W. R. Anderson and C. C. Davis. 2005. “The Mascagnia cordifolia group (Malpighiaceae).” Contributions from the University of Michigan Herbarium, 24, Pp. 33-44. PDF
C. C. Davis, C.O. Webb, K. J. Wurdack, C.A. Jaramillo, and M. J. Donoghue. 2005. “Explosive radiation of Malpighiales supports a mid-Cretaceous origin of modern tropical rain forests.” Am Nat, 165, Pp. E36-E65. PDF
C. C. Davis, W. R. Anderson, and K. J. Wurdack. 2005. “Gene transfer from a parasitic flowering plant to a fern.” Proc Biol Sci, 272, Pp. 2237-42.Abstract

The rattlesnake fern (Botrychium virginianum (L.) Sw.) is obligately mycotrophic and widely distributed across the northern hemisphere. Three mitochondrial gene regions place this species with other ferns in Ophioglossaceae, while two regions place it as a member of the largely parasitic angiosperm order Santalales (sandalwoods and mistletoes). These discordant phylogenetic placements suggest that part of the genome in B. virginianum was acquired by horizontal gene transfer (HGT), perhaps from root-parasitic Loranthaceae. These transgenes are restricted to B. virginianum and occur across the range of the species. Molecular and life-history traits indicate that the transfer preceded the global expansion of B. virginianum, and that the latter may have happened very rapidly. This is the first report of HGT from an angiosperm to a fern, through either direct parasitism or the mediation of interconnecting fungal symbionts.

R. Samuel, H. Kathriarachchi, P. Hoffmann, M. H. Barfuss, K. J. Wurdack, C. C. Davis, and M. W. Chase. 2005. “Molecular phylogenetics of Phyllanthaceae: evidence from plastid MATK and nuclear PHYC sequences.” Am J Bot, 92, Pp. 132-41.Abstract

Plastid matK and a fragment of the low-copy nuclear gene PHYC were sequenced for 30 genera of Phyllanthaceae to evaluate tribal and generic delimitation. Resolution and bootstrap percentages obtained with matK are higher than that of PHYC, but both regions show nearly identical phylogenetic patterns. Phylogenetic relationships inferred from the independent and combined data are congruent and differ from previous, morphology-based classifications but are highly concordant with those of the plastid gene rbcL previously published. Phyllanthaceae is monophyletic and gives rise to two well-resolved clades (T and F) that could be recognized as subfamilies. DNA sequence data for Keayodendron and Zimmermanniopsis are presented for the first time. Keayodendron is misplaced in tribe Phyllantheae and belongs to the Bridelia alliance. Zimmermanniopsis is sister to Zimmermannia. Phyllanthus and Cleistanthus are paraphyletic. Savia and Phyllanthus subgenus Kirganelia are not monophyletic.

Y.-L. Qiu, O. Dombrovska, J. Lee, L. Li, B.A. Whitlock, F. Bernasconi-Quadroni, J. S. Rest, C. C. Davis, T. Borsch, K. W. Hilu, S. S. Renner, D. E. Soltis, P. S. Soltis, M.J. Zanis, J.J. Cannone, R.R. Gutell, M. Powell, V. Savolainen, L.W. Chatrou, and M. W. Chase. 2005. “Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes.” Int J Plant Sci, 166, Pp. 815-842. PDF
W. R. Anderson and C. C. Davis. 2005. “Transfer of Mascagnia leticiana to Malpighia (Malpighiaceae).” Contributions from the University of Michigan Herbarium, 24, Pp. 45-49. PDF
C. C. Davis and M. W. Chase. 2004. “Elatinaceae are sister to Malpighiaceae; Peridiscaceae belong to Saxifragales.” Am J Bot, 91, Pp. 262-273. PDF
C. C. Davis, P. W. Fritsch, C. D. Bell, and S. Mathews. 2004. “High latitude Tertiary migrations of an exclusively tropical clade: evidence from Malpighiaceae.” Int. J Plant Sci, 165, Pp. S107-S121. PDF
C. C. Davis and K. J. Wurdack. 2004. “Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales.” Science, 305, Pp. 676-8.Abstract

