Table of Contents
  • Volume 59 Issue 5

    Cover illustration: Left to right, top to bottom: Abelia forrestii (Linnaeoideae) (Photo by S. Landrein), Kolkwitzia amabilis (Linnaeoideae) (Photo by G.M. Li), Lonicera hypoglauca (Caprifolioideae) (Photo by H.X. Wang), Zabelia trifl ora (Photo by S. Landrein), Vesalea floribunda (Linnaeoideae) (Photo by S. Landrein), Zabelia integrifolia (Photo by S. Landrein), Scabiosa comosa (Dipsacoideae) (Photo by J.L. Zhang), Valeriana flaccidissima (Valerianoideae) (Photo by S.H. Xia), Pterocephalus hookeri (Dipsacoideae) (P [Detail] ...
      
      Issue Information
    • 2021, 59 (5): 1–4
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    • Research Articles
    • Hong‐Xin Wang, Diego F. Morales‐Briones, Michael J. Moore, Jun Wen, and Hua‐Feng Wang
      2021, 59 (5): 897–914
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      The use of diverse data sets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we used target enrichment data, species tree, and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and 46 complete plastome sequence data from 43 samples representing 38 species from all major clades to reconstruct the phylogeny of the family using concatenation and coalescence approaches. We found significant nuclear gene tree conflict as well as cytonuclear discordance. Additionally, coalescent simulations and phylogenetic species network analyses suggested putative ancient hybridization among subfamilies of Caprifoliaceae, which seems to be the main source of phylogenetic discordance. Ancestral state reconstruction of six morphological characters revealed some homoplasy for each character examined. By dating the branching events, we inferred the origin of Caprifoliaceae at approximately 66.65 Ma in the late Cretaceous. By integrating evidence from molecular phylogeny, divergence times, and morphology, we here recognize Zabelioideae as a new subfamily in Caprifoliaceae. This work shows the necessity of using a combination of multiple approaches to identify the sources of gene tree discordance. Our study also highlights the importance of using data from both nuclear and plastid genomes to reconstruct deep and shallow phylogenies of plants.
    • 1. Species tree of the nuclear concatenated dataset inferred with ASTRAL-Ⅲ.
      2. Tanglegram of the nuclear concatenated (left) and plastid (right) phylogenies.
    • Mario Rincón‐Barrado, Sanna Olsson, Tamara Villaverde, Belén Moncalvillo, Lisa Pokorny, Alan Forrest, Ricarda Riina, and Isabel Sanmartín
      2021, 59 (5): 915–934
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      Wide-range geographically discontinuous distributions have long intrigued scientists. We explore the role of ecology, geology, and dispersal in the formation of these large-scale disjunctions, using the angiosperm tribe Putorieae (Rubiaceae) as a case study. From DNA sequences of nuclear ITS and six plastid markers, we inferred a phylogeny with 65% of all known Putorieae species. Divergence times, ancestral ranges, and diversification rate shifts were then estimated using Bayesian inference. We further explored species climatic tolerances and performed ancestral niche reconstruction to discriminate among alternative speciation modes, including geographical and ecological vicariance, and ecogeographical, ecological, and dispersal-mediated speciation. As a result, we identified seven major clades in Putorieae, some of which exhibit striking geographical disjunctions, matching the Rand Flora pattern, with sister species in the Canary Islands and eastern and southern Africa. Initial diversification within the tribe occurred in the early Miocene, coincident with a period of climate warming; however, most clades diverged within the last 10 Myr. Aridification and high extinction rates, coupled with ecological vicariance, explain the oldest disjunctions. Adaptation to new environmental conditions, after allopatry, is observed in several clades. Dispersal, either long-distance or via corridors made available by mountain uplift, is behind the most recent disjunctions. Some of these events were followed by ecological speciation and rapid diversification, with species becoming adapted to xeric or increasingly colder continental climates. We show that an integrative approach may help discriminate among speciation modes invoked to explain disjunctions at macroevolutionary time scales, even when extinction has erased the signature of past events.
