Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)

Abstract

With the continued adoption of genome‐scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent‐based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent‐based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent‐based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.

Evaluating taxonomic inflation: towards evidence-based species delimitation in Eurasian vipers (Serpentes: Viperinae)

“…This applies even to introns and other fast-evolving single copy nuclear genes (e.g., NT3, PRLR, Townsend et al, 2008). Consequently, other molecular approaches such as even faster evolving markers (e.g., Kindler and Fritz, 2018;Pöschel et al, 2018), phylogenomic methods (e.g., Blair et al, 2019;Heinicke et al, 2018), and increased sampling to evaluate current or past gene flow between most-proximate populations or contact zones of two or more closely related species (Mebert, 2008(Mebert, , 2015a(Mebert, , b, 2020Hillis, 2019) should be favoured to infer evolutionary histories and resolve species limits among these taxa.…”

“…Ultimately, the taxonomic status of candidate species should be best addressed in an integrative fashion, that is, by searching for concordant differences in genetic, morphological and ecological traits (Padial et al, 2010). Since mtDNA could be particularly misleading in vipers, both by inflating the number of taxa or by missing lineages that have lost their mtDNA due to introgression (e.g., Zinenko et al, 2016), we encourage the use of multilocus genetic data (e.g., UCE loci, Blair et al, 2019). Until now, among all Eurasian vipers, only three species have been described using integrative approaches (i.e., by addressing phylogenetic divergence and characterizing phenotypic variability; Vipera walser Ghielmi et al, 2016; Macrovipera razii Oraie et al, 2018; Vipera sakoi Tuniyev et al, 2018).…”

Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data

“…For instance, Burbrink and Gehara (2018) discovered ancient reticulation in New World kingsnakes using species networks, and used tree-based methods to estimate divergence times and ancestral geographical areas. Similarly, using thousands of UCE loci, Blair et al (2019) combined tree-based approaches to delimit species of rattlesnakes and estimate species trees and divergence times with a network approach to estimate the history of deep reticulation. By combining both types of analyses these studies were able to provide a more comprehensive picture into the evolutionary history of these groups.…”

“…parsimony, likelihood, Bayesian). Nowadays, it is common to perform a suite of coalescentbased species tree analyses in addition to concatenation, the latter of which is widely used to test for species monophyly and help assign individuals to species prior to species tree inference (Blair et al 2019). If gene flow is expected or present, adding networks to the list of tools seems like a natural extension to the field as a whole, and will no doubt provide novel insight into the propensity for reticulation/hybridization throughout the Tree of Life.…”

Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex

“…The wide use of DNA sequence data in taxonomy (e.g., Hebert, Cywinska, Ball, & DeWaard, 2003;Tautz, Arctander, Minelli, Thomas, & Vogler, 2003) and the application of phylogenetic/coalescentbased species delimitation approaches (e.g., Fujita, Leaché, Burbrink, McGuire, & Moritz, 2012;Pons et al, 2006;Yang & Rannala, 2010) have allowed the discovery of cryptic species and the resolution of many taxonomic uncertainties (e.g., Blair et al, 2019;Burbrink et al, 2011;Leavitt, Johnson, Goward, & St Clair, 2011;Niemiller, Near, & Fitzpatrick, 2012). In particular, the incorporation of coalescent theory under an integrative taxonomic framework has increased the statistical rigor of species delimitation and has helped to move away from subjective decisions on the degree of differentiation (e.g., phenotypic, genetic, ecological, etc) that is needed for considering different lineages or populations as distinct taxa (Fujita et al, 2012;Jones & Weisrock, 2018;Wiens & Servedio, 2000).…”