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Genetic structure can be influenced by local adaptation to environmental heterogeneity and biogeographic barriers, resulting in discrete population clusters. Geographic distance among populations, however, can result in continuous clines of genetic divergence that appear as structured populations. Here, we evaluate the relevant importance of these three factors over a landscape characterized by environmental heterogeneity and the presence of a hypothesized biogeographic barrier in producing population genetic structure within 13 codistributed snake species using a genomic data set. We demonstrate that geographic distance and environmental heterogeneity across western North America contribute to population genomic divergence. Surprisingly, landscape features long thought to contribute to biogeographic barriers play little role in divergence community wide. Our results suggest that isolation by environment is the most important contributor to genomic divergence. Furthermore, we show that models of population clustering that incorporate spatial information consistently outperform nonspatial models, demonstrating the importance of considering geographic distances in population clustering. We argue that environmental and geographic distances as drivers of community-wide divergence should be explored before assuming the role of biogeographic barriers., (© 2019 John Wiley & Sons Ltd.)

Most phylogenies are typically represented as purely bifurcating. However, as genomic data have become more common in phylogenetic studies, it is not unusual to find reticulation among terminal lineages or among internal nodes (deep time reticulation; DTR). In these situations, gene flow must have happened in the same or adjacent geographic areas for these DTRs to have occurred and therefore biogeographic reconstruction should provide similar area estimates for parental nodes, provided extinction or dispersal has not eroded these patterns. We examine the phylogeny of the widely distributed New World kingsnakes (Lampropeltis), determine if DTR is present in this group, and estimate the ancestral area for reticulation. Importantly, we develop a new method that uses coalescent simulations in a machine learning framework to show conclusively that this phylogeny is best represented as reticulating at deeper time. Using joint probabilities of ancestral area reconstructions on the bifurcating parental lineages from the reticulating node, we show that this reticulation likely occurred in northwestern Mexico/southwestern US, and subsequently, led to the diversification of the Mexican kingsnakes. This region has been previously identified as an area important for understanding speciation and secondary contact with gene flow in snakes and other squamates. This research shows that phylogenetic reticulation is common, even in well-studied groups, and that the geographic scope of ancient hybridization is recoverable.

Inferring the evolutionary and biogeographic history of taxa occurring in a particular region is one way to determine the processes by which the biodiversity of that region originated. Tree boas of the genus Corallus are an ancient clade and occur throughout Central and South America and the Lesser Antilles, making it an excellent group for investigating Neotropical biogeography. Using sequenced portions of two mitochondrial and three nuclear loci for individuals of all recognized species of Corallus, we infer phylogenetic relationships, present the first molecular analysis of the phylogenetic placement of the enigmatic C. cropanii, develop a time-calibrated phylogeny, and explore the biogeographic history of the genus. We found that Corallus diversified within mainland South America, via over-water dispersals to the Lesser Antilles and Central America, and via the traditionally recognized Panamanian land bridge. Divergence time estimates reject the South American Caribbean-Track as a general biogeographic model for Corallus and implicate a role for events during the Oligocene and Miocene in diversification such as marine incursions and the uplift of the Andes. Our findings also suggest that recognition of the island endemic species, C. grenadensis and C. cookii, is questionable as they are nested within the widely distributed species, C. hortulanus. Our results highlight the importance of using widespread taxa when forming and testing biogeographic hypotheses in complex regions and further illustrate the difficulty of forming broadly applicable hypotheses regarding patterns of diversification in the Neotropical region., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Numerous taxa show ancient intertropical disjunct distributions. Many can be explained by well-known processes of historical vicariance, such as the breakup of Gondwanaland. Others, such as Asian-Neotropical divergences are not as well understood. To clarify the phylogenetic position and understand biogeographic and temporal origins of the geographically disjunct and morphologically unique genera of hinged-teeth snakes, Scaphiodontophis (n=1) and Sibynophis (n=9; Colubridae), we inferred a time-calibrated phylogeny with additional 107 taxa representing the superfamily Colubroidea using four genes (c-mos, cyt-b, ND2, RAG-1; 3085 bp). We used this tree to estimate ancestral areas for the group. The results show that Scaphiodontophis is sister to Sibynophis, both originated in the late Eocene/Oligocene in Asia and likely dispersed through Beringia to the New World, but unlike other snake groups left no extant species in temperate North America. Current recognition of Scaphiodontophiinae renders Colubrinae paraphyletic, and we resurrect the previously named subfamily Sibynophiinae to encompass both genera and use the tribes Sibynophiini (Sibynophis) and Scaphiodontophiini (Scaphiodontophis) to highlight the geographically distinct areas occupied by these taxa. These results suggest that intercontinental dispersal with extinction in intermediate areas can explain puzzling patterns of ancient intertropical disjunct distributions., (Copyright © 2012 Elsevier Inc. All rights reserved.)

