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  • Yun-Feng Li, Lian Luo, Yang Liu, Qiang He, Ning-Ning Yu, Naren Gaowa, Zhao-Qin Yi, Jun-Jie Wang, Wei Han, Tao Peng, Boon-Chuan Ho, Xiaolan He, Li Zhang, Zhi-Duan Chen, Yu Jia, Qing-Hua Wang
    J Syst Evol. 2024, 62(4): 577-588.
    https://doi.org/10.1111/jse.13063
    Bryophytes, a monophyletic group comprising three major lineages, diversified soon after the terrestrialization of land plants. However, their internal phylogenetic relationships remain controversial. In this study, we reconstructed the ordinal and familial phylogeny of bryophytes using the largest plastid data set to date, including 549 taxa that represent almost all known orders and two-thirds of families. The strongly supported phylogenetic inference enabled us to propose in mosses seven newly segregated families, that is, Baldwiniellaceae, Calyptrochaetaceae, Ctenidiaceae, Herpetineuraceae, Isodrepaniaceae, Pseudotaxiphyllaceae, and Rozeaceae, and one reduced family, that is, Climaciaceae. We also transferred the liverwort family Calyculariaceae from Fossombroniales to Pelliales. Recent advancements in molecular phylogeny have revolutionized bryophyte classification, tending to be more fragmental. Hence, we further propose a revised familial classification system for bryophytes that includes 45 orders and 142 families in mosses, 23 orders and 85 families in liverworts, and five orders and five families in hornworts.
    Bryophytes are morphologically distinct and diverse in land plants, and their internal phylogenetic relationships remain controversial. We reconstructed the ordinal and familial phylogeny of bryophytes using the largest plastome data set to date, including 549 taxa that represent almost all known orders and two-third families. Based on the plastid genomic phylogeny presented here and the recently published systems, we further propose a revised familial classification system for bryophytes that includes seven newly segregated families and one reduced family in mosses.
  • Li-Ying Luo, Gui-Hua Jin, Peng-Fei Ma, De-Zhu Li
    J Syst Evol. 2024, 62(4): 702-714.
    https://doi.org/10.1111/jse.13038
    Many examples of phenotypic modifications resulting from high-elevation adaptation have been documented, however, the underlying processes responsible for these modifications and whether the continuity of the adaptation process remain elusive, particularly in plants. The alpine plants distributed along wide elevational gradients provide an ideal system to address this question. Here, we collected transcriptomes from multiple tissues of three species with different elevations (~1500, ~2500, and ~3600 m in the Hengduan Mountains, Southwest China) in two genera Fargesia and Yushania of alpine bamboos, respectively, and conducted evolutionary and expressional analyses. Results showed that high-elevation adaptation emerged earlier in the evolutionary history of both genera and evolved continuously as the elevation increased. Moreover, convergence of genetic changes was observed in the two genera, with amounts of candidate genes responsible for high-elevation adaptation identified under positive selection. Overall, our study provides an empirical example and valuable genetic resource for further investigation of high-elevation adaptation in plants and sheds new light on how plants adapting to high-elevation environments in a biodiversity hotspot.
    This figure displays two points: (i) both genera of alpine bamboo (Fargesia and Yushania) have already experienced selection for genes showing signals of adaptation to the high elevation despite when distributed at relatively low elevations; and (ii) as the elevation increased, a growing number of new elevation-specific positively selected genes (PSGs) (genes identified to be positively selected exclusively at a certain elevational gradient) associated with high-elevation adaptation continued to emerge in both genera. Based on the results above, we obtained two significant outcomes: (i) the early appearance of high-elevation adaptation in bamboo evolutionary history; and (ii) the process of high-elevation adaptation and their underlying genetic changes were continuous as the elevational gradients increased in both alpine bamboo genera.
  • Guo-Qing Wang, Rosa A. Scherson, Diego Vera, Yun-Hao Bai, Jun Wen, Lin-Yuan Guo, Alice C. Hughes, Hua-Feng Wang
    J Syst Evol. 2024, 62(4): 603-620.
    https://doi.org/10.1111/jse.13017
    Hainan Island has the most extensive and well-preserved tropical forests in China. With rapid economic development of Hainan, biodiversity is increasingly at risk. Determining the spatial patterns of plant diversity in Hainan and explaining the drivers behind plant diversity are important considerations in assessing and maximizing the effectiveness of national parks, such as the newly designated Hainan Rainforest National Park. We assessed phylogenetic diversity patterns, and species richness using 106,252 georeferenced specimen records and a molecular phylogeny of 3,792 native plant species. Based on phylogenetic range-weighted turnover metrics, we divided Hainan flora into four major floristic units. The Grade of Membership model was used to further verify the four units, and to understand their boundaries and the internal structure of each floristic unit. Finally, the best combination model was used to explore the driving mechanisms underlying the division. Our results reveal that central Hainan is the most important hotspot for plant endemism and diversity, followed by the southern area. Environmental energy is the main factor determining the spatial patterns of native plant diversity on the island, and accessibility has the greatest impact on native plant diversity among social factors. We explore patterns of spatial phylogenetics and biogeography to identify potential priorities for management and conservation drivers of plant diversity patterns across Hainan, to provide the basis for the effective protection of native plant diversity and the improvement of national parks of Hainan Island.
    Representative species of the four floristic units. The bold line on the map represents the boundaries of four floristic units as shown in Fig. 6. (i) Tropical coastal vegetation; (ii) Tropical rainforest; (iii) Tropical mountain rainforest. (iv) Tropical shrubland. Species morphological adaptations to different habitats, from southern forests and mountains to northern plantations and coastal wetland plants, can be observed.
  • Hong Zhang, Yu-Tao Mao, Ming-Xia Ma, Guang-Can Tao, Tian-Peng Wei, Yu-Lan Jiang
    J Syst Evol. 2024, 62(4): 637-676.
    https://doi.org/10.1111/jse.13035
    Rosa-associated fungi are rich in species and diverse in function, with many potential new taxa. However, only a few publications have reported Rosa-associated endophytic fungi using a combination of molecular systematics and morphology. Rosa roxburghii is an economically important source of medicine and food. We reported earlier the diversity and antimicrobial activities of the fungal endophytes of this plant, but further confirmation is needed for possible new taxa. In this study, we describe 10 novel species and two new host records isolated from healthy tissues of R. roxburghii while identifying three new combinations, all belonging to the Sordariomycetes. The new species described herein include Chaetomium rosifloricola, Chaetomium rosiradicicola, Chrysofolia fructicola, Coniella cili, Hypoxylon florendophyticum, Hypoxylon rosicaulendophyticum, Ilyonectria radicigena, Neopestalotiopsis caulicola, Neopestalotiopsis fructicola, and Seimatosporium endophyticum. Monochaetia bulbophylli, Neopestalotiopsis anacardii, and Neopestalotiopsis termitarii were introduced as new combinations, while Coniella quercicola and Hypoxylon pulicicidum were described as new host records on R. roxburghii. All the taxa have been described, illustrated, and phylogenetically analyzed, in addition to the lifestyles of each genus. Altogether, the results of this study have important implications for identifying novel endophytic fungi and developing potential applications of these fungi in the future.
    Healthy Rosa roxburghii tissues were collected, six media were used to isolate endophytic fungi, and the isolates were subjected to multigene phylogenetic analyses and morphological identification. As a result, 10 new species, three new combinations, and two new host records were found.
  • Biao-Biao Niu, Qi-Xiang Zheng, Yang Liu, Nina Lundholm, Sing Tung Teng, Xu-Dan Lu, Rui-Wei Ran, Li Zhang, Yang Li
    J Syst Evol. 2024, 62(4): 621-636.
    https://doi.org/10.1111/jse.13016
    Pseudo-nitzschia is a group of widely distributed planktonic diatoms. Some species produce the neurotoxin domoic acid. Herein, two new Pseudo-nitzschia species were described from Chinese coastal waters and the South China Sea after combining morphological and molecular data, together with biogeographical traits. Pseudo-nitzschia punctionis sp. nov. was similar to Pseudo-nitzschia bipertita morphologically, but differed in poroid structure, which was undivided in P. punctionis but divided in two sectors in P. bipertita. This difference corresponded to the presence of two hemicompensatory base changes (HCBCs) in the secondary structure of internal transcribed spacer 2. Pseudo-nitzschia polymorpha sp. nov. was sister to Pseudo-nitzschia limii phylogenetically, but distinct by the various shapes of perforations on the valve and copula, which was supported by four HCBCs. In a metabarcoding analysis, multiple new ribotypes were identified within the two new species, and intraspecific genetic divergences were analyzed. Metabarcoding data revealed that P. punctionis had a broader temperature range (12.9–30.5°C) than P. polymorpha (22.3–30.5°C). Within the two new species, different traits were found among the amplicon sequence variants regarding temperature and biogeography, representing different microevolutionary directions under environmental selection. The two new species had different biogeographical traits when compared to their closely related species. Domoic acid was detected in strains of P. punctionis at a concentration of 13.5–17.7 fg/cell, but the toxin was not found in strains of P. polymorpha. A combination of characters based on laboratory strains and field metabarcoding data provided more data for delimiting Pseudo-nitzschia species and gave new insights into their diversity and biogeography.
    Two new Pseudo-nitzschia species were described based on morphology and molecular phylogeny. A metabarcoding analysis revealed different biogeographical and temperature characters between two new species and their closely related species, which help to define the Pseudo-nitzschia species.
  • Dong-Mei Jin, Quan Yuan, Xi-Ling Dai, Gregor Kozlowski, Yi-Gang Song
    J Syst Evol. 2024, 62(4): 677-686.
    https://doi.org/10.1111/jse.13022
    Subtropical evergreen broad-leaved forest (EBLF) is the predominant vegetation type in eastern China. However, the majority of the region it covers in eastern China was an arid area during the Paleogene. The temporal history and essential factors involved in the evolution of subtropical EBLFs in eastern China remain enigmatic. Here we report on the niche evolution of Quercus section Cyclobalanopsis, which appeared in south China and Japan during the Eocene and became a dominant component of subtropical EBLFs since the Miocene in eastern Asia, using integrative analysis of occurrences, climate data and a dated phylogeny of 35 species in Cyclobalanopsis. Species within clades Cyclobalanoides, Lamellosa, and Helferiana mainly exist in the Himalaya–Hengduan region, adapting to a plateau climate, while species within the other clades mainly live in eastern China under the control of the East Asian monsoon. Reconstructed history showed that significant divergence of climatic tolerance in Cyclobalanopsis began around 19 million years ago (Ma) in the early Miocene. Simultaneously, disparities in precipitation of wettest/warmest quarter and annual precipitation were markedly enhanced in Cyclobalanopsis, especially in the recent eastern clades. During the Miocene, the marked radiation of Cyclobalanopsis and many other dominant taxa of subtropical EBLFs strongly suggest the rapid formation and expansion of subtropical EBLFs in eastern China. Our research highlights that the intensification of the East Asian monsoon and subsequent occupation of new niches by the ancient clades already present in the south may have jointly promoted the formation of subtropical EBLFs in eastern China since the early Miocene.
    Subtropical evergreen broad-leaved forest (EBLF) is the predominant vegetation type in eastern China, of which the evolutionary history remains enigmatic. Quercus section Cyclobalanopsis has been dominant component of subtropical EBLFs since the Miocene in eastern Asia. Here we report on the niche evolution of Quercus section Cyclobalanopsis, using integrative analysis of occurrences, climate data and a dated phylogeny of 35 species in Cyclobalanopsis. Species belong to clades Cyclobalanoides, Lamellosa, and Helferiana usually habitat in the Himalaya–Hengduan region, adapting to a plateau climate; while species belonging to Semiserrata, Acuta, Glauca, and Gilva mainly live in eastern China, under the control of the East Asian monsoon. The disparity of tolerance to precipitation of the wettest quarter in Cyclobalanopsis has been markedly enhanced since 19 Ma. Meanwhile, significant divergence of climatic tolerance to precipitation began around the early Miocene. Our research highlights that the intensification of the East Asian monsoon system and subsequent species diversification and occupation of new niches by the ancient clades already present in the south may have jointly promoted the formation of subtropical EBLFs in eastern China since the early Miocene.
  • Xiao-Min Yang, Hai-Liang Meng, Jian-Lin Zhang, Yao Yu, Edward Allen, Zi-Yang Xia, Kong-Yang Zhu, Pan-Xin Du, Xiao-Ying Ren, Jian-Xue Xiong, Xiao-Yu Lu, Yi Ding, Sheng Han, Wei-Peng Liu, Li Jin, Chuan-Chao Wang, and Shao-Qing Wen
    J Syst Evol. 2023, 61(6): 1056-1064.
    https://doi.org/10.1111/jse.12938
  • Jacopo Franzoni, Giovanni Astuti, Gianluigi Bacchetta, Giulio Barone, Fabrizio Bartolucci, Liliana Bernardo, Angelino Carta, Fabio Conti, Gianniantonio Domina, Božo Frajman, Gianpietro Giusso del Galdo, Duilio Iamonico, Mauro Iberite, Luigi Minuto, Marco Sarigu, Ana Terlević, Alessia Turini, Lucia Varaldo, Daniel Volgger, Lorenzo Peruzzi
    J Syst Evol. 2024, 62(4): 589-602.
    https://doi.org/10.1111/jse.13025
    European wild carnations (Dianthus) are represented by a high number of taxa organized in unresolved taxonomies. In particular, taxa belonging to the Dianthus virgineus L. complex in the Central Mediterranean have been delimited mainly with qualitative morphological data and still await quantitative investigations, which are vital to understand boundaries and relations among plant diversity groups. Here, we examine the phenotypic features of nuclear genome organization testing for species boundaries in this complex. We have studied the chromosome number, the total haploid length (THL), and the relative genome size (RGS) in 122 populations belonging to 25 out of 33 taxa of the complex. All the studied populations have 2n = 2x = 30 chromosomes, and the THL ranges from 14.09 to 20.71 μm. Genome size estimations support the absence of polyploidization events, but show a certain degree of variation (0.318–0.423 arbitrary units). The RGS variation is not in agreement with current taxonomic treatment, but rather shows a geographical pattern, with higher values in Sicily and Sardinia. No correlation between the THL and the RGS was detected, possibly due to the stable chromosome number and the small size of chromosomes. A number of evolutionary unique groups lower than the number of currently accepted taxa may be hypothesized.
    Taxa belonging to the Dianthus virgineus L. complex in the Central Mediterranean have been delimited mainly with qualitative morphological data and still await quantitative investigations. Here, we examined phenotypic features of nuclear genome organization testing for species boundaries in this complex. A constant diploid chromosome number, coupled with few relative genome size (RGS) differences, was observed among taxa of the D. virgineus complex in the Central Mediterranean. A geographical, rather than taxonomic, RGS variation allowed speculations on the actual evolutionary relationships within this complex.
  • Cai-Xia Wei, Phillip E. Jardine, Li-Mi Mao, Luke Mander, Mao Li, William D. Gosling, Carina Hoorn
    J Syst Evol. 2024, 62(4): 687-701.
    https://doi.org/10.1111/jse.13021
    The grasses are one of the most diverse plant families on Earth. However, their classification and evolutionary history are obscured by their pollen stenopalynous (similar) morphology. A combination of high-resolution imaging of pollen surface ornamentation and computational analysis has previously been proposed as a promising tool to classify grass taxonomic boundaries. In this study, we test this hypothesis by studying Poaceae pollen across the phylogeny from plants collected in northern South America and also from published literature across the globe. We assessed if morphotypes that we establish using descriptive terminology are supported by computational analysis, if they vary along six (a)biotic variables and vary across the phylogeny. Based on this analysis, we constructed a reference framework for pollen surface ornamentation morphotypes. Our results showed that there is a wide variation of grass pollen surface ornamentation. We identified nine new and confirmed six known morphotypes, establishing a data set for 223 species (243 individual plant specimens) that represent 11 subfamilies. Computational analysis showed that our morphotypes are well-supported by two quantitative features of pollen sculptural elements (size and density). The specific data set and mapping of the phylogeny confirmed that pollen morphological sculpture is unrelated to (a)biotic variables and is diverse across the phylogeny.
    Pollen surface ornamentation shows a high diversity across the Poaceae phylogeny. The different colors and the number of symbols (square or circle) in the grid show the distribution of the 15-grass pollen morphotypes identified for each specimen in each subfamily.
  • Ya-Dong Zhou, Hong Qian, Ke-Yan Xiao, Qing-Feng Wang, and Xue Yan
    J Syst Evol. 2023, 61(6): 979-989.
    https://doi.org/10.1111/jse.12939
    Studies on large-scale geographic patterns of aquatic plant diversity can promote research on the generality of macroecological patterns in different ecosystems. Here, we compiled a checklist of 889 aquatic angiosperms in China, including 738 helophytes (emergent and marshy plants) and 151 hydrophytes (submerged, free-floating, and floating-leaved plants). We explore the geographic patterns and environmental correlates of aquatic plant diversity based on six metrics including species richness (SR), weighted endemism (WE), phylogenetic diversity (PD), phylogenetic endemism (PE), the standardized effect size of phylogenetic diversity (PDses), and the standardized effect size of mean phylogenetic distance (MPDses). Our results show that the diversity of aquatic plants in China is extremely uneven, with high diversity in southeastern China and low diversity in northwestern China, and the geographic patterns of taxonomic and PD are generally consistent. The pattern of helophytes differs from that of hydrophytes. Notably, the wavy-shaped pattern of aquatic plant diversity (especially SR and PD for hydrophytes) across the latitude observed in this study is not consistent with those previously observed for aquatic plants in other continents. Climatic variables and water environmental variables are the main drivers of aquatic plant diversity in China; however, the effects of individual variables differ between helophytes and hydrophytes. Water environmental variables have a greater impact on PDses and MPDses of hydrophytes than those of helophytes. Overall, our work provides insight into understanding the large-scale patterns of aquatic plant diversity and is a critical addition to previous studies on the macroecological pattern of terrestrial organisms.
    Terrestrial ecosystems are more directly influenced by climate, whereas the water environment is more important to aquatic organisms, thus the geographic patterns of aquatic plant diversity might differ from the general pattern observed for most terrestrial groups. Here, we compiled a checklist of 889 aquatic angiosperms in China, based on several floras, monographs, research papers, and online sources, and explored the geographic patterns and environmental correlates of the taxonomic and phylogenetic diversity of these aquatic plants. We obtained some interesting results, for example, the wavy-shaped pattern of aquatic plant diversity across latitudes observed in this study is not consistent with that previously observed for aquatic plants on other continents. The shoreline complexity could affect aquatic plant diversity. Climatic variables and water environmental variables are the main drivers of the aquatic plant diversity in China; however, the effects of individual variables differ between helophytes and hydrophytes. Water environmental variables have a greater impact on the diversity of hydrophytes than that of helophytes. Our work provides insight into understanding the large-scale pattern of aquatic plant diversity, and is a critical addition to previous studies on the macroecological pattern of terrestrial organisms.
  • Kai-Lai Wang, Pu-Rong Deng, Zhi Yao, Jin-Yi Dong, Zhi He, Peng Yang, and Yong-Bo Liu
    J Syst Evol. 2023, 61(5): 776-789.
    https://doi.org/10.1111/jse.12909
    Exploring the frequency and distribution pattern of polyploid species in geographic parameters is of significance in understanding the mechanisms of polyploid speciation and evolutionary drivers of biodiversity. We here explored polyploid and paleopolyploid incidence frequency in a scale of 100×100 km grids in China. We found 33% of angiosperm species are polyploidy in China, and 23% of polyploid speciation. Western China and eastern China showed a significantly different polyploid and paleopolyploid frequency, with an evolutionary cradle of polyploid angiosperms in the Qinghai-Tibetan plateau. Herbaceous species exhibited higher polyploid frequency but lower paleopolyploid frequency than woody species, indicating the former experienced more rapid differentiation and speciation than the latter. Our results indicate that western China is an evolutionary cradle for polyploid angiosperms where harsh environment facilitates the establishment and survival of polyploids, while polyploid lineages tend to rediploidize to be diploids with sufficient time in suitable environment.
