Caballero-López Violeta, Lundberg Max, Sokolovskis Kristaps, Bensch Staffan
Department of Biology, Lund University, Lund, Sweden.
Mol Ecol. 2022 Feb;31(4):1128-1141. doi: 10.1111/mec.16292. Epub 2021 Dec 5.
The genetic basis of bird migration has been the focus of several studies. Two willow warbler subspecies (Phylloscopus trochilus trochilus and Phylloscopus trochilus acredula) follow different migratory routes to wintering grounds in Africa. Their breeding populations overlap in contact areas or "migratory divides" located in central Scandinavia and in eastern Poland. Earlier analyses demonstrated that the genetic differences between these two migratory phenotypes are few and cluster on chromosomes 1 and 5. In addition, an amplified fragment length polymorphism-derived biallelic marker (known as WW2) presents steep clines across both migratory divides but failed to be mapped in the genome. Here, we characterize the WW2 marker and describe its two variants (WW2 ancestral and WW2 derived) as portions of long terminal repeat retrotransposons originating from an ancient infection by an endogenous retrovirus. We used quantitative polymerase chain reaction techniques to quantify copy numbers of the WW2 derived variant in the two subspecies and their hybrids. This, together with genome analyses revealed that WW2 derived variants are much more abundant in P. t. acredula and appear embedded in a large repeat-rich region (>12 Mbp), not associated with the divergent regions of chromosomes 1 or 5. However, it might interact with genetic elements controlling migration direction. Testing this hypothesis further will require knowing the exact location of this region, such as by obtaining more complete genome assemblies preferably in combination with techniques like fluorescence in situ hybridization applied to a willow warbler karyotype, and finally to investigate the copy number of this marker in hybrids with known migratory tracks.
鸟类迁徙的遗传基础一直是多项研究的重点。两种柳莺亚种（黄腹柳莺指名亚种和黄腹柳莺东方亚种）遵循不同的迁徙路线前往非洲的越冬地。它们的繁殖种群在位于斯堪的纳维亚半岛中部和波兰东部的接触区域或“迁徙分界线”重叠。早期分析表明，这两种迁徙表型之间的遗传差异很少，且集中在1号和5号染色体上。此外，一种基于扩增片段长度多态性的双等位基因标记（称为WW2）在两条迁徙分界线上呈现出陡峭的渐变，但未能在基因组中定位。在这里，我们对WW2标记进行了表征，并将其两个变体（WW2祖先型和WW2衍生型）描述为源自内源性逆转录病毒古老感染的长末端重复逆转座子的一部分。我们使用定量聚合酶链反应技术来量化两个亚种及其杂交种中WW2衍生变体的拷贝数。这与基因组分析一起表明，WW2衍生变体在黄腹柳莺东方亚种中更为丰富，并且似乎嵌入在一个大的富含重复序列的区域（>12 Mbp）中，该区域与1号或5号染色体的差异区域无关。然而，它可能与控制迁徙方向的遗传元件相互作用。进一步验证这一假设需要知道该区域的确切位置，例如通过获得更完整的基因组组装，最好结合应用于柳莺核型的荧光原位杂交等技术，最后研究具有已知迁徙轨迹的杂交种中该标记的拷贝数。
