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Forest, F.

Publications and source records attributed to Forest, F..

At least 19 recordsLinked to original sources

A framework for measuring national trends in the extinction risk of evolutionarily distinct species using the EDGE Index

The biodiversity crisis is threatening evolutionarily distinct species, those that constitute long periods of unique evolutionary history or that are from highly imperilled lineages. The EDGE (Evolutionarily Distinct and Globally Endangered) index was designed to track the changing extinction risks of these species and is listed as an indicator in the Kunming-Montreal Global Biodiversity Framework. Here, we provide a set of guidelines for calculating the EDGE index at the national level and for addressing data uncertainty. We distinguish two approaches for calculating a country-level EDGE index, either generated directly by using national data or from disaggregated global data. Using two national Red Lists, we show the contrasting state of high evolutionarily distinct nesting birds across French territories, and the elevated threat status of high evolutionarily distinct endemic species for South African vertebrates. Using global extinction risk data, we then reveal the deteriorating state of birds, mammals, and amphibians over time, and we highlight the countries with the highest proportions of threatened evolutionarily distinct species. Application of these guidelines should aid countries in monitoring their evolutionarily irreplaceable species, which in turn can help target local conservation actions, while contributing to global efforts to preserve the tree of life.

evolutionary biology↗

Self-Supervised AI Discovery of Histomorphological Phenotypes from Routine Mesothelioma Biopsies

Accurate subtype diagnosis is essential for guiding therapy and predicting patient outcome in malignant mesothelioma. Most computational pathology models are trained on large tissue images from resection specimens, which maximises information for training but limits model relevance in real-world diagnostic settings where small biopsies are the most usual tissue source. In this work, we assembled a large multicentre cohort of HES- and HPS-stained mesothelioma biopsy slides. We used a self-supervised learning model to evaluate the associations of biopsy-driven morphology patterns with histological subtype, molecular markers, and survival. The discovered histomorphology patterns captured a continuum of tissue phenotypes spanning epithelioid, sarcomatoid, and non-tumour morphologies. Also, patient-level HPC representations achieved excellent performance for distinguishing epithelioid from non-epithelioid mesothelioma (AUC = 0.94) and demonstrated predictive value for immunohistochemistry (IHC) markers. Additionally, HPC-derived features alone achieved performance comparable to established clinical and molecular variables (C-index = 0.65), while integration of HPCs with clinical and marker information improved performance to a C-index of 0.69. Several HPCs were significantly associated with favourable or adverse prognosis and reflected known subtype-specific biological patterns. In conclusion, self-supervised learning can discover interpretable histomorphological phenotypes directly from routine mesothelioma biopsies without further training. These AI-derived phenotypes capture clinically and biologically relevant information, linking tissue architecture to molecular characteristics, histological subtypes, and patient outcomes. The proposed framework provides a thorough evaluation of real-world biopsy data using a pre-trained model, without the need for computationally intensive retraining, and addresses the question of whether SSL-based AI can be deployed out of the box in clinical settings.

cancer biology↗

Integrating lineage-specific and universal genomic probes illuminates phylogenetic relationships and molecular evolution in Sauvagesieae (Ochnaceae)

Obtaining large and well-resolved phylogenetic trees for neotropical clades is challenging, as many species inhabit remote regions, and sampling often relies on herbarium specimens with highly degraded DNA. Target capture provides an effective solution for retrieving molecular data from fragmentary material. However, data processing using tools generally designed for diploid organisms and single-copy loci is also challenging, particularly when events such as genome duplication and hybridisation have shaped the lineage evolution. We used dual-hybridisation to integrate Ochnaceae-specific and universal probes to reconstruct the phylogenetic relationships of Sauvagesieae, a pantropical clade with ca. 90 species mainly distributed in the northern Andes, the Brazilian Espinhaco Range, and the Amazon-Guyana region. We tested different filtering strategies involving missing data and paralogs to assess probable sources of tree discordance and topological uncertainty. We found no significant benefit in reducing tree discordance after removing entire genes due to the presence of paralogs or a high amount of missing data. Removing fragmentary sequences instead improved alignments and increased branch support of gene trees. By quantifying the proportion of SNPs, analysing the distribution of the allele frequencies, and gene-tree quartet frequencies, we found evidence of polyploidisation and hybridisation, which could reduce resolution at internal nodes, particularly in mountain clades. Our results underscore the importance of exploring the complexities of target-capture data, not only to improve phylogenetic resolution but also to understand the sources of phylogenetic conflict and the underlying molecular evolutionary processes.

