Table of Contents

01 May 2025, Volume 63 Issue 3

Cover illustration: Most Annonaceae species possess apocarpous flowers with diverse gynoecia. A study (pp. 495–509) by Chen et al. of 20 species across all four subfamilies revealed the widespread occurrence of extragynoecial compita (EGC), which facilitate intercarpellary pollen-tube growth. Suprastylar EGC, mediated by stigmatic exudate and stigma connections, was identifi ed in all subfamilies, while infrastylar EGC—newly documented in genera such as Artabotrys, Annona, and Miliusa—involves openings along carpel ventral grooves and/or basal placentation. Although Cyathocalyx exhibits a solitary carpel, vascular and developmental evidence contradicts syncarpy, suggesting that increased ovule numbers in the solitary carpel might compensate for the limitations of apocarpy. These adaptations likely enhance reproductive effi ciency, supporting the family’s diversifi cation. The image shows the gynoecium of Artabotrys hainanensis R.E.Fr., featuring moist stigmas that are in contact with each other, providing suitable conditions for suprastylar EGC. Photograph by Yanwen Chen. [Detail] ...

  

Research Article
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  Gynoecial diversity in the Annonaceae and the evolution of functional traits that overcome the limitations of apocarpy

  Yanwen Chen, Junhao Chen, Bine Xue, Bin Yang, Daniel C. Thomas, Richard M. K. Saunders

  J Syst Evol. 2025, 63(3): 495-509.
  https://doi.org/10.1111/jse.13143

  Abstract  |  Full Text PDF  |  Save

  Most species in the early divergent angiosperm family Annonaceae are apocarpous, with very diverse gynoecial morphologies. Although several Annonaceae genera with apocarpous flowers are known to possess an extragynoecial compitum (EGC) that enables intercarpellary pollen-tube growth to enhance fertilization success, the occurrence of EGC across the whole family remains obscure. Twenty Annonaceae species from all four subfamilies (Anaxagoreoideae, Ambavioideae, Annonoideae, and Malmeoideae) are examined here, with anatomical evidence revealing the occurrence of stigmatic exudate-mediated suprastylar EGC in all four subfamilies. Histological and ontogenetic studies furthermore indicate that trichomes in Cananga and Drepananthus form a confluent zone that connects adjacent stigmas, providing a structural premise for suprastylar EGC. Infrastylar EGC are reported in the Annonaceae for the first time in several genera, including Artabotrys, Annona, and Miliusa, associated with the opening on the ovary ventral groove and/or basal placentation. In addition to the sister genera Isolona and Monodora that are clearly syncarpous, flowers of the distantly related genus Cyathocalyx with a unicarpellate gynoecium have also been hypothesized to be syncarpous. Evidence of carpel vasculature and primordium development does not support that the solitary Cyathocalyx carpel is originated from carpel fusion, however, although the increased number of ovules renders it functionally similar to syncarpy. Gynoecial features, including the extensive occurrence of EGC and the increased number of ovules per carpel (consonant with reduction to a solitary carpel) in Cyathocalyx, may have evolved to overcome limitations associated with apocarpy and possibly contribute to the reproductive success and diversification of the family.

  Morphologically diverse gynoecia in the Annonaceae reflect five strategies to overcome the limitations of apocarpy in the family: our family-wide study provides anatomical evidence showing the presence of (A) suprastylar extragynoecial compitum (EGC), (B) ovarian EGC, and (C) receptacular EGC, as well as histological and ontogenetic evidence revealing (D) syncarpy and (E) increased number of ovules per carpel, with inference of their phylogenetic occurrence and potential reproductive significance.
Review
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  Fast and furious: The rapid turnover of microRNAs in plants

  Zhonglong Guo, Yixiang Yang, Xiaozeng Yang

  J Syst Evol. 2025, 63(3): 510-522.
  https://doi.org/10.1111/jse.13158

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  Plant miRNAs exhibit a dynamic and complex evolutionary landscape. Despite their rapid turnover, miRNAs play crucial roles in regulating key biological processes, underscoring their functional significance even when evolutionarily transient. This review explores the phenomenon of miRNA turnover through a comprehensive survey of miRNA conservation across land plants. We discuss how de novo miRNAs overcome challenges such as transcriptional activation, structural requirements for biogenesis, and functional integration into gene regulatory networks. Furthermore, we review the mechanisms of miRNA origination, including inverted duplication of target genes, derivation from retrotransposons or DNA transposons, spontaneous evolution, and a newly proposed mechanism through template switching mutations. Duplication of existing miRNAs plays a significant role in miRNA family expansion, driving the functional diversification and strengthening regulatory networks. While the phenomenon of miRNA loss has been preliminarily explored, its mechanisms remain insufficiently understood. To address this, we proposed three detailed steps to advance research into miRNA loss. This review provides an integrated perspective on the gain, expansion, and loss of plant miRNAs, offering insights into their evolutionary and biological significance.

