An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes, atp1, matR, nad5, and rps3, from 380 species that represent 376 genera and 296 families of seed plants. It is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB, matK, and rbcL, and nuclear 18S rDNA. The basalmost lineage consists of Amborella and Nymphaeales (including Hydatellaceae). Austrobaileyales follow this clade and are sister to the mesangiosperms, which include Chloranthaceae, Ceratophyllum, magnoliids, monocots, and eudicots. With the exception of Chloranthaceae being sister to Ceratophyllum, relationships among these five lineages are not well supported. In eudicots, Ranunculales, Sabiales, Proteales, Trochodendrales, Buxales, Gunnerales, Saxifragales, Vitales, Berberidopsidales, and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and asterids. Within rosids, the COM (Celastrales–Oxalidales–Malpighiales) clade is sister to malvids (or rosid II), instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of angiosperms. Santalales and Caryophyllales are members of an expanded asterid clade. This study shows that the mitochondrial genes are informative markers for resolving relationships among genera, families, or higher rank taxa across angiosperms. The low substitution rates and low homoplasy levels of the mitochondrial genes relative to the chloroplast genes, as found in this study, make them particularly useful for reconstructing ancient phylogenetic relationships. A mitochondrial gene-based angiosperm phylogeny provides an independent and essential reference for comparison with hypotheses of angiosperm phylogeny based on chloroplast genes, nuclear genes, and non-molecular data to reconstruct the underlying organismal phylogeny.

Recent phylogenetic analyses of molecular data have supported different hypotheses of relationships among Cornales, Ericales, and core asterids. Such hypotheses have implications for the evolution of important morphological and embryological features of asterids. In this study we generated plastid genome-scale data of Davidia (Cornales) and Franklinia (Ericales) and combined them with published sequence data of eudicots. Our maximum parsimony, maximum likelihood, and Bayesian analyses generated strongly supported and congruent phylogenetic relationships among the three major lineages of the asterids. Cornales diverges first in asterids; Ericales is sister to the core asterids. Adding two more taxa helps mitigate long branch attraction in parsimony analyses. Sampling 26–28 plastid protein-coding genes may provide satisfactory resolution and support for relationships of eudicots including basal lineages of asterids.

Cordyceps is an endoparasite ascomycetous genus containing approximately 450 species with a diversity of insect hosts, traditionally included in the family Clavicipitaceae of Ascomycota. Establishing the relationships among species with a varied range of morphologies and hosts is of importance to our understanding of the phylogeny and co-evolution of parasites and hosts in entomopathogenic ascomycetes. To this end, we used a combination of molecular index and morphological characters from 40 representative species to carry out comprehensive molecular phylogenetic analyses. Based on the phylogenetic tree, we used the program DISCRETE for inferring the rates of evolution and finding ancestral states of morphological character. The phylogenetic analyses revealed two important points. (i) Types of perithecia attached to stroma reflected an evolutionary trend in Cordyceps. The vertically immersed perithecia form was the ancestral state, superficial and obliquely immersed perithecia were derived characters, obliquely immersed was irreversible. Species with obliquely immersed perithecia were in a closely related group and were the derived group. (ii) A strong correlation between fungal relatedness and the microhabitat supported the hypothesis that the host jumps through commingling in soil microhabitats. Based on the results of these analyses, host switching explains the diversity of entomopathogenic fungi of the genus Cordyceps.

Adenophora is an extremely variable genus, and its taxonomy is very controversial. Of the genus, Adenophora potaninii complex, including A. potaninii, A. bockiana, A. wawreana, A. lobophylla, A. biformifolia, A. polydentata, and A. wawreana var. lanceifolia, is a typical group with different taxonomical treatments due to high level of morphological diversity. We carried out extensive biosystematic studies based on population sampling, transplantation experiments and offspring tests, cluster analysis, and a crossing experiment. The results reveal four main findings. (i) Leaf forms of the A. potaninii complex were extremely polymorphic; the leaf form of A. potaninii and A. bockiana, and that of A. wawreana and A. biformifolia could be found, respectively, on a single population or among the offsprings of a single plant. (ii) Cluster analysis and a crossing experiment indicated that A. bockiana and A. polydentata could not be separated from A. potaninii, nor A. biformifolia from A. wawreana. (iii) Adenophora potaninii and A. wawreana were gradational in morphology and their compatibility value was slightly reduced compared to that within each entity. (iv) Adenophora lobophylla was distinct from the other members of the complex in shape and size of corolla, relative length of style, and shape of capsule. This species was incompatible reproductively with the other members of the complex, but partly compatible with A. stenanthina, a species in another section. Therefore, we recognized only one species with two subspecies in the complex, A. potaninii subsp. potaninii and subsp. wawreana, moved A. lobophylla out of the complex, and reduced all the other names as new synonyms.