    • Wide-range geographically discontinuous distributions have long intrigued scientists. We explore the role of ecology, geology, and dispersal in the formation of these large-scale disjunctions, using the angiosperm tribe Putorieae (Rubiaceae) as a case study. From DNA sequences of nuclear ITS and six plastid markers, we inferred a phylogeny, obtained an ancestral niche reconstruction, and estimated divergence times, ancestral ranges, and diversification rate shifts using Bayesian inference. As a result, we identified seven major clades in Putorieae, some of which exhibit striking geographical disjunctions and a probable reason for their distribution, including ecological and geographical vicariance, ecological and ecogeographical speciation, and long-distance dispersal.
    • Patricia Rivera, José Luis Villaseñor, Teresa Terrazas, and José L. Panero
      2021, 59 (5): 935–952
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      Asteraceae is the largest plant family in México with about 417 genera and 3113 species, and with more than 60% of them being endemic. Phylogenetic relationships at subfamily and tribal levels have been previously resolved employing both nuclear and plastid molecular markers. However, Asteraceae species native to Mexico have been underrepresented in such phylogenies. To tackle this issue, the taxon sampling of this study included 90 Asteraceae species native to México, four species from the Caribbean, 119 previously sequenced species, and six outgroups. With this sampling, all the Asteraceae subfamilies and all of the tribes recognized to date are represented. The analyzed dataset consisted of eleven chloroplast markers (atpB, matK, ndhC, ndhD, ndhF, ndhI, ndhJ, ndhK, rbcL, trnL-trnF, and 23S-trnA). We present two phylogenetic reconstructions obtained by maximum likelihood and pseudocoalescent methods. Besides, we present a time-calibrated phylogeny, which is used to infer the best configuration of diversification rate shifts. Our results show that Mexican species are distributed mainly in the subfamily Asteroideae (80 species), followed by Cichorioideae (6 species), Carduoideae (2 species), and Mutisioideae (2 species). Four net diversification rate shifts were found: One near the base of the tree and four within Asteroideae subfamily. Our extended sampling of the family with the representation of native species to Mexico allowed us to identify important events in the evolutionary history of the family.
    • Results from the Bayesian analysis of macroevolutionary mixtures (BAMM) analysis revealed four shifts in the diversification rates in Asteraceae through its history. Three of the shifts occur within Asteroideae subfamily, which is the most diverse in Mexico.
    • Yves Bawin, Tom Ruttink, Ariane Staelens, Annelies Haegeman, Piet Stoffelen, Jean‐Claude Ithe Mwanga Mwanga, Isabel Roldán‐Ruiz, Olivier Honnay, and Steven B. Janssens
      2021, 59 (5): 953–963
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      Interspecific hybridization events have played a major role in plant speciation, yet the evolutionary origin of hybrid species often remains enigmatic. Here, we inferred the evolutionary origin of the allotetraploid species Coffea arabica, which is widely cultivated for Arabica coffee production. We estimated genetic distances between C. arabica and all species that are known to be closely related to C. arabica using genotyping-by-sequencing (GBS) data. In addition, we reconstructed a time-calibrated multilabeled phylogenetic tree of 24 species to estimate the age of the C. arabica hybridization event. Ancestral states of self-compatibility were also inferred to shed new light on the evolution of self-compatibility in Coffea. Coffea canephora and C. eugenioides were confirmed as the putative progenitor species of C. arabica. These species most likely hybridized between 1.08 million and 543 000 years ago, coinciding with periods of environmental upheaval, which may have induced range shifts of the progenitor species that facilitated the emergence of C. arabica.
    • In this study, with broader species sampling and higher genetic resolution as compared with previous studies, we confirmed C. canephora and C. eugenioides as putative progenitors of the allotetraploid species C. arabica using genotyping-by-sequencing data and a multilabeled phylogenetic tree. We also estimated the age of the hybridization event giving rise to C. arabica between 1.08 million and 543 000 years, and inferred that self-compatible Coffea species (namely C. arabica, C. anthonyi, and C. heterocalyx) comprise a paraphyletic group.
