Department of Biology, University of Florence, Firenze, Italy.
Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
Mol Ecol. 2021 Dec;30(23):6309-6324. doi: 10.1111/mec.16121. Epub 2021 Aug 30.
Population and conservation genetics studies have greatly benefited from the development of new techniques and bioinformatic tools associated with next-generation sequencing. Analysis of extensive data sets from whole-genome sequencing of even a few individuals allows the detection of patterns of fine-scale population structure and detailed reconstruction of demographic dynamics through time. In this study, we investigated the population structure, genomic diversity and demographic history of the Komodo dragon (Varanus komodoensis), the world's largest lizard, by sequencing the whole genomes of 24 individuals from the five main Indonesian islands comprising the entire range of the species. Three main genomic groups were observed. The populations of the Island of Komodo and the northern coast of Flores, in particular, were identified as two distinct conservation units. Degrees of genomic divergence among island populations were interpreted as a result of changes in sea level affecting connectivity across islands. Demographic inference suggested that Komodo dragons probably experienced a relatively steep population decline over the last million years, reaching a relatively stable N during the Saalian glacial cycle (400-150 thousand years ago) followed by a rapid N decrease. Genomic diversity of Komodo dragons was similar to that found in endangered or already extinct reptile species. Overall, this study provides an example of how whole-genome analysis of a few individuals per population can help define population structure and intraspecific demographic dynamics. This is particularly important when applying population genomics data to conservation of rare or elusive endangered species.
种群和保护遗传学研究极大地受益于与下一代测序相关的新技术和生物信息工具的发展。即使对少数个体进行全基因组测序的广泛数据集的分析也可以检测到细微的种群结构模式，并通过时间详细重建人口动态。在这项研究中，我们通过对来自包括该物种整个分布范围的五个印度尼西亚主要岛屿的 24 个个体的全基因组进行测序，研究了科莫多巨蜥（Varanus komodoensis）的种群结构、基因组多样性和历史动态，科莫多巨蜥是世界上最大的蜥蜴。观察到三个主要的基因组群体。科莫多岛和弗洛雷斯岛北部海岸的种群被确定为两个不同的保护单元。岛屿种群之间的基因组差异程度被解释为海平面变化影响岛屿间连通性的结果。人口推断表明，科莫多龙在过去的一百万年中可能经历了相对陡峭的人口下降，在萨勒冰期循环（40 万至 15 万年前）期间达到相对稳定的 N，随后 N 迅速下降。科莫多龙的基因组多样性与濒危或已灭绝的爬行动物物种相似。总的来说，这项研究提供了一个例子，说明对每个种群中的少数个体进行全基因组分析如何有助于定义种群结构和种内人口动态。当将群体基因组学数据应用于稀有或难以捉摸的濒危物种的保护时，这一点尤其重要。
