Rui-Qi Li

A nonflowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial, and nuclear genes

Nucleotide sequences of seven chloroplast (atpB and rbcL, SSU and LSU rDNAs), mitochondrial (atp1, LSU rDNA), and nuclear (18S rDNA) genes from 192 land plants and their algal relatives were analyzed using maximum likelihood and maximum parsimony methods. Liverworts, mosses, hornworts, lycophytes, monilophytes (ferns), seed plants, and angiosperms all represent strongly supported monophyletic groups. Three bryophyte lineages form a paraphyletic group to vascular plants, with liverworts representing the sister to all other land plants and hornworts being sister to vascular plants. Lycophytes are sister to all other vascular plants, which are divided into two clades, one being monilophytes, which include Equisetum, Psilotaceae‐Ophioglossaceae, Marattiaceae, and leptosporangiate ferns, and the other being seed plants. Relationships among the monilophyte lineages remain unresolved. Within seed plants, extant gymnosperms form a moderately supported clade in which Gnetales are related to conifers. This clade is sister to angiosperms. Most of the relationships among all major lineages of nonflowering land plants are supported by bootstrap values of 75% or higher, except those among basal monilophyte lineages and among some gymnosperm lineages, probably because of extinctions. The closest algal relative of land plants is Characeae, and this relationship is well supported. Several methodological issues on reconstructing large, deep phylogenies are also discussed.

Reconstructing the basal angiosperm phylogeny: Evaluating information content of mitochondrial genes

Three mitochondrial (atp1, matR, nad5), four chloroplast (atpB, matK, rbcL, rpoC2), and one nuclear (18S) genes from 162 seed plants, representing all major lineages of gymnosperms and angiosperms, were analyzed together in a supermatrix or in various partitions using likelihood and parsimony methods. The results show that Amborella + Nymphaeales together constitute the first diverging lineage of angiosperms, and that the topology of Amborella alone being sister to all other angiosperms likely represents a local long branch attraction artifact. The monophyly of magnoliids, as well as sister relationships between Magnoliales and Laurales, and between Canellales and Piperales, are all strongly supported. The sister relationship to eudicots of Ceratophyllum is not strongly supported by this study; instead a placement of the genus with Chloranthaceae receives moderate support in the mitochondrial gene analyses. Relationships among magnoliids, monocots, and eudicots remain unresolved. Direct comparisons of analytic results from several data partitions with or without RNA editing sites show that in multigene analyses, RNA editing has no effect on well supported relationships, but minor effect on weakly supported ones. Finally, comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloroplast genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.

PHYLOGENETIC RELATIONSHIPS IN FAGALES BASED ON DNA SEQUENCES FROM THREE GENOMES

Nucleotide sequences of six regions from three plant genomes—trnL‐F, matK, rbcL, atpB (plastid), matR (mtDNA), and 18S rDNA (nuclear)—were used to analyze inter‐ and infrafamilial relationships of Fagales. All 31 extant genera representing eight families of the order were sampled. Congruence among data sets was assessed using the partition homogeneity test, and five different combined data sets were analyzed using maximum parsimony and the Bayesian approach. At the familial level, the same phylogenetic relationships were inferred from five different analyses of these data. Nothofagus, followed by Fagaceae, are subsequent sisters to the rest of the order. Fagaceae are then sister to the core “higher” hamamelids, which consist of two main subclades, one being Myricaceae (Rhoipteleaceae (Juglandaceae)) and the other Casuarinaceae (Ticodendraceae (Betulaceae)). The combined data sets provide the best‐supported estimate of evolutionary relationships within Fagales. Our results suggest that the combination of different sequences from several species within the same genus representing a terminal taxon has little influence on phylogenetic accuracy. Inclusion of taxa with some missing data in combined data sets also does not have a major impact on the topology.

Phylogenetic and Biogeographic Diversification of Berberidaceae in the Northern Hemisphere

Abstract Sequences of the chloroplast genes matK and rbcL and nuclear ribosomal ITS2 were used for phylogenetic analyses of Berberidaceae. Three major clades were recognized, corresponding to the chromosome base numbers x = 6, 7, and 8/10. Bongardia was sister to the clade containing Achlys and the Podophyllum group, which consists of Diphylleia, Sinopodophyllum, Podophyllum, and Dysosma. The estimated times of divergence of six disjunct genera between Eurasia and North America ranged from 7.5 ± 2.3 Ma to 1.0 ± 0.7 Ma. The intercontinental disjunct lineages of Berberidaceae may have originated in eastern Asia and then migrated to Europe and North America. However, long-distance dispersal may explain the distribution pattern of Achlys. Desert xerophytes of Berberidaceae in southwestern Asia originated in response to the advent of dry climate at different times; Bongardia diverged from its closest relatives at 46.5 ± 3.6 Ma, whereas Leontice differentiated from Gymnospermium at 10.3 ± 3.2 Ma.

Menispermaceae and the diversification of tropical rainforests near the Cretaceous–Paleogene boundary

• Modern tropical rainforests have the highest biodiversity of terrestrial biomes and are restricted to three low-latitude areas. However, the actual timeframe during which tropical rainforests began to appear on a global scale has been intensely disputed. Here, we used the moonseed family (Menispermaceae), an important physiognomic and structural component of tropical rainforests on a worldwide basis, to obtain new insights into the diversification of this biome. • We integrated phylogenetic, biogeographic and molecular dating methods to analyse temporal and spatial patterns of global diversification in Menispermaceae. • Importantly, a burst of moonseed diversification occurred in a narrow window of time, which coincides with the Cretaceous-Paleogene (K-Pg) boundary. Our data also suggest multiple independent migrations from a putative ancestral area of Indo-Malay into other tropical regions. • Our data for Menispermaceae suggest that modern tropical rainforests may have appeared almost synchronously throughout the three major tropical land areas close to, or immediately following, the K-Pg mass extinction.

Large-scale phylogenetic analyses reveal multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms associated with climate change

Nitrogen is fundamental to all life forms and is also one of the most limiting of nutrients for plant growth. Several clades of angiosperms have developed symbiotic relationships with actinorhizal bacteria that fix atmospheric nitrogen and increase access to this nutrient. However, the evolutionary patterns of actinorhizal nitrogen-fixing symbioses remain unclear to date. Furthermore the underlying environmental pressures that led to the gain of symbiotic actinorhizal nitrogen fixation have never been investigated. Here, we present the most comprehensive genus-level phylogenetic analysis of the nitrogen-fixing angiosperms based on three plastid loci. We found that actinorhizal nitrogen-fixing species are distributed in nine distinct lineages. By dating the branching events, we determined that seven actinorhizal nitrogen-fixing lineages originated during the Late Cretaceous, and two more emerged during the Eocene. We put forward a hypothesis that multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms may have been associated with increased global temperatures and high levels of atmospheric carbon dioxide during these two time periods, as well as the availability of open habitats with high light conditions. Our nearly complete genus-level time-tree for the nitrogen-fixing clade is a significant advance in understanding the evolutionary and ecological background of this important symbiosis between plants and bacteria.

Integrated Fossil and Molecular Data Reveal the Biogeographic Diversification of the Eastern Asian-Eastern North American Disjunct Hickory Genus (Carya Nutt.)

