Table of Contents

01 July 2024, Volume 62 Issue 4
Cover illustration: In this issue, Li et al. (577-588) reconstructed the ordinal and familial phylogeny of bryophytes using the largest plastid data set available to date. Based on the phylogenetic inference, they proposed seven newly segregated moss families and 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. The cover shows the typical morphologies of seven new families. [Detail] ...
  
    Issue Information
  • Research Articles
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Suellen M. Gales, Kristene T. Parsons, Ellen E. Biesack, Jonathan Ready, Raquel Siccha-Ramirez, Leonardo C. Rosa, Ricardo Rosa, Matheus M. Rotundo, Roger Bills, Alan Erik S. Rodrigues, Luis Fernando S. Rodrigues-Filho, Jan McDowell, João Bráullio L. Sales
    J Syst Evol. 2024, 62(4): 715-738.
    https://doi.org/10.1111/jse.13027
    Gymnurid rays are found in tropical, subtropical, and temperate regions around the world, where they are associated with sandy or muddy bottoms in coastal areas, being easily distinguished from other rays by the width of the disc. In recent years, the systematics of this family have been revised extensively. However, there has been no comprehensive molecular review of the family based on an adequate sample of species and localities, which may have obscured the presence of distinct evolutionary lineages. The present study was based on samples of 12 of the 13 valid species of the genus Gymnura, which were used for a multilocus reconstruction of the evolutionary history of the family Gymnuridae. Our results indicate the existence of several cryptic gymnurid lineages, within the species Gymnura micrura, Gymnura lessae, Gymnura altavela, and Gymnura poecilura. Also, we indicate that only half of the species that compose the genus are known, as well their conservation status. The analyses also indicate that the gymnurids originated during the Paleocene, with events of dispersal and vicariance occurring through the formation of oceanographic barriers, and species diversification peaking during the Oligocene and Miocene. The results of the present study reinforce the need for a comprehensive revision of the systematics of the family, in particular, the widely distributed species that are considered valid taxa, but may, in fact, represent different cryptic species. The inadequate classification of this cryptic diversity may have negative implications for the development of effective conservation measures.
    Summary of the hidden diversity of the species inside Gymnura, with the main biogeographical events that shape its origin and diversification.
  • Xiu-Yan Feng, Yi-Qing Gong, Khang Sinh Nguyen, Hiep Tien Nguyen, Yong-Bo Liu, Jian Liu, Xun Gong
    J Syst Evol. 2024, 62(4): 739-757.
    https://doi.org/10.1111/jse.13031
    Understanding the driving forces of speciation is a central question in evolutionary biology. Cycas bifida (Dyer) K. D. Hill and Cycas micholitzii Dyer are two morphologically similar Cycas (Cycadaceae) species with deeply pectinate megasporophylls and dichotomously divided leaflets. Geographically, they are isolated by the Red River Fault Zone (RRFZ), which acts as a biogeographical barrier for many Cycas species. In this study, we investigated the divergence, genetic diversity, genetic structure, and demographic history of C. bifida and C. micholitzii to uncover the speciation mechanisms for the two endangered species. Results revealed high historical gene flow but low contemporary gene flow between the two species, with a deep divergence occurring in the Late Miocene. The long-term geographical isolation and ecological niche differentiation were identified as important factors in driving the divergence of the two species, supported by significant isolation by distance testing, barrier analysis, and niche consistency detection. Geographical isolation by the RRFZ played a pivotal role in facilitating their divergence by constraining gene flow. Conservation genetic analyses indicated high genetic diversity within both species, coupled with disparate responses to Pleistocene climate fluctuations: C. micholitzii experienced population expansion, while C. bifida displayed a mild bottleneck effect. To ensure the protection and long-term sustainability of two threatened species, relevant conservation guidelines were proposed based on the assessment of their genetic diversity and structure. This study furnishes valuable insights into the mechanisms underpinning species divergence and delivers actionable recommendations for cycad conservation.
    Cycas bifida and Cycas micholitzii are two leaflets dichotomously divided Cycas species that have morphological similarities with deeply pectinate megasporophylls. Population genetics revealed that the two species had high genetic differentiation and occupied different niches with a deep divergence that occurred in the Late Miocene. The long-term geographical isolation and ecological niche differentiation were identified as important factors in driving the divergence of the two species. Subsequently, each species made its own response to the Pleistocene climate fluctuations: a weak bottleneck effect in C. bifida and a population expansion in C. micholitzii.
