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Schneller NM, Strugnell JM, Field MA, Johannesson K, Cooke I. Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments. Mol Ecol 2025:e17776. [PMID: 40342214 DOI: 10.1111/mec.17776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 04/01/2025] [Accepted: 04/14/2025] [Indexed: 05/11/2025]
Abstract
Major threats to marine species and ecosystems include overfishing, invasive species, pollution and climate change. The changing climate not only imposes direct threats through the impacts of severe marine heatwaves, cyclones and ocean acidification but also complicates fisheries and invasive species management by driving species range shifts. The dynamic nature of these threats means that the future of our oceans will depend on the ability of species to adapt. This has led to calls for genetic interventions focussed on enhancing species' adaptive capacity, including translocations, restocking and selective breeding. Assessing the benefits and risks of such approaches requires an improved understanding of the genetic architecture of adaptive variation, not only in relation to climate-resilient phenotypes but also locally adapted populations and the fitness of hybrids. Large structural genetic variants such as chromosomal inversions play an important role in local adaptation by linking multiple adaptive loci. Consequently, inversions are likely to be particularly important when managing for adaptive capacity. However, under some circumstances, they also accumulate deleterious mutations, potentially increasing the risk of inbreeding depression. Genetic management that takes account of these dual roles on fitness is likely to be more effective at ensuring population persistence. We summarise evolutionary factors influencing adaptive and deleterious variation of inversions, review inversions found in marine taxa, and provide a framework to predict the consequences of ignoring inversions in key management scenarios. We conclude by describing practical methods to bridge the gap between evolutionary theory and practical application of inversions in conservation.
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Affiliation(s)
- Nadja M Schneller
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Jan M Strugnell
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- Securing Antarctica's Environmental Future, James Cook University, Townsville, Queensland, Australia
| | - Matt A Field
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Ira Cooke
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Securing Antarctica's Environmental Future, James Cook University, Townsville, Queensland, Australia
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2
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Ravagni S, Montero-Mendieta S, Leonard JA, Webster MT, Christmas MJ, Bunikis I, Rodríguez-Teijeiro JD, Sanchez-Donoso I, Vilà C. Large Inversions Shape Diversification and Genome Evolution in Common Quails. Mol Ecol 2025; 34:e17740. [PMID: 40183764 DOI: 10.1111/mec.17740] [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: 07/01/2024] [Revised: 03/05/2025] [Accepted: 03/10/2025] [Indexed: 04/05/2025]
Abstract
Chromosomal inversions, by suppressing recombination, can profoundly shape genome evolution and drive adaptation. In the common quail (Coturnix coturnix), a highly mobile bird with a vast Palearctic breeding range, we previously identified a massive inversion on chromosome 1 associated with distinct phenotypes and restricted geographic distribution. Here, using a new de novo genome assembly, we characterise this inversion and uncover additional, ancient structural variation on chromosome 2 that segregates across the species' range: either two putatively linked inversions or a single, large inversion that appears as two due to scaffolding limitations. Together, the inversions encompass a remarkable 15.6% of the quail genome (153.6 Mbp), creating highly divergent haplotypes that diverged over a million years ago. While the chromosome 1 inversion is linked to phenotypic differences, including morphology and migratory behaviour, the chromosome 2 inversion(s) show no such association. Notably, all inversion regions exhibit reduced effective population size and a relaxation of purifying selection, evidenced by elevated nonsynonymous-to-synonymous substitution ratios (N/S). This suggests that inversions, particularly the geographically restricted one on chromosome 1, may act as engines of diversification, accelerating the accumulation of functional variation and potentially contributing to local adaptation, especially within isolated island populations. Our findings demonstrate how large-scale chromosomal rearrangements can compartmentalise a genome, fostering distinct evolutionary trajectories within a single, highly mobile species.
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Affiliation(s)
- Sara Ravagni
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Seville, Spain
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome La Sapienza, Rome, Italy
| | - Santiago Montero-Mendieta
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Seville, Spain
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, National Genomics Infrastructure Hosted by SciLifeLab, Uppsala, Sweden
| | | | - Ines Sanchez-Donoso
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Seville, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Seville, Spain
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3
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Jiang J, Chen JF, Li XT, Wang L, Mao JF, Wang BS, Guo YL. Incorporating genetic load contributes to predicting Arabidopsis thaliana's response to climate change. Nat Commun 2025; 16:2752. [PMID: 40113777 PMCID: PMC11926394 DOI: 10.1038/s41467-025-58021-z] [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: 10/30/2023] [Accepted: 03/06/2025] [Indexed: 03/22/2025] Open
Abstract
Understanding how species respond to climate change can facilitate species conservation and crop breeding. Current prediction frameworks about population vulnerability focused on predicting range shifts or local adaptation but ignored genetic load, which is also crucial for adaptation. By analyzing 1115 globally distributed Arabidopsis thaliana natural accessions, we find that effective population size (Ne) is the major contributor of genetic load variation, both along genome and among populations, and can explain 74-94% genetic load variation in natural populations. Intriguingly, Ne affects genetic load by changing both effectiveness of purifying selection and GC biased gene conversion strength. In particular, by incorporating genetic load, genetic offset and species distribution models (SDM), we predict that, the populations at species' range edge are generally at higher risk. The populations at the eastern range perform poorer in all aspects, southern range have higher genetic offset and lower SDM suitability, while northern range have higher genetic load. Among the diverse natural populations, the Yangtze River basin population is the most vulnerable population under future climate change. Overall, here we deciphered the driving forces of genetic load in A. thaliana, and incorporated SDM, local adaptation and genetic load to predict the fate of populations under future climate change.
