When standard DNA barcodes do not work for species identification: intermixed mitochondrial haplotypes in the Jaera albifrons complex (Crustacea: Isopoda)

Here, we characterise the standard “Folmer region” of the mitochondrial cytochrome c oxidase subunit 1 (CO1) marker and a fragment of nuclear 28S marker in four species of the Jaera albifrons complex. Jaera albifrons (Leach, 1814), Jaera ischiosetosa Forsman, 1949, Jaera praehirsuta Forsman, 1949, and Jaera forsmani Bocquet, 1950 were collected from localities on the Norwegian coast and identified with morphological characters. We compared DNA sequences with sequences available in GenBank and BOLDsystems and calculated haplotype networks and interspecific versus intraspecific genetic distances. These analyses revealed low interspecific genetic distance (CO1 0.00–1.57%, 28S 0.00–0.39%) and extensive haplotype sharing between J. albifrons group species and specimens from both sides of the North Atlantic for both CO1 and 28S. Genetic distances between J. albifrons group species and other Jaera species, however, exceeded 29% for both CO1 and 28S, with no haplotype sharing. These assessments, together with taxonomically unconstrained analyses with software ABGD and ASAP, show that these markers are unable to distinguish between the J. albifrons group of morphospecies. The sequences do, however, clearly identify J. albifrons species complex from other Jaera species. Thus, a likely hypothesis is that taxa in this complex represent a single species. Our results corroborate previous finds where discordance between mitochondrial gene clusters, AFLP, and other data highlights the potential conflict between different “species criteria” and the well-established distinction between gene trees and species trees. In operational terms, common protocols for metabarcoding will potentially underestimate sympatric species diversity with cases like the J. albifrons complex, if the members of this complex indeed represent different species.