1
|
Charlesworth D, Qiu S, Bergero R, Gardner J, Keegan K, Yong L, Hastings A, Konczal M. Has recombination changed during the recent evolution of the guppy Y chromosome? Genetics 2024; 226:iyad198. [PMID: 37956094 DOI: 10.1093/genetics/iyad198] [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: 09/27/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Genome sequencing and genetic mapping of molecular markers have demonstrated nearly complete Y-linkage across much of the guppy (Poecilia reticulata) XY chromosome pair. Predominant Y-linkage of factors controlling visible male-specific coloration traits also suggested that these polymorphisms are sexually antagonistic (SA). However, occasional exchanges with the X are detected, and recombination patterns also appear to differ between natural guppy populations, suggesting ongoing evolution of recombination suppression under selection created by partially sex-linked SA polymorphisms. We used molecular markers to directly estimate genetic maps in sires from 4 guppy populations. The maps are very similar, suggesting that their crossover patterns have not recently changed. Our maps are consistent with population genomic results showing that variants within the terminal 5 Mb of the 26.5 Mb sex chromosome, chromosome 12, are most clearly associated with the maleness factor, albeit incompletely. We also confirmed occasional crossovers proximal to the male-determining region, defining a second, rarely recombining, pseudo-autosomal region, PAR2. This fish species may therefore have no completely male-specific region (MSY) more extensive than the male-determining factor. The positions of the few crossover events suggest a location for the male-determining factor within a physically small repetitive region. A sex-reversed XX male had few crossovers in PAR2, suggesting that this region's low crossover rate depends on the phenotypic, not the genetic, sex. Thus, rare individuals whose phenotypic and genetic sexes differ, and/or occasional PAR2 crossovers in males can explain the failure to detect fully Y-linked variants.
Collapse
Affiliation(s)
- Deborah Charlesworth
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3LF, UK
| | - Suo Qiu
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3LF, UK
| | - Roberta Bergero
- Scottish Rural Agricultural College, Peter Wilson Building, King's Buildings, W Mains Rd, Edinburgh EH9 3JG, UK
| | - Jim Gardner
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3LF, UK
| | - Karen Keegan
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3LF, UK
| | - Lengxob Yong
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn TR10 9FE, UK
- South Carolina Department of Natural Resources, Marine Resources Research Institute, P.O. Box 12559 Charleston, SC 29422-2559, USA
| | - Abigail Hastings
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3LF, UK
| | - Mateusz Konczal
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, 60-614 Poznań, Poland
| |
Collapse
|
2
|
Heckley AM, Pearce AE, Gotanda KM, Hendry AP, Oke KB. Compiling forty years of guppy research to investigate the factors contributing to (non)parallel evolution. J Evol Biol 2022; 35:1414-1431. [PMID: 36098479 DOI: 10.1111/jeb.14086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/29/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
Examples of parallel evolution have been crucial for our understanding of adaptation via natural selection. However, strong parallelism is not always observed even in seemingly similar environments where natural selection is expected to favour similar phenotypes. Leveraging this variation in parallelism within well-researched study systems can provide insight into the factors that contribute to variation in adaptive responses. Here we analyse the results of 36 studies reporting 446 average trait values in Trinidadian guppies, Poecilia reticulata, from different predation regimes. We examine how the extent of predator-driven phenotypic parallelism is influenced by six factors: sex, trait type, rearing environment, ecological complexity, evolutionary history, and time since colonization. Analyses show that parallel evolution in guppies is highly variable and weak on average, with only 24.7% of the variation among populations being explained by predation regime. Levels of parallelism appeared to be especially weak for colour traits, and parallelism decreased with increasing complexity of evolutionary history (i.e., when estimates of parallelism from populations within a single drainage were compared to estimates of parallelism from populations pooled between two major drainages). Suggestive - but not significant - trends that warrant further research include interactions between the sexes and different trait categories. Quantifying and accounting for these and other sources of variation among evolutionary 'replicates' can be leveraged to better understand the extent to which seemingly similar environments drive parallel and nonparallel aspects of phenotypic divergence.
Collapse
Affiliation(s)
- Alexis M Heckley
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Allegra E Pearce
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Kiyoko M Gotanda
- Department of Biology, Université Sherbrooke, Sherbrooke, Quebec, Canada.,Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Krista B Oke
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| |
Collapse
|
3
|
Meisel RP. Ecology and the evolution of sex chromosomes. J Evol Biol 2022; 35:1601-1618. [PMID: 35950939 DOI: 10.1111/jeb.14074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes are common features of animal genomes, often carrying a sex determination gene responsible for initiating the development of sexually dimorphic traits. The specific chromosome that serves as the sex chromosome differs across taxa as a result of fusions between sex chromosomes and autosomes, along with sex chromosome turnover-autosomes becoming sex chromosomes and sex chromosomes 'reverting' back to autosomes. In addition, the types of genes on sex chromosomes frequently differ from the autosomes, and genes on sex chromosomes often evolve faster than autosomal genes. Sex-specific selection pressures, such as sexual antagonism and sexual selection, are hypothesized to be responsible for sex chromosome turnovers, the unique gene content of sex chromosomes and the accelerated evolutionary rates of genes on sex chromosomes. Sex-specific selection has pronounced effects on sex chromosomes because their sex-biased inheritance can tilt the balance of selection in favour of one sex. Despite the general consensus that sex-specific selection affects sex chromosome evolution, most population genetic models are agnostic as to the specific sources of these sex-specific selection pressures, and many of the details about the effects of sex-specific selection remain unresolved. Here, I review the evidence that ecological factors, including variable selection across heterogeneous environments and conflicts between sexual and natural selection, can be important determinants of sex-specific selection pressures that shape sex chromosome evolution. I also explain how studying the ecology of sex chromosome evolution can help us understand important and unresolved aspects of both sex chromosome evolution and sex-specific selection.
