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Li T, Zhang RS, True JR. Genetic variation for sexual dimorphism in developmental traits in Drosophila melanogaster. G3 (BETHESDA, MD.) 2024; 14:jkae010. [PMID: 38427952 PMCID: PMC10989870 DOI: 10.1093/g3journal/jkae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/10/2024] [Indexed: 03/03/2024]
Abstract
Sexual dimorphism in traits of insects during the developmental stages could potentially be the direct or indirect result of sex-specific selection provided that genetic variation for sexual dimorphism is present. We investigated genetic variation in sexual dimorphism in a set of Drosophila melanogaster inbred lines for 2 traits: egg to adult development time and pupation site preference. We observed considerable genetic variation in sexual dimorphism among lines in both traits. The sexual dimorphic patterns remained relatively consistent across multiple trials, despite both traits being sensitive to environmental conditions. Additionally, we measured 2 sexually dimorphic adult morphological traits in 6 sampled lines and investigated correlations in the sexual dimorphism patterns with the 2 developmental traits. The abundance of genetic variation in sexual dimorphism for D. melanogaster developmental traits demonstrated in this study provides evidence for a high degree of evolvability of sex differences in preadult traits in natural populations.
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Affiliation(s)
- Tianyu Li
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Rebecca S Zhang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John R True
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
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2
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Kaufmann P, Howie JM, Immonen E. Sexually antagonistic selection maintains genetic variance when sexual dimorphism evolves. Proc Biol Sci 2023; 290:20222484. [PMID: 36946115 PMCID: PMC10031426 DOI: 10.1098/rspb.2022.2484] [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: 12/12/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
Genetic variance (VG) in fitness related traits is often unexpectedly high, evoking the question how VG can be maintained in the face of selection. Sexually antagonistic (SA) selection favouring alternative alleles in the sexes is common and predicted to maintain VG, while directional selection should erode it. Both SA and sex-limited directional selection can lead to sex-specific adaptations but how each affect VG when sexual dimorphism evolves remain experimentally untested. Using replicated artificial selection on the seed beetle Callosobruchus maculatus body size we recently demonstrated an increase in size dimorphism under SA and male-limited (ML) selection by 50% and 32%, respectively. Here we test their consequences on genetic variation. We show that SA selection maintained significantly more ancestral, autosomal additive genetic variance than ML selection, while both eroded sex-linked additive variation equally. Ancestral female-specific dominance variance was completely lost under ML, while SA selection consistently sustained it. Further, both forms of selection preserved a high genetic correlation between the sexes (rm,f). These results demonstrate the potential for sexual antagonism to maintain more genetic variance while fuelling sex-specific adaptation in a short evolutionary time scale, and are in line with predicted importance of sex-specific dominance reducing sexual conflict over alternative alleles.
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Affiliation(s)
- Philipp Kaufmann
- Department of Ecology and Genetics (Evolutionary Biology program), Uppsala University, Norbyvägen 18D, 75234 Uppsala, Sweden
| | - James Malcolm Howie
- Department of Ecology and Genetics (Evolutionary Biology program), Uppsala University, Norbyvägen 18D, 75234 Uppsala, Sweden
- Institute of Forest Entomology, Forest Pathology and Forest Protection, Boku, University of Natural Resources and Life Sciences, Peter-Jordan-Straße 82/I, 1190, Vienna, Austria
| | - Elina Immonen
- Department of Ecology and Genetics (Evolutionary Biology program), Uppsala University, Norbyvägen 18D, 75234 Uppsala, Sweden
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3
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Layh S, Nagarajan-Radha V, Lemos B, Dowling DK. Y chromosome-linked variation affects locomotor activity in male Drosophila melanogaster and is robust to differences in thermal environment. Heredity (Edinb) 2023; 130:312-319. [PMID: 36914794 PMCID: PMC10163223 DOI: 10.1038/s41437-023-00604-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/16/2023] Open
Abstract
Although containing genes important for sex determination, genetic variation within the Y chromosome was traditionally predicted to contribute little to the expression of sexually dimorphic traits. This prediction was shaped by the assumption that the chromosome harbours few protein-coding genes, and that capacity for Y-linked variation to shape adaptation would be hindered by the chromosome's lack of recombination and holandric inheritance. Consequently, most studies exploring the genotypic contributions to sexually dimorphic traits have focused on the autosomes and X chromosome. Yet, several studies have now demonstrated that the Y chromosome harbours variation affecting male fitness, moderating the expression of hundreds of genes across the nuclear genome. Furthermore, emerging results have shown that expression of this Y-linked variation may be sensitive to environmental heterogeneity, leading to the prediction that Y-mediated gene-by-environment interactions will shape the expression of sexually dimorphic phenotypes. We tested this prediction, investigating whether genetic variation across six distinct Y chromosome haplotypes affects the expression of locomotor activity, at each of two temperatures (20 and 28 °C) in male fruit flies (Drosophila melanogaster). Locomotor activity is a sexually dimorphic trait in this species, previously demonstrated to be under intralocus sexual conflict. We demonstrate Y haplotype effects on male locomotor activity, but the rank order and magnitude of these effects were unaltered by differences in temperature. Our study contributes to a growing number of studies demonstrating Y-linked effects moderating expression of traits evolving under sexually antagonistic selection, suggesting a role for the Y chromosome in shaping outcomes of sexual conflict.
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Affiliation(s)
- Sean Layh
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Venkatesh Nagarajan-Radha
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia.,Behaviour Ecology and Evolution Lab, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Bernardo Lemos
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia.
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4
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Immonen E, Sayadi A, Stojković B, Savković U, Đorđević M, Liljestrand-Rönn J, Wiberg RAW, Arnqvist G. Experimental Life History Evolution Results in Sex-specific Evolution of Gene Expression in Seed Beetles. Genome Biol Evol 2022; 15:6948356. [PMID: 36542472 PMCID: PMC9830990 DOI: 10.1093/gbe/evac177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The patterns of reproductive timing and senescence vary within and across species owing to differences in reproductive strategies, but our understanding of the molecular underpinnings of such variation is incomplete. This is perhaps particularly true for sex differences. We investigated the evolution of sex-specific gene expression associated with life history divergence in replicated populations of the seed beetle Acanthoscelides obtectus, experimentally evolving under (E)arly or (L)ate life reproduction for >200 generations which has resulted in strongly divergent life histories. We detected 1,646 genes that were differentially expressed in E and L lines, consistent with a highly polygenic basis of life history evolution. Only 30% of differentially expressed genes were similarly affected in males and females. The evolution of long life was associated with significantly reduced sex differences in expression, especially in non-reproductive tissues. The expression differences were overall more pronounced in females, in accordance with their greater phenotypic divergence in lifespan. Functional enrichment analysis revealed differences between E and L beetles in gene categories previously implicated in aging, such as mitochondrial function and defense response. The results show that divergent life history evolution can be associated with profound changes in gene expression that alter the transcriptome in a sex-specific way, highlighting the importance of understanding the mechanisms of aging in each sex.
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Affiliation(s)
| | - Ahmed Sayadi
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Biljana Stojković
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia,Faculty of Biology, Institute of Zoology, University of Belgrade, Belgrade, Serbia
| | - Uroš Savković
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Mirko Đorđević
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - R Axel W Wiberg
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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5
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Xu R, Martelossi J, Smits M, Iannello M, Peruzza L, Babbucci M, Milan M, Dunham JP, Breton S, Milani L, Nuzhdin SV, Bargelloni L, Passamonti M, Ghiselli F. Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam. Genome Biol Evol 2022; 14:6889380. [PMID: 36508337 PMCID: PMC9803972 DOI: 10.1093/gbe/evac171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/26/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The molecular factors and gene regulation involved in sex determination and gonad differentiation in bivalve molluscs are unknown. It has been suggested that doubly uniparental inheritance (DUI) of mitochondria may be involved in these processes in species such as the ubiquitous and commercially relevant Manila clam, Ruditapes philippinarum. We present the first long-read-based de novo genome assembly of a Manila clam, and a RNA-Seq multi-tissue analysis of 15 females and 15 males. The highly contiguous genome assembly was used as reference to investigate gene expression, alternative splicing, sequence evolution, tissue-specific co-expression networks, and sexual contrasting SNPs. Differential expression (DE) and differential splicing (DS) analyses revealed sex-specific transcriptional regulation in gonads, but not in somatic tissues. Co-expression networks revealed complex gene regulation in gonads, and genes in gonad-associated modules showed high tissue specificity. However, male gonad-associated modules showed contrasting patterns of sequence evolution and tissue specificity. One gene set was related to the structural organization of male gametes and presented slow sequence evolution but high pleiotropy, whereas another gene set was enriched in reproduction-related processes and characterized by fast sequence evolution and tissue specificity. Sexual contrasting SNPs were found in genes overrepresented in mitochondrial-related functions, providing new candidates for investigating the relationship between mitochondria and sex in DUI species. Together, these results increase our understanding of the role of DE, DS, and sequence evolution of sex-specific genes in an understudied taxon. We also provide resourceful genomic data for studies regarding sex diagnosis and breeding in bivalves.