  The evolution of plant miRNAs is a dynamic process marked by rapid turnover, meaning frequent gain and loss events occurring over relatively short evolutionary timescales. Mechanisms of miRNA origination have been extensively studied, including inverted duplication of target genes, derivation from retrotransposons or DNA transposons, random repeats, and a newly proposed mechanism in animals through template switching mutations. However, the phenomenon, mechanisms, and evolutionary significance of miRNA loss, particularly in plants, remains poorly understood.
Research Article
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  A comparative analysis of gamete production in distylous Primula: Associations with floral traits and elevation

  Shuai Yuan, Gui Zeng, Spencer C. H. Barrett, Yuan Xu, Kai Hao, Shixiao Luo, Dianxiang Zhang

  J Syst Evol. 2025, 63(3): 523-535.
  https://doi.org/10.1111/jse.13146

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  Despite the importance of gamete production this topic has rarely been investigated in angiosperms using comparative approaches. Here, we investigated pollen and ovule numbers per flower in 73 species and 99 populations of Primula comprising both distylous and homostylous reproductive systems. We investigated whether phylogenetic relationships influenced associations between variation in gamete production, floral traits and elevation, and whether the evolutionary breakdown of distyly to homostyly resulted in parallel changes to gamete production. We used a Bayesian approach facilitated by the MCMCglmm method to model pollen and ovule traits across species and determined whether they exhibited phylogenetic signals. We detected significant positive correlations between pollen number and elevation in both the long‐styled and short‐styled morphs (L‐morph and S‐morph, respectively), whereas ovule number was not influenced by elevation. Pollen production was significantly higher in the L‐morph than in the S‐morph, but there was no significant difference between morphs in ovule number. Pollen volume exhibited a positive correlation with the style length of compatible morphs. The transition from distyly to homostyly was associated with significant decreases in pollen production but not ovule number. Our findings demonstrate the importance of elevation on pollen production, perhaps because of selection to improve pollen‐transfer efficiency in uncertain pollinator environments. In contrast, ovule number variation appears to be more constrained by phylogenetic relationships. Our comparative analyses of a well defined angiosperm lineage highlight the complex interactions between intrinsic and extrinsic factors influencing gamete production in plants and emphasize the importance of considering pollen and ovule data separately.

  By sampling a large number of species and populations in Primula, we aimed to investigate the possible causes of variation in gamete production within this genus. We showed that pollen number per flower was significantly positively correlated with elevation independently of phylogenetic relationships among species, whereas ovule number was not affected by elevation but showed significant phylogenetic conservatism. Our comparative analyses of a well resolved angiosperm lineage highlighted the complex interplay between intrinsic and extrinsic factors affecting gamete production in plants.
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  Integrated genomic analysis reveals the fine-scale population genetic structure and variety differentiation of Taihangia rupestris, a rare cliff plant

  Meng Liu, Wen-Long Xing, Bin Zhang, Ming-Lu Wen, Yue-Qin Cheng, Yan-Yan Liu, Ya-Nan Cao, Hong-Wei Wang

  J Syst Evol. 2025, 63(3): 536-550.
  https://doi.org/10.1111/jse.13148

  Abstract  |  Full Text PDF  |  Save

  Taihangia rupestris Yu & Li, an early spring flowering plant of the Rosaceae family, is classified as a second-level protected species in China. Endemic to the cliff faces of the Taihang Mountains in central China, this rare species requires a comprehensive understanding and conservation approach. In this study, we analyzed population-level genetic variations in both chloroplast and nuclear genomes. Taihangia rupestris var. ciliata exhibited higher genetic diversity than T. rupestris var. rupestris in both genome types. All individuals of T. rupestris var. rupestris formed a single cluster, while individuals of T. rupestris var. ciliata were grouped into three distinct clusters. Approximately 29.82 Ma, T. rupestris diverged from its closely related species. Taihangia rupestris var. ciliata appeared first, followed by the differentiation of T. rupestris var. rupestris, which adapted to the climate of the southern Taihang Mountains, around 3.55 Ma. Additionally, our study identified several chloroplast genes potentially involved in variety adaptive differentiation. These findings enhance our understanding of environmental adaptation and differentiation in the two T. rupestris varieties, providing valuable genetic insights for the conservation and utilization of this species.

  Population genetic structure and phylogenetic analysis of Taihangia rupestris. (A) Principal component analysis results of T. rupestris. (B) Phylogenetic tree based on SLAF-seq data. (C) Phylogenetic tree reconstructed based on complete chloroplast genome sequences (maximum likelihood [ML], Bayesian inference [BI]). (D) Estimation of divergence time of T. rupestris based on the chloroplast genome.
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  Lineage‐specific duplication of a CYCLOIDEA2 gene and the diversification of capitula in the tribe Anthemideae (Asteraceae)

  Yu‐Lin Rong, Chen‐Yu Niu, Chu‐Jie Zhang, Yan‐Ping Guo, Guang‐Yuan Rao

  J Syst Evol. 2025, 63(3): 551-566.
  https://doi.org/10.1111/jse.13134

  Abstract  |  Full Text PDF  |  Save

  Gene duplications have contributed to the innovation of morphological traits during plant evolution. An outstanding example is the role of CYCLOIDEA2 (CYC2) gene duplications in the formation of the complex structure of Asteraceae capitula. Previous studies have shown that Chrysanthemum lavandulifolium (Fischer ex Trautv.) Makino and a few other species of the Asteraceae harbor two copies of CYC2e. Here, we identified a lineagespecific CYC2e duplication event at the root of the phylogeny of the tribe Anthemideae by analyzing the evolutionary history of CYC2 genes across the Asteraceae. Although the gene expression patterns of CYC2e1 and CYC2e2 were similar in most of floral organs, CYC2e1 promoted ligule elongation by promoting cell expansion, whereas CYC2e2 showed a weak inhibiting effect on the ray‐floret development, and overexpression of CYC2e2 resulted in the maldevelopment of stamens in disc florets. These results indicated differentiated functions of CYC2e1 and CYC2e2 in the capitulum development of the Anthemideae. Given the previous data that identified CYC2g and CYC2d as main regulators in ligule morphogenesis, we comparatively analyzed 10 Asteraceae genomic data, and identified tandem arrays of CYC2g, CYC2d, and CYC2e. We further investigated the regulatory relationships between CYC2g/CYC2d and CYC2e genes, and found that CYC2g can activate the expression of CYC2e1. The findings of this study elucidate the synergistic roles of CYC2 genes in regulating the formation of the Asteraceae capitula and enhance understanding of the mechanism of duplicated gene retention during plant evolution.

