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分子钟速率和日期的膨胀:来自澳大拉西亚的全球蝉辐射的分子系统发育、生物地理学和多样化(半翅目:蝉科:蝉小蜂科)。

Inflation of Molecular Clock Rates and Dates: Molecular Phylogenetics, Biogeography, and Diversification of a Global Cicada Radiation from Australasia (Hemiptera: Cicadidae: Cicadettini).

机构信息

Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA;

Entomology Department, Australian Museum, 6 College Street, Sydney NSW 2010, Australia;

出版信息

Syst Biol. 2016 Jan;65(1):16-34. doi: 10.1093/sysbio/syv069. Epub 2015 Oct 22.

Abstract

Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1[Formula: see text] intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from: (i) an extrapolated EF-1[Formula: see text] exon clock derived from COI-calibrated analysis within the largest New Zealand subclade; (ii) post hoc scaling of the tribe-level chronogram using results from subclade analyses; and (iii) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera.

摘要

有时间关系的系统发育树对于研究多样化机制非常重要,而分子钟对于研究缺乏良好化石记录的生物也非常重要。然而,研究已经开始发现由于模型化分子替换过程的不确定性而导致分子钟日期出现问题。在这里,我们在研究全球蝉族 Cicadettini 约 200 种物种的生物地理学时,探索了贝叶斯松弛时钟分子定年法。由于可用的化石很少且没有信息,因此我们的树在一定程度上使用包含文献中对节肢动物估计的范围的细胞色素氧化酶 I(COI)时钟进行了校准。我们表明,仅使用 COI 时钟校准的部落水平分析得出的日期非常古老,与 Cicadettini 内两个经过充分研究的新西兰亚群的已发表估计值相冲突。额外的亚群分析表明,随着支系年龄的增加,COI 松弛时钟速率和最大似然分支长度相对于 EF-1[Formula: see text]内含子和外显子速率和分支长度会膨胀。我们提出了从以下方面得出的更正估计值:(i)从最大的新西兰亚群中 COI 校准分析中得出的外推 EF-1[Formula: see text]外显子时钟;(ii)使用亚群分析的结果对部落水平时标进行事后缩放;(iii)利用与新喀里多尼亚相关的地质校准点进行利用。我们警告说,由于替代估计值既依赖于分类群样本,又依赖于模型的选择,包括伽马类别数以及对经验与估计的基本频率的选择,因此会产生相当大的不确定性。我们的结果表明,蝉族的多样化始于新生代早期至中期,并随着澳大利亚和全球开阔干旱栖息地的发展而继续进行。我们发现,蝉族是一个罕见的具有澳大利亚起源的全球陆地动物群的例子,所有非澳大利亚属都属于两个远端分支。在澳大利亚内部,我们表明蝉族比任何其他蝉族都分布更广泛,在温带,干旱和季风性栖息地中多样化,并且几乎不存在于雨林中。我们对我们的发现对十三个蝉属的分类学影响发表了评论。

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