Table of Contents

01 November 2025, Volume 63 Issue 6
Cover illustration: The genus Oxera (Lamiaceae) is known for its showy ornamental flowers. Oxera species show remarkable morphological corolla diversity and are thought to be pollinated by insects (especially moths and butterflies), birds (especially Meliphagidae) and mammals (bats and flying foxes) depending on the clades and subclades they belong to. Gâteblé et al. (pp. 1299–1311) hypothesized that two New Caledonian sympatric sister species, Oxera palmatinervia and O. sympatrica [Detail] ...
  
    Commentary
  • Hao Li, Qiong Zhao, Tian Wu, Xin-Yi Liao, Yu-Han Fang
    J Syst Evol. 2025, 63(6): 1293-1298.
    https://doi.org/10.1111/jse.70033
    A recent 123-genome bryophyte super-pangenome reshapes our understanding of plant systematics and gene-family innovation. This commentary examines its key findings of expanded gene-family space, new genes and horizontal transfers, refined signals of whole-genome duplications, and the lineage-balanced, genome-wide approach behind them, with implications for early terrestrial adaptation and cellular novelties.
  • Research Article
  • Gildas Gâteblé, Ryusuke Ikeda, Giliane Karnadi-Abdelkader, Jacqueline Ounémoa, Yoshihisa Suyama, Yuji Isagi
    J Syst Evol. 2025, 63(6): 1299-1311.
    https://doi.org/10.1111/jse.70011
    While conducting a population genetic study aiming at refining previous conclusions about cladogenesis in the Oxera genus (Lamiaceae) in New Caledonia, we uncovered an unexpected result for the well-known Oxera palmatinervia Dubard species. To better understand the preliminary molecular results that revealed two distinct sister species, we performed extensive field studies in order to sample, measure, hand-pollinate, and observe the flower and fruit visitors on different populations of O. palmatinervia and other species of the “robusta” clade. We found flower morphology differences to be congruent with the molecular results, so that we propose to describe a new species as O. sympatrica Gâteblé & Karnadi sp. nov. The differences in flower morphology between the two species, which can grow in true sympatry and flower at the same time of the year, are striking so that flower visitors and pollination syndromes were investigated as far as possible. We find that two species of honeyeaters Glycifohia undulata and Philemon diemenensis are likely the preferred pollinators, respectively, of O. palmatinervia and O. sympatrica sp. nov. because of their respective sizes, bill and tongue lengths, and behavior. Even though, to date, it cannot be proven that initial speciation of both Oxera occurred in sympatry, today's sympatry is observed along with a remarkable supposed coevolution pollination syndrome. The new species is fully described, mapped, evaluated against Red List criteria, and illustrated. Pollination syndromes are discussed and illustrated.
    Investigating the morphology and ecology of two sympatric species of the Oxera (Lamiaceae) genus in New Caledonia and their respective putative pollinators showed that two species of honeyeaters are likely the preferred pollinators because of their respective sizes, bill and tongue lengths, and behavior.
  • Ying Wang, Xiuxiu Zhu, Kaibin Wang, Jiayue Zhou, Zechen Tang, Siying Fu, Chenguang Zheng, Wenjun Bu
    J Syst Evol. 2025, 63(6): 1312-1326.
    https://doi.org/10.1111/jse.13197
    East Asia has been hypothesized to be separated into distinct northern and southern regions by a climatic barrier, which is an east–west-oriented arid zone at approximately 40° N in eastern China. However, the impacts of climate change and local environmental selection on widespread species in this area are still poorly understood. In this study, we generated extensive genomic data for the crop pest Aelia fieberi (Hemiptera: Pentatomidae), which was sampled across its entire distribution in China, and we used these data in combination with niche analyses to investigate its phylogeographic pattern and examine the impact of climate change on its population structure and demographic history. We found that A. fieberi comprised two genetic lineages (southern and northern) that diverged during the middle Pleistocene, leading to a distinct “south–north” genetic pattern; this divergence was probably triggered by Pleistocene climate change in the arid belt. The two lineages of A. fieberi both experienced population expansion after the Last Interglacial (LIG) until the Last Glacial Maximum (LGM) and experienced secondary contact in the late Pleistocene. Local environmental adaptation may play an important role in maintaining and/or reinforcing the south–north divergence. Our study provides a detailed example of how climatic barriers and local environmental selection collaborate to facilitate adaptation to heterogeneous landscapes in East Asia from a phylogeographic perspective.
