1
|
Foster LJ, Tsvetkov N, McAfee A. Mechanisms of Pathogen and Pesticide Resistance in Honey Bees. Physiology (Bethesda) 2024; 39:0. [PMID: 38411571 DOI: 10.1152/physiol.00033.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024] Open
Abstract
Bees are the most important insect pollinators of the crops humans grow, and Apis mellifera, the Western honey bee, is the most commonly managed species for this purpose. In addition to providing agricultural services, the complex biology of honey bees has been the subject of scientific study since the 18th century, and the intricate behaviors of honey bees and ants, fellow hymenopterans, inspired much sociobiological inquest. Unfortunately, honey bees are constantly exposed to parasites, pathogens, and xenobiotics, all of which pose threats to their health. Despite our curiosity about and dependence on honey bees, defining the molecular mechanisms underlying their interactions with biotic and abiotic stressors has been challenging. The very aspects of their physiology and behavior that make them so important to agriculture also make them challenging to study, relative to canonical model organisms. However, because we rely on A. mellifera so much for pollination, we must continue our efforts to understand what ails them. Here, we review major advancements in our knowledge of honey bee physiology, focusing on immunity and detoxification, and highlight some challenges that remain.
Collapse
Affiliation(s)
- Leonard J Foster
- Department of Biochemistry and Molecular Biology and Michael Smith LaboratoriesUniversity of British Columbia, Vancouver, British Columbia, Canada
| | - Nadejda Tsvetkov
- Department of Biochemistry and Molecular Biology and Michael Smith LaboratoriesUniversity of British Columbia, Vancouver, British Columbia, Canada
| | - Alison McAfee
- Department of Biochemistry and Molecular Biology and Michael Smith LaboratoriesUniversity of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
2
|
Obšteter J, Strachan LK, Bubnič J, Prešern J, Gorjanc G. SIMplyBee: an R package to simulate honeybee populations and breeding programs. Genet Sel Evol 2023; 55:31. [PMID: 37161307 PMCID: PMC10169377 DOI: 10.1186/s12711-023-00798-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/31/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND The Western honeybee is an economically important species globally, but has been experiencing colony losses that lead to economical damage and decreased genetic variability. This situation is spurring additional interest in honeybee breeding and conservation programs. Stochastic simulators are essential tools for rapid and low-cost testing of breeding programs and methods, yet no existing simulator allows for a detailed simulation of honeybee populations. Here we describe SIMplyBee, a holistic simulator of honeybee populations and breeding programs. SIMplyBee is an R package and hence freely available for installation from CRAN http://cran.r-project.org/package=SIMplyBee . IMPLEMENTATION SIMplyBee builds upon the stochastic simulator AlphaSimR that simulates individuals with their corresponding genomes and quantitative genetic values. To enable honeybee-specific simulations, we extended AlphaSimR by developing classes for global simulation parameters, SimParamBee, for a honeybee colony, Colony, and multiple colonies, MultiColony. We also developed functions to address major honeybee specificities: honeybee genome, haplodiploid inheritance, social organisation, complementary sex determination, polyandry, colony events, and quantitative genetics at the individual- and colony-levels. RESULTS We describe its implementation for simulating a honeybee genome, creating a honeybee colony and its members, addressing haplodiploid inheritance and complementary sex determination, simulating colony events, creating and managing multiple colonies at the same time, and obtaining genomic data and honeybee quantitative genetics. Further documentation, available at http://www.SIMplyBee.info , provides details on these operations and describes additional operations related to genomics, quantitative genetics, and other functionalities. DISCUSSION SIMplyBee is a holistic simulator of honeybee populations and breeding programs. It simulates individual honeybees with their genomes, colonies with colony events, and individual- and colony-level genetic and breeding values. Regarding the latter, SIMplyBee takes a user-defined function to combine individual- into colony-level values and hence allows for modeling any type of interaction within a colony. SIMplyBee provides a research platform for testing breeding and conservation strategies and their effect on future genetic gain and genetic variability. Future developments of SIMplyBee will focus on improving the simulation of honeybee genomes, optimizing the simulator's performance, and including spatial awareness in mating functions and phenotype simulation. We invite the honeybee genetics and breeding community to join us in the future development of SIMplyBee.
Collapse
Affiliation(s)
- Jana Obšteter
- Department of Animal Science, The Agricultural Institute of Slovenia, Ljubljana, Slovenia.
| | - Laura K Strachan
- The Roslin Institute and Royal (Dick) School of Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
| | - Jernej Bubnič
- Department of Animal Science, The Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - Janez Prešern
- Department of Animal Science, The Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
- Biotechnical Faculty, Department of Animal Science, The University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
3
|
Buswell VG, Ellis JS, Huml JV, Wragg D, Barnett MW, Brown A, Knight ME. When One's Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression in Apis mellifera mellifera. INSECTS 2023; 14:insects14050421. [PMID: 37233049 DOI: 10.3390/insects14050421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023]
Abstract
The human management of honey bees (Apis mellifera) has resulted in the widespread introduction of subspecies outside of their native ranges. One well known example of this is Apis mellifera mellifera, native to Northern Europe, which has now been significantly introgressed by the introduction of C lineage honey bees. Introgression has consequences for species in terms of future adaptive potential and long-term viability. However, estimating introgression in colony-living haplodiploid species is challenging. Previous studies have estimated introgression using individual workers, individual drones, multiple drones, and pooled workers. Here, we compare introgression estimates via three genetic approaches: SNP array, individual RAD-seq, and pooled colony RAD-seq. We also compare two statistical approaches: a maximum likelihood cluster program (ADMIXTURE) and an incomplete lineage sorting model (ABBA BABA). Overall, individual approaches resulted in lower introgression estimates than pooled colonies when using ADMIXTURE. However, the pooled colony ABBA BABA approach resulted in generally lower introgression estimates than all three ADMIXTURE estimates. These results highlight that sometimes one individual is not enough to assess colony-level introgression, and future studies that do use colony pools should not be solely dependent on clustering programs for introgression estimates.
Collapse
Affiliation(s)
- Victoria G Buswell
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
| | - Jonathan S Ellis
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - J Vanessa Huml
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - David Wragg
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Mark W Barnett
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Andrew Brown
- B4, Newton Farm Metherell, Cornwall, Callington PL17 8DQ, UK
| | - Mairi E Knight
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| |
Collapse
|
4
|
Sokół R, Michalczyk M. A Preliminary Study on “Personalised Treatment” against Varroa destructor Infestations in Honey Bee (Apis mellifera) Colonies. Animals (Basel) 2023; 13:ani13060987. [PMID: 36978527 PMCID: PMC10044234 DOI: 10.3390/ani13060987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
The requirement for the protection of bee colonies against Varroa destructor invasions has been noted by many breeders and is included as an aspect of the development of beekeeping. This research aimed to check the effect of the development of a colony exposed to laying eggs (brood surface) by queen bees with similar chemical potential (sisters) on the effect of a preparation combating V. destructor depending on the number of mites found in a given colony. We chose this as a standard model of conduct that treats each bee colony as one organism subjected to individual parasite control. For this purpose, we created a bee colony with a mother-of-one breeding line and fertilised drones from one colony. Infection with V. destructor occurred naturally and uncontrollably. Without interfering with the colony’s development, the frame insulator helped each colony’s brood (mothers’ reproductive potential) and the initial and final individuals from the mites themselves. The study was carried out in four species (two control species and two species with up to 20 and over 21 mites, respectively). Treatments with amitraz to combat damage were divided into four treatment subgroups: two treatments every four days or four treatments every two days. We observed the number of individuals that were protected in all subgroups in the average brood area. The reproductive potential of the sisters’ mothers did not change after the treatments with amitraz, which indicated that amitraz did not affect the delegation of egg laying. The invasion rate was also tracked relative to the control group, which allowed us to conclude that a two-time treatment with amitraz reduced the frequency of mites and a four-time treatment checked the effectiveness. Tailoring the control of V. destructor in bee colonies may be an effective measure in the fight against this parasite.
Collapse
|
5
|
Guichard M, Dainat B, Dietemann V. Prospects, challenges and perspectives in harnessing natural selection to solve the ‘varroa problem’ of honey bees. Evol Appl 2023; 16:593-608. [PMID: 36969141 PMCID: PMC10035043 DOI: 10.1111/eva.13533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/24/2023] Open
Abstract
Honey bees, Apis mellifera, of European origin are major pollinators of crops and wild flora. Their endemic and exported populations are threatened by a variety of abiotic and biotic factors. Among the latter, the ectoparasitic mite Varroa destructor is the most important single cause behind colony mortality. The selection of mite resistance in honey bee populations has been deemed a more sustainable solution to its control than varroacidal treatments. Because natural selection has led to the survival of some European and African honey bee populations to V. destructor infestations, harnessing its principles has recently been highlighted as a more efficient way to provide honey bee lineages that survive infestations when compared with conventional selection on resistance traits against the parasite. However, the challenges and drawbacks of harnessing natural selection to solve the varroa problem have only been minimally addressed. We argue that failing to consider these issues could lead to counterproductive results, such as increased mite virulence, loss of genetic diversity reducing host resilience, population collapses or poor acceptance by beekeepers. Therefore, it appears timely to evaluate the prospects for the success of such programmes and the qualities of the populations obtained. After reviewing the approaches proposed in the literature and their outcomes, we consider their advantages and drawbacks and propose perspectives to overcome their limitations. In these considerations, we not only reflect on the theoretical aspects of host-parasite relationships but also on the currently largely neglected practical constraints, that is, the requirements for productive beekeeping, conservation or rewilding objectives. To optimize natural selection-based programmes towards these objectives, we suggest designs based on a combination of nature-driven phenotypic differentiation and human-directed selection of traits. Such a dual strategy aims at allowing field-realistic evolutionary approaches towards the survival of V. destructor infestations and the improvement of honey bee health.
