Molecular Phylogenetics Laboratory

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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.


Just some of the publications from work done in the MPL:

Andreasen, K., and B.G. Baldwin. 2003. Nuclear ribosomal DNA sequence polymorphism and hybridization in checker mallows (Sidalcea, Malvaceae). Molecular Phylogenetics and Evolution 29:563-581.

Andreasen, K., and B.G. Baldwin. 2003. Reexamination of relationships, habital evolution, and phylogeography of checker mallows (Sidalcea, Malvaceae) based on molecular phylogenetic data. American Journal of Botany 90:436-444.

Andreasen, K., and B.G. Baldwin. 2001. Unequal evolutionary rates between annual and perennial lineages of checker mallows (Sidalcea, Malvaceae): Evidence from 18S-26S rDNA internal and external transcribed spacers. Molecular Biology and Evolution 18:936-944.

Andreasen, K., and B. Bremer. 2000. Combined phylogenetic analysis in the Rubiaceae-Ixoroideae: Morphology, nuclear, and chloroplast DNA data. American Journal of Botany 87:1731-1748.

Andreasen, K., E.A. Cypher, and B.G. Baldwin. 2002. Sympatry between desert mallow, Eremalche exilis, and Kern mallow, E. kernenesis (Malvaceae): Molecular and morphological perspectives. Madroño 49:22-24.

Andreasen, K., B.G. Baldwin, and B. Bremer. 1999. Phylogenetic utility of the nuclear rDNA ITS region in subfamily Ixoroideae (Rubiaceae): Comparisons with cpDNA rbcL sequence data. Plant Systematics and Evolution 217:119-135.

Armbruster, W.S., and B.G. Baldwin. 2003. Pollination and evolution of euphorb vines in Madagascar. In S.M. Goodman and J.P. Benstead (eds.), The Natural History of Madagascar. University of Chicago Press, Chicago. Pp. 390-393.

Armbruster, W.S., C.P.H. Mulder, B.G. Baldwin, S. Kalisz, B. Wessa, and H. Nute. 2002. Comparative analysis of late floral development and mating-system evolution in tribe Collinsieae (Scrophulariaceae s. l.). American Journal of Botany 89:37-49.

Baldwin, B.G. 2006. Contrasting patterns and processes of evolutionary change in the tarweed-silversword lineage: Revisiting Clausen, Keck, and Hiesey's findings. Annals of the Missouri Botanical Garden 93:64-93.

Baldwin B.G. 2005. Origin of the serpentine-endemic herb Layia discoidea from the widespread L. glandulosa (Compositae). Evolution 59(11):2473-2479.

Baldwin, B.G. 2003. A phylogenetic perspective on the origin and evolution of Madiinae. In S. Carlquist, B.G. Baldwin, and G.D. Carr (eds.), Tarweeds and Silverswords: Evolution of the Madiinae. Missouri Botanical Garden Press, St. Louis. Pp. 193-228.

Baldwin, B.G. 2001. Harmonia guggolziorum (Compositae-Madiinae), a new tarweed from ultramafics of southern Mendocino County, California. Madroño 48:293-297.

Baldwin, B.G, and W.S. Armbruster. 2002. Collinsia antonina is evolutionarily distinct from C. parryi. Madroño 49:295-297.

Baldwin, B.G., and G.D. Carr. 2005. Dubautia kalalauensis, a new species of the Hawaiian silversword alliance from northwestern Kaua`i, U.S.A. Novon 15:259-263.

Baldwin, B.G., R.E. Preston, B.L. Wessa, and M. Wetherwax. 2001. A biosystematic and phylogenetic assessment of sympatric taxa in Blepharizonia (Compositae-Madiinae). Systematic Botany 26:184-194.

Baldwin, B.G., B.L. Wessa, and J. Panero. 2002. Nuclear rDNA evidence for major lineages of helenioid Heliantheae (Compositae). Systematic Botany 27:161-198.

Baldwin, B.G., and B.L. Wessa. 2000. Phylogenetic placement of Pelucha and new subtribes in Helenieae sensu stricto (Compositae). Systematic Botany 25:522-538.

Baldwin, B.G., and B.L. Wessa. 2000. Origin and relationships of the tarweed-silversword lineage (Compositae-Madiinae). American Journal of Botany 87:1890-1908.

Baldwin, B.G., and S. Markos. 1998. Phylogenetic utility of the external transcribed spacer (ETS) of 18S-26S rDNA: Congruence of ETS and ITS trees of Calycadenia (Compositae). Molecular Phylogenetics and Evolution 10:449-463.

Baldwin, B.G., and M.J. Sanderson. 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proceedings of the National Academy of Sciences, USA 95:9402-9406.

