Extending phylogeography to account for lineage fusion
Extending phylogeography to account for lineage fusion
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DOI：
10.1111/jbi.13503
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发表时间：
2019-02-01
影响因子：
3.9
通讯作者：
Symula, Rebecca E.
中科院分区：
文献类型：
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作者：
Garrick, Ryan C.;Banusiewicz, John D.;Symula, Rebecca E.
长期隔离人群之间的二次接触有几种可能的结果。这些包括通过强化来加强预先存在的生殖隔离机制，出现与其现存的亲本谱系不同并且占据它们之间的空间限制区的杂交谱系，或者两个种群完全合并使得亲本谱系不再存在（本文中的“谱系融合”）。后一种情况很少被明确考虑在单一物种和比较地理学研究，但它有可能影响人口历史和一致性水平的推断。在本文中，我们探讨的想法，洞察过去的谱系融合现在可能是可能的，由于下一代测序的出现。使用模拟的DNA序列单倍型数据集（即，基因座与等位基因组成的一组连锁的核苷酸多态性），我们检查了基本要求（基因座和采样的个人数），以确定案件时，目前的panmictic人口是产品的谱系融合，使用一个范例的统计框架近似贝叶斯计算。我们发现，大约有100个定相的单倍型基因座（每个400 bp长）和适度的个体样本量（每个群体10个），可以在相当具有挑战性的情况下检测到谱系融合。这包括在末次盛冰期时间范围内完全包含网状结构的一些情况，前提是混合是对称的，祖先基因库中度至深度分歧，融合事件和基因库采样之间的滞后时间相对较短。然而，如果额外的遗传数据（例如，400个位点）。尽管我们的模拟和知识的差距，仍然存在一些简化的假设下，血统融合的情况下，可能是可检测的，我们建议，最近发布的数据限制，允许地理学家扩大范围的推断长期的人口历史。
Secondary contact between long isolated populations has several possible outcomes. These include the strengthening of preexisting reproductive isolating mechanisms via reinforcement, the emergence of a hybrid lineage that is distinct from its extant parental lineages and which occupies a spatially restricted zone between them, or complete merging of two populations such that parental lineages are no longer extant ("lineage fusion" herein). The latter scenario has rarely been explicitly considered in single-species and comparative phylogeographic studies, yet it has the potential to impact inferences about population history and levels of congruence. In this paper, we explore the idea that insights into past lineage fusion may now be possible, owing to the advent of next-generation sequencing. Using simulated DNA sequence haplotype datasets (i.e., loci with alleles comprised of a set of linked nucleotide polymorphisms), we examined basic requirements (number of loci and individuals sampled) for identifying cases when a present-day panmictic population is the product of lineage fusion, using an exemplar statistical framework-approximate Bayesian computation. We found that with approximately 100 phased haplotype loci (each 400 bp long) and modest sample sizes of individuals (10 per population), lineage fusion can be detected under rather challenging scenarios. This included some scenarios where reticulation was fully contained within a Last Glacial Maximum timeframe, provided that mixing was symmetrical, ancestral gene pools were moderately to deeply diverged, and the lag time between the fusion event and gene pool sampling was relatively short. However, the more realistic case of asymmetrical mixing is not prohibitive if additional genetic data (e.g., 400 loci) are available. Notwithstanding some simplifying assumptions of our simulations and the knowledge gaps that remain about the circumstances under which lineage fusion is potentially detectable, we suggest that the recent release from data limitation allows phylogeographers to expand the scope of inferences about long-term population history.