Loss of recombination between sex chromosomes often depletes Y chromosomes of functional content and genetic variation, which might limit their potential to generate adaptive diversity. Males of the freshwater fish Poecilia parae occur as one of five discrete morphs, all of which shoal together in natural populations where morph frequency has been stable for over 50 years. Each morph uses a different complex reproductive strategy and morphs differ dramatically in colour, body size and mating behaviour. Morph phenotype is passed perfectly from father to son, indicating there are five Y haplotypes segregating in the species, which encode the complex male morph characteristics. Here, we examine Y diversity in natural populations of P. parae. Using linked-read sequencing on multiple P. parae females and males of all five morphs, we find that the genetic architecture of the male morphs evolved on the Y chromosome after recombination suppression had occurred with the X. Comparing Y chromosomes between each of the morphs, we show that, although the Ys of the three minor morphs that differ in colour are highly similar, there are substantial amounts of unique genetic material and divergence between the Ys of the three major morphs that differ in reproductive strategy, body size and mating behaviour. Altogether, our results suggest that the Y chromosome is able to overcome the constraints of recombination loss to generate extreme diversity, resulting in five discrete Y chromosomes that control complex reproductive strategies.
This is a preview of subscription content, access via your institution
Open Access articles citing this article.
Sex-limited chromosomes and non-reproductive traits
BMC Biology Open Access 06 July 2022
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 digital issues and online access to articles
$119.00 per year
only $9.92 per issue
Rent or buy this article
Get just this article for as long as you need it
Prices may be subject to local taxes which are calculated during checkout
All of the data generated for this study have been made available in the NCBI repository under the BioProject accession number PRJNA714257.
All scripts and pipelines for analyses are available at https://github.com/manklab/Poecilia_parae_Y_Diversity
Bachtrog, D. Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration. Nat. Rev. Genet. 14, 113–124 (2013).
Tobler, R., Nolte, V. & Schlotterer, C. High rate of translocation-based gene birth on the Drosophila Y chromosome. Proc. Natl Acad. Sci. USA 114, 11721–11726 (2017).
Mahajan, S. & Bachtrog, D. Convergent evolution of Y chromosome gene content in flies. Nat. Commun. 8, 785 (2017).
Bachtrog, D., Mahajan, S. & Bracewell, R. Massive gene amplification on a recently formed Drosophila Y chromosome. Nat. Ecol. Evol. 3, 1587–1597 (2019).
Hall, A. B. et al. Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. Proc. Natl Acad. Sci. USA 113, E2114–E2123 (2016).
Todesco, M. et al. Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 584, 602–607 (2020).
Schwander, T., Libbrecht, R. & Keller, L. Supergenes and complex phenotypes. Curr. Biol. 24, 288–294 (2014).
Wang, J. et al. A Y-like social chromosome causes alternative colony organization in fire ants. Nature 493, 664–668 (2013).
Lamichhaney, S. et al. Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nat. Genet. 48, 84–88 (2016).
Kupper, C. et al. A supergene determines highly divergent male reproductive morphs in the ruff. Nat. Genet. 48, 79–83 (2016).
Branco, S. et al. Multiple convergent supergene evolution events in mating-type chromosomes. Nat. Commun. 9, 2000 (2018).
Yan, Z. et al. Evolution of a supergene that regulates a trans-species social polymorphism. Nat. Ecol. Evol. 4, 240–249 (2020).
Lindholm, A. K., Brooks, R. & Breden, F. Extreme polymorphism in a Y-linked sexually selected trait. Heredity 92, 156–162 (2004).
Hurtado-Gonzales, J. L. & Uy, J. A. Alternative mating strategies may favour the persistence of a genetically based colour polymorphism in a pentamorphic fish. Anim. Behav. 77, 1187–1194 (2009).
Hurtado-Gonzales, J. L. & Uy, J. A. Intrasexual competition facilitates the evolution of alternative mating strategies in a colour polymorphic fish. BMC Evol. Biol. 10, 391 (2010).
Hurtado-Gonzales, J. L., Baldassarre, D. T. & Uy, J. A. Interaction between female mating preferences and predation may explain the maintenance of rare males in the pentamorphic fish Poecilia parae. J. Evol. Biol. 23, 1293–1301 (2010).
Hurtado-Gonzales, J. L., Loew, E. R. & Uy, J. A. Variation in the visual habitat may mediate the maintenance of color polymorphism in a poeciliid fish. PLoS ONE 9, e101497 (2014).