    We analyzed the biogeographical patterns of polyploid and paleopolyploid frequency at a scale of 100×100km grids in China, and revealed the role of polyploidization and rediploidization of polyploids in understanding the mechanisms of speciation and evolutionary drivers of biodiversity. Our results indicate that western China is an evolutionary cradle for polyploid angiosperms where harsh environment facilitates the establishment and survival of polyploids, while polyploid lineages tend to rediploidize to be diploids with sufficient time in suitable environment.
  • Xiao-Gang Fu, Shui-Yin Liu, Robin van Velzen, Gregory W. Stull, Qin Tian, Yun-Xia Li, Ryan A. Folk, Robert P. Guralnick, Heather R. Kates, Jian-Jun Jin, Zhong-Hu Li, Douglas E. Soltis, Pamela S. Soltis, and Ting-Shuang Yi
    J Syst Evol. 2023, 61(5): 806-826.
    https://doi.org/10.1111/jse.12920
    Cannabaceae are a relatively small family of angiosperms, but they include several species of huge economic and cultural significance: marijuana or hemp (Cannabis sativa) and hops (Humulus lupulus). Previous phylogenetic studies have clarified the most deep relationships in Cannabaceae, but relationships remain ambiguous among several major lineages. Here, we sampled 82 species representing all genera of Cannabaceae and utilized a new dataset of 90 nuclear genes and 82 chloroplast loci from Hyb-Seq to investigate the phylogenomics of Cannabaceae. Nuclear phylogenetic analyses revealed a robust and consistent backbone for Cannabaceae. We observed nuclear gene-tree conflict at several deep nodes in inferred species trees, also cyto- nuclear discordance concerning the relationship between Gironniera and Lozanella and the relationships among Trema s.l. (including Parasponia), Cannabis + Humulus, and Chaetachme + Pteroceltis. Coalescent simulations and network analyses suggest that observed deep cyto-nuclear discordances were most likely to stem from incomplete lineage sorting (ILS); nuclear gene-tree conflict might be caused by both ILS and gene flow between species. All genera of Cannabaceae were recovered as monophyletic, except for Celtis, which consisted of two distinct clades: Celtis I (including most Celtis species) and Celtis II (including Celtis gomphophylla and Celtis schippii). We suggest that Celtis II should be recognized as the independent genus Sparrea based on both molecular and morphological evidence. Our work provides the most comprehensive and reliable phylogeny to date for Cannabaceae, enabling further exploration of evolutionary patterns across this family and highlighting the necessity of comparing nuclear with chloroplast data to examine the evolutionary history of plant groups.
    Tanglegram showing the incongruence between the nuclear (left) and chloroplast (right) trees of Cannabaceae both inferred by partitioned RAxML analyses. Black lines connect the same taxa between the two trees. The colored branches indicate the major clades of Cannabaceae: black, outgroups; brown, Aphananthe; medium aquamarine, Gironniera; purple, Lozanella; red, Celtis II; light green, Chaetachme+Pteroceltis; green, Cannabis+Humulus; orange, Trema s.l.; and blue, Celtis I.
  • Su-Juan Wei, Yong-Qing Liufu, He-Wen Zheng, Hai-Ling Chen, Yan-Chi Lai, Yan Liu, Quan-Qing Ye, and Shao-Qing Tang
    J Syst Evol. 2023, 61(5): 748-763.
    https://doi.org/10.1111/jse.12915
    All yellow Camellia plants in China are threatened, but their classification is contentious. Here, we performed a phylogenetic reconstruction based on nuclear double-digest restriction site-associated DNA sequencing (ddRAD), transcriptomes, nuclear ribosomal internal transcribed spacer (nrITS), and the small single-copy region of the chloroplast genome, in combination with morphological evidence to help resolve taxonomic ambiguity of those rare and threatened species. Conflicting relationships were derived from nuclear and chloroplast sequences. The strong hybridization/introgression signal detected suggests reticulate evolution mainly caused this discordance pattern. The nuclear-ddRAD and RNA-seq phylogenies fit better to the yellow camellias' morphology, providing a clear resolution for inferring their relationships in China. Based on present phylogenetic analyses and morphological characters, we propose these taxonomic suggestions: (i) Camellia petelotii and Camellia nitidissima are distinct species; (ii) Camellia ptilosperma, Camellia longruiensis, Camellia longgangensis, and C. longgangensis var. grandis are conspecific with Camellia flavida; (iii) Camellia multipetala and C. longgangensis var. patens are synonyms of Camellia quinqueloculosa, and C. quinqueloculosa should be recognized as an independent species; (iv) Camellia wumingensis should be formally recognized as an independent species; (v) Camellia longzhouensis is a synonym of Camellia chrysanthoides; (vi) Camellia xiashiensis and Camellia parvipetala should be treated as synonyms of Camellia micrantha; (vii) Camellia achrysantha is a good species; (viii) Camellia tunghinensis is an independent species; (ix) species status of Camellia huana is well-supported; and (x) Camellia pingguoensis var. terminals should be correctly identified to species level as Camellia terminalis. These results provide the basis for the recognition 20 yellow Camellia species in China.
    All yellow Camellia species in China are threatened. To avoid mistakes in species conservation, high-resolution phylogenetic analyses were performed by using genome-scale double-digest restriction site-associated (ddRAD) and transcriptomes sequencing, in combination with morphological evidences to resolve taxonomic incongruence of yellow-flowered Camellia species in China. These results provide the basis for the recognition at least 20 yellow Camellia species in China.
  • Jessica M. Budke, Nikisha R. Patel, GoFlag Consortium, Mark D. Wienhold, and Maria A. Bruggeman-Nannenga
    J Syst Evol. 2023, 61(5): 868-889.
    https://doi.org/10.1111/jse.12926
    Morphological evolution in mosses has long been hypothesized to accompany shifts in microhabitats, which can be tested using comparative phylogenetics. These lines of inquiry have been developed to include target capture sequencing, which can yield phylogenomic scale data from herbarium specimens. Here, we test the relationship between taxonomically important morphological characters in the moss genus Fissidens, using a 400- locus data set generated using a target-capture approach in tandem with a three-locus phylogeny generated using Sanger sequencing. Phylogenetic trees generated using ASTRAL and Bayesian inference were used to test the monophyly of subgenera/sections. These trees provide the basis for ancestral character state reconstructions and phylogenetic correlation analyses for five morphological characters and characters related to the moisture habitat, scored from the literature and by specimen inspection. Many of these characters exhibit statistically significant phylogenetic signal. Significant correlations were found between the limbidium (phyllid/leaf border of the gametophyte) and habitat moisture niche breadth, which could be interpreted as the more extensive limbidium enabling species to survive across a wider variety of habitats. We also found correlations between costa anatomy, peristome morphology, and the limbidium, which could reflect the evolutionary recruitment of genetic networks from the gametophyte to the sporophyte phase. The correlation found between average habitat moisture and the sexual system indicates that dioicous and polyoicous species are more likely to be found in moist habitats and that these higher moisture levels could be particularly, reproductively advantageous to species with separate sexes.
    Phylogenetic trees were generated from both a 400-locus data set generated using a target-capture approach as well as a three-locus phylogeny generated using Sanger sequencing for mosses in the genus Fissidens. Taxonomically important morphological characters for the genus were found to exhibit statistically significant phylogenetic signals. Significant correlations were found between the limbidium and habitat moisture niche breadth, which could be interpreted as the more extensive limbidium enabling species to survive across a wider variety of habitats. We also found correlations between costa anatomy, peristome morphology, and the limbidium, which could reflect the evolutionary recruitment of genetic networks from the gametophyte to the sporophyte phase. The correlation found between average habitat moisture and the sexual system indicates that dioicous and polyoicous species are more likely to be found in moist habitats, and these higher moisture levels could be particularly reproductively advantageous to species with separate sexes.
  • Shu-Fen Li, Xin-Yu Zhang, Long-Long Yang, Ke-Li Jia, Jia-Rong Li, Li-Na Lan, Yu-Lan Zhang, Ning Li, Chuan-Liang Deng, and Wu-Jun Gao
    J Syst Evol. 2023, 61(5): 919-931.
    https://doi.org/10.1111/jse.12929
    Helitron transposons play an important role in host genome evolution due to their ability to capture genes and regulatory elements. In this study, we developed a pipeline to identify and annotate Helitrons systematically from 358 plant and 178 animal high-quality genomes. All these data were organized into HelDB, a database where Helitrons can be explored with a user-friendly Web interface and related software. Based on these data, further analysis showed that the number or the cumulative length of Helitrons is positively correlated with genome size. Helitrons had experienced two expansion periods in plants, with the first occurring 20-30 Ma and peaking at approximately 24 Ma. The second expansion occurred in the last 4 million years. The expansions might be due to stimulation of paleogeographic environment. Detailed investigation of gene capture by Helitrons in Brassicaceae and Solanaceae plants showed that the captured genes showed diverse functions. Interestingly, metal ion binding function was enriched in these captured genes in most species. This phenomenon might be due to the need for binding of divalent metal ions to the Rep domain required for Helitron transposition. This study improves our knowledge of the landscape and evolution of Helitron transposons in plants and paves a way for further functional studies of this kind of transposable element.
    Helitron transposons play an important role in host genome evolution due to their ability to capture genes and regulatory elements. In this study, we developed a pipeline to identify and annotate Helitrons systematically from 358 plant and 178 animal high-quality genomes. All these data were organized into HelDB, a database where Helitrons can be explored with a user-friendly Web interface and related software. Based on these data, further analysis showed that the number or the cumulative length of Helitrons is positively correlated with genome size. Helitrons had experienced two expansion periods in plants, with the first occurring 20-30 Ma and peaking at approximately 24Ma. The second expansion occurred in the last 4 million years. The expansions might be due to stimulation of paleogeographic environment. Detailed investigation of gene capture by Helitrons in Brassicaceae and Solanaceae plants showed that the captured genes showed diverse functions. Interestingly, metal ion binding function was enriched in these captured genes in most species. This phenomenon might be due to the need for binding of divalent metal ions to the Rep domain required for Helitron transposition. This study improves our knowledge of the landscape and evolution of Helitron transposons in plants and paves a way for further functional studies of this kind of transposable element.