The statistical rigor of species delimitation has increased dramatically over the past decade. Coalescent theory provides powerful models for population genetic inference, and is now increasingly important in phylogenetics and speciation research. By applying probabilistic models, coalescent-based species delimitation provides clear and objective testing of alternative hypotheses of evolutionary independence. As acquisition of multilocus data becomes increasingly automated, coalescent-based species delimitation will improve the discovery, resolution, consistency, and stability of the taxonomy of species. Along with other tools and data types, coalescent-based species delimitation will play an important role in an integrative taxonomy that emphasizes the identification of species limits and the processes that have promoted lineage diversification., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Molecular phylogenies are often used to test hypotheses about the tempo and mode of speciation and extinction. One commonly used statistic is Pybus and Harvey's γ, which measures the density of ordered internode distances on an ultrametric tree to infer earlier (negative γ) or later (positive γ) bursts of diversification. However, coalescent theory predicts that γ might be biased toward negative values (inferring early bursts of diversification) when using gene trees rather than species trees. Gene divergences predate species divergences, increasingly so at higher effective population sizes (N(e)), and proportionally more so toward the tips of the tree. Thus, gene trees will have a higher density of older nodes in many cases (particularly at higher N(e)), due to the disproportionate lengthening of terminal branches. This will yield an artifactual signature of early bursts of diversification when estimating γ from gene trees. We simulate gene trees within species trees under both Yule (pure-birth) and birth-death processes, and demonstrate support for these predictions. However, for most realistic estimates of θ in natural populations, gene trees provide relatively good estimates of γ, despite the disproportionate overestimation of younger node ages. This is corroborated with an empirical dataset of North American fence lizards (Sceloporus)., (© 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.)

Climatic changes associated with Pleistocene glacial cycles profoundly affected species distributions, patterns of interpopulation gene flow, and demography. In species restricted to montane habitats, ranges may expand and contract along an elevational gradients in response to environmental fluctuations and create high levels of genetic variation among populations on different mountains. The salamander Plethodon fourchensis is restricted to high-elevation, mesic forest on five montane isolates in the Ouachita Mountains. We used DNA sequence data along with ecological niche modelling and coalescent simulations to test several hypotheses related to the effects of Pleistocene climatic fluctuations on species in montane habitats. Our results revealed that P. fourchensis is composed of four well-supported, geographically structured lineages. Geographic breaks between lineages occurred in the vicinity of major valleys and a narrow high-elevation pass. Ecological niche modelling predicted that environmental conditions in valleys separating most mountains are suitable; however, interglacial periods like the present are predicted to be times of range expansion in P. fourchensis. Divergence dating and coalescent simulations indicated that lineage diversification occurred during the Middle Pleistocene via the fragmentation of a wide-ranging ancestor. Bayesian skyline plots showed gradual decreases in population size in three of four lineages over the most recent glacial period and a slight to moderate amount of population growth during the Holocene. Our results not only demonstrate that climatic changes during the Pleistocene had profound effects on species restricted to montane habitats, but comparison of our results for P. fourchensis with its parapatric, sister taxon, P. ouachitae, also emphasizes how responses can vary substantially even among closely related, similarly distributed taxa.

