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Heterogeneous Models Place the Root of the Placental Mammal Phylogeny
Open accessAbstract
Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size, and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and data set, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and data set heterogeneity have been applied to mammal data. Here, we show the impact of accurate model assignment and the importance of data sets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, data set power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root.
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“CAT/CATGTR offers improved resilience to long-branch attraction artefacts (LBA)22 and is almost always better fitting than standard site-homogeneous amino acid substitution models (e.g. WAG)8–10,23–29.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [26]
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Metadata
- Authors
- Morgan, C. C., Foster, P. G., Webb, A. E., Pisani, D., McInerney, J. O., & O’Connell, M. J.
- Affiliations
- Dublin City University (IE)
- Natural History Museum (GB)
- National University of Ireland, Maynooth (IE)
- Corresponding author
- O’Connell, Mary J.
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-06-29
- Volume
- 30
- Issue
- 9
- Pages
- 2145-2156
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC3748356
- OpenAlex
- W2129747243
- Cited by
- 123
- References
- 63
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 6 · 2023: 9 · 2022: 7 · 2021: 9 · 2020: 7 · 2019: 14 · 2018: 9 · 2017: 10 · 2016: 19 · 2015: 14 · 2014: 10 · 2013: 4
- FWCI
- 10.66
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Repository@Nottingham (University of Nottingham) (publishedVersion, other-oa)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- Repository@Nottingham (University of Nottingham) (submittedVersion, cc-by-nc)
- Research Explorer (The University of Manchester) (submittedVersion)
- Explore Bristol Research (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion)
- Funders
- US-UK Fulbright Commission
- Irish Research Council for Science, Engineering and Technology
- Science Foundation Ireland
- Irish Research Council
- Irish Centre for High-End Computing
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Keywords
- Xenarthra, Afrotheria, phylogenetic conflict, compositional heterogeneity, amino acid substitution rates, model adequacy
- MeSH terms
- Animals, Female, Mammals, Models, Genetic, Phylogeny, Placenta, Pregnancy, Recombination, Genetic, Genetic Heterogeneity, Evolution, Molecular, Amino Acid Substitution, Mutation Rate
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