Collapse
Affiliation(s)
- Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| |
Collapse
|
4
|
Paris JR, Whiting JR, Daniel MJ, Ferrer Obiol J, Parsons PJ, van der Zee MJ, Wheat CW, Hughes KA, Fraser BA. A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy. Nat Commun 2022; 13:1233. [PMID: 35264556 PMCID: PMC8907176 DOI: 10.1038/s41467-022-28895-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 02/16/2022] [Indexed: 11/22/2022] Open
Abstract
Male colour patterns of the Trinidadian guppy (Poecilia reticulata) are typified by extreme variation governed by both natural and sexual selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been hypothesised that many of the colour trait genes must be physically linked to sex determining loci as a ‘supergene’ on the sex chromosome. Here, we phenotype and genotype four guppy ‘Iso-Y lines’, where colour was inherited along the patriline for 40 generations. Using an unbiased phenotyping method, we confirm the breeding design was successful in creating four distinct colour patterns. We find that genetic differentiation among the Iso-Y lines is repeatedly associated with a diverse haplotype on an autosome (LG1), not the sex chromosome (LG12). Moreover, the LG1 haplotype exhibits elevated linkage disequilibrium and evidence of sex-specific diversity in the natural source population. We hypothesise that colour pattern polymorphism is driven by Y-autosome epistasis. Extreme colour pattern variation in male Trinidadian guppies are influenced by natural selection and sexual selection. Here, the authors phenotype and genotype four guppy lineages finding that colour pattern is associated with a diverse haplotype on an autosome.
Collapse
Affiliation(s)
- Josephine R Paris
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - James R Whiting
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Mitchel J Daniel
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32304, USA
| | - Joan Ferrer Obiol
- Departament de Microbiologia, Genètica i Estadística and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Paul J Parsons
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.,NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mijke J van der Zee
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | | | - Kimberly A Hughes
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32304, USA
| | - Bonnie A Fraser
- Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| |
Collapse
|
5
|
Harrison LM, Noble DWA, Jennions MD. A meta-analysis of sex differences in animal personality: no evidence for the greater male variability hypothesis. Biol Rev Camb Philos Soc 2021; 97:679-707. [PMID: 34908228 DOI: 10.1111/brv.12818] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022]
Abstract
The notion that men are more variable than women has become embedded into scientific thinking. For mental traits like personality, greater male variability has been partly attributed to biology, underpinned by claims that there is generally greater variation among males than females in non-human animals due to stronger sexual selection on males. However, evidence for greater male variability is limited to morphological traits, and there is little information regarding sex differences in personality-like behaviours for non-human animals. Here, we meta-analysed sex differences in means and variances for over 2100 effects (204 studies) from 220 species (covering five broad taxonomic groups) across five personality traits: boldness, aggression, activity, sociality and exploration. We also tested if sexual size dimorphism, a proxy for sex-specific sexual selection, explains variation in the magnitude of sex differences in personality. We found no significant differences in personality between the sexes. In addition, sexual size dimorphism did not explain variation in the magnitude of the observed sex differences in the mean or variance in personality for any taxonomic group. In sum, we find no evidence for widespread sex differences in variability in non-human animal personality.
Collapse
Affiliation(s)
- Lauren M Harrison
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, 46 Sullivans Creek Road, Canberra, ACT, 2600, Australia
| | - Daniel W A Noble
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, 46 Sullivans Creek Road, Canberra, ACT, 2600, Australia
| | - Michael D Jennions
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, 46 Sullivans Creek Road, Canberra, ACT, 2600, Australia
| |
Collapse
|
6
|
Mank JE, Rideout EJ. Developmental mechanisms of sex differences: from cells to organisms. Development 2021; 148:272484. [PMID: 34647574 DOI: 10.1242/dev.199750] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Male-female differences in many developmental mechanisms lead to the formation of two morphologically and physiologically distinct sexes. Although this is expected for traits with prominent differences between the sexes, such as the gonads, sex-specific processes also contribute to traits without obvious male-female differences, such as the intestine. Here, we review sex differences in developmental mechanisms that operate at several levels of biological complexity - molecular, cellular, organ and organismal - and discuss how these differences influence organ formation, function and whole-body physiology. Together, the examples we highlight show that one simple way to gain a more accurate and comprehensive understanding of animal development is to include both sexes.
Collapse
Affiliation(s)
- Judith E Mank
- Department of Zoology, Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Elizabeth J Rideout
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| |
Collapse
|
7
|
Fraser BA, Whiting JR, Paris JR, Weadick CJ, Parsons PJ, Charlesworth D, Bergero R, Bemm F, Hoffmann M, Kottler VA, Liu C, Dreyer C, Weigel D. Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata). Genome Biol Evol 2021; 12:1789-1805. [PMID: 32853348 PMCID: PMC7643365 DOI: 10.1093/gbe/evaa187] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 02/06/2023] Open
Abstract
Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favor the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male color patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low-predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female guppy. Here, we present a new guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.
Collapse
Affiliation(s)
| | | | | | | | | | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Roberta Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Margarete Hoffmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Verena A Kottler
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Chang Liu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Christine Dreyer
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| |
Collapse
|
8
|
Valvo JJ, Aponte JD, Daniel MJ, Dwinell K, Rodd H, Houle D, Hughes KA. Using Delaunay triangulation to sample whole-specimen color from digital images. Ecol Evol 2021; 11:12468-12484. [PMID: 34594513 PMCID: PMC8462138 DOI: 10.1002/ece3.7992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/21/2021] [Indexed: 11/26/2022] Open
Abstract
Color variation is one of the most obvious examples of variation in nature, but biologically meaningful quantification and interpretation of variation in color and complex patterns are challenging. Many current methods for assessing variation in color patterns classify color patterns using categorical measures and provide aggregate measures that ignore spatial pattern, or both, losing potentially important aspects of color pattern.Here, we present Colormesh, a novel method for analyzing complex color patterns that offers unique capabilities. Our approach is based on unsupervised color quantification combined with geometric morphometrics to identify regions of putative spatial homology across samples, from histology sections to whole organisms. Colormesh quantifies color at individual sampling points across the whole sample.We demonstrate the utility of Colormesh using digital images of Trinidadian guppies (Poecilia reticulata), for which the evolution of color has been frequently studied. Guppies have repeatedly evolved in response to ecological differences between up- and downstream locations in Trinidadian rivers, resulting in extensive parallel evolution of many phenotypes. Previous studies have, for example, compared the area and quantity of discrete color (e.g., area of orange, number of black spots) between these up- and downstream locations neglecting spatial placement of these areas. Using the Colormesh pipeline, we show that patterns of whole-animal color variation do not match expectations suggested by previous work.Colormesh can be deployed to address a much wider range of questions about color pattern variation than previous approaches. Colormesh is thus especially suited for analyses that seek to identify the biologically important aspects of color pattern when there are multiple competing hypotheses or even no a priori hypotheses at all.