  • María J. Bena, Matias C. Baranzelli, Santiago M. Costas, Andrea Cosacov, María C. Acosta, Andrés Moreira-Muñoz, Alicia N. Sérsic
    J Syst Evol. 2024, 62(4): 758-774.
    https://doi.org/10.1111/jse.13023
    Geoclimatic events driving South American aridization have generated biota differentiation due to barriers and new environment formation. New environments allow species climatic niche evolution, or the geographical expansion of an existing one. Understanding the role these processes play may clarify the evolution of South American biota. Gomphrena L. ranges across almost all the continent's arid environments. We tested whether South American drylands are biogeographically connected through the Gran Chaco but, due to different aridity levels, lineage diversification could have also been associated with the evolution of climatic niches and morphological or physiological traits. With available data, we generated a dated phylogeny, estimated ancestral ranges, performed diversification analyses, reconstructed ancestral states of two characters, and examined if niches have changed between lineages. Results showed that Gomphrena diversified throughout the easternmost South American drylands ~15.4 Ma, and subsequently three independent clades colonized the western arid regions during the last Andean pulse, and after the marine transgressions (~4.8–0.4 Ma) via the Gran Chaco. The colonization implied an increase in the diversification rate of annuals over perennials and the progressive east–west differentiation of the occupied climatic niche. This diversification was influenced by C4 photosynthesis, which could have acted as a niche opener to conquer new environments after the Paranaean Sea withdrew. Spatiotemporal patterns found in Gomphrena suggest that geographical expansion and evolution of climatic niches played a common but decoupled role in promoting diversification. These results show that the Gran Chaco may have acted as a historical connection linking South American drylands.
    We tested whether South American dry and arid biomes are linked through the Gran Chaco but, due to the difference in the aridity level, lineage diversification could have been also associated with the evolution of climatic niches and morphological or physiological traits. Results showed that Gomphrena diversified throughout the easternmost South American drylands ~15.4 Ma, and that three independent clades subsequently colonized the western arid regions (~4.8–0.4 Ma) during the last Andean pulse, and after the last marine transgressions via the Gran Chaco. The colonization implied an increase in the rate of diversification of annual over perennial species and the progressive east–west differentiation of the occupied climatic niche. This diversification was influenced by C4 photosynthesis, which could have acted as a niche opener for the conquest of new environments after the Paranaean Sea withdrew and allowed colonization of the western drylands. Spatiotemporal patterns found in Gomphrena suggest that geographical expansion and the evolution of climatic niches played a common but decoupled role in promoting diversification. These results show that the Gran Chaco may have acted as a historical connection generating a link between dry and arid South American regions.
  • Xiao-Fei Tian, Maki Toyota, Hajime Ohtsuki, Jotaro Urabe
    J Syst Evol. 2024, 62(4): 775-784.
    https://doi.org/10.1111/jse.13015
    Evolutionary theory suggests the hypothesis that among genetically isolated populations, phenotypic variation should be smaller in populations with smaller ratios of nonsynonymous to synonymous substitutions (dN/dS) because smaller dN/dS ratios occur under greater purification selections. Two distinct lineages (JPN1 and JPN2) of panarctic Daphnia cf. pulex sensu Hebert (1995), invaded independently into Japan from North America, provide an excellent opportunity to test this hypothesis because the earlier invader JPN1 has a lower dN/dS ratio than JPN2. Therefore, we examined phenotypic variations in fitness-related traits, including digestive, life-history, and morphological traits, among several genotypes within these two lineages. We found that phenotypic variations were smaller within the JPN1 lineage than within the JPN2 lineage. Furthermore, within-lineage variation of the phenotypic plasticity to changing food levels was smaller in the JPN1 lineage than in the JPN2 lineage. These results support the hypothesis that the JPN1 lineage has been more efficiently subjected to negative selection. However, the magnitude of the phenotypic plasticity of these traits was, on average, at the same level between the JPN1 and JPN2 lineages and its direction differed among genotypes of these lineages, suggesting that the JPN2 genotypes might have exploited niches that were different from those of the JPN1 genotypes.
