{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T08:45:39Z","timestamp":1772268339277,"version":"3.50.1"},"reference-count":117,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2022,7,26]],"date-time":"2022-07-26T00:00:00Z","timestamp":1658793600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Posgrado en Ciencias Biol\u00f3gicas"},{"DOI":"10.13039\/501100003141","name":"Consejo Nacional de Ciencia y Tecnolog\u00eda","doi-asserted-by":"crossref","award":["1085698"],"award-info":[{"award-number":["1085698"]}],"id":[{"id":"10.13039\/501100003141","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Direcci\u00f3n General de Ausuntos del Personal Acad\u00e9mico-Universidad Nacional Aut\u00f3noma de M\u00e9xico","award":["IA201616"],"award-info":[{"award-number":["IA201616"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>\n                    The most recent glacial cycles of the Pleistocene affected the distribution, population sizes, and levels of genetic structure of temperate-forest species in the main Mexican mountain systems. Our objective was to investigate the effects these cycles had on the genetic structure and distribution of a dominant species of the \u201cmexical\u201d vegetation across North and Central America. We studied the genetic diversity of\n                    <jats:italic>Juniperus deppeana<\/jats:italic>\n                    , a conifer distributed from the Southwestern United States to the highlands of Central America. We combined information of one plastid marker and two nuclear markers to infer phylogeographic structure, genetic diversity and demographic changes. We also characterized the climatic niche for each variety to infer the plausible area of suitability during past climatic conditions and to evaluate climatic niche discontinuities along with the species distribution. We found a marked phylogeographic structure separating the populations North and South of the Isthmus of Tehuantepec, with populations to the South of this barrier forming a distinct genetic cluster corresponding to\n                    <jats:italic>Juniperus deppeana<\/jats:italic>\n                    var.\n                    <jats:italic>gamboana<\/jats:italic>\n                    . We also found signals of population expansion in the Northern genetic cluster. Ecological niche modeling results confirmed climatic niche differences and discontinuities among\n                    <jats:italic>J. deppeana<\/jats:italic>\n                    varieties and heterogeneous responses to climatic oscillations. Overall,\n                    <jats:italic>J. deppeana<\/jats:italic>\n                    \u2019s genetic diversity has been marked by distribution shifts, population growth and secondary contact the North, and\n                    <jats:italic>in situ<\/jats:italic>\n                    permanence in the South since the last interglacial to the present. High genetic variation suggests a wide and climatically diverse distribution during climatic oscillations. We detected the existence of two main genetic clusters, supporting previous proposals that\n                    <jats:italic>Juniperus deppeana<\/jats:italic>\n                    and\n                    <jats:italic>Juniperus gamboana<\/jats:italic>\n                    may be considered two separate species.\n                  <\/jats:p>","DOI":"10.7717\/peerj.13802","type":"journal-article","created":{"date-parts":[[2022,7,26]],"date-time":"2022-07-26T04:24:39Z","timestamp":1658809479000},"page":"e13802","source":"Crossref","is-referenced-by-count":9,"title":["Incipient speciation, high genetic diversity, and ecological divergence in the alligator bark juniper suggest complex demographic changes during the Pleistocene"],"prefix":"10.7717","volume":"10","author":[{"given":"Rodrigo","family":"Mart\u00ednez de Le\u00f3n","sequence":"first","affiliation":[{"name":"Posgrado en Ciencias Biol\u00f3gicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Ciudad de M\u00e9xico, Mexico"},{"name":"Jard\u00edn Bot\u00e1nico, Instituto de Biolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Ciudad de M\u00e9xico, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2000-4741","authenticated-orcid":true,"given":"Gabriela","family":"Castellanos-Morales","sequence":"additional","affiliation":[{"name":"Departamento de Conservaci\u00f3n de la Biodiversidad, Colegio de la Frontera Sur, Villahermosa, M\u00e9xico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7524-7639","authenticated-orcid":true,"given":"Alejandra","family":"Moreno-Letelier","sequence":"additional","affiliation":[{"name":"Jard\u00edn Bot\u00e1nico, Instituto de Biolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Ciudad de M\u00e9xico, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"4443","published-online":{"date-parts":[[2022,7,26]]},"reference":[{"issue":"3","key":"10.7717\/peerj.13802\/ref-1","doi-asserted-by":"publisher","first-page":"284","DOI":"10.2307\/2805588","article-title":"Reevaluation of the biological status of Juniperus deppeana var. sperryi Correll","volume":"25","author":"Adams","year":"1973","journal-title":"Brittonia"},{"issue":"10","key":"10.7717\/peerj.13802\/ref-2","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1016\/S0305-1978(00)00022-3","article-title":"The serrate leaf margined Juniperus (Section Sabina) of the western hemisphere: systematics and evolution based on leaf essential oils and Random Amplified Polymorphic DNAs (RAPDs)","volume":"28","author":"Adams","year":"2000","journal-title":"Biochemical Systematics and Ecology"},{"key":"10.7717\/peerj.13802\/ref-3","volume-title":"Junipers of the world: the genus Juniperus","author":"Adams","year":"2014","edition":"4"},{"key":"10.7717\/peerj.13802\/ref-4","doi-asserted-by":"publisher","first-page":"227","DOI":"10.5962\/bhl.part.10450","article-title":"Infraspecific adjustments in Juniperus deppeana (Cupressaceae)","volume":"88","author":"Adams","year":"2006","journal-title":"Phytologia"},{"key":"10.7717\/peerj.13802\/ref-5","first-page":"179","article-title":"Phylogeny of Juniperus using nrDNA and four cpDNA regions","volume":"95","author":"Adams","year":"2013","journal-title":"Phytologia"},{"key":"10.7717\/peerj.13802\/ref-6","doi-asserted-by":"publisher","first-page":"870","DOI":"10.3389\/fgene.2020.00870","article-title":"Evaluation of the minimum sampling design for population genomic and microsatellite studies: an analysis based on wild maize","volume":"11","author":"Aguirre-Liguori","year":"2020","journal-title":"Frontiers in Genetics"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-7","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1016\/j.ympev.2011.09.021","article-title":"Phylogeny, diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context","volume":"62","author":"Aguirre-Planter","year":"2012","journal-title":"Molecular Phylogenetics and Evolution"},{"key":"10.7717\/peerj.13802\/ref-8","doi-asserted-by":"publisher","first-page":"863","DOI":"10.3389\/fpls.2020.00863","article-title":"Phylogeography and genetic diversity in a southern North American desert: Agave kerchovei from the Tehuac\u00e1n-Cuicatl\u00e1n valley Mexico","volume":"11","author":"Aguirre-Planter","year":"2020","journal-title":"Frontiers in Plant Science"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-9","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1016\/j.quaint.2015.04.043","article-title":"Past vegetation influence on the hydrological cycle in the Chihuahuan Desert, North Mexico as indicated by data of four pollen sites","volume":"374","author":"Albert","year":"2015","journal-title":"Quaternary International"},{"key":"10.7717\/peerj.13802\/ref-10","doi-asserted-by":"crossref","DOI":"10.2307\/j.ctv1nzfgj7","volume-title":"Phylogeography: the history and formation of species","author":"Avise","year":"2000"},{"issue":"2","key":"10.7717\/peerj.13802\/ref-11","doi-asserted-by":"publisher","first-page":"280","DOI":"10.2307\/2395199","article-title":"Evolution and biogeography of the Madrean-Tethyan sclerophyll vegetation","volume":"62","author":"Axelrod","year":"1975","journal-title":"Annals of the Missouri Botanical Garden"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-12","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1093\/oxfordjournals.molbev.a026036","article-title":"Median-joining networks for inferring intraspecific phylogenies","volume":"46","author":"Bandelt","year":"1999","journal-title":"Molecular Biology and Evolution"},{"issue":"1\u20134","key":"10.7717\/peerj.13802\/ref-13","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/S0040-1951(98)80062-0","article-title":"Neotectonic evolution of the Isthmus of Tehuantepec (southeastern Mexico)","volume":"287","author":"Barrier","year":"1998","journal-title":"Tectonophysics"},{"issue":"18","key":"10.7717\/peerj.13802\/ref-14","doi-asserted-by":"publisher","first-page":"e2021GL093678","DOI":"10.1029\/2021GL093678","article-title":"Wetter summers mitigated tempetature stress on Rocky Mountain forests during the last interglacial warm period","volume":"48","author":"Berkelhammer","year":"2021","journal-title":"Geophysical Research Letters"},{"issue":"1\u20132","key":"10.7717\/peerj.13802\/ref-15","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/S0031-0182(00)00154-1","article-title":"Late Quaternary vegetation history of Rough Canyon, south-central New Mexico, USA","volume":"165","author":"Betancourt","year":"2001","journal-title":"Palaeogeography, Palaeoclimatology, Palaeoecology"},{"issue":"4","key":"10.7717\/peerj.13802\/ref-16","doi-asserted-by":"publisher","first-page":"e1006650","DOI":"10.1371\/journal.pcbi.1006650","article-title":"BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis","volume":"15","author":"Bouckaert","year":"2019","journal-title":"PLOS Computational Biology"},{"issue":"2\u20133","key":"10.7717\/peerj.13802\/ref-17","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/S0304-3800(02)00200-4","article-title":"Evaluating resource selection functions","volume":"157","author":"Boyce","year":"2002","journal-title":"Ecological Modelling"},{"issue":"4","key":"10.7717\/peerj.13802\/ref-18","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1111\/j.1466-8238.2011.00698.x","article-title":"Measuring ecological niche overlap from occurrence and spatial environmental data","volume":"21","author":"Broennimann","year":"2012","journal-title":"Global Ecology and Biogeography"},{"key":"10.7717\/peerj.13802\/ref-19","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1894\/0038-4909","article-title":"Digitized