It is unlikely that taxonomically diverse phylogenetic studies will be completed rapidly in the near future for nonmodel organisms on a whole-genome basis. However, one approach to advancing the field of "phylogenomics" is to estimate the structure of poorly known genomes by mining libraries of clones from suites of taxa, rather than from single species. The present analysis adopts this approach by taking advantage of megabase-scale end-sequence scanning of reptilian genomic clones to characterize diversity of CR1-like LINEs, the dominant family of transposable elements (TEs) in the sister group of mammals. As such, it helps close an important gap in the literature on the molecular systematics and evolution of retroelements in nonavian reptiles. Results from aligning more than 14 Mb of sequence from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta), Bahamian green anole (Anolis smaragdinus), Tuatara (Sphenodon punctatus), Emu (Dromaius novaehollandiae), and Zebra Finch (Taeniopygia guttata) against a comprehensive library approximately 3000 TE-encoding peptides reflect an increasing abundance of LINE and non-long-terminal-repeat (non-LTR) retrotransposon repeat types with the age of common ancestry among exemplar reptilian clades. The hypothesis that repeat diversity is correlated with basal metabolic rate was tested using comparative methods and a significant nonlinear relationship was indicated. This analysis suggests that the age of divergence between an exemplary clade and its sister group as well as metabolic correlates should be considered in addition to genome size in explaining patterns of retroelement diversity. The first phylogenetic analysis of the largely unexplored chicken repeat 1 (CR1) 3' reverse transcriptase (RT) conserved domains 8 and 9 in nonavian reptiles reveals a pattern of multiple lineages with variable branch lengths, suggesting presence of both old and young elements and the existence of several distinct well-supported clades not apparent from previous characterization of CR1 subfamily structure in birds and the turtle. This mode of CR1 evolution contrasts with historical patterns of LINE 1 diversification in mammals and hints toward the existence of a rich but still largely unexplored diversity of nonavian retroelements of importance to advancing both comparative vertebrate genomics and amniote systematics.

中文翻译：

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爬行动物CR1 LINE多样性的系统发育研究

在不久的将来，基于全基因组的非模式生物的分类学多样性系统发育研究不太可能迅速完成。然而，推进“系统基因组学”领域的一种方法是通过从分类群而不是单个物种中挖掘克隆文库来估计鲜为人知的基因组的结构。本分析采用这种方法，利用爬虫类基因组克隆的百万碱基规模的末端序列扫描来表征 CR1 样 LINEs 的多样性，CR1 样 LINEs 是哺乳动物姐妹群中转座因子 (TE) 的主要家族。因此，它有助于弥补非鸟类爬行动物分子系统学和逆向元素进化文献中的一个重要空白。比对来自美洲短吻鳄 (Alligator Mississippiensis)、锦龟 (Chrysemys picta)、巴哈马绿蜥蜴 (Anolis smaragdinus)、大蜥蜴 (Sphenodon punctatus)、鸸鹋 (Dromaius novaehollandiae) 和斑纹斑马 (Taenio Finch) 的超过 14 Mb 序列的结果Guttata）针对一个综合库，大约 3000 条 TE 编码肽反映了 LINE 和非长末端重复（非 LTR）反转录转座子重复类型的丰度随着示例爬行动物进化枝之间的共同祖先的年龄而增加。使用比较方法检验了重复多样性与基础代谢率相关的假设，并表明存在显着的非线性关系。该分析表明，在解释逆向元件多样性模式时，除了基因组大小之外，还应考虑示范进化枝与其姊妹组之间的分化年龄以及代谢相关性。对非鸟类爬行动物中大部分未探索的鸡重复序列 1 (CR1) 3' 逆转录酶 (RT) 保守域 8 和 9 的首次系统发育分析揭示了具有可变分支长度的多个谱系的模式，表明存在年老和年轻元素以及从先前对鸟类和乌龟的 CR1 亚科结构的表征来看，存在几个不同的得到良好支持的进化枝。