{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T05:04:24Z","timestamp":1789707864656,"version":"4.0.1"},"reference-count":130,"publisher":"Elsevier BV","issue":"17","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T00:00:00Z","timestamp":1785110400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000270","name":"UK Research and Innovation Natural Environment Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000270","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Current Biology"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.cub.2026.07.055","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T14:47:40Z","timestamp":1787150860000},"page":"4415-4428.e8","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-wide barriers to gene flow reveal the genetic basis of viviparity evolution in a lizard"],"prefix":"10.1016","volume":"36","author":[{"given":"Hongxin","family":"Xie","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans","family":"Recknagel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Capstick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Guillaume","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maureen M.","family":"Bain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean","family":"Clobert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9219-7001","authenticated-orcid":false,"given":"Kathryn R.","family":"Elmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.cub.2026.07.055_bib1","series-title":"Evolution, the Extended Synthesis","year":"2010"},{"key":"10.1016\/j.cub.2026.07.055_bib2","series-title":"Models in Paleobiology","article-title":"Punctuated equilibria: an alternative to phyletic gradualism","author":"Eldredge","year":"1972"},{"key":"10.1016\/j.cub.2026.07.055_bib3","series-title":"The Material Basis of Evolution","author":"Goldschmidt","year":"1982"},{"key":"10.1016\/j.cub.2026.07.055_bib4","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1006\/jtbi.1995.0092","article-title":"Saltationist and punctuated equilibrium models for the evolution of viviparity and placentation","volume":"174","author":"Blackburn","year":"1995","journal-title":"J. Theor. Biol."},{"key":"10.1016\/j.cub.2026.07.055_bib5","doi-asserted-by":"crossref","first-page":"3646","DOI":"10.1073\/pnas.1816086116","article-title":"Genomic and transcriptomic investigations of the evolutionary transition from oviparity to viviparity","volume":"116","author":"Gao","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2026.07.055_bib6","doi-asserted-by":"crossref","first-page":"3226","DOI":"10.1093\/gbe\/evw229","article-title":"Reptile pregnancy is underpinned by complex changes in uterine gene expression: a comparative analysis of the uterine transcriptome in viviparous and oviparous lizards","volume":"8","author":"Griffith","year":"2016","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib7","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1111\/mec.15409","article-title":"Emergence of an evolutionary innovation: gene expression differences associated with the transition between oviparity and viviparity","volume":"29","author":"Foster","year":"2020","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.cub.2026.07.055_bib8","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1111\/brv.12836","article-title":"Understanding the evolution of viviparity using intraspecific variation in reproductive mode and transitional forms of pregnancy","volume":"97","author":"Whittington","year":"2022","journal-title":"Biol. Rev. Camb. Philos. Soc."},{"key":"10.1016\/j.cub.2026.07.055_bib9","first-page":"556","article-title":"Are viviparity and egg-guarding evolutionarily labile in squamates?","volume":"55","author":"Blackburn","year":"1999","journal-title":"Herpetologica"},{"key":"10.1016\/j.cub.2026.07.055_bib10","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1002\/jez.b.22593","article-title":"Contrasting models of parity-mode evolution in squamate reptiles","volume":"324","author":"Pyron","year":"2015","journal-title":"J. Exp. Zool. B Mol. Dev. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib11","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1002\/jez.b.22614","article-title":"Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles","volume":"324","author":"Griffith","year":"2015","journal-title":"J. Exp. Zool. B Mol. Dev. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib12","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1002\/jmor.20272","article-title":"Evolution of vertebrate viviparity and specializations for fetal nutrition: A quantitative and qualitative analysis","volume":"276","author":"Blackburn","year":"2015","journal-title":"J. Morphol."},{"key":"10.1016\/j.cub.2026.07.055_bib13","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1111\/brv.12189","article-title":"Matrotrophy and placentation in invertebrates: a new paradigm","volume":"91","author":"Ostrovsky","year":"2016","journal-title":"Biol. Rev. Camb. Philos. Soc."