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Affiliation(s)
- Ran Xu
- Corresponding authors: E-mail: (R.X.); E-mail: (F.G.)
| | | | | | | | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Joseph P Dunham
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA,SeqOnce Biosciences Inc., Pasadena, CA, USA
| | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Sergey V Nuzhdin
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
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6
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Parker DJ, Jaron KS, Dumas Z, Robinson‐Rechavi M, Schwander T. X chromosomes show relaxed selection and complete somatic dosage compensation across
Timema
stick insect species. J Evol Biol 2022; 35:1734-1750. [PMID: 35933721 PMCID: PMC10087215 DOI: 10.1111/jeb.14075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/06/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes have evolved repeatedly across the tree of life. As they are present in different copy numbers in males and females, they are expected to experience different selection pressures than the autosomes, with consequences including a faster rate of evolution, increased accumulation of sexually antagonistic alleles and the evolution of dosage compensation. Whether these consequences are general or linked to idiosyncrasies of specific taxa is not clear as relatively few taxa have been studied thus far. Here, we use whole-genome sequencing to identify and characterize the evolution of the X chromosome in five species of Timema stick insects with XX:X0 sex determination. The X chromosome had a similar size (approximately 12% of the genome) and gene content across all five species, suggesting that the X chromosome originated prior to the diversification of the genus. Genes on the X showed evidence of relaxed selection (elevated dN/dS) and a slower evolutionary rate (dN + dS) than genes on the autosomes, likely due to sex-biased mutation rates. Genes on the X also showed almost complete dosage compensation in somatic tissues (heads and legs), but dosage compensation was absent in the reproductive tracts. Contrary to prediction, sex-biased genes showed little enrichment on the X, suggesting that the advantage X-linkage provides to the accumulation of sexually antagonistic alleles is weak. Overall, we found the consequences of X-linkage on gene sequences and expression to be similar across Timema species, showing the characteristics of the X chromosome are surprisingly consistent over 30 million years of evolution.
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Affiliation(s)
- Darren J. Parker
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Natural Sciences Bangor University Bangor UK
| | - Kamil S. Jaron
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Biological Sciences Institute of Evolutionary Biology University of Edinburgh Edinburgh UK
| | - Zoé Dumas
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
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7
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Rowe L, Rundle HD. The Alignment of Natural and Sexual Selection. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012021-033324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sexual selection has the potential to decrease mean fitness in a population through an array of costs to nonsexual fitness. These costs may be offset when sexual selection favors individuals with high nonsexual fitness, causing the alignment of sexual and natural selection. We review the many laboratory experiments that have manipulated mating systems aimed at quantifying the net effects of sexual selection on mean fitness. These must be interpreted in light of population history and the diversity of ways manipulations have altered sexual interactions, sexual conflict, and sexual and natural selection. Theory and data suggest a net benefit is more likely when sexually concordant genetic variation is enhanced and that ecological context can mediate the relative importance of these different effects. Comparative studies have independently examined the consequences of sexual selection for population/species persistence. These provide little indication of a benefit, and interpreting these higher-level responses is challenging.
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Affiliation(s)
- Locke Rowe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Howard D. Rundle
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
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8
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Grieshop K, Maurizio PL, Arnqvist G, Berger D. Selection in males purges the mutation load on female fitness. Evol Lett 2021; 5:328-343. [PMID: 34367659 PMCID: PMC8327962 DOI: 10.1002/evl3.239] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/26/2022] Open
Abstract
Theory predicts that the ability of selection and recombination to purge mutation load is enhanced if selection against deleterious genetic variants operates more strongly in males than females. However, direct empirical support for this tenet is limited, in part because traditional quantitative genetic approaches allow dominance and intermediate-frequency polymorphisms to obscure the effects of the many rare and partially recessive deleterious alleles that make up the main part of a population's mutation load. Here, we exposed the partially recessive genetic load of a population of Callosobruchus maculatus seed beetles via successive generations of inbreeding, and quantified its effects by measuring heterosis-the increase in fitness experienced when masking the effects of deleterious alleles by heterozygosity-in a fully factorial sex-specific diallel cross among 16 inbred strains. Competitive lifetime reproductive success (i.e., fitness) was measured in male and female outcrossed F1s as well as inbred parental "selfs," and we estimated the 4 × 4 male-female inbred-outbred genetic covariance matrix for fitness using Bayesian Markov chain Monte Carlo simulations of a custom-made general linear mixed effects model. We found that heterosis estimated independently in males and females was highly genetically correlated among strains, and that heterosis was strongly negatively genetically correlated to outbred male, but not female, fitness. This suggests that genetic variation for fitness in males, but not in females, reflects the amount of (partially) recessive deleterious alleles segregating at mutation-selection balance in this population. The population's mutation load therefore has greater potential to be purged via selection in males. These findings contribute to our understanding of the prevalence of sexual reproduction in nature and the maintenance of genetic variation in fitness-related traits.
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Affiliation(s)
- Karl Grieshop
- Animal Ecology, Department of Ecology and GeneticsUppsala UniversityUppsalaSE‐75236Sweden
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM5S 3B2Canada
- Department of Molecular BiosciencesThe Wenner‐Gren InstituteStockholm UniversityStockholmSE‐10691Sweden
| | - Paul L. Maurizio
- Section of Genetic Medicine, Department of MedicineUniversity of ChicagoChicagoIllinois60637
| | - Göran Arnqvist
- Animal Ecology, Department of Ecology and GeneticsUppsala UniversityUppsalaSE‐75236Sweden
| | - David Berger
- Animal Ecology, Department of Ecology and GeneticsUppsala UniversityUppsalaSE‐75236Sweden
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9
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van der Bijl W, Mank JE. Widespread cryptic variation in genetic architecture between the sexes. Evol Lett 2021; 5:359-369. [PMID: 34367661 PMCID: PMC8327960 DOI: 10.1002/evl3.245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/06/2021] [Accepted: 06/13/2021] [Indexed: 11/08/2022] Open
Abstract
The majority of the genome is shared between the sexes, and it is expected that the genetic architecture of most traits is shared as well. This common architecture has been viewed as a major source of constraint on the evolution of sexual dimorphism (SD). SD is nonetheless common in nature, leading to assumptions that it results from differential regulation of shared genetic architecture. Here, we study the effect of thousands of gene knockout mutations on 202 mouse phenotypes to explore how regulatory variation affects SD. We show that many traits are dimorphic to some extent, and that a surprising proportion of knockouts have sex-specific phenotypic effects. Many traits, regardless whether they are monomorphic or dimorphic, harbor cryptic differences in genetic architecture between the sexes, resulting in sexually discordant phenotypic effects from sexually concordant regulatory changes. This provides an alternative route to dimorphism through sex-specific genetic architecture, rather than differential regulation of shared architecture.
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Affiliation(s)
- Wouter van der Bijl
- Department of ZoologyUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Judith E. Mank
- Department of ZoologyUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- BiosciencesUniversity of ExeterPenryn CampusPenrynTR10 9FEUK
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10
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Abstract
Sexual dimorphism in gene expression is likely to be the underlying source of dimorphism in a variety of traits. Many analyses implicitly make the assumption that dimorphism only evolves when selection favors different phenotypes in the two sexes, although theory makes clear that it can also evolve as an indirect response to other kinds of selection. Furthermore, previous analyses consider the evolution of a single transcript or trait at a time, ignoring the genetic covariance with other transcripts and traits. We first show which aspects of the genetic-variance-covariance matrix, G, affect dimorphism when these assumptions about selection are relaxed. We then reanalyze gene expression data from Drosophila melanogaster with these predictions in mind. Dimorphism of gene expression for individual transcripts shows the signature of both direct selection for dimorphism and indirect responses to selection. To account for the effect of measurement error on evolutionary predictions, we estimated a G matrix for eight linear combinations of expression traits. Sex-specific genetic variances in female- and male-biased transcription, as well as one relatively unbiased combination, were quite unequal, ensuring that most forms of selection on these traits will have large effects on dimorphism. Predictions of response to selection based on the whole G matrix showed that sexually concordant and antagonistic selection are equally capable of changing sexual dimorphism. In addition, the indirect responses of dimorphism due to cross-trait covariances were quite substantial. The assumption that sexual dimorphism in transcription is an adaptation could be incorrect in many specific cases.
