@article{fan_xiang_remington_purugganan_wiegmann_2007, title={Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae)}, volume={130}, ISSN={0016-6707, 1573-6857}, url={http://link.springer.com/10.1007/s10709-006-0016-3}, DOI={10.1007/s10709-006-0016-3}, abstractNote={The evolutionary pattern of the myc-like anthocyanin regulatory gene antR-Cor was examined in the dwarf dogwood species complex (Cornus Subgenus Arctocrania) that contains two diploid species (C. canadensis and C. suecica), their putative hybrids with intermediate phenotypes, and a tetraploid derivative (C. unalaschkensis). Full-length sequences of this gene ( approximately 4 kb) were sequenced and characterized for 47 dwarf dogwood samples representing all taxa categories from 43 sites in the Pacific Northwest. Analysis of nucleotide diversity indicated departures from neutral evolution, due most likely to local population structure. Neighbor-joining and haplotype network analyses show that sequences from the tetraploid and diploid intermediates are much more strongly diverged from C. suecica than from C. canadensis, and that the intermediate phenotypes may represent an ancestral group to C. canadensis rather than interspecific hybrids. Seven amino acid mutations that are potentially linked to myc-like anthocyanin regulatory gene function correlate with petal colors differences that characterize the divergence between two diploid species and the tetraploid species in this complex. The evidence provides a working hypothesis for testing the role of the gene in speciation and its link to the petal coloration. Sequencing and analysis of additional nuclear genes will be necessary to resolve questions about the evolution of the dwarf dogwood complex.}, number={1}, journal={Genetica}, author={Fan, Chuanzhu and Xiang, Qiu-Yun (Jenny) and Remington, David L. and Purugganan, Michael D. and Wiegmann, Brian M.}, year={2007}, month={Apr}, pages={19–34} }
 @article{houston_fan_xiang_schulze_jung_boston_2005, title={Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins}, volume={137}, DOI={10.1104/pp.104.056507}, abstractNote={Abstract}, number={2}, journal={Plant Physiology}, author={Houston, N. L. and Fan, C. Z. and Xiang, Qiu-Yun and Schulze, J. M. and Jung, R. and Boston, R. S.}, year={2005}, pages={762–778} }
 @article{fan_purugganan_thomas_wiegmann_xiang_2004, title={Heterogeneous evolution of the Myc-like Anthocyanin regulatory gene and its phylogenetic utility in Cornus L. (Cornaceae)}, volume={33}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2004.08.002}, abstractNote={Anthocyanin is a major pigment in vegetative and floral organs of most plants and plays an important role in plant evolution. The anthocyanin regulatory genes are responsible for regulating transcription of genes in the anthocyanin synthetic pathway. To assess evolutionary significance of sequence variation and evaluate the phylogenetic utility of an anthocyanin regulatory gene, we compared nucleotide sequences of the myc-like anthocyanin regulatory gene in the genus of dogwoods (Cornus: Cornaceae). Phylogenetic analyses demonstrate that the myc-like anthocyanin regulatory gene has potential as an informative phylogenetic marker at different taxonomic levels, depending on the data set considered (DNA or protein sequences) and regions applied (exons or introns). Pairwise nonsynonymous and synonymous substitution rate tests and codon-based substitution models were applied to characterize variation and to identify sites under diversifying selection. Mosaic evolution and heterogeneous rates among different domains and sites were detected.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Fan, CZ and Purugganan, MD and Thomas, DT and Wiegmann, BM and Xiang, QY}, year={2004}, month={Dec}, pages={580–594} }
 @misc{fan_xiang_2003, title={Phylogenetic analyses of Cornales based on 26S rRNA and combined 26S rDNA-matK-rbcL sequence data}, volume={90}, ISSN={["1537-2197"]}, DOI={10.3732/ajb.90.9.1357}, abstractNote={Nuclear 26S rDNA sequences were used to corroborate and test previously publishedmatK‐rbcL‐based hypotheses of phylogenetic relationships in Cornales. Sequences were generated for 53 taxa includingAlangium,Camptotheca,Cornus,Curtisia,Davidia,Diplopanax,Mastixia,Nyssa, and four families: Grubbiaceae, Hydrangeaceae, Hydrostachyaceae, and Loasaceae. Fifteen taxa from asterids were used as outgroups. The 26S rDNA sequences were initially analyzed separately and then combined withmatK‐rbcLsequences, using both parsimony and maximum likelihood methods. Eight strongly supported major clades were identified within Cornales by all analyses:Cornus,Alangium, nyssoids (Nyssa,Davidia, andCamptotheca), mastixioids (MastixiaandDiplopanax), Hydrangeaceae, Loasaceae,Grubbia‐Curtisia, andHydrostachys. However, relationships among the major lineages are not strongly supported in either 26S rDNA or combined 26S rDNA‐matK‐rbcLtopologies, except for the sister relationships betweenCornusandAlangiumand between nyssoids and mastixioids in the tree from combined data. Discrepancies in relationships among major lineages, especially the placement of the long‐branchedHydrostachys, were found between parsimony and maximum likelihood trees in all analyses. Incongruence between the 26S rDNA andmatK‐rbcLdata sets was suggested, where Hydrangeaceae was found to be largely responsible for the incongruence. The long branch ofHydrostachysrevealed in previous analyses was reduced significantly with more sampling. Maximum likelihood analysis of combined 26S rDNA‐matK‐rbcLsequences suggested thatHydrostachysmight be sister to the remainder of Cornales, thatCornus‐Alangiumare sisters, that nyssoids‐mastixioids are sisters, and that Hydrangeaceae‐Loasaceae are sisters, consistent with previous analyses ofmatK‐rbcLsequence data.}, number={9}, journal={AMERICAN JOURNAL OF BOTANY}, author={Fan, CZ and Xiang, QY}, year={2003}, month={Sep}, pages={1357–1372} }