genomics↗

Assembling a fully-dated complete tree of life

Time-scaled phylogenetic trees summarising evolutionary relationships are fundamental to many analyses in biology, from diversification rate estimation to conservation prioritisation. The most comprehensive available summary of these relationships, the Open Tree of Life, synthesises information from over two thousand studies into a supertree covering the full range of global biodiversity, but its use in downstream analyses is limited by the lack of divergence times. Previous work has mapped dates from Open Trees database of trees to certain nodes in the supertree, but for the majority of nodes no date is available. While algorithms exist to interpolate missing dates in a tree, we found that their time and memory requirements scaled quadratically with the number of nodes, which made it computationally infeasible to run them on the entire tree. In this work, we describe novel date interpolation algorithms that scale linearly with the number of nodes. These enabled us to produce a distribution of fully-dated trees containing 2.3 million extant described species, greatly expanding the scope of feasible phylogenetic analyses. We illustrate the utility of these trees by computing the most robust estimate yet of the phylogenetic diversity of the complete tree of life, incorporating both topological and temporal uncertainty.

evolutionary biology↗

A large phylogenetic tree for euphyllophytes

PremiseMolecular datasets for estimating phylogenetic trees increasingly include more species and gene regions. Often trees are constructed using backbone phylogenies, subtrees, and other techniques to address the challenges of large dataset size. Currently, there is no established approach to integrate these rapidly expanding datasets. MethodsWe generated a phylogenetic tree (and 1,000 bootstrap trees) with divergence times that span euphyllophytes. To do this, we integrated taxonomically broad dated backbone phylogenies with species-level trees generated from phylogenetic analysis of individual clades. Datasets for species-level trees were assembled using PyPHLAWD. ResultsThe resulting dated phylogenetic tree includes: 121,641 angiosperm species; 1,026 gymnosperms; and 5,603 ferns. This is the largest euphyllophyte phylogenetic tree constructed to date. Topological uncertainty spikes at the start of the Cretaceous and gradually increases during the Cenozoic. Uncertainty in age estimates gradually increases in the Cenozoic but increases dramatically in the most recent 5 Myrs. DiscussionThis dated phylogenetic framework can underpin evolutionary studies spanning euphyllophytes, and enable the integration of insights from the recent to the distant past. Our approach also enables the tree to be easily updated in the future to reflect future increases in data availability, and systematic and taxonomic advances within specific clades.

plant biology↗

A ligand/receptor trafficking clock governs self-renewal and abscission dynamics in pluripotent stem cells

Summary/AbstractHow extracellular cues are temporally integrated to regulate self-renewal and differentiation propensities across the cell cycle remains largely unresolved. We identify a ligand/receptor trafficking clock in rodent and human pluripotent stem cells (PSCs) in which the cyclic turnover of Netrin-1 and its receptors Neo1 and Unc5b (NNU) governs self-renewal capacity and abscission dynamics. In G1, NNU complexes undergo Clathrin-mediated internalization and lysosomal degradation, a process required for timely post-mitotic bridge abscission. At later stages of the cycle, NNU activate Src within early endosomes, inducing a genome-wide redistribution of the transcriptional co-activator Yap1. This reshapes gene regulatory networks by activating stemness- and ectoderm-associated transcriptional programs enriched for Sox2/Nanog binding and by repressing mesodermal- and cell cycle-related targets enriched for Sox2 and Tcf3. Functionally, recombinant Netrin-1 reduces functional heterogeneity and enhances clonogenicity in G1, uncovering a tractable strategy to canalize stem cell behavior. Collectively, our results reveal cell cycle-dependent ligand/receptor trafficking as a temporal clock that directly links membrane dynamics to epigenetic regulation and stem cell fate, opening new avenues for regenerative medicine.