    Integrating mitochondrial fragments, nuclear SNPs, whole genome data sets, and geographic distribution elucidated the phylogeographical pattern of Aelia fieberi. Population structure analyses revealed that A. fieberi comprises distinct southern and northern genetic lineages, possibly related to middle Pleistocene climate change in the arid belt and maintained by local environmental adaptation.
  • Long-Fei Fu, Chi Xiong, Jian He, Feng Chen, Zi-Bing Xin, Fang Wen, Xin-Yun Lv, Yi-Gang Wei, Alexandre K. Monro
    J Syst Evol. 2025, 63(6): 1327-1343.
    https://doi.org/10.1111/jse.13199
    Apomixis can confer fertility upon spontaneous hybrids and allopolyploids, both of which have played a pivotal role in the evolutionary trajectory and diversification of flowering plants. We hypothesized that an unusual morphotype of Elatostema represents a viable hybrid species between E. scabrum and E. hirticaule, as opposed to a sterile F1 hybrid. To test this, we employed phylogenomic, flow cytometry (FC), cytological, and morphological analyses. A two-step phylogenomic approach was used. Genome skimming was performed on one E. longpingii population, three populations of each parent (E. scabrum, E. hirticaule), and ten Elatostema and one Pilea species. Population genetic analyses were then conducted using RAD sequencing data from the type population of hybrid and parent species. Phylogenomic analyses using genome skimming and RAD sequencing data consistently supported a hybrid origin, placing E. longpingii close to or nested within E. scabrum and distant from E. hirticaule. Chromosome counts revealed pentaploid, triploid, and tetraploid ploidy levels in E. longpingii, E. scabrum, and E. hirticaule, respectively. FC suggested apomixis in E. longpingii and E. scabrum, while E. hirticaule exhibited sexual reproduction. Morphological studies indicated that E. longpingii shares traits from both parents. Our findings demonstrate a novel reproductively viable hybrid species in Elatostema, likely originated through a natural hybridization event involving heteroploidy, coupled with the inheritance of an apomictic reproductive pathway from its maternal parent. These results provide compelling evidence that hybridization and apomixis have played pivotal roles in driving reticulate evolution and promoting diversification within the Elatostema.
    Elatostema longpingii, hypothesized to be a heteroploid hybrid between E. scabrum and E. hirticaule, was investigated using phylogenomic, flow cytometric, cytological, and morphological analyses. Results confirmed its hybrid origin, with E. longpingii inheriting apomixis from its maternal parent, E. scabrum. This provides a case how hybridization and apomixis contribute to diversification in Elatostema.
  • Jia-Rui Yu, Si-Ao Li, Dong-Xue Zhao, Francis M. Martin, Hai-Sheng Yuan
    J Syst Evol. 2025, 63(6): 1344-1357.
    https://doi.org/10.1111/jse.70006
    Ectomycorrhizal (ECM) fungi form symbiotic relationships with woody plants, completing their life cyclesthrough mutualistic associations. The evolution of this symbiosis involves genomic adaptations including gene gain andloss. However, how these genomic characteristics reflect speciation and adaptation throughout the evolutionaryhistory of ECM fungi remains unclear. In the present study, we explored speciation and host adaptation in Tricholoma species, an ecologically relevant clade of ECM basidiomycetes. We compared the genomes of three species, Tricholoma matsutakeT. populinum, and T. bakamatsutake, which despite their close phylogenetic relationships, have different tree hosts. A phylogenetic tree constructed using single‐copy orthologous genes estimated the divergence time of T. populinum to be approximately 28.48 Mya, coinciding with the diversification of subg. Eupopulus in East Asia. The split between T. matsutake and T. bakamatsutake was estimated at around 8.08 Mya, corresponding to the diversification period of evergreen broadleaved forests in East Asia. In this study, we identified 19, 13, and 13 positively selected genes in the genomes of T. bakamatsutake, T. matsutake, and T. populinum, respectively. Additionally, 2983, 2783, and 1548 genes have undergone rapid evolution in their genomes. Gene ontology enrichment analysis revealed the functions of these rapidly evolving genes, including those associated with cell cycle, cytoplasmic components, and GTPase mediation. Gene flow analysis indicated unidirectional migration from the ancestor of Tpopulinum to Tmatsutake and Tbakamatsutake, whereas bidirectional gene flow was observed in the ancestors of T. matsutake and T. bakamatsutake. This study suggested that host‐induced immigrant unviability in symbiotic fungi is the primary causeof prezygotic isolation. The combination of ecology‐based genomic evidence and gene flow analysis offers new insightinto the speciation and evolutionary mechanisms of symbiotic fungi.