},{"key":"10.1016\/j.cub.2026.07.055_bib14","doi-asserted-by":"crossref","first-page":"2614","DOI":"10.1111\/evo.12130","article-title":"Evolution of viviparity: a phylogenetic test of the cold-climate hypothesis in phrynosomatid lizards","volume":"67","author":"Lambert","year":"2013","journal-title":"Evolution"},{"key":"10.1016\/j.cub.2026.07.055_bib15","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms11271","article-title":"Viviparity stimulates diversification in an order of fish","volume":"7","author":"Helmstetter","year":"2016","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cub.2026.07.055_bib16","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1111\/ele.12168","article-title":"Early origin of viviparity and multiple reversions to oviparity in squamate reptiles","volume":"17","author":"Pyron","year":"2014","journal-title":"Ecol. Lett."},{"key":"10.1016\/j.cub.2026.07.055_bib17","doi-asserted-by":"crossref","first-page":"R15","DOI":"10.1530\/REP-13-0309","article-title":"The evolution of viviparity: Molecular and genomic data from squamate reptiles advance understanding of live birth in amniotes","volume":"147","author":"Van Dyke","year":"2014","journal-title":"Reproduction"},{"key":"10.1016\/j.cub.2026.07.055_bib18","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.1038\/s41559-021-01555-4","article-title":"The functional genetic architecture of egg-laying and live-bearing reproduction in common lizards","volume":"5","author":"Recknagel","year":"2021","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib19","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1095\/biolreprod.110.085019","article-title":"What makes an egg unique? Clues from evolutionary scenarios of egg-specific genes","volume":"83","author":"Tian","year":"2010","journal-title":"Biol. Reprod."},{"key":"10.1016\/j.cub.2026.07.055_bib20","doi-asserted-by":"crossref","DOI":"10.1038\/s41559-017-0072","article-title":"The placenta as a model for understanding the origin and evolution of vertebrate organs","volume":"1","author":"Griffith","year":"2017","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib21","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1002\/jez.b.22642","article-title":"Which came first: the lizard or the egg? Robustness in phylogenetic reconstruction of ancestral states","volume":"324","author":"Wright","year":"2015","journal-title":"J. Exp. Zool. B Mol. Dev. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib22","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1111\/jeb.13886","article-title":"Evolutionary origins of viviparity consistent with palaeoclimate and lineage diversification","volume":"34","author":"Recknagel","year":"2021","journal-title":"J. Evol. Biol."},{"key":"10.1016\/j.cub.2026.07.055_bib23","first-page":"3491","article-title":"Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny","volume":"279","author":"dos Reis","year":"2012","journal-title":"Proc. Biol. Sci."},{"key":"10.1016\/j.cub.2026.07.055_bib24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1095-8312.2006.00552.x","article-title":"Multiple origins of viviparity, or reversal from viviparity to oviparity? The European common lizard (Zootoca vivipara, Lacertidae) and the evolution of parity","volume":"87","author":"Surget-Groba","year":"2006","journal-title":"Biol. J. Linn. Soc."},{"key":"10.1016\/j.cub.2026.07.055_bib25","doi-asserted-by":"crossref","DOI":"10.1111\/geb.13812","article-title":"SquamBase\u2014A database of squamate (Reptilia: Squamata) traits","volume":"33","author":"Meiri","year":"2024","journal-title":"Glob. Ecol. Biogeogr."},{"key":"10.1016\/j.cub.2026.07.055_bib26","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1002\/jez.b.22625","article-title":"Evolution of viviparity in squamate reptiles: Reversibility reconsidered","volume":"324","author":"Blackburn","year":"2015","journal-title":"J. Exp. Zool. B Mol. Dev. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib28","first-page":"333","article-title":"Hybridization experiment between oviparous and viviparous strains of Lacerta vivipara: A new insight into the evolution of viviparity in reptiles","volume":"52","author":"Arrayago","year":"1996","journal-title":"Herpetologica"},{"key":"10.1016\/j.cub.2026.07.055_bib29","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.1139\/z92-301","article-title":"Caract\u00e9ristiques de la coquille des oeufs chez la souche hybride (ovipare \u00d7 vivipare) du l\u00e9zard Lacerta vivipara","volume":"70","author":"Heulin","year":"1992","journal-title":"Can. J. Zool."},{"key":"10.1016\/j.cub.2026.07.055_bib30","first-page":"73","article-title":"Identification of a contact zone between oviparous and viviparous common lizards (Zootoca vivipara) in central Europe: reproductive strategies and natural hybridization","volume":"46","author":"Lindtke","year":"2010","journal-title":"Salamandra"},{"key":"10.1016\/j.cub.2026.07.055_bib31","doi-asserted-by":"crossref","first-page":"1917","DOI":"10.1111\/1365-2435.13408","article-title":"Distinct telomere differences within a reproductively bimodal common lizard population","volume":"33","author":"McLennan","year":"2019","journal-title":"Funct. Ecol."