Collapse
Affiliation(s)
| | | | - Vincent Dietemann
- Swiss Bee Research Centre Agroscope Bern Switzerland
- Department of Ecology and Evolution, Biophore, UNIL‐Sorge University of Lausanne Lausanne Switzerland
| |
Collapse
|
6
|
Huang Q, Sim SB, Geib SM, Childers A, Liu J, Wei X, Han W, Posada-Florez F, Xue AZ, Li Z, Evans JD. Identification of sex chromosomes and primary sex ratio in the small hive beetle, a worldwide parasite of honey bees. Gigascience 2022; 12:giad056. [PMID: 37489752 PMCID: PMC10367126 DOI: 10.1093/gigascience/giad056] [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: 02/08/2023] [Revised: 04/20/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND The small hive beetle (SHB), Aethina tumida, has emerged as a worldwide threat to honey bees in the past two decades. These beetles harvest nest resources, feed on larval bees, and ultimately spoil nest resources with gelatinous slime together with the fungal symbiont Kodamaea ohmeri. RESULTS Here, we present the first chromosome-level genome assembly for the SHB. With a 99.1% representation of conserved (BUSCO) arthropod genes, this resource enables the study of chemosensory, digestive, and detoxification traits critical for SHB success and possible control. We use this annotated assembly to characterize features of SHB sex chromosomes and a female-skewed primary sex ratio. We also found chromosome fusion and a lower recombination rate in sex chromosomes than in autosomes. CONCLUSIONS Genome-enabled insights will clarify the traits that allowed this beetle to exploit hive resources successfully and will be critical for determining the causes of observed sex ratio asymmetries.
Collapse
Affiliation(s)
- Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, 330045, Nanchang, China
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sheina B Sim
- Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research, USDA, Agricultural Research Service, Hilo, HI 96720, USA
| | - Scott M Geib
- Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research, USDA, Agricultural Research Service, Hilo, HI 96720, USA
| | - Anna Childers
- Beltsville Agricultural Research Center, Bee Research Laboratory, USDA, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Junfeng Liu
- Periodicals Agency, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Xiuxiu Wei
- Honeybee Research Institute, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Wensu Han
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Francisco Posada-Florez
- Beltsville Agricultural Research Center, Bee Research Laboratory, USDA, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Allen Z Xue
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Zheng Li
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jay D Evans
- Beltsville Agricultural Research Center, Bee Research Laboratory, USDA, Agricultural Research Service, Beltsville, MD 20705, USA
| |
Collapse
|
7
|
Avalos A, Bilodeau L. Russian honey bee genotype identification through enhanced marker panel set. FRONTIERS IN INSECT SCIENCE 2022; 2:998310. [PMID: 38468798 PMCID: PMC10926385 DOI: 10.3389/finsc.2022.998310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/14/2022] [Indexed: 03/13/2024]
Abstract
Russian honey bees (RHB) are a breeding population developed by USDA-ARS as an effort to provide Varroa-resistant honey bees to beekeepers. The selection strategy for this breeding population was the first in honey bees to incorporate genetic stock identification (GSI). The original GSI approach has been in use for over a decade, and though effective, novel technologies and analytical approaches recently developed provide an opportunity for improvement. Here we outline a novel genotyping assay that capitalizes on the markers used in the GSI as well as new loci recently identified in a whole genome pooled study of commercial honey bee stocks. Our approach utilizes a microfluidic platform and machine learning analyses to arrive at an accurate, high throughput assay. This novel approach provides an improved tool that can be readily incorporated into breeding decisions towards healthier more productive bees.
Collapse
Affiliation(s)
- Arian Avalos
- Honey Bee Breeding, Genetics, and Physiology Research Laboratory, USDA-ARS, Baton Rouge, LA, United States
| | | |
Collapse
|
8
|
Sless TJL, Searle JB, Danforth BN. Genome of the bee Holcopasites calliopsidis—a species showing the common apid trait of brood parasitism. G3 GENES|GENOMES|GENETICS 2022; 12:6619165. [PMID: 35762966 PMCID: PMC9339306 DOI: 10.1093/g3journal/jkac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/31/2022] [Indexed: 11/22/2022]
Abstract
Brood parasites represent a substantial but often poorly studied fraction of the wider diversity of bees. Brood parasitic bees complete their life cycles by infiltrating the nests of solitary host bees thereby enabling their offspring to exploit the food provisions intended for the host’s offspring. Here, we present the draft assembly of the bee Holcopasites calliopsidis, the first brood parasitic species to be the subject of detailed genomic analysis. Consistent with previous findings on the genomic signatures of parasitism more broadly, we find that H. calliopsidis has the smallest genome currently known among bees (179 Mb). This small genome does not appear to be the result of purging of repetitive DNA, with some indications of novel repetitive elements which may show signs of recent expansion. Nor does H. calliopsidis demonstrate any apparent net loss of genic content in comparison with nonparasitic species, though many individual gene families do show significant contractions. Although the basis of the small genome size of this species remains unclear, the identification of over 12,000 putative genes—with functional annotation for nearly 10,000 of these—is an important step in investigating the genomic basis of brood parasitism and provides a valuable dataset to be compared against new genomes that remain to be sequenced.
Collapse
Affiliation(s)
- Trevor J L Sless
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, NY 14853, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, NY 14853, USA
| | - Bryan N Danforth
- Department of Entomology, Cornell University , Ithaca, NY 14853, USA
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Page RE. Societies to genes: can we get there from here? Genetics 2021; 219:6330772. [PMID: 34849914 PMCID: PMC8633090 DOI: 10.1093/genetics/iyab104] [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: 01/22/2021] [Accepted: 07/01/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the organization and evolution of social complexity is a major task because it requires building an understanding of mechanisms operating at different levels of biological organization from genes to social interactions. I discuss here, a unique forward genetic approach spanning more than 30 years beginning with human-assisted colony-level selection for a single social trait, the amount of pollen honey bees (Apis mellifera L.) store. The goal was to understand a complex social trait from the social phenotype to genes responsible for observed trait variation. The approach combined the results of colony-level selection with detailed studies of individual behavior and physiology resulting in a mapped, integrated phenotypic architecture composed of correlative relationships between traits spanning anatomy, physiology, sensory response systems, and individual behavior that affect individual foraging decisions. Colony-level selection reverse engineered the architecture of an integrated phenotype of individuals resulting in changes in the social trait. Quantitative trait locus (QTL) studies combined with an exceptionally high recombination rate (60 kb/cM), and a phenotypic map, provided a genotype-phenotype map of high complexity demonstrating broad QTL pleiotropy, epistasis, and epistatic pleiotropy suggesting that gene pleiotropy or tight linkage of genes within QTL integrated the phenotype. Gene expression and knockdown of identified positional candidates revealed genes affecting foraging behavior and confirmed one pleiotropic gene, a tyramine receptor, as a target for colony-level selection that was under selection in two different tissues in two different life stages. The approach presented here has resulted in a comprehensive understanding of the structure and evolution of honey bee social organization.
Collapse
Affiliation(s)
- Robert E Page
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA.,Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| |
Collapse
|
11
|
Bernstein R, Du M, Hoppe A, Bienefeld K. Simulation studies to optimize genomic selection in honey bees. Genet Sel Evol 2021; 53:64. [PMID: 34325663 PMCID: PMC8323320 DOI: 10.1186/s12711-021-00654-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/07/2021] [Indexed: 12/04/2022] Open
Abstract
Background With the completion of a single nucleotide polymorphism (SNP) chip for honey bees, the technical basis of genomic selection is laid. However, for its application in practice, methods to estimate genomic breeding values need to be adapted to the specificities of the genetics and breeding infrastructure of this species. Drone-producing queens (DPQ) are used for mating control, and usually, they head non-phenotyped colonies that will be placed on mating stations. Breeding queens (BQ) head colonies that are intended to be phenotyped and used to produce new queens. Our aim was to evaluate different breeding program designs for the initiation of genomic selection in honey bees. Methods Stochastic simulations were conducted to evaluate the quality of the estimated breeding values. We developed a variation of the genomic relationship matrix to include genotypes of DPQ and tested different sizes of the reference population. The results were used to estimate genetic gain in the initial selection cycle of a genomic breeding program. This program was run over six years, and different numbers of genotyped queens per year were considered. Resources could be allocated to increase the reference population, or to perform genomic preselection of BQ and/or DPQ. Results Including the genotypes of 5000 phenotyped BQ increased the accuracy of predictions of breeding values by up to 173%, depending on the size of the reference population and the trait considered. To initiate a breeding program, genotyping a minimum number of 1000 queens per year is required. In this case, genetic gain was highest when genomic preselection of DPQ was coupled with the genotyping of 10–20% of the phenotyped BQ. For maximum genetic gain per used genotype, more than 2500 genotyped queens per year and preselection of all BQ and DPQ are required. Conclusions This study shows that the first priority in a breeding program is to genotype phenotyped BQ to obtain a sufficiently large reference population, which allows successful genomic preselection of queens. To maximize genetic gain, DPQ should be preselected, and their genotypes included in the genomic relationship matrix. We suggest, that the developed methods for genomic prediction are suitable for implementation in genomic honey bee breeding programs. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00654-x.
