DOI: 10.5061/dryad.413f4
title: Data from: A multilocus molecular phylogeny for the avian genus Liocichla (Passeriformes: Leiothrichidae: Liocichla)

description: Background: Historically the babblers have been assigned to the family
 Timaliidae but several recent studies have attempted to rest the taxonomy
 of this diverse passerine assemblage on a more firm evolutionary footing.
 The result has been a major rearrangement of the group. A well-supported
 and comprehensive phylogeny for this widespread avian group is an
 important part of testing evolutionary and biogeographic hypotheses,
 especially in Asia where the babblers are a key component of many forest
 ecosystems. However, the genus Liocichla is poorly represented in these
 prior studies of babbler systematics. Methods: We used a multilocus
 molecular genetic approach to generate a phylogenetic hypothesis for all
 five currently recognized species in the avian genus Liocichla. Multilocus
 DNA sequence data was used to construct individual gene trees using
 maximum likelihood and species trees were estimated from gene trees using
 Bayesian analyses. Divergence dates were obtained using a molecular clock
 approach. Results: Molecular data estimate a probable window of time for
 the origin for the Liocichla from the mid to late Miocene, between 5.55
 and 12.87 Ma. Despite plumage similarities between the insular Taiwan
 endemic, L. steerii, and the continental L. bugunorum and L. omeiensis,
 molecular data suggest that L. steerii is the sister taxon to all
 continental Liocichla. The continental Liocichla are comprised of two
 lineages; a lineage containing L. omeiensis and L. bugunorum and a lineage
 comprised of L. phoenicea and L. ripponi. The comparatively early
 divergence of L. steerii within the Liocichla may be illusory due to
 extinct and therefore unsampled lineages. L. ripponi and L. phoenicea are
 parapatric with a Pleistocene split (0.07–1.88 Ma) occurring between an
 Eastern Himalayan L. phoenicea and a Northern Indochina distributed L.
 ripponi. L. bugunorum and L. omeiensis underwent a similar split between
 the Eastern Himalaya (L. bugunorum) and Central China (L. omeiensis)
 divided by the Hengduan Mountains. Conclusions: This study supports an
 origin of the Liocichla occurring sometime prior to the Miocene–Pliocene
 boundary, a period of significant climatic upheaval in Asia. The
 biogeographical patterns within the Liocichla mirror those of other birds
 in the region and allude to common geological and climatic drivers of
 avian diversification in Asia.
description: Nexus alignments
 including all taxaNexus alignments that
 include all taxa even those taxa (Minla ignotincta and Liocichla
 bugunorum) for which there are missing sequences for some
 loci.Nexus
 alignments ALL TAXA.zipNexus alignments without
 MI and LBNexus alignments used in
 BEAST in which taxa with missing data for one or more loci (Minla
 ignotincta and Liocichla bugunorum) were excluded.BEAST23_run1_analysis23BEAUti xml file for analysis with partitioning only by locus.BEAST23_run1_analysis24BEAUti xml file with partitioning by both locus and codon positionCombined results from BEAST codon partitioned analysislog and tree files from four replicate BEAST runs using partitioning by both codon and locus combined in LogCombinerCombined results from BEAST gene only partitioned analysislog and tree files from four replicate BEAST runs using only partitioning by locus combined in LogCombinerBEAST analysis with gene partitioning and nuclear loci onlylog and tree files from single run of BEAST (100,000,000 generations) with partitioning by gene and only the nuclear intron loci.Supplemental file 1 GenBank accession numbersGenBank accession numbers for all sequences used in this study.