1
|
Wang Y, Zeng B, Deng M, Zhao T, Liao Y, Ren R, Wang H, Yuan Y. Whole-genome resequencing reveals genetic diversity and adaptive evolution in Chinese honeybee ( Apis cerana cerana) in Guizhou, China. Front Genet 2024; 15:1352455. [PMID: 38826805 PMCID: PMC11140131 DOI: 10.3389/fgene.2024.1352455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/29/2024] [Indexed: 06/04/2024] Open
Abstract
Introduction: Guizhou Province, characterized by complex and diverse geographic and climatic environments, has rich genetic resources for the Chinese honeybee (Apis cerana cerana) and is one of the main bee-producing areas in China. However, research on the genetic diversity of Chinese honeybee in the Guizhou region is very limited, despite implications for conservation of biodiversity. Methods: In this study, we analyzed the genetic diversity, differentiation, and selection signals based on 116 Chinese honeybees from 12 regions in Guizhou Province using whole-genome sequencing. Results: We identified 1,400,430 high-quality SNPs across all samples. A population structure analysis revealed two independent genetic subgroups of Chinese honeybees in Guizhou, a Yunnan-Guizhou Plateau population in western Guizhou and a hilly-mountainous population in eastern Guizhou. The average nucleotide diversity (Pi) ranged from 0.00138 to 0.00161 and average expected heterozygosity (He) ranged from 0.2592 to 0.2604. The average genetic differentiation index (F ST) for Chinese honeybees in pairwise comparisons of 12 regions ranged from 0.0094 to 0.0293. There was clear genetic differentiation between the western plateau and the eastern hilly mountainous areas of Guizhou; however, F ST values between the eastern and western populations ranged from 0.0170 to 0.0293, indicating a low degree of differentiation. A genome-wide scan revealed a number of genes under selection in the Yunnan-Guizhou Plateau environment. These genes were related to growth and development, reproduction, and cold resistance, and several candidate genes involved in environmental adaptation were identified, including CTR, MAPK, MAST, HSF, and MKKK. Discussion: The results of the present study provide important theoretical bases for the conservation, evaluation, development, and utilization of genetic resources for Chinese honeybees in the Guizhou region and for further investigations of environmental adaptation and underlying mechanisms in the species.
Collapse
Affiliation(s)
- Yinchen Wang
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Bing Zeng
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Mengqing Deng
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Tian Zhao
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Yan Liao
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Rongqing Ren
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Hua Wang
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Yang Yuan
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| |
Collapse
|
2
|
Dong JH, Xu X, Ren ZX, Zhao YH, Zhang Y, Chen L, Wu Y, Chen G, Cao R, Wu Q, Wang H. The adaptation of bumblebees to extremely high elevation associated with their gut microbiota. mSystems 2024; 9:e0121923. [PMID: 38329353 PMCID: PMC10949452 DOI: 10.1128/msystems.01219-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024] Open
Abstract
Bumblebees are among the most abundant and important pollinators for sub-alpine and alpine flowering plant species in the Northern Hemisphere, but little is known about their adaptations to high elevations. In this article, we focused on two bumblebee species, Bombus friseanus and Bombus prshewalskyi, and their respective gut microbiota. The two species, distributed through the Hengduan Mountains of southwestern China, show species replacement at different elevations. We performed genome sequencing based on 20 worker bee samples of each species. Applying evolutionary population genetics and metagenomic approaches, we detected genes under selection and analyzed functional pathways between bumblebees and their gut microbes. We found clear genetic differentiation between the two host species and significant differences in their microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. These extremely high-elevation bumblebees show evidence of positive selection related to diverse biological processes. Positively selected genes involved in host immune systems probably contributed to gut microbiota changes, while the butyrate generated by gut microbiota may influence both host energy metabolism and immune systems. This suggests a close association between the genomes of the host species and their microbiomes based on some degree of natural selection.IMPORTANCETwo closely related and dominant bumblebee species, distributed at different elevations through the Hengduan Mountains of southwestern China, showed a clear genomic signature of adaptation to elevation at the molecular level and significant differences in their respective microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. Bumblebees' adaptations to higher elevations are closely associated with their gut microbiota through two biological processes: energy metabolism and immune response. Information allowing us to understand the adaptive mechanisms of species to extreme conditions is implicit if we are to conserve them as their environments change.
Collapse
Affiliation(s)
- Jiu-Hong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin Xu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zong-Xin Ren
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yan-Hui Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yaran Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - You Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guotao Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruiqing Cao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
3
|
Li Y, Yao J, Sang H, Wang Q, Su L, Zhao X, Xia Z, Wang F, Wang K, Lou D, Wang G, Waterhouse RM, Wang H, Luo S, Sun C. Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees. Mol Ecol Resour 2024; 24:e13905. [PMID: 37996991 DOI: 10.1111/1755-0998.13905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
The Asian honeybee, Apis cerana, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group of A. cerana. Integrating this with 525 resequencing data sets, we constructed the first pan-genome of A. cerana, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions; however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novel A. cerana ecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in the Atpalpha gene, indicated that this SV may promote the cold adaptation of A. cerana by altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation of A. cerana.