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Affiliation(s)
- David Houle
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Changde Cheng
- Department of Integrative Biology, University of Texas, Austin, TX, USA
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11
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Development of a Set of Microsatellite Markers to Investigate Sexually Antagonistic Selection in the Invasive Ant Nylanderia fulva. INSECTS 2021; 12:insects12070643. [PMID: 34357303 PMCID: PMC8306888 DOI: 10.3390/insects12070643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022]
Abstract
Simple Summary The two sexes of a species usually exhibit phenotypic differences, such as in behavior, body size or color. They, however, share most of their genomes, preventing fixation of distinct alleles for genes coding for those traits in each sex. The different optima between the sexes on these loci lead to genomic conflicts, called sexually antagonistic selection (SAS). Under SAS, distinct alleles are therefore selected in each sex. In the invasive tawny crazy ant, Nylanderia fulva, a genomic region is under SAS, while the rest of the genome is randomly selected in males and females. Here, we provide a suite of 15 polymorphic microsatellite markers located in the SAS genomic region to study the origin and evolution of SAS in N. fulva. These markers have allelic frequencies that are highly different between males and females. All males carry only a subset of the alleles present in the population, while females are reliably heterozygous, with one allele from the male gene pool and a different allele inherited from their mother. The SAS markers may be used to test for the strength and the extent of the genomic regions under SAS in both the native and introduced ranges of N. fulva. These markers may serve to answer similar questions in other introduced species of the Nylanderia genus, yielding insights into the origin and evolution of SAS within and among species of the genus Nylanderia. Abstract Sexually antagonistic selection (SAS) occurs when distinct alleles are differentially selected in each sex. In the invasive tawny crazy ant, Nylanderia fulva, a genomic region is under SAS, while the rest of the genome is randomly selected in males and females. In this study, we designed a suite of 15 microsatellite markers to study the origin and evolution of SAS in N. fulva. These SAS markers were polymorphic, with allelic frequencies that are highly different between males and females. All haploid males carry only a subset of the alleles present in the population, while females are reliably heterozygous, with one allele from the male gene pool and a different allele inherited from their mother. In addition, we identified six polymorphic markers not associated with SAS and six markers yielding consistent, yet monomorphic, amplification in the introduced range of this species. Reaction condition optimizations allowed all retained markers to be co-amplified in four PCR mixes. The SAS markers may be used to test for the strength and the extent of the genomic regions under SAS in both the native and introduced ranges of N. fulva, while the set of non-SAS loci may be used to assess the invasion route of this species. Overall, the application of these microsatellite markers will yield insights into the origin and evolution of SAS within and among species of the genus Nylanderia.
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12
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Ruzicka F, Connallon T. Is the X chromosome a hot spot for sexually antagonistic polymorphisms? Biases in current empirical tests of classical theory. Proc Biol Sci 2020; 287:20201869. [PMID: 33081608 PMCID: PMC7661300 DOI: 10.1098/rspb.2020.1869] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022] Open
Abstract
Females and males carry nearly identical genomes, which can constrain the evolution of sexual dimorphism and generate conditions that are favourable for maintaining sexually antagonistic (SA) polymorphisms, in which alleles beneficial for one sex are deleterious for the other. An influential theoretical prediction, by Rice (Rice 1984 Evolution38, 735-742), is that the X chromosome should be a 'hot spot' (i.e. enriched) for SA polymorphisms. While important caveats to Rice's theoretical prediction have since been highlighted (e.g. by Fry (2010) Evolution64, 1510-1516), several empirical studies appear to support it. Here, we show that current tests of Rice's theory-most of which are based on quantitative genetic measures of fitness (co)variance-are frequently biased towards detecting X-linked effects. We show that X-linked genes tend to contribute disproportionately to quantitative genetic patterns of SA fitness variation whether or not the X is enriched for SA polymorphisms. Population genomic approaches for detecting SA loci, including genome-wide association study of fitness and analyses of intersexual FST, are similarly biased towards detecting X-linked effects. In the light of our models, we critically re-evaluate empirical evidence for Rice's theory and discuss prospects for empirically testing it.
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13
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Cheng 成常德 C, Houle D. Predicting Multivariate Responses of Sexual Dimorphism to Direct and Indirect Selection. Am Nat 2020; 196:391-405. [PMID: 32970462 DOI: 10.1086/710353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractSexual dimorphism is often assumed to result from balancing the strength of antagonistic selection in favor of dimorphism against the degree of constraint imposed by the shared genome of the sexes, reflected in the B matrix of genetic intersexual covariances. To investigate the totality of forces shaping dimorphism, we reparameterized the Lande equation to predict changes in trait averages and trait differences between the sexes. As genetic constraints on the evolution of dimorphism in response to antagonistic selection become larger, dimorphism will tend to respond more rapidly to concordant selection (which favors the same direction of change in male and female traits) than to antagonistic selection. When we apply this theory to four empirical estimates of B in Drosophila melanogaster, the indirect responses of dimorphism to concordant selection are of comparable or larger magnitude than the direct responses of dimorphism to antagonistic selection in two suites of traits with typical levels of intersex correlation. Antagonistic selection is more important in two suites of traits where the intersex correlations are unusually low. This suggests that the evolution of sexual dimorphism may sometimes be dominated by concordant selection rather than antagonistic selection.
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14
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Khodursky S, Svetec N, Durkin SM, Zhao L. The evolution of sex-biased gene expression in the Drosophila brain. Genome Res 2020; 30:874-884. [PMID: 32554780 PMCID: PMC7370887 DOI: 10.1101/gr.259069.119] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/16/2020] [Indexed: 01/08/2023]
Abstract
Genes with sex-biased expression in Drosophila are thought to underlie sexually dimorphic phenotypes and have been shown to possess unique evolutionary properties. However, the forces and constraints governing the evolution of sex-biased genes in the somatic tissues of Drosophila are largely unknown. By using population-scale RNA sequencing data, we show that sex-biased genes in the Drosophila brain are highly enriched on the X Chromosome and that most are biased in a species-specific manner. We show that X-linked male-biased genes, and to a lesser extent female-biased genes, are enriched for signatures of directional selection at the gene expression level. By examining the evolutionary properties of gene-flanking regions on the X Chromosome, we find evidence that adaptive cis-regulatory changes are more likely to drive the expression evolution of X-linked male-biased genes than other X-linked genes. Finally, we examine whether constraint owing to broad expression across multiple tissues and genetic constraint owing to the largely shared male and female genomes could be responsible for the observed patterns of gene expression evolution. We find that expression breadth does not constrain the directional evolution of gene expression in the brain. Additionally, we find that the shared genome between males and females imposes a substantial constraint on the expression evolution of sex-biased genes. Overall, these results significantly advance our understanding of the patterns and forces shaping the evolution of sexual dimorphism in the Drosophila brain.
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Affiliation(s)
- Samuel Khodursky
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, New York 10065, USA
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, New York 10065, USA
| | - Sylvia M Durkin
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, New York 10065, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, New York 10065, USA
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15
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Li J, Yu H, Wang W, Fu C, Zhang W, Han F, Wu H. Genomic and transcriptomic insights into molecular basis of sexually dimorphic nuptial spines in Leptobrachium leishanense. Nat Commun 2019; 10:5551. [PMID: 31804492 PMCID: PMC6895153 DOI: 10.1038/s41467-019-13531-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 11/13/2019] [Indexed: 12/21/2022] Open
Abstract
Sexually dimorphic (SD) traits are important in sexual selection and species survival, yet the molecular basis remains elusive, especially in amphibians where SD traits have evolved repeatedly. We focus on the Leishan moustache toad (Leptobrachium leishanense), in which males develop nuptial spines on their maxillary skin. Here we report a 3.5 Gb genome assembly with a contig N50 of 1.93 Mb. We find a specific expansion of the intermediate filament gene family including numerous keratin genes. Within these genes, a cluster of duplicated hair keratin genes exhibits male-biased and maxillary skin-specific expression, suggesting a role in developing nuptial spines. We identify a module of coexpressed genes significantly associated with spine formation. In addition, we find several hormones likely to be involved in regulating spine development. This study not only presents a high-quality anuran genome but also provides a reference for studying skin-derived SD traits in amphibians. The basis of sexual dimorphism in non-model species may be elusive, in part due to a lack of genomic and molecular resources. Here, Li et al. report a high-quality anuran genome and reveal candidate genes and pathways associated with shaping sexually dimorphic nuptial spines in a moustache toad.
