Comparison between morphological and DNA barcode-suggested species boundaries among shallow-water amphipod fauna from the southern European Atlantic coast

Abstract

Background: Amphipods are one of the most diverse and widely distributed groups of crustaceans, often constituting dominant or key elements of marine and coastal communities. As with many other marine invertebrate taxa, rigorous species identifications can be rather challenging, and cryptic species reports have been increasing. In this study we compared DNA barcode-suggested species boundaries with morphology-based species identifications in the amphipod fauna of the southern European Atlantic coast. Results: DNA sequences of the cytochrome c oxidase subunit I barcode region (COI-5P) were obtained from 197 specimens collected along the coast and estuaries of continental Portugal, which were then assigned to 41 morphospecies and 21 families. To this dataset we added publicly available COI-5P sequences of the same species or genus, hence producing a final BOLD dataset comprising 60 species and 273 sequences. Sequences from this dataset were in turn assigned to 68 BINs (Barcode Index Numbers), of which 38 were concordant (i.e., 1 BIN = 1 species), 11 were taxonomically discordant BINs, and 19 were singletons. A detailed examination of the discordant BINs revealed that in most cases discordances likely result from misidentifications. Rigorously identified specimens of Corophium multisetosum (Stock, 1952) were split into two BINs, which diverged 18%. Albeit fairly divergent, these BINs correspond to two geographically close populations (≈115 km), lacking any apparent geographic barrier between them. Significance: Our results suggest that specimens of C. multisetosum here analyzed comprise two overlooked cryptic species. This morphospecies is locally abundant and frequently dominant in the benthic communities of the investigated estuaries, which makes these findings particularly relevant. For less-known faunal groups as the amphipods, DNA barcodes offer great potential to assist taxonomic revisions and inventories, species discovery, and routine species identifications.

Full text

Comparison between morphological and DNA barcode-suggested species
boundaries among shallow-water amphipod fauna from the southern European
Atlantic coast
Ilisa C. Antunes 1, Maria S. Ferreira1, Jorge Lobo1,2 , Marcos A.L. Teixeira1, Luisa M.S. Borges1,3,
Ronaldo Sousa1,4, Pedro A. Gomes1, Maria Helena Costa2, Marina R. Cunha5 and Filipe O. Costa1
1 CBMA – Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
2 MARE – Marine and Environmental Sciences Centre, New University of Lisbon, 2829-516 Monte de Caparica, Portugal.
3 Helmholtz-Zentrum Geesthacht, Centre for Material and Coastal Research, Max-Planck-Straße 1, 21502, Germany.
4 CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 123,
4050-123, Porto, Portugal.
5 CESAM – Centre for Environmental and Marine Studies, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
Corresponding author: Ilisa C. Antunes (e-mail: ilisaantunes@gmail.com).
Background: Amphipods are one of the most diverse and widely distributed groups of
crustaceans, often constituting dominant or key elements of marine and coastal communities. As
with many other marine invertebrate taxa, rigorous species identifications can be rather
challenging, and cryptic species reports have been increasing. In this study we compared DNA
barcode-suggested species boundaries with morphology-based species identifications in the
amphipod fauna of the southern European Atlantic coast.
Results: DNA sequences of the cytochrome c oxidase subunit I barcode region (COI-5P) were
obtained from 197 specimens collected along the coast and estuaries of continental Portugal, which
were then assigned to 41 morphospecies and 21 families. To this dataset we added publicly
available COI-5P sequences of the same species or genus, hence producing a final BOLD dataset
comprising 60 species and 273 sequences. Sequences from this dataset were in turn assigned to 68
BINs (Barcode Index Numbers), of which 38 were concordant (i.e., 1 BIN = 1 species), 11 were
taxonomically discordant BINs, and 19 were singletons. A detailed examination of the discordant
BINs revealed that in most cases discordances likely result from misidentifications. Rigorously
identified specimens of Corophium multisetosum (Stock, 1952) were split into two BINs, which
diverged 18%. Albeit fairly divergent, these BINs correspond to two geographically close
populations (˜115 km), lacking any apparent geographic barrier between them.
Significance: Our results suggest that specimens of C. multisetosum here analyzed comprise two
overlooked cryptic species. This morphospecies is locally abundant and frequently dominant in
the benthic communities of the investigated estuaries, which makes these findings particularly
relevant. For less-known faunal groups as the amphipods, DNA barcodes offer great potential to
assist taxonomic revisions and inventories, species discovery, and routine species identifications.