L. Lacey Knowles, Ph.D - Publications

Ecology and Evolutionary Biology University of Michigan, Ann Arbor, Ann Arbor, MI 
speciation, phylogeography, phylogenetics, population genetics

76 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Wan T, Oaks JR, Jiang XL, Huang H, Knowles LL. Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species. Proceedings. Biological Sciences. 288: 20202567. PMID 33402075 DOI: 10.1098/rspb.2020.2567  1
2020 Friedman NR, Lecroq Bennet B, Fischer G, Sarnat EM, Huang JP, Knowles LLK, Economo EP. Macroevolutionary integration of phenotypes within and across ant worker castes. Ecology and Evolution. 10: 9371-9383. PMID 32953067 DOI: 10.1002/ece3.6623  0.48
2020 Fischer G, Friedman NR, Huang JP, Narula N, Knowles LL, Fisher BL, Mikheyev AS, Economo EP. Socially Parasitic Ants Evolve a Mosaic of Host-Matching and Parasitic Morphological Traits. Current Biology : Cb. PMID 32707068 DOI: 10.1016/j.cub.2020.06.078  0.48
2018 Knowles LL, Huang H, Sukumaran J, Smith SA. A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories. American Journal of Botany. PMID 29710372 DOI: 10.1002/ajb2.1064  1
2018 Sukumaran J, Knowles LL. Trait-Dependent Biogeography: (Re)Integrating Biology into Probabilistic Historical Biogeographical Models. Trends in Ecology & Evolution. PMID 29685579 DOI: 10.1016/j.tree.2018.03.010  1
2017 He Q, Prado JR, Knowles LL. Inferring the geographic origin of a range expansion: latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program x-origin. Molecular Ecology. PMID 29044712 DOI: 10.1111/mec.14380  0.44
2017 Sukumaran J, Knowles LL. Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences of the United States of America. PMID 28137871 DOI: 10.1073/pnas.1607921114  1
2016 Wachter GA, Papadopoulou A, Muster C, Arthofer W, Knowles LL, Steiner FM, Schlick-Steiner BC. Glacial refugia, recolonisation patterns, and diversification forces in Alpine-endemic Megabunus harvestmen. Molecular Ecology. PMID 27037513 DOI: 10.1111/mec.13634  0.92
2016 He Q, Knowles LL. Identifying targets of selection in mosaic genomes with machine learning: applications in Anopheles gambiae for detecting sites within locally adapted chromosomal inversions. Molecular Ecology. PMID 26994406 DOI: 10.1111/mec.13619  0.44
2016 Thomaz AT, Christie MR, Knowles LL. The architecture of river networks can drive the evolutionary dynamics of aquatic populations. Evolution; International Journal of Organic Evolution. PMID 26888211 DOI: 10.1111/evo.12883  0.92
2016 Massatti R, Reznicek AA, Knowles LL. Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae. American Journal of Botany. PMID 26851268 DOI: 10.3732/ajb.1500315  0.92
2015 Economo EP, Sarnat EM, Janda M, Clouse R, Klimov PB, Fischer G, Blanchard BD, Ramirez LN, Andersen AN, Berman M, Guénard B, Lucky A, Rabeling C, Wilson EO, Knowles LL. Breaking out of biogeographical modules: range expansion and taxon cycles in the hyperdiverse ant genus Pheidole. Journal of Biogeography. 42: 2289-2301. PMID 27660394 DOI: 10.1111/jbi.12592  0.48
2015 Sukumaran J, Economo EP, Knowles LL. Machine Learning Biogeographic Processes from Biotic Patterns: A New Trait-Dependent Dispersal and Diversification Model with Model Choice By Simulation-Trained Discriminant Analysis. Systematic Biology. PMID 26715585 DOI: 10.1093/sysbio/syv121  1
2015 Oneal E, Knowles LL. Paternity analyses in wild-caught and laboratory-reared Caribbean cricket females reveal the influence of mating environment on post-copulatory sexual selection. Journal of Evolutionary Biology. PMID 26348983 DOI: 10.1111/jeb.12754  0.92
