Population structure and evolutionary history of the greater cane rat (Thryonomys swinderianus) from the Guinean Forests of West Africa

Isaac A Babarinde; Adeniyi C Adeola; Chabi A M S Djagoun; Lotanna M Nneji; Agboola O Okeyoyin; George Niba; Ndifor K Wanzie; Ojo C Oladipo; Ayotunde O Adebambo; Semiu F Bello; Said I Ng'ang'a; Wasiu A Olaniyi; Victor M O Okoro; Babatunde E Adedeji; Omotoso Olatunde; Adeola O Ayoola; Moise M Matouke; Yun-Yu Wang; Oscar J Sanke; Saidu O Oseni; Christopher D Nwani; Robert W Murphy

doi:10.3389/fgene.2023.1041103

Population structure and evolutionary history of the greater cane rat (Thryonomys swinderianus) from the Guinean Forests of West Africa

Front Genet. 2023 Feb 27:14:1041103. doi: 10.3389/fgene.2023.1041103. eCollection 2023.

Authors

Isaac A Babarinde^{1

2}, Adeniyi C Adeola^{3

4

5}, Chabi A M S Djagoun⁶, Lotanna M Nneji⁷, Agboola O Okeyoyin⁸, George Niba⁹, Ndifor K Wanzie^{10

11}, Ojo C Oladipo¹², Ayotunde O Adebambo¹³, Semiu F Bello¹⁴, Said I Ng'ang'a³, Wasiu A Olaniyi¹⁵, Victor M O Okoro¹⁶, Babatunde E Adedeji¹⁷, Omotoso Olatunde¹⁷, Adeola O Ayoola^{3

4}, Moise M Matouke¹⁸, Yun-Yu Wang¹⁹, Oscar J Sanke²⁰, Saidu O Oseni²¹, Christopher D Nwani²², Robert W Murphy²³

Affiliations

¹ Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
² Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
³ State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
⁴ Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China.
⁵ Centre for Biotechnology Research, Bayero University, Kano, Nigeria.
⁶ Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Benin.
⁷ Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States.
⁸ National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria.
⁹ National Centre for Animal Husbandry and Veterinary Training, Jakiri, North West Region, Cameroon.
¹⁰ Department of Zoology, University of Douala, Douala, Cameroon.
¹¹ Department of Zoology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria.
¹² Old Oyo National Park, Oyo, Nigeria.
¹³ Animal Genetics & Biotechnology, Federal University of Agriculture, Abeokuta, Nigeria.
¹⁴ Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.
¹⁵ Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria.
¹⁶ Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria.
¹⁷ Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria.
¹⁸ Department of Fisheries and Aquatic Resources Management, University of Buea, Buea, Cameroon.
¹⁹ Wild Forensic Center, Kunming, China.
²⁰ Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria.
²¹ Department of Animal Sciences, Faculty of Agriculture, Obafemi Awolowo University, Ile-Ife, Nigeria.
²² Department of Zoology and Environmental Biology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria.
²³ Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada.

Abstract

Grasscutter (Thryonomys swinderianus) is a large-body old world rodent found in sub-Saharan Africa. The body size and the unique taste of the meat of this major crop pest have made it a target of intense hunting and a potential consideration as a micro-livestock. However, there is insufficient knowledge on the genetic diversity of its populations across African Guinean forests. Herein, we investigated the genetic diversity, population structures and evolutionary history of seven Nigerian wild grasscutter populations together with individuals from Cameroon, Republic of Benin, and Ghana, using five mitochondrial fragments, including D-loop and cytochrome b (CYTB). D-loop haplotype diversity ranged from 0.571 (± 0.149) in Republic of Benin to 0.921 (± 0.013) in Ghana. Within Nigeria, the haplotype diversity ranged from 0.659 (± 0.059) in Cross River to 0.837 (± 0.075) in Ondo subpopulation. The fixation index (F_ST), haplotype frequency distribution and analysis of molecular variance revealed varying levels of population structures across populations. No significant signature of population contraction was detected in the grasscutter populations. Evolutionary analyses of CYTB suggests that South African population might have diverged from other populations about 6.1 (2.6-10.18, 95% CI) MYA. Taken together, this study reveals the population status and evolutionary history of grasscutter populations in the region.

Keywords: Thryonomys swinderianus; genetic diversity; lower guinean forests; mitochondrial sequences; population structure.

Copyright © 2023 Babarinde, Adeola, Djagoun, Nneji, Okeyoyin, Niba, Wanzie, Oladipo, Adebambo, Bello, Ng’ang’a, Olaniyi, Okoro, Adedeji, Olatunde, Ayoola, Matouke, Wang, Sanke, Oseni, Nwani and Murphy.

Grants and funding

This work was supported by the Sino-Africa Joint Research Center, the Chinese Academy of Sciences (SAJC202103), the Animal Branch of the Germplasm Bank of Wild Species, and the Chinese Academy of Sciences (the Large Research Infrastructure Funding). The Chinese Academy of Sciences President’s International Fellowship Initiative provided support to ACA (2021FYB0006).