Collapse
Affiliation(s)
- Richard Bernstein
- Institute for Bee Research Hohen Neuendorf, Friedrich-Engels-Str. 32, 16540, Hohen Neuendorf, Germany. .,Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, 10099, Berlin, Germany.
| | - Manuel Du
- Institute for Bee Research Hohen Neuendorf, Friedrich-Engels-Str. 32, 16540, Hohen Neuendorf, Germany
| | - Andreas Hoppe
- Institute for Bee Research Hohen Neuendorf, Friedrich-Engels-Str. 32, 16540, Hohen Neuendorf, Germany
| | - Kaspar Bienefeld
- Institute for Bee Research Hohen Neuendorf, Friedrich-Engels-Str. 32, 16540, Hohen Neuendorf, Germany.,Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, 10099, Berlin, Germany
| |
Collapse
|
12
|
Chak STC, Harris SE, Hultgren KM, Jeffery NW, Rubenstein DR. Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements. Proc Natl Acad Sci U S A 2021; 118:e2025051118. [PMID: 34099551 PMCID: PMC8214670 DOI: 10.1073/pnas.2025051118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite progress uncovering the genomic underpinnings of sociality, much less is known about how social living affects the genome. In different insect lineages, for example, eusocial species show both positive and negative associations between genome size and structure, highlighting the dynamic nature of the genome. Here, we explore the relationship between sociality and genome architecture in Synalpheus snapping shrimps that exhibit multiple origins of eusociality and extreme interspecific variation in genome size. Our goal is to determine whether eusociality leads to an accumulation of repetitive elements and an increase in genome size, presumably due to reduced effective population sizes resulting from a reproductive division of labor, or whether an initial accumulation of repetitive elements leads to larger genomes and independently promotes the evolution of eusociality through adaptive evolution. Using phylogenetically informed analyses, we find that eusocial species have larger genomes with more transposable elements (TEs) and microsatellite repeats than noneusocial species. Interestingly, different TE subclasses contribute to the accumulation in different species. Phylogenetic path analysis testing alternative causal relationships between sociality and genome architecture is most consistent with the hypothesis that TEs modulate the relationship between sociality and genome architecture. Although eusociality appears to influence TE accumulation, ancestral state reconstruction suggests moderate TE abundances in ancestral species could have fueled the initial transitions to eusociality. Ultimately, we highlight a complex and dynamic relationship between genome and social evolution, demonstrating that sociality can influence the evolution of the genome, likely through changes in demography related to patterns of reproductive skew.
Collapse
Affiliation(s)
- Solomon T C Chak
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027;
- Department of Biological Sciences, State University of New York College at Old Westbury, Old Westbury, NY 11568
| | - Stephen E Harris
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
- Department of Biology, State University of New York Purchase College, Purchase, NY 10577
| | | | - Nicholas W Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS B2Y 4A2, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Dustin R Rubenstein
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
| |
Collapse
|
13
|
Li R, Qu H, Chen J, Wang S, Chater JM, Zhang L, Wei J, Zhang YM, Xu C, Zhong WD, Zhu J, Lu J, Feng Y, Chen W, Ma R, Ferrante SP, Roose ML, Jia Z. Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes. Mol Biol Evol 2021; 37:3684-3698. [PMID: 32668004 PMCID: PMC7743722 DOI: 10.1093/molbev/msaa176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor’s chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.
Collapse
Affiliation(s)
- Ruidong Li
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
| | - Han Qu
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Jinfeng Chen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Shibo Wang
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - John M Chater
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Le Zhang
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
| | - Julong Wei
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI
| | - Yuan-Ming Zhang
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chenwu Xu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wei-De Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jianguo Zhu
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China
| | - Jianming Lu
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yuanfa Feng
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Weiming Chen
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China
| | - Renyuan Ma
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Department of Mathematics, Bowdoin College, Brunswick, ME
| | - Sergio Pietro Ferrante
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
| |
Collapse
|
14
|
Short-term effects of controlled mating and selection on the genetic variance of honeybee populations. Heredity (Edinb) 2021; 126:733-747. [PMID: 33785894 PMCID: PMC8102520 DOI: 10.1038/s41437-021-00411-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 02/01/2023] Open
Abstract
Directional selection in a population yields reduced genetic variance due to the Bulmer effect. While this effect has been thoroughly investigated in mammals, it is poorly studied in social insects with biological peculiarities such as haplo-diploidy or the collective expression of traits. In addition to the natural adaptation to climate change, parasites, and pesticides, honeybees increasingly experience artificial selection pressure through modern breeding programs. Besides selection, many honeybee breeding schemes introduce controlled mating. We investigated which individual effects selection and controlled mating have on genetic variance. We derived formulas to describe short-term changes of genetic variance in honeybee populations and conducted computer simulations to confirm them. Thereby, we found that the changes in genetic variance depend on whether the variance is measured between queens (inheritance criterion), worker groups (selection criterion), or both (performance criterion). All three criteria showed reduced genetic variance under selection. In the selection and performance criteria, our formulas and simulations showed an increased genetic variance through controlled mating. This newly described effect counterbalanced and occasionally outweighed the Bulmer effect. It could not be observed in the inheritance criterion. A good understanding of the different notions of genetic variance in honeybees, therefore, appears crucial to interpreting population parameters correctly.
Collapse
|
15
|
Reproductive success of the parasitic mite (Varroa destructor) is lower in honeybee colonies that target infested cells with recapping. Sci Rep 2021; 11:9133. [PMID: 33911144 PMCID: PMC8080770 DOI: 10.1038/s41598-021-88592-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/05/2021] [Indexed: 01/06/2023] Open
Abstract
Cell recapping is a behavioural trait of honeybees (Apis mellifera) where cells with developing pupae are uncapped, inspected, and then recapped, without removing the pupae. The ectoparasitic mite Varroa destructor, unarguably the most destructive pest in apiculture world-wide, invades the cells of developing pupae to feed and reproduce. Honeybees that target mite infested cells with this behaviour may disrupt the reproductive cycle of the mite. Hence, cell recapping has been associated with colony-level declines in mite reproduction. In this study we compared the colony-level efficacy of cell recapping (how often infested cells are recapped) to the average mite fecundity in A. mellifera. Our study populations, known to be adapted to V. destructor, were from Avignon, France, Gotland, Sweden, and Oslo, Norway, and were compared to geographically similar, treated control colonies. The results show that colonies with a higher recapping efficacy also have a lower average mite reproductive success. This pattern was likely driven by the adapted populations as they had the largest proportion of highly-targeted cell recapping. The consistent presence of this trait in mite-resistant and mite-susceptible colonies with varying degrees of expression may make it a good proxy trait for selective breeding on a large scale.
Collapse
|
16
|
Kushwaha B, Pandey M, Das P, Joshi CG, Nagpure NS, Kumar R, Kumar D, Agarwal S, Srivastava S, Singh M, Sahoo L, Jayasankar P, Meher PK, Shah TM, Hinsu AT, Patel N, Koringa PG, Das SP, Patnaik S, Bit A, Iquebal MA, Jaiswal S, Jena J. The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes. DNA Res 2021; 28:6070145. [PMID: 33416875 PMCID: PMC7934567 DOI: 10.1093/dnares/dsaa031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
The walking catfish Clarias magur (Hamilton, 1822) (magur) is an important catfish species inhabiting the Indian subcontinent. It is considered as a highly nutritious food fish and has the capability to walk to some distance, and survive a considerable period without water. Assembly, scaffolding and several rounds of iterations resulted in 3,484 scaffolds covering ∼94% of estimated genome with 9.88 Mb largest scaffold, and N50 1.31 Mb. The genome possessed 23,748 predicted protein encoding genes with annotation of 19,279 orthologous genes. A total of 166 orthologous groups represented by 222 genes were found to be unique for this species. The Computational Analysis of gene Family Evolution (CAFE) analysis revealed expansion of 207 gene families and 100 gene families have rapidly evolved. Genes specific to important environmental and terrestrial adaptation, viz. urea cycle, vision, locomotion, olfactory and vomeronasal receptors, immune system, anti-microbial properties, mucus, thermoregulation, osmoregulation, air-breathing, detoxification, etc. were identified and critically analysed. The analysis clearly indicated that C. magur genome possessed several unique and duplicate genes similar to that of terrestrial or amphibians’ counterparts in comparison to other teleostean species. The genome information will be useful in conservation genetics, not only for this species but will also be very helpful in such studies in other catfishes.
Collapse
Affiliation(s)
- Basdeo Kushwaha
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Manmohan Pandey
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Naresh S Nagpure
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Suyash Agarwal
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Shreya Srivastava
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Pallipuram Jayasankar
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Prem K Meher
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Tejas M Shah
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Namrata Patel
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Sofia P Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Siddhi Patnaik
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Amrita Bit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Mir A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Joykrushna Jena
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| |
Collapse
|
17
|
Saelao P, Simone-Finstrom M, Avalos A, Bilodeau L, Danka R, de Guzman L, Rinkevich F, Tokarz P. Genome-wide patterns of differentiation within and among U.S. commercial honey bee stocks. BMC Genomics 2020; 21:704. [PMID: 33032523 PMCID: PMC7545854 DOI: 10.1186/s12864-020-07111-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/29/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The population genetics of U.S. honey bee stocks remain poorly characterized despite the agricultural importance of Apis mellifera as the major crop pollinator. Commercial and research-based breeding programs have made significant improvements of favorable genetic traits (e.g. production and disease resistance). The variety of bees produced by artificial selection provides an opportunity to characterize the genetic diversity and regions of the genome undergoing selection in commonly managed stocks. RESULTS Pooled sequencing of eight honey bee stocks found strong genetic similarity among six of the stocks. Two stocks, Pol-line and Hilo, showed significant differentiation likely due to their intense and largely closed breeding for resistance to the parasitic Varroa mite. Few variants were identified as being specific to any one stock, indicating potential admixture among the sequenced stocks. Juxtaposing the underlying genetic variation of stocks selected for disease- and parasite-resistance behavior, we identified genes and candidate regions putatively associated with resistance regulated by hygienic behavior. CONCLUSION This study provides important insights into the distinct genetic characteristics and population diversity of honey bee stocks used in the United States, and provides further evidence of high levels of admixture in commercially managed honey bee stocks. Furthermore, breeding efforts to enhance parasite resistance in honey bees may have created unique genetic profiles. Genomic regions of interest have been highlighted for potential future work related to developing genetic markers for selection of disease and parasite resistance traits. Due to the vast genomic similarities found among stocks in general, our findings suggest that additional data regarding gene expression, epigenetic and regulatory information are needed to more fully determine how stock phenotypic diversity is regulated.
