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25 March 2023, Volume 45 Issue 02
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  • Correspondence
    New insights into intergeneric relationships of Hickeliinae (Poaceae: Bambusoideae) revealed by complete plastid genomes
    Rivontsoa A. Rakotonasolo, Soejatmi Dransfield, Thomas Haevermans, Helene Ralimanana, Maria S. Vorontsova, Meng-Yuan Zhou, De-Zhu Li
    2023, 45(02):  125-132.  doi:10.1016/j.pld.2022.06.001
    Abstract ( 24 )   HTML ( )   PDF (2123KB) ( 14 )   Save
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    The Hickeliinae (Poaceae: Bambusoideae) is an ecologically and economically significant subtribe of tropical bamboos restricted to Madagascar, Comoros, Reunion Island, and a small part of continental Africa (Tanzania). Because these bamboos rarely flower, field identification is challenging, and inferring the evolutionary history of Hickeliinae from herbarium specimens is even more so. Molecular phylogenetic work is critical to understanding this group of bamboos. Here, comparative analysis of 22 newly sequenced plastid genomes showed that members of all genera of Hickeliinae share evolutionarily conserved plastome structures. We also determined that Hickeliinae plastome sequences are informative for phylogenetic reconstructions. Phylogenetic analysis showed that all genera of Hickeliinae are monophyletic, except for Nastus, which is paraphyletic and forms two distant clades. The type species of Nastus (Clade II) is endemic to Reunion Island and is not closely related to other sampled species of Nastus endemic to Madagascar (Clade VI). Clade VI (Malagasy Nastus) is sister to the Sokinochloa + Hitchcockella clade (Clade V), and both clades have a clumping habit with short-necked pachymorph rhizomes. The monotypic Decaryochloa is remarkable in having the longest floret in Bambuseae and forms a distinct Clade IV. Clade III, which has the highest generic diversity, consists of Cathariostachys, Perrierbambus, Sirochloa, and Valiha, which are also morphologically diverse. This work provides significant resources for further genetic and phylogenomic studies of Hickeliinae, an understudied subtribe of bamboo.
    The identity of Dinochloa species and enumeration of Melocalamus (Poaceae: Bambusoideae) in China
    Jing-Xia Liu, Zu-Chang Xu, Yu-Xiao Zhang, Meng-Yuan Zhou, De-Zhu Li
    2023, 45(02):  133-146.  doi:10.1016/j.pld.2022.07.001
    Abstract ( 19 )   HTML ( )   PDF (49283KB) ( 18 )   Save
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    Three woody bamboo species collected in Hainan, China in 1940 have been described as Dinochloa based on vegetative specimens. However, the identity of these species has long been in doubt, largely because the vegetative phase in species of Dinochloa is morphologically similar to that in species of Melocalamus, a climbing or scrambling bamboo genus of the paleotropical woody bamboos (Poaceae: Bambusoideae) that consists of about 15 species and one variety. To determine the phylogenetic affinity of the three Dinochloa species from Hainan, we sampled almost all recognized Chinese species of Melocalamus and representative species of Dinochloa as well as other closely related genera, performed molecular phylogenetic analysis, and compared their morphology based on herbarium and fieldwork investigation. Our ddRAD data indicate that the three species from Hainan are closely related to Melocalamus, not Dinochloa. Morphological analysis showed that these three species have a climbing habit but do not grow spirally, their culm leaves have smooth bases, and there is a ring of powder and/or tomenta above and below the nodes. Taken together our findings indicate that the three species from Hainan originally published in Dinochloa should be transferred to Melocalamus, i.e., Melocalamus orenudus (McClure) D.Z. Li & J.X. Liu, Melocalamus puberulus (McClure) D.Z. Li & J.X. Liu, and Melocalamus utilis (McClure) D.Z. Li & J.X. Liu, respectively. This study concludes with an enumeration of Chinese species of Melocalamus, with a key to nine recognized species and one variety, and a lectotypification for M.compatiflorus.
    Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia
    Shi-Yu Lv, Xia-Ying Ye, Zhong-Hu Li, Peng-Fei Ma, De-Zhu Li
    2023, 45(02):  147-155.  doi:10.1016/j.pld.2022.04.002
    Abstract ( 29 )   HTML ( )   PDF (2402KB) ( 12 )   Save
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    Fargesia, the largest genus within the temperate bamboo tribe Arundinarieae, has more than 90 species mainly distributed in the mountains of Southwest China. The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals, including the giant panda. However, species-level identification of Fargesia is difficult. Moreover, the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes (rbcL, matK, and ITS) in bamboos. With progress in the sequencing technologies, complete plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) sequences have been proposed as organelle barcodes for species identification; however, these have not been tested in bamboos. We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes. Our analysis indicates that complete plastomes have substantially higher discriminatory power (28.6%) than standard barcodes (5.7%), whereas nrDNA sequences show a moderate improvement (65.4%) compared to ITS (47.2%). We also found that nuclear markers performed better than plastid markers, and ITS alone had higher discriminatory power than complete plastomes. The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia. However, neither of these sequences were able to discriminate all the sampled species, and therefore, more nuclear markers need to be identified.
