{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T09:23:50Z","timestamp":1788341030158,"version":"build-2803163510"},"reference-count":66,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T00:00:00Z","timestamp":1785888000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Azenta\u2013GENEWIZ"},{"DOI":"10.13039\/100000001","name":"US National Science Foundation","doi-asserted-by":"publisher","award":["NSF 2218671"],"award-info":[{"award-number":["NSF 2218671"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Reference-quality genomes remain scarce for true crocodiles (Crocodylus), limiting comparative analyses of genome evolution and demographic history. Here, we generated and analyzed 2 long-read genomes, 1 for Crocodylus intermedius and 1 for C. niloticus, to investigate genome architecture, coalescent effective population size (Ne), and patterns of molecular evolution across crocodilians. Comparative analyses revealed broadly similar repeat landscapes in both species and extensive macro-synteny with Alligator sinensis, indicating strong structural conservation across crocodilian genomes. Using phased diploid assemblies and MSMC2, we reconstructed historical Ne trajectories and found marked differences between species. Crocodylus intermedius exhibited persistently low Ne throughout most of the late Quaternary, with a pronounced decline during the Late Pleistocene\u2013early Holocene transition. In contrast, C. niloticus showed substantially larger Ne over comparable time intervals. Genome-wide codon-based analyses identified significant heterogeneity in dN\/dS (\u03c9) among crocodilian lineages. Crocodylus niloticus showed the lowest genome-wide \u03c9, whereas elevated values in C. intermedius and other lineages were consistent with reduced long-term efficacy of purifying selection under smaller historical population sizes. Branch-site tests identified candidate genes under positive selection in both focal species, with functional categories related to ion transport, endocrine regulation, and cellular signaling. Together, these results provide genomic resources for Crocodylus and support an association between long-term demographic history and genome-wide patterns of molecular evolution across crocodilians.<\/jats:p>","DOI":"10.1093\/g3journal\/jkag178","type":"journal-article","created":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T15:28:37Z","timestamp":1785943717000},"source":"Crossref","is-referenced-by-count":0,"title":["Genome evolution and long-term demographic history in true crocodiles"],"prefix":"10.1093","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3466-6313","authenticated-orcid":false,"given":"Ana M","family":"Saldarriaga-G\u00f3mez","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Fordham University , Bronx, NY 10458 ,","place":["United States"]},{"name":"American Museum of Natural History , NewYork, NY 10024 ,","place":["United States"]},{"name":"Grupo de Biodiversidad y Conservaci\u00f3n Gen\u00e9tica, Instituto de Gen\u00e9tica, Universidad Nacional de Colombia , Bogot, Cundinamarca 111321 ,","place":["Colombia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5516-9661","authenticated-orcid":false,"given":"Agusto","family":"Luzuriaga-Neira","sequence":"additional","affiliation":[{"name":"Department of Ornithology, American Museum of Natural History , NewYork, NY 10024 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8974-3430","authenticated-orcid":false,"given":"Mario","family":"Vargas-Ram\u00edrez","sequence":"additional","affiliation":[{"name":"Grupo de Biodiversidad y Conservaci\u00f3n Gen\u00e9tica, Instituto de Gen\u00e9tica, Universidad Nacional de Colombia , Bogot, Cundinamarca 111321 ,","place":["Colombia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-5740-6939","authenticated-orcid":false,"given":"George","family":"Amato","sequence":"additional","affiliation":[{"name":"American Museum of Natural History , NewYork, NY 10024 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9250-3091","authenticated-orcid":false,"given":"Evon","family":"Hekkala","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Fordham University , Bronx, NY 10458 ,","place":["United States"]},{"name":"American Museum of Natural History , NewYork, NY 10024 