{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T01:51:06Z","timestamp":1791597066166,"version":"4.3.4"},"reference-count":105,"publisher":"Elsevier BV","issue":"9","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":[[2026,7,23]],"date-time":"2026-07-23T00:00:00Z","timestamp":1784764800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002808","name":"Carlsberg Foundation","doi-asserted-by":"publisher","award":["CF20-0539"],"award-info":[{"award-number":["CF20-0539"]}],"id":[{"id":"10.13039\/501100002808","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF23SA0084103"],"award-info":[{"award-number":["NNF23SA0084103"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["iScience"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.isci.2026.117121","type":"journal-article","created":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T09:01:40Z","timestamp":1787043700000},"page":"117121","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["From forests to deserts: Sequencing of the giant forest hog completes the genomic history of the African suids"],"prefix":"10.1016","volume":"29","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8998-4899","authenticated-orcid":false,"given":"Marta Maria","family":"Ciucani","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabhrina Gita","family":"Aninta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nuno Filipe","family":"Gomes Martins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Duch\u00eane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ignacio A.","family":"Lazagabaster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaodong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frederik Filip","family":"St\u00e6ger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikkel","family":"Schubert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"B\u00f8ggild","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shixu","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zilong","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael","family":"Reyna","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik","family":"Meijaard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas M.","family":"Butynski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent B.","family":"Muwanika","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Masembe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvain","family":"Dufour","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Gaubert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans R.","family":"Siegismund","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ida","family":"Moltke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anders","family":"Albrechtsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rasmus","family":"Heller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.isci.2026.117121_bib1","series-title":"Pigs, Peccaries and Hippos: Status Survey and Conservation Action Plan","first-page":"84","article-title":"The Forest Hog (Hylochoerus meinertzhageni)","author":"d\u2019Huart","year":"1993"},{"key":"10.1016\/j.isci.2026.117121_bib2","series-title":"Mammals of Africa. Vol. VI. Pigs, deer, giraffe, bovids and hippos","first-page":"64","article-title":"Hylochoerus meinertzhageni - Forest Hog","year":"2013"},{"key":"10.1016\/j.isci.2026.117121_bib3","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1038\/070577a0","article-title":"The Forest-pig of Central Africa","volume":"70","author":"Thomas","year":"1904","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117121_bib4","series-title":"Mammals of Africa: Volume VI: Hippopotamuses, Pigs, Deer, Giraffe","author":"Kingdon","year":"2013"},{"key":"10.1016\/j.isci.2026.117121_bib5","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.1098\/rstb.2004.1535","article-title":"Mechanisms and tempo of evolution in the African Guineo-Congolian rainforest","volume":"359","author":"Plana","year":"2004","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"10.1016\/j.isci.2026.117121_bib6","series-title":"Hylochoerus meinertzhageni (The IUCN Red List of Threatened Species in 2016)","author":"d\u2019Huart","year":"2016"},{"key":"10.1016\/j.isci.2026.117121_bib7","article-title":"Predicting near-future deforestation in West African Key Biodiversity Areas to inform conservation urgency","author":"Trew","year":"2024","journal-title":"bioRxiv"},{"key":"10.1016\/j.isci.2026.117121_bib8","doi-asserted-by":"crossref","first-page":"742","DOI":"10.3201\/eid2904.221022","article-title":"Mapping global bushmeat activities to improve zoonotic spillover surveillance by using geospatial modeling","volume":"29","author":"Jagadesh","year":"2023","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.isci.2026.117121_bib9","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1038\/s41893-024-01494-5","article-title":"Regional patterns of wild animal hunting in African tropical forests","volume":"8","author":"Ingram","year":"2025","journal-title":"Nat. Sustain."