    • Natalia P. Maslova, Aleksandra B. Sokolova, Тatiana M. Kodrul, Anna V. Tobias, Natalia V. Bazhenova, Xin‐Kai Wu, and Jian‐Hua Jin
      2021, 59 (5): 964–984
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      The unique co-occurrence of thyriothecia belonging to three fossil genera of epiphyllous fungi, Stomiopeltites Alvin & Muir (Micropeltidaceae), Callimothallus Dilcher, and Trichothyrites Rosendahl (Microthyriaceae), are reported on the leaves of the same host plant, Cunninghamia shangcunica Kodrul, Gordenko & Sokolova from the Oligocene Shangcun Formation of the Maoming Basin, South China. In China, Stomiopeltites is identified for the first time, Callimothallus is known from the Oligocene and Miocene of Guangxi and Zhejiang provinces, and Trichothyrites previously has been found only in the Eocene palynological assemblages of the Maoming Basin. The presence of abundant and diverse epiphyllous micromycetes, together with the taxonomic composition of the Shangcun megaflora and pollen assemblage, as well as quantitative climatic estimates obtained using Climate Leaf Analysis Multivariate Program, confirm the existence of a warm and humid climate in this region during the late early Oligocene. The geographic and stratigraphic distributions, comparisons with extant analogues, as well as ecological and paleoclimatic implications of the fossil fungi are discussed.
    • The unique co-occurrence of thyriothecia belonging to three fossil genera of epiphyllous fungi are reported on the leaves of the same host plant Cunninghamia from the Oligocene of South China. Together with the taxonomic composition of the megaflora and pollen assemblage, as well as quantitative climatic estimates, they confirm the existence of a warm and humid climate in this region during the late early Oligocene.
    • Xiao‐Long Jiang, Zhi‐Hao Su, Gang‐Biao Xu, and Min Deng
      2021, 59 (5): 985–997
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      Understanding the past and future evolutionary dynamics of dominant species in a forest is important for guiding decisions for biodiversity conservation, forest management, and vegetation restoration. This study used Quercus schottkyana, a dominant tree in subtropical evergreen broad-leaved forests in southwest China, to investigate the influences of past environmental fluctuations and future changes in climate on the dynamics of tree demographics. Genomic data were obtained for 133 samples of Q. schottkyana from 22 populations using double-digest genotyping by sequencing. The single-nucleotide polymorphisms in the genome showed a uniform distribution. Based on principal component analysis and Admixture analysis, two distinct lineages and one mixed group were identified that corresponded to their geographical distribution. Approximate Bayesian computation analyses provided evidence that the divergence among Q. schottkyana populations could be driven by the collision between the Asian and Indian plates during the Miocene, and that climatic fluctuations in the late Pleistocene led to the introgression. The analysis of genotype-environment relationships showed that annual precipitation and geographic distance were associated with spatial genetic variation. Populations of Q. schottkyana in the northern area of the Jinsha River basin were predicted to be the most vulnerable to future climate change. To increase genetic diversity in the northern Jinsha River basin and to buffer threats from future climate change, managers could use a mixture of local and alien seeds during forest restoration and management. This case study can promote further investigations into assessing how past and future climate change impacts genetic divergence and local adaptation of trees in forests.
    • Genomic vulnerability to future climate change across the Quercus schottkyana range, and its relationship with annual precipitation.