    Wind-dispersed seeds blur phylogeographic breaks: The complex evolutionary history of Populus lasiocarpa around the Sichuan Basin
    Xue Li, Markus Ruhsam, Yi Wang, Hong-Ying Zhang, Xiao-Yan Fan, Lei Zhang, Jing Wang, Kang-Shan Mao
    2023, 45(02):  156-168.  doi:10.1016/j.pld.2022.10.003
    Abstract ( 21 )   HTML ( )   PDF (12434KB) ( 5 )   Save
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    The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits. Several important phylogeographic breaks exist around the Sichuan Basin in Southwest China but few studies have focused on wind-dispersed plants. Here, we investigated the phylogeographic patterns and the evolutionary history of Populus lasiocarpa, a wind-pollinated and wind-dispersed tree species with a circum-Sichuan Basin distribution in southwest China. We sequenced and analyzed three plastid DNA fragments (ptDNA) and eight nuclear microsatellites (nSSRs) of 265 individuals of P.lasiocarpa from 21 populations spanning the entire distribution range. Distribution patterns based on nSSR data revealed that there are three genetic groups in P.lasiocarpa. This is consistent with the three phylogeographic breaks (Sichuan Basin, the Kaiyong Line and the 105°E line), where the Sichuan basin acts as the main barrier to gene flow between western and eastern groups. However, the distribution pattern based on ptDNA haplotypes poorly matched the phylogeographic breaks, and wind-dispersed seeds may be one of the main contributing factors. Species distribution modelling suggested a larger potential distribution in the last glacial maximum with a severe bottleneck during the last interglacial. A DIYABC model also suggested a population contraction and expansion for both western and eastern lineages. These results indicate that biological traits are likely to affect the evolutionary history of plants, and that nuclear molecular markers, which experience higher levels of gene flow, might be better indicators of phylogeographic breaks.
    Patterns of phylogenetic relatedness of non-native plants across the introduction-naturalization-invasion continuum in China
    Hong Qian
    2023, 45(02):  169-176.  doi:10.1016/j.pld.2022.12.005
    Abstract ( 17 )   HTML ( )   PDF (1045KB) ( 7 )   Save
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    Human activities have caused the exchange of species among different parts of the world. When introduced species become naturalized and invasive, they may cause great negative impacts on the environment and human societies, and pose significant threats to biodiversity and ecosystem structure. Knowledge on phylogenetic relatedness between native and non-native species and among non-native species at different stages of species invasion may help for better understanding the drivers of species invasion. Here, I analyze a comprehensive data set including both native and non-native angiosperm species in China to determine phylogenetic relatedness of introduced species across a full invasion continuum (from introduction through naturalization to invasion). This study found that (1) introduced plants are a phylogenetically clustered subset of overall (i.e. native plus non-native) angiosperm flora, (2) naturalized plants are a phylogenetically clustered subset of introduced plants, and (3) invasive plants are a phylogenetically clustered subset of naturalized plants. These patterns hold regardless of spatial scales examined (i.e. national versus provincial scale) and whether basal- or tip-weighted metric of phylogenetic relatedness is considered. These findings are consistent with Darwin's preadaptation hypothesis.
    Geographic patterns of taxonomic and phylogenetic β-diversity of aquatic angiosperms in China
    Ya-Dong Zhou, Hong Qian, Yi Jin, Ke-Yan Xiao, Xue Yan, Qing-Feng Wang
    2023, 45(02):  177-184.  doi:10.1016/j.pld.2022.12.006
    Abstract ( 24 )   HTML ( )   PDF (3837KB) ( 8 )   Save
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    China covers a vast territory harbouring a large number of aquatic plants. Although there are many studies on the β-diversity of total, herbaceous or woody plants in China and elsewhere, few studies have focused on aquatic plants. Here, we analyse a comprehensive data set of 889 aquatic angiosperm species in China, and explore the geographic patterns and climatic correlates of total taxonomic and phylogenetic β-diversity as well as their turnover and nestedness components. Our results show that geographic patterns of taxonomic and phylogenetic β-diversity are highly congruent for aquatic angiosperms, and taxonomic β-diversity is consistently higher than phylogenetic β-diversity. The ratio between the nestedness component and total β-diversity is high in northwestern China and low in southeastern China. The geographic patterns of taxonomic and phylogenetic β-diversity of aquatic angiosperms in China are obviously affected by geographic and climatic distances, respectively. In conclusion, the geographic patterns of taxonomic and phylogenetic β-diversity of aquatic angiosperms are consistent across China. Climatic and geographic distances jointly affect the geographic patterns of β-diversity of aquatic angiosperms. Overall, our work provides insight into understanding the large-scale patterns of aquatic angiosperm β-diversity, and is a critical addition to previous studies on the macroecological patterns of terrestrial organisms.