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Affiliation(s)
- Juan Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Fu Chen
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Tong Li
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li Wang
- Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jian-Feng Mao
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Bao-Sheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ya-Long Guo
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- China National Botanical Garden, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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4
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Li G, Ren Y, Yang Y, Chen S, Zheng J, Zhang X, Li J, Chen M, Sun X, Lv C, Li X, Zhang B, Sun X, Li Y, Zhao M, Dong C, Tang J, Huang Z, Peng Y, Gu D, Wang Z, Zheng H, Shi C, Kang G, Zheng T, Chen F, Wang D, Zhang K, Yin G. Genomic analysis of Zhou8425B, a key founder parent, reveals its genetic contributions to elite agronomic traits in wheat breeding. PLANT COMMUNICATIONS 2025; 6:101222. [PMID: 39690740 PMCID: PMC11956103 DOI: 10.1016/j.xplc.2024.101222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/14/2024] [Accepted: 12/12/2024] [Indexed: 12/19/2024]
Abstract
High-quality genome information is essential for efficiently deciphering and improving crop traits. Here, we report a highly contiguous and accurate hexaploid genome assembly for the key wheat breeding parent Zhou8425B, an elite 1BL/1RS translocation line with durable adult plant resistance (APR) against yellow rust (YR) disease. By integrating HiFi and Hi-C sequencing reads, we have generated a 14.75-Gb genome assembly for Zhou8425B with a contig N50 of 70.94 and a scaffold N50 of 735.11 Mb. Comparisons with previously sequenced common wheat cultivars shed light on structural changes in the 1RS chromosome arm, which has been extensively used in wheat improvement. Interestingly, Zhou8425B 1RS carries more genes encoding AP2/ERF-ERF or B3 transcription factors than its counterparts in four previously sequenced wheat and rye genotypes. The Zhou8425B genome assembly aided in the fine mapping of a new APR locus (YrZH3BS) that confers resistance to YR disease and promotes grain yield under field conditions. Notably, pyramiding YrZH3BS with two previously characterized APR loci (YrZH22 and YrZH84) can further reduce YR severity and enhance grain yield, with the triple combination (YrZH3B + YrZH22 + YrZH84) having the greatest effect. Finally, the founder genotype effects of Zhou8425B were explored using publicly available genome resequencing data, which reveals the presence of important Zhou8425B genomic blocks in its derivative cultivars. Our data demonstrate the value of the Zhou8425B genome assembly for further study of the structural and functional characteristics of 1RS, the genetic basis of durable YR resistance, and founder genotype effects in wheat breeding. Our resources will facilitate the development of elite wheat cultivars through genomics-assisted breeding.
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Affiliation(s)
- Guangwei Li
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Yan Ren
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Yuxin Yang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Shulin Chen
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Jizhou Zheng
- Henan Fengdekang Seed Industry Co., Ltd, Zhengzhou 450001, China
| | - Xiaoqing Zhang
- National Agro-Tech Extension and Service Center, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Junlong Li
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Mengen Chen
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Xiaonan Sun
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Chunlei Lv
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Xiaode Li
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Bingbing Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Xiao Sun
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Yujia Li
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Mingtian Zhao
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Chunhao Dong
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Jianwei Tang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Zhenpu Huang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Yanyan Peng
- Henan Fengdekang Seed Industry Co., Ltd, Zhengzhou 450001, China
| | - Dengbin Gu
- Henan Fengdekang Seed Industry Co., Ltd, Zhengzhou 450001, China
| | - Zhiyong Wang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Hongyuan Zheng
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Cuilan Shi
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Guozhang Kang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China
| | - Tiancun Zheng
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China; Henan Fengdekang Seed Industry Co., Ltd, Zhengzhou 450001, China
| | - Feng Chen
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China.
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China.
| | - Kunpu Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China.
| | - Guihong Yin
- State Key Laboratory of Wheat and Maize Crop Science, Henan Center for Crop Genomics and Rice Engineering, College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou 450046, China; National Wheat Engineering Research Center, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China.