},{"key":"10.1016\/j.isci.2026.117121_bib10","series-title":"Movement Ecology of Afrotropical Forest Mammals","first-page":"9","article-title":"Movement patterns and population dynamics of giant forest hog groups in Kibale National Park, Uganda","author":"Reyna-Hurtado","year":"2023"},{"key":"10.1016\/j.isci.2026.117121_bib11","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2013-14-9-r107","article-title":"Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus","volume":"14","author":"Frantz","year":"2013","journal-title":"Genome Biol."},{"key":"10.1016\/j.isci.2026.117121_bib12","article-title":"Genetic origins and diversity of bushpigs from Madagascar (Potamochoerus larvatus, family Suidae)","volume":"10","author":"Lee","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.isci.2026.117121_bib13","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msac256","article-title":"African Suid genomes provide insights into the local adaptation to diverse African environments","volume":"39","author":"Xie","year":"2022","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.isci.2026.117121_bib14","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msac134","article-title":"Warthog genomes resolve an evolutionary conundrum and reveal introgression of disease resistance genes","volume":"39","author":"Garcia-Erill","year":"2022","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.isci.2026.117121_bib15","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1038\/s41467-023-44105-1","article-title":"African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival","volume":"15","author":"Balboa","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117121_bib16","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1111\/j.1463-6409.2011.00480.x","article-title":"Rethinking the evolution of extant sub-Saharan African suids (Suidae, Artiodactyla)","volume":"40","author":"Gongora","year":"2011","journal-title":"Zool. Scr."},{"key":"10.1016\/j.isci.2026.117121_bib17","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.isci.2026.117121_bib18","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2200016119","article-title":"Insights into bear evolution from a Pleistocene polar bear genome","volume":"119","author":"Lan","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.isci.2026.117121_bib19","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-026-71262-w","article-title":"The genomic impact of population connectivity and decline in Africa\u2019s elephants","volume":"17","author":"Pe\u010dnerov\u00e1","year":"2026","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117121_bib20","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1016\/j.cub.2024.02.051","article-title":"Giraffe lineages are shaped by major ancient admixture events","volume":"34","author":"Bertola","year":"2024","journal-title":"Curr. Biol."},{"key":"10.1016\/j.isci.2026.117121_bib21","series-title":"An Evaluation of the Taxonomic Status of Giraffe (Giraffa spp.)","year":"2025"},{"key":"10.1016\/j.isci.2026.117121_bib22","doi-asserted-by":"crossref","first-page":"2921","DOI":"10.1038\/s41467-024-47015-y","article-title":"Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations","volume":"15","author":"Liu","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117121_bib23","doi-asserted-by":"crossref","first-page":"3102","DOI":"10.1016\/j.cell.2025.03.040","article-title":"Genomes of critically endangered saola are shaped by population structure and purging","volume":"188","author":"Garcia-Erill","year":"2025","journal-title":"Cell"},{"key":"10.1016\/j.isci.2026.117121_bib24","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1038\/s41559-017-0406-1","article-title":"Forest extent and deforestation in tropical Africa since 1900","volume":"2","author":"Aleman","year":"2018","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.isci.2026.117121_bib25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2307\/1006288","article-title":"Evolution of the Plio-Pleistocene African Suidae","volume":"69","author":"Harris","year":"1979","journal-title":"Trans. Am. Phil. Soc."