  A lineage-specific CYC2e duplication happened to the tribe Anthemideae (Asteraceae). The two CYC2e paralogs play important roles in the development of both ray and disc florets, and the synergistic effect of multiple CYC2 genes contributes to the capitular diversification of the Anthemideae.
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  Chromosome‐scale genomes of Toona fargesii provide insights into competency of root sprouting

  Jikai Ma, Qiangqiang Cheng, Qiuwei Zhong, Fangfang Fu, Ting Jia, Xuanjin Du, Wen Cao, Ling Xu, Fuliang Cao, Chunce Guo, Lu Zhang

  J Syst Evol. 2025, 63(3): 567-582.
  https://doi.org/10.1111/jse.13144

  Abstract  |  Full Text PDF  |  Save

  Toona fargesii A. Chev., a versatile tree in the Toona genus of the Meliaceae family, is renowned for its exquisite timber and medicinal properties, offering promising benefits. Due to natural regeneration obstacles and long‐term excessive exploitation, it has been threatened in China. Intriguingly, root sprouting, which may diminish the genetic diversity and hinder population development, dominates the reproductive pattern of T. fargesii in the wild. However, the lack of complete genome information has hampered basic studies on the regeneration, classification, evolution and conservation of this species. Here, we report the genome of T. fargesii, which was sequenced using the PacBio platform and assembled into a high‐quality genome with a total size of 535.24 Mb. Of this, 97.93% of the assembled contigs were anchored onto 28 pseudochromosomes, achieving a chromosomelevel genome. The long terminal repeat assembly index score was 21.34, and the consensus quality value was 39.90%, indicating the accuracy and completeness of the genome. Comparative genome analysis suggested that a recent whole genome duplication event occurred between 22.1 and 50.1 Mya in the Toona genus, with the divergence time between T. fargesii and its relative T. sinensis estimated at approximately ~16.7 Mya. Additionally, 13 TfARR genes, which play integral roles in root sprouting by mediating cytokinin signaling, underwent rapid gene expansion and showed significant enrichment in the plant hormone signal transduction pathway. Furthermore, transcriptomic analysis demonstrated that differentially expressed genes between root sprouts and nonroot sprouts were significantly enriched in the zeatin biosynthesis pathway, indicating that cytokinin regulation is involved in root sprouting development. Collectively, the findings provide valuable genomic resources for the Toona genus and genetic insights into the mechanisms of root sprouting in T. fargesii.

  Toona fargesii, a valuable tree species in the Meliaceae family, is exquisite for its high-quality timber and medicinal properties. However, due to natural regeneration challenges and overexploitation, it is now threatened in China. Toona fargesii primarily reproduces through root sprouting, which can reduce genetic diversity and hinder population growth. The lack of complete genome of T. fargesii has limited studies on its regeneration, classification, evolution and conservation. In this study, we reported the high-quality, chromosome-level genome of T. fargesii, which was sequenced using the PacBio platform, with a total size of 535.24 Mb. Comparative genomic analysis revealed a recent whole genome duplication event between 22.1 and 50.1 Mya. We identified 13 TfARR genes involved in cytokinin signaling, which showed rapid expansion. Zeatin biosynthesis was also highly enriched, suggesting cytokinin regulation in root sprouting, as supported by transcriptomic analysis of three types of roots. Taken together, these findings provide valuable genomic resources and insights into the genetic mechanisms underlying root sprouting in T. fargesii.
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  New mid‐Cretaceous macrothelids showing a similar living mode to extant Macrothelidae (Araneae: Mygalomorphae)

  Xuying Wang, Kun Yu, Paul A. Selden, Dong Ren, Xiangbo Guo

  J Syst Evol. 2025, 63(3): 583-600.
  https://doi.org/10.1111/jse.13139

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  Five new spider fossils of the family Macrothelidae (Araneae: Mygalomorphae) are described from mid‐ Cretaceous Kachin amber, Myanmar. A new genus Acanthomacrothele gen. nov. is established for three new species: Acanthomacrothele pauciverrucae sp. nov., Acanthomacrothele geminata sp. nov., and Acanthomacrothele longicaudata sp. nov. Both male and female specimens of A. pauciverrucae sp. nov. are described, representing a rare case of a fossil spider with both sexes known. We also describe an unidentified juvenile of Macrothelidae to document different developmental stages of Cretaceous species. To test the phylogenetic position of the new fossils, we undertook phylogenetic analyses using both topology‐unconstrained and topology‐constrained methods. Our analyses supported the placement of Acanthomacrothele gen. nov. in Macrothelidae, although its phylogenetic relationship to other genera of Macrothelidae differed among different analytical methods. The fossils documented here have elongated, widely spaced posterior lateral spinnerets, compact rectangular group of eyes on a tubercle, and more spines on male tibia of anterior legs than female, similar to extant macrothelids, suggesting that they probably have similar retreat construction behavior, habitat preference, and mating position to their living relatives.

