Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

Morgan, Claire C.; Foster, Peter G.; Webb, Andrew E.; Pisani, Davide; McInerney, James O.; O’Connell, Mary J.

doi:10.1093/molbev/mst117

Cited by 123Evolution and Paleontology StudiesGenomics and Phylogenetic StudiesPlant Diversity and Evolution

Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

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Morgan, Claire C., Foster, Peter G., Webb, Andrew E., Pisani, Davide, McInerney, James O., O’Connell, Mary J.·2013·Molecular Biology and Evolution

DOI 10.1093/molbev/mst117PMC PMC3748356

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Abstract

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 and is almost always better fitting than standard site-homogeneous amino acid substitution models.
“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]
In Results and Discussion, the 66TaxonSet and 39TaxonSet analyses find CAT or CAT-GTR better fitting than the homogeneous models tested on their amino-acid datasets. That supports the fit comparison for these datasets, but not the broader claim that CAT/CAT-GTR is almost always better fitting. The Introduction identifies long-branch attraction as a phylogenetic problem; the passages do not show that CAT/CAT-GTR is more resilient to it. (LLM, conf=0.86)
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Data from: Heterogeneous models place the root of the placental mammal phylogeny
Morgan, C. C., Foster, P. G., Webb, A. E., Pisani, D., McInerney, J. O., & O'Connell, M. J. (2013) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.vh49j
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A rticle Heterogeneous Models Place the Root of the Placental Mammal
Morgan, C. C., Foster, P. G., Webb, A. E., Pisani, D., McInerney, J. O., & Z, M. J. O. (2016)
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The molecular phylogeny of placental mammals and its application to uncovering signatures of molecular adaptation.
Morgan, C. C. (2013) · Dublin City University Open Access Institutional Repository (Dublin City University)
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Making the Impossible Possible: Rooting the Tree of Placental Mammals
Teeling, E. C., & Hedges, S. B. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst118 · Cited by 40 · see citing works
Article A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree
Moran, R. J., Morgan, C. C., & O’connell, M. J. (2015)
Self-citation

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: Morgan, Claire C.
Foster, Peter G.
Webb, Andrew E.
Pisani, Davide
McInerney, James O.
O’Connell, Mary J.
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
DOI: 10.1093/molbev/mst117
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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Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

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