},{"key":"10.1016\/j.cub.2026.07.055_bib27","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1016\/j.ympev.2018.05.029","article-title":"Common lizards break Dollo\u2019s law of irreversibility: Genome-wide phylogenomics support a single origin of viviparity and re-evolution of oviparity","volume":"127","author":"Recknagel","year":"2018","journal-title":"Mol. Phylogenet. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib32","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1038\/s41437-019-0201-7","article-title":"Genetic introgression among differentiated clades is lower among clades exhibiting different parity modes","volume":"123","author":"Horreo","year":"2019","journal-title":"Heredity"},{"key":"10.1016\/j.cub.2026.07.055_bib33","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1111\/bij.12478","article-title":"Reproductive isolation between oviparous and viviparous lineages of the Eurasian common lizard Zootoca vivipara in a contact zone","volume":"114","author":"Cornetti","year":"2015","journal-title":"Biol. J. Linn. Soc. Lond."},{"key":"10.1016\/j.cub.2026.07.055_bib34","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1006\/mpev.2000.0896","article-title":"Intraspecific phylogeography of Lacerta vivipara and the evolution of viviparity","volume":"18","author":"Surget-Groba","year":"2001","journal-title":"Mol. Phylogenet. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib35","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0085912","article-title":"Mitochondrial and nuclear DNA survey of Zootoca vivipara across the eastern Italian Alps: evolutionary relationships, historical demography and conservation implications","volume":"9","author":"Cornetti","year":"2014","journal-title":"PLOS One"},{"key":"10.1016\/j.cub.2026.07.055_bib36","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1080\/11250008809386761","article-title":"Progressive differentiation of the W sex-chromosome between oviparous and viviparous populations of Zootoca vivipara (Reptilia, Lacertidae)","volume":"65","author":"Odierna","year":"1998","journal-title":"Ital. J. Zool."},{"key":"10.1016\/j.cub.2026.07.055_bib37","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.tree.2024.09.010","article-title":"Dollo\u2019s law of irreversibility in the post-genomic age","volume":"40","author":"Elmer","year":"2025","journal-title":"Trends Ecol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib38","doi-asserted-by":"crossref","DOI":"10.1186\/s12983-021-00403-2","article-title":"Climatic niche differences among Zootoca vivipara clades with different parity modes: implications for the evolution and maintenance of viviparity","volume":"18","author":"Horreo","year":"2021","journal-title":"Front. Zool."},{"key":"10.1016\/j.cub.2026.07.055_bib39","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1111\/evo.12832","article-title":"Irrational exuberance for resolved species trees","volume":"70","author":"Hahn","year":"2016","journal-title":"Evolution"},{"key":"10.1016\/j.cub.2026.07.055_bib40","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1002967","article-title":"Inference of population splits and mixtures from genome-wide allele frequency data","volume":"8","author":"Pickrell","year":"2012","journal-title":"PLOS Genet."},{"key":"10.1016\/j.cub.2026.07.055_bib41","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1534\/genetics.116.194720","article-title":"Exploring evolutionary relationships across the genome using topology weighting","volume":"206","author":"Martin","year":"2017","journal-title":"Genetics"},{"key":"10.1016\/j.cub.2026.07.055_bib42","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1038\/ng.937","article-title":"Bayesian inference of ancient human demography from individual genome sequences","volume":"43","author":"Gronau","year":"2011","journal-title":"Nat. Genet."},{"key":"10.1016\/j.cub.2026.07.055_bib43","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/nature10231","article-title":"Inference of human population history from individual whole-genome sequences","volume":"475","author":"Li","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.cub.2026.07.055_bib44","doi-asserted-by":"crossref","first-page":"4882","DOI":"10.1093\/bioinformatics\/btab468","article-title":"fastsimcoal2: demographic inference under complex evolutionary scenarios","volume":"37","author":"Excoffier","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2026.07.055_bib45","doi-asserted-by":"crossref","first-page":"5684","DOI":"10.1111\/mec.16697","article-title":"Genetic decline and recovery of a demographically rebuilt fishery species","volume":"31","author":"Hoey","year":"2022","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.cub.2026.07.055_bib46","doi-asserted-by":"crossref","first-page":"msac064","DOI":"10.1093\/molbev\/msac064","article-title":"Species persistence with hybridization in toad-headed lizards driven by divergent selection and low recombination","volume":"39","author":"Gao","year":"2022","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib47","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1016\/j.celrep.2013.09.042","article-title":"Hybridization reveals the evolving genomic architecture of speciation","volume":"5","author":"Kronforst","year":"2013","journal-title":"Cell Rep."