2015 Papadopoulou A, Knowles LL. Species-specific responses to island connectivity cycles: refined models for testing phylogeographic concordance across a Mediterranean Pleistocene Aggregate Island Complex. Molecular Ecology. 24: 4252-68. PMID 26154606 DOI: 10.1111/mec.13305  0.92
2015 Lanier HC, Massatti R, He Q, Olson LE, Knowles LL. Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris). Molecular Ecology. PMID 26096099 DOI: 10.1111/mec.13270  0.44
2015 Christie MR, Knowles LL. Habitat corridors facilitate genetic resilience irrespective of species dispersal abilities or population sizes. Evolutionary Applications. 8: 454-63. PMID 26029259 DOI: 10.1111/eva.12255  0.92
2015 Papadopoulou A, Knowles LL. Genomic tests of the species-pump hypothesis: Recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands. Evolution; International Journal of Organic Evolution. 69: 1501-17. PMID 25903255 DOI: 10.1111/evo.12667  0.92
2015 Solís-Lemus C, Knowles LL, Ané C. Bayesian species delimitation combining multiple genes and traits in a unified framework. Evolution; International Journal of Organic Evolution. 69: 492-507. PMID 25495061 DOI: 10.1111/evo.12582  0.92
2015 Lanier HC, Knowles LL. Applying species-tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies. Molecular Phylogenetics and Evolution. 83: 191-9. PMID 25450097 DOI: 10.1016/j.ympev.2014.10.022  0.92
2015 Thomaz AT, Malabarba LR, Bonatto SL, Knowles LL. Testing the effect of palaeodrainages versus habitat stability on genetic divergence in riverine systems: Study of a Neotropical fish of the Brazilian coastal Atlantic Forest Journal of Biogeography. 42: 2389-2401. DOI: 10.1111/jbi.12597  0.92
2015 Economo EP, Sarnat EM, Janda M, Clouse R, Klimov PB, Fischer G, Blanchard BD, Ramirez LN, Andersen AN, Berman M, Guénard B, Lucky A, Rabeling C, Wilson EO, Knowles LL. Breaking out of biogeographical modules: Range expansion and taxon cycles in the hyperdiverse ant genus Pheidole Journal of Biogeography. 42: 2289-2301. DOI: 10.1111/jbi.12592  0.92
2014 Massatti R, Knowles LL. Microhabitat differences impact phylogeographic concordance of codistributed species: genomic evidence in montane sedges (Carex L.) from the Rocky Mountains. Evolution; International Journal of Organic Evolution. 68: 2833-46. PMID 25041894 DOI: 10.1111/evo.12491  0.92
2014 Huang H, Knowles LL. Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences. Systematic Biology. PMID 24996413 DOI: 10.1093/sysbio/syu046  1
2014 Huang H, Tran LA, Knowles LL. Do estimated and actual species phylogenies match? Evaluation of East African cichlid radiations. Molecular Phylogenetics and Evolution. 78: 56-65. PMID 24837624 DOI: 10.1016/j.ympev.2014.05.010  0.92
2014 Edwards DL, Knowles LL. Species detection and individual assignment in species delimitation: can integrative data increase efficacy? Proceedings. Biological Sciences / the Royal Society. 281: 20132765. PMID 24403337 DOI: 10.1098/rspb.2013.2765  0.92
2014 Olave M, Solà E, Knowles LL. Upstream analyses create problems with DNA-based species delimitation. Systematic Biology. 63: 263-71. PMID 24361591 DOI: 10.1093/sysbio/syt106  0.92
2014 Alvarado-Serrano DF, Knowles LL. Ecological niche models in phylogeographic studies: applications, advances and precautions. Molecular Ecology Resources. 14: 233-48. PMID 24119244 DOI: 10.1111/1755-0998.12184  0.92
