DOI: 10.5061/dryad.gd74v
title: Data from: The identification of the closest living relative(s) of tetrapods: phylogenomic lessons for resolving short ancient internodes

description: Identifying the closest living relative(s) of tetrapods is an important,
 yet still contested question in vertebrate phylogenetics. Three hypotheses
 are possible and ruling out alternatives has proven difficult even with
 large molecular data sets due to weak phylogenetic signal coupled
 nonphylogenetic noise resulting from relatively rapid speciation events
 that occurred a long time ago (&gt;400 Ma). Here, we revisit the
 identity of the closest living relative of land vertebrates from a
 phylogenomic perspective and include new genomic data for all extant
 lungfish genera. RNA-seq proves to be a great alternative to genomic
 sequencing, which currently is technically not feasible in lungfishes due
 to their huge (50–130 Gb) and repetitive genomes. We examined the most
 important sources of systematic error, namely long-branch attraction
 (LBA), compositional heterogeneity and distribution of missing data and
 applied different correction techniques. A multispecies coalescent
 approach is used to account for deep coalescence that might come from the
 short and deep internodes separating early sarcopterygian splits.
 Concatenation methods favored lungfishes as the closest living relatives
 of tetrapods with strong statistical support. Amino acid profile mixture
 models can unambiguously resolve this difficult internode thanks to their
 ability to avoid systematic error. We assessed the performance of
 different site-heterogeneous models and data partitioning and compared the
 ability of different strategies designed to overcome LBA, including taxon
 manipulation, reduction of among-lineage rate heterogeneity and removal of
 fast-evolving or compositionally heterogeneous positions. The
 identification of lungfish as sister group of tetrapods is robust
 regarding the effects of nonstationary composition and distribution of
 missing data. The multispecies coalescent method reconstructed strongly
 supported topologies that were congruent with concatenation, despite
 pervasive gene tree heterogeneity. We reject alternative topologies for
 early sarcopterygian relationships by increasing the signal-to-noise ratio
 in our alignments. The analytical pipeline outlined here combines
 probabilistic phylogenomic inference with methods for evaluating data
 quality, model adequacy, and assessing systematic error, and thus is
 likely to help resolve similarly difficult internodes in the tree of life.
description: 2960_smx_3lf251_amemiya_3lf1821_smx_3lf1821_homog_blocks251_heterog_blocks251_homog_blocks1821_heterog_blocksget_support_values_from_treePerl script to extract support values from a tree for a predefined cladeclade_support_from_site_patternsPerl script to identify sites supporting a predefined clade, classified by the method of Waegele and Rodding (1998)parse_trees_test_alt_topologiesPerl script to test tree topologies. Specifically, it checks if the tree conforms to T1, T2 or T3 hypotheses.parse_tree_check_outparalogsPerl script to identify putative instances of paralogy by testing the monophyly of a specified clade on gene trees.Supplementary Information, Tables and FiguresIrisarri_Meyer_supplement_20160607.pdf