Journal of Systematics and Evolution

Demographic factors are intrinsically crucial to evaluate species' extinction risk. However, measuring them remains difficult and time-consuming and the use of genomic summary statistics has been advocated to assess the conservation status of a species. In the present study, we estimated (i) the census number (Nc), (ii) effective population size (Ne) over three different time periods, recent, historical and ancient, (iii) neutral genetic diversity ({pi}4), and (iv) a measure of the efficacy of purifying selection ({pi}0/{pi}4) for 101 plant species using population genomic sequencing data. Twenty-one species are from the Plant Species with Extremely Small Populations (PSESP) program of SW China. Threatened species exhibited significantly lower Ne, Nc, {pi}4, and weaker purifying selection, but had a higher Ne/Nc ratio than non-threatened ones. Nc was the main determinant in identifying conservation status, and contemporary neutral genetic diversity was predominantly influenced by historical Ne. In the absence of demographic information, genetic parameters are a good proxy of conservation status, likely because currently threatened species also had a low historical population size. In summary, our findings suggest that direct estimates of Nc are more useful than {pi}4, although the latter remains a valuable conservation indicator. Hence, efforts such as the PSESP should be extended.

Zingiberales includes eight morphologically distinctive families, but its family-level backbone has remained unstable, especially around Musaceae, Heliconiaceae, Lowiaceae, and Strelitziaceae. We analysed 1566 low-copy nuclear genes from 52 samples, representing all eight families and Pontederia crassipes as outgroup. Concatenated maximum likelihood and multispecies coalescent analyses recovered the same backbone: ((Zingiberaceae, Costaceae), (Cannaceae, Marantaceae)) is sister to (Musaceae, (Heliconiaceae, (Lowiaceae, Strelitziaceae))). Penalized-likelihood dating placed the sampled crown group in the Late Cretaceous, with several deep family-level divergences occurring on short internodes. Analysis of 1248 rerooted gene trees showed that conflict is concentrated on these deep branches and in several shallow clades. HyDe tests of empirical and simulated matrices, each including 62,475 triples, did not support widespread ancient hybridization among the major family-level lineages after filtering against the simulated null model. The nuclear data recover a stable Zingiberales backbone, and the long-standing instability of several deep nodes is best explained by rapid early divergence and extensive incomplete lineage sorting.

This investigation aimed at compiling all phylogenetic lineages within and around genus Cyanoboletus. The evolutionary inference obtained from the nuclear ribosomal genes internal transcribed spacer region (ITS) suggests that part of the species currently classified in Cyanoboletus belong in lineages separate from the genus, thus suggesting a narrower boundary that includes only the species that develop a strong staining reaction to touch and to air exposure of the context. The separate lineages are the monotypic Cupreoboletus genus and a few species that do not develop such reaction, which are part of a clade together with genera Cacaoporus and Acyanoboletus, thus broadening the concept of Cacaoporus to encompass all of them. The emerging 3C perspective of Cupreoboletus, Cacaoporus and Cyanoboletus offers a remarkably consistent morphological diagnosis, overcoming the problems of a too broad concept for Cyanoboletus. This work reveals that Boletus neotropicus, B. novae-zelandiae and B. sensibilis belong respectively in Cyanoboletus, Cacaoporus and Lanmaoa, and by studying multigene alignment concatenates it identifies lineages that probably represent undescribed species: at least four in Cacaoporus and at least five in Cyanoboletus. Diagnostic tables and dichotomic keys are presented by geographic region. The present work also includes a study of the phylogenetic position of Neoboletus flavosanguineus, a species once classified in Cyanoboletus. The complexity of assigning species epithets in some lineages is addressed, namely for the boundaries between Cacaoporus instabilis and Ca. fagaceophilus as well as the diversity under the names Cyanoboletus sinopulverulentus and Cy. pulverulentus. The overall picture of evolutionary lineages sets a framework for the choice of reference data that can provide, in future phylogenetic studies that involve the 3C, a balanced and efficient coverage. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC="FIGDIR/small/724631v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@7f618corg.highwire.dtl.DTLVardef@dd6a14org.highwire.dtl.DTLVardef@5f7399org.highwire.dtl.DTLVardef@9e7443_HPS_FORMAT_FIGEXP M_FIG C_FIG

