Journal of Systematics and Evolution

Although Cinnamomum includes globally important spice and medicinal plants, genome-scale knowledge of Cinnamomum species native to Japan remains limited. The Nansei Islands are an approximately 1,200-km-long archipelago located between the Pacific Ocean and the East China Sea and represent a key biogeographic region shaped by deep-sea barriers such as the Tokara and Kerama Gaps. Here, we integrated chloroplast and nuclear genome data generated in this study with public datasets to examine the phylogenetic relationships of four Cinnamomum species native to the Nansei Islands and ten related species. Chloroplast genomes showed no major structural differences among the four island species, whereas nuclear genome data resolved two distinct evolutionary lineages in the Nansei Islands: C. yabunikkei, C. x durifruticeticola, and C. daphnoides formed a distinct Nansei Islands lineage separate from Sri Lankan, Indonesian, and Taiwanese lineages, whereas C. sieboldii was placed in a Taiwanese lineage. Ancestry estimation indicated that C. x durifruticeticola and C. daphnoides share a common ancestral component, while C. sieboldii exhibited a single homogeneous ancestral component, suggesting reduced ancestral diversity after divergence from a Taiwanese lineage. These findings reveal previously unrecognized genomic differentiation among Japanese Cinnamomum species and suggest that deep-sea barriers, dispersal, and long-term isolation shaped their diversification.

Speciation can be a slow process for long-lived organisms with large populations due to persistent incomplete lineage sorting, while hybridisation can further obscure species boundaries through admixture. In eucalypts, there is tremendous morphological and environmental variation with almost a thousand described species, subspecies, and hybrid taxa falling into multiple subgenera and intermediate sections. Multilocus molecular studies have generated concatenated species trees supporting deeper divergence between the Corymbia + Blakella + Angophora clade with the rest of eucalypts. However, the proportion of gene trees that recover the concatenated tree topology, including the taxonomic relationships among individual subgenera and sections, remains underappreciated. In this study, we assessed the predictive power of current eucalypt taxonomy - represented as a concatenated tree - in explaining topological variation across gene trees. To do this, we first extracted 1,187 BUSCO loci from short-read data of 701 samples representing roughly 500 described species using CAPTUS. We then inferred individual gene trees and a concatenated species tree using IQ-TREE2. Finally, we calculated the concordance factors for every described subgenus and section on the concatenated tree, and developed a taxonomic consistency test that tracks the taxonomic placement of each sample across gene trees. We show that, even though most taxonomic groups are monophyletic on the concatenated tree with 100% bootstrap support, several groups exhibit very low concordance, indicating that most gene trees do not recover their relationships as represented by the concatenated tree. These results highlight important considerations for current eucalypt taxonomic classification and provide a phylogenomic inference pipeline that can be applied not only to future eucalypt studies, but also to other evolutionarily complex groups of taxa.

The Asparagaceae is an economically and ecologically important angiosperm (monocot) clade, containing iconic garden plants such as asparagus, hyacinth and agave, and arid-adapted keystone species like Joshua tree and dragon blood tree. The approximately 2,500 species in the family are spread across seven subfamilies: Agavoideae, Aphyllanthoideae, Asparagoideae, Brodiaeoideae, Lomandroideae, Nolinoideae and Scilloideae. Relationships among the seven subfamilies are generally unresolved and the sources of gene tree-species tree discordance are largely unknown. Investigating the biology underlying such discordance requires a robust sampling of both taxa and molecular markers, due to the extremely short branches that form the backbone of the Asparagaceae phylogeny. Using targeted sequencing of 1,726 low-copy nuclear genes, and a nearly complete sampling of genera, we interrogate relationships among all seven Asparagaceae subfamilies and investigate the underlying sources of discordance across the phylogeny. Analyses using different phylogenomic approaches (multispecies coalescence vs. nuclear gene supermatrix vs. chloroplast gene supermatrix) each revealed extensive discordance across the Asparagaceae backbone, which may be associated with rapid lineage diversifications that occurred in Africa shortly following the origin of the family ~49 Ma. Specifically, we found that two branches, representing ancestors of Aphyllanthoideae and Nolinoideae, may be responsible for much of the backbone discordance. The placement of Aphyllanthoideae, represented by one extant taxon (Aphyllanthes monspeliensis), is controversial with discordant topologies across many studies. However, multispecies coalescence-based analyses from this study strongly support a sister relationship between Aphyllanthoideae and a larger Agavoideae + Scilloideae + Brodiaeoideae clade. According to gene tree quartet frequencies and ABBA-BABA tests, we cannot reject incomplete lineage sorting (ILS) as the main source of discordance for the placement of Aphyllanthoideae; our results leave open the possibility of an ancient reticulation involving an ancestor of Aphyllanthoideae and an extinct basal Asparagaceae lineage. Regarding Nolinoideae, we found that conflicting support for two possible bifurcating clades (Asparagoideae + Nolinoideae vs. Asparagoideae + Lomandroideae) was associated with skewed support for alternative gene tree topologies, suggesting that phenomena other than ILS may explain the observed discordance. A quartet-based ABBA-BABA analysis, used to test for signatures of introgression, revealed a putative ancient hybridization event between two divergent, ancestral lineages which may have contributed to the origin of the Nolinoideae clade in Africa ~45 Ma. In sum, this study elucidates the long-troublesome backbone of the Asparagaceae phylogeny and advances our understanding of the evolutionary and biogeographical origins of all extant subfamilies. More broadly, this study expands our understanding of the various sources of gene tree discordance that may arise from natural processes associated with rapid lineage radiations across the tree of life.

