Évolution, Génomes, Comportement, Écologie, CNRS, IRD, Univ Paris-Sud. Université Paris-Saclay, F-91198, Gif-sur-Yvette, France.
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, F-91198, Paris, France.
BMC Evol Biol. 2018 Apr 18;18(1):43. doi: 10.1186/s12862-018-1156-7.
Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called "old" and "new" lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations.
We reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages. Using IMa2, a program that allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (< 20,000 years). We identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of pools of embryos (Pool-seq) belonging to Pachón cave population and a surface population from Texas. Based on summary statistics that can be computed with this SNP data set together with simulations of evolution of SNP polymorphisms in two recently isolated populations, we looked for sets of demographic parameters that allow the computation of summary statistics with simulated populations that are similar to the ones with the sampled populations. In most simulations for which we could find a good fit between the summary statistics of observed and simulated data, the best fit occurred when the divergence between simulated populations was less than 30,000 years.
Although it is often assumed that some cave populations have a very ancient origin, a recent origin of these populations is strongly supported by our analyses of independent sets of nuclear DNA polymorphism. Moreover, the observation of two divergent haplogroups of mitochondrial and nuclear genes with different geographic distributions support a recent admixture of two divergent surface populations, before the isolation of cave populations. If cave populations are indeed only several thousand years old, many phenotypic changes observed in cavefish would thus have mainly involved the fixation of genetic variants present in surface fish populations and within a very short period of time.
属于墨西哥四齿鱼物种的洞穴鱼种群是研究适应剧烈环境变化的时间和模式的杰出模型。它们目前被分为两个主要群体，即所谓的“旧”和“新”谱系，它们应该是在不同时间独立地进入几个洞穴的。然而，我们还没有这些种群进化的时间框架的准确估计。
我们重新分析了线粒体和核 DNA 多态性的地理分布，发现这些数据不支持存在两种洞穴鱼谱系。使用允许除人口参数外还可以对种群分歧进行定年的 IMa2 程序，我们发现微卫星多态性强烈支持洞穴种群的起源非常近（<20000 年）。我们在属于帕雄洞穴种群和来自德克萨斯州的一个地表种群的胚胎混合池（Pool-seq）的转录序列中鉴定出大量单核苷酸多态性（SNP）。基于可以用这个 SNP 数据集计算的汇总统计数据以及在两个最近隔离的种群中 SNP 多态性进化的模拟，我们寻找了允许用模拟种群计算汇总统计数据的参数集，这些模拟种群与采样种群相似。在大多数我们可以找到观察数据和模拟数据之间汇总统计数据的良好拟合的模拟中，当模拟种群之间的分歧小于 30000 年时，最佳拟合出现。
尽管人们通常认为一些洞穴种群起源非常古老，但我们对独立的核 DNA 多态性数据集的分析强烈支持这些种群的起源非常近。此外，具有不同地理分布的线粒体和核基因的两个分歧单倍型群体的观察结果支持在洞穴种群隔离之前，两个分歧的地表种群之间的混合。如果洞穴种群确实只有几千年的历史，那么在洞穴鱼中观察到的许多表型变化主要涉及到存在于地表鱼类种群中的遗传变异的固定，而且在很短的时间内完成。
