C. C. Davis, E.J. Edwards, and M. J. Donoghue. 2010. “A clades-eye view of global climate change.” In Evolution Since Darwin: The First 150 Years, edited by M.A. Bell, D. J. Futuyma, W.F. Eanes, and J.S. Levinton, Pp. 623-627. Sunderland, Massachusetts: Sinauer. PDF
C. C. Davis and W. R. Anderson. 2010. “A complete generic phylogeny of Malpighiaceae inferred from nucleotide sequence data and morphology.” Am J Bot, 97, Pp. 2031-48.Abstract

PREMISE OF THE STUDY: The Malpighiaceae include approximately 1300 tropical flowering plant species in which generic definitions and intergeneric relationships have long been problematic. The goals of our study were to resolve relationships among the 11 generic segregates from the New World genus Mascagnia, test the monophyly of the largest remaining Malpighiaceae genera, and clarify the placement of Old World Malpighiaceae. * METHODS: We combined DNA sequence data for four genes (plastid ndhF, matK, and rbcL and nuclear PHYC) from 338 ingroup accessions that represented all 77 currently recognized genera with morphological data from 144 ingroup species to produce a complete generic phylogeny of the family. * KEY RESULTS AND CONCLUSIONS: The genera are distributed among 14 mostly well-supported clades. The interrelationships of these major subclades have strong support, except for the clade comprising the wing-fruited genera (i.e., the malpighioid+Amorimia, Ectopopterys, hiraeoid, stigmaphylloid, and tetrapteroid clades). These results resolve numerous systematic problems, while others have emerged and constitute opportunities for future study. Malpighiaceae migrated from the New to Old World nine times, with two of those migrants being very recent arrivals from the New World. The seven other Old World clades dispersed much earlier, likely during the Tertiary. Comparison of floral morphology in Old World Malpighiaceae with their closest New World relatives suggests that morphological stasis in the New World likely results from selection by neotropical oil-bee pollinators and that the morphological diversity found in Old World flowers has evolved following their release from selection by those bees.

C. G. Willis, B. R. Ruhfel, R. B. Primack, A. J. Miller-Rushing, J. B. Losos, and C. C. Davis. 2010. “Favorable climate change response explains non-native species' success in Thoreau's woods.” PLoS One, 5, Pp. e8878.Abstract

Invasive species have tremendous detrimental ecological and economic impacts. Climate change may exacerbate species invasions across communities if non-native species are better able to respond to climate changes than native species. Recent evidence indicates that species that respond to climate change by adjusting their phenology (i.e., the timing of seasonal activities, such as flowering) have historically increased in abundance. The extent to which non-native species success is similarly linked to a favorable climate change response, however, remains untested. We analyzed a dataset initiated by the conservationist Henry David Thoreau that documents the long-term phenological response of native and non-native plant species over the last 150 years from Concord, Massachusetts (USA). Our results demonstrate that non-native species, and invasive species in particular, have been far better able to respond to recent climate change by adjusting their flowering time. This demonstrates that climate change has likely played, and may continue to play, an important role in facilitating non-native species naturalization and invasion at the community level.

W. Zhang, E. M. Kramer, and C. C. Davis. 2010. “Floral symmetry genes and the origin and maintenance of zygomorphy in a plant-pollinator mutualism.” Proc Natl Acad Sci U S A, 107, Pp. 6388-93.Abstract

