Jiménez-Mena Belén, Tataru Paula, Brøndum Rasmus F, Sahana Goutam, Guldbrandtsen Bernt, Bataillon Thomas
Bioinformatics Research Center (BiRC), Aarhus University, Aarhus, Denmark INRA, UMR1313 Génétique animale et biologie intégrative, 78350 Jouy-en-Josas, France AgroParisTech, UMR1313 Génétique animale et biologie intégrative, 16 rue Claude Bernard, 75231 Paris 05, France.
Bioinformatics Research Center (BiRC), Aarhus University, Aarhus, Denmark.
Biol Lett. 2016 Jul;12(7). doi: 10.1098/rsbl.2016.0426.
Effective population size (Ne) is a central parameter in population and conservation genetics. It measures the magnitude of genetic drift, rates of accumulation of inbreeding in a population, and it conditions the efficacy of selection. It is often assumed that a single Ne can account for the evolution of genomes. However, recent work provides indirect evidence for heterogeneity in Ne throughout the genome. We study this by examining genome-wide diversity in the Danish Holstein cattle breed. Using the differences in allele frequencies over a single generation, we directly estimated Ne among autosomes and smaller windows within autosomes. We found statistically significant variation in Ne at both scales. However, no correlation was found between the detected regional variability in Ne, and proxies for the intensity of linked selection (local recombination rate, gene density), or the presence of either past strong selection or current artificial selection on traits of economic value. Our findings call for further caution regarding the wide applicability of the Ne concept for understanding quantitatively processes such as genetic drift and accumulation of consanguinity in both natural and managed populations.
有效种群大小（Ne）是种群遗传学和保护遗传学中的核心参数。它衡量遗传漂变的程度、种群中近亲繁殖的积累速率，并决定选择的效力。人们通常认为单一的Ne能够解释基因组的进化。然而，近期的研究提供了全基因组范围内Ne存在异质性的间接证据。我们通过研究丹麦荷斯坦奶牛品种的全基因组多样性来探究这一问题。利用单代内等位基因频率的差异，我们直接估计了常染色体以及常染色体内较小窗口间的Ne。我们在两个尺度上均发现了Ne具有统计学意义的变异。然而，在检测到的Ne区域变异性与连锁选择强度的代理指标（局部重组率、基因密度）之间，以及与过去对经济价值性状的强选择或当前人工选择的存在之间，均未发现相关性。我们的研究结果提醒人们，在理解自然种群和管理种群中的遗传漂变和近亲繁殖积累等定量过程时，对于Ne概念的广泛适用性需进一步谨慎对待。