Asian Passifloraceae occupy a distinctive evolutionary and ecological position within the family despite their relatively low species diversity compared with the Neotropics. Many Asian representatives are highly localized, small and often ephemeral climbers that persist seasonally through rhizomes, tuberous stems or dormant seeds, while considerable morphological plasticity may obscure species limits and evolutionary relationships. Xishuangbanna, southwestern China, lies at the convergence of Southeast Asian, Indian-Himalayan and southern Chinese floristic elements and represents an important regional centre of Passifloraceae diversity, with two species of Adenia and five species of Passiflora, including the recently described P. xishuangbannaensis and P. menghaiensis. We investigate the evolutionary relationships, plastome evolution and population genomics of these taxa using complete plastome assemblies, a concatenated dataset of 68 selected plastid protein-coding genes, 356 reconstructed nuclear Coding Sequences (CDS), and Genotyping-By-Sequencing (GBS) across the known wild distribution of P. xishuangbannaensis. Plastid, concatenated nuclear and nuclear coalescent phylogenies were strongly incongruent and differed from published classifications based on morphology and earlier phylogenies (ITS, ncpGS, ctyGS, ndhF and trnL-F). Gene-tree discordance and phylogenetic-network inference indicated widespread incomplete lineage sorting together with introgression. The two statistically best-supported network models placed P. menghaiensis, which showed high genetic similarity to the Indian P. napalensis, as a sister lineage involved in independent reticulation events associated with P. altebilobata, P. xishuangbannaensis and P. sumatrana. A pronounced biogeographic pattern was evident within Passiflora supersection Disemma, particularly in the P. siamica-P. cochinchinensis lineage across the Hua Line, whereas relationships among other Asian Passiflora blurred this boundary. This pattern suggests that diversification and reticulation within the Asian lineage may have overlapped temporally with the development of the biogeographic divide represented by the Hua Line. The concentration of early-diverging lineages around Xishuangbanna and the eastern Himalayan-Indian region further points to this area as an important centre in the early diversification of Asian Passiflora. Within this context, the highly localized P. xishuangbannaensis may represent either a relictual of an early Asian lineage or the surviving product of an ancient reticulate complex, contrasting with lineages such as P. siamica that subsequently expanded farther across Southeast Asia. Comparative plastome analyses revealed extensive structural and gene-content evolution within subgenus Decaloba, including pseudogenization, gene and intron losses, and repeated Inverted-Repeat (IR) expansions and contractions; substantial plastome modification also characterized supersection Disemma. Passiflora sumatrana exhibited a particularly distinctive IR expansion extending into the accD-pafII region, potentially characterizing this lineage. Adenia plastomes were generally more structurally conservative, although A. penangiana displayed an IR-boundary contraction involving the rps19-rpl2 region. Mitochondrial CDS and non-coding regions provided the best-resolved phylogenetic signal and revealed strong discordance with the chloroplast phylogeny, consistent with maternal mitochondrial inheritance and variable plastid transmission, potentially involving paternal or biparental inheritance and heteroplasmy. GBS analyses of P. xishuangbannaensis using complementary distant-reference, de novo and closely related-reference approaches showed that mapping to P. organensis provided the clearest SNP distribution and population resolution. ADMIXTURE, PCA and FST analyses revealed two strongly geographically structured populations with additional substructure and substantial differentiation (FST = 0.112). Linkage disequilibrium based demographic reconstruction using GONE2 indicated declining effective population size (Ne) toward the present in both populations, with a particularly abrupt recent decline in Pop1 and a more gradual decline in Pop2. Few candidate Self-Incompatibility (SI) genes could be confidently reconstructed, including limited recovery of highly variable docking regions. However, the intracellular region of an S-locus Receptor Kinases (SRK) contained a distinctive non-synonymous substitution predicted to alter protein configuration without major disruption of overall folding, potentially contributing to compatibility differences between populations. Together, these results reveal a complex evolutionary history combining historical dispersal, incomplete lineage sorting, reticulation, morphological plasticity, plastome structural evolution and strong population differentiation. The narrow distributions and recent demographic decline of these newly recognized Xishuangbanna taxa emphasize their conservation importance, while broader Asian taxon sampling and deeper genomic sequencing will be essential to resolve the evolutionary history of this discreet and poorly known Passifloraceae radiation.

