@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}, 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 Protein disulfide isomerases (PDIs) are molecular chaperones that contain thioredoxin (TRX) domains and aid in the formation of proper disulfide bonds during protein folding. To identify plant PDI-like (PDIL) proteins, a genome-wide search of Arabidopsis (Arabidopsis thaliana) was carried out to produce a comprehensive list of 104 genes encoding proteins with TRX domains. Phylogenetic analysis was conducted for these sequences using Bayesian and maximum-likelihood methods. The resulting phylogenetic tree showed that evolutionary relationships of TRX domains alone were correlated with conserved enzymatic activities. From this tree, we identified a set of 22 PDIL proteins that constitute a well-supported clade containing orthologs of known PDIs. Using the Arabidopsis PDIL sequences in iterative BLAST searches of public and proprietary sequence databases, we further identified orthologous sets of 19 PDIL sequences in rice (Oryza sativa) and 22 PDIL sequences in maize (Zea mays), and resolved the PDIL phylogeny into 10 groups. Five groups (I–V) had two TRX domains and showed structural similarities to the PDIL proteins in other higher eukaryotes. The remaining five groups had a single TRX domain. Two of these (quiescin-sulfhydryl oxidase-like and adenosine 5′-phosphosulfate reductase-like) had putative nonisomerase enzymatic activities encoded by an additional domain. Two others (VI and VIII) resembled small single-domain PDIs from Giardia lamblia, a basal eukaryote, and from yeast. Mining of maize expressed sequence tag and RNA-profiling databases indicated that members of all of the single-domain PDIL groups were expressed throughout the plant. The group VI maize PDIL ZmPDIL5-1 accumulated during endoplasmic reticulum stress but was not found within the intracellular membrane fractions and may represent a new member of the molecular chaperone complement in the cell.}, 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 published matK‐rbcL ‐based hypotheses of phylogenetic relationships in Cornales. Sequences were generated for 53 taxa including Alangium , 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 with matK‐rbcL sequences, using both parsimony and maximum likelihood methods. Eight strongly supported major clades were identified within Cornales by all analyses: Cornus , Alangium , nyssoids ( Nyssa , Davidia , and Camptotheca ), mastixioids ( Mastixia and Diplopanax ), Hydrangeaceae, Loasaceae, Grubbia ‐ Curtisia , and Hydrostachys . However, relationships among the major lineages are not strongly supported in either 26S rDNA or combined 26S rDNA‐ matK‐rbcL topologies, except for the sister relationships between Cornus and Alangium and between nyssoids and mastixioids in the tree from combined data. Discrepancies in relationships among major lineages, especially the placement of the long‐branched Hydrostachys , were found between parsimony and maximum likelihood trees in all analyses. Incongruence between the 26S rDNA and matK‐rbcL data sets was suggested, where Hydrangeaceae was found to be largely responsible for the incongruence. The long branch of Hydrostachys revealed in previous analyses was reduced significantly with more sampling. Maximum likelihood analysis of combined 26S rDNA‐ matK‐rbcL sequences suggested that Hydrostachys might be sister to the remainder of Cornales, that Cornus ‐ Alangium are sisters, that nyssoids‐mastixioids are sisters, and that Hydrangeaceae‐Loasaceae are sisters, consistent with previous analyses of matK‐rbcL sequence 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} }