Nuclear phylogenomics, but not mitogenomics, resolves the most
successful Late Miocene radiation of African mammals (Rodentia:
Muridae: Arvicanthini)

J 2021

Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini)

MIKULA, Ondřej, Violaine NICOLAS, Radim ŠUMBERA, Adam KONEČNÝ, Christiane DENYS et. al.

Basic information

Original name

Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini)

Authors

MIKULA, Ondřej, Violaine NICOLAS, Radim ŠUMBERA, Adam KONEČNÝ (203 Czech Republic, belonging to the institution), Christiane DENYS, Erik VERHEYEN, Anna BRYJOVÁ, Alan R. LEMMON, Emily Moriarty LEMMON and Josef BRYJA (203 Czech Republic, guarantor, belonging to the institution)

Edition

Molecular Phylogenetics and Evolution, Academic Press Inc. 2021, 1055-7903

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10613 Zoology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.019

RIV identification code

RIV/00216224:14310/21:00121517

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1016/j.ympev.2021.107069

UT WoS

000618942200001

Keywords in English

Late Miocene; Radiation; Anchored phylogenomics; Rodentia; Tropical Africa; Complete mitochondrial DNA

Abstract

V originále

The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes.

Links

90042, large research infrastructures

Name: CESNET II

Citovat

MIKULA, Ondřej, Violaine NICOLAS, Radim ŠUMBERA, Adam KONEČNÝ, Christiane DENYS, Erik VERHEYEN, Anna BRYJOVÁ, Alan R. LEMMON, Emily Moriarty LEMMON and Josef BRYJA. Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini). Molecular Phylogenetics and Evolution. Academic Press Inc., 2021, vol. 157, April, p. "107069", 9 pp. ISSN 1055-7903. Available from: https://dx.doi.org/10.1016/j.ympev.2021.107069.

@article{1765336,
   author = {Mikula, Ondřej and Nicolas, Violaine and Šumbera, Radim and Konečný, Adam and Denys, Christiane and Verheyen, Erik and Bryjová, Anna and Lemmon, Alan R. and Lemmon, Emily Moriarty and Bryja, Josef},
   article_number = {April},
   doi = {http://dx.doi.org/10.1016/j.ympev.2021.107069},
   keywords = {Late Miocene; Radiation; Anchored phylogenomics; Rodentia; Tropical Africa; Complete mitochondrial DNA},
   language = {eng},
   issn = {1055-7903},
   journal = {Molecular Phylogenetics and Evolution},
   title = {Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini)},
   url = {https://doi.org/10.1016/j.ympev.2021.107069},
   volume = {157},
   year = {2021}
}

TY  - JOUR
ID  - 1765336
AU  - Mikula, Ondřej - Nicolas, Violaine - Šumbera, Radim - Konečný, Adam - Denys, Christiane - Verheyen, Erik - Bryjová, Anna - Lemmon, Alan R. - Lemmon, Emily Moriarty - Bryja, Josef
PY  - 2021
TI  - Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini)
JF  - Molecular Phylogenetics and Evolution
VL  - 157
IS  - April
SP  - "107069"
EP  - "107069"
PB  - Academic Press Inc.
SN  - 10557903
KW  - Late Miocene
KW  - Radiation
KW  - Anchored phylogenomics
KW  - Rodentia
KW  - Tropical Africa
KW  - Complete mitochondrial DNA
UR  - https://doi.org/10.1016/j.ympev.2021.107069
N2  - The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes.
ER  -

MIKULA, Ondřej, Violaine NICOLAS, Radim ŠUMBERA, Adam KONEČNÝ, Christiane DENYS, Erik VERHEYEN, Anna BRYJOVÁ, Alan R. LEMMON, Emily Moriarty LEMMON and Josef BRYJA. Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini). \textit{Molecular Phylogenetics and Evolution}. Academic Press Inc., 2021, vol.~157, April, p.~''107069'', 9 pp. ISSN~1055-7903. Available from: https://dx.doi.org/10.1016/j.ympev.2021.107069.

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