DOI: 10.7291/d1wq2p
title: Bewildering biogeography: waves of dispersal and diversification across southern Wallacea by bent-toed geckos (genus: Cyrtodactylus)

description: Bent-toed Geckos, genus Cyrtodactylus, are one of the most diverse
 terrestrial vertebrate groups, and their range extends from South Asia
 into Australo-Papua and adjacent Pacific islands. Given the generally high
 faunal endemism on Wallacean islands, it is rather paradoxical that the
 diversity in these geckos appears to be so low (21 species in Wallacea, 15
 in the Philippines) compared with continental shelf assemblages
 (&gt;300 species on Sunda + Sahul Shelves + adjacent islands). To
 determine whether this shortfall was real or an artifact of historical
 undersampling, we analyzed mitochondrial DNA sequences of hundreds of
 southern Wallacean samples (Lesser Sundas + southern Maluku). After
 screening to guide sample selection for target capture data collection, we
 obtained a 1150-locus genomic dataset (1,476,505 bp) for 119 samples of
 southern Wallacean and closely related lineages. The results suggest that
 species diversity of Cyrtodactylus in southern Wallacea is vastly
 underestimated, with phylogenomic and clustering analyses suggesting as
 many as 25 candidate species, in contrast to the 8 currently described.
 Gene exchange between adjacent candidate species is absent or minimal
 across the archipelago with only one case of &gt;0.5 migrants per
 generation. Biogeographical analysis suggests that the hitherto
 unrecognized diversity is the result of at least three independent
 dispersals from Sulawesi or its offshore islands into southern Wallacea
 between 6–14 Ma, with one invasion producing small-bodied geckos and the
 other two or three producing larger-bodied geckos. The smaller-bodied
 laevigatus group appears to be able to coexist with members of either
 larger-bodied clade, but we have yet to find members of the two
 larger-bodied clades occurring in sympatry, suggesting that ecological
 partitioning or competitive exclusion may be shaping individual island
 assemblages.
description: Genome-wide sequence data were collected following the
 transcriptome-based exon-capture protocol of Bi et al. (2012).
 Transcriptomes of four samples were sequenced, including representatives
 from the <em>Cyrtodactylus darmandvillei, C. laevigatus,
 </em>and<em> C. wetariensis</em> species complexes
 (Table S2). Orthologous exon loci target regions were derived from aligned
 contigs, and after a number of filtering steps, 1200 loci (target size
 ~1.06 MB) from three of the transcripts were used to design 120-bp,
 2.5X-tiled RNA library baits (57,552 unique probes) for an in-solution
 targeted capture experiment (Mybaits, Mycroarray). Genomic library
 preparation included 31 samples from the
 <em>darmandvillei</em> complex, 25 from the
 <em>laevigatus</em> complex, 16 from the
 <em>wetariensis</em> complex, 28 from the
 <em>sadleiri</em> complex, and 19 outgroup samples or samples
 believed to be closely related to our focal clades (Table S1). Genomic
 library pools of 5–6 samples were hybridized to the probes for an
 incubation period of 24 h, and target sequences were isolated with
 magnetic streptavidin beads. The target sequences were then PCR-amplified,
 pooled, and sequenced on an Illumina HiSeq 2500 with 100 bp paired-end
 reads. Bi, K., Vanderpool, D., Singhal, S., Linderoth,
 T., Moritz, C., Good, J.M., 2012. Transcriptome-based exon capture enables
 highly cost-effective comparative genomic data collection at moderate
 evolutionary scales. BMC Genomics 13, 403.
description: All files can be opened with a standard text editor such as
 BBEdit. See materials and methods in the published paper for details on
 which files are analyzed with which software packages.