Collapse
Affiliation(s)
- Jennifer J. Valvo
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| | - Jose David Aponte
- Department of Cell Biology and AnatomyUniversity of CalgaryCalgaryABCanada
| | - Mitch J. Daniel
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| | - Kenna Dwinell
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| | - Helen Rodd
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - David Houle
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| | - Kimberly A. Hughes
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| |
Collapse
|
9
|
Darolti I, Wright AE, Mank JE. Guppy Y Chromosome Integrity Maintained by Incomplete Recombination Suppression. Genome Biol Evol 2021; 12:965-977. [PMID: 32426836 PMCID: PMC7337182 DOI: 10.1093/gbe/evaa099] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
The loss of recombination triggers divergence between the sex chromosomes and promotes degeneration of the sex-limited chromosome. Several livebearers within the genus Poecilia share a male-heterogametic sex chromosome system that is roughly 20 Myr old, with extreme variation in the degree of Y chromosome divergence. In Poecilia picta, the Y is highly degenerate and associated with complete X chromosome dosage compensation. In contrast, although recombination is restricted across almost the entire length of the sex chromosomes in Poecilia reticulata and Poecilia wingei, divergence between the X chromosome and the Y chromosome is very low. This clade therefore offers a unique opportunity to study the forces that accelerate or hinder sex chromosome divergence. We used RNA-seq data from multiple families of both P. reticulata and P. wingei, the species with low levels of sex chromosome divergence, to differentiate X and Y coding sequences based on sex-limited SNP inheritance. Phylogenetic tree analyses reveal that occasional recombination has persisted between the sex chromosomes for much of their length, as X- and Y-linked sequences cluster by species instead of by gametolog. This incomplete recombination suppression maintains the extensive homomorphy observed in these systems. In addition, we see differences between the previously identified strata in the phylogenetic clustering of X–Y orthologs, with those that cluster by chromosome located in the older stratum, the region previously associated with the sex-determining locus. However, recombination arrest appears to have expanded throughout the sex chromosomes more gradually instead of through a stepwise process associated with inversions.
Collapse
Affiliation(s)
- Iulia Darolti
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison E Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Judith E Mank
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| |
Collapse
|
10
|
Charlesworth D, Zhang Y, Bergero R, Graham C, Gardner J, Yong L. Using GC Content to Compare Recombination Patterns on the Sex Chromosomes and Autosomes of the Guppy, Poecilia reticulata, and Its Close Outgroup Species. Mol Biol Evol 2021; 37:3550-3562. [PMID: 32697821 DOI: 10.1093/molbev/msaa187] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genetic and physical mapping of the guppy (Poecilia reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, as in pseudoautosomal regions of mammalian sex chromosomes. We used GC content to indirectly infer recombination patterns on guppy chromosomes, based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and third positions of codons to make comparisons between sequences that are matched, as far as possible, and are all probably under weak selection. Almost all guppy chromosomes, including the sex chromosome (LG12), have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localization in male meiosis. Our test does not suggest that the guppy XY pair has stronger crossover localization than the autosomes, or than the homologous chromosome in the close relative, the platyfish (Xiphophorus maculatus). We therefore conclude that the guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. We also identify the centromere ends of guppy chromosomes, which were not determined in the genome assembly.
Collapse
Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yexin Zhang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Roberta Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Chay Graham
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jim Gardner
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Lengxob Yong
- Centre for Ecology and Conservation, University of Exeter, Falmouth, Cornwall, United Kingdom
| |
Collapse
|
11
|
Almeida P, Sandkam BA, Morris J, Darolti I, Breden F, Mank JE. Divergence and Remarkable Diversity of the Y Chromosome in Guppies. Mol Biol Evol 2021; 38:619-633. [PMID: 33022040 PMCID: PMC7826173 DOI: 10.1093/molbev/msaa257] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared with their downstream pair. Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female preference for rare Y-linked color variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence.
Collapse
Affiliation(s)
- Pedro Almeida
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Benjamin A Sandkam
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Jake Morris
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
12
|
Morris J, Darolti I, van der Bijl W, Mank JE. High-resolution characterization of male ornamentation and re-evaluation of sex linkage in guppies. Proc Biol Sci 2020; 287:20201677. [PMID: 33081622 DOI: 10.1098/rspb.2020.1677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Coloration plays a key role in the ecology of many species, influencing how an organism interacts with its environment, other species and conspecifics. Guppies are sexually dimorphic, with males displaying sexually selected coloration resulting from female preference. Previous work has suggested that much of guppy colour pattern variation is Y-linked. However, it remains unclear how many individual colour patterns are Y-linked in natural populations as much of the previous work has focused on phenotypes either not found in the wild, or aggregate measures such as total colour area. Moreover, ornaments have traditionally been identified and delineated by hand, and computational methods now make it possible to extract pixels and identify ornaments with automated methods, reducing the potential for human bias. Here we developed a pipeline for semi-automated ornament identification and high-resolution image analysis of male guppy colour patterns and applied it to a multigenerational pedigree. Our results show that loci controlling the presence or the absence of individual male ornaments in our population are not predominantly Y-linked. However, we find that ornaments of similar colour are not independent of each other, and modifier loci that affect whole animal coloration appear to be at least partially Y-linked. Considering these results, Y-linkage of individual ornaments may not be important in driving colour changes in natural populations of guppies, or in expansions of the non-recombining Y region, while Y-linked modifier loci that affect aggregate traits may well play an important role.