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5
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De-Kayne R, Gordon IJ, Terblanche RF, Collins S, Saitoti Omufwoko K, Martins DJ, Martin SH. Incomplete recombination suppression fuels extensive haplotype diversity in a butterfly colour pattern supergene. PLoS Biol 2025; 23:e3003043. [PMID: 40019922 PMCID: PMC11918383 DOI: 10.1371/journal.pbio.3003043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Revised: 03/18/2025] [Accepted: 01/28/2025] [Indexed: 03/19/2025] Open
Abstract
Supergenes can evolve when recombination-suppressing mechanisms like inversions promote co-inheritance of alleles at two or more polymorphic loci that affect a complex trait. Theory shows that such genetic architectures can be favoured under balancing selection or local adaptation in the face of gene flow, but they can also bring costs associated with reduced opportunities for recombination. These costs may in turn be offset by rare 'gene flux' between inverted and ancestral haplotypes, with a range of possible outcomes. We aimed to shed light on these processes by investigating the 'BC supergene', a large genomic region comprising multiple rearrangements associated with three distinct wing colour morphs in Danaus chrysippus, a butterfly known as the African monarch, African queen and plain tiger. Using whole-genome resequencing data from 174 individuals, we first confirm the effects of BC on wing colour pattern: background melanism is associated with SNPs in the promoter region of yellow, within an inverted subregion of the supergene, while forewing tip pattern is most likely associated with copy-number variation in a separate subregion of the supergene. We then show that haplotype diversity within the supergene is surprisingly extensive: there are at least six divergent haplotype groups that experience suppressed recombination with respect to each other. Despite high divergence between these haplotype groups, we identify an unexpectedly large number of natural recombinant haplotypes. Several of the inferred crossovers occurred between adjacent inversion 'modules', while others occurred within inversions. Furthermore, we show that new haplotype groups have arisen through recombination between two pre-existing ones. Specifically, an allele for dark colouration in the promoter of yellow has recombined into distinct haplotype backgrounds on at least two separate occasions. Overall, our findings paint a picture of dynamic evolution of supergene haplotypes, fuelled by incomplete recombination suppression.
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Affiliation(s)
- Rishi De-Kayne
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Ian J. Gordon
- Centre of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye, Rwanda
| | - Reinier F. Terblanche
- Department of Conservation Ecology & Entomology, University of Stellenbosch, Stellenbosch, South Africa
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | - Kennedy Saitoti Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Dino J. Martins
- Turkana Basin Institute, Stony Brook University, Stony Brook, New York, United States of America
- Mpala Research Centre, Nanyuki, Kenya
| | - Simon H. Martin
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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6
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Huang K, Ostevik KL, Jahani M, Todesco M, Bercovich N, Andrew RL, Owens GL, Rieseberg LH. Inversions contribute disproportionately to parallel genomic divergence in dune sunflowers. Nat Ecol Evol 2025; 9:325-335. [PMID: 39633041 PMCID: PMC11807836 DOI: 10.1038/s41559-024-02593-4] [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: 04/19/2024] [Accepted: 10/30/2024] [Indexed: 12/07/2024]
Abstract
The probability of parallel genetic evolution is a function of the strength of selection and constraints imposed by genetic architecture. Inversions capture locally adapted alleles and suppress recombination between them, which limits the range of adaptive responses. In addition, the combined phenotypic effect of alleles within inversions is likely to be greater than that of individual alleles; this should further increase the contributions of inversions to parallel evolution. We tested the hypothesis that inversions contribute disproportionately to parallel genetic evolution in independent dune ecotypes of Helianthus petiolaris. We analysed habitat data and identified variables underlying parallel habitat shifts. Genotype-environment association analyses of these variables indicated parallel responses of inversions to shared selective pressures. We also confirmed larger seed size across the dunes and performed quantitative trait locus mapping with multiple crosses. Quantitative trait loci shared between locations fell into inversions more than expected by chance. We used whole-genome sequencing data to identify selective sweeps in the dune ecotypes and found that the majority of shared swept regions were found within inversions. Phylogenetic analyses of shared regions indicated that within inversions, the same allele typically was found in the dune habitat at both sites. These results confirm predictions that inversions drive parallel divergence in the dune ecotypes.
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Affiliation(s)
- Kaichi Huang
- School of Ecology, Sun Yat-sen University, Shenzhen, China.
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Kate L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA.
| | - Mojtaba Jahani
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco Todesco
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada
| | - Natalia Bercovich
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rose L Andrew
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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7
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Wilkinson MJ, McLay K, Kainer D, Elphinstone C, Dillon NL, Webb M, Wijesundara UK, Ali A, Bally ISE, Munyengwa N, Furtado A, Henry RJ, Hardner CM, Ortiz-Barrientos D. Centromeres are hotspots for chromosomal inversions and breeding traits in mango. THE NEW PHYTOLOGIST 2025; 245:899-913. [PMID: 39548673 DOI: 10.1111/nph.20252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 10/15/2024] [Indexed: 11/18/2024]
Abstract
Chromosomal inversions can preserve combinations of favorable alleles by suppressing recombination. Simultaneously, they reduce the effectiveness of purifying selection enabling deleterious alleles to accumulate. This study explores how areas of low recombination, including centromeric regions and chromosomal inversions, contribute to the accumulation of deleterious and favorable loci in 225 Mangifera indica genomes from the Australian Mango Breeding Program. Here, we identify 17 chromosomal inversions that cover 7.7% (29.7 Mb) of the M. indica genome: eight pericentric (inversion includes the centromere) and nine paracentric (inversion is on one arm of the chromosome). Our results show that these large pericentric inversions are accumulating deleterious loci, while the paracentric inversions show deleterious levels above and below the genome wide average. We find that despite their deleterious load, chromosomal inversions contain small effect loci linked to variation in crucial breeding traits. These results indicate that chromosomal inversions have likely facilitated the evolution of key mango breeding traits. Our study has important implications for selective breeding of favorable combinations of alleles in regions of low recombination.
