Combosch David J, Lemer Sarah, Ward Peter D, Landman Neil H, Giribet Gonzalo
Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
Marine Laboratory, University of Guam, Mangilao, GU, USA.
Mol Ecol. 2017 Nov;26(21):5923-5938. doi: 10.1111/mec.14344. Epub 2017 Oct 7.
Living fossils are survivors of previously more diverse lineages that originated millions of years ago and persisted with little morphological change. Therefore, living fossils are model organisms to study both long-term and ongoing adaptation and speciation processes. However, many aspects of living fossil evolution and their persistence in the modern world remain unclear. Here, we investigate three major aspects of the evolutionary history of living fossils: cryptic speciation, population genetics and effective population sizes, using members of the genera Nautilus and Allonautilus as classic examples of true living fossils. For this, we analysed genomewide ddRAD-Seq data for all six currently recognized nautiloid species throughout their distribution range. Our analyses identified three major allopatric Nautilus clades: a South Pacific clade, subdivided into three subclades with no signs of admixture between them; a Coral Sea clade, consisting of two genetically distinct populations with significant admixture; and a widespread Indo-Pacific clade, devoid of significant genetic substructure. Within these major clades, we detected five Nautilus groups, which likely correspond to five distinct species. With the exception of Nautilus macromphalus, all previously described species are at odds with genomewide data, testifying to the prevalence of cryptic species among living fossils. Detailed F analyses further revealed significant genome-wide and locus-specific signatures of selection between species and differentiated populations, which is demonstrated here for the first time in a living fossil. Finally, approximate Bayesian computation (ABC) simulations suggest large effective population sizes, which may explain the low levels of population differentiation commonly observed in living fossils.
活化石是先前更为多样化谱系的幸存者，它们起源于数百万年前，形态变化极小地存续至今。因此，活化石是研究长期和正在进行的适应及物种形成过程的模式生物。然而，活化石进化的许多方面及其在现代世界中的存续情况仍不清楚。在此，我们以鹦鹉螺属和异鹦鹉螺属的成员作为真正活化石的经典例子，研究活化石进化历史的三个主要方面：隐秘物种形成、种群遗传学和有效种群大小。为此，我们分析了目前已确认的所有六种鹦鹉螺物种在其分布范围内的全基因组ddRAD-Seq数据。我们的分析确定了三个主要的异域鹦鹉螺分支：一个南太平洋分支，细分为三个亚分支，它们之间没有混合的迹象；一个珊瑚海分支，由两个基因上不同但有显著混合的种群组成；以及一个广泛分布的印度-太平洋分支，没有明显的遗传亚结构。在这些主要分支中，我们检测到五个鹦鹉螺类群，它们可能对应于五个不同的物种。除了大脐鹦鹉螺外，所有先前描述的物种都与全基因组数据不符，这证明了隐秘物种在活化石中很普遍。详细的F分析进一步揭示了物种和分化种群之间在全基因组和基因座特异性上的显著选择特征，这在活化石中是首次得到证明。最后，近似贝叶斯计算（ABC）模拟表明有效种群大小很大，这可能解释了在活化石中通常观察到的低水平种群分化。