Collapse
Affiliation(s)
- Perot Saelao
- USDA-ARS, Honey Bee Breeding, Genetics and Physiology Laboratory, Baton Rouge, LA 70820 USA
- Present Address: USDA-ARS Knipling-Bushland U.S. Livestock Arthropod Pests Research Unit, Kerrville, TX 78028 USA
| | | | - Arian Avalos
- USDA-ARS, Honey Bee Breeding, Genetics and Physiology Laboratory, Baton Rouge, LA 70820 USA
| | - Lelania Bilodeau
- USDA-ARS, Honey Bee Breeding, Genetics and Physiology Laboratory, Baton Rouge, LA 70820 USA
| | - Robert Danka
- USDA-ARS, Honey Bee Breeding, Genetics and Physiology Laboratory, Baton Rouge, LA 70820 USA
| | - Lilia de Guzman
- USDA-ARS, Honey Bee Breeding, Genetics and Physiology Laboratory, Baton Rouge, LA 70820 USA
| | - Frank Rinkevich
- USDA-ARS, Honey Bee Breeding, Genetics and Physiology Laboratory, Baton Rouge, LA 70820 USA
| | - Philip Tokarz
- USDA-ARS, Honey Bee Breeding, Genetics and Physiology Laboratory, Baton Rouge, LA 70820 USA
| |
Collapse
|
18
|
A Single Gene Causes Thelytokous Parthenogenesis, the Defining Feature of the Cape Honeybee Apis mellifera capensis. Curr Biol 2020; 30:2248-2259.e6. [DOI: 10.1016/j.cub.2020.04.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/05/2020] [Accepted: 04/15/2020] [Indexed: 02/01/2023]
|
19
|
Evans JD. Selection for barriers between honey bees and a devastating parasite. Mol Ecol 2020; 28:2955-2957. [PMID: 31317607 DOI: 10.1111/mec.15142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/26/2022]
Abstract
Rivaling pesticides and a dearth of flowers, the parasitic mite Varroa destructor presents a tremendous threat to western honey bees, Apis mellifera. A longstanding, but minor, pest for the Asian honey bee Apis cerana, these obligate bee parasites feast on developing and adult A. mellifera across several continents. Varroa reproduction is limited to a short window when developing bee pupae are concealed in wax cells. Mated females target developing bees just before pupation and then have about one day to initiate reproduction, eventually laying one male and up to several female offspring. Female mites often fail to reproduce at all, instead waiting in cells until their bee host finishes development and then hitching dangerous rides on a succession of adult bees for up to several weeks, before scouting for a new host pupa. In this issue of Molecular Ecology, Conlon et al. (2019) have explored mite reproductive success via a clever and thought-provoking association study. In so doing, they have identified a protein whose actions could be integral to the dance between bees and their mite parasites.
Collapse
Affiliation(s)
- Jay D Evans
- USDA-ARS Bee Research Laboratory, Beltsville, MD, USA
| |
Collapse
|
20
|
Honey bee survival mechanisms against the parasite Varroa destructor: a systematic review of phenotypic and genomic research efforts. Int J Parasitol 2020; 50:433-447. [PMID: 32380096 DOI: 10.1016/j.ijpara.2020.03.005] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/12/2020] [Accepted: 03/24/2020] [Indexed: 11/22/2022]
Abstract
The ectoparasitic mite Varroa destructor is the most significant pathological threat to the western honey bee, Apis mellifera, leading to the death of most colonies if left untreated. An alternative approach to chemical treatments is to selectively enhance heritable honey bee traits of resistance or tolerance to the mite through breeding programs, or select for naturally surviving untreated colonies. We conducted a literature review of all studies documenting traits of A. mellifera populations either selectively bred or naturally selected for resistance and tolerance to mite parasitism. This allowed us to conduct an analysis of the diversity, distribution and importance of the traits in different honey bee populations that can survive V. destructor globally. In a second analysis, we investigated the genetic bases of these different phenotypes by comparing 'omics studies (genomics, transcriptomics, and proteomics) of A. mellifera resistance and tolerance to the parasite. Altogether, this review provides a detailed overview of the current state of the research projects and breeding efforts against the most devastating parasite of A. mellifera. By highlighting the most promising traits of Varroa-surviving bees and our current knowledge on their genetic bases, this work will help direct future research efforts and selection programs to control this pest. Additionally, by comparing the diverse populations of honey bees that exhibit those traits, this review highlights the consequences of anthropogenic and natural selection in the interactions between hosts and parasites.
Collapse
|
21
|
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.
Collapse
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,
| |
Collapse
|
22
|
|
23
|
Acevedo‐Gonzalez JP, Galindo‐Cardona A, Avalos A, Whitfield CW, Rodriguez DM, Uribe‐Rubio JL, Giray T. Colonization history and population differentiation of the Honey Bees ( Apis mellifera L.) in Puerto Rico. Ecol Evol 2019; 9:10895-10902. [PMID: 31641443 PMCID: PMC6802029 DOI: 10.1002/ece3.5330] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 11/25/2022] Open
Abstract
Honey bees (Apis mellifera L.) are the primary commercial pollinators across the world. The subspecies A. m. scutellata originated in Africa and was introduced to the Americas in 1956. For the last 60 years, it hybridized successfully with European subspecies, previous residents in the area. The result of this hybridization was called Africanized honey bee (AHB). AHB has spread since then, arriving to Puerto Rico (PR) in 1994. The honey bee population on the island acquired a mosaic of features from AHB or the European honey bee (EHB). AHB in Puerto Rico shows a major distinctive characteristic, docile behavior, and is called gentle Africanized honey bees (gAHB). We used 917 SNPs to examine the population structure, genetic differentiation, origin, and history of range expansion and colonization of gAHB in PR. We compared gAHB to populations that span the current distribution of A. mellifera worldwide. The gAHB population is shown to be a single population that differs genetically from the examined populations of AHB. Texas and PR groups are the closest genetically. Our results support the hypothesis that the Texas AHB population is the source of gAHB in Puerto Rico.
Collapse
Affiliation(s)
| | - Alberto Galindo‐Cardona
- National Scientific and Technical Research Council (CONICET)TucumanArgentina
- Miguel Lillo FoundationTucumánArgentina
| | - Arian Avalos
- USDA, Agricultural Research ServiceHoney Bee Breeding, Genetics and Physiology ResearchBaton RougeLouisiana
- Department of EntomologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | - Charles W. Whitfield
- Department of EntomologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | | | | | - Tugrul Giray
- Department of BiologyUniversity of Puerto RicoSan JuanPuerto Rico
| |
Collapse
|
24
|
Behavioral Genetics of the Interactions between Apis mellifera and Varroa destructor. INSECTS 2019; 10:insects10090299. [PMID: 31527402 PMCID: PMC6780334 DOI: 10.3390/insects10090299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 01/06/2023]
Abstract
The western honeybee Apis mellifera exhibits a diverse set of adaptations in response to infestations by its most virulent disease-causing agent, the ectoparasitic mite Varroa destructor. In this study, we investigated the effect of honeybee pupae genotype on the expression of four host and parasite traits that are associated with the reproductive phase of the mite in the brood of its host. We first phenotyped cells containing bee pupae to assess their infestation status, their infestation level, the reproductive status of the mites, and the recapping of cells by adult workers. We then genotyped individual pupae with five microsatellites markers to compare these phenotypes across full sister groups. We found that the four phenotypes varied significantly in time but did not across the subfamilies within the colonies. These findings show that V. destructor mites do not differentially infest or reproduce on some particular honeybee patrilines, and that workers do not target preferentially specific pupae genotypes when performing recapping. These findings bring new insights that can help designing sustainable mite control strategies through breeding and provide new insights into the interactions between A. mellifera and V. destructor.
Collapse
|
25
|
Karssene Y, Godinho R, Chammem M, Cocchiararo B, Nouira S, Nowak C. Noninvasive DNA sampling and camera trapping suggest dramatic regional conservation status of an understudied carnivore: the Rüppell’s fox in Tunisia. J NAT HIST 2019. [DOI: 10.1080/00222933.2019.1656295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Yamna Karssene
- Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El- Manar, Tunis, Tunisia
- Laboratoire d’Elevage et de la Faune Sauvage, Institut des Régions Arides de Médenine, Médenine, Tunisia
| | - Raquel Godinho
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| | - Mohsen Chammem
- Laboratoire d’Elevage et de la Faune Sauvage, Institut des Régions Arides de Médenine, Médenine, Tunisia
| | - Berardino Cocchiararo
- Senckenberg Research Institute and Natural History Museum Frankfurt, Conservation Genetics Group, Gelnhausen, Germany
| | - Said Nouira
- Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El- Manar, Tunis, Tunisia
| | - Carsten Nowak
- Senckenberg Research Institute and Natural History Museum Frankfurt, Conservation Genetics Group, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| |
Collapse
|
26
|
Yunusbaev UB, Kaskinova MD, Ilyasov RA, Gaifullina LR, Saltykova ES, Nikolenko AG. The Role of Whole-Genome Studies in the Investigation of Honey Bee Biology. RUSS J GENET+ 2019. [DOI: 10.1134/s102279541906019x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
27
|
Kawakami T, Wallberg A, Olsson A, Wintermantel D, de Miranda JR, Allsopp M, Rundlöf M, Webster MT. Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees. Genetics 2019; 212:1101-1119. [PMID: 31152071 PMCID: PMC6707477 DOI: 10.1534/genetics.119.302008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/30/2019] [Indexed: 12/30/2022] Open
Abstract
Meiotic recombination shuffles genetic variation and promotes correct segregation of chromosomes. Rates of recombination vary on several scales, both within genomes and between individuals, and this variation is affected by both genetic and environmental factors. Social insects have extremely high rates of recombination, although the evolutionary causes of this are not known. Here, we estimate rates of crossovers and gene conversions in 22 colonies of the honeybee, Apis mellifera, and 9 colonies of the bumblebee, Bombus terrestris, using direct sequencing of 299 haploid drone offspring. We confirm that both species have extremely elevated crossover rates, with higher rates measured in the highly eusocial honeybee than the primitively social bumblebee. There are also significant differences in recombination rate between subspecies of honeybee. There is substantial variation in genome-wide recombination rate between individuals of both A. mellifera and B. terrestris and the distribution of these rates overlap between species. A large proportion of interindividual variation in recombination rate is heritable, which indicates the presence of variation in trans-acting factors that influence recombination genome-wide. We infer that levels of crossover interference are significantly lower in honeybees compared to bumblebees, which may be one mechanism that contributes to higher recombination rates in honeybees. We also find a significant increase in recombination rate with distance from the centromere, mirrored by methylation differences. We detect a strong transmission bias due to GC-biased gene conversion associated with noncrossover gene conversions. Our results shed light on the mechanistic causes of extreme rates of recombination in social insects and the genetic architecture of recombination rate variation.
Collapse
Affiliation(s)
- Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, 752 36, Sweden
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, United Kingdom
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 05. Sweden
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 05. Sweden
| | - Dimitry Wintermantel
- INRA, UE 1255 APIS, Le Magneraud, 17700 Surgères, France
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS and Université de La Rochelle, 79360 Villiers-en-Bois, France
| | - Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Mike Allsopp
- Plant Protection Research Institute, Agricultural Research Council, Stellenbosch, 7608, South Africa
| | - Maj Rundlöf
- Department of Biology, Lund University, 223 62, Sweden
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 05. Sweden
| |
Collapse
|
28
|
Harpur BA, Guarna MM, Huxter E, Higo H, Moon KM, Hoover SE, Ibrahim A, Melathopoulos AP, Desai S, Currie RW, Pernal SF, Foster LJ, Zayed A. Integrative Genomics Reveals the Genetics and Evolution of the Honey Bee's Social Immune System. Genome Biol Evol 2019; 11:937-948. [PMID: 30768172 PMCID: PMC6447389 DOI: 10.1093/gbe/evz018] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2019] [Indexed: 12/13/2022] Open
Abstract
Social organisms combat pathogens through individual innate immune responses or through social immunity—behaviors among individuals that limit pathogen transmission within groups. Although we have a relatively detailed understanding of the genetics and evolution of the innate immune system of animals, we know little about social immunity. Addressing this knowledge gap is crucial for understanding how life-history traits influence immunity, and identifying if trade-offs exist between innate and social immunity. Hygienic behavior in the Western honey bee, Apis mellifera, provides an excellent model for investigating the genetics and evolution of social immunity in animals. This heritable, colony-level behavior is performed by nurse bees when they detect and remove infected or dead brood from the colony. We sequenced 125 haploid genomes from two artificially selected highly hygienic populations and a baseline unselected population. Genomic contrasts allowed us to identify a minimum of 73 genes tentatively associated with hygienic behavior. Many genes were within previously discovered QTLs associated with hygienic behavior and were predictive of hygienic behavior within the unselected population. These genes were often involved in neuronal development and sensory perception in solitary insects. We found that genes associated with hygienic behavior have evidence of positive selection within honey bees (Apis), supporting the hypothesis that social immunity contributes to fitness. Our results indicate that genes influencing developmental neurobiology and behavior in solitary insects may have been co-opted to give rise to a novel and adaptive social immune phenotype in honey bees.
Collapse
Affiliation(s)
- Brock A Harpur
- Department of Entomology, Purdue University.,Department of Biology, York University, Toronto, Ontario, Canada
| | - Maria Marta Guarna
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada
| | | | - Heather Higo
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shelley E Hoover
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada.,Alberta Agriculture and Forestry, Agriculture Centre, Lethbridge, Alberta, Canada
| | - Abdullah Ibrahim
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada
| | - Andony P Melathopoulos
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada.,Department of Horticulture, College of Agricultural Sciences, Oregon State University
| | - Suresh Desai
- Department of Entomology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Robert W Currie
- Department of Entomology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Stephen F Pernal
- Agriculture and Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, Alberta, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amro Zayed
- Department of Biology, York University, Toronto, Ontario, Canada
| |
Collapse
|
29
|
Jones JC, Wallberg A, Christmas MJ, Kapheim KM, Webster MT. Extreme Differences in Recombination Rate between the Genomes of a Solitary and a Social Bee. Mol Biol Evol 2019; 36:2277-2291. [DOI: 10.1093/molbev/msz130] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Abstract
Social insect genomes exhibit the highest rates of crossing over observed in plants and animals. The evolutionary causes of these extreme rates are unknown. Insight can be gained by comparing recombination rate variation across the genomes of related social and solitary insects. Here, we compare the genomic recombination landscape of the highly social honey bee, Apis mellifera, with the solitary alfalfa leafcutter bee, Megachile rotundata, by analyzing patterns of linkage disequilibrium in population-scale genome sequencing data. We infer that average recombination rates are extremely elevated in A. mellifera compared with M. rotundata. However, our results indicate that similar factors control the distribution of crossovers in the genomes of both species. Recombination rate is significantly reduced in coding regions in both species, with genes inferred to be germline methylated having particularly low rates. Genes with worker-biased patterns of expression in A. mellifera and their orthologs in M. rotundata have higher than average recombination rates in both species, suggesting that selection for higher diversity in genes involved in worker caste functions in social taxa is not the explanation for these elevated rates. Furthermore, we find no evidence that recombination has modulated the efficacy of selection among genes during bee evolution, which does not support the hypothesis that high recombination rates facilitated positive selection for new functions in social insects. Our results indicate that the evolution of sociality in insects likely entailed selection on modifiers that increased recombination rates genome wide, but that the genomic recombination landscape is determined by the same factors.
Collapse
Affiliation(s)
- Julia C Jones
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
30
|
Comparison of infinitesimal and finite locus models for long-term breeding simulations with direct and maternal effects at the example of honeybees. PLoS One 2019; 14:e0213270. [PMID: 30840680 PMCID: PMC6402681 DOI: 10.1371/journal.pone.0213270] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 02/19/2019] [Indexed: 01/01/2023] Open
Abstract
Stochastic simulation studies of animal breeding have mostly relied on either the infinitesimal genetic model or finite polygenic models. In this study, we investigated the long-term effects of the chosen model on honeybee breeding schemes. We implemented the infinitesimal model, as well as finite locus models, with 200 and 400 gene loci and simulated populations of 300 and 1000 colonies per year over the course of 100 years. The selection was of a directly and maternally influenced trait with maternal heritability of hm2=0.42, direct heritability of hd2=0.27, and a negative correlation between the effects of rmd = − 0.18. Another set of simulations was run with parameters hm2=0.53, hd2=0.34, and rmd = − 0.53. All models showed similar behavior for the first 20 years. Throughout the study, we observed a higher genetic gain in the direct than in the maternal effects and a smaller gain with a stronger negative covariance. In the long-term, however, only the infinitesimal model predicted sustainable linear genetic progress, while the finite locus models showed sublinear behavior and, after 100 years, only reached between 58% and 62% of the mean breeding values in the infinitesimal model. While the infinitesimal model suggested a reduction of genetic variance by 33% to 49% after 100 years, the finite locus models saw a more drastic loss of 76% to 92%. When designing sustainable breeding strategies, one should, therefore, not blindly trust the infinitesimal model as the predictions may be overly optimistic. Instead, the more conservative choice of the finite locus model should be favored.
Collapse
|
31
|
Dogantzis KA, Zayed A. Recent advances in population and quantitative genomics of honey bees. CURRENT OPINION IN INSECT SCIENCE 2019; 31:93-98. [PMID: 31109680 DOI: 10.1016/j.cois.2018.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/09/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
The increase in the availability of individual Apis mellifera genomes has resulted in significant progress toward understanding the evolution and adaptation of the honey bee. These efforts have identified new subspecies, evolutionary lineages, and a significant number of genes involved with adaptations and colony-level quantitative traits. Many studies have also developed genetic assays that are being used to monitor the movement and admixture of honey bee populations. These resources are valuable for conservation and breeding programs that seek to improve the economic value of colonies or preserve locally adapted populations and subspecies. This review provides a brief discussion on how population and quantitative genomic studies has improved our understanding of the honey bee.
