DOI: 10.5061/dryad.kp400
title: Data from: Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

description: Background: Using molecular data generated by high throughput next
 generation sequencing (NGS) platforms to infer phylogeny is becoming
 common as costs go down and the ability to capture loci from across the
 genome goes up. While there is a general consensus that greater numbers of
 independent loci should result in more robust phylogenetic estimates, few
 studies have compared phylogenies resulting from smaller datasets for
 commonly used genetic markers with the large datasets captured using NGS.
 Here, we determine how a 5-locus Sanger dataset compares with a 377-locus
 anchored genomics dataset for understanding the evolutionary history of
 the pseudoxyrhophiine snake radiation centered in Madagascar. The
 Pseudoxyrhophiinae comprise ~86 % of Madagascar’s serpent diversity, yet
 they are poorly known with respect to ecology, behavior, and systematics.
 Using the 377-locus NGS dataset and the summary statistics species-tree
 methods STAR and MP-EST, we estimated a well-supported species tree that
 provides new insights concerning intergeneric relationships for the
 pseudoxyrhophiines. We also compared how these and other methods performed
 with respect to estimating tree topology using datasets with varying
 numbers of loci. Methods: Using Sanger sequencing and an anchored
 phylogenomics approach, we sequenced datasets comprised of 5 and 377 loci,
 respectively, for 23 pseudoxyrhophiine taxa. For each dataset, we
 estimated phylogenies using both gene-tree (concatenation) and
 species-tree (STAR, MP-EST) approaches. We determined the similarity of
 resulting tree topologies from the different datasets using
 Robinson-Foulds distances. In addition, we examined how subsets of these
 data performed compared to the complete Sanger and anchored datasets for
 phylogenetic accuracy using the same tree inference methodologies, as well
 as the program *BEAST to determine if a full coalescent model for species
 tree estimation could generate robust results with fewer loci compared to
 the summary statistics species tree approaches. We also examined the
 individual gene trees in comparison to the 377-locus species tree using
 the program MetaTree. Results: Using the full anchored dataset under a
 variety of methods gave us the same, well-supported phylogeny for
 pseudoxyrhophiines. The African pseudoxyrhophiine Duberria is the sister
 taxon to the Malagasy pseudoxyrhophiines genera, providing evidence for a
 monophyletic radiation in Madagascar. In addition, within Madagascar, the
 two major clades inferred correspond largely to the aglyphous and
 opisthoglyphous genera, suggesting that feeding specializations associated
 with tooth venom delivery may have played a major role in the early
 diversification of this radiation. The comparison of tree topologies from
 the concatenated and species-tree methods using different datasets
 indicated the 5-locus dataset cannot be used to infer a correct phylogeny
 for the pseudoxyrhophiines under any method tested here and that summary
 statistics methods require 50 or more loci to consistently recover the
 species-tree inferred using the complete anchored dataset. However, as few
 as 15 loci may infer the correct topology when using the full coalescent
 species tree method *BEAST. MetaTree analyses of each gene tree from the
 Sanger and anchored datasets found that none of the individual gene trees
 matched the 377-locus species tree, and that no gene trees were identical
 with respect to topology. Conclusions: Our results suggest that ≥50 loci
 may be necessary to confidently infer phylogenies when using summary
 species-tree methods, but that the coalescent-based method *BEAST
 consistently recovers the same topology using only 15 loci. These results
 reinforce that datasets with small numbers of markers may result in
 misleading topologies, and further, that the method of inference used to
 generate a phylogeny also has a major influence on the number of loci
 necessary to infer robust species trees.
description: Anchored loci probe
 design informationThe alignments of probe
 regions, probes, and probe region coordinates used to generate the
 anchored loci for the pseudoxyrhophiine dataset, as described in the
 methods of the manuscript.AHE_Snake_ProbeDesign.zipDatasets used for analysesThis zip files contains the Sanger and NGS alignments, information for the Robinson-Foulds distances for all trees, the gene trees for both the Sanger and NGS alignments, resulting trees from phylogenetic analyses, and the complete MetaTree analysis data.All_files_for_Pseudoxyrhophiines.zip