  • Meng-Ting Wang, Zhen-Yu Hou, Chao Li, Jia-Peng Yang, Zhi-Tao Niu, Qing-Yun Xue, Wei Liu, and Xiao-Yu Ding
    J Syst Evol. 2023, 61(5): 790-805.
    https://doi.org/10.1111/jse.12912
    Reconstructing mitochondrial genomes of angiosperms is extremely intricate due to frequent recombinations which give rise to varied sized in Dendrobium mitogenomes and their structural variations, even in most orchid species. In this study, we first sequenced two complete and five draft mitochondrial genomes of Dendrobium using next-generation and third-generation sequencing technologies. The mitochondrial genomes were 420 538-689 048 bp long, showing multipartite (multichromosomal) structures that consisted of variably sized circular or linear-mapping isoforms (chromosomes). The comparison of mitochondrial genomes showed frequent gene losses in Dendrobium species. To explore structure variations of mitochondrial genomes in vivo, we quantified copy numbers of five mitochondrial genes and DNA contents per mitochondrion. The gene copy numbers and the DNA contents showed extreme differences during Dendrobium development, suggesting dynamic structures of mitochondrial genomes. Furthermore, phylogenetic relationships of 97 accessions from 39 Dendrobium species were constructed based on 12 nuclear single-copy genes and 15 mitochondrial genes. We discovered obvious discordance between the nuclear and mitochondrial trees. Reticulate evolution was inferred from the species network analysis in Dendrobium. Our findings revealed the rapid structural evolution of Dendrobium mitochondrial genomes and the existence of hybridization events in Dendrobium species, which provided new insights into in vivo structural variations of plant mitochondrial genomes and the strong potential of mitochondrial genes in deciphering plant evolution history.
    Mitochondrial genomes of Dendrobium showed multichromosomal structures with variably sized circular or linear isoforms. Mitochondrial protein-coding genes underwent frequent lost events in Dendrobium species. The structures of mitochondrial genomes were dynamic during Dendrobium development. The mitochondrial tree and the nuclear tree displayed obvious phylogenetic discordances in Dendrobium.
  • Han-Yang Lin, Yue Yang, Wen-Hao Li, Yu-Xin Luo, Xiao-Hua Bai, Tetsuo Ohi-Toma, Changkyun Kim, Joo-Hwan Kim, and Yun-Peng Zhao
    J Syst Evol. 2024, 62(1): 73-83.
    https://doi.org/10.1111/jse.12950
    Clear species boundaries are crucial for plans and actions on biodiversity conservation. However, morphological similarities among allied species can result in taxonomic difficulties, thus impeding conservation efforts. In China, Cinnamomum japonicum Siebold is a well-known endangered plant, yet suffers from longstanding taxonomic issues. Here, we explicitly evaluate whether C. japonicum, C. chenii, and C. chekiangense are the same phylogenetic species on the basis of a multi-individual sampling strategy. We identified three sets of low-copy orthologous genes from 19 Lauraceae taxa for phylogenetic inferences. Both the concatenation and coalescent-based phylogenies supported that C. chenii individuals were embedded in the C. japonicum clade, indicating these two taxa are conspecific. Meanwhile, C. chekiangense accessions formed a monophyly which was not sister to C. japonicum. This result, together with the morphological differences that the leaves of C. japonicum are glabrous with a faveolate pattern of venation while those of C. chekiangense have trichomes and inevident lateral veins, led us to consider both as two distinct species. Based on 17 728 neutral single nucleotide polymorphisms (SNPs), the ADMIXTURE analysis suggested that the Chinese C. japonicum populations in Zhoushan Archipelago (=C. chenii) were genetically differentiated from the Japanese and Korean ones. Furthermore, ecological niche modeling predicted that the present distribution area of Chinese C. japonicum is likely to be unsuitable under global warming scenarios. Together with its limited distribution and genetic uniqueness, we recommend that Chinese C. japonicum deserves conservation priorities.
    Cinnamomum chenii (purple) individuals were embedded in the Cinnamomum japonicum clade, suggesting these are the same species. Cinnamomum japonicum (blue) (including C. chenii) and Cinnamomum chekiangense (red) showed reciprocal monophyly with full supports, and they were not sister species. Scanning electron microscope observations indicated clear morphological differences between C. japonicum and C. chekiangense. Based on 17 728 neutral single nucleotide polymorphisms (SNPs), the assignment analysis suggested that Chinese C. japonicum showed unique genetic compositions. Moreover, the predictions of ecological niche modeling showed that the present distribution area of Chinese C. japonicum will no longer be suitable in the future. To sum up, we recommend that Chinese C. japonicum deserves ex situ conservation priorities.
  • Sheng-Yuan Qin, Kai Chen, Wen-Ju Zhang, Xiao-Guo Xiang, Zheng-Yu Zuo, Cen Guo, Yao Zhao, Lin-Feng Li, Yu-Guo Wang, Zhi-Ping Song, Ji Yang, Xiao-Qiang Yang, Jian Zhang, Wei-Tao Jin, Qiang Wen, Song-Zi Zhao, Jia-Kuan Chen, De-Zhu Li, and Jun Rong
    J Syst Evol. 2024, 62(1): 38-54.
    https://doi.org/10.1111/jse.12948
    Polyploids are common in Camellia sect. Paracamellia, which contain many important oil crop species. However, their complex evolutionary history is largely unclear. In this study, 22 transcriptomes and 19 plastomes of related species of Camellia were sequenced and assembled, providing the most completed taxa sampling of Camellia sect. Oleifera and C. sect. Paracamellia. Phylogenetic trees were reconstructed with predicted single-copy nuclear genes and plastomes. Phylogenetic trees with nuclear genes demonstrated that C. sect. Oleifera should be merged into C. sect. Paracamellia. Cytonuclear discordance and network analyses suggested hybridizations among polyploid species and relatives. The divergence of major clades in C. sect. Paracamellia was dated to be during the middle to late Miocene from the ancestral Lingnan region, and a rapid diversification during the Quaternary was found, probably through hybridization and polyploidization. The tetraploid Camellia meiocarpa Hu may have originated from hybridization between closely related diploid species. The hexaploid Camellia oleifera C. Abel probably originated from hybridization between closely related diploid and tetraploid (e.g., C. meiocarpa) species. The octoploid Camellia vietnamensis T. C. Huang ex Hu could have originated from hybridization between hexaploid C. oleifera and the closely related diploid species. Hybridization and polyploidization played an important role in generating the rich variation of important fruit traits, especially increased fruit size in polyploid species.
    Our study supports the incorporation of Camellia sect. Oleifera into C. sect. Paracamellia. The reticulate evolution and biogeographic history of polyploid oil crop species were inferred. Hybridization and polyploidization may drive diversification of C. sect. Paracamellia and generate rich variation in fruit traits.
  • Yi Yang, Lei Jiang, En-De Liu, Wei-Li Liu, Li Chen, Yi-Xuan Kou, Deng-Mei Fan, Shan-Mei Cheng, Zhi-Yong Zhang, and Hua Peng
    J Syst Evol. 2023, 61(6): 1036-1046.
    https://doi.org/10.1111/jse.12935
    Resolving the infrageneric classification of species-rich genera has been challenging in plant taxonomy. Ilex L. is a subcosmopolitan genus with over 600 species of dioecious trees and shrubs. Many classification systems based on morphological data have been proposed during the past 250 years. However, these systems (such as Loesener's and Galle's systems) may not truly reflect Ilex's evolutionary trajectories because most of those system's infrageneric hierarchies are not monophyletic. In this study, we reconstructed a phylogeny of Ilex L. comprising 15 moderately to highly supported clades using rigorously identified samples (202 species) and closely authenticated gene sequences of three nuclear genes [internal transcribed spacer (ITS), external transcribed spacer (ETS), and nepGS]. The newly generated phylogenetic tree resembles essentially that of the nuclear tree of Manen et al., but shows conspicuous topological differences with the phylogeny of Yao et al. Closely scrutinizing morphological variation and distributional patterns of 202 species, this study found that most lineages of Ilex identified herein are well defined by a particular trait or a combination of morphological and distributional traits, displaying phylogeny–morphology–distribution conformity that has seldom been uncovered in previous studies. Given the general phylogeny–morphology–distribution conformity revealed in this genus, we put forward an updated sectional classification system for Ilex that temporarily contains 14 sections. The new classification will provide a robust framework for studying the evolution and diversification of this ecologically and economically important genus.
    The genus Ilex comprises at least 15 moderately to highly supported clades. The newly generated phylogenetic tree resembles essentially that of the nuclear tree of Manen et al., but shows conspicuous topological differences with the phylogeny of Yao et al. Most lineages of Ilex identified herein are well defined by a particular trait or a combination of morphological and distributional traits, displaying a phylogeny–morphology–distribution conformity that has seldom been uncovered in previous studies. We put forward an updated sectional classification system for Ilex that temporarily contains 14 sections.
  • Chang Qu, Hong-Na Kao, Hui Xu, Bao-Sheng Wang, Zhi-Ling Yang, Qi Yang, Gui-Feng Liu, Xiao-Ru Wang, Yan-Jing Liu, and Qing-Yin Zeng
    J Syst Evol. 2024, 62(1): 135-148.
    https://doi.org/10.1111/jse.12953
    Hybrid genomes usually harbor asymmetrical parental contributions. However, it is challenging to infer the functional significance of asymmetrical retention of parental alleles in hybrid populations of conifer trees. Here we investigated the diversity in the glutathione S-transferase (GST) gene family in a hybrid pine Pinus densata and its parents (Pinus tabuliformis and Pinus yunnanensis). Plant GSTs play major roles in protecting plants against biotic and abiotic stresses. In this study, 19 orthologous groups of GST genes were identified and cloned from these three species. We examined their expression in different tissues, and then purified the corresponding proteins to characterize their enzymatic activities and specificities toward different substrates. We found that among the 19 GST orthologous groups, divergence in gene expression and in enzymatic activities toward different substrates was prevalent. P. densata preferentially retained P. yunnanensis-like GSTs for 17 out of the 19 gene loci. We determined the first GST crystal structure from conifer species at a resolution of 2.19??. Based on this structure, we performed site-directed mutagenesis to replace amino acid residuals in different wild-types of GSTs to understand their functional impacts. Reciprocal replacement of amino acid residuals in native GSTs of P. densata and P. tabuliformis demonstrated significant changes in enzyme functions and identified key sites controlling GSTs activities. This study illustrates an approach to evaluating the functional significance of sequence variations in conifer genomes. Our study also sheds light on plausible mechanisms for controlling the selective retention of parental alleles in the P. densata genome.