Collapse
Affiliation(s)
- Kathleen A Dogantzis
- Department of Biology, York University, 4700 Keele St., Toronto, Ontario, Canada
| | - Amro Zayed
- Department of Biology, York University, 4700 Keele St., Toronto, Ontario, Canada.
| |
Collapse
|
32
|
Smith NMA, Wade C, Allsopp MH, Harpur BA, Zayed A, Rose SA, Engelstädter J, Chapman NC, Yagound B, Oldroyd BP. Strikingly high levels of heterozygosity despite 20 years of inbreeding in a clonal honey bee. J Evol Biol 2018; 32:144-152. [DOI: 10.1111/jeb.13397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/11/2018] [Accepted: 11/05/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Nicholas M. A. Smith
- Behaviour and Genetics of Social Insects Laboratory The University of Sydney Sydney New South Wales Australia
| | - Claire Wade
- Faculty of Veterinary Science The University of Sydney Sydney New South Wales Australia
| | - Michael H. Allsopp
- Honey Bee Research Section ARC‐Plant Protection Research Institute Stellenbosch South Africa
| | - Brock A. Harpur
- Department of Biology Faculty of Science York University Toronto Ontario Canada
| | - Amro Zayed
- Department of Biology Faculty of Science York University Toronto Ontario Canada
| | - Stephen A. Rose
- Department of Biology Faculty of Science York University Toronto Ontario Canada
| | - Jan Engelstädter
- School of Biological Sciences The University of Queensland Brisbane Queensland Australia
| | - Nadine C. Chapman
- Behaviour and Genetics of Social Insects Laboratory The University of Sydney Sydney New South Wales Australia
| | - Boris Yagound
- Behaviour and Genetics of Social Insects Laboratory The University of Sydney Sydney New South Wales Australia
| | - Benjamin P. Oldroyd
- Behaviour and Genetics of Social Insects Laboratory The University of Sydney Sydney New South Wales Australia
| |
Collapse
|
33
|
Guiding recombinant antivenom development by omics technologies. N Biotechnol 2018; 45:19-27. [DOI: 10.1016/j.nbt.2017.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/16/2017] [Indexed: 11/23/2022]
|
34
|
Complete mitogenome of Anopheles sinensis and mitochondrial insertion segments in the nuclear genomes of 19 mosquito species. PLoS One 2018; 13:e0204667. [PMID: 30261042 PMCID: PMC6160108 DOI: 10.1371/journal.pone.0204667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/12/2018] [Indexed: 11/19/2022] Open
Abstract
Anopheles sinensis is a major malarial vector in China and Southeast Asia. The mitochondria is involved in many important biological functions. Nuclear mitochondrial DNA segments (NUMTs) are common in eukaryotic organisms, but their characteristics are poorly understood. We sequenced and analyzed the complete mitochondrial (mt) genome of An. sinensis. The mt genome is 15,418 bp long and contains 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs and a large non-coding region. Its gene arrangement is similar to previously published mosquito mt genomes. We identified and analyzed the NUMTs of 19 mosquito species with both nuclear genomes and mt genome sequences. The number, total length and density of NUMTs are significantly correlated with genome size. About half of NUMTs are short (< 200 bp), but larger genomes can house longer NUMTs. NUMTs may help explain genome size expansion in mosquitoes. The expansion due to mitochondrial insertion segments is variable in different insect groups. PCGs are transferred to nuclear genomes at a higher frequency in mosquitoes, but NUMT origination is more different than in mammals. Larger-sized nuclear genomes have longer mt genome sequences in both mosquitoes and mammals. The study provides a foundation for the functional research of mitochondrial genes in An. sinensis and helps us understand the characteristics and origin of NUMTs and the potential contribution to genome expansion.
Collapse
|
35
|
Henriques D, Wallberg A, Chávez-Galarza J, Johnston JS, Webster MT, Pinto MA. Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Sci Rep 2018; 8:11145. [PMID: 30042407 PMCID: PMC6057950 DOI: 10.1038/s41598-018-29469-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/06/2018] [Indexed: 12/25/2022] Open
Abstract
The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.
Collapse
Affiliation(s)
- Dora Henriques
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE -751 23, Uppsala, Sweden
| | - Julio Chávez-Galarza
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, La Molina, Lima, Peru
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE -751 23, Uppsala, Sweden
| | - M Alice Pinto
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal.
| |
Collapse
|
36
|
Haenel Q, Laurentino TG, Roesti M, Berner D. Meta-analysis of chromosome-scale crossover rate variation in eukaryotes and its significance to evolutionary genomics. Mol Ecol 2018; 27:2477-2497. [PMID: 29676042 DOI: 10.1111/mec.14699] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 01/02/2023]
Abstract
Understanding the distribution of crossovers along chromosomes is crucial to evolutionary genomics because the crossover rate determines how strongly a genome region is influenced by natural selection on linked sites. Nevertheless, generalities in the chromosome-scale distribution of crossovers have not been investigated formally. We fill this gap by synthesizing joint information on genetic and physical maps across 62 animal, plant and fungal species. Our quantitative analysis reveals a strong and taxonomically widespread reduction of the crossover rate in the centre of chromosomes relative to their peripheries. We demonstrate that this pattern is poorly explained by the position of the centromere, but find that the magnitude of the relative reduction in the crossover rate in chromosome centres increases with chromosome length. That is, long chromosomes often display a dramatically low crossover rate in their centre, whereas short chromosomes exhibit a relatively homogeneous crossover rate. This observation is compatible with a model in which crossover is initiated from the chromosome tips, an idea with preliminary support from mechanistic investigations of meiotic recombination. Consequently, we show that organisms achieve a higher genome-wide crossover rate by evolving smaller chromosomes. Summarizing theory and providing empirical examples, we finally highlight that taxonomically widespread and systematic heterogeneity in crossover rate along chromosomes generates predictable broad-scale trends in genetic diversity and population differentiation by modifying the impact of natural selection among regions within a genome. We conclude by emphasizing that chromosome-scale heterogeneity in crossover rate should urgently be incorporated into analytical tools in evolutionary genomics, and in the interpretation of resulting patterns.
Collapse
Affiliation(s)
- Quiterie Haenel
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | - Marius Roesti
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| |
Collapse
|
37
|
Testing the effect of paraquat exposure on genomic recombination rates in queens of the western honey bee, Apis mellifera. Genetica 2018; 146:171-178. [PMID: 29397499 DOI: 10.1007/s10709-018-0009-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 01/30/2018] [Indexed: 10/18/2022]
Abstract
The rate of genomic recombination displays evolutionary plasticity and can even vary in response to environmental factors. The western honey bee (Apis mellifera L.) has an extremely high genomic recombination rate but the mechanistic basis for this genome-wide upregulation is not understood. Based on the hypothesis that meiotic recombination and DNA damage repair share common mechanisms in honey bees as in other organisms, we predicted that oxidative stress leads to an increase in recombination rate in honey bees. To test this prediction, we subjected honey bee queens to oxidative stress by paraquat injection and measured the rates of genomic recombination in select genome intervals of offspring produced before and after injection. The evaluation of 26 genome intervals in a total of over 1750 offspring of 11 queens by microsatellite genotyping revealed several significant effects but no overall evidence for a mechanistic link between oxidative stress and increased recombination was found. The results weaken the notion that DNA repair enzymes have a regulatory function in the high rate of meiotic recombination of honey bees, but they do not provide evidence against functional overlap between meiotic recombination and DNA damage repair in honey bees and more mechanistic studies are needed.
Collapse
|
38
|
RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates. Genetics 2018; 208:1585-1599. [PMID: 29437826 PMCID: PMC5887150 DOI: 10.1534/genetics.117.300567] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/31/2018] [Indexed: 12/30/2022] Open
Abstract
Conflict between organisms can lead to a reciprocal adaptation that manifests as an increased evolutionary rate in genes mediating the conflict. This adaptive signature has been observed in RNA-interference (RNAi) pathway genes involved in the suppression of viruses and transposable elements in Drosophila melanogaster, suggesting that a subset of Drosophila RNAi genes may be locked in an arms race with these parasites. However, it is not known whether rapid evolution of RNAi genes is a general phenomenon across invertebrates, or which RNAi genes generally evolve adaptively. Here we use population genomic data from eight invertebrate species to infer rates of adaptive sequence evolution, and to test for past and ongoing selective sweeps in RNAi genes. We assess rates of adaptive protein evolution across species using a formal meta-analytic framework to combine data across species and by implementing a multispecies generalized linear mixed model of mutation counts. Across species, we find that RNAi genes display a greater rate of adaptive protein substitution than other genes, and that this is primarily mediated by positive selection acting on the genes most likely to defend against viruses and transposable elements. In contrast, evidence for recent selective sweeps is broadly spread across functional classes of RNAi genes and differs substantially among species. Finally, we identify genes that exhibit elevated adaptive evolution across the analyzed insect species, perhaps due to concurrent parasite-mediated arms races.
Collapse
|
39
|
Doyle SR, Laing R, Bartley DJ, Britton C, Chaudhry U, Gilleard JS, Holroyd N, Mable BK, Maitland K, Morrison AA, Tait A, Tracey A, Berriman M, Devaney E, Cotton JA, Sargison ND. A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry. Genome Biol Evol 2018; 10:396-409. [PMID: 29267942 PMCID: PMC5793844 DOI: 10.1093/gbe/evx269] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2017] [Indexed: 12/27/2022] Open
Abstract
The parasitic nematode Haemonchus contortus is an economically and clinically important pathogen of small ruminants, and a model system for understanding the mechanisms and evolution of traits such as anthelmintic resistance. Anthelmintic resistance is widespread and is a major threat to the sustainability of livestock agriculture globally; however, little is known about the genome architecture and parameters such as recombination that will ultimately influence the rate at which resistance may evolve and spread. Here, we performed a genetic cross between two divergent strains of H. contortus, and subsequently used whole-genome resequencing of a female worm and her brood to identify the distribution of genome-wide variation that characterizes these strains. Using a novel bioinformatic approach to identify variants that segregate as expected in a pseudotestcross, we characterized linkage groups and estimated genetic distances between markers to generate a chromosome-scale F1 genetic map. We exploited this map to reveal the recombination landscape, the first for any helminth species, demonstrating extensive variation in recombination rate within and between chromosomes. Analyses of these data also revealed the extent of polyandry, whereby at least eight males were found to have contributed to the genetic variation of the progeny analyzed. Triploid offspring were also identified, which we hypothesize are the result of nondisjunction during female meiosis or polyspermy. These results expand our knowledge of the genetics of parasitic helminths and the unusual life-history of H. contortus, and enhance ongoing efforts to understand the genetic basis of resistance to the drugs used to control these worms and for related species that infect livestock and humans throughout the world. This study also demonstrates the feasibility of using whole-genome resequencing data to directly construct a genetic map in a single generation cross from a noninbred nonmodel organism with a complex lifecycle.
