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Cao L, Dai Z, Tan H, Zheng H, Wang Y, Chen J, Kuang H, Chong RA, Han M, Hu F, Sun W, Sun C, Zhang Z. Population Structure, Demographic History, and Adaptation of Giant Honeybees in China Revealed by Population Genomic Data. Genome Biol Evol 2023; 15:7044694. [PMID: 36799935 PMCID: PMC9991589 DOI: 10.1093/gbe/evad025] [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: 06/26/2022] [Revised: 02/05/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
There have been many population-based genomic studies on human-managed honeybees (Apis mellifera and Apis cerana), but there has been a notable lack of analysis with regard to wild honeybees, particularly in relation to their evolutionary history. Nevertheless, giant honeybees have been found to occupy distinct habitats and display remarkable characteristics, which are attracting an increased amount of attention. In this study, we de novo sequenced and then assembled the draft genome sequence of the Himalayan giant honeybee, Apis laboriosa. Phylogenetic analysis based on genomic information indicated that A. laboriosa and its tropical sister species Apis dorsata diverged ∼2.61 Ma, which supports the speciation hypothesis that links A. laboriosa to geological changes throughout history. Furthermore, we re-sequenced A. laboriosa and A. dorsata samples from five and six regions, respectively, across their population ranges in China. These analyses highlighted major genetic differences for Tibetan A. laboriosa as well as the Hainan Island A. dorsata. The demographic history of most giant honeybee populations has mirrored glacial cycles. More importantly, contrary to what has occurred among human-managed honeybees, the demographic history of these two wild honeybee species indicates a rapid decline in effective population size in the recent past, reflecting their differences in evolutionary histories. Several genes were found to be subject to selection, which may help giant honeybees to adapt to specific local conditions. In summary, our study sheds light on the evolutionary and adaptational characteristics of two wild giant honeybee species, which was useful for giant honeybee conservation.
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Affiliation(s)
- Lianfei Cao
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhijun Dai
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Hongwei Tan
- School of Life Sciences, Chongqing University, Chongqing, China.,Chongqing General Station of Animal Husbandry Technology Extension, Chongqing, China
| | - Huoqing Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yun Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jie Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Haiou Kuang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Rebecca A Chong
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| | - Minjin Han
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Fuliang Hu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Wei Sun
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Ze Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
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