Sandkam, B. A., Young, C. M., Breden, F. M., Bourne, G. R. & Breden, F. Color vision varies more among populations than among species of live-bearing fish from South America. BMC Evol. Biol. 15, 225 (2015).
Bourne, G. R., Breden, F. & Allen, T. C. Females prefer carotenoid colored males as mates in the pentamorphic livebearing fish, Poecilia parae. Naturwissenschaften 90, 402–405 (2003).
Liley, N. R. Reproductive Isolation in Some Sympatric Species of Fishes. PhD thesis, Oxford Univ. (1963).
Bachtrog, D. et al. Are all sex chromosomes created equal? Trends Genet. 27, 350–357 (2011).
Rice, W. R. Evolution of the Y sex chromosome in animals. BioScience 46, 331–343 (1996).
Wright, A. E., Dean, R., Zimmer, F. & Mank, J. E. How to make a sex chromosome. Nat. Commun. 7, 12087 (2016).
Furman, B. L. S. et al. Sex chromosome evolution: so many exceptions to the rules. Genome Biol. Evol. 12, 750–763 (2020).
Darolti, I. et al. Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers. Proc. Natl Acad. Sci. USA 116, 19031–19036 (2019).
Wright, A. et al. Convergent recombination suppression suggests a role of sexual selection in guppy sex chromosome formation. Nat. Commun. 8, 14251 (2017).
Darolti, I., Wright, A. E. & Mank, J. E. Guppy Y chromosome integrity maintained by incomplete recombination suppression. Genome Biol. Evol. 12, 965–977 (2020).
Almeida, P. et al. Divergence and remarkable diversity of the Y chromosome in guppies. Mol. Biol. Evol. 38, 619–633 (2021).
Rabosky, D. L. et al. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559, 392–395 (2018).
Reznick, D. N., Miles, D. B. & Winslow, S. Life history of Poecilia picta (Poeciliidae) from the Island of Trinidad. Copeia 1992, 782–790 (1992).
Haskins, C. P. & Haskins, E. F. The role of sexual selection as an isolating mechanism in three species of poeciliid fishes. Evolution 3, 160–169 (1949).
Liley, N. R. Ethological isolating mechanisms in four sympatric species of poeciliid fishes. Behav. Suppl. 14, 1–197 (1966).
Vicoso, B. & Bachtrog, D. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature 499, 332–335 (2013).
Vicoso, B. & Bachtrog, D. Numerous transitions of sex chromosomes in Diptera. PLoS Biol. 13, e1002078 (2015).
Vicoso, B., Emerson, J. J., Zektser, Y., Mahajan, S. & Bachtrog, D. Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation. PLoS Biol. 11, e1001643 (2013).
Kim, J. et al. Reference-assisted chromosome assembly. Proc. Natl Acad. Sci. USA 110, 1785–1790 (2013).
Pucholt, P., Wright, A. E., Conze, L. L., Mank, J. E. & Berlin, S. Recent sex chromosome divergence despite ancient dioecy in the willow Salix viminalis. Mol. Biol. Evol. 34, 1991–2001 (2017).
Akagi, T., Henry, I. M., Tao, R. & Comai, L. A Y-chromosome-encoded small RNA acts as a sex determinant in persimmons. Science 346, 646–650 (2014).
Torres, M. F. et al. Genus-wide sequencing supports a two-locus model for sex-determination in Phoenix. Nat. Commun. 9, 3969 (2018).
Morris, J., Darolti, I., Bloch, N. I., Wright, A. E. & Mank, J. E. Shared and species-specific patterns of nascent Y chromosome evolution in two guppy species. Genes 9, 238 (2018).
Napolitano, L. M. & Meroni, G. TRIM family: pleiotropy and diversification through homomultimer and heteromultimer formation. IUBMB Life 64, 64–71 (2012).
Sardiello, M., Cairo, S., Fontanella, B., Ballabio, A. & Meroni, G. Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties. BMC Evol. Biol. 8, 225 (2008).
Karki, R. et al. NLRC3 is an inhibitory sensor of PI3K-mTOR pathways in cancer. Nature 540, 583–587 (2016).
Sandkam, B. A. et al. Tbx2a modulates switching of RH2 and LWS opsin gene expression. Mol. Biol. Evol. 37, 2002–2014 (2020).
