Phylogenomics,biogeography, and evolution of the blue‐ or white‐fruited dogwoods (Cornus)—Insights into morphological and ecological niche divergence following intercontinental geographic isolation

The eastern Asian (EA)–eastern North American (ENA) floristic disjunction represents a major pattern of phytogeography of the Northern Hemisphere. Despite 20 years of studies dedicated to identification of taxa that display this disjunct pattern, its origin and evolution remain an open question, especially regarding post‐isolation evolution. The blue‐ or white‐fruited dogwoods (BW) are the most species‐rich among the four major clades of Cornus L., consisting of ~35 species divided into three subgenera (subg. Yinquania, subg. Mesomora, and subg. Kraniopsis). The BW group provides an excellent example of the EA–ENA floristic disjunction for biogeographic study due to its diversity distribution centered in eastern Asia and eastern North America, yet its species relationships and delineation have remained poorly understood. In this study, we combined genome‐wide markers from RAD‐seq, morphology, fossils, and climate data to understand species relationships, biogeographic history, and ecological niche and morphological evolution. Our phylogenomic analyses with RAxML and MrBayes recovered a strongly supported and well‐resolved phylogeny of the BW group with three intercontinental disjunct clades in EA and ENA or Eurasia and North America, of which two are newly identified within subg. Kraniopsis. These analyses also recovered a potential new species but failed to resolve relationships within the C. hemsleyi–C. schindleri complex. In an effort to develop an approach to reduce computation time, analysis of different nodal age settings in treePL suggests setting a node's minimum age constraint to the lower bound of a fossil's age range to obtain similar ages to that of BEAST. Divergence time analyses with BEAST and treePL dated the BW stem back to the very Late Cretaceous and the divergence of the three subgenera in the Paleogene. By integrating fossil ages and morphology, a total evidence‐based dating approach was used in conjunction with time‐slice probabilities of dispersal under a DEC model to resolve ancestral ranges of each disjunct in the Miocene: Eurasia and ENA (disjunct 1), EA and western North America (disjunct 2), and EA (disjunct 3). The dated biogeographic history supports dispersal via the North Atlantic Land Bridge in the late Paleogene in disjunct 1 and dispersal via the Bering Land Bridge in the Miocene for disjuncts 2 and 3. Character mapping with a stochastic model in phytools and comparison of ecological niche, morphospace, and rate of evolution indicated differential divergence patterns in morphology, ecological niche, and molecules between disjunct sisters. Although morphological stasis was observed in most of the characters, evolutionary changes in growth habit and some features of leaf, flower, and fruit morphology occurred in one or both sister clades. A significant differentiation of ecological habitats in temperature, precipitation, and elevation between disjunct sisters was observed, suggesting a role of niche divergence in morphological evolution post‐isolation. The patterns of evolutionary rate between morphology and molecules varied among disjunct clades and were not always congruent between morphology and molecules, suggesting cases of non‐neutral morphological evolution driven by ecological selection. Our phylogenetic evidence and comparisons of evolutionary rate among disjunct lineages lend new insights into the formation of the diversity anomaly between EA and ENA, with particular support of an early diversification in EA. These findings, in conjunction with previous studies, again suggest that the EA–ENA disjunct floras are an assembly of lineages descended from the Mesophytic Forests that evolved from the early Paleogene “boreotropical flora” through varied evolutionary pathways across lineages.     

Differential diversifications of South American and Eastern Asian disjunct genera Bocconia and Macleaya (Papaveraceae)