    Through structural and functional assays of the glutathione S-transferase family, this study revealed molecular mechanisms of asymmetrical retention of parental alleles in a homoploid hybrid Pinus densata.
  • Fei Qin, Xiao-Xia Zhang, Yun-Feng Huang, Lei Wu, Wei-Bin Xu, Tian-Tian Xue, Wen-Di Zhang, Qin Liu, Jiang-Hong Yu, Jie-Jing Gao, Rainer W. Bussmann, Juan Wang, and Sheng-Xiang Yu
    J Syst Evol. 2023, 61(6): 967-978.
    https://doi.org/10.1111/jse.12941
    National key protected wild plants (NKPWPs) are species with important conservation value based on genetics, ecology, culture, and/or scientific research, which are also confronted with serious threats. However, their geographical distribution patterns and conservation status remain unclear. In this study, we compiled 1032 species of NKPWPs. We measured the diversity to identify hotspots of NKPWPs based on species richness, weighted range size rarity and a complementarity-based analysis. Comparing the distribution and hotspots of NKPWPs with the coverage of Chinese nature reserves (NRs), we assessed conservation effectiveness and identified conservation gaps. The results identified 13 diversity hotspots; only 9.5% of them were covered by NRs with >30% of the grid cell area, and even 19.5% were not covered at all by NRs. Overall, 44.7% of NKPWPs were effectively protected by national NRs. Despite this success, 571 species in Yunnan, Guizhou, Sichuan, Chongqing, Guangxi, Guangdong, southern Hainan, Taiwan, and northern Xinjiang remain unprotected by NRs. The protected proportion of plants with first-level protection was lower than that of plants with second-level protection. The low overall proportion of protected hotspots indicates that the conservation outlook for NKPWPs is not optimistic. This study identifies priority conservation areas and conservation gaps and provides a scientific reference for the conservation of wild plants in China.
    This study identified hotspots for priority conservation and conservation gaps of national key protected wild plants (NKPWPs) based on species richness, weighted range size rarity and a complementarity-based analysis. The protected proportion of plants with first-level protection is lower than that with second-level protection, and the low proportion of protected hotspots indicates that the conservation status of NKPWPs is not optimistic.
  • Yang Tian, Shu-Yu Liu, Pär K. Ingvarsson, Dan-Dan Zhao, Li Wang, Baoerjiang Abuduhamiti, Jin-Feng Cai, Zhi-Qiang Wu, Jian-Guo Zhang, and Zhao-Shan Wang
    J Syst Evol. 2023, 61(5): 852-867.
    https://doi.org/10.1111/jse.12911
    Identifying the factors that cause reproductive isolation and their relative importance in species divergence is crucial to our understanding of speciation processes. In most species, natural selection is commonly considered to play a large role in driving speciation. Based on whole genome re-sequencing data from 27 Populus alba and 28 Populus adenopoda individuals, we explored the factors related to reproductive isolation of these two closely related species. The results showed that the two species diverged ~5-10 million years ago (Ma), when the Qinghai-Tibet Plateau reached a certain height and the inland climate of the Asian continent became arid. In highly differentiated genomic regions, the relative divergence (FST) and absolute divergence (dxy) were significantly higher than the genomic background, θπ and shared polymorphisms decreased whereas fixed differences increased, which indicated that natural selection played a key role in the reproductive isolation of the two species. In addition, we found several genes that were related to reproduction that may be involved in explaining the reproductive isolation. Using phylogenetic trees resolved from haplotype data of Populus tomentosa and P. adenopoda, the maternal origin of P. tomentosa from P. adenopoda was likely to be located in Hubei and Chongqing Provinces.
    Using the re-sequencing data of 27 Populus alba and 28 Populus adenopoda, it was identified that the two species have obvious genetic structure. The uplift of the Qinghai-Tibet Plateau and climate change make the two populations differentiate and produce post-zygotic isolation. The hybrid offspring of Populus tomentosa are sterile. Natural selection plays an important role in this process.
  • Zhe-Chen Qi, Pan Li, Jun-Jie Wu, Alexander Gamisch, Tuo Yang, Yun-Peng Zhao, Wu-Qing Xu, Shi-Chao Chen, Kenneth M. Cameron, Ying-Xiong Qiu, and Cheng-Xin Fu
    J Syst Evol. 2023, 61(5): 733-747.
    https://doi.org/10.1111/jse.12998
    Geographical variation in species richness in plant groups is determined by the interplay between historical, evolutionary, and ecological processes. However, the processes underlying the striking disparity in species richness between Asia and the Americas remain poorly understood. Here, we synthesize global phylogenetic and macroecological data on the diversification of Smilacaceae, deciphering potential drivers underlying the species diversity pattern biased toward Asia. We compiled global distributions of all Smilacaceae species, and reconstructed the biogeographic history and niche evolution using a new time-calibrated phylogeny (eight genes, 135 species). Integrating these data sets, we estimated evolutionary histories and diversification rates for each region, and tested correlations among species diversification, niche evolution, and niche divergence. Smilacaceae probably originated during the Late Cretaceous/Early Palaeocene and began to diversify in middle to low latitudes in Central America and Eurasia during the Late Eocene. Both the Old and New World clades exhibited a steady, albeit slight, increase of species diversification from the Late Eocene to Early Miocene. However, the Old World clade experienced an abrupt increase in net diversification during the Late Miocene. Our findings also revealed that species diversification rates were positively correlated with ecological niche evolution and niche divergence. Niche shifts and climatic niche evolution since the Middle Miocene played crucial roles in species diversification dynamics within Smilacaceae. The high plant richness in Asia may be explained by greater diversification in this region, potentially promoted by heterogeneous environments.
    ·By integrating the global phylogenetic and macroecological data on the diversification of Smilacaceae, the evolutionary histories and diversification patterns were reconstructed.
    ·The origin of the family Smilacaceae is estimated during the Late Cretaceous/Early Palaeocene, and began to diversify in the middle to low latitudes in Central America and Eurasia during the Late Eocene.
    ·The species diversification rate was positively correlated with ecological niche evolution and niche divergence. Niche shifts and climatic niche evolution since the Middle Miocene are proved to play important roles in species diversification dynamics within Smilacaceae.
  • Antonio Giacò, Lucia Varaldo, Gabriele Casazza, Daniele De Luca, Paolo Caputo, Marco Sarigu, Gianluigi Bacchetta, Llorenç Sáez, and Lorenzo Peruzzi
    J Syst Evol. 2023, 61(5): 827-842.
    https://doi.org/10.1111/jse.12925
    Santolina is a clear example of a genus lying in an alpha-taxonomic status, with species accepted only based on qualitative morphological descriptions. In particular, taxonomic issues still need to be resolved for Santolina populations from southern France and north-eastern Spain, and so, we carried out an integrative taxonomic study involving morphometrics, cypsela morphometrics, niche overlap, and phylogenetic analysis based on six plastid markers (trnH-psbA, trnL-trnF, trnQ-rps16, rps15-ycf1, psbM-trnD, and trnS-trnG). Our results revealed that the current taxonomic circumscription is not adequate. In particular, the Santolina populations at the foothills of eastern Pyrenees, previously included in the variability of Santolina benthamiana, have to be considered as a distinct species, namely, Santolina intricata. In addition, despite their high phylogenetic relatedness, S. benthamiana s.str. and Santolina ericoides can still be considered as distinct species due to clear morphological and ecological differentiation. Finally, we demonstrated that three different subspecies can be recognized in Santolina decumbens, a species endemic to Provence. For one of these subspecies, due to its extremely restricted distribution range, conservation issues are pointed out.
    An integrative taxonomic approach involving morphometrics, niche analysis, and molecular systematics with plastid markers (trnH-psbA, trnL-trnF, trnQ-rps16, rps15-ycf1, psbM-trnD, and trnS-trnG) revealed new endemic taxa of Santolina in southern France and north-eastern Spain. In particular, Santolina intricata, previously considered as a synonym of Santolina benthamiana, has to be considered as a distinct species, endemic to eastern Pyrenees. Then, for Santolina decumbens, a species endemic to Provence, three subspecies can be recognized. Finally, despite a high phylogenetic relatedness, Santolina ericoides and S. benthamiana can still be considered as distinct species due to both morphological and ecological differentiation.
  • Gui-Lin Wu, Qing Ye, Hui Liu, De-Xiang Chen, Zhang Zhou, Ming Kang, Hang-Hui Kong, Zhi-Jing Qiu, and Hui Wang
    J Syst Evol. 2023, 61(5): 843-851.
    https://doi.org/10.1111/jse.12914
    Leaf water storage capacity and osmotic strength are important traits enabling species to adapt to environments that are often moisture limited. However, whether these drought tolerance traits are correlated with the species diversification rate (DR) of plant lineages is yet to be determined. In this study, we selected a species-rich genus (Primulina) of plants widely distributed in karst regions in which species frequently experience variable periods of drought. We measured water storage capacity-related traits (including leaf thickness and water content per mass) and saturated osmotic strength in the leaves of 58 Primulina species growing in a common garden. Subsequently, using phylogenetic methods, we examined the relationships between the rate of species diversification and the drought tolerance traits and between the species DR and evolutionary rates of these traits. We found that neither water storage capacity nor saturated osmotic strength showed significant relationships with the rate of species diversification. However, the evolutionary rate of saturated osmotic strength showed a significant correlation with the species DR, although no comparable significant relationship was detected regarding the evolutionary rate of water storage capacity. Our study indicates that the diversification among Primulina species has typically been accompanied by an extensive divergence of leaf osmotic strength but not a divergence in leaf water storage capacity. These findings will enhance our current understanding of how drought tolerance influences the diversification of plant species in karst regions.
    Leaf drought tolerance (including leaf water storage capacity and osmotic strength) was hypothesized drive diversification in Primulina which are widely distributed in karst regions. We found the evolutionary rate of saturated osmotic strength showed a significant correlation with the rate of diversification in Primulina. By contrast, leaf water storage capacity showed nonsignificant relationship with diversification rate in this genus. Our study indicate that the diversification among Primulina species has typically been accompanied by an extensive divergence of leaf osmotic strength, not a divergence in leaf water storage capacity.