map of biotic communities for plotting and comparing distributions of North American animals","volume":"52","author":"Brown","year":"2007","journal-title":"The Southwestern Naturalist"},{"issue":"4","key":"10.7717\/peerj.13802\/ref-20","doi-asserted-by":"publisher","first-page":"e44158","DOI":"10.21425\/F5FBG44158","article-title":"A tale of two niches: methods, concepts, and evolution","volume":"11","author":"Brown","year":"2019","journal-title":"Frontiers of Biogeography"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-21","doi-asserted-by":"publisher","first-page":"180254","DOI":"10.1038\/sdata.2018.254","article-title":"PaleoClim, high spatial resolution paleoclimate surfaces for global land areas","volume":"5","author":"Brown","year":"2018","journal-title":"Scientific Data"},{"issue":"12","key":"10.7717\/peerj.13802\/ref-22","doi-asserted-by":"publisher","first-page":"2299","DOI":"10.1111\/j.1365-2699.2011.02565.x","article-title":"Ephemeral Pleistocene woodlands connect the dots for highland rattlesnakes of the Crotalus intermedius group","volume":"38","author":"Bryson","year":"2011","journal-title":"Journal of Biogeography"},{"key":"10.7717\/peerj.13802\/ref-23","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1016\/j.ympev.2015.08.027","article-title":"Peripatric speciation of an endemic species driven by Pleistocene climate change: the case of the Mexican prairie dog (Cynomys mexicanus)","volume":"94","author":"Castellanos-Morales","year":"2016","journal-title":"Molecular Phylogenetics and Evolution"},{"issue":"8","key":"10.7717\/peerj.13802\/ref-24","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1038\/nmeth.2109","article-title":"jModelTest 2: more models, new heuristics and parallel computing","volume":"9","author":"Darriba","year":"2012","journal-title":"Nature Methods"},{"issue":"6","key":"10.7717\/peerj.13802\/ref-25","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1111\/ecog.02671","article-title":"Ecospat: an R package to support spatial analyses and modeling of species niches and distributions","volume":"40","author":"Di Cola","year":"2017","journal-title":"Ecography"},{"key":"10.7717\/peerj.13802\/ref-26","first-page":"11","article-title":"A rapid DNA isolation procedure from small quantities of fresh leaf tissues","volume":"19","author":"Doyle","year":"1987","journal-title":"Phytochemical Bulletin"},{"key":"10.7717\/peerj.13802\/ref-27","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1007\/s12686-011-9548-7","article-title":"STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method","volume":"4","author":"Earl","year":"2012","journal-title":"Conservation Genetics Resources"},{"key":"10.7717\/peerj.13802\/ref-28","volume-title":"Conifers of the world. The complete reference","author":"Eckenwalder","year":"2009"},{"issue":"5","key":"10.7717\/peerj.13802\/ref-29","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Research"},{"issue":"8","key":"10.7717\/peerj.13802\/ref-30","doi-asserted-by":"publisher","first-page":"2611","DOI":"10.1111\/j.1365-294X.2005.02553.x","article-title":"Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study","volume":"14","author":"Evanno","year":"2005","journal-title":"Molecular Ecology"},{"key":"10.7717\/peerj.13802\/ref-31","volume-title":"A monograph of cupressaceae and sciadopitys","author":"Farjon","year":"2005"},{"key":"10.7717\/peerj.13802\/ref-32","doi-asserted-by":"crossref","DOI":"10.1163\/9789004211810","volume-title":"An atlas of the world\u2019s conifers: an analysis of their distribution, biogeography, diversity and conservation status","author":"Farjon","year":"2013"},{"issue":"19","key":"10.7717\/peerj.13802\/ref-33","doi-asserted-by":"publisher","first-page":"4973","DOI":"10.1175\/2011JCLI4083.1","article-title":"The community climate system model version 4","volume":"24","author":"Gent","year":"2011","journal-title":"Journal of Climate"},{"key":"10.7717\/peerj.13802\/ref-34","doi-asserted-by":"publisher","first-page":"126","DOI":"10.7550\/rmb.32195","article-title":"Biodiversidad de Pinophyta (con\u00edferas) en M\u00e9xico","volume":"85","author":"Gernandt","year":"2014","journal-title":"Revista Mexicana de Biodiversidad"},{"issue":"4","key":"10.7717\/peerj.13802\/ref-35","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1111\/j.1469-8137.2010.03559.x","article-title":"Southward Pleistocene migration of Douglas-fir into Mexico: phylogeography, ecological niche modeling, and conservation of \u201crear edge\u201d populations","volume":"189","author":"Gugger","year":"2011","journal-title":"New Phytologist"},{"issue":"17\u201318","key":"10.7717\/peerj.13802\/ref-36","doi-asserted-by":"publisher","first-page":"2052","DOI":"10.1016\/j.quascirev.2010.04.022","article-title":"Glacial populations and postglacial migration of Douglas-fir based on fossil pollen and macrofossil evidence","volume":"29","author":"Gugger","year":"2010","journal-title":"Quaternary Science Reviews"},{"issue":"6","key":"10.7717\/peerj.13802\/ref-37","doi-asserted-by":"publisher","first-page":"1872","DOI":"10.1111\/nph.16647","article-title":"Niche conservatism promotes speciation in cycads: the case of Dioon merolae (Zamiaceae) in Mexico","volume":"227","author":"Guti\u00e9rrez-Ortega","year":"2020","journal-title":"New