Department of Anthropology, University of Missouri, Columbia, MO 65211, United States; Nocturnal Primate Research Group, Oxford Brookes University, Oxford OX3 0BP, UK.
Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
Mol Phylogenet Evol. 2018 Oct;127:556-567. doi: 10.1016/j.ympev.2018.05.025. Epub 2018 May 25.
Extensive phylogenetic studies have found robust phylogenies are modeled by using a multi-gene approach and sampling from the majority of the taxa of interest. Yet, molecular studies focused on the lorises, a cryptic primate family, have often relied on one gene, or just mitochondrial DNA, and many were unable to include all four genera in the analyses, resulting in inconclusive phylogenies. Past phylogenetic loris studies resulted in lorises being monophyletic, paraphyletic, or an unresolvable trichotomy with the closely related galagos. The purpose of our study is to improve our understanding of loris phylogeny and evolutionary history by using a multi-gene approach. We used the mitochondrial genes cytochrome b, and cytochrome c oxidase subunit 1, along with a nuclear intron (recombination activating gene 2) and nuclear exon (the melanocortin 1 receptor). Maximum Likelihood and Bayesian phylogenetic analyses were conducted based on data from each locus, as well as on the concatenated sequences. The robust, concatenated results found lorises to be a monophyletic family (Lorisidae) (PP ≥ 0.99) with two distinct subfamilies: the African Perodictinae (PP ≥ 0.99) and the Asian Lorisinae (PP ≥ 0.99). Additionally, from these analyses all four genera were all recovered as monophyletic (PP ≥ 0.99). Some of our single-gene analyses recovered monophyly, but many had discordances, with some showing paraphyly or a deep-trichotomy. Bayesian partitioned analyses inferred the most recent common ancestors of lorises emerged ∼42 ± 6 million years ago (mya), the Asian Lorisinae separated ∼30 ± 9 mya, and Perodictinae arose ∼26 ± 10 mya. These times fit well with known historical tectonic shifts of the area, as well as with the sparse loris fossil record. Additionally, our results agree with previous multi-gene studies on Lorisidae which found lorises to be monophyletic and arising ∼40 mya (Perelman et al., 2011; Pozzi et al., 2014). By taking a multi-gene approach, we were able to recover a well-supported, monophyletic loris phylogeny and inferred the evolutionary history of this cryptic family.
广泛的系统发育研究发现，使用多基因方法并从大多数感兴趣的分类群中采样，可以构建稳健的系统发育。然而，针对灵长类动物中一个隐蔽的科——懒猴的分子研究往往依赖于一个基因，或者只是线粒体 DNA，而且许多研究无法将所有四个属都包括在分析中，导致系统发育关系不确定。过去的懒猴系统发育研究结果表明，懒猴是单系的、并系的，或者与密切相关的夜猴形成不可解决的三分叉。我们研究的目的是通过使用多基因方法来提高对懒猴系统发育和进化历史的理解。我们使用了线粒体基因细胞色素 b 和细胞色素 c 氧化酶亚基 1，以及一个核内含子（重组激活基因 2）和一个核外显子（黑色素皮质素 1 受体）。最大似然法和贝叶斯系统发育分析是基于每个基因座的数据以及串联序列进行的。稳健的串联结果发现，懒猴是一个单系科（懒猴科）（PP≥0.99），分为两个不同的亚科：非洲 Perodictinae（PP≥0.99）和亚洲 Lorisinae（PP≥0.99）。此外，从这些分析中，所有四个属都被回收为单系（PP≥0.99）。我们的一些单基因分析结果显示单系性，但许多结果存在分歧，有些显示并系性或深三分叉。贝叶斯分区分析推断，懒猴的最近共同祖先出现在约 4200 万年前（mya），亚洲 Lorisinae 大约在 3000 万年前分离，而 Perodictinae 大约在 2600 万年前出现。这些时间与该地区已知的历史构造变化以及稀疏的懒猴化石记录非常吻合。此外，我们的结果与之前关于懒猴科的多基因研究结果一致，该研究发现懒猴是单系的，起源于约 4000 万年前（Perelman 等人，2011 年；Pozzi 等人，2014 年）。通过采用多基因方法，我们能够重建一个支持度良好的单系懒猴系统发育，并推断这个隐蔽家族的进化历史。