Forest trees pose numerous potential challenges to phylogenomic inference. Their large effective population sizes and relatively long generation times lead to deep allele coalescence and consequently incomplete lineage sorting (ILS), which biases inferences of divergence times toward older ages and introduces gene tree discordance. Deep phylogenetic divergences, reaching back into the Paleocene, introduce reference-mapping biases. Introgression--the movement of genes between lineages--may result in different phylogenies being inferred depending on which individuals are included in analysis, even if the plurality of the genome favors the divergence history unaffected by introgression. These factors influence phylogenetic inference across the Tree of Life but are particularly prevalent in forest trees. Oaks (Quercus) are notable for all three influences. In addition, our knowledge of the oak phylogeny is currently based strongly on restriction site associated DNA sequencing (RADseq) datasets published over the past decade, which may introduce additional sources of uncertainty. In this chapter, we analyze a 322-species RADseq dataset and genome resequencing data from across the genus to address sources of uncertainty in our understanding of the global oak phylogeny, which we hope will serve as a model for other research groups working on comparable woody plant groups.

The climatic transition from Marine Isotope Stage 3 (MIS3) to the Last Glacial Maximum (LGM) had caused widespread vegetation change. Despite the dynamic equilibrium between vegetation and climate, the specific role of functional composition in vegetation response to climate change was inadequately understood. Here, we analyzed the long-term trajectories of palynological diversity, vegetation coverage and community-weighted-mean (CWM) functional traits based on EH22 pollen record (35-18 cal ka BP) from Erhai Lake, southwestern China. The results disclosed a vegetation transition from temperate deciduous broadleaf forest dominance in late MIS3 to cold coniferous and mixed broadleaved/coniferous forests in LGM. This vegetation dynamic involved functional composition shifts from competitive-driven functional convergence to partial recovery via niche differentiation during the late MIS3, and finally to a low-diversity but functional differentiation state through trait complementarity and diversification strategies during the cold LGM. Our results likely support a function-mediated climate filtering process whereby climate change regulated long-term vegetation dynamics during the MIS3 to LGM transition primarily through shifts in CWM functional composition. These findings underscore the potential of pollen-based trait approaches to reconstruct ecosystem properties and advance our understanding of ecosystem change over decadal to millennial time-scales.

Oaks (Quercus L.) are among the most ecologically important tree genera in the northern hemisphere, with an intricate evolutionary history reflected in a reticulated phylogeny. Oak diversity has been profoundly shaped by introgression and diversification, yet the Iberian Peninsula remains an understudied natural laboratory for understanding these evolutionary processes. We used RAD-seq to characterize 38 taxa (including nothotaxa) and investigate the evolutionary history of the Iberian white oaks, with an emphasis on hybrid swarms. Results led to a readdressing of Iberian white oak species, expanding our current understanding of the phylogeography of the European Section Quercus. Furthermore, molecular evidence led to the circumscription of two new subsections, reflecting the contrast between typical temperate and Atlantic distributed species (Group A), and the submediterranean marcescent oaks (Group B). The former unveiled the recovery of Q. estremadurensis and a Northwestern Iberian lineage represented by Q. broteroana and Q. orocantabrica as southwestern representatives of the broad European pedunculate oaks (Q. robur s.l.). The latter led to the validation of hybrid swarms, emphasizing the Iberian oak syngameon and the importance of gene flow to oak evolution. Ultimately, our approach advances the understanding of European white oak evolution across different evolutionary scales, establishing the Iberian Peninsula as an important reservoir of oak diversity.