Phytologist"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-38","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1111\/jzs.12142","article-title":"A temporally dynamic approach for cladistic biogeography and the processes underlying the biogeographic patterns of North American deserts","volume":"55","author":"G\u00e1mez","year":"2017","journal-title":"Journal of Zoological Systematics and Evolutionary Research"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-39","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1186\/1471-2148-8-289","article-title":"Bayesian inference of population size history from multiple loci","volume":"8","author":"Heled","year":"2008","journal-title":"BMC Evolutionary Biology"},{"issue":"3","key":"10.7717\/peerj.13802\/ref-40","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1093\/molbev\/msp274","article-title":"Bayesian inference of species trees from multilocus data","volume":"27","author":"Heled","year":"2010","journal-title":"Molecular Biology and Evolution"},{"issue":"6789","key":"10.7717\/peerj.13802\/ref-41","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/35016000","article-title":"The genetic legacy of the Quaternary ice ages","volume":"405","author":"Hewitt","year":"2000","journal-title":"Nature"},{"key":"10.7717\/peerj.13802\/ref-42","doi-asserted-by":"publisher","first-page":"1965","DOI":"10.1002\/(ISSN)1097-0088","article-title":"Very high resolution interpolated climate surfaces for global land areas","volume":"25","author":"Hijmans","year":"2005","journal-title":"International Journal of Climatology"},{"issue":"3\u20134","key":"10.7717\/peerj.13802\/ref-43","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1016\/j.palaeo.2006.02.017","article-title":"A 36,000-yr vegetation history from the Peloncillo Mountains, southeastern Arizona, USA","volume":"240","author":"Holmgren","year":"2006","journal-title":"Palaeogeography, Palaeoclimatology, Palaeoecology"},{"key":"10.7717\/peerj.13802\/ref-44","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1002\/(ISSN)1099-1417","article-title":"Inferences about winter temperatures and summer rains from the late Quaternary record of C4 perennial grasses and C3 desert shrubs in the northern Chihuahuan Desert","volume":"22","author":"Holmgren","year":"2007","journal-title":"Journal of Quaternary Science"},{"issue":"5","key":"10.7717\/peerj.13802\/ref-45","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1111\/j.1755-0998.2009.02591.x","article-title":"Inferring weak population structure with the assistance of sample group information","volume":"9","author":"Hubisz","year":"2009","journal-title":"Molecular Ecology Resources"},{"issue":"11","key":"10.7717\/peerj.13802\/ref-46","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.1093\/bioinformatics\/btn129","article-title":"adegenet: a R package for the multivariate analysis of genetic markers","volume":"24","author":"Jombart","year":"2008","journal-title":"Bioinformatics"},{"issue":"4","key":"10.7717\/peerj.13802\/ref-47","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1111\/2041-210X.12945","article-title":"Wallace: a flexible platform for reproducible modeling of species niches and distributions built for community expansion","volume":"9","author":"Kass","year":"2018","journal-title":"Methods in Ecology and Evolution"},{"key":"10.7717\/peerj.13802\/ref-48","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1111\/2041-210X.12410","article-title":"PopART: full-feature software for haplotype network construction","volume":"6","author":"Leigh","year":"2015","journal-title":"Methods in Ecology and Evolution"},{"key":"10.7717\/peerj.13802\/ref-49","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1111\/j.1365-2699.2010.02400.x","article-title":"The Pleistocene demography of an alpine juniper of the Qinghai-Tibetan Plateau: tabula rasa, cryptic refugia or something else?","volume":"38","author":"Li","year":"2011","journal-title":"Journal of Biogeography"},{"issue":"12","key":"10.7717\/peerj.13802\/ref-50","doi-asserted-by":"publisher","first-page":"2706","DOI":"10.1111\/jbi.13064","article-title":"Pleistocene refugia in the Chihuahuan Desert: the phylogeographic and demographic history of the gymnosperm Ephedra compacta","volume":"44","author":"Loera","year":"2017","journal-title":"Journal of Biogeography"},{"key":"10.7717\/peerj.13802\/ref-51","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1006\/qres.2002.2361","article-title":"Mid-to late-Wisconsin pollen record of San Felipe basin, Baja California","volume":"58","author":"Lozano-Garca","year":"2002","journal-title":"Quaternary Research"},{"key":"10.7717\/peerj.13802\/ref-52","doi-asserted-by":"publisher","first-page":"113","DOI":"10.17129\/botsci.1492","article-title":"Late Quarterly vegetation from central Mexico: palynological records and their paleoclimatic implications","volume":"58","author":"Lozano-Garc\u00eda","year":"1996","journal-title":"Botanical Sciences"},{"issue":"2","key":"10.7717\/peerj.13802\/ref-53","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1016\/j.yqres.2015.07.002","article-title":"Climatic variability in the northern sector of the American tropics since the latest MIS 3","volume":"84","author":"Lozano-Garc\u00eda","year":"2015","journal-title":"Quaternary Research"},{"issue":"3","key":"10.7717\/peerj.13802\/ref-54","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1016\/j.palaeo.2012.12.006","article-title":"Ecosystem responses to climate and disturbances in western central Mexico during the late Pleistocene and Holocene","volume":"370","author":"Lozano-Garc\u00eda","year":"2013","journal-title":"Paleogeography, Paleaoclimatology, Paleoecology"},{"issue":"2","key":"10.7717\/peerj.13802\/ref-55","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1111\/mec.12614","article-title":"Postglacial northward expansion and genetic differentiation between migratory and sedentary populations of the broad-tailed hummingbird (Selasphorus platycercus)","volume":"23","author":"Malpica","year":"2014","journal-title":"Molecular Ecology"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-56","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1111\/j.1469-8137.2010.03351.x","article-title":"Diversification and biogeography of Juniperus (Cupressaceae): variable diversification rates and multiple intercontinental dispersals","volume":"188","author":"Mao","year":"2010","journal-title":"New Phytologist"},{"issue":"3","key":"10.7717\/peerj.13802\/ref-57","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/j.gecco.2014.12.008","article-title":"Biodiversity hotspots: a shortcut for a more complicated concept","volume":"3","author":"Marchese","year":"2015","journal-title":"Global Ecology and Conservation"},{"key":"10.7717\/peerj.13802\/ref-58","volume-title":"Las pin\u00e1ceas mexicanas","author":"Mart\u00ednez","year":"1963","edition":"3"},{"key":"10.7717\/peerj.13802\/ref-59","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1111\/jbi.12546","article-title":"Biodiversity in the Mexican highlands and the interaction of geology, geography and climate within the Trans-Mexican Volcanic Belt","volume":"42","author":"Mastretta-Yanes","year":"2015","journal-title":"Journal of Biogeography"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-60","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1007\/s10592-011-0277-y","article-title":"Distinctiveness, rarity and conservation in a subtropical highland conifer","volume":"13","author":"Mastretta-Yanes","year":"2012","journal-title":"Conservation Genetics"},{"issue":"2","key":"10.7717\/peerj.13802\/ref-61","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1111\/mec.14461","article-title":"Long-term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics","volume":"27","author":"Mastretta-Yanes","year":"2018","journal-title":"Molecular Ecology"},{"key":"10.7717\/peerj.13802\/ref-62","doi-asserted-by":"publisher","first-page":"258","DOI":"10.3417\/0026-6493","article-title":"Late quaternary environments of the northern deserts and central transvolcanic belt of Mexico 1","volume":"93","author":"Metcalfe","year":"2006","journal-title":"Annals of the Missouri Botanical Garden"},{"key":"10.7717\/peerj.13802\/ref-63","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1006\/qres.2001.2292","article-title":"Wet conditions during the last glaciation in the Chihuahuan Desert, Alta Babicora Basin Mexico","volume":"57","author":"Metcalfe","year":"2002","journal-title":"Quaternary Research"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-64","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1111\/nph.12761","article-title":"Late Miocene lineage divergence and ecological differentiation of rare endemic Juniperus blancoi: clues for the diversification of North American conifers","volume":"203","author":"Moreno-Letelier","year":"2014","journal-title":"New Phytologist"},{"issue":"10","key":"10.7717\/peerj.13802\/ref-65","doi-asserted-by":"publisher","first-page":"e78228","DOI":"10.1371\/journal.pone.0078228","article-title":"Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently Diverged Pine Species","volume":"8","author":"Moreno-Letelier","year":"2013","journal-title":"PLOS ONE"},{"key":"10.7717\/peerj.13802\/ref-66","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/978-3-642-20992-5_5","article-title":"Vascular plant diversity in a changing world: global centres and biome-specific patterns","volume-title":"Biodiversity Hotspots: Distribution and Protection of Conservation Priority Areas","author":"Mutke","year":"2011"},{"key":"10.7717\/peerj.13802\/ref-67","doi-asserted-by":"crossref","DOI":"10.7312\/nei-92038","volume-title":"Molecular evolutionary genetics","author":"Nei","year":"1987"},{"key":"10.7717\/peerj.13802\/ref-68","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1093\/bioinformatics\/bts091","article-title":"Unipro UGENE: a unified bioinformatics toolkit","volume":"28","author":"Okonechnikov","year":"2012","journal-title":"Bioinformatics"},{"issue":"12","key":"10.7717\/peerj.13802\/ref-69","doi-asserted-by":"publisher","first-page":"2384","DOI":"10.1111\/j.1365-2699.2010.02372.x","article-title":"Phylogeography of Podocarpus matudae (Podocarpaceae): pre-Quaternary relics in northern Mesoamerican cloud forests","volume":"37","author":"Ornelas","year":"2010","journal-title":"Journal of Biogeography"},{"key":"10.7717\/peerj.13802\/ref-70","doi-asserted-by":"publisher","first-page":"25","DOI":"10.17129\/botsci.1786","article-title":"Fragmentation and demographic expansion in the Mexican populations