  A new extinct spider genus Acanthomacrothele gen. nov. is established for three new species of the family Macrothelidae from the mid-Cretaceous Kachin amber, Myanmar. Phylogenetic analyses based on morphological data using both topology-unconstrained and topology-constrained methods were carried out to test the familial placement of these new fossils. These new fossils have elongated, widely spaced posterior lateral spinnerets, compact rectangular eye group on tubercle, and more spines on male tibia of anterior legs than female, similar to extant macrothelids, suggesting that they probably have similar retreat construction behavior, habitat preference, and mating position to their living relatives. A, Results of the unconstrained phylogenetic analyses. B, Holotype male of Acanthomacrothele pauciverrucae sp. nov. C, Web and habitat of an extant macrothelid spider.
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  Two new species of Late Devonian seed Cosmosperma from Zhejiang and Anhui, South China

  Le Liu, De‐Ming Wang, Yi Zhou, Min Qin, Peng Xu, Jia‐Jun Mu

  J Syst Evol. 2025, 63(3): 601-611.
  https://doi.org/10.1111/jse.13140

  Abstract  |  Full Text PDF  |  Save

  The earliest ovules or seeds widely reported from the Late Devonian (Famennian) are crucial for understanding the evolution of seed plants. Cosmosperma, the first Devonian seed documented in China and East Asia, is characterized by cupules with multiple segments enclosing a single ovule and covered by prickles. Two new Cosmosperma species, Cosmosperma dicrana sp. nov. and Cosmosperma lepta sp. nov., are now identified from the Upper Devonian (Wutong Formation) of Zhejiang and Anhui provinces, China, respectively. C. dicrana exhibits dichotomized fertile branches terminating in pairs of cupulate ovules, with centrifugally extending cupule segments at their distal portions. C. lepta displays slender cupulate ovules on pinnate fertile branches. Both species possess prickles on their cupules. A comparison with coeval seed plant taxa reveals differences in fertile branch types and suggests different evolutionary levels. The potentially weak dispersal ability of Cosmosperma is suggested by the absence of specialized structures for wind or water transport. Prickles on Cosmosperma cupules do not suggest adaptations for epizoochory but facilitate entanglement and friction. The adaptations for short‐distance dispersal can be advantageous in a disturbed and heterogeneous environment. The presence of Late Devonian seed plant taxa with dispersal‐adapted traits hints at habitat divergence, with some possibly inhabiting uplands or areas away fromthe coast. The pricklesmay also be an adaptation for maintaining stability in small‐ to medium‐sized plants of the Late Devonian coastal communities.

  We describe two new species of the Late Devonian seed Cosmosperma as Cosmosperma dicrana sp. nov. (A–C) and Cosmosperma lepta sp. nov. (D–G), based on specimens from Anhui and Zhejiang Provinces, South China. While the cupules of both new species feature prickles on their outer surface, they exhibit varied dimensions compared to the type species (H) and are borne on fertile branches with distinct patterns. Comparison with contemporaneous seed plant taxa suggests potential differences in evolutionary levels. The prickled cupules of Cosmosperma may be adapted for short-distance dispersal, offering advantages in disturbed, heterogeneous environments.
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  Reconstructing evolutionary history of Chinese walnuts (Juglans)

  Meng Dang, Hui‐Juan Zhou, Hang Ye, Shao‐Hong Zhu, Rui Wang, Gui‐Fang Zhao, Keith Woeste, Ming Yue, Xiao Zhang, Peng Zhao

  J Syst Evol. 2025, 63(3): 612-628.
  https://doi.org/10.1111/jse.13153

  Abstract  |  Full Text PDF  |  Save

  Members of the genus Juglans (walnuts, family Juglandaceae) are typical Tertiary relict tree species. They are widely distributed in China and are well known for their edible nuts and high‐quality wood. The genetic structure and historical gene flow patterns of Chinese Juglans still need to be resolved. Here, we collected samples from a total of 2242 trees from 142 populations of three walnut species (Juglans regia L., Juglans sigillata Dode, and Juglans mandshurica Maxim.) and a hybrid taxon Juglans × hopeiensis. These samples were distributed throughout China. We analyzed population genetic structure, interspecific relationships, lineage differentiation, and speciation using 21 EST‐SSR genetic markers. All populations of J. regia and J. sigillata clustered into one lineage, corresponding to the Juglans sect. Dioscaryon, and all J. mandshurica and Juglans × hopeiensis populations (section Cardiocaryon) clustered into a second lineage. For J. mandshurica, there was an obvious north-south genetic cline. Interestingly, except for seven populations of the hybrid Juglans × hopeiensis, there was almost no gene flow between the populations of section Juglans/Dioscaryon and section Cardiocaryon. A DIYABC analysis showed that J. regia and J. mandshurica differentiated during the Oligocene. Juglans sigillata originated during the Pliocene to the Pleistocene. Subsequently, during the Middle Pleistocene, J. regia and J. mandshurica hybridized within a narrow zone to produce Juglans × hopeiensis. These results demonstrate the impact of repeated turbulent climate changes in the Quaternary on the evolutionary history of Tertiary relict plants.