cell biology↗

The Pioneer Transcription Factor Oct4 Differentially Co-opts Bcl11a and Bcl11b to Regulate Reprogramming to Pluripotency

Pioneer transcription factors (TFs) orchestrate development, reprogramming, and cancer. Yet, the molecular mechanisms by which they cooperate with endogenous TFs and chromatin to trigger cell fate conversions remain largely unknown. Here, we identified antagonistic functions in reprogramming to pluripotency for the two paralogous somatic zinc finger TFs Bcl11a and Bcl11b. We reveal that Bcl11a and Bcl11b are initially co-expressed in mouse embryonic fibroblasts and then segregate in cellular intermediates respectively prone or refractory to reprogramming, transdifferentiation, and oncogenic transformation. They exert opposite functions - with Bcl11a promoting and Bcl11b hindering - the efficacy of induced pluripotent stem cells generation. During reprogramming, we uncover that Bcl11b safeguards cellular identity by persistently binding to differentiation genes with Runx1 in refractory intermediates. In contrast, in reprogramming intermediates, Bcl11a interacts with Oct4 and is initially displaced from MEF enhancers. Bcl11a then binds transiently and contributes to activate the E3 ubiquitin ligase Pja1 that regulates Smad3, thus promoting mesenchymal-epithelial transition and constraining senescence. Collectively, our work unveils how the differential repurposing of paralogous TFs by Oct4 orchestrates reprogramming to pluripotency.

cell biology↗

Setting priorities for the acquisition of primary plant occurrence data

AimEffective implementation of the Global Biodiversity Framework and Global Strategy for Plant Conservation depends on accurate species distribution data. Current vascular plant distribution data, while crucial for understanding terrestrial ecosystems, is often sparse and biased and requires significant expansion. This study developed a scalable approach to prioritize areas for plant occurrence data acquisition, adaptable to national priorities and providing a framework for botanical institutions to coordinate efforts and allocate resources. LocationGlobal. MethodsUsing a Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) analysis, we prioritized areas based on: (a) ecosystem service value; (b) floristic value threatened by climate or land-use change; and (c) uncertainty in species richness estimates, stratified by biome and region. Regional prioritization maps for Africa & Madagascar; East, South and Southeast Asia; Siberia and the Russian Far East; South America; and North & Central America were reviewed by botanical experts for validation. Scalability was assessed by comparing regional and global analyses. ResultsData-driven priority maps, divided into tree-dominated and grassland/deforested areas, largely received expert support. High similarity between global and regional maps demonstrated scalability. Main conclusionsOur approach provides a framework for supporting national implementation of the Global Biodiversity Framework. Variables and their weights can be tailored to national or local needs. The methods flexibility and adaptability extend to other taxonomic groups and objectives, such as protected area selection By prioritizing data acquisition, whether field-based or digital, this research promotes the efficient use of resources. A key advantage of this approach is its capacity to systematically translate expert opinion into explicit and quantitative criteria, which in turn facilitates clear communication with policymakers and funders.

plant biology↗

Big angiosperm genera are priorities for conservation

Species in big angiosperm genera ([≥]500 species) are often considered to be less well-known than those in smaller genera. Consequently, species in big genera are likely underrepresented in conservation at all levels, from analyses to actions. However, emerging evidence indicates that species in larger genera tend to have smaller geographic ranges (a strong correlate of increased extinction risk). Here, we test the generality of this pattern by quantifying the relationships between plant taxon size, extinction risk and climatic zone on a global scale. We find that species in larger genera are more likely to have small ranges, less likely to have a global Red List assessment, and, when assessed, are more likely to be threatened. Persistent obstacles to improving conservation documentation of big genera include taxonomic uncertainty, data shortfalls and number of species involved, requiring continued collaboration between taxonomy and conservation to reduce this bias and enable effective conservation of the quarter of plant species that big genera encompass. Article Impact StatementSpecies in big angiosperm genera are under-studied, under-assessed, and their extinction risk has been underestimated.