Collapse
Affiliation(s)
- Yancan Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Jun Yao
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiling Sang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Quangui Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Su
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiaomeng Zhao
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
| | - Zhenyu Xia
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feiran Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Kai Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Delong Lou
- Shandong Provincial Animal Husbandry Station, Jinan, China
| | - Guizhi Wang
- Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Huihua Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shudong Luo
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing, China
| |
Collapse
|
4
|
Wakamiya T, Kamioka T, Ishii Y, Takahashi J, Maeda T, Kawata M. Genetic differentiation and local adaptation of the Japanese honeybee, Apis cerana japonica. Ecol Evol 2023; 13:e10573. [PMID: 37780082 PMCID: PMC10541296 DOI: 10.1002/ece3.10573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023] Open
Abstract
We examine the population genetic structure and divergence among the regional populations of the Japanese honeybee, Apis cerana japonica, by re-sequencing the genomes of 105 individuals from the three main Japanese islands with diverse climates. The genetic structure results indicated that these individuals are distinct from the mainland Chinese A. cerana samples. Furthermore, population structure analyses have identified three genetically distinct geographic regions in Japan: Northern (Tohoku-Kanto-Chubu districts), Central (Chugoku district), and Southern (Kyushu district). In some districts, "possible non-native" individuals, likely introduced from other regions in recent years, were discovered. Then, genome-wide scans were conducted to detect candidate genes for adaptation by two different approaches. We performed a population branch statistics (PBS) analysis to identify candidate genes for population-specific divergence. A latent factor mixed model (LFMM) was used to identify genes associated with climatic variables along a geographic gradient. The PBSmax analysis identified 25 candidate genes for population-specific divergence whereas the LFMM analysis identified 73 candidate genes for adaptation to climatic variables along a geographic gradient. However, no common genes were identified by both methods.
Collapse
Affiliation(s)
- Takeshi Wakamiya
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
- Department of Biological SciencesTokyo Metropolitan UniversityHachiojiJapan
| | | | - Yuu Ishii
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | | | - Taro Maeda
- Institute for Agro‐Environmental Sciences (NIAES)NAROTsukubaJapan
| | - Masakado Kawata
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| |
Collapse
|
5
|
Hao Y, Song G, Zhang YE, Zhai W, Jia C, Ji Y, Tang S, Lv H, Qu Y, Lei F. Divergent contributions of coding and noncoding sequences to initial high-altitude adaptation in passerine birds endemic to the Qinghai-Tibet Plateau. Mol Ecol 2023; 32:3524-3540. [PMID: 37000417 DOI: 10.1111/mec.16942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/27/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023]
Abstract
Early events in the evolution of an ancestral lineage can shape the adaptive patterns of descendant species, but the evolutionary mechanisms driving initial adaptation from an ancestor remain largely unexplored. High-altitude adaptations have been extensively explored from the viewpoint of protein-coding genes; however, the contribution of noncoding regions remains relatively neglected. Here, we integrate genomic and transcriptomic data to investigate adaptive evolution in the ancestor of three high-altitude snowfinch species endemic to the Qinghai-Tibet Plateau. Our genome-wide scan for adaptation in the snowfinch ancestor identifies strong adaptation signals in functions of development and metabolism for the coding genes, but in functions of the nervous system development for noncoding regions. This pattern is exclusive to the snowfinch ancestor compared to a control ancestral lineage subject to weak selection. Changes in noncoding regions in the snowfinch ancestor, especially those nearest to coding genes, may be disproportionately associated with the differential expression of genes in the brain tissue compared to other tissues. Extensive gene expression in the brain tissue can be further altered via genetic regulatory networks of transcription factors harbouring potential accelerated regulatory regions (e.g., the development-related transcription factor YEATS4). Altogether, our study provides new evidence concerning how coding and noncoding sequences work through decoupled pathways in initial adaptation to the selective pressure of high-altitude environments. The analysis highlights the idea that noncoding sequences may be promising elements in facilitating the rapid evolution and adaptation to high altitudes.