Collapse
Affiliation(s)
- Stephen R Doyle
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Roz Laing
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - David J Bartley
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Collette Britton
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Umer Chaudhry
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Alberta, Canada
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Barbara K Mable
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Kirsty Maitland
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Alison A Morrison
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Andy Tait
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Alan Tracey
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Eileen Devaney
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - James A Cotton
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Neil D Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
| |
Collapse
|
40
|
Rueppell O, Kuster R, Miller K, Fouks B, Rubio Correa S, Collazo J, Phaincharoen M, Tingek S, Koeniger N. A New Metazoan Recombination Rate Record and Consistently High Recombination Rates in the Honey Bee Genus Apis Accompanied by Frequent Inversions but Not Translocations. Genome Biol Evol 2018; 8:3653-3660. [PMID: 28173114 PMCID: PMC5521732 DOI: 10.1093/gbe/evw269] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2016] [Indexed: 12/31/2022] Open
Abstract
Western honey bees (Apis mellifera) far exceed the commonly observed 1–2 meiotic recombination events per chromosome and exhibit the highest Metazoan recombination rate (20 cM/Mb) described thus far. However, the reasons for this exceptional rate of recombination are not sufficiently understood. In a comparative study, we report on the newly constructed genomic linkage maps of Apis florea and Apis dorsata that represent the two honey bee lineages without recombination rate estimates so far. Each linkage map was generated de novo, based on SNP genotypes of haploid male offspring of a single female. The A. florea map spans 4,782 cM with 1,279 markers in 16 linkage groups. The A. dorsata map is 5,762 cM long and contains 1,189 markers in 16 linkage groups. Respectively, these map sizes result in average recombination rate estimates of 20.8 and 25.1 cM/Mb. Synteny analyses indicate that frequent intra-chromosomal rearrangements but no translocations among chromosomes accompany the high rates of recombination during the independent evolution of the three major honey bee lineages. Our results imply a common cause for the evolution of very high recombination rates in Apis. Our findings also suggest that frequent homologous recombination during meiosis might increase ectopic recombination and rearrangements within but not between chromosomes. It remains to be investigated whether the resulting inversions may have been important in the evolutionary differentiation between honey bee species.
Collapse
Affiliation(s)
- Olav Rueppell
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Ryan Kuster
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Katelyn Miller
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Bertrand Fouks
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Sara Rubio Correa
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Juan Collazo
- Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Mananya Phaincharoen
- Ratchaburi Campus, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Salim Tingek
- Agricultural Research Station, Tenom, Sabah, Malaysia
| | - Nikolaus Koeniger
- Molecular Ecology, Institute of Biology/Zoology, Martin-Luther-University Halle-Wittenberg, Halle an der Saale, Germany
| |
Collapse
|
41
|
Avalos A, Pan H, Li C, Acevedo-Gonzalez JP, Rendon G, Fields CJ, Brown PJ, Giray T, Robinson GE, Hudson ME, Zhang G. A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee. Nat Commun 2017; 8:1550. [PMID: 29142254 PMCID: PMC5688081 DOI: 10.1038/s41467-017-01800-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/16/2017] [Indexed: 12/30/2022] Open
Abstract
Highly aggressive Africanized honeybees (AHB) invaded Puerto Rico (PR) in 1994, displacing gentle European honeybees (EHB) in many locations. Gentle AHB (gAHB), unknown anywhere else in the world, subsequently evolved on the island within a few generations. Here we sequence whole genomes from gAHB and EHB populations, as well as a North American AHB population, a likely source of the founder AHB on PR. We show that gAHB retains high levels of genetic diversity after evolution of gentle behaviour, despite selection on standing variation. We observe multiple genomic loci with significant signatures of selection. Rapid evolution during colonization of novel habitats can generate major changes to characteristics such as morphological or colouration traits, usually controlled by one or more major genetic loci. Here we describe a soft selective sweep, acting at multiple loci across the genome, that occurred during, and may have mediated, the rapid evolution of a behavioural trait. Africanized honey bees (AHB) are notoriously aggressive, but in Puerto Rico they have a ‘gentle’ phenotype. Here, Avalos et al. show that there has been a soft selective sweep at several loci in the Puerto Rican AHB population and suggest a role in the rapid evolution of gentle behaviour.
Collapse
Affiliation(s)
- Arian Avalos
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hailin Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.,China National Genebank, BGI-Shenzhen, 518083, Shenzhen, Guangdong, China.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Cai Li
- China National Genebank, BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | | | - Gloria Rendon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,High-Performance Computing for Biology (HPCBio), Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher J Fields
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,High-Performance Computing for Biology (HPCBio), Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Patrick J Brown
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tugrul Giray
- Departamento de Biología, Universidad de Puerto Rico, Río Piedras, PR, 00931, USA
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Matthew E Hudson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,High-Performance Computing for Biology (HPCBio), Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China. .,China National Genebank, BGI-Shenzhen, 518083, Shenzhen, Guangdong, China. .,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100, Copenhagen, Denmark.
| |
Collapse
|
42
|
Forfert N, Troxler A, Retschnig G, Gauthier L, Straub L, Moritz RFA, Neumann P, Williams GR. Neonicotinoid pesticides can reduce honeybee colony genetic diversity. PLoS One 2017; 12:e0186109. [PMID: 29059234 PMCID: PMC5653293 DOI: 10.1371/journal.pone.0186109] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/25/2017] [Indexed: 12/02/2022] Open
Abstract
Neonicotinoid insecticides can cause a variety of adverse sub-lethal effects in bees. In social species such as the honeybee, Apis mellifera, queens are essential for reproduction and colony functioning. Therefore, any negative effect of these agricultural chemicals on the mating success of queens may have serious consequences for the fitness of the entire colony. Queens were exposed to the common neonicotinoid pesticides thiamethoxam and clothianidin during their developmental stage. After mating, their spermathecae were dissected to count the number of stored spermatozoa. Furthermore, their worker offspring were genotyped with DNA microsatellites to determine the number of matings and the genotypic composition of the colony. Colonies providing the male mating partners were also inferred. Both neonicotinoid and control queens mated with drones originating from the same drone source colonies, and stored similar number of spermatozoa. However, queens reared in colonies exposed to both neonicotinoids experienced fewer matings. This resulted in a reduction of the genetic diversity in their colonies (i.e. higher intracolonial relatedness). As decreased genetic diversity among worker bees is known to negatively affect colony vitality, neonicotinoids may have a cryptic effect on colony health by reducing the mating frequency of queens.
Collapse
Affiliation(s)
- Nadège Forfert
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Aline Troxler
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gina Retschnig
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Lars Straub
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Robin F. A. Moritz
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
- Social Insect Research Group, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Geoffrey R. Williams
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| |
Collapse
|
43
|
Nelson RM, Wallberg A, Simões ZLP, Lawson DJ, Webster MT. Genomewide analysis of admixture and adaptation in the Africanized honeybee. Mol Ecol 2017; 26:3603-3617. [PMID: 28378497 DOI: 10.1111/mec.14122] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/08/2016] [Accepted: 03/20/2017] [Indexed: 02/03/2023]
Abstract
Genetic exchange by hybridization or admixture can make an important contribution to evolution, and introgression of favourable alleles can facilitate adaptation to new environments. A small number of honeybees (Apis mellifera) with African ancestry were introduced to Brazil ~60 years ago, which dispersed and hybridized with existing managed populations of European origin, quickly spreading across much of the Americas in an example of a massive biological invasion. Here, we analyse whole-genome sequences of 32 Africanized honeybees sampled from throughout Brazil to study the effect of this process on genome diversity. By comparison with ancestral populations from Europe and Africa, we infer that these samples have 84% African ancestry, with the remainder from western European populations. However, this proportion varies across the genome and we identify signals of positive selection in regions with high European ancestry proportions. These observations are largely driven by one large gene-rich 1.4-Mbp segment on chromosome 11 where European haplotypes are present at a significantly elevated frequency and likely confer an adaptive advantage in the Africanized honeybee population. This region has previously been implicated in reproductive traits and foraging behaviour in worker bees. Finally, by analysing the distribution of ancestry tract lengths in the context of the known time of the admixture event, we are able to infer an average generation time of 2.0 years. Our analysis highlights the processes by which populations of mixed genetic ancestry form and adapt to new environments.
Collapse
Affiliation(s)
- Ronald M Nelson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Andreas Wallberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Zilá Luz Paulino Simões
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, Brazil.,Department of Genetics, FMRP, University of São Paulo, Ribeirão Preto, Brazil
| | - Daniel J Lawson
- Department of Mathematics, University of Bristol, Bristol, UK
| | - Matthew T Webster
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
44
|
Cridge AG, Lovegrove MR, Skelly JG, Taylor SE, Petersen GEL, Cameron RC, Dearden PK. The honeybee as a model insect for developmental genetics. Genesis 2017; 55. [PMID: 28432809 DOI: 10.1002/dvg.23019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/08/2017] [Accepted: 01/15/2017] [Indexed: 11/11/2022]
Abstract
Honeybees are an important component of modern agricultural systems, and a fascinating and scientifically engrossing insect. Honeybees are not commonly used as model systems for understanding development in insects despite their importance in agriculture. Honeybee embryogenesis, while being superficially similar to Drosophila, is molecularly very different, especially in axis formation and sex determination. In later development, much of honeybee biology is modified by caste development, an as yet poorly understood, but excellent, system to study developmental plasticity. In adult stages, developmental plasticity of the ovaries, related to reproductive constraint exhibits another aspect of plasticity. Here they review the tools, current knowledge and opportunities in honeybee developmental biology, and provide an updated embryonic staging scheme to support future studies.