Bocconia (10 species) and Macleaya (2 species) are two disjunct genera between South America and eastern Asia (EAS) in the Papaveraceae offering an opportunity to compare its biogeographic history with that of the well‐known disjunction between EAS and eastern North American (ENA). Our phylogenetic analyses of the chloroplast matK and rbcL gene sequences of Ranunculales including two species of Macleaya and six species of Bocconia supported the monophyly of Bocconia, Macleaya, and Chelidonioideae to which Bocconia and Macleaya belong. Nucleotide sequences of matK, rbcL, and nrDNA ITS supported the sister relationship of Bocconia and Macleaya. Biogeographic analyses of Chelidonioideae using S‐DIVA (statistical dispersal vicariance analysis) and DEC (dispersal extinction cladogenesis) methods inferred Eurasia as the most likely ancestral area of Bocconia and Macleaya and suggested no extinction events in either Bocconia or Macleaya. This agrees with the “Out‐of‐Asia” pattern of the EAS‐ENA disjunction. Molecular dating of Ranunculales with fossil‐based calibrations showed that Bocconia and Macleaya diverged in the late Eocene and early Oligocene, which is much earlier than most EAS‐ENA disjunct taxa. The disjunction may have formed via long distance dispersal or boreotropical connections via the North Atlantic and Bering land bridges. Both Bocconia and Macleaya diversified in the late mid‐Miocene, but Bocconia has apparently experienced a greater diversification probably aided by the evolution of the bird dispersal syndrome in fruit and seed after migration to South America. The greater diversification of Bocconia is also evidenced by the diverse leaf morphology and growth habit in response to colonization in various local habitats in South America.     

Evolutionary and ecological causes of the latitudinal diversity gradient in hylid frogs: treefrog trees unearth the roots of high tropical diversity

Why are there more species in the tropics than in temperate regions? In recent years, this long-standing question has been addressed primarily by seeking environmental correlates of diversity. But to understand the ultimate causes of diversity patterns, we must also examine the evolutionary and biogeographic processes that directly change species numbers (i.e., speciation, extinction, and dispersal). With this perspective, we dissect the latitudinal diversity gradient in hylid frogs. We reconstruct a phylogeny for 124 hylid species, estimate divergence times and diversification rates for major clades, reconstruct biogeographic changes, and use ecological niche modeling to identify climatic variables that potentially limit dispersal. We find that hylids originated in tropical South America and spread to temperate regions only recently (leaving limited time for speciation). There is a strong relationship between the species richness of each region and when that region was colonized but not between the latitudinal positions of clades and their rates of diversification. Temperature seasonality seemingly limits dispersal of many tropical clades into temperate regions and shows significant phylogenetic conservatism. Overall, our study illustrates how two general principles (niche conservatism and the time-for-speciation effect) may help explain the latitudinal diversity gradient as well as many other diversity patterns across taxa and regions.     

Evolution of biogeographic disjunction between eastern Asia and eastern North America in Phryma (Phrymaceae)

This study examines molecular and morphological differentiation in Phryma L., which has only one species with a well-known classic intercontinental disjunct distribution between eastern Asia (EA) and eastern North America (ENA). Phylogenetic analysis of nuclear ribosomal ITS and chloroplast rps16 and trnL-F sequences revealed two highly distinct clades corresponding to EA and ENA. The divergence time between the intercontinental populations was estimated to be 3.68 ± 2.25 to 5.23 ± 1.37 million years ago (mya) based on combined chloroplast data using Bayesian and penalized likelihood methods. Phylogeographic and dispersal-vicariance (DIVA) analysis suggest a North American origin of Phryma and its migration into EA via the Bering land bridge. Multivariate analysis based on 23 quantitative morphological characters detected no geographic groups at the intercontinental level. The intercontinental populations of Phryma thus show distinct molecular divergence with little morphological differentiation. The discordance of the molecular and morphological patterns may be explained by morphological stasis due to ecological similarity in both continents. The divergence of Phryma from its close relatives in the Phrymaceae was estimated to be at least 32.32 ± 4.46 to 49.35 ± 3.18 mya.     

