In plants, the mitochondrial DNA has evolved in peculiar ways. Simple circular mitochondrial genomes found in most other eukaryotic lineages have expanded tremendously in size. Mitochondrial DNAs in some flowering plants may in fact be larger than genomes of free-living bacteria. Introns, retrotransposons, pseudogene fragments, and promiscuous DNA copied from the chloroplast or nuclear genome contribute to the size expansion but most intergenic DNA remains unaccounted for so far. Additionally, frequent recombination results in heterogeneous pools of coexisting, subgenomic mtDNA molecules in angiosperms. In contrast, the mitochondrial DNAs of bryophytes, the extant representatives of very early splits in plant phylogeny, are more conservative in structural evolution and seem to be devoid of active recombination. However, whereas mitochondrial introns are highly conserved among seed plants (spermatophytes), not a single one of more than 80 different introns in bryophyte mtDNAs is conserved among the three divisions, liverworts, mosses, and hornworts. Lycophytes are now unequivocally identified as living representatives of the earliest vascular plant branch in a crucial phylogenetic position between bryophytes and later diversifying tracheophytes including spermatophytes. Very recently, mtDNAs have become available for the three orders of extant lycophytes—Isoetales, Selaginellales, and Lycopodiales. As I will discuss here, the lycophyte mtDNAs not only show a surprising diversity of features but also previously unseen novelties of plant mitochondrial DNA evolution. The transition from a gametophyte-dominated bryophyte lifestyle to a sporophyte-dominated vascular plant lifestyle apparently gave rise to several peculiar independent changes in plant chondrome evolution.

Horizontal gene transfer (HGT) may not only create genome mosaicism, but also introduce evolutionary novelties to recipient organisms. HGT in plastid genomes, though relatively rare, still exists. HGT-derived genes are particularly common in unicellular photosynthetic eukaryotes and they also occur in multicellular plants. In particular, ancient HGT events occurring during the early evolution of primary photosynthetic eukaryotes were probably frequent. There is clear evidence that anciently acquired genes played an important role in the establishment of primary plastids and in the transition of plants from aquatic to terrestrial environments. Although algal genes have often been used to infer historical plastids in plastid-lacking eukaryotes, reliable approaches are needed to distinguish endosymbionts-derived genes from those independently acquired from preferential feeding or other activities.

Divergence time estimation using molecular sequence data relying on uncertain fossil calibrations is an unconventional statistical estimation problem. As the sequence data provide information about the distances only, estimation of absolute times and rates has to rely on information in the prior, so that the model is only semi-identifiable. In this paper, we use a combination of mathematical analysis, computer simulation, and real data analysis to examine the uncertainty in posterior time estimates when the amount of sequence data increases. The analysis extends the infinite-sites theory of Yang and Rannala, which predicts the posterior distribution of divergence times and rate when the amount of data approaches infinity. We found that the posterior credibility interval in general decreases and reaches a non-zero limit when the data size increases. However, for the node with the most precise fossil calibration (as measured by the interval width divided by the mid value), sequence data do not really make the time estimate any more precise. We propose a finite-sites theory which predicts that the square of the posterior interval width approaches its infinite-data limit at the rate 1/n, where n is the sequence length. We suggest a procedure to partition the uncertainty of posterior time estimates into that due to uncertainties in fossil calibrations and that due to sampling errors in the sequence data. We evaluate the impact of conflicting fossil calibrations on posterior time estimation and point out that narrow credibility intervals or overly precise time estimates can be produced by conflicting or erroneous fossil calibrations.

Genetic differentiation of populations has been traditionally quantified by Wright's F-statistics, typically assuming mutation–migration–drift equilibrium. However, the equilibrium perspective can be unrealistic as many natural populations are likely not yet in equilibrium. Therefore, understanding the behaviors, robustness, and power of the differentiation indexes under non-equilibrium conditions has important implications. Here, we report an extensive examination of the properties of two major indexes G_ST and D under non-equilibrium conditions by theoretical deduction under the infinite allele model (IAM) and simulation under the stepwise mutation model (SMM). Several properties of G_ST and D valid under both SMM and IAM, which have not been recognized under the equilibrium perspective, were unveiled. First, if gene flow is very weak (e.g., m < 10⁻⁴), G_ST, like D, also takes a fairly long time to reach equilibrium if mutation rate is not very large. When G_ST (D) is in equilibrium depends on when H_S and H_T are both in equilibrium. Under IAM and complete isolation, this is determined by the product of µ and t: G_ST will not approach equilibrium as long as µt ≪ 1. Under SMM, 10⁻⁴ appears to be the rough threshold migration rate; when m < 10⁻⁴, G_ST approaches equilibrium much slower and later than H_S, whereas the opposite is true when m > 10⁻⁴. Second, contrary to the popular belief, µ ≪ m is neither an obligatory request for G_ST to be an effective differentiation measure nor a sufficient condition for using G_ST to estimate gene flow level (Nm), if G_ST is not yet approaching equilibrium. Third, under SMM (but not IAM) and complete isolation, when population size is large (e.g., ≥1000), mutation rate shows a great impact on G_ST but only a mild influence on D; hence D can be much less sensitive to mutation rate heterogeneity than G_ST in certain situations. Fourth, whatever the level of gene flow, drift plays a dominant role on G_ST, whereas gene flow appears to have a stronger influence on D when subpopulations exchange individuals (even only infrequently). Moreover, G_ST appears to have a larger power to detect recent population genetic events than D. Finally, it is the migration rate (m), not the absolute number of migrants (Nm), that determines the speed at which G_ST or D approaches equilibrium. These results suggest that G_ST and D bear unique revealing powers under non-equilibrium conditions.

