Geographic variation in morphology in the Mohave Rattlesnake (Crotalus scutulatus Kennicott 1861) (Serpentes: Viperidae): implications for species boundaries

Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation

Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study, we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single-nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genus Ehrharta, whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree of Ehrharta and to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualizes multiple values of K. Given that the two genomic data sets are independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both of which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in the E. setacea and E. rehmannii complexes, with the E. ramosa complex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach. [Species delimitation; genotyping-by-sequencing; population structure; integrative taxonomy; cryptic species; Ehrharta (Poaceae).].

A new species of Chrysemys (Emydidae: Deirochelyinae) from the latest Miocene-Early Pliocene of Tennessee, USA and its implications for the evolution of painted turtles

Chrysemys, commonly known as painted turtles, have the largest native biogeographic range of all North American turtles. The presence of a new species, Chrysemys corniculata sp. nov., in the Late Hemphillian-Early Blancan North American Land Mammal Age (latest Miocene-Early Pliocene) of Tennessee provides further data on the evolution of Chrysemys, deirochelyines and emydids. The new fossil species lies basally in Deirochelyinae and suggests that either Chrysemys represents a basal deirochelyine morphology and is one of the oldest genera in the family, or that similar basal morphologies have evolved multiple times throughout deirochelyine evolution. Its occurrence at the same time as Chrysemys picta, during the Hemphillian-Early Blancan, a time of high biodiversity in emydid turtles, suggests either multiple species of Chrysemys during the Late Hemphillian-Early Blancan (at least one in the mid-west and one farther east), or multiple lineages with basal morphologies during this time. Early fossil deirochelyines occur after the greenhouse conditions of the Eocene and the Mid-Miocene Climatic Optimum. Vicariance led to deirochelyines becoming more speciose, including the occurrence of C. corniculata, after the Mid-Miocene Climatic Optimum, potentially suggesting cooler temperatures aided in the evolution of the subfamily and their speciation during the Hemphillian and into the Early Blancan.

Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus)

Hybridization and introgression are important, but often overlooked processes when inferring phylogenies. When these processes are not accounted for and a strictly diverging phylogenetic model is applied to groups with a history of hybridization, phylogenetic inference and parameter estimation can be inaccurate. Recent developments in phylogenetic network approaches coupled with the increasing availability of genomic data allow inferences of reticulate evolutionary histories across the tree of life. The western rattlesnake species group (C. viridis species complex, C. mitchellii species complex, C. scutulutas, and C. tigris) is an iconic snake lineage that is widespread across western North America. This group is composed of several species complexes with unclear species limits, likely the result of ongoing gene flow among nascent lineages. Here I generate reduced representation genomic data and test for a history of reticulation within this group. I demonstrate that all species have undergone hybridization with at least one other lineage, suggesting introgression is widespread in this group. Topologies differ between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, indicating that gene flow has obscured phylogenetic relationships within this group. These past introgression events are predominantly restricted to species that co-occur geographically. However, within species that have a history of introgression, this signature is detected regardless of specimen sampling across geography. Overall, my results suggest the accumulation of reproductive isolating barriers occurs slowly in rattlesnakes which likely leads to the difficulty in delimiting species, furthermore, the results of this study have implications for trait evolution in this group.

A symphony of destruction: Dynamic differential fibrinogenolytic toxicity by rattlesnake (Crotalus and Sistrurus) venoms

What factors influence the evolution of a heavily selected functional trait in a diverse clade? This study adopts rattlesnakes as a model group to investigate the evolutionary history of venom coagulotoxicity in the wider context of phylogenetics, natural history, and biology. Venom-induced clotting of human plasma and fibrinogen was determined and mapped onto the rattlesnake phylogenetic tree to reconstruct the evolution of coagulotoxicity across the group. Our results indicate that venom phenotype is often independent of phylogenetic relationships in rattlesnakes, suggesting the importance of diet and/or other environmental variables in driving venom evolution. Moreover, the striking inter- and intraspecific variability in venom activity on human blood highlights the considerable variability faced by physicians treating envenomation. This study is the most comprehensive effort to date to describe and characterize the evolutionary and biological aspects of coagulotoxins in rattlesnake venom. Further research at finer taxonomic levels is recommended to elucidate patterns of variation within species and lineages.