},{"key":"10.1016\/j.cub.2026.07.055_bib48","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1111\/jeb.13738","article-title":"The pitfalls and virtues of population genetic summary statistics: Detecting selective sweeps in recent divergences","volume":"34","author":"Schneider","year":"2021","journal-title":"J. Evol. Biol."},{"key":"10.1016\/j.cub.2026.07.055_bib49","doi-asserted-by":"crossref","first-page":"3133","DOI":"10.1111\/mec.12796","article-title":"Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow","volume":"23","author":"Cruickshank","year":"2014","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.cub.2026.07.055_bib50","doi-asserted-by":"crossref","first-page":"11006","DOI":"10.1073\/pnas.1801832115","article-title":"Selection and gene flow shape genomic islands that control floral guides","volume":"115","author":"Tavares","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2026.07.055_bib51","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1126\/science.adi2982","article-title":"The genetic basis of a recent transition to live-bearing in marine snails","volume":"383","author":"Stankowski","year":"2024","journal-title":"Science"},{"key":"10.1016\/j.cub.2026.07.055_bib52","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1010999","article-title":"Demographically explicit scans for barriers to gene flow using gIMble","volume":"19","author":"Laetsch","year":"2023","journal-title":"PLOS Genet."},{"key":"10.1016\/j.cub.2026.07.055_bib53","doi-asserted-by":"crossref","first-page":"1450","DOI":"10.1111\/jeb.13047","article-title":"Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow","volume":"30","author":"Ravinet","year":"2017","journal-title":"J. Evol. Biol."},{"key":"10.1016\/j.cub.2026.07.055_bib54","doi-asserted-by":"crossref","first-page":"88","DOI":"10.3109\/13813455.2013.777078","article-title":"Adenosine deaminase activity in normal pregnancy and pregnancy associated disorders","volume":"119","author":"Jadhav","year":"2013","journal-title":"Arch. Physiol. Biochem."},{"key":"10.1016\/j.cub.2026.07.055_bib55","article-title":"Screening candidate genes regulating placental development from trophoblast transcriptome at early pregnancy in Dazu Black Goats (Capra hircus)","volume":"11","author":"Luo","year":"2021","journal-title":"Animals (Basel)"},{"key":"10.1016\/j.cub.2026.07.055_bib56","doi-asserted-by":"crossref","first-page":"16285","DOI":"10.1074\/jbc.M110.217026","article-title":"A phosphodiesterase 3B-based signaling complex integrates exchange protein activated by cAMP 1 and phosphatidylinositol 3-kinase signals in human arterial endothelial cells","volume":"286","author":"Wilson","year":"2011","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.cub.2026.07.055_bib57","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1530\/JME-15-0248","article-title":"Interaction of steroid receptor coactivators and estrogen receptors in the human placenta","volume":"56","author":"Kim","year":"2016","journal-title":"J. Mol. Endocrinol."},{"key":"10.1016\/j.cub.2026.07.055_bib58","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.70753","article-title":"Disrupted PGR-B and ESR1 signaling underlies defective decidualization linked to severe preeclampsia","volume":"10","author":"Garrido-Gomez","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.cub.2026.07.055_bib59","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1038\/s41559-025-02748-x","article-title":"Cell type and cell signalling innovations underlying mammalian pregnancy","volume":"9","author":"Stadtmauer","year":"2025","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib60","doi-asserted-by":"crossref","first-page":"2941","DOI":"10.1172\/JCI87715","article-title":"p53 coordinates decidual sestrin 2\/AMPK\/mTORC1 signaling to govern parturition timing","volume":"126","author":"Deng","year":"2016","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.cub.2026.07.055_bib61","doi-asserted-by":"crossref","DOI":"10.1111\/aji.13222","article-title":"Sestrin2 alleviates palmitate-induced endoplasmic reticulum stress, apoptosis, and defective invasion of human trophoblast cells","volume":"83","author":"Lee","year":"2020","journal-title":"Am. J. Reprod. Immunol."