Speijer, D., Lukeš, J. & Eliáš, M. Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life. Proc. Natl Acad. Sci. USA 112, 8827–8834 (2015).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

Muller, H. J. Some genetic aspects of sex. Am. Nat. 66, 118–138 (1932).

Article 

Google Scholar
 

Muller, H. J. The relation of recombination to mutational advance. Mutat. Res. 106, 2–9 (1964).

Article 
CAS 

Google Scholar
 

Felsenstein, J. The evolutionary advantage of recombination. Genetics 78, 737–756 (1974).

Article 
CAS 
PubMed Central 

Google Scholar
 

Quattro, J. M., Avise, J. C. & Vrijenhoek, R. C. An ancient clonal lineage in the fish genus Poeciliopsis (Atheriniformes: Poeciliidae). Proc. Natl Acad. Sci. USA 89, 348–352 (1992).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

Welch, M. D. & Meselson, M. Evidence for the evolution of bdelloid rotifers without sexual reproduction or genetic exchange. Science 288, 1211–1215 (2000).

Article 
ADS 
CAS 

Google Scholar
 

Schwander, T., Henry, L. & Crespi, B. J. Molecular evidence for ancient asexuality in timema stick insects. Curr. Biol. 21, 1129–1134 (2011).

Article 
CAS 

Google Scholar
 

Hubbs, C. L. & Hubbs, L. C. Apparent parthenogenesis in nature, in a form of fish of hybrid origin. Science 76, 628–630 (1932).

Article 
ADS 
CAS 

Google Scholar
 

Stöck, M., Lampert, K. P., Möller, D., Schlupp, I. & Schartl, M. Monophyletic origin of multiple clonal lineages in an asexual fish (Poecilia formosa). Mol. Ecol. 19, 5204–5215 (2010).

Article 

Google Scholar
 

Warren, W. C. et al. Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly. Nat. Ecol. Evol. 2, 669–679 (2018).

Article 
PubMed Central 

Google Scholar
 

Smith, J. M. The Evolution of Sex (Cambridge Univ. Press, 1978).

Birky, C. W. Jr. Heterozygosity, heteromorphy, and phylogenetic trees in asexual eukaryotes. Genetics 144, 427–437 (1996).

Article 
PubMed Central 

Google Scholar
 

Judson, O. P. & Normark, B. B. Ancient asexual scandals. Trends Ecol. Evol. 11, 41–46 (1996).

Article 
CAS 

Google Scholar
 

Lynch, M., Conery, J. & Burger, R. Mutation accumulation and the extinction of small populations. Am. Nat. 146, 489–518 (1995).

Article 

Google Scholar
 

Bell, G. The Masterpiece of Nature: Evolution and Genetics of Sexuality (Croom Helm, 1982).

Smith, J. M. in Group Selection (ed. Williams, G. C.) Ch. 9 (Routledge, 1971).

Williams, G. C. Sex and Evolution (Princeton Univ. Press, 1975).

Tree of Sex Consortium Tree of Sex: a database of sexual systems. Sci. Data 1, 140015 (2014).

Article 

Google Scholar
 

Lynch, M. & Gabriel, W. Mutation load and the survival of small populations. Evolution 44, 1725–1737 (1990).

Article 

Google Scholar
 

Jaron, K. S. et al. Genomic features of parthenogenetic animals. J. Hered. 112, 19–33 (2021).

Article 
CAS 
PubMed Central 

Google Scholar
 

Dawley, R. M. & Bogart, J. P. Evolution and Ecology of Unisexual Vertebrates (New York State Museum, 1989).

Avise, J. C. Clonality: The Genetics, Ecology, and Evolution of Sexual Abstinence in Vertebrate Animals (Oxford Univ. Press, 2008).

Barley, A. J., Nieto-Montes de Oca, A., Manríquez-Morán, N. L. & Thomson, R. C. The evolutionary network of whiptail lizards reveals predictable outcomes of hybridization. Science 377, 773–777 (2022).

Article 
ADS 
CAS 

Google Scholar
 

Avise, J. C., Trexler, J. C., Travis, J. & Nelson, W. S. Poecilia mexicana is the recent female parent of the unisexual fish P. formosa. Evolution 45, 1530–1533 (1991).

