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Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships
Systematic Biology ( IF 6.5 ) Pub Date : 2019-09-24 , DOI: 10.1093/sysbio/syz062
Frank T Burbrink 1 , Felipe G Grazziotin 2 , R Alexander Pyron 3 , David Cundall 4 , Steve Donnellan 5, 6 , Frances Irish 7 , J Scott Keogh 8 , Fred Kraus 9 , Robert W Murphy 10 , Brice Noonan 11 , Christopher J Raxworthy 1 , Sara Ruane 12 , Alan R Lemmon 13 , Emily Moriarty Lemmon 14 , Hussam Zaher 15, 16
Affiliation  

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards and snakes, amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. Here, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites, phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of parsimony informative sites), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; and between the three toxiferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

中文翻译:

询问有鳞动物(蜥蜴、蛇和两栖动物)的基因组规模数据显示不支持关键的传统形态学关系

基因组学正在缩小许多羊膜动物群系统发育结构的不确定性。对于最多样化和物种最丰富的群体之一,有鳞爬行动物(蜥蜴和蛇,两栖动物),使用 DNA 序列数据并就这些关系达成共识的所有出版物中,采样的分类群和基因座数量之间仍然存在负相关其中问题很大。在这里,我们使用来自 75 个有鳞类家族的 289 个样本的高通量序列数据来解决系统发育亲和性,估计分歧时间,并在存在基​​因组规模数据的情况下表征残余拓扑不确定性。重要的是,我们使用新颖的机器学习技术解决了对传统分类群 Scleroglossa 和 Macrostomata 的基因组支持。我们使用这些基因座固有的各种指标来询问基因,包括简约信息位点、系统发育信息、长度、间隙、替换数量和位点一致性,以了解为什么某些基因座未能找到先前得到充分支持的分子进化枝以及它们如何失败支持物种树估计。我们表明,不完整的谱系排序和较差的基因树估计(由于一些不受欢迎的基因特性,例如简约信息站点数量不足),可能是大多数基因和物种树不一致的原因。我们发现 Toxicofera 的压倒性信号,并且还表明本研究中包含的基因座均不支持 Scleroglossa 或 Macrostomata。
更新日期:2019-09-24
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