DOI: 10.5061/dryad.7n42q35
title: Data from: Reticulate evolution in nuclear Middle America causes discordance in the phylogeny of palm‐pitvipers (Viperidae: Bothriechis)

description: 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 in Nuclear Middle American 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. 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 in Nuclear Middle American 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.
description: Data files from
 Reticulate evolution in Nuclear Middle America causes discordance in the
 phylogeny of palm-pitvipers (Viperidae: Bothriechis)This DRYAD package
 contains the input files and data used for the project: Reticulate
 evolution in Nuclear Middle America causes discordance in the phylogeny of
 palm-pitvipers (Viperidae: Bothriechis). These include command files and
 data for maximum likelihood and coalescence-based species tree
 phylogenetic estimation, reticulate evolution inference methods using
 Phylonet, SNaQ, and Treemix, calibration based tree dating with MCMCtree,
 and ancestral area reconstruction with BioGeoBEARS.Mason_et_al_2019_data_files.zip