The evolution of floral zygomorphy is an important innovation in flowering plants and is thought to arise principally from specialization on various insect pollinators. Floral morphology of neotropical Malpighiaceae is distinctive and highly conserved, especially with regard to symmetry, and is thought to be caused by selection by its oil-bee pollinators. We sought to characterize the genetic basis of floral zygomorphy in Malpighiaceae by investigating CYCLOIDEA2-like (CYC2-like) genes, which are required for establishing symmetry in diverse core eudicots. We identified two copies of CYC2-like genes in Malpighiaceae, which resulted from a gene duplication in the common ancestor of the family. A likely role for these loci in the development of floral zygomorphy in Malpighiaceae is demonstrated by the conserved pattern of dorsal gene expression in two distantly related neotropical species, Byrsonima crassifolia and Janusia guaranitica. Further evidence for this function is observed in a Malpighiaceae species that has moved to the paleotropics and experienced coincident shifts in pollinators, floral symmetry, and CYC2-like gene expression. The dorsal expression pat-tern observed in Malpighiaceae contrasts dramatically with their actinomorphic-flowered relatives, Centroplacaceae (Bhesa paniculata) and Elatinaceae (Bergia texana). In particular, B. texana exhibits a previously undescribed pattern of uniform CYC2 expression, suggesting that CYC2 expression among the actinomorphic ancestors of zygomorphic lineages may be much more complex than previously thought. We consider three evolutionary models that may have given rise to this patterning, including the hypothesis that floral zygomorphy in Malpighiaceae arose earlier than standard morphology-based character reconstructions suggest.

C. C. Davis, C. G. Willis, R. B. Primack, and A. J. Miller-Rushing. 2010. “The importance of phylogeny to the study of phenological response to global climate change.” Philos Trans R Soc Lond B Biol Sci, 365, Pp. 3201-13.Abstract

Climate change has resulted in major changes in the phenology--i.e. the timing of seasonal activities, such as flowering and bird migration--of some species but not others. These differential responses have been shown to result in ecological mismatches that can have negative fitness consequences. However, the ways in which climate change has shaped changes in biodiversity within and across communities are not well understood. Here, we build on our previous results that established a link between plant species' phenological response to climate change and a phylogenetic bias in species' decline in the eastern United States. We extend a similar approach to plant and bird communities in the United States and the UK that further demonstrates that climate change has differentially impacted species based on their phylogenetic relatedness and shared phenological responses. In plants, phenological responses to climate change are often shared among closely related species (i.e. clades), even between geographically disjunct communities. And in some cases, this has resulted in a phylogenetically biased pattern of non-native species success. In birds, the pattern of decline is phylogenetically biased but is not solely explained by phenological response, which suggests that other traits may better explain this pattern. These results illustrate the ways in which phylogenetic thinking can aid in making generalizations of practical importance and enhance efforts to predict species' responses to future climate change.

K. J. Wurdack and C. C. Davis. 2009. “Malpighiales phylogenetics: Gaining ground on one of the most recalcitrant clades in the angiosperm tree of life.” Am J Bot, 96, Pp. 1551-70.Abstract

The eudicot order Malpighiales contains approximately 16000 species and is the most poorly resolved large rosid clade. To clarify phylogenetic relationships in the order, we used maximum likelihood, Bayesian, and parsimony analyses of DNA sequence data from 13 gene regions, totaling 15604 bp, and representing all three genomic compartments (i.e., plastid: atpB, matK, ndhF, and rbcL; mitochondrial: ccmB, cob, matR, nad1B-C, nad6, and rps3; and nuclear: 18S rDNA, PHYC, and newly developed low-copy EMB2765). Our sampling of 190 taxa includes representatives from all families of Malpighiales. These data provide greatly increased support for the recent additions of Aneulophus, Bhesa, Centroplacus, Ploiarium, and Rafflesiaceae to Malpighiales; sister relations of Phyllanthaceae + Picrodendraceae, monophyly of Hypericaceae, and polyphyly of Clusiaceae. Oxalidales + Huaceae, followed by Celastrales are successive sisters to Malpighiales. Parasitic Rafflesiaceae, which produce the world's largest flowers, are confirmed as embedded within a paraphyletic Euphorbiaceae. Novel findings show a well-supported placement of Ctenolophonaceae with Erythroxylaceae + Rhizophoraceae, sister-group relationships of Bhesa + Centroplacus, and the exclusion of Medusandra from Malpighiales. New taxonomic circumscriptions include the addition of Bhesa to Centroplacaceae, Medusandra to Peridiscaceae (Saxifragales), Calophyllaceae applied to Clusiaceae subfamily Kielmeyeroideae, Peraceae applied to Euphorbiaceae subfamily Peroideae, and Huaceae included in Oxalidales.

C. G. Willis, B. Ruhfel, R. B. Primack, A. J. Miller-Rushing, and C. C. Davis. 2009. “Reply to McDonald et al.: Climate change, not deer hebivory, has shaped species decline in Concord, Massachusetts.” Proc Natl Acad Sci U S A, 106, Pp. E29. PDF
H. Wang, M. J. Moore, P. S. Soltis, C. D. Bell, S. F. Brockington, R. Alexandre, C. C. Davis, M. Latvis, S. R. Manchester, and D. E. Soltis. 2009. “Rosid radiation and the rapid rise of angiosperm-dominated forests.” Proc Natl Acad Sci U S A, 106, Pp. 3853-8.Abstract

The rosid clade (70,000 species) contains more than one-fourth of all angiosperm species and includes most lineages of extant temperate and tropical forest trees. Despite progress in elucidating relationships within the angiosperms, rosids remain the largest poorly resolved major clade; deep relationships within the rosids are particularly enigmatic. Based on parsimony and maximum likelihood (ML) analyses of separate and combined 12-gene (10 plastid genes, 2 nuclear; >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening spacers; >25,000 bp) datasets for >100 rosid species, we provide a greatly improved understanding of rosid phylogeny. Vitaceae are sister to all other rosids, which in turn form 2 large clades, each with a ML bootstrap value of 100%: (i) eurosids I (Fabidae) include the nitrogen-fixing clade, Celastrales, Huaceae, Zygophyllales, Malpighiales, and Oxalidales; and (ii) eurosids II (Malvidae) include Tapisciaceae, Brassicales, Malvales, Sapindales, Geraniales, Myrtales, Crossosomatales, and Picramniaceae. The rosid clade diversified rapidly into these major lineages, possibly over a period of <15 million years, and perhaps in as little as 4 to 5 million years. The timing of the inferred rapid radiation of rosids [108 to 91 million years ago (Mya) and 107-83 Mya for Fabidae and Malvidae, respectively] corresponds with the rapid rise of angiosperm-dominated forests and the concomitant diversification of other clades that inhabit these forests, including amphibians, ants, placental mammals, and ferns.

C. C. Davis, P. K. Endress, and D. A. Baum. 2008. “The evolution of floral gigantism.” Curr Opin Plant Biol, 11, Pp. 49-57.Abstract

Flowers exhibit tremendous variation in size (>1000-fold), ranging from less than a millimeter to nearly a meter in diameter. Numerous studies have established the importance of increased floral size in species that exhibit relatively normal-sized flowers, but few studies have examined the evolution of floral size increase in species with extremely large flowers or flower-like inflorescences (collectively termed blossoms). Our review of these record-breakers indicates that blossom gigantism has evolved multiple times, and suggests that the evolutionary forces operating in these species may differ from their ordinary-sized counterparts. Surprisingly, rather than being associated with large-bodied pollinators, gigantism appears to be most common in species with small-bodied beetle or carrion-fly pollinators. Such large blossoms may be adapted to these pollinators because they help to temporarily trap animals, better facilitate thermal regulation, and allow for the mimicry of large animal carcasses. Future phylogenetic tests of these hypotheses should be conducted to determine if the transition to such pollination systems correlates with significant changes in the mode and tempo of blossom size evolution.

C. C. Davis. 2008. “Floral evolution: dramatic size change was recent and rapid in the world's largest flowers.” Curr Biol, 18, Pp. R1102-4.Abstract

Recent studies clarifying the closest relatives of the world's largest flowers, Rafflesiaceae, whose floral diameters range from approximately 11 to approximately 100 cm, indicated that they evolved from tiny-flowered ancestors in a burst of floral gigantism. New data now suggest that floral size evolution within Rafflesiaceae may be more dynamic than expected, with both recent and rapid changes in flower size.

