| Year |
Citation |
Score |
| 2023 |
Duckett DJ, Calder K, Sullivan J, Tank DC, Carstens BC. Reduced representation approaches produce similar results to whole genome sequencing for some common phylogeographic analyses. Plos One. 18: e0291941. PMID 38032899 DOI: 10.1371/journal.pone.0291941 |
0.758 |
|
| 2023 |
Tumendemberel O, Hendricks SA, Hohenlohe PA, Sullivan J, Zedrosser A, Saebø M, Proctor MF, Koprowski JL, Waits LP. Range-wide evolutionary relationships and historical demography of brown bears (Ursus arctos) revealed by whole-genome sequencing of isolated central Asian populations. Molecular Ecology. 32: 5156-5169. PMID 37528604 DOI: 10.1111/mec.17091 |
0.465 |
|
| 2022 |
Leducq JB, Sneddon D, Santos M, Condrain-Morel D, Bourret G, Martinez-Gomez NC, Lee JA, Foster JA, Stolyar S, Shapiro BJ, Kembel SW, Sullivan JM, Marx CJ. Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity. Genome Biology and Evolution. 14. PMID 35906926 DOI: 10.1093/gbe/evac123 |
0.376 |
|
| 2022 |
Smith ML, Wallace J, Tank DC, Sullivan J, Carstens BC. The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest. Molecular Ecology. PMID 35780485 DOI: 10.1111/mec.16595 |
0.784 |
|
| 2022 |
Herrera ND, Bell KC, Callahan CM, Nordquist E, Sarver BAJ, Sullivan J, Demboski JR, Good JM. Genomic resolution of cryptic species diversity in chipmunks. Evolution; International Journal of Organic Evolution. PMID 35778920 DOI: 10.1111/evo.14546 |
0.834 |
|
| 2022 |
Ruffley M, Smith ML, Espíndola A, Turck DF, Mitchell N, Carstens B, Sullivan J, Tank DC. Genomic evidence of an ancient Inland Temperate Rainforest in the Pacific Northwest of North America. Molecular Ecology. PMID 35322900 DOI: 10.1111/mec.16431 |
0.797 |
|
| 2021 |
Duckett DJ, Sullivan J, Pirro S, Carstens BC. Genomic Resources for the North American Water Vole () and the Montane Vole (). Gigabyte (Hong Kong, China). 2021: gigabyte19. PMID 36824326 DOI: 10.46471/gigabyte.19 |
0.725 |
|
| 2021 |
Rankin AM, Anderson FE, Clutts SA, Espíndola A, Carstens BC, Lucid M, Sullivan J. Comparative phylogeography of two Northern Rocky Mountain endemics: the widespread Anguispira kochi occidentalis and the narrow-range Anguispira nimapuna (Gastropoda: Discidae). Biological Journal of the Linnean Society. Linnean Society of London. 133: 817-834. PMID 34220190 DOI: 10.1093/biolinnean/blab030 |
0.794 |
|
| 2021 |
Sarver BAJ, Herrera ND, Sneddon D, Hunter SS, Settles ML, Kronenberg Z, Demboski JR, Good JM, Sullivan J. Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias). Systematic Biology. PMID 33410870 DOI: 10.1093/sysbio/syaa085 |
0.841 |
|
| 2020 |
Lucid M, Cushman S, Robinson L, Kortello A, Hausleitner D, Mowat G, Ehlers S, Gillespie S, Svancara LK, Sullivan J, Rankin A, Paetkau D. Carnivore Contact: A Species Fracture Zone Delineated Amongst Genetically Structured North American Marten Populations ( and ). Frontiers in Genetics. 11: 735. PMID 32754203 DOI: 10.3389/Fgene.2020.00735 |
0.498 |
|
| 2019 |
Grond K, Bell KC, Demboski JR, Santos M, Sullivan JM, Hird SM. No evidence for phylosymbiosis in western chipmunk species. Fems Microbiology Ecology. PMID 31730167 DOI: 10.1093/Femsec/Fiz182 |
0.809 |
|
| 2019 |
Tumendemberel O, Zedrosser A, Proctor MF, Reynolds HV, Adams JR, Sullivan JM, Jacobs SJ, Khorloojav T, Tserenbataa T, Batmunkh M, Swenson JE, Waits LP. Phylogeography, genetic diversity, and connectivity of brown bear populations in Central Asia. Plos One. 14: e0220746. PMID 31408475 DOI: 10.1371/journal.pone.0220746 |
0.416 |
|
| 2019 |
Sarver BAJ, Pennell MW, Brown JW, Keeble S, Hardwick KM, Sullivan J, Harmon LJ. The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates. Peerj. 7: e6334. PMID 30886768 DOI: 10.7717/Peerj.6334 |
0.4 |
|
| 2019 |
Sullivan J, Smith ML, Espíndola A, Ruffley M, Rankin A, Tank D, Carstens B. Integrating life history traits into predictive phylogeography. Molecular Ecology. PMID 30667113 DOI: 10.1111/Mec.15029 |
0.737 |
|
| 2019 |
Rankin AM, Wilke T, Lucid M, Leonard W, Espíndola A, Smith ML, Carstens BC, Sullivan J. Complex interplay of ancient vicariance and recent patterns of geographical speciation in north-western North American temperate rainforests explains the phylogeny of jumping slugs (Hemphillia spp.) Biological Journal of the Linnean Society. 127: 876-889. DOI: 10.1093/Biolinnean/Blz040 |
0.798 |
|
| 2019 |
Lucid MK, Rankin A, Sullivan J, Robinson L, Ehlers S, Cushman S. A carnivores’ oasis? An isolated fisher (Pekania pennanti) population provides insight on persistence of a metapopulation Conservation Genetics. 20: 585-596. DOI: 10.1007/S10592-019-01160-W |
0.473 |
|
| 2018 |
Pelletier TA, Carstens BC, Tank DC, Sullivan J, Espíndola A. Predicting plant conservation priorities on a global scale. Proceedings of the National Academy of Sciences of the United States of America. 115: 13027-13032. PMID 30509998 DOI: 10.1073/Pnas.1804098115 |
0.734 |
|
| 2018 |
Ruffley M, Smith ML, Espíndola A, Carstens BC, Sullivan J, Tank DC. Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Molecular Ecology. PMID 29334417 DOI: 10.1111/Mec.14491 |
0.777 |
|
| 2018 |
Lucid M, Rankin A, Espíndola A, Chichester L, Ehlers S, Robinson L, Sullivan J. Taxonomy and biogeography of Hemphillia (Gastropoda: Pulmonata: Arionidae) in North American rainforests, with description of a new species (Skade’s jumping-slug, Hemphillia skadei sp. nov.) Canadian Journal of Zoology. 96: 305-316. DOI: 10.1139/Cjz-2017-0260 |
0.445 |
|
| 2018 |
Smith ML, Ruffley M, Rankin AM, Espíndola A, Tank DC, Sullivan J, Carstens BC. Testing for the presence of cryptic diversity in tail-dropper slugs (Prophysaon) using molecular data Biological Journal of the Linnean Society. 124: 518-532. DOI: 10.1093/Biolinnean/Bly067 |
0.733 |
|
| 2017 |
Smith ML, Ruffley M, Espíndola A, Tank DC, Sullivan J, Carstens BC. Demographic Model Selection using Random Forests and the Site Frequency Spectrum. Molecular Ecology. PMID 28665011 DOI: 10.1111/Mec.14223 |
0.74 |
|
| 2017 |
Sarver BA, Demboski JR, Good JM, Forshee N, Hunter SS, Sullivan J. Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (Tamias). Genome Biology and Evolution. 9: 7-19. PMID 28172670 DOI: 10.1093/Gbe/Evw254 |
0.828 |
|
| 2016 |
Espíndola A, Ruffley M, Smith ML, Carstens BC, Tank DC, Sullivan J. Identifying cryptic diversity with predictive phylogeography. Proceedings. Biological Sciences. 283. PMID 27798300 DOI: 10.1098/Rspb.2016.1529 |
0.778 |
|
| 2016 |
Sarver BA, Demboski JR, Good JM, Forshee N, Hunter SS, Sullivan J. Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (TAMIAS). Genome Biology and Evolution. PMID 27797954 DOI: 10.1093/gbe/evw254 |
0.83 |
|
| 2015 |
Metzger G, Espindola A, Waits LP, Sullivan J. Genetic Structure across Broad Spatial and Temporal Scales: Rocky Mountain Tailed Frogs (Ascaphus montanus; Anura: Ascaphidae) in the Inland Temperate Rainforest. The Journal of Heredity. 106: 700-10. PMID 26285914 DOI: 10.1093/Jhered/Esv061 |
0.459 |
|
| 2015 |
Sullivan J. Mammalogy. 6th ed. Journal of Mammalogy. 96: 246.1-248. DOI: 10.1093/Jmammal/Gyu018 |
0.341 |
|
| 2014 |
Sullivan J, Demboski JR, Bell KC, Hird S, Sarver B, Reid N, Good JM. Divergence with gene flow within the recent chipmunk radiation (Tamias). Heredity. 113: 185-94. PMID 24781803 DOI: 10.1038/Hdy.2014.27 |
0.788 |
|
| 2013 |
Carstens BC, Brennan RS, Chua V, Duffie CV, Harvey MG, Koch RA, McMahan CD, Nelson BJ, Newman CE, Satler JD, Seeholzer G, Posbic K, Tank DC, Sullivan J. Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis. Molecular Ecology. 22: 4014-28. PMID 23848064 DOI: 10.1111/Mec.12347 |
0.763 |
|
| 2013 |
Sen D, Brown CJ, Top EM, Sullivan J. Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Molecular Biology and Evolution. 30: 154-66. PMID 22936717 DOI: 10.1093/Molbev/Mss210 |
0.386 |
|
| 2012 |
Reid N, Demboski JR, Sullivan J. Phylogeny estimation of the radiation of western North American chipmunks (Tamias) in the face of introgression using reproductive protein genes. Systematic Biology. 61: 44-62. PMID 21878471 DOI: 10.1093/Sysbio/Syr094 |
0.777 |
|
| 2012 |
Evans J, Sullivan J. Generalized mixture models for molecular phylogenetic estimation. Systematic Biology. 61: 12-21. PMID 21873377 DOI: 10.1093/Sysbio/Syr093 |
0.393 |
|
| 2012 |
Hoisington-Lopez JL, Waits LP, Sullivan J. Species limits and integrated taxonomy of the Idaho ground squirrel (Urocitellus brunneus): genetic and ecological differentiation Journal of Mammalogy. 93: 589-604. DOI: 10.1644/11-Mamm-A-021.1 |
0.5 |
|
| 2011 |
Evans J, Sullivan J. Approximating model probabilities in Bayesian information criterion and decision-theoretic approaches to model selection in phylogenetics. Molecular Biology and Evolution. 28: 343-9. PMID 20671039 DOI: 10.1093/Molbev/Msq195 |
0.358 |
|
| 2010 |
Hird S, Reid N, Demboski J, Sullivan J. Introgression at differentially aged hybrid zones in red-tailed chipmunks Genetica. 138: 869-883. PMID 20623163 DOI: 10.1007/S10709-010-9470-Z |
0.798 |
|
| 2010 |
Ripplinger J, Sullivan J. Assessment of substitution model adequacy using frequentist and Bayesian methods. Molecular Biology and Evolution. 27: 2790-803. PMID 20616145 DOI: 10.1093/Molbev/Msq168 |
0.637 |
|
| 2010 |
Ripplinger J, Abdo Z, Sullivan J. Effects of parameter estimation on maximum-likelihood bootstrap analysis. Molecular Phylogenetics and Evolution. 56: 642-8. PMID 20434567 DOI: 10.1016/J.Ympev.2010.04.035 |
0.628 |
|
| 2010 |
Reid N, Hird S, Schulte-Hostedde A, Sullivan J. Examination of nuclear loci across a zone of mitochondrial introgression between Tamias ruficaudus and T. amoenus Journal of Mammalogy. 91: 1389-1400. DOI: 10.1644/09-Mamm-A-082.1 |
0.833 |
|
| 2009 |
Hird S, Sullivan J. Assessment of gene flow across a hybrid zone in red-tailed chipmunks (Tamias ruficaudus). Molecular Ecology. 18: 3097-109. PMID 19538343 DOI: 10.1111/J.1365-294X.2009.04196.X |
0.825 |
|
| 2008 |
Good JM, Hird S, Reid N, Demboski JR, Steppan SJ, Martin-Nims TR, Sullivan J. Ancient hybridization and mitochondrial capture between two species of chipmunks. Molecular Ecology. 17: 1313-27. PMID 18302691 DOI: 10.1111/J.1365-294X.2007.03640.X |
0.812 |
|
| 2008 |
Ripplinger J, Sullivan J. Does choice in model selection affect maximum likelihood analysis? Systematic Biology. 57: 76-85. PMID 18275003 DOI: 10.1080/10635150801898920 |
0.645 |
|
| 2007 |
Nagler JJ, Cavileer T, Sullivan J, Cyr DG, Rexroad C. The complete nuclear estrogen receptor family in the rainbow trout: discovery of the novel ERalpha2 and both ERbeta isoforms. Gene. 392: 164-73. PMID 17307310 DOI: 10.1016/J.Gene.2006.12.030 |
0.378 |
|
| 2006 |
Nielson M, Lohman K, Daugherty CH, Allendorf FW, Knudsen KL, Sullivan J. Allozyme and mitochondrial DNA variation in the tailed frog (Anura: Ascaphus): The influence of geography and gene flow Herpetologica. 62: 235-258. DOI: 10.1655/0018-0831(2006)62[235:Aamdvi]2.0.Co;2 |
0.543 |
|
| 2006 |
Brunsfeld SJ, Sullivan J. A multi-compartmented glacial refugium in the northern Rocky Mountains: Evidence from the phylogeography of Cardamine constancei (Brassicaceae) Conservation Genetics. 6: 895-904. DOI: 10.1007/S10592-005-9076-7 |
0.51 |
|
| 2005 |
Carstens BC, Brunsfeld SJ, Demboski JR, Good JM, Sullivan J. Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework. Evolution; International Journal of Organic Evolution. 59: 1639-52. PMID 16331838 DOI: 10.1111/J.0014-3820.2005.Tb01815.X |
0.811 |
|
| 2005 |
Carstens BC, Bankhead A, Joyce P, Sullivan J. Testing population genetic structure using parametric bootstrapping and MIGRATE-N. Genetica. 124: 71-5. PMID 16011004 DOI: 10.1007/S10709-004-8358-1 |
0.76 |
|
| 2005 |
Steele CA, Carstens BC, Storfer A, Sullivan J. Testing hypotheses of speciation timing in Dicamptodon copei and Dicamptodon aterrimus (Caudata: Dicamptodontidae). Molecular Phylogenetics and Evolution. 36: 90-100. PMID 15904859 DOI: 10.1016/J.Ympev.2004.12.001 |
0.766 |
|
| 2005 |
Sullivan J. Maximum-likelihood methods for phylogeny estimation. Methods in Enzymology. 395: 757-79. PMID 15865994 DOI: 10.1016/S0076-6879(05)95039-8 |
0.358 |
|
| 2005 |
Sullivan J, Abdo Z, Joyce P, Swofford DL. Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Molecular Biology and Evolution. 22: 1386-92. PMID 15758203 DOI: 10.1093/Molbev/Msi129 |
0.328 |
|
| 2005 |
Carstens BC, Degenhardt JD, Stevenson AL, Sullivan J. Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Molecular Ecology. 14: 255-65. PMID 15643968 DOI: 10.1111/J.1365-294X.2004.02404.X |
0.787 |
|
| 2005 |
Abdo Z, Minin VN, Joyce P, Sullivan J. Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimation. Molecular Biology and Evolution. 22: 691-703. PMID 15548751 DOI: 10.1093/Molbev/Msi050 |
0.352 |
|
| 2005 |
Sullivan J, Joyce P. Model Selection in Phylogenetics Annual Review of Ecology, Evolution, and Systematics. 36: 445-466. DOI: 10.1146/Annurev.Ecolsys.36.102003.152633 |
0.345 |
|
| 2004 |
Carstens BC, Stevenson AL, Degenhardt JD, Sullivan J. Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Systematic Biology. 53: 781-92. PMID 15545255 DOI: 10.1080/10635150490522296 |
0.793 |
|
| 2004 |
Carstens BC, Sullivan J, Davalos LM, Larsen PA, Pedersen SC. Exploring population genetic structure in three species of Lesser Antillean bats. Molecular Ecology. 13: 2557-66. PMID 15315670 DOI: 10.1111/J.1365-294X.2004.02250.X |
0.78 |
|
| 2003 |
Minin V, Abdo Z, Joyce P, Sullivan J. Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology. 52: 674-83. PMID 14530134 DOI: 10.1080/10635150390235494 |
0.343 |
|
| 2003 |
Good JM, Demboski JR, Nagorsen DW, Sullivan J. Phylogeography and introgressive hybridization: chipmunks (genus Tamias) in the northern Rocky Mountains. Evolution; International Journal of Organic Evolution. 57: 1900-16. PMID 14503631 DOI: 10.1111/J.0014-3820.2003.Tb00597.X |
0.835 |
|
| 2003 |
Demboski JR, Sullivan J. Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America. Molecular Phylogenetics and Evolution. 26: 389-408. PMID 12644399 DOI: 10.1016/S1055-7903(02)00363-9 |
0.757 |
|
| 2002 |
Winchell CJ, Sullivan J, Cameron CB, Swalla BJ, Mallatt J. Evaluating hypotheses of deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data. Molecular Biology and Evolution. 19: 762-76. PMID 11961109 DOI: 10.1093/Oxfordjournals.Molbev.A004134 |
0.434 |
|
| 2002 |
Good JM, Sullivan J. Phylogeography of the red-tailed chipmunk (Tamias ruficaudus), a northern Rocky Mountain endemic. Molecular Ecology. 10: 2683-95. PMID 11883882 DOI: 10.1046/J.0962-1083.2001.01397.X |
0.73 |
|
| 2001 |
Sullivan J, Swofford DL. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Systematic Biology. 50: 723-9. PMID 12116942 DOI: 10.1080/106351501753328848 |
0.371 |
|
| 2001 |
Nielson M, Lohman K, Sullivan J. Phylogeography of the tailed frog (Ascaphus truei): implications for the biogeography of the Pacific Northwest. Evolution; International Journal of Organic Evolution. 55: 147-60. PMID 11263735 DOI: 10.1111/J.0014-3820.2001.Tb01280.X |
0.519 |
|
| 2000 |
Harris D, Rogers DS, Sullivan J. Phylogeography of Peromyscus furvus (Rodentia; muridae) based on cytochrome b sequence data. Molecular Ecology. 9: 2129-35. PMID 11123624 DOI: 10.1046/J.1365-294X.2000.01135.X |
0.512 |
|
| 2000 |
Sullivan J, Arellano E, Rogers DS. Comparative Phylogeography of Mesoamerican Highland Rodents: Concerted versus Independent Response to Past Climatic Fluctuations. The American Naturalist. 155: 755-768. PMID 10805642 DOI: 10.1086/303362 |
0.433 |
|
| 2000 |
Steppan SJ, Sullivan J. The emerging statistical perspective in systematics: A comment on Mares and Braun Journal of Mammalogy. 81: 260-270. DOI: 10.1644/1545-1542(2000)081<0260:Tespis>2.0.Co;2 |
0.312 |
|
| 1999 |
Waits LP, Sullivan J, O'Brien SJ, Ward RH. Rapid radiation events in the family Ursidae indicated by likelihood phylogenetic estimation from multiple fragments of mtDNA. Molecular Phylogenetics and Evolution. 13: 82-92. PMID 10508542 DOI: 10.1006/Mpev.1999.0637 |
0.513 |
|
| 1999 |
Mallatt J, Sullivan J. 28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes. Molecular Biology and Evolution. 15: 1706-18. PMID 9866205 DOI: 10.1093/Oxfordjournals.Molbev.A025897 |
0.457 |
|
| 1997 |
Sullivan J, Markert JA, Kilpatrick CW. Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood. Systematic Biology. 46: 426-40. PMID 11975329 DOI: 10.1093/Sysbio/46.3.426 |
0.522 |
|
| 1997 |
Frati F, Simon C, Sullivan J, Swofford DL. Evolution of the mitochondrial cytochrome oxidase II gene in collembola. Journal of Molecular Evolution. 44: 145-58. PMID 9069175 DOI: 10.1007/Pl00006131 |
0.503 |
|
| 1997 |
Sullivan J, Swofford DL. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics Journal of Mammalian Evolution. 4: 77-86. DOI: 10.1023/A:1027314112438 |
0.455 |
|
| 1996 |
Sullivan J, Holsinger KE, Simon C. The effect of topology on estimates of among-site rate variation. Journal of Molecular Evolution. 42: 308-12. PMID 8919882 DOI: 10.1007/Bf02198857 |
0.306 |
|
| 1996 |
Simon C, Nigro L, Sullivan J, Holsinger K, Martin A, Grapputo A, Franke A, McIntosh C. Large differences in substitutional pattern and evolutionary rate of 12S ribosomal RNA genes Molecular Biology and Evolution. 13: 923-932. PMID 8752001 DOI: 10.1093/Oxfordjournals.Molbev.A025660 |
0.396 |
|
| 1996 |
Hickson RE, Simon C, Cooper A, Spicer GS, Sullivan J, Penny D. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Molecular Biology and Evolution. 13: 150-69. PMID 8583888 DOI: 10.1093/Oxfordjournals.Molbev.A025552 |
0.406 |
|
| 1996 |
Sullivan J. Combining Data with Different Distributions of Among-Site Rate Variation Systematic Biology. 45: 375-380. DOI: 10.1093/Sysbio/45.3.375 |
0.337 |
|
| 1995 |
Sullivan J, Holsinger KE, Simon C. Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents. Molecular Biology and Evolution. 12: 988-1001. PMID 8524051 DOI: 10.1093/Oxfordjournals.Molbev.A040292 |
0.457 |
|
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