Collapse
Affiliation(s)
- A G Cridge
- Laboratory for Evolution and Development, Genetics Otago, Biochemistry Department, University of Otago, Dunedin, 9054, P.O. Box 56, Aotearoa-New Zealand
| | - M R Lovegrove
- Laboratory for Evolution and Development, Genetics Otago, Biochemistry Department, University of Otago, Dunedin, 9054, P.O. Box 56, Aotearoa-New Zealand
| | - J G Skelly
- Laboratory for Evolution and Development, Genetics Otago, Biochemistry Department, University of Otago, Dunedin, 9054, P.O. Box 56, Aotearoa-New Zealand
| | - S E Taylor
- Laboratory for Evolution and Development, Genetics Otago, Biochemistry Department, University of Otago, Dunedin, 9054, P.O. Box 56, Aotearoa-New Zealand
| | - G E L Petersen
- Laboratory for Evolution and Development, Genetics Otago, Biochemistry Department, University of Otago, Dunedin, 9054, P.O. Box 56, Aotearoa-New Zealand.,AbacusBio Ltd, Public Trust Building, 442 Moray Place, Dunedin 9016, Aotearoa-New Zealand
| | - R C Cameron
- Department of Developmental and Molecular Biology and Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - P K Dearden
- Laboratory for Evolution and Development, Genetics Otago, Biochemistry Department, University of Otago, Dunedin, 9054, P.O. Box 56, Aotearoa-New Zealand
| |
Collapse
|
45
|
Bossert S, Murray EA, Blaimer BB, Danforth BN. The impact of GC bias on phylogenetic accuracy using targeted enrichment phylogenomic data. Mol Phylogenet Evol 2017; 111:149-157. [PMID: 28390323 DOI: 10.1016/j.ympev.2017.03.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/06/2017] [Accepted: 03/24/2017] [Indexed: 01/08/2023]
Abstract
The field of sequence based phylogenetic analyses is currently being transformed by novel hybrid-based targeted enrichment methods, such as the use of ultraconserved elements (UCEs). Rather than analyzing relationships among organisms using a small number of genes, these methods now allow us to evaluate relationships with many hundreds to thousands of individual gene loci. However, the inclusion of thousands of loci does not necessarily overcome the long-standing challenge of incongruence among phylogenetic trees derived from different genes or gene regions. One factor that impacts the level of incongruence in phylogenomic data sets is the level of GC bias. GC rich gene regions are prone to higher recombination rates than AT rich regions, driven by a process referred to as "GC biased gene conversion". As a result, high GC content can be negatively associated with phylogenetic accuracy, but the extent to which this impacts incongruence among UCEs is currently unstudied. We investigated the impact of GC content on phylogeny reconstruction using in silico captured UCE data for the corbiculate bees (Hymenoptera: Apidae). The phylogeny of this group has been the subject of extensive study, and incongruence among gene trees is thought to be a source of phylogenetic error. We conducted coalescent- and concatenation-based analyses of 810 individual gene loci from all 13 currently available bee genomes, including 8 corbiculate taxa. Both coalescent- and concatenation-based methods converged on a single topology for the corbiculate tribes. In contrast to concatenation, the coalescent-based methods revealed significant topological conflict at nodes involving the orchid bees (Euglossini) and honeybees (Apini). Partitioning the loci by GC content reveals decreasing support for the inferred topology with increasing GC bias. Based on the results of this study, we report the first evidence that GC biased gene conversion may contribute to topological incongruence in studies based on ultraconserved elements.
Collapse
Affiliation(s)
- Silas Bossert
- Department of Entomology, Cornell University, Ithaca, New York, USA.
| | | | - Bonnie B Blaimer
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Ithaca, New York, USA
| |
Collapse
|
46
|
Trapp J, McAfee A, Foster LJ. Genomics, transcriptomics and proteomics: enabling insights into social evolution and disease challenges for managed and wild bees. Mol Ecol 2017; 26:718-739. [DOI: 10.1111/mec.13986] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Judith Trapp
- Department of Biochemistry & Molecular Biology; Michael Smith Laboratories; University of British Columbia; 2125 East Mall Vancouver BC V6T 1Z4 Canada
| | - Alison McAfee
- Department of Biochemistry & Molecular Biology; Michael Smith Laboratories; University of British Columbia; 2125 East Mall Vancouver BC V6T 1Z4 Canada
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology; Michael Smith Laboratories; University of British Columbia; 2125 East Mall Vancouver BC V6T 1Z4 Canada
| |
Collapse
|
47
|
Liu H, Jia Y, Sun X, Tian D, Hurst LD, Yang S. Direct Determination of the Mutation Rate in the Bumblebee Reveals Evidence for Weak Recombination-Associated Mutation and an Approximate Rate Constancy in Insects. Mol Biol Evol 2017; 34:119-130. [PMID: 28007973 PMCID: PMC5854123 DOI: 10.1093/molbev/msw226] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Accurate knowledge of the mutation rate provides a base line for inferring expected rates of evolution, for testing evolutionary hypotheses and for estimation of key parameters. Advances in sequencing technology now permit direct estimates of the mutation rate from sequencing of close relatives. Within insects there have been three prior such estimates, two in nonsocial insects (Drosophila: 2.8 × 10-9 per bp per haploid genome per generation; Heliconius: 2.9 × 10-9) and one in a social species, the honeybee (3.4 × 10-9). Might the honeybee's rate be ∼20% higher because it has an exceptionally high recombination rate and recombination may be directly or indirectly mutagenic? To address this possibility, we provide a direct estimate of the mutation rate in the bumblebee (Bombus terrestris), this being a close relative of the honeybee but with a much lower recombination rate. We confirm that the crossover rate of the bumblebee is indeed much lower than honeybees (8.7 cM/Mb vs. 37 cM/Mb). Importantly, we find no significant difference in the mutation rates: we estimate for bumblebees a rate of 3.6 × 10-9 per haploid genome per generation (95% confidence intervals 2.38 × 10-9 and 5.37 × 10-9) which is just 5% higher than the estimate that of honeybees. Both genomes have approximately one new mutation per haploid genome per generation. While we find evidence for a direct coupling between recombination and mutation (also seen in honeybees), the effect is so weak as to leave almost no footprint on any between-species differences. The similarity in mutation rates suggests an approximate constancy of the mutation rate in insects.
Collapse
Affiliation(s)
- Haoxuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yanxiao Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaoguang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Laurence D Hurst
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| |
Collapse
|
48
|
Dukić M, Berner D, Roesti M, Haag CR, Ebert D. A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna. BMC Genet 2016; 17:137. [PMID: 27737627 PMCID: PMC5064971 DOI: 10.1186/s12863-016-0445-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 10/04/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome. RESULTS A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates. CONCLUSIONS Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.
Collapse
Affiliation(s)
- Marinela Dukić
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland.
| | - Daniel Berner
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland
| | - Marius Roesti
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland.,Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive - CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, campus CNRS, 1919, route de Mende, 34293, Montpellier Cedex 5, France.,Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Muśee 10, 1700, Fribourg, Switzerland
| | - Dieter Ebert
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland
| |
Collapse
|
49
|
Viral prevalence increases with regional colony abundance in honey bee drones (Apis mellifera L). INFECTION GENETICS AND EVOLUTION 2016; 44:549-554. [DOI: 10.1016/j.meegid.2016.07.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/07/2016] [Accepted: 07/16/2016] [Indexed: 01/06/2023]
|
50
|
Łopuch S, Tofilski A. The relationship between asymmetry, size and unusual venation in honey bees (Apis mellifera). BULLETIN OF ENTOMOLOGICAL RESEARCH 2016; 106:304-313. [PMID: 27241228 DOI: 10.1017/s0007485315000784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Despite the fact that symmetry is common in nature, it is rarely perfect. Because there is a wide range of phenotypes which differs from the average one, the asymmetry should increase along with deviation. Therefore, the aim of this study was to assess the level of asymmetry in normal individuals as well as in phenodeviants categorized as minor or major based on abnormalities in forewing venation in honey bees. Shape fluctuating asymmetry (FA) was lower in normal individuals and minor phenodeviants compared with major phenodeviants, whereas the former two categories were comparable in drones. In workers and queens, there were not significant differences in FA shape between categories. FA size was significantly lower in normal individuals compared with major phenodeviant drones and higher compared with minor phenodeviant workers. In queens, there were no significant differences between categories. The correlation between FA shape and FA size was significantly positive in drones, and insignificant in workers and queens. Moreover, a considerable level of directional asymmetry was found as the right wing was constantly bigger than the left one. Surprisingly, normal individuals were significantly smaller than minor phenodeviants in queens and drones, and they were comparable with major phenodeviants in all castes. The correlation between wing size and wing asymmetry was negative, indicating that smaller individuals were more asymmetrical. The high proportion of phenodeviants in drones compared with workers and queens confirmed their large variability. Thus, the results of the present study showed that minor phenodeviants were not always intermediate as might have been expected.
Collapse
Affiliation(s)
- S Łopuch
- Department of Pomology and Apiculture,Agricultural University,29 Listopada 54,31-425 Krakow,Poland
| | - A Tofilski
- Department of Pomology and Apiculture,Agricultural University,29 Listopada 54,31-425 Krakow,Poland
| |
Collapse
|