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Affiliation(s)
- Melanie J Wilkinson
- School of the Environment, The University of Queensland, Brisbane, Qld, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Qld, 4072, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Kathleen McLay
- School of the Environment, The University of Queensland, Brisbane, Qld, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - David Kainer
- School of the Environment, The University of Queensland, Brisbane, Qld, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Natalie L Dillon
- Queensland Department of Agriculture and Fisheries, Mareeba, Qld, 4880, Australia
| | - Matthew Webb
- Queensland Department of Agriculture and Fisheries, Brisbane, Qld, 4001, Australia
| | - Upendra K Wijesundara
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Asjad Ali
- Queensland Department of Agriculture and Fisheries, Mareeba, Qld, 4880, Australia
| | - Ian S E Bally
- Queensland Department of Agriculture and Fisheries, Mareeba, Qld, 4880, Australia
| | - Norman Munyengwa
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Robert J Henry
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Qld, 4072, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Craig M Hardner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of the Environment, The University of Queensland, Brisbane, Qld, 4072, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Qld, 4072, Australia
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8
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Nocchi G, Whiting JR, Yeaman S. Repeated global adaptation across plant species. Proc Natl Acad Sci U S A 2024; 121:e2406832121. [PMID: 39705310 DOI: 10.1073/pnas.2406832121] [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: 04/04/2024] [Accepted: 11/09/2024] [Indexed: 12/22/2024] Open
Abstract
Global adaptation occurs when all populations of a species undergo selection toward a common optimum. This can occur by a hard selective sweep with the emergence of a new globally advantageous allele that spreads throughout a species' natural range until reaching fixation. This evolutionary process leaves a temporary trace in the region affected, which is detectable using population genomic methods. While selective sweeps have been identified in many species, there have been few comparative and systematic studies of the genes involved in global adaptation. Building upon recent findings showing repeated genetic basis of local adaptation across independent populations and species, we asked whether certain genes play a more significant role in driving global adaptation across plant species. To address this question, we scanned the genomes of 17 plant species to identify signals of repeated global selective sweeps. Despite the substantial evolutionary distance between the species analyzed, we identified several gene families with strong evidence of repeated positive selection. These gene families tend to be enriched for reduced pleiotropy, consistent with predictions from Fisher's evolutionary model and the cost of complexity hypothesis. We also found that genes with repeated sweeps exhibit elevated levels of gene duplication. Our findings contrast with recent observations of increased pleiotropy in genes driving local adaptation, consistent with predictions based on the theory of migration-selection balance.
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Affiliation(s)
- Gabriele Nocchi
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Samuel Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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9
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Mykhailenko A, Zieliński P, Bednarz A, Schlyter F, Andersson MN, Antunes B, Borowski Z, Krokene P, Melin M, Morales-García J, Müller J, Nowak Z, Schebeck M, Stauffer C, Viiri H, Zaborowska J, Babik W, Nadachowska-Brzyska K. Complex Genomic Landscape of Inversion Polymorphism in Europe's Most Destructive Forest Pest. Genome Biol Evol 2024; 16:evae263. [PMID: 39656753 DOI: 10.1093/gbe/evae263] [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: 11/15/2024] [Revised: 11/29/2024] [Accepted: 12/02/2024] [Indexed: 12/17/2024] Open
Abstract
In many species, polymorphic genomic inversions underlie complex phenotypic polymorphisms and facilitate local adaptation in the face of gene flow. Multiple polymorphic inversions can co-occur in a genome, but the prevalence, evolutionary significance, and limits to complexity of genomic inversion landscapes remain poorly understood. Here, we examine genome-wide genetic variation in one of Europe's most destructive forest pests, the spruce bark beetle Ips typographus, scan for polymorphic inversions, and test whether inversions are associated with key traits in this species. We analyzed 240 individuals from 18 populations across the species' European range and, using a whole-genome resequencing approach, identified 27 polymorphic inversions covering ∼28% of the genome. The inversions vary in size and in levels of intra-inversion recombination, are highly polymorphic across the species range, and often overlap, forming a complex genomic architecture. We found no support for mechanisms such as directional selection, overdominance, and associative overdominance that are often invoked to explain the presence of large inversion polymorphisms in the genome. This suggests that inversions are either neutral or maintained by the combined action of multiple evolutionary forces. We also found that inversions are enriched in odorant receptor genes encoding elements of recognition pathways for host plants, mates, and symbiotic fungi. Our results indicate that the genome of this major forest pest of growing social, political, and economic importance harbors one of the most complex inversion landscapes described to date and raise questions about the limits of intraspecific genomic architecture complexity.