},{"key":"10.1016\/j.isci.2026.117121_bib26","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/S0016-6995(97)80262-8","article-title":"The status of the african fossil suids Kolpochoerus limnetes (Hopwood, 1926), K. Phacochoeroides (Thomas 1884) and K. Afarensis (Cooke, 1978)","volume":"30","author":"Cooke","year":"1997","journal-title":"Geobios"},{"key":"10.1016\/j.isci.2026.117121_bib27","series-title":"Hominin environments in the east African Pliocene: An assessment of the faunal evidence","author":"Cooke","year":"2007"},{"key":"10.1016\/j.isci.2026.117121_bib28","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/s10914-012-9207-0","article-title":"A new species of Kolpochoerus (Mammalia: Suidae) from the Pliocene of Central Afar, Ethiopia: Its Taxonomy and Phylogenetic Relationships","volume":"20","author":"Haile-Selassie","year":"2013","journal-title":"J. Mamm. Evol."},{"key":"10.1016\/j.isci.2026.117121_bib29","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1515\/mammalia-2014-0023","article-title":"Three-dimensional dental microwear texture analysis and diet in extant Suidae (Mammalia: Cetartiodactyla)","volume":"79","author":"Souron","year":"2015","journal-title":"Mammalia"},{"key":"10.1016\/j.isci.2026.117121_bib30","doi-asserted-by":"crossref","first-page":"329","DOI":"10.37520\/fi.2024.025","article-title":"Kolpochoerus (Suidae, Mammalia) dento-gnathic remains from Algeria: biostratigraphic implications","volume":"80","author":"Pickford","year":"2024","journal-title":"Foss. Impr."},{"key":"10.1016\/j.isci.2026.117121_bib31","first-page":"337","article-title":"A new wild boar belonging to the genus Potamochoerus (Suidae, Artiodactyla, Mammalia) from the Eurasian Late Upper Pliocene (Fonelas P-1, Cuenca de Guadix, Granada)","volume":"10","author":"Arribas","year":"2008","journal-title":"Quad. Mus. Geominero"},{"key":"10.1016\/j.isci.2026.117121_bib32","first-page":"57","article-title":"First record of maxillary dentition of Potamochoerus theobaldi (Suidae, Mammalia) from the upper siwaliks of India","volume":"119","author":"Kumar","year":"2013","journal-title":"Riv Ital Paleontol S"},{"key":"10.1016\/j.isci.2026.117121_bib33","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1080\/0035919X.2012.689265","article-title":"Ancestors of broom\u2019s pigs","volume":"67","author":"Pickford","year":"2012","journal-title":"Trans. R. Soc. S. Afr."},{"key":"10.1016\/j.isci.2026.117121_bib34","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1080\/00359190609519953","article-title":"Synopsis of the biochronology of African Neogene and Quaternary suiformes","volume":"61","author":"Pickford","year":"2006","journal-title":"Trans. R. Soc. S. Afr."},{"key":"10.1016\/j.isci.2026.117121_bib35","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1016\/j.jhevol.2008.05.015","article-title":"The large-mammal fauna from the Kibish Formation","volume":"55","author":"Assefa","year":"2008","journal-title":"J. Hum. Evol."},{"key":"10.1016\/j.isci.2026.117121_bib36","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1080\/08912963.2022.2057226","article-title":"The scarcity of fossils in the African rainforest. Archaeo-paleontological surveys and actualistic taphonomy in Equatorial Guinea","volume":"34","author":"Rosas","year":"2022","journal-title":"Hist. Biol."},{"key":"10.1016\/j.isci.2026.117121_bib37","doi-asserted-by":"crossref","first-page":"3673","DOI":"10.1080\/08912963.2021.1887861","article-title":"A Late Pleistocene third molar of Hylochoerus (Suidae, Mammalia) from Rusinga Island, Kenya: paleoenvironmental implications and a note on the hypsodonty of African forest hogs","volume":"33","author":"Lazagabaster","year":"2021","journal-title":"Hist. Biol."},{"key":"10.1016\/j.isci.2026.117121_bib38","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1016\/j.palaeo.2018.05.029","article-title":"Fossil Suidae (Mammalia, Artiodactyla) from Lee Adoyta, Ledi-Geraru, lower Awash Valley, Ethiopia: Implications for late Pliocene turnover and paleoecology","volume":"504","author":"Lazagabaster","year":"2018","journal-title":"Palaeogeogr. Palaeoclimatol. Palaeoecol."