Knowles LL, PB Klimov. 2011. Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse group of feather mites (Acari: Proctophyllodidae). Parasitology (special issue on phylogenetics), in press.
Klimov PB, LL Knowles. 2011. Repeated parallel evolution of minimal rRNAs revealed from detailed comparative analyses. J. of Heredity 102:283-293.
McCormack J, Heled J, Delaney KS, Peterson TA, Knowles LL. 2011. Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays. Evolution 65:184-202.
Carstens BC, Knowles LL. 2010. Navigating the unknown: model selection in phylogeography. Mol. Ecol. 19:4581-4582.
Knowles LL. 2010. Sampling Strategies for Species-Tree Estimation. In: Estimating Species Trees: Practical and Theoretical Aspects (L. L. Knowles and L. S. Kubatko, eds.), pp. 1-12. Wiley-Blackwell.
Knowles LL, LS Kubatko. 2010. Estimating species trees: an introduction to concepts and models. In: Estimating Species Trees: Practical and Theoretical Aspects (L. L. Knowles and L. S. Kubatko, eds.), pp. 163-172. Wiley-Blackwell.
Edwards D, S Keogh, LL Knowles. 2010. Model-based comparative phylogeographic hypothesis testing of co-distributed Australian reptiles with coupled ENM and ABC analyses. Mol. Ecol., in review.
Oneal E, D Otte, LL Knowles (2010) Testing for biogeographic mechanisms promoting divergence in Caribbean crickets (genus Amphiacusta). J. Biogeogr. 37:530-540.
Knowles LL, DF Alvarado-S (2010) Exploring the population genetic consequences of the colonization process with spatio-temporally explicit models: insights from coupled ecological, demographic, and genetic models in montane grasshoppers. Mol. Ecol.19:3727-3745.
McCormack JE, AJ Zellmer, LL Knowles (2010) Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation?: insights from tests with niche models. Evolution 64:1231-1244.
Huang H, He Q, Kubatko LS, Knowles LL (2010) Sources of Error for Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing Among Different Methods. Syst. Biol. 59:573-583.
Beaumont M, Rasmus N, Robert C, Hey J, Gaggiotti O, Knowles LL , Estoup A, Panchal M, Corander J, Hickerson M, Sisson S, Fagundes N, Chikhi L, Beerli P, Vitalis R, Cornuet J-M, Huelsenbeck J, Foll M, Yang ZH, Rousset F, Balding D, Excoffier L (2010) In defense of model-based inference in phylogeography. Mol. Ecol. 19:436-446.
Knowles LL (2009) Statistical phylogeography. Annu. Rev. Ecol. Syst. 40:593-612.
Knowles LL (2009) Species tree estimation: methods of phylogenetic analysis when there is incongruence across genes. Syst. Biol. 58:463-467.
Zellmer AJ, LL Knowles (2009) Disentangling the effects of historic versus contemporary landscape structure on population genetic divergence. Mol. Ecol. 18:3593-3602.
Huang H, LL Knowles (2009) What's the biological reality of the anomaly zone? Syst. Biol. 58:527-536.
McCormack JE, H Huang, LL Knowles (2009) Maximum-likelihood Estimates of Species Trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Syst. Biol. 58:501-508.
Kubatko L, BC Carstens, LL Knowles (2009) STEM: Species tree estimation using Maximum likelihood for gene trees under coalescence, Bioinformatics 25:971-973.
McCormack JE, H Huang, LL Knowles (2009) Sky islands. in R. Gillespie and D. Clague, eds. Encyclopedia of Islands. University of California Press, Berkeley, CA.
Knowles LL (2008) Why does a method that fails continued to be used? Evolution 62:2713-17.
Gray, D.A., H. Huang, & L.L. Knowles. 2008. 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. Mol. Ecol., in press.
Knowles, L.L & Y-H Chan. 2008. Resolving species phylogenies of recent evolutionary radiations. Ann. Missouri Bot. Gard. 95:224-231.
Connallon, T. & L.L. Knowles. 2007. Recombination rate and protein evolution in yeast. BMC Evolutionary Biology, 7:235.doi:10.1186/1471-2148-7-235.
Richards, C.L., B.C. Carstens, L.L. Knowles. 2007. Distribution modeling and statistical phylogeography: an integrative framework for testing biogeographic hypotheses. J. Biogeogr. 34:1833-1845.
Marquez, E.J. & Knowles, L.L., 2007. Correlated Evolution in multivariate traits: detecting codivergence across multiple dimensions. J. Evol. Biol. 20:2334-2348. doi:10.1111/j.1420-9101.2007.01415
Knowles, L.L., B.C.Carstens, & M. L. Keat. 2007. Coupled Genetic and Ecological-Niche Models to Examine How Past Population Distributions Contribute to Divergence. Current Biol. 17:1-7.
Knowles, L.L., & B.C. Carstens. 2007. Delimiting species without monophyletic gene trees. Syst. Biol. 56:887-895.
Knowles, L.L. & B.C. Carstens. 2007. Estimating a geographically explicit model of population divergence. Evolution 61:477-493.
Richards, C.L. & Knowles, L.L. 2007. Tests of phenotypic and genetic concordance and their application to the conservation of Panamanian golden frogs (Anura, Bufonidae). Mol. Ecol. 16:3119-3133.
Klimov, P.B., B.M. OConnor, & L.L. Knowles. 2007. Museum specimens and phylogenies elucidate ecology's role in determining coevoutionary associations between chaetodactylid mites and their bee hosts. Evolution 61:1368-1379.
