بتوقيت بيروت - 9/7/2025 4:32:54 AM - GMT (+2 )


Darwin, C. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (J. Murray, 1859).
Mayr, E. Systematics and the Origin of Species, from the Viewpoint of a Zoologist (Columbia Univ. Press, 1942).
Lehtonen, J., Schmidt, D. J., Heubel, K. & Kokko, H. Evolutionary and ecological implications of sexual parasitism. Trends Ecol. Evol. 28, 297–306 (2013).
PubMed Google Scholar
Loi, P. et al. Genetic rescue of an endangered mammal by cross-species nuclear transfer using post-mortem somatic cells. Nat. Biotechnol. 19, 962–964 (2001).
CAS PubMed Google Scholar
Bolton, R. L. et al. Resurrecting biodiversity: advanced assisted reproductive technologies and biobanking. Reprod. Fertil. 3, R121–R146 (2022).
PubMed PubMed Central Google Scholar
Avise, J. Clonality: The Genetics, Ecology, and Evolution of Sexual Abstinence in Vertebrate Animals (Oxford Univ. Press, 2008).
Bachtrog, D. et al. Sex determination: why so many ways of doing it? PLoS Biol. 12, e1001899 (2014).
PubMed PubMed Central Google Scholar
Simpson, S. J., Sword, G. A. & Lo, N. Polyphenism in insects. Curr. Biol. 22, 352 (2012).
CAS Google Scholar
Schwander, T., Lo, N., Beekman, M., Oldroyd, B. P. & Keller, L. Nature versus nurture in social insect caste differentiation. Trends Ecol. Evol. 25, 275–282 (2010).
PubMed Google Scholar
Shapiro, A. M. in Evolutionary Biology (eds Hecht, M. K., Steere, W. C. & Wallace, B.) 259–333 (Springer US, 1976).
Applebaum, S. W. & Heifetz, Y. Density-dependent physiological phase in insects. Annu. Rev. Entomol. 44, 317–341 (1999).
CAS PubMed Google Scholar
Romiguier, J., Fournier, A., Yek, S. H. & Keller, L. Convergent evolution of social hybridogenesis in Messor harvester ants. Mol. Ecol. 26, 1108–1117 (2017).
PubMed Google Scholar
Steiner, F. M. et al. Turning one into five: integrative taxonomy uncovers complex evolution of cryptic species in the harvester ant Messor ‘structor’. Mol. Phylogenet. Evol. 127, 387–404 (2018).
PubMed Google Scholar
Smith, C. R., Toth, A. L., Suarez, A. V. & Robinson, G. E. Genetic and genomic analyses of the division of labour in insect societies. Nat. Rev. Genet. 9, 735–748 (2008).
CAS PubMed Google Scholar
Weyna, A., Bourouina, L., Galtier, N. & Romiguier, J. Detection of F1 hybrids from single-genome data reveals frequent hybridization in hymenoptera and particularly ants. Mol. Biol. Evol. 39, msac071 (2022).
CAS PubMed PubMed Central Google Scholar
Raj, A., Stephens, M. & Pritchard, J. K. fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197, 573–589 (2014).
PubMed PubMed Central Google Scholar
Umphrey, G. J. Sperm parasitism in ants: selection for interspecific mating and hybridization. Ecology 87, 2148–2159 (2006).
PubMed Google Scholar
Helms Cahan, S. & Keller, L. Complex hybrid origin of genetic caste determination in harvester ants. Nature 424, 306–309 (2003).
ADS CAS PubMed Google Scholar
Darras, H. et al. Obligate chimerism in male yellow crazy ants. Science 380, 55–58 (2023).
ADS CAS PubMed Google Scholar
Lacy, K. D., Shoemaker, D. & Ross, K. G. Joint evolution of asexuality and queen number in an ant. Curr. Biol. 29, 1394–1400 (2019).
CAS PubMed Google Scholar
Kuhn, A., Darras, H., Paknia, O. & Aron, S. Repeated evolution of queen parthenogenesis and social hybridogenesis in Cataglyphis desert ants. Mol. Ecol. 29, 549–564 (2020).
PubMed Google Scholar
Seifert, B. The Ants of Central and North Europe (lutra Verlags- und Vertriebsgesellschaft, 2018).
Lebas, C. Influence des activités humaines sur la répartition des fourmis du genre Messor dans les Pyrénées-Orientales (Hymenoptera: Formicidae: Myrmicinae). Osmia https://doi.org/10.47446/osmia9.9 (2021).
Heimpel, G. E. & de Boer, J. G. Sex determination in the hymenoptera. Annu. Rev. Entomol. 53, 209–230 (2008).
CAS PubMed Google Scholar
Schwander, T. & Oldroyd, B. P. Androgenesis: where males hijack eggs to clone themselves. Philos. Trans. R. Soc. Lond. B 371, 20150534 (2016).