  • Dong-Ling Cao, Xue-Jie Zhang, Xiao-Jian Qu, and Shou-Jin Fan
    J Syst Evol. 2023, 61(6): 1004-1019.
    https://doi.org/10.1111/jse.12946
    Previous phylogenetic analyses indicated that Polygonoideae, the largest subfamily in the Polygonaceae, is monophyletic. Phylogenetic relationships within the Polygonoideae have been substantially controversial. We collected 160 samples representing all currently recognized tribes for a more comprehensive phylogenetic analysis of the subfamily. Here, we reconstructed phylogenetic relationships of the Polygonoideae, inferred ancestral character states, and estimated the divergence time with a dense taxon sampling. This study corroborated and expanded previous results regarding the phylogenetic relationships of the Polygonoideae clade, and resolved the phylogenetic status of some controversial taxa by integrating molecular and morphological evidence. Phylogenetic analyses based on the complete plastomes suggested strong support for six primary clades that correspond to the most recent circumscription of tribes: Polygoneae, Rumiceae, Calligoneae, Pteroxygoneae, Fagopyreae, and Persicarieae. In addition, we provided further morphological data and assessed characters that supported different clades. The 3-colpate pollen, 5-parted perianth, and 3 styles were inferred to be the ancestral states of Polygonoideae. Divergence time estimation revealed that Polygonoideae originated around the late Cretaceous, and diversification was concentrated in the Eocene and Miocene. Time estimation indicated that the rapid uplift of the Tibetan Plateau and the intensification of the Asian monsoons might be potential driving forces for the diversification of Polygonoideae. Overall, this study advances our understanding of the phylogeny and diversification of the Polygonoideae and highlights the adaptive evolution of the taxa.
    Our study represents the largest plastid phylogenomic investigation of the Polygonoideae and offers critically important insights into the deep phylogenetic relationships of Polygonaceae. In particular, we revealed that the rapid uplift of the Qinghai–Tibetan Plateau and the intensification of Asian monsoons were the driving forces in the origin and diversification of Polygonoideae species. Taken together, our study advances our understanding of the origin and diversification of Polygonoideae species and highlights the adaptive evolution of the taxa.
  • Yan-Fei Li, Shu-Jing Wang, Jia-Yue Zhou, Cui-Qing Gao, Chen-Guang Zheng, Huai-Jun Xue, and Wen-Jun Bu
    J Syst Evol. 2023, 61(5): 932-947.
    https://doi.org/10.1111/jse.12931
    Economically significant bean pests of the genus Chauliops are species rich in the areas surrounding the Qinghai-Tibet Plateau and provide an excellent system for speciation studies. Here, an integrative taxonomic approach, employing morphological analyses, population genetic methods, and multiple molecular species delimitation methods, was used to clarify the taxonomy of Chauliops in East and Southeast Asia. Four new species (Chauliops parahorizontalis Li & Bu, sp. nov., Chauliops albida Li & Bu, sp. nov., Chauliops bicoloripes Li & Bu, sp. nov., and Chauliops paraconica Li & Bu, sp. nov.) were described, which increases the number of Chauliops species in this area from six to 10; a key for Chauliops species is also provided. Phylogenetic analysis and divergence time estimation revealed that Chauliops was divided into four clades: Clade A (Chauliops bisontula + [Chauliops horizontalis + C. parahorizontalis sp. nov.]), Clade B (C. albida sp. nov. and C. bicoloripes sp. nov.), Clade C (Chauliops quaternaria and Chauliops zhengi), and Clade D (Chauliops fallax + [Chauliops conica + C. paraconica sp. nov.]). Two species diversification events of Chauliops estimated to have occurred 7-1 million years ago (Ma) and 25-13 Ma were detected. These speciation events were consistent with the two historical uplift events of the Qinghai-Tibet Plateau, suggesting that orogeny might have provided opportunities for the diversification of Chauliops species on the southeastern margin of the Qinghai-Tibet Plateau. Our findings show that population genetic analyses can be used to delimit related species and that orogeny is a key driver of species diversification on the southeastern margin of the Qinghai-Tibet Plateau.
    An integrative taxonomic approach employing morphology, population genetic methods based, was used to clarify the taxonomy of Chauliops in East and Southeast Asia, four new species were described. Two species diversification events of Chauliops suggested that orogeny might have provided opportunities for the diversification of Chauliops species in the southeast margin of the Qinghai-Tibet Plateau. Population genetic analyses can be used to delimit related species and orogeny is a key driver of species diversification in the southeast margin of the Qinghai-Tibet Plateau.
  • Jie Gao, Kyle W. Tomlinson, Wei Zhao, Baosheng Wang, Ralph Sedricke Lapuz, Jing-Xin Liu, Bonifacio O. Pasion, Bach T. Hai, Souvick Chanthayod, Jin Chen, and Xiao-Ru Wang
    J Syst Evol. 2024, 62(1): 120-134.
    https://doi.org/10.1111/jse.12949
    Southeast Asia (SEA) has seen strong climatic oscillations and fluctuations in sea levels during the Quaternary. The impact of past climate changes on the evolution and distribution of local flora in SEA is still poorly understood. Here we aim to infer how the Quaternary climate change affects the evolutionary process and range shifts in two pine species. We investigated the population genetic structure and diversity using cytoplasmic DNA markers, and performed ecological niche modeling to reconstruct the species past distribution and to project range shift under future climates. We found substantial gene flow across the continuous distribution of the subtropical Pinus yunnanensis. In contrast, the tropical Pinus kesiya showed a strong population structure in accordance with its disjunct distribution across montane islands in Indochina and the Philippines. A broad hybrid zone of the two species occurs in southern Yunnan. Asymmetric introgression from the two species was detected in this zone with dominant mitochondrial gene flow from P. yunnanensis and chloroplast gene flow from P. kesiya. The observed population structure suggests a typical postglaciation expansion in P. yunnanensis, and a glacial expansion and interglacial contraction in P. kesiya. Ecological niche modeling supports the inferred demographic history and predicts a decrease in range size for P. kesiya under future climates. Our results suggest that tropical pine species in SEA have undergone evolutionary trajectories different from high latitude species related to their Quaternary climate histories. We also illustrate the need for urgent conservation actions in this fragmented landscape.
    We studied the great impacts of Quaternary climate fluctuations on the distribution and evolution of Pinus yunnanensis and P. kesiya in Southeast Asia (SEA). The past climate change resulted in contrasting patterns of populations history in the two pine species and a large introgression zone between them. Range shifts caused by Quaternary glacial–interglacial climate oscillations created secondary contact zones between the two species, leading to a zone of introgression with complex genetic composition. Our results suggest that the Quaternary climate history in SEA strongly shaped the diversity and evolutionary trajectories of pine species in the region and illustrate the need for guided conservation actions in this dispersed and isolated landscape.
  • Jong-Soo Kang, Jigao Yu, Xian-Chun Zhang, and Qiao-Ping Xiang
    J Syst Evol. 2023, 61(5): 890-905.
    https://doi.org/10.1111/jse.12927
    Extensive C-to-U editing has been reported from plastid genomes (plastomes) and mitochondrial genomes (mitogenomes) of spikemoss. While “reverse” U-to-C editing was recorded in other seed-free plants such as hornworts, quillworts, and ferns, it was not observed in spikemosses. However, no comprehensive study on the association between RNA editing and other genomic features was conducted for the organelle genomes of spikemosses. Here, we report thousands of C-to-U editing sites from plastomes and mitogenomes of two species: 1767 and 2394 edits in Selaginella remotifolia, and 4091 and 2786 edits in Selaginella nipponica, respectively. Comparative analyses revealed two different editing frequencies among plastomes, but one similar frequency in mitogenomes. The different editing frequency in the Selaginella organelle genomes is related to the nonsynonymous substitution rate and the genome structural complexity. The high guanine and cytosine (GC) content caused by GC-biased mutations in organelle genomes might be related to the absence of U-to-C editing in Selaginellaceae. Using RNA-seq and whole-genome data, we screened the pentatricopeptide repeat (PPR) family and discovered that the number of aspartic acid-tyrosine-tryptophan (DYW) domain-containing PPR proteins corresponded roughly to the editing abundance in the Selaginella organelle genomes. Consequently, we hypothesize that associated evolution among RNA editing, GC-biased mutation in organelle genomes, and the PPR protein family encoded in the nuclear genome, is probably triggered by the aberrant DNA repair system in Selaginellaceae. Our study provides new insights into the association between organelle and nuclear genomes in Selaginellaceae, which would contribute to understanding the evolution of post-transcriptional modifications of organelle genomes in land plants.
    Organelle genomes in Selaginellaceae are notorious for genome architecture and extensive RNA editing. In order to understand the editing pattern in Selaginellaceae organelle genomes, thousands of RNA editing sites in the plastid and mitochondrial genomes of two Selaginella species were newly identified and compared with those from other previously reported Selaginella organelle genomes. Additionally, the analysis of pentatricopeptide repeat (PPR) genes using RNA-seq and whole-genome data demonstrated that the expansion of PPR proteins with the aspartic acid-tyrosine-tryptophan (DYW) domain corresponded to the editing abundance in their organelle genomes.
  • Sergio Castro, Audrey Muratet, Magdalena Szczepaniak, Julie Nguefack, and Laurent Hardion
    J Syst Evol. 2023, 61(5): 764-775.
    https://doi.org/10.1111/jse.12940
    Melica (Poaceae) consist of about 92 species distributed across temperate regions of the world. Within section Dalycum, Melica ciliata sensu lato forms a taxonomic complex of several species and subspecies with clinal morphological variation causing conflicting identifications. To resolve taxonomic confusion, we used three complementary approaches, through molecular, morphological, and phytoecological analyses. The double-digest restriction-associated DNA markers significantly support the monophyly of three taxa: (i) the Mediterranean Melica magnolii, (ii) the Eurasian Melica transsilvanica subsp. transsilvanica, and (iii) the west-European M. ciliata subsp. glauca. This differentiation is corroborated by the analysis of 22 morphometric variables. Furthermore, phytoecological analysis of 221 floristic inventories revealed habitat distinctions among these taxa. Our approach of integrative taxonomy argues for a specific distinction for these three taxa, and we include a key to separate these forms. These new molecular data on the section Dalycum, subsection Ciliatae, call for further phylogenetic analyses including samples of M. ciliata subsp. ciliata and other East-Mediterranean and South African taxa.