Article 

Google Scholar
 

Schartl, M., Wilde, B., Schlupp, I. & Parzefall, J. Evolutionary origin of a parthenoform, the Amazon molly Poecilia formosa, on the basis of a molecular genealogy. Evolution 49, 827 (1995).

CAS 

Google Scholar
 

Turner, B. J. The evolutionary genetics of a unisexual fish, Poecilia formosa. Prog. Clin. Biol. Res. 96, 265–305 (1982).

CAS 

Google Scholar
 

Costa, G. C. & Schlupp, I. Placing the hybrid origin of the asexual Amazon molly (Poecilia formosa) based on historical climate data. Biol. J. Linn. Soc. Lond. 129, 835–843 (2020).

Article 

Google Scholar
 

Costa, G. C. & Schlupp, I. Biogeography of the Amazon molly: ecological niche and range limits of an asexual hybrid species. Glob. Ecol. Biogeogr. 19, 442–451 (2010).

Article 

Google Scholar
 

Dedukh, D. et al. Achiasmatic meiosis in the unisexual Amazon molly, Poecilia formosa. Chromosome Res. 30, 443–457 (2022).

Article 
CAS 
PubMed Central 

Google Scholar
 

Kallman, K. D. Population genetics of the gynogenetic teleost, Mollienesia formosa (Girard). Evolution 16, 497–504 (1962).

Article 

Google Scholar
 

Turner, B. J., Elder, J. F. Jr, Laughlin, T. F. & Davis, W. P. Genetic variation in clonal vertebrates detected by simple-sequence DNA fingerprinting. Proc. Natl Acad. Sci. USA 87, 5653–5657 (1990).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

Schartl, M. et al. On the stability of dispensable constituents of the eukaryotic genome: stability of coding sequences versus truly hypervariable sequences in a clonal vertebrate, the amazon molly, Poecilia formosa. Proc. Natl Acad. Sci. USA. 88, 8759–8763 (1991).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

Loewe, L. & Lamatsch, D. K. Quantifying the threat of extinction from Muller’s ratchet in the diploid Amazon molly (Poecilia formosa). BMC Evol. Biol. 8, 88 (2008).

Article 
PubMed Central 

Google Scholar
 

Koren, S. et al. De novo assembly of haplotype-resolved genomes with trio binning. Nat. Biotechnol. 36, 1174–1182 (2018).

Article 
ADS 
CAS 

Google Scholar
 

Rice, E. S. et al. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. GigaScience 9, giaa029 (2020).

Article 
PubMed Central 

Google Scholar
 

Moran, N. A. Accelerated evolution and Muller’s rachet in endosymbiotic bacteria. Proc. Natl Acad. Sci. USA 93, 2873–2878 (1996).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

Nesta, A. V., Tafur, D. & Beck, C. R. Hotspots of human mutation. Trends Genet. 37, 717–729 (2021).

Article 
CAS 

Google Scholar
 

Gonzalez-Perez, A., Sabarinathan, R. & Lopez-Bigas, N. Local determinants of the mutational landscape of the human genome. Cell 177, 101–114 (2019).

Article 
CAS 

Google Scholar
 

Omilian, A. R., Cristescu, M. E. A., Dudycha, J. L. & Lynch, M. Ameiotic recombination in asexual lineages of Daphnia. Proc. Natl Acad. Sci. USA 103, 18638–18643 (2006).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

Weir, W. et al. Population genomics reveals the origin and asexual evolution of human infective trypanosomes. eLife 5, e11473 (2016).

Article 
PubMed Central 

Google Scholar
 

Brandt, A. et al. Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova. Proc. Natl Acad. Sci. USA 118, e2101485118 (2021).

Article 
CAS 
PubMed Central 

Google Scholar
 

Tubbs, A. et al. Dual roles of poly(dA:dT) tracts in replication initiation and fork collapse. Cell 174, 1127–1142.e19 (2018).

Article 
CAS 
PubMed Central 

Google Scholar
 

Stewart, J. A. et al. Noncanonical outcomes of break-induced replication produce complex, extremely long-tract gene conversion events in yeast. G3 11, jkab245 (2021).

Article 
PubMed Central 

Google Scholar
 

Chen, J.-M., Cooper, D. N., Chuzhanova, N., Férec, C. & Patrinos, G. P. Gene conversion: mechanisms, evolution and human disease. Nat. Rev. Genet. 8, 762–775 (2007).