    • Peter C. van Welzen, Susana Arias Guerrero, Deby Arifiani, Tjut J.F. Bangun, Roderick W. Bouman, Marcel C.M. Eurlings, Iska Gushilman, Peter B. Phillipson, Iris Tabak, Esmée Winkel, and Kenneth J. Wurdack
      2021, 59 (5): 1000–1017
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      During the environmental impact study for a proposed nickel mine near Weda Bay on Halmahera in North Moluccas (Maluku Utara Province), Indonesia, two unknown Euphorbiaceae were discovered. Morphological comparisons and molecular phylogenetic analyses using four markers (plastid trnL-F and rbcL, and nuclear ribosomal internal transcribed spacer and external transcribed spacer) indicated that they should be recognized as constituting a new, distinct genus of two species, which are described and illustrated here as Weda fragarioides and Weda lutea. The new taxa are members of the Australasian tribe Ricinocarpeae in subfamily Crotonoideae, and they are most closely related to Alphandia. In contrast with the otherwise mostly sclerophyllous Ricinocarpeae, Weda possesses stellate to dendritic hairs, large, long-petiolate, glandular leaves, and inflorescences with a pair of large, leafy, subopposite bracts. The two narrowly distributed species are distinguished from each other by vegetative and floral features, molecular data, and elevational preferences. Leaf elemental analysis of Weda indicated manganese, but not nickel, accumulation. Newly resolved generic relationships and potential morphological synapomorphies within Crotonoideae are discussed, and the circumscription of Ricinocarpeae is expanded from 7 to 11 genera.
    • Ying Bao, Yu-Qin Mei, Xin Xu, Ye Liu, and Zhen-Yang Wu
      2021, 59 (5): 1018–1026
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      The DAD1 (defender against apoptotic cell death) gene is a negative regulator of programmed cell death. It plays important roles in plant growth, development, environmental adaptation, and aging. We examined whether and how the expression of DAD1 gene is affected by the promoter changes in the allotetraploid upland cotton (Gossypium hirsutum L.). We compared the expression status of the genes in the leaves of an elite cultivar and a wild variety of G. hirsutum, and cloned and analyzed a 1.3-kb promoter region of the genes in two cotton types. Results revealed that the expression of a subgenomic homoeolog of DAD1 (DAD1 At ) was significantly upregulated in leaves of the cultivated cotton when compared with that in a wild cotton. In addition, we identified 18 variations, including 14 single nucleotide polymorphisms and four indels between the promoters of the two cotton types. We detected at least 10 of 18 variations in the promoters related to possible cis-regulatory elements. Further transient tobacco assays using heterogeneous DAD1 At promoter::GUS fusion showed that the activity of the DAD1 At promoter in the cultivated cotton was stronger than that in the wild cotton, which suggested a dynamic change in the DAD1 At promoter during genetic divergence of the two cottons. This study provides an example of how gene expression could be affected by specific changes in the gene promoter.
    • Zhi‐Zhong Li, Andrew W. Gichira, John K. Muchuku, Wei Li, Guang‐Xi Wang, and Jin‐Ming Chen
      2021, 59 (5): 1027–1039
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      Monochoria C. Presl is a genus of Pontederiaceae and confined to the Old World, with species mainly distributed in tropical and subtropical Africa, Asia, and Australia. However, phylogenetic relationships and biogeography within Monochoria are yet to be fully resolved. Here, we sequenced 14 Monochoria plastomes, representing around eight of the ~10 species of Monochoria, and two plastomes from related genera. We undertook comparative analyses and phylogenetic reconstructions of Monochoria using these and other available sequences. We found the plastomes of Pontederiaceae to be highly conserved in structure, and identified six regions as mutational hotspots among species of Monochoria. Our data strongly support the monophyly of Monochoria and two main clades within the genus. We confirm that Monochoria australasica Ridl. is sister to the rest of the genus and that Monochoria korsakowii (Regel & Maack) defines the second split within Monochoria. In addition, we inferred the African endemic species Monochoria africana (Solms) N. E. Br. to be closely related to Monochoria plantaginea (Roxb.) Kunth and an undetermined specimen from Australia (Monochoria sp. AU63). Estimation of divergence times and biogeography implied that the African species M. africana originated in Asia, and the most recent common ancestor of Monochoria was distributed in Australasia/Asia at approximately 15 Ma, followed by diversification in Asia during the late Miocene and Pliocene. Long-distance dispersal, likely mediated by migratory birds, to Africa and Australia during the Pliocene and Pleistocene, might have contributed to the extant transoceanic distribution of the genus. Additionally, based on our phylogenetic results, we revised the description of Monochoria valida G. X. Wang & Nagam here.