ecology↗

Safeguarding evolutionary history in a biodiversity hotspot: downscaling the EDGE metric to a regional application

In the face of accelerating biodiversity loss, phylogenetically informed approaches offer critical insights for conservation planning from an evolutionary perspective. The EDGE (Evolutionarily Distinct and Globally Endangered) metric combines phylogenetic singularity with extinction risk to identify taxa that represent unique evolutionary history under threat. In this study, we focus on the global conservation relevance of angiosperms native to a regional biodiversity hotspot, the Iberian Peninsula. Our aim was to identify areas with a high concentration of EDGE species and to evaluate how effectively the current protected area network encompasses them. Our findings reveal that threatened evolutionary history is primarily concentrated in mountainous and coastal regions. While several EDGE zones --areas containing unique and endangered evolutionary lineages-- overlap with existing protected areas, particularly in mountains, others harbouring few but evolutionarily unique and highly threatened taxa remain largely unprotected. This study highlights the value of applying global conservation metrics such as EDGE at regional scales. Our results provide a foundation for integrating evolutionary history into conservation prioritization in the Iberian Peninsula and offer a replicable framework for implementing the EDGE approach in other biodiversity-rich regions. Impact statementIn the Iberian Peninsula, there are 22 EDGE zones that account for over 90% of angiosperm threatened evolutionary history.

plant biology↗

Classification of Urticaceae based on morphology and phylogenetic inference

The Urticaceae (ca. 2600 species) were first formally recognized by Jussieu in the 18th century and last comprehensively monographed by Weddell in the 19th century. Since Weddells work, family delimitation has been modified and many genera described in a fragmented manner. Over the past two decades, numerous molecular studies have supported the inclusion of Cecropiaceae within Urticaceae and identified paraphyly in several genera, notably Laportea, Urera, Boehmeria, Parietaria, Pellionia, and Pouzolzia. However, few studies have translated these molecular insights into a revised taxonomy. This study aimed to provide a robust, updated classification for Urticaceae by: a) increasing taxon and genomic locus sampling through the integration of newly generated sequence data with previously published datasets; and b) incorporating morphological data to support a revised delimitation of tribes and genera, and to establish a new linear sequence for the family. We also sought to identify remaining taxonomic challenges. Using Sanger and Angiosperms353 sequence data, we constructed a phylogenetic framework for 57 out of 59 currently accepted genera. We also assessed the phylogenetic informativeness of 57 morphological characters by mapping them onto the phylogeny. Our analyses support the delimitation of 61 monophyletic genera and an infrafamilial classification comprising seven tribes, two of which we describe as new: Myriocarpeae and Leukosykeae. We provide a revised linear sequence for the family. Our classification reinstates several names previously treated as synonyms (Fleurya, Leptocnide, Margarocarpus, Polychroa, Scepocarpus, Sceptrocnide), places several genera in synonymy (Hemistylus and Rousselia under Pouzolzia; Hesperocnide under Urtica; Gesnouinia and Soleirolia under Parietaria), and proposes the recognition of two new genera, Muimar gen. nov. and Pouzolziella gen. nov., to accommodate Boehmeria nivea and Pouzolzia australis, respectively. Mapping morphological characters onto the phylogeny indicates that while most states are homoplastic at the family level, their combination is valuable for recognizing genera. Geographic character mapping suggests a high degree of spatial conservatism at the genus rank. Our dated ultrametric tree suggests an origin for Urticaceae in Indomalaya during the mid-Cretaceous, followed by establishment in the Laurasian boreotropical flora and subsequent dispersal to the neotropics and Africa. Once classified within an evolutionary framework we believe that the Urticaceae represent a valuable study system in evolutionary biology for investigating transitions across biomes, the drivers of floral trait evolution, and intrinsic speciation mechanisms. New tribes: --Leukosykeae, Myriocarpeae New genera: --Muimar, Pouzolziella