  We collected samples from a total of 2242 trees from 142 populations of three walnut species (Juglans regia L., Juglans sigillata Dode, and Juglans mandshurica Maxim.), and a hybrid taxon Juglans × hopeiensis. These samples were distributed across all China. We analyzed population genetic structure, interspecific relationship, lineage differentiation, and the processes of speciation using 21 EST-SSR genetic markers. Based on the results of this study, we propose a hypothesis on the speciation process of J. regia and J. mandshurica in China.
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  Phylogenetics and reticulation among koelerioid clades, part I: Contraction of Trisetum, expansion of Acrospelion, Graphephorum, and Tzveleviochloa; Graciliotrisetum gen. nov. and resurrection of Aegialina (Poaceae, Pooideae, Poeae, Aveninae)

  Patricia Barberá, Robert J. Soreng, Paul M. Peterson, Joan Garcia‐Porta, Konstantin Romaschenko, Carlos Aedo, and Alejandro Quintanar

  J Syst Evol. 2025, 63(3): 629-655.
  https://doi.org/10.1111/jse.13133

  Abstract Full Text PDF  |  Save

  Koelerioid grasses (subtribe Aveninae, tribe Poeae; Pooideae) resolve into two major clades, here called Koelerioid Clades A and B. Phylogenetic relationships among koelerioid grasses are investigated using plastid DNA sequences of rpl32‐trnL, rps16‐trnK, rps16 intron, and ITS regions, focusing on Trisetum, Acrospelion, and some annual species (Rostraria p.p. and Trisetaria p.p.) closely related to Trisetum flavescens in Koelerioid Clade A. Phylogenetic analyses of several selected data sets performed for 80 taxa and using maximum likelihood and Bayesian methods, revealed mostly congruent topologies in the nuclear and plastid trees, but also reticulation affecting several lineages. Trisetum is restricted to one species, T. flavescens, which is a sister to the clade formed by Trisetum gracile and Trisetaria aurea. The latter two species are classified here in the genus Graciliotrisetum gen. nov. The sister clade includes three species of Rostraria and Trisetaria lapalmae, all of which are classified here in a resurrected genus, Aegialina, which includes four species. Acrospelion is enlarged to include 13 species after the addition of other species formerly classified in Trisetum sect. Trisetum and T. sect. Acrospelion. We also transfer Trisetum ambiguum, Trisetum longiglume, and Koeleria mendocinensis to Graphephorum; and Helictotrichon delavayi to Tzveleviochloa, expanding these genera to eight and six species, respectively. We evaluate cases of reticulate evolution between Koelerioid Clades A and B and within Koelerioid Clade A, which probably gave rise to Graphephorum, Rostraria cristata, and Rostraria obtusiflora. Finally, we comment on polyploidy and biogeographic patterns in koelerioid grasses. We propose the following 26 new combinations: Acrospelion alpestre, Acrospelion altaicum, Acrospelion argenteum, Acrospelion bertolonii, Acrospelion buschianum, Acrospelion buschianum subsp. transcaucasicum, Acrospelion fuscum, Acrospelion laconicum, Acrospelion macrotrichum, Acrospelion rigidum, Acrospelion rigidum subsp. teberdense, Acrospelion tamonanteae, Acrospelion velutinum, Aegialina lapalmae, Aegialina pubescens, Aegialina pumila, Aegialina pumila subsp. fuscescens, Aegialina salzmannii, Aegialina salzmannii subsp. cossoniana, Graciliotrisetum aureum, Graciliotrisetum gracile, Graphephorum ambiguum, Graphephorum longiglume, Graphephorum mendocinense, Graphephorum orthochaetum, and Tzveleviochloa delavayi. Lectotypes are designated for the names Aegialitis tenuis, Aira melicoides, Avena aspera var. parviflora, Avena delavayi, Koeleria grisebachii var. mendocinensis, Koeleria pubescens subsp. cossoniana, Koeleria pumila, Koeleria salzmannii, Phalaris pubescens, Trisetum aureum, Trisetum cernuum, Trisetum fuscescens, Trisetum longiglume, and Trisetum wolfii; and we designate one neotype for Alopecurus litoreus.

  Phylogenetic relationships within Koeleriinae clades A and B are examined using DNA sequences of plastid rpl32-trnL, rps16-trnK, rps16 intron, and ITS regions. Phylogenetic analyses of different selected data sets yielded mostly congruent topologies in nuclear and plastid trees. Several lineages resolve in strikingly incongruent positions in the trees obtained from our different data sets, suggesting a reticulate origin for these taxa. Twenty-six new combinations have been made and 14 lectotypes and one neotype have been designated.
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  Generation of genomic resources and phylogenetic contributions in Oxalis from desert fog oases in Peru

  Leonardo Gaspar, Feng Song, Ning Fu, Lu Jin, Frank Guzmán, Asunción Cano, Mónica Arakaki, Xue‐Jun Ge

  J Syst Evol. 2025, 63(3): 656-669.
  https://doi.org/10.1111/jse.13135

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  Several species in the genus Oxalis occupy Peruvian fog oases (Lomas) with a significant habitatadapted and endemic diversity. Acknowledging this aspect, the genus Oxalis is a conceivable group for evolutionary and biogeographic hypothesis testing; however, molecular resources for the genus still need improvement. We conducted a genome skimming approach to assemble new plastomes from 18 accessions (six species) of Oxalis collected in Lomas locations in Peru. These complete plastomes of Oxalis species (several reported for the first time) present a highly conserved composition. Our phylogenetic results were congruent with previous section‐based backbone phylogenies of Oxalis; however, a closer look at the phylogeny of sect. Carnosae revealed nonmonophyletic arrangements involving Oxalis megalorrhiza and Oxalis bulbocastanum individuals. We also propose a set of three hypervariable plastid regions as potential molecular markers. Likewise, an array of primers for nuclear simple sequence repeat markers based on the most widely distributed species, O. megalorrhiza, were listed and evaluated for their transferability to the other species under examination. These new genomic resources represent a significant development for future population, phylogenetic, and biogeographic studies in Oxalis.

