DOI: 10.5061/dryad.07h0n14
title: Data from: The origins and diversification of the exceptionally rich gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar

description: Processes leading to spectacular diversity of both form and species on
 islands have been well documented under island biogeography theory, where
 distance from source and island size are key factors determining
 immigration and extinction resistance. Less understood are the processes
 governing in-situ diversification on the world’s mega islands, where large
 and isolated land masses produced morphologically distinct radiations from
 related taxa on continental regions. Madagascar has long been recognized
 as a natural laboratory due to its isolation, lack of influence from
 adjacent continents, and diversification of spectacular vertebrate
 radiations. However, only a handful of studies have examined rate shifts
 of in-situ diversification for this island. Here we examine rates of
 diversification in the Malagasy snakes of the family Pseudoxyrhophiinae
 (gemsnakes) to understand if rates of speciation were initially high,
 enhanced by diversification into distinct biomes, and associated with key
 dentition traits. Using a genomic sequence-capture dataset for 366
 samples, we determine that all previously described and newly discovered
 species are delimitable and therefore useful candidates for understanding
 diversification trajectories through time. Our analysis detected no shifts
 in diversification rate between clades or changes in biome or dentition
 type. However, we did detect a significant slowdown in diversification
 during the Pleistocene. We comment on the apparent paradox where most
 living species originated in the Pleistocene, yet diversification rates
 were highest during the previous 15 million years.
description: 1_AHA_Genomic_datazip1. AHA Genomic Data for Pseudoxyrhophiinae and outgroups.2_Phylogenies_comparative_dataIncludes the following files: BAMM_control.txt BioGeoBEARS Code_Match_Nodes_Dates_Among_Methods.R Comparative_Phylo_Table_AICc Conversions_for_732_Tree_Tips.txt Ecological_data_w_outgroups.txt Locus_Models_372_individuals.txt Partitions_models_732_IQ_Tree.txt Tree_Astral_130_taxa Tree_Astral_II_732 Tree_Beast_dated_130_not_Burned_in_R Tree_CMOS_alignment.phy Tree_CMOS_phy.tre Tree_COI_alignment.phy Tree_COI_phy.tre Tree_concat_sanger_alignment.phy Tree_concat_sanger_tree.tre Tree_Dated_Point_PL_Astral_topology_130 Tree_Dated_Raxml_BootStrap_Point_tree_130 Tree_DatedPLTREE_Astral_Topology_Fitted_Raxml_732 Tree_IQ_Boot_SH_130.treefile Tree_IQ_Tree_Concatenated_Partitioned_732_tips.treefile Tree_IQTree_130_Conca_Partitionedt Tree_MCMC_Dated_tree.txt Tree_mcmc_rate_gram.txt Tree_MG_ASTRAL_130_multi_individual_IQ_Trees Tree_NAV5_alignment.phy Tree_NAV5_phy.tre Tree_PL_Dated_IQ_Bootstraps_130_root_edge Tree_PLTree_Dated_1000_IQ_BS_130_Taxa_Tree_Annotator Tree_RAG2_alignment.phy Tree_RAG2_Phy.tre Tree_RAxML_bestTree_732_with_partitions_raxml Tree_RF_Comparisons.xlsx Tree_SVD_130_taxa.tre3_CodeIncludes the following files: Code_Add_Tips_Test_Diversification_TESS.R Code_BPP_Dater.R Code_BPP_Maker.R Code_Character_Reconstruction.R Code_Match_Nodes_Dates_Among_Methods.R Code_Morlon_Model_Diversification.R Code_Reprojection_species_points.R Code_TESS_COMET_Modified.R4_Shapefiles_Species_Coordinates_EcoRegionsIncludes the following files: Madagascar terrestrial ecosystem shape files zip.zip MG_ecoregion_attribute_summary.csv species_coordinates.csv Yoder & Nowak (2006) _shapefiles.zip5_BPP_by_Genus_Dates5. BPP Files with results organized by genus6_Sample_Data_Names_Sanger_AHAAdditional_Text_MethodsFig_S1_Sanger_Tree_AHA_tree_incongruencies_redFig_S2_Astral_Tree_732_Tips