of Pinus ayacahuite var. ayacahuite","volume":"83","author":"Ort\u00edz-Medrano","year":"2008","journal-title":"Botanical Sciences"},{"key":"10.7717\/peerj.13802\/ref-71","doi-asserted-by":"publisher","first-page":"2886","DOI":"10.1002\/ece3.1994","article-title":"Morphological and niche divergence of pinyon pines","volume":"6","author":"Ort\u00edz-Medrano","year":"2016","journal-title":"Ecology and Evolution"},{"issue":"5768","key":"10.7717\/peerj.13802\/ref-72","doi-asserted-by":"publisher","first-page":"1751","DOI":"10.1126\/science.1120808","article-title":"Simulating Arctic climate warmth and icefield retreat in the last interglaciation","volume":"311","author":"Otto-Bliesner","year":"2006","journal-title":"Science"},{"key":"10.7717\/peerj.13802\/ref-73","article-title":"Geodist: fast, dependency-free geodesic distance calculations. (R package version 0.0.4.)","author":"Padgham","year":"2020"},{"issue":"2","key":"10.7717\/peerj.13802\/ref-74","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1111\/jbi.13731","article-title":"Why mountains matter for biodiversity","volume":"47","author":"Perrigo","year":"2020","journal-title":"Journal of Biogeography"},{"issue":"5431","key":"10.7717\/peerj.13802\/ref-75","doi-asserted-by":"publisher","first-page":"1265","DOI":"10.1126\/science.285.5431.1265","article-title":"Conservatism of ecological niches in evolutionary time","volume":"285","author":"Peterson","year":"1999","journal-title":"Science"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-76","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1146\/annurev.ecolsys.37.091305.110215","article-title":"Some evolutionary consequences of being a tree","volume":"37","author":"Petit","year":"2006","journal-title":"Annual Review of Ecology Evolution and Systematics"},{"issue":"10","key":"10.7717\/peerj.13802\/ref-77","doi-asserted-by":"publisher","first-page":"4204","DOI":"10.1002\/ece3.6189","article-title":"High genetic diversity and stable Pleistocene distributional ranges in the widespread Mexican red oak Quercus castanea N\u00e9e, 1801 (Fagaceae)","volume":"10","author":"Pe\u00f1aloza-Ram\u00edrez","year":"2020","journal-title":"Ecology and Evolution"},{"issue":"7","key":"10.7717\/peerj.13802\/ref-78","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1111\/ecog.03049","article-title":"Opening the black box: an open-source release of Maxent","volume":"40","author":"Phillips","year":"2017","journal-title":"Ecography"},{"issue":"2","key":"10.7717\/peerj.13802\/ref-79","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","article-title":"Inference of population structure using multilocus genotype data","volume":"155","author":"Pritchard","year":"2000","journal-title":"Genetics"},{"key":"10.7717\/peerj.13802\/ref-80","volume-title":"R: a language and environment for statistical computing","author":"R Core Team","year":"2013"},{"issue":"6458","key":"10.7717\/peerj.13802\/ref-81","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1126\/science.aax0151","article-title":"Building mountain biodiversity: geological and evolutionary processes","volume":"365","author":"Rahbek","year":"2019","journal-title":"Science"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-82","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1186\/2193-1801-3-431","article-title":"STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user-friendly interface","volume":"3","author":"Ramasamy","year":"2014","journal-title":"SpringerPlus"},{"issue":"5","key":"10.7717\/peerj.13802\/ref-83","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in Bayesian phylogenetics using Tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Systematic Biology"},{"key":"10.7717\/peerj.13802\/ref-84","doi-asserted-by":"publisher","first-page":"3299","DOI":"10.1093\/molbev\/msx248","article-title":"DnaSP v6: DNA sequence polymorphism analysis of large datasets","volume":"34","author":"Rozas","year":"2017","journal-title":"Molecular Biology and Evolution"},{"key":"10.7717\/peerj.13802\/ref-85","first-page":"375","article-title":"M\u00e9xico como \u00e1rea de origen y diversificaci\u00f3n de linajes vegetales","volume-title":"Regionalizaci\u00f3n Biogeogr\u00e1fica En Iberoam\u00e9rica Y Tr\u00f3picos Afines","author":"Rzedowski","year":"2005"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-86","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1146\/annurev.ecolsys.38.091206.095646","article-title":"Gene flow and local adaptation in trees","volume":"38","author":"Savolainen","year":"2007","journal-title":"Annual Review of Ecology, Evolution, and Systematics"},{"key":"10.7717\/peerj.13802\/ref-87","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1111\/jbi.12851","article-title":"Neogene and Pleistocene history of Agave lechuguilla in the Chihuahuan Desert","volume":"44","author":"Scheinvar","year":"2017","journal-title":"Journal of Biogeography"},{"key":"10.7717\/peerj.13802\/ref-88","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/978-3-030-44963-6_2","article-title":"Phylogeography of the Chihuahuan Desert: diversification and evolution over the pleistocene","volume-title":"Plant Diversity and Ecology in the Chihuahuan Desert","author":"Scheinvar","year":"2020"},{"key":"10.7717\/peerj.13802\/ref-89","doi-asserted-by":"publisher","first-page":"704","DOI":"10.2307\/1935534","article-title":"Anolis