},{"key":"10.1016\/j.isci.2026.117121_bib39","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1007\/s10592-020-01304-3","article-title":"Evidence of hybridisation between the common Indonesian banded pig (Sus scrofa vitattus) and the endangered Java warty pig (Sus verrucosus)","volume":"21","author":"Drygala","year":"2020","journal-title":"Conserv. Genet."},{"key":"10.1016\/j.isci.2026.117121_bib40","doi-asserted-by":"crossref","first-page":"1992","DOI":"10.1038\/s41467-019-10017-2","article-title":"Genomic analysis on pygmy hog reveals extensive interbreeding during wild boar expansion","volume":"10","author":"Liu","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117121_bib41","doi-asserted-by":"crossref","DOI":"10.1126\/science.adv4963","article-title":"Genomic and morphometric evidence for Austronesian-mediated pig translocation in the Pacific","volume":"391","author":"Stanton","year":"2026","journal-title":"Science"},{"key":"10.1016\/j.isci.2026.117121_bib42","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1111\/brv.12644","article-title":"Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna","volume":"96","author":"Couvreur","year":"2021","journal-title":"Biol. Rev. Camb. Philos. Soc."},{"key":"10.1016\/j.isci.2026.117121_bib43","doi-asserted-by":"crossref","first-page":"3656","DOI":"10.1111\/j.1365-294X.2012.05650.x","article-title":"Comparative phylogeography of African savannah ungulates","volume":"21","author":"Lorenzen","year":"2012","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.isci.2026.117121_bib44","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1742-9994-1-4","article-title":"The structure of biodiversity - insights from molecular phylogeography","volume":"1","author":"Hewitt","year":"2004","journal-title":"Front. Zool."},{"key":"10.1016\/j.isci.2026.117121_bib45","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1111\/j.1365-294X.2007.03610.x","article-title":"Phylogeography of a Sahelian rodent species Mastomys huberti: a Plio-Pleistocene story of emergence and colonization of humid habitats","volume":"17","author":"Mouline","year":"2008","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.isci.2026.117121_bib46","doi-asserted-by":"crossref","first-page":"6133","DOI":"10.1002\/ece3.7429","article-title":"Rivers, not refugia, drove diversification in arboreal, sub-Saharan African snakes","volume":"11","author":"Allen","year":"2021","journal-title":"Ecol. Evol."},{"key":"10.1016\/j.isci.2026.117121_bib47","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1111\/j.1365-2486.2007.01524.x","article-title":"Simulated glacial and interglacial vegetation across Africa: implications for species phylogenies and trans-African migration of plants and animals: AFRICAN GLACIAL AND INTERGLACIAL VEGETATION","volume":"14","author":"Cowling","year":"2008","journal-title":"Glob. Chang. Biol."},{"key":"10.1016\/j.isci.2026.117121_bib48","doi-asserted-by":"crossref","first-page":"3589","DOI":"10.1016\/j.quascirev.2011.09.019","article-title":"Orbital scale vegetation change in Africa","volume":"30","author":"Dupont","year":"2011","journal-title":"Quat. Sci. Rev."},{"key":"10.1016\/j.isci.2026.117121_bib49","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1130\/0091-7613(2001)029<0195:MPECIT>2.0.CO;2","article-title":"Mid-Pleistocene environmental change in tropical Africa began as early as 1.05 Ma","volume":"29","author":"Dupont","year":"2001","journal-title":"Geology"},{"key":"10.1016\/j.isci.2026.117121_bib50","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0012-821X(04)00003-2","article-title":"African climate change and faunal evolution during the Pliocene\u2013Pleistocene","volume":"220","author":"deMenocal","year":"2004","journal-title":"Earth Planet Sci. Lett."},{"key":"10.1016\/j.isci.2026.117121_bib51","doi-asserted-by":"crossref","first-page":"4016","DOI":"10.1038\/s41467-023-39480-8","article-title":"Disruption of trait-environment relationships in African megafauna occurred in the middle Pleistocene","volume":"14","author":"Lauer","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117121_bib52","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1126\/science.1141038","article-title":"Orbital and millennial Antarctic climate variability over the past 800,000 years","volume":"317","author":"Jouzel","year":"2007","journal-title":"Science"},{"key":"10.1016\/j.isci.2026.117121_bib53","doi-asserted-by":"crossref","first-page":"1230","DOI":"10.1016\/j.jseaes.2010.08.002","article-title":"A prolonged warm and humid interval during marine isotope stage 13\u201315 as revealed by hydrographic reconstructions from the South China Sea (IMAGES MD972142)","volume":"40","author":"Yu","year":"2011","journal-title":"J. Asian Earth Sci."