1
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Wragg D, Eynard SE, Basso B, Canale‐Tabet K, Labarthe E, Bouchez O, Bienefeld K, Bieńkowska M, Costa C, Gregorc A, Kryger P, Parejo M, Pinto MA, Bidanel J, Servin B, Le Conte Y, Vignal A. Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones. Mol Ecol Resour 2022; 22:3068-3086. [PMID: 35689802 PMCID: PMC9796960 DOI: 10.1111/1755-0998.13665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 01/07/2023]
Abstract
Honey bee subspecies originate from specific geographical areas in Africa, Europe and the Middle East, and beekeepers interested in specific phenotypes have imported genetic material to regions outside of the bees' original range for use either in pure lines or controlled crosses. Moreover, imported drones are present in the environment and mate naturally with queens from the local subspecies. The resulting admixture complicates population genetics analyses, and population stratification can be a major problem for association studies. To better understand Western European honey bee populations, we produced a whole genome sequence and single nucleotide polymorphism (SNP) genotype data set from 870 haploid drones and demonstrate its utility for the identification of nine genetic backgrounds and various degrees of admixture in a subset of 629 samples. Five backgrounds identified correspond to subspecies, two to isolated populations on islands and two to managed populations. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long and represents 21% of chromosome 11, with two major haplotypes corresponding to the two dominant genetic backgrounds identified. This large naturally phased data set is available as a single vcf file that can now serve as a reference for subsequent populations genomics studies in the honey bee, such as (i) selecting individuals of verified homogeneous genetic backgrounds as references, (ii) imputing genotypes from a lower-density data set generated by an SNP-chip or by low-pass sequencing, or (iii) selecting SNPs compatible with the requirements of genotyping chips.
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Affiliation(s)
- David Wragg
- GenPhySEUniversité de Toulouse, INRAE, INPT, INP‐ENVTCastanet TolosanFrance,Roslin InstituteUniversity of EdinburghMidlothianUK
| | - Sonia E. Eynard
- GenPhySEUniversité de Toulouse, INRAE, INPT, INP‐ENVTCastanet TolosanFrance
| | - Benjamin Basso
- Institut de l'abeille (ITSAP), UMT PrADEAvignonFrance,INRAE, UR 406 Abeilles et Environment, UMT PrADEAvignonFrance
| | | | | | | | | | | | - Cecilia Costa
- CREA Research Centre for Agriculture and EnvironmentBolognaItaly
| | - Aleš Gregorc
- Faculty of Agriculture and Life SciencesUniversity of MariborPivolaSlovenia
| | - Per Kryger
- Department of Agroecology, Science and TechnologyAarhus UniversitySlagelseDenmark
| | - Melanie Parejo
- Agroscope, Swiss Bee Research CentreBernSwitzerland,Applied Genomics and Bioinformatics, Department of Genetics, Physical Anthropology and Animal PhysiologyUniversity of the Basque CountryLeioaSpain
| | - M. Alice Pinto
- Centro de Investigação de Montanha (CIMO)Instituto Politécnico de BragançaBragançaPortugal
| | | | - Bertrand Servin
- GenPhySEUniversité de Toulouse, INRAE, INPT, INP‐ENVTCastanet TolosanFrance
| | - Yves Le Conte
- INRAE, UR 406 Abeilles et Environment, UMT PrADEAvignonFrance
| | - Alain Vignal
- GenPhySEUniversité de Toulouse, INRAE, INPT, INP‐ENVTCastanet TolosanFrance
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2
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Cohen ZP, Chen YH, Groves R, Schoville SD. Evidence of hard‐selective sweeps suggests independent adaptation to insecticides in Colorado potato beetle (Coleoptera: Chrysomelidae) populations. Evol Appl 2022; 15:1691-1705. [DOI: 10.1111/eva.13498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Zachary P. Cohen
- Department of Entomology University of Wisconsin‐Madison Madison Wisconsin USA
| | - Yolanda H. Chen
- Department of Plant and Soil Sciences University of Vermont Burlington Vermont USA
| | - Russell Groves
- Department of Entomology University of Wisconsin‐Madison Madison Wisconsin USA
| | - Sean D. Schoville
- Department of Entomology University of Wisconsin‐Madison Madison Wisconsin USA
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3