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Affiliation(s)
- Anastasiia Mykhailenko
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-348 Kraków, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
| | - Aleksandra Bednarz
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
| | - Fredrik Schlyter
- Chemical Ecology, Department of Plant Protection Biology, Swedish University of Agricultural Sciences Alnarp, 234 22 Lomma, Sweden
- ETM, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, 165 00 Praha, Czechia
| | | | - Bernardo Antunes
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
| | - Zbigniew Borowski
- Departament of Forest Ecology, Forest Research Institute, 05-090 Raszyn, Poland
| | - Paal Krokene
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, 1433 Ås, Norway
| | - Markus Melin
- Forest Health and Bidiversity Group, Natural Resources Institute Finland, 80100 Joensuu, Finland
| | - Julia Morales-García
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-348 Kraków, Poland
| | - Jörg Müller
- Field Station Fabrikschleichach, Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, 96181 Rauhenebrach, Germany
- Bavarian Forest National Park, 94481 Grafenau, Germany
| | - Zuzanna Nowak
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
| | - Martin Schebeck
- Institute of Forest Entomology, Forest Pathology and Forest Protection, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Christian Stauffer
- Institute of Forest Entomology, Forest Pathology and Forest Protection, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Heli Viiri
- UPM Forest, UPM-Kymmene, 33100 Tampere, Finland
| | - Julia Zaborowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland
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10
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Meyer L, Barry P, Riquet F, Foote A, Der Sarkissian C, Cunha RL, Arbiol C, Cerqueira F, Desmarais E, Bordes A, Bierne N, Guinand B, Gagnaire PA. Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse. Mol Ecol 2024; 33:e17277. [PMID: 38279695 DOI: 10.1111/mec.17277] [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: 06/20/2023] [Revised: 12/18/2023] [Accepted: 01/04/2024] [Indexed: 01/28/2024]
Abstract
Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine-lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome-level genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked-read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo-overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation.
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Affiliation(s)
- Laura Meyer
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Pierre Barry
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto, Vairão, Portugal
| | | | - Andrew Foote
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Clio Der Sarkissian
- Centre for Anthropobiology and Genomics of Toulouse, CNRS, University of Toulouse Paul Sabatier, Toulouse, France
| | - Regina L Cunha
- Centre of Marine Sciences-CCMAR, University of Algarve, Faro, Portugal
| | | | | | - Erick Desmarais
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Anaïs Bordes
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Bruno Guinand
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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11
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Liao X, Xie D, Bao T, Hou M, Li C, Nie B, Sun S, Peng D, Hu H, Wang H, Tao Y, Zhang Y, Li W, Wang L. Inversions encounter relaxed genetic constraints and balance birth and death of TPS genes in Curcuma. Nat Commun 2024; 15:9349. [PMID: 39472560 PMCID: PMC11522489 DOI: 10.1038/s41467-024-53719-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 10/21/2024] [Indexed: 11/02/2024] Open
Abstract
Evolutionary dynamics of inversion and its impact on biochemical traits are a puzzling question. Here, we show abundance of inversions in three Curcuma species (turmeric, hidden ginger and Siam tulip). Genes within inversions display higher long terminal repeat content and lower expression level compared with genomic background, suggesting inversions in Curcuma experience relaxed genetic constraints. It is corroborated by depletion of selected SNPs and enrichment of deleterious mutations in inversions detected among 56 Siam tulip cultivars. Functional verification of tandem duplicated terpene synthase (TPS) genes reveals that genes within inversions become pseudogenes, while genes outside retain catalytic function. Our findings suggest that inversions act as a counteracting force against tandem duplication in balancing birth and death of TPS genes and modulating terpenoid contents in Curcuma. This study provides an empirical example that inversions are likely not adaptive but affect biochemical traits.