},{"key":"10.1016\/j.isci.2026.117121_bib54","doi-asserted-by":"crossref","first-page":"361","DOI":"10.5194\/cp-7-361-2011","article-title":"Interglacial and glacial variability from the last 800 ka in marine, ice and terrestrial archives","volume":"7","author":"Lang","year":"2011","journal-title":"Clim. Past"},{"key":"10.1016\/j.isci.2026.117121_bib55","article-title":"A Pliocene-Pleistocene stack of 57 globally distributed benthic \u03b418O records: Pliocene-pleistocene benthic stack","volume":"20","author":"Lisiecki","year":"2005","journal-title":"Paleoceanography"},{"key":"10.1016\/j.isci.2026.117121_bib56","doi-asserted-by":"crossref","DOI":"10.1038\/srep30807","article-title":"Phylogeographic patterns in Africa and high resolution delineation of genetic clades in the lion (Panthera leo)","volume":"6","author":"Bertola","year":"2016","journal-title":"Sci. Rep."},{"key":"10.1016\/j.isci.2026.117121_bib57","doi-asserted-by":"crossref","first-page":"2929","DOI":"10.1016\/j.cub.2021.04.033","article-title":"Whole-genome analysis of giraffe supports four distinct species","volume":"31","author":"Coimbra","year":"2021","journal-title":"Curr. Biol."},{"key":"10.1016\/j.isci.2026.117121_bib58","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1186\/1471-2148-9-83","article-title":"Mitochondrial phylogeography of baboons (Papio spp.): indication for introgressive hybridization?","volume":"9","author":"Zinner","year":"2009","journal-title":"BMC Evol. Biol."},{"key":"10.1016\/j.isci.2026.117121_bib59","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0056235","article-title":"Pan-African genetic structure in the African buffalo (Syncerus caffer): investigating intraspecific divergence","volume":"8","author":"Smitz","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.isci.2026.117121_bib60","doi-asserted-by":"crossref","first-page":"2435","DOI":"10.1093\/molbev\/msi244","article-title":"The population history of extant and extinct hyenas","volume":"22","author":"Rohland","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.isci.2026.117121_bib61","doi-asserted-by":"crossref","first-page":"2049","DOI":"10.1111\/jbi.12570","article-title":"The phylogeography of the rodent genus Malacomys suggests multiple Afrotropical Pleistocene lowland forest refugia","volume":"42","author":"Bohoussou","year":"2015","journal-title":"J. Biogeogr."},{"key":"10.1016\/j.isci.2026.117121_bib62","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1017\/S0952836902000365","article-title":"Patterns of species richness and narrow endemism of terrestrial bird species in the Afrotropical Region","volume":"256","author":"de Klerk","year":"2002","journal-title":"J. Zool."},{"key":"10.1016\/j.isci.2026.117121_bib63","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1046\/j.1472-4642.2002.00142.x","article-title":"Biogeographical patterns of endemic terrestrial Afrotropical birds","volume":"8","author":"De Klerk","year":"2002","journal-title":"Divers. Distrib."},{"key":"10.1016\/j.isci.2026.117121_bib64","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.ecolmodel.2015.09.009","article-title":"A high-resolution model of bat diversity and endemism for continental Africa","volume":"320","author":"Herkt","year":"2016","journal-title":"Ecol. Modell."},{"key":"10.1016\/j.isci.2026.117121_bib65","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.actao.2017.11.018","article-title":"Modelling the spatial baseline for amphibian conservation in West Africa","volume":"94","author":"Penner","year":"2019","journal-title":"Acta Oecol."},{"key":"10.1016\/j.isci.2026.117121_bib66","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1093\/zoolinnean\/zlab029","article-title":"A new species of tree hyrax (Procaviidae: Dendrohyrax) from West Africa and the significance of the Niger\u2013Volta interfluvium in mammalian biogeography","volume":"194","author":"Oates","year":"2022","journal-title":"Zool. J. Linn. Soc."},{"key":"10.1016\/j.isci.2026.117121_bib67","doi-asserted-by":"crossref","DOI":"10.1002\/ajp.23320","article-title":"Quantitative estimates of glacial refugia for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP)","volume":"83","author":"Barratt","year":"2021","journal-title":"Am. J. Primatol."