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Affiliation(s)
- Jun Li
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Wenxia Wang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China
| | - Chao Fu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China
| | - Wei Zhang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China
| | - Fengming Han
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Hua Wu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
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16
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Sayadi A, Martinez Barrio A, Immonen E, Dainat J, Berger D, Tellgren-Roth C, Nystedt B, Arnqvist G. The genomic footprint of sexual conflict. Nat Ecol Evol 2019; 3:1725-1730. [DOI: 10.1038/s41559-019-1041-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/15/2019] [Indexed: 12/28/2022]
Abstract
AbstractGenes with sex-biased expression show a number of unique properties and this has been seen as evidence for conflicting selection pressures in males and females, forming a genetic ‘tug-of-war’ between the sexes. However, we lack studies of taxa where an understanding of conflicting phenotypic selection in the sexes has been linked with studies of genomic signatures of sexual conflict. Here, we provide such a link. We used an insect where sexual conflict is unusually well understood, the seed beetle Callosobruchus maculatus, to test for molecular genetic signals of sexual conflict across genes with varying degrees of sex-bias in expression. We sequenced, assembled and annotated its genome and performed population resequencing of three divergent populations. Sex-biased genes showed increased levels of genetic diversity and bore a remarkably clear footprint of relaxed purifying selection. Yet, segregating genetic variation was also affected by balancing selection in weakly female-biased genes, while male-biased genes showed signs of overall purifying selection. Female-biased genes contributed disproportionally to shared polymorphism across populations, while male-biased genes, male seminal fluid protein genes and sex-linked genes did not. Genes showing genomic signatures consistent with sexual conflict generally matched life-history phenotypes known to experience sexually antagonistic selection in this species. Our results highlight metabolic and reproductive processes, confirming the key role of general life-history traits in sexual conflict.
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17
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Sexually antagonistic selection promotes genetic divergence between males and females in an ant. Proc Natl Acad Sci U S A 2019; 116:24157-24163. [PMID: 31719204 DOI: 10.1073/pnas.1906568116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic diversity acts as a reservoir for potential adaptations, yet selection tends to reduce this diversity over generations. However, sexually antagonistic selection (SAS) may promote diversity by selecting different alleles in each sex. SAS arises when an allele is beneficial to one sex but harmful to the other. Usually, the evolution of sex chromosomes allows each sex to independently reach different optima, thereby circumventing the constraint of a shared autosomal genome. Because the X chromosome is found twice as often in females than males, it represents a hot spot for SAS, offering a refuge for recessive male-beneficial but female-costly alleles. Hymenopteran species do not have sex chromosomes; females are diploid and males are haploid, with sex usually determined by heterozygosity at the complementary sex-determining locus. For this reason, their entire genomes display an X-linked pattern, as every chromosome is found twice as often in females than in males, which theoretically predisposes them to SAS in large parts of their genome. Here we report an instance of sexual divergence in the Hymenoptera, a sexually reproducing group that lacks sex chromosomes. In the invasive ant Nylanderia fulva, a postzygotic SAS leads daughters to preferentially carry alleles from their mothers and sons to preferentially carry alleles from their grandfathers for a substantial region (∼3%) of the genome. This mechanism results in nearly all females being heterozygous at these regions and maintains diversity throughout the population, which may mitigate the effects of a genetic bottleneck following introduction to an exotic area and enhance the invasion success of this ant.
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18
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Yuan W, Jiang S, Sun D, Wu Z, Wei C, Dai C, Jiang L, Peng S. Transcriptome profiling analysis of sex-based differentially expressed mRNAs and lncRNAs in the brains of mature zebrafish (Danio rerio). BMC Genomics 2019; 20:830. [PMID: 31703616 PMCID: PMC6842217 DOI: 10.1186/s12864-019-6197-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 10/16/2019] [Indexed: 12/18/2022] Open
Abstract
Background Similar to humans, the zebrafish brain plays a central role in regulating sexual reproduction, maturation and sexual behavior. However, systematic studies of the dimorphic patterns of gene expression in the brain of male and female zebrafish are lacking. Results In this study, the mRNA and lncRNA expression profiles were obtained from the brain tissue samples of the three male and three female zebrafish by high-throughput transcriptome sequencing. We identified a total of 108 mRNAs and 50 lncRNAs with sex-based differential expression. We randomly selected four differentially expressed genes for RT-qPCR verification and the results certified that the expression pattern showed a similar trend between RNA-seq and RT-qPCR results. Protein-protein interaction network analysis, Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to obtain the biological significance of differentially expressed mRNA in the brain dimorphism of zebrafish. Finally, a Pearson correlation analysis was performed to construct the co-expression network of the mRNAs and lncRNAs. Conclusions We found that 12 new lncRNAs not only have significant gender specificity in the brain of zebrafish, and this finding may provide a clue to further study of the functional difference between male and female zebrafish brain.
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Affiliation(s)
- Wenliang Yuan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China.,School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.,College of Mathematics and Information Engineering, Jiaxing University, Jiaxing, 314001, China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China
| | - Dan Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China
| | - Zhichao Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China
| | - Cai Wei
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China
| | | | - Linhua Jiang
- School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
| | - Sihua Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China. .,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China. .,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China.
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19
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Puixeu G, Pickup M, Field DL, Barrett SCH. Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. THE NEW PHYTOLOGIST 2019; 224:1108-1120. [PMID: 31291691 PMCID: PMC6851585 DOI: 10.1111/nph.16050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/27/2019] [Indexed: 06/09/2023]
Abstract
Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less information is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigated patterns of genetically based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1 Y2 ) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life-cycle.
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Affiliation(s)
- Gemma Puixeu
- Institute of Science and Technology AustriaAm Campus 1Klosterneuburg3400Austria
| | - Melinda Pickup
- Institute of Science and Technology AustriaAm Campus 1Klosterneuburg3400Austria
- Department of Ecology and Evolutionary BiologyUniversity of Toronto25 Willcocks St.TorontoONM5S 3B2Canada
| | - David L. Field
- Department of Ecology and Evolutionary BiologyUniversity of Toronto25 Willcocks St.TorontoONM5S 3B2Canada
- School of ScienceEdith Cowan University270 Joondalup DriveJoondalupWA6027Australia
| | - Spencer C. H. Barrett
- Department of Ecology and Evolutionary BiologyUniversity of Toronto25 Willcocks St.TorontoONM5S 3B2Canada
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20
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Bissegger M, Laurentino TG, Roesti M, Berner D. Widespread intersex differentiation across the stickleback genome – The signature of sexually antagonistic selection? Mol Ecol 2019; 29:262-271. [DOI: 10.1111/mec.15255] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Mirjam Bissegger
- Department of Environmental Sciences, Zoology University of Basel Basel Switzerland
| | - Telma G. Laurentino
- Department of Environmental Sciences, Zoology University of Basel Basel Switzerland
| | - Marius Roesti
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Zoology University of Basel Basel Switzerland
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21
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Comparative analysis of the multivariate genetic architecture of morphological traits in three species of Gomphocerine grasshoppers. Heredity (Edinb) 2019; 124:367-382. [PMID: 31649325 DOI: 10.1038/s41437-019-0276-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/08/2019] [Accepted: 09/18/2019] [Indexed: 11/08/2022] Open
Abstract
Evolutionary change is the change in trait values across generations, and usually occurs in multidimensional trait space rather than along isolated traits. Genetic covariation influences the magnitude and direction of evolutionary change and can be statistically summarized by the additive genetic (co)variance matrix, G. While G can affect the response to selection, it is exposed to evolutionary change by selection and genetic drift, but the magnitude and speed of these changes are poorly understood. We use comparative G matrix analyses to assess evolution of the shape and orientation of G over longer timescales in three species of Gomphocerine grasshoppers. We estimate 10 × 10 G matrices for five morphological traits expressed in both sexes. We find low-to-moderate heritabilities (average 0.36), mostly large cross-sex correlations (average 0.54) and moderate between-trait correlations (average 0.34). G matrices differ significantly among species with wing length contributing most to these differences. Wing length is the trait that is most divergent among species, suggesting it has been under selection during species divergence. The more distantly related species, Pseudochorthippus parallelus, was the most different in the shape of G. Projection of contemporary genetic variation into the divergence space D illustrates that the major axis of genetic variation in Gomphocerippus rufus is aligned with divergence from Chorthippus biguttulus, while the major axis of genetic variation in neither of the species is aligned with the divergence between Pseudochorthippus parallelus and the other two species. Our results demonstrate significant differences in G matrices with a phylogenetic signal in the differentiation.
