DOI: 10.5061/dryad.r2280gbcd
title: Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics.

description: The crustacean marine isopod species Haploniscus bicuspis (G.O. Sars,
 1877) shows circum-Icelandic distribution in a wide range of environmental
 conditions and along well-known geographic barriers, such as the
 Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population
 genetics, phylogeography and cryptic speciation as well as to investigate
 whether previously described, but unaccepted subspecies have any merit.
 Using the same set of specimens, we combined mitochondrial COI sequences,
 thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected
 morphological characters using Confocal Laser Scanning Microscopy (CLSM).
 Five divergent genetic lineages were identified by COI and ddRAD, two
 south and three north of the GIF Ridge. Assignment of populations to the
 three northern lineages varied and detailed analyses revealed
 hybridization and gene flow between them, suggesting a single northern
 species with a complex phylogeographic history. No apparent hybridization
 was observed among lineages south of the Ridge, inferring the existence of
 two more species. Differences in proteomic profiles between the three
 putative species were minimal, implying an ongoing or recent speciation
 process. Population differentiation was high, even among closely
 associated populations, and higher in mitochondrial COI than nuclear ddRAD
 loci. Gene flow is apparently male-biased, leading to hybrid zones and
 instances of complete exchange of the local nuclear genome through
 immigrating males. This study did not confirm the existence of subspecies
 defined by male characters, which probably characterize different male
 developmental stages.
description: All <i>H. bicuspis</i> specimens examined were
 sampled aboard the research vessels RV Meteor (M85/3), RV Poseidon
 (POS456) and RV Maria S. Merian (MSM75) during the IceAGE (2011), IceAGE2
 (2013) and IceAGE_RR (2018) expeditions. The specimens were sorted at the
 laboratories of the DZMB (German Centre for Marine Biodiversity Research)
 and deposited in the collections of the Center of Natural History
 (Hamburg, Germany; see Supplementary Table S1). Specimens were collected
 using an epibenthic sledge or VanVeen grab. DNA extractions were performed
 using the mid-sections of the animals, leaving the cephalothorax and the
 pleon intact for subsequent morphological analyses and as partial vouchers
 in the collections. The animals were dissected carefully using a micro
 scissor and the gut was removed to avoid contaminations. If possible, the
 same animal was used for proteomics, COI barcoding and ddRAD, transferring
 half of the dissected tissue in a vial for genetics and the other half
 into a vial for proteomics. DNA was extracted using the Marine Animal
 Tissue Genomic DNA Extraction Kit (Neo Biotech) or the Genomic DNA from
 tissue kit (Macherey-Nagel). DNA was eluted in 70 µL elution buffer.
 Chelex (Chelating Ion Exchange Resin, Bio-Rad) was used for some of the
 animals, for which only the COI fragment was sequenced (for protocol see
 Jennings, Golovan, & Brix, 2020). Based on DNA yield, a subset of
 samples was selected for ddRAD sequencing. Usually selected samples had
 &gt;150 ng DNA, to include certain relevant populations a few samples
 with &gt; 30 ng DNA were selected as well. DNA concentration was
 measured with a Qubit 3.0 (Invitrogen). If samples had less than 150 ng,
 they were concentrated via drying. All samples were brought to 24 µl. The
 protocol described by Peterson et al. (2012) was mostly adhered to, with a
 few modifications (see also Schwentner & Lörz, 2021; Franchini,
 Monné Parera, Kautt, & Meyer, 2017).
description: The files MetaDataxlsx.xlsx and Hellinger_Matrix.csv refer to the
 proteomic data. All other data belong to the ddRAD.