly in the central and southern Andes. Here, we investigated the diversification patterns for the largest South American-endemic lineage of Brassicaceae, composed of tribes Cremolobeae, Eudemeae and Schizopetaleae (CES clade). Species of this group inhabit nearly all Andean biomes and adjacent areas including the Atacama-Sechura desert, the Chilean Matorral and the Patagonian Steppe. First, we studied diversification times and historical biogeography of the CES clade. Second, we analysed diversification rates through time, lineages and associated life forms. Results demonstrate that early diversification of the CES clade occurred in the early to mid-Miocene (c. 12-19 Mya) and involved the central Andes, the southern Andes and the Patagonian Steppe, and the Atacama-Sechura desert. The Chilean Matorral and northern Andes were colonized subsequently in the early Pliocene (4-5 Mya). Diversification of the CES clade was recovered as a gradual process without any evidence for rate shifts or rapid radiation, in contrast to many other Andean groups analysed so far. Diversification time/rates and biogeographical patterns obtained for the CES clade are discussed and compared with patterns and conclusions reported for other Andean plant lineages.
Historical biogeography has been characterized by a large diversity of methods and unresolved debates about which processes, such as dispersal or vicariance, are most important for explaining distributions. A new R package, BioGeoBEARS, implements many models in a common likelihood framework, so that standard statistical model selection procedures can be applied to let the data choose the best model. Available models include a likelihood version of DIVA (“DIVALIKE”), LAGRANGE’s DEC model, and BAYAREA, as well as “+J” versions of these models which include founder-event speciation, an important process left out of most inference methods. I use BioGeoBEARS on a large sample of island and non-island clades (including two fossil clades) to show that founder-event speciation is a crucial process in almost every clade, and that most published datasets reject the non-J models currently in widespread use. BioGeoBEARS is open-source and freely available for installation at the Comprehensive R Archive Network at http://CRAN.R-project.org/package=BioGeoBEARS. A step-by-step tutorial is available at http://phylo.wikidot.com/biogeobears.
I. II. III. IV. V. VI. References SUMMARY: Alpine plant radiations are compared across the world's major mountain ranges and shown to be overwhelmingly young and fast, largely confined to the Pliocene and Pleistocene, and some of them apparently in the early explosive phase of radiation. Accelerated diversification triggered by island-like ecological opportunities following the final phases of mountain uplift, and in many cases enabled by the key adaptation of perennial habit, provides a general model for alpine plant radiations. Accelerated growth form evolution facilitated by perenniality provides compelling evidence of ecological release and suggests striking parallels between island-like alpine, and especially tropicalpine radiations, and island radiations more generally. These parallels suggest that the world's mountains offer an excellent comparative system for explaining evolutionary radiation.
© 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.
Abstract—
This taxonomic treatment is the first in the genus Calycera based on a detailed study of morphology and a critical analysis of species boundaries. In this revision, nine species and four varieties are recognized, one new combination (
C. crassifolia
var.
spinulosa
), nine new synonymies (Anomocarpus axillaris, Boopis integrifolia, Calycera boopidea, C. crenata, C. foliosa, C. intermedia, C. pulvinata f. cauligera, C. squarrosa, and Gymnocaulus viridiflorus),
six new lectotypifications (for Anomocarpus, Boopis gracilis, Calycera crenata, C. pulvinata f. cauligera, C. sessiliflora, and C. sympaganthera), and one neotypification (for Calycera involucrata) are established. Updated morphological
descriptions (including an emended description of C. herbacea var. sinuata) and geographical distributions are included for each species. Analyses of their life forms and inflorescence, flower, and fruit morphology are presented.
Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and modify it to create a new model, DEC+J, which adds founder-event speciation, the importance of which is governed by a new free parameter, j. The identifiability of DEC and DEC+J is tested on datasets simulated under a wide range of macroevolutionary models where geography evolves jointly with lineage birth/death events. The results confirm that DEC and DEC+J are identifiable even though these models ignore the fact that molecular phylogenies are missing many cladogenesis and extinction events. The simulations also indicate that DEC will have substantially increased errors in ancestral range estimation and parameter inference when the true model includes +J. DEC and DEC+J are compared on 13 empirical datasets drawn from studies of island clades. Likelihood ratio tests indicate that all clades reject DEC, and AICc model weights show large to overwhelming support for DEC+J, for the first time verifying the importance of founder-event speciation in island clades via statistical model choice. Under DEC+J, ancestral nodes are usually estimated to have ranges occupying only one island, rather than the widespread ancestors often favored by DEC. These results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods.
The nomenclatural revision of 51 names previously published, combined or synonymyzed under the genus Nastanthus (Calyceraceae) is presented. Six species are recognized with correct names and new synonyms established. The nomenclature of Nastanthus ventosus, Nastanthus scapigerus and Nastanthus compactus is updated, giving a total of 45 synonyms. Lectotypes for Boopis caespitosa, Boopis scapigera, Boopis spathulata, Nastanthus laciniatus, Boopis araucana, Calycera ventosa, Nastanthus pinnatifidus and Boopis breviflora are here designated. A map with the geographic distributions, complete species descriptions, corrected illustrations, and a new key to accepted species of Nastanthus, are included.
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.
Diversification rates vary across species as a response to various factors, including environmental conditions and species-specific features. Phylogenetic models that allow accounting for and quantifying this heterogeneity in diversification rates have proven particularly useful for understanding clades diversification. Recently, we introduced the cladogenetic diversification rate shift model (ClaDS), which allows inferring multiple rate changes of small magnitude across lineages. Here we present a new inference technique for this model that considerably reduces computation time through the use of data augmentation and provide an implementation of this method in Julia. In addition to drastically reducing computation time, this new inference approach provides a posterior distribution of the augmented data, that is the tree with extinct and unsampled lineages as well as associated diversification rates. In particular, this allows extracting the distribution through time of both the mean rate and the number of lineages. We assess the statistical performances of our approach using simulations and illustrate its application on the entire bird radiation.
Disjunct clades between the southern and the tropical Andes represent a biogeographical pattern that has not been studied. One of the plant groups showing this disjunction is the clade formed by the genera Archidasyphyllum, Arnaldoa and Fulcaldea (Asteraceae, Barnadesioideae). Archidasyphyllum is distributed in central and southern Chile and adjacent Argentina and is sister to the latter two, which in turn form a clade centered in northern Peru and southern Ecuador, with one species of Fulcaldea in Bahia, Brazil. The western American clades are separated by a distance of ca. 2500 km in direct line and have no representatives through the entire arid and hyperarid regions of the Pacific deserts and the dry Puna. We hypothesized that the Neogene origin of aridity in this intervening area might be responsible for this disjunction. To address this hypothesis, we estimated divergence times and ancestral range and quantified the climatic niches of the respective clades and compared them to each other and with the intervening area. Our results suggest a Miocene split of this clade from an ancestor previously distributed in the Central Andes, where the species of this clade are currently absent. Colonization of NE Brazil by Fulcaldea may have occurred during the Pliocene. The niche analysis rejects climatic niche conservatism and the intervening area is found to be climatically different from the current ranges occupied by either clade. We suggest that the global cooling trend in the Miocene and concomitant hyperaridity in the Pacific deserts and southern Central Andean highlands played a crucial role in the formation of this disjunct pattern and that the climatic niches of each clade have subsequently shifted in different directions.
