Data from: Range size variably predicts genetic diversity in Gehyra geckos
Data files
Mar 24, 2025 version files 45.91 GB
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cohort_vcf.zip
14.91 MB
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DArT_raw_data.zip
39.99 GB
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expanded_aus_gvcf.zip
3.26 GB
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expanded_nana_gvcf.zip
2.65 GB
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Gehyra_62species_Starbeast2_100loci_renamed2024.tre
1.80 KB
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README.md
1.46 KB
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starbeast_tree_alignments_100loci.zip
301.63 KB
Abstract
Genetic diversity is a fundamental population genetic parameter, and predicts adaptive capacity. Neutral theory predicts a positive correlation between population (or range) size and genetic diversity, but this can be confounded by other demographic processes. To investigate the role of range size, population fluctuation and introgression in determining genetic diversity, we generate and analyse population-level, genomic-scale SNP data from 21 species of Australian Gehyra geckos (769 samples) that vary in range size over three orders of magnitude. Using a best-practice approach to estimate SNP-based heterozygosity, we found a significantly positive overall correlation between range size and heterozygosity, although with a shallow slope (R2 = 0.30), consistent with Lewontin’s Paradox. At a clade level, we show a stronger relationship between range size and heterozygosity in the australis group (R2 = 0.74, p < 0.01) than the nana group (R2 = 0.15, n.s.). A significantly negative correlation between Tajima’s D and range size in both groups, and evidence for introgression in the nana group, suggest a role for both population fluctuation and introgression in driving deviations from theoretical expectations. Our results provide insight into the biological and demographic processes that influence genetic diversity, in addition to neutral expectations.
https://doi.org/10.5061/dryad.cvdncjtc0
Raw data and processed final .vcf files underlying the analysis for Lau et al. ‘Range size variably predicts genetic diversity in Gehyra geckos’. Metadata and geographical information for each sample ID are provided in Supplementary Table 1 of the manuscript.
Description of the data and file structure
Population genomic data
DArT_raw_data.zip - contains raw DArT reads for each sample, named as according to IDs provided in Supplementary Table 1
expanded_aus_gvcf.zip - contains single-sample, expanded gvcf files for each sample in the Gehyra australis group, as used for individual heterozygosity calculations
expanded_nana_gvcf.zip - contains single-sample, expanded gvcf files for each sample in the Gehyra nana group, as used for individual heterozygosity calculations
cohort_vcf.zip - contains cohort-genotyped files (by species, clades and sympatric groups), underlying Tajima’s D and introgression analyses
Species tree data
starbeast_tree_alignments_100loci.zip - contains 100 gene tree alignments of two haplotypes from 62 species or lineages, underlying the Starbeast2 species tree reconstruction
Gehyra_62species_Starbeast2_100loci_renamed2024.tre - is the final 62-species Starbeast2 species tree underlying phylogenetic comparative analysis