The genus Wisteria (Fabaceae) is disjunctly distributed in eastern Asian and eastern North American temperate deciduous forests, and it is widely cultivated around the world as spectacular garden plants. It is a member of inverted repeat-lacking clade (IRLC). The IRLC Species are characterized by the loss of an IR region in their plastomes, which has long been of great interest. In this research, we report whole plastome sequences from all four Wisteria species and a Wisteriopsis japonica, combining these with existing data to explore phylogenetic relationships and biogeography of Wisteria, as well as plastome evolution of IRLC species. Phylogenetic analyses recognized a clade containing Glycyrrhiza–Wisteriopsis–Wisteria as sister to the remaining genera of IRLC. North American Wisteria frutescens and the three Asian species formed reciprocal clades, and Wisteria brachybotrys was sister to Wisteria floribunda and Wisteria sinensis. Wisteria may have originated in Japan near the boundary of the Oligocene and Miocene. The disappearance of Bering Land Bridge in the late Miocene might lead to the Eastern Asian–Eastern North American disjunction of Wisteria. Allopatric speciation of Wisteria between the Japanese archipelago and the Asian continent in the Quaternary increased the species richness of eastern Asia in comparison with eastern North America. Synonymous substitution rates (d_S) of protein-coding genes in the IRLC species were around 2-fold (SC genes) or 11-fold (IR genes) higher than those of non-IRLC species. For both SC and IR genes, herbaceous legumes have around 3-fold higher d_S than woody ones. Both loss of one IR region and herbaceous habit elevated substitution rates of the plastomes.

This analysis corroborates and expands our previous results regarding the phylogenetic position of Cheilanthes species from South America. We sequenced three plastid genetic regions, one genic (rbcL) and two genic plus intergenic spacers (trnL + trnL-F and rps4 + rps4-trnS) from 25 South American cheilanthoid species. This allowed us to elucidate phylogenetic relationships that have been historically unresolved or were lowly supported. Here, we analyzed 45 Cheilanthes species (23 from South America) and circumscribed Cheilanthes s.s. in a strongly supported clade that contains three subclades: (i) exclusively from South America, (ii) from Australasia + South America, and (iii) from Africa. The position of three South American species, previously referred to the informal “Cheilanthes geraniifolia group”, is confirmed as a highly supported group outside Cheilanthes s.s. and within the Adiantopsis–Doryopteris clade. This group is described here as the new genus Mineirella. The new combinations for the genus and illustrations are included. Additionally, we discuss the morphological innovations that provide evidence to support the different clades.

Didymodon s.l. is one of the largest genera in the moss family Pottiaceae, with about 122 species distributed in all continents. This, together with its high degree of morphological variation, has made it one of the taxonomically most challenging genera of Pottiaceae. Circumscription of Didymodon s.l. has been, and still is, controversial. To date, the only molecular study that has investigated the delimitation of the genus has been far from comprehensive (35 samples from 27 species), limited in geographical scope (mainly restricted to Europe), and based exclusively on ITS sequences. To evaluate the circumscription of Didymodon s.l. and its relationships with the allied genera Andinella, Gertrudiella, and Tridontium, we conducted phylogenetic analyses of DNA sequences for three plastid markers (atpB–rbcL, trnG, and trnL-F) and one nuclear locus (ITS) for 335 samples representing 86 species of Didymodon s.l. (ca. 70%), and all taxa of the genera Andinella, Gertrudiella, and Tridontium. Individual markers and concatenated matrices were analyzed using maximum likelihood and Bayesian approaches. Our results indicate that Didymodon s.l. is not monophyletic, because Andinella, Gertrudiella, and Tridontium species are nested within it. Species of these four genera can be divided into eight well-supported and morphologically distinct genera: Didymodon s.s., Geheebia, Gertrudiella, Husnotiella, Trichostomopsis, Tridontium, Vinealobryum, and Zanderella. In correspondence with the results presented, 38 new combinations, 10 new synonyms, and a new name are provided for those taxa where required, and lectotypes are designated for 13 names. A diagnostic key to the eight recognized genera is provided.

Roegneria is a polyploid perennial genus in the tribe Triticeae. Some species of Roegneria are morphologically similar to genus Elymus and have been classified in Elymus. To investigate the delimitation and phylogenetic relationships of Roegneria, nuclear (ITS, Acc1, and Pgk1) and chloroplast (trnL–trnF) DNA regions were sequenced for 38 allopolyploid species and 32 diploid species of Triticeae. Phylogenetic analyses of nuclear DNA revealed that all Roegneria species were included in the St and Y genome clades, and that the Y genome was closely related to the V and Xp genomes. The chloroplast DNA dataset showed that Roegneria species were grouped with Pseudoroegneria species. The Pseudoroegneria species from the Middle East (P. libanotica and P. tauri) and Central Asia (P. strigosa) were more closely related to Roegneria species. The results suggested that: (i) the species containing the St and Y genomes should be segregated from Elymus and treated as a distinct genus, Roegneria, based on the genomic constitution; (ii) P. libanotica, P. tauri, and/or P. strigosa potentially served as the maternal donor of the St genome in Roegneria; (iii) The Y genome of Roegneria originated from a diploid Y genome species, and the V and Xp genomes may have contributed to Y genome formation; (iv) among Roegneria species of previously uncertain genomic constitution, R. seriotina was tetraploid and possessed the StY genomes, E. calcicolus was hexaploid with the StYH genomic constitution and should be classified in Campeiostachys, R. glaucifolia possessed the StStY genomes, and R. tschimganica had the genomic constitution St₁St₂Y.

Schizachyrium (Poaceae, Andropogoneae) includes about 60 species distributed in tropical and subtropical regions of the world. In all recent molecular phylogenies of Andropogoneae, representatives of Schizachyrium appear closely related to Andropogon species. The objective of this study was to contribute to the delimitation of Schizachyrium. We performed a phylogenetic study including 38 taxa (>63%) of Schizachyrium, along with representatives of related genera, mainly of Andropogon, yielding a total of 49 taxa. This is the first phylogenetic analysis to include the type species of Schizachyrium, S. condensatum. DNA sequences of two plastid markers (ndhF and trnL-F) were analyzed under Bayesian methods. The results indicate that Schizachyrium is not monophyletic: 26 of the 38 Schizachyrium taxa analyzed are placed in a Schizachyrium s.s. clade that includes the type species of the genus, while 10 taxa are related to Andropogon species and two other species, S. delavayi (from China and India) and S. jeffreysii (from Africa), appear clearly separated. Additionally, 58 morphological characters (41 qualitative and 17 quantitative) were scored for the same 49 taxa and analyzed under the parsimony criterion. Character optimizations showed that (i) the reduced pedicellate spikelets, (ii) with lower glume less than or equal to 0.5 mm wide, (iii) awned, and (iv) without lemma and palea support the Schizachyrium s.s. clade. We propose these four characters as diagnostic features for the delimitation of Schizachyrium s.s.

Despite its amazing biodiversity, the Eastern Mediterranean remains a highly understudied region when compared with the Western Mediterranean, restricting our understanding of diversity across the entire Mediterranean. Here we use a combination of molecular markers and presence/absence data from all species of the Eastern Mediterranean genus Ricotia collected across its full geographic range to determine historical, ecological, and evolutionary factors responsible for lineage-specific diversification in the Eastern Mediterranean. Network analysis based on molecular data revealed a high genetic structure within all lineages, and phylogenetic reconstructions based on the multispecies coalescent showed that within-lineage diversification corresponded to the onset of the Mediterranean climate. Reconstruction of ancestral histories indicates that the genus originated within Anatolia and spread across the Eastern Mediterranean and Levant using the Taurus mountains. Ecological niche models suggest that local populations did not go through any major distributional shifts and have persisted in present-day habitats since the Last Glacial Maximum. Furthermore, niche differentiation tests revealed significant differences between closely related species and showed the main variables predicting species limits to be different for each species. Our results give crucial information on the patterns and processes shaping diversity in the Eastern Mediterranean and show the main factors promoting diversification to be local environmental dynamics and ecological specialization and not large-scale latitudinal movements, as often reported for southern Europe. By determining local and regional patterns of diversification in an Eastern Mediterranean genus, we further our understanding of the major trends influencing plant diversity in the Mediterranean basin as a whole.

The genus Elymus L. in the tribe Triticeae (Poaceae) includes economically and ecologically important forage grasses. The genus contains the pivotal St genome from Pseudoroegneria in combination with other genomes in the tribe. Many Elymus species are tetraploids containing the StY genomes. It is thought that polyploidization characterizes the speciation of the genus in which the Y is considered as another key genome. Based on data from cytological, genome in situ hybridization, and molecular studies, we hypothesized an endo-allopolyploidy origin of the StY-genome species from the autotetraploid Pseudoroegneria species. To test this hypothesis, we amplified, cloned, and sequenced five single-copy nuclear genes (i.e., alcohol dehydrogenase 1–3, Adh1–Adh3, RNA polymerase II, Rpb2; and Waxy) from Elymus, Pseudoroegneria, and Hordeum species. The phylogenetic trees constructed based on the sequencing analyses of all genes indicated that diploid and autotetraploid Pseudoroegneria species were closely related, although with considerable genetic variation in tetraploids. In addition, the StY-genome Elymus species tended to have a close relationship with the diploid and autotetraploid Pseudoroegneria species, although different phylogenetic relationships among the gene trees were detected. These results indicated that the StY-genome species may have an autotetraploid origin and experienced recurrent hybridization. The complex St genomes in Pseudoroegneria in the polyploid state may gain more opportunities for within-species differentiation and recurrent hybridization. As a result, series modified versions of St genomes evolved into the StY genomes in some Elymus species.