The palaeogeographic history of the Neotropics has inspired multiple diversification models, emphasizing either the Andes or Amazonia as primary drivers of biodiversity. However, the extensive Pebas wetland system that covered western Amazonia during the Miocene has gained attention as a potential barrier to dispersal and diversification. This system may have contributed to the modern diversity imbalance between the Andes and Amazonia, known as the Gentry pattern. Most evidence for this hypothesis comes from isolated case studies and fossils. Here, we conduct a meta-analysis including 1,361 species of Neotropical butterflies to evaluate the role of the Pebas wetland on the dynamics of dispersal and diversification. We found that Andean- and Amazonian-centred clades show complementary but temporarily distinct biogeographic patterns. High Andean diversity reflects an Andean origin, with early occupancy and diversification occurring within the Andes, followed by post-Pebas dispersal into Amazonia. By contrast, Amazonian-centred clades, reflect an Amazonian origin, with an early diversification in Amazonia and subsequent post-Pebas colonization of the Andes. While several clades show little evidence of Pebas influence, our study suggests that the Pebas wetland did not uniformly restrict diversification, but rather selectively constrained dispersal between the Andes and Amazonia, preventing simultaneous diversification in both regions and thereby creating a diversity imbalance that characterizes the modern Neotropic.

Myricaria Desv. (Tamaricaceae) is a genus of shrubs that play a keystone role in montane riparian ecosystems across Eurasia, shaping riverine habitats and supporting ecological function. The genus has a centre of origin in the Qinghai-Tibetan Plateau and exhibits a broad distribution, but many species boundaries are unresolved. Here, we present the first phylogenomic analysis of Myricaria using the Angiosperms353 target enrichment bait set, with sampling across its full geographic range. Off-target plastid loci were extracted from next-generation sequencing data using the CAPTUS bioinformatics pipeline. We infer species relationships using ASTRAL-IV and network analysis with SplitsTree, in conjunction with morphology. We also provide a taxonomic treatment of the genus, integrating our morphological observations and phylogenomic analyses for species delimitations. Based on our analyses, recognise two infrageneric sections: sect. Parallelantherae (containing only M. elegans) and sect. Myricaria (the remainder of the genus, with type species M. germanica). We also propose synonymising M. davurica, M. bracteata and M. squamosa with M. germanica. Although species boundaries in the Asian highlands remain unresolved, we conclude that the species M. elegans, M. germanica, M. laxiflora, M. longifolia, M. platyphylla, and M. pulcherrima are well-supported both phylogenomically and morphologically.

Rapid diversification can generate regional biodiversity through ancestral polymorphism, admixture, and ecological differentiation, while leaving complex genomic signals. We analysed whole-genome variation in 325 butterflies, including 166 individuals of the Papilio bianor species complex and six outgroup species, to reconstruct lineage relationships and demographic history. Nuclear genomic analyses recovered three major clades corresponding to the recognized species and placed the island lineage as sister to continental P. bianor. Analyses of 18,635 autosomal window trees revealed extensive genealogical discordance, with incomplete lineage sorting predominating among continental lineages and the strongest introgression signals involving island related ancestry. Demographic modelling supported early island continental divergence followed by continental diversification and ancient admixture. The best fitting fastsimcoal2 model inferred an admixed origin of the Eastern China lineage, while BPP analyses supported ancient island-related introgression into the Eastern China ancestor, Western Himalaya and southwestern Thailand. Peripheral populations exhibited pronounced genetic differentiation and distinct demographic histories; Western Himalaya additionally showed mitochondrial affinity with Yaeyama despite its placement within the Himalayan nuclear lineage. Together, these findings suggest that introgression among deeply differentiated ancestral populations and incomplete lineage sorting during rapid divergence jointly shaped lineage diversity in the P. bianor complex. This study provides an empirical framework for investigating how lineage diversity emerges rapidly during the early stages of speciation, particularly in groups with deep ancestral population structure.

Telomeres have the crucial role of protecting chromosome ends and its length varies significantly between organisms. What evolutionary factor shapes this natural variation has been a long standing question, with answers providing insights into chromosome function and evolution. In animals life-history variation relating to senescence or tumorigenesis explains telomere length variation. For plants, however, we lack knowledge of what factor is driving their length variation in nature. Is life-history differences also driving telomere length variation among plant species? We answer this question by analyzing the telomeres of 257 plant species spanning the major orders of the green plant kingdom. Telomere lengths were estimated for species that vary significantly in their life-history, geographical distribution, and trait characters. Results showed telomere length increased with the evolution of terrestrialization, where Chlorophytes had the shortest telomeres and Spermatophytes had the longest telomeres. Surprisingly, plants with different life-histories had minimal telomere length differences, but biogeographic clines had significant effect on telomere length variation. Plant telomere length increases closer to the equator, while telomere length decreases at higher altitude. Domestication was previously proposed to lengthen telomeres, but we found no consistent domestication effect on telomere lengths comparing crops and their wild progenitors. From our results we conclude plant telomere length contrasts with animal telomeres, in that life-history has minimal effect on length variation. Instead we propose the ecological adaptation hypothesis, where telomere length in plants is determined by selection from abiotic conditions, and suggest temperature is a major factor shaping telomere length in plants.

Premise of the study: Doryopteris J.Sm. is a genus of dry-adapted ferns found widely across the southern hemisphere and the tropics. In the Hawaiian Islands, the genus is represented by four endemic species and one putative hybrid. Two of the endemic species (D. decora and D. decipiens) are widespread across all major islands, while two (D. angelica and D. takeuchii) are federally and state-listed endangered single-island endemics.We aimed to resolve the evolutionary relationships and biogeographic history of Hawaiian Doryopteris. Methods: We used a target-capture approach and the GoFlag 408 flagellate land plant probe set to sequence more than 400 nuclear loci for 40 Hawaiian and 29 non-Hawaiian individuals in Doryopteris and the related genera Lytoneuron and Ormopteris. After processing the sequences into alignments and single nucleotide polymorphism sites, we performed phylogenetic inference and population-level principal component analyses. Key results: We infer that Hawaiian Doryopteris are monophyletic and are nested within the pantropical species D. concolor. Within Hawai'i, clades and clusters of individuals correspond to geographical, geological, and climatological factors, more so than species identifications, with a few exceptions. We posit that Hawaiian Doryopteris represents an incipient radiation at the very earliest stages of divergence, and that budding speciation has led to non-monophyly of several taxa. Conclusions Our inference using genome-wide sequencing data sheds light on the complex evolutionary history of Hawaiian Doryopteris. Overall, the phylogeny of Hawaiian Doryopteris shows strong links with geographical, geological, and climatological processes and little with morphological evolution.

The evolutionary processes underlying successful invasions are often difficult to disentangle. Historical collections provide a temporal perspective, offering great potential to reconstruct invasion histories and identify the processes driving invasions. Japanese stiltgrass (Microstegium vimineum) is an invasive C4 grass introduced to eastern North America over a century ago and now established in 31 USA states. To reconstruct its invasion history, we leveraged low-coverage whole-genome sequencing of 142 herbarium and 330 contemporary samples spanning the temporal and spatial extent of the North American invasion and the native range in Asia. We identified three independent introductions in the USA: an awnless form in the South and two independent introductions of awned forms in the North, with limited admixture among introductions across space and time. In both regions, we observed high genetic diversity in the earliest available collections despite demographic bottlenecks and identified several putative selective sweeps in or near flowering-time genes, suggesting rapid evolution in the introduced range. Our analyses support separate invasions in the USA, likely facilitated by standing genetic variation and selection, but provide little support for admixture playing a major role. Our study highlights the power of historical collections to uncover the processes and mechanisms underlying successful biological invasions.