Plant growth forms effectively reflect profound evolutionary adaptations that underpin ecosystem functioning; however, how their biogeographic disparities influence conservation prioritization remains poorly understood. We here integrate a comprehensive phylogeny with high-resolution distribution data for 14,468 vascular plant species across the Qinghai-Tibet Plateau, showing that growth-form identity decouples the spatial patterns of taxonomic and phylogenetic diversity, with distinct forms exhibiting marked differences in geographic range sizes and elevational optima (2,200-3,300 m). Although herbs dominate plant assemblages across spatial scales, their proportional abundance decreases along a northwest-to-southeast aridity gradient, yielding to structurally complex, non-herbaceous forms in humid, species-rich regions. Consequently, priority conservation areas derived for individual growth forms exhibit low spatial similarity. Despite this divergence, we identify trees and climbers as highly effective umbrella growth forms: prioritizing these functional groups captures [≥]75% of the multidimensional diversity of all other growth forms within a minimal spatial footprint. Our findings demonstrate that accounting for growth-form-based functional identity is essential for maximizing conservation efficacy, providing a scalable framework for biodiversity hotspots worldwide.

[vrecto] Hybridization, incomplete lineage sorting and climatic oscillations can interact across evolutionary timescales, but their combined effects on plant diversification remain difficult to resolve. We investigated how these processes shaped the origin and geographic structure of Linum bienne, the putative progenitor of cultivated flax. [vrecto]We integrated genus-level Angiosperms353 phylogenomics across Linum with plastome analyses, low-depth nuclear resequencing, demographic inference and environmental niche modelling across the range of L. bienne. This framework allowed us to assess phylogenetic discordance, test for reticulation and reconstruct lineage history through time. [vrecto]Phylogenetic discordance was widespread across our genus-level sampling and largely consistent with incomplete lineage sorting. However, branch-length and maximum-likelihood network analyses detected additional signal of gene flow at the node including L. bienne, cultivated flax and the closest relatives. Within L. bienne, plastid and nuclear data recovered four geographically structured lineages across the species range, with cytonuclear discordance and demographic analyses supporting repeated secondary contact. [vrecto]Our results show that the evolutionary history of L. bienne reflects the interaction between deep reticulation, incomplete lineage sorting and Pleistocene range dynamics. This multiscale perspective highlights L. bienne as a genetically complex species and illustrates how reticulate evolution and climatic change can jointly shape plant diversification.

AimThe overarching aim of this study is to reconstruct the spatiotemporal evolutionary history of Australian Dysphania, including testing the littoral connection hypothesis, assessing the role of reticulation, and identifying the major drivers of diversification within the lineage. LocationAustralia and New Zealand TaxonDysphania, Chenopodioideae, Amaranthaceae, Caryophyllales, Angiosperms MethodsUsing a DNA sequence dataset based on a target enrichment approach with custom baits designed for Chenopodioideae, we compared alternative biogeographic and ancestral habitat models to infer the spatiotemporal evolutionary history of Australian Dysphania. In addition, we applied several complementary analyses to assess concordance and conflict within our phylogenomic datasets, estimate ploidy levels, and compare ecological niches among closely related species. Results and Main conclusionsOur results reveal a close evolutionary relationship between Sub-Saharan African and Australian desert ephemerals and indicate that Australian Dysphania originated through an ancestral reticulation event. The last common ancestor reached northwestern Australia during the Miocene, occupied riverine desert habitats, and migrated eastward with their expansion, potentially undergoing ecological speciation. Four major Australian clades subsequently diversified across Miocene to Pleistocene landscapes, from riverine deserts to salt lake mosaics, with divergence likely driven by salinity gradients, flood regimes, and microhabitat partitioning rather than polyploidisation or geographic isolation.

Ledebouria, a geophytic herb native genus to Africa and represented by a few species in the Arabian Peninsula, Madagascar, India and Sri Lanka. For a long time Indian species were named as L. revoluta until recent molecular work clarified African L. revoluta is distinct from Indian and Sri Lankan species. Hence the name L. hyacinthina was resurrected. However, there is no clear molecular or morphological clarification of the different morphotypes and karyotypes observed in various accessions from peninsular India. Since plastid DNA sequence markers failed to detect diversity, we used the high density, low copy number marker set, the Angiosperms353, for phylogenomic analysis of eight accessions and analysed with the same markers from the global dataset from published work. Our analysis shows L. hyderabadensis is a distinct species, whereas other widely distributed Indian accessions under the other name L. hyacinthina are young lineages representing incipient species. Our results indicate that Ledebouria has not diversified enough at the molecular sequence level for the marker set used. The same is also true of the chloroplast sequences.

Species distribution forecasts commonly overlook intraspecific genetic variation, missing a potentially important mechanism of ecosystem change: climate-driven range shifts among lineages within a species native range. Here we integrate population genomic analysis of 495 individuals, multi-site common garden experiments, and species distribution modeling based on 837 occurrence records for three major genetic lineages of the foundation grass Phragmites australis in China. The octoploid FEAU lineage (haplotype P) exhibits superior heat tolerance (critical temperature Tcrit and T50) and produces significantly greater total biomass in three of four common gardens compared to the cold-adapted CN lineage (tetraploid, haplotypes O/M), which occupies a climatic niche with lower annual mean temperature (Bio1) and mean temperature of the wettest quarter (Bio8). Genomic analyses further reveal bidirectional but asymmetric introgression, with admixed individuals showing a systematic bias toward FEAU ancestry. Under the high-emission scenario (SSP5-8.5) by 2070, projected highly suitable habitat for the FEAU lineage expands by 18.6%, while the CN lineage shows a smaller relative increase. By contrast, the subtropical SW lineage (haplotypes U/I) exhibits limited and stable suitable habitat. These results demonstrate that climate change interacts with intraspecific variation rooted in polyploidy, thermal tolerance, and asymmetric gene flow to drive potential lineage replacement within a native range, a process already suggested by field observations of FEAU expansion in a plateau lake. Our findings argue for integrating evolutionary history and genetic identity into ecological forecasting to better anticipate ecosystem responses under ongoing climate warming.

Ectomycorrhizal (EM) fungi are vital to forest ecosystems, supporting tree growth and survival. However, their inclusion in conservation policy and action remains limited and little is known about the status of their genetic diversity, which is essential for their long-term survival and adaptation. The Global Biodiversity Framework adopted a genetic indicator based on the effective population size, Ne, to monitor genetic diversity in all species. To date, it is still uncertain how Ne, a key parameter, can be reliably assessed in species with complex life history traits. Ectomycorrhizal fungi are a highly diverse group of taxa displaying haplodiplontic life cycles with partially clonal reproduction. Here, we review the literature to understand how these life history traits might affect Ne and its estimation in six species of EM fungi. We estimated Ne in 19 populations using eight genetic and genomic datasets from selected studies. We compared Ne estimates using Linkage Disequilibrium (LD) and Sibship Frequency (SF) methods. We tested how Ne estimates change due to partial clonality and genetic structure gradients and whether the number of genetic markers influence the precision of the estimates. We show a systematic bias in Ne estimations when large clones are present and when populations are not correctly delimited. We found both methods are not robust to these factors, which makes them unreliable for conservation assessment purposes in EM fungi. This study provides new perspectives for further research into the links between life history traits and the effective population size of ectomycorrhizal fungi.

Computational workshops are common in evolutionary biology and are used to share discipline-specific tools and skills with researchers. Despite the perceived importance of these workshops, there is no common set of criteria for workshop success, and there are few peer-reviewed studies investigating the efficacy of workshops or assessing the value of particular instructional techniques in this context. Here, we focused on one key element of a successful workshop: its ability to increase participants motivation to use the methods and tools presented during the workshop. We analyzed the goals, perceptions, and future plans of research practitioners engaging in a workshop on phylogenetic methods of historical biogeography using pre- and post-workshop surveys. Overall, the workshop was successful at motivating participants, and survey responses provided insights into participants perceptions of different activities, including "participatory live coding". Apart from this case study, we aim to highlight the importance of developing a common set of workshop goals in collaboration with other workshop stakeholders and the need for specialized, validated tools for assessing the efficacy of computational workshops for researchers.

