Systematists have long been fascinated by the astounding variation in species diversity across the various branches of the tree of life, a net result of the uneven rates at which lineages undergo speciation and extinction over time. The past 30 years have seen the development and widespread application of tools that allow diversification to be quantified and characterized in empirical data sets. These advances have, in turn, enabled the statistical evaluation of hypotheses about the causes behind the uneven distribution of species richness among lineages, leading to a more nuanced understanding of diversification rate variation, as reflected in an ever-expanding literature. Here, we provide a brief review of the current understanding of these models, the types of questions they address, and some of their collective limitations, with a focus on tree-based analyses of reconstructed phylogenies. Based on this overview, we outline future considerations in the lineage diversification research program, including the potential for machine learning to revolutionize the field by making model selection and parameter estimation more efficient in highly complex models. We interpret the recent slowdown in publication pace as a sign of a maturing field, where systematists are taking a step back after becoming better equipped to understand the technicalities and current limitations of these methods, leading to more careful applications and a greater embrace of uncertainty.

Climate change is creating mismatches between species' current environments and their historical niches. Locations that once had the abiotic and biotic conditions to support the persistence of a species may now be too warm, too dry, or simply too different, to meet their niche requirements. Changes in behaviors, altered phenology, and range shifts are common responses to climate change. Though these responses are often studied in isolation by scientists from disparate subfields of ecology, they all represent variants of the same solution-strategies to realign the conditions populations experience with their niche. Here, we aim to (1) identify the physiological and ecological effects, and potential alignment, of these three ecological responses: shifts in behavior, phenology, or ranges, (2) determine the circumstances under which each type of response may be more or less effective at mitigating the effects of climate change, and (3) consider how these strategies might interact with each other. Each response has been previously reviewed, but efforts to consider relationships between ecological (or with evolutionary) responses have been limited. A synthetic perspective that considers the similarities among ecological responses and how they interact with each other and with evolutionary responses offers a more robust view on species' resilience to climate change.

Early burst patterns of speciation—the disproportionate concentration of speciation events early in the history of a radiating clade—are predicted under some models of adaptive radiation. Using time-calibrated phylogenetic trees, researchers have inferred evidence of an early burst for a wide range of organisms. However, the interpretation of these patterns can be fraught with controversy, because taxonomic and sampling biases—a phenomenon we refer to as ‘taxon murk’—can lead to apparent decelerations in the rate of speciation through time. Using Australia’s diverse sphenomorphine scincid lizards as a model, we tested whether multiple forms of tip-level uncertainty, including taxonomic undersampling and lag time for species recognition, could bias inference of speciation rates. To explore the impacts of taxon murk on diversification inference, we constructed a phylogenomic tree for 1941 individuals spanning 211 nominate species of sphenomorphines, including extensive sampling of intraspecific diversity. We found that the Australian sphenomorphine radiation is characterized by a robust early burst pattern that cannot be explained by uncertainty in the nature of tip units. These results are surprising, because extinction-mediated turnover should erode the signal of early burst speciation from molecular phylogenies. We provide a possible resolution to this paradox and consider the implications of our findings for continental radiations more generally. However, profound gaps in our knowledge of sphenomorphine behaviour and ecology limit our ability to test whether sphenomorphine macroevolutionary dynamics are consistent with paradigmatic patterns observed in better-studied radiations.

Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.