 @article{xiang_moody_soltis_fan_soltis_2002, title={Relationships within Cornales and circumscription of Cornaceae – matK and rbcL sequence data and effects of outgroups and long branches}, volume={24}, ISSN={["1095-9513"]}, DOI={10.1016/S1055-7903(02)00267-1}, abstractNote={Phylogenetic relationships in Cornales were assessed using sequences rbcL and matK. Various combinations of outgroups were assessed for their suitability and the effects of long branches and outgroups on tree topology were examined using RASA 2.4 prior to conducting phylogenetic analyses. RASA identified several potentially problematic taxa having long branches in individual data sets that may have obscured phylogenetic signal, but when data sets were combined RASA no longer detected long branch problems. t(RASA) provides a more conservative measurement for phylogenetic signal than the PTP and skewness tests. The separate matK and rbcL sequence data sets were measured as not containing phylogenetic signal by RASA, but PTP and skewness tests suggested the reverse [corrected]. Nonetheless, the matK and rbcL sequence data sets suggested relationships within Cornales largely congruent with those suggested by the combined matK-rbcL sequence data set that contains significant phylogenetic signal as measured by t(RASA), PTP, and skewness tests. Our analyses also showed that a taxon having a long branch on the tree may not be identified as a "long-branched" taxon by RASA. The long branches identified by RASA had little effect on the arrangement of other taxa in the tree, but the placements of the long-branched taxa themselves were often problematic. Removing the long-branched taxa from analyses generally increased bootstrap support, often substantially. Use of non-optimal outgroups (as identified by RASA) decreased phylogenetic resolution in parsimony analyses and suggested different relationships in maximum likelihood analyses, although usually weakly supported clades (less than 50% support) were impacted. Our results do not recommend using t(RASA) as a sole criterion to discard data or taxa in phylogenetic analyses, but t(RASA) and the taxon variance ratio obtained from RASA may be useful as a guide for improved phylogenetic analyses. Results of parsimony and ML analyses of the sequence data using optimal outgroups suggested by RASA revealed four major clades within Cornales: (1) Curtisia-Grubbia, (2) Cornus-Alangium, (3) Nyssa-Camptotheca-Davidia-Mastixia-Diplopanax, and (4) Hydrangeaceae-Loasaceae, with clades (2) and (3) forming a monophyletic group sister to clade (4) and clade (1) sister to the remainder of Cornales. However, there was not strong bootstrap support for relationships among the major clades. The placement of Hydrostachys could not be reliably determined, although most analyses place the genus within Hydrangeaceae; ML analyses, for example, placed the genus as the sister of Hydrangeeae. Our results supported a Cornales including the systematically problematic Hydrostachys, a Cornaceae consisting of Cornus and Alangium, a Nyssaceae consisting of Nyssa and Camptotheca, a monogeneric Davidiaceae, a Mastixiaceae consisting of Mastixia and Diplopanax, and an expanded Grubbiaceae consisting of Grubbia and Curtisia, and two larger families, Hydrangeaceae and Loasaceae.}, number={1}, journal={Molecular Phylogeneics and Evolution}, author={Xiang, Q.Y. and Moody, M. and Soltis, D.E. and Fan, C.Z. and Soltis, P.S.}, year={2002}, pages={35–57} }
 @article{fan_xiang_2001, title={Phylogenetic relationships within Cornus (Cornaceae) based on 26S rDNA sequences}, volume={88}, ISSN={00029122}, url={http://doi.wiley.com/10.2307/2657096}, DOI={10.2307/2657096}, abstractNote={Phylogenetic relationships within the dogwood genus Cornus have been highly controversial due to the great morphological heterogeneity. Earlier phylogenetic analyses of Cornus using chloroplast DNA (cpDNA) data (including rbcL and matK sequences, as well as restriction sites) and morphological characters suggested incongruent relationships within the genus. The present study generated sequence data from the nuclear gene 26S rDNA for Cornus to test the phylogenetic hypotheses based on cpDNA and morphological data. The 26S rDNA sequence data obtained represent 16 species, 13 from Cornus and three from outgroups, having an aligned length of 3380 bp. Both parsimony and maximum likelihood analyses of these sequences were conducted. Trees resulting from these analyses suggest relationships among subgroups of Cornus consistent with those inferred from cpDNA data. That is, the dwarf dogwood (subg. Arctocrania) and the big‐bracted dogwood (subg. Cynoxylon and subg. Syncarpea) clades are sisters, which are, in turn, sister to the cornelian cherries (subg. Cornus and subg. Afrocrania). This red‐fruited clade is sister to the blue‐ or white‐fruited dogwoods (subg. Mesomora, subg. Kraniopsis, and subg. Yinquania). Within the blue‐ or white‐fruited clade, C. oblonga (subg. Yinquania) is sister to the remainder, and subg. Mesomora is sister to subg. Kraniopsis. These relationships were also suggested by the combined 26S rDNA and cpDNA data, but with higher bootstrap and Bremer support in the combined analysis. The 26S rDNA sequence data of Cornus consist of 12 expansion segments spanning 1034 bp. These expansion segments evolve approximately four times as fast as the conserved core regions. The study provides an example of phylogenetic utility of 26S rDNA sequences below the genus level.}, number={6}, journal={American Journal of Botany}, author={Fan, Chuanzhu and Xiang, Jenny Qiu-Yun}, year={2001}, month={Jun}, pages={1131–1138} }