dispersal sweepstakes: biotic interchange propelled air-breathing fishes across the globe

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 comprehens..., 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., 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., # Synbranchiformes UCE data

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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 > 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 > The output tree from IQTree analysis of concatenated UCE_only sequence data matrix.
UCE_only_75percent_matrix.phylip > The alignment for UCE sequence data (all loci 75% taxonomically complete), concatenated in phylip format.
UCE_only_75percent_matrix_partitions.txt > The partitioning scheme for the IQTree analysis of concatenated UCE sequence data (all loci 75% taxonomically complete).

UCE_composite_matrix_IQTree.tre > The output tree from IQTree analysis of the concatenated UCE-composite (95% complete UCE loci plus t...