    Three types of markers were used to clarify the taxonomic status of Melica magnolii, Melica ciliata subsp. glauca, and Melica transsilvanica subsp. transsilvanica. RAD sequencing-based phylogenetic analyses reveal the monophyletic nature of each taxon, which is congruent with morphometric clustering and habitat distinctions. Useful information for field recognition is presented. More work is needed to fully understand the evolution and diversification of this intricate taxonomic complex.
  • Rui-Yun Li, Lin-Hao Cui, Dong-Jing Fu, and Xing-Liang Zhang
    J Syst Evol. 2023, 61(6): 1091-1101.
    https://doi.org/10.1111/jse.12942
    Macroalgae have been a key ecological component of marine ecosystems since the Proterozoic period and are common fossil forms in Cambrian Burgess Shale-type Lagerstätten. However, in most cases, it is difficult to place these early fossil algae into modern groups because little distinctive morphology is preserved. Here, we describe a new form of macroalgae, Qingjiangthallus cystocarpium gen. & sp. nov., from the Qingjiang biota of South China. The new taxon is represented by 546 specimens remarkably preserved with characteristics that allow a phylogenetic placement into crown groups of red algae. Centimeter-sized thalli resemble members of the extant Rhodymeniophycidae (a subclass of the class Florideophyceae), and hence suggest a florideophycean affinity, which indicates that ahnfeltiophycidaen and rhodymeniophycidaen algae may have diverged at least 518Ma, accordant with estimations of molecular studies. The presence of possible cystocarps on Qingjiangthallus thalli suggests that evolutionary innovation of a triphasic life cycle in red algae may have occurred no later than the Early Cambrian. The branching patterns and branch width of Qingjiangthallus are consistent with the coarsely dichotomously branched morphogroup, which was previously present in the Ediacaran, Ordovician, and afterward, but absent in the Cambrian.
    The new form of macroalgae, Qingjiangthallus cystocarpium gen. et sp. nov., is placed in the crown-group Rhodophyta, and probably has an affinity with the Florideophyceae. Its comparability with Rhodymeniophycidae and early age indicate that ahnfeltiophycidaen and rhodymeniophycidaen algae may have diverged at least 518Ma. The presence of possible cystocarps on Qingjiangthallus thalli suggests that evolutionary innovations of triphasic life history in red algae may have occurred no later than the Early Cambrian. Morphologically, Qingjiangthallus fills the Cambrian gap in the fossil record of the coarsely dichotomously branched morphogroup.
  • Jorge Cruz-Nicolás, Norberto Martínez-Méndez, Erika Aguirre-Planter, Luis E. Eguiarte, and Juan P. Jaramillo-Correa
    J Syst Evol. 2024, 62(3): 368-383.
    https://doi.org/10.1111/jse.13000
    Interspecific trait divergence may reflect adaptation and reproductive isolation, particularly after the rapid differentiation that may follow the colonization of new environments. Although new lineages are generally expected to be morphologically and ecologically similar to their ancestors, environmental forces can also drive adaptive differentiation along specific phenotypic axes. We used climate niche models and comparative analyses based on a previously inferred phylogeny to examine the history of ecological and morphological divergence of Neotropical firs (Abies Mill., Pinaceae), a group of conifers that have recently colonized and diversified in the mountains of Mexico and northern Central America. We inferred past secondary contact zones by comparing current and past climate niche projections and looked for evidence of recent interspecific gene flow using genomic data. Neotropical firs have similar niches to each other and show a strong phylogenetic signal for most evaluated morphological traits. Analyses based on individual variables suggested a random walk model of differentiation. However, early adaptation to tropical conditions is inferred in the ancestor of the southernmost firs, as all modern southern taxa are differentiated climatically from Abies concolor, the northernmost species. In addition, observed autapomorphic traits for soil properties and the number of resin ducts in needles are consistent with possible species-specific adaptations. Thus, a combination of nonadaptive and adaptive processes along different phenotypic axes, some related to the environment, likely operated after the southward migration of this plant lineage from North America and its subsequent radiation in the Neotropics.
    Past climate niche projections of Neotropical firs revealed larger past than current distributions, which translated in recent interspecific gene flow, according to genome data analyses. Neotropical firs have similar niches and show strong phylogenetic signals for most traits evaluated, which predominantely fitted the random walk model, as expected for nonadaptive radiations. However, an early adaptation to tropical conditions in the ancestor of southernmost firs was inferred; all modern southern taxa are climatically differentiated from northernmost Abies concolor, suggesting the possible contribution of nonadaptive and adaptive processes to fir differentiation.
  • Shao-Jun Ling, Xiao-Lan Yao, Juli Caujapé-Castells, Jordi López-Pujol, Ke Tan, and Ming-Xun Ren
    J Syst Evol. 2023, 61(6): 1020-1035.
    https://doi.org/10.1111/jse.12937
    Disjunct distribution is a key issue in biogeography and ecology, but it is often difficult to determine the relative roles of dispersal vs. vicariance in disjunctions. We studied the phylogeographic pattern of the monotypic Conandron ramondioides (Gesneriaceae), which shows Sino-Japanese disjunctions, with ddRAD sequencing based on a comprehensive sampling of 11 populations from mainland China, Taiwan Island, and Japan. We found a very high degree of genetic differentiation among these three regions, with very limited gene flow and a clear Isolation by Distance pattern. Mainland China and Japan clades diverged first from a widespread ancestral population in the middle Miocene, followed by a later divergence between mainland China and Taiwan Island clades in the early Pliocene. Three current groups have survived in various glacial refugia during the Last Glacial Maximum, and experienced contraction and/or bottlenecks since their divergence during Quaternary glacial cycles, with strong niche divergence between mainland China+Japan and Taiwan Island ranges. Thus, we verified a predominant role of vicariance in the current disjunction of the monotypic genus Conandron. The sharp phylogenetic separation, ecological niche divergence among these three groups, and the great number of private alleles in all populations sampled indicated a considerable time of independent evolution, and suggests the need for a taxonomic survey to detect potentially overlooked taxa.
    Using single nuclear polymorphisms obtained by restriction site-associated DNA sequencing, it was identified that the monotypic Conandron ramondioides (Gesneriaceae) has an obvious genetic structure caused by geographical barriers. Three major genetic boundaries were detected among the 11 populations using BARRIER v.2.2, corresponding to Tokyo Bay, East China Sea, and Taiwan Strait. Vicariance resulting from an historical sea level rise associated with the Last Glacial Maximum plays an important role in this process.
  • Jean-Yves Dubuisson, Adèle Nivart, Ehoarn Bidault, Vincent Deblauwe, Vincent Droissart, Narcisse G. Kamdem, Germinal Rouhan, Atsushi Ebihara, and Timothée le Péchon
    J Syst Evol. 2024, 62(1): 84-101.
    https://doi.org/10.1111/jse.12951
    The fern genus Didymoglossum (Hymenophyllaceae) is not so diverse in Africa with seven species at most. However, its local taxonomy is surprisingly still strongly debated, in particular within the Didymoglossum erosum complex interpreted either as a single polymorphic species or as a group of at least three distinct but morphologically very close taxa (D. erosum, Didymoglossum chamaedrys, and Didymoglossum benlii). Investigating these taxonomic issues and more generally the diversity of the genus in Africa and its origin, we conducted a complete anatomo–morphological analysis coupled with a molecular phylogenetic work based on rbcL. Our results support the recognition of all seven species, including Didymoglossum robinsonii that is likely distinct from the Neotropical Didymoglossum reptans to which the African populations were traditionally attributed. We here propose new characters and a novel key to distinguish the seven African species which also include Didymoglossum ballardianum, Didymoglossum lenormandii, and Didymoglossum liberiense. Once the taxonomy is clarified with respect to the distinct evolutionary lineages evidenced, the biogeographic history of the genus in Africa is discussed based on a divergence time estimation and the reconstruction of the ancestral geographic areas. These analyses reveal a Mesozoic (Cretaceous) vicariance event within Didymoglossum which is the second one hypothesized for the family Hymenophyllaceae.
    Analyses combining morphology and molecules confirmed the presence in tropical Africa of at least seven species of Didymoglossum ferns (Hymenophyllaceae) and traced the history of the genus in Africa, which would imply numerous multiple dispersals from the Neotropics or the western Indian Ocean and at least one local diversification in the Cenozoic. A new identification key is produced and phylogenetic inferences also suggest a possible Mesozoic vicariance event at the genus scale.
  • Ya Li, Carole T. Gee, Zhen-Zhen Tan, Yan-Bin Zhu, Tie-Mei Yi, and Cheng-Sen Li
    J Syst Evol. 2024, 62(1): 164-180.
    https://doi.org/10.1111/jse.12952
    Tsuga (hemlock) is a small genus of 10 extant species in the Pinaceae, with a disjunct distribution in East Asia and eastern and western North America. Reliable species-level identification of Tsuga fossils depends on the discovery of seed cones with intact bracts, but such cones are rare in the fossil record. Here we describe a new fossil species of hemlock as T. weichangensis sp. nov. based on exquisitely preserved seed cones with nearly complete bracts from the Lower Miocene of Weichang, Hebei Province, North China. This fossil species displays a mosaic of characters between Tsuga and Nothotsuga. The well-developed and slightly exserted bract scales of T. weichangensis are reminiscent of Nothotsuga, but other characters, such as nonleaved peduncles and tongue-shaped bract scales, in addition to monosaccate pollen found at the same fossil locality, suggest an affinity closer to Tsuga. Cladistic analysis based on 15 morphological characters and a molecular backbone constraint supports the assignment of these fossil cones to Tsuga rather than Nothotsuga, and places the fossil species of T. weichangensis in an unresolved polytomy within the genus Tsuga. The occurrence of Tsuga seed cone fossils indicate the paleoclimate in the Miocene of Weichang was warmer and more humid than today's climate, which is consistent with the paleoclimate reconstructed by paleopalynology.