},{"key":"10.1016\/j.isci.2026.117121_bib68","doi-asserted-by":"crossref","DOI":"10.21425\/fob.18.139537","article-title":"Towards a comprehensive view on evolutionary refugia in West African rainforests","volume":"18","author":"Ernst","year":"2025","journal-title":"Front. Biogeogr."},{"key":"10.1016\/j.isci.2026.117121_bib69","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1093\/molbev\/msp298","article-title":"The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses","volume":"27","author":"Hey","year":"2010","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.isci.2026.117121_bib70","doi-asserted-by":"crossref","first-page":"2706","DOI":"10.1111\/jbi.13716","article-title":"Exploring rain forest diversification using demographic model testing in the African foam-nest treefrog Chiromantis rufescens","volume":"46","author":"Leach\u00e9","year":"2019","journal-title":"J. Biogeogr."},{"key":"10.1016\/j.isci.2026.117121_bib71","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1111\/evo.13941","article-title":"Comparative phylogeography of West African amphibians and reptiles","volume":"74","author":"Leach\u00e9","year":"2020","journal-title":"Evolution"},{"key":"10.1016\/j.isci.2026.117121_bib72","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1038\/nprot.2014.063","article-title":"Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX","volume":"9","author":"Schubert","year":"2014","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.isci.2026.117121_bib73","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1186\/s13104-016-1900-2","article-title":"AdapterRemoval v2: rapid adapter trimming, identification, and read merging","volume":"9","author":"Schubert","year":"2016","journal-title":"BMC Res. Notes"},{"key":"10.1016\/j.isci.2026.117121_bib74","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013","journal-title":"arXiv"},{"key":"10.1016\/j.isci.2026.117121_bib75","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.isci.2026.117121_bib76","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1186\/s12859-014-0356-4","article-title":"ANGSD: Analysis of Next Generation Sequencing Data","volume":"15","author":"Korneliussen","year":"2014","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.isci.2026.117121_bib77","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.isci.2026.117121_bib78","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.isci.2026.117121_bib79","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: Improving the Ultrafast Bootstrap Approximation","volume":"35","author":"Hoang","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.isci.2026.117121_bib80","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.isci.2026.117121_bib81","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/s12859-018-2129-y","article-title":"ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees","volume":"19","author":"Zhang","year":"2018","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.isci.2026.117121_bib82","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.85492","article-title":"On the limits of fitting complex models of population history to f-statistics","volume":"12","author":"Maier","year":"2023","journal-title":"eLife"},{"key":"10.1016\/j.isci.2026.117121_bib83","doi-asserted-by":"crossref","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":"10.1016\/j.isci.2026.117121_bib84","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","article-title":"APE: Analyses of Phylogenetics and Evolution in R language","volume":"20","author":"Paradis","year":"2004","journal-title":"Bioinformatics"},{"key":"10.1016\/j.isci.2026.117121_bib85","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Paradis","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.isci.2026.117121_bib86","doi-asserted-by":"crossref","first-page":"5321","DOI":"10.1093\/bioinformatics\/btz554","article-title":"MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees","volume":"35","author":"Puttick","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.isci.2026.117121_bib87","doi-asserted-by":"crossref","DOI":"10.1093\/genetics\/iyab008","article-title":"Estimating divergence times from DNA