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Wall JD, Robinson JA, Cox LA. High-Resolution Estimates of Crossover and Noncrossover Recombination from a Captive Baboon Colony. Genome Biol Evol 2022; 14:evac040. [PMID: 35325119 PMCID: PMC9048888 DOI: 10.1093/gbe/evac040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2022] [Indexed: 11/17/2022] Open
Abstract
Homologous recombination has been extensively studied in humans and a handful of model organisms. Much less is known about recombination in other species, including nonhuman primates. Here, we present a study of crossovers (COs) and noncrossover (NCO) recombination in olive baboons (Papio anubis) from two pedigrees containing a total of 20 paternal and 17 maternal meioses, and compare these results to linkage disequilibrium (LD) based recombination estimates from 36 unrelated olive baboons. We demonstrate how COs, combined with LD-based recombination estimates, can be used to identify genome assembly errors. We also quantify sex-specific differences in recombination rates, including elevated male CO and reduced female CO rates near telomeres. Finally, we add to the increasing body of evidence suggesting that while most NCO recombination tracts in mammals are short (e.g., <500 bp), there is a non-negligible fraction of longer (e.g., >1 kb) NCO tracts. For NCO tracts shorter than 10 kb, we fit a mixture of two (truncated) geometric distributions model to the NCO tract length distribution and estimate that >99% of all NCO tracts are very short (mean 24 bp), but the remaining tracts can be quite long (mean 4.3 kb). A single geometric distribution model for NCO tract lengths is incompatible with the data, suggesting that LD-based methods for estimating NCO recombination rates that make this assumption may need to be modified.
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Affiliation(s)
- Jeffrey D. Wall
- Institute for Human Genetics, University of California San Francisco, USA
| | | | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, USA
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4
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Waiker P, de Abreu FCP, Luna-Lucena D, Freitas FCP, Simões ZLP, Rueppell O. Recombination mapping of the Brazilian stingless bee Frieseomelitta varia confirms high recombination rates in social hymenoptera. BMC Genomics 2021; 22:673. [PMID: 34536998 PMCID: PMC8449902 DOI: 10.1186/s12864-021-07987-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/04/2021] [Indexed: 11/26/2022] Open
Abstract
Background Meiotic recombination is a fundamental genetic process that shuffles allele combinations and promotes accurate segregation of chromosomes. Analyses of the ubiquitous variation of recombination rates within and across species suggest that recombination is evolving adaptively. All studied insects with advanced eusociality have shown exceptionally high recombination rates, which may represent a prominent case of adaptive evolution of recombination. However, our understanding of the relationship between social evolution and recombination rates is incomplete, partly due to lacking empirical data. Here, we present a linkage map of the monandrous, advanced eusocial Brazilian stingless bee, Frieseomelitta varia, providing the first recombination analysis in the diverse Meliponini (Hymenoptera, Apidae). Results Our linkage map includes 1417 markers in 19 linkage groups. This map spans approximately 2580 centimorgans, and comparisons to the physical genome assembly indicate that it covers more than 75 % of the 275 Megabasepairs (Mbp) F. varia genome. Thus, our study results in a genome-wide recombination rate estimate of 9.3–12.5 centimorgan per Mbp. This value is higher than estimates from nonsocial insects and comparable to other highly social species, although it does not support our prediction that monandry and strong queen-worker caste divergence of F. varia lead to even higher recombination rates than other advanced eusocial species. Conclusions Our study expands the association between elevated recombination and sociality in the order Hymenoptera and strengthens the support for the hypothesis that advanced social evolution in hymenopteran insects invariably selects for high genomic recombination rates. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07987-3.