    Comparative genomics of three Tricholoma species with differing host spectra identified genes and gene families related to adaptive evolution and statistical analysis revealed the role of repetitive sequences in adaptive evolution, allowing an exploration of how hosts promote speciation.
  • Ke-Yi Wang, Peng Zhou, Yan-Fang Cui, Yi-Zhen Liu, Wen-Gen Zhang, Bo Pan, Yu-Song Huang, Zhi-You Guo, Zhen-Yu Li, Wei-Tao Jin, Qiang Zhang, Chun-Ce Guo, Xiao-Guo Xiang
    J Syst Evol. 2025, 63(6): 1358-1369.
    https://doi.org/10.1111/jse.70007
    Karst areas are well known for their extreme biodiversity and the investigation of plant adaptation in these unique environments is a research hotspot. Previous studies have primarily focused on the genomic adaptation of karst endemic species, but the specific adaptation of facultative species remains unclear. Hemiboea subcapitata, a traditional medicinal plant growing in both karst and non-karst areas serves as a valuable model for understanding these genomic mechanisms. Here, the H. subcapitata genome was sequenced using the PacBio and Illumina platforms and de novo assembled with a contig N50 value of 21.11 Mb. The assembled genomic size was 763.59 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) quality value was 98.10%, and 92.87% of sequences were anchored to 16 chromosomes. Comparative genome analyses identified three whole-genome duplication (WGD) events: the γ-WGT event (115–130 Ma) shared by all eudicots, WGD2 shared within Lamiales except Oleaceae (67.57 Ma) and the recently independent WGD1 unique to H. subcapitata (16.92 Ma). These three WGD events probably facilitate the expansion of stress-responsive gene families, which in turn influence functional pathway regulation. In particular, genomic and transcriptome analyses identified 25 key genes in the flavonoid pathway and candidate MYB transcription factors related to environmental adaptation. Compared with the karst endemic Primulina tabacum, H. subcapitata showed the upregulation of 25 key flavonoid pathway genes (96% in roots, 92% in leaves, 88% in flowers). This mechanism of expanding ecological niches through metabolic pathway regulation is a unique adaptive strategy of H. subcapitata. This study provides valuable data for further resource utilization and conservation of Hemiboea.
    Analysis of a chromosome-level genome for Hemiboea subcapitata identified three whole-genome duplication events and 25 flavonoid pathway genes cooperating with MYB transcription factors, which might promote unique facultative adaptation to karst and non-karst environments by H. subcapitata.
  • Xin-Yu Lin, Yan Liu, Jing-Fei Zhang, Jia-Xiu Zhong, Shu-Han Duan, Xiang-Ping Li, Hao-Ran Su, Qing-Xin Yang, Xiao-Jun Liu, Qiu-Xia Sun, Chao Liu, Meng-Ge Wang, Guang-Lin He, Yong-Xin Ma
    J Syst Evol. 2025, 63(6): 1370-1389.
    https://doi.org/10.1111/jse.70009
    The genetic structure and population history of ethno-linguistically diverse populations from the Yunnan–Guizhou Plateau remain underrepresented in human genomic research. We analyzed genome-wide data from 239 individuals in Guizhou, combined with modern and ancient datasets, to investigate their fine-scale genetic structure, demographic events, and functional consequences of adaptive genomic signatures. Our findings revealed three genetically distinct groups corresponding to linguistic categories, shaped by differential gene flow from ancient millet farmers and southern Chinese populations. We identified population-specific adaptive candidate genomic regions associated with immune, metabolic, and hematological functions. Additionally, we detected clinically relevant variants with implications for disease risk prediction and precision medicine. These findings underscore the importance of genetic diversity in understanding human adaptation and health disparities, offering a framework for equitable genomic research in underrepresented populations.
