Genetic differentiation among local populations of medaka fish (Oryzias latipes) evaluated through grid- and deme-based sampling
Genetic differentiation among local populations of medaka fish (Oryzias latipes) evaluated through grid- and deme-based sampling
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DOI：
10.1016/j.gene.2009.04.017
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发表时间：
2009-08-15
期刊：
影响因子：
3.5
通讯作者：
Kawamura, Shoji
中科院分区：
文献类型：
--
作者：
Katsumura, Takafumi;Oda, Shoji;Kawamura, Shoji
青鳉（Oryzias latipes）是一种微小的鱼类，是分子遗传学和发育遗传学的极好实验模型。并且被期望作为群体遗传学的“脊椎动物”模式动物，因为1）存在丰富的种内变异，和2）已经确定了近交系之一的全基因组序列。尽管它的潜在用途，有没有全面的研究量化之间和种群内的遗传多样性野生青鳉。为了研究种群结构，我们研究了非编码D-环区和线粒体（mt）基因组的细胞色素B基因的核苷酸序列的青鳉个体收集不同的两种采样方法。采用种群抽样法，在3个地方种群（2个野生种群和1个生境）的373个个体中，只发现16种不同的mt D-loop序列类型，而采用网格抽样法，在东亚不同地理区域的35个个体中，发现26种不同的mt D-loop序列类型。我们进行统计检验，以评估标准中性模型下的分离位点之间的核苷酸频率的分布模式，我们表明，deme抽样人口可能经历了人口规模的减少和/或自然或人工迁移造成的子结构。遗传变异的减少在生活小区的种群中更为明显，这表明人类活动可能对青鳉的人口统计历史产生影响。然而，我们的研究结果表明，基于网格的采样提供了更丰富的变异比基于deme的采样，而基于deme的采样提供了更多的信息的等位基因频率谱的本地野生特性比基于网格的采样。这为青鳉作为脊椎动物模式动物进行比较群体基因组学研究奠定了基础。(C)2009爱思唯尔有限公司版权所有。
The medaka (Oryzias latipes), a tiny fish, has been an excellent experimental model for molecular and developmental genetics. and is expected for being a "vertebrate" model animal for population genetics, because 1) there is abundant within-species variation, and 2) the whole genome sequence has been determined for one of the inbred strains. In spite of its potential usefulness, there is no comprehensive study on quantifying between- and within-population genetic diversity of wild medaka. To investigate population structure, we examine nucleotide sequences of the non-coding D-loop region and the cytochrome b gene of the mitochondrial (mt) genome for medaka individuals collected with distinct two sampling-methods. Using deme-based sampling, out of 373 total individuals from three local (two wild and one biotope) populations only 16 distinct sequence types of mt D-loop are found. However, we find 26 D-loop types in 35 individuals collected with grid-based sampling from various geographical regions in East Asia. We carry out statistical tests to evaluate the distribution pattern of nucleotide frequencies among segregating sites under the standard neutral model, and we show that the deme-sampled populations might have experienced population size reduction and/or sub-structuring caused by natural or artificial migration. The reduction of genetic variation has been driven more markedly in the populations from the biotope, suggesting that human activities can pose an impact on the demographic history of medaka. Nevertheless, our results suggest that the grid-based sampling gives more abundant variations than the deme-based sampling, while the deme-based sampling gives more information about the local-wild characteristics of allele frequency spectrum than grid-based sampling. This could be a basis of strategy to use medaka as a vertebrate model animal for comparative population genomics. (C) 2009 Elsevier B.V. All rights reserved.