Nature ( 2026 ) Cite this article
Sexual reproduction is ancient and ubiquitous despite its obvious disadvantages 1 .
Theory predicts that the reassortment of alleles that results from sex is necessary for natural selection to act effectively on individual loci; therefore, a purely clonal organism should rapidly accumulate deleterious mutations and go extinct 2 , 3 , 4 .
Nevertheless, many asexual species have existed for longer than theory predicts is possible 5 , 6 , 7 , such as the Amazon molly ( Poecilia formosa ), a clonally reproducing fish arising from a single hybridization event more than 100,000 years ago 8 , 9 , 10 .
Here we show that although the Amazon molly has accumulated mutations faster than its sexual progenitor species, this has not led to functional mutational decay, defying theoretical expectations.
Instead, gene conversion facilitates both adaptive and purifying selection by generating new clonal lineages in which previous mutations are either reverted or fixed, and by resolving hybrid incompatibilities between the ancestral haplotypes.
The transition to clonality altered chromatin structure, but the asexual haplotypes of the Amazon molly nonetheless maintain the divergent mutational landscapes of their progenitor species.
Together, these results provide new insights into long-standing questions about the trade-offs involved in asexual reproduction.
This is a preview of subscription content, access via your institution
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
Receive 51 print issues and online access
Prices may be subject to local taxes which are calculated during checkout
Fig.
1: Origin and phylogeny of the Amazon molly P.
formosa.
Fig.
2: Asexual P.
formosa genomes show at most limited mutational decay compared with sexual progenitor species.
Fig.
3: Asexual genomes have diverged more than their sexual counterparts, but haplotypes of P.
formosa have diverged at different rates.
Fig.
4: Gene conversion slows Muller’s ratchet, facilitating both positive and negative selection.
Similar content being viewed by others
Parallel loss of sexual reproduction in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality
Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus ) show that hybridization preceded speciation
Multi-omics integration identifies diverse transcripts and chromatin accessibility profiles in Monopterus albus gonads
All sequence data generated for this project, as well as the assembled genomes, are deposited in the relevant NCBI databases under the following BioProject IDs: PRJNA1398340 ( P.
latipinna ), PRJNA1398337 ( P.
mexicana ), and PRJNA1398335 and PRJNA1398336 ( P.
formosa ).
Hi-C reads for P.
latipinna and P.
mexicana are available under BioProject ID PRJNA614959 .
Previously published accessions from the NCBI Sequence Read Archive are listed in Supplementary Table 2 .
Code used to perform the analyses described in this manuscript is open-source licensed under the GNU General Public License and publicly available on GitHub ( https://github.com/esrice/amazon-molly-paper ) and at https://doi.org/10.5281/zenodo.17976427 (ref.
104 ).
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 PubMed Google Scholar
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).
Article CAS PubMed Google Scholar
Felsenstein, J.
The evolutionary advantage of recombination.
Genetics 78 , 737–756 (1974).
Article CAS PubMed Central PubMed 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).
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).
Article ADS CAS PubMed 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).
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 PubMed 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).
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).
We thank M.
Baldwin, L.
Frantz, G.
Hickey, P.
Jern, N.
Luscombe, D.
Metzler, F.
Rheindt and M.
Tobler for discussions about the project; G.
Schneider and P.
Weber for breeding and care of the fish sequenced for these analyses; M.
Tobler for permission to use his photo to create the silhouette of P.
mexicana used in the figures; K.
S.
Jaron for dedicating silhouettes of P.
latipinna and P.
formosa available on PhyloPic to the public domain; F.
Berio for dedicating a silhouette of P.
reticulata available on PhyloPic to the public domain; and I.
Schlupp for supplying the P.
mexicana and P.
latipinna individuals for reference genome sequencing.
Computation for this work was performed on the high performance computing infrastructure provided by Research Computing Support Services and in part by the National Science Foundation under grant number CNS-1429294 at the University of Missouri, Columbia MO.
The authors gratefully acknowledge the Leibniz Supercomputing Centre for funding this project by providing computing time on its Linux cluster.
Research in the Lupiañez lab was funded by the European Research Council (grant no.
101045439, 3D-REVOLUTION) and by the Spanish “Agencia Estatal de Investigación” (grant number PID2022-143253NB-I00/ AEI/10.13039/501100011033/ FEDER, UE).
Funded by the European Union.
Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency.
Neither the European Union nor the granting authority can be held responsible for them.
These authors contributed equally: Edward S.
Ricemeyer, Nathan K.
Schaefer
These authors jointly supervised this work: Manfred Schartl, Wesley C.
Warren
Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
Edward S.
Ricemeyer, Rachel A.
Carroll & Wesley C.
Warren
Institute of Animal Systems Genomics, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
Edward S.
Ricemeyer & Rosie Drinkwater
The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
Rafael D.
Acemel & Darío G.
