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Abstract The diversity of life forms that surround us formed through a variety of processes. Speciation researchers use a suite of comparative approaches to understand both the generalities and the variance underpinning this diversification. Here, we summarize these approaches and what they have taught us, and we then apply them to understand speciation in the night lizards Xantusia, a genus of small lizards found in the arid regions of western North America. Although Xantusia species span both a range of phenotypic and genetic divergence, we find that speciation in Xantusia appears to be a predictable consequence of divergence in extended periods of allopatry. We conclude by identifying possible areas of growth for comparative studies of speciation. 

ABSTRACT Coalescent modelling of hybrid zones can provide novel insights into the historical demography of populations, including divergence times, population sizes, introgression proportions, migration rates and the timing of hybrid zone formation. We used coalescent analysis to determine whether the hybrid zone between phylogeographic lineages of the Plateau Fence Lizard (Sceloporus tristichus) in Arizona formed recently due to human‐induced landscape changes, or if it originated during Pleistocene climatic shifts. Given the presence of mitochondrial DNA from another species in the hybrid zone (Southwestern Fence Lizard,S. cowlesi), we tested for the presence ofS. cowlesinuclear DNA in the hybrid zone as well as reassessed the species boundary betweenS. tristichusandS. cowlesi. No evidence ofS. cowlesinuclear DNA is found in the hybrid zone, and the paraphyly of both species raises concerns about their taxonomic validity. Introgression analysis placed the divergence time between the parental hybrid zone populations at approximately 140 kya and their secondary contact and hybridization at approximately 11 kya at the end of the Pleistocene. Introgression proportions estimated for hybrid populations are correlated with their geographic distance from parental populations. The multispecies coalescent with migration provided significant support for unidirectional migration moving from south to north, which is consistent with spatial cline analyses that suggest a slow but steady northward shift of the centre of the hybrid zone over the last two decades. When analysing hybrid populations sampled along a linear transect, coalescent methods can provide novel insights into hybrid zone dynamics. 

In the face of anthropogenic change and the potential loss of species, documenting biodiversity – including accurately delimiting species complexes – is of tantamount importance. Genome-wide data are powerful for investigating lineage divergence, though deciding if this divergence represents species-level differentiation remains challenging. Here, we use genome-wide data to investigate species limits in four currently recognized species of Earless Lizards (Phrynosomatidae: Holbrookia), with a focus on H. lacerata and H. subcaudalis, the latter having potentially imperiled populations. This group’s taxonomy has been repeatedly revised; most recently, H. lacerata and H. subcaudalis were elevated to species status using conserved morphological data and a few molecular markers. In this study, we used double-digest restriction-site associated DNA sequencing to delineate species limits for our focal taxa. We recovered five populations that corresponded to five well-supported lineages with very little gene flow among them. Our results support the recognition of H. lacerata and H. subcaudalis as two separate species, based on strong phylogenetic support for these lineages and genetic divergence measures that exceed those of currently recognized species within Holbrookia. Genomic methods for species delimitation offer a promising approach to assess biodiversity in taxonomically confounded taxa or organisms of conservation priority. 

Inquiry-based course experiences provide a scalable and equitable way to engage students in research. In this study, we describe how we introduced inquiry-based experiences to ten lower-division and upper-division courses across the biology curriculum at a regionally comprehensive public university serving the diverse population in a major metropolitan area. Student survey data suggest this redesign effectively developed students’ scientific skills and nurtured their sense of belonging. This project illustrates how inquiry-based experiences can be implemented sustainably across institutional context. 

Complex patterns of genome evolution associated with the end-Cretaceous [Cretaceous-Paleogene (K–Pg)] mass extinction limit our understanding of the early evolutionary history of modern birds. Here, we analyzed patterns of avian molecular evolution and identified distinct macroevolutionary regimes across exons, introns, untranslated regions, and mitochondrial genomes. Bird clades originating near the K–Pg boundary exhibited numerous shifts in the mode of molecular evolution, suggesting a burst of genomic heterogeneity at this point in Earth’s history. These inferred shifts in substitution patterns were closely related to evolutionary shifts in developmental mode, adult body mass, and patterns of metabolic scaling. Our results suggest that the end-Cretaceous mass extinction triggered integrated patterns of evolution across avian genomes, physiology, and life history near the dawn of the modern bird radiation. 

Abstract Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (Elgaria coerulea), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single-nucleotide polymorphism data from 120 samples of E. coerulea. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for E. coerulea, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least 10 distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in E. coerulea is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in E. coerulea are consistent with predictions from co-distributed species. 

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. 

Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process—the propensity for population isolation—as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates. These results suggest that other stages of speciation—including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist—are likely to play a larger role than population isolation in controlling speciation rate variation in squamates. 

Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should be at least as divergent as other species. Here, we develop a reference-based taxonomy for Horned Lizards ( Phrynosoma ; 17 species) using phylogenomic data (ddRADseq data) to provide a framework for delimiting species in the Greater Short-horned Lizard species complex ( P. hernandesi ). Previous species delimitation studies of this species complex have produced conflicting results, with morphological data suggesting that P. hernandesi consists of five species, whereas mitochondrial DNA support anywhere from 1 to 10 + species. To help address this conflict, we first estimated a time-calibrated species tree for P. hernandesi and close relatives using SNP data. These results support the paraphyly of P. hernandesi; we recommend the recognition of two species to promote a taxonomy that is consistent with species monophyly. There is strong evidence for three populations within P. hernandesi , and demographic modeling and admixture analyses suggest that these populations are not reproductively isolated, which is consistent with previous morphological analyses that suggest hybridization could be common. Finally, we characterize the population-species boundary by quantifying levels of genetic divergence for all 18 Phrynosoma species. Genetic divergence measures for western and southern populations of P. hernandesi failed to exceed those of other Phrynosoma species, but the relatively small population size estimated for the northern population causes it to appear as a relatively divergent species. These comparisons underscore the difficulties associated with putting a reference-based approach to species delimitation into practice. Nevertheless, the reference-based approach offers a promising framework for the consistent assessment of biodiversity within clades of organisms with similar life histories and ecological traits.