The Calyceraceae (47 spp.) is a small family of plants that is sister to the Asteraceae (∼ 25,000 spp.), one of the largest families of angiosperms. Most members of Calyceraceae are endemic to the Andes and Patagonia, representing an excellent model within which to study diversification patterns in these regions. The single phylogenetic study of Calyceraceae conducted to date revealed that the boundaries of most genera and several species of this family require further analyses, especially the “Nastanthus–Gamocarpha” clade. In this study, we reconstructed the phylogeny of the “Nastanthus Gamocarpha” clade using multispecies coalescent models under BPP and StarBeast2 programs, sampling 63 individuals from 13 of the 14 species recognized to date. We then used this phylogenetic framework to delimit species using BFD and the A11 method implemented in BPP. Species limits suggested through a coalescent approach were then re-evaluated in the light of morphology, geography, and phenology. Coalescent-based methods indicated that most putative lineages could be recognized as distinct species. Morphological, geographical, ecological, and phenological data further supported species delimitation. Necessary taxonomic changes are proposed. Namely, the paraphyletic Nastanthus is synonymized under Gamocarpha, while five species of Boopis are transferred into Gamocarpha. We used an integrative taxonomic approach to recognize 13 species and one subspecies within the newly circumscribed genus Gamocarpha.
An update of the Angiosperm Phylogeny Group (APG) classification of the orders and families of angiosperms is presented. Several new orders are recognized: Boraginales, Dilleniales, Icacinales, Metteniusiales and Vahliales. This brings the total number of orders and families recognized in the APG system to 64 and 416, respectively. We propose two additional informal major clades, superrosids and superasterids, that each comprise the additional orders that are included in the larger clades dominated by the rosids and asterids. Families that made up potentially monofamilial orders, Dasypogonaceae and Sabiaceae, are instead referred to Arecales and Proteales, respectively. Two parasitic families formerly of uncertain positions are now placed: Cynomoriaceae in Saxifragales and Apodanthaceae in Cucurbitales. Although there is evidence that some families recognized in APG III are not monophyletic, we make no changes in Dioscoreales and Santalales relative to APG III and leave some genera in Lamiales unplaced (e.g. Peltanthera). These changes in familial circumscription and recognition have all resulted from new results published since APG III, except for some changes simply due to nomenclatural issues, which include substituting Asphodelaceae for Xanthorrhoeaceae (Asparagales) and Francoaceae for Melianthaceae (Geraniales); however, in Francoaceae we also include Bersamaceae, Ledocarpaceae, Rhynchothecaceae and Vivianiaceae. Other changes to family limits are not drastic or numerous and are mostly focused on some members of the lamiids, especially the former Icacinaceae that have long been problematic with several genera moved to the formerly monogeneric Metteniusaceae, but minor changes in circumscription include Aristolochiaceae (now including Lactoridaceae and Hydnoraceae; Aristolochiales), Maundiaceae (removed from Juncaginaceae; Alismatales), Restionaceae (now re-including Anarthriaceae and Centrolepidaceae; Poales), Buxaceae (now including Haptanthaceae; Buxales), Peraceae (split from Euphorbiaceae; Malpighiales), recognition of Petenaeaceae (Huerteales), Kewaceae, Limeaceae, Macarthuriaceae and Microteaceae (all Caryophyllales), Petiveriaceae split from Phytolaccaceae (Caryophyllales), changes to the generic composition of Ixonanthaceae and Irvingiaceae (with transfer of Allantospermum from the former to the latter; Malpighiales), transfer of Pakaraimaea (formerly Dipterocarpaceae) to Cistaceae (Malvales), transfer of Borthwickia, Forchhammeria, Stixis and Tirania (formerly all Capparaceae) to Resedaceae (Brassicales), Nyssaceae split from Cornaceae (Cornales), Pteleocarpa moved to Gelsemiaceae (Gentianales), changes to the generic composition of Gesneriaceae (Sanango moved from Loganiaceae) and Orobanchaceae (now including Lindenbergiaceae and Rehmanniaceae) and recognition of Mazaceae distinct from Phrymaceae (all Lamiales).
Slowdowns in lineage accumulation in phylogenies suggest that speciation rates decline as diversity increases. Likelihood methods have been developed to detect such diversity dependence. However, a thorough test of whether such approaches correctly infer diversity dependence is lacking.