    Two new species of Polyalthiopsis (Annonaceae) based on morphological characters and phylogenetic evidence, with a supplementary description of P.chinensis from China
    Bin Yang, Jin-Yue Li, Rui-Jie Yang, Hong-Bo Ding, Min Deng, Chun-Fen Xiao, Yun-Juan Zuo, Yun-Hong Tan
    2023, 45(02):  185-198.  doi:10.1016/j.pld.2022.05.001
    Abstract ( 18 )   HTML ( )   PDF (24630KB) ( 7 )   Save
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    Two new species of Polyalthiopsis (Annonaceae), P.nigra Y.H. Tan & Bin Yang from Guangxi and Yunnan Provinces and P.xui Y.H. Tan & Bin Yang from Yunnan Province, are described and illustrated. P.nigra is morphologically similar to P.chinensis in having narrowly elliptic-oblong, lemon to yellowish green petals, but differs by having obovoid monocarps, a higher number of leaf secondary veins, leaf blades usually widest above the middle, and a lower ratio of leaf blade length to width. P.xui is morphologically similar to P.floribunda in having axillary inflorescences, 1-3(-4) flowers, elliptic leaves, and elliptic-ovate petals, but differs in the numbers of carpels per flower and ovules per carpel. The molecular phylogenetic analysis using five plastid markers confirm that the two new species belong to the genus Polyalthiopsis and show clear interspecific divergences between P.nigra and P.xui and between them and other species in the genus. Detailed descriptions, colored photographs, and habitat and distribution data for the two new species are provided. In addition, the fruit morphology of P.chinensis is described for the first time, based on living collections. Geographical distributions and a diagnostic key for all Polyalthiopsis species are also presented.
    Legumes from the Paleocene sediments of India and their ecological significance
    Harshita Bhatia, Gaurav Srivastava, R. C. Mehrotra
    2023, 45(02):  199-210.  doi:10.1016/j.pld.2022.08.001
    Abstract ( 22 )   HTML ( )   PDF (45705KB) ( 2 )   Save
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    During the early Paleogene, greenhouse gases created warm global climates. These warm climates redistributed the habitat of marine and terrestrial biota globally. Understanding the ecology of biotas under extremely warm climates is important to decipher their behavior in future climate warming. Here we report two new legume fossils (Leguminocarpum meghalayensis Bhatia, Srivastava et Mehrotra sp. nov., and Parvileguminophyllum damalgiriensis Bhatia, Srivastava et Mehrotra sp. nov.) from the late Paleocene sediments of Tura Formation of Meghalaya, northeast India. Globally, the Paleocene legume fossil records indicate that legumes most likely immigrated to India from Africa via the Ladakh-Kohistan Arc during the early Paleogene. Moreover, previously reconstructed climate data from the Tura Formation indicate that legumes were well adapted to a warm seasonal climate with monsoon rains.
    Ecological and habitat ranges of orchids in the northernmost regions of their distribution areas: A case study from Ural Mountains, Russia
    Irina A. Kirillova, Yuriy A. Dubrovskiy, Svetlana V. Degteva, Alexander B. Novakovskiy
    2023, 45(02):  211-218.  doi:10.1016/j.pld.2022.08.005
    Abstract ( 18 )   HTML ( )   PDF (5288KB) ( 17 )   Save
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    The Orchidaceae, which is one of the most interesting families of angiosperms, contains a large number of rare species. Despite their acknowledged importance, little attention has been paid to the study of orchids distributed in northern territories. In this study, we determined the syntaxonomical diversity and ecological parameters of orchid habitats in two of Europe's largest protected areas, the Pechoro-Ilychsky Reserve and the Yugyd Va National Park (northeastern European Russia), and then compared our findings to those in other parts of orchid distribution ranges. For this purpose, we studied 345 descriptions of plant communities (releves) containing species from Orchidaceae and defined habitat parameters using Ellenberg indicator values with the community weight mean approach, nonmetric multidimensional scaling (NMS), and relative niche width. We found that orchids were distributed in eight habitat types and 97 plant associations. The largest number of orchid species is found in forest communities. Half of the orchid species under study occur in the mires and rock habitats with open vegetation. Several orchids consistently occur in areas disturbed by human activity. In addition, our study indicates that the main drivers of orchid distribution across the vegetation types are light and soil nitrogen. Our analysis of the ecological parameters of orchid habitats indicates that some orchid species can be classified as habitat specialists that are confined to a relatively narrow ecological niche in the Urals (e.g., Goodyera repens, Cypripedium guttatum and Dactylorhiza maculata). Several other species (e.g. Neottia cordataand Dactylorhiza fuchsia) grow under diverse ecological parameters.