Collapse
Affiliation(s)
- Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanzhu Ji
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shiyu Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hongrui Lv
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
6
|
Huang X, Du Q, Wang L, Chen B. Impacts of oxygen deficiency on embryo life-history traits of migratory locust Locusta migratoria from low and high altitudes. INSECT SCIENCE 2023; 30:867-879. [PMID: 36325760 DOI: 10.1111/1744-7917.13129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/08/2022] [Accepted: 10/13/2022] [Indexed: 06/15/2023]
Abstract
Hypoxia challenges aerobic organisms in numerous environments, and hypoxic conditions may become more severe under future climate-change scenarios. The impact of hypoxia on the development of terrestrial insect embryos is not well understood. Here, to address this gap, embryonic life-history traits of migratory locust Locusta migratoria from low-altitude and high-altitude regions were compared under 2 oxygen levels: normoxia (i.e., 21 kPa oxygen partial pressure and mild hypoxia (i.e., 10 kPa oxygen partial pressure). Our results demonstrated that, whether reared under normoxia or mild hypoxia, L. migratoria from high-altitude populations had longer developmental times, reduced weight, and lower mean relative growth rate as compared with those from low-altitude populations. When transferred from normoxia to mild hypoxia, nearly all the tested life-history traits presented significant negative changes in the low-altitude populations, but not in the high-altitude populations. The factor 'strain' alone explained 18.26%-54.59% of the total variation for traits, suggesting that the phenotypic differences between L. migratoria populations from the 2 altitudes could be driven by genetic variation. Significant genetic correlations were found between life-history traits, and most of these showed differentiation between the 2 altitudinal gradients. G-matrix comparisons showed significant structural differences between L. migratoria from the 2 regions, as well as several negative covariances (i.e., trade-offs) between traits in the low-altitude populations. Overall, our study provides clear evidence that evolutionary divergence of embryonic traits between L. migratoria populations from different altitudes has occurred.
Collapse
Affiliation(s)
- Xianliang Huang
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, Hebei Province, China
| | - Qianli Du
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, Hebei Province, China
| | - Lijing Wang
- Kenli Municipal Bureau of Agriculture and Rural Affairs, Dongying, Shandong Province, China
| | - Bing Chen
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, Hebei Province, China
| |
Collapse
|
7
|
Tang X, Yao Y, Li Y, Song H, Luo R, Shi P, Zhou Z, Xu J. Comparison of the mitochondrial genomes of three geographical strains of Apis laboriosa indicates high genetic diversity in the black giant honeybee (Hymenoptera: Apidae). Ecol Evol 2023; 13:e9782. [PMID: 36744074 PMCID: PMC9891905 DOI: 10.1002/ece3.9782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 12/26/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Apis laboriosa is the largest honeybee that lives mainly on cliff faces, with strong migratory ability. In this study, we firstly sequenced and assembled two complete mitochondrial genomes of A. laboriosa isolated from two distant locations in China (Chongqing and Shangri-La regions). Combined with the published mitochondrial genome of A. laboriosa from Nepal, comparative genomic analyses were conducted to gain insight into the genetic diversity of giant honeybees from different geographical distributions. The mitochondrial genomes of A. laboriosa from Chongqing and Shangri-La regions were 15,579 and 15,683 bp in length, respectively, both larger than that from Nepal with the length of 15,510 bp. Three mitochondrial genomes all harbor 37 common genes and present the same AT bias and the frequency of codon usage. However, the fragments including COX1, SSUrRNA, LSUrRNA, and the AT-rich region of the mitochondrial genome from Shangri-La region demonstrate distinctive insertions and deletions compared to those from Chongqing and Nepal regions. Phylogenetic trees of mitochondrial genomes show that A. laboriosa from Chongqing is most closely related to that from Nepal, rather than to Shangri-La. Genetic distance between Shangri-La and Chongqing or Nepal was even larger than that between the various subspecies of Apis mellifera. Overall, these results unmark that A. laboriosa in different geographical distributions can exhibit high genetic diversity at the mitochondrial genomic level, and therein, A. laboriosa from Shangri-La may be the subspecies. All these studies will contribute to our understanding of the geographical distribution and genetic differentiation of black giant honeybee in Asian region.
Collapse
Affiliation(s)
- Xiang‐You Tang
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Yu‐Xin Yao
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Yao‐Hui Li
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Hua‐Li Song
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Rui Luo
- College of Life SciencesChongqing Normal UniversityChongqingChina
| | - Peng Shi
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Ze‐Yang Zhou
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| | - Jin‐Shan Xu
- College of Life SciencesChongqing Normal UniversityChongqingChina,Key Laboratory of Conservation and Utilization of Pollinator Insect of the Upper Reaches of the Yangtze RiverMinistry of Agriculture and Rural AffairsChongqingChina
| |
Collapse
|
8
|
Lozier JD, Strange JP, Heraghty SD. Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee. Ecol Evol 2023; 13:e9778. [PMID: 36744081 PMCID: PMC9889631 DOI: 10.1002/ece3.9778] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Understanding historical range shifts and population size variation provides an important context for interpreting contemporary genetic diversity. Methods to predict changes in species distributions and model changes in effective population size (N e) using whole genomes make it feasible to examine how temporal dynamics influence diversity across populations. We investigate N e variation and climate-associated range shifts to examine the origins of a previously observed latitudinal heterozygosity gradient in the bumble bee Bombus vancouverensis Cresson (Hymenoptera: Apidae: Bombus Latreille) in western North America. We analyze whole genomes from a latitude-elevation cline using sequentially Markovian coalescent models of N e through time to test whether relatively low diversity in southern high-elevation populations is a result of long-term differences in N e. We use Maxent models of the species range over the last 130,000 years to evaluate range shifts and stability. N e fluctuates with climate across populations, but more genetically diverse northern populations have maintained greater N e over the late Pleistocene and experienced larger expansions with climatically favorable time periods. Northern populations also experienced larger bottlenecks during the last glacial period, which matched the loss of range area near these sites; however, bottlenecks were not sufficient to erode diversity maintained during periods of large N e. A genome sampled from an island population indicated a severe postglacial bottleneck, indicating that large recent postglacial declines are detectable if they have occurred. Genetic diversity was not related to niche stability or glacial-period bottleneck size. Instead, spatial expansions and increased connectivity during favorable climates likely maintain diversity in the north while restriction to high elevations maintains relatively low diversity despite greater stability in southern regions. Results suggest genetic diversity gradients reflect long-term differences in N e dynamics and also emphasize the unique effects of isolation on insular habitats for bumble bees. Patterns are discussed in the context of conservation under climate change.
