Ferrer Obiol et al. (2023) applied double digest restriction-site associated sequencing (ddRAD-seq) data to delimit species in North Atlantic and Mediterranean Puffinus shearwaters. These authors concluded that the Balearic/Yelkouan shearwaters (P. mauretanicus/P. yelkouan) sister-species pair comprised a single species based on analyses of ddRAD-seq data and a very brief and deficient review of other evidence. While it is clear that reduced representation genomic data are often suitable for the discovery and documentation of species and their relationships, the issue of whether such data are sufficient to falsify hypotheses of species taxa has received only limited attention so far. Here, we note that detection of species in phylogenomic analyses based on reduced representation sequencing methods will be problematic if species differences are only found in a small portion of the genome (so-called ‘genomic islands of differentiation’), as has been documented in multiple case studies. This means that genomic differences between some species may only be detected if (i) entire genomes are sequenced, and (ii) a formal search for islands of differentiation is conducted. Valid species may be overlooked in reduced representation approaches, such as ddRAD sequencing. Consequently, an apparent lack of overall phylogenomic divergence (e.g. lack of reciprocal monophyly, low genome-wide FST) should not be used by taxonomists as evidence that such taxa are not valid species. We conclude that the apparent lack of divergence in the ddRAD-seq data of Ferrer Obiol et al. (2023) does not represent credible evidence that P. mauretanicus and P. yelkouan are conspecific. In addition, we show that the authors misrepresented other available taxonomic data, failing to properly follow an integrative approach.
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