Genetic variation in populations of the earthworm, Lumbricus rubellus, across contaminated mine sites.
Genetic variation in populations of the earthworm, Lumbricus rubellus, across contaminated mine sites.
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DOI：
10.1186/s12863-017-0557-8
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发表时间：
2017-11-17
期刊：
影响因子：
2.9
通讯作者：
Spurgeon D
中科院分区：
文献类型：
--
作者：
Anderson C;Cunha L;Sechi P;Kille P;Spurgeon D
蚯蚓种群（Lumbricus rubellus）常见于高度污染的前矿区，被认为经过了选择以减轻金属毒性。将适应种群与污染较少的土壤上发现的种群进行比较，可以深入了解生态过程，从而证明土壤污染的长期影响。现代测序方法可以描述人口统计推断并突出表明特定基因选择的遗传变异。此外，英国各地 L. rubellus 谱系的出现可以推断与物种形成和局部适应驱动因素相关的机制。使用 RADseq，我们能够通过使用每个谱系的基因组草案来定义两个谱系之间的种群结构，证明谱系之间不存在混合，并且跨越广泛地理距离的种群形成离散种群。在这两个英国谱系之间，我们能够为与表观遗传和形态功能相关的基因以及编码信息素的基因附近的选择提供证据。居住在高度污染土壤中的蚯蚓与来自邻近对照土壤的蚯蚓的基因组非常相似。我们能够定义许多 SNP，这些 SNP 在很大程度上隔离了种群，并且表明可能正在选择用于管理金属毒性的基因。这包括分别与铅和砷污染物相关的钙和磷酸盐处理机制，同时我们还观察到多个人群中与谷胱甘肽相关机制（包括金属硫蛋白）的证据。群体基因组终点表明，相对于暴露史，核苷酸多样性没有持续减少，近交系数没有增加。尽管我们可以使用基因组标记清楚地定义谱系成员身份，以及地理区域之间的种群结构，但很难解析因土壤金属浓度而在种群之间完全隔离的标记。这可能代表了一系列高度可变的性状，以响应土壤环境的异质性，但最终证明了当地人群中谱系特异性遗传变异的维持。 L. rubellus 似乎为探索物种形成驱动因素提供了一个示范系统，其谱系连续体在欧洲大陆共存，而不同的谱系在英国各地孤立存在。本文的在线版本 (10.1186/s12863-017-0557-8) 包含补充材料，可供授权用户使用。
Populations of the earthworm, Lumbricus rubellus, are commonly found across highly contaminated former mine sites and are considered to have under-gone selection for mitigating metal toxicity. Comparison of adapted populations with those found on less contaminated soils can provide insights into ecological processes that demonstrate the long-term effects of soil contamination. Contemporary sequencing methods allow for portrayal of demographic inferences and highlight genetic variation indicative of selection at specific genes. Furthermore, the occurrence of L. rubellus lineages across the UK allows for inferences of mechanisms associated with drivers of speciation and local adaptation. Using RADseq, we were able to define population structure between the two lineages through the use of draft genomes for each, demonstrating an absence of admixture between lineages and that populations over extensive geographic distances form discrete populations. Between the two British lineages, we were able to provide evidence for selection near to genes associated with epigenetic and morphological functions, as well as near a gene encoding a pheromone. Earthworms inhabiting highly contaminated soils bare close genomic resemblance to those from proximal control soils. We were able to define a number of SNPs that largely segregate populations and are indicative of genes that are likely under selection for managing metal toxicity. This includes calcium and phosphate-handling mechanisms linked to lead and arsenic contaminants, respectively, while we also observed evidence for glutathione-related mechanisms, including metallothionein, across multiple populations. Population genomic end points demonstrate no consistent reduction in nucleotide diversity, or increase in inbreeding coefficient, relative to history of exposure. Though we can clearly define lineage membership using genomic markers, as well as population structure between geographic localities, it is difficult to resolve markers that segregate entirely between populations in response to soil metal concentrations. This may represent a highly variable series of traits in response to the heterogenous nature of the soil environment, but ultimately demonstrates the maintenance of lineage-specific genetic variation among local populations. L. rubellus appears to provide an exemplary system for exploring drivers for speciation, with a continuum of lineages coexisting across continental Europe, while distinct lineages exist in isolation throughout the UK. The online version of this article (10.1186/s12863-017-0557-8) contains supplementary material, which is available to authorized users.
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影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
DOI：
10.1534/g3.115.023655
发表时间：
2016-01-15
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Davey JW;Chouteau M;Barker SL;Maroja L;Baxter SW;Simpson F;Merrill RM;Joron M;Mallet J;Dasmahapatra KK;Jiggins CD
通讯作者：
Jiggins CD
影响因子：
11.4
作者：
Burgos, MG;Winters, C;Morgan, AJ
通讯作者：
Morgan, AJ
影响因子：
11.4
作者：
Hanson, Niklas;Stark, John D.
通讯作者：
Stark, John D.
影响因子：
4.8
作者：
Hines, Rochelle M.;Kang, Rujun;Quamme, Gary A.
通讯作者：
Quamme, Gary A.