Collapse
Affiliation(s)
- Jeffrey D. Lozier
- Department of Biological SciencesThe University of AlabamaTuscaloosaAlabamaUSA
| | - James P. Strange
- Department of EntomologyThe Ohio State UniversityColumbusOhioUSA
| | - Sam D. Heraghty
- Department of Biological SciencesThe University of AlabamaTuscaloosaAlabamaUSA
| |
Collapse
|
9
|
Geometric morphology and population genomics provide insights into the adaptive evolution of Apis cerana in Changbai Mountain. BMC Genomics 2022; 23:64. [PMID: 35045823 PMCID: PMC8772121 DOI: 10.1186/s12864-022-08298-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/07/2022] [Indexed: 01/27/2023] Open
Abstract
Abstract
Background
Exploration of adaptive evolution of organisms in response to environmental change can help to understand the evolutionary history of species and the underlying mechanisms of adaptation to local environments, thus guiding future conservation programmes. Before the introduction of Apis mellifera in China, eastern honey bees (Apis cerana) were the only species used for beekeeping in this region. In the mountains of Changbai, populations of A. cerana are considered a distinct ecotype of the species which formed through the distinct selective pressures in this area over time.
Result
We performed a measure of 300 wing specimens of eastern honey bees and obtained the geometric morphological variation in the wing of A. cerana in Changbai Mountain. A total of 3,859,573 high-quality SNP loci were yielded via the whole-genome resequencing of 130 individuals in 5 geographic regions.
Conclusion
Corresponding geometric morphology and population genomics confirmed the particularity of the A. cerana in Changbai Mountain. Genetic differentiation at the subspecies level exists between populations in Changbai Mountain and remaining geographic regions, and a significant reduction in the effective population size and an excessive degree of inbreeding may be responsible for a substantial loss of population genetic diversity. Candidate genes potentially associated with cold environmental adaptations in populations under natural selection were identified, which may represent local adaptations in populations. Our study provided insights into the evolutionary history and adaptation of A. cerana in Changbai Mountain, as well as its conservation.
Collapse
|
10
|
Zhang J, Zhang F, Tay WT, Robin C, Shi Y, Guan F, Yang Y, Wu Y. Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm. Mol Ecol Resour 2022; 22:1875-1891. [PMID: 35007400 DOI: 10.1111/1755-0998.13581] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/20/2021] [Accepted: 01/05/2022] [Indexed: 11/28/2022]
Abstract
The cotton bollworm Helicoverpa armigera is a cosmopolitan pest and its diverse habitats plausibly contribute to the formation of diverse lineages. Despite the significant threat it poses to economic crops worldwide, its evolutionary history and genetic basis of local adaptation are poorly understood. In this study, we de novo assembled a high-quality chromosome-level reference genome of H. a. armigera (contig N50 = 7.34 Mb), with 99.13% of the HaSCD2 assembly assigned into 31 chromosomes (Z-chromosome + 30 autosomes). We constructed an ultra-dense variation map across 14 cotton bollworm populations and identified a novel lineage in northwestern China. Historical inference showed that effective population size changes coincided with global temperature fluctuation. We identified nine differentiated genes in the three H. armigera lineages (H. a. armigera, H. a. conferta, and the new northwestern Chinese lineage), of which per and clk genes are involved in circadian rhythm. Selective sweep analyses identified a series of GO categories related to climate adaptation, feeding behavior and insecticide tolerance. Our findings reveal fundamental knowledge of the local adaptation of different cotton bollworm lineages and will guide the formulation of cotton bollworm management measures at different scales.