2014 Lanier HC, Huang H, Knowles LL. How low can you go? The effects of mutation rate on the accuracy of species-tree estimation. Molecular Phylogenetics and Evolution. 70: 112-9. PMID 24060367 DOI: 10.1016/j.ympev.2013.09.006  0.92
2013 He Q, Edwards DL, Knowles LL. Integrative testing of how environments from the past to the present shape genetic structure across landscapes. Evolution; International Journal of Organic Evolution. 67: 3386-402. PMID 24299395 DOI: 10.1111/evo.12159  0.92
2013 Alvarado-Serrano DF, Luna L, Knowles LL. Localized versus generalist phenotypes in a broadly distributed tropical mammal: how is intraspecific variation distributed across disparate environments? Bmc Evolutionary Biology. 13: 160. PMID 23899319 DOI: 10.1186/1471-2148-13-160  0.92
2013 Oneal E, Knowles LL. Ecological selection as the cause and sexual differentiation as the consequence of species divergence? Proceedings. Biological Sciences / the Royal Society. 280: 20122236. PMID 23173206 DOI: 10.1098/rspb.2012.2236  0.92
2013 Lanier HC, Edwards DL, Knowles LL. Phylogenetic structure of vertebrate communities across the Australian arid zone Journal of Biogeography. 40: 1059-1070. DOI: 10.1111/jbi.12077  0.92
2012 Knowles LL, Lanier HC, Klimov PB, He Q. Full modeling versus summarizing gene-tree uncertainty: method choice and species-tree accuracy. Molecular Phylogenetics and Evolution. 65: 501-9. PMID 22835380 DOI: 10.1016/j.ympev.2012.07.004  0.44
2012 Brown JL, Knowles LL. Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika. Molecular Ecology. 21: 3757-75. PMID 22702844 DOI: 10.1111/j.1365-294X.2012.05640.x  0.92
2012 Edwards DL, Keogh JS, Knowles LL. Effects of vicariant barriers, habitat stability, population isolation and environmental features on species divergence in the south-western Australian coastal reptile community. Molecular Ecology. 21: 3809-22. PMID 22646317 DOI: 10.1111/j.1365-294X.2012.05637.x  0.92
2012 Lanier HC, Knowles LL. Is recombination a problem for species-tree analyses? Systematic Biology. 61: 691-701. PMID 22215721 DOI: 10.1093/sysbio/syr128  0.92
2011 Knowles LL, Klimov PB. Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae). Parasitology. 138: 1750-9. PMID 21554840 DOI: 10.1017/S003118201100031X  0.92
2011 Klimov PB, Knowles LL. Repeated parallel evolution of minimal rRNAs revealed from detailed comparative analysis. The Journal of Heredity. 102: 283-93. PMID 21422103 DOI: 10.1093/jhered/esr005  0.92
2011 McCormack JE, Heled J, Delaney KS, Peterson AT, Knowles LL. Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays. Evolution; International Journal of Organic Evolution. 65: 184-202. PMID 20681982 DOI: 10.1111/j.1558-5646.2010.01097.x  0.92
2010 Carstens BC, Knowles LL. Navigating the unknown: model selection in phylogeography. Models of population structure: tools for thinkers. Molecular Ecology. 19: 4581-2. PMID 20958809 DOI: 10.1111/j.1365-294X.2010.04851.x  0.92
2010 Huang H, He Q, Kubatko LS, Knowles LL. Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Systematic Biology. 59: 573-83. PMID 20833951 DOI: 10.1093/sysbio/syq047  0.92
2010 McCormack JE, Zellmer AJ, Knowles LL. Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation? Insights from tests with niche models. Evolution; International Journal of Organic Evolution. 64: 1231-44. PMID 19922442 DOI: 10.1111/j.1558-5646.2009.00900.x  0.92
2010 Beaumont MA, Nielsen R, Robert C, Hey J, Gaggiotti O, Knowles L, Estoup A, Panchal M, Corander J, Hickerson M, Sisson SA, Fagundes N, Chikhi L, Beerli P, Vitalis R, et al. In defence of model-based inference in phylogeography Molecular Ecology. 19: 436-446. DOI: 10.1111/j.1365-294X.2009.04515.x  0.92