Collapse
Affiliation(s)
- Jake Morris
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wouter van der Bijl
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, London, UK.,Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
13
|
Charlesworth D, Bergero R, Graham C, Gardner J, Yong L. Locating the Sex Determining Region of Linkage Group 12 of Guppy ( Poecilia reticulata). G3 (BETHESDA, MD.) 2020; 10:3639-3649. [PMID: 32753367 PMCID: PMC7534449 DOI: 10.1534/g3.120.401573] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/29/2020] [Indexed: 01/04/2023]
Abstract
Despite over 100 years of study, the location of the fully sex-linked region of the guppy (Poecilia reticulata) carrying the male-determining locus, and the regions where the XY pair recombine, remain unclear. Previous population genomics studies to determine these regions used small samples from recently bottlenecked captive populations, which increase the false positive rate of associations between individuals' sexes and SNPs. Using new data from multiple natural populations, we show that a recently proposed candidate for this species' male-determining gene is probably not completely sex-linked, leaving the maleness factor still unidentified. Variants in the chromosome 12 region carrying the candidate gene sometimes show linkage disequilibrium with the sex-determining factor, but no consistently male-specific variant has yet been found. Our genetic mapping with molecular markers spread across chromosome 12 confirms that this is the guppy XY pair. We describe two families with recombinants between the X and Y chromosomes, which confirm that the male-determining locus is in the region identified by all previous studies, near the terminal pseudo-autosomal region (PAR), which crosses over at a very high rate in males. We correct the PAR marker order, and assign two unplaced scaffolds to the PAR. We also detect a duplication, with one copy in the male-determining region, explaining signals of sex linkage in a more proximal region.
Collapse
Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, EH9 3LF, UK
| | - Roberta Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, EH9 3LF, UK
| | - Chay Graham
- University of Cambridge, Department of Biochemistry, Sanger Building, 80 Tennis Ct Rd, Cambridge CB2 1GA, UK
| | - Jim Gardner
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, EH9 3LF, UK
| | - Lengxob Yong
- Centre for Ecology and Conservation, University of Exeter, Penryn, Falmouth, Cornwall, TR10 9FE, UK
| |
Collapse
|
14
|
Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers. Proc Natl Acad Sci U S A 2019; 116:19031-19036. [PMID: 31484763 PMCID: PMC6754558 DOI: 10.1073/pnas.1905298116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Once recombination is halted between the X and Y chromosomes, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about the variation in sex chromosome differentiation within clades. Here, we combined whole-genome and transcriptome sequencing data to characterize the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged roughly 20 million years ago. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata and P. wingei are largely homomorphic, with recombination in the former persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely nonrecombining and strikingly heteromorphic. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of functional chromosome-wide dosage compensation in this species, which has not been previously observed in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation.
Collapse
|
15
|
Exaggerated heterochiasmy in a fish with sex-linked male coloration polymorphisms. Proc Natl Acad Sci U S A 2019; 116:6924-6931. [PMID: 30894479 DOI: 10.1073/pnas.1818486116] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
It is often stated that polymorphisms for mutations affecting fitness of males and females in opposite directions [sexually antagonistic (SA) polymorphisms] are the main selective force for the evolution of recombination suppression between sex chromosomes. However, empirical evidence to discriminate between different hypotheses is difficult to obtain. We report genetic mapping results in laboratory-raised families of the guppy (Poecilia reticulata), a sexually dimorphic fish with SA polymorphisms for male coloration genes, mostly on the sex chromosomes. Comparison of the genetic and physical maps shows that crossovers are distributed very differently in the two sexes (heterochiasmy); in male meiosis, they are restricted to the termini of all four chromosomes studied, including chromosome 12, which carries the sex-determining locus. Genome resequencing of male and female guppies from a population also indicates sex linkage of variants across almost the entire chromosome 12. More than 90% of the chromosome carrying the male-determining locus is therefore transmitted largely through the male lineage. A lack of heterochiasmy in a related fish species suggests that it originated recently in the lineage leading to the guppy. Our findings do not support the hypothesis that suppressed recombination evolved in response to the presence of SA polymorphisms. Instead, a low frequency of recombination on a chromosome that carries a male-determining locus and has not undergone genetic degeneration has probably facilitated the establishment of male-beneficial coloration polymorphisms.
Collapse
|
16
|
Dick C, Reznick DN, Hayashi CY. Sex-biased expression between guppies varying in the presence of ornamental coloration. PeerJ 2018; 6:e5782. [PMID: 30324034 PMCID: PMC6186404 DOI: 10.7717/peerj.5782] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/18/2018] [Indexed: 01/21/2023] Open
Abstract
Sex-biased gene expression provides a means to achieve sexual dimorphism across a genome largely shared by both sexes. Trinidadian guppies are ideal to examine questions of sex-bias as they exhibit sexual dimorphism in ornamental coloration with male only expression. Here we use RNA-sequencing to quantify whole transcriptome gene expression differences, with a focus on differential expression of color genes between the sexes. We determine whether males express genes positively correlated with coloration at higher levels than females. We find that all the differentially expressed color genes were more highly expressed by males. Males also expressed all known black melanin synthesis genes at higher levels than females, regardless of whether the gene was significantly differentially expressed in the analysis. These differences correlated with the visual color differences between sexes at the stage sampled, as all males had ornamental black coloration apparent. We propose that sexual dimorphism in ornamental coloration is caused by male-biased expression of color genes.