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Affiliation(s)
- Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Dejin Xie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Tingting Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Mengmeng Hou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Bao Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Shichao Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Haixiao Hu
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yongfu Tao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yu Zhang
- School of Agriculture, Sun Yat-sen University, Shenzhen, 518107, China
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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12
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Jamsandekar M, Ferreira MS, Pettersson ME, Farrell ED, Davis BW, Andersson L. The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring. Nat Commun 2024; 15:9136. [PMID: 39443489 PMCID: PMC11499932 DOI: 10.1038/s41467-024-53079-7] [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: 10/26/2023] [Accepted: 09/26/2024] [Indexed: 10/25/2024] Open
Abstract
Chromosomal inversions are associated with local adaptation in many species. However, questions regarding how they are formed, maintained and impact various other evolutionary processes remain elusive. Here, using a large genomic dataset of long-read and short-read sequencing, we ask these questions in one of the most abundant vertebrates on Earth, the Atlantic herring. This species has four megabase-sized inversions associated with ecological adaptation that correlate with water temperature. The S and N inversion alleles at these four loci dominate in the southern and northern parts, respectively, of the species distribution in the North Atlantic Ocean. By determining breakpoint coordinates of the four inversions and the structural variations surrounding them, we hypothesize that these inversions are formed by ectopic recombination between duplicated sequences immediately outside of the inversions. We show that these are old inversions (>1 MY), albeit formed after the split between the Atlantic herring and its sister species, the Pacific herring. There is evidence for extensive gene flux between inversion alleles at all four loci. The large Ne of herring combined with the common occurrence of opposite homozygotes across the species distribution has allowed effective purifying selection to prevent the accumulation of genetic load and repeats within the inversions.
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Affiliation(s)
- Minal Jamsandekar
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, USA
| | - Mafalda S Ferreira
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mats E Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, USA
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, USA.
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
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13
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Zhang J, Schneller NM, Field MA, Chan CX, Miller DJ, Strugnell JM, Riginos C, Bay L, Cooke I. Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef. Mol Ecol 2024; 33:e17468. [PMID: 39046252 DOI: 10.1111/mec.17468] [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: 04/17/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/25/2024]
Abstract
The future survival of coral reefs in the Anthropocene depends on the capacity of corals to adapt as oceans warm and extreme weather events become more frequent. Targeted interventions designed to assist evolutionary processes in corals require a comprehensive understanding of the distribution and structure of standing variation, however, efforts to map genomic variation in corals have so far focussed almost exclusively on SNPs, overlooking structural variants that have been shown to drive adaptive processes in other taxa. Here, we show that the reef-building coral, Acropora kenti, harbours at least five large, highly polymorphic structural variants, all of which exhibit signatures of strongly suppressed recombination in heterokaryotypes, a feature commonly associated with chromosomal inversions. Based on their high minor allele frequency, uniform distribution across habitats and elevated genetic load, we propose that these inversions in A. kenti are likely to be under balancing selection. An excess of SNPs with high impact on protein-coding genes within these loci elevates their importance both as potential targets for adaptive selection and as contributors to genetic decline if coral populations become fragmented or inbred in future.
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Affiliation(s)
- Jia Zhang
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Nadja M Schneller
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Matt A Field
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Miller
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Jan M Strugnell
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Cynthia Riginos
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Line Bay
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Ira Cooke
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
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14
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Mee JA, Carson B, Yeaman S. Conditionally Deleterious Mutation Load Accumulates in Genomic Islands of Local Adaptation but Can Be Purged with Sufficient Genotypic Redundancy. Am Nat 2024; 204:43-54. [PMID: 38857343 DOI: 10.1086/730186] [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] [Indexed: 06/12/2024]
Abstract
AbstractLocal adaptation frequently evolves in patches or environments that are connected via migration. In these cases, genomic regions that are linked to a locally adapted locus experience reduced effective migration rates. Via individual-based simulations of a two-patch system, we show that this reduced effective migration results in the accumulation of conditionally deleterious mutations, but not universally deleterious mutations, adjacent to adaptive loci. When there is redundancy in the genetic basis of local adaptation (i.e., genotypic redundancy), turnover of locally adapted polymorphisms allows conditionally deleterious mutation load to be purged. The amount of mutational load that accumulates adjacent to locally adapted loci is dependent on redundancy, recombination rate, migration rate, population size, strength of selection, and the phenotypic effect size of adaptive alleles. Our results highlight the need to be cautious when interpreting patterns of local adaptation at the level of phenotype or fitness, as the genetic basis of local adaptation can be transient, and evolution may confer a degree of maladaptation to nonlocal environments.
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15
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Zhang T, Peng W, Xiao H, Cao S, Chen Z, Su X, Luo Y, Liu Z, Peng Y, Yang X, Jiang GF, Xu X, Ma Z, Zhou Y. Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1408-1426. [PMID: 38578160 DOI: 10.1111/jipb.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/04/2024] [Indexed: 04/06/2024]
Abstract
Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.