  The genus Oxalis occupies fog oases (Lomas) with a significant habitat-adapted and endemic diversity. We assembled 18 new plastomes (six species) of Oxalis collected in Lomas locations in Peru. Our phylogenetic reconstruction is consistent with taxonomic sectional grouping; however, further evaluation of sect. Carnosae revealed nonmonophyletic arrangements. In addition, we propose a set of three hypervariable plastomic regions as potential molecular markers. Likewise, an array of primers for nuclear simple sequence repeat markers based on the most widely distributed species O. megalorrhiza were listed and evaluated for their transferability to the other species under examination.
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  An integrative taxonomy of Oecanthinae in China (Orthoptera: Grylloidea; Oecanthidae) and its implication as a model for investigating sexual selection

  Yan‐Na Zheng, Xuan Jing, Rui Wang, Tao Zhang, Jun‐Jie Gu, Li‐Bin Ma

  J Syst Evol. 2025, 63(3): 670-692.
  https://doi.org/10.1111/jse.13136

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  Rich materials can provide more opportunities for exploring the mechanisms of speciation driven by sexual selection. Being the fastest‐evolving arthropods to date, the sword‐tailed crickets of Nudilla Gorochov, 1988 (= Laupala Otte, 1994) have rapidly diverged primarily due to the variability of their calling songs (sexual signals). In addition, they also exhibit morphological conservatism, with little variation between species. Similar circumstances can be seen in tree crickets (Oecanthinae), which have conservative morphology and a diverse range of song variations. Thus, we believe that tree crickets could serve as a model for research on sexual selection since they share a similar evolutionary history and mode of differentiation with Nudilla. However, due to the improper methods in analyzing the calling songs and nearly identical morphological features between taxa, there are many problems with the taxonomy of Oecanthinae in China. To solve these problems, we conducted an integrative taxonomic study of Chinese Oecanthinae based on comparative morphology, species delimitation, acoustical analysis, and phylogenetic analysis. This study recognized 12 Oecanthinae species in China, including four new species, and confirmed one new synonym and two misidentifications. Meanwhile, we confirmed the morphological stability of Oecanthinae, and revealed that variation in color, size, and morphology may be intraspecific polymorphism, which sometimes does not reflect the species relationships. The result indicates that the acoustic parameter freq.median can be used for efficient and accurate species delimitation in Oecanthinae. We speculate that incomplete species divergence leads to complexity in species relationships at the genetic level of Oecanthinae. The conservation of morphological characters, the interspecificity of songs and the complexity of species relationships suggest that sexual selection have played a role in the evolution of Oecanthinae. Our study resolves some systematic and taxonomic problems of Oecanthinae, clarifies the species relationships of Oecanthinae in China, and provides clues for expanding the cricket groups to be used in speciation studies.

  The study conducted an integrated taxonomic for Chinese crickets of Oecanthinae. It verified the existence of 12 species in China. It was discovered that the Oecanthinae morphology was conservative in terms of size, color, and morphology. It also confirmed the interspecific specificity of acoustic parameter in Oecanthinae. Finally, it is possible that sexual selection contributed to the evolution of Oecanthinae due to the conservation of morphological traits, the interspecificity of songs, and the complexity of species relationships.
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  A phylogenetic analysis of scale insects (Hemiptera, Coccoidea) based on genomic and transcriptomic data

  Nan Song, Miaomiao Wang, Huiji Tang, Zhihao Dang

  J Syst Evol. 2025, 63(3): 693-707.
  https://doi.org/10.1111/jse.13141

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  Coccoidea (Hemiptera, Sternorrhyncha) are widely distributed and agriculturally significant insects known for their distinctive morphology and biological traits. The Coccoidea are often called scales or mealybugs because many species have a shell‐like covering resembling a scale or are covered with mealy wax. Knowledge of scale insects beyond the female adult stage is limited, partly because other life stages are less conspicuous, shorter‐lived, and less impactful on host plants. This complicates accurate classification, further compounded by limited molecular phylogenetic studies. This study presents the first phylogenetic analyses combining genome and transcriptome sequence data. We sequenced five whole genomes and one transcriptome from Pseudococcidae and integrated these new genome‐scale data with existing genome and transcriptome sequences to perform phylogenomic analysis of scale insects. The analysis yielded robustly supported relationships within Coccoidea, resolving several high‐level relationships. The current genome‐scale data support the monophyly of Monophlebidae, Pseudococcidae, Kerriidae, and Diaspididae, while not supporting the monophyly of Coccidae and Eriococcidae. Bayesian inferences using site‐heterogeneous models corroborated Pseudococcidae as the sister group of all other neococcoid families. Within Pseudococcidae, two subfamilies, Phenacoccinae and Pseudococcinae, were supported. At the tribe level, Phenacoccini was found to be monophyletic, whereas Planococcini, Trabutinini, and Pseudococcini were not.

  In this study, we sequenced five whole genomes and one transcriptome from the family Pseudococcidae, marking the first phylogenetic analyses of Coccoidea based on genome-scale data. Our findings strongly support the monophyly of Monophlebidae, Pseudococcidae, Kerriidae, and Diaspididae, while failing to support the monophyly of Coccidae and Eriococcidae. Bayesian analyses using site-heterogeneous models further corroborated Pseudococcidae as the sister group to all other neococcoid families.
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  Key stage of evolution of endemism in Gaoligong Shan after the late Pliocene