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,5]]},"reference":[{"key":"2026090205043750800_jkag178-B1","doi-asserted-by":"publisher","first-page":"892","DOI":"10.1111\/1755-0998.13160","article-title":"MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics","volume":"20","author":"Allio","year":"2020","journal-title":"Mol Ecol Resour"},{"key":"2026090205043750800_jkag178-B2","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1186\/s13059-022-02823-7","article-title":"Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing","volume":"23","author":"Alonge","year":"2022","journal-title":"Genome Biol"},{"key":"2026090205043750800_jkag178-B3","volume-title":"The IUCN red list of threatened Species","author":"Balaguera-Reina","year":"2018"},{"key":"2026090205043750800_jkag178-B4","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1016\/j.tig.2025.03.003","article-title":"Can genomic analysis actually estimate past population size?","volume":"41","author":"Bansal","year":"2025","journal-title":"Trends Genet"},{"key":"2026090205043750800_jkag178-B5","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msae068","article-title":"Earl grey: a fully automated user-friendly transposable element annotation and analysis pipeline","volume":"41","author":"Baril","year":"2024","journal-title":"Mol Biol Evol"},{"key":"2026090205043750800_jkag178-B6","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1191\/0959683602h1518rp","article-title":"Late quaternary savanna history of the Colombian llanos orientales from lagunas chenevo and Mozambique: a transect synthesis","volume":"12","author":"Berr\u00edo","year":"2002","journal-title":"Holocene"},{"key":"2026090205043750800_jkag178-B7","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.1660","article-title":"AMAS: a fast tool for alignment manipulation and computing of summary statistics","volume":"4","author":"Borowiec","year":"2016","journal-title":"PeerJ"},{"key":"2026090205043750800_jkag178-B8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0311412","article-title":"First genetic evaluation of a wild population of Crocodylus intermedius: new insights for the recovery of a critically endangered species","volume":"19","author":"Castillo-Rodr\u00edguez","year":"2024","journal-title":"PLoS One"},{"key":"2026090205043750800_jkag178-B9","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1038\/nrg2526","article-title":"Effective population size and patterns of molecular evolution and variation","volume":"10","author":"Charlesworth","year":"2009","journal-title":"Nat Rev Genet"},{"key":"2026090205043750800_jkag178-B10","doi-asserted-by":"publisher","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":"2026090205043750800_jkag178-B11","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1186\/s12977-014-0071-2","article-title":"Evolution and gene capture in ancient endogenous retroviruses: insights from the crocodilian genomes","volume":"11","author":"Chong","year":"2014","journal-title":"Retrovirology"},{"key":"2026090205043750800_jkag178-B12","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"2026090205043750800_jkag178-B13","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol"},{"key":"2026090205043750800_jkag178-B14","doi-asserted-by":"publisher","first-page":"1517","DOI":"10.1093\/molbev\/msw033","article-title":"Life history traits, protein evolution, and the nearly neutral theory in amniotes","volume":"33","author":"Figuet","year":"2016","journal-title":"Mol Biol Evol"},{"key":"2026090205043750800_jkag178-B15","doi-asserted-by":"publisher","first-page":"1500","DOI":"10.1046\/j.1523-1739.1996.10061500.x","article-title":"Relationship of genetic variation to population size in wildlife","volume":"10","author":"Frankham","year":"1996","journal-title":"Conserv Biol"},{"key":"2026090205043750800_jkag178-B16","doi-asserted-by":"publisher","first-page":"3635","DOI":"10.1093\/gbe\/evz269","article-title":"A high-quality reference genome assembly of the saltwater crocodile, Crocodylus porosus, reveals patterns of selection in crocodylidae","volume":"12","author":"Ghosh","year":"2020","journal-title":"Genome Biol Evol"},{"key":"2026090205043750800_jkag178-B17","doi-asserted-by":"publisher","first-page":"1254449","DOI":"10.1126\/science.1254449","article-title":"Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs","volume":"346","author":"Green","year":"2014","journal-title":"Science"},{"key":"2026090205043750800_jkag178-B18","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"2026090205043750800_jkag178-B19","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/s42003-021-02017-0","article-title":"Paleogenomics