Mining rare Earth elements: Identifying the plant species most threatened by ore extraction in an insular hotspot

Conservation efforts in global biodiversity hotspots often face a common predicament: an urgent need for conservation action hampered by a significant lack of knowledge about that biodiversity. In recent decades, the computerisation of primary biodiversity data worldwide has provided the scientific community with raw material to increase our understanding of the shared natural heritage. These datasets, however, suffer from a lot of geographical and taxonomic inaccuracies. Automated tools developed to enhance their reliability have shown that detailed expert examination remains the best way to achieve robust and exhaustive datasets. In New Caledonia, one of the most important biodiversity hotspots worldwide, the plant diversity inventory is still underway, and most taxa awaiting formal description are narrow endemics, hence by definition hard to discern in the datasets. In the meantime, anthropogenic pressures, such as nickel-ore mining, are threatening the unique ultramafic ecosystems at an increasing rate. The conservation challenge is therefore a race against time, as the rarest species must be identified and protected before they vanish. In this study, based on all available datasets and resources, we applied a workflow capable of highlighting the lesser known taxa. The main challenges addressed were to aggregate all data available worldwide, and tackle the geographical and taxonomic biases, avoiding the data loss resulting from automated filtering. Every doubtful specimen went through a careful taxonomic analysis by a local and international taxonomist panel. Geolocation of the whole dataset was achieved through dataset cross-checking, local botanists’ field knowledge, and historical material examination. Field studies were also conducted to clarify the most unresolved taxa. With the help of this method and by analysing over 85,000 data, we were able to double the number of known narrow endemic taxa, elucidate 68 putative new species, and update our knowledge of the rarest species’ distributions so as to promote conservation measures

Application of a Simplified Method of Chloroplast Enrichment to Small Amounts of Tissue for Chloroplast Genome Sequencing

Premise of the study: High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms. Methods: Chloroplasts were enriched using a high-salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high-throughput sequencing. Results: Using this simple method, significant enrichment of chloroplast DNA-derived reads was attained, allowing deep sequencing of chloroplast genomes. As an example, the chloroplast genome of the conifer Callitris sulcata was assembled, from which polymorphic microsatellite loci were isolated successfully. Discussion: This chloroplast enrichment method from small amounts of plant tissue will be particularly useful for studies that use sequencers with relatively small throughput and that cannot use large amounts of tissue (e.g., for endangered species)

Le genre Ilex (Aquifoliaceae) en Nouvelle-Calédonie

International audienceTwo names of Ilex L. (Aquifoliaceae) were published at the end of the 19 th century for New Caledonia. We confirm placing Ilex neocaledonica Maxim. under Ilex sebertii Pancher, a synonymy proposed in 1901. Both names are lectotypified. The single New Caledonian endemic species is represented on mainland Grande Terre both on ultramafic and nonultramafic substrates but appears quite variable morphologically.Deux noms de Ilex L. (Aquifoliaceae) ont été publiés pour la Nouvelle-Calédonie à la fin du 19 e siècle. Nous proposons ici de confirmer et d’argumenter la synonymie faite en 1901, plaçant Ilex neocaledonica Maxim. en synonymie de Ilex sebertii Pancher et de lectotypifier ces deux noms. L’unique espèce endémique de Nouvelle-Calédonie se rencontre sur l’ensemble de la Grande Terre sur substrats ultramafique et non ultramafique mais apparaît assez variable morphologiquement

Alyxia Banks ex R.Br. in New Caledonia: a clarification of several species complexes, nomenclatural notes, and a description of three new species

International audienceThe genus Alyxia Banks ex R.Br. is partially revised for New Caledonia, with 31 species recognised. The species complex Alyxia tisserantii Montrouz. is discussed and divided into seven species with existing names, and the synonymy is updated accordingly. Alyxia loeseneriana var. macrocarpa Boiteau is elevated to species status due to new flowering material with the name A. paniensis Lannuzel nom. nov., stat. nov. created to accommodate it, due to the preexisting Alyxia macrocarpa Koord. Detailed study of Alyxia caletioides (Baill.) Guillaumin ex Däniker revealed it was in fact made up of two distinct taxa; a new separate species, Alyxia urceolata Lannuzel, sp.nov. is therefore described. Two new species are also described following their recent collection: Alyxia humboldtensis Lannuzel & Gâteblé, sp.nov. is restricted to the summit of Mount Humboldt, and Alyxia minimiflora Lannuzel, sp.nov. is known from schistaceous cliffs around Nouméa. Finally, several nomenclatural issues are discussed, and an updated key to the genus in New Caledonia is provided

FIGURE 6 in Three new species threatened by mining activity in New Caledonia

FIGURE 6. Pictures of Tristaniopsis planidisca. A—General habit; B—Abaxial surface of the leaf; C—Flowering branch; D—Flower; E—Young fruits; F—Old fruit. Photographer: Lannuzel G. from Gâteblé et al. 1240.Published as part of Bruy, David, Lannuzel, Guillaume, Gâteblé, Gildas & Munzinger, Jérôme, 2023, Three new species threatened by mining activity in New Caledonia, pp. 228-240 in Phytotaxa 578 (3) on page 236, DOI: 10.11646/phytotaxa.578.3.2, http://zenodo.org/record/752309

Three new species threatened by mining activity in New Caledonia

International audienceNew Caledonia is a tropical archipelago with very high biodiversity conservation challenges. Its flora is still imperfectly known while its ecosystems are increasingly degraded by various threats, including mining activity. In this context, there is an urgent need to describe the most threatened species so they can be accounted for in situ conservation programs. In this article, three species new to science are described and illustrated: Croton barrabeae Bruy (Euphorbiaceae), Geijera tartarea T.G.Hartley ex Munzinger & Bruy (Rutaceae) and Tristaniopsis planidisca Lannuzel (Myrtaceae). According to IUCN criteria, each of these species is highly threatened by mining activity

Lagenophora (Asteraceae, Astereae) in New Caledonia

The genus Lagenophora Cass. is taxonomically revised for New Caledonia with two species recognised. Lagenophora sