{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T16:33:41Z","timestamp":1786120421762,"version":"build-2736575974"},"reference-count":78,"publisher":"Elsevier BV","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":[[2026,5,26]],"date-time":"2026-05-26T00:00:00Z","timestamp":1779753600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100017014","name":"University of Delaware Delaware Biotechnology Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100017014","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002805","name":"Carl Trygger Foundation for Scientific Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002805","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100016022","name":"Data Center of Management Science National Natural Science Foundation of China Peking University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100016022","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"USDA","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007516","name":"National Park Service","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007516","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000202","name":"US Fish & Wildlife Service","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000202","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Molecular Phylogenetics and Evolution"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.ympev.2026.108642","type":"journal-article","created":{"date-parts":[[2026,5,10]],"date-time":"2026-05-10T22:19:56Z","timestamp":1778451596000},"page":"108642","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["Phylogenomic analyses reveal introgression and cryptic speciation in the globally distributed, vector-transmitted pathogen Plasmodium relictum"],"prefix":"10.1016","volume":"222","author":[{"given":"Esther","family":"Weyer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela N.","family":"Theodosopoulos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vaidas","family":"Palinauskas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Staffan","family":"Bensch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helena","family":"Westerdahl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00e9lanie","family":"Duc","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arif","family":"Ciloglu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyeong Soon","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshio","family":"Tsuda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carter T.","family":"Atkinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavel","family":"Zehtindjiev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert C.","family":"Fleischer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nichelle M.","family":"VanTassel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott A.","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olof","family":"Hellgren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7193-9408","authenticated-orcid":false,"given":"Vincenzo A.","family":"Ellis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"16","key":"10.1016\/j.ympev.2026.108642_b0005","doi-asserted-by":"crossref","first-page":"3357","DOI":"10.1111\/mec.14805","article-title":"Co\u2010occurrence among three divergent plant\u2010castrating fungi in the same Silene host species","volume":"27","author":"Abbate","year":"2018","journal-title":"Mol. Ecol."},{"issue":"4","key":"10.1016\/j.ympev.2026.108642_b0010","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msad041","article-title":"Beginner\u2019s Guide on the use of PAML to detect positive selection","volume":"40","author":"\u00c1lvarez-Carretero","year":"2023","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ympev.2026.108642_b0015","article-title":"FastQC (Version 0.11.9) [Computer software]","author":"Andrews","year":"2020","journal-title":"Babraham Bioinform."},{"key":"10.1016\/j.ympev.2026.108642_b0020","unstructured":"Arbor Biosciences. (2020). MyBaits Hybridization Capture for Targeted NGS User Manual (5.00). Daicel Arbor Biosciences. https:\/\/arborbiosci.com\/wp-content\/uploads\/2020\/08\/myBaits_v5.0_Manual.pdf."},{"issue":"Database","key":"10.1016\/j.ympev.2026.108642_b0025","doi-asserted-by":"crossref","first-page":"D539","DOI":"10.1093\/nar\/gkn814","article-title":"PlasmoDB: a functional genomic database for malaria parasites","volume":"37","author":"Aurrecoechea","year":"2009","journal-title":"Nucleic Acids Res."},{"issue":"1604","key":"10.1016\/j.ympev.2026.108642_b0030","first-page":"2935","article-title":"Global phylogeographic limits of Hawaii\u2019s avian malaria","volume":"273","author":"Beadell","year":"2006","journal-title":"Proc. Biol. Sci."},{"issue":"8","key":"10.1016\/j.ympev.2026.108642_b0035","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.pt.2013.03.011","article-title":"How can we determine the molecular clock of malaria parasites?","volume":"29","author":"Bensch","year":"2013","journal-title":"Trends Parasitol."