Rates of climatic niche evolution are correlated with species richness in a large and ecologically diverse radiation of songbirds

By employing a recently inferred phylogeny and museum occurrence records, we examine the relationship of ecological niche evolution to diversification in the largest family of songbirds, the tanagers (Thraupidae). We test whether differences in species numbers in the major clades of tanagers can be explained by differences in rate of climatic niche evolution. We develop a methodological pipeline to process and filter occurrence records. We find that, of the ecological variables examined, clade richness is higher in clades with higher climatic niche rate, and that this rate is also greater for clades that occupy a greater extent of climatic space. Additionally, we find that more speciose clades contain species with narrower niche breadths, suggesting that clades in which species are more successful at diversifying across climatic gradients have greater potential for speciation or are more buffered from the risk of extinction.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111277/1/ele12422.pd

Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates?

Species‐specific diversification rates, or ‘tip rates’, can be computed quickly from phylogenies and are widely used to study diversification rate variation in relation to geography, ecology and phenotypes. These tip rates provide a number of theoretical and practical advantages, such as the relaxation of assumptions of rate homogeneity in trait‐dependent diversification studies. However, there is substantial confusion in the literature regarding whether these metrics estimate speciation or net diversification rates. Additionally, no study has yet compared the relative performance and accuracy of tip rate metrics across simulated diversification scenarios.We compared the statistical performance of three model‐free rate metrics (inverse terminal branch lengths; node density metric; DR statistic) and a model‐based approach (Bayesian analysis of macroevolutionary mixtures [BAMM]). We applied each method to a large set of simulated phylogenies that had been generated under different diversification processes. We summarized performance in relation to the type of rate variation, the magnitude of rate heterogeneity and rate regime size. We also compared the ability of the metrics to estimate both speciation and net diversification rates.We show decisively that model‐free tip rate metrics provide a better estimate of the rate of speciation than of net diversification. Error in net diversification rate estimates increases as a function of the relative extinction rate. In contrast, error in speciation rate estimates is low and relatively insensitive to extinction. Overall, and in particular when relative extinction was high, BAMM inferred the most accurate tip rates and exhibited lower error than non‐model‐based approaches. DR was highly correlated with true speciation rates but exhibited high error variance, and was the best metric for very small rate regimes.We found that, of the metrics tested, DR and BAMM are the most useful metrics for studying speciation rate dynamics and trait‐dependent diversification. Although BAMM was more accurate than DR overall, the two approaches have complementary strengths. Because tip rate metrics are more reliable estimators of speciation rate, we recommend that empirical studies using these metrics exercise caution when drawing biological interpretations in any situation where the distinction between speciation and net diversification is important.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149536/1/mee313153-sup-0001-FigS1-S10.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149536/2/mee313153.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149536/3/mee313153_am.pd

Tests of species‐specific models reveal the importance of drought in postglacial range shifts of a Mediterranean‐climate tree: insights from integrative distributional, demographic and coalescent modelling and ABC model selection

Past climate change has caused shifts in species distributions and undoubtedly impacted patterns of genetic variation, but the biological processes mediating responses to climate change, and their genetic signatures, are often poorly understood. We test six species‐specific biologically informed hypotheses about such processes in canyon live oak (Quercus chrysolepis) from the California Floristic Province. These hypotheses encompass the potential roles of climatic niche, niche multidimensionality, physiological trade‐offs in functional traits, and local‐scale factors (microsites and local adaptation within ecoregions) in structuring genetic variation. Specifically, we use ecological niche models (ENMs) to construct temporally dynamic landscapes where the processes invoked by each hypothesis are reflected by differences in local habitat suitabilities. These landscapes are used to simulate expected patterns of genetic variation under each model and evaluate the fit of empirical data from 13 microsatellite loci genotyped in 226 individuals from across the species range. Using approximate Bayesian computation (ABC), we obtain very strong support for two statistically indistinguishable models: a trade‐off model in which growth rate and drought tolerance drive habitat suitability and genetic structure, and a model based on the climatic niche estimated from a generic ENM, in which the variables found to make the most important contribution to the ENM have strong conceptual links to drought stress. The two most probable models for explaining the patterns of genetic variation thus share a common component, highlighting the potential importance of seasonal drought in driving historical range shifts in a temperate tree from a Mediterranean climate where summer drought is common.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134178/1/mec13804-sup-0001-Supinfo.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134178/2/mec13804.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134178/3/mec13804_am.pd

Genetic variation among western populations of the Horned Lark (Eremophila alpestris) indicates recent colonization of the Channel Islands off southern California, mainland-bound dispersal, and postglacial range shifts

