FORESEA: a note on a dataset of 160 marine fish genomes

A watch note, and not a data page of this site. This page describes an external dataset, concerning fish and not cetaceans. It appears here because fifteen of the hundred species sequenced belong to the diet of the common dolphin and the harbour porpoise, and because the catalogue record that references it contains errors which we flag below. The link with cetaceans is prospective, not established: no result from this project has been published to date. For data that genuinely concern cetaceans, see our distribution maps and the strandings map.

This dataset sheds light on a question that touches cetaceans indirectly, that of the capacity of marine species to absorb change in their environment. The Sextant catalogue record indicates access on request, but the sequencing data are in fact publicly deposited in the European Nucleotide Archive under accession PRJEB116067. The visualisations below are reconstructed from that deposit.

Where the 160 fish were sampled

Each point is a sequenced individual. The circles ringed in white mark the species documented as prey of the common dolphin or the harbour porpoise.

One hundred species, twenty-three orders

Number of species sequenced per order. The dark portion corresponds to the species documented as prey of cetaceans in these waters.

What this sampling design allows, and what it does not

The number of individuals per species says a great deal about the question being asked. The median isa single genome per species.

What the dataset allows. With a diploid genome sequenced at 15×, a single individual is enough to estimate the heterozygosity of a species, that is, the proportion of positions where its two chromosome copies differ. The design is therefore built to compare diversity entre espèces. Les 43 espèces prélevées dans plusieurs bassins add a second dimension, the comparison of a single species between the Atlantic and the Mediterranean.

What it does not allow. With one to four individuals per species, no population study is possible: measuring the genetic structure of a population would require dozens per site. And above all, genetic diversity itself does not appear in what is released : the ENA exposes only the raw reads, about 5,000 billion bases. Obtaining a heterozygosity value per species requires aligning each genome and calling the variants. As no associated publication can be found, the question the project asks, why diversity varies so much from one species to another, remains without a published answer.

In other words, this page documents a research resource and the design that produced it, not a result.

160individuals sequenced

100distinct species

47familles

15cetacean prey species

Reconstructed from the public repository ENA PRJEB116067, which holds 273 read sets for 160 samples. The sampling coordinates and dates are those declared with the samples. Assigning a species to the diet of cetaceans draws on the literature on the common dolphin and the harbour porpoise of the North-East Atlantic, not on the FORESEA dataset itself.

What the dataset contains

Within the FORESEA project, the whole genomes of 160 marine fish were sequenced to a minimum depth of 15×, which allows almost the whole of each diploid genome to be reconstructed, both copies of each chromosome included.

The aim was not to describe one species in particular, but to understand why genetic diversity varies so much from one species to another. This diversity is generally regarded as a key factor in the capacity to adapt: a genetically varied population has more combinations on which selection can act when the environment changes. Yet the biological, ecological and biogeographical determinants of that variability remain poorly understood, particularly in certain groups.

Why this concerns cetaceans

By two routes, and it has to be said honestly that neither is direct.

First, these fish are prey. Of the 100 species sequenced, 15 appear in the documented diet of the common dolphin or the harbour porpoise in the North-East Atlantic: anchovy, sprat, mackerel, horse mackerel, whiting, blue whiting, sandeel, smooth sandeel, sand goby, lesser argentine, boarfish and poor cod. These are waters where the common dolphin and the harbour porpoise feed. The capacity of the fish to adapt conditions the resource of the predators that depend on them.

Second, the question posed holds for cetaceans themselves, and more acutely so. The large cetaceans combine everything that impoverishes a genetic heritage: small numbers, late maturity, rare offspring, and, for many species, the demographic bottleneck of twentieth-century industrial whaling. Our pages on sequenced genomes and on hybridisation cover this ground.

How to access it

The Sextant record indicates access on request from the authors, and the location it mentions is a space internal to Ifremer. But the raw data do indeed exist in open access: the project has deposited 273 read sets for 160 samples in the European Nucleotide Archive, under accession PRJEB116067. It is from that deposit that the map and the chart above are drawn, including the sampling coordinates and the species identifications. Two discrepancies with the catalogue record are worth flagging. The actual extent is much wider than the one announced: the samples range from 35.3 to 50.2 degrees north and from 5.8 west to 25.4 east, that is, from the southern North Sea to the eastern Mediterranean, whereas the record describes an Atlantic extent stopping at 8.7 east. And the sampling dates spread from 2018 to 2022, the record mentioning only March 2021 to January 2022. We have not, on the other hand, found an associated publication that would open up the results of the analysis itself.

For an access request, the catalogue record lists the contacts, among them Pierre-Alexandre Gagnaire (CNRS, ISEM), Sébastien Villéger (CNRS, MARBEC), Laurène Gaillard (CNRS, MARBEC), Ahmed Souissi (University of Perpignan, MARBEC), together with Sylvie Lapègue, Florence Cornette and Bruno Ernande for Ifremer.

Dataset summary

Title	Whole genome sequencing of 160 marine fish for the FORESEA project, 2022
Producers	CNRS (ISEM, MARBEC), University of Montpellier, University of Perpignan, Ifremer
Type	Whole genomes, minimum depth 15×, 160 individuals
Extent	Declared: North-East Atlantic, from 41.5 to 50.8 degrees north and from 8.4 west to 8.7 east. Actual, according to the ENA deposit: from 35.3 to 50.2 north and from 5.8 west to 25.4 east
Period	Declared: March 2021 to January 2022. Actual, according to the ENA deposit: 2018 to 2022
Licence	CC-BY. Record: access on request. Raw data in open access in the ENA, accession PRJEB116067
Identifier	10.12770/47a8e408-9612-4228-a655-e26d9e70745c
Catalogue	Sextant record (Ifremer)

For data that are genuinely open on the cetaceans of the same waters, see instead our maps of cetacean distribution in French waters, from the same institutional source but freely downloadable.