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Affiliation(s)
- Prashant Waiker
- Biology Department, University of North Carolina at Greensboro, 321 McIver St, Greensboro, NC, 27412, USA.
| | - Fabiano Carlos Pinto de Abreu
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, SP, Ribeirão Preto, Brazil
| | - Danielle Luna-Lucena
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Flávia Cristina Paula Freitas
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.,Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG, Brazil
| | - Zilá Luz Paulino Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, SP, Ribeirão Preto, Brazil
| | - Olav Rueppell
- Biology Department, University of North Carolina at Greensboro, 321 McIver St, Greensboro, NC, 27412, USA.,Department of Biological Sciences, University of Alberta, AB, T6G 2E9, Edmonton, Canada
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5
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Fruciano C, Franchini P, Jones JC. Capturing the rapidly evolving study of adaptation. J Evol Biol 2021; 34:856-865. [PMID: 34145685 DOI: 10.1111/jeb.13871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 11/30/2022]
Abstract
Research on the genomics of adaptation is rapidly changing. In the last few decades, progress in this area has been driven by methodological advances, not only in the way increasingly large amounts of molecular data are generated (e.g. with high-throughput sequencing), but also in the way these data are analysed. This includes a growing appreciation and quantitative treatment of covariation among units within the same data type (e.g. genes) or across data types (e.g. genes and phenotypes). The development and adoption of more and more integrative tools have resulted in richer and more interesting empirical work. This special issue - comprising methodological, empirical, and review papers - aims to capture a 'snapshot' of this rapidly evolving field. We discuss in particular three important themes in the study of adaptation: the genetic architecture of adaptive variation, protein-coding and regulatory changes, and parallel evolution. We highlight how more traditional key themes in the study of genetic architecture (e.g. the number of loci underlying adaptive traits and the distribution of their effects) are now being complemented by other factors (e.g. how patterns of linkage and number of loci interact to affect the ability to adapt). Similarly, apart from addressing the relative importance of protein-coding and regulatory changes, we now have the tools to look in-depth at specific types of regulatory variation to gain a clearer picture of regulatory networks. Finally, parallel evolution has always been central to the study of adaptation, but now we are often able to address the question of whether - and to what extent - parallelism at the organismal or phenotypic level is matched by parallelism at the genetic level. Perhaps most importantly, we can now determine what mechanisms are driving parallelism (or lack thereof) across levels of biological organization. All these recent methodological developments open up new directions for future studies of adaptive changes across traits, levels of biological organization, demographic contexts and time scales.
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Affiliation(s)
- Carmelo Fruciano
- National Research Council - Institute of Marine Biological Resources and Biotechnologies, Messina, Italy.,Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, PSL Université Paris, Paris, France.,School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Julia C Jones
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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6
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Kelemen EP, Rehan SM. Conservation insights from wild bee genetic studies: Geographic differences, susceptibility to inbreeding, and signs of local adaptation. Evol Appl 2021; 14:1485-1496. [PMID: 34178099 PMCID: PMC8210791 DOI: 10.1111/eva.13221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/19/2021] [Accepted: 03/07/2021] [Indexed: 12/12/2022] Open
Abstract
Conserving bees are critical both ecologically and economically. Genetic tools are valuable for monitoring these vital pollinators since tracking these small, fast-flying insects by traditional means is difficult. By surveying the current state of the literature, this review discusses how recent advances in landscape genetic and genomic research are elucidating how wild bees respond to anthropogenic threats. Current literature suggests that there may be geographic differences in the vulnerability of bee species to landscape changes. Populations of temperate bee species are becoming more isolated and more genetically depauperate as their landscape becomes more fragmented, but tropical bee species appear unaffected. These differences may be an artifact of historical differences in land-use, or it suggests that different management plans are needed for temperate and tropical bee species. Encouragingly, genetic studies on invasive bee species indicate that low levels of genetic diversity may not lead to rapid extinction in bees as once predicted. Additionally, next-generation sequencing has given researchers the power to identify potential genes under selection, which are likely critical to species' survival in their rapidly changing environment. While genetic studies provide insights into wild bee biology, more studies focusing on a greater phylogenetic and life-history breadth of species are needed. Therefore, caution should be taken when making broad conservation decisions based on the currently few species examined.