    • A robust phylogenetic framework for Monochoria was constructed using the whole plastome. Monochoria is monophyletic and consists of two major clades. The most recent common ancestor of Monochoria was distributed in Australasian/Asian areas at approximately 15 Ma, followed by diversification in Asia during the late Miocene and Pliocene. Long-distance dispersal likely aided by migratory birds contributed to the transoceanic distribution of the genus.
    • Dong‐Mei Jin, Xi‐Le Zhou, Harald Schneider, Hong‐Jin Wei, Hong‐Yu Wei, and Yue‐Hong Yan
      2021, 59 (5): 1040–1050
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      Ferns that evolved from 400 million years ago show various functional traits and ecological strategies in extant species, over 80% of which belong to the youngest order Polypodiales. How the functional traits and strategies of ferns have changed during their evolutionary history remains unexplored. Here, we measured functional traits that are sensitive to environmental light and water availability in 345 fern species across fern phylogeny, and reconstructed their evolutionary histories. We found that ferns, mainly Polypodiales, have developed diversified functional traits in response to forest environments. Terrestrial species, especially Thelypteridaceae and Athyriaceae in eupolypods II, since the late Jurassic period, have shown decreased leaf mass per area (LMA) and area-based leaf nitrogen (Narea), but increased mass-based leaf nitrogen (Nmass) compared with early-derived polypods. Epiphytic species, mainly those in Polypodiaceae, have shown reductions in Nmass and individual leaf area (Area) since the late Cretaceous period. The adaption of functional traits of Polypodiales to forest environment may have played a crucial role in fern radiation since the late Jurassic period. Integrative analysis of functional traits, especially numerical ones, may shed new light on plant evolution.
    • Phylogenetic analysis of functional traits from extant ferns revealed how ferns have adapted to forest environments, including the shade and moist forest floor and the exposed and xeric forest canopy.
    • Lei Huang, Xiao‐Cheng Xing, Wan‐Wan Li, Yun Zhou, Yu‐Qu Zhang, Cheng Xue, Yi Ren, and Ju‐Qing Kang
      2021, 59 (5): 1051–1064
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      The taxonomy of woody bamboo presents many difficulties due to its long blooming interval and complex morphological variation. Whether the current taxonomy reflects genuine species divergence within woody bamboo is an intriguing question. The Fargesia spathacea Franch. complex comprises 15 closely related species with a sympatric distribution in China. Their classification has long been controversial because only a handful of vegetative traits are available, providing a good opportunity to explore the evolutionary relationships and genetic differentiation in woody bamboo. Here, we present a study involving 750 individuals from 39 representative populations in the F. spathacea complex using 14 simple sequence repeat markers. We found varying degrees of genetic diversity across populations of the F. spathacea complex (He = 0.07–0.81) and largely negative F-values at the population level, implying an excess of heterozygotes in the populations. Phylogenetic analyses revealed that all populations were divided into two major groups (clusters A and B), with the majority of the 15 species representing distinct genetic lineages. Based on population genetic analysis along with morphological evidence, we confirmed the identity of three species (F. decurvata J. L. Lu, F. spathacea, and F. murielae Gamble) and suggested the invalidation of four other species (F. scabrida T. P. Yi, F. robusta T. P. Yi, F. denudata T. P. Yi F. murielae (Gamble) T. P. Yi, and F. nitida (Mitford) Keng f. ex T. P. Yi). The delimitation of the remaining eight species has yet to be explored. The analysis of ecological factors and spatial autocorrelation suggested that altitudinal differences might account for the distinct genetic divergence between the two major groups.
