The woodrats or packrats of the genus Neotoma have been the subject of a wide array of research including paleoecology, physiology, morphological evolution, systematics, speciation, and hybridization. In recent years, much work has been done to elucidate evolutionary relationships within and between closely related species of the genus; in particular the addition of newly collected specimens from critical geographic regions has provided new opportunities for taxonomic assessment. Given these new data and their potential, parsimony (PARS), maximum likelihood (ML), and Bayesian inference (BI) analyses were conducted on DNA sequences obtained from nine individual genes (four mitochondrial loci: 12S, 16S, CoII, and Cytb; five nuclear loci: AdhI2, BfibI7, En2, Mlr, and Myh6) to estimate the phylogenetic relationships among 23 species of Neotoma. Results of these analyses depicted a wide array of phylogenetic relationships among taxa; with substantial nodal support recovered in both the ML and PARS analyses at some mid-level and terminal positions. Several individual genes, particularly 12S, AdhI2, BfibI7, CoII, and Cytb, provided support at several basal positions; however, phylogenetic resolution was limited in the other genes. A final BI analysis where the nine genes were concatenated into a single data set produced several supported clades that corresponded to previously recognized species groups (floridana, micropus, mexicana, and lepida) and the subgenus Homodontomys. Levels of genetic divergence for within-species comparisons (estimated from the Cytb data set) ranged from 0.88% (N. magister) to 6.82% (N. fuscipes); for between sister species comparisons ranged from 4.68% (N. devia and N. lepida) to 12.70% (N. angustapalata and N. nelsoni); and for members within closely related clades ranged from 8.70% (N. bryanti and N. lepida) to 12.57% (N. goldmani and N. magister). Evaluations of generic, subgeneric, and species group boundaries were explored using phylogenetic principles on the DNA sequence data presented herein, as well as morphological findings from previous studies. Results obtained suggest that the most conservative taxonomic interpretation involves the abandonment of subgeneric delineations and relies on the recognition of eight species groups (cinerea, floridana, fuscipes, lepida, mexicana, micropus, phenax, and stephensi) as the backbone of the woodrat classification.

中文翻译：

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重新评估 Neotomini 啮齿动物（Hodomys、Neotoma 和 Xenomys）之间的系统发育关系以及对 woodrat 分类的评论

Neotoma 属的林鼠或袋鼠已成为广泛研究的主题，包括古生态学、生理学、形态进化、系统学、物种形成和杂交。近年来，已经做了大量工作来阐明该属密切相关的物种内部和之间的进化关系；特别是从关键地理区域添加新收集的标本，为分类学评估提供了新的机会。鉴于这些新数据及其潜力，对从九个单独基因（四个线粒体基因座：12S、16S、CoII 和 Cytb；五个核位点：AdhI2、BfibI7、En2、Mlr 和 Myh6）来估计 23 种 Neotoma 之间的系统发育关系。这些分析的结果描述了类群之间广泛的系统发育关系；在一些中级和终端位置的 ML 和 PARS 分析中恢复了大量节点支持。几个单独的基因，特别是 12S、AdhI2、BfibI7、CoII 和 Cytb，在几个基础位置提供支持；然而，系统发育分辨率在其他基因中是有限的。将九个基因连接成一个数据集的最终 BI 分析产生了几个支持的进化枝，这些进化枝对应于先前识别的物种组（floridana、micropus、mexicana 和 lepida）和 Homodontomys 亚属。种内比较的遗传差异水平（根据 Cytb 数据集估计）范围从 0.88%（N. magister）到 6.82%（N. fuscipes）；姐妹物种之间的比较范围为 4.68% (N. devia 和 N. lepida）至 12.70%（N. angustapalata 和 N. nelsoni）；对于密切相关的进化枝内的成员，范围从 8.70%（N. bryanti 和 N. lepida）到 12.57%（N. goldmani 和 N. magister）。使用系统发育原理对此处提供的 DNA 序列数据以及先前研究的形态学发现，对属、亚属和种群边界的评估进行了探索。获得的结果表明，最保守的分类学解释涉及放弃亚属划分，并依赖于将八个种群（cinerea、floridana、fuscipes、lepida、mexicana、micropus、phenax 和 stephensi）识别为林鼠分类的主干。lepida) 到 12.57% (N. goldmani 和 N. magister)。使用系统发育原理对此处提供的 DNA 序列数据以及先前研究的形态学发现，对属、亚属和种群边界的评估进行了探索。获得的结果表明，最保守的分类学解释涉及放弃亚属划分，并依赖于将八个种群（cinerea、floridana、fuscipes、lepida、mexicana、micropus、phenax 和 stephensi）识别为林鼠分类的主干。lepida) 到 12.57% (N. goldmani 和 N. magister)。使用系统发育原理对此处提供的 DNA 序列数据以及先前研究的形态学发现，对属、亚属和种群边界的评估进行了探索。获得的结果表明，最保守的分类学解释涉及放弃亚属划分，并依赖于将八个种群（cinerea、floridana、fuscipes、lepida、mexicana、micropus、phenax 和 stephensi）识别为林鼠分类的主干。