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7
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Schrader L, Pan H, Bollazzi M, Schiøtt M, Larabee FJ, Bi X, Deng Y, Zhang G, Boomsma JJ, Rabeling C. Relaxed selection underlies genome erosion in socially parasitic ant species. Nat Commun 2021; 12:2918. [PMID: 34006882 PMCID: PMC8131649 DOI: 10.1038/s41467-021-23178-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/06/2021] [Indexed: 02/03/2023] Open
Abstract
Inquiline ants are highly specialized and obligate social parasites that infiltrate and exploit colonies of closely related species. They have evolved many times convergently, are often evolutionarily young lineages, and are almost invariably rare. Focusing on the leaf-cutting ant genus Acromyrmex, we compared genomes of three inquiline social parasites with their free-living, closely-related hosts. The social parasite genomes show distinct signatures of erosion compared to the host lineages, as a consequence of relaxed selective constraints on traits associated with cooperative ant colony life and of inquilines having very small effective population sizes. We find parallel gene losses, particularly in olfactory receptors, consistent with inquiline species having highly reduced social behavioral repertoires. Many of the genomic changes that we uncover resemble those observed in the genomes of obligate non-social parasites and intracellular endosymbionts that branched off into highly specialized, host-dependent niches.
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Affiliation(s)
- Lukas Schrader
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
| | | | - Martin Bollazzi
- Entomología, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Fredrick J Larabee
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | | | - Guojie Zhang
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Christian Rabeling
- Department of Biology, University of Rochester, Rochester, NY, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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8
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Christmas MJ, Jones JC, Olsson A, Wallerman O, Bunikis I, Kierczak M, Peona V, Whitley KM, Larva T, Suh A, Miller-Struttmann NE, Geib JC, Webster MT. Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics. Mol Biol Evol 2021; 38:3126-3143. [PMID: 33823537 PMCID: PMC8321533 DOI: 10.1093/molbev/msab086] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Evidence is accumulating that gene flow commonly occurs between recently diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to gene flow and how such barriers form. Here, we compare genetic differentiation across the genomes of bumblebee species living in sympatry and allopatry to reveal the potential impact of gene flow during species divergence and uncover genetic barrier loci. We first compared the genomes of the alpine bumblebee Bombus sylvicola and a previously unidentified sister species living in sympatry in the Rocky Mountains, revealing prominent islands of elevated genetic divergence in the genome that colocalize with centromeres and regions of low recombination. This same pattern is observed between the genomes of another pair of closely related species living in allopatry (B. bifarius and B. vancouverensis). Strikingly however, the genomic islands exhibit significantly elevated absolute divergence (dXY) in the sympatric, but not the allopatric, comparison indicating that they contain loci that have acted as barriers to historical gene flow in sympatry. Our results suggest that intrinsic barriers to gene flow between species may often accumulate in regions of low recombination and near centromeres through processes such as genetic hitchhiking, and that divergence in these regions is accentuated in the presence of gene flow.