  Jun‐Wei Ye, De‐Zhu Li

  J Syst Evol. 2025, 63(3): 708-717.
  https://doi.org/10.1111/jse.13142

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  In the Mountains of Southwest China (MSC), accelerated diversification triggered by mountain uplift and monsoon intensification in the Miocene is widely revealed, but less is known about the stage after the Pliocene. Thus, the tempo‐spatial evolution of the endemism of Gaoligong Shan (GLGS), a young and isolated mountain with the highest biodiversity in the MSC, was determined. Temporal patterns were inferred by the stem ages of the endemic species and spatial patterns were inferred through ancestral area reconstructions and the distributions of the sister taxa. Temporally, the calibrated origin times of 114 phylogenetically well resolved endemic species (75 plants, 33 animals and six fungi) ranged from the early Miocene to the Holecene. Spatially, 82 centric origin species (mean = 3.08 Ma) were significantly younger than 32 eccentric origin species (6.84 Ma). Eccentric origins accumulated smoothly while centric origins burst after the late Pliocene, especially after the Pleistocene (n = 52). In centric origins, most of the sister taxa showed sympatric (n = 47) or allopatric (n = 23) distributions in the GLGS. The eccentric origins were mainly dispersed from the southern lower latitude region (n = 20). Principle component analysis indicated that niche conservatism exerted greater contribution to the speciation of the endemic species. Uplift of the GLGS and monsoon intensification during the late Pliocene accelerated the formation of its endemism. The “Species pump” effect of the Pleistocene climatic fluctuations is further revealed. Speciation triggered by geological isolation by mountain and river barriers through niche conservatism exceeds adaptive evolution.

  In Gaoligong Shan (GLGS), the origin times of 114 phylogenetically well resolved endemic species ranged from the early Miocene to the Holecene. Eccentric origins (n = 32) accumulated smoothly while centric origins (n = 82) burst after the late Pliocene, especially after the Pleistocene. In centric origins, most of the sister taxa showed sympatric or allopatric distribution in the GLGS. The eccentric origins were mainly dispersed from the southern lower latitude region. Uplift of the GLGS and monsoon intensification during the late Pliocene accelerated the formation of its endemism. The “Species pump” effect of the Pleistocene climatic fluctuations is further revealed.
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  Cryptic diversity and evolutionary history of the fish species Xenotoca variata (Cyprinodontiformes: Goodeidae) in the Mexican Plateau: Implications for taxonomy and conservation

  Rosa Gabriela Beltrán‐López, Omar Domínguez‐Domínguez, Gerardo Pérez‐Ponce de León, Adan Fernando Mar‐Silva, Silvia Perea, Rodolfo Pérez‐Rodríguez, Kyle R. Piller, Humberto Mejía‐Mojica, Ignacio Doadrio

  J Syst Evol. 2025, 63(3): 718-736.
  https://doi.org/10.1111/jse.13147

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  Geological and climatic events frequently represent the primary explanations to describe evolutionary processes among species. Freshwater fishes have been used previously as models to uncover evolutionary and historical biogeographic patterns in central Mexico, hydrologic systems and biotas. Xenotoca variata (Cyprinodontiformes: Goodeidae) is one of the most widely distributed species across central Mexico. The species represents a highly dimorphic and sexually selective species. In this study, the phylogenetic and phylogeographic patterns of populations of X. variata, using one mitochondrial locus (cytb) and three nuclear loci (S7, RHO, and RAG1), were described in order to understand the evolutionary history of the species throughout its distributional range. Two well‐defined and highly supported clades were recovered with all analyses and genes studied, with an estimated divergence time of ca. 2.42 Mya, corroborating the existence of an independent evolutionary unit in Cuitzeo Lake and its recognition as a putative new species. Also, a phylogeographic structure in two genes was found within the widely distributed clades. The role played by climate change events and geological history as well as the possible influence of reproductive traits in the phylogeographic pattern of the species are discussed.

  Xenotoca variata (Cyprinodontiformes: Goodeidae) is one of the most widely distributed species across central Mexico, showing high sexual dimorphism and varying coloration patterns according to its distribution. The populations studied display a clear genetic structure that varies according to the markers analyzed. Two well-defined and highly supported clades were observed across the four markers, with an estimated divergence time of approximately 2.42 Mya. The population of Cuitzeo Lake (highlighted in red) is supported as a possible new species.
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  Integrated analyses reveal extensive cytonuclear discordance and two new members of Rhodiola

  Long Huang, Ya‐Peng Yang, Xiao‐Ying Liu, Lin‐Feng Qiu, Yue‐Yi Li, Zi‐Wei Ma, Shi‐Yu Wang, Xin‐Yue Wang, Jian‐Qiang Zhang

  J Syst Evol. 2025, 63(3): 737-752.
  https://doi.org/10.1111/jse.13149

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  Our knowledge of species diversity in biodiversity hotspots remains incomplete. The Qinghai-Tibet Plateau (QTP) and the mountainous region of southwestern China have long been regarded as biodiversity hotspots. However, despite considerable efforts, numerous plant species may still elude formal description. Rhodiola L. (Crassulaceae) encompasses ca. 58 perennial herb species, which have been used as an important traditional medicinal plant for centuries. Rampant exploitation has put some species at risk of extinction. Rhodiola has also been recognized as a promising model for investigating radiation speciation in the QTP. However, the phylogenetic relationships among major clades in the genus are still not well resolved, and the underlying causes of cytonuclear discordance briefly mentioned in previous studies remain unexplored. Through phylogenomic analyses utilizing data from both the nuclear genome and plastome of 42 species, we identified six major clades in Rhodiola and found extensive cytonuclear discordance, which was primarily attributed to hybridization and introgression occurring among clades or closely related species. In addition, the integration of morphological, phylogenomic, population genomic, and ecological evidence resulted in the identification and description of a new species of Rhodiola: R. renii sp. nov., and the reclassification of a previously Pseudosedum species merged into Rhodiola. Our results highlight the significant role of hybridization and introgression in the evolution of Rhodiola and probably other rapid‐radiated groups in the QTP, and emphasize the need for increased species discovery efforts in biodiversity hotspots such as the QTP and its adjacent mountainous areas.