Collapse
Affiliation(s)
- Cynthia Dick
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA, United States of America
| | - David N Reznick
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA, United States of America
| | - Cheryl Y Hayashi
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, United States of America
| |
Collapse
|
17
|
Levell ST, Travis J. Activity Level and Predation Risk in the Least Killifish, Heterandria formosa. COPEIA 2018. [DOI: 10.1643/ce-17-703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
18
|
Charlesworth D. Evolution of recombination rates between sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0456. [PMID: 29109220 DOI: 10.1098/rstb.2016.0456] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 11/12/2022] Open
Abstract
In species with genetic sex-determination, the chromosomes carrying the sex-determining genes have often evolved non-recombining regions and subsequently evolved the full set of characteristics denoted by the term 'sex chromosomes'. These include size differences, creating chromosomal heteromorphism, and loss of gene functions from one member of the chromosome pair. Such characteristics and changes have been widely reviewed, and underlie molecular genetic approaches that can detect sex chromosome regions. This review deals mainly with the evolution of new non-recombining regions, focusing on how certain evolutionary situations select for suppressed recombination (rather than the proximate mechanisms causing suppressed recombination between sex chromosomes). Particularly important is the likely involvement of sexually antagonistic polymorphisms in genome regions closely linked to sex-determining loci. These may be responsible for the evolutionary strata of sex chromosomes that have repeatedly formed by recombination suppression evolving across large genome regions. More studies of recently evolved non-recombining sex-determining regions should help to test this hypothesis empirically, and may provide evidence about whether other situations can sometimes lead to sex-linked regions evolving. Similarities with other non-recombining genome regions are discussed briefly, to illustrate common features of the different cases, though no general properties apply to all of them.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
Collapse
Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratory, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK
| |
Collapse
|
19
|
Charlesworth D. The Guppy Sex Chromosome System and the Sexually Antagonistic Polymorphism Hypothesis for Y Chromosome Recombination Suppression. Genes (Basel) 2018; 9:genes9050264. [PMID: 29783761 PMCID: PMC5977204 DOI: 10.3390/genes9050264] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/11/2018] [Accepted: 05/16/2018] [Indexed: 02/06/2023] Open
Abstract
Sex chromosomes regularly evolve suppressed recombination, distinguishing them from other chromosomes, and the reason for this has been debated for many years. It is now clear that non-recombining sex-linked regions have arisen in different ways in different organisms. A major hypothesis is that a sex-determining gene arises on a chromosome and that sexually antagonistic (SA) selection (sometimes called intra-locus sexual conflict) acting at a linked gene has led to the evolution of recombination suppression in the region, to reduce the frequency of low fitness recombinant genotypes produced. The sex chromosome system of the guppy (Poecilia reticulata) is often cited as supporting this hypothesis because SA selection has been demonstrated to act on male coloration in natural populations of this fish, and probably contributes to maintaining polymorphisms for the genetic factors involved. I review classical genetic and new molecular genetic results from the guppy, and other fish, including approaches for identifying the genome regions carrying sex-determining loci, and suggest that the guppy may exemplify a recently proposed route to sex chromosome evolution.
Collapse
Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| |
Collapse
|
20
|
The Colorful Sex Chromosomes of Teleost Fish. Genes (Basel) 2018; 9:genes9050233. [PMID: 29751562 PMCID: PMC5977173 DOI: 10.3390/genes9050233] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 12/14/2022] Open
Abstract
Teleost fish provide some of the most intriguing examples of sexually dimorphic coloration, which is often advantageous for only one of the sexes. Mapping studies demonstrated that the genetic loci underlying such color patterns are frequently in tight linkage to the sex-determining locus of a species, ensuring sex-specific expression of the corresponding trait. Several genes affecting color synthesis and pigment cell development have been previously described, but the color loci on the sex chromosomes have mostly remained elusive as yet. Here, we summarize the current knowledge about the genetics of such color loci in teleosts, mainly from studies on poeciliids and cichlids. Further studies on these color loci will certainly provide important insights into the evolution of sex chromosomes.
Collapse
|
21
|
Bergeron ZT, Fuller RC. Using Human Vision to Detect Variation in Avian Coloration: How Bad Is It? Am Nat 2018; 191:269-276. [DOI: 10.1086/695282] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
22
|
|
23
|
Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam B, Buechel SD, Kolm N, Breden F, Vicoso B, Mank JE. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nat Commun 2017; 8:14251. [PMID: 28139647 PMCID: PMC5290318 DOI: 10.1038/ncomms14251] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/13/2016] [Indexed: 01/19/2023] Open
Abstract
Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution.
Collapse
Affiliation(s)
- Alison E. Wright
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Iulia Darolti
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Natasha I. Bloch
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Vicencio Oostra
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Ben Sandkam
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Severine D. Buechel
- Department of Zoology, Stockholm University, Svante Arrheniusväg 18 B, Stockholm 106 91, Sweden
| | - Niclas Kolm
- Department of Zoology, Stockholm University, Svante Arrheniusväg 18 B, Stockholm 106 91, Sweden
| | - Felix Breden
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Beatriz Vicoso
- Institute of Science and Technology, Am Campus 1A, Klosterneuburg 3400, Austria
| | - Judith E. Mank
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| |
Collapse
|
24
|
Gordon SP, López-Sepulcre A, Rumbo D, Reznick DN. Rapid Changes in the Sex Linkage of Male Coloration in Introduced Guppy Populations. Am Nat 2016; 189:196-200. [PMID: 28107058 DOI: 10.1086/689864] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Theory predicts that the sex linkage of sexually selected traits can influence the direction and rate of evolution and should itself evolve in response to sex-specific selection. Some studies have found intraspecific differences in sex linkage associated with differences in selection pressures, but we know nothing about how fast these differences can evolve. Here we show that introduced guppy populations showing rapid evolution of male coloration also show rapid changes in sex-linkage patterns. A comparison, using hormonal manipulations in females, of introduced populations of different ages suggests a consistent increase of autosomal or X-linked coloration 2 years after introduction from high- to low-predation environments. Twenty years after introduction, populations already show the same pattern of coloration inheritance typical of natural low-predation populations in similar habitats. These results highlight that the contemporary evolution of sexually selected traits ought to be studied in concert with contemporary changes in linkage relationships.