illuminates the evolutionary history of the extinct Holocene \u201chorned\u201d crocodile of Madagascar, Voay robustus","volume":"4","author":"Hekkala","year":"2021","journal-title":"Commun Biol"},{"key":"2026090205043750800_jkag178-B20","doi-asserted-by":"publisher","first-page":"4199","DOI":"10.1111\/j.1365-294X.2011.05245.x","article-title":"An ancient icon reveals new mysteries: mummy DNA resurrects a cryptic species within the Nile crocodile","volume":"20","author":"Hekkala","year":"2011","journal-title":"Mol Ecol"},{"key":"2026090205043750800_jkag178-B21","doi-asserted-by":"publisher","first-page":"1435","DOI":"10.1007\/s10592-009-9970-5","article-title":"Molecular assessment of population differentiation and individual assignment potential of Nile crocodile (Crocodylus niloticus) populations","volume":"11","author":"Hekkala","year":"2010","journal-title":"Conserv Genet"},{"key":"2026090205043750800_jkag178-B22","doi-asserted-by":"publisher","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":"2026090205043750800_jkag178-B23","author":"International Union for Conservation of Nature (IUCN) Crocodile Specialist Group","year":"2023"},{"key":"2026090205043750800_jkag178-B24","author":"International Union for Conservation of Nature (IUCN) Crocodile Specialist Group","year":"2023"},{"key":"2026090205043750800_jkag178-B25","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2026090205043750800_jkag178-B26","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1007\/978-1-4939-9173-0_9","article-title":"Gemoma: homology-based gene prediction utilizing intron position conservation and RNA-seq data","volume":"1962","author":"Keilwagen","year":"2019","journal-title":"Methods Mol Biol"},{"key":"2026090205043750800_jkag178-B27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0076514","article-title":"Dynamics of Green Sahara periods and their role in hominin evolution","volume":"8","author":"Larrasoa\u00f1a","year":"2013","journal-title":"PLoS One"},{"key":"2026090205043750800_jkag178-B28","doi-asserted-by":"publisher","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":"2026090205043750800_jkag178-B29","doi-asserted-by":"publisher","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":"2026090205043750800_jkag178-B30","doi-asserted-by":"publisher","first-page":"evab277","DOI":"10.1093\/gbe\/evab277","article-title":"Rates of protein evolution across the marsupial phylogeny: heterogeneity and link to life-history traits","volume":"14","author":"Luzuriaga-Neira","year":"2022","journal-title":"Genome Biol Evol"},{"key":"2026090205043750800_jkag178-B31","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","article-title":"A fast, lock-free approach for efficient parallel counting of occurrences of k-mers","volume":"27","author":"Mar\u00e7ais","year":"2011","journal-title":"Bioinformatics"},{"key":"2026090205043750800_jkag178-B32","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1016\/S0277-3791(00)00182-7","article-title":"Mid- to late-hHolocene pollen-based biome reconstructions for Colombia","volume":"20","author":"Marchant","year":"2001","journal-title":"Quat Sci Rev"},{"key":"2026090205043750800_jkag178-B33","doi-asserted-by":"publisher","first-page":"1829","DOI":"10.1098\/rstb.2007.0019","article-title":"Impact of a drier early\u2013mid-Holocene climate upon Amazonian forests","volume":"363","author":"Mayle","year":"2008","journal-title":"Philos Trans R Soc B"},{"key":"2026090205043750800_jkag178-B34","volume-title":"Los crocodylia de sur am\u00e9rica. Volumen I. Los crocodylia de Colombia","author":"Medem","year":"1981"},{"key":"2026090205043750800_jkag178-B35","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1186\/s12863-024-01240-y","article-title":"Draft assembly and annotation of the Cuban crocodile (Crocodylus rhombifer) genome","volume":"25","author":"Meredith","year":"2024","journal-title":"BMC Genomics Data"},{"key":"2026090205043750800_jkag178-B36","doi-asserted-by":"publisher","first-page":"D419","DOI":"10.1093\/nar\/gky1038","article-title":"PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools","volume":"47","author":"Mi","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026090205043750800_jkag178-B37","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.5836","article-title":"Genetic evidence supports a distinct lineage of American crocodile (Crocodylus acutus) in the Greater Antilles","volume":"6","author":"Mili\u00e1n-Garc\u00eda","year":"2018","journal-title":"PeerJ"},{"key":"2026090205043750800_jkag178-B38","doi-asserted-by":"publisher","first-page":"106924","DOI":"10.1016\/j.ympev.2020.106924","article-title":"Phylogenomics reveals novel relationships among neotropical crocodiles (Crocodylus spp.)","volume":"152","author":"Mili\u00e1n-Garc\u00eda","year":"2020","journal-title":"Mol Phylogenet Evol"},{"key":"2026090205043750800_jkag178-B39","doi-asserted-by":"publisher","first-page":"329","DOI":"10.5343\/bms.2016.1134","article-title":"Mitogenomic investigation reveals a cryptic lineage of Crocodylus in Cuba","volume":"94","author":"Mili\u00e1n-Garc\u00eda","year":"2018","journal-title":"Bull Mar Sci"},{"key":"2026090205043750800_jkag178-B40","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1038\/s41587-024-02147-w","article-title":"Quality assessment of gene repertoire annotations with OMArk","volume":"43","author":"Nevers","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2026090205043750800_jkag178-B41","doi-asserted-by":"publisher","first-page":"3285","DOI":"10.1111\/j.1558-5646.2011.01373.x","article-title":"A time-calibrated species tree of crocodylia reveals a recent radiation of the true crocodiles","volume":"65","author":"Oaks","year":"2011","journal-title":"Evolution"},{"key":"2026090205043750800_jkag178-B42","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1038\/246096a0","article-title":"Slightly deleterious mutant substitutions in evolution","volume":"246","author":"Ohta","year":"1973","journal-title":"Nature"},{"key":"2026090205043750800_jkag178-B43","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1146\/annurev.es.23.110192.001403","article-title":"The nearly neutral theory of molecular evolution","volume":"23","author":"Ohta","year":"1992","journal-title":"Annu Rev Ecol Syst"},{"key":"2026090205043750800_jkag178-B44","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1111\/nyas.13443","article-title":"Evolutionary ecology of telomeres: a review","volume":"1422","author":"Olsson","year":"2018","journal-title":"Ann N Y Acad Sci"},{"key":"2026090205043750800_jkag178-B45","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adm7980","article-title":"Genomic insights and the conservation potential of captive breeding: the case of Chinese alligator","volume":"11","author":"Pan","year":"2025","journal-title":"Sci Adv"},{"key":"2026090205043750800_jkag178-B46","doi-asserted-by":"publisher","DOI":"10.1093\/bioadv\/vbad161","article-title":"syntenyPlotter: a user-friendly R package to visualize genome synteny","volume":"3","author":"Quigley","year":"2023","journal-title":"Bioinform Adv"},{"key":"2026090205043750800_jkag178-B47","doi-asserted-by":"publisher","first-page":"1432","DOI":"10.1038\/s41467-020-14998-3","article-title":"GenomeScope 2.0 and smudgeplot for reference-free profiling of polyploid genomes","volume":"11","author":"Ranallo-Benavidez","year":"2020","journal-title":"Nat Commun"},{"key":"2026090205043750800_jkag178-B48","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","article-title":"Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies","volume":"21","author":"Rhie","year":"2020","journal-title":"Genome Biol"},{"key":"2026090205043750800_jkag178-B49","doi-asserted-by":"publisher","first-page":"2866","DOI":"10.1093\/bioinformatics\/btab219","article-title":"OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches","volume":"37","author":"Rossier","year":"2021","journal-title":"Bioinformatics"},{"key":"2026090205043750800_jkag178-B50","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1038\/ng.3015","article-title":"Inferring human population size and separation history from multiple genome sequences","volume":"46","author":"Schiffels","year":"2014","journal-title":"Nat Genet"},{"key":"2026090205043750800_jkag178-B51","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1007\/978-1-0716-0199-0_7","article-title":"MSMC and MSMC2: the multiple sequentially Markovian coalescent","volume":"2090","author":"Schiffels","year":"2020","journal-title":"Methods Mol Biol"},{"key":"2026090205043750800_jkag178-B52","first-page":"59","volume-title":"Crocodiles Status survey and conservation action plan","author":"Seijas","year":"2010","edition":"3rd ed"},{"key":"2026090205043750800_jkag178-B53","doi-asserted-by":"publisher","first-page":"20132483","DOI":"10.1098\/rspb.2013.2483","article-title":"Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation","volume":"281","author":"Shirley","year":"2014","journal-title":"Proc Biol Sci."