Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials

Gao-Ming Liu; Qi Pan; Juan Du; Ping-Fen Zhu; Wei-Qiang Liu; Zi-Hao Li; Ling Wang; Chun-Yan Hu; Yi-Chen Dai; Xiao-Xiao Zhang; Zhan Zhang; Yang Yu; Meng Li; Peng-Cheng Wang; Xiao Wang; Ming Li; Xu-Ming Zhou

doi:10.24272/j.issn.2095-8137.2023.189

Volume 44 Issue 6

Nov. 2023

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Gao-Ming Liu, Qi Pan, Juan Du, Ping-Fen Zhu, Wei-Qiang Liu, Zi-Hao Li, Ling Wang, Chun-Yan Hu, Yi-Chen Dai, Xiao-Xiao Zhang, Zhan Zhang, Yang Yu, Meng Li, Peng-Cheng Wang, Xiao Wang, Ming Li, Xu-Ming Zhou. Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials. Zoological Research, 2023, 44(6): 1064-1079. doi: 10.24272/j.issn.2095-8137.2023.189

Citation:

Gao-Ming Liu, Qi Pan, Juan Du, Ping-Fen Zhu, Wei-Qiang Liu, Zi-Hao Li, Ling Wang, Chun-Yan Hu, Yi-Chen Dai, Xiao-Xiao Zhang, Zhan Zhang, Yang Yu, Meng Li, Peng-Cheng Wang, Xiao Wang, Ming Li, Xu-Ming Zhou. Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials. Zoological Research, 2023, 44(6): 1064-1079. doi: 10.24272/j.issn.2095-8137.2023.189

Citation:

Gao-Ming Liu, Qi Pan, Juan Du, Ping-Fen Zhu, Wei-Qiang Liu, Zi-Hao Li, Ling Wang, Chun-Yan Hu, Yi-Chen Dai, Xiao-Xiao Zhang, Zhan Zhang, Yang Yu, Meng Li, Peng-Cheng Wang, Xiao Wang, Ming Li, Xu-Ming Zhou. Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials. Zoological Research, 2023, 44(6): 1064-1079. doi: 10.24272/j.issn.2095-8137.2023.189

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Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials

doi: 10.24272/j.issn.2095-8137.2023.189

Gao-Ming Liu¹,
Qi Pan^{1, 2},
Juan Du^{1, 2},
Ping-Fen Zhu¹,
Wei-Qiang Liu^{1, 2},
Zi-Hao Li^{1, 2},
Ling Wang^{1, 2},
Chun-Yan Hu^{1, 2},
Yi-Chen Dai¹,
Xiao-Xiao Zhang^{1, 2},
Zhan Zhang^{1, 2},
Yang Yu³,
Meng Li¹,
Peng-Cheng Wang^{1, 4},
Xiao Wang¹,
Ming Li¹,
Xu-Ming Zhou^{1
,
,}

1.
Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
2.
University of Chinese Academy of Sciences, Beijing 100049, China
3.
School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
4.
College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China

The field-collected Taphozous melanopogon, Aselliscus stoliczkanus, Chaerephon plicatus, and Hipposideros larvatus samples used in this study are not from endangered species and are not included in the “List of Protected Animals in China”. No specific permissions were required for sampling activities.
The generated sequences were submitted to GenBank (accession numbers OR503106–OR504069). Custom Perl scripts and alignments are available at Dryad (DOI: 10.5061/dryad.crjdfn36w).
Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
X.M.Z. conceived and supervised the project. J.D., Z.H.L., L.W., X.X.Z., Z.Z., Y.Y., M.L. P.C.W., X.W., and M.L. performed data curation. G.M.L., Q.P., P.F.Z., W.Q.L., C.Y.H., and Y.C.D. conducted hypothesis testing, phylogenetic analyses, and divergence time estimation. G.M.L. and X.M.Z. wrote the manuscript with input from all authors. All authors read and approved the final version of the manuscript.

Funds: This work was supported by the National Key Research and Development Projects of the Ministry of Science and Technology of China (2021YFC2301300), National Natural Science Foundation of China (82050002, 32070528, 32100335, 32000287), and Beijing Natural Sciences Foundation for Distinguished Young Scholars (JQ19022)

More Information

Corresponding author: E-mail: zhouxuming@ioz.ac.cn
Received Date: 2023-09-04
Accepted Date: 2023-10-23

Published Online: 2023-10-25

Publish Date: 2023-11-18

Abstract

Abstract

The timing of mammalian diversification in relation to the Cretaceous-Paleogene (KPg) mass extinction continues to be a subject of substantial debate. Previous studies have either focused on limited taxonomic samples with available whole-genome data or relied on short sequence alignments coupled with extensive species samples. In the present study, we improved an existing dataset from the landmark study of Meredith et al. (2011) by filling in missing fragments and further generated another dataset containing 120 taxa and 98 exonic markers. Using these two datasets, we then constructed phylogenies for extant mammalian families, providing improved resolution of many conflicting relationships. Moreover, the timetrees generated, which were calibrated using appropriate molecular clock models and multiple fossil records, indicated that the interordinal diversification of placental mammals initiated before the Late Cretaceous period. Additionally, intraordinal diversification of both extant placental and marsupial lineages accelerated after the KPg boundary, supporting the hypothesis that the availability of numerous vacant ecological niches subsequent to the mass extinction event facilitated rapid diversification. Thus, our results support a scenario of placental radiation characterized by both basal cladogenesis and active interordinal divergences spanning from the Late Cretaceous into the Paleogene.
- Mammals,
- Phylogeny,
- Diversification,
- Evolutionary model

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References(116)

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