DOI: 10.5061/dryad.59zw3r2c0
title: Data from: dispersal sweepstakes: biotic interchange propelled air-breathing fishes across the globe

description: Synbranchiformes is a phenotypically diverse and species rich clade of
 freshwater acanthomorph fishes, which include eel- and perch-like,
 air-breathing and non-air-breathing fishes. The ability to breathe out of
 water has presumably aided lineages of Synbranchiformes in dispersing
 across all southern continents except Antarctica. The lack of a
 well-resolved, time-calibrated phylogeny of Synbranchiformes limits our
 understanding of the timing and geographic patterns of diversification of
 these anatomically and ecologically diverse fishes. As a consequence,
 contemporary interpretations of synbranchiform biogeography invoke
 scenarios as disparate as Gondwana vicariance and pan-global rafting to
 explain their modern-day geographic distribution. In this study, we use
 high-throughput sequencing of ultra-conserved elements (UCEs) to infer a
 phylogeny for all major synbranchiform lineages. We combine this dataset
 with existing Sanger sequenced genes and fossil calibrations to infer a
 comprehensive time-calibrated phylogeny of Synbranchiformes. Then, we use
 Bayesian methods of biogeographical reconstruction to document the history
 of dispersal of synbranchiforms, finding support for Southeast Asia as the
 likely ancestral area of all major lineages. Our results reject the
 hypothesis of Gondwanan vicariance explaining synbranchiform biogeography,
 and instead the historical biogeographic analyses support a hypothesis of
 independent continental invasions by snakeheads, anabantids, and spiny
 eels. However, there is no signal of elevated lineage diversification
 rates after these invasions. Instead, higher rates of lineage
 diversification in spiny eels pre-dates their arrival to Africa, while the
 high levels of lineage diversification observed in Betta were
 initiated prior to the flooding of insular Sundaland in SE Asia.
description: UCE DNA sequence data were obtained through hybrid enrichment of
 genomic libraries. Library preparation of sheared, genomic DNA samples
 were performed using Kapa HyperPrep kits; UCE probes were purchased from
 Daicel Arbor Biosciences to target ~1300 ultraconserved elements from
 Acanthomorph fishes. Sequencing was performed on Illumina HiSeq4000.
 Demultiplexed data were processed using the Phyluce software package,
 which applies other programs to: trim tag sequences from raw reads and
 remove low quality sequence data; match raw reads to UCE probes; and
 construct alignments to meet various thresholds of completeness (75% or
 95% taxonically complete). Trees were inferred using the program IQTree;
 divergence times were estimated using BEAST; lineage diversification
 dynamics were estimated using BAMM and MiSSE; biogeographic history was
 inferred using BioGeoBears.
description: Alignment files and their associated character set/partition
 delimitation files can be opened with any text editor. Tree files can be
 opened with FigTree or other program that reads newick- or nexus-
 formatted phylogenetic files.
description: # Synbranchiformes UCE data --- Included are concatenated sequence data
 files, files that denote the partitions of UCE loci, and the output tree
 files from analyses using IQTree and BEAST. ## Description of the Data and
 file structure UCE_loci_75p_complete.gzip &gt; gzip directory of
 nexus-formatted alignments for individual UCE loci. All alignments in this
 directory contain at least 75% of taxa in our total dataset.
 UCE_only_matrix_IQTree.tre &gt; The output tree from IQTree analysis of
 concatenated UCE_only sequence data matrix.
 UCE_only_75percent_matrix.phylip &gt; The alignment for UCE sequence data
 (all loci 75% taxonomically complete), concatenated in phylip format.
 UCE_only_75percent_matrix_partitions.txt &gt; The partitioning scheme for
 the IQTree analysis of concatenated UCE sequence data (all loci 75%
 taxonomically complete). UCE_composite_matrix_IQTree.tre &gt; The output
 tree from IQTree analysis of the concatenated UCE-composite (95% complete
 UCE loci plus the data obtained from Genbank) matrix.
 UCE_composite_matrix.phylip &gt; The alignment for UCE sequence data
 (UCE-genbank-composite matrix), concatenated in phylip format.
 UCE_composite_matrix_partitions.txt &gt; The partitioning scheme for the
 IQTree analysis of concatenated UCE-genbank-composite sequence data.
 UCE_loci_trees_for_ASTRAL.trees &gt; Individual UCE loci trees obtained by
 maximum likelihood analysis in IQTree. BEAST_divtimes_set1.xml &gt; XML
 file for BEAST divergence time analysis of 30 UCE loci (set 1) and three
 Genbank loci (cytb, coi, rag1). BEAST_divtimes_set2.xml &gt; XML file for
 BEAST divergence time analysis of 30 UCE loci (set 2) and three Genbank
 loci (cytb, coi, rag1). BEAST_divtimes_set3.xml &gt; XML file for BEAST
 divergence time analysis of 30 UCE loci (set 3) and three Genbank loci
 (cytb, coi, rag1). BEAST_divtimes_set1.tre &gt; Time tree obtained from
 BEAST analysis of 30 UCE loci (set 1) and three Genbank loci (cytb, coi,
 rag1) BEAST_divtimes_set2.tre &gt; Time tree obtained from BEAST analysis
 of 30 UCE loci (set 2) and three Genbank loci (cytb, coi, rag1)
 BEAST_divtimes_set3.tre &gt; Time tree obtained from BEAST analysis of 30
 UCE loci (set 3) and three Genbank loci (cytb, coi, rag1)