The hickory genus (Carya) contains ca. 17 species distributed in subtropical and tropical regions of eastern Asia and subtropical to temperate regions of eastern North America. Previously, the phylogenetic relationships between eastern Asian and eastern North American species of Carya were not fully confirmed even with an extensive sampling, biogeographic and diversification patterns had thus never been investigated in a phylogenetic context. We sampled 17 species of Carya and 15 species representing all other genera of the Juglandaceae as outgroups, with eight nuclear and plastid loci to reconstruct the phylogeny of Carya. The phylogenetic positions of seven extinct genera of the Juglandaceae were inferred using morphological characters and the molecular phylogeny as a backbone constraint. Divergence times within Carya were estimated with relaxed Bayesian dating. Biogeographic analyses were performed in DIVA and LAGRANGE. Diversification rates were inferred by LASER and APE packages. Our results support two major clades within Carya, corresponding to the lineages of eastern Asia and eastern North America. The split between the two disjunct clades is estimated to be 21.58 (95% HPD 11.07-35.51) Ma. Genus-level DIVA and LAGRANGE analyses incorporating both extant and extinct genera of the Juglandaceae suggested that Carya originated in North America, and migrated to Eurasia during the early Tertiary via the North Atlantic land bridge. Fragmentation of the distribution caused by global cooling in the late Tertiary resulted in the current disjunction. The diversification rate of hickories in eastern North America appeared to be higher than that in eastern Asia, which is ascribed to greater ecological opportunities, key morphological innovations, and polyploidy.

Tree of life for the genera of Chinese vascular plants

We reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We produced a matrix comprising 6098 species and including 13 695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 families of Chinese vascular plants, covering more than 93% of all genera known from China. The comprehensive large phylogeny supports most relationships among and within families recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafamilial relationships of several large families and monophyly of some large genera are well supported by our dense taxonomic sampling. Our results showed that two species of Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except Sarcosperma. We have made our phylogeny of Chinese vascular plants publically available for the creation of subtrees via SoTree (http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.

Organogenesis of the inflorescence and flowers in Platycarya strobilacea (Juglandaceae)

The reproductive structures of the monotypic genus Platycarya (Juglandaceae), in particular the nature of the fruit wings, have been interpreted variously. We investigated organogenesis of inflorescence and flowers with scanning electron microscopy (SEM). This is the first SEM study to show the whole developmental process of male, female, and bisexual flowers in a member of the Fagales. In staminate and bisexual flowers, only a subtending bract is present, while bracteole and perianth are absent. Four to 10 stamen primordia of different sizes are arranged as an irregular circle or two semicircles. With further development of the stamens, the receptacle, which is fused to the base of the bract, enlarges, and the whorled arrangement of stamens becomes less and less distinct. In pistillate flowers, the transversely ellipsoidal floral primordium develops a central depression. Two bracteoles are initiated in the lateral position of the floral primordium. Soon, the inconspicuous circular perianth primordium appears around the central depression, and two carpels are initiated bordering the central depression opposite to the bracteoles. The perianth is highly reduced and fused with the ovary wall from the initial stage. Each wing of the fruit of Platycarya strobilacea is formed by a combination of one bracteole and the lateral lobe of the perianth.

Global versus Chinese perspectives on the phylogeny of the N‐fixing clade

There has been increasing interest in integrating a regional tree of life with community assembly rules in the ecological research. This raises questions regarding the impacts of taxon sampling strategies at the regional versus global scales on the topology. To address this concern, we constructed two trees for the nitrogen‐fixing clade: (i) a genus‐level global tree including 1023 genera; and (ii) a regional tree comprising 303 genera, with taxon sampling limited to China. We used the supermatrix approach and performed maximum likelihood analyses on combined matK, rbcL, and trnL‐F plastid sequences. We found that the topology of the global and the regional tree of the N‐fixing clade were generally congruent. However, whereas relationships among the four orders obtained with the global tree agreed with the accepted topology obtained in focused analyses with more genes, the regional topology obtained different relationships, albeit weakly supported. At a finer scale, the phylogenetic position of the family Myricaceae was found to be sensitive to sampling density. We expect that internal support throughout the phylogeny could be improved with denser taxon sampling. The taxon sampling approach (global vs. regional) did not have a major impact on fine‐level branching patterns of the N‐fixing clade. Thus, a well‐resolved phylogeny with relatively dense taxon sampling strategy at the regional scale appears, in this case, to be a good representation of the overall phylogenetic pattern and could be used in ecological research. Otherwise, the regional tree should be adjusted according to the correspondingly reliable global tree.