},{"key":"10.1016\/j.cub.2026.07.055_bib62","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1111\/j.1558-5646.2007.00105.x","article-title":"The locus of evolution: evo devo and the genetics of adaptation","volume":"61","author":"Hoekstra","year":"2007","journal-title":"Evolution"},{"key":"10.1016\/j.cub.2026.07.055_bib63","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.1630","article-title":"GREAT improves functional interpretation of cis-regulatory regions","volume":"28","author":"McLean","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cub.2026.07.055_bib64","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.110280","article-title":"Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages","volume":"38","author":"Roscito","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.cub.2026.07.055_bib65","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1111\/jbi.13349","article-title":"Phylogeography, evolutionary history and effects of glaciations in a species (Zootoca vivipara) inhabiting multiple biogeographic regions","volume":"45","author":"Horreo","year":"2018","journal-title":"J. Biogeogr."},{"key":"10.1016\/j.cub.2026.07.055_bib66","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1007\/BF00137351","article-title":"Dollo on Dollo\u2019s law: irreversibility and the status of evolutionary laws","volume":"3","author":"Gould","year":"1970","journal-title":"J. Hist. Biol."},{"key":"10.1016\/j.cub.2026.07.055_bib67","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1016\/j.tree.2008.06.013","article-title":"Reversing opinions on Dollo\u2019s Law","volume":"23","author":"Collin","year":"2008","journal-title":"Trends Ecol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib68","doi-asserted-by":"crossref","DOI":"10.1016\/j.ympev.2024.108197","article-title":"Reticulate evolution: Detection and utility in the phylogenomics era","volume":"201","author":"Bjornson","year":"2024","journal-title":"Mol. Phylogenet. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib69","doi-asserted-by":"crossref","DOI":"10.1093\/nsr\/nwab127","article-title":"Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow","volume":"8","author":"Jiao","year":"2021","journal-title":"Natl. Sci. Rev."},{"key":"10.1016\/j.cub.2026.07.055_bib70","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msae214","article-title":"The meaning and measure of concordance factors in phylogenomics","volume":"41","author":"Lanfear","year":"2024","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib71","doi-asserted-by":"crossref","DOI":"10.1186\/s12915-024-01837-w","article-title":"Convergent genomic signatures associated with vertebrate viviparity","volume":"22","author":"Eastment","year":"2024","journal-title":"BMC Biol."},{"key":"10.1016\/j.cub.2026.07.055_bib72","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msad208","article-title":"Genomic signatures associated with transitions to viviparity in Cyprinodontiformes","volume":"40","author":"Yusuf","year":"2023","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib73","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1146\/annurev.ecolsys.36.102003.152631","article-title":"Life-history evolution in reptiles","volume":"36","author":"Shine","year":"2005","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"10.1016\/j.cub.2026.07.055_bib74","doi-asserted-by":"crossref","first-page":"12787","DOI":"10.1073\/pnas.1811268115","article-title":"Quantifying the risk of hemiplasy in phylogenetic inference","volume":"115","author":"Guerrero","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2026.07.055_bib75","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab098","article-title":"A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles","volume":"11","author":"Koochekian","year":"2022","journal-title":"GigaScience"},{"key":"10.1016\/j.cub.2026.07.055_bib76","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giy160","article-title":"Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation","volume":"8","author":"Kolora","year":"2019","journal-title":"GigaScience"},{"key":"10.1016\/j.cub.2026.07.055_bib77","doi-asserted-by":"crossref","DOI":"10.1111\/mec.17278","article-title":"Genetic basis and expression of ventral colour in polymorphic common lizards","volume":"33","author":"Recknagel","year":"2024","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.cub.2026.07.055_bib78","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.gpb.2015.08.002","article-title":"PacBio sequencing and its applications","volume":"13","author":"Rhoads","year":"2015","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"10.1016\/j.cub.2026.07.055_bib79","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","article-title":"Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm","volume":"18","author":"Cheng","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cub.2026.07.055_bib80","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","article-title":"Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst."},{"key":"10.1016\/j.cub.2026.07.055_bib81","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.aal3327","article-title":"De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds","volume":"356","author":"Dudchenko","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.cub.2026.07.055_bib82","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.cels.2015.07.012","article-title":"Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst."},{"key":"10.1016\/j.cub.2026.07.055_bib83","doi-asserted-by":"crossref","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib84","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"RepeatModeler2 for automated genomic discovery of transposable element families","volume":"117","author":"Flynn","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.cub.2026.07.055_bib85","article-title":"Using RepeatMasker to identify repetitive elements in genomic sequences","volume":"Chapter","author":"Chen","year":"2004","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"10.1016\/j.cub.2026.07.055_bib86","doi-asserted-by":"crossref","first-page":"W435","DOI":"10.1093\/nar\/gkl200","article-title":"AUGUSTUS: ab initio prediction of alternative transcripts","volume":"34","author":"Stanke","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2026.07.055_bib87","series-title":"Gene Prediction: Methods and Protocols","first-page":"161","article-title":"GeMoMa: homology-based gene prediction utilizing intron position conservation and RNA-seq data","author":"Keilwagen","year":"2019"},{"key":"10.1016\/j.cub.2026.07.055_bib88","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cub.2026.07.055_bib89","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.cub.2026.07.055_bib90","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nmeth.4078","article-title":"TACO produces robust multisample transcriptome assemblies from RNA-seq","volume":"14","author":"Niknafs","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cub.2026.07.055_bib91","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2008-9-1-r7","article-title":"Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments","volume":"9","author":"Haas","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.cub.2026.07.055_bib92","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J."},{"key":"10.1016\/j.cub.2026.07.055_bib93","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2026.07.055_bib94","series-title":"IEEE International Parallel and Distributed Processing Symposium (IPDPS) (IEEE)","first-page":"314","article-title":"Efficient architecture-aware acceleration of BWA-MEM for multicore systems","author":"Vasimuddin","year":"2019"},{"key":"10.1016\/j.cub.2026.07.055_bib95","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2026.07.055_bib96","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"10.1016\/j.cub.2026.07.055_bib97","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"10.1016\/j.cub.2026.07.055_bib98","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2026.07.055_bib99","unstructured":"Ortiz, E.M. (2019). vcf2phylip v2.0: Convert a VCF Matrix into Several Matrix Formats for Phylogenetic Analysis. Zenodo. https:\/\/doi.org\/10.5281\/zenodo.2540861."},{"key":"10.1016\/j.cub.2026.07.055_bib100","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib101","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib102","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.cub.2026.07.055_bib103","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res."},{"key":"10.1016\/j.cub.2026.07.055_bib104","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkt371","article-title":"Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach","volume":"41","author":"Hahn","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2026.07.055_bib105","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib106","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: molecular evolutionary genetics analysis version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib107","doi-asserted-by":"crossref","first-page":"W573","DOI":"10.1093\/nar\/gks485","article-title":"T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks","volume":"40","author":"Boc","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.cub.2026.07.055_bib108","doi-asserted-by":"crossref","first-page":"3194","DOI":"10.1093\/bioinformatics\/btz030","article-title":"admixr\u2014R package for reproducible analyses using ADMIXTOOLS","volume":"35","author":"Petr","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2026.07.055_bib109","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1534\/genetics.112.145037","article-title":"Ancient admixture in human history","volume":"192","author":"Patterson","year":"2012","journal-title":"Genetics"},{"key":"10.1016\/j.cub.2026.07.055_bib110","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1016\/j.ajhg.2021.08.005","article-title":"Fast two-stage phasing of large-scale sequence data","volume":"108","author":"Browning","year":"2021","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.cub.2026.07.055_bib111","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"key":"10.1016\/j.cub.2026.07.055_bib112","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v087.c03","article-title":"ggtern: Ternary Diagrams Using ggplot2","volume":"87","author":"Hamilton","year":"2018","journal-title":"J. Stat. Softw."