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22
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Sex-biased gene expression is repeatedly masculinized in asexual females. Nat Commun 2019; 10:4638. [PMID: 31604947 PMCID: PMC6789136 DOI: 10.1038/s41467-019-12659-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/23/2019] [Indexed: 12/21/2022] Open
Abstract
Males and females feature strikingly different phenotypes, despite sharing most of their genome. A resolution of this apparent paradox is through differential gene expression, whereby genes are expressed at different levels in each sex. This resolution, however, is likely to be incomplete, leading to conflict between males and females over the optimal expression of genes. Here we test the hypothesis that gene expression in females is constrained from evolving to its optimum level due to sexually antagonistic selection on males, by examining changes in sex-biased gene expression in five obligate asexual species of stick insect, which do not produce males. We predicted that the transcriptome of asexual females would be feminized as asexual females do not experience any sexual conflict. Contrary to our prediction we find that asexual females feature masculinized gene expression, and hypothesise that this is due to shifts in female optimal gene expression levels following the suppression of sex.
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23
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Matthews G, Hangartner S, Chapple DG, Connallon T. Quantifying maladaptation during the evolution of sexual dimorphism. Proc Biol Sci 2019; 286:20191372. [PMID: 31409252 DOI: 10.1098/rspb.2019.1372] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Females and males have distinct trait optima, resulting in selection for sexual dimorphism. However, most traits have strong cross-sex genetic correlations, which constrain evolutionary divergence between the sexes and lead to protracted periods of maladaptation during the evolution of sexual dimorphism. While such constraints are thought to be costly in terms of individual and population fitness, it remains unclear how severe such costs are likely to be. Building upon classical models for the 'cost of selection' in changing environments (sensu Haldane), we derived a theoretical expression for the analogous cost of evolving sexual dimorphism; this cost is a simple function of genetic (co)variances of female and male traits and sex differences in trait optima. We then conducted a comprehensive literature search, compiled quantitative genetic data from a diverse set of traits and populations, and used them to quantify costs of sexual dimorphism in the light of our model. For roughly 90% of traits, costs of sexual dimorphism appear to be modest, and comparable to the costs of fixing one or a few beneficial substitutions. For the remaining traits (approx. 10%), sexual dimorphism appears to carry a substantial cost-potentially orders of magnitude greater than costs of selection during adaptation to environmental changes.
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Affiliation(s)
- Genevieve Matthews
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Sandra Hangartner
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - David G Chapple
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia.,Centre for Geometric Biology, Monash University, Clayton, Victoria 3800, Australia
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24
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Allen SL, Bonduriansky R, Chenoweth SF. Genetic constraints on microevolutionary divergence of sex-biased gene expression. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0427. [PMID: 30150225 DOI: 10.1098/rstb.2017.0427] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2018] [Indexed: 12/18/2022] Open
Abstract
The evolution of sex-specific phenotypes is an important dimension of diversification and local adaptation. The sex-dependent regulation of gene expression is considered a key genomic mechanism facilitating sex-dependent adaptation. In many species, genes with male-biased expression evolve faster in DNA sequence and expression level than genes with female-biased or sexually monomorphic expression. While positive selection may be responsible for rapid DNA sequence evolution, why expression of male-biased genes also evolves rapidly remains unclear. Beyond sex differences in selection, some aspects of the genetic architecture of gene expression could contribute to the rapid evolution of male-biased gene expression. First, male-biased genes might simply have greater standing genetic variance than female-biased genes. Second, male-biased genes could be less constrained by pleiotropy, either within or between sexes. Here, we evaluate these alternative explanations on an intraspecific scale using a series of quantitative genetic experiments conducted on natural variation in male and female gene expression in the fly Drosophila serrata Male-biased genes had significantly higher genetic variance than female-biased genes and were generally more narrowly expressed across tissues, suggesting lower within-individual pleiotropy. However, consistent with stronger constraints due to between-sex pleiotropy, their between-sex genetic correlations, rMF, were higher than for female-biased genes and more strongly negatively associated with sex bias. Using an extensive clinal dataset, we tested whether sex differences in gene expression divergence among populations have been shaped by pleiotropy. Here too, male-biased gene divergence was more strongly associated with between-sex pleiotropy than was female-biased gene divergence. Systematic differences in genetic variance and pleiotropy may be important factors influencing sex-specific adaptation arising through changes in gene expression.This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.
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Affiliation(s)
- Scott L Allen
- The School of Biological Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Russell Bonduriansky
- Evolution and Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, New South Wales, Australia
| | - Stephen F Chenoweth
- The School of Biological Sciences, The University of Queensland, St Lucia 4072, Australia
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25
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Connallon T, Débarre F, Li XY. Linking local adaptation with the evolution of sex differences. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0414. [PMID: 30150215 DOI: 10.1098/rstb.2017.0414] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 01/21/2023] Open
Abstract
Many conspicuous forms of evolutionary diversity occur within species. Two prominent examples include evolutionary divergence between populations differentially adapted to their local environments (local adaptation), and divergence between females and males in response to sex differences in selection (sexual dimorphism sensu lato). These two forms of diversity have inspired vibrant research programmes, yet these fields have largely developed in isolation from one another. Nevertheless, conceptual parallels between these research traditions are striking. Opportunities for local adaptation strike a balance between local selection, which promotes divergence, and gene flow-via dispersal and interbreeding between populations-which constrains it. Sex differences are similarly constrained by fundamental features of inheritance that mimic gene flow. Offspring of each sex inherit genes from same-sex and opposite-sex parents, leading to gene flow between each differentially selected half of the population, and raising the question of how sex differences arise and are maintained. This special issue synthesizes and extends emerging research at the interface between the research traditions of local adaptation and sex differences. Each field can promote understanding of the other, and interactions between local adaptation and sex differences can generate new empirical predictions about the evolutionary consequences of selection that varies across space, time, and between the sexes.This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Florence Débarre
- CNRS, UMR 7241 Centre Interdisciplinaire de Recherche en Biologie (CIRB), Collège de France, Paris, France
| | - Xiang-Yi Li
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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26
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Malacrinò A, Kimber CM, Brengdahl M, Friberg U. Heightened condition-dependence of the sexual transcriptome as a function of genetic quality in Drosophila melanogaster head tissue. Proc Biol Sci 2019; 286:20190819. [PMID: 31288700 DOI: 10.1098/rspb.2019.0819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Theory suggests sexual traits should show heightened condition-dependent expression. This prediction has been tested extensively in experiments where condition has been manipulated through environmental quality. Condition-dependence as a function of genetic quality has, however, only rarely been addressed, despite its central importance in evolutionary theory. To address the effect of genetic quality on expression of sexual and non-sexual traits, we here compare gene expression in Drosophila melanogaster head tissue between flies with intact genomes (high condition) and flies carrying a major deleterious mutation (low condition). We find that sex-biased genes show heightened condition-dependent expression in both sexes, and that expression in low condition males and females regresses towards a more similar expression profile. As predicted, sex-biased expression was more sensitive to condition in males compared to females, but surprisingly female-biased, rather than male-biased, genes show higher sensitivity to condition in both sexes. Our results thus support the fundamental predictions of the theory of condition-dependence when condition is a function of genetic quality.
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Affiliation(s)
- Antonino Malacrinò
- 1 IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University , 581 83 Linköping , Sweden.,2 Department of Evolution, Ecology and Organismal Biology, The Ohio State University , Columbus, OH 43210 , USA
| | - Christopher M Kimber
- 1 IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University , 581 83 Linköping , Sweden
| | - Martin Brengdahl
- 1 IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University , 581 83 Linköping , Sweden
| | - Urban Friberg
- 1 IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University , 581 83 Linköping , Sweden
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27
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Cossard GG, Toups MA, Pannell JR. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. ANNALS OF BOTANY 2019; 123:1119-1131. [PMID: 30289430 PMCID: PMC6612945 DOI: 10.1093/aob/mcy183] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/06/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species. METHODS The present study documents differences in gene expression in both above- and below-ground tissues of early pre-reproductive individuals of the wind-pollinated dioecious annual herb, Mercurialis annua, which otherwise shows clear sexual dimorphism only at the adult stage. KEY RESULTS Whereas males and females differed in their gene expression at the first leaf stage, sex-biased gene expression peaked just prior to, and after, flowering, as might be expected if sexual dimorphism is partly a response to differential costs of reproduction. Sex-biased genes were over-represented among putative sex-linked genes in M. annua but showed no evidence for more rapid evolution than unbiased genes. CONCLUSIONS Sex-biased gene expression in M. annua occurs as early as the first whorl of leaves is produced, is highly dynamic during plant development and varies substantially between vegetative tissues.