    • Yong‐Hui Wang, Sayaka Ban, Wen‐Jing Wang, Yi Li, Ke Wang, Paul M. Kirk, Kathryn E. Bushley, Cai‐Hong Dong, David L. Hawksworth, and Yi‐Jian Yao
      2021, 59 (5): 1065–1080
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      Since the discovery of the Pleurocordyceps/Polycephalomyces” clade unaffiliated with the clades of Clavicipitaceae s. str., Ophiocordycipitaceae, and Cordycipitaceae of clavicipitaceous fungi, some taxa have been published and more fungal material relevant to the group have become available for further study. Here, a multigene phylogeny using nrSSU, nrLSU, tef1, rpb1, and rpb2 was constructed with some of the recently discovered additional taxa using maximum likelihood and Bayesian analyses (BI) to test and refine the current phylogenetic framework for Cordyceps s. lat. and other clavicipitaceous fungi. In addition to the well supported major Pleurocordyceps/“Polycephalomyces” clade revealed previously, another clade with newly added taxa referred to as “Polycephalomyces formosus-like” from Japan was found to be sister to the Pleurocordyceps/“Polycephalomyces” clade. Extensive investigation revealed that strains named “P. formosus-like” grouped in this new clade and do indeed represent the true P. formosus and that species previously included in the genus Polycephalomyces required a new generic name. Based on the phylogenetic analyses and morphological characteristics, including both sexual and asexual morphs when available, the new generic name Pleurocordyceps is introduced and relevant new combinations are made. A newly designated lectotype and a supporting epitype for P. formosus is selected and the circumscription of Polycephalomyces is discussed.
    • Phylogenetic tree from ML and BI analyses of multigene (nrSSU, nrLSU, tef1, rpb1, and rpb2) data sets showing the relationships within Hypocreales. Bootstrap proportions (equal to or above 70%) of ML analyses (ML-BP) and posterior probabilities (PP) (equal to or above 95%) are shown above internodes before and after the backslash, respectively. The names of taxa (e.g., clades, families) are provided to the right of the species names.
    • Qian‐Yi Yin, Qiang Fan, Pan Li, DoVan Truong, Wan‐Yi Zhao, Ren‐Chao Zhou, Su‐Fang Chen, and Wen‐Bo Liao
      2021, 59 (5): 1081–1099
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      Historical climate oscillations and tectonic events have influenced the speciation and evolutionary history of many organisms. In this study, we chose Fokienia hodginsii (Dunn) A. Henry & H. H. Thomas (Cupressaceae s.l.), a Tertiary relict conifer, for the inference of the demographic history since the Neogene. Five chloroplast regions and two single-copy nuclear genes were amplified and sequenced in 497 individuals from 28 populations. The chloroplast data showed that F. hodginsii presented a high level of genetic diversity (H T  = 0.860 ± 0.0279) and significant phylogeographic structure (N ST  > G ST , P < 0.05). According tobeast analysis, the divergence time of the two major lineages indicated by the phylogenetic construction produced from chloroplast and nuclear data could be dated to the early Miocene (ca. 19.34–19.95 Ma), which coincided with the onset and intensification of the Asian monsoon. During this time, environmental adaption under the different climatic conditions on either side of the Tanaka Line could have played important roles in maintaining and/or reinforcing the divergence of the two major lineages. The ecological niche modeling results showed that F. hodginsii experienced habitat fragmentation and strengthening of genetic barriers during the Last Glacial Maximum, followed by local expansion during postglacial periods. Our findings show that paleoclimate changes since the Neogene might have triggered the extinction of all but one Fokienia species and its intraspecific lineage differentiation. This study also suggests that Tertiary relicts in subtropical and tropical areas might have had a complex evolutionary history and their intraspecific differentiation time might have been earlier than expected.