Collapse
Affiliation(s)
- Jianpeng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wee Tek Tay
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia
| | - Charles Robin
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yu Shi
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fang Guan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yihua Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yidong Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
11
|
Trense D, Hoffmann AA, Fischer K. Large- and small-scale geographic structures affecting genetic patterns across populations of an Alpine butterfly. Ecol Evol 2021; 11:14697-14714. [PMID: 34765135 PMCID: PMC8571576 DOI: 10.1002/ece3.8157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding factors influencing patterns of genetic diversity and the population genetic structure of species is of particular importance in the current era of global climate change and habitat loss. These factors include the evolutionary history of a species as well as heterogeneity in the environment it occupies, which in turn can change across time. Most studies investigating spatio-temporal genetic patterns have focused on patterns across wide geographic areas rather than local variation, but the latter can nevertheless be important particularly in topographically complex areas. Here, we consider these issues in the Sooty Copper butterfly (Lycaena tityrus) from the European Alps, using genome-wide SNPs identified through RADseq. We found strong genetic differentiation within the Alps with four genetic clusters, indicating western, central, and eastern refuges, and a strong reduction of genetic diversity from west to east. This reduction in diversity may suggest that the southwestern refuge was the largest one in comparison to other refuges. Also, the high genetic diversity in the west may result from (a) admixture of different western refuges, (b) more recent demographic changes, or (c) introgression of lowland L. tityrus populations. At small spatial scales, populations were structured by several landscape features and especially by high mountain ridges and large river valleys. We detected 36 outlier loci likely under altitudinal selection, including several loci related to membranes and cellular processes. We suggest that efforts to preserve alpine L. tityrus should focus on the genetically diverse populations in the western Alps, and that the dolomite populations should be treated as genetically distinct management units, since they appear to be currently more threatened than others. This study demonstrates the usefulness of SNP-based approaches for understanding patterns of genetic diversity, gene flow, and selection in a region that is expected to be particularly vulnerable to climate change.
Collapse
Affiliation(s)
- Daronja Trense
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
| | - Ary A. Hoffmann
- Pest & Environmental Adaptation Research GroupSchool of BiosciencesBio21 InstituteParkvilleVic.Australia
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
| |
Collapse
|
12
|
Liu Y, Henkel J, Beaurepaire A, Evans JD, Neumann P, Huang Q. Comparative genomics suggests local adaptations in the invasive small hive beetle. Ecol Evol 2021; 11:15780-15791. [PMID: 34824789 PMCID: PMC8601931 DOI: 10.1002/ece3.8242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 01/01/2023] Open
Abstract
Invasive species are a major driver of ecological and environmental changes that affect human health, food security, and natural biodiversity. The success and impact of biological invasions depend on adaptations to novel abiotic and biotic selective pressures. However, the molecular mechanisms underlying adaptations in invasive parasitic species are inadequately understood. Small hive beetles, Aethina tumida, are parasites of bee nests. Originally endemic to sub-Saharan Africa, they are now found nearly globally. Here, we investigated the molecular bases of the adaptations to novel environments underlying their invasion routes. Genomes of historic and recent adults A. tumida from both the endemic and introduced ranges were compared. Analysis of gene-environment association identified 3049 candidate loci located in 874 genes. Functional annotation showed a significant bias toward genes linked to growth and reproduction. One of the genes from the apoptosis pathway encodes an "ecdysone-related protein," which is a crucial regulator in controlling body size in response to environmental cues for holometabolous insects during cell death and renewal. Genes whose proteins regulate organ size, ovary activation, and oviposition were also detected. Functions of these enriched pathways parallel behavioral differences between introduced and native A. tumida populations, which may reflect patterns of local adaptation. The results considerably improve our understanding of the underlying mechanisms and ecological factors driving adaptations of invasive species. Deep functional investigation of these identified loci will help clarify the mechanisms of local adaptation in A. tumida.