Sky islands provide ideal opportunities for understanding how climatic changes associated with Pleistocene glacial cycles influenced species distributions, genetic diversification, and demography. The salamander Plethodon ouachitae is largely restricted to high-elevation, mesic forest on six major mountains in the Ouachita Mountains. Because these mountains are separated by more xeric, low-elevation valleys, the salamanders appear to be isolated on sky islands where gene flow among populations on different mountains may be restricted. We used DNA sequence data along with ecological niche modelling and coalescent simulations to test several hypotheses related to diversifications in sky island habitats. Our results revealed that P. ouachitae is composed of seven well-supported lineages structured across six major mountains. The species originated during the Late Pliocene, and lineage diversification occurred during the Middle Pleistocene in a stepping stone fashion with a cyclical pattern of dispersal to a new mountain followed by isolation and divergence. Diversification occurred primarily on an east-west axis, which is likely related to the east-west orientation of the Ouachita Mountains and the more favourable cooler and wetter environmental conditions on north slopes compared to south-facing slopes and valleys. All non-genealogical coalescent methods failed to detect significant population expansion in any lineages. Bayesian skyline plots showed relatively stable population sizes over time, but indicated a slight to moderate amount of population growth in all lineages starting approximately 10 000-12 000 years ago. Our results provide new insight into sky island diversifications from a previously unstudied region, and further demonstrate that climatic changes during the Pleistocene had profound effects on lineage diversification and demography, especially in species from environmentally sensitive habitats in montane regions.

Background: The mitochondrial genomes of snakes are characterized by an overall evolutionary rate that appears to be one of the most accelerated among vertebrates. They also possess other unusual features, including short tRNAs and other genes, and a duplicated control region that has been stably maintained since it originated more than 70 million years ago. Here, we provide a detailed analysis of evolutionary dynamics in snake mitochondrial genomes to better understand the basis of these extreme characteristics, and to explore the relationship between mitochondrial genome molecular evolution, genome architecture, and molecular function. We sequenced complete mitochondrial genomes from Slowinski's corn snake (Pantherophis slowinskii) and two cottonmouths (Agkistrodon piscivorus) to complement previously existing mitochondrial genomes, and to provide an improved comparative view of how genome architecture affects molecular evolution at contrasting levels of divergence., Results: We present a Bayesian genetic approach that suggests that the duplicated control region can function as an additional origin of heavy strand replication. The two control regions also appear to have different intra-specific versus inter-specific evolutionary dynamics that may be associated with complex modes of concerted evolution. We find that different genomic regions have experienced substantial accelerated evolution along early branches in snakes, with different genes having experienced dramatic accelerations along specific branches. Some of these accelerations appear to coincide with, or subsequent to, the shortening of various mitochondrial genes and the duplication of the control region and flanking tRNAs., Conclusion: Fluctuations in the strength and pattern of selection during snake evolution have had widely varying gene-specific effects on substitution rates, and these rate accelerations may have been functionally related to unusual changes in genomic architecture. The among-lineage and among-gene variation in rate dynamics observed in snakes is the most extreme thus far observed in animal genomes, and provides an important study system for further evaluating the biochemical and physiological basis of evolutionary pressures in vertebrate mitochondria.

To examine Holarctic snake dispersal, we inferred a phylogenetic tree from four mtDNA genes and one scnDNA gene for most species of the Old World (OW) and New World (NW) colubrid group known as ratsnakes. Ancestral area distributions are estimated for various clades using divergence-vicariance analysis and maximum likelihood on trees produced using Bayesian inference. Dates of divergence for the same clades are estimated using penalized likelihood with statistically crosschecked calibration references obtained from the Miocene fossil record. With ancestral areas and associated dates estimated, various hypotheses concerning the age and environment associated with the origin of ratsnakes and the dispersal of NW taxa from OW ancestors were tested. Results suggest that the ratsnakes originated in tropical Asia in the late Eocene and subsequently dispersed to the Western and Eastern Palearctic by the early Oligocene. These analyses also suggest that the monophyletic NW ratsnakes (the Lampropeltini) diverged from OW ratsnakes and dispersed through Beringia in the late Oligocene/early Miocene when this land bridge was mostly composed of deciduous and coniferous forests.

Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.