Species limits within the Mexican garter snakes of the \u3cem\u3eThamnophis godmani\u3c/em\u3e complex

The highly variable Thamniphis godmani complex of southern Mexico, comprised of four apparently allopatric populations, was examined by using 28 morphological characters scored on 214 specimens. Character values were tested with univariate and multivariate statistics to determine if populations are morphologically distinct. The results suggest that the four populations represent independently evolving lineages. Four species, three previously undescribed, are recognized in the T. godmani complex. A lectotype is designated for T. godmani. For each species, a diagnosis description of holotype or lectotype, summary of interspecific variation, and statement of distribution are provided. Comparisons are made with T. errans, alleged to be the closest relative to members of the complex

Systematics of the Polymorphic North American Rat Snake (Elaphe Obsoleta).

The North American rat snake (Elaphe obsoleta) complex is composed of seven uniquely colored subspecies of E. obsoleta and the sister species E. bairdi. Maximum parsimony (MP) and maximum likelihood (ML) analysis of two mitochondrial DNA genes from 73 E. obsoleta and E. bairdi, produced well-supported trees that do not conform to the currently accepted subspecies. Both ML and MP trees were significantly shorter than the trees in which each subspecies was constrained to be monophyletic. The subspecies of E. obsoleta do not represent genetic lineages. Instead, molecular evidence revealed the existence of four well-supported mtDNA clades confined to particular geographic areas in North America. Lack of genetic variability in each clade of E. obsoleta may indicate that the lineages expanded from southern glacial refugia recently. Univariate and multivariate analysis of 67 morphological characters scored from 1006 specimens provided additional statistical support for the existence of the same four evolutionary lineages identified in the molecular phylogeographic study. Specimens could be classified using canonical discriminant function analysis into the four molecular clades better than they could be partitioned into subspecific categories. Moreover, the identification of these subspecies proved difficult when using the traditional characters ascribed to them. In light of the corroborating molecular and morphological evidence, it is suggested that the recognition of the subspecies of Elaphe obsoleta be discontinued. Instead, the four molecular clades should be recognized as four species: E. alleghaniensis, E. spiloides, E. obsoleta, and E. bairdi. This research demonstrates that the recognition of subspecies from one or two characters may be detrimental to understanding evolutionary history

Independent Demographic Responses to Climate Change among Temperate and Tropical Milksnakes (Colubridae: Genus Lampropeltis)

The effects of Late Quaternary climate change have been examined for many temperate New World taxa, but the impact of Pleistocene glacial cycles on Neotropical taxa is less well understood, specifically with respect to changes in population demography. Here, we examine historical demographic trends for six species of milksnake with representatives in both the temperate and tropical Americas to determine if species share responses to climate change as a taxon or by area (i.e., temperate versus tropical environments). Using a multilocus dataset, we test for the demographic signature of population expansion and decline using non-genealogical summary statistics, as well as coalescent-based methods. In addition, we determine whether range sizes are correlated with effective population sizes for milksnakes. Results indicate that there are no identifiable trends with respect to demographic response based on location, and that species responded to changing climates independently, with tropical taxa showing greater instability. There is also no correlation between range size and effective population size, with the largest population size belonging to the species with the smallest geographic distribution. Our study highlights the importance of not generalizing the demographic histories of taxa by region and further illustrates that the New World tropics may not have been a stable refuge during the Pleistocene

Claims of Potential Expansion throughout the U.S. by Invasive Python Species Are Contradicted by Ecological Niche Models

Background Recent reports from the United States Geological Survey (USGS) suggested that invasive Burmese pythons in the Everglades may quickly spread into many parts of the U.S. due to putative climatic suitability. Additionally, projected trends of global warming were predicted to significantly increase suitable habitat and promote range expansion by these snakes. However, the ecological limitations of the Burmese python are not known and the possible effects of global warming on the potential expansion of the species are also unclear. Methodology/Principal Findings Here we show that a predicted continental expansion is unlikely based on the ecology of the organism and the climate of the U.S. Our ecological niche models, which include variables representing climatic extremes as well as averages, indicate that the only suitable habitat in the U.S. for Burmese pythons presently occurs in southern Florida and in extreme southern Texas. Models based on the current distribution of the snake predict suitable habitat in essentially the only region in which the snakes are found in the U.S. Future climate models based on global warming forecasts actually indicate a significant contraction in suitable habitat for Burmese pythons in the U.S. as well as in their native range. Conclusions/Significance The Burmese python is strongly limited to the small area of suitable environmental conditions in the United States it currently inhabits due to the ecological niche preferences of the snake. The ability of the Burmese python to expand further into the U.S. is severely limited by ecological constraints. Global warming is predicted to significantly reduce the area of suitable habitat worldwide, underscoring the potential negative effects of climate change for many species

Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region

<p>Abstract</p> <p>Background</p> <p>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 (<it>Pantherophis slowinskii</it>) and two cottonmouths (<it>Agkistrodon piscivorus</it>) 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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p

Environmental heterogeneity and not vicariant biogeographic barriers generate community-wide population structure in desert-adapted snakes

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.see also the Perspective by Alencar and QuentalPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/1/mec15182-sup-0004-AppendixS4.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/2/mec15182_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/3/mec15182-sup-0005-AppendixS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/4/mec15182-sup-0002-AppendixS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/5/mec15182-sup-0010-AppendixS10.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/6/mec15182.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/7/mec15182-sup-0003-AppendixS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/8/mec15182-sup-0006-AppendixS6.pd

Environmental heterogeneity and not vicariant biogeographic barriers generate community-wide population structure in desert-adapted snakes