Collapse
|
25
|
Mcnair A, Lokman PM, Closs GP, Nakagawa S. ECOLOGICAL AND EVOLUTIONARY APPLICATIONS FOR ENVIRONMENTAL SEX REVERSAL OF FISH. QUARTERLY REVIEW OF BIOLOGY 2015; 90:23-44. [PMID: 26434164 DOI: 10.1086/679762] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Environmental sex reversal (ESR), which results in a mismatch between genotypic and phenotypic sex, is well documented in numerous fish species and may be induced by chemical exposure. Historically, research involving piscine ESR has been carried out with a view to improving profitability in aquaculture or to elucidate the processes governing sex determination and sexual differentiation. However, recent studies in evolution and ecology suggest research on ESR now has much wider applications and ramifications. We begin with an overview of ESR in fish and a brief review of the traditional applications thereof. We then discuss ESR and its potential demographic consequences in wild populations. Theory even suggests sex-reversed fish may be purposefully released to manipulate population dynamics. We suggest new research directions that may prove fruitful in understanding how ESR at the individual level translates to population-level processes. In the latter portion of the review we focus on evolutionary applications of ESR. Sex-reversal studies from the aquaculture literature provide insight in to the evolvability of determinants of sexual phenotype. Additionally, induced sex reversal can provide information about the evolution of sex chromosomes and sex-linked traits. Recently, naturally occurring ESR has been implicated as a mechanism contributing to the evolution of sex chromosomes.
Collapse
|
26
|
Charlesworth D. The status of supergenes in the 21st century: recombination suppression in Batesian mimicry and sex chromosomes and other complex adaptations. Evol Appl 2015; 9:74-90. [PMID: 27087840 PMCID: PMC4780387 DOI: 10.1111/eva.12291] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/16/2015] [Indexed: 02/06/2023] Open
Abstract
I review theoretical models for the evolution of supergenes in the cases of Batesian mimicry in butterflies, distylous plants and sex chromosomes. For each of these systems, I outline the genetic evidence that led to the proposal that they involve multiple genes that interact during ‘complex adaptations’, and at which the mutations involved are not unconditionally advantageous, but show advantages that trade‐off against some disadvantages. I describe recent molecular genetic studies of these systems and questions they raise about the evolution of suppressed recombination. Nonrecombining regions of sex chromosomes have long been known, but it is not yet fully understood why recombination suppression repeatedly evolved in systems in distantly related taxa, but does not always evolve. Recent studies of distylous plants are tending to support the existence of recombination‐suppressed genome regions, which may include modest numbers of genes and resemble recently evolved sex‐linked regions. For Batesian mimicry, however, molecular genetic work in two butterfly species suggests a new supergene scenario, with a single gene mutating to produce initial adaptive phenotypes, perhaps followed by modifiers specifically refining and perfecting the new phenotype.
Collapse
|
27
|
Dean R, Mank JE. The role of sex chromosomes in sexual dimorphism: discordance between molecular and phenotypic data. J Evol Biol 2015; 27:1443-53. [PMID: 25105198 DOI: 10.1111/jeb.12345] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In addition to initial sex determination, genes on the sex chromosomes are theorized to play a particularly important role in phenotypic differences between males and females. Sex chromosomes in many species display molecular signatures consistent with these theoretical predictions, particularly through sex-specific gene expression. However, the phenotypic implications of this molecular signature are unresolved, and the role of the sex chromosomes in quantitative genetic studies of phenotypic sex differences is largely equivocal. In this article, we examine molecular and phenotypic data in the light of theoretical predictions about masculinization and feminization of the sex chromosomes. Additionally, we discuss the role of genetic and regulatory complexities in the genome–phenotype relationship, and ultimately how these affect the overall role of the sex chromosomes in sex differences.
Collapse
|
28
|
Senior AM, Nakagawa S, Grimm V. The evolutionary consequences of disrupted male mating signals: an agent-based modelling exploration of endocrine disrupting chemicals in the guppy. PLoS One 2014; 9:e103100. [PMID: 25047080 PMCID: PMC4105596 DOI: 10.1371/journal.pone.0103100] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/27/2014] [Indexed: 11/19/2022] Open
Abstract
Females may select a mate based on signalling traits that are believed to accurately correlate with heritable aspects of male quality. Anthropogenic actions, in particular chemicals released into the environment, are now disrupting the accuracy of mating signals to convey information about male quality. The long-term prediction for disrupted mating signals is most commonly loss of female preference. Yet, this prediction has rarely been tested using quantitative models. We use agent-based models to explore the effects of rapid disruption of mating signals. In our model, a gene determines survival. Males signal their level of genetic quality via a signal trait, which females use to select a mate. We allowed this system of sexual selection to become established, before introducing a disruption between the male signal trait and quality, which was similar in nature to that induced by exogenous chemicals. Finally, we assessed the capacity of the system to recover from this disruption. We found that within a relatively short time frame, disruption of mating signals led to a lasting loss of female preference. Decreases in mean viability at the population-level were also observed, because sexual-selection acting against newly arising deleterious mutations was relaxed. The ability of the population to recover from disrupted mating signals was strongly influenced by the mechanisms that promoted or maintained genetic diversity in traits under sexual selection. Our simple model demonstrates that environmental perturbations to the accuracy of male mating signals can result in a long-term loss of female preference for those signals within a few generations. What is more, the loss of this preference can have knock-on consequences for mean population fitness.
