ArticleMolecular biology and evolution2008
Confirming the phylogeny of mammals by use of large comparative sequence data sets.
Article in Molecular biology and evolution, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Potentiation of Tumor Hallmarks by the Loss of GULO, a Vitamin C Biosynthesis Gene in Humans.Current molecular medicine · 2025Review
- Advancing microbial diagnostics: a universal phylogeny guided computational algorithm to find unique sequences for precise microorganism detection.Briefings in bioinformatics · 2024Article
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- Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses.Systematic biology · 2024Article
- Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference.Genome biology and evolution · 2022Article
- Deformity Index: A Semi-Reference Clade-Based Quality Metric of Phylogenetic Trees.Journal of molecular evolution · 2021Article
- Is Phylotranscriptomics as Reliable as Phylogenomics?Molecular biology and evolution · 2020Article
- Molecular evolution of the meiotic recombination pathway in mammals.Evolution; international journal of organic evolution · 2019Article
- Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae).BMC evolutionary biology · 2019Article
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- Correlated Selection on Amino Acid Deletion and Replacement in Mammalian Protein Sequences.Journal of molecular evolution · 2018Article
- Split-inducing indels in phylogenomic analysis.Algorithms for molecular biology : AMB · 2018Article
- Molecular evolution of type II MAGE genes from ancestral MAGED2 gene and their phylogenetic resolution of basal mammalian clades.Mammalian genome : official journal of the International Mammalian Genome Society · 2017Article
- Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences.Genome biology and evolution · 2017Article
- Speciation network in Laurasiatheria: retrophylogenomic signals.Genome research · 2017Article
- Selective evolution of Toll-like receptors 3, 7, 8, and 9 in bats.Immunogenetics · 2017Article
- Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species.Genome biology and evolution · 2017Article
- Comparative genomics reveals contraction in olfactory receptor genes in bats.Scientific reports · 2017Article
- Resolving the relationships of Paleocene placental mammals.Biological reviews of the Cambridge Philosophical Society · 2017Article
32 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
The ongoing generation of prodigious amounts of genomic sequence data from myriad vertebrates is providing unparalleled opportunities for establishing definitive phylogenetic relationships among species. The size and complexities of such comparative sequence data sets not only allow smaller and more difficult branches to be resolved but also present unique challenges, including large computational requirements and the negative consequences of systematic biases. To explore these issues and to clarify the phylogenetic relationships among mammals, we have analyzed a large data set of over 60 megabase pairs (Mb) of high-quality genomic sequence, which we generated from 41 mammals and 3 other vertebrates. All sequences are orthologous to a 1.9-Mb region of the human genome that encompasses the cystic fibrosis transmembrane conductance regulator gene (CFTR). To understand the characteristics and challenges associated with phylogenetic analyses of such a large data set, we partitioned the sequence data in several ways and utilized maximum likelihood, maximum parsimony, and Neighbor-Joining algorithms, implemented in parallel on Linux clusters. These studies yielded well-supported phylogenetic trees, largely confirming other recent molecular phylogenetic analyses. Our results provide support for rooting the placental mammal tree between Atlantogenata (Xenarthra and Afrotheria) and Boreoeutheria (Euarchontoglires and Laurasiatheria), illustrate the difficulty in resolving some branches even with large amounts of data (e.g., in the case of Laurasiatheria), and demonstrate the valuable role that very large comparative sequence data sets can play in refining our understanding of the evolutionary relationships of vertebrates.
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