1
|
Fisher KJ, Vignogna RC, Lang GI. Overdominant Mutations Restrict Adaptive Loss of Heterozygosity at Linked Loci. Genome Biol Evol 2021; 13:6345346. [PMID: 34363476 PMCID: PMC8382679 DOI: 10.1093/gbe/evab181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2021] [Indexed: 12/29/2022] Open
Abstract
Loss of heterozygosity is a common mode of adaptation in asexual diploid populations. Because mitotic recombination frequently extends the full length of a chromosome arm, the selective benefit of loss of heterozygosity may be constrained by linked heterozygous mutations. In a previous laboratory evolution experiment with diploid yeast, we frequently observed homozygous mutations in the WHI2 gene on the right arm of Chromosome XV. However, when heterozygous mutations arose in the STE4 gene, another common target on Chromosome XV, loss of heterozygosity at WHI2 was not observed. Here, we show that mutations at WHI2 are partially dominant and that mutations at STE4 are overdominant. We test whether beneficial heterozygous mutations at these two loci interfere with one another by measuring loss of heterozygosity at WHI2 over 1,000 generations for ∼300 populations that differed initially only at STE4 and WHI2. We show that the presence of an overdominant mutation in STE4 reduces, but does not eliminate, loss of heterozygosity at WHI2. By sequencing 40 evolved clones, we show that populations with linked overdominant and partially dominant mutations show less parallelism at the gene level, more varied evolutionary outcomes, and increased rates of aneuploidy. Our results show that the degree of dominance and the phasing of heterozygous beneficial mutations can constrain loss of heterozygosity along a chromosome arm, and that conflicts between partially dominant and overdominant mutations can affect evolutionary outcomes.
Collapse
Affiliation(s)
- Kaitlin J Fisher
- Department of Biological Sciences, Lehigh University, USA.,Laboratory of Genetics, University of Wisconsin-Madison, USA
| | | | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, USA
| |
Collapse
|
2
|
Oldroyd BP, Yagound B, Allsopp MH, Holmes MJ, Buchmann G, Zayed A, Beekman M. Adaptive, caste-specific changes to recombination rates in a thelytokous honeybee population. Proc Biol Sci 2021; 288:20210729. [PMID: 34102886 PMCID: PMC8187994 DOI: 10.1098/rspb.2021.0729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/13/2021] [Indexed: 11/12/2022] Open
Abstract
The ability to clone oneself has clear benefits-no need for mate hunting or dilution of one's genome in offspring. It is therefore unsurprising that some populations of haplo-diploid social insects have evolved thelytokous parthenogenesis-the virgin birth of a female. But thelytokous parthenogenesis has a downside: the loss of heterozygosity (LoH) as a consequence of genetic recombination. LoH in haplo-diploid insects can be highly deleterious because female sex determination often relies on heterozygosity at sex-determining loci. The two female castes of the Cape honeybee, Apis mellifera capensis, differ in their mode of reproduction. While workers always reproduce thelytokously, queens always mate and reproduce sexually. For workers, it is important to reduce the frequency of recombination so as to not produce offspring that are homozygous. Here, we ask whether recombination rates differ between Cape workers and Cape queens that we experimentally manipulated to reproduce thelytokously. We tested our hypothesis that Cape workers have evolved mechanisms that restrain genetic recombination, whereas queens have no need for such mechanisms because they reproduce sexually. Using a combination of microsatellite genotyping and whole-genome sequencing we find that a reduction in recombination is confined to workers only.
Collapse
Affiliation(s)
- Benjamin P. Oldroyd
- Behaviour, Ecology and Evolution (BEE) Laboratory, University of Sydney, Macleay Building A12, NSW 2006, Australia
- Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany
| | - Boris Yagound
- Behaviour, Ecology and Evolution (BEE) Laboratory, University of Sydney, Macleay Building A12, NSW 2006, Australia
| | - Michael H. Allsopp
- Michael H Allsopp, Honeybee Research Section, ARC-Plant Protection Research Institute, Stellenbosch 7600, South Africa
| | - Michael J. Holmes
- Behaviour, Ecology and Evolution (BEE) Laboratory, University of Sydney, Macleay Building A12, NSW 2006, Australia
| | - Gabrielle Buchmann
- Behaviour, Ecology and Evolution (BEE) Laboratory, University of Sydney, Macleay Building A12, NSW 2006, Australia
| | - Amro Zayed
- Department of Biology, Faculty of Science, York University, Toronto, Ontario M3J 1P3, Canada
| | - Madeleine Beekman
- Behaviour, Ecology and Evolution (BEE) Laboratory, University of Sydney, Macleay Building A12, NSW 2006, Australia
- Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany
| |
Collapse
|
3
|
Carpentier F, Rodríguez de la Vega RC, Branco S, Snirc A, Coelho MA, Hood ME, Giraud T. Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi. Genome Res 2019; 29:944-953. [PMID: 31043437 PMCID: PMC6581054 DOI: 10.1101/gr.242578.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 04/29/2019] [Indexed: 12/28/2022]
Abstract
The degree of selfing has major impacts on adaptability and is often controlled by molecular mechanisms determining mating compatibility. Changes in compatibility systems are therefore important evolutionary events, but their underlying genomic mechanisms are often poorly understood. Fungi display frequent shifts in compatibility systems, and their small genomes facilitate elucidation of the mechanisms involved. In particular, linkage between the pre- and postmating compatibility loci has evolved repeatedly, increasing the odds of gamete compatibility under selfing. Here, we studied the mating-type chromosomes of two anther-smut fungi with unlinked mating-type loci despite a self-fertilization mating system. Segregation analyses and comparisons of high-quality genome assemblies revealed that these two species displayed linkage between mating-type loci and their respective centromeres. This arrangement renders the same improved odds of gamete compatibility as direct linkage of the two mating-type loci under the automictic mating (intratetrad selfing) of anther-smut fungi. Recombination cessation was found associated with a large inversion in only one of the four linkage events. The lack of trans-specific polymorphism at genes located in nonrecombining regions and linkage date estimates indicated that the events of recombination cessation occurred independently in the two sister species. Our study shows that natural selection can repeatedly lead to similar genomic patterns and phenotypes, and that different evolutionary paths can lead to distinct yet equally beneficial responses to selection. Our study further highlights that automixis and gene linkage to centromeres have important genetic and evolutionary consequences, while being poorly recognized despite being present in a broad range of taxa.