Background and AimsThe evolution of reproductive isolation between previously interbreeding populations is a fundamental driver of plant speciation. Within Amaryllidaceae, Nothoscordum represents an evolutionarily complex genus, characterized by an unusually high incidence of chromosomal rearrangements. During fieldwork, Nothoscordum montevidense and Nothoscordum bonariense were found growing in sympatry, along with individuals exhibiting intermediate morphological traits, suggesting a putative hybrid origin. To test this hypothesis, we employed an integrative approach to characterize the morphologically intermediate specimens and the two sympatric populations. Materials and methodsTo characterize the putative hybrids we have combined morphological, cytogenetic analyses (chromosome counts, CMA/DAPI banding, and FISH) and flow cytometry-based genome size estimation. Phylogenetic relationships and genomic structure were also investigated through Genotyping-by-Sequencing (GBS), complete chloroplast genome assembly, and comparative repetitive DNA analysis. We also performed species distribution modeling and phenological analyses of the putative parental species. Key ResultsMultiple lines of evidence confirm the hybrid origin of the studied plants. Cytogenetic analyses revealed specimens with 2n = 21 (1C {approx} 33 pg = 32.274 Mbp) and 2n = 25 (1C {approx} 37 pg = 36.186 Mbp), accompanied by meiotic irregularities consistent with interspecific hybridization. Chloroplast genome phylogeny identified N. montevidense (2n = 16, 1C {approx} 25 pg) as the maternal lineage, while GBS data confirmed N. bonariense (2n = 26, 1C {approx} 41 pg) as the paternal contributor and revealed evidence of subsequent backcrossing. Comparative analysis of repetitive DNA showed reduced 35S rDNA diversity in the hybrid, indicative of post-hybridization genomic restructuring. Despite the observed genomic complexity, no clear morphological differentiation was detected among hybrid individuals. Phenological analyses and species distribution models demonstrated broad overlap between parental species. ConclusionsOur findings highlight the role of hybridization in shaping genome architecture in cytogenetically labile plant lineages. Furthermore, our results underscore that morphological similarity can mask profound genomic complexity, reinforcing the value of integrative approaches to understand genera characterized by reticulate evolution and genomic instability.

Conservation strategies for at-risk species can be aided significantly by research on topics such as ecology, life history, and threats, yet research effort is lacking for many species facing elevated extinction risk. Here we investigated whether listing under the U.S. Endangered Species Act (ESA) was associated with research effort for U.S. butterflies, and whether that effort was higher before or after ESA listing. We found that ESA-listed species had significantly more peer-reviewed publications than non-listed species after accounting for species range and taxonomic family. Further, we showed that more papers were published per year after ESA listing than before. These findings confirm that ESA-listed species benefit from greater research attention that can support data-informed conservation efforts. However, the relative scarcity of studies prior to ESA listing, as well as the lack of research for many unlisted, at-risk taxa, underscores the need for proactive, strategic research effort to inform conservation action.

The diversity of the brown frog genus Rana may be underestimated as the high similarity of morphological characters. A new species belonging to the genus Rana is delineated based on eight specimens obtained from the Tianma National Nature Reserve, Jinzhai County, Luan City, Anhui Province, China. The phylogenetic analysis based on three mitochondrial genes (12S, ND2, and Cyt b) and one nuclear gene (BDNF) showed that the new species formed an independent clade closely related to R. culainensis and received strong support. In addition, morphological differentiation confirmed the phylogenetic results, and both supported the validity of a new species (Rana tianmaensis sp. nov.) in the R. japonica species group. The discovery of this new species enhances peoples understanding of the biodiversity of Rana and can provide important foundational data for scientific decision-making on protected area construction, ecological conservation, and species diversity. With the inclusion of newly described species in this study, the distribution of Rana genus in China now includes 31 recognized species.

The preparation of multi panel figures remains a labor intensive step in scientific publication. Albeit there are specific tools available to solve this problem, they are often highly specialized, difficult to install, or time consuming to learn. Griphus is a standalone graphical application designed for rapid composition and experimentation with multi panel figures, developed by and for zoological taxonomists. Functions specifically designed for multi panel composition include automatic figure numbering and placement, aspect ratio operations, spacers, layout rotation, layout suggestions, and automatic generation of figure legends, including scale bar descriptions. The software can perform both spatial interpretation of images on the canvas and work with a simple, editable layout formula. It also enables instant multi panel composition, with numbered images and automatic contrast selection for the numbers, obtained simply by loading images. User defined parameters such as target printable dimensions, resolution, spacing, and color mode are preserved throughout the work. The program produces coordinated outputs consisting of the final composite figure, a readable file describing the layout structure, and a .gri file storing images, transformations, and parameters for exact regeneration. Griphus is intended as a complementary tool to professional image software, providing a simple and efficient environment for constructing high quality multi panel figures.