lizards of Bimini: resource partitioning in a complex fauna","volume":"49","author":"Schoener","year":"1968","journal-title":"Ecology"},{"key":"10.7717\/peerj.13802\/ref-90","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1086\/319501","article-title":"A new statistical method for haplotype reconstruction from population data","volume":"68","author":"Stephens","year":"2001","journal-title":"American Journal of Human Genetics"},{"issue":"1912","key":"10.7717\/peerj.13802\/ref-91","doi-asserted-by":"publisher","first-page":"20191887","DOI":"10.1098\/rspb.2019.1887","article-title":"Accumulation over evolutionary time as a major cause of biodiversity hotspots in conifers","volume":"286","author":"Sundaram","year":"2019","journal-title":"Proceedings of the Royal Society B: Biological Sciences"},{"issue":"9","key":"10.7717\/peerj.13802\/ref-92","doi-asserted-by":"publisher","first-page":"1296","DOI":"10.1002\/ajb2.1536","article-title":"High phylogeographic and genetic diversity of Tidestromia lanuginosa supports full-glacial refugia for arid-adapted plants in southern and central Coahuila, Mexico","volume":"107","author":"S\u00e1nchez-del Pino","year":"2020","journal-title":"American Journal of Botany"},{"key":"10.7717\/peerj.13802\/ref-93","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1007\/BF00037152","article-title":"Universal primers for amplification of three non-coding regions of chloroplast DNA","volume":"17","author":"Taberlet","year":"1991","journal-title":"Plant Molecular Biology"},{"key":"10.7717\/peerj.13802\/ref-94","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1093\/genetics\/105.2.437","article-title":"Evolutionary relationship of DNA sequences in finite populations","volume":"105","author":"Tajima","year":"1983","journal-title":"Genetics"},{"key":"10.7717\/peerj.13802\/ref-95","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1093\/genetics\/123.3.585","article-title":"Statistical method for testing the neutral mutation hypothesis by DNA polymorphism","volume":"123","author":"Tajima","year":"1989","journal-title":"Genetics"},{"key":"10.7717\/peerj.13802\/ref-96","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1046\/j.1365-2699.2000.00427.x","article-title":"Biomes of western North America at 18,000, 6000 and 0 14Cyr BP reconstructed from pollen and packrat midden data","volume":"27","author":"Thompson","year":"2000","journal-title":"Journal of Biogeography"},{"issue":"6\u20137","key":"10.7717\/peerj.13802\/ref-97","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1007\/s001220050476","article-title":"Sequence-tagged-sites (STSs) of cDNA clones in Cryptomeria japonica and their evaluation as molecular markers in conifers","volume":"94","author":"Tsumura","year":"1997","journal-title":"Theoretical and Applied Genetics"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-98","doi-asserted-by":"publisher","first-page":"107022","DOI":"10.1016\/j.ympev.2020.107022","article-title":"Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny","volume":"156","author":"Uckele","year":"2021","journal-title":"Molecular Phylogenetics and Evolution"},{"key":"10.7717\/peerj.13802\/ref-99","doi-asserted-by":"publisher","first-page":"33","DOI":"10.17129\/botsci.1692","article-title":"Diversidad del g\u00e9nero Quercus (Fagaceae) en M\u00e9xico","volume":"75","author":"Valencia","year":"2004","journal-title":"Botanical Sciences"},{"issue":"10","key":"10.7717\/peerj.13802\/ref-100","doi-asserted-by":"publisher","first-page":"1398","DOI":"10.2307\/2446398","article-title":"The chaparral vegetation in Mexico under non mediterranean climate: the convergence and Madrean-Tethyan hypotheses reconsidered","volume":"85","author":"Valiente-Banuet","year":"1998","journal-title":"American Journal of Botany"},{"key":"10.7717\/peerj.13802\/ref-101","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511802256","volume-title":"Asymptotic statistics","author":"Van der Vaart","year":"1998"},{"key":"10.7717\/peerj.13802\/ref-102","first-page":"104","article-title":"Late quaternary vegetation and climate of the Chihuahuan desert","volume-title":"Packrat Middens: The Last 40 000 Years of Biotic Change","author":"Van Devender","year":"1990"},{"issue":"4394","key":"10.7717\/peerj.13802\/ref-103","doi-asserted-by":"publisher","first-page":"701","DOI":"10.1126\/science.204.4394.701","article-title":"Development of vegetation and climate in the southwestern United States","volume":"204","author":"Van Devender","year":"1979","journal-title":"Science"},{"issue":"118","key":"10.7717\/peerj.13802\/ref-104","doi-asserted-by":"publisher","first-page":"65","DOI":"10.21829\/abm118.2017.1201","article-title":"El elemento end\u00e9mico de la flora vascular del Desierto Chihuahuense","volume":"118","author":"Villareal-Quintanilla","year":"2017","journal-title":"Acta Bot\u00e1nica Mexicana"},{"issue":"2","key":"10.7717\/peerj.13802\/ref-105","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1111\/jbi.13745","article-title":"Assembly and origin of the flora of the Chihuahuan Desert: the case of sclerophyllous Rosaceae","volume":"47","author":"V\u00e1squez-Cruz","year":"2020","journal-title":"Journal of