Species delimitation in the Eviota sigillata species complex, a widely distributed group of cryptobenthic coral reef fishes

Cryptobenthic reef fishes (CRF) are the smallest vertebrates on coral reefs but represent about 40% of the fish species and about 50% of fish abundance in coral reef ecosystems. Their diversity can be explained by their extremely limited dispersal abilities and short generation times (promoting allopatric speciation) coupled with their ability to partition microhabitats at a very fine scale. Importantly, for some groups of CRF, their small size, cryptic nature, and conserved morphology have resulted in many undetected cryptic species, which may require a genome-wide species delimitation approach to discern how many species are present. One of the most species-rich groups of CRF, the genus Eviota, has 132 species described to date, is widely distributed from the Red Sea to Hawaii and French Polynesia, and is known to comprise numerous cryptic species. We focused on the Eviota sigillata complex which is represented by two nominal species described by morphological characters, yet prelimin..., Sample Collection
A total of 123 specimens in the E. sigillata complex were collected from locations across the Indo-Pacific region (Figure 1; see Table S1 for specific location of 102 samples passing the bioinformatic filtering). Specimens were determined to belong to the E. sigillata complex if they keyed out to E. sigillata, E. shimadai, or an ambiguous combination of the two using the key from Greenfield and Winterbottom (2016) or very closely resembled live photographs of these two species from the taxonomic literature. All specimens were captured after being anesthetized using 5% quinaldine sulphate dissolved in seawater or a solution of 5% clove oil dissolved in ethanol dispersed from a squirt bottle (see Tornabene et al., 2013). Specimens were photographed in the field and then preserved in 95% ethanol. We also used two tissue samples of E. sigillata from two specimens from the South African Institute for Aquatic Biodiversity (SAIAB) that were available for genomic analysis and ..., , # Eviota sigillata data

Dataset DOI: [https://doi.org/10.5061/dryad.69p8cz9cn](https://doi.org/10.5061/dryad.69p8cz9cn)

## Description of the data and file structure

To estimate the number of species in the *E. sigillata* complex we took an integrative approach that combined multiple data sources and analyses. Using a combination of freshly collected samples and museum specimens, we holistically evaluated the number of species estimated from: (i) species delimitation analysis of mitochondrial COI data using both tree-based and non-tree-based approaches; (ii) genome-wide phylogenetic analyses of thousands of loci from ddRADseq data; for several clades, we performed a (iii) multispecies coalescent species-tree analysis coupled with Bayes Factor species delimitation using SNAPP + BFD*, as well as (iv) a genome wide analysis of population genetic variation using STRUCTURE; and (v) an analysis of morphology to identify putatively diagnostic characters for different clades. Information fro...,