Google Scholar
Pichot, C., Borrut, A. & El Maâtaoui, M. Unexpected DNA content in the endosperm of Cupressus dupreziana A. Camus seeds and its implications in the reproductive process. Sex. Plant Reprod. 11, 148–152 (1998).
CAS Google Scholar
Komaru, A., Ookubo, K. & Kiyomoto, M. All meiotic chromosomes and both centrosomes at spindle pole in the zygotes discarded as two polar bodies in clam Corbicula leana: unusual polar body formation observed by antitubulin immunofluorescence. Dev. Genes Evol. 210, 263–269 (2000).
CAS PubMed Google Scholar
Fournier, D. et al. Clonal reproduction by males and females in the little fire ant. Nature 435, 1230–1234 (2005).
ADS CAS PubMed Google Scholar
Ohkawara, K., Nakayama, M., Satoh, A., Trindl, A. & Heinze, J. Clonal reproduction and genetic caste differences in a queen-polymorphic ant, Vollenhovia emeryi. Biol. Lett. 2, 359–363 (2006).
PubMed PubMed Central Google Scholar
Pearcy, M., Goodisman, M. A. D. & Keller, L. Sib mating without inbreeding in the longhorn crazy ant. Proc. Biol. Sci. 278, 2677–2681 (2011).
PubMed PubMed Central Google Scholar
Okita, I. & Tsuchida, K. Clonal reproduction with androgenesis and somatic recombination: the case of the ant Cardiocondyla kagutsuchi. Naturwissenschaften 103, 22 (2016).
PubMed Google Scholar
Weyna, A., Romiguier, J. & Mullon, C. Hybridization enables the fixation of selfish queen genotypes in eusocial colonies. Evol. Lett. 5, 582–594 (2021).
PubMed PubMed Central Google Scholar
Norman, V., Darras, H., Tranter, C., Aron, S. & Hughes, W. O. H. Cryptic lineages hybridize for worker production in the harvester ant Messor barbarus. Biol. Lett. 12, 20160542 (2016).
PubMed PubMed Central Google Scholar
Purugganan, M. D. What is domestication? Trends Ecol. Evol. 37, 663–671 (2022).
PubMed Google Scholar
Jaron, K. S. et al. Convergent consequences of parthenogenesis on stick insect genomes. Sci. Adv. 8, eabg3842 (2022).
CAS PubMed PubMed Central Google Scholar
Glémin, S., François, C. M. & Galtier, N. Genome evolution in outcrossing vs. selfing vs. asexual species. Methods Mol. Biol. 1910, 331–369 (2019).
PubMed Google Scholar
Excoffier, L., Foll, M. & Petit, R. J. Genetic consequences of range expansions. Annu. Rev. Ecol. Evol. Syst. 40, 481–501 (2009).
Google Scholar
de Pedro, M. et al. Demography, genetic diversity and expansion load in the colonizing species Leontodon longirostris (Asteraceae) throughout its native range. Mol. Ecol. 30, 1190–1205 (2021).
PubMed Google Scholar
Glémin, S. & Bataillon, T. A comparative view of the evolution of grasses under domestication. New Phytol. 183, 273–290 (2009).
PubMed Google Scholar
Frantz, L. A. F., Bradley, D. G., Larson, G. & Orlando, L. Animal domestication in the era of ancient genomics. Nat. Rev. Genet. 21, 449–460 (2020).
CAS PubMed Google Scholar
Darwin, C. The Variation of Animals and Plants under Domestication (John Murray, 1868).
Gentry, A., Clutton-Brock, J. & Groves, C. P. The naming of wild animal species and their domestic derivatives. J. Archaeol. Sci. 31, 645–651 (2004).
Google Scholar
Anderson, K. E. et al. Distribution and evolution of genetic caste determination in Pogonomyrmex seed-harvester ants. Ecology 87, 2171–2184 (2006).
PubMed Google Scholar
Spribille, T., Resl, P., Stanton, D. E. & Tagirdzhanova, G. Evolutionary biology of lichen symbioses. New Phytol. 234, 1566–1582 (2022).
PubMed Google Scholar
Martin, W. F., Garg, S. & Zimorski, V. Endosymbiotic theories for eukaryote origin. Philos. Trans. R. Soc. Lond. B 370, 20140330 (2015).
Google Scholar
Martijn, J., Vosseberg, J., Guy, L., Offre, P. & Ettema, T. J. G. Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature 557, 101–105 (2018).
ADS CAS PubMed Google Scholar
Wheeler, W. M. The ant‐colony as an organism. J. Morphol. 22, 307–325 (1911).
Google Scholar
Boomsma, J. J. & Gawne, R. Superorganismality and caste differentiation as points of no return: how the major evolutionary transitions were lost in translation. Biol. Rev. Camb. Philos. Soc. 93, 28–54 (2018).
PubMed Google Scholar
Maynard-Smith, J. & Szathmary, E. The Major Transitions in Evolution, Vol. 49 (Oxford Univ. Press, 1997).
West, S. A., Fisher, R. M., Gardner, A. & Kiers, E. T. Major evolutionary transitions in individuality. Proc. Natl Acad. Sci. USA 112, 10112–10119 (2015).