},{"issue":"5","key":"10.1016\/j.ympev.2026.108642_b0040","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1111\/j.1755-0998.2009.02692.x","article-title":"MalAvi: a public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochrome b lineages","volume":"9","author":"Bensch","year":"2009","journal-title":"Mol. Ecol. Resour."},{"issue":"4","key":"10.1016\/j.ympev.2026.108642_b0045","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1101\/gr.218123.116","article-title":"Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals","volume":"28","author":"B\u00f6hme","year":"2018","journal-title":"Genome Res."},{"issue":"Pt A","key":"10.1016\/j.ympev.2026.108642_b0050","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.ympev.2015.09.003","article-title":"Phylogeny of haemosporidian blood parasites revealed by a multi-gene approach","volume":"94","author":"Borner","year":"2016","journal-title":"Mol. Phylogenet. Evol."},{"issue":"1","key":"10.1016\/j.ympev.2026.108642_b0055","doi-asserted-by":"crossref","DOI":"10.1186\/s12864-015-1634-x","article-title":"Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi","volume":"16","author":"Carpi","year":"2015","journal-title":"BMC Genomics"},{"issue":"5","key":"10.1016\/j.ympev.2026.108642_b0060","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1093\/sysbio\/syac012","article-title":"The implications of incongruence between gene tree and species tree topologies for divergence time estimation","volume":"71","author":"Carruthers","year":"2022","journal-title":"Syst. Biol."},{"issue":"2","key":"10.1016\/j.ympev.2026.108642_b0065","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"},{"issue":"6","key":"10.1016\/j.ympev.2026.108642_b0070","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1080\/10635150701701083","article-title":"Species concepts and species delimitation","volume":"56","author":"De Queiroz","year":"2007","journal-title":"Syst. Biol."},{"key":"10.1016\/j.ympev.2026.108642_b0075","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msaf049","article-title":"Misspecification strikes: ASTRAL can mislead in the presence of hybridization, even for non-anomalous scenarios","author":"Dinh","year":"2025","journal-title":"Mol. Biol. Evol."},{"issue":"5","key":"10.1016\/j.ympev.2026.108642_b0080","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004888","article-title":"Admixture in humans of two divergent plasmodium knowlesi populations associated with different macaque host species","volume":"11","author":"Divis","year":"2015","journal-title":"PLoS Pathog."},{"issue":"3","key":"10.1016\/j.ympev.2026.108642_b0085","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1016\/j.ympev.2008.09.008","article-title":"Does gene flow destroy phylogenetic signal? the performance of three methods for estimating species phylogenies in the presence of gene flow","volume":"49","author":"Eckert","year":"2008","journal-title":"Mol. Phylogenet. Evol."},{"issue":"12","key":"10.1016\/j.ympev.2026.108642_b0090","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1016\/j.ijpara.2018.05.005","article-title":"Host specificity of avian haemosporidian parasites is unrelated among sister lineages but shows phylogenetic signal across larger clades","volume":"48","author":"Ellis","year":"2018","journal-title":"Int. J. Parasitol."},{"issue":"3","key":"10.1016\/j.ympev.2026.108642_b0095","doi-asserted-by":"crossref","DOI":"10.1098\/rsbl.2022.0459","article-title":"Host shift and natural long-distance dispersal to an oceanic island of a host-specific parasite","volume":"19","author":"Ellis","year":"2023","journal-title":"Biol. Lett."},{"key":"10.1016\/j.ympev.2026.108642_b0100","article-title":"A generalist vector-transmitted parasite exhibits population genetic structure among host genera","volume":"1\u201310","author":"Ellis","year":"2025","journal-title":"Parasitology"},{"issue":"1","key":"10.1016\/j.ympev.2026.108642_b0105","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1186\/s13071-022-05373-w","article-title":"Genomic sequence capture of Plasmodium relictum in experimentally infected birds","volume":"15","author":"Ellis","year":"2022","journal-title":"Parasit. Vectors"},{"issue":"1","key":"10.1016\/j.ympev.2026.108642_b0110","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/s13059-015-0721-2","article-title":"OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy","volume":"16","author":"Emms","year":"2015","journal-title":"Genome Biol."},{"issue":"19","key":"10.1016\/j.ympev.2026.108642_b0115","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"issue":"10","key":"10.1016\/j.ympev.2026.108642_b0125","doi-asserted-by":"crossref","first-page":"2585","DOI":"10.1093\/molbev\/msy147","article-title":"Species tree inference with BPP using genomic sequences and the multispecies coalescent","volume":"35","author":"Flouri","year":"2018","journal-title":"Mol. Biol. Evol."