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Affiliation(s)
- Tianhao Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenjing Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhuyifu Chen
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiangnian Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Yuanyuan Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiping Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Guo-Feng Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
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16
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Bock DG, Baeckens S, Kolbe JJ, Losos JB. When adaptation is slowed down: Genomic analysis of evolutionary stasis in thermal tolerance during biological invasion in a novel climate. Mol Ecol 2024; 33:e17075. [PMID: 37489260 DOI: 10.1111/mec.17075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/25/2023] [Accepted: 07/04/2023] [Indexed: 07/26/2023]
Abstract
Research conducted during the past two decades has demonstrated that biological invasions are excellent models of rapid evolution. Even so, characteristics of invasive populations such as a short time for recombination to assemble optimal combinations of alleles may occasionally limit adaptation to new environments. Here, we investigated such genetic constraints to adaptation in the invasive brown anole (Anolis sagrei)-a tropical ectotherm that was introduced to the southeastern United States, a region with a much colder climate than in its native Caribbean range. We examined thermal physiology for 30 invasive populations and tested for a climatic cline in cold tolerance. Also, we used genomics to identify mechanisms that may limit adaptation. We found no support for a climatic cline, indicating that thermal tolerance did not shift adaptively. Concomitantly, population genomic results were consistent with the occurrence of recombination cold spots that comprise more than half of the genome and maintain long-range associations among alleles in invasive populations. These genomic regions overlap with both candidate thermal tolerance loci that we identified using a standard genome-wide association test. Moreover, we found that recombination cold spots do not have a large contribution to population differentiation in the invasive range, contrary to observations in the native range. We suggest that limited recombination is constraining the contribution of large swaths of the genome to adaptation in invasive brown anoles. Our study provides an example of evolutionary stasis during invasion and highlights the possibility that reduced recombination occasionally slows down adaptation in invasive populations.
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Affiliation(s)
- Dan G Bock
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Simon Baeckens
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Evolution and Optics of Nanostructures Lab, Department of Biology, Ghent University, Ghent, Belgium
- Functional Morphology Lab, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Jason J Kolbe
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Jonathan B Losos
- Department of Biology, Washington University, St. Louis, Missouri, USA
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17
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Charlesworth B. The fitness consequences of genetic divergence between polymorphic gene arrangements. Genetics 2024; 226:iyad218. [PMID: 38147527 PMCID: PMC11090464 DOI: 10.1093/genetics/iyad218] [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: 10/15/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023] Open
Abstract
Inversions restrict recombination when heterozygous with standard arrangements, but often have few noticeable phenotypic effects. Nevertheless, there are several examples of inversions that can be maintained polymorphic by strong selection under laboratory conditions. A long-standing model for the source of such selection is divergence between arrangements with respect to recessive or partially recessive deleterious mutations, resulting in a selective advantage to heterokaryotypic individuals over homokaryotypes. This paper uses a combination of analytical and numerical methods to investigate this model, for the simple case of an autosomal inversion with multiple independent nucleotide sites subject to mildly deleterious mutations. A complete lack of recombination in heterokaryotypes is assumed, as well as constancy of the frequency of the inversion over space and time. It is shown that a significantly higher mutational load will develop for the less frequent arrangement. A selective advantage to heterokaryotypes is only expected when the two alternative arrangements are nearly equal in frequency, so that their mutational loads are very similar in size. The effects of some Drosophila pseudoobscura polymorphic inversions on fitness traits seem to be too large to be explained by this process, although it may contribute to some of the observed effects. Several population genomic statistics can provide evidence for signatures of a reduced efficacy of selection associated with the rarer of two arrangements, but there is currently little published data that are relevant to the theoretical predictions.
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Affiliation(s)
- Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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18
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Hu H, Scheben A, Wang J, Li F, Li C, Edwards D, Zhao J. Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:544-554. [PMID: 37961986 PMCID: PMC10893937 DOI: 10.1111/pbi.14224] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.
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Affiliation(s)
- Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Fangping Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Centre for Crop & Food Innovation, Food Futures Institute, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - David Edwards
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
- Australia & Centre for Applied BioinformaticsUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
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19
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Hill J, Enbody ED, Bi H, Lamichhaney S, Lei W, Chen J, Wei C, Liu Y, Schwochow D, Younis S, Widemo F, Andersson L. Low Mutation Load in a Supergene Underpinning Alternative Male Mating Strategies in Ruff (Calidris pugnax). Mol Biol Evol 2023; 40:msad224. [PMID: 37804117 DOI: 10.1093/molbev/msad224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves 2 rare inversion haplotypes (satellite and faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (independent) haplotype indicates that the inversion could be as old as 4 million years. Here, we have constructed a highly contiguous genome assembly of the inversion region for both the independent and satellite haplotypes. Based on the new data, we estimate that the recombination event(s) creating the satellite haplotype occurred only about 70,000 yr ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the satellite and faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N (CENPN) gene is disrupted by the inversion and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.
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Affiliation(s)
- Jason Hill
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Huijuan Bi
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Sangeet Lamichhaney
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Biological Sciences, Kent State University, Kent, OH 44241, USA
| | - Weipan Lei
- Key Laboratory for Biodiversity Science and Ecological Engineering, National Demonstration Center for Experimental Life Sciences and Biotechnology Education, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
| | - Juexin Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Chentao Wei
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Doreen Schwochow
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Division of Immunology and Rheumatology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Fredrik Widemo
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
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20
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Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. How chromosomal inversions reorient the evolutionary process. J Evol Biol 2023; 36:1761-1782. [PMID: 37942504 DOI: 10.1111/jeb.14242] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.
