Giarla Thomas C, Voss Robert S, Jansa Sharon A
Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA; J.F. Bell Museum of Natural History, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA.
Mol Phylogenet Evol. 2014 Jan;70:137-51. doi: 10.1016/j.ympev.2013.09.019. Epub 2013 Oct 2.
Cryptic genetic diversity is a significant challenge for systematists faced with ever-increasing amounts of DNA sequence data. Computationally intensive coalescent-based analyses involving multiple unlinked loci are the only currently viable methods by which to assess the extent to which phenotypically similar populations (or metapopulations) are genetically distinct lineages. Although coalescent-based approaches have been tested extensively via simulations, few empirical studies have examined the impact of prior assumptions and dataset size on the ability to assess genetic isolation (evolutionary independence) using molecular data alone. Here, we consider the efficacy of two coalescent-based approaches (BPP and SpeDeSTEM) for testing the evolutionary independence of cryptic mtDNA haplogroups within three morphologically diagnosable species of Andean mouse opossums (Thylamys pallidior, T. sponsorius, and T. venustus). Fourteen anonymous nuclear loci, one X-linked nuclear intron, and one mitochondrial gene were analyzed for multiple individuals within each haplogroup of interest. We inferred individual gene trees for each locus and considered all of the nuclear loci jointly in a species-tree analysis. Using only the nuclear loci, we performed "species validation" tests for the cryptic mitochondrial lineages in SpeDeSTEM and BPP. For BPP, we also tested a wide range of prior assumptions, assessed performance of the rjMCMC algorithm, and examined how many loci were necessary to confidently delimit lineages. Results from BPP provided strong support for two independent evolutionary lineages each within T. pallidior, T. sponsorius, and T. venustus, whereas SpeDeSTEM results did not support splitting out mtDNA haplogroups as distinct evolutionary units. For most tests, BPP was robust to prior assumptions, although priors were shown to have an effect on both the strength of lineage recognition among T. venustus haplotypes and on the efficiency of the rjMCMC algorithm. Comparisons of results from datasets with different numbers of loci revealed that some cryptic lineages could be confidently delimited with as few as two loci.
隐秘遗传多样性对于面对不断增加的DNA序列数据量的分类学家来说是一个重大挑战。涉及多个不连锁基因座的计算密集型基于溯祖的分析是目前唯一可行的方法，通过这些方法可以评估表型相似的种群（或复合种群）在多大程度上是遗传上不同的谱系。尽管基于溯祖的方法已经通过模拟进行了广泛测试，但很少有实证研究考察先验假设和数据集大小对仅使用分子数据评估遗传隔离（进化独立性）能力的影响。在这里，我们考虑两种基于溯祖的方法（BPP和SpeDeSTEM）在测试安第斯小鼠负鼠（苍白负鼠、斯氏负鼠和威氏负鼠）三个形态可诊断物种内隐秘线粒体单倍型类群的进化独立性方面的功效。对每个感兴趣的单倍型类群中的多个个体分析了14个匿名核基因座、一个X连锁核内含子和一个线粒体基因。我们推断了每个基因座的个体基因树，并在物种树分析中联合考虑所有核基因座。仅使用核基因座，我们在SpeDeSTEM和BPP中对隐秘线粒体谱系进行了“物种验证”测试。对于BPP，我们还测试了广泛的先验假设，评估了rjMCMC算法的性能，并研究了确定谱系需要多少个基因座。BPP的结果为苍白负鼠、斯氏负鼠和威氏负鼠各自内部的两个独立进化谱系提供了有力支持，而SpeDeSTEM的结果不支持将线粒体单倍型类群划分为不同的进化单元。对于大多数测试，BPP对先验假设具有鲁棒性，尽管先验被证明对威氏负鼠单倍型之间的谱系识别强度和rjMCMC算法的效率都有影响。对不同基因座数量的数据集结果的比较表明，一些隐秘谱系仅用两个基因座就可以可靠地确定。