Collapse
Affiliation(s)
- Yuanzhen Liu
- Vetsuisse FacultyInstitute of Bee HealthUniversity of BernBernSwitzerland
| | - Jan Henkel
- Vetsuisse FacultyInstitute of GeneticsUniversity of BernBernSwitzerland
| | - Alexis Beaurepaire
- Vetsuisse FacultyInstitute of Bee HealthUniversity of BernBernSwitzerland
| | - Jay D. Evans
- USDA‐ARS Beltsville Bee Research LaboratoryBeltsvilleMarylandUSA
| | - Peter Neumann
- Vetsuisse FacultyInstitute of Bee HealthUniversity of BernBernSwitzerland
- AgroscopeSwiss Bee Research CentreBernSwitzerland
| | - Qiang Huang
- Honeybee Research InstituteJiangxi Agricultural UniversityNanchangChina
| |
Collapse
|
13
|
McCulloch GA, Guhlin J, Dutoit L, Harrop TWR, Dearden PK, Waters JM. Genomic signatures of parallel alpine adaptation in recently evolved flightless insects. Mol Ecol 2021; 30:6677-6686. [PMID: 34592029 DOI: 10.1111/mec.16204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/16/2021] [Accepted: 09/27/2021] [Indexed: 12/01/2022]
Abstract
Natural selection along elevational gradients has potential to drive predictable adaptations across distinct lineages, but the extent of such repeated evolution remains poorly studied for many widespread alpine taxa. We present parallel genomic analyses of two recently evolved flightless alpine insect lineages to test for molecular signatures of repeated alpine adaptation. Specifically, we compare low-elevation vs. alpine stonefly ecotypes from parallel stream populations in which flightless upland ecotypes have been independently derived. We map 67,922 polymorphic genetic markers, generated across 176 Zelandoperla fenestrata specimens from two independent alpine stream populations in New Zealand's Rock and Pillar Range, to a newly developed plecopteran reference genome. Genome-wide scans revealed 31 regions with outlier single nucleotide polymorphisms (SNPs) differentiating lowland vs. alpine ecotypes in Lug Creek, and 37 regions with outliers differentiating ecotypes in Six Mile Creek. Of these regions, 13% (8/60) yielded outlier SNPs across both within-stream ecotype comparisons, implying comparable genomic shifts contribute to this repeated alpine adaptation. Candidate genes closely linked to repeated outlier regions include several with documented roles in insect wing-development (e.g., dishevelled), suggesting that they may contribute to repeated alpine wing reduction. Additional candidate genes have been shown to influence insect fecundity (e.g., ovo) and lifespan (e.g., Mrp4), implying that they might contribute to life history differentiation between upland and lowland ecotypes. Additional outlier genes have potential roles in the evolution of reproductive isolation among ecotypes (hedgehog and Desaturase 1). These results demonstrate how replicated outlier tests across independent lineages can potentially contribute to the discovery of genes underpinning repeated adaptation.
Collapse
Affiliation(s)
| | - Joseph Guhlin
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Thomas W R Harrop
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Peter K Dearden
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | |
Collapse
|
14
|
Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, Paten B, Penso-Dolfin L, Wang L, Chang Y, Gao Q, Ma L, Ma L, Zhang Z, Zhang H, Zhang H, Ruzzante L, Robertson HM, Zhu Y, Liu Y, Yang H, Ding L, Wang Q, Ma D, Xu W, Liang C, Itgen MW, Mee L, Cao G, Zhang Z, Sadd BM, Hahn MW, Schaack S, Barribeau SM, Williams PH, Waterhouse RM, Mueller RL. Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits. Mol Biol Evol 2021; 38:486-501. [PMID: 32946576 PMCID: PMC7826183 DOI: 10.1093/molbev/msaa240] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships, whereas incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. Our study reveals how bumblebee genes and genomes have evolved across the Bombus phylogeny and identifies variations potentially linked to key ecological and behavioral traits of these important pollinators.
Collapse
Affiliation(s)
- Cheng Sun
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaxing Huang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yun Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xiaomeng Zhao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Su
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gregg W C Thomas
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Mengya Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Saverio Vicario
- Institute of Atmospheric Pollution Research-Italian National Research Council C/O Department of Physics, University of Bari, Bari, Italy
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA.,Department of Cytology and Genetics, Tomsk State University, Tomsk, Russian Federation
| | - Semen M Bondarenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA
| | - Martin Hasselmann
- Department of Livestock Population Genomics, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Chang N Kim
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA
| | | | - Li Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuxiao Chang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ling Ma
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lina Ma
- China National Center for Bioinformation & Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhang Zhang
- China National Center for Bioinformation & Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Hongbo Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Huahao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Livio Ruzzante
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL
| | - Yihui Zhu
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA
| | - Yanjie Liu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huipeng Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lele Ding
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Quangui Wang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongna Ma
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilin Xu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Liang
- Institute of Sericultural and Apiculture, Yunnan Academy of Agricultural Sciences, Mengzi, China
| | - Michael W Itgen
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Lauren Mee
- Department of Ecology, Evolution and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Ze Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Ben M Sadd
- School of Biological Sciences, Illinois State University, Normal, IL
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN.,Department of Computer Science, Indiana University, Bloomington, IN
| | | | - Seth M Barribeau
- Department of Ecology, Evolution and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Paul H Williams
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | |
Collapse
|
15
|
Shi P, Zhou J, Song H, Wu Y, Lan L, Tang X, Ma Z, Vossbrinck CR, Vossbrinck B, Zhou Z, Xu J. Genomic analysis of Asian honeybee populations in China reveals evolutionary relationships and adaptation to abiotic stress. Ecol Evol 2020; 10:13427-13438. [PMID: 33304549 PMCID: PMC7713975 DOI: 10.1002/ece3.6946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 01/12/2023] Open
Abstract
The geographic and biological diversity of China has resulted in the differential adaptation of the eastern honeybee, Apis cerana, to these varied habitats. A. cerana were collected from 14 locations in China. Their genomes were sequenced, and nucleotide polymorphisms were identified at more than 9 million sites. Both STRUCTURE and principal component analysis placed the bees into seven groups. Phylogenomic analysis groups the honeybees into many of the same clusters with high bootstrap values (91%-100%). Populations from Tibet and South Yunnan are sister taxa and together represent the earliest diverging lineage included in this study. We propose that the evolutionary origin of A. cerana in China was in the southern region of Yunnan Province and expanded from there into the southeastern regions and into the northeastern mountain regions. The Cold-Temperate West Sichuan Plateau and Tropical Diannan populations were compared to identify genes under adaptive selection in these two habitats. Pathway enrichment analysis showing genes under selection, including the Hippo signaling pathway, GABAergic pathway, and trehalose-phosphate synthase, indicates that most genes under selection pressure are involved in the process of signal transduction and energy metabolism. qRT-PCR analysis reveals that one gene under selection, the AcVIAAT gene, involved in the GABAergic pathway, is responding to cold temperature stress. Through homologous recombination, we show that the AcVIAAT gene is able to replace the CNAG_01904 gene in the fungus Cryptococcus neoformans and that it makes the fungus less sensitive to conditions of oxidative stress and variations in temperature. Our results contribute to our understanding of the evolutionary origin of A. cerana in China and the molecular basis of environmental adaptation.