AimBiodiversity-rich regions often lack the scientific infrastructure needed to document and curate their own biodiversity, creating inequalities in access to taxonomic reference material. We investigated how biological, institutional, and geopolitical factors shape the retention, extraction, and appropriation of reptile holotypes, the name-bearing specimens upon which species descriptions are based. LocationGlobal. TaxonReptiles. MethodsWe compiled a historical dataset of reptile holotype origins and destinations spanning 1758-2024 to reconstruct long-term patterns of retention and international specimen flows. We then quantified species-level holotype retention, holotype flows between country pairs, and country-level patterns of retention, appropriation, and network centrality for the period 1990-2024, and used generalised linear mixed models to assess the biological, institutional, and geopolitical determinants of these contemporary circulation processes. ResultsAlthough nearly 90% of reptile species described originated in the Global South, less than a quarter of their holotypes remain housed there. Historically, exported holotypes consistently outnumbered retained holotypes on a decadal basis until the early twenty-first century. Retention was promoted by local scientific capacity, institutional infrastructure, collector involvement in species descriptions, and environmental governance. In contrast, extraction was concentrated in highly endemic regions with limited scientific infrastructure and was associated with taxonomic revisions, socioeconomic interest, and disparities in political stability and colonial history. Appropriation of foreign holotypes was greatest in countries with high research investment, strong environmental governance, and historical geopolitical influence. Main conclusionsGlobal patterns of holotype circulation reflect a persistent geography of scientific inequality. The distribution of taxonomic reference material emerges from the interaction of retention, extraction, and appropriation processes, linking local biodiversity discovery to uneven global scientific capacity. Reducing these inequalities will require investments in taxonomic expertise, institutional infrastructure, and governance frameworks that promote more equitable stewardship of biodiversity knowledge and its material foundations.

The tribe Spermacoceae (Rubiaceae) comprises a morphologically diverse assemblage of approximately 1,400 species distributed across the Neotropics, Africa, Asia, Australia, and Pacific region. It remains one of the most taxonomically intractable groups in the family, with generic limits repeatedly redefined for more than two centuries. Previous phylogenetic studies based on a limited number of plastid and nuclear markers left numerous relationships unresolved and provided sparse representation of Neotropical lineages. Here, we present the first phylogenomic study of the tribe based on plastome-scale data and expanded sampling of Neotropical taxa. We sampled 121 species representing 55 genera spanning all major clades and generated 123 new plastomes, including 25 species incorporated into a molecular phylogenetic framework for the first time. Maximum-likelihood and Bayesian analyses recovered a highly resolved and strongly supported phylogeny, with uncertainty restricted to a small number of deep backbone nodes. Pollen and seed micromorphology provided additional evidence for evaluating phylogenetic relationships. The resulting phylogenetic framework clarifies generic boundaries across several problematic lineages and supports multiple taxonomic changes. Pervasive homoplasy in seed and floral characters rendered several traditionally recognized genera non-monophyletic, warranting new combinations, including Edrastima oxycoccoides, Stenotis alexanderae, and S. prostrata, and a reassessment of taxa such as Terrellianthus serpyllaceus and Oldenlandia dusenii. We further identify genera requiring additional study and provide an updated key to the 82 recognized genera of Spermacoceae. Together, these results provide the most robust phylogenetic framework yet available for the tribe and establish a foundation for future systematic, biogeographic, and evolutionary research.

Last winter, community scientists recorded anomalous winter flowering by Joshua trees (Yucca brevifolia and Y. jaegeriana), and some speculated the bloom was caused by climate change. We trained machine learning models that reliably identify weather triggers for seasonal Joshua tree flowering, then applied frontier methods from climate science to simulate flowering in a counterfactual world without human-caused climate change. Surprisingly, we found winter blooms in 2018-9 and 2025-6 were driven by high winter rainfall, not rising temperatures--and therefore, are probably the result of natural weather variability, not climate change.