Global patterns of diversification and species richness in amphibians

Geographic patterns of species richness ultimately arise through the processes of speciation, extinction, and dispersal, but relatively few studies consider evolutionary and biogeographic processes in explaining these diversity patterns. One explanation for high tropical species richness is that many species-rich clades originated in tropical regions and spread to temperate regions infrequently and more recently, leaving little time for species richness to accumulate there (assuming similar rates of diversification in temperate and tropical regions). However, the major clades of anurans (frogs) and salamanders may offer a compelling counterexample. Most salamander families are predominately temperate in distribution, but the one primarily tropical clade (Bolitoglossinae) contains nearly half of all salamander species. Similarly, most basal clades of anurans are predominately temperate, but one largely tropical clade (Neobatrachia) contains approximately 96% of anurans. In this article, I examine patterns of diversification in frogs and salamanders and their relationship to large-scale patterns of species richness in amphibians. I find that diversification rates in both frogs and salamanders increase significantly with decreasing latitude. These results may shed light on both the evolutionary causes of the latitudinal diversity gradient and the dramatic but poorly explained disparities in the diversity of living amphibian clades.     

Floristic relationships between Eastern Asia and North America: test of Gray's hypothesis

Similarities in the temperate floras of eastern Asia and North America have been appreciated for more than 200 yr, but the generality of the floristic relationships among eastern Asia (EAS), eastern North America (ENA), and western North America (WNA), postulated by Asa Gray about 150 yr ago, has not been tested until now. In this article, floristic relationships based on genera shared among EAS, ENA, and WNA were examined at different spatial scales for different phylogenetic groups using complete floras. Floristic similarity between EAS and ENA is higher than that between EAS and WNA, and the floras of ENA and WNA are more closely related to each other than are the floras of EAS and ENA. Compared with ENA and WNA, the number of genera common to EAS and ENA is significantly higher in basal angiosperms and significantly lower in asterids. Floristic similarities tend to decrease from more basal to more modern lineages between EAS and ENA and between EAS and WNA but not between ENA and WNA. Similarly, from more basal to more modern divisions, the fraction of shared genera decreases between EAS and ENA and between EAS and WNA, whereas the floristic similarity between ENA and WNA tends to increase. Furthermore, floristic similarity between EAS and ENA increases with latitude. The causes of the observed patterns of floristic similarity between EAS, ENA, and WNA are discussed.     

Evolutionary origins of the eastern North American–Mesoamerican floristic disjunction: Current status and future prospects

Biogeographic disjunction patterns, where multiple taxa are shared between isolated geographic areas, represent excellent systems for investigating the historical assembly of modern biotas and fundamental biological processes such as speciation, diversification, niche evolution, and evolutionary responses to climate change. Studies on plant genera disjunct across the northern hemisphere, particularly between eastern North America (ENA) and eastern Asia (EAS), have yielded tremendous insight on the geologic history and assembly of rich temperate floras. However, one of the most prevalent disjunction patterns involving ENA forests has been largely overlooked: that of taxa disjunct between ENA and cloud forests of Mesoamerica (MAM), with examples including Acer saccharum, Liquidambar styraciflua, Cercis canadensis, Fagus grandifolia, and Epifagus virginiana. Despite the remarkable nature of this disjunction pattern, which has been recognized for over 75 years, there have been few recent efforts to empirically examine its evolutionary and ecological origins. Here I synthesize previous systematic, paleobotanical, phylogenetic, and phylogeographic studies to establish what is known about this disjunction pattern to provide a roadmap for future research. I argue that this disjunction pattern, and the evolution and fossil record of the Mexican flora more broadly, represents a key missing piece in the broader puzzle of northern hemisphere biogeography. I also suggest that the ENA–MAM disjunction represents an excellent system for examining fundamental questions about how traits and life history strategies mediate plant evolutionary responses to climate change and for predicting how broadleaf temperate forests will respond to the ongoing climatic pressures of the Anthropocene.     

Phylogenomics,biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North American Nyssa (Nyssaceae)