Lupiáñez
Institute of Pathology, University of Würzburg, Würzburg, Germany
Institute for Molecular Life Sciences, Texas State University, San Marcos, TX, USA
Research Department for Limnology, University of Innsbruck, Mondsee, Austria
Division of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
Search author on: PubMed Google Scholar
This project was conceived and led by W.C.W.
and M.S.
with input from E.S.R.
N.K.S.
performed admixture, selection and gene function-related analyses.
R.A.C.
performed DNA extraction and library preparation.
K.D.
annotated genome assemblies.
I.d.C.
assisted with genome assembly curation.
S.K.
performed allele-specific expression analysis.
R.D.
built trees.
R.D.A.
and D.G.L.
analysed chromatin structure.
E.S.R.
performed all other analyses.
E.S.R.
and M.S.
wrote the first draft of the manuscript, which all authors edited and approved.
Correspondence to Edward S.
Ricemeyer .
The authors declare no competing interests.
Nature thanks Daniel Berner and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data figures and tables
Extended Data Fig.
1 Gene flow among P.
latipinna , P.
mexicana and P.
formosa .
a , Gene-order based synteny mapping shows high structural conservation between P.
latipinna and P.
mexicana.
The best path through both annotations was found using a Needleman-Wunsch-like algorithm, which identifies inversions (none found) and translocations (highlighted red).
Each dot is a gene present in both annotations.
b , ADMIXTURE analysis shows signs of at most limited gene flow among the species.
c , D-statistics of the form D( latipinna , mexicana , X, reticulata ), with each formosa genome standing in for X and all individuals from the other species included in each calculation.
Negative D indicates greater sharing of derived alleles between the shown formosa genome and latipinna individuals than with mexicana individuals, whereas positive D indicates greater sharing between formosa and mexicana than formosa and latipinna .
Error bars show maximum and minimum values of each genome-wide D calculation including individual X; points are median values.
d , D-statistics of the form D(X, Y, formosa , reticulata ), where X and Y are either every permutation of two latipinna genomes (orange) or two mexicana genomes (purple).
Positive D indicates greater derived allele sharing between the Y individual and formosa than between the X individual and formosa , which could result either from gene flow or the Y individual sharing more ancestral drift with the conspecific ancestor of P.
formosa .
e , Sub-clades defined for admixture analysis.
f , \(\hat{f}\) statistics for P.
latipinna and P.
mexicana individuals showing the highest rates of allele sharing with the opposite species.
D-statistics were computed using all conspecific individuals not belonging to the same clade, and with every individual from the opposite population; denominators were computed using every possible combination of two individuals from the opposite population, but with the same P1 individual as the numerator.
Points are medians across all possible computations; error bars show minimum and maximum values.
Extended Data Fig.
2 Admixture graph suggests possible inter-species gene flow into one population of P.
latipinna and one population of P.
mexicana .
a , ADMIXTOOLS2 qpGraph showing the best fit model of those we tested.
Solid edges represent parent/child relationships, and solid edge labels quantify drift along those edges.
Dotted edges show ancestry derived from multiple groups (admixture), and dotted edge labels quantify the amount of ancestry derived from each group.
b-c , Best fit TreeMix graphs with one ( b ) and two ( c ) gene flow edges.
Extended Data Fig.
3 Neighbor-joining tree of genome assemblies.
A neighbor-joining tree using mash distances between each pair among the five assemblies shows the same two patterns as the tree based on ancestral reconstruction: both asexual genomes have diverged more quickly than their sexual counterparts, and the mexicana -ancestry genomes are more diverged from their common ancestor than the latipinna -ancestry genomes with comparable reproduction strategies.
Leaf branches are labeled with mash distances, multiplied by 10 3 for readability.
P.
formosa and P.
latipinna silhouettes by Kamil S.
Jaron ( CC0 1.0 ); P.
mexicana silhouette by Michael Tobler ( CC0 1.0 ); P.
reticulata silhouette by Fidji Berio ( CC0 1.0 ).
Extended Data Fig.
4 The single origin and clonal reproduction of P.
formosa allow confident inference of the ancestral state of both haplotypes of 19 P.
formosa samples.
Extended Data Fig.
5 Chromatin conformation shows that although TAD boundaries are conserved, switch to asexual reproduction increased insulation genome-wide.
Extended Data Fig.
6 Local divergence rates are correlated between sister genomes.
a , Single-base divergence from ancestral genome within 50 kb windows on LG2 for each assembly, in Pmex coordinates.
b , Bivariate distributions of genome-wide window divergence rates for each pair of assemblies, with Pearson correlation coefficients above (all correlations p < 10 −3 , values for all comparisons in Supplementary Data Table 6 ).
P.
formosa and P.
latipinna silhouettes by Kamil S.
Jaron ( CC0 1.0 ); P.
mexicana silhouette by Michael Tobler ( CC0 1.0 ).
Extended Data Fig.
7 The mutation spectrum shows a possible derived shift in P.
latipinna lineages relative to others.
On each branch (A-F) shown in the tree, we compared reference genome sequences and counted mutations by considering their trimer context (e.g.
AAA to ACA or CGG to CTG), then divided these counts by the total mutations on the branch, to generate a branch-specific mutation spectrum.
a , Kullback-Leibler (KL) divergence between each pair of mutation spectra are shown in the heatmap.
The dendrogram is the result of hierarchically clustering the KL distances.
KL divergence is not symmetrical; the heatmap values correspond to \({D}_{{KL}}({Branch}1{||Branch}2)\) .
b , Each bar represents the normalized count of a specific mutation type on a specific branch.
Boxes correspond to labeled branches in the tree, and mutations are colored by their context (the base immediately upstream and the base immediately downstream of the mutation).
Extended Data Fig.
8 Long read alignments show rare crossing-over recombination.
a-b , Aligning long reads from all three species to both haplotypes of P.
formosa reveals a crossing-over recombination between the haplotypes.
a , Comparing mismatched base percentages of long reads from P.
latipinna vs.
P.
mexicana aligned to both P.
formosa haplotypes shows locations of two breakpoints where a P.
formosa contig switches ancestry.
These two breakpoints are in homologous positions between the two haplotypes.
b , Many individual P.
formosa long reads span the breakpoint, supporting the inference of a crossing-over recombination.
c , Linkage disequilibrium on AncMol chr0 measured by the Rogers-Huff r 2 estimator at 1 kb bins for biallelic pairs from 0-100 kb apart with 5% of all pairs sampled (top), and 10 kb bins from 0-1 Mb apart with 1% of all pairs sampled (bottom).
n = 19 biologically independent P.
formosa individuals; bootstrapped 95% confidence intervals are shown based on 1,000 resamples.
As expected, LD is stable with increasing distance between loci in P.
formosa .
The only exception to this is for loci less than 1 kb apart, which have higher mean linkage disequilibrium than loci pairs in all other distance bins, consistent with gene conversion, which acts on relatively small pieces of the genome, but not crossing-over and reassortment during sexual reproduction, which should affect LD over greater distances.
Extended Data Fig.
9 Gene conversions arise repeatedly at the same loci and often near polyA/T repeats.
a , Gene conversion tracts arise repeatedly at the same loci.
For each consensus gene conversion tract, we determined how many times at minimum it must have arisen independently, according to maximum parsimony and the consensus phylogenetic tree using SNP data.
We then compared these numbers with those expected, assuming that non-overlapping genomic segments undergo gene conversion following the Poisson distribution.
b , Numbers of occurrences of each possible type of mononucleotide or dinucleotide repeat within 50 bp of a gene conversion breakpoint, minus numbers of occurrences of the same types of repeats in matched, randomly sampled 50 bp intervals.
Each point corresponds to repeats of the given length or longer.
c , Due to clonal reproduction in P.
formosa , the ancestry of all parts of the genome must be the same outside of regions of gene conversion; this can be used to detect gene conversion using Fitch’s algorithm.
In the example tree shown, the most parsimonious set of mutations to explain the genotypes is an earlier mutation from homozygous (0,0) to heterozygous (0,1) followed by a gene conversion back to homozygous (0,0), both represented with stars.
Supplementary Information (download PDF )
Supplementary Methods and Notes.
Reporting Summary (download PDF )
Supplementary Table 1 (download XLSX )
Basic statistics for all assemblies discussed in the article.
Supplementary Table 2 (download XLSX )
Accessions for all short-read samples used in this study.
Supplementary Table 3 (download XLSX )
Wright’s Fixation index ( F ST ) between all pairs of species included in the study.
Standard errors were computed using a 10 Mb weighted block jackknife.
Supplementary Table 4 (download XLSX )
Residual values for qpGraph models.
Supplementary Table 5 (download XLSX )
Test statistics for allele-biased expression analysis.
Supplementary Table 6 (download XLSX )
Pearson correlation test results for all pairwise comparisons between window mutation rates.
Supplementary Table 7 (download XLSX )
GO enrichment for coding substitutions within gene conversion tracts.
Results are from Mann - Whitney U -tests, with genes ranked by the maximum frequency of a gene conversion tract including a substitution in a first or second codon position.
Supplementary Table 8 (download XLSX )
GO enrichment for the nearest genes to noncoding sequence within gene conversion tracts, ranked by the maximum frequency of a tract near the gene.
Supplementary Table 9 (download XLSX )
GO enrichment for the nearest genes to noncoding sequence within gene conversion tracts, ranked by the maximum indicator of positive selection in the sequence (Fay and Wu’s H within P.
latipinna , if converted to P.
latipinna haplotype, or Fay and Wu’s H in P.
mexicana , if converted to P.
mexicana haplotype).
Springer Nature or its licensor (e.g.
a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
Version of record : 11 March 2026
DOI : https://doi.org/10.1038/s41586-026-10180-9
Related Stories
Source: This article was originally published by Nature News
Read Full Original Article →
Comments (0)
No comments yet. Be the first to comment!
Leave a Comment