  Rhodiola has been used as traditional Tibetan medicine since ancient times and has been identified as a promising model for investigating radiation speciation. Nevertheless, the phylogenetic relationships among major clades and its relationship with Pseudosedum are still elusive. We reconstructed the most comprehensively sampled phylogeny based on nuclear and plastid genomes. We found that hybridization and introgression have led to extensive cytonuclear discordance within Rhodiola. Furthermore, we integrated morphological, phylogenetic, and population genomic data to delineate a previously undescribed species within Rhodiola (R. renii sp. nov.) and reassigned a former Pseudosedum species (P. lievenii) to the genus Rhodiola.
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  Alpine refugial isolation drove divergence of the cold‐adapted montane scorpionfly Cerapanorpa obtusa (Mecoptera: Panorpidae)

  Kai Gao, Yuan Hua, Le‐Le He, Bao‐Zhen Hua

  J Syst Evol. 2025, 63(3): 753-766.
  https://doi.org/10.1111/jse.13150

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  Quaternary climate fluctuations and complex mountain systems had a prominent impact on the genetic diversification and speciation of montane organisms. However, the genetic imprints of the interplay between past climate events and rugged relief on montane species remain largely unresolved. Here, we analyzed the phylogeny, population structure, divergence time, demographic simulations, and ecological niche modeling of the montane scorpionfly Cerapanorpa obtusa (Cheng) from 36 populations in the mountains of central China (MCC) using three mitochondrial and two nuclear genes to explore its evolutionary history. The results show that C. obtusa originated from the Minshan Mountains, and currently consists of six genetically fragmented lineages that diverged 1.25-0.52 Ma. Four minor lineages (S1-S4) are confined to the topographically rugged Minshan Mountains, and two major lineages (NW and NE) are widely distributed in the northern MCC with relatively homogeneous landscapes. The Minshan Mountains are likely interglacial microrefugia for C. obtusa, and as spatial buffers in response to past climate changes. These findings provide some evidence that the interplay between climate changes and rugged relief may play a significant role in shaping the distinct phylogeographical pattern of cold‐adapted montane insects. These results would also seem to suggest the importance of topographically rugged mountain systems in the conservation of evolutionary diversity and endemic species.

  We assessed the phylogeographical pattern of the montane scorpionfly Cerapanorpa obtusa, revealing that alpine refugial isolation may promote divergence in such a cold-adapted species. The findings highlight that the interplay between climate changes and rugged relief may play a significant role in shaping the distinct phylogeographical pattern of cold-adapted montane insects, providing new insights into the importance of topographically rugged mountain systems in the conservation of evolutionary diversity and endemic species.
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  Inconsistent geographical patterns of phylogenetic relatedness among different plant growth forms: A case study in woody and herbaceous angiosperms of China

  Yang‐Yang Liu, Hong Qian, Ya‐Dong Zhou

  J Syst Evol. 2025, 63(3): 767-777.
  https://doi.org/10.1111/jse.13157

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  Plants exhibiting different growth forms possess different capabilities in adapting to their respective environments, consequently displaying distinct geographical patterns of phylogenetic relatedness across a broad environmental gradient. Here, we compare the geographical patterns of phylogenetic relatedness between woody and herbaceous angiosperms in China, based on three phylogenetic relatedness metrics, namely, the standardized effect sizes of phylogenetic diversity (PD_ses), mean pairwise distance (MPD_ses), and mean nearest taxon distance (MNTD_ses). Additionally, we explore the effects of three categories of environmental variables (current climate, historical climate change, and environmental heterogeneity) on the geographical patterns of phylogenetic relatedness of both plant groups. Our results indicate that the geographical patterns of phylogenetic relatedness of herbaceous and woody plants are inconsistent, and the deviations of phylogenetic relatedness between woody and herbaceous angiosperms have geographical patterns and vary along environmental gradients. Our study found that environmental variables have a greater influence on the phylogenetic relatedness of herbaceous plants than on that of woody plants, emphasizing that environmental variables, especially current climatic variables, are the primary drivers of the deviations of phylogenetic relatedness between woody and herbaceous angiosperms. In summary, we illustrate the distinct differences in phylogenetic relatedness among plants of different growth forms, providing valuable insights into the driving factors of species coexistence at various spatial scales.

  Plants exhibiting different life forms possess different capabilities in adapting to their respective environments, consequently displaying distinct geographical patterns of phylogenetic relatedness across a broad environmental gradient. Here, we compare the geographical patterns of phylogenetic relatedness between woody and herbaceous angiosperms in China, based on three phylogenetic relatedness metrics, that is, the standardized effect sizes of phylogenetic diversity (PD_ses), mean pairwise distance (MPD_ses), and mean nearest taxon distance (MNTD_ses). Additionally, we explore the effects of three categories of environmental variables (current climate, historical climate change, and environmental heterogeneity) on the geographical patterns of phylogenetic relatedness of both plant groups. Our results indicate that the geographical patterns of phylogenetic relatedness of herbaceous and woody plants are inconsistent, and the deviations of phylogenetic relatedness between woody and herbaceous angiosperms have geographical patterns, and vary along environmental gradients. Our study found that environmental variables have a greater influence on the phylogenetic relatedness of herbaceous plants than on that of woody plants, emphasizing that environmental variables, especially current climatic variables, are the primary drivers of the deviations of phylogenetic relatedness between woody and herbaceous angiosperms. In summary, we illustrate the distinct differences in phylogenetic relatedness among plants of different life forms, providing valuable insights into the driving factors of species coexistence at various spatial scales.