    Exploring the genomic diversity of underrepresented Guizhou multi-ethnic populations by analysis of the fine-scale genetic structure and admixture patterns, revealed substructures tied to linguistic categories, adaptive signatures linked to key functions, and clinical-related variants, highlighting the critical role of population-specific genomic diversity in refining precision medicine for tailored therapeutic interventions.
  • Xinkun Kang, Zhixin Wen, Jin Wang, Liang Lu, Alexei Abramov, Wenjuan Shan, Deyan Ge
    J Syst Evol. 2025, 63(6): 1390-1400.
    https://doi.org/10.1111/jse.13200
    The rodent family Platacanthomyidae encompasses both the Malabar spiny tree mouse (genus Platacanthomys) and the soft-furred tree mice (genus Typhlomys). This family represents a typical relict group of ancient origin, and its evolutionary history and dynamics warrant further investigation. A critical scientific question concerns whether the evolutionary trajectory of this ancient taxon has been shaped by environmental perturbations, such as the periodic climatic oscillations of the Quaternary glacial periods. This study aims to elucidate the evolutionary trajectory of the Platacanthomyidae by examining fossil records alongside extant species. Molecular dating revealed that the most speciose genus Typhlomys within this family began diverging approximately 21.15 Ma. The speciation rate and net diversification rate of the Platacanthomyidae was notably high around 20 Ma, but it has shown a continuous decline since then, while the extinction rate of this taxa has remained stable. The current dataset indicates that the evolutionary trajectory of this family appears to have remained unaffected by late Cenozoic climatic fluctuations and subsequent anthropogenic influences associated with societal development. The ancestral distribution reconstruction has not yielded conclusive evidence regarding the origin of this family, thereby positioning it among the most enigmatic taxa within Rodentia. Moreover, the evolutionary mechanisms underlying the divergence of these ancestral species and their subsequent ecological adaptations to paleoenvironmental changes require future studies.
    Elucidating the evolutionary trajectory of the Platacanthomyidae based on fossil occurrences and genomic data of extant species suggested that the evolutionary trajectory of this family has remained unaffected by major climatic oscillation and lead to a hypothesis of its origin in Central Asia.
  • Su-Xin Yin, Chong Dong, Biao Pan, Zhuo Feng, Jian-Guo Hui, Fabiany Herrera, Patrick S. Herendeen, Peter R. Crane, and Gong-Le Shi
    J Syst Evol. 2025, 63(6): 1401-1414.
    https://doi.org/10.1111/jse.70000
    Pinaceae are one of the most economically and ecologically important tree families and play a key role in boreal, temperate, and montane forests of the Northern Hemisphere. The family have a rich fossil record with the earliest occurrence of the Pinaceae crown group probably from the Late Jurassic, and diverse seed cones, woods, leaves, and pollen grains from the Early Cretaceous of the Northern Hemisphere. However, the origin and early evolutionary history of Pinaceae is not well understood, in part because of uncertainty about the phylogenetic position of early fossils. In this article we describe a new woody stem of Pinaceae based on well-preserved material from the Early Cretaceous Huolinhe Formation in Jarud Banner, eastern Inner Mongolia, Northeast China. Piceoxylon jarudense sp. nov. has distinct growth rings with secondary xylem composed of tracheids, ray tracheids, ray parenchyma cells, axial parenchyma cells, and axial and radial resin canals. Pitting on radial walls of tracheids is abietinean; cross-field pitting is piceoid and taxodioid with two to six pits arranged in one to two rows per cross-field. Axial and radial resin canals are lined by thick-walled epithelial cells. Piceoxylon has been considered to include species with wood anatomy comparable to extant Larix, Pseudotsuga, Picea, and Cathaya. Comparisons of wood anatomy and constrained phylogenetic analyses of P. jarudense, one of the earliest records of Piceoxylon, both suggest that P. jarudense is most likely allied with Larix and Pseudotsuga within the pinoid clade suggesting divergence of the Larix–Pseudotsuga clade before ~125.6 Ma.