    • Sheng‐Lan Xu, Tatiana M. Kodrul, Yan Wu, Natalia P. Maslova, and Jian‐Hua Jin
      2021, 59 (5): 1100–1110
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      The genus Burretiodendron Rehder is currently endemic to an area near the China–Vietnam border and the limestone mountains of Thailand and Myanmar. The fossil records of this genus were previously found only from the Miocene of Yunnan, Southwest China, and the Oligocene of Guangxi, South China. Here, we describe fossil fruits and associated leaves of Burretiodendron, which were discovered in the lower Oligocene Shangcun Formation of the Maoming Basin, Guangdong, South China. Morphological comparison with extant and fossil Burretiodendron taxa indicates that fruit fossils belong to the species Burretiodendron parvifructum J. Lebreton Anberrée & Z. K. Zhou. This is one of the earliest fossil records of the genus, providing additional evidence for the early biogeographic history of this genus and supporting the inference that the genus originated in South China. According to the habitat conditions of modern species, we speculate that there were limestone mountains around the Maoming Basin in the early Oligocene.
    • Dan Xie, Bo Liu, Li‐Na Zhao, Tirtha Raj Pandey, Hui‐Yuan Liu, Zhang‐Jian Shan, and Hai‐Ning Qin
      2021, 59 (5): 1111–1123
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      The Species Catalogue of China: Volume 1: Plants (SCCP) is a new, comprehensive, hardcopy inventory of Chinese higher plants that combines several datasets and references to recent taxonomic treatments. The database, with all attached additional information, is freely accessible via the internet (http://www.sp2000.org.cn/) and on CD-ROM, and will be updated yearly. It includes bryophytes (157 families, 599 genera, and 3167 specific and infraspecific taxa), lycophytes and ferns (41 families, 181 genera, and 2336 specific and infraspecific taxa), gymnosperms (10 families, 45 genera, and 311 specific and infraspecific taxa), and angiosperms (270 families, 3227 genera, and 35 873 specific and infraspecific taxa); in total 478 families, 4052 genera, and 41 687 specific and infraspecific taxa. Several other important statistics can also be drawn from the database, such as the distribution pattern of the four major groups of higher plants, as well as number of endemic and naturalized or cultivated genera/taxa. Entries in SCCP are also compared with Flora of China, and Flora reipublicae popularis Sinicae at the genus level. The SCCP will not only be a useful reference for floristic or biodiversity studies in China, but will also serve as a key resource to direct action and monitor progress. It is intended to be a useful resource for achieving Target 1 of the Global Strategy for Plant Conservation (GSPC).
    • Higher plants of China are mainly distributed in the southwestern region of the country, especially in the area between 95°E and 110°E longitude and 20°N and 34°N latitude. The number of higher plants in the south is more than that in the north which makes the 34°N latitudinal line a floristic border for the south and the north of China.
    • Bin‐Bin Liu, Zhi‐Yao Ma, Chen Ren, Richard G. J. Hodel, Miao Sun, Xiu‐Qun Liu, Guang‐Ning Liu, De‐Yuan Hong, Elizabeth A. Zimmer, and Jun Wen
      2021, 59 (5): 1124–1138
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      With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 data sets with different sequencing coverage in silico. We tested the performance of four data sets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the Vitis clade at the genus level and Vitaceae at the family level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10× coverage. Without the steps of synthesizing baits and enrichment experiments, coupled with incredibly low sequencing costs, we showcase that deep genome skimming (DGS) is as effective for capturing large data sets of SCNs as the widely used Hyb-Seq approach, in addition to capturing plastomes, mtDNA, and entire nrDNA repeats. DGS may serve as an efficient and economical alternative and may be superior to the popular target enrichment/Hyb-Seq approach.
    • We proposed a new method, deep genome skimming (DGS), for recovering single-copy nuclear genes (SCNs), in addition to plastomes, mitochondrial DNA, and entire nuclear ribosomal DNA repeats, and this method may serve as an efficient and economical alternative and may be superior to the popular target enrichment/Hyb-Seq approach.
Editors-in-Chief
Song Ge
Jun Wen
Impact Factor
4.098
JCR 2020 IF ranking: 41/235 (Plant Sciences, top 17.24%, Q1 quartile)
Journal Abbreviation: J Syst Evol
ISSN: 1674-4918 (Print)
1759-6831 (Online)
CN: 11-5779/Q
Frequency: Bi-monthly

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