Speciation network in Laurasiatheria: retrophylogenomic signals.
Speciation network in Laurasiatheria: retrophylogenomic signals.
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DOI：
10.1101/gr.210948.116
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发表时间：
2017-06
期刊：
影响因子：
7
通讯作者：
Schmitz J
中科院分区：
文献类型：
--
作者：
Doronina L;Churakov G;Kuritzin A;Shi J;Baertsch R;Clawson H;Schmitz J
由于适应性变化或新的生态空间的占领，物种的快速辐射挑战了我们对祖先物种形成和现代物种关系的理解。在分子水平上，在短时间内连续物种形成的快速辐射——太短而无法固定多态等位基因——被描述为不完整的谱系分类。不完整的谱系分类导致遗传标记的随机固定，因此，在系统发育重建中，关系的随机信号。当你考虑到基因组是祖先和现代未完全排序的序列块的马赛克时，情况就更加复杂了，这些序列块会导致与其中一个或另一个亲属的重建关系，这取决于他们共同的祖先多态性等位基因的固定。翼翅目、蛇足目、鲸足目和食肉目之间的捕食者关系是这种神秘的隶属关系的最好例子。我们对蝙蝠（翼翅目）、马（扑趾目）、牛（鲸趾目）和狗（食肉目）等代表动物进行了系统发育诊断性反转录转座子插入的全基因组筛选，并从162,000个预先选择的病例中提取了102个几乎无同源性的、系统发育信息丰富的反转录元件，以绘制出Laurasiatheria中高度复杂的进化关系的完整画面。所有可能的进化场景都得到了相当多的反转录转座子支持，给我们留下了一个联系网络。然而，鲸目动物与肉目动物的关系、翼目动物的基础位置和祖先月牙兽的杂交过程确实显示出一些非常清晰、明显的信号。反转录转座子存在/缺失模式和侧翼核苷酸变化的显著一致性表明，镶嵌基因组结构在物种历史重建中具有重要影响。
Rapid species radiation due to adaptive changes or occupation of new ecospaces challenges our understanding of ancestral speciation and the relationships of modern species. At the molecular level, rapid radiation with successive speciations over short time periods—too short to fix polymorphic alleles—is described as incomplete lineage sorting. Incomplete lineage sorting leads to random fixation of genetic markers and hence, random signals of relationships in phylogenetic reconstructions. The situation is further complicated when you consider that the genome is a mosaic of ancestral and modern incompletely sorted sequence blocks that leads to reconstructed affiliations to one or the other relative, depending on the fixation of their shared ancestral polymorphic alleles. The laurasiatherian relationships among Chiroptera, Perissodactyla, Cetartiodactyla, and Carnivora present a prime example for such enigmatic affiliations. We performed whole-genome screenings for phylogenetically diagnostic retrotransposon insertions involving the representatives bat (Chiroptera), horse (Perissodactyla), cow (Cetartiodactyla), and dog (Carnivora), and extracted among 162,000 preselected cases 102 virtually homoplasy-free, phylogenetically informative retroelements to draw a complete picture of the highly complex evolutionary relations within Laurasiatheria. All possible evolutionary scenarios received considerable retrotransposon support, leaving us with a network of affiliations. However, the Cetartiodactyla–Carnivora relationship as well as the basal position of Chiroptera and an ancestral laurasiatherian hybridization process did exhibit some very clear, distinct signals. The significant accordance of retrotransposon presence/absence patterns and flanking nucleotide changes suggest an important influence of mosaic genome structures in the reconstruction of species histories.