The origin of the latitudinal biodiversity gradient has been studied using various approaches. Here, we employ a comparative phylogenetic approach to infer evidence for the hypothesis that differences in diversification rates are one of the main factors contributing to the assembly of this gradient. We infer the phylogeny of the two sister genera Phegopteris and Pseudophegopteris. The two genera are distinct in their species richness (4 vs. 20 spp.) and their preferences to temperate to subtropical (Phegopteris) or tropical climates (Pseudophegopteris). Using sequences of three plastid DNA regions, we confirm the monophyly of each genus and infer the inter- and intra-generic phylogenetic differentiation of the sister clades. We recover evidence for distinct net-diversification rate between the two genera, which may be caused either by a higher extinction risk of temperate Phegopteris or a higher speciation rate of tropical Pseudophegopteris. We discuss our results in the context of our current knowledge on the speciation processes of ferns. We conclude on the crucial influence of other factors such as the rise of the Himalaya on the diversification of these ferns.

Various mechanistic theories of community assembly have been proposed ranging from niche-based theory to neutral theory. Analyses of beta diversity in a phylogenetic context could provide an excellent opportunity for testing many of these hypotheses. We analyzed the patterns of phylogenetic beta diversity in tropical tree communities in Panama to test several community assembly hypotheses. In particular, the degree to which the phylogenetic dissimilarity between communities can be explained by geographical or environmental distance can yield support for stochastic or deterministic assembly processes, respectively. Therefore, we examined: (i) the existence of distance decay of phylogenetic similarity among communities and its degree of departure from that expected under a null model; and (ii) the relative importance of geographical versus environmental distance in predicting the phylogenetic dissimilarity of communities. We found evidence that the similarity in the phylogenetic composition of communities decayed with geographical distance and environmental gradients. Null model evidence showed that beta diversity in the study system was phylogenetically non-random. Our results highlighted not only the role of local ecological mechanisms, including environmental filtering and competitive exclusion, but also biogeographical processes such as speciation, dispersal limitation, and niche evolution in structuring phylogenetic turnover. These results also highlight the importance of niche conservatism in structuring species diversity patterns.

The utility of pollination syndromes in predicting pollinators has been controversial. Flowers of Guihaiothamnus acaulis are tubular and vivid in color, indicating that butterflies might be the dominant pollinators of this species, based on the theory of pollination syndromes. To test this prediction, observations on the floral biology, pollinator behaviors, and breeding system were carried out in two wild populations. The results showed that diurnal and protandrous flowers of G. acaulis could last 7–10 days, and this species was self-incompatible. Thus, the fruit set was pollinator-dependent. In addition, pollen-consuming hoverflies and halictid bees were identified as the major pollinators of G. acaulis; butterflies were recorded as visiting the flower only once. The expanded corolla throat, massive pollen per flower, and high floral longevity suggest that G. acaulis had experienced the process of pollinator shift. Our results indicated that the actual pollinating fauna of plants were determined by complex factors including floral syndromes, the availability of pollinators, and historical adaptation to habitat. Pollination syndromes should be used carefully to predict pollinators of a particular flowering plant species.

Over 70 species and infraspecific taxa have been described in the Symplocos nakaharae (Hayata) Masam. complex (Symplocaceae), and the taxonomy of this complex has been controversial. To provide a rational taxonomic revision of the complex, extensive field observations were carried out and approximately 800 herbarium specimens, covering the whole distribution range, were examined to evaluate the taxonomic importance of morphological characteristics. Our studies recognized 13 species and one subspecies, including S. boninensis, S. henryi, S. kawakamii, S. lucida, S. nakaharae, S. migoi, S. multipes, S. pergracilis, S. setchuensis, S. shilanensis, S. tanakae, S. tetragona, S. theifolia, and S. lucida subsp. howii comb. nov. One new combination is made and two new synonyms, S. ernestii Dunn var. pubicalyx C. Chen syn. nov. and S. kuroki Nagam. syn. nov., are recognized. Two identification keys are provided, based primarily on flower and fruit characters. Detailed morphological descriptions and geographical distribution information of the 14 taxa are given.