The pollen morphology of 11 species of the genus Glycyrrhiza L. with one from each of the genera Glycyrrhizopsis Boiss. & Bal. and Meristotropis Fisch. & C. A. Mey. was investigated by scanning electron microscopy. In pollen morphology, the main differences between Glycyrrhizopsis and Glycyrrhiza are: Glycyrrhizopsis—pollen grains 36.63 × 40.42 μm in size, oblate spheroidal in shape; and Glycyrrhiza—pollen grains 24.47–33.18 × 23.82–31.83 μm in size, prolate spheroidal in shape. Glycyrrhizopsis and Glycyrrhiza should be recognized as two distinct genera based on palynological and morphological characters. Meristotropis and Glycyrrhiza are similar in many important palynological and morphological characters, suggesting that the two should be merged. In Glycyrrhiza, two types of pollen grains, 3-lobed-circular or subtriangular in polar view, are found in different species, in accordance with morphological differences in the two groups, shedding light on the classification and evolution of the genus.

The pollen morphology of 13 taxa (34 specimens) of the genera Glechoma L., and Marmoritis Benth. was investigated in detail using light, scanning electron, and transmission electron microscopy. Pollen grains of all studied taxa are small to large in size (P= 32.5–60.4 μm, E= 20.2–50.5 μm), prolate-spheroidal to prolate in shape and mostly hexacolpate (the amb more or less circular or rarely ellipsoid) with granular membranes. The sexine ornamentation of Glechoma is bireticulate; the muri of the primary reticulum are irregularly circled, and lumen size is short. In contrast, the sexine surfaces of the Marmoritis pollen tend to more elongate or wider at the muri of the primary reticulum than those of the Glechoma. The pollen wall stratification of selected taxa (three from Glechoma and one from Marmoritis) is characterized by unbranched columellae, and continuous or distinctly discontinuous endexine based on transmission electron microscopy observation. The results of Glechoma and Marmoritis reveal rather similar pollen morphological features, however, fine details of sexine ornamentation are characteristic to differentiate the pollen taxa. Although these differences may be useful in establishing the taxonomic boundary between two genera, they are too weak to segregate diagnostic characters.

Phylogeny and infrageneric relationships were reconstructed for Korean Viola (Violaceae) using eight chloroplast sequences: the atpB-rbcL intergenic spacer, the atpF-H intergenic spacer, the matK gene, the psbA-trnH intergenic spacer, the psbK-I intergenic spacer, the rpl16 intron, the rpoC1 exon 2, and the trnL-trnF regions. The combined analyses of the eight chloroplast regions suggest that sections Dischidium and Chamaemelanium are monophyletic, whereas section Nomimium is paraphyletic; sections Dischidium and Chamaemelanium form a clade with subsections Hypocarpae and Trigonocarpae of section Nomimium, but unresolved within the clade; two subsections (subsects. Bilobatae and Vaginatae) of section Nomimium form a clade and are placed between the stem and stemless species group; and subsection Patellares of section Nomimium is monophyletic, and Viola dissecta is diverged first in the clade with high support (BS = 100, PP = 100). Our present results support the subsectional grouping based on morphological characteristics, although discordance remained at the series level.

The phylogenetic relationships of Osmanthus Lour. were investigated using the nuclear ribosomal internal transcribed spacer (ITS) regions and non-coding chloroplast regions (psbA-trnH, trnL-F). The two datasets support the conclusion that Osmanthus is polyphyletic, with some species of the subtribe Oleinae nested within Osmanthus. Osmanthus didymopetalus P. S. Green is nested within the clade formed by species of section Osmanthus in two trees. Osmanthus attenuatus P. S. Green, O. yunnanensis P. S. Green, and O. gracilinervis R. L. Lu of traditional section Osmanthus are clearly divergent from other accessions, and do not form a monophyletic group with other Osmanthus accessions. Osmanthus marginatus Hemsl. is embedded in the clade formed by species of section Osmanthus in the ITS tree. In cpDNA trees all species of section Osmanthus are placed in the large clade and all species of section Leiolea formed a group. The taxonomic incongruence among trees for ITS and cpDNA indicate hybridization, as introgression may have occurred among some species of sections Osmanthus and Leiolea. Phylogeny of Osmanthus is discussed in light of molecular and morphological data, and a revised infrageneric classification with three sections (Leiolea, Siphosmanthu, and Osmanthus) is presented. The section Linocieroides is abandoned and united with section Osmanthus.

The Tibetan antelope (chiru, Pantholops hodgsoni), a heavily poached species and symbol of the Qinghai-Tibetan Plateau (QTP), is noted worldwide for its special calving migration. This species originated in the early Quaternary and it is interesting to know how the following climatic oscillations affected its demographic dynamics in the climate-sensitive QTP. In this study, we analyzed the mitochondrial D-loop region from 312 individuals sampled in all of the six major populations. We found high rates of gene flow and little genetic differentiation between populations, suggesting that the calving migration may have homogenized the genetic pool of this species. Both mismatch distribution analyses and coalescent simulations suggested that this species experienced a demographic expansion approximately 600–200 Kyr following the retreat of the large glaciers developed in the QTP at 800–600 Kyr, rather than at the end of the last glacial age, as previously suggested, based on a limited sample size. In addition, we found evidence of a chiru population decrease probably related to the human settings at the QTP during the middle Holocene.