Carstens, B.C., & L.L. Knowles. 2007. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 56:1-12.
Carstens, B.C. & L.L. Knowles. 2007. Shifting distributions and speciation: species divergence during rapid climate change. Mol. Ecol. 16:619-627.
E. Oneal, T. Connallon, & L.L. Knowles. 2007. Conflict between direct and indirect benefits of female choice in desert Drosophila. Biology Letters, Proc. R. Soc. Lond. B. 3:29-32.
Connallon, T.M. & L.L. Knowles. 2006. Evidence for overdominant selection maintaining X-linked fitness variation in Drosophila melanogaster. Evolution 60:1445-1453.
Maddison, W.P. & L.L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
Carstens, B.C. & L.L. Knowles. 2006. Variable nuclear markers for Melanoplus oregonensis identified from the screening of a genomic library. Mol Ecol. Notes 6:683-685 doi:10.1111/j.1471-8286.2006.01309.x
Knowles, L.L. & Richards, C.L. 2005. Importance of genetic drifts during Pleistocene divergence as revealed by analysis of genomic variation. Mol. Ecol.14:4023-4032.
Connallon, T. & L.L. Knowles. 2005. Intergenomic conflict revealed by patterns of sex-biased gene expression. Trends in Genetics 21:495-499.
Pfeiler, E., L.A. Hurtado, L.L. Knowles, J. Torre-Cosio, L. Bourillon-Moreno, J.F. Marquez-Farias, & G. Montemayor-Lopez. 2005. Population genetics of the swimming crab Callinectes bellicosus (Brachyura: Portunidae) from the eastern Pacific Ocean. Mar. Biol. 146:559-569. (doi:10.1007/s00227-004-1463-y).
Knowles, L.L. , B.B. Hernandez, & T.A. Markow. 2005. Non-antagonistic interactions between the sexes revealed by the ecological consequences of reproductive traits.J. Evol. Biol. 18:156-161 (doi:10.1111/j.1420-9101.2004.00779.x)
Knowles, L.L. 2004. The burgeoning field of statistical phylogeography. J. Evol. Biol. 17:1-10 (doi: 10.1046/j.1420-9101.2003.0064.x).
Knowles, L.L. , B.B. Hernandez, & T.A. Markow. 2004. Exploring the consequences of postmating-prezygotic interactions between the sexes. Proc. R. Soc. Lond. Series B 271:S357-S359 (doi: 10.1098/rsbl.2004.0192).
Knowles, L.L. & W.P. Maddison. 2002. Statistical phylogeography. Mol. Ecol. 11:2623-2635.
Kurdziel, J.P. & L.L. Knowles. 2002. The mechanisms of morph determination in the amphipod Jassa: implications for the evolution of alternative male phenotypes. Proc. R. Soc. Lond. Series B. 269:1749-1754.
Knowles, L.L. & T. A. Markow. 2001. Sexually antagonistic coevolution of a postmating-prezygotic reproductive character in desert Drosophila. Proc. Natl. Academy Sci. USA 98:8692-8696.
Knowles, L.L. 2001.Genealogical portraits of speciation in montane grasshoppers (genus Melanoplus) from the sky islands of the Rocky Mountains. Proc. R. Soc. Lond. Series B. 268:319-324.
Knowles, L.L. 2001. Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Mol. Ecol. 10:691-701.
Knowles, L.L. 2000. Tests of Pleistocene speciation in montane grasshoppers from the sky islands of western North America (genus Melanoplus). Evolution 54:1337-1348.
Knowles, L.L. & D. Otte. 2000. Phylogenetic analysis of montane grasshoppers from western North America (genus Melanoplus, Acrididae: Melanoplinae). Annals Entom. Soc. Am. 93:421-431
Knowles, L.L., D.J. Futuyma, W.F. Eanes & B. Rannala. 1999. Insights into speciation mode from historical demography in the phytophagous beetle Ophraella. Evolution 53:1846-1856.
Knowles, L.L., A. Coelho, J. McNellis, K.P. Greene, & D.J. Futuyma. 1999. Tests of inbreeding effects on host shift potential in the phytophagous beetle Ophraella communa. Evolution 53:561-567.
Knowles, L.L. & S.S. Bell. 1998. The influence of habitat structure on faunal-habitat associations in a Tampa Bay seagrass system, Florida. Bulletin of Marine Science 62:781-894.
Meyer, A., L.L. Knowles & E. Verheyen. 1995. Widespread distribution of mitochondrial haplotypes in rock-dwelling cichlid fishes from Lake Tanganyika. Mol. Ecol. 5:341-350.
Knowles, L.L. 2003. Research update: Nonstochastic variation of species-level diversification rates within angiosperms. BioMedNet record 1404200381.
Knowles, L.L. 2002. Reconstructing rapid climate change from a snail’s pace. TREE 17:355.
Knowles, L.L. 2001. An evolutionary slant on species-area curves. TREE 16:174-175.
Knowles, L.L. 2000. Conflict begets diversity? TREE 15:488-489.
Knowles, L.L. 1998. Book review of: The Ice-Age History of Southwestern National Parks, by S.A. Elias. Quarterly Review of Biology 73:67.
Knowles, L.L. 1997. Book review of: The Ice-Age History of National Parks in the Rocky Mountains, by S.A. Elias. Quarterly Review of Biology 72:66.