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Affiliation(s)
- Guillaume G Cossard
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Melissa A Toups
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - John R Pannell
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
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Connallon T, Matthews G. Cross-sex genetic correlations for fitness and fitness components: Connecting theoretical predictions to empirical patterns. Evol Lett 2019; 3:254-262. [PMID: 31171981 PMCID: PMC6546386 DOI: 10.1002/evl3.116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/21/2019] [Accepted: 04/07/2019] [Indexed: 11/18/2022] Open
Abstract
Sex differences in morphology, physiology, development, and behavior are widespread, yet the sexes inherit nearly identical genomes, causing most traits to exhibit strong and positive cross‐sex genetic correlations. In contrast to most other traits, estimates of cross‐sex genetic correlations for fitness and fitness components (rW fm ) are generally low and occasionally negative, implying that a substantial fraction of standing genetic variation for fitness might be sexually antagonistic (i.e., alleles benefitting one sex harm the other). Nevertheless, while low values of rW fm are often regarded as consequences of sexually antagonistic selection, it remains unclear exactly how selection and variation in quantitative traits interact to determine the sign and magnitude of rW fm , making it difficult to relate empirical estimates of cross‐sex genetic correlations to the evolutionary processes that might shape them. We present simple univariate and multivariate quantitative genetic models that explicitly link patterns of sex‐specific selection and trait genetic variation to the cross‐sex genetic correlation for fitness. We show that rW fm provides an unreliable signal of sexually antagonistic selection for two reasons. First, rW fm is constrained to be less than the cross‐sex genetic correlation for traits affecting fitness, regardless of the nature of selection on the traits. Second, sexually antagonistic selection is an insufficient condition for generating negative cross‐sex genetic correlations for fitness. Instead, negative fitness correlations between the sexes (rW fm <0) can only emerge when selection is sexually antagonistic and the strength of directional selection on each sex is strong relative to the amount of shared additive genetic variation in female and male traits. These results imply that empirical tests of sexual antagonism that are based on estimates of rW fm will be conservative and underestimate its true scope. In light of these theoretical results, we revisit current data on rW fm and sex‐specific selection and find that they are consistent with the theory.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences, and Centre for Geometric Biology Monash University Clayton Victoria 3800 Australia
| | - Genevieve Matthews
- School of Biological Sciences, and Centre for Geometric Biology Monash University Clayton Victoria 3800 Australia
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Ruzicka F, Hill MS, Pennell TM, Flis I, Ingleby FC, Mott R, Fowler K, Morrow EH, Reuter M. Genome-wide sexually antagonistic variants reveal long-standing constraints on sexual dimorphism in fruit flies. PLoS Biol 2019; 17:e3000244. [PMID: 31022179 PMCID: PMC6504117 DOI: 10.1371/journal.pbio.3000244] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/07/2019] [Accepted: 04/09/2019] [Indexed: 01/02/2023] Open
Abstract
The evolution of sexual dimorphism is constrained by a shared genome, leading to ‘sexual antagonism’, in which different alleles at given loci are favoured by selection in males and females. Despite its wide taxonomic incidence, we know little about the identity, genomic location, and evolutionary dynamics of antagonistic genetic variants. To address these deficits, we use sex-specific fitness data from 202 fully sequenced hemiclonal Drosophila melanogaster fly lines to perform a genome-wide association study (GWAS) of sexual antagonism. We identify approximately 230 chromosomal clusters of candidate antagonistic single nucleotide polymorphisms (SNPs). In contradiction to classic theory, we find no clear evidence that the X chromosome is a hot spot for sexually antagonistic variation. Characterising antagonistic SNPs functionally, we find a large excess of missense variants but little enrichment in terms of gene function. We also assess the evolutionary persistence of antagonistic variants by examining extant polymorphism in wild D. melanogaster populations and closely related species. Remarkably, antagonistic variants are associated with multiple signatures of balancing selection across the D. melanogaster distribution range and in their sister species D. simulans, indicating widespread and evolutionarily persistent (about 1 million years) genomic constraints on the evolution of sexual dimorphism. Based on our results, we propose that antagonistic variation accumulates because of constraints on the resolution of sexual conflict over protein coding sequences, thus contributing to the long-term maintenance of heritable fitness variation. This study characterises antagonistic loci across the genome of the fruit fly Drosophila melanogaster, finding them to be preferentially associated with variation in coding sequences and to be selectively maintained across worldwide populations of D. melanogaster, and even its sister species D. simulans.
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Affiliation(s)
- Filip Ruzicka
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Mark S. Hill
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tanya M. Pennell
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Ilona Flis
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Fiona C. Ingleby
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Richard Mott
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Kevin Fowler
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Edward H. Morrow
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- * E-mail: (MR); (EHM)
| | - Max Reuter
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- * E-mail: (MR); (EHM)
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Fraïsse C, Puixeu Sala G, Vicoso B. Pleiotropy Modulates the Efficacy of Selection in Drosophila melanogaster. Mol Biol Evol 2019; 36:500-515. [PMID: 30590559 PMCID: PMC6389323 DOI: 10.1093/molbev/msy246] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative "gender load," it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.
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Affiliation(s)
- Christelle Fraïsse
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Gemma Puixeu Sala
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
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31
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Connallon T, Sharma S, Olito C. Evolutionary Consequences of Sex-Specific Selection in Variable Environments: Four Simple Models Reveal Diverse Evolutionary Outcomes. Am Nat 2019; 193:93-105. [DOI: 10.1086/700720] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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32
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Oke KB, Motivans E, Quinn TP, Hendry AP. Sexual dimorphism modifies habitat‐associated divergence: Evidence from beach and creek breeding sockeye salmon. J Evol Biol 2018; 32:227-242. [DOI: 10.1111/jeb.13407] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/17/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Krista B. Oke
- Department of Biology and Redpath Museum McGill University Montreal Quebec Canada
- College of Fisheries and Ocean Sciences University of Alaska Fairbanks Juneau Alaska
| | - Elena Motivans
- Department of Biology and Redpath Museum McGill University Montreal Quebec Canada
- Helmholtz Centre for Environmental Research Leipzig Germany
| | - Thomas P. Quinn
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Andrew P. Hendry
- Department of Biology and Redpath Museum McGill University Montreal Quebec Canada
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33
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Grieshop K, Arnqvist G. Sex-specific dominance reversal of genetic variation for fitness. PLoS Biol 2018; 16:e2006810. [PMID: 30533008 PMCID: PMC6303075 DOI: 10.1371/journal.pbio.2006810] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 12/21/2018] [Accepted: 11/27/2018] [Indexed: 11/18/2022] Open
Abstract
The maintenance of genetic variance in fitness represents one of the most longstanding enigmas in evolutionary biology. Sexually antagonistic (SA) selection may contribute substantially to maintaining genetic variance in fitness by maintaining alternative alleles with opposite fitness effects in the two sexes. This is especially likely if such SA loci exhibit sex-specific dominance reversal (SSDR)-wherein the allele that benefits a given sex is also dominant in that sex-which would generate balancing selection and maintain stable SA polymorphisms for fitness. However, direct empirical tests of SSDR for fitness are currently lacking. Here, we performed a full diallel cross among isogenic strains derived from a natural population of the seed beetle Callosobruchus maculatus that is known to exhibit SA genetic variance in fitness. We measured sex-specific competitive lifetime reproductive success (i.e., fitness) in >500 sex-by-genotype F1 combinations and found that segregating genetic variation in fitness exhibited pronounced contributions from dominance variance and sex-specific dominance variance. A closer inspection of the nature of dominance variance revealed that the fixed allelic variation captured within each strain tended to be dominant in one sex but recessive in the other, revealing genome-wide SSDR for SA polymorphisms underlying fitness. Our findings suggest that SA balancing selection could play an underappreciated role in maintaining fitness variance in natural populations.
