When One's Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression in Apis mellifera mellifera.
When One's Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression in Apis mellifera mellifera.
复制标题
作者：
人类对蜜蜂的管理导致了本土亚种的范围和完整性的减少，因为它们被具有被认为更可取的特征的外来亚种所取代。渗透--通过杂交和重复回交在不同的遗传谱系之间转移等位基因(基因变体)--可能会导致由于适应而随着时间的推移而积累起来的等位基因组合的丢失。对于育种者和自然资源保护者来说，测量渐渗对于评估群体的遗传完整性是很重要的。然而，目前还没有一种公认的方法来衡量蜜蜂群体中的渗入。在这里，我们比较了两种常用的统计方法来估计蜜蜂的导入，从个体和群体的遗传数据：聚类法(混合)和等位基因模式方法(ABBA BABA)。总体而言，来自一个群体的单个个体的数据比使用混合的群体样本的数据导致更低的回归估计。然而，ABBA BABA始终产生比混合更低的渐进估计值。这项研究强调，有时一个个体不足以评估群体水平的引入，未来使用混合群体方法的研究不应完全依赖于混合来进行引入估计。人类对蜜蜂的管理导致了蜜蜂亚种在其本土范围之外的广泛引入。一个著名的例子是意大利蜜蜂，原产于北欧，现在已经通过引入C系蜜蜂而显著引入。就未来的适应潜力和长期生存能力而言，导入会对物种产生影响。然而，估计群居生活的单倍体物种的渗入是具有挑战性的。以前的研究已经估计了个体工蚁、个体工蜂、多只工蜂和集体工蜂的内向。在这里，我们通过三种遗传方法来比较自回归估计：SNP阵列、个体RAD-SEQ和集合群体RAD-SEQ。我们还比较了两种统计方法：最大似然聚类程序(混合)和不完全世系排序模型(ABBA BABA)。总体而言，当使用混合方法时，单独的方法导致比混合群体更低的渐渗估计。然而，混合群体ABBA BABA方法的结果通常比三种混合估计值都要低。这些结果强调，有时一个个体不足以评估群体水平的导入，未来的研究，确实使用菌落池不应该完全依赖于集群程序的导入估计。
The human management of honey bees (Apis mellifera) has led to a reduction in the range and integrity of native subspecies, as they are replaced by foreign subspecies with traits that are perceived to be more desirable. Introgression—the transfer of alleles (gene variants) between genetically distinct lineages via hybridisation and repeated backcrossing—can lead to the loss of combinations of alleles that have built up over time as a result of adaptation. Measuring introgression is important for assessing the genetic integrity of colonies for breeders and conservationists. However, there is no agreed upon approach for measuring introgression in honey bee colonies. Here, we compare two commonly applied statistical methods for estimating introgression in honey bees from both individual and colony-pooled genetic data: a clustering approach (ADMIXTURE) and an allele pattern approach (ABBA BABA). Overall, data from a single individual from a colony resulted in lower introgression estimates than those from pooled colony samples using ADMIXTURE. However, ABBA BABA consistently yielded lower introgression estimates than ADMIXTURE. This study highlights that sometimes one individual is not enough to assess colony-level introgression and future studies using pooled colony approaches should not be solely dependent on ADMIXTURE for introgression estimates. The human management of honey bees (Apis mellifera) has resulted in the widespread introduction of subspecies outside of their native ranges. One well known example of this is Apis mellifera mellifera, native to Northern Europe, which has now been significantly introgressed by the introduction of C lineage honey bees. Introgression has consequences for species in terms of future adaptive potential and long-term viability. However, estimating introgression in colony-living haplodiploid species is challenging. Previous studies have estimated introgression using individual workers, individual drones, multiple drones, and pooled workers. Here, we compare introgression estimates via three genetic approaches: SNP array, individual RAD-seq, and pooled colony RAD-seq. We also compare two statistical approaches: a maximum likelihood cluster program (ADMIXTURE) and an incomplete lineage sorting model (ABBA BABA). Overall, individual approaches resulted in lower introgression estimates than pooled colonies when using ADMIXTURE. However, the pooled colony ABBA BABA approach resulted in generally lower introgression estimates than all three ADMIXTURE estimates. These results highlight that sometimes one individual is not enough to assess colony-level introgression, and future studies that do use colony pools should not be solely dependent on clustering programs for introgression estimates.
登录
查看更多内容
影响因子：
7
作者：
Beye, Martin;Gattermeier, Irene;Page, Robert E., Jr.
通讯作者：
Page, Robert E., Jr.
影响因子：
3.3
作者：
Mughal MR;DeGiorgio M
通讯作者：
DeGiorgio M
影响因子：
3.6
作者：
Bienkowska, Malgorzata;Splitt, Aleksandra;Maciorowski, Robert
通讯作者：
Maciorowski, Robert
影响因子：
2.4
作者：
Dall'Olio, Raffaele;Marino, Alberto;Moritz, Robin F. A.
通讯作者：
Moritz, Robin F. A.
影响因子：
3.3
作者：
Bachtrog, D;Thornton, K;Andolfatto, P
通讯作者：
Andolfatto, P