© 2014 American Ornithologists\u27 Union. The Channel Islands off the coast of southern California host \u3e50 species of terrestrial vertebrates with varying degrees of phenotypic differentiation. However, most organisms that breed on the Channel Islands remain unstudied with respect to genetic differentiation from mainland populations. By comparing patterns of genetic variation between the Channel Islands and the mainland, we aimed to further our understanding of the role that the Channel Islands have played in diversification of the North American biota. We evaluated long-standing, untested hypotheses regarding colonization patterns and evolutionary relationships among western populations of the Horned Lark (Eremophila alpestris), including the endemic Channel Island subspecies E. a. insularis. We also examined how many times Horned Larks have colonized the Channel Islands, whether the species exhibits asymmetrical patterns of gene flow between mainland and island populations, and whether E. a. strigata of the Pacific Northwest is closely related to the phenotypically similar, but geographically separated, island subspecies. We found that E. a. insularis is polyphyletic, which suggests either multiple colonization events from the mainland or incomplete lineage sorting of a large ancestral population. We also inferred higher rates of migration from the Channel Islands to the mainland, with E. a. strigata being closely related to individuals from the Channel Islands and coastal southern California. Moreover, ecological niche models for E. a. strigata identified suitable abiotic conditions in southern California and the Pacific Northwest during the Last Glacial Maximum, which suggests that E. a. strigata experienced a postglacial range shift in addition to a population bottleneck. Our results provide novel insight regarding the origins of the Channel Island avifauna and the evolutionary history of the Horned Lark in the western United States. Moreover, our findings suggest that Channel Island birds may be weakly differentiated from mainland populations despite phenotypic differences between recognized subspecies

Niche evolution in relation to diversification in tanagers, the largest radiation of songbirds in the Neotropics

Includes bibliographical references (p. 49-59).Increasing availability of species occurrence data, coupled with sophistication of niche modeling techniques, has made it possible to quantify species ecological niches based on large-scale environmental data for the first time. Using these data in conjunction with emerging, large-scale phylogenies of widespread groups has made it possible to address broad questions regarding the interplay between ecology and evolution. Tanagers are an ideal group for the study of the evolution of ecological niches. They are the largest group of Neotropical songbirds and are found in nearly all habitats across Central and South America. Thanks to the recent inference of a well-supported species-level phylogeny for the group, questions regarding their extensive ecological diversity can now be addressed appropriately in a phylogenetic framework. Specifically, questions regarding species climatic niches can be framed in an evolutionary context to examine the role of ecology in diversification. My first objective was to test whether differences in species numbers in the major clades of tanagers could be explained by differences in niche evolutionary rate among these major clades. This was accomplished by testing for correlations between rates of lineage diversification and rates of climatic niche evolution. I first tested whether or not constant-rate diversification was an appropriate descriptor of tanager lineage accumulation. As I found that tanagers are better described by density-dependent models of diversification, I used species richness and the carrying capacity K as descriptors of lineage diversity, as traditional measures of net diversification were not appropriate. I found that rates of niche evolution are correlated with K, which indicates that differences in species numbers can be explained by rates of niche evolution and thus niche evolution may be driving diversification in tanagers. I also found that tanagers with greater rates of niche evolution occupy greater environmental volume. My second objective was to examine niche evolution at a finer scale by examining niche characteristics among sister species pairs. There has been debate in the scientific literature in recent years regarding the role of ecology in speciation, and whether sister species should be expected to have similar or different niches. To address this, I took multiple approaches at several phylogenetic depths to examine niche evolution in tanagers. I measured niche overlap for 55 sister species pairs and found niche similarity to be low, implying niche divergence among sister species. I also calculated relative disparity through time and found that tanagers had partitioned available niche space early in evolutionary time, and that niche evolution eventually shifted toward convergence closer to the present. There was also significant variation in niche evolution dynamics across tanager subfamilies. The findings of my second chapter support the findings of my first chapter, in that both sets of results support the hypothesis that niche evolution might drive diversification in tanagers, and both suggest an important role for ecology in speciation in tanager

Data from: Do macrophylogenies yield stable macroevolutionary inferences? An example from squamate reptiles

Advances in the generation, retrieval, and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies"—large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches—provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life. These trees are characterized by substantial phylogenetic uncertainty on multiple levels, and the stability of macroevolutionary inferences from these data sets has not been rigorously explored. As a case study, we tested whether five recently published phylogenies for squamate reptiles—each consisting of more than 4000 species—yield congruent inferences about the processes that underlie variation in species richness across replicate evolutionary radiations of Australian snakes and lizards. We find discordance across the five focal phylogenies with respect to clade age and several diversification rate metrics, and in the effects of clade age on species richness. We also find that crown clade ages reported in the literature on these Australian groups are in conflict with all of the large phylogenies examined. Macrophylogenies offer an unprecedented opportunity to address evolutionary and ecological questions at broad phylogenetic scales, but accurately representing the uncertainty that is inherent to such analyses remains a critical challenge to our field.TitleRabosky_Macrophylogenies_suppltables and figuresspeciesSpecificDivRateR script for calculating the per-species diversification rate from Jetz et al. (2012)richness_cladeAge_powerAnalysisR script for replicating the statistical power analysis shown in Figure 3 of main text.phylogenic treesMacrophylogenies that were included in analyses.phylogenies.zipBAMM_filescontrol files and trees for BAMM analyse

treesForTipRates

Directory of all phylogenies used to evaluate tip rate metrics

tipRatesDataScripts

R scripts and data files needed to reproduce all analyses and figures