C. G. Willis, B. Ruhfel, R. B. Primack, A. J. Miller-Rushing, and C. C. Davis. 2008. “Phylogenetic patterns of species loss in Thoreau's woods are driven by climate change.” Proc Natl Acad Sci U S A, 105, Pp. 17029-33.Abstract

Climate change has led to major changes in the phenology (the timing of seasonal activities, such as flowering) of some species but not others. The extent to which flowering-time response to temperature is shared among closely related species might have important consequences for community-wide patterns of species loss under rapid climate change. Henry David Thoreau initiated a dataset of the Concord, Massachusetts, flora that spans approximately 150 years and provides information on changes in species abundance and flowering time. When these data are analyzed in a phylogenetic context, they indicate that change in abundance is strongly correlated with flowering-time response. Species that do not respond to temperature have decreased greatly in abundance, and include among others anemones and buttercups [Ranunculaceae pro parte (p.p.)], asters and campanulas (Asterales), bluets (Rubiaceae p.p.), bladderworts (Lentibulariaceae), dogwoods (Cornaceae), lilies (Liliales), mints (Lamiaceae p.p.), orchids (Orchidaceae), roses (Rosaceae p.p.), saxifrages (Saxifragales), and violets (Malpighiales). Because flowering-time response traits are shared among closely related species, our findings suggest that climate change has affected and will likely continue to shape the phylogenetically biased pattern of species loss in Thoreau's woods.

B. Ruhfel, S. Lindsay, and C. C. Davis. 2008. “Phylogenetic placement of Rheopteris and the polyphyly of Momogramma (Pteridaceae s.l.): evidencre from rbcl sequence data.” Sys Bot, 11, Pp. 49-57. PDF
C. C. Davis, M. Latvis, D. L. Nickrent, K. J. Wurdack, and D. A. Baum. 2007. “Floral gigantism in Rafflesiaceae.” Science, 315, Pp. 1812. PDF
W. R. Anderson and C. C. Davis. 2007. “Generic adjustments in neotropical Malpighiaceae.” Contributions from the University of Michigan Herbarium, 25, Pp. 137-166. PDF
D. E. Soltis, J.W. Clayton, C. C. Davis, M. A. Gitzendanner, M. Cheek, V. Savolainen, A. M. Amorim, and P. S. Soltis. 2007. “Monophyly and relationships of the enigmatic family Peridiscaceae.” Taxon, 56, Pp. 65-73. PDF
Y. L. Qiu, L. Li, B. Wang, Z. Chen, V. Knoop, M. Groth-Malonek, O. Dombrovska, J. Lee, L. Kent, J. Rest, G. F. Estabrook, T. A. Hendry, D. W. Taylor, C. M. Testa, M. Ambros, B. Crandall-Stotler, R. J. Duff, M. Stech, W. Frey, D. Quandt, and C. C. Davis. 2006. “The deepest divergences in land plants inferred from phylogenomic evidence.” Proc Natl Acad Sci U S A, 103, Pp. 15511-6.Abstract

Phylogenetic relationships among the four major lineages of land plants (liverworts, mosses, hornworts, and vascular plants) remain vigorously contested; their resolution is essential to our understanding of the origin and early evolution of land plants. We analyzed three different complementary data sets: a multigene supermatrix, a genomic structural character matrix, and a chloroplast genome sequence matrix, using maximum likelihood, maximum parsimony, and compatibility methods. Analyses of all three data sets strongly supported liverworts as the sister to all other land plants, and analyses of the multigene and chloroplast genome matrices provided moderate to strong support for hornworts as the sister to vascular plants. These results highlight the important roles of liverworts and hornworts in two major events of plant evolution: the water-to-land transition and the change from a haploid gametophyte generation-dominant life cycle in bryophytes to a diploid sporophyte generation-dominant life cycle in vascular plants. This study also demonstrates the importance of using a multifaceted approach to resolve difficult nodes in the tree of life. In particular, it is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences.

W. R. Anderson and C. C. Davis. 2006. “Expansion of Diplopterys at the expense of Banisteriopsis (Malpighiaceae).” Harvard Papers in Botany, 11, Pp. 1-16. PDF