    Rapid evolution of T2/S-RNase genes in Fragaria linked to multiple transitions from self-incompatibility to self-compatibility
    Wu Chen, Hong Wan, Fang Liu, Haiyuan Du, Chengjun Zhang, Weishu Fan, Andan Zhu
    2023, 45(02):  219-228.  doi:10.1016/j.pld.2022.04.003
    Abstract ( 16 )   HTML ( )   PDF (10343KB) ( 2 )   Save
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    The T2/RNase gene family is widespread in eukaryotes, and particular members of this family play critical roles in the gametophytic self-incompatibility (GSI) system in plants. Wild diploid strawberry (Fragaria) species have diversified their sexual systems via self-incompatible and self-compatible traits, yet how these traits evolved in Fragaria remains elusive. By integrating the published and de novo assembled genomes and the newly generated RNA-seq data, members of the RNase T2 gene family were systematically identified in six Fragaria species, including three self-incompatible species (Fragaria nipponica, Fragaria nubicola, and Fragaria viridis) and three self-compatible species (Fragaria nilgerrensis, Fragaria vesca, and Fragaria iinumae). In total, 115 RNase T2 genes were identified in the six Fragaria genomes and can be classified into three classes (I-III) according to phylogenetic analysis. The identified RNase T2 genes could be divided into 22 homologous gene sets according to amino acid sequence similarity and phylogenetic and syntenic relationships. We found that extensive gene loss and pseudogenization coupled with small-scale duplications mainly accounted for variations in the RNase T2 gene numbers in Fragaria. Multiple copies of homologous genes were mainly generated from tandem and segmental duplication events. Furthermore, we newly identified five S-RNase genes in three self-incompatible Fragaria genomes, including two in F.nipponica, two in F.viridis, and one in F.nubicola, which fit for typical features of a pistil determinant, including highly pistil-specific expression, highly polymorphic proteins and alkaline isoelectric point (pI), while no S-RNase genes were found in all three self-compatible Fragaria species. Surprisingly, these T2/ S-RNase genes contain at least one large intron (>10kb). This study revealed that the rapid evolution of T2/ S-RNase genes within the Fragaria genus could be associated with its sexual mode, and repeated evolution of the self-compatible traits in Fragaria was convergent via losses of S-RNase.
    Short communication
    Are allometric model parameters of aboveground biomass for trees phylogenetically constrained?
    Xing-Zhao Huang, Fang-Bing Li, Zi-Xuan Wang, Yi Jin, Hong Qian
    2023, 45(02):  229-233.  doi:10.1016/j.pld.2022.11.005
    Abstract ( 22 )   HTML ( )   PDF (488KB) ( 11 )   Save
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    Knowledge of which biological and functional traits have, or lack, phylogenetic signal in a particular group of organisms is important to understanding the formation and functioning of biological communities. Allometric biomass models reflecting tree growth characteristics are commonly used to predict forest biomass. However, few studies have examined whether model parameters are constrained by phylogeny. Here, we use a comprehensive database (including 276 tree species) compiled from 894 allometric biomass models published in 302 articles to examine whether parameters a and b of the model W=aDb (where W stands for aboveground biomass, D is diameter at breast height) exhibit phylogenetic signal for all tree species as a whole and for different groups of tree species. For either model parameter, we relate difference in model parameter between different tree species to phylogenetic distance and to environmental distance between pairwise sites. Our study shows that neither model parameter exhibits phylogenetic signals (Pagel's λ and Blomberg's K both approach zero). This is the case regardless of whether all tree species in our data set were analyzed as a whole or tree species in different taxonomic groups (gymnosperm and angiosperm), leaf duration groups (evergreen and deciduous), or ecological groups (tropical, temperate and boreal) were analyzed separately. Our study also shows that difference in each parameter of the allometric biomass model is not significantly related to phylogenetic and environmental distances between tree species in different sites.
    Applying image clustering to phylogenetic analysis: A trial
    Li-Dan Tao, Wei-Bang Sun
    2023, 45(02):  234-237.  doi:10.1016/j.pld.2022.11.001
    Abstract ( 18 )   HTML ( )   PDF (12206KB) ( 31 )   Save
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