Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure.
Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure.
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DOI：
10.1111/1755-0998.12369
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发表时间：
2015-09
影响因子：
7.7
通讯作者：
Walton C
中科院分区：
文献类型：
--
作者：
Kemppainen P;Knight CG;Sarma DK;Hlaing T;Prakash A;Maung Maung YN;Somboon P;Mahanta J;Walton C
测序方面的最新进展使几乎任何物种的种群基因组数据都能被生成。然而，分析这类数据的方法落后于生成数据的能力，特别是在非模式物种中。连锁不平衡(LD，来自不同座位的等位基因的非随机关联)是包括染色体倒置、局部适应和地理结构在内的许多进化现象的高度敏感的指标。在这里，我们提出了连锁不平衡网络分析(LDNA)，它访问关于全基因组多个座位之间共享的LD的信息。在LD网络中，顶点表示轨迹，顶点之间的连接表示它们之间的LD。我们在两个测试案例中分析了这样的网络：东南亚疟疾媒介白脉按蚊的新限制酶位点相关DNA序列(RAD-seq)数据集，以及来自21个三棘刺鱼个体的特征良好的单核苷酸多态(SNP)数据集。在每种情况下，我们都很容易地识别出五个不同的LD网络簇(单一异常值簇，SOC)，每个簇都包含由高LD连接的多个基因座。在白脉曲霉中，进一步的群体遗传学分析支持这样的推断，即每个SOC对应于一个大的倒位，这与以前的细胞学研究一致。对于刺鱼，我们推断每个SOC都与一个不同的进化现象有关：两个染色体倒置、局部适应、人口-人口历史和地理结构。因此，LDNA是一个有用的探索性工具，能够给出与各种进化现象相关的LD的全球概况，并确定可能涉及的基因座。LDNA不需要连锁图谱或参考基因组，因此它适用于任何种群基因组数据集，使其对非模式物种特别有价值。
Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species.