Caballero, S., H. Hamilton, L. Flórez-Gonzalez, J. Capella, C. Olavarría, H. Rosenbaum, and C.S. Baker. 2000. Stock identity and diversity of humpback whale mitochondrial DNA lineages on the Colombian winter breeding grounds. Report to the Scientific Commitee of the International Whaling Commission. SC/52/IA14.

Caballero, S., H. Hamilton, C. Jaramillo, J. Capella, L. Flórez-Gonzalez, C. Olavarría, H. Rosenbaum, F. Guhl, and C.S. Baker. 2000. Genetic characterization of the Colombian Pacific Coast humpback whale population using RAPDs and mitochondrial DNA sequences. Humpback Whale Conference, Queensland, Australia.

Carter, B.E., S. Nosratinia and J.R. Shevock. 2014. A revisitation of species circumscriptions and evolutionary relationships in Scouleria (Scouleriaceae). Systematic Botany 39: 4-9.

Chan, R., B.G. Baldwin, and R. Ornduff. 2002. Cryptic goldfields: A molecular phylogenetic re-investigation of Lasthenia californica sensu lato and close relatives (Compositae: Heliantheae sensu lato). American Journal of Botany 89:1103-1112.

Chan, R., B.G. Baldwin, , and R. Ornduff. 2001. Goldfields revisited: A molecular phylogenetic perspective on the evolution of Lasthenia (Compositae: Heliantheae sensu lato). International Journal of Plant Sciences 162:1347-1360.

Collins, A.G. 1998. Evaluating multiple alternative hypotheses for the origin of Bilateria: An analysis of 18S rRNA molecular evidence. Proceedings of the National Academy of Sciences, USA 95:15458-15463.

Collins, A.G. 1999. Molecules and evolutionary history. In D. Springer and J. Scotchmoor (eds.), Evolution: Investigating the Evidence. Paleontological Society Papers, Vol. 3.

Collins, A.G. 2001 Towards understanding the phylogenetic history of Hydrozoa: Hypothesis testing with 18S gene sequence data. Scientia Marina 65 (Suppl. 1).

Fine, P.V.A., T. M. Misiewicz, A.S. Chavez, and R.Q. Cuthrell. 2013. Population genetic structure of California hazelnut, an important food source for people in the Quiroste Valley in the Late Holocene. California Archaeology 5:353-370.

Fine, P.V.A., F. Zapata, and D. C. Daly. 2014. Investigating processes of Neotropical rain forest tree diversification by examining the evolution and historical biogeography of Protieae (Burseraceae). Evolution 68: 1988-2004.

Fine, P.V.A., F. Zapata, D. C. Daly, I. Mesones, T. M. Misiewicz, H. F. Cooper, and C. E. A. Barbosa. 2013. The importance of environmental heterogeneity and spatial distance in generating phylogeographic structure in edaphic specialist and generalist species of Protium (Burseraceae) across the Amazon basin. Journal of Biogeography 60: 646-661.

Ford, V.S., J. Lee, B.G. Baldwin, and L.D. Gottlieb. 2006. Species divergence and relationships in Stephanomeria (Compositae): PgiC phylogeny compared to prior biosystematic studies. American Journal of Botany 93:480-490.

Hamilton, H., S. Caballero, A.G. Collins, and R.L. Brownell, Jr. 2001. Evolution of river dolphins. The Royal Society Proceedings: Biological Sciences 268:549-556.

Harbaugh, D T. 2007. A taxonomic revision of Australian northern sandalwood (Santalum lanceolatum, Santalaceae). Australian Systematic Botany 20:409-416.

Harbaugh, D.T. 2008. Polyploid and hybrid origins of Pacific island sandalwoods (Santalum, Santalaceae) inferred from low-copy nuclear and flow cytometry data. International Journal of Plant Sciences 169:677-685.

Kelch, D.G., and B.G. Baldwin. 2003. Phylogeny and ecological radiation of New World thistles (Cirsium, Compositae - Carduae) based on ITS and ETS rDNA sequence data. Molecular Ecology 12:141-151.

La Farge, C., B.D. Mishler, J.A. Wheeler, D.P. Wall, K. Johannes, S. Schaffer, and A.J. Shaw. 2000. Phylogenetic relationships within the haplolepideous mosses. The Bryologist 103:257-276.

Lee, J., B.G. Baldwin, and L.D. Gottlieb. 2002. Phylogeny of Stephanomeria and related genera (Compositae-Lactuceae) based on analysis of 18S-26S nuclear rDNA ITS and ETS sequences. American Journal of Botany 89:160-168.

Lee, J., B.G. Baldwin, and L.D. Gottlieb. 2003. Phylogenetic relationships among the primarily North American genera of Cichorieae (Compositae) based on analysis of 18S-26S nuclear rDNA ITS and ETS sequences. Systematic Botany 28:616-626.

