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).
Muller, H. J. Some genetic aspects of sex. Am. Nat. 66, 118–138 (1932).
Muller, H. J. The relation of recombination to mutational advance. Mutat. Res. 106, 2–9 (1964).
Felsenstein, J. The evolutionary advantage of recombination. Genetics 78, 737–756 (1974).
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).
Welch, M. D. & Meselson, M. Evidence for the evolution of bdelloid rotifers without sexual reproduction or genetic exchange. Science 288, 1211–1215 (2000).
Schwander, T., Henry, L. & Crespi, B. J. Molecular evidence for ancient asexuality in timema stick insects. Curr. Biol. 21, 1129–1134 (2011).
Hubbs, C. L. & Hubbs, L. C. Apparent parthenogenesis in nature, in a form of fish of hybrid origin. Science 76, 628–630 (1932).
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).
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).
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).
Judson, O. P. & Normark, B. B. Ancient asexual scandals. Trends Ecol. Evol. 11, 41–46 (1996).
Lynch, M., Conery, J. & Burger, R. Mutation accumulation and the extinction of small populations. Am. Nat. 146, 489–518 (1995).
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).
Lynch, M. & Gabriel, W. Mutation load and the survival of small populations. Evolution 44, 1725–1737 (1990).
Jaron, K. S. et al. Genomic features of parthenogenetic animals. J. Hered. 112, 19–33 (2021).
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).
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).
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).
Turner, B. J. The evolutionary genetics of a unisexual fish, Poecilia formosa. Prog. Clin. Biol. Res. 96, 265–305 (1982).
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).
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).
Dedukh, D. et al. Achiasmatic meiosis in the unisexual Amazon molly, Poecilia formosa. Chromosome Res. 30, 443–457 (2022).
Kallman, K. D. Population genetics of the gynogenetic teleost, Mollienesia formosa (Girard). Evolution 16, 497–504 (1962).
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).
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).
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).
Koren, S. et al. De novo assembly of haplotype-resolved genomes with trio binning. Nat. Biotechnol. 36, 1174–1182 (2018).
Rice, E. S. et al. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. GigaScience 9, giaa029 (2020).
Moran, N. A. Accelerated evolution and Muller’s rachet in endosymbiotic bacteria. Proc. Natl Acad. Sci. USA 93, 2873–2878 (1996).
Nesta, A. V., Tafur, D. & Beck, C. R. Hotspots of human mutation. Trends Genet. 37, 717–729 (2021).
Gonzalez-Perez, A., Sabarinathan, R. & Lopez-Bigas, N. Local determinants of the mutational landscape of the human genome. Cell 177, 101–114 (2019).
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).
Weir, W. et al. Population genomics reveals the origin and asexual evolution of human infective trypanosomes. eLife 5, e11473 (2016).
Brandt, A. et al. Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova. Proc. Natl Acad. Sci. USA 118, e2101485118 (2021).
Tubbs, A. et al. Dual roles of poly(dA:dT) tracts in replication initiation and fork collapse. Cell 174, 1127–1142.e19 (2018).
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).
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).
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).
Mikocziova, I., Greiff, V. & Sollid, L. M. Immunoglobulin germline gene variation and its impact on human disease. Genes Immun. 22, 205–217 (2021).
Kravitz, S. N. et al. Random allelic expression in the adult human body. Cell Rep. 42, 111945 (2023).
Schaefer, N. K., Shapiro, B. & Green, R. E. An ancestral recombination graph of human, Neanderthal, and Denisovan genomes. Sci. Adv. 7, eabc0776 (2021).
Johnson, N. A. & Porter, A. H. Rapid speciation via parallel, directional selection on regulatory genetic pathways. J. Theor. Biol. 205, 527–542 (2000).
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).
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).
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).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Di Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316–319 (2017).
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).
Zhou, C., McCarthy, S. A. & Durbin, R. YaHS: yet another Hi-C scaffolding tool. Bioinformatics 39, btac808 (2023).
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).
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).
Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–9 (2006).
Boutet, E., Lieberherr, D., Tognolli, M., Schneider, M. & Bairoch, A. UniProtKB/Swiss-Prot. Methods Mol. Biol. 406, 89–112 (2007).
Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988–995 (2004).
Slater, G. S. C. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005).
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).
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).
Kapustin, Y., Souvorov, A., Tatusova, T. & Lipman, D. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol. Direct 3, 20 (2008).
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).
Darolti, I. et al. Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers. Proc. Natl Acad. Sci. USA 116, 19031–19036 (2019).
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).
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).
Herzeel, C. et al. Multithreaded variant calling in elPrep 5. PLoS ONE 16, e0244471 (2021).
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).
Armstrong, J. et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 587, 246–251 (2020).
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).
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).
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).
The Gene Ontology Consortium The Gene Ontology knowledgebase in 2023. Genetics 224, iyad031 (2023).
Smedley, D. et al. BioMart-biological queries made easy. BMC Genomics 10, 22 (2009).
Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555–556 (1997).
Yang, Z. & Nielsen, R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17, 32–43 (2000).
McDonald, J. H. & Kreitman, M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351, 652–654 (1991).
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6, 80–92 (2012).
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).
Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).
Cock, P. J. A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422–1423 (2009).
Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).
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).
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).
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).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
Rogers, A. R. & Huff, C. Linkage disequilibrium between loci with unknown phase. Genetics 182, 839–844 (2009).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
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).
Fitch, W. M. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20, 406 (1971).
Prüfer, K. et al. FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8, 41 (2007).
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).
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).

