Shedlock Andrew M, Takahashi Kazuhiko, Okada Norihiro
Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
Trends Ecol Evol. 2004 Oct;19(10):545-53. doi: 10.1016/j.tree.2004.08.002.
The value of short interspersed elements (SINEs) for diagnosing common ancestry is being expanded to examine the differential sorting of lineages through the course of speciation events. Because most SINEs are neutral markers of identical descent, are not precisely excised from the genome and have a known ancestral condition, they are advantageous for reconciling gene trees and species trees with minimal phylogenetic error. A population perspective on SINE evolution combined with coalescence theory provides a context for investigating the phenomenon of ancestral polymorphism and its role in producing incongruent SINE insertion patterns among multiple loci. Studies of human Alu repeats demonstrate the value of young polymorphic SINEs for assessing human genomic diversity and tracking ancient demographics of human populations, whereas incongruent insertion patterns revealed by older fixed SINE loci, such as those in African cichlid fishes, contain information that might help identify ancient radiations that are otherwise obscured by accumulated mutations in sequence data. Here, we review the utility of retroposons for inferring common ancestry, discuss limits to the method, and clarify confusion by providing examples from the literature that illustrate how discordant multi-locus insertion patterns of retroelements can indicate lineage-sorting events that should not be misinterpreted as phylogenetic noise.
短散在元件（SINEs）在诊断共同祖先方面的价值正在得到扩展，以研究在物种形成事件过程中谱系的差异分选。由于大多数SINEs是相同谱系的中性标记，不会从基因组中精确切除且具有已知的祖先状态，因此它们有利于以最小的系统发育误差来协调基因树和物种树。从群体角度看待SINE进化并结合溯祖理论，为研究祖先多态性现象及其在多个位点产生不一致的SINE插入模式中的作用提供了背景。对人类Alu重复序列的研究证明了年轻的多态性SINEs在评估人类基因组多样性和追踪人类群体古代人口统计学方面的价值，而较古老的固定SINE位点（如非洲丽鱼科鱼类中的那些位点）所揭示的不一致插入模式，则包含了可能有助于识别那些在序列数据中因累积突变而被掩盖的古代辐射的信息。在这里，我们回顾了反转录转座子在推断共同祖先方面的效用，讨论了该方法的局限性，并通过提供文献中的例子来澄清混淆，这些例子说明了反转录元件不一致的多位点插入模式如何能够指示谱系分选事件，而不应将其误解为系统发育噪声。