},{"key":"10.1016\/j.cub.2026.07.055_bib113","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2026.07.055_bib114","doi-asserted-by":"crossref","first-page":"3478","DOI":"10.1093\/molbev\/msab113","article-title":"The pop-gen pipeline platform: A software platform for population genomic analyses","volume":"38","author":"Webb","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib115","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2026.07.055_bib116","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib117","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/bioinformatics\/btl140","article-title":"Improved scoring of functional groups from gene expression data by decorrelating GO graph structure","volume":"22","author":"Alexa","year":"2006","journal-title":"Bioinformatics"},{"key":"10.1016\/j.cub.2026.07.055_bib118","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly"},{"key":"10.1016\/j.cub.2026.07.055_bib119","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.cub.2026.07.055_bib120","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.cub.2026.07.055_bib121","article-title":"Full-length transcriptome data for the white cloud mountain minnow (Tanichthys albonubes) from a wild population based on isoform sequencing","volume":"9","author":"Li","year":"2022","journal-title":"Front. Mar. Sci."},{"key":"10.1016\/j.cub.2026.07.055_bib122","article-title":"A brief review of meiotic chromosomes in early spermatogenesis and oogenesis and mitotic chromosomes in the viviparous Lizard Zootoca vivipara (Squamata: Lacertidae) with multiple sex chromosomes","volume":"13","author":"Kurpyianova","year":"2022","journal-title":"Animals (Basel)"},{"key":"10.1016\/j.cub.2026.07.055_bib123","first-page":"83","article-title":"Karyotype dispersal of the common lizard Zootoca vivipara (Lichtenstein, 1823) in eastern and northeastern Fennoscandia","volume":"90","author":"Kupriyanova","year":"2014","journal-title":"Memo. Soc. Fauna Flora Fenn."},{"key":"10.1016\/j.cub.2026.07.055_bib124","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/j.ympev.2016.04.016","article-title":"Evaluating the phylogenetic signal limit from mitogenomes, slow evolving nuclear genes, and the concatenation approach. New insights into the Lacertini radiation using fast evolving nuclear genes and species trees","volume":"100","author":"Mendes","year":"2016","journal-title":"Mol. Phylogenet. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib125","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1016\/j.cub.2024.09.028","article-title":"Avoidable false PSMC population size peaks occur across numerous studies","volume":"35","author":"Hilgers","year":"2025","journal-title":"Curr. Biol."},{"key":"10.1016\/j.cub.2026.07.055_bib126","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1093\/evlett\/qrad027","article-title":"Experimental estimates of germline mutation rate in eukaryotes: a phylogenetic meta-analysis","volume":"7","author":"Wang","year":"2023","journal-title":"Evol. Lett."},{"key":"10.1016\/j.cub.2026.07.055_bib127","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1111\/j.1365-2435.2011.01837.x","article-title":"An integrative study of ageing in a wild population of common lizards","volume":"25","author":"Massot","year":"2011","journal-title":"Funct. Ecol."},{"key":"10.1016\/j.cub.2026.07.055_bib128","doi-asserted-by":"crossref","first-page":"3001","DOI":"10.1111\/j.1558-5646.2007.00238.x","article-title":"Population size changes reshape genomic patterns of diversity","volume":"61","author":"Pool","year":"2007","journal-title":"Evolution"},{"key":"10.1016\/j.cub.2026.07.055_bib129","doi-asserted-by":"crossref","first-page":"1953","DOI":"10.1093\/gbe\/evaa161","article-title":"Chromosome-level assembly of the common lizard (Zootoca vivipara) genome","volume":"12","author":"Yurchenko","year":"2020","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.cub.2026.07.055_bib130","first-page":"309","article-title":"Table de developpement du lezard vivipare: Lacerta (Zootoca) vivipara Jacquin","volume":"50","author":"Hubert","year":"1962","journal-title":"Arch. Anat. Microsc. Morphol. Exp."}],"container-title":["Current Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0960982226009541?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0960982226009541?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T04:27:47Z","timestamp":1789705667000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0960982226009541"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":130,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["S0960982226009541"],"URL":"https:\/\/doi.org\/10.1016\/j.cub.2026.07.055","relation":{},"ISSN":["0960-9822"],"issn-type":[{"value":"0960-9822","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Genome-wide barriers to gene flow reveal the genetic basis of viviparity evolution in a lizard","name":"articletitle","label":"Article Title"},{"value":"Current Biology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cub.2026.07.055","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}