Article 
CAS 

Google Scholar
 

Zeng, K., Fu, Y.-X., Shi, S. & Wu, C.-I. Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 174, 1431–1439 (2006).

Article 
PubMed Central 

Google Scholar
 

Mikocziova, I., Greiff, V. & Sollid, L. M. Immunoglobulin germline gene variation and its impact on human disease. Genes Immun. 22, 205–217 (2021).

Article 
CAS 
PubMed Central 

Google Scholar
 

Kravitz, S. N. et al. Random allelic expression in the adult human body. Cell Rep. 42, 111945 (2023).

Article 
CAS 
PubMed Central 

Google Scholar
 

Schaefer, N. K., Shapiro, B. & Green, R. E. An ancestral recombination graph of human, Neanderthal, and Denisovan genomes. Sci. Adv. 7, eabc0776 (2021).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

Johnson, N. A. & Porter, A. H. Rapid speciation via parallel, directional selection on regulatory genetic pathways. J. Theor. Biol. 205, 527–542 (2000).

Article 
ADS 
CAS 

Google Scholar
 

Go, A., Alhazmi, D. & Civetta, A. Altered expression of cell adhesion genes and hybrid male sterility between subspecies of Drosophila pseudoobscura. Genome 62, 657–663 (2019).

Article 
CAS 

Google Scholar
 

Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).

Article 
CAS 
PubMed Central 

Google Scholar
 

Rice, E. S. Trio_binning: programs implementing the trio-binning genome assembly method. Github https://github.com/esrice/trio_binning (2022).

Kokot, M., Dlugosz, M. & Deorowicz, S. KMC 3: counting and manipulating k-mer statistics. Bioinformatics 33, 2759–2761 (2017).

Article 
CAS 

Google Scholar
 

Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).

Article 
CAS 
PubMed Central 

Google Scholar
 

Di Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316–319 (2017).

Article 

Google Scholar
 

Rice, E. S. hic-scaffolding-nf: nextflow pipeline for scaffolding genome assemblies with Hi-C reads. Github https://github.com/WarrenLab/hic-scaffolding-nf (2022).

Zhang, H. et al. Fast alignment and preprocessing of chromatin profiles with Chromap. Nat. Commun. 12, 6566 (2021).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

Zhou, C., McCarthy, S. A. & Durbin, R. YaHS: yet another Hi-C scaffolding tool. Bioinformatics 39, btac808 (2023).

Article 
CAS 
PubMed Central 

Google Scholar
 

Dudchenko, O. et al. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. Preprint at bioRxiv https://doi.org/10.1101/254797 (2018).

Lu, Y. et al. High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Genome Res. 33, 557–571 (2023).

Article 
CAS 
PubMed Central 

Google Scholar
 

Dfam Consortium. TETools: Dfam transposable element tools docker container. Github https://github.com/Dfam-consortium/TETools (2022).

Du, K. et al. Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation. Nat. Commun. 15, 6609 (2024).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–9 (2006).

Article 
CAS 
PubMed Central 

Google Scholar
 

Boutet, E., Lieberherr, D., Tognolli, M., Schneider, M. & Bairoch, A. UniProtKB/Swiss-Prot. Methods Mol. Biol. 406, 89–112 (2007).

CAS 

Google Scholar
 

Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988–995 (2004).

Article 
CAS 
PubMed Central 

Google Scholar
 

Slater, G. S. C. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005).

Article 
PubMed Central 

Google Scholar
 

She, R., Chu, J. S.-C., Wang, K., Pei, J. & Chen, N. GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Res. 19, 143–149 (2009).

Article 
CAS 

Google Scholar
 

Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).

Article 
CAS 
PubMed Central 

Google Scholar
 

Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).

Article 
CAS 
PubMed Central 

Google Scholar
 

Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).

Article 
CAS 
PubMed Central 

Google Scholar
 

Kapustin, Y., Souvorov, A., Tatusova, T. & Lipman, D. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol. Direct 3, 20 (2008).

Article 
PubMed Central 

Google Scholar
 

Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).

Article 

Google Scholar
 

Darolti, I. et al. Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers. Proc. Natl Acad. Sci. USA 116, 19031–19036 (2019).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

Greenway, R. et al. Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments. Proc. Natl Acad. Sci. USA 117, 16424–16430 (2020).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

De-Kayne, R. et al. Evolutionary rate shifts in coding and regulatory regions underpin repeated adaptation to sulfidic streams in poeciliid fishes. Genome Biol. Evol. 16, evae087 (2024).

