Will Freyman


Chamerion latifolium (Onagraceae)

Articles

Freyman, W.A., McManus, K.F., Shringarpure, S.S., Jewett, E.M., and A. Auton. Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform. In prep.

Micheletti, S.J., Bryc, K., Esselmann, S.G.A., Freyman, W.A., Moreno, M.E., Shastri, A.J., Beleza, S., and J.L. Mountain. The genetic consequences in the Americas of the transatlantic slave trade. In review.

Furness, A.I., Springer, M.S., Freyman, W.A., and S. Höhna. Placental invasiveness and Eutherian mammal diversification. In review.

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 syz076 [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. In review. [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]

Abstracts

Freyman, W.A., McManus, K.F., Shringarpure, S.S., Jewett, E.M., and A. Auton. Fast and accurate identity-by-descent inference despite haplotype and phasing errors. Bay Area Population Genomics XVIII, Berkeley, CA.

Micheletti, S.J., Bryc, K., Esselmann, S.G.A., Freyman, W.A., Moreno, M.E., Shastri, A.J., Beleza, S., and J.L. Mountain. The genetic consequences in the Americas of the transatlantic slave trade. American Society of Human Genetics Annual Meeting 2019, Houston TX.

Jewett, E.M., McManus, K.F., Freyman, W.A., and A. Auton. Bonsai and Big Bonsai: Efficient methods for pedigree inference. Probabilistic Modeling in Genomics 2019, Aussois, France.

Freyman, W.A., McManus, K.F., Shringarpure, S.S., Jewett, E.M., and A. Auton. Fast and accurate identity-by-descent inference despite haplotype and phasing errors. Probabilistic Modeling in Genomics 2019, Aussois, France.

Qiao, Y., Jewett, E.M., McManus, K.F., Freyman, W.A., Blangero, J., and A. Williams. Reconstructing the genotypes of parents from siblings and close relatives. Probabilistic Modeling in Genomics 2019, Aussois, France.

Freyman, W.A., McManus, K.F., Shringarpure, S.S., Jewett, E.M., and A. Auton. Fast and accurate identity-by-descent inference despite haplotype and phasing errors. SMBE 2019, Manchester, England.

Baldwin, B.G., Wood, K.R., and W.A. Freyman. Revisiting cytonuclear discordance, habitat shifts, and biogeographic patterns in the Hawaiian silversword alliance (Compositae). Botany 2019, Tucson, AZ.

Song, M., Tribble, C., Martinez-Gomez, J., Freyman, W.A. Hohna, S., Specht, C. and C. Rothfels. Diversification rates across lineages: how does biological meaning differ across model-based approaches? Botany 2019, Tucson, AZ.

Freyman, W.A. and E.E. Goldberg. 2018. Testing the adequacy of trait-dependent speciation and extinction models with posterior predictive checks. Evolution 2018, Montpellier, France

Zenil-Ferguson, R., Freyman, W.A., Jordan, K. 2018. RevBayes: An introduction to Bayesian inference in phylogenetics. Botany 2018, Rochester, MN

Lichter Marck, I.H., Freyman, W.A., Schneider, A., Tian, E., Baldwin, B. 2018. Phylogenomics of the rock daisies (Perityleae; Asteraceae). Botany 2018, Rochester, MN

Wilson, C., Freyman, W.A. 2018. Phylogenomics of subgenus Hermodactyloides, a small lineage of bulbous Iris that are mostly narrow endemics. Botany 2018, Rochester, MN

Puente-Lelievre, C., Crayn, D., Freyman, W.A., Potter, B. 2018. Historical biogeography of the Australasian Ericaceae: evaluating competing vicariance and dispersal scenarios. Botany 2018, Rochester, MN

Mitine, C., Lehman, K., Thornhill, A., Freyman, W.A., Wright, C., Hernandez, A.I. Baldwin, B., Mishler, B., Guilliams, C.M. 2018. Using spatial phylogenetics to inform conservation at the archipelago-scale: an introduction to the Channel Islands Phylodiversity Project. Botany 2018, Rochester, MN

Landis, M.J., Freyman, W.A., and B.G. Baldwin. Dating the Hawaiian silversword radiation in the face of phylogenetic, biogeographic, and paleogeographic uncertainty. GSA 2017, Seattle, WA

Freyman, W.A. 2017. Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible lineages. Evolution 2017, Portland, OR

Furness, A., Springer, M., Freyman, W.A., and S. Höhna. 2017. Placental invasiveness and Eutherian mammal diversification. Evolution 2017, Portland, OR