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Affiliation(s)
- Karl Grieshop
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Göran Arnqvist
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
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34
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35
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Stewart AD, Rice WR. Arrest of sex-specific adaptation during the evolution of sexual dimorphism in Drosophila. Nat Ecol Evol 2018; 2:1507-1513. [DOI: 10.1038/s41559-018-0613-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/22/2018] [Indexed: 11/09/2022]
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36
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Lasne C, Hangartner SB, Connallon T, Sgrò CM. Cross‐sex genetic correlations and the evolution of sex‐specific local adaptation: Insights from classical trait clines in
Drosophila melanogaster. Evolution 2018; 72:1317-1327. [DOI: 10.1111/evo.13494] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/03/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Clémentine Lasne
- School of Biological Sciences Monash University Clayton Victoria 3800 Australia
| | | | - Tim Connallon
- School of Biological Sciences Monash University Clayton Victoria 3800 Australia
| | - Carla M. Sgrò
- School of Biological Sciences Monash University Clayton Victoria 3800 Australia
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37
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Zajitschek F, Connallon T. Antagonistic pleiotropy in species with separate sexes, and the maintenance of genetic variation in life-history traits and fitness. Evolution 2018; 72:1306-1316. [PMID: 29667189 DOI: 10.1111/evo.13493] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/21/2018] [Accepted: 03/23/2018] [Indexed: 01/01/2023]
Abstract
Antagonistic pleiotropy (AP)-where alleles of a gene increase some components of fitness at a cost to others-can generate balancing selection, and contribute to the maintenance of genetic variation in fitness traits, such as survival, fecundity, fertility, and mate competition. Previous theory suggests that AP is unlikely to maintain variation unless antagonistic selection is strong, or AP alleles exhibit pronounced differences in genetic dominance between the affected traits. We show that conditions for balancing selection under AP expand under the likely scenario that the strength of selection on each fitness component differs between the sexes. Our model also predicts that the vast majority of balanced polymorphisms have sexually antagonistic effects on total fitness, despite the absence of sexual antagonism for individual fitness components. We conclude that AP polymorphisms are less difficult to maintain than predicted by prior theory, even under our conservative assumption that selection on components of fitness is universally sexually concordant. We discuss implications for the maintenance of genetic variation, and for inferences of sexual antagonism that are based on sex-specific phenotypic selection estimates-many of which are based on single fitness components.
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Affiliation(s)
- Felix Zajitschek
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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38
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Cheng C, Kirkpatrick M. Environmental Plasticity in the Intersexual Correlation and Sex Bias of Gene Expression. J Hered 2018; 108:754-758. [PMID: 29036352 DOI: 10.1093/jhered/esx083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/22/2017] [Indexed: 11/13/2022] Open
Abstract
Intersexual genetic correlations are expected to constrain the evolution of sexual dimorphic traits, including the degree of sex-biased gene expression. Consistent with that expectation, studies in fruit flies and birds have reported that genes whose expression has a strong intersexual genetic correlation (rMF) show a lower level of sex-biased expression (SBE). However, it is known that both rMF and SBE can be affected by the environment. It is therefore unclear whether there is a consistent relationship between these 2 quantities across multiple environments. In this paper, we study this relationship in the African malaria mosquito Anopheles gambiae. We show that both rMF and SBE change between environments. The change in SBE across environments is significantly correlated with dN/dS: greater changes in SBE are associated with higher values of dN/dS. Furthermore, the relationship between rMF and SBE is sensitive to the environment. We conclude that this relationship is sufficiently plastic that environmental effects should be considered in future studies.
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Affiliation(s)
- Changde Cheng
- Department of Integrative Biology, University of Texas, Austin, TX 78712.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX 78712
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39
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Connallon T, Hall MD. Genetic constraints on adaptation: a theoretical primer for the genomics era. Ann N Y Acad Sci 2018; 1422:65-87. [PMID: 29363779 DOI: 10.1111/nyas.13536] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/20/2017] [Accepted: 09/28/2017] [Indexed: 12/14/2022]
Abstract
Genetic constraints are features of inheritance systems that slow or prohibit adaptation. Several population genetic mechanisms of constraint have received sustained attention within the field since they were first articulated in the early 20th century. This attention is now reflected in a rich, and still growing, theoretical literature on the genetic limits to adaptive change. In turn, empirical research on constraints has seen a rapid expansion over the last two decades in response to changing interests of evolutionary biologists, along with new technologies, expanding data sets, and creative analytical approaches that blend mathematical modeling with genomics. Indeed, one of the most notable and exciting features of recent progress in genetic constraints is the close connection between theoretical and empirical research. In this review, we discuss five major population genetic contexts of genetic constraint: genetic dominance, pleiotropy, fitness trade-offs between types of individuals of a population, sign epistasis, and genetic linkage between loci. For each, we outline historical antecedents of the theory, specific contexts where constraints manifest, and their quantitative consequences for adaptation. From each of these theoretical foundations, we discuss recent empirical approaches for identifying and characterizing genetic constraints, each grounded and motivated by this theory, and outline promising areas for future work.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences, and Centre for Geometric Biology, Monash University, Clayton, Victoria, Australia
| | - Matthew D Hall
- School of Biological Sciences, and Centre for Geometric Biology, Monash University, Clayton, Victoria, Australia
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40
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Griffin RM, Hayward AD, Bolund E, Maklakov AA, Lummaa V. Sex differences in adult mortality rate mediated by early-life environmental conditions. Ecol Lett 2017; 21:235-242. [PMID: 29210148 DOI: 10.1111/ele.12888] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/18/2017] [Accepted: 11/06/2017] [Indexed: 12/16/2022]
Abstract
Variation in sex differences is affected by both genetic and environmental variation, with rapid change in sex differences being more likely due to environmental change. One case of rapid change in sex differences is human lifespan, which has become increasingly female-biased in recent centuries. Long-term consequences of variation in the early-life environment may, in part, explain such variation in sex differences, but whether the early-life environment mediates sex differences in life-history traits is poorly understood in animals. Combining longitudinal data on 60 cohorts of pre-industrial Finns with environmental data, we show that the early-life environment is associated with sex differences in adult mortality and expected lifespan. Specifically, low infant survival rates and high rye yields (an important food source) in early-life are associated with female-bias in adult lifespan. These results support the hypothesis that environmental change has the potential to affect sex differences in life-history traits in natural populations of long-lived mammals.
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Affiliation(s)
- Robert M Griffin
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Adam D Hayward
- Department of Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Elisabeth Bolund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, 752 36, Sweden
| | - Alexei A Maklakov
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, 752 36, Sweden.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Virpi Lummaa
- Department of Biology, University of Turku, 20014, Turku, Finland
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41
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Kutch IC, Fedorka KM. A test for Y-linked additive and epistatic effects on surviving bacterial infections in Drosophila melanogaster. J Evol Biol 2017; 30:1400-1408. [DOI: 10.1111/jeb.13118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/11/2017] [Indexed: 02/03/2023]
Affiliation(s)
- I. C. Kutch
- University of Central Florida; Orlando FL USA
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42
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Zajitschek F, Connallon T. Partitioning of resources: the evolutionary genetics of sexual conflict over resource acquisition and allocation. J Evol Biol 2017; 30:826-838. [DOI: 10.1111/jeb.13051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/15/2017] [Accepted: 01/27/2017] [Indexed: 01/20/2023]
Affiliation(s)
- F. Zajitschek
- Department of Biological Sciences Monash University Clayton Vic. Australia
| | - T. Connallon
- Department of Biological Sciences Monash University Clayton Vic. Australia
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43
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Allen SL, Bonduriansky R, Sgro CM, Chenoweth SF. Sex-biased transcriptome divergence along a latitudinal gradient. Mol Ecol 2017; 26:1256-1272. [PMID: 28100025 DOI: 10.1111/mec.14015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/23/2016] [Accepted: 11/28/2016] [Indexed: 12/26/2022]
Abstract
Sex-dependent gene expression is likely an important genomic mechanism that allows sex-specific adaptation to environmental changes. Among Drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex-biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex-specific selection and the evolution of sex-biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male-biased genes, there was no overrepresentation of X-linked genes in males. By contrast, X-linked divergence was elevated in females, especially for female-biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro- and micro-ecological spatial scales.