evolutionary biology↗

300 billion years of angiosperm evolution at risk of extinction

Extinction results in not only loss of species, but also loss of the unique evolutionary history that they represent and the irreplaceable features they exhibit. There is broad consensus regarding the necessity to optimise the preservation of the tree of life by including evolutionary information in conservation prioritisation, a notion also endorsed by major policy frameworks1-4. However, evolutionarily-informed prioritisations are lacking for most plants, resulting in a taxonomic imbalance in the evolutionary information incorporated in global biodiversity analyses, which has undermined conservation for decades. Here, we use comprehensive species-level phylogenetic trees, and extinction risk estimates, to generate the first global assessment of angiosperm evolutionary history at risk, and to identify phylogenetically-informed conservation priorities for the worlds flowering plants. We estimate that more than one fifth of angiosperm evolutionary history is at risk of extinction in the short term. Using the Evolutionarily Distinct and Globally Endangered5,6 approach, we identify 9,945 threatened plant species that disproportionately account for total evolutionary history at risk. Species and area prioritisations incorporating evolutionary history are urgently needed to correct imbalances between plants and animals, monitor the effectiveness of conservation efforts, and optimise conservation resource allocation in the face of increasing human pressures on Earths biodiversity.

evolutionary biology↗

Expanding Ventilago to incorporate Smythea: new combinations in Ventilagineae (Rhamnaceae) based on novel sequence data and phylogenetic analysis

Ventilagineae (Rhamnaceae) is a tribe of palaeotropical climbing plants, comprising two genera: Smythea and Ventilago. Previous studies have established the monophyly of the tribe, but the relationships within it remain unclear. This research includes six species of Smythea and seven species of Ventilago in a molecular phylogeny using the Angiosperms353 probe set. The results show that Ventilago is paraphyletic, with Smythea nested within it. To resolve this issue, we propose to merge Smythea into Ventilago. To achieve this, we make seven new combinations in Ventilago as well as resurrecting five names previously published in Ventilago but subsequently transferred to Smythea. In addition, we typify Ventilago.

evolutionary biology↗

Phylogenetic biome niche conservatism underlies the evolution of forest paleoendemic legume trees in tropical Africa

Niche conservatism is prevalent during the evolution of plant lineages. However, inferring biome niche lability and its impact on tropical tree species diversification is currently limited. To better understand biome niche lability and its effect on diversification rates, we analyzed an endemic lineage of African tropical trees, testing whether biome niche type (forest vs savanna) and biome lability are non-randomly distributed. We reconstructed a time-calibrated phylogeny of the Berlinia clade (16 genera, ca 201 species) using 140 nuclear genes, 75% of its extant species, and eight fossil calibrations. We also analyzed the phylogenetic signal of biome shifts across the group and its effect on diversification and extinction rates. We found the forest biome as the ancestral condition and a directional shift from forest to savanna (no reversals). The forest biome type is conserved in the Berlinia clade, but the lability to shift biomes is randomly distributed in the group. We did not find evidence that biome shift was associated with higher diversification or lower extinction rates. Our analyses identified five paleoendemic genera that have persisted solely in the forest biome since the Eocene. These paleoendemic and forest-restricted lineages are potentially more susceptible to habitat alterations of human related activities and future climate change, due to perhaps an innate limitation to adapt to new habitat types.

evolutionary biology↗

Early Cretaceous Origin and Evolutionary History of Palms (Arecaceae) inferred from 1,033 Nuclear Genes and a New Synthesis of Fossil Evidence

AO_SCPLOWBSTRACTC_SCPLOWTropical rainforests are home to almost half of all known plant diversity, yet a shortfall in tropical plant phylogenetic hypotheses is hindering our understanding of how rainforests have formed and adapted to past global changes. Phylogenetic and historical biogeographic evidence from key rainforest lineages, including palms (Arecaceae), are required to illuminate the history of these ecosystems. However, our current understanding of the palm tree of life is based on uneven sampling of data from the plastid and nuclear genome, and numerous palm genera and palm fossils have been described or revised over the past decade, casting doubt on many palm relationships, ages and ancestral ranges inferred in previous studies. Here, we infer the phylogenetic relationships of all palm genera based on data from 1,033 nuclear genes generated using target sequence capture. Our palm tree of life is highly resolved and supported. Remaining areas of ambiguity reflect the complex dynamics of palm evolution, including many rapid diversification events in subfamily Arecoideae and putative cases of ancient reticulation throughout the family. We review the phylogenetic placement and age of hundreds of palm fossils and use a vetted selection to estimate divergence times and ancestral ranges for all palm genera. We show that the family is older than previously thought, likely first diversifying in the Early Cretaceous in Laurasia, and that three quarters of the genera had originated by the Oligocene. The early spread of palms across the world involved at least 40 long-distance dispersals across oceanic gaps. Dispersals away from northern latitudes vastly outnumber dispersals into these latitudes, consistent with the ancient affinity of palms for megathermal climates, and suggesting that global cooling during the Oligocene was a major constraint on early palm distribution. Our dated phylogenomic tree and curated fossil dataset provide a new foundation for evolutionary studies on palms, opening the door to deeper research on the rainforest biome in which they thrive.