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Affiliation(s)
- Emma L Berdan
- Bioinformatics Core, Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Nicholas H Barton
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Roger Butlin
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Ecology and Evolutionary Biology, School of Bioscience, The University of Sheffield, Sheffield, UK
| | - Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Rui Faria
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Inês Fragata
- CHANGE - Global Change and Sustainability Institute/Animal Biology Department, cE3c - Center for Ecology, Evolution and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | | | - Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Martin Kapun
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- Central Research Laboratories, Natural History Museum of Vienna, Vienna, Austria
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Claire Mérot
- UMR 6553 Ecobio, Université de Rennes, OSUR, CNRS, Rennes, France
| | - Esra Durmaz Mitchell
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anja M Westram
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Stephen W Schaeffer
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kerstin Johannesson
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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21
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Huang K, Jahani M, Gouzy J, Legendre A, Carrere S, Lázaro-Guevara JM, González Segovia EG, Todesco M, Mayjonade B, Rodde N, Cauet S, Dufau I, Staton SE, Pouilly N, Boniface MC, Tapy C, Mangin B, Duhnen A, Gautier V, Poncet C, Donnadieu C, Mandel T, Hübner S, Burke JM, Vautrin S, Bellec A, Owens GL, Langlade N, Muños S, Rieseberg LH. The genomics of linkage drag in inbred lines of sunflower. Proc Natl Acad Sci U S A 2023; 120:e2205783119. [PMID: 36972449 PMCID: PMC10083583 DOI: 10.1073/pnas.2205783119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/18/2022] [Indexed: 03/29/2023] Open
Abstract
Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here, we analyzed the genomic and phenotypic impacts of wild introgressions in inbred lines of cultivated sunflower to estimate the impacts of linkage drag. First, we generated reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge-regression best linear unbiased prediction (BLUP) model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including >3,000 new genes. While introgressions reduced genetic load at protein-coding sequences, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low-frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.
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Affiliation(s)
- Kaichi Huang
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Mojtaba Jahani
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Alexandra Legendre
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Sébastien Carrere
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - José Miguel Lázaro-Guevara
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Eric Gerardo González Segovia
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Marco Todesco
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Baptiste Mayjonade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Nathalie Rodde
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Stéphane Cauet
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Isabelle Dufau
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - S. Evan Staton
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Research and Development Department, NRGene Canada Inc., Saskatoon, SKS7N 3R3, Canada
| | - Nicolas Pouilly
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Marie-Claude Boniface
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Camille Tapy
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Brigitte Mangin
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Alexandra Duhnen
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Véronique Gautier
- Gentyane Genomic Platform, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Clermont Ferrand, 63000France
| | - Charles Poncet
- Gentyane Genomic Platform, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Clermont Ferrand, 63000France
| | - Cécile Donnadieu
- Plateforme Génome et Transcriptome (GeT-PlaGe), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Tali Mandel
- MIGAL Galilee Research Institute, Tel-Hai Academic College, Upper Galilee, 11016Israel
| | - Sariel Hübner
- MIGAL Galilee Research Institute, Tel-Hai Academic College, Upper Galilee, 11016Israel
| | - John M. Burke
- Department of Plant Biology, University of Georgia, Athens, GA30602
| | - Sonia Vautrin
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Arnaud Bellec
- Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326France
| | - Gregory L. Owens
- Department of Biology, University of Victoria, Victoria, BCV8W 2Y2, Canada
| | - Nicolas Langlade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Stéphane Muños
- Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326France
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
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22
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Harringmeyer OS, Hoekstra HE. Chromosomal inversion polymorphisms shape the genomic landscape of deer mice. Nat Ecol Evol 2022; 6:1965-1979. [PMID: 36253543 PMCID: PMC9715431 DOI: 10.1038/s41559-022-01890-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/17/2022] [Indexed: 12/15/2022]
Abstract
Chromosomal inversions are an important form of structural variation that can affect recombination, chromosome structure and fitness. However, because inversions can be challenging to detect, the prevalence and hence the significance of inversions segregating within species remains largely unknown, especially in natural populations of mammals. Here, by combining population-genomic and long-read sequencing analyses in a single, widespread species of deer mouse (Peromyscus maniculatus), we identified 21 polymorphic inversions that are large (1.5-43.8 Mb) and cause near-complete suppression of recombination when heterozygous (0-0.03 cM Mb-1). We found that inversion breakpoints frequently occur in centromeric and telomeric regions and are often flanked by long inverted repeats (0.5-50 kb), suggesting that they probably arose via ectopic recombination. By genotyping inversions in populations across the species' range, we found that the inversions are often widespread and do not harbour deleterious mutational loads, and many are likely to be maintained as polymorphisms by divergent selection. Comparisons of forest and prairie ecotypes of deer mice revealed 13 inversions that contribute to differentiation between populations, of which five exhibit significant associations with traits implicated in local adaptation. Taken together, these results show that inversion polymorphisms have a significant impact on recombination, genome structure and genetic diversity in deer mice and likely facilitate local adaptation across the widespread range of this species.
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Affiliation(s)
- Olivia S Harringmeyer
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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