Biology subjects

Larridon, I.

Publications and source records attributed to Larridon, I..

10 recordsLinked to original sources

bioRxiv2025

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↗

bioRxiv2025

Traditional uses, population, threats and conservation of the bansouman or gingerbread plum Neocarya macrophylla (Chrysobalanaceae) in Republic of Guinea (West Africa)

The flora of the Republic of Guinea (West Africa) includes nearly 4000 vascular plants species, of which c. 10% have been documented to have local socio-economic uses. These socio-economic plants provide among others, foods, medicines, materials and a source of income for the people of Guinea. One example is the bansouman or gingerbread plum, Neocarya macrophylla (Chrysobalanaceae) which is locally valued for its large, delicious seeds (nuts), edible fruit flesh, and medicinal bark (among other medicinal parts). Through a field survey of 17 local communities adjacent to Neocarya populations and the Neocarya populations themselves (780 mature individuals measured), in seven of the ten Guinean prefectures from which the species is recorded, this study documents (1) the local names, harvesting methods, uses and seed sale prices at different points in the value chain, partitions the species by habitat, records perceived threats to trees, key elements of the population structure and relative frequency of Neocarya macrophylla in Guinea, (2) map and re assesses its global conservation status as Near Threatened using the 2012 IUCN Red List categories and criteria, and (3) construct a species conservation action plan. Analysis of our survey data suggests that the largest number of mature trees (75% of the total) is in the three northern prefectures (Gaoual, Koundara, Pita) at the western foot of the Fouta massif whence seeds are exported internationally. Trees mainly occurred in shrub savannah (45% of mature individuals), with lower numbers in three other habitats. Human set bush fires appear to be the most ubiquitous threat (55%) in Guinea, but sand quarrying (18%), agricultural conversion and debarking are also key threats. Natural regeneration levels seem low compared with data from Niger with juveniles (<1 m tall) less than 10 % of the number of mature, fruiting trees (> 11 cm circumference) recorded. This is the first study focused on Neocarya macrophylla in the Republic of Guinea. In contrast the species has been the subject of numerous other papers elsewhere in its range, and we document 14 studies from Niger alone in the last 15 years. While the species is well known as an important Indigenous Fruit Tree with multiple uses in some countries, it is currently not among the top 10 such species listed for Guinea. Compared with Nigeria where numerous other uses including industrial are derived from the species, Neocarya macrophylla appears under utilised in Guinea. We suggest that studies of the chemistry and nutritional value of the seeds of Guinean Neocarya are made, since there are indications that these differ between Guinea and e.g. Niger. Follow up studies to map tree distribution in Guinea in more detail, quantify tree density, fruit yield per tree and per Ha, and duration between germination and fruiting are advised. Field trials to select elite individuals are recommended. Development of a machine to extract seeds from the endocarp (decortication) is a priority as this is the major factor limiting wild harvesting and availability of seed for human consumption.

plant biology↗

bioRxiv2025

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↗

bioRxiv2024

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↗

bioRxiv2024

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↗

bioRxiv2024

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↗

bioRxiv2023

Global analysis of Poales diversification - parallel evolution in space and time into open and closed habitats

O_LIPoales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test the hypotheses that Poales species are assembled into distinct phyloregions, with centres of high phylogenetic diversity and endemism clustered in tropical regions, and that cosmopolitan families show parallel transitions into open and closed habitats at different times. C_LIO_LIWe sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts. A dated supertree of Poales was constructed. We integrated spatial phylogenetics with regionalization analyses, historical biogeography, ancestral state estimations, and models of contingent evolution. C_LIO_LIDiversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time, space, and traits, most prominently in tropical and southern latitudes. Our results reveal parallel and recurrent patterns of habitat and trait transitions in the species-rich families Poaceae and Cyperaceae, yet other smaller families display unique evolutionary trajectories. C_LIO_LIThe Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats. C_LI

ecology↗

bioRxiv2021

Plastid phylogenomics of the Sansevieria clade (Dracaena; Asparagaceae) resolves a rapid evolutionary radiation

Sansevierias are a diverse group of flowering plants native to Africa, Madagascar, the Arabian Peninsula and the Indian subcontinent, popular outside their native range as low maintenance houseplants. Traditionally recognized as a distinct genus, Sansevieria was recently merged with the larger genus Dracaena based on molecular phylogenetic data. Within the Sansevieria clade, taxonomic uncertainties remain despite numerous attempts to classify the species. We aim to arrive at a robust phylogeny using a plastid phylogenomic approach, and estimate a time-frame of diversification to infer the evolutionary history of the group, including geographical and morphological evolution. Molecular data was obtained using genome skimming for 50 Sansevieria, representing all informal groups previously instated based on morphology, and two Dracaena sensu stricto species. The resulting Maximum Likelihood phylogenetic hypotheses are generally well supported, except for some very short branches along the backbone of the tree. The time-calibrated phylogeny indicates a recent rapid radiation with the main clades emerging in the Pliocene. Two well-supported clades align with previously defined informal groups, i.e., Sansevieria section Dracomima, characterised by the Dracomima-type inflorescence, and the Zeylanica group, native to the Indian subcontinent. Other morphologically defined informal groups are shown to be polyphyletic: a pattern due to convergent evolution of the identifying characters. Cylindrical leaves arose multiple times independently in the evolution of the Sansevieria clade and similarly, the Cephalantha-type inflorescence has originated multiple times from an ancestor with a Sansevieria-type inflorescence. To provide a more accessible tool for species identification and delimitation, genes and spacer regions were screened for variability and phylogenetic informativeness to investigate their potential as chloroplast DNA barcodes. Candidate chloroplast DNA barcodes include the trnH-rpl12, ndhH-rps15, psbE-petL, psbT-psbN, rps18-rpl20 intergenic spacers, the chloroplast gene rps8 and the first intron of ycf3.

evolutionary biology↗

bioRxiv2020

An analysis of Species Conservation Action Plans in Guinea

To achieve conservation success, we need to support the recovery of threatened species. Yet, <5% of plant species listed as threatened on the IUCN Red List have Species Conservation Action Plans (CAPs). If we are to move from a Red List to a Green List for threatened plant species, CAPs need to be devised and implemented. Guinea is one of the most botanically diverse countries in West Africa. Recent research found that nearly 4000 vascular plants occur in Guinea, a 30% increase from previous estimates. 273 of these plant species are now assessed as threatened with global extinction. There is increasing pressure on the environment from the extractive industry and a growing population. In parallel with implementation of an Important Plant Area programme in Guinea, CAPs were developed for 20 threatened plant species. These plans elaborate conservation efforts needed first to safeguard threatened species both in situ and ex situ and then to support their recovery. We document the approach used to assemble the Species Conservation Action Plans, and we discuss the importance of having up to date field information, IUCN Red List assessments, and use of a collaborative approach. The need for these plans is increasingly important with recent calculations suggesting a third of African plants are threatened with extinction. This paper outlines initial detailed plant conservation planning in Guinea and offers a template for conservation practitioners in other tropical African countries to follow.

ecology↗

bioRxiv2019

Introgression in Brownea suggests that reticulate evolution contributes to Amazonian tree diversity

Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization in Amazonias megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by introgression, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using [~]19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species which co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and a persistence of hybridization over time. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridizations rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.

evolutionary biology↗