Here, we simulate phylogenetic branching under linear negative diversity‐dependent and diversity‐independent models and estimate from the simulated phylogenies the maximum‐likelihood parameters for three different conditionings – on survival of the birth–death process given the crown age, on tree size ( N ) and on tree size given the crown age. We report the accuracy of recovering the simulation parameters and the reliability of the model selection based on the χ ² likelihood ratio test.
Parameter estimate accuracy: Conditioning on survival given the crown age yields a severe bias of the carrying capacity K towards N and an upward bias of the speciation rate, particularly in clades where diversity‐dependent feedbacks are still weak ( N « K ). Conditioning on N yields an overestimate of K and an underestimate of speciation rate, particularly when saturation has been reached. Dual conditioning yields relatively unbiased parameter estimates on average, but the deviation from the true value for any single estimate may be large.
Model selection reliability: The frequency of incorrectly rejecting a diversity‐independent model when the simulation was diversity‐independent (type I error) differs substantially from the significance level α used in the likelihood ratio test, rendering the likelihood ratio test inappropriate. The frequency of correctly rejecting the diversity‐independent model when the simulation was diversity‐dependent (power) is larger when the clade is closer to equilibrium and for conditioning on crown age.
We conclude that conditioning on crown age has the best statistical properties overall, but caution that parameter estimates may be biased. To assess parameter uncertainty in future studies of diversity dependence on real data, we recommend parametric bootstrapping, examination of the likelihood surface and comparison of estimates across the types of conditioning. To assess model selection reliability, we discourage the use of the χ ² likelihood ratio test or AIC (which are equivalent in this case), but recommend a likelihood ratio test based on parametric bootstrap. We illustrate this method for the diversification of Dendroica warblers.
Spatial and temporal differences in ecological opportunity can result in disparity of net species diversification rates and consequently uneven distribution of taxon richness across the tree of life. The largest eudicotyledonous plant family Asteraceae has a global distribution and at least 460 times more species than its South American endemic sister family Calyceraceae. In this study, diversification rate dynamics across Asteraceae are examined in light of the several hypothesized causes for the family’s evolutionary success that could be responsible for rate change. The innovations of racemose capitulum and pappus, and a whole genome duplication event occurred near the origin of the family, yet we found the basal lineages of Asteraceae that evolved in South America share background diversification rates with Calyceraceae and their Australasian sister Goodeniaceae. Instead we found diversification rates increased gradually from the origin of Asteraceae approximately 69.5 Ma in the late Cretaceous through the Early Eocene Climatic Optimum at least. In contrast to earlier studies, significant rate shifts were not strongly correlated with intercontinental dispersals or polyploidization. The difference is due primarily to sampling more backbone nodes, as well as calibrations placed internally in Asteraceae that resulted in earlier divergence times than those found in most previous relaxed clock studies. Two clades identified as having transformed rate processes are the Vernonioid Clade and a clade within the Heliantheae alliance characterized by phytomelanic fruit (PF Clade) that represents an American radiation. In Africa, subfamilies Carduoideae, Pertyoideae, Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae diverged in a relatively short span of only 6.5 million years during the Middle Eocene.