    To examine whether when an invasive organism exploits a new habitat, their phenotypic variations are large at first but eventually decrease with increasing the age of colonized populations because of the increased competitive interactions among the mutants. We examined two different asexual lineages (JPN1 and JPN2) of panarctic Daphnia pulex with different ratios of nonsynonymous to synonymous mutation rates, which invaded Japan from North America at different time points. Our results found that the variations of the phenotypic traits and plasticity of organisms increase due to the relaxation of selection when they first exploit new habitats but eventually decrease through adaptation to the habitats.
  • Kong-Yang Zhu, Zhi-Ping Zhang, Le Tao, Run-Qi Jiang, Wen-Bo Huang, Yong-Gang Sun, Hai-Feng He, Hui-Lin Fu, Hao Ma, Xiao-Min Yang, Jian-Xin Guo, Xin Jia, Chuan-Chao Wang
    J Syst Evol. 2024, 62(4): 785-793.
    https://doi.org/10.1111/jse.13029
    The West Liao River (WLR) and Yellow River (YR) basins are two major centers of millet farming in northern China. The result from flotation analyses and the spatial distribution of archeological sites indicate that two distinct survival strategies—agriculture and pastoralism were adopted in the southern and western regions of the WLR. Previous studies of ancient populations from the western area of the WLR suggested a correlation between a pastoral economy in the Bronze Age Upper Xiajiadian culture with a decreased genetic affinity with YR farmers. However, the population history of the southern WLR is unknown mainly due to the lack of ancient genetic data. Here we report the genomic data of an ancient individual from the Majiazishan site from the Late Bronze Age southern WLR region associated with Upper Xiajiadian culture. Unlike individuals from western WLR, this individual derived ancestry entirely from Late Neolithic YR farmers. We found a genetic substructure of the ancient human population of Upper Xiajiadian culture, which is consistent with the differences in the subsistence strategies of western and southern WLR. Climate deterioration led to different populations occupying the west and the south, respectively, in the WLR: the nomadic population from the Amur River (AR) in the west and the agricultural population from the YR in the south.
    A principal components analysis (PCA) with various East Asian groups was first performed to investigate the overall genetic structure of the WLR_BA_o2. In the PCA result, WLR_BA_o2 and other ancient individuals from the West Liao Region, projected between the Yellow River (YR) and Amur River (AR) groups. WLR_BA_o2 cluster with WLR_LN projected most close to the Late Neolithic to Iron Age YR groups (YR_LN and YR_LBIA), while WLR_MN and WLR_BA shifts toward the AR groups and WLR_BA_o fully cluster with AR groups.
  • Yi Xiong, Yan-Li Xiong, Xue-Jie Jia, Jun-Ming Zhao, Li-Jun Yan, Li-Na Sha, Lin Liu, Qing-Qing Yu, Xiong Lei, Shi-Qie Bai, Xiao Ma
    J Syst Evol. 2024, 62(4): 794-808.
    https://doi.org/10.1111/jse.13020
    Quaternary glacial climate oscillation and geographical isolation have significantly influenced the geographic distribution pattern and lineage evolution history of species. However, understanding how these factors specifically impact the genealogical structure of dominant Gramineous species in the Qinghai–Tibet Plateau (QTP) remains a subject of investigation. Elymus sibiricus L. (Gramineae), indigenous to the QTP and widely distributed in Eurasia, exhibits remarkable environmental adaptation and phenotypic diversity, making it an ideal candidate for phylogeographic studies. Based on the analysis of 175 complete chloroplast genome sequences, our results indicated that the ancestors of E. sibiricus originated from the QTP and underwent a complex migration history. After the speciation of E. sibiricus, several geo-groups exhibited independent differentiation, showing minimal gene flow among them. The current phylogeographic patterns of E. sibiricus are a result of frequent climate alternations and the cold climate during the Quaternary glacial, as well as the presence of several geographical barriers that have restricted the gene flow among different geo-groups. Our research has revealed for the first time that E. sibiricus has a multilineage origin, and its maternal donors are not limited to a single species. Furthermore, the high quality and mapping depth of the variant file provided reliable data for analyzing the patterns based on raw sequencing data. These findings enhance our understanding of the relationship between plant differentiation and climatic and geographical factors of Eurasia.