Africa hosts remarkable biodiversity across diverse biomes, yet its evolutionary history at continental-scale remains poorly understood. We integrate a time-calibrated phylogeny covering 93% of African vascular plant genera with continental-scale distribution data to jointly evaluate phylogenetic diversity (PD), endemism, and diversification rates (DR). We reveal a pronounced decoupling between DR and accumulated evolutionary history across Africa. Mountain, arid, and semi-arid areas emerge as centers of neo-endemism and elevated diversification, whereas lowland and humid regions, particularly the Guineo-Congolian zone, are dominated by older lineages with low recent diversification. Several DR hotspots do not overlap with Global Biodiversity Hotspots, indicating a mismatch between rapid diversification and accumulated evolutionary history. High net diversification and speciation rates during the last 15 million years were likely driven by cooling, aridification, and mountain uplift that created new ecological gradients and isolation barriers. These abiotic changes, interacting with lineage-specific traits, shaped African modern flora and highlight conservation gaps, especially in arid regions

Climate affects biological processes and organisms. It is extensively recorded, and its effects are frequently studied. Climatic variables are recorded as time series of measurements, but these are often summarized as long-term averages, throwing away biologically relevant information. Subsequent analyses can therefore miss important climate effects or suffer from low predictive power. Here, we propose a new method, StatClim, inferring the most informative climatic summary from the data. Instead of taking a fixed arbitrary summary of a time series, StatClim automatically estimates the beginning and width of a climatic window and simultaneously calculates data aggregation, which best predicts a response variable. We implemented the proposed approach as a Bayesian hierarchical model in Stan. We illustrated the potential of StatClim on published data on mast seeding of Fagus sylvatica. StatClim correctly identified known climatic windows relevant for this tree species, but also uncovered that mast seeding is triggered by high temperatures within these windows. We demonstrated flexibility of the model to account for complex data structures, we ran power analysis showing the ability of the model to identify climatic effects even with modest datasets, and we evaluated its false positive rate, which is lower than 0.01. We discuss the advantages and limitations of StatClim. Compared to existing alternatives, it is suitable for hypothesis testing and offers important advances, such as estimation of the type of aggregation. In combination with existing methods, StatClim will facilitate data-driven use of climatic and microclimatic data and therefore discovering so far unknown climatic effects on biological processes and ecosystem functioning.

Lineages that have undergone little apparent evolutionary change over long geological intervals are often described as "living fossils", with iconic examples including the coelacanth, tuatara, and Ginkgo. However, studies of morphological and molecular data have produced mixed evidence regarding whether living fossils have evolved more slowly than their relatives. We tested for reduced evolutionary rates using a sister-pairs approach, analysing a comprehensive set of morphological and molecular data for 45 living-fossil lineages and their close relatives across the Tree of Life. Living-fossil lineages showed substantially reduced rates of morphological evolution, whereas evidence for reduced molecular rates was weaker. To test whether this pattern could be explained by species poverty, we also analysed other depauperate lineages (species-poor clades contrasted with species-rich sister clades) and found a weak tendency towards reduced molecular rates but without a corresponding slowdown in morphological evolution. Our study reveals that the living-fossil concept captures a quantifiable pattern of prolonged morphological conservatism, but also suggests that living fossils lack other shared biological or life-history characteristics that might unite them as a group.

Abstract Habitat configuration influences population connectivity and, consequently, genetic structure. River networks provide heterogeneous, hierarchically arranged environments that shift drastically from upstream to downstream. We compared congeneric species across Ephemeroptera, Plecoptera, and Trichoptera, emphasizing longitudinal replacement (upstream to downstream) and the rarely studied wet rock (hygropetric) habitats. We surveyed six rivers on the Muroto Peninsula, Japan, qualitatively sampling aquatic insects at 63 sites. Cluster analysis based on the environmental data classified surveyed sites into four clusters. We analyzed a total of 10 species from four genera that exhibit longitudinal replacement patterns within genera. Genetic analyses based on the mitochondrial cytochrome c oxidase subunit I region revealed that upstream species showed higher genetic diversity than downstream species. In contrast, species adapted to hygropetric exhibited the lowest genetic differentiation among all habitat types. A novel contribution of this study is the inclusion of hygropetric species. The surprisingly low differentiation in hygropetric species suggests high connectivity, similar to lentic species. By comparing congeneric taxa across orders within environmentally similar rivers, we reduce phylogenetic and environmental confounds, strengthening inference that habitat configuration and dispersal traits jointly shape genetic structure. These findings provide a new perspective on riverine spatial ecology and underscore the importance of microhabitat-aware comparisons for evolutionary inference.

Megadiverse countries concentrate most of the World's biodiversity. These countries encompass different levels of research infrastructure, and nearly all of them have been historically committed to the Convention of Biological Diversity, often setting precedents and leading new approaches. Here, we ask whether the assessment of genetic diversity indicators provide novel insights for biodiversity management and conservation in one of those countries, Mexico. We evaluated the first national application of the Kunming-Montreal Global Biodiversity Framework (GBF), genetic diversity indicators in Mexico. The data covered 97 taxa across diverse ecosystem types and taxonomic groups, including crop wild relatives, to assess the capacity of genetic diversity indicators to provide novel insights, as well as their relevance for strengthening national conservation strategies. We calculated two indicators: the proportion of populations with an effective population size greater than 500 (Ne 500) and the proportion of populations maintained (PM). Data were sufficient to estimate the Ne 500 indicator for 47 taxa and the PM for 28 taxa, with mean indicator values of 0.217 and 0.936, respectively. Species' geographic range was positively associated with Ne 500, whereas national endemicity had no significant effect. Comparisons with the IUCN Red List and Mexico's national extinction-risk legislation revealed that genetic vulnerability occurs even among taxa not currently recognized as threatened. Our findings highlight a gap in legal recognition of genetic diversity protection that could be strengthened by incorporating population-level assessments focused on maintaining adaptive potential in the long-term. Additionally, the indicators allowed to highlight conservation concerns within crop wild relatives, though fully realizing their potential requires integrating the entire wild-to-domesticated complex. The Mexican experience highlights that the main challenge for scaling the monitoring of genetic diversity is not only generating new data, but integrating existing information into systems that strengthen collaboration and communication among researchers, local communities, and government institutions.

The Peruvian Andes, and especially its slopes towards the Amazonian Basin are well-known biodiversity hotspots for plants and animals, which represent the visible part of biodiversity. However, not much is known about microeukaryotic diversity, despite the significant role protists play in the ecosystem. Based on a molecular survey of the diversity of Arcellinida (a group of amoebae well known for its environmental sensitivity and restricted geographical distributions), we estimated its diversity along an elevation gradient spanning more than 3000 meters. Surprisingly, Neotropical forest Arcellinida were less abundant and diverse than in most other extratropical biomes; nevertheless, communities differed strongly in their taxonomic composition as compared with forests in higher latitudes. Notably, sequences related to Trigonopyxis were most abundant, whereas this group occurs only marginally in extratropical settings. Elevation influenced beta diversity, showing different assembly processes occurring at different elevation belts. Canopy cover positively influenced both phylogenetic and taxonomic diversity, showing the importance of above and below ground integration in tropical forests.

Underlying diversification patterns and potential drivers of land plants remain puzzling, particularly at deep-time and global scales. Here, we reconstruct the diversification dynamics of land plants using an updated time-calibrated phylogeny comprising approximately 30,000 extant species, and nearly 40,000 fossil occurrences within the Bayesian birth-death frameworks. Our analyses indicate that angiosperms exhibit the highest diversification rates, whereas ferns underwent a marked diversification increase during the Cretaceous, coincident with the rapid radiation of angiosperms. Among the major Phanerozoic mass extinctions, the Cretaceous-Paleogene event has the most significant impact on land plant diversity, with estimated genus-level losses of 13%, 14%, and 4% in bryophytes, pteridophytes, and gymnosperms. We identify a pattern consistent with competitive displacement scenario, in which pteridophytes origination rates declined as gymnosperm diversity increased, accompanying the transition from pteridophyte- to gymnosperm-dominated floras. We find that plant-insect interactions have originated as early as the emergence of pteridophytes, potentially promoting the diversification of pteridophytes and gymnosperms. During the Cretaceous, these associations shifted toward angiosperms, as indicated by a positive relationship between insect diversity and angiosperm origination rates. Finally, continental fragmentation, fluctuations in aridity, atmospheric carbon and sedimentary dynamics, showed stronger associations with the successive rise and decline of major land plant groups.

1. Plant populations at high elevation persist near their physiological limits, and treeline position is one of the clearest expressions of this constraint. In many mountain regions, however, this limit reflects historical land use as much as climate. Treeline shift is most often tracked as the displacement of a boundary line (1D) overlooking structural changes only visible when the ecotone is analysed as a surface (2D). 2. We reconstructed treeline ecotone dynamics at nine sites in the Italian Alps using aerial imagery from 1954 and 2017. At each site we detected the timberline and tree species line, quantified elevational displacement, and measured ecotonal surface change, relating them to climatic, land-use, and topographic predictors. 3. Both boundaries advanced upslope at all nine sites, with timberlines shifting faster (1.6 m/yr) than tree species lines (1.1 m/yr). This decoupled velocity caused the ecotonal surface to contract by ~17%. Land-use variables consistently explained more variance than climatic ones. 4. Land-use legacy and abandonment have a major role in shaping treeline dynamics. Boundary displacement reveals vegetation advance at both margins, while the surface view reveals concurrent narrowing of the habitat available for tree establishment. Both perspectives are needed to fully characterize how plant populations respond to shifting limiting factors at the treeline ecotone.

Distinct from plants which directly parasitise other plants (parasites), non-photosynthetic mycoheterophic plants (MHPs, previously known as achlorophyllous mycotrophs or saprophytes) depend upon fungal hyphae for their carbon and have been viewed as cheaters or parasites in their fungal partnerships rather than mutualistic as in most other plant-mycorrhizal interactions. Over 400 such species in 87 genera and 11 families are recorded which maintain this lifeform through their life-cycle, while an estimate 30,000 further species, mainly orchids, depend on this mode of life to establish themselves from seeds. In most cases the fungal partners and the ultimate carbon sources, usually autotrophic plants, are unknown. High fungal specificity is the norm in those MHPs researched. We describe a new MHP genus and species, Denisea fonensis that we discovered in the Simandou range of the Republic of Guinea, West Africa in October 2025 on the footprint of a mining project. While clearly placed in Dioscoreales (which has three MHP families), the features of Denisea are so unusual that it was not initially clear in which family to place it. Finally, with molecular data we placed Denisea in Thismiaceae, corroborated by morphology. The new discovery is all the more unexpected as this is the first record of Thismiaceae from West Africa. Until now the family has only been recorded in Africa from three species of the very different genus Oxygyne, of Cameroon and Central African Republic. We provisionally assess Denisea fonensis as Critically Endangered since less than ten individuals are recorded in only a few square metres at one site, where there are imminent threats from animals. We propose urgent measures to conserve this species to reduce the risk of global extinction that has eliminated other African MHP species such as Oxygyne triandra, and further research to determine the fungal and autotrophic plant partners of this remarkable plant genus.

During biogeographical ancestry (BGA) analysis, an unknown individual for whom ancestry informative markers (AIMs) were analyzed is often assigned to one of a few reference populations. For some individuals, such an assignment is not meaningful: the two parents of the individual may come from different populations, or the individual may come from a population not included in the reference database. In this study, we examined classification methods in combination with 104 AIMs from the VISAGE Enhanced Tool to provide one of the following three possible outcomes: (i) in-reference (IR), with an assignment to one of the reference populations; (ii) admixed (AD), with parents from two in-reference populations; and (iii) out-of-reference (OR), where the individual's ancestry is not sufficiently represented by the reference populations. We therefore compared seven classifiers in combination with class-specific acceptance thresholds for the OR decision. The best-performing method according to our selection criterion was a naive Bayes classifier over pairs of populations, which we call the recent naive Bayes (RNB) classifier. Populations held out of the reference panel were correctly rejected in $84.9\%$ of cases. We further tested the method on $800$ individuals from seven additional groups not included in the reference panel. Only $29.4\%$ of individuals from four non-admixed populations were rejected, resembling joint ancestry with reference populations. In addition, we investigated the prediction accuracy in a newly collected dataset of 28 individuals with self-reported ancestry by analyzing AIMs using massively parallel sequencing.