Landis, M.J., Brown, J.M., Coghill, L.M., Freyman, W.A., Heath, T.A., Pett, W.C., Wright, A.M., and S. Höhna. 2017. RevBayes. iEvoBio 2017, Portland, OR

Freund, F.D., Freyman, W.A., and C. Rothfels. 2017. Inferring the evolution of corm lobation in Isoëtes using Bayesian model-averaged ancestral state reconstruction. Botany 2017, Fort Worth, TX

Jordon-Thaden, I.E., Freyman, W.A., Cantley, J., Stoughton, T., Tank, D., Hayes, D., Koch, M.A., Sharbel, T., and C.T. Martine. 2017. Alpine plants scoff at mountain valleys and migrate anyway. Botany 2017, Fort Worth, TX

Klingman, B., Jordon-Thaden, I.E., Martine, C.T., and Freyman, W.A. 2017. Ancestral area reconstruction of population-level sampling of an alpine species, Draba oligosperma (Brassicaceae). Botany 2017, Fort Worth, TX

Lichter Marck, I., Freyman, W.A., Schneider, A.C., and B.G. Baldwin. 2017. Systematics of the rock daisies (subtribe Perityleae; Asteraceae). Botany 2017, Fort Worth, TX

Freyman, W.A. 2017. Novel approaches to stochastic character mapping and applications to the evolution of Onagraceae. Graduate Student Meeting of the California Botanical Society, Santa Barbara, CA

Freyman, W.A. and S. Höhna. 2017. Phylogenetic models of chromosome number evolution and chromosomal speciation. SSB 2017 Standalone Meeting, Baton Rouge, LA

Freyman, W.A. 2016. Cladogenetic and anagenetic models of chromosome number evolution: model averaging using reversible jump MCMC. Evolution 2016, Austin, TX

Sheth, S.N., Freyman, W.A., Baldwin, B.G., and D.D. Ackerly. 2016. Relationships among rates of climatic niche evolution and diversification. Evolution 2016, Austin, TX

Freyman, W.A. Höhna, S., and B.G. Baldwin. Phylogenetic models of chromosome number evolution and chromosomal speciation. Botany 2016, Savannah, GA

Jordon-Thaden, I.E., Freyman, W.A., Ruhfel, B.R., Martine, C. 2016. Glacial relict speciation of the Appalachian diploid Draba ramosissima (Brassicaceae). Botany 2016, Savannah, GA

Thornhill, A.H., Baldwin, B,G., Freyman, W.A., Nosratinia, S., Morueta-Holme, N., Kling, M., Baxter, D., Madsen, T., Ackerly, D.D., B.D. Mishler. Hotspots of phylogenetic richness and endemism in the California flora. Botany 2016, Savannah, GA

Mishler, B.D., Thornhill, A.H., Kling, M., Freyman, W.A., Ackerly, D.D., B.G. Baldwin. Hotspots of species richness and endemism in the California flora. Botany 2016, Savannah, GA

Urbina-Cassanova, R., Freyman, W.A., Thornhill, A.H., Mishler, B.D., R. Scherson. 2016. Phylogenetic diversity and endemism in the vascular flora of Chile. VIII Southern Connection Congress 2016, Punta Arenas, Chile

Freyman, W.A. and B.G. Baldwin. 2015. Integrating cytogenetic, molecular, and paleontological data in a joint Bayesian phylogenetic analysis: a case study in Onagraceae. Graduate Student Meeting of the California Botanical Society, Claremont, CA. Won Best Overall Presentation Prize.

Schneider, A.C., Guilliams, C.M., Freyman, W.A., Springer, Y., and B.G. Baldwin. 2014. Species relationships in Hesperolinon (Linaceae) inferred from ITS and chloroplast sequence data. Northern California Botanists Symposium, Chico, CA

Freyman, W.A. and J.P. Olfelt. 2013. Phylogeny and divergence times among the North American Rhodiola (Crassulaceae) species. Botany 2013, New Orleans, LA

Freyman, W.A. and K.A. Glennemeier. 2013. Restoration Map: a tool for stewards to plan and assess restoration projects. Wild Things Conference, Chicago, IL

Freyman, W.A., M.J. Rios, and J.P. Olfelt. 2012. Molecular phylogeny of the North American Rhodiola (Crassulaceae). SACNAS National Conference, Seattle, WA

Freyman, W.A., S. Packard, and J. Pepper. 2012. Restoration Map: a web-based tool for spatially explicit planning of ecological restoration projects. Ecological Society of America Annual Meeting, Portland, OR