Abstract Late Pliocene and Pleistocene climatic instability has been invoked to explain the buildup of Neotropical biodiversity, although other theories date Neotropical diversification to earlier periods. If these climatic fluctuations drove Neotropical diversification, then a large proportion of species should date to this period and faunas should exhibit accelerated rates of speciation. However, the unique role of recent climatic fluctuations in promoting diversification could be rejected if late Pliocene and Pleistocene rates declined. To test these temporal predictions, dateable molecular phylogenies for 27 avian taxa were used to contrast the timing and rates of diversification in lowland and highland Neotropical faunas. Trends in diversification rates were analyzed in two ways. First, rates within taxa were analyzed for increasing or decreasing speciation rates through time. There was a significant trend within lowland taxa towards decreasing speciation rates, but no significant trend was observed within most highland taxa. Second, fauna wide diversification rates through time were estimated during one-million-year intervals by combining rates across taxa. In the lowlands, rates were highest during the late Miocene and then decreased towards the present. The decline in rates observed both within taxa and for the fauna as a whole probably resulted from density dependent cladogenesis. In the highlands, faunawide rates did not vary greatly before the Pleistocene but did increase significantly during the last one million years of the Pleistocene following the onset of severe glacial cycles in the Andes. These contrasting patterns of species accumulation suggest that lowland and highland regions were affected differently by recent climatic fluctuations. Evidently, habitat alterations associated with global climate change were not enough to promote an increase in the rate of diversification in lowland faunas. In contrast, direct fragmentation of habitats by glaciers and severe altitudinal migration of montane vegetation zones during climatic cycles may have resulted in the late Pleistocene increase in highland diversification rates. This increase resulted in a fauna with one third of its species dating to the last one million years.
A number of approaches for studying macroevolution using phylogenetic trees have been developed in the last few years. Here, we present RPANDA , an R package that implements model‐free and model‐based phylogenetic comparative methods for macroevolutionary analyses.
The model‐free approaches implemented in RPANDA are recently developed approaches stemming from graph theory that allow summarizing the information contained in phylogenetic trees, computing distances between trees, and clustering them accordingly. They also allow identifying distinct branching patterns within single trees.
RPANDA also implements likelihood‐based models for fitting various diversification models to phylogenetic trees. It includes birth–death models with i) constant, ii) time‐dependent and iii) environmental‐dependent speciation and extinction rates. It also includes models with equilibrium diversity derived from the coalescent process, as well as a likelihood‐based inference framework to fit the individual‐based model of Speciation by Genetic Differentiation, which is an extension of Hubbell's neutral theory of biodiversity.
RPANDA can be used to (i) characterize trees by plotting their spectral density profiles (ii) compare trees and cluster them according to their similarities, (iii) identify and plot distinct branching patterns within trees, (iv) compare the fit of alternative diversification models to phylogenetic trees, (v) estimate rates of speciation and extinction, (vi) estimate and plot how these rates have varied with time and environmental variables and (vii) deduce and plot estimates of species richness through geological time.
RPANDA provides investigators with a set of tools for exploring patterns in phylogenetic trees and fitting various models to these trees, thereby contributing to the ongoing development of phylogenetics in the life sciences.
1. The R package ‘diversitree’ contains a number of classical and contemporary comparative phylogenetic methods. Key included methods are BiSSE (binary state speciation and extinction), MuSSE (a multistate extension of BiSSE), and QuaSSE (quantitative state speciation and extinction). Diversitree also includes methods for analysing trait evolution and estimating speciation/extinction rates independently.
2. In this note, I describe the features and demonstrate use of the package, using a new method, MuSSE (multistate speciation and extinction), to examine the joint effects of two traits on speciation.
3. Using simulations, I found that MuSSE could reliably detect that a binary trait that affected speciation rates when simultaneously accounting for additional thats that had no effect on speciation rates.
4. Diversitree is an open source and available on the Comprehensive R Archive Network (cran). A tutorial and worked examples can be downloaded from http://www.zoology.ubc.ca/prog/diversitree.
Studies of phylogenetic diversification often show evidence for slowdowns in diversification rates over the history of clades. Recent studies seeking biological explanations for this pattern have emphasized the role of niche differentiation, as in hypotheses of adaptive radiation and ecological limits to diversity. Yet many other biological explanations might underlie diversification slowdowns. In this paper, we focus on the geographic context of diversification, environment-driven bursts of speciation, failure of clades to keep pace with a changing environment, and protracted speciation. We argue that, despite being currently underemphasized, these alternatives represent biologically plausible explanations that should be considered along with niche differentiation. Testing the importance of these alternative hypotheses might yield fundamentally different explanations for what influences species richness within clades through time.