Article 
PubMed Central 

Google Scholar
 

Herzeel, C. et al. Multithreaded variant calling in elPrep 5. PLoS ONE 16, e0244471 (2021).

Article 
CAS 
PubMed Central 

Google Scholar
 

Van der Auwera, G. A. & O’Connor, B. D. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra (O’Reilly Media, 2020).

Martin, M., Ebert, P. & Marschall, T. Read-based phasing and analysis of phased variants with WhatsHap. Methods Mol. Biol. 2590, 127–138 (2023).

Article 
CAS 

Google Scholar
 

Armstrong, J. et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 587, 246–251 (2020).

Article 
ADS 
CAS 
PubMed Central 

Google Scholar
 

Fraser, B. A. et al. Improved reference genome uncovers novel sex-linked regions in the guppy (Poecilia reticulata). Genome Biol. Evol. 12, 1789–1805 (2020).

Article 
CAS 
PubMed Central 

Google Scholar
 

Fraser, B. A., Künstner, A., Reznick, D. N., Dreyer, C. & Weigel, D. Population genomics of natural and experimental populations of guppies (Poecilia reticulata). Mol. Ecol. 24, 389–408 (2015).

Article 

Google Scholar
 

Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

Article 
CAS 

Google Scholar
 

The Gene Ontology Consortium The Gene Ontology knowledgebase in 2023. Genetics 224, iyad031 (2023).

Article 

Google Scholar
 

Smedley, D. et al. BioMart-biological queries made easy. BMC Genomics 10, 22 (2009).

Article 
PubMed Central 

Google Scholar
 

Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555–556 (1997).

CAS 

Google Scholar
 

Yang, Z. & Nielsen, R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17, 32–43 (2000).

Article 
CAS 

Google Scholar
 

McDonald, J. H. & Kreitman, M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351, 652–654 (1991).

Article 
ADS 
CAS 

Google Scholar
 

Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6, 80–92 (2012).

Article 
CAS 
PubMed Central 

Google Scholar
 

Hickey, G., Paten, B., Earl, D., Zerbino, D. & Haussler, D. HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics 29, 1341–1342 (2013).

Article 
CAS 
PubMed Central 

Google Scholar
 

Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).

Article 
PubMed Central 

Google Scholar
 

Cock, P. J. A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422–1423 (2009).

Article 
CAS 
PubMed Central 

Google Scholar
 

Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).

Article 
CAS 
PubMed Central 

Google Scholar
 

Li, A., Zeng, G., Wang, H., Li, X. & Zhang, Z. DeDoc2 identifies and characterizes the hierarchy and dynamics of chromatin TAD-like domains in the single cells. Adv. Sci. 10, e2300366 (2023).

Article 

Google Scholar
 

Kruse, K., Hug, C. B. & Vaquerizas, J. M. FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data. Genome Biol. 21, 303 (2020).

Article 
PubMed Central 

Google Scholar
 

Gu, Z., Eils, R., Schlesner, M. & Ishaque, N. EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations. BMC Genomics 19, 234 (2018).

Article 
PubMed Central 

Google Scholar
 

Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).

Article 
PubMed Central 

Google Scholar
 

Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).

Article 
CAS 
PubMed Central 

Google Scholar
 

Rogers, A. R. & Huff, C. Linkage disequilibrium between loci with unknown phase. Genetics 182, 839–844 (2009).

Article 
PubMed Central 

Google Scholar
 

Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

Article 
CAS 
PubMed Central 

Google Scholar
 

Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).

Article 
CAS 
PubMed Central 

Google Scholar
 

Fitch, W. M. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20, 406 (1971).

Article 

Google Scholar
 

Prüfer, K. et al. FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8, 41 (2007).

Article 
PubMed Central 

Google Scholar
 

Szklarczyk, D. et al. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51, D638–D646 (2023).

Article 
CAS 
PubMed Central 

Google Scholar
 

Ricemeyer, E. S., Schaefer, N. & Acemel, R. D. esrice/amazon-molly-paper: Zenodo DOI release (v0.0.3). Zenodo https://doi.org/10.5281/zenodo.17976428 (2025).