Biogeography"},{"issue":"10","key":"10.7717\/peerj.13802\/ref-106","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1016\/j.tree.2014.08.003","article-title":"Mistaking geography for biology: inferring processes from species distributions","volume":"29","author":"Warren","year":"2014","journal-title":"Trends in Ecology & Evolution"},{"issue":"11","key":"10.7717\/peerj.13802\/ref-107","doi-asserted-by":"publisher","first-page":"2868","DOI":"10.1111\/j.1558-5646.2008.00482.x","article-title":"Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution","volume":"62","author":"Warren","year":"2008","journal-title":"Evolution"},{"key":"10.7717\/peerj.13802\/ref-108","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1111\/j.1600-0587.2009.06142.x","article-title":"ENMTools: a toolbox for comparative studies of environmental niche models","volume":"33","author":"Warren","year":"2010","journal-title":"Ecography"},{"issue":"4","key":"10.7717\/peerj.13802\/ref-109","doi-asserted-by":"publisher","first-page":"845","DOI":"10.5194\/gmd-4-845-2011","article-title":"MIROC-ESM 2010: model description and basic results of CMIP5-20c3m experiments","volume":"4","author":"Watanabe","year":"2011","journal-title":"Geoscientific Model Development"},{"key":"10.7717\/peerj.13802\/ref-110","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1016\/0040-5809(75)90020-9","article-title":"On the number of segregating sites in genetical models without recombination","volume":"276","author":"Watterson","year":"1975","journal-title":"Theoretical Population Biology"},{"key":"10.7717\/peerj.13802\/ref-111","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1007\/978-3-642-20992-5_16","article-title":"Forests of east Australia: The 35th biodiversity hotspot","volume-title":"Biodiversity Hotspots: Distribution and Protection of Conservation Priority Areas","author":"Williams","year":"2011"},{"key":"10.7717\/peerj.13802\/ref-112","doi-asserted-by":"publisher","first-page":"299","DOI":"10.3732\/ajb.95.3.299","article-title":"Hydraulic traits are influenced by phylogenetic history in the drought-resistant, invasive genus Juniperus (Cupressaceae)","volume":"95","author":"Willson","year":"2008","journal-title":"American Journal of Botany"},{"issue":"1","key":"10.7717\/peerj.13802\/ref-113","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1093\/molbev\/msl131","article-title":"Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus","volume":"24","author":"Willyard","year":"2007","journal-title":"Molecular Biology and Evolution"},{"issue":"2","key":"10.7717\/peerj.13802\/ref-114","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1093\/BIOLINNEAN\/BLAA043","article-title":"Phylogeography of the widespread white-eared hummingbird (Hylocharis leucotis): pre-glacial expansion and genetic differentiation of populations separated by the Isthmus of Tehuantepec","volume":"130","author":"Zamudio-Beltr\u00e1n","year":"2020","journal-title":"Biological Journal of the Linnean Society"},{"key":"10.7717\/peerj.13802\/ref-115","doi-asserted-by":"publisher","first-page":"69","DOI":"10.17129\/botsci.1154","article-title":"The Genus Juniperus (Cupressaceae) in Mexico and Guatemala: numerical and morphological analysis","volume":"35","author":"Zanoni","year":"1975","journal-title":"Botanical Sciences"},{"key":"10.7717\/peerj.13802\/ref-116","doi-asserted-by":"publisher","first-page":"83","DOI":"10.17129\/botsci.1171","article-title":"The genus Juniperus (Cupressaceae) in Mexico and Guatemala: synonymy, key and distributions of the taxa","volume":"38","author":"Zanoni","year":"1979","journal-title":"Botanical Sciences"},{"key":"10.7717\/peerj.13802\/ref-117","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-3-030-44963-6_1","article-title":"Diversity and uniqueness at its best: vegetation of the Chihuahuan Desert","volume-title":"Plant Diversity and Ecology in the Chihuahuan Desert","author":"Zavala-Hurtado","year":"2020"}],"container-title":["PeerJ"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/peerj.com\/articles\/13802.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/13802.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/13802.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/13802.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,26]],"date-time":"2022-07-26T04:25:10Z","timestamp":1658809510000},"score":1,"resource":{"primary":{"URL":"https:\/\/peerj.com\/articles\/13802"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,7,26]]},"references-count":117,"alternative-id":["10.7717\/peerj.13802"],"URL":"https:\/\/doi.org\/10.7717\/peerj.13802","archive":["CLOCKSS","LOCKSS","Portico"],"relation":{"has-review":[{"id-type":"doi","id":"10.7287\/peerj.13802v0.1\/reviews\/1","asserted-by":"object"},{"id-type":"doi","id":"10.7287\/peerj.13802v0.1\/reviews\/2","asserted-by":"object"},{"id-type":"doi","id":"10.7287\/peerj.13802v0.1\/reviews\/3","asserted-by":"object"},{"id-type":"doi","id":"10.7287\/peerj.13802v0.2\/reviews\/3","asserted-by":"object"},{"id-type":"doi","id":"10.7287\/peerj.13802v0.2\/reviews\/1","asserted-by":"object"},{"id-type":"doi","id":"10.7287\/peerj.13802v0.2\/reviews\/2","asserted-by":"object"}]},"ISSN":["2167-8359"],"issn-type":[{"value":"2167-8359","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,7,26]]},"article-number":"e13802"}}