Horizontal gene transfer (HGT) between sexually unrelated species has recently been documented for higher plants, but mechanistic explanations for HGTs have remained speculative. We show that a parasitic relationship may facilitate HGT between flowering plants. The endophytic parasites Rafflesiaceae are placed in the diverse order Malpighiales. Our multigene phylogenetic analyses of Malpighiales show that mitochondrial (matR) and nuclear loci (18S ribosomal DNA and PHYC) place Rafflesiaceae in Malpighiales, perhaps near Ochnaceae/Clusiaceae. Mitochondrial nad1B-C, however, groups them within Vitaceae, near their obligate host Tetrastigma. These discordant phylogenetic hypotheses strongly suggest that part of the mitochondrial genome in Rafflesiaceae was acquired via HGT from their hosts.

Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae
C. C. Davis, C. D. Bell, S. Mathews, and M. J. Donoghue. 2002. “Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae.” Proc Natl Acad Sci U S A, 99, Pp. 6833-7.Abstract

Explanations for biogeographic disjunctions involving South America and Africa typically invoke vicariance of western Gondwanan biotas or long distance dispersal. These hypotheses are problematical because many groups originated and diversified well after the last known connection between Africa and South America (approximately 105 million years ago), and it is unlikely that "sweepstakes" dispersal accounts for many of these disjunctions. Phylogenetic analyses of the angiosperm clade Malpighiaceae, combined with fossil evidence and molecular divergence-time estimates, suggest an alternative hypothesis to account for such distributions. We propose that Malpighiaceae originated in northern South America, and that members of several clades repeatedly migrated into North America and subsequently moved via North Atlantic land connections into the Old World during episodes starting in the Eocene, when climates supported tropical forests. This Laurasian migration route may explain many other extant lineages that exhibit western Gondwanan distributions.

C. C. Davis. 2002. “Madagasikaria (Malpighiaceae): a new genus from Madagascar with implications for floral evolution in Malpighiaceae.” Am J Bot, 89, Pp. 699-706.Abstract

Madagasikaria andersonii is described here as a new genus and species of Malpighiaceae from Madagascar. The phylogenetic placement of Madagasikaria was estimated by using combined data from ndhF and trnL-F chloroplast sequences and phytochrome (PHYC) and ITS nuclear sequences. It forms a strongly supported clade with the Malagasy endemic genera Rhynchophora and Microsteira. Despite nearly identical floral morphology among species in this clade (here called the madagasikarioid clade), these genera are easily distinguishable on the basis of their fruits. The schizocarpic fruits of Madagasikaria have distinctive mericarps. Each mericarp has a lateral wing, which completely encircles the nut, and a peculiar dorsal wing, which folds over on itself. The morphology of this fruit suggests that the homology of the unusual wing in Rhynchophora is lateral in nature and represents a reduced wing similar to the lateral wing in Madagasikaria. Taxa in the madagasikarioid clade all appear to be morphologically androdioecious and functionally dioecious, producing both staminate and "bisexual" (i.e., functionally carpellate) individuals. This condition appears to be exceedingly rare in flowering plants and has important implications for floral evolution within Malpighiaceae. Neotropical Malpighiaceae are pollinated by specialized oil-collecting anthophorine bees of the tribe Centridini and exhibit highly conserved floral morphology despite tremendous diversity in fruit morphology and habit. These oil-collecting bees are absent from the paleotropics, where most members of the Malpighiaceae lack both the oil glands and the typical floral orientation crucial to pollination by neotropical oil-collecting bees. The madagasikarioids represent one shift from the neotropical pollination syndrome among Old World Malpighiaceae.