sequences","volume":"217","author":"Sj\u00f6din","year":"2021","journal-title":"Genetics"},{"key":"10.1016\/j.isci.2026.117121_bib88","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.isci.2026.117121_bib89","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.isci.2026.117121_bib90","doi-asserted-by":"crossref","DOI":"10.1093\/genetics\/iyac148","article-title":"Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage","volume":"222","author":"Rasmussen","year":"2022","journal-title":"Genetics"},{"key":"10.1016\/j.isci.2026.117121_bib91","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"GigaScience"},{"key":"10.1016\/j.isci.2026.117121_bib92","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.isci.2026.117121_bib93","first-page":"99","article-title":"Long-term preservation of whale skin for DNA analysis","volume":"13","author":"Amos","year":"1991","journal-title":"Rep. Int. Whal. Comm."},{"key":"10.1016\/j.isci.2026.117121_bib94","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.isci.2026.117121_bib95","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.isci.2026.117121_bib96","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1534\/g3.117.300192","article-title":"Powerful inference with the D-statistic on low-coverage whole-genome data","volume":"8","author":"Soraggi","year":"2018","journal-title":"G3 (Bethesda)"},{"key":"10.1016\/j.isci.2026.117121_bib97","first-page":"329","article-title":"European Suinae (Artiodactyla) from the Late Miocene onwards","volume":"28","author":"van der Made Jan","year":"1989","journal-title":"Boll. Soc. Paleontol. Ital."},{"key":"10.1016\/j.isci.2026.117121_bib98","first-page":"51","article-title":"Deux nouvelles esp\u00e8ces de Suini (Mammalia, Suidae) du continent Africain (\u00c9thiopie; Tchad)","volume":"332","author":"Brunet","year":"2001","journal-title":"C. R. Acad. Sci."},{"key":"10.1016\/j.isci.2026.117121_bib99","doi-asserted-by":"crossref","first-page":"2161","DOI":"10.1093\/molbev\/msr045","article-title":"Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times","volume":"28","author":"dos Reis","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.isci.2026.117121_bib100","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1038\/nature11622","article-title":"Analyses of pig genomes provide insight into porcine demography and evolution","volume":"491","author":"Groenen","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117121_bib101","doi-asserted-by":"crossref","DOI":"10.1126\/science.aav6202","article-title":"Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits","volume":"364","author":"Chen","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.isci.2026.117121_bib102","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/s41586-023-05752-y","article-title":"Evolution of the germline mutation rate across vertebrates","volume":"615","author":"Bergeron","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117121_bib103","doi-asserted-by":"crossref","first-page":"89","DOI":"10.3897\/natureconservation.5.5734","article-title":"Generation length for mammals","volume":"5","author":"Di Marco","year":"2013","journal-title":"Nat. Conserv."},{"key":"10.1016\/j.isci.2026.117121_bib104","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1126\/science.aao6266","article-title":"Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago","volume":"358","author":"Schlebusch","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.isci.2026.117121_bib105","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1101\/gr.154831.113","article-title":"Estimating and interpreting FST: the impact of rare variants","volume":"23","author":"Bhatia","year":"2013","journal-title":"Genome Res."}],"container-title":["iScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004226024995?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004226024995?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T01:29:41Z","timestamp":1791595781000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2589004226024995"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":105,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["S2589004226024995"],"URL":"https:\/\/doi.org\/10.1016\/j.isci.2026.117121","relation":{},"ISSN":["2589-0042"],"issn-type":[{"value":"2589-0042","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"From forests to deserts: Sequencing of the giant forest hog completes the genomic history of the African suids","name":"articletitle","label":"Article Title"},{"value":"iScience","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.isci.2026.117121","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"117121"}}