Dataset Information

Phylogeography in an "oyster" shell provides first insights into the genetic structure of an extinct Ostrea edulis population.

ABSTRACT: The historical phylogeography of Ostrea edulis was successfully depicted in its native range for the first time using ancient DNA methods on dry shells from museum collections. This research reconstructed the historical population structure of the European flat oyster across Europe in the 1870s-including the now extinct population in the Wadden Sea. In total, four haplogroups were identified with one haplogroup having a patchy distribution from the North Sea to the Atlantic coast of France. This irregular distribution could be the result of translocations. The other three haplogroups are restricted to narrow geographic ranges, which may indicate adaptation to local environmental conditions or geographical barriers to gene flow. The phylogenetic reconstruction of the four haplogroups suggests the signatures of glacial refugia and postglacial expansion. The comparison with present-day O. edulis populations revealed a temporally stable population genetic pattern over the past 150 years despite large-scale translocations. This historical phylogeographic reconstruction was able to discover an autochthonous population in the German and Danish Wadden Sea in the late nineteenth century, where O. edulis is extinct today. The genetic distinctiveness of a now-extinct population hints at a connection between the genetic background of O. edulis in the Wadden Sea and for its absence until today.

SUBMITTER: Hayer S

PROVIDER: S-EPMC7840910 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Phylogeography in an "oyster" shell provides first insights into the genetic structure of an extinct Ostrea edulis population.

Hayer Sarah S Brandis Dirk D Immel Alexander A Susat Julian J Torres-Oliva Montserrat M Ewers-Saucedo Christine C Krause-Kyora Ben B

Scientific reports 20210127 1

The historical phylogeography of Ostrea edulis was successfully depicted in its native range for the first time using ancient DNA methods on dry shells from museum collections. This research reconstructed the historical population structure of the European flat oyster across Europe in the 1870s-including the now extinct population in the Wadden Sea. In total, four haplogroups were identified with one haplogroup having a patchy distribution from the North Sea to the Atlantic coast of France. This ...[more]

PMID: 33504886

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Project description:Reefs formed by Ostrea edulis, the European native oyster, are among many biogenic habitats that have declined globally. European oyster habitats are now rare, and undisturbed examples have not been described. As more is understood of the ecosystem services provided by the reefs, oyster restoration efforts are on the rise, becoming a more prominent component of Europe's portfolio of marine conservation practices. It is therefore important to establish the relationship between the development of oyster reefs and their associated biotic community if the biodiversity benefits are to be accurately predicted and the progress of restoration projects assessed. The Loch Ryan oyster fishery in Southwest Scotland is the last of its type and uses a rotational harvest system where different areas are fished each year and then left for six years before they are fished again. This provided an opportunity to study the effect of oyster reef development and biodiversity gain at different stages of habitat recovery. In this study three treatments were surveyed for faunal biodiversity, oyster shell density and oyster shell percentage cover. Treatments were plots that had been harvested one year before, two years before, and six years before the study. The treatments were surveyed with SCUBA using a combination of video transects and photo quadrats. Oyster shell density, oyster shell percent cover and macrofaunal biodiversity differed significantly between treatments, with the highest values observed in the six-year treatment. Shell density was 8.5 times higher in the six-year treatment compared to the one-year treatment, whilst Shannon-Wiener's diversity was 60.5% higher, and Margalef's richness 68.8% higher. Shell density and percent cover had a significant positive relationship with macrofaunal biodiversity. This is probably due to the provision of increased structural complexity in the matrix of live and dead oyster shells. Projecting forward the trend of biodiversity increase in relation to time since disturbance indicates that full recovery would take approximately ten years in which time diversity (Shannon-Wiener) would probably have doubled. The findings from the present study indicate the probable biodiversity benefits of oyster habitat restoration and a cost-effective metric (shell density) to judge progress in restoration projects.

Project description:BackgroundBecause of its typical architecture, inheritance and small size, mitochondrial (mt) DNA is widely used for phylogenetic studies. Gene order is generally conserved in most taxa although some groups show considerable variation. This is particularly true in the phylum Mollusca, especially in the Bivalvia. During the last few years, there have been significant increases in the number of complete mitochondrial sequences available. For bivalves, 35 complete mitochondrial genomes are now available in GenBank, a number that has more than doubled in the last three years, representing 6 families and 23 genera. In the current study, we determined the complete mtDNA sequence of O. edulis, the European flat oyster. We present an analysis of features of its gene content and genome organization in comparison with other Ostrea, Saccostrea and Crassostrea species.ResultsThe Ostrea edulis mt genome is 16 320 bp in length and codes for 37 genes (12 protein-coding genes, 2 rRNAs and 23 tRNAs) on the same strand. As in other Ostreidae, O. edulis mt genome contains a split of the rrnL gene and a duplication of trnM. The tRNA gene set of O. edulis, Ostrea denselamellosa and Crassostrea virginica are identical in having 23 tRNA genes, in contrast to Asian oysters, which have 25 tRNA genes (except for C. ariakensis with 24). O. edulis and O. denselamellosa share the same gene order, but differ from other Ostreidae and are closer to Crassostrea than to Saccostrea. Phylogenetic analyses reinforce the taxonomic classification of the 3 families Ostreidae, Mytilidae and Pectinidae. Within the Ostreidae family the results also reveal a closer relationship between Ostrea and Saccostrea than between Ostrea and Crassostrea.ConclusionsOstrea edulis mitogenomic analyses show a high level of conservation within the genus Ostrea, whereas they show a high level of variation within the Ostreidae family. These features provide useful information for further evolutionary analysis of oyster mitogenomes.

Project description:The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed across Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to overexploitation and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was in the low-moderate range, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels was assessed. Genomic prediction accuracies using the full density panel were high (> 0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e., 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relatedness should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

Dataset Information

Phylogeography in an "oyster" shell provides first insights into the genetic structure of an extinct Ostrea edulis population.

Publications

Phylogeography in an "oyster" shell provides first insights into the genetic structure of an extinct Ostrea edulis population.

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