    Characterization of the pan-chloroplast genomes of Elymus sibiricus endemic to Qinghai–Tibet Plateau (QTP) was performed. Ancestors of E. sibiricus (with the genome constitution of StStHH) from different origins may be different, and the St genome is of multiline origin. Elymus sibiricus originated from the QTP and underwent a complex migration process during the Quaternary ice age.
  • Eliise Kara, Jérémie Bardin, Dario De Franceschi, Cédric Del Rio
    J Syst Evol. 2024, 62(4): 809-828.
    https://doi.org/10.1111/jse.13033
    Menispermaceae are an angiosperm family of mostly climbing plants distributed throughout tropical regions. The fruits in this family have a strong sclerified endocarp and can be used for reliable species-level identifications, even in a fossilized form. New Paleocene-age menispermaceous endocarps have recently been discovered in South America and Asia, while in Europe, they are mostly found in the Eocene. This paper focuses on the study of fossil endocarps belonging to Menispermaceae, found in the Petit-Pâtis locality, which is one of the few Paleocene localities in Europe. The locality is dated to the late Paleocene (57–56 Ma) and the fossils represent flora and fauna in the Paris Basin before the onset of the Paleocene–Eocene Thermal Maximum. Lignitized fossils were photographed and their morphology was analyzed using computed tomography, scanning electron microscope, and geometric morphometric analysis. The analysis of 36 fossils belonging to Menispermaceae revealed that three genera (Stephania, Palaeosinomenium, Tinospora) were present in the late Paleocene of Paris Basin. Differences in internal morphology and a more inflated endocarp base led to a description of a new fossil species—Palaeosinomenium oisensis sp. nov. The occurrence of these genera in the Paleocene of France is consistent with the suggestion that megathermal flora was present in the Paris Basin before the Paleocene–Eocene Thermal Maximum. These three genera are currently the oldest occurrences in Europe, highlighting the connection between paleofloras of the Americas, Europe, and Asia in the Paleocene.
    This paper focuses on the study of fossil endocarps belonging to Menispermaceae, found in the Petit-Pâtis locality, which is one of the few Paleocene localities in Europe. Three genera (Stephania, Palaeosinomenium, Tinospora) and one new fossil species (Palaeosinomenium oisensis) are recognized in the Late Paleocene of Paris Basin before the onset of the Paleocene–Eocene Thermal Maximum. These three genera are currently the oldest occurrences in Europe, highlighting the connection between paleofloras of the Americas, Europe, and Asia in the Paleocene.
  • Raman Patel, Rajendra Singh Rana, Ashif Ali, Taposhi Hazra, Mahasin Ali Khan
    J Syst Evol. 2024, 62(4): 829-841.
    https://doi.org/10.1111/jse.13024
    Fossil leaves, fruits, and woods assigned to Rhamnaceae have been recorded from India, however, there are no previous reports of rhamnaceous fossil flowers from India. Here, we report the first fossil flowers in appreciable numbers from the early Eocene (Palana Formation) sedimentary sequences of Gurha Lignite Mine, Rajasthan, western India, and show that they are attributable to Rhamnaceae. We examined variation in flower morphology among extant and extinct rhamnaceous species as a basis for interpreting our fossil flowers. The specimens are small star-like, pentamerous, actinomorphic, gamosepalous flowers with triangular, keeled sepals with acute apices, spathulate, short-clawed petals alternating with sepals, shallow, five-lobed nectary disc with prominent pentagonal outer margin, and a centrally placed globose ovary with stigma scar. The flowers co-occur with ziziphoid leaves and are recognized as a new species Eopaliura indica Patel, Rana & Khan sp. nov. Because of aforesaid characteristics, fossil flowers are easily identifiable as Rhamnaceae and should provide a reliable means of documenting the evolutionary history of this family during the Cenozoic.
    Here, we report the first Rhamnaceae fossil flowers from the early Eocene (Palana Formation) sedimentary sequences of the Gurha Lignite Mine, Rajasthan, and western India. The present Eocene flower specimens are recognized as a new species namely, Eopaliura indica Patel, Rana, and Khan sp. nov. and should provide a reliable means of documenting the evolutionary history of this family during the Cenozoic.