ADS CAS PubMed PubMed Central Google Scholar
Rafiqi, A. M., Rajakumar, A. & Abouheif, E. Origin and elaboration of a major evolutionary transition in individuality. Nature 585, 239–244 (2020).
ADS CAS PubMed Google Scholar
Rhoads, A. & Au, K. F. PacBio sequencing and its applications. Genom. Proteom. Bioinform. 13, 278–289 (2015).
Google Scholar
Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17, 155–158 (2019).
PubMed PubMed Central Google Scholar
Zimin, A. V. & Salzberg, S. L. The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. PLoS Comput. Biol. 16, e1007981 (2020).
ADS CAS PubMed PubMed Central Google Scholar
Hu, J., Fan, J., Sun, Z. & Liu, S. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36, 2253–2255 (2020).
CAS PubMed Google Scholar
Alonge, M. et al. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 20, 224 (2019).
PubMed PubMed Central Google Scholar
Boomsma, J. J. et al. The Global Ant Genomics Alliance (GAGA). Myrmecol. News 25, 61–66 (2017).
Google Scholar
Xu, M. et al. TGS-GapCloser: a fast and accurate gap closer for large genomes with low coverage of error-prone long reads. Gigascience 9, giaa094 (2020).
PubMed PubMed Central Google Scholar
Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).
CAS PubMed PubMed Central Google Scholar
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).
CAS PubMed PubMed Central Google Scholar
Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness. Methods Mol. Biol. 1962, 227–245 (2019).
CAS PubMed Google Scholar
Tilak, M.-K. et al. A cost-effective straightforward protocol for shotgun Illumina libraries designed to assemble complete mitogenomes from non-model species. Conserv. Genet. Resour. 7, 37–40 (2015).
Google Scholar
Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, db.prot5448 (2010).
Google Scholar
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
PubMed PubMed Central Google Scholar
Vasimuddin, M., Misra, S., Li, H. & Aluru, S. Efficient architecture-aware acceleration of BWA-MEM for multicore systems. In 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) 314–324 (IEEE, 2019).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
PubMed PubMed Central Google Scholar
Chevreux, B. et al. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14, 1147–1159 (2004).
CAS PubMed PubMed Central Google Scholar
Li, D. et al. MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102, 3–11 (2016).
CAS PubMed Google Scholar
Allio, R. et al. MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol. Ecol. Resour. 20, 892–905 (2020).
CAS PubMed PubMed Central Google Scholar
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
CAS PubMed PubMed Central Google Scholar
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
CAS PubMed PubMed Central Google Scholar
Juvé, Y. et al. One mother for two species: obligate cross-species cloning in ants. Zenodo https://doi.org/10.5281/zenodo.11506545 (2025).
Kuznetsov, D. et al. OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic Acids Res. 51, D445–D451 (2023).
CAS PubMed Google Scholar
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
PubMed PubMed Central Google Scholar
Katoh, K. & Toh, H. Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform. 9, 286–298 (2008).
CAS PubMed Google Scholar
Ranwez, V., Douzery, E. J. P., Cambon, C., Chantret, N. & Delsuc, F. MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons. Mol. Biol. Evol. 35, 2582–2584 (2018).
CAS PubMed PubMed Central Google Scholar
Romiguier, J. et al. Ant phylogenomics reveals a natural selection hotspot preceding the origin of complex eusociality. Curr. Biol. 32, 2942–2947 (2022).
CAS PubMed Google Scholar
Lau, M. K. et al. Draft Aphaenogaster genomes expand our view of ant genome size variation across climate gradients. PeerJ 7, e6447 (2019).
PubMed PubMed Central Google Scholar
Nygaard, S. et al. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res. 21, 1339–1348 (2011).
CAS PubMed PubMed Central Google Scholar
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
CAS PubMed PubMed Central Google Scholar
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
PubMed PubMed Central Google Scholar
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
CAS PubMed Google Scholar
dos Reis, M. & Yang, Z. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol. Biol. Evol. 28, 2161–2172 (2011).
PubMed Google Scholar
Branstetter, M. G., Longino, J. T., Reyes-López, J. L., Brady, S. G. & Schultz, T. R. Out of the temperate zone: a phylogenomic test of the biogeographical conservatism hypothesis in a contrarian clade of ants. J. Biogeogr. 49, 1640–1653 (2022).
Google Scholar
Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904 (2018).
CAS PubMed 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).
CAS PubMed PubMed Central Google Scholar
Romiguier, J. et al. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature 515, 261–263 (2014).
ADS CAS PubMed Google Scholar
Schlupp, I. The evolutionary ecology of gynogenesis. Annu. Rev. Ecol. Evol. Syst. 36, 399–417 (2005).
Google Scholar
Lavanchy, G. & Schwander, T. Hybridogenesis. Curr. Biol. 29, 539 (2019).
CAS PubMed Google Scholar
إقرأ المزيد