Nyssa (Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian–eastern North American floristic disjunction. The genus consists of three species in eastern Asia, four species in eastern North America, and one species in Central America. Species of the genus are ecologically important trees in eastern North American and eastern Asian forests. The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin and evolution of the eastern Asian–eastern North American floristic disjunction. However, despite the small number of species, relationships within the genus have remained unclear and have not been elucidated using a molecular approach. Here, we integrate data from 48 nuclear genes, fossils, morphology, and ecological niche to resolve species relationships, elucidate its biogeographical history, and investigate the evolution of morphology and ecological niches, aiming at a better understanding of the well‐known EA–ENA floristic disjunction. Results showed that the Central American (CAM) Nyssa talamancana was sister to the remaining species, which were divided among three, rapidly diversified subclades. Estimated divergence times and biogeographical history suggested that Nyssa had an ancestral range in Eurasia and western North America in the late Paleocene. The rapid diversification occurred in the early Eocene, followed by multiple dispersals between and within the Erasian and North American continents. The genus experienced two major episodes of extinction in the early Oligocene and end of Neogene, respectively. The Central American N. talamancana represents a relic lineage of the boreotropical flora in the Paleocene/Eocene boundary that once diversified in western North America. The results supported the importance of both the North Atlantic land bridge and the Bering land bridge (BLB) for the Paleogene dispersals of Nyssa and the Neogene dispersals, respectively, as well as the role of Central America as refugia of the Paleogene flora. The total‐evidence‐based dated phylogeny suggested that the pattern of macroevolution of Nyssa coincided with paleoclimatic changes. We found a number of evolutionary changes in morphology (including wood anatomy and leaf traits) and ecological niches (precipitation and temperature) between the EA–ENA disjunct, supporting the ecological selection driving trait evolutions after geographic isolation. We also demonstrated challenges in phylogenomic studies of lineages with rapid diversification histories. The concatenation of gene data can lead to inference of strongly supported relationships incongruent with the species tree. However, conflicts in gene genealogies did not seem to impose a strong effect on divergence time dating in our case. Furthermore, we demonstrated that rapid diversification events may not be recovered in the divergence time dating analysis using BEAST if critical fossil constraints of the relevant nodes are not available. Our study provides an example of complex bidirectional exchanges of plants between Eurasia and North America in the Paleogene, but “out of Asia” migrations in the Neogene, to explain the present disjunct distribution of Nyssa in EA and ENA.     

A phylogenetic perspective on the evolutionary processes of floristic assemblages within a biodiversity hotspot in eastern Asia

Abstract How to maximize the conservation of biodiversity is critical for conservation planning, particularly given rapid habitat loss and global climatic change. The importance of preserving phylogenetic diversity has gained recognition due to its ability to identify some influences of evolutionary history on contemporary patterns of species assemblages that traditional taxonomic richness measures cannot identify. In this study, we evaluate the relationship between taxonomic richness and phylogenetic diversity of angiosperms at genus and species levels and explore the spatial pattern of the residuals of this relationship. We then incorporate data on historical biogeography to understand the process that shaped contemporary floristic assemblages in a global biodiversity hotspot, Yunnan Province, located in southwestern China. We identified a strong correlation between phylogenetic diversity residuals and the biogeographic affinity of the lineages in the extant Yunnan angiosperm flora. Phylogenetic diversity is well correlated with taxonomic richness at both genus and species levels between floras in Yunnan, where two diversity centers of phylogenetic diversity were identified (the northwestern center and the southern center). The northwestern center, with lower phylogenetic diversity than expected based on taxonomic richness, is rich in temperate‐affinity lineages and signifies an area of rapid speciation. The southern center, with higher phylogenetic diversity than predicted by taxonomic richness, contains a higher proportion of lineages with tropical affinity and seems to have experienced high immigration rates. Our results highlight that maximizing phylogenetic diversity with historical interpretation can provide valuable insights into the floristic assemblage of a region and better‐informed decisions can be made to ensure different stages of a region's evolutionary history are preserved.     

Beta diversity of angiosperms in temperate floras of eastern Asia and eastern North America

The diversity of a region reflects both local diversity and the turnover of species (beta diversity) between areas. The angiosperm flora of eastern Asia (EAS) is roughly twice as rich as that of eastern North America (ENA), in spite of similar area and climate. Using province/state‐level angiosperm species floras, we calculated beta diversity as the slope of the relationship between the log of species similarity (S ) and either geographic distance or difference in climate. Distance‐based beta diversity was 2.6 times greater in the north–south direction in EAS than in ENA and 3.3 times greater in the east–west direction. When ln S was related to distance and climate difference in multiple regressions, both distance and climate PC1 were significant effects in the north–south direction, but only geographic distance had a significant, unique influence in the east–west direction. The general predominance of distance over environment in beta diversity suggests that history and geography have had a strong influence on the regional diversity of these temperate floras.     

