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Genetic diversity across the globe
Genetic diversity across the globe
The spatial distribution of neutral genetic diversity across the species range provides key insights to the species demographic history, and its knowledge is essential to understand and predict the evolution of species ranges under changing environmental conditions. GenDivRange is a unified database of geo-referenced estimates of genetic diversity for over 1000 species and nearly 20'000 populations across the globe and across most major taxa, including terrestrial and marine organisms.
Populations with an estimate of genetic diversity in GenDivRange.
2020 Distributed Graduate Seminar in Landscape Genetics group project meeting via zoom. We were pre-covid zoom users! From top left to bottom right: Kati, Jonny, Michael, Kirsten, Vivi, Priscila, Tin Hang (alias Henry).
Crowd science to create a database
Crowd science to create a database
A unique crowd science approach was used to collect the data: the participant group of the 2020 Distributed Graduate Seminar in Landscape Genetics searched suitable studies as part of their semester project. Every person picked his or her favourite taxa! The group project was proposed and supervised by Dr Katalin Csillery. Later, Haonan Yang and Dr Yohann Chauvier-Mendes joined the efforts to check and clean the data. And when Dr Michael Nobis joined, we started to develop the R Shiny interactive map tool. We also integrated existing databases: VarVer, MacroPopGen and data from de Kort et al (2020) after data filtering and cleaning. See more about us.
We like plants! Overcoming taxonomic biases
We like plants! Overcoming taxonomic biases
There are considerably less population genetic studies on plants than on animals. This is reflected in the databases: early databases of genetic diversity, VarVer and MacroPopGen contained only vertebrates. Before us, Hanne de Kort et al (2020) collected genetic diversity for several plant species. We continued this effort and collected data from several woody plants and herbaceous plant species. As a result, the combination of these four data sources allowed us to obtain a more taxonomically balanced dataset than any of the previous databases.
Expected heterozygosity is by far the most reported proxy for genetic diversity, followed by the observed heterozygosity and allelic richness.
Which indices of population genetic diversity?
Which indices of population genetic diversity?
The best would be to have a database of the full genotype tables. In 2016, the ‘FAIR Guiding Principles for scientific data management and stewardship’ were proposed, however, earlier studies often did not publish the raw data. Thereby, we collected as many data summaries as possible about the genetic diversity and the sample size. Here is the full list of statistics, even though many of them were rare across publications:
N: Number of individuals genotyped per population
A: Mean number of alleles per population across all loci
A_tot: Total number of alleles per population across all loci
N_eff: Effective number of alleles per population across all loci
N_private: Number of private alleles per population across all loci
N_genot: Number of genotypes
A_mean: Mean number of alleles across all loci and all populations
Ar: Mean allelic richness
Ho: Observed heterozygosity
He: Expected heterozygosity
GD_Nei: Nei’s genetic diversity
D_clonal: Clonal richness
F_is: Inbreeding coefficient
F_is_sig: Significance of F_is, S: p-values < 0.05, NS: p-value > 0.05
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