    We describe a new species of hemlock as Tsuga weichangensis sp. nov. (Pinaceae) based on exquisitely preserved seed cones from the Early Miocene of Weichang, Hebei Province, North China. This fossil species displays a mosaic of characters between Nothotsuga and Tsuga. The well-developed and slightly exserted bract scales of T. weichangensis are reminiscent of Nothotsuga, but other characters, such as nonleaved peduncles and tongue-shaped bract scales, in addition to monosaccate pollen found at the same fossil cite, suggest an affinity closer to Tsuga. Cladistic analysis based on 15 morphological characters and a molecular backbone constraint supports the assignment of the fossil seed cones to Tsuga rather than Nothotsuga, and places T. weichangensis in an unresolved polytomy within the genus Tsuga.
  • Jun-Jie Ge, Hong-Fei Ying, Sheng-Quan Xu, and Hua-Teng Huang
    J Syst Evol. 2023, 61(6): 1047-1055.
    https://doi.org/10.1111/jse.12943
    Gomphomastacinae is a grasshopper subfamily in Eumastacidae, with a morphology and distribution distinct from other subfamilies. The alpine genera of Gomphomastacinae that inhabit the Qinghai–Tibet Plateau in China show unique characteristics adapted to high-altitude life. However, their phylogenetic position and biogeographic history remain controversial. Thus, to determine the diversification history of these alpine genera and the origin of the subfamily, we obtained mitochondrial genome sequences from all seven Gomphomastacinae genera distributed in China. The reconstructed phylogeny was well supported and confirmed the phylogenetic position of Gomphomastacinae within Eumastacidae. Time calibration revealed a deep-time origin of the subfamily dating back to the Cretaceous period, and the diversification among alpine genera was also an ancient pre-Miocene event (30–50 Ma). Based on phylogeny and time estimates, the most likely biogeographic scenario is that Gomphomastacinae originated from an ancestral lineage that lived in East Gondwana and dispersed to Central and Western Asia through India. Subsequently, the alpine genera likely diverged along with the uplift of the Qinghai–Tibet Plateau and survived drastic climate change by in situ adaptation to high-altitude dwellings.
    ·Gomphomastacinae is a unique subfamily in Eumastacidae—distinct morphology and distributed in central Asia, far away from all other subfamilies in America.
    ·Our time-calibrated phylogeny based on mitogenomes confirmed the phylogenetic position of Gomphomastacinae and provided information for distinguishing alternative hypotheses regarding the biogeographic origin of this subfamily.
    ·The phylogeny also revealed that diversifications among this subfamily's alpine genera on the Qinghai–Tibet Plateau are ancient pre-Miocene events, suggesting an in-situ adaptation process to high-altitude living.
  • Julián Aguirre-Santoro, Alejandro Zuluaga, Emma Stonesmyth, Julio Betancur, and Rachel S. Jabaily
    J Syst Evol. 2024, 62(2): 257-274.
    https://doi.org/10.1111/jse.13062
    Phylogenomics enhances our understanding of plant radiations in the biodiverse Andes. Our study focuses on Puya, primarily Andean and a part of the Bromeliaceae family. Using a phylogenomic framework based on the Angiosperms353 probe set for 80 species, we explored Puya′s phenotypic evolution and biogeography. Divergence time analyses and ancestral area estimations suggested that Puya originated in Central Coastal Chile around 9 million years ago (Ma). Subsequently, it dispersed to the dry valleys of the Central Andes and Puna regions between 5–8 Ma, leading to the emergence of major lineages. Key events in the last 2–4 million years include the recolonization of Chilean lowlands and dispersal to the northern Andes via Peru's Jalcas, facilitating passage through the Huancabamba depression. This event gave rise to the high-elevation Northern Andes clade. Using phylogenetic comparative methods, we tested the hypothesis that adaptation to the Andes' island-like high-elevation ecosystems was facilitated by unique leaf and floral traits, life history, and inflorescence morphology. Our findings suggest correlations between inflorescence axis compression, protective bract overlap, and high-elevation living, potentially preventing reproductive structure freezing. Semelparity evolved exclusively at high elevations, although its precise adaptive value remains uncertain. Our framework offers insights into Andean evolution, highlighting that lineages adapted to life in dry ecosystems can easily transition to high-elevation biomes. It also underscores how the island-like nature of high-elevation ecosystems influences phenotypic evolution rates. Moreover, it opens avenues to explore genetic mechanisms underlying adaptation to extreme mountain conditions.
    By employing phylogenomics, we elucidate the evolutionary relationships within Puya (Bromeliaceae), providing valuable insights into its biogeography and trait evolution in the biodiverse Andes. Our study reveals the origin of Puya in Central Coastal Chile approximately 10 Ma, followed by dispersal to the dry valleys of the Central Andes, and subsequent emergence of major lineages. Semelparity and inflorescence traits related to thermoregulation in Puya are associated with life in high-elevation ecosystems, offering new perspectives on adaptation to extreme conditions in mountain systems.
  • Bao-Xia Du, Ming-Zhen Zhang, Jing Zhang, Ai-Jing Li, Shao-Hua Lin, Guo-Rong Ma, and Jian-Guo Hui
    J Syst Evol. 2023, 61(6): 1065-1078.
    https://doi.org/10.1111/jse.12934
    Eudicots exhibit diverse life forms and occupy a wide variety of habitats in the modern terrestrial ecosystems, and the diversification began during the Early Cretaceous; however, few Early Cretaceous fossils are preserved as multiorgan whole plants that can provide sufficient morphological characters for detailed phylogenetic assessment. Here, Fairlingtonia microgyna sp. nov. is reported from the upper Lower Cretaceous of Zhonggou Formation, Hanxia Section, Yumen City, western Gansu Province, Northwest China. The specimen is exceptionally preserved as multiorgan whole plant fossil with fibrous adventitious roots, simple and deeply dissected leaves, solitary and dehiscent capsular fruits attached to the creeping stems. As such, it was interpreted as a herbaceous eudicot. Phylogenetic analyses support a placement within the Papaveraceae, most likely in Papaveroideae, but there are obvious differences in morphological characteristics, which cannot confirm the systematic position within the Papaveraceae. Fossil records of Fairlingtonia from contemporaneous deposits (late Aptian to early Albian) in Northwest China and eastern North America provide direct evidence of the geographical radiation of Fairlingtonia on Laurasia. And the morphological characters of F. microgyna, including creeping leafy branches, fibrous adventitious roots, small and deeply dissected leaves as well as small capsular fruits with tiny seeds probably indicate that it was a colonizer of lake-shore environments under wet and bright conditions and possessed fast-growing and rapid propagation habitats, which allowed it to expand its geographic range with both sexual and asexual reproduction.
    A new herbaceous eudicot, Fairlingtonia microgyna sp. nov. was described based on multiorgan whole preserved plant fossils from the Lower Cretaceous of Northwest China. Phylogenetic analysis suggested an similarity with Papaveraceae, while they still show distinction in morphological characters. Fossil records from contemporaneous deposits (late Aptian to early Albian) in NW China and eastern North America indicate geographical radiation of Fairlingtonia in Laurasia.
  • Jie Zhang, Francisco Pina-Martins, Zu-Shi Jin, Yong-Peng Cha, Zu-Yao Liu, Jun-Chu Peng, Jian-Li Zhao, and Qing-Jun Li
    J Syst Evol. 2023, 61(5): 906-918.
    https://doi.org/10.1111/jse.12928
    Techniques of reduced-representation sequencing (RRS) have revolutionized ecological and evolutionary genomics studies. Precise establishment of orthologs is a critical challenge for RRS, especially when a reference genome is absent. The proportion of shared heterozygous sites across samples is an alternative criterion for filtering paralogs. In the prevailing pipeline for variant calling of RRS data - PYRAD/ IPYRAD, maxSH is an often overlooked parameter with implications to detecting and filtering paralogs according to shared heterozygosity. Using empirical genotyping by sequencing data of two primroses (Primula alpicola Stapf and Primula florindae Ward) and their putative hybrids, and extra data sets of Californian golden cup oaks, we explore the impact of maxSH on filtering paralogs and further downstream analyses. Our study sheds light on the simultaneous validity and risk of filtering paralogs using maxSH, and its significant effects on downstream analyses of outlier detection, population assignment, and demographic modeling, emphasizing the importance of attention to detail during bioinformatic processes. The mutual confirmation between results of population assignment and demographic modeling in this study suggested maxSH = 0.10 has a potentially excessive and asymmetrical effect on the removal of truly shared heterozygous sites as paralogs. These results indicate that hybridization origin hypotheses of putative hybrids represented by results with maxSH = 0.25 and 0.50 are more credible. In conclusion, we revealed the critical hazard of paralogs filtration according to sharing heterozygosity at first, so that we propose to use specific protocols, rather than maxSH, to filter potential paralogs for closely related lineages.
    Tuning an overlooked parameter (maxSH) in PYRAD/IPYRAD, a prevalent pipeline for reduced-representation sequencing assembly and analysis, can strongly influence our biological inferences of the origin of putative hybrids.
  • Martha Kandziora, Juan M. Gorospe, Luciana Salomon, Diana L. A. Vásquez, Maria Pinilla Vargas, Filip Kolář, Petr Sklenář, and Roswitha Schmickl
    J Syst Evol. 2024, 62(2): 275-290.
    https://doi.org/10.1111/jse.13048
    Habitat stability is important for maintaining biodiversity by preventing species extinction, but this stability is being challenged by climate change. The tropical alpine ecosystem is currently one of the ecosystems most threatened by global warming, and the flora close to the permanent snow line is at high risk of extinction. The tropical alpine ecosystem, found in South and Central America, Malesia and Papuasia, Africa, and Hawaii, is of relatively young evolutionary age, and it has been exposed to changing climates since its origin, particularly during the Pleistocene. Estimating habitat loss and gain between the Last Glacial Maximum (LGM) and the present allows us to relate current biodiversity to past changes in climate and habitat stability. In order to do so, (i) we developed a unifying climate-based delimitation of tropical alpine regions across continents, and (ii) we used this delimitation to assess the degree of habitat stability, that is, the overlap of suitable areas between the LGM and the present, in different tropical alpine regions. Finally, we discuss the link between habitat stability and tropical alpine plant diversity. Our climate-based delimitation approach can be easily applied to other ecosystems using our developed code, facilitating macro-comparative studies of habitat dynamics through time.
    Using a climate-based delimitation to compare the extent of tropical alpine areas between the present and during the last glacial maximum permits us to estimate the degree of habitat stability. This new approach facilitates macro-comparative studies of habitat dynamics through time.