Collapse
Affiliation(s)
- Peng Shi
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Jun Zhou
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Huali Song
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Yujuan Wu
- State Key Laboratory of Silkworm Genome BiologySouthwest UniversityChongqingChina
| | - Lan Lan
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Xiangyou Tang
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Zhengang Ma
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| | - Charles R. Vossbrinck
- Department of Environmental ScienceConnecticut Agricultural Experiment StationNew HavenCTUSA
| | | | - Zeyang Zhou
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
- State Key Laboratory of Silkworm Genome BiologySouthwest UniversityChongqingChina
| | - Jinshan Xu
- College of Life SciencesChongqing Normal UniversityChongqingChina
- Engineering Research Center of Biotechnology for Active SubstancesMinistry of EducationChongqingChina
| |
Collapse
|
16
|
Trense D, Schmidt TL, Yang Q, Chung J, Hoffmann AA, Fischer K. Anthropogenic and natural barriers affect genetic connectivity in an Alpine butterfly. Mol Ecol 2020; 30:114-130. [PMID: 33108010 DOI: 10.1111/mec.15707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/22/2022]
Abstract
Dispersal is a key biological process serving several functions including connectivity among populations. Habitat fragmentation caused by natural or anthropogenic structures may hamper dispersal, thereby disrupting genetic connectivity. Investigating factors affecting dispersal and gene flow is important in the current era of anthropogenic global change, as dispersal comprises a vital part of a species' resilience to environmental change. Using finescale landscape genomics, we investigated gene flow and genetic structure of the Sooty Copper butterfly (Lycaena tityrus) in the Alpine Ötz valley system in Austria. We found surprisingly high levels of gene flow in L. tityrus across the region. Nevertheless, ravines, forests, and roads had effects on genetic structure, while rivers did not. The latter is surprising as roads and rivers have a similar width and run largely in parallel in our study area, pointing towards a higher impact of anthropogenic compared with natural linear structures. Additionally, we detected eleven loci potentially under thermal selection, including ones related to membranes, metabolism, and immune function. This study demonstrates the usefulness of molecular approaches in obtaining estimates of dispersal and population processes in the wild. Our results suggest that, despite high gene flow in the Alpine valley system investigated, L. tityrus nevertheless seems to be vulnerable to anthropogenically-driven habitat fragmentation. With anthropogenic rather than natural linear structures affecting gene flow, this may have important consequences for the persistence of species such as the butterfly studied here in altered landscapes.
Collapse
Affiliation(s)
- Daronja Trense
- Institute for Integrated Natural Sciences, Zoology, University Koblenz-Landau, Koblenz, Germany
| | - Thomas L Schmidt
- Pest & Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, Parkville, Vic., Australia
| | - Qiong Yang
- Pest & Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, Parkville, Vic., Australia
| | - Jessica Chung
- Pest & Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, Parkville, Vic., Australia
| | - Ary A Hoffmann
- Pest & Environmental Adaptation Research Group, School of Biosciences, Bio21 Institute, Parkville, Vic., Australia
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, Zoology, University Koblenz-Landau, Koblenz, Germany
| |
Collapse
|
17
|
Small-scale population divergence is driven by local larval environment in a temperate amphibian. Heredity (Edinb) 2020; 126:279-292. [PMID: 32958927 DOI: 10.1038/s41437-020-00371-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
Genomic variation within and among populations is shaped by the interplay between natural selection and the effects of genetic drift and gene flow. Adaptive divergence can be found in small-scale natural systems even when population sizes are small, and the potential for gene flow is high, suggesting that local environments exert selection pressures strong enough to counteract the opposing effects of drift and gene flow. Here, we investigated genomic differentiation in nine moor frog (Rana arvalis) populations in a small-scale network of local wetlands using 16,707 ddRAD-seq SNPs, relating levels of differentiation with local environments, as well as with properties of the surrounding landscape. We characterized population structure and differentiation, and partitioned the effects of geographic distance, local larval environment, and landscape features on total genomic variation. We also conducted gene-environment association studies using univariate and multivariate approaches. We found small-scale population structure corresponding to 6-8 clusters. Local larval environment was the most influential component explaining 2.3% of the total genetic variation followed by landscape features (1.8%) and geographic distance (0.8%), indicative of isolation-by-environment, -by-landscape, and -by-distance, respectively. We identified 1000 potential candidate SNPs putatively under divergent selection mediated by the local larval environment. The candidate SNPs were involved in, among other biological functions, immune system function and development. Our results suggest that small-scale environmental differences can exert selection pressures strong enough to counteract homogenizing effects of gene flow and drift in this small-scale system, leading to observable population differentiation.
