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Babarinde IA, Adeola AC, Djagoun CAMS, Nneji LM, Okeyoyin AO, Niba G, Wanzie NK, Oladipo OC, Adebambo AO, Bello SF, Ng'ang'a SI, Olaniyi WA, Okoro VMO, Adedeji BE, Olatunde O, Ayoola AO, Matouke MM, Wang YY, Sanke OJ, Oseni SO, Nwani CD, Murphy RW. Population structure and evolutionary history of the greater cane rat ( Thryonomys swinderianus) from the Guinean Forests of West Africa. Front Genet 2023; 14:1041103. [PMID: 36923796 PMCID: PMC10010571 DOI: 10.3389/fgene.2023.1041103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023] Open
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 (FST), 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.
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Affiliation(s)
- Isaac A Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China.,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Chabi A M S Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Agboola O Okeyoyin
- National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria
| | - George Niba
- National Centre for Animal Husbandry and Veterinary Training, Jakiri, North West Region, Cameroon
| | - Ndifor K Wanzie
- Department of Zoology, University of Douala, Douala, Cameroon.,Department of Zoology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | - Ayotunde O Adebambo
- Animal Genetics & Biotechnology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Semiu F Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Said I Ng'ang'a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wasiu A Olaniyi
- Department of Animal Science, Faculty of Agriculture, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Victor M O Okoro
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | | | - Omotoso Olatunde
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Adeola O Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Kunming, China
| | - Moise M Matouke
- Department of Fisheries and Aquatic Resources Management, University of Buea, Buea, Cameroon
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Saidu O Oseni
- Department of Animal Sciences, Faculty of Agriculture, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Christopher D Nwani
- Department of Zoology and Environmental Biology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
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Nneji LM, Adeola AC, Yan F, Okeyoyin AO, Oladipo OC, Saidu Y, Samuel D, Nneji IC, Adeyi AO, Onadeko AB, Olagunju TE, Omotoso O, Oladipo SO, Iyiola OA, Usongo JY, Auta T, Usman AD, Abdullahi H, Ikhimiukor OO, Zhou WW, Jin JQ, Ugwumba OA, Ugwumba AAA, Peng MS, Murphy RW, Che J. Genetic variation and cryptic lineage diversity of the Nigerian red-headed rock agama Agama agama associate with eco-geographic zones. Curr Zool 2019; 65:713-724. [PMID: 31857818 PMCID: PMC6911843 DOI: 10.1093/cz/zoz002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 01/28/2019] [Indexed: 11/14/2022] Open
Abstract
Nigeria is an Afrotropical region with considerable ecological heterogeneity and levels of biotic endemism. Among its vertebrate fauna, reptiles have broad distributions, thus, they constitute a compelling system for assessing the impact of ecological variation and geographic isolation on species diversification. The red-headed rock agama, Agama agama, lives in a wide range of habitats and, thus, it may show genetic structuring and diversification. Herein, we tested the hypothesis that ecology affects its genetic structure and population divergence. Bayesian inference phylogenetic analysis of a mitochondrial DNA (mtDNA) gene recovered four well-supported matrilines with strong evidence of genetic structuring consistent with eco-geographic regions. Genetic differences among populations based on the mtDNA also correlated with geographic distance. The ecological niche model for the matrilines had a good fit and robust performance. Population divergence along the environmental axes was associated with climatic conditions, and temperature ranked highest among all environmental variables for forest specialists, while precipitation ranked highest for the forest/derived savanna, and savanna specialists. Our results cannot reject the hypothesis that niche conservatism promotes geographic isolation of the western populations of Nigerian A. agama. Thus, ecological gradients and geographic isolation impact the genetic structure and population divergence of the lizards. This species might be facing threats due to recent habitat fragmentation, especially in western Nigeria. Conservation actions appear necessary.
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Affiliation(s)
- Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Agboola O Okeyoyin
- National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria
| | | | - Yohanna Saidu
- Gashaka Gumti National Park, Serti, Taraba State, Nigeria
| | - Dinatu Samuel
- Gashaka Gumti National Park, Serti, Taraba State, Nigeria
| | - Ifeanyi C Nneji
- Department of Biological Sciences, University of Abuja, FCT, Abuja, Nigeria
| | - Akindele O Adeyi
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | | | - Olatunde Omotoso
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Segun O Oladipo
- Department of Biosciences and Biotechnology, Kwara State University, Malete, Kwara State, Nigeria
| | - Oluyinka A Iyiola
- Department of Zoology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - John Y Usongo
- Department of Zoology, Modibbo Adama University of Technology, Yola, Nigeria
| | - Timothy Auta
- Department of Biological Sciences, Federal University Dutsin-Ma, Katsina State, Nigeria
| | - Abbas D Usman
- Department of Biology, Kashim Ibrahim College of Education, Maiduguri, Borno State, Nigeria
| | - Halima Abdullahi
- Department of Biology, Kashim Ibrahim College of Education, Maiduguri, Borno State, Nigeria
| | - Odion O Ikhimiukor
- Department of Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Obih A Ugwumba
- Department of Zoology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Nneji LM, Adeola AC, Okeyoyin AO, Oladipo OC, Saidu Y, Usongo JY, Ugwumba AAA. Assessing the effectiveness of molecular data for species identification and diversity studies of Nigerian herpetofauna. Mitochondrial DNA Part B 2019. [DOI: 10.1080/23802359.2018.1561219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Lotanna M. Nneji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Agboola O. Okeyoyin
- National Park Service Headquarter, Abuja, Federal Capital Territory, Nigeria
| | | | | | - John Y. Usongo
- Department of Zoology, Modibbo Adama University of Technology, Yola, Nigeria
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Nneji LM, Adeola AC, Yan F, Okeyoyin AO, Oladipo OC, Olagunju TE, Omotoso O, Oladipo SO, Iyiola OA, Auta T, Usman AD, Abdullahi H, Peng MS, Jin JQ, Murphy RW, Ugwumba AAA, Che J. Cryptic Lineages of Nigerian Agama (Squamata: Agamidae) within the West African Radiation. RUSS J HERPETOL 2018. [DOI: 10.30906/1026-2296-2019-25-2-97-112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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