Collapse
Affiliation(s)
- Alistair McNair Senior
- Zoology Department, The University of Otago, Dunedin, Otago, New Zealand
- The Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
| | - Shinichi Nakagawa
- Zoology Department, The University of Otago, Dunedin, Otago, New Zealand
| | - Volker Grimm
- Department of Ecological Modelling, Helmholtz Centre for Environmental Research, Leipzig, Saxony, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Brandenburg, Germany
| |
Collapse
|
29
|
Sharma E, Künstner A, Fraser BA, Zipprich G, Kottler VA, Henz SR, Weigel D, Dreyer C. Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata. BMC Genomics 2014; 15:400. [PMID: 24886435 PMCID: PMC4059875 DOI: 10.1186/1471-2164-15-400] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/09/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Sexually dimorphic phenotypes are generally associated with differential gene expression between the sexes. The study of molecular evolution and genomic location of these differentially expressed, or sex-biased, genes is important for understanding inter-sexual divergence under sex-specific selection pressures. Teleost fish provide a unique opportunity to examine this divergence in the presence of variable sex-determination mechanisms of recent origin. The guppy, Poecilia reticulata, displays sexual dimorphism in size, ornaments, and behavior, traits shaped by natural and sexual selection in the wild. RESULTS To gain insight into molecular mechanisms underlying the guppy's sexual dimorphism, we assembled a reference transcriptome combining genome-independent as well as genome-guided assemblies and analyzed sex-biased gene expression between different tissues of adult male and female guppies. We found tissue-associated sex-biased expression of genes related to pigmentation, signal transduction, and spermatogenesis in males; and growth, cell-division, extra-cellular matrix organization, nutrient transport, and folliculogenesis in females. While most sex-biased genes were randomly distributed across linkage groups, we observed accumulation of ovary-biased genes on the sex linkage group, LG12. Both testis-biased and ovary-biased genes showed a significantly higher rate of non-synonymous to synonymous substitutions (dN/dS) compared to unbiased genes. However, in somatic tissues only female-biased genes, including those co-expressed in multiple tissues, showed elevated ratios of non-synonymous substitutions. CONCLUSIONS Our work identifies a set of annotated gene products that are candidate factors affecting sexual dimorphism in guppies. The differential genomic distribution of gonad-biased genes provides evidence for sex-specific selection pressures acting on the nascent sex chromosomes of the guppy. The elevated rates of evolution of testis-biased and female-biased genes indicate differing evolution under distinct selection pressures on the reproductive versus non-reproductive tissues.
Collapse
Affiliation(s)
| | - Axel Künstner
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany.
| | | | | | | | | | | | | |
Collapse
|
30
|
Gotanda KM, Hendry AP. Using adaptive traits to consider potential consequences of temporal variation in selection: male guppy colour through time and space. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12261] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Kiyoko M. Gotanda
- Department of Biology; McGill University; 1205 Docteur Penfield Avenue Montreal Quebec H3A 1B1 Canada
- Redpath Museum; McGill University; 859 Sherbrooke West Montreal Quebec H3A 0C4 Canada
| | - Andrew P. Hendry
- Department of Biology; McGill University; 1205 Docteur Penfield Avenue Montreal Quebec H3A 1B1 Canada
- Redpath Museum; McGill University; 859 Sherbrooke West Montreal Quebec H3A 0C4 Canada
| |
Collapse
|
31
|
Charlesworth B, Jordan CY, Charlesworth D. The evolutionary dynamics of sexually antagonistic mutations in pseudoautosomal regions of sex chromosomes. Evolution 2014; 68:1339-50. [PMID: 24476564 PMCID: PMC4289941 DOI: 10.1111/evo.12364] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 01/08/2014] [Indexed: 11/30/2022]
Abstract
Sex chromosomes can evolve gene contents that differ from the rest of the genome, as well as larger sex differences in gene expression compared with autosomes. This probably occurs because fully sex-linked beneficial mutations substitute at different rates from autosomal ones, especially when fitness effects are sexually antagonistic (SA). The evolutionary properties of genes located in the recombining pseudoautosomal region (PAR) of a sex chromosome have not previously been modeled in detail. Such PAR genes differ from classical sex-linked genes by having two alleles at a locus in both sexes; in contrast to autosomal genes, however, variants can become associated with gender. The evolutionary fates of PAR genes may therefore differ from those of either autosomal or fully sex-linked genes. Here, we model their evolutionary dynamics by deriving expressions for the selective advantages of PAR gene mutations under different conditions. We show that, unless selection is very strong, the probability of invasion of a population by an SA mutation is usually similar to that of an autosomal mutation, unless there is close linkage to the sex-determining region. Most PAR genes should thus evolve similarly to autosomal rather than sex-linked genes, unless recombination is very rare in the PAR.
Collapse
Affiliation(s)
- Brian Charlesworth
- Institute of Evolutionary Biology, Ashworth Laboratory, School of Biological Sciences, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JT, United Kingdom
| | | | | |
Collapse
|
32
|
Abstract
Sex-antagonistic (SA) selection has major evolutionary consequences: it can drive genomic change, constrain adaptation, and maintain genetic variation for fitness. The recombining (or pseudoautosomal) regions of sex chromosomes are a promising setting in which to study SA selection because they tend to accumulate SA polymorphisms and because recombination allows us to deploy the tools of molecular evolution to locate targets of SA selection and quantify evolutionary forces. Here we use coalescent models to characterize the patterns of polymorphism expected within and divergence between recombining X and Y (or Z and W) sex chromosomes. SA selection generates peaks of divergence between X and Y that can extend substantial distances away from the targets of selection. Linkage disequilibrium between neutral sites is also inflated. We show how the pattern of divergence is altered when the SA polymorphism or the sex-determining region was recently established. We use data from the flowering plant Silene latifolia to illustrate how the strength of SA selection might be quantified using molecular data from recombining sex chromosomes.
Collapse
|
33
|
Testing for the footprint of sexually antagonistic polymorphisms in the pseudoautosomal region of a plant sex chromosome pair. Genetics 2013; 194:663-72. [PMID: 23733787 DOI: 10.1534/genetics.113.152397] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The existence of sexually antagonistic (SA) polymorphism is widely considered the most likely explanation for the evolution of suppressed recombination of sex chromosome pairs. This explanation is largely untested empirically, and no such polymorphisms have been identified, other than in fish, where no evidence directly implicates these genes in events causing loss of recombination. We tested for the presence of loci with SA polymorphism in the plant Silene latifolia, which is dioecious (with separate male and female individuals) and has a pair of highly heteromorphic sex chromosomes, with XY males. Suppressed recombination between much of the Y and X sex chromosomes evolved in several steps, and the results in Bergero et al. (2013) show that it is still ongoing in the recombining or pseudoautosomal, regions (PARs) of these chromosomes. We used molecular evolutionary approaches to test for the footprints of SA polymorphisms, based on sequence diversity levels in S. latifolia PAR genes identified by genetic mapping. Nucleotide diversity is high for at least four of six PAR genes identified, and our data suggest the existence of polymorphisms maintained by balancing selection in this genome region, since molecular evolutionary (HKA) tests exclude an elevated mutation rate, and other tests also suggest balancing selection. The presence of sexually antagonistic alleles at a locus or loci in the PAR is suggested by the very different X and Y chromosome allele frequencies for at least one PAR gene.
Collapse
|
34
|
Ruell EW, Handelsman CA, Hawkins CL, Sofaer HR, Ghalambor CK, Angeloni L. Fear, food and sexual ornamentation: plasticity of colour development in Trinidadian guppies. Proc Biol Sci 2013; 280:20122019. [PMID: 23466982 DOI: 10.1098/rspb.2012.2019] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolution of male ornamentation often reflects compromises between sexual and natural selection, but it may also be influenced by phenotypic plasticity. We investigated the developmental plasticity of male colour ornamentation in Trinidadian guppies in response to two environmental variables that covary in nature: predation risk and food availability. We found that exposure to chemical predator cues delayed the development of pigment-based colour elements, which are conspicuous to visual-oriented predators. Predator cues also reduced the size of colour elements at the time of maturity and caused adult males to be less colourful. To the best of our knowledge, these findings provide the first example of a plastic reduction in the development of a sexually selected male ornament in response to predator cues. The influence of predator cues on ornamentation probably affects individual fitness by reducing conspicuousness to predators, but could reduce attractiveness to females. Reduced food availability during development caused males to delay the development of colour elements and mature later, probably reflecting a physiological constraint, but their coloration at maturity and later in adulthood was largely unaffected, suggesting that variation in food quantity without variation in quality does not contribute to condition dependence of the trait.
Collapse
Affiliation(s)
- E W Ruell
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
| | | | | | | | | | | |
Collapse
|
35
|
Schaefer JF, Duvernell DD, Kreiser BR, Champagne C, Clark SR, Gutierrez M, Stewart LK, Coleman C. Evolution of a sexually dimorphic trait in a broadly distributed topminnow (Fundulus olivaceus). Ecol Evol 2012; 2:1371-81. [PMID: 22957146 PMCID: PMC3434935 DOI: 10.1002/ece3.242] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 02/21/2012] [Accepted: 02/24/2012] [Indexed: 11/23/2022] Open
Abstract
Understanding the interaction between sexual and natural selection within variable environments is crucial to our understanding of evolutionary processes. The handicap principle predicts females will prefer males with exaggerated traits provided those traits are indicators of male quality to ensure direct or indirect female benefits. Spatial variability in ecological factors is expected to alter the balance between sexual and natural selection that defines the evolution of such traits. Male and female blackspotted topminnows (Fundulidae: Fundulus olivaceus) display prominent black dorsolateral spots that are variable in number across its broad range. We investigated variability in spot phenotypes at 117 sites across 13 river systems and asked if the trait was sexually dimorphic and positively correlated with measures of fitness (condition and gonadosomatic index [GSI]). Laboratory and mesocosm experiments assessed female mate choice and predation pressure on spot phenotypes. Environmental and community data collected at sampling locations were used to assess predictive models of spot density at the individual, site, and river system level. Greater number of spots was positively correlated with measures of fitness in males. Males with more spots were preferred by females and suffered greater mortality due to predation. Water clarity (turbidity) was the best predictor of spot density on the drainage scale, indicating that sexual and natural selection for the trait may be mediated by local light environments.
Collapse
|
36
|
Shenoy K. Environmentally realistic exposure to the herbicide atrazine alters some sexually selected traits in male guppies. PLoS One 2012; 7:e30611. [PMID: 22312428 PMCID: PMC3270011 DOI: 10.1371/journal.pone.0030611] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 12/25/2011] [Indexed: 11/18/2022] Open
Abstract
Male mating signals, including ornaments and courtship displays, and other sexually selected traits, like male-male aggression, are largely controlled by sex hormones. Environmental pollutants, notably endocrine disrupting compounds, can interfere with the proper functioning of hormones, thereby impacting the expression of hormonally regulated traits. Atrazine, one of the most widely used herbicides, can alter sex hormone levels in exposed animals. I tested the effects of environmentally relevant atrazine exposures on mating signals and behaviors in male guppies, a sexually dimorphic freshwater fish. Prolonged atrazine exposure reduced the expression of two honest signals: the area of orange spots (ornaments) and the number of courtship displays performed. Atrazine exposure also reduced aggression towards competing males in the context of mate competition. In the wild, exposure levels vary among individuals because of differential distribution of the pollutants across habitats; hence, differently impacted males often compete for the same mates. Disrupted mating signals can reduce reproductive success as females avoid mating with perceptibly suboptimal males. Less aggressive males are at a competitive disadvantage and lose access to females. This study highlights the effects of atrazine on ecologically relevant mating signals and behaviors in exposed wildlife. Altered reproductive traits have important implications for population dynamics, evolutionary patterns, and conservation of wildlife species.
Collapse
Affiliation(s)
- Kausalya Shenoy
- Department of Biology, University of Kentucky, Lexington, Kentucky, United States of America.
| |
Collapse
|