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Affiliation(s)
- Scott L Allen
- The School of Biological Sciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
| | - Russell Bonduriansky
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Carla M Sgro
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
| | - Stephen F Chenoweth
- The School of Biological Sciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
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44
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Cox RM, Cox CL, McGlothlin JW, Card DC, Andrew AL, Castoe TA. Hormonally Mediated Increases in Sex-Biased Gene Expression Accompany the Breakdown of Between-Sex Genetic Correlations in a Sexually Dimorphic Lizard. Am Nat 2017; 189:315-332. [PMID: 28221827 DOI: 10.1086/690105] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The evolution of sexual dimorphism is predicted to occur through reductions in between-sex genetic correlations (rmf) for shared traits, but the physiological and genetic mechanisms that facilitate these reductions remain largely speculative. Here, we use a paternal half-sibling breeding design in captive brown anole lizards (Anolis sagrei) to show that the development of sexual size dimorphism is mirrored by the ontogenetic breakdown of rmf for body size and growth rate. Using transcriptome data from the liver (which integrates growth and metabolism), we show that sex-biased gene expression also increases dramatically between ontogenetic stages bracketing this breakdown of rmf. Ontogenetic increases in sex-biased expression are particularly evident for genes involved in growth, metabolism, and cell proliferation, suggesting that they contribute to both the development of sexual dimorphism and the breakdown of rmf. Mechanistically, we show that treatment of females with testosterone stimulates the expression of male-biased genes while inhibiting the expression of female-biased genes, thereby inducing male-like phenotypes at both organismal and transcriptomic levels. Collectively, our results suggest that sex-specific modifiers such as testosterone can orchestrate sex-biased gene expression to facilitate the phenotypic development of sexual dimorphism while simultaneously reducing genetic correlations that would otherwise constrain the independent evolution of the sexes.
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45
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The transcriptional architecture of phenotypic dimorphism. Nat Ecol Evol 2017; 1:6. [PMID: 28812569 DOI: 10.1038/s41559-016-0006] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/06/2016] [Indexed: 12/11/2022]
Abstract
The profound differences in gene expression between the sexes are increasingly used to study the molecular basis of sexual dimorphism, sexual selection and sexual conflict. Studies of transcriptional architecture, based on comparisons of gene expression, have also been implemented for a wide variety of other intra-specific polymorphisms. These efforts are based on key assumptions regarding the relationship between transcriptional architecture, phenotypic variation and the target of selection. Some of these assumptions are better supported by available evidence than others. In all cases, the evidence is largely circumstantial, leaving considerable gaps in our understanding of the relationship between transcriptional and phenotypic dimorphism.
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46
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Autosomal and X-Linked Additive Genetic Variation for Lifespan and Aging: Comparisons Within and Between the Sexes in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2016; 6:3903-3911. [PMID: 27678519 PMCID: PMC5144961 DOI: 10.1534/g3.116.028308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Theory makes several predictions concerning differences in genetic variation between the X chromosome and the autosomes due to male X hemizygosity. The X chromosome should: (i) typically show relatively less standing genetic variation than the autosomes, (ii) exhibit more variation in males compared to females because of dosage compensation, and (iii) potentially be enriched with sex-specific genetic variation. Here, we address each of these predictions for lifespan and aging in Drosophila melanogaster. To achieve unbiased estimates of X and autosomal additive genetic variance, we use 80 chromosome substitution lines; 40 for the X chromosome and 40 combining the two major autosomes, which we assay for sex-specific and cross-sex genetic (co)variation. We find significant X and autosomal additive genetic variance for both traits in both sexes (with reservation for X-linked variation of aging in females), but no conclusive evidence for depletion of X-linked variation (measured through females). Males display more X-linked variation for lifespan than females, but it is unclear if this is due to dosage compensation since also autosomal variation is larger in males. Finally, our results suggest that the X chromosome is enriched for sex-specific genetic variation in lifespan but results were less conclusive for aging overall. Collectively, these results suggest that the X chromosome has reduced capacity to respond to sexually concordant selection on lifespan from standing genetic variation, while its ability to respond to sexually antagonistic selection may be augmented.
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47
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Cheng C, Kirkpatrick M. Sex-Specific Selection and Sex-Biased Gene Expression in Humans and Flies. PLoS Genet 2016; 12:e1006170. [PMID: 27658217 PMCID: PMC5033347 DOI: 10.1371/journal.pgen.1006170] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/14/2016] [Indexed: 12/02/2022] Open
Abstract
Sexual dimorphism results from sex-biased gene expression, which evolves when selection acts differently on males and females. While there is an intimate connection between sex-biased gene expression and sex-specific selection, few empirical studies have studied this relationship directly. Here we compare the two on a genome-wide scale in humans and flies. We find a distinctive "Twin Peaks" pattern in humans that relates the strength of sex-specific selection, quantified by genetic divergence between male and female adults at autosomal loci, to the degree of sex-biased expression. Genes with intermediate degrees of sex-biased expression show evidence of ongoing sex-specific selection, while genes with either little or completely sex-biased expression do not. This pattern apparently results from differential viability selection in males and females acting in the current generation. The Twin Peaks pattern is also found in Drosophila using a different measure of sex-specific selection acting on fertility. We develop a simple model that successfully recapitulates the Twin Peaks. Our results suggest that many genes with intermediate sex-biased expression experience ongoing sex-specific selection in humans and flies.
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Affiliation(s)
- Changde Cheng
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
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48
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Joag R, Stuglik M, Konczal M, Plesnar-Bielak A, Skrzynecka A, Babik W, Radwan J. Transcriptomics of Intralocus Sexual Conflict: Gene Expression Patterns in Females Change in Response to Selection on a Male Secondary Sexual Trait in the Bulb Mite. Genome Biol Evol 2016; 8:2351-7. [PMID: 27401174 PMCID: PMC5010903 DOI: 10.1093/gbe/evw169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Intralocus sexual conflict (IASC) prevents males and females from reaching their disparate phenotypic optima and is widespread, but little is known about its genetic underpinnings. In Rhizoglyphus robini, a mite species with alternative male morphs, elevated sexual dimorphism of the armored fighter males (compared to more feminized scramblers males) was previously reported to be associated with increased IASC. Because IASC persists if gene expression patterns are correlated between sexes, we compared gene expression patterns of males and females from the replicate lines selected for increased proportion of fighter or scrambler males (F- and S-lines, respectively). Specifically, we tested the prediction that selection for fighter morph caused correlated changes in gene expression patterns in females. We identified 532 differentially expressed genes (FDR < 0.05) between the F-line and S-line males. Consistent with the prediction, expression levels of these genes also differed between females from respective lines. Thus, significant proportion of genes differentially expressed between sexually selected male phenotypes showed correlated expression levels in females, likely contributing to elevated IASC in F-lines reported in a previous study.
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Affiliation(s)
- Richa Joag
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Krakow, Poland
| | - Michal Stuglik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Krakow, Poland Integrative Animal Sciences, Scotland's Rural College, Easter Bush Campus, Midlothian, Scotland
| | - Mateusz Konczal
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Agata Plesnar-Bielak
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Krakow, Poland
| | - Anna Skrzynecka
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Krakow, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Krakow, Poland
| | - Jacek Radwan
- Faculty of Biology, Evolutionary Biology Group, Adam Mickiewicz University, Poznan, Poland
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49
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Connallon T, Hall MD. Genetic correlations and sex‐specific adaptation in changing environments. Evolution 2016; 70:2186-2198. [DOI: 10.1111/evo.13025] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 07/20/2016] [Accepted: 07/26/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Tim Connallon
- School of Biological Sciences Monash University Clayton Victoria 3800 Australia
| | - Matthew D. Hall
- School of Biological Sciences Monash University Clayton Victoria 3800 Australia
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50
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Dean R, Mank JE. Tissue Specificity and Sex-Specific Regulatory Variation Permit the Evolution of Sex-Biased Gene Expression. Am Nat 2016; 188:E74-84. [PMID: 27501094 DOI: 10.1086/687526] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Genetic correlations between males and females are often thought to constrain the evolution of sexual dimorphism. However, sexually dimorphic traits and the underlying sexually dimorphic gene expression patterns are often rapidly evolving. We explore this apparent paradox by measuring the genetic correlation in gene expression between males and females (Cmf) across broad evolutionary timescales, using two RNA-sequencing data sets spanning multiple populations and multiple species. We find that unbiased genes have higher Cmf than sex-biased genes, consistent with intersexual genetic correlations constraining the evolution of sexual dimorphism. However, we found that highly sex-biased genes (both male and female biased) also had higher tissue specificity, and unbiased genes had greater expression breadth, suggesting that pleiotropy may constrain the breakdown of intersexual genetic correlations. Finally, we show that genes with high Cmf showed some degree of sex-specific changes in gene expression in males and females. Together, our results suggest that genetic correlations between males and females may be less important in constraining the evolution of sex-biased gene expression than pleiotropy. Sex-specific regulatory variation and tissue specificity may resolve the paradox of widespread sex bias within a largely shared genome.
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