},{"issue":"4","key":"10.1016\/j.ympev.2026.108642_b0130","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1093\/molbev\/msz296","article-title":"A Bayesian implementation of the multispecies coalescent model with introgression for phylogenomic analysis","volume":"37","author":"Flouri","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ympev.2026.108642_b0135","article-title":"Hypothesis testing with BPP [Github Wiki]","author":"Flouri","year":"2024","journal-title":"Phylogenomics"},{"issue":"11","key":"10.1016\/j.ympev.2026.108642_b0140","doi-asserted-by":"crossref","first-page":"1803","DOI":"10.1046\/j.1365-294x.2000.01070.x","article-title":"Bottlenecks and multiple introductions: Population genetics of the vector of avian malaria in Hawaii","volume":"9","author":"Fonseca","year":"2000","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.ympev.2026.108642_b0145","doi-asserted-by":"crossref","unstructured":"Fonseca, D. M., Smith, J. L., Wilkerson, R. C., & Fleischer, R. C. (2006). Pathways of expansion and multiple introductions illustrated by large genetic differentiation among worldwide populations of the southern house mosquito.","DOI":"10.4269\/ajtmh.2006.74.284"},{"issue":"10","key":"10.1016\/j.ympev.2026.108642_b0150","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3000490","article-title":"Resurrection of the ancestral RH5 invasion ligand provides a molecular explanation for the origin of P. falciparum malaria in humans","volume":"17","author":"Galaway","year":"2019","journal-title":"PLoS Biol."},{"issue":"1","key":"10.1016\/j.ympev.2026.108642_b0155","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/s12862-018-1242-x","article-title":"Integrating coalescent species delimitation with analysis of host specificity reveals extensive cryptic diversity despite minimal mitochondrial divergence in the malaria parasite genus Leucocytozoon","volume":"18","author":"Galen","year":"2018","journal-title":"BMC Evol. Biol."},{"issue":"3","key":"10.1016\/j.ympev.2026.108642_b0160","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1093\/molbev\/msaa278","article-title":"Common adaptive strategies underlie within-host evolution of bacterial pathogens","volume":"38","author":"Gatt","year":"2021","journal-title":"Mol. Biol. Evol."},{"issue":"8","key":"10.1016\/j.ympev.2026.108642_b0165","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1111\/ecog.01158","article-title":"Global phylogeography of the avian malaria pathogen Plasmodium relictum based on MSP1 allelic diversity","volume":"38","author":"Hellgren","year":"2015","journal-title":"Ecography"},{"issue":"5","key":"10.1016\/j.ympev.2026.108642_b0170","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/sysbio\/syq047","article-title":"Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods","volume":"59","author":"Huang","year":"2010","journal-title":"Syst. Biol."},{"key":"10.1016\/j.ympev.2026.108642_b0175","article-title":"Species delimitation with gene flow","volume":"syw117","author":"Jackson","year":"2016","journal-title":"Syst. Biol."},{"issue":"12","key":"10.1016\/j.ympev.2026.108642_b0180","doi-asserted-by":"crossref","DOI":"10.1093\/nsr\/nwab127","article-title":"Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow","volume":"8","author":"Jiao","year":"2021","journal-title":"Natl. Sci. Rev."},{"issue":"430","key":"10.1016\/j.ympev.2026.108642_b0185","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1080\/01621459.1995.10476572","article-title":"Bayes factors","volume":"90","author":"Kass","year":"1995","journal-title":"J. Am. Stat. Assoc."},{"key":"10.1016\/j.ympev.2026.108642_b0190","unstructured":"Kassambara, A. (2023). ggpubr: \u201cggplot2\u201d Based Publication Ready Plots. https:\/\/rpkgs.datanovia.com\/ggpubr\/."},{"key":"10.1016\/j.ympev.2026.108642_b0195","article-title":"Trim Galore (Version 0.6.6) [Computer software]","author":"Krueger","year":"2020","journal-title":"Babraham Bioinform."},{"issue":"1","key":"10.1016\/j.ympev.2026.108642_b0200","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1093\/sysbio\/syy051","article-title":"The spectre of too many species","volume":"68","author":"Leach\u00e9","year":"2019","journal-title":"System. Biol."},{"key":"10.1016\/j.ympev.2026.108642_b0205","unstructured":"Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM (No. arXiv:1303.3997). arXiv. DOI: 10.48550\/arXiv.1303.3997."},{"issue":"5","key":"10.1016\/j.ympev.2026.108642_b0210","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1093\/sysbio\/syy011","article-title":"Comparison of methods for molecular species delimitation across a range of speciation scenarios","volume":"67","author":"Luo","year":"2018","journal-title":"System. Biol."},{"issue":"1","key":"10.1016\/j.ympev.2026.108642_b0215","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J."