Collapse
Affiliation(s)
- Fantin Carpentier
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Sara Branco
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Marco A Coelho
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Michael E Hood
- Department of Biology, Amherst College, Amherst, Massachusetts 01002, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France
| |
Collapse
|
4
|
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
|
5
|
O’Reilly GD, Jabot F, Gunn MR, Sherwin WB. Predicting Shannon’s information for genes in finite populations: new uses for old equations. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1079-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
6
|
Engelstädter J. Asexual but Not Clonal: Evolutionary Processes in Automictic Populations. Genetics 2017; 206:993-1009. [PMID: 28381586 PMCID: PMC5499200 DOI: 10.1534/genetics.116.196873] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/21/2017] [Indexed: 11/18/2022] Open
Abstract
Many parthenogenetically reproducing animals produce offspring not clonally but through different mechanisms collectively referred to as automixis. Here, meiosis proceeds normally but is followed by a fusion of meiotic products that restores diploidy. This mechanism typically leads to a reduction in heterozygosity among the offspring compared to the mother. Following a derivation of the rate at which heterozygosity is lost at one and two loci, depending on the number of crossovers between loci and centromere, a number of models are developed to gain a better understanding of basic evolutionary processes in automictic populations. Analytical results are obtained for the expected neutral genetic variation, effective population size, mutation-selection balance, selection with overdominance, the spread of beneficial mutations, and selection on crossover rates. These results are complemented by numerical investigations elucidating how associative overdominance (two off-phase deleterious mutations at linked loci behaving like an overdominant locus) can in some cases maintain heterozygosity for prolonged times, and how clonal interference affects adaptation in automictic populations. These results suggest that although automictic populations are expected to suffer from the lack of gene shuffling with other individuals, they are nevertheless, in some respects, superior to both clonal and outbreeding sexual populations in the way they respond to beneficial and deleterious mutations. Implications for related genetic systems such as intratetrad mating, clonal reproduction, selfing, as well as different forms of mixed sexual and automictic reproduction are discussed.
Collapse
Affiliation(s)
- Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, 4072, Australia
| |
Collapse
|
7
|
An invasive social insect overcomes genetic load at the sex locus. Nat Ecol Evol 2016; 1:11. [PMID: 28812560 DOI: 10.1038/s41559-016-0011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/09/2016] [Indexed: 11/08/2022]
Abstract
Some invasive hymenopteran social insects found new populations with very few reproductive individuals. This is despite the high cost of founder effects for such insects, which generally require heterozygosity at a single locus-the complementary sex determiner, csd-to develop as females. Individuals that are homozygous at csd develop as either infertile or subfertile diploid males or not at all. Furthermore, diploid males replace the female workers that are essential for colony function. Here we document how the Asian honey bee (Apis cerana) overcame the diploid male problem during its invasion of Australia. Natural selection prevented the loss of rare csd alleles due to genetic drift and corrected the skew in allele frequencies caused by founder effects to restore high average heterozygosity. Thus, balancing selection can alleviate the genetic load at csd imposed by severe bottlenecks, and so facilitate invasiveness.
Collapse
|
8
|
Oxley PR, Ji L, Fetter-Pruneda I, McKenzie SK, Li C, Hu H, Zhang G, Kronauer DJC. The genome of the clonal raider ant Cerapachys biroi. Curr Biol 2014; 24:451-8. [PMID: 24508170 DOI: 10.1016/j.cub.2014.01.018] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/26/2013] [Accepted: 01/09/2014] [Indexed: 11/17/2022]
Abstract
Social insects are important models for social evolution and behavior. However, in many species, experimental control over important factors that regulate division of labor, such as genotype and age, is limited. Furthermore, most species have fixed queen and worker castes, making it difficult to establish causality between the molecular mechanisms that underlie reproductive division of labor, the hallmark of insect societies. Here we present the genome of the queenless clonal raider ant Cerapachys biroi, a powerful new study system that does not suffer from these constraints. Using cytology and RAD-seq, we show that C. biroi reproduces via automixis with central fusion and that heterozygosity is lost extremely slowly. As a consequence, nestmates are almost clonally related (r = 0.996). Workers in C. biroi colonies synchronously alternate between reproduction and brood care, and young workers eclose in synchronized cohorts. We show that genes associated with division of labor in other social insects are conserved in C. biroi and dynamically regulated during the colony cycle. With unparalleled experimental control over an individual's genotype and age, and the ability to induce reproduction and brood care, C. biroi has great potential to illuminate the molecular regulation of division of labor.
Collapse
Affiliation(s)
- Peter R Oxley
- Laboratory of Insect Social Evolution, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Lu Ji
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
| | - Ingrid Fetter-Pruneda
- Laboratory of Insect Social Evolution, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean K McKenzie
- Laboratory of Insect Social Evolution, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Cai Li
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
| | - Haofu Hu
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
| | - Guojie Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China; Centre for Social Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Daniel J C Kronauer
- Laboratory of Insect Social Evolution, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| |
Collapse
|