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Affiliation(s)
- Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Julia C Jones
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Valentina Peona
- Department of Organismal Biology-Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Kaitlyn M Whitley
- Department of Biology, Appalachian State University, Boone, NC, USA.,U.S. Department of Agriculture, Agriculture Research Service, Charleston, SC, USA
| | - Tuuli Larva
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Alexander Suh
- Department of Organismal Biology-Systematic Biology, Uppsala University, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | | | - Jennifer C Geib
- Department of Biology, Appalachian State University, Boone, NC, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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9
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Calfee E, Agra MN, Palacio MA, Ramírez SR, Coop G. Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas. PLoS Genet 2020; 16:e1009038. [PMID: 33075065 PMCID: PMC7595643 DOI: 10.1371/journal.pgen.1009038] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/29/2020] [Accepted: 08/09/2020] [Indexed: 02/07/2023] Open
Abstract
Recent biological invasions offer 'natural' laboratories to understand the genetics and ecology of adaptation, hybridization, and range limits. One of the most impressive and well-documented biological invasions of the 20th century began in 1957 when Apis mellifera scutellata honey bees swarmed out of managed experimental colonies in Brazil. This newly-imported subspecies, native to southern and eastern Africa, both hybridized with and out-competed previously-introduced European honey bee subspecies. Populations of scutellata-European hybrid honey bees rapidly expanded and spread across much of the Americas in less than 50 years. We use broad geographic sampling and whole genome sequencing of over 300 bees to map the distribution of scutellata ancestry where the northern and southern invasions have presently stalled, forming replicated hybrid zones with European bee populations in California and Argentina. California is much farther from Brazil, yet these hybrid zones occur at very similar latitudes, consistent with the invasion having reached a climate barrier. At these range limits, we observe genome-wide clines for scutellata ancestry, and parallel clines for wing length that span hundreds of kilometers, supporting a smooth transition from climates favoring scutellata-European hybrid bees to climates where they cannot survive winter. We find no large effect loci maintaining exceptionally steep ancestry transitions. Instead, we find most individual loci have concordant ancestry clines across South America, with a build-up of somewhat steeper clines in regions of the genome with low recombination rates, consistent with many loci of small effect contributing to climate-associated fitness trade-offs. Additionally, we find no substantial reductions in genetic diversity associated with rapid expansions nor complete dropout of scutellata ancestry at any individual loci on either continent, which suggests that the competitive fitness advantage of scutellata ancestry at lower latitudes has a polygenic basis and that scutellata-European hybrid bees maintained large population sizes during their invasion. To test for parallel selection across continents, we develop a null model that accounts for drift in ancestry frequencies during the rapid expansion. We identify several peaks within a larger genomic region where selection has pushed scutellata ancestry to high frequency hundreds of kilometers past the present cline centers in both North and South America and that may underlie high-fitness traits driving the invasion.
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Affiliation(s)
- Erin Calfee
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | | | - María Alejandra Palacio
- Instituto Nacional de Tecnología Agropecuaria (INTA), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad de Mar del Plata, Balcarce, Argentina
| | - Santiago R. Ramírez
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Graham Coop
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
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10
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DeLory T, Funderburk K, Miller K, Smith WZ, McPherson S, Pirk CW, Costa C, Teixeira ÉW, Dahle B, Rueppell O. Local Variation in Recombination Rates of the Honey Bee ( Apis mellifera) Genome among Samples from Six Disparate Populations. INSECTES SOCIAUX 2020; 67:127-138. [PMID: 33311731 PMCID: PMC7732154 DOI: 10.1007/s00040-019-00736-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Meiotic recombination is an essential component of eukaryotic sexual reproduction but its frequency varies within and between genomes. Although it is well-established that honey bees have a high recombination rate with about 20 cM/Mbp, the proximate and ultimate causes of this exceptional rate are poorly understood. Here, we describe six linkage maps of the Western Honey Bee Apis mellifera that were produced with consistent methodology from samples from distinct parts of the species' near global distribution. We compared the genome-wide rates and distribution of meiotic crossovers among the six maps and found considerable differences. Overall similarity of local recombination rates among our samples was unrelated to geographic or phylogenetic distance of the populations that our samples were derived from. However, the limited sampling constrains the interpretation of our results because it is unclear how representative these samples are. In contrast to previous studies, we found only in two datasets a significant relation between local recombination rate and GC content. Focusing on regions of particularly increased or decreased recombination in specific maps, we identified several enriched gene ontologies in these regions and speculate about their local adaptive relevance. These data are contributing to an increasing comparative effort to gain an understanding of the intra-specific variability of recombination rates and their evolutionary role in honey bees and other social insects.
