Reticulate evolution in nuclear Middle America causes discordance in the phylogeny of palm‐pitvipers (Viperidae: Bothriechis)

Abstract

Aim A number of processes can lead to weak or conflicting phylogenetic signals, especially in geographically dynamic regions where unstable landscapes and climates promote complex evolutionary histories. The Middle American pitviper genus Bothriechis has a complex biogeographic distribution and previous phylogenetic analyses have recovered conflicting topologies based on the data type used. Here, we tested whether historic conflicts in the phylogeny were the result of reticulate evolution and whether the inferred biogeographic history of the group would enable contact among reticulate lineages. Location Middle America. Taxon Palm‐pitvipers (genus Bothriechis). Methods We generated a phylogenomic dataset using an anchored phylogenomics approach and inferred a genomics‐based species tree and mitochondrial tree to assess incongruence among datasets. We then generated a dated phylogeny and conducted ancestral area reconstruction to examine the biogeographic history surrounding the diversification of these species. We additionally tested whether the discordance among trees is better explained by lineage sorting or reticulate evolution by testing models of reticulate evolution inferred through multiple methods. Results We found strong support for discordance in the phylogeny of Bothriechis and corresponding evidence for reticulate evolution among lineages with incongruent placement. Ancestral area reconstruction placed these taxa in adjacent regions during the time period when reticulation was projected to take place and suggested a biogeographic history heavily influenced by vicariant processes. Main conclusions Reticulation among geographically proximate lineages has driven apparent genomic discordance in Bothriechis and is responsible for historical incongruence in the phylogeny. Inference of the order of events suggests that reticulation among nuclear Middle American taxa occurred during a time of geologic upheaval, promoting lineage divergence and secondary contact. Reticulate evolution and similar processes can have substantial impacts on the evolutionary trajectory of taxa and are important to explicitly test for in biogeographically complex regions.

Trait differentiation and modular toxin expression in palm-pitvipers

“…We recovered 1517 total transcripts for B. nigroviridis, which included 43 toxins from 13 toxin families. The venom transcriptome of B. nigroviridis was largely dominated by the expression of the heterodimeric neurotoxic [33] and a distribution map for B. nigroviridis and B. nubestris made in R v.3.5.3 (https://www.R-project.org/) based on ranges described in [74] and [33] and publicly available specimen localities in [32]. Sampled localities are shown as dots with specimen labels.…”

“…The sister species to B. nigroviridis, B. nubestris, appears to occupy an extremely similar ecological niche based on its documented range and conserved morphology [32]. Although empirical studies of B.nubestris' venom have yet to be conducted, its divergence from B. nigroviridis 6-10 mya would provide sufficient temporal opportunity for venom diversification [33]. Bothriechis nigroviridis and B. nubestris can therefore provide a test case for examining mechanisms of phenotypic diversification in a modular framework.…”

Genomic Adaptations to Salinity Resist Gene Flow in the Evolution of Floridian Watersnakes

“…2013 ; Pease et al. 2016 ; Mason et al. 2019 ); therefore, gene flow is likely responsible for the limited nodal support recovered in our phylogenies and further demonstrates the most probable cause of historical phylogenetic discrepancies, with regard to the separation of N. fasciata and N. clarkii , and limitations of single-gene phylogenies.…”

A new species of Bolitoglossa (Caudata: Plethodontidae) of the Bolitoglossa franklini group from an isolated cloud forest in northern Guatemala

“…The complex tectonic background of Guatemala, with multiple events of fragmentation and isolation overall its geological history, has been reported as a plausible promotor of species divergence for the isolated cloud forests in the mountain ridges of Nuclear Central America region (Castoe et al 2009, Ornelas et al 2013. This has produced disjunct distributions of several taxa such as passalid beetles Proculus (Schuster et al 2003) and Ogyges ), Cryptotriton salamanders (Vásquez-Almazán et al 2009, Rovito et al 2015, Abronia lizards (Campbell & Frost 1993, Gutiérrez-Rodríguez et al 2021, Bothriechis pit vipers (Mason et al 2019) and shrews (Woodman et al 2012).…”