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.see also the Perspective by Alencar and QuentalPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/1/mec15182-sup-0004-AppendixS4.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/2/mec15182_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/3/mec15182-sup-0005-AppendixS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/4/mec15182-sup-0002-AppendixS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/5/mec15182-sup-0010-AppendixS10.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/6/mec15182.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/7/mec15182-sup-0003-AppendixS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152024/8/mec15182-sup-0006-AppendixS6.pd

Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family

The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary relationships, often with very low statistical support. We sought to resolve this situation by sequencing over 4,500 ultraconserved element loci from multiple representatives of every elapoid family/sub-family level taxon and inferring their phylogenetic relationships with multiple methods. Concatenation and multispecies coalescent based species trees yielded largely congruent and well-supported topologies. Hypotheses of a hard polytomy were not retained for any deep branches. Our phylogenies recovered Cyclocoridae and Elapidae as diverging early within Elapoidea. The Afro-Malagasy radiation of elapoid snakes, classified as multiple subfamilies of an inclusive Lamprophiidae by some earlier authors, was found to be monophyletic in all analyses. The genus Micrelaps was consistently recovered as sister to Lamprophiidae. We establish a new family, Micrelapidae fam. nov., for Micrelaps and assign Brachyophis to this family based on cranial osteological syn-apomorphy. We estimate that Elapoidea originated in the early Eocene and rapidly diversified into all the major lineages during this epoch. Ecological opportunities presented by the post-Cretaceous-Paleogene mass extinction event may have promoted the explosive radiation of elapoid snakes.Peer reviewe

Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

Background Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS. Here, we determine how a 5-locus Sanger dataset compares with a 377-locus anchored genomics dataset for understanding the evolutionary history of the pseudoxyrhophiine snake radiation centered in Madagascar. The Pseudoxyrhophiinae comprise ~86 % of Madagascar’s serpent diversity, yet they are poorly known with respect to ecology, behavior, and systematics. Using the 377-locus NGS dataset and the summary statistics species-tree methods STAR and MP-EST, we estimated a well-supported species tree that provides new insights concerning intergeneric relationships for the pseudoxyrhophiines. We also compared how these and other methods performed with respect to estimating tree topology using datasets with varying numbers of loci. Methods Using Sanger sequencing and an anchored phylogenomics approach, we sequenced datasets comprised of 5 and 377 loci, respectively, for 23 pseudoxyrhophiine taxa. For each dataset, we estimated phylogenies using both gene-tree (concatenation) and species-tree (STAR, MP-EST) approaches. We determined the similarity of resulting tree topologies from the different datasets using Robinson-Foulds distances. In addition, we examined how subsets of these data performed compared to the complete Sanger and anchored datasets for phylogenetic accuracy using the same tree inference methodologies, as well as the program *BEAST to determine if a full coalescent model for species tree estimation could generate robust results with fewer loci compared to the summary statistics species tree approaches. We also examined the individual gene trees in comparison to the 377-locus species tree using the program MetaTree. Results Using the full anchored dataset under a variety of methods gave us the same, well-supported phylogeny for pseudoxyrhophiines. The African pseudoxyrhophiine Duberria is the sister taxon to the Malagasy pseudoxyrhophiines genera, providing evidence for a monophyletic radiation in Madagascar. In addition, within Madagascar, the two major clades inferred correspond largely to the aglyphous and opisthoglyphous genera, suggesting that feeding specializations associated with tooth venom delivery may have played a major role in the early diversification of this radiation. The comparison of tree topologies from the concatenated and species-tree methods using different datasets indicated the 5-locus dataset cannot beused to infer a correct phylogeny for the pseudoxyrhophiines under any method tested here and that summary statistics methods require 50 or more loci to consistently recover the species-tree inferred using the complete anchored dataset. However, as few as 15 loci may infer the correct topology when using the full coalescent species tree method *BEAST. MetaTree analyses of each gene tree from the Sanger and anchored datasets found that none of the individual gene trees matched the 377-locus species tree, and that no gene trees were identical with respect to topology. Conclusions Our results suggest that ≥50 loci may be necessary to confidently infer phylogenies when using summaryspecies-tree methods, but that the coalescent-based method *BEAST consistently recovers the same topology using only 15 loci. These results reinforce that datasets with small numbers of markers may result in misleading topologies, and further, that the method of inference used to generate a phylogeny also has a major influence on the number of loci necessary to infer robust species trees. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0503-1) contains supplementary material, which is available to authorized users

A generalized method to determine detectability of rare and cryptic species using the ornate box turtle as a model

Estimates regarding population parameters are often based on data from surveys. To ensure that such estimates are as accurate as possible, it is important to know the detectability resulting from the particular survey method used. We used radiotelemetry to measure detectability of ornate box turtles (Terrapene ornata), using visual-encounter surveys in a sand prairie in northwestern Illinois, USA. We found that the overall detection probability of visual-encounter surveys was 0.03, and our high frequency of nondetection was due to a failure to detect visible turtles rather than turtles being underground or hidden in dense vegetation. Despite the substantial population density at our study site, visual-encounter surveys failed to detect box turtles on most visits, which resulted in a prohibitively high number of surveys that would be required to accurately estimate population size or to infer absence of the species from a site. Our method of using radiotelemetry to measure detection probability of a survey method could be easily applied to other small, cryptic, or rare species. However, our low detection probability and high frequency of nondetections recommend against use of visual-encounter surveys alone in estimating population parameters for ornate box turtles. © 2011 The Wildlife Society