Mimicry of non-rewarding flowers to rewarding flowers has been accepted as a strategy to improve pollination success in angiosperms. It has been proposed that this mechanism depends on whether potential pollinators can discriminate between the flowers. In this study, the intersexual mimicry and deceit pollination were studied in a threatened dioecious aquatic herb, Ottelia acuminata. Its female flowers resemble male flowers in morphology and odor compounds, to avoid discrimination by pollinators and outcompete male flowers in attracting the pollinators using stronger scents and bigger flowers. However, an obvious visit bias of its pollinator (Apis cerana) to male flowers was detected, suggesting that bees can distinguish the rewarding males from non-rewarding females. Although the deceit was not successful, pollination was not seriously undermined because pollen limitation was found to be low in the sampled natural population. We speculate that, due to “accidental” visits on female flowers and “mistake” pollinations, pollen limitation could be mitigated by a high frequency of pollen donors, and is correlated with the size and sex ratio of a population. Ottelia acuminata is a threatened dioecious aquatic herb. We suggest that developing multi-stakeholder coalitions should be encouraged to save the threatened edible and ornamental plant species in China. We hope this study could provide new insights into understanding of the role of intersexual mimicry in other flowering plants.

Understanding the genetic basis underpinning local adaptation is one of the fundamental issues in ecological and evolutionary biology. In this study, we investigated the genomic basis underlying local adaptation of the Chinese wingnut (Pterocarya stenoptera C. DC). Our population genomic analyses revealed nine spatial genetic clusters across the current distribution range of this species. Based on the assessment of genetic–environment association, we found that adaptive divergence of the P. stenoptera populations were mainly shaped by solar radiation during fruit development, temperature seasonality, annual temperature, precipitation, and air humidity. In particular, our genome-wide scanning identified a total of 801 candidate single nucleotide polymorphisms (SNPs) that are highly correlated with diverse environmental factors. Further functional annotation of the SNPs identified some candidate genes that are involved into temperature, water, and light adaptation. Taken together, our results suggest that natural selection during local adaptation has contributed to the success of survival to diverse heterogenous environmental conditions. Our study provides important insights into the fundamental knowledge of the genetic basis underlying the local adaptation of non-model species.

Polyploidization and hybridization are very common in natural plant species, and mixed-ploidy species provide a unique opportunity to study the effects of evolutionary history, local abundance, and ploidy level on the direction and extent of introgression between intraspecific lineages. First, we delimited two morphologically cryptic lineages of Phragmites australis Trin. ex Steud. in temperate China using 11 nuclear microsatellites and two chloroplast DNA fragments with 225 samples from China as well as 11 samples from Oceania and Europe. Our evidence supported that haplotype O and haplotype P were two relatively independent lineages with low and high ploidy levels, respectively; haplotype M might be ancient and could have undergone a complex evolutionary history. Then we examined the lineage divergence and compared the introgression patterns between two major lineages along geographical and abundance gradients with a large number of samples (n = 1067) collected from China. The sympatric coexistence of two lineages in north and northeast China implies an ongoing or potential introgression between them. Cline analysis showed that the level of genetic admixture were significantly correlated with longitude rather than latitude. Our results also suggested that ploidy level could deeply influence the introgression asymmetry, and the effect of the current local abundance on introgression might be covered by the past coexistence time driven by phylogeographic history. Our study draws a baseline for future research on the ecological and evolutionary consequences of migration and introgression of Chinese P. australis under global change.

Past climatic oscillations and complex geodynamic processes had tremendous effects on the current distributions of species in East Asia. Previous studies have revealed that spermatophytes experienced different demographic histories and survived in multiple refuges. However, very few studies involving ferns have been conducted over a large geographical area like East Asia. The monophyletic epiphytic fern genus Lemmaphyllum, which is composed of four species, is widespread in East Asia and offers a good model for exploring how geoclimatic oscillations influence the diversification and demographic history of fern species. We studied the phylogeography of Lemmaphyllum based on 115 populations using plastid sequences and ecological niche modeling. A total of 91 haplotypes were found in Lemmaphyllum. Molecular clock estimation revealed that speciation coincided with the three phases of the Qingzang Movement at beginning of the third uplift of Qinghai-Tibetan Plateau. The “Tanaka-Kaiyong Line” demarcated lineages within L. carnosum. The split of the mainland and island lineages of L. rostratum and L. carnosum var. microphyllum may have resulted from ancestral isolation whereby land-bridges acted as a “barrier” rather than as a “corridor” between mainland and island lineages. Multiple glacial refuges such as Sichuan Basin, Jinggangshan region, YGG region, HDM region, and the islands of the China East Sea during the LGM were revealed. The entities of Lemmaphyllum experienced species-specific demographic histories in response to the Pleistocene climate change. The case study of epiphytic ferns may provide evidences for understanding the migration of evergreen broad-leaf forest under climate oscillation.

Gymnosphaera represents a minor lineage within the scaly tree-fern family Cyatheaceae. Tropical and subtropical mainland Asia is a main distribution area of Gymnosphaera. However, the species diversity of Gymnosphaera is currently incompletely known in mainland Asia due to lacking critical revision. Here we present new findings of species diversity and their relationships to mainland Asian Gymnosphaera based on field surveys, the examination of herbarium collections, and phylogenetic analyses of sequences of multiple chloroplast and nuclear regions. Two new species, G. saxicola from southwestern Yunnan and G. bachmaensis from central Vietnam, are established. Traditionally recognized G. podophylla is revealed to be a complex, from which G. bonii is reinstated as a distinct species. Our phylogenetic analyses identified four clades within Gymnosphaera in mainland Asia: G. denticulata clade, G. gigantea clade, G. podophylla clade, and G. salletii clade. The new species G. saxicola, which is special for its saxicolous habitat, was resolved as sister to G. austroyunnanensis in the G. salletii clade. The newly discovered G. bachmaensis, which is characterized specially by the spathulate frond, was positioned in the G. podophylla clade, being sister to G. bonii. The mountainous region from south-central Vietnam northwards to western Yunnan is a diverse center of Gymnosphaera and more species of this group are probably to be discovered there.

Icacinaceae are well represented in the modern tropical flora of East Asia, but this family has no confirmed macrofossils from this region. Most of the unambiguous fossils (e.g., endocarps) are from the Paleogene of North America and Europe, where the family is no longer present. Here we report a fossil endocarp of the liana genus Iodes from the Oligocene Wenshan flora, southwestern China. The fossil is relatively large (ca. 20 mm length, 11 mm width) and documents a vascular bundle inside the endocarp wall, a pattern of ridges enclosing few areoles, and an asymmetrical apex and rounded base. On the basis of these characteristics, we described a new species, Iodes elliptica, which represents the first Icacinaceae fruit fossil record from Asia. This fossil, consistent with recent reports of Iodes pollen from the Eocene of Hainan, indicates a long-standing presence of the genus in SE Asia, dating back to the Paleogene. Based on the climatic data of modern Iodes, and other fossil occurrences from Wenshan, we hypothesize that the climate in the region was subtropical during the Oligocene, supporting a rainforest, with an overall mixed regional flora of subtropical and tropical elements.

The genus Elaeocarpus contains approximately 360 species and occurs in mesic forest communities from India, through to China, Southeast Asia, New Guinea, Australia, and New Caledonia. Elaeocarpus fossils are best known from the Eocene to the Miocene of Australia and the late Pliocene–early Pleistocene of India, but have not been documented from East Asia before. Here we describe six new species of Elaeocarpus, E. nanningensis sp. nov. from the late Oligocene Yongning Formation of the Nanning Basin, E. presikkimensis sp. nov. from the Miocene Erzitang Formation of the Guiping Basin, E. prerugosus sp. nov., E. prelacunosus sp. nov., E. preserratus sp. nov., and E. preprunifolioides sp. nov. from the late Miocene Foluo Formation of the Nankang Basin in Guangxi, South China. This is the first reliable report for the genus occurring in East Asia, and the fossils indicate that Elaeocarpus had colonized this region by the late Oligocene and represented by a morphologically diverse group of species by the late Miocene. This sheds new insights into the timing and migration patterns of the genus in East Asia. Elaeocarpus is typically a rainforest genus occurring in mesic forests. Based on the habitat of their morphologically similar modern relatives we propose that these three sedimentary basins were warm and wet adjacent to mountainous regions with the evergreen or rain forests during the late Oligocene to Miocene.