evolutionary biology↗

Identifying conservation priorities of a pantropical plant lineage: a case study in Scleria (Cyperaceae)

Scleria is a pantropical genus of annual and perennial herbs and the sixth largest genus in the Cyperaceae family with around 261 species. In this study, we produced preliminary extinction risk assessments for the [~]30% of Scleria species that do not yet have a global Red List assessment and followed the Evolutionarily Distinct and Globally Endangered (EDGE2) and Ecologically Distinct and Globally Endangered (EoDGE) protocols to identify evolutionary and ecologically unique Scleria species at greatest risk of extinction and hotspots of rare and endangered species. Our results indicate that 38 of the 78 Scleria species not yet included in the Red List, and 26% of species in the genus, are potentially threatened with extinction. The risk of extinction is not equally distributed across the phylogeny, and the Afrotropics and the Neotropics accumulate most threatened species. Eleven ecoregions mostly from four African (Madagascar, D.R. Congo, Zambia and Tanzania) and two South American (Brazil, Venezuela) countries accumulate almost half of Scleria species and stand out in terms of their sum of EDGE2 scores. Phylogenetic and functional distinctiveness metrics were largely uncorrelated, and the EcoDGE metric mostly points towards South American countries as reservoirs of ecologically distinctive and endangered species: Brazil, Venezuela, Bolivia, Peru, Colombia, Guyana and Dominican Republic. Recent methodological advances in the identification of species at-risk of extinction and the novel EDGE2 framework emerge as powerful tools to identify conservation priorities.

ecology↗

Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation

O_LIGrasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. C_LIO_LIWe inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1,153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a 910-tip plastome tree. C_LIO_LIThe nuclear phylogeny matches that of the plastome at most deep branches, with only a few instances of incongruence. Gene tree-species tree reconciliation suggests that reticulation events occurred repeatedly in the history of grasses. C_LIO_LIWe provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture. C_LI

plant biology↗

Towards a phylogenomic classification of Magnoliidae

PremiseMagnoliidae are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses of a limited number of mostly plastid markers have led to the current classification of magnoliids into four orders and 18 families. However, uncertainty remains regarding the placement of several families. MethodsHere we present the first comprehensive phylogenomic analysis of Magnoliidae as a whole, sampling 235 species from 199 (74%) genera and representing all families and most previously accepted subfamilies and tribes. We analyze newly generated data from the Angiosperms353 probe set using both coalescent and concatenation analyses and testing the impact of multiple filtering and alignment strategies. ResultsWhile our results generally provide further support for previously established phylogenetic relationships in both magnoliids as a whole and large families including Annonaceae and Lauraceae, they also provide new evidence for previously ambiguous relationships. In particular, we find support for the position of Hydnoraceae as sister to the remainder of Piperales and, for the first time, resolve the backbone of relationships among most genera of Myristicaceae. ConclusionsAlthough some of our results are limited by low gene recovery for a number of taxa and significant gene tree conflict for some relationships, this study represents a significant step towards reconstructing the evolutionary history of a major lineage of angiosperms. Based on these results, we present an updated phylogenetic classification for Magnoliidae, recognizing 21 families, summarizing previously established subfamilies and tribes, and describing new tribes for Myristicaceae.

evolutionary biology↗