Family size evolution in Drosophila chemosensory gene families: a comparative analysis with a critical appraisal of methods.
Family size evolution in Drosophila chemosensory gene families: a comparative analysis with a critical appraisal of methods.
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DOI：
10.1093/gbe/evu130
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发表时间：
2014-06-19
影响因子：
3.3
通讯作者：
Rozas J
中科院分区：
文献类型：
--
作者：
Almeida FC;Sánchez-Gracia A;Campos JL;Rozas J
基因更新率和基因家族大小的进化是基因组进化的重要方面。在这里，我们使用策划的序列数据的主要化学感受基因家族果蝇的味觉受体，气味受体，离子型受体，气味结合蛋白家族进行比较分析家庭之间，探索不同的方法来估计基因的出生率和死亡率，包括特设模拟研究。值得注意的是，我们发现，最先进的方法可能会产生非常不同的速率估计，这可能会导致不同的结论在果蝇的化学感受基因家族大小的演变。在生物学因素中，我们发现D. sechellia的基因更新率是全球估计偏差的主要来源，而基因转换对本文分析的家庭的影响可以忽略不计。周转率有很大的不同，家庭，亚家庭，和直系同源群体，虽然所有分析的家庭是相当动态的基因周转。计算机模拟表明，使用直系同源群信息的方法似乎是最准确的果蝇化学感受家庭。最重要的是，这些结果揭示了潜在的谱系之间的利率异质性严重偏见的一些周转率估计方法和需要进一步评估这些方法的性能在一个更多样化的基因家族和系统发育背景下的采样。使用分支特异性密码子替换模型，我们发现了最近重复的基因中正选择的进一步证据，这证明了基因出生和死亡过程的非中性方面。
Gene turnover rates and the evolution of gene family sizes are important aspects of genome evolution. Here, we use curated sequence data of the major chemosensory gene families from Drosophila—the gustatory receptor, odorant receptor, ionotropic receptor, and odorant-binding protein families—to conduct a comparative analysis among families, exploring different methods to estimate gene birth and death rates, including an ad hoc simulation study. Remarkably, we found that the state-of-the-art methods may produce very different rate estimates, which may lead to disparate conclusions regarding the evolution of chemosensory gene family sizes in Drosophila. Among biological factors, we found that a peculiarity of D. sechellia’s gene turnover rates was a major source of bias in global estimates, whereas gene conversion had negligible effects for the families analyzed herein. Turnover rates vary considerably among families, subfamilies, and ortholog groups although all analyzed families were quite dynamic in terms of gene turnover. Computer simulations showed that the methods that use ortholog group information appear to be the most accurate for the Drosophila chemosensory families. Most importantly, these results reveal the potential of rate heterogeneity among lineages to severely bias some turnover rate estimation methods and the need of further evaluating the performance of these methods in a more diverse sampling of gene families and phylogenetic contexts. Using branch-specific codon substitution models, we find further evidence of positive selection in recently duplicated genes, which attests to a nonneutral aspect of the gene birth-and-death process.
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影响因子：
64.8
作者：
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通讯作者：
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DOI：
10.1073/pnas.0608424104
发表时间：
2007-03-20
影响因子：
11.1
作者：
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通讯作者：
McBride, Carolyn S.