    Comparisons of wood anatomy and constrained phylogenetic analyses of a woody stem of Piceoxylon jarudense sp. nov. (Pinaceae) from the Early Cretaceous of Northeast China suggest that it is allied with Larix and Pseudotsuga within the pinoid clade and that the Larix-Pseudotsuga clade diverged before ~125.6 Ma.
  • Michael Heads
    J Syst Evol. 2025, 63(6): 1415-1440.
    https://doi.org/10.1111/jse.70002
    The 26 genera of aurantioids and the 28 species of one genus, Citrus, are mapped. The distributions are explained, not by using fossil-calibrated clade ages and ancestral-area algorithms, but by focusing on the geometry of the clade distributions and the tectonic history at the break zones (nodes). Allopatry is attributed to vicariance, while overlap is attributed to normal dispersal. Subfamily Aurantioideae is allopatric with its sister groups in Eurasia and the Americas. In contrast, the seven main clades within Aurantioideae show a high level of overlap. But within each of these seven main clades, there is again a high level of allopatry. The pattern is explained by vicariance events at the first and third levels. The overlap at the second level can be accounted for if vicariance (now obscured) generated the clades and subsequent dispersal caused secondary overlap of the clades. This latter phase of mobilism can be explained by the migration of coastlines and maritime flora far inland during marine transgressions, especially in the mid-Cretaceous. Many aurantioids inhabit mangrove-associated vegetation, beach thicket, limestone substrate, and areas with high levels of disturbance. Within Citrus, the five main clades overlap in South-Central China (Nanling Mountains) and are allopatric elsewhere. The overlap zone has been interpreted as a center of origin, but it is explained here as a break zone, the site of vicariance in a widespread ancestor, where localized, secondary overlap has developed later. The zone coincides with a belt of mid-Cretaceous deformation manifested in voluminous magmatism, subsidence, rifting, back-arc extension, and the opening of the East China Sea.
    Distribution of the Rutaceae subfamily Aurantioideae can be explained through vicariance and secondary range expansion. Citrus originated in situ by vicariance with its allopatric sisters, and the origin of Citrus in southern China is likely to represent a break zone in a widespread ancestor.
  • Francisco Fajardo‐Gutiérrez, Mariasole Calbi, Markus S. Dillenberger, Sebastian Tello, AlfredoFuentes, Nora H. Oleas, Ricardo A. Segovia, Christine E. Edwards, Yohan Pillon, James E.Richardson, Thomas Borsch
    J Syst Evol. 2025, 63(6): 1441-1457.
    https://doi.org/10.1111/jse.70004
    The tribe Cunonieae comprises five genera and 214 species of shrubs and trees currently distributed in the Southern Hemisphere and the tropics, exhibiting an amphi‐Pacific disjunct distribution shared with Araucariaceae, Myrtaceae, Nothofagaceae, Podocarpaceae, and Proteaceae, among others. To address the central question of how historical geological forces have shaped the distribution of plant diversity in the southern hemisphere, we aimed to provide evidence from the biogeographical history of Cunonieae. We generated themost densely sampled phylogenetic trees of Cunonieae available to date, with 121 samples and 81 species, basedon 404 new sequences of plastid and nuclear DNA regions with high hierarchical phylogenetic signal (matK, trnL‐F, rpl16, and internal transcribed spacer (ITS)). We included 184 samples of Rosids to estimate divergence times using fossil calibration points. For biogeographic inference, we employed a time‐stratified model including fossils as tips. Cunonia and Pterophylla were paraphyletic in the ITS tree, and Cunonia was paraphyletic in the plastid tree. Pancheria, Vesselowskya, and Weinmannia were monophyletic, the latter with conflicting nuclear and plastid phylogenies. The crown group Cunonieae was dated at ~56 Ma, and its ancestral areas were Antarctica and Patagonia. Antarctica acted as a bridge between Australia and South America before the consolidation of the Antarctic Ice Sheet and the extinction of the lineage in Antarctica from the Oligocene to the Miocene. Following that, Cunonieae spread to lower latitudes via Zealandia/Oceania and Patagonia/South America. Geological changes during the Pliocene facilitated a further burst in diversification along the Andes, in Madagascar, and in New Caledonia, where at least three colonization events occurred.
    Fossil calibration reveals recent radiations and biogeographical history of the Cunonieae tribe. The most densely sampled phylogeny indicated Antarctica and Patagonia as areas of origin, confirming the reestablishment of Pterophylla and revealing the northward movement of Weinmannia into the tropical Andes. Conflicting plastid and nuclear phylogenies suggest past chloroplast capture.
  • Paranchai Malailkanok, Friðgeir Grímsson, Reinhard Zetter, Paul J. Grote, Thomas Denk, Wongkot Phuphumirat
    J Syst Evol. 2025, 63(6): 1458-1480.
    https://doi.org/10.1111/jse.70010
    Fossil Ericales pollen from late Oligocene to Early Miocene sediments of the Ban Pa Kha Subbasin, Li Basin, northern Thailand, were examined using the single-grain method. A total of 24 different ericalean pollen types belonging to Ebenaceae (Diospyros), Ericaceae (Cassiope, Vaccinium, and Rhododendron), Pentaphylacaceae (Adinandra), Sapotaceae, Styracaceae (Rehderodendron and Styrax), and Symplocaceae (Symplocos) were identified. All the fossil pollen, except that of Sapotaceae, represent families/genera that are described for the first time from the Cenozoic of Thailand. By considering present terrestrial biome occupancy, Köppen–Geiger climate profiles, and vertical distributions of potential modern analogs of the parent plants producing the fossil pollen, the phytosociological and paleoecological preferences of the fossil taxa were assessed. Our results demonstrate that modern analogs of most of the ericalean taxa have wide ecological and climatic amplitudes with a broad zone of convergence in warm and cold temperate humid or seasonally dry climates. Exceptions are Sapotaceae, which rarely occur outside lowland tropical forests, and Cassiope, which at present occurs at high elevations and, besides Rehderodendron, is one of two modern analogs absent from the modern flora of Thailand. Along with a review of phytosociological studies in montane forests of northern Thailand and neighboring regions, this suggests that the assemblage of dispersed ericalean pollen of the Ban Pa Kha Subbasin likely derives from more than one vegetation type and possibly from different vertical zones.
    Ericalean pollen was recovered from the Ban Pa Kha Subbasin, Li Basin, northern Thailand. Based on the ecological preferences of their modern analogs, the assemblage of dispersed ericalean pollen likely derives from more than one vegetation type and possibly from different vertical zones of mountainous areas.
  • Jianyu Chen, Yunshan Yang, Bo Liu, Weihang Wang, Daochuan Zhang, Ming Bai, Xinjiang Li
    J Syst Evol. 2025, 63(6): 1481-1500.
    https://doi.org/10.1111/jse.13196
    Grylloblattids are an ancient insect lineage crucial for understanding insect evolution and phylogeny. Systematic and in-depth studies of this taxon are still needed. This investigation advances grylloblattid systematics through three principal contributions: taxonomic revision of extant Grylloblattidae with redesigned diagnostic keys; description of a new species Grylloblattella aletaiensis sp. nov.; and geometric morphometrics analyses to quantify interspecific differentiation in the first tergum morphology across all genera of extant Grylloblattidae. We further sequenced and assembled the first complete mitochondrial genome (16 625 bp) from an Asian-lineage grylloblattid, revealing conserved gene arrangement and structural conservation shared with polyneopteran lineages. Phylogenetic delineation of basal lineages within Grylloblattidae was conducted using concatenated mitochondrial and nuclear loci, coupled with divergence time estimation analyses to reconstruct historical biogeographic dynamics. This multidisciplinary operational framework synthesizes molecular phylogenetics and temporal biogeography, establishing a robust empirical foundation for interdisciplinary research in paleoentomology, evolutionary developmental biology, and evidence-based conservation prioritization for relict insect lineages. The evolutionary history of grylloblattids is closely coupled with global geo-climate changes since the Mesozoic Era, serving as a model system for investigating the macroevolution of insects.
    Review of the extant Grylloblattidae species and description of a new species, Grylloblattella aletaiensis sp. nov., with the biology of Grylloblattella, along with geometric morphometrics and phylogenetic analysis clarified the genetic relationships among the genera of extant Grylloblattidae.
  • Jairo Arroyave, Adán Fernando Mar-Silva, Bruno F. Melo, Sonia Gabriela Hernández-Ávila, Jesús M. López-Vila, Gabriel S. C. Silva, Píndaro Díaz-Jáimes
    J Syst Evol. 2025, 63(6): 1501-1518.
    https://doi.org/10.1111/jse.70003
    Neotropical catfishes of the genus Rhamdia are divided into cis- and trans-Andean/Middle American reciprocally monophyletic components, the latter notable for its considerable cave-dwelling diversity. Despite previous research, uncertainties regarding the systematics and historical biogeography of the Middle American clade remain. To test previous phylogenetic hypotheses and improve our understanding of the evolutionary history of this group of Middle American freshwater fishes, we generated and analyzed comparative mitogenome-wide data from most valid species and known cave-dwelling forms. Our results corroborate this clade as divided into two reciprocally monophyletic groups (split dated at ~9 Ma): a clade representing the species Rhamdia guatemalensis (crown group dated at ~2.8 Ma) and a clade consisting of the remaining Middle American species (i.e., the Rhamdia laticauda species group; crown group dated at ~4 Ma). Our results also confirm the notion that R. laticauda is deeply paraphyletic and that phylogenetically scattered geographic lineages of this taxon could represent different species. Our divergence time estimates, coupled with present-day distribution patterns, support the biogeographic scenario in which northward dispersal and colonization of Central America and southern North America by Rhamdia was catalyzed by the emergence of the Panamanian Isthmus land bridge and stream captures across Lower Central America. Cave colonization in Middle American Rhamdia is widespread, convergent, relatively recent (dating from the Pleistocene), and most likely opportunistic, with established cave-dwelling populations possibly representing “evolutionary dead ends.”
    Investigating the systematics and biogeography of Neotropical catfishes of the genus Rhamdia refined phylogenetic hypotheses, including deep paraphyly of Rhamdia laticauda, supported northward dispersal catalyzed by emergence of the Panamanian Isthmus and imply that cave colonization is widespread, convergent, and recent, with established cave-dwelling populations possibly representing “evolutionary dead ends”.
  • Xin Yao, Zhi-Rong Zhang, Jun-Bo Yang, Richard T. Corlett, De-Zhu Li, Wen-Bin Yu
    J Syst Evol. 2025, 63(6): 1519-1535.
    https://doi.org/10.1111/jse.70014
    Investigating the evolutionary history and species diversification patterns in hyperdiverse lineages is essential for understanding how species diversity accumulates and how floras assemble historically across diverse regions. A large angiosperm family, Apocynaceae, exhibited remarkable diversity in functional traits including growth form, fruit types, and pollen aggregation, which may have a substantial impact on species diversification rates. However, the lack of a robust and well dated phylogeny has hindered our understanding of Apocynaceae diversification. To address this gap, we reconstructed a robust phylogeny covering 22 of 25 tribes using plastome sequences, then employed this framework to estimate divergence times, analyze diversification patterns, and investigate associations between species diversification and functional traits. The plastome phylogenies received strong nodal support across most branches. Among higher taxonomic groupings, three subfamilies (Asclepiadoideae, Secamonoideae, and Periplocoideae) were monophyletic. At the tribal levels, 19 tribes were strongly supported as monophyletic except Melodineae, Willughbeieae, and Vinceae. Additionally, five genera (Vincetoxicum, Cynanchum, Hoya, Marsdenia, and Aganosma) were identified as nonmonophyletic. Our analyses revealed that Apocynaceae originated in the paleotropics during the middle Late Cretaceous. Integrating binary state speciation and extinction (BiSSE), hidden state speciation and extinction (HiSSE), and fast, intuitive state-dependent speciation-extinction (FiSSE) analyses, we found that species with pollinia had a higher speciation rate than those without. Dry-fruited species had a higher speciation rate than those with fleshy fruits. Furthermore, Bayesian analysis of macro-evolutionary mixtures (BAMM) detected a diversification rate increase coinciding with the evolution of pollinia with clip-type attachment mechanisms in the subfamily Asclepiadoideae. Herbs had the highest speciation rate, followed by climbers and self-supporting species. Our findings contribute to understanding the historical assembly of floras in tropical and subtropical Asia.
    Our results showed the Apocynaceae originated in the middle Late Cretaceous in the paleotropics. We found that changes in speciation rate are associated with changes in growth form, fruit type, and pollen aggregation. We further detected a diversification rate shift to increase at the node in which pollinia with clip-type attachment started to evolve in BAMM.
  • Shabir A. Rather, Sajjad Asaf, Amish Kumar, Hongmei Liu, Harald Schneider
    J Syst Evol. 2025, 63(6): 1536-1559.
    https://doi.org/10.1111/jse.70015
    The generic delimitation of the Caesalpinia group continues to be under contention, similar to several other lineages of the hyper diverse legume family. Despite its known ecological and economic importance and role as a model to explore correlations between ecological diversification and genomic traits, both intergeneric and infrageneric relationships remain unresolved, despite recent phylogenetic analyses. While phylogenomic approaches have elucidated complex relationships within the angiosperm tree of life, the phylogenetic backbone of the Caesalpinia group remains poorly defined owing to limited genomic data. To address this gap, this study combined de novo assembled and characterized plastomes from 19 samples across nine genera, along with 27 previously published plastomes, to achieve a comprehensive dataset of 46 plastomes representing 16 of the 26 genera. The phylogenomic analysis generated a robust phylogenetic hypothesis, distinguishing two main clades, of which one occurs exclusively in the Neotropics in contrast to the other Pantropical clade, in addition to resolving several previously ambiguous relationships. Notable changes in the plastome gene content were observed, including six gene losses (psbL, rpl22, rps2, rpl32, ycf1, ycf2) and six gene duplications (ndhB, rpl23, rps7, rps12, ycf1, ycf2). Other changes included shifts in inverted repeat (IR) boundaries and genome rearrangements, indicating lineage-specific plastome evolution. Hypervariable regions were identified as potential mini-barcodes, with cpSSRs providing valuable resources for species delimitation and population genetics studies. Codon usage revealed a strong AT bias, while relaxed purifying selection in genes such as accD, clpP, and rps16. These findings offer novel insights into Caesalpinia group evolution, emphasizing the utility of plastome data for resolving complex evolutionary questions and establishing a genomic toolkit for future research in systematics, conservation, and evolutionary biology of legumes.
    Studying plastome evolution within the Caesalpinia group revealed key genomic features and their variations across species. It visualized the chloroplast genome structure, illustrating gene duplications, losses, and rearrangements, providing insights that deepened our understanding of the Caesalpinia group's diversity and have significant implications for systematics, conservation, and population genetics.
  • Xiao-Xu Pang, Da-Yong Zhang
    J Syst Evol. 2025, 63(6): 1560-1576.
    https://doi.org/10.1111/jse.70013
    Population genetic clustering methods are widely used to detect hybridization events between closely related populations within species, as well as between deeply diverged lineages across phylogenetic time scales. Their strengths and limitations in the latter cases, however, remain poorly explored. This study presents a systematic evaluation of the performance of the most popular population clustering method, STRUCTURE, under a variety of cross-species hybridization scenarios, including hybrid speciation, as well as introgression involving ghost (i.e., extinct or unsampled) lineages or otherwise. Our simulations demonstrate that STRUCTURE performs well in identifying hybrids and their parental donors when admixture happens very recently between sampled extant lineages, but generally fails to detect signals of admixture when hybridization occurs in deep time or when gene flow stems from ghost lineages. We find that symmetrical parental contribution in cases of hybrid speciation will often be revealed as extremely asymmetrical in STRUCTURE, especially when the admixture event occurred a long time ago. Our results suggest that population genetic clustering methods may be inefficient for detecting ancient or ghost admixtures, which may partly explain why ghost introgression has escaped the attention of evolutionary biologists until recently.
    Simulations provide a systematic evaluation of STRUCTURE in cross-species hybridization scenarios, showing that STRUCTURE performs well in identifying hybrids and their parental donors only when admixture happens very recently, but generally fails to detect hybridization when admixture occurs in deep time or when gene flow stems from ghost lineages.