Spatial patterns of species richness, phylogenetic and morphological diversity are key to answering many questions in ecology and evolution. Across spatial scales, geographical and environmental features, as well as evolutionary history and phenotypic traits, are thought to play roles in shaping both local species communities and regional assemblages. By examining these geographical patterns, it is possible to infer how different axes of biodiversity influence one another, and how their interaction with abiotic factors has led to the spatial distribution of species assemblages—and their attributes—that we observe in the present. Although there has been interest in this area of research for some time, it has recently become more tractable to include multivariate shape data in such analyses. Shape information has the potential to provide a more direct measure of the functional morphology of species as compared to individual trait measurements and might be more relevant to understanding community composition. However, few tools currently exist to explore geographical patterns of both phylogenetic and shape diversity. We present the EcoPhyloMapper r package (epm) that aims to streamline the handling of geographical range polygons or point occurrences and integration of resulting species metacommunities with phylogenetic trees and morphological shape. Geographical maps can be generated that demonstrate spatial patterns in diversity metrics pertaining to phylogenetic similarity, multivariate shape similarity and disparity, and combinations of the two. Patterns of taxonomic, phylogenetic and shape disparity turnover can also be visualized. Biodiversity indices summarized across grid cells can easily be exported to GIS software as well as to other r packages that specialize in community assembly or geospatial statistics. This r package will facilitate the geographical exploration of multivariate shape data in concert with phylogenetic diversity, which will, in turn, support macroecological research exploring how species assemblages are structured. Furthermore, this r package should prove useful across a wide range of macroecological applications that extend beyond the study of morphology.

The relationship between ecology and morphology is a cornerstone of evolutionary biology, and quantifying variation across environments can shed light on processes that give rise to biodiversity. Three morphotypes of the Steller’s Jay (Cyanocitta stelleri) occupy different ecoregions in western North America that vary in climate and landcover. These morphotypes (Coastal, Interior, Rocky Mountain) differ in size, plumage coloration, and head pattern. We sampled 1,080 Steller’s Jays from 68 populations (plus 11 outgroups) to address three main questions using data on morphology, plumage, genetics (mtDNA, microsatellites), and ecological niches: (1) How do phenotypic and genetic traits vary within and among populations, morphotypes, and ecoregions? (2) How do population-level differences in Steller’s Jays compare to other sister species pairs of North American birds? (3) What can we infer about the population history of Steller’s Jays in relation to past climates, paleoecology, and niche evolution? We found substantial morphological, genetic, and ecological differentiation among morphotypes. The greatest genetic divergence separated Coastal and Interior morphotypes from the Rocky Mountain morphotype, which was associated with warmer, drier, and more open habitats. Microsatellites revealed additional structure between Coastal and Interior groups. The deep mtDNA split between Coastal/Interior and Rocky Mountain lineages of Steller’s Jay (ND2 ~7.8%) is older than most North American avian sister species and dates to approximately 4.3 mya. Interior and Rocky Mountain morphotypes contact across a narrow zone with steep clines in traits and reduced gene flow. The distribution of the three morphotypes coincides with divergent varieties of ponderosa pine and Douglas fir. Species distribution models support multiple glacial refugia for Steller’s Jays. Our integrative dataset combined with extensive geographic sampling provides compelling evidence for recognizing at least two species of Steller’s Jay.

As society confronts a multitude of wicked problems without clear solutions, transdisciplinary research institutes have the opportunity to meet the increasingly important challenge to foster research capable of addressing such problems—that is, cross-disciplinary and societally relevant research. There is a growing body of literature on how to conduct effective interdisciplinary, transdisciplinary, and team-based research, but there is less work that evaluates (1) the lessons learned, pitfalls, and successes involved in creating and maintaining transdisciplinary institutes that support this research and (2) how early-career researchers are shaped by and shape such institutes. In this commentary, we share insights and critical questions germane for those involved in the formation of, or participation in (especially as early-career, non-tenure-track researchers), transdisciplinary institutes. From our perspective as part of a unique cohort of research fellows developed as part of a new transdisciplinary institute at Indiana University, we explore facilitators and barriers to our ability to support the institute’s mission. Topics addressed include tensions between research and implementation, rapidly achieving collaborative research, and community building, especially in the context of nurturing an institute with temporary employees as a key component. We reflect on what our experiences as part of such an institute mean for our career pathways, especially in the context of current academic structures and incentives. Our insights are in the context of an environmental-focused institute, but the issues raised are likely relevant to transdisciplinary institutes formed around a wide range of other themes or topics, especially those seeking to learn from the experiences of the first few years of an institute.

Aim We investigate geographic patterns across taxonomic, ecological and phylogenetic diversity to test for spatial (in)congruency and identify aggregate diversity hotspots in relationship to present land use and future climate. Simulating extinctions of imperilled species, we demonstrate where losses across diversity dimensions and geography are predicted. Location North America. Time period Present day, future. Major taxa studied Rodentia. Methods Using geographic range maps for rodent species, we quantified spatial patterns for 11 dimensions of diversity: taxonomic (species, range weighted), ecological (body size, diet and habitat), phylogenetic (mean, variance, and nearest‐neighbour patristic distances, phylogenetic distance and genus‐to‐species ratio) and phyloendemism. We tested for correlations across dimensions and used spatial residual analyses to illustrate regions of pronounced diversity. We aggregated diversity hotspots in relationship to predictions of land‐use and climate change and recalculated metrics following extinctions of IUCN‐listed imperilled species. Results Topographically complex western North America hosts high diversity across multiple dimensions: phyloendemism and ecological diversity exceed predictions based on taxonomic richness, and phylogenetic variance patterns indicate steep gradients in phylogenetic turnover. An aggregate diversity hotspot emerges in the west, whereas spatial incongruence exists across diversity dimensions at the continental scale. Notably, phylogenetic metrics are uncorrelated with ecological diversity. Diversity hotspots overlap with land‐use and climate change, and extinctions predicted by IUCN status are unevenly distributed across space, phylogeny or ecological groups. Main conclusions Comparison of taxonomic, ecological and phylogenetic diversity patterns for North American rodents clearly shows the multifaceted nature of biodiversity. Testing for geographic patterns and (in)congruency across dimensions of diversity facilitates investigation into underlying ecological and evolutionary processes. The geographic scope of this analysis suggests that several explicit regional challenges face North American rodent fauna in the future. Simultaneous consideration of multi‐dimensional biodiversity allows us to assess what critical functions or evolutionary history we might lose with future extinctions and maximize the potential of our conservation efforts.

—Ecological interactions such as those involving arthropod predators and parasitoids and their prey or hosts provide evidence for selective pressures influencing small vertebrate populations, and are key to understanding the many connections that shape food webs in tropical rainforests. Here, we document 15 predator-prey interactions involving different types of arthropod predators and vertebrate prey including frogs, lizards, snakes, and a mammal. Documented also are three cases of fly myiasis in frogs, and provide further evidence of a commensal relationship involving a tarantula and a narrow-mouthed frog in lowland Amazonian Peru.

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.

Population divergence is the first step in allopatric speciation, as has long been recognized in both theoretical models of speciation and empirical explorations of natural systems. All else being equal, lineages with substantial population differentiation should form new species more quickly than lineages that maintain range-wide genetic cohesion through high levels of gene flow. However, there have been few direct tests of the extent to which population differentiation predicts speciation rates as measured on phylogenetic trees. Here, we explicitly test the links between organismal traits, population-level processes, and phylogenetic speciation rates across a diverse clade of Australian lizards that shows remarkable variation in speciation rate. Using genome-wide double digest restriction site-associated DNA data from 892 individuals, we generated a comparative data set on isolation by distance and population differentiation across 104 putative species-level lineages (operational taxonomic units). We find that species show substantial variation in the extent of population differentiation, and this variation is predicted by organismal traits that are thought to be proxies for dispersal and deme size. However, variation in population structure does not predict variation in speciation rate. Our results suggest that population differentiation is not the rate-limiting step in species formation and that other ecological and historical factors are primary determinants of speciation rates at macroevolutionary scales.

Far more species of organisms are found in the tropics than in temperate and polar regions, but the evolutionary and ecological causes of this pattern remain controversial1,2. Tropical marine fish communities are much more diverse than cold-water fish communities found at higher latitudes3,4, and several explanations for this latitudinal diversity gradient propose that warm reef environments serve as evolutionary 'hotspots' for species formation5-8. Here we test the relationship between latitude, species richness and speciation rate across marine fishes. We assembled a time-calibrated phylogeny of all ray-finned fishes (31,526 tips, of which 11,638 had genetic data) and used this framework to describe the spatial dynamics of speciation in the marine realm. We show that the fastest rates of speciation occur in species-poor regions outside the tropics, and that high-latitude fish lineages form new species at much faster rates than their tropical counterparts. High rates of speciation occur in geographical regions that are characterized by low surface temperatures and high endemism. Our results reject a broad class of mechanisms under which the tropics serve as an evolutionary cradle for marine fish diversity and raise new questions about why the coldest oceans on Earth are present-day hotspots of species formation.

Species distribution modeling is a valuable tool with many applications across ecology and evolutionary biology. The selection of biologically meaningful environmental variables that determine relative habitat suitability is a crucial aspect of the modeling pipeline. The 19 bioclimatic variables from WorldClim are frequently employed, primarily because they are easily accessible and available globally for past, present and future climate scenarios. Yet, the availability of relatively few other comparable environmental datasets potentially limits our ability to select appropriate variables that will most successfully characterize a species’ distribution. We identified a set of 16 climatic and two topographic variables in the literature, which we call the envirem dataset, many of which are likely to have direct relevance to ecological or physiological processes determining species distributions. We generated this set of variables at the same resolutions as WorldClim, for the present, mid-Holocene, and Last Glacial Maximum (LGM). For 20 North American vertebrate species, we then assessed whether including the envirem variables led to improved species distribution models compared to models using only the existing WorldClim variables. We found that including the ENVIREM dataset in the pool of variables to select from led to substantial improvements in niche modeling performance in 17 out of 20 species. We also show that, when comparing models constructed with different environmental variables, differences in projected distributions were often greater in the LGM than in the present. These variables are worth consideration in species distribution modeling applications, especially as many of the variables have direct links to processes important for species ecology. We provide these variables for download at multiple resolutions and for several time periods at envirem.github.io. Furthermore, we have written the ‘envirem’ R package to facilitate the generation of these variables from other input datasets.

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. [Australia; macroevolution; macrophylogeny; squamates; time calibration.].

1 Materials and Methods 2 1.1 Sampling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2 Library Preparation and Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.3 Testing Methods for ddRAD data assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.4 Species Delimitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1.5 Measures of Genetic Diversity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.5.1 Generating Pseudo-reference Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.5.2 Within-population π . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.5.3 Species-wide π . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.5.4 mtDNA π . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.5.5 Calculating diversity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.6 Demographic Analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.6.1 Running ADMIXTURE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.6.2 Running ANGSD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.6.3 Running LAMARC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 1.7 Species Tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 1.8 Collecting data on possible drivers of genetic diversity . . . . . . . . . . . . . . . . . . . . . . 7 1.8.1 Proxies for census population size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.8.2 Environmental hetereogeneity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.8.3 Historical demography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.8.4 Possible confounders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.9 Model-Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus . To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic diversity. Using a phylogenetically informed approach, we tested whether variation in genetic diversity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic diversity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic diversity, suggesting that genetic diversity might be difficult to predict at shallower phylogenetic scales.

The Bell’s Vireo ( Vireo bellii ) is a widespread North American species of bird that has declined since the mid-1960s primarily due to habitat modification. Throughout its range, Bell’s Vireo populations are regulated under varying degrees of protection; however, the species has never been characterized genetically. Therefore, the current taxonomy used to guide management decisions may misrepresent the true evolutionary history for the species. We sequenced 86 individuals for ND2 and genotyped 48 individuals for genome-wide SNPs to identify distinct lineages within Bell’s Vireo. Phylogenetic analyses uncovered two distinct clades that are separated in the arid southwestern United States, near the border of the Chihuahuan and Sonoran Deserts. These clades diverged from each other approximately 1.11–2.04 mya. The timing of diversification, geographic location, and niche modeling of the east/west divergence suggest vicariance as a mode of diversification for these two lineages. Analyses of the SNP dataset provided additional resolution and indicated the Least Bell’s Vireo populations are a distinct evolutionary lineage. Our genetic evidence, together with information from morphology and behavior, suggests that the Bell’s Vireo complex involves two species, each containing two separate subspecies. This new information has implications for the federal, state and other listing status of Bell’s Vireo throughout its range.

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.