The causes of species richness patterns across space, time, and clades and the role of "ecological limits"

A major goal of research in ecology and evolution is to explain why species richness varies across habitats, regions, and clades. Recent reviews have argued that species richness patterns among regions and clades may be explained by "ecological limits" on diversity over time, which are said to offer an alternative explanation to those invoking speciation and extinction (diversification) and time. Further, it has been proposed that this hypothesis is best supported by failure to find a positive relationship between time (e.g., clade age) and species richness. Here, I critically review the evidence for these claims, and propose how we might better study the ecological and evolutionary origins of species richness patterns. In fact, ecological limits can only influence species richness in clades by influencing speciation and extinction, and so this new "alternative paradigm" is simply one facet of the traditional idea that ecology influences diversification. The only direct evidence for strict ecological limits on richness (i.e., constant diversity over time) is from the fossil record, but many studies cited as supporting this pattern do not, and there is evidence for increasing richness over time. Negative evidence for a relationship between clade age and richness among extant clades is not positive evidence for constant diversity over time, and many recent analyses finding no age-diversity relationship were biased to reach this conclusion. More comprehensive analyses strongly support a positive age-richness relationship. There is abundant evidence that both time and ecological influences on diversification rates are important drivers of both large-scale and small-scale species richness patterns. The major challenge for future studies is to understand the ecological and evolutionary mechanisms underpinning the relationships between time, dispersal, diversification, and species richness patterns.     

EVOLUTIONARY AND BIOGEOGRAPHIC ORIGINS OF HIGH TROPICAL DIVERSITY IN OLD WORLD FROGS (RANIDAE)

Differences in species richness between regions are ultimately explained by patterns of speciation, extinction, and biogeographic dispersal. Yet, few studies have considered the role of all three processes in generating the high biodiversity of tropical regions. A recent study of a speciose group of predominately New World frogs (Hylidae) showed that their low diversity in temperate regions was associated with relatively recent colonization of these regions, rather than latitudinal differences in diversification rates (rates of speciation–extinction). Here, we perform parallel analyses on the most species-rich group of Old World frogs (Ranidae; ∼1300 species) to determine if similar processes drive the latitudinal diversity gradient. We estimate a time-calibrated phylogeny for 390 ranid species and use this phylogeny to analyze patterns of biogeography and diversification rates. As in hylids, we find a strong relationship between the timing of colonization of each region and its current diversity, with recent colonization of temperate regions from tropical regions. Diversification rates are similar in tropical and temperate clades, suggesting that neither accelerated tropical speciation rates nor greater temperate extinction rates explain high tropical diversity in this group. Instead, these results show the importance of historical biogeography in explaining high species richness in both the New World and Old World tropics.     

Rates of morphological evolution are correlated with species richness in salamanders

The tempo and mode of species diversification and phenotypic evolution vary widely across the tree of life, yet the relationship between these processes is poorly known. Previous tests of the relationship between rates of phenotypic evolution and rates of species diversification have assumed that species richness increases continuously through time. If this assumption is violated, simple phylogenetic estimates of net diversification rate may bear no relationship to processes that influence the distribution of species richness among clades. Here, we demonstrate that the variation in species richness among plethodontid salamander clades is unlikely to have resulted from simple time-dependent processes, leading to fundamentally different conclusions about the relationship between rates of phenotypic evolution and species diversification. Morphological evolutionary rates of both size and shape evolution are correlated with clade species richness, but are uncorrelated with simple estimators of net diversification that assume constancy of rates through time. This coupling between species diversification and phenotypic evolution is consistent with the hypothesis that clades with high rates of morphological trait evolution may diversify more than clades with low rates. Our results indicate that assumptions about underlying processes of diversity regulation have important consequences for interpreting macroevolutionary patterns.     