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Affiliation(s)
- Timothy DeLory
- Department of Biology, University of North Carolina at Greensboro, NC, USA
- Current address: Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT, USA
| | - Karen Funderburk
- Department of Biology, University of North Carolina at Greensboro, NC, USA
- Current address: Applied Mathematics for the Life & Social Sciences, College of Liberal Arts and Sciences, Arizona State University, Tempe, AZ, USA
| | - Katelyn Miller
- Department of Biology, University of North Carolina at Greensboro, NC, USA
| | | | - Samantha McPherson
- Department of Biology, University of North Carolina at Greensboro, NC, USA
- Current address: Current address: NCSU Department of Entomology & Plant Pathology, Campus Box 7613, 100 Derieux Place, Raleigh, NC, USA
| | - Christian W. Pirk
- Social Insects Research Group, Department of Zoology & Entomology, University of Pretoria, South Africa
| | - Cecilia Costa
- Consiglio per la Ricerca in Agricolturae l’Analisi dell’Economia Agraria, Via Po, 14 - 00198 Rome, Italy
| | - Érica Weinstein Teixeira
- Honey Bee Health Specialized Laboratory, Biological Institute, São Paulo State Agribusiness Technology Agency, Av. Prof. Manoel César Ribeiro, 1920, Pindamonhangaba, São Paulo 12411-010, Brazil
| | - Bjørn Dahle
- Norwegian Beekeepers Association, Kløfta, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, NC, USA
- Corresponding author: 312 Eberhart Bldg, 321 McIver Street, Greensboro NC 27403, USA. Phone: (+1) 336-2562591,
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11
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Brand P, Hinojosa-Díaz IA, Ayala R, Daigle M, Yurrita Obiols CL, Eltz T, Ramírez SR. The evolution of sexual signaling is linked to odorant receptor tuning in perfume-collecting orchid bees. Nat Commun 2020; 11:244. [PMID: 31932598 PMCID: PMC6957680 DOI: 10.1038/s41467-019-14162-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/18/2019] [Indexed: 12/16/2022] Open
Abstract
Sexual signaling is an important reproductive barrier known to evolve early during the formation of new species, but the genetic mechanisms that facilitate the divergence of sexual signals remain elusive. Here we isolate a gene linked to the rapid evolution of a signaling trait in a pair of nascent neotropical orchid bee lineages, Euglossa dilemma and E. viridissima. Male orchid bees acquire chemical compounds from their environment to concoct species-specific perfumes to later expose during courtship. We find that the two lineages acquire chemically distinct perfumes and are reproductively isolated despite low levels of genome-wide differentiation. Remarkably, variation in perfume chemistry coincides with rapid divergence in few odorant receptor (OR) genes. Using functional assays, we demonstrate that the derived variant of Or41 in E. dilemma is specific towards its species-specific major perfume compound, whereas the ancestral variant in E. viridissima is broadly tuned to multiple odorants. Our results show that OR evolution likely played a role in the divergence of sexual communication in natural populations.
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Affiliation(s)
- Philipp Brand
- Department of Evolution and Ecology, Center for Population Biology, University of California, 1 Shields Avenue, 95616, Davis, California, USA.
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, 1230 York Avenue, 10065, New York, New York, USA.
| | - Ismael A Hinojosa-Díaz
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n Ciudad Universitaria Delegación Coyoacán, Apartado Postal 70-153, Ciudad de México, 04510, Mexico
| | - Ricardo Ayala
- Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 21, San Patricio, Jalisco, 48980, Mexico
| | - Michael Daigle
- Department of Evolution and Ecology, Center for Population Biology, University of California, 1 Shields Avenue, 95616, Davis, California, USA
| | - Carmen L Yurrita Obiols
- Centro de Estudios Conservacionistas, Universidad de San Carlos de Guatemala, Avenida La Reforma, 0-63, Guatemala, 01000, Guatemala
| | - Thomas Eltz
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Santiago R Ramírez
- Department of Evolution and Ecology, Center for Population Biology, University of California, 1 Shields Avenue, 95616, Davis, California, USA.
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