Collapse
|
18
|
Parejo M, Wragg D, Henriques D, Charrière JD, Estonba A. Digging into the Genomic Past of Swiss Honey Bees by Whole-Genome Sequencing Museum Specimens. Genome Biol Evol 2020; 12:2535-2551. [PMID: 32877519 PMCID: PMC7720081 DOI: 10.1093/gbe/evaa188] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 11/20/2022] Open
Abstract
Historical specimens in museum collections provide opportunities to gain insights into the genomic past. For the Western honey bee, Apis mellifera L., this is particularly important because its populations are currently under threat worldwide and have experienced many changes in management and environment over the last century. Using Swiss Apis mellifera mellifera as a case study, our research provides important insights into the genetic diversity of native honey bees prior to the industrial-scale introductions and trade of non-native stocks during the 20th century—the onset of intensive commercial breeding and the decline of wild honey bees following the arrival of Varroa destructor. We sequenced whole-genomes of 22 honey bees from the Natural History Museum in Bern collected in Switzerland, including the oldest A. mellifera sample ever sequenced. We identify both, a historic and a recent migrant, natural or human-mediated, which corroborates with the population history of honey bees in Switzerland. Contrary to what we expected, we find no evidence for a significant genetic bottleneck in Swiss honey bees, and find that genetic diversity is not only maintained, but even slightly increased, most probably due to modern apicultural practices. Finally, we identify signals of selection between historic and modern honey bee populations associated with genes enriched in functions linked to xenobiotics, suggesting a possible selective pressure from the increasing use and diversity of chemicals used in agriculture and apiculture over the last century.
Collapse
Affiliation(s)
- Melanie Parejo
- Agroscope, Swiss Bee Research Center, Bern, Switzerland.,Lab. Genetics, Department of Genetics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - David Wragg
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Dora Henriques
- Instituto Politécnico de Bragança, Centro de Investigação de Montanha (CIMO), Bragança, Portugal
| | | | - Andone Estonba
- Lab. Genetics, Department of Genetics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| |
Collapse
|
19
|
Corrigendum. Mol Ecol 2020. [DOI: 10.1111/mec.15302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
20
|
Jackson JM, Pimsler ML, Oyen KJ, Strange JP, Dillon ME, Lozier JD. Local adaptation across a complex bioclimatic landscape in two montane bumble bee species. Mol Ecol 2020; 29:920-939. [PMID: 32031739 DOI: 10.1111/mec.15376] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 01/21/2020] [Accepted: 02/02/2020] [Indexed: 12/21/2022]
Abstract
Understanding evolutionary responses to variation in temperature and precipitation across species ranges is of fundamental interest given ongoing climate change. The importance of temperature and precipitation for multiple aspects of bumble bee (Bombus) biology, combined with large geographic ranges that expose populations to diverse environmental pressures, make these insects well-suited for studying local adaptation. Here, we analyzed genome-wide sequence data from two widespread bumble bees, Bombus vosnesenskii and Bombus vancouverensis, using multiple environmental association analysis methods to investigate climate adaptation across latitude and altitude. The strongest signatures of selection were observed in B. vancouverensis, but despite unique responses between species for most loci, we detected several shared responses. Genes relating to neural and neuromuscular function and ion transport were especially evident with respect to temperature variables, while genes relating to cuticle formation, tracheal and respiratory system development, and homeostasis were associated with precipitation variables. Our data thus suggest that adaptive responses for tolerating abiotic variation are likely to be complex, but that several parallels among species can emerge even for these complex traits and landscapes. Results provide the framework for future work into mechanisms of thermal and desiccation tolerance in bumble bees and a set of genomic targets that might be monitored for future conservation efforts.
Collapse
Affiliation(s)
- Jason M Jackson
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
| | - Meaghan L Pimsler
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
| | - Kennan J Oyen
- Department of Zoology & Physiology and Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - James P Strange
- Department of Entomology, The Ohio State University, Columbus, OH, USA
| | - Michael E Dillon
- Department of Zoology & Physiology and Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Jeffrey D Lozier
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
| |
Collapse
|