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Gradients of genetic diversity and differentiation across the distribution range of a Mediterranean coral: patterns, processes and conservation implications.

Citation

Ledoux, Jean-Baptiste (2021), Gradients of genetic diversity and differentiation across the distribution range of a Mediterranean coral: patterns, processes and conservation implications., Dryad, Dataset, https://doi.org/10.5061/dryad.xgxd254gw

Abstract

The aim of this study was to determine how historical and contemporary eco-evolutionary processes shape the patterns of genetic diversity and differentiation across species’ distribution range remains an open question with strong conservation implications. Focusing on the orange stony coral, Astroides calycularis, we i) characterized the pattern of neutral genetic diversity across the distribution range; ii) gave insights into the underlying processes; and iii) discussed conservation implications with emphasis on a national park located on a hotspot of genetic diversity.

Location: South Mediterranean Sea and Zembra National Park.

We combined new data from 12 microsatellites in 13 populations located in the Centre and in the Western Periphery of the distribution range with a published dataset including 16 populations from the Western and Eastern Peripheries. We analysed the relationship among parameters of genetic diversity (HeAr(g)) and structure (population-specific FST) and two measures of geographic peripherality. We compared two estimators of pairwise genetic structure (GSTDEST) across the distribution range. The evolutionary and demographic history of the populations following the Last Glacial Maximum was reconstructed using approximate Bayesian computations and Maximum Likelihood analyses. We inferred the contemporary connectivity among populations from Zembra National Park and with the neighbouring area of Cap Bon. We demonstrate a decrease of genetic diversity and an increase of genetic differentiation from the Centre to the Eastern and Western Peripheries of the distribution rangePopulations from Zembra show the highest genetic diversity reported in the species. We identified a spillover effect towards Cap Bon. The patterns of genetic diversity and differentiation are most likely explained by “the postglacial range expansion hypothesis” rather than the “central-peripheral hypothesis”. Enforcement of conservation measures should be considered to protect this genetic diversity pattern, in particular when considering the low effective population size inferred at many sites.

Methods

The dataset is a genotyping dataset in Genepop format (see https://kimura.univ-montp2.fr/~rousset/Genepop4.7.pdf).
It is composed by the genotypes at 12 microsatellites of 655 individuals coming from 29 populations (see Table 1 in Ledoux et al. 2021, Diversity and Distributions for details).
The first line of the dataset corresponds to the title, the following 12 lines are the locus names.
Each line contains the name of the individual and the genotype at each of the 12 microsatellites.
The populations are delimited by a "pop" line.
Part of the data came from Casado-Amueza et al. 2012 (Molecular Ecology, 21, 3671-3685). The remaining samples were genotyped during the study (see Ledoux et al. 2021, Diversity and Distributions for details).

Usage Notes

The standardization of the allele scoring between the two datasets (Casado-Amueza et al vs. Ledoux et al) is detailled in the Appendix 2 in Ledoux et al. 2021, Diversity and Distributions. Briefly, it is based on the comparison of allele frequencies in three populations (ALF, ALM and PC; Table 1, Figure 1), that were sampled in the same location among the two studies. 

Missing genotypes are coded with "000000".