The potential usage of genomic open data can help us to understand biodiversity, for example by analyzing species boundaries in morphologically similar species. An example of taxon in which this can be useful is Nematomorpha (horsehair worms), one of the less studied animal phyla, in which species identification can be challenging due to lack of morphological characters. This study started as an evaluation of population-level analyses of effective population size (Ne) with open data using the genus Chordodes. An RNA sequencing (RNA-seq) dataset originally labelled as Chordodes fukuii was first examined by extracting sequences of the mitochondrial barcoding gene cytochrome c oxidase subunit I (COXI) from it. After surprising results from such gene, which showed two potential distinct Chordodes species in the datasets (C. formosanus and C. japonensis), further analyses were run by combining these data with a previously published double-digest restriction-site-associated DNA sequencing (ddRADseq) dataset. PCA, adegenet, and ADMIXTURE analyses consistently recovered two distinct genetic clusters, indicating that the RNA-seq dataset contains specimens from two species rather. While most individuals were consistently assigned, some specimens identified as C. japonensis based on COXI clustered with individuals labelled as C. formosanus or exhibited mixed ancestry when genome-wide markers were analyzed, suggesting possible introgression, incomplete lineage sorting, or biases related to missing data. The study shows how previously released data can be used for evaluating species delimitation, potential previous demographic events, and potential needs in DNA barcoding and genomics for avoiding future misidentification of morphologically similar species.
Nematomorph, Taiwan, Japan, Species recognition, Phylogenomics