},{"key":"2026090205043750800_jkag178-B54","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"2026090205043750800_jkag178-B55","doi-asserted-by":"publisher","first-page":"10295","DOI":"10.5808\/GI.2015.13.4.102","article-title":"Role of chromosome changes in Crocodylus evolution and diversity","volume":"14","author":"Srikulnath","year":"2015","journal-title":"Genet Mol Res"},{"key":"2026090205043750800_jkag178-B56","doi-asserted-by":"publisher","first-page":"W609","DOI":"10.1093\/nar\/gkl315","article-title":"PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments","volume":"34","author":"Suyama","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2026090205043750800_jkag178-B57","doi-asserted-by":"publisher","first-page":"D325","DOI":"10.1093\/nar\/gkaa1113","article-title":"The gene ontology resource: enriching a GOld mine","volume":"49","author":"The Gene Ontology Consortium","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026090205043750800_jkag178-B58","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.1601503","article-title":"Rainfall regimes of the green sahara","volume":"3","author":"Tierney","year":"2017","journal-title":"Sci Adv"},{"key":"2026090205043750800_jkag178-B59","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1016\/j.quascirev.2008.11.003","article-title":"Trends, rhythms and events in plio-pleistocene African climate","volume":"28","author":"Trauth","year":"2009","journal-title":"Quat Sci Rev"},{"key":"2026090205043750800_jkag178-B60","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1038\/nrg3117","article-title":"Repetitive DNA and next-generation sequencing: computational challenges and solutions","volume":"13","author":"Treangen","year":"2011","journal-title":"Nat Rev Genet"},{"key":"2026090205043750800_jkag178-B61","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1186\/s12859-023-05385-y","article-title":"Mitohifi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads","volume":"24","author":"Uliano-Silva","year":"2023","journal-title":"BMC Bioinformatics"},{"key":"2026090205043750800_jkag178-B62","first-page":"261","article-title":"Upper pleistocene and holocene climate and vegetation of the sabana de bogot\u00e1 (Colombia, South America)","volume":"25","author":"van der Hammen","year":"1960","journal-title":"Leidse Geol Meded"},{"key":"2026090205043750800_jkag178-B63","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1038\/cr.2013.104","article-title":"Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator","volume":"23","author":"Wan","year":"2013","journal-title":"Cell Res"},{"key":"2026090205043750800_jkag178-B64","first-page":"71","article-title":"Palynological data on the history of tropical savannas in Northern South America","volume":"38","author":"Wijmstra","year":"1966","journal-title":"Leidse Geol Meded"},{"key":"2026090205043750800_jkag178-B65","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol Biol Evol"},{"key":"2026090205043750800_jkag178-B66","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1016\/S0169-5347(00)01994-7","article-title":"Statistical methods for detecting molecular adaptation","volume":"15","author":"Yang","year":"2000","journal-title":"Trends Ecol Evol"}],"container-title":["G3: Genes, Genomes, Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/g3journal\/advance-article-pdf\/doi\/10.1093\/g3journal\/jkag178\/70496563\/jkag178.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/16\/9\/jkag178\/70496563\/jkag178.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/16\/9\/jkag178\/70496563\/jkag178.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T09:06:40Z","timestamp":1788340000000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/g3journal\/article\/doi\/10.1093\/g3journal\/jkag178\/8752653"}},"subtitle":[],"editor":[{"given":"R","family":"Mallarino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,5]]},"references-count":66,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,8,5]]},"published-print":{"date-parts":[[2026,9,2]]}},"URL":"https:\/\/doi.org\/10.1093\/g3journal\/jkag178","relation":{},"ISSN":["2160-1836"],"issn-type":[{"value":"2160-1836","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,8,5]]},"article-number":"jkag178"}}