2010 Oneal E, Otte D, Knowles LL. Testing for biogeographic mechanisms promoting divergence in Caribbean crickets (genus Amphiacusta) Journal of Biogeography. 37: 530-540. DOI: 10.1111/j.1365-2699.2009.02231.x  0.92
2009 Huang H, Knowles LL. What is the danger of the anomaly zone for empirical phylogenetics? Systematic Biology. 58: 527-36. PMID 20525606 DOI: 10.1093/sysbio/syp047  0.92
2009 McCormack JE, Huang H, Knowles LL. Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Systematic Biology. 58: 501-8. PMID 20525604 DOI: 10.1093/sysbio/syp045  0.92
2009 Knowles LL. Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Systematic Biology. 58: 463-7. PMID 20525600 DOI: 10.1093/sysbio/syp061  0.92
2009 Zellmer AJ, Knowles LL. Disentangling the effects of historic vs. contemporary landscape structure on population genetic divergence. Molecular Ecology. 18: 3593-602. PMID 19674302 DOI: 10.1111/j.1365-294X.2009.04305.x  0.92
2009 Kubatko LS, Carstens BC, Knowles LL. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics (Oxford, England). 25: 971-3. PMID 19211573 DOI: 10.1093/bioinformatics/btp079  0.92
2008 Knowles LL. Why does a method that fails continue to be used? Evolution; International Journal of Organic Evolution. 62: 2713-7. PMID 18973487 DOI: 10.1111/j.1558-5646.2008.00481.x  0.92
2008 Gray DA, Huang H, Knowles LL. Molecular evidence of a peripatric origin for two sympatric species of field crickets (Gryllus rubens and G. texensis) revealed from coalescent simulations and population genetic tests. Molecular Ecology. 17: 3836-55. PMID 18647239 DOI: 10.1111/j.1365-294X.2008.03827.x  0.92
2008 Knowles LL, Chan YH. Resolving species phylogenies of recent evolutionary radiations Annals of the Missouri Botanical Garden. 95: 224-231. DOI: 10.3417/2006102  0.92
2007 Connallon T, Knowles LL. Recombination rate and protein evolution in yeast. Bmc Evolutionary Biology. 7: 235. PMID 18042299 DOI: 10.1186/1471-2148-7-235  0.92
2007 Knowles LL, Carstens BC. Delimiting species without monophyletic gene trees. Systematic Biology. 56: 887-95. PMID 18027282 DOI: 10.1080/10635150701701091  0.92
2007 Márquez EJ, Knowles LL. Correlated evolution of multivariate traits: detecting co-divergence across multiple dimensions. Journal of Evolutionary Biology. 20: 2334-48. PMID 17956395 DOI: 10.1111/j.1420-9101.2007.01415.x  0.92
2007 Richards CL, Knowles LL. Tests of phenotypic and genetic concordance and their application to the conservation of Panamanian golden frogs (Anura, Bufonidae). Molecular Ecology. 16: 3119-33. PMID 17651191 DOI: 10.1111/j.1365-294X.2007.03369.x  0.92
2007 Klimov PB, O'Connor BM, Knowles LL. Museum specimens and phylogenies elucidate ecology's role in coevolutionary associations between mites and their bee hosts. Evolution; International Journal of Organic Evolution. 61: 1368-79. PMID 17542846 DOI: 10.1111/j.1558-5646.2007.00119.x  0.92
2007 Carstens BC, Knowles LL. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Systematic Biology. 56: 400-11. PMID 17520504 DOI: 10.1080/10635150701405560  0.92
2007 Knowles LL, Carstens BC, Keat ML. Coupling genetic and ecological-niche models to examine how past population distributions contribute to divergence. Current Biology : Cb. 17: 940-6. PMID 17475496 DOI: 10.1016/j.cub.2007.04.033  0.92
