Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.
Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.
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DOI：
10.1371/journal.pgen.1000862
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发表时间：
2010-02-26
期刊：
影响因子：
4.5
通讯作者：
Cresko WA
中科院分区：
文献类型：
--
作者：
Hohenlohe PA;Bassham S;Etter PD;Stiffler N;Johnson EA;Cresko WA
新一代测序技术为收集自然种群的基因组尺度序列数据提供了新的机会，为种群基因组学领域的发展奠定了经验基础。本文对三刺棘鱼（Gasterosteus aculeatus）自然种群的核苷酸多样性和分化进行了基因组扫描。我们使用illumina测序的RAD标签在来自两个海洋和三个淡水种群的100个个体中识别和分型超过45,000个单核苷酸多态性（snp）。对种群间遗传多样性和分化的总体估计证实了生物地理学的假设，即大型泛海种群反复产生表型上不同的淡水种群。在多个独立衍生的种群中，表现出平衡选择和分化选择特征的基因组区域是非常一致的，这表明在全基因组范围内，刺鱼的重复平行表型进化可能是通过广泛的、平行的遗传进化发生的。其中一些基因组区域与先前通过实验室定位杂交鉴定的棘鱼表型变异QTL共定位。此外，我们还发现了几个在独立种群中显示平行分化的新区域。这些区域的注释揭示了许多基因，这些基因是刺鱼表型进化的候选基因，并将形成未来刺鱼和其他生物遗传分析的基础。本研究首次对野生三刺鱼种群的遗传多样性和分化进行了高密度单核苷酸多态性基因组扫描。这些数据通过确认先前确定的基因组区域的适应性意义，阐明这些区域在自然种群中的特定进化和人口统计学历史，以及确定新的基因组区域和具有进化意义的候选基因，说明了实验室杂交和种群基因组扫描的互补性。海洋三刺棘鱼无数次入侵并适应了北半球的淡水栖息地。这些淡水种群往往以相似的方式从它们独立派生的祖先海洋种群进化而来。除了少数已确定的基因外，这种显著的平行适应的遗传基础尚不清楚。在这里，我们表明平行表型进化与核苷酸多样性和种群分化在基因组中的平行模式相匹配。我们使用了一种新的基于序列的高通量基因分型方法，对三刺棘鱼种群进行了首次高密度全基因组扫描，并确定了几个表明分化选择和平衡选择的基因组区域。其中一些地区以前与淡水适应的重要特征有关，但其他地区以前未被发现。在这些基因组区域内，我们确定了候选基因，为进一步研究关键通路的遗传和功能奠定了基础。这项研究说明了实验室制图、功能遗传学和群体基因组学的互补性。
Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field of population genomics. Here we conducted a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback (Gasterosteus aculeatus). We used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs) in each of 100 individuals from two oceanic and three freshwater populations. Overall estimates of genetic diversity and differentiation among populations confirm the biogeographic hypothesis that large panmictic oceanic populations have repeatedly given rise to phenotypically divergent freshwater populations. Genomic regions exhibiting signatures of both balancing and divergent selection were remarkably consistent across multiple, independently derived populations, indicating that replicate parallel phenotypic evolution in stickleback may be occurring through extensive, parallel genetic evolution at a genome-wide scale. Some of these genomic regions co-localize with previously identified QTL for stickleback phenotypic variation identified using laboratory mapping crosses. In addition, we have identified several novel regions showing parallel differentiation across independent populations. Annotation of these regions revealed numerous genes that are candidates for stickleback phenotypic evolution and will form the basis of future genetic analyses in this and other organisms. This study represents the first high-density SNP–based genome scan of genetic diversity and differentiation for populations of threespine stickleback in the wild. These data illustrate the complementary nature of laboratory crosses and population genomic scans by confirming the adaptive significance of previously identified genomic regions, elucidating the particular evolutionary and demographic history of such regions in natural populations, and identifying new genomic regions and candidate genes of evolutionary significance. Oceanic threespine stickleback have invaded and adapted to freshwater habitats countless times across the northern hemisphere. These freshwater populations have often evolved in similar ways from the ancestral marine stock from which they independently derived. With the exception of a few identified genes, the genetic basis of this remarkable parallel adaptation is unclear. Here we show that the parallel phenotypic evolution is matched by parallel patterns of nucleotide diversity and population differentiation across the genome. We used a novel high-throughput sequence-based genotyping approach to produce the first high density genome-wide scans of threespine stickleback populations and identified several genomic regions indicative of both divergent and balancing selection. Some of these regions have been associated previously with traits important for freshwater adaptation, but others were previously unidentified. Within these genomic regions we identified candidate genes, laying the foundation for further genetic and functional study of key pathways. This research illustrates the complementary nature of laboratory mapping, functional genetics, and population genomics.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
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作者：
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通讯作者：
BELL, MA
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作者：
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作者：
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通讯作者：
Schluter, Dolph
种群基因组学：果蝇果蝇中多态性和差异的全基因组分析。
影响因子：
9.8
作者：
Begun, David J.;Holloway, Alisha K.;Stevens, Kristian;Hillier, LaDeana W.;Poh, Yu-Ping;Hahn, Matthew W.;Nista, Phillip M.;Jones, Corbin D.;Kern, Andrew D.;Dewey, Colin N.;Pachter, Lior;Myers, Eugene;Langley, Charles H.
通讯作者：
Langley, Charles H.