{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T13:49:07Z","timestamp":1762177747906,"version":"3.40.3"},"reference-count":43,"publisher":"American Society of Parasitologists","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Journal of Parasitology"],"published-print":{"date-parts":[[2025,3,24]]},"DOI":"10.1645\/24-135","type":"journal-article","created":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T03:12:44Z","timestamp":1742958764000},"source":"Crossref","is-referenced-by-count":2,"title":["Genomics and Morphology Resolve Chipmunk Sucking Louse Systematics (Genus Hoplopleura)"],"prefix":"10.1645","volume":"111","author":[{"given":"Priscilla A.","family":"San Juan","sequence":"first","affiliation":[{"name":"Department of Mammalogy, Research and Collections, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lance A.","family":"Durden","sequence":"additional","affiliation":[{"name":"Department of Biology, Georgia Southern University, 4324 Old Register Road, Statesboro, Georgia 30458."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julie M.","family":"Allen","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, Virginia 24061."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna J.","family":"Phillips","sequence":"additional","affiliation":[{"name":"Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, D.C. 20560."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kayce C.","family":"Bell","sequence":"additional","affiliation":[{"name":"Department of Mammalogy, Research and Collections, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007."}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1220","reference":[{"key":"28","unstructured":"B. Q. Minh, H. A. Schmidt, O. Chernomor, et al.  \"Molecular Biology and Evolution.\"  37, \"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era.\" 1530 (2020)"},{"key":"1","doi-asserted-by":"crossref","unstructured":"J. M. Allen, B. Boyd, N. Nguyen, et al.  \"Systematic Biology.\"  66, \"Phylogenomics from whole genome sequences using aTRAM.\" 786 (2017)","DOI":"10.1093\/sysbio\/syw105"},{"key":"2","doi-asserted-by":"publisher","unstructured":"J. M. Allen, D. I. Huang, Q. C. Cronk, et al.  \"BMC Bioinformatics.\"  16, \"aTRAM\u2014Automated target restricted assembly method: A fast method for assembling loci across divergent taxa from next-generation sequencing data.\" 98 (2015)","DOI":"10. 1186\/s12859-015-0515-2"},{"key":"3","doi-asserted-by":"publisher","unstructured":"J. M. Allen, R. Lafrance, R. A. Folk, et al.  \"Evolutionary Bioinformatics Online.\"  14, \"aTRAM 2.0: An improved, flexible locus assembler for NGS data.\" 1176934318774546 (2018)","DOI":"10.1177\/1176934318774546"},{"key":"5","doi-asserted-by":"publisher","unstructured":"K. C. Bell, J. M. Allen, K. P. Johnson, et al.  \"Molecular Phylogenetics and Evolution.\"  155, \"Disentangling lousy relationships: Comparative phylogenomics of two sucking louse lineages parasitizing chipmunks.\" 106998 (2021)","DOI":"10.1016\/j.ympev.2020.106998"},{"key":"6","doi-asserted-by":"crossref","unstructured":"K. C. Bell, D. Matek, J. R. Demboski, et al.  \"Comparative Parasitology.\"  82, \"Expanded host range of sucking lice and pinworms of western North American chipmunks.\" 312 (2015)","DOI":"10.1654\/4756.1"},{"key":"10","doi-asserted-by":"crossref","unstructured":"L. A. Durden, S. E. Kessler, L. Boundenga, et al.  \"Journal of Parasitology.\"  106, \"A new species of sucking louse from the mandrill from Gabon with a review of host associations and geographical distributions, and identification keys to members of the genus Pedicinus (Phthiraptera: Anoplura: Pedicinidae).\" 221 (2020)","DOI":"10.1645\/19-170"},{"key":"12","unstructured":"G. F. Ferris,  \"Stanford University Publications, University Series, Biological Sciences.\"  2, \"Contributions toward a monograph of the sucking lice, Part II.\" 52 (1921)"},{"key":"16","unstructured":"G. J. Hannon,  \"FASTX-Toolkit.\"  (2010)"},{"key":"17","doi-asserted-by":"crossref","unstructured":"P. D. Hebert, S. Ratnasingham, J. R. Dewaard,  \"Proceedings of the Royal Society B: Biological Sciences.\"  270, \"Bar-coding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species.\" S96 (2003)","DOI":"10.1098\/rsbl.2003.0025"},{"key":"19","doi-asserted-by":"crossref","unstructured":"E. W. Jameson,  \"Acta Theriologica.\"  44, \"Host\u2013ectoparasite relationships among North American chipmunks.\" 225 (1999)","DOI":"10.4098\/AT.arch.99-21"},{"key":"23","doi-asserted-by":"crossref","unstructured":"V. L. Kellogg  and G. F. Ferris  \"Anoplura and Mallophaga of North American Mammals.\"  74 (1915)","DOI":"10.5962\/bhl.title.60046"},{"key":"25","doi-asserted-by":"publisher","unstructured":"J. E. Light, V. S. Smith, J. M. Allen, et al.  \"BMC Evolutionary Biology.\"  10, \"Evolutionary history of mammalian sucking lice (Phthiraptera: Anoplura).\" 292 (2010)","DOI":"10.1186\/1471-2148-10-292"},{"key":"26","doi-asserted-by":"crossref","unstructured":"A. L\u00f6ytynoja,  \"Methods in Molecular Biology.\"  1079, \"Phylogeny-aware alignment with PRANK.\" 155 (2014)","DOI":"10.1007\/978-1-62703-646-7_10"},{"key":"27","doi-asserted-by":"crossref","unstructured":"B. S. Mclean, K. C. Bell, J. M. Allen, et al.  \"Systematic Biology.\"  68, \"Impacts of inference method and data set filtering on phylogenomic resolution in a rapid radiation of ground squirrels (Xerinae: Marmotini).\" 298 (2019)","DOI":"10.1093\/sysbio\/syy064"},{"key":"29","doi-asserted-by":"crossref","unstructured":"H. Osborn,  \"Bulletin of the U.S. Department of Agriculture, Bureau (Division) of Entomology No. 5.\"  \"Insects affecting domestic animals: An account of the species of importance in North America, with mention of forms occurring on other animals.\" 302 (1896)","DOI":"10.5962\/bhl.title.64990"},{"key":"31","doi-asserted-by":"crossref","unstructured":"J. L. Penner  and L. D. Devenport  \"Journal of Comparative Psychology.\"  125, \"A comparative study of caching and pilfering behavior in two sympatric species, least chipmunks (Tamias minimus) and eastern chipmunks (Tamias striatus).\" 375 (2011)","DOI":"10.1037\/a0024562"},{"key":"33","unstructured":"A. Rambaut,  \"FigTree, version 1.4.4.\"  (2018)"},{"key":"34","doi-asserted-by":"publisher","unstructured":"L. J. Revell,  \"PeerJ.\"  12, \"phytools 2.0: An updated R ecosystem for phylogenetic comparative methods (and other things).\" e16505 (2024)","DOI":"10.7717\/peerk\/16505"},{"key":"37","doi-asserted-by":"publisher","unstructured":"G. S. Slater  and E. Birney  \"BMC Bioinformatics.\"  6, \"Automated generation of heuristics for biological sequence comparison.\" 31 (2005)","DOI":"10.1186\/1471-2105-6-31"},{"key":"38","doi-asserted-by":"crossref","unstructured":"C. J. Stojanovich  and H. D. Pratt  \"Journal of Parasitology.\"  47, \"Key to the North American sucking lice in the genera Hoplopleura and Neohaematopinus with descriptions of two species.\" 312 (1961)","DOI":"10.2307\/3275316"},{"key":"39","unstructured":"C. J. Stojanovich  and H. D. Pratt  \"Key to Anoplura of North America.\"  24 (1965)"},{"key":"40","doi-asserted-by":"crossref","unstructured":"J. Sullivan, J. R. Demboski, K. C. Bell, et al.  \"Heredity.\"  113, \"Divergence with gene flow within the recent chipmunk radiation (Tamias).\" 185 (2014)","DOI":"10.1038\/hdy.2014.27"},{"key":"41","doi-asserted-by":"crossref","unstructured":"D. A. Sutton  and B. D. Patterson  \"Journal of Mammalogy.\"  81, \"Geographic variation of the western chipmunks Tamias senex and T. siskiyou, with two new subspecies from California.\" 299 (2000)","DOI":"10.1093\/jmammal\/81.2.299"},{"key":"32","unstructured":"R. D. Price, R. A. Hellenthal, R. L. Palma, et al.  \"The Chewing Lice: World Checklist and Biological Overview.\"  501 (2003)"},{"key":"36","doi-asserted-by":"crossref","unstructured":"R. S. Sikes,  \"Journal of Mammalogy.\"  97, \"2016 Guidelines of the American Society of Mammalogists for the use of wild mammals in research and education.\" 663 (2016)","DOI":"10.1093\/jmammal\/gyw078"},{"key":"22","unstructured":"K. Katoh  and D. M. Standley  \"Molecular Biology and Evolution.\"  30, \"MAFFT multiple sequence alignment software version 7: improvements in performance and usability.\" 772 (2013)"},{"key":"35","doi-asserted-by":"crossref","unstructured":"E. Sayyari  and S. Mirarab  \"Molecular Biology and Evolution.\"  33, \"Fast coalescent-based computation of local branch support from quartet frequencies.\" 1654 (2016)","DOI":"10.1093\/molbev\/msw079"},{"key":"42","doi-asserted-by":"crossref","unstructured":"G. Yu, D. Smith, H. Zhu, et al.  \"Methods in Ecology and Evolution.\"  8, \"ggtree: An R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.\" 28 (2017)","DOI":"10.1111\/2041-210X.12628"},{"key":"43","doi-asserted-by":"crossref","unstructured":"C. Zhang, M. Rabiee, E. Sayyari, et al.  \"BMC Bioinformatics.\"  19, \"ASTRAL-III: Polynomial time species tree reconstruction from partially resolved gene trees.\" 153 (2018)","DOI":"10.1186\/s12859-018-2129-y"},{"key":"30","doi-asserted-by":"publisher","unstructured":"E. Paradis  and K. Schliep  \"Bioinformatics.\"  35, \"Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.\" 526 (2019)","DOI":"10.1093\/bioinformatics\/bty633"},{"key":"15","doi-asserted-by":"crossref","unstructured":"M. S. Hafner, P. D. Sudman, F. X. Villablanca, et al.  \"Science.\"  265, \"Disparate rates of molecular evolution in cospeciating hosts and parasites.\" 1087 (1994)","DOI":"10.1126\/science.8066445"},{"key":"21","unstructured":"S. Kalyaanamoorthy, B. Q. Minh, T. K. F. Wong, et al.  \"Nature Methods.\"  14, \"ModelFinder: fast model selection for accurate phylogenetic estimates.\" 587 (2017)"},{"key":"14","doi-asserted-by":"crossref","unstructured":"M. Gouy, S. Guindon, O. Gascuel,  \"Molecular Biology and Evolution.\"  27, \"SeaView Version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building.\" 221 (2010)","DOI":"10.1093\/molbev\/msp259"},{"key":"11","unstructured":"L. A. Durden  and G. G. Musser  \"Bulletin of the American Museum of Natural History.\"  218, \"The sucking lice (Insecta, Anoplura) of the world: A taxonomic checklist with records of mammalian hosts and geographical distributions.\" 1 (1994)"},{"key":"13","doi-asserted-by":"crossref","unstructured":"G. F. Ferris,  \"Memoirs of the Pacific Coast Entomological Society.\"  1, \"The sucking lice.\" 1 (1951)","DOI":"10.5962\/bhl.title.149669"},{"key":"7","doi-asserted-by":"crossref","unstructured":"S. Capella-Gutierrez, J. M. Silla-Martinez, T. Gabaldon,  \"Bioinformatics.\"  25, \"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.\" 1972 (2009)","DOI":"10.1093\/bioinformatics\/btp348"},{"key":"18","doi-asserted-by":"crossref","unstructured":"S. D. Jackman, B. P. Vandervalk, H. Mohamadi, et al.  \"Genome Research.\"  27, \"ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter.\" 768 (2017)","DOI":"10.1101\/gr.214346.116"},{"key":"4","unstructured":"S. Andrews,  \"FastQC: A quality control tool for high throughput sequence data.\"  (2010)"},{"key":"9","doi-asserted-by":"crossref","unstructured":"E. F. Cook  and J. R. Beer  \"Journal of Parasitology.\"  45, \"The immature stages of the genus Hoplopleura (Anoplura: Hoplopleuridae) in North America, with descriptions of two new species.\" 405 (1959)","DOI":"10.2307\/3274391"},{"key":"24","unstructured":"K. C. Kim, H. D. Pratt, C. J. Stojanovich,  \"The Sucking Lice of North America: An Illustrated Manual for Identification.\"  241 (1986)"},{"key":"8","doi-asserted-by":"publisher","unstructured":"D. H. Clayton  and K. P. Johnson  \"Evolution.\"  57, \"Linking coevolutionary history to ecological process: Doves and lice.\" 2335 (2003)","DOI":"10.1554\/03-123"},{"key":"20","doi-asserted-by":"crossref","unstructured":"K. P. Johnson, D. L. Reed, S. L. Hammond Parker, et al.  \"Molecular Phylogenetics and Evolution.\"  45, \"Phylogenetic analysis of nuclear and mitochondrial genes supports species groups for Columbicola (Insecta: Phthiraptera).\" 506 (2007)","DOI":"10.1016\/j.ympev.2007.07.005"}],"container-title":["Journal of Parasitology"],"original-title":[],"deposited":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T03:13:36Z","timestamp":1742958816000},"score":1,"resource":{"primary":{"URL":"https:\/\/bioone.org\/journals\/journal-of-parasitology\/volume-111\/issue-2\/24-135\/Genomics-and-Morphology-Resolve-Chipmunk-Sucking-Louse-Systematics-Genus-Hoplopleura\/10.1645\/24-135.full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,24]]},"references-count":43,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,4,1]]}},"URL":"https:\/\/doi.org\/10.1645\/24-135","relation":{},"ISSN":["0022-3395"],"issn-type":[{"value":"0022-3395","type":"print"}],"subject":[],"published":{"date-parts":[[2025,3,24]]}}}