Herbaceous invaders in temperate forests: a systematic review of their ecology and proposed mechanisms of invasion

We present a systematic literature review of exotic understory forest herbaceous invasions with a focus on the forests of East Asia (EAS) and Eastern North America (ENA), two dominant regions of the north temperate deciduous forest biome. We examined the biogeographic origins of herbaceous invaders in EAS and ENA forests, summarized their life histories and ecology, and compiled the relevant literature on the 10 leading mechanistic hypotheses proposed for these invasions. We asked whether invasions of EAS and ENA forests by herbs are shared between regions, and whether a common suite of ecological traits unite these invaders into a functionally distinct group. In a focused summary of the empirical literature, we investigated if leading hypothesized mechanisms for biological invasions at large are also invoked and supported for this ecologically important, but relatively understudied, group of species. In contrast to ENA, forest invaders in EAS are overwhelmingly herbaceous (78% of forest invasions vs. 34% for ENA) and originate from different regions. Plant families represented and species traits between regions differed. Within a single species, multiple invasion mechanisms were often supported, highlighting the need for future research that simultaneously investigates multiple mechanistic hypotheses. Further, because results for a single invader often differed across space and time, a shift in focus to incorporate the complex dynamics across temporal and spatial scales with the consideration of spatial heterogeneity and the interplays among natural and anthropogenic factors to study exotic invasions is needed.     

Extinction as a driver of avian latitudinal diversity gradients

The role of historical factors in driving latitudinal diversity gradients is poorly understood. Here, we used an updated global phylogeny of terrestrial birds to test the role of three key historical factors—speciation, extinction, and dispersal rates—in generating latitudinal diversity gradients for eight major clades. We fit a model that allows speciation, extinction, and dispersal rates to differ, both with latitude and between the New and Old World. Our results consistently support extinction (all clades had lowest extinction where species richness was highest) as a key driver of species richness gradients across each of eight major clades. In contrast, speciation and dispersal rates showed no consistent latitudinal patterns across replicate bird clades, and thus are unlikely to represent general underlying drivers of latitudinal diversity gradients.     

Multiple hybrid formation in natural populations: concerted evolution of the internal transcribed spacer of nuclear ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae)

DNA sequence variation of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA from Arabis holboellii, A. drummondii, and its putative hybrid A. divaricarpa was analyzed to study hybrid speciation in a species system geographically covering nearly the entire North American continent. Based on molecular systematics the investigated species are better combined under the genus Boechera. Multiple intraindividual ITS copies were detected in numerous accessions of A. divaricarpa, and, to a minor extent, in the parental taxa. Comparative phylogenetic analysis demonstrates that reticulate evolution is common. Consequently, concerted evolution of ITS regions resulted in different types of ITS fragments not only in hybrid populations but also in one of the parental taxa, A. holboellii. Hybrid formation often occurred independently at different sites and at different times, which is reflected by ITS copies resampling the original parental sequence variation in different ways. Some biogeographic structuring of genetic diversity is apparent and mirrors postglacial migration routes. Hybridization, reticulation, and apomixis are assumed to be the major forces driving speciation processes in this species complex. Analysis of conserved regions and secondary structures of the ITS region provided no evidence that, in this system, hybrid ITS evolution is predominantly driven in a particular direction. However, two regions in the ITS1 and ITS2, respectively, show higher mutation rates than expected from outgroup comparisons. Strong evidence for the occurrence of apomixis in A. holboellii and A. divaricarpa has come from pollen size measurements and estimations of pollen quality, which favor the hypothesis that A. drummondii served as paternal hybridization partner more frequently than A. holboellii.     

Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity

Many groups show higher species richness in tropical regions but the underlying causes remain unclear. Despite many competing hypotheses to explain latitudinal diversity gradients, only three processes can directly change species richness across regions: speciation, extinction and dispersal. These processes can be addressed most powerfully using large-scale phylogenetic approaches, but most previous studies have focused on small groups and recent time scales, or did not separate speciation and extinction rates. We investigate the origins of high tropical diversity in amphibians, applying new phylogenetic comparative methods to a tree of 2871 species. Our results show that high tropical diversity is explained by higher speciation in the tropics, higher extinction in temperate regions and limited dispersal out of the tropics compared with colonization of the tropics from temperate regions. These patterns are strongly associated with climate-related variables such as temperature, precipitation and ecosystem energy. Results from models of diversity dependence in speciation rate suggest that temperate clades may have lower carrying capacities and may be more saturated (closer to carrying capacity) than tropical clades. Furthermore, we estimate strikingly low tropical extinction rates over geological time scales, in stark contrast to the dramatic losses of diversity occurring in tropical regions presently.     