},{"issue":"7","key":"10.1016\/j.ympev.2026.108642_b0220","doi-asserted-by":"crossref","DOI":"10.1002\/ecy.3038","article-title":"The role of native and introduced birds in transmission of avian malaria in Hawaii","volume":"101","author":"McClure","year":"2020","journal-title":"Ecology"},{"key":"10.1016\/j.ympev.2026.108642_b0225","first-page":"33","article-title":"Patterns of success among introduced birds in the Hawaiian Islands","volume":"22","author":"Moulton","year":"2001","journal-title":"Stud. Avian Biol."},{"issue":"14","key":"10.1016\/j.ympev.2026.108642_b0230","doi-asserted-by":"crossref","first-page":"2490","DOI":"10.1093\/bioinformatics\/bty121","article-title":"Parallelization of MAFFT for large-scale multiple sequence alignments","volume":"34","author":"Nakamura","year":"2018","journal-title":"Bioinformatics"},{"issue":"6","key":"10.1016\/j.ympev.2026.108642_b0235","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1038\/s41564-018-0162-2","article-title":"Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria","volume":"3","author":"Otto","year":"2018","journal-title":"Nat. Microbiol."},{"issue":"7","key":"10.1016\/j.ympev.2026.108642_b0240","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1016\/j.pt.2023.04.004","article-title":"Origin and diversity of malaria parasites and other Haemosporida","volume":"39","author":"Pacheco","year":"2023","journal-title":"Trends Parasitol.."},{"key":"10.1016\/j.ympev.2026.108642_b0245","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.molbiopara.2017.08.002","article-title":"Experimental evidence for hybridization of closely related lineages in Plasmodium relictum","volume":"217","author":"Palinauskas","year":"2017","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.ympev.2026.108642_b0250","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"},{"issue":"1459","key":"10.1016\/j.ympev.2026.108642_b0255","doi-asserted-by":"crossref","first-page":"2345","DOI":"10.1098\/rspb.2000.1290","article-title":"Species concepts and malaria parasites: Detecting a cryptic species of Plasmodium","volume":"267","author":"Perkins","year":"2000","journal-title":"Proc. Royal Soc. London. Series B: Biol. Sci."},{"issue":"10","key":"10.1016\/j.ympev.2026.108642_b0260","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1016\/j.pt.2016.06.001","article-title":"A Modern Menagerie of Mammalian Malaria","volume":"32","author":"Perkins","year":"2016","journal-title":"Trends Parasitol.."},{"issue":"6","key":"10.1016\/j.ympev.2026.108642_b0265","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.ympev.2026.108642_b0270","unstructured":"R Core Team. (2023). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. https:\/\/www.R-project.org\/."},{"issue":"41","key":"10.1016\/j.ympev.2026.108642_b0275","doi-asserted-by":"crossref","first-page":"14816","DOI":"10.1073\/pnas.1416356111","article-title":"Species formation by host shifting in avian malaria parasites","volume":"111","author":"Ricklefs","year":"2014","journal-title":"Proc. Nat. Acad. Sci."},{"issue":"8","key":"10.1016\/j.ympev.2026.108642_b0280","doi-asserted-by":"crossref","first-page":"2960","DOI":"10.1890\/10-1311.1","article-title":"The dynamics, transmission, and population impacts of avian malaria in native hawaiian birds: a modeling approach","volume":"21","author":"Samuel","year":"2011","journal-title":"Ecol. Appl."},{"key":"10.1016\/j.ympev.2026.108642_b0285","series-title":"Avian Malaria and Related Parasites in the Tropics: Ecology, Evolution and Systematics","year":"2020"},{"issue":"7","key":"10.1016\/j.ympev.2026.108642_b0290","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1093\/molbev\/msw079","article-title":"Fast coalescent-based computation of local branch support from quartet frequencies","volume":"33","author":"Sayyari","year":"2016","journal-title":"Mol. Biol. Evolut."},{"issue":"6","key":"10.1016\/j.ympev.2026.108642_b0295","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.02275-20","article-title":"Hidden diversity within common protozoan parasites as revealed by a novel genomotyping scheme","volume":"87","author":"Seabolt","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"issue":"1","key":"10.1016\/j.ympev.2026.108642_b0300","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1146\/annurev-ecolsys-102723-055311","article-title":"A genomic perspective on species delimitation","volume":"56","author":"Singhal","year":"2025","journal-title":"Ann. Rev. Ecol. Evol. System."},{"issue":"9","key":"10.1016\/j.ympev.2026.108642_b0305","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/j.ympev.2026.108642_b0310","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1471-2148-14-38","article-title":"Discord between morphological and phylogenetic species boundaries: Incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen","volume":"14","author":"Stewart","year":"2014","journal-title":"BMC Evol. Biol."},{"issue":"1","key":"10.1016\/j.ympev.2026.108642_b0315","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1111\/jpy.13304","article-title":"An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis","volume":"59","author":"Struneck\u00fd","year":"2023","journal-title":"J. Phycol."