Lewis, L.A., B.D. Mishler, and R. Vilgalys. 1997. Phylogenetic relationships of the liverworts (Hepaticae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene rbcL. Molecular Phylogenetics and Evolution 7:377-393.

Markos, S., and B.G. Baldwin. 2001. Higher-level relationships and major lineages of Lessingia (Compositae, Astereae) based on nuclear rDNA internal and external transcribed spacer (ITS and ETS) sequences. Systematic Botany 26:168-183

Markos, S., and B.G. Baldwin. 2002. Structure, molecular evolution, and phylogenetic utility of the 5' region of the external transcribed spacer of 18S-26S rDNA in Lessingia (Compositae, Astereae). Molecular Phylogenetics and Evolution 23:214-228.

McCourt, R.M., K.G. Karol, J. Bell., S. Fritz, K. Helm-Bychowski, A. Grajewska, M.F. Wojciechowski, and R.W. Hoshaw. 2000. Phylogeny of the conjugating green algae (Zygnemophyceae) based on rbcLsequences. Journal of Phycology 36:747-758.

Mishler, B.D. 2014. Phylogenetic diversity and phylogenetic endemism in the California flora: a new NSF-funded initiative. The Jepson Globe 24(1): 1-6.

Misiewicz, T. M. and P. V. A. Fine. 2014. Evidence for ecological divergence across a mosaic of soil types in an Amazonian tropical tree: Protium subserratum (Burseraceae). Molecular Ecology 23: 2543-2558.

Moore AJ, Moore WL, Baldwin BG. 2014. Genetic and ecotypic differentiation in a Californian plant polyploid complex (Grindelia, Asteraceae). PLoS ONE 9: e95656.

Newton, A.E., C.J. Cox, J.G. Duckett, J.A. Wheeler, B. Goffinet, T.A.J. Hedderson, and B.D. Mishler. 2000. Evolution of the major moss lineages: Phylogenetic analyses based on multiple gene sequences and morphology. The Bryologist 103:187-211.

Pryer, K.M., H. Schneider, A.R. Smith, R. Cranfill, P.G. Wolf, J.S. Hunt, and S.D. Sipes. 2001. Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409:618-622.

Rajakaruna, N., B.G. Baldwin, R. Chan, A.M. Desrochers, B.A. Bohm, and J. Whitton. 2003. Edaphic races and phylogenetic taxa in the Lasthenia californica (Asteraceae) complex: An hypothesis of parallel evolution. Molecular Ecology 12:1675-1679.

Sanderson, M.J., M.F. Wojciechowski, J.-M. Hu, T. Sher Khan, and S.G. Brady. 2000. Error, bias and long branch attraction in data for two chloroplast photosystem genes in seed plants. Molecular Biology and Evolution 17:782-797.

Schneider, A.C., Freyman, W.A., Guilliams, C.M., Springer, Y., and B.G. Baldwin. Submitted. Pleistocene radiation of the serpentine-adapted genus Hesperolinon and other divergence times in Linaceae (Malpighiales). Submitted to American Journal of Botany

Schultheis, L.M. 2001. Systematics of Downingia (Campanulaceae) based on molecular sequence data: Implications for floral and chromosomal evolution. Systematic Botany 26:603-621.

Stone, R.D. 2006. Phylogeny of major in lineages in Melastomataceae, subfamily Olisbeioideae: Utility of nuclear glyceraldehydes 3-phosphate dehydrogenase (GapC) gene sequences. Systematic Botany 31:107-121.

Urbatsch, L.E., B.G. Baldwin, and M.J. Donoghue. 2000. Phylogeny of the coneflowers and relatives (Heliantheae: Asteraceae) based on nuclear rDNA internal transcribed spacer (ITS) sequences and chloroplast DNA restriction site data. Systematic Botany 25: 539-565.

Valentine, J.W., and A.G. Collins. 2000. The significance of moulting in ecdysozoan evolution. Evolution and Development 2:152-156.

Wheeler, J.A. 2000. Molecular phylogenetic reconstructions of the Marchantioid liverwort radiation. The Bryologist 103:314-333.

Wojciechowski, M.F., M.J. Sanderson, and J-M. Hu. 1999. Evidence on the monophyly of Astragalus (Fabaceae) and its major subgroups based on nuclear ribosomal DNA ITS and chloroplast DNA trnL intron data. Systematic Botany 24:409-437.

Zapata, F. and P. V. A. Fine. 2013. Molecular evolution of monoterpene synthases (TPSb genes) in a highly diverse genus of tropical trees. Molecular Phylogenetics and Evolution 68: 432-442.

Molecular Phylogenetics Laboratory
University/Jepson Herbaria
University of California Berkeley
1123 Valley Life Sciences Building
Berkeley CA 94720 USA

Phone: 510-643-2519

This page last modified October 30, 2015