Into the Andes: multiple independent colonizations drive montane diversity in the Neotropical clearwing butterflies Godyridina

Understanding why species richness peaks along the Andes is a fundamental question in the study of Neotropical biodiversity. Several biogeographic and diversification scenarios have been proposed in the literature, but there is confusion about the processes underlying each scenario, and assessing their relative contribution is not straightforward. Here, we propose to refine these scenarios into a framework which evaluates four evolutionary mechanisms: higher speciation rate in the Andes, lower extinction rates in the Andes, older colonization times and higher colonization rates of the Andes from adjacent areas. We apply this framework to a species‐rich subtribe of Neotropical butterflies whose diversity peaks in the Andes, the Godyridina (Nymphalidae: Ithomiini). We generated a time‐calibrated phylogeny of the Godyridina and fitted time‐dependent diversification models. Using trait‐dependent diversification models and ancestral state reconstruction methods we then compared different biogeographic scenarios. We found strong evidence that the rates of colonization into the Andes were higher than the other way round. Those colonizations and the subsequent local diversification at equal rates in the Andes and in non‐Andean regions mechanically increased the species richness of Andean regions compared to that of non‐Andean regions (‘species‐attractor’ hypothesis). We also found support for increasing speciation rates associated with Andean lineages. Our work highlights the importance of the Andean slopes in repeatedly attracting non‐Andean lineages, most likely as a result of the diversity of habitats and/or host plants. Applying this analytical framework to other clades will bring important insights into the evolutionary mechanisms underlying the most species‐rich biodiversity hotspot on the planet.     

Evolutionary rates and species diversity in flowering plants

Genetic change is a necessary component of speciation, but the relationship between rates of speciation and molecular evolution remains unclear. We use recent phylogenetic data to demonstrate a positive relationship between species numbers and the rate of neutral molecular evolution in flowering plants (in both plastid and nuclear genes). Rates of protein and morphological evolution also correlate with the neutral substitution rate, but not with species numbers. Our findings reveal a link between the rate of neutral molecular change within populations and the evolution of species diversity.     

Testing for unequal rates of morphological diversification in the absence of a detailed phylogeny: a case study from Characiform fishes

This study develops the random phylogenies rate test (RAPRATE), a likelihood method that simulates morphological evolution along randomly generated phylogenies, and uses it to determine whether a considerable difference in morphological diversity between two sister clades of South American fishes should be taken as evidence of differing rates of morphological change or lineage turnover. Despite identical ages of origin, similar species richness, and sympatric geographic distributions, the morphological and ecological diversity of the superfamily Anostomoidea exceeds that of the Curimatoidea. The test shows with 90% confidence (using variance among species as the measure of morphological diversity) or 99% confidence (using volume of occupied morphospace) that the rate of morphological change per unit time in the Anostomoidea likely exceeded that of the Curimatoidea. Variation in the rate of lineage turnover (speciation and extinction rates) is not found to affect greatly the morphological diversity of simulated clades and is not a likely explanation of the observed difference in morphological diversity in this case study. Though a 17% or greater delay in the onset of diversification in the Curimatoidea remains a possible alternative explanation of unequal morphological diversification, further simulations suggest that two clades drawn from the possible treespace of the Anostomoidea and Curimatoidea will rarely differ so greatly in the onset of diversification. Several uniquely derived morphological and ecological features of the Anostomoidea and Curimatoidea may have accelerated or decelerated their rate of morphological change, including a marked lengthening of the quadrate that may have relaxed structural constraints on the evolution of the anostomoid jaw.