Data from: Range size variably predicts genetic diversity in Gehyra geckos

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.

遗传多样性是种群遗传学的核心参数之一，可预测物种的适应能力。中性理论（Neutral Theory）预测种群（或分布区）大小与遗传多样性呈正相关，但这一关系可能会受到其他种群统计过程的干扰。为探究分布区大小、种群波动与基因渐渗（introgression）在调控遗传多样性中的作用，本研究获取并分析了21种澳原趾虎属（Gehyra）壁虎的种群级基因组尺度单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据，共包含769份样本；这些物种的分布区大小跨度达三个数量级。本研究采用标准化最优方法估算基于SNP的杂合度，结果显示总体上分布区大小与杂合度呈显著正相关，但回归斜率较平缓（决定系数R²=0.30），这与莱文廷悖论（Lewontin's Paradox）的结论一致。在演化支层面，australis组（australis group）的分布区大小与杂合度之间的相关性强于nana组（nana group）：前者决定系数R²=0.74，p<0.01，后者R²=0.15，无统计学显著性。两个类群中，塔伊马D统计量（Tajima's D）与分布区大小均呈显著负相关；而nana组存在基因渐渗的证据，这表明种群波动与基因渐渗均会导致遗传多样性偏离中性理论预期。本研究结果不仅验证了中性理论的预期，还为解析影响遗传多样性的生物学与种群统计过程提供了新视角。