Showell, C., Christine, K. S., Mandel, E. M. & Conlon, F. L. Developmental expression patterns of Tbx1, Tbx2, Tbx5, and Tbx20 in Xenopus tropicalis. Dev. Dyn. 235, 1623–1630 (2006).
Gibson-Brown, J. J., S, I. A., Silver, L. M. & Papaioannou, V. E. Expression of T-box genes Tbx2-Tbx5 during chick organogenesis. Mech. Dev. 74, 165–169 (1998).
Tomaszkiewicz, M., Chalopin, D., Schartl, M., Galiana, D. & Volff, J.-N. A multicopy Y-chromosomal SGNH hydrolase gene expressed in the testis of the platyfish has been captured and mobilized by a Helitron transposon. BMC Genet. 15, 44 (2014).
Smit, A. F. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9, 657–663 (1999).
Sotero-Caio, C. G., Platt, R. N. 2nd, Suh, A. & Ray, D. A. Evolution and diversity of transposable elements in vertebrate genomes. Genome Biol. Evol. 9, 161–177 (2017).
Felsenstein, J. The evolutionary advantage of recombination. Genetics 78, 737–756 (1974).
Lenormand, T., Fyon, F., Sun, E. & Roze, D. Sex chromosome degeneration by regulatory evolution. Curr. Biol. 30, 3001–3006 (2020).
Hough, J., Wang, W., Barrett, S. C. H. & Wright, S. I. Hill–Robertson interference reduces genetic diversity on a young plant Y-chromosome. Genetics 207, 685 (2017).
Marais, G. A. et al. Evidence for degeneration of the Y chromosome in the dioecious plant Silene latifolia. Curr. Biol. 18, 545–549 (2008).
Bachtrog, D. & Charlesworth, B. Reduced adaptation of a non-recombining neo-Y chromosome. Nature 416, 323–326 (2002).
Mank, J. E. Small but mighty: the evolutionary dynamics of W and Y sex chromosomes. Chromosome Res. 20, 21–33, (2012).
Kaiser, V. B. & Charlesworth, B. Muller’s ratchet and the degeneration of the Drosophila miranda neo-Y chromosome. Genetics 185, 339–348 (2010).
Keightley, P. D. & Otto, S. P. Interference among deleterious mutations favours sex and recombination in finite populations. Nature 443, 89–92 (2006).
Ritz, K. R., Noor, M. A. F. & Singh, N. D. Variation in recombination rate: adaptive or not? Trends Genet. 33, 364–374 (2017).
Metzger, D. C. H., Sandkam, B. A., Darolti, I. & Mank, J. E. Rapid evolution of complete dosage compensation in Poecilia. Preprint at bioRxiv https://doi.org/10.1101/2021.02.12.431036 (2021).
Lemos, B., Araripe, L. O. & Hartl, D. L. Polymorphic Y chromosomes harbor cryptic variation with manifold functional consequences. Science 319, 91–93 (2008).
Ellegren, H. Characteristics, causes and evolutionary consequences of male-biased mutation. Proc. Biol. Sci. 274, 1–10 (2007).
Tennessen, J. A. et al. Repeated translocation of a gene cassette drives sex-chromosome turnover in strawberries. PLoS Biol. 16, e2006062 (2018).
Bourque, G. et al. Ten things you should know about transposable elements. Genome Biol. 19, 199 (2018).
Carleton, K. L. et al. Movement of transposable elements contributes to cichlid diversity. Mol. Ecol. 29, 4956–4969 (2020).
Brawand, D. et al. The genomic substrate for adaptive radiation in African cichlid fish. Nature 513, 375–381 (2014).
Auvinet, J. et al. Mobilization of retrotransposons as a cause of chromosomal diversification and rapid speciation: the case for the Antarctic teleost genus Trematomus. BMC Genom. 19, 339 (2018).
Naville, M. et al. Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates. Clin. Microbiol. Infect. 22, 312–323 (2016).
Sinervo, B. & Calsbeek, R. The developmental, physiological, neural, and genetical causes and consequences of frequency-dependent selection in the wild. Annu. Rev. Ecol. Evol. Syst. 37, 581–610 (2006).
Sinervo, B. & Lively, C. M. The rock-paper-scissors game and the evolution of alternative male strategies. Nature 380, 240–243 (1996).
Hartl, D. L. & Clark, A. G. Principles of Population Genetics (Sinauer Associates, 1997).
