Will Freyman

Publications

Harney, É., Micheletti, S., Bruwelheide, K.S., Freyman, W.A., Bryc, K., Akbari, A., Jewett, E., Comer, E., Gates Jr, H.L., Heywood, L., Thornton, J., Curry, R., Esselmann, S.A., Barca, K.G., Sedig, J., Sirak, K., Olalde, I., Adamski, N., Bernardos, R., Broomandkhoshbacht, N., Ferry, M., Qiu, L., Stewardson, K., Workman, J.N., Zalzala, F., Mallick, S., Micco, A., Mah, M., Zhang, Z., Rohland, N., Mountain, J.L., Owsley, D.W., and D. Reich. 2023. The genetic legacy of African Americans from Catoctin Furnace. Science, 381 (6657), 482-483. [journal] [pdf]

Shi, J., O'Connell, J., Hicks, B., Wang, W., Bryc, K., Brady, J.J., Vacic, V., Freyman, W.A., Abul-Husn, N.S., Auton, A., and S. Shringarpure. 2023. GWAS of cataract in Puerto Ricans identifies a novel large-effect variant in ITGA6. medRxiv 2023.07.25.23293. [preprint]

Freyman, W.A., Johnson, M.G., and C.J. Rothfels. 2023. Homologizer: phylogenetic phasing of gene copies into polyploid subgenomes. Methods in Ecology and Evolution 14 (5), 1230–1244 [journal] [preprint]

Freyman, W.A. and C.J. Rothfels. 2023. Phasing gene copies into polyploid subgenomes using a Bayesian phylogenetic approach. Chapter in Polyploidy: Methods and Protocols (pp. 123-138). New York, NY: Springer US. [publisher] [pdf]

Martínez-Gómez, J., Song, M.J., Tribble, C.M., Kopperud, B.T., Höhna, S., Freyman, W.A., Specht, C.D., and C.J. Rothfels. 2023. Commonly used Bayesian diversification-rate models produce biologically meaningful differences on empirical phylogenies. bioRxiv 2023.05.17.541228. [preprint]

Schwery, O., Freyman, W.A., and E.E. Goldberg. 2023. adequaSSE: Model adequacy testing for trait-dependent diversification models. bioRxiv 2023.03.06.531416. [preprint]

Tribble, C.M., Freyman, W.A., Landis, M.J., Lim, J.Y., Barido-Sottani, J., Kopperud, B.T., Höhna, S., and M.R. May. 2022. RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes. Methods in Ecology and Evolution 13(2), 314-323. [journal] [preprint]

Baldwin, B.G., Wood, K.R., and Freyman, W.A. 2021. Directionally biased habitat shifts and biogeographically informative cytonuclear discordance in the Hawaiian silversword alliance (Compositae). American Journal of Botany 108(10) 2015-2037. [journal] [pdf]

Jewett, E.M., McManus, K.F., Freyman, W.A., and A. Auton. 2021. Bonsai: an efficient method for inferring large human pedigrees from genotype data. American Journal of Human Genetics 108(11) 2052-2070. [journal] [preprint]

Freyman, W.A., McManus, K.F., Shringarpure, S.S., Jewett, E.M., and A. Auton. 2021. Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform. Molecular Biology and Evolution 38(5) 2131–2151. [preprint] [journal] [pdf]

Lichter‐Marck, I.H., Freyman, W.A., Siniscalchi, C.M., Mandel, J.R., Castro‐Castro, A., Johnson, G., and B.G. Baldwin. 2020. Phylogenomics of Perityleae (Compositae) provides new insights into morphological and chromosomal evolution of the rock daisies. Journal of Systematics and Evolution 58(6) 853-880. [journal] [pdf]

Micheletti, S.J., Bryc, K., Esselmann, S.G.A., Freyman, W.A., Moreno, M.E., Shastri, A.J., Beleza, S., and J.L. Mountain. 2020. Genetic consequences of the transatlantic slave trade in the Americas. American Journal of Human Genetics 107(2) 265-277. [journal] [pdf]

Verboom, G.A., Boucher, F.C., Ackerly, D.A., Wootton, L.M., and W.A. Freyman. 2020. Species selection regime and phylogenetic tree shape. Systematic Biology 69(4) 774-794 [journal] [pdf]

Höhna, S., Freyman, W.A., Nolen, Z., Huelsenbeck, J., May, M.R., and B.R. Moore. 2019. A Bayesian approach for estimating branch-specific speciation and extinction rates. bioRxiv 555805. [preprint]

Zenil‐Ferguson, R., Burleigh, J.G., Freyman, W.A., Igić, B., Mayrose, I., and E.E. Goldberg. 2019. Interaction among ploidy, breeding system and lineage diversification. New Phytologist. 224(3) 1252-1265 [journal]

Freyman, W.A. and S. Höhna. 2019. Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible lineages. Systematic Biology. 68(3) 505-519 [preprint] [journal]

Landis, M.J., Freyman, W.A., and B.G. Baldwin. 2018. Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty. Evolution 72(11) 2343-2359. [preprint] [journal]

Freund, F.D., Freyman, W.A. and C.J. Rothfels. 2018. Inferring the evolutionary reduction of corm lobation in Isoëtes using Bayesian model-averaged ancestral state reconstruction. American Journal of Botany 105(2) 275-286 [preprint] [journal]

Thornhill, A.H., Baldwin, B.G., Freyman, W.A., Nosratinia, S., Kling, M.M., Morueta-Holme, N., Madsen, T.P., Ackerly, D.D., and B.D. Mishler. 2017. Spatial phylogenetics of the native California flora. BMC Biology 15:96 [journal] [pdf]

Freyman, W.A. and S. Höhna. 2018. Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach. Systematic Biology 67(2) 195-215 [journal] [preprint] [pdf]

Scherson, R.A., Thornhill, A.H., Urbina-Casanova, R., Freyman, W.A., Pliscoff, P.A., B.D. Mishler. 2017. Spatial phylogenetics of the vascular flora of Chile. Molecular Phylogenetics and Evolution 112: 88-95 [journal] [pdf]

Baldwin, B.G., Thornhill, A.H., Freyman, W.A., Ackerly, D.D., Kling, M.M., Morueta-Holme, N., and B.D. Mishler. 2017. Species richness and endemism in the California flora. American Journal of Botany 104(3): 487-501 [journal] [pdf]

Schneider, A.C., Freyman, W.A., Guilliams, C.M., Springer, Y., and B.G. Baldwin. 2016. Pleistocene radiation of the serpentine-adapted genus Hesperolinon and other divergence times in Linaceae (Malpighiales). American Journal of Botany 103(1): 1-12 [journal] [pdf]

Freyman, W.A., L.A. Masters, and S. Packard. 2016. The Universal Floristic Quality Assessment (FQA) Calculator: an online tool for ecological assessment and monitoring. Methods in Ecology and Evolution 7(3): 380–383 [journal] [pdf]

Freyman, W.A. 2015. SUMAC: constructing phylogenetic supermatrices and assessing partially decisive taxon coverage. Evolutionary Bioinformatics 2015:11 263-266 [journal] [pdf]

Olfelt, J.P. and W.A. Freyman. 2014. Relationships of North American members of Rhodiola (Crassulaceae). Botany 92(12): 901-910 [journal] [pdf]

Freyman, W.A. and K.A. Glennemeier. 2014. Restoration Map: a web-based tool for spatial and participatory adaptive management of ecological restoration projects. Ecological Restoration (32-1) [journal] [pdf]