},{"issue":"7","key":"10.1016\/j.ympev.2026.108642_b0320","doi-asserted-by":"crossref","first-page":"1607","DOI":"10.1073\/pnas.1607921114","article-title":"Multispecies coalescent delimits structure, not species","volume":"114","author":"Sukumaran","year":"2017","journal-title":"Proc. Nat. Acad. Sci."},{"issue":"4","key":"10.1016\/j.ympev.2026.108642_b0325","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1093\/sysbio\/syad015","article-title":"Estimation of species divergence times in presence of cross-species gene flow","volume":"72","author":"Tiley","year":"2023","journal-title":"System. Biol."},{"issue":"4","key":"10.1016\/j.ympev.2026.108642_b0330","doi-asserted-by":"crossref","first-page":"327","DOI":"10.2307\/1942550","article-title":"The epizootiology and ecological significance of malaria in Hawaiian land birds","volume":"56","author":"Van Riper","year":"1986","journal-title":"Ecol. Monogr."},{"issue":"2","key":"10.1016\/j.ympev.2026.108642_b0335","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1093\/sysbio\/syab051","article-title":"Evolutionary rate variation among lineages in gene trees has a negative impact on species-tree inference","volume":"71","author":"Vankan","year":"2022","journal-title":"Syst. Biol."},{"issue":"3","key":"10.1016\/j.ympev.2026.108642_b0340","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/j.pt.2018.12.005","article-title":"Genomic advances in avian malaria research","volume":"35","author":"Videvall","year":"2019","journal-title":"Trends Parasitol."},{"issue":"2","key":"10.1016\/j.ympev.2026.108642_b0345","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1093\/molbev\/msz240","article-title":"Treeio: an R package for phylogenetic tree input and output with richly annotated and associated data","volume":"37","author":"Wang","year":"2020","journal-title":"Mol. Biol. Evol."},{"issue":"2","key":"10.1016\/j.ympev.2026.108642_b0350","doi-asserted-by":"crossref","first-page":"101","DOI":"10.2307\/1365954","article-title":"The role of introduced diseases in the extinction of the endemic Hawaiian Avifauna","volume":"70","author":"Warner","year":"1968","journal-title":"Condor"},{"issue":"3","key":"10.1016\/j.ympev.2026.108642_b0355","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1093\/molbev\/msx335","article-title":"Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes","volume":"35","author":"Weaver","year":"2018","journal-title":"Mol. Biol. Evol."},{"issue":"3","key":"10.1016\/j.ympev.2026.108642_b0360","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1093\/molbev\/msu400","article-title":"RELAX: detecting relaxed selection in a phylogenetic framework","volume":"32","author":"Wertheim","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ympev.2026.108642_b0365","series-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"issue":"5","key":"10.1016\/j.ympev.2026.108642_b0370","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1093\/bioinformatics\/13.5.555","article-title":"PAML: a program package for phylogenetic analysis by maximum likelihood","volume":"13","author":"Yang","year":"1997","journal-title":"Bioinformatics"},{"issue":"8","key":"10.1016\/j.ympev.2026.108642_b0375","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."},{"issue":"12","key":"10.1016\/j.ympev.2026.108642_b0380","doi-asserted-by":"crossref","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."},{"issue":"1","key":"10.1016\/j.ympev.2026.108642_b0385","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol. Evol."},{"issue":"Suppl 6","key":"10.1016\/j.ympev.2026.108642_b0390","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."},{"issue":"6","key":"10.1016\/j.ympev.2026.108642_b0395","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1093\/sysbio\/syr071","article-title":"Evaluation of a Bayesian coalescent method of species delimitation","volume":"60","author":"Zhang","year":"2011","journal-title":"Syst. Biol."}],"container-title":["Molecular Phylogenetics and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1055790326001120?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1055790326001120?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T21:28:35Z","timestamp":1786051715000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1055790326001120"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":78,"alternative-id":["S1055790326001120"],"URL":"https:\/\/doi.org\/10.1016\/j.ympev.2026.108642","relation":{},"ISSN":["1055-7903"],"issn-type":[{"value":"1055-7903","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Phylogenomic analyses reveal introgression and cryptic speciation in the globally distributed, vector-transmitted pathogen Plasmodium relictum","name":"articletitle","label":"Article Title"},{"value":"Molecular Phylogenetics and Evolution","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ympev.2026.108642","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":"108642"}}