Lank, D. B., Smith, C. M., Hanotte, O., Burke, T. & Cooke, F. Genetic polymorphism for alternative mating behaviour in lekking male ruff Philomachus pugnax. Nature 378, 59–62 (1995).
Tuttle, E. M. et al. Divergence and functional degradation of a sex chromosome-like supergene. Curr. Biol. 26, 344–350 (2016).
Hunt, B. G. Supergene evolution: recombination finds a way. Curr. Biol. 30, 73–76, (2020).
Charlesworth, D. The status of supergenes in the 21st century: recombination suppression in Batesian mimicry and sex chromosomes and other complex adaptations. Evol. Appl. 9, 74–90 (2016).
Joron, M. et al. Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry. Nature 477, 203–206 (2011).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Elyanow, R., Wu, H.-T. & Raphael, B. J. Identifying structural variants using linked-read sequencing data. Bioinformatics 34, 353–360 (2018).
Harris, R. S. Improved Pairwise Alignment of Genomic DNA. PhD thesis, Pennsylvania State Univ. (2007).
Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W. & Haussler, D. Evolution’s cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA 100, 11484–11489 (2003).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357 (2012).
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).
Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1, 2047–217X–1–18 (2012).
Palmer, D. H., Rogers, T. F., Dean, R. & Wright, A. E. How to identify sex chromosomes and their turnover. Mol. Ecol. 28, 4709–4724 (2019).
Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012).
Carvalho, A. B. & Clark, A. G. Efficient identification of Y chromosome sequences in the human and Drosophila genomes. Genome Res. 23, 1894–1907 (2013).
Carvalho, A. B., Vicoso, B., Russo, C. A., Swenor, B. & Clark, A. G. Birth of a new gene on the Y chromosome of Drosophila melanogaster. Proc. Natl Acad. Sci. USA 112, 12450–12455 (2015).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Holt, C. & Yandell, M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinform. 12, 491 (2011).
Smit, A., Hubley, R. RepeatModeler Open-1.0. (ISB, 2013-2015); http://www.repeatmasker.org
Smit, A., Hubley, R. & Green, P. RepeatMasker Open-4.0. (ISB, 2013-2015); http://www.repeatmasker.org
Howe, K. L. et al. Ensembl Genomes 2020-enabling non-vertebrate genomic research. Nucleic Acids Res. 48, D689–D695 (2020).
Dreyer, C. et al. ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata. BMC Genom. 8, 269 (2007).
Sharma, E. et al. Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata. BMC Genom. 15, 400 (2014).
Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).
Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–W439 (2006).
Seppey, M., Manni, M. & Zdobnov, E. M. in Gene Prediction (ed. Kollmar, M.) 227–245 (Humana, 2019).
Korf, I. Gene finding in novel genomes. BMC Bioinform. 5, 59 (2004).
Katoh, K., Asimenos, G. & Toh, H. Multiple alignment of DNA sequences with MAFFT. Methods Mol. Biol. 537, 39–64 (2009).
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
We thank the members of the Mank lab and N. Prior for stimulating conversations and excellent feedback on early drafts of the manuscript. This was supported by the Natural Sciences and Engineering Research Council of Canada through a Banting Postdoctoral Fellowship (to B.A.S.), the European Research Council (grant nos. 260233 and 680951 to J.E.M.) and a Canada 150 Research Chair (to J.E.M.). Field work was conducted under Permit 120616 SP: 015 from the Environmental Protection Agency of Guyana. Sequencing was performed by the SNP&SEQ Technology Platform in Uppsala, Sweden. The CEIBA Biological Center partially subsidized our expenses during field collection in Guyana. We thank C. Lacy for the fish illustrations.
The authors declare no competing interests.
Peer review information Nature Ecology & Evolution thanks the anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended Data Fig. 1 Divergence between X and Y in Poecilia parae and the sister species Poecilia picta indicate recombination was stopped before the five morphs controlled by the Y chromosome evolved in Poecilia parae.
a, M:F log2 coverage of RACA anchored scaffolds for all five morphs of P. parae (red) and the close relative P. picta (black)25. Lines represent sliding window of 15 scaffolds. Shaded bars represent the 95% confidence interval based on bootstrapping coverage across the autosomes for P. parae (pink) and P. picta (grey). b, Phylogeny from The Fish Tree of Life29. Orange indicate species for which chr 8 is known to be the Y and is highly diverged from the X. Blue indicates species for which chr 8 is known to be not degraded25. Green star denotes the branch on which X–Y recombination was arrested and the Y chromosome diverged. None of the male morphs of P. parae are found in other species, making the most parsimonious explanation that all five morphs arose after recombination stopped. (Note, a version of the phylogeny in b is also presented in ref. 59).