C. C. Davis, PA Fritsch, J. Li, and M. J. Donoghue. 2002. “Phylogeny and biogeography of Cercis (Fabaceae): evidence from nuclear ribosomal ITS and chloroplast ndhF sequence data.” Sys. Bot., 27, Pp. 289-302. PDF
C. C. Davis, C. D. Bell, P. W. Fritsch, and S. Mathews. 2002. “Phylogeny of Acridocarpus-Brachylophon (Malpighiaceae): implications for tertiary tropical floras and Afroasian biogeography.” Evolution, 56, Pp. 2395-405.Abstract

A major tenet of African Tertiary biogeography posits that lowland rainforest dominated much of Africa in the late Cretaceous and was replaced by xeric vegetation as a response to continental uplift and consequent widespread aridification beginning in the late Paleogene. The aridification of Africa is thought to have been a major factor in the extinction of many African humid-tropical lineages, and in the present-day disparity of species diversity between Africa and other tropical regions. This primarily geologically based model can be tested with independent phylogenetic evidence from widespread African plant groups containing both humid- and xeric-adapted species. We estimated the phylogeny and lineage divergence times within one such angiosperm group, the acridocarpoid clade (Malpighiaceae), with combined ITS, ndhF, and trnL-F data from 15 species that encompass the range of morphological and geographic variation within the group. Dispersal-vicariance analysis and divergence-time estimates suggest that the basal acridocarpoid divergence occurred between African and Southeast Asian lineages approximately 50 million years ago (mya), perhaps after a southward ancestral retreat from high-latitude tropical forests in response to intermittent Eocene cooling. Dispersion of Aeridocarpus from Africa to Madagascar is inferred between approximately 50 and 35 mya, when lowland humid tropical forest was nearly continuous between these landmasses. A single dispersal event within Acridocarpus is inferred from western Africa to eastern Africa between approximately 23 and 17 mya, coincident with the widespread replacement of humid forests by savannas in eastern Africa. Although the spread of xeric environments resulted in the extinction of many African plant groups, our data suggest that for others it provided an opportunity for further diversification.

W. R. Anderson and C. C. Davis. 2001. “Monograph of Lophopterys (Malpighiaceae).” Contributions from the University of Michigan Herbarium, 23, Pp. 83-105. PDF
J. Li, C. C. Davis, M. J. Donoghue, S. Kelley, and P. Del Tredici. 2001. “Phylogenetic relationships of Torreya (Taxaceae) inferred from sequences of nuclear ribosomal DNA ITS region.” Harvard Papers in Botany, 6, Pp. 275-281. PDF
J. Li, C. C. Davis, P. Del Tredici, and M. J. Donoghue. 2001. “Phylogeny and biogeography of Taxus (Taxaceae) inferred from sequences of the internal transcribed spacer region of nuclear ribosomal DNA.” Harvard Papers in Botany, 6, Pp. 267-274. PDF
C. C. Davis, W. R. Anderson, and M. J. Donoghue. 2001. “Phylogeny of Malpighiaceae: evidence from chloroplast ndhF and trnl-F nucleotide sequences.” Am J Bot, 88, Pp. 1830-46.Abstract

The Malpighiaceae are a family of approximately 1250 species of predominantly New World tropical flowering plants. Infrafamilial classification has long been based on fruit characters. Phylogenetic analyses of chloroplast DNA nucleotide sequences were analyzed to help resolve the phylogeny of Malpighiaceae. A total of 79 species, representing 58 of the 65 currently recognized genera, were studied. The 3' region of the gene ndhF was sequenced for 77 species and the noncoding intergenic spacer region trnL-F was sequenced for 65 species; both sequences were obtained for the outgroup, Humiria (Humiriaceae). Phylogenetic relationships inferred from these data sets are largely congruent with one another and with results from combined analyses. The family is divided into two major clades, recognized here as the subfamilies Byrsonimoideae (New World only) and Malpighioideae (New World and Old World). Niedenzu's tribes are all polyphyletic, suggesting extensive convergence on similar fruit types; only de Jussieu's tribe Gaudichaudieae and Anderson's tribes Acmanthereae and Galphimieae are monophyletic. Fleshy fruits evolved three times in the family and bristly fruits at least three times. Among the wing-fruited vines, which constitute more than half the diversity in the family, genera with dorsal-winged samaras are fairly well resolved, while the resolution of taxa with lateral-winged samaras is poor. The trees suggest a shift from radially symmetrical pollen arrangement to globally symmetrical pollen at the base of one of the clades within the Malpighioideae. The Old World taxa fall into at least six and as many as nine clades.