2007 Onealt E, Connallon T, Knowles LL. Conflict between direct and indirect benefits of female choice in desert Drosophila. Biology Letters. 3: 29-32. PMID 17443958 DOI: 10.1098/rsbl.2006.0565  0.92
2007 Knowles LL, Carstens BC. Estimating a geographically explicit model of population divergence. Evolution; International Journal of Organic Evolution. 61: 477-93. PMID 17348914 DOI: 10.1111/j.1558-5646.2007.00043.x  0.92
2007 Carstens BC, Knowles LL. Shifting distributions and speciation: species divergence during rapid climate change. Molecular Ecology. 16: 619-27. PMID 17257117 DOI: 10.1111/j.1365-294X.2006.03167.x  0.92
2006 Connallon T, Knowles LL. Evidence for overdominant selection maintaining X-linked fitness variation in Drosophila melanogaster. Evolution; International Journal of Organic Evolution. 60: 1445-53. PMID 16929661 DOI: 10.1554/06-119.1  0.92
2006 Maddison WP, Knowles LL. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology. 55: 21-30. PMID 16507521 DOI: 10.1080/10635150500354928  0.92
2005 Knowles LL, Richards CL. Importance of genetic drift during Pleistocene divergence as revealed by analyses of genomic variation. Molecular Ecology. 14: 4023-32. PMID 16262856 DOI: 10.1111/j.1365-294X.2005.02711.x  0.92
2005 Connallon T, Knowles LL. Intergenomic conflict revealed by patterns of sex-biased gene expression. Trends in Genetics : Tig. 21: 495-9. PMID 16039005 DOI: 10.1016/j.tig.2005.07.006  0.92
2004 Knowles LL, Hernandez BB, Markow TA. Exploring the consequences of postmating-prezygotic interactions between the sexes. Proceedings. Biological Sciences / the Royal Society. 271: S357-9. PMID 15504017 DOI: 10.1098/rsbl.2004.0192  0.92
2004 Knowles LL. The burgeoning field of statistical phylogeography. Journal of Evolutionary Biology. 17: 1-10. PMID 15000642 DOI: 10.1046/j.1420-9101.2003.00644.x  0.92
2002 Knowles LL, Maddison WP. Statistical phylogeography. Molecular Ecology. 11: 2623-35. PMID 12453245 DOI: 10.1046/j.1365-294X.2002.01637.x  0.92
2002 Kurdziel JP, Knowles LL. The mechanisms of morph determination in the amphipod Jassa: implications for the evolution of alternative male phenotypes. Proceedings. Biological Sciences / the Royal Society. 269: 1749-54. PMID 12350261 DOI: 10.1098/rspb.2002.2089  0.92
2001 Knowles LL, Markow TA. Sexually antagonistic coevolution of a postmating-prezygotic reproductive character in desert Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 98: 8692-6. PMID 11447265 DOI: 10.1073/pnas.151123998  0.92
2001 Knowles LL. Genealogical portraits of speciation in montane grasshoppers (genus Melanoplus) from the sky islands of the Rocky Mountains. Proceedings. Biological Sciences / the Royal Society. 268: 319-24. PMID 11217904 DOI: 10.1098/rspb.2000.1364  0.92
1999 Knowles LL, Futuyma DJ, Eanes WF, Rannala B. INSIGHT INTO SPECIATION FROM HISTORICAL DEMOGRAPHY IN THE PHYTOPHAGOUS BEETLE GENUS OPHRAELLA. Evolution; International Journal of Organic Evolution. 53: 1846-1856. PMID 28565438 DOI: 10.1111/j.1558-5646.1999.tb04567.x  0.64
1999 Knowles LL, Levy A, McNellis JM, Greene KP, Futuyma DJ. TESTS OF INBREEDING EFFECTS ON HOST-SHIFT POTENTIAL IN THE PHYTOPHAGOUS BEETLE OPHRAELLA COMMUNA. Evolution; International Journal of Organic Evolution. 53: 561-567. PMID 28565413 DOI: 10.1111/j.1558-5646.1999.tb03791.x  0.64
1996 Meyer A, Knowles LL, Verheyen E. Widespread geographical distribution of mitochondrial haplotypes in rock-dwelling cichlid fishes from Lake Tanganyika. Molecular Ecology. 5: 341-50. PMID 8688956  0.92
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