Extended Data Fig. 2 Bayesian phylogeny built on presence/absence of the 27,950,090 P. parae Y-mers and the 646,754 P. picta Y-mers in each individual and rooted on P. picta (as in Fig. 2).
The posterior probability is presented at each node. The number of Y-mers each individual shares with P. picta Y-mers is denoted to the right. P. picta Y-mers are distributed across all morphs indicating that they have been segregating on non-recombining regions of the Y chromosome since recombination was stopped in the common ancestor of P. parae and P. picta.
Extended Data Fig. 3 Validation of morph-mer identification pipeline using random sets of individuals from each of the different morphs.
Different samples were used for each set except for blue where the 1 sample was used in validation set 2 and validation set 3. There were a low number of Y-mers unique to sets of four random individuals and zero Y-mers unique to sets with more than four individuals. This demonstrates the false positive rate of our morph-mer analysis was quite low because all major morphs had at least four individuals.
Extended Data Fig. 4 Mapping distribution for each set of morph-mers mapped to de novo scaffolds of males of that morph with no mismatches, gaps, or trimming.
There was a low incidence of individual morph-mers mapping to more than one scaffold (0 of the 59 Y-mers were contained in more than one scaffold across all males; 0 of the 1,435 parae-mers were contained in more than one scaffold in parae males; 131 of the 87,629 melanzona-mers were contained in more than one scaffold in melanzona males; 138 of the 64,515 immaculata-mers were contained in more than one scaffold in immaculata males). Left: cumulative morph-mers mapped for each individual, each change in hue is a different scaffold. A large percentage of morph-mers generally map to just one or a few scaffolds indicating that our k-mer approach reveals regions of highly diverged morph-specific sequence rather than single SNPs distributed throughout the genome. Right: cumulative morph-mers mapped presented as a function of the number of scaffolds. The strong deviation from 1:1 shows morph-mer mapping is non-random and further supports the morph-mers approach is identifying regions of morph-specific sequence. The total number of unique morph-mers identified for that morph is indicated in red on the axis (note the variation in number of morph-mers mapped is due to some individuals having morph-mers map to multiple scaffolds). Astrix in P02 of the melanzona-mers indicates the example alignment scaffold with melanzona-mers presented in Extended Data Fig. 5.
Extended Data Fig. 5 Melanzona-mers aligned to scaffold 104666 of sample P02 with no mismatches, gaps, or trimming.
Each 31 bp melanzona-mer is shown aligned below the reference sequence, and coverage is shown in purple above the reference sequence. Of the 87,629 unique melanzona-mers; 23,773 aligned to this scaffold. Regions of Ns are denoted on the reference genome in grey and explain a lack of melanzona-mers aligning to these regions. The strong clustering and overlapping nature of the melanzona-mers indicates sequence is highly diverged both from females and from the other morphs.
Extended Data Fig. 6 Morph-specific Y chromosome sequence is composed of significantly more interspersed repeats than the autosomes and X chromosome.
For males, only scaffolds containing >5 morph-specific Y-mers were evaluated, ensuring sequence is morph-specific and Y-linked. To determine rates of autosomes and X chromosomes, female full de novo genomes were evaluated. Stars indicate significant differences between morphs (* P<0.05, ** P<0.01).
Extended Data Fig. 7 Unrooted approximately-maximum-likelihood trees (FastTree) of each of the autosomes confirm that the extreme divergence across morphs is specific to the Y chromosome, and not the result of cryptic subpopulations.
Trees were built using the consensus sequence of the longest scaffold from each chromosome (as identified by RACA). Tips denote sample name, colour indicates morph, and numbers on branches indicate FastTree support value.
Supplementary Tables 1–12.
Rights and permissions
About this article
Cite this article
Sandkam, B.A., Almeida, P., Darolti, I. et al. Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish. Nat Ecol Evol 5, 939–948 (2021). https://doi.org/10.1038/s41559-021-01452-w
This article is cited by
Sex-specific morphs: the genetics and evolution of intra-sexual variation
Nature Reviews Genetics (2023)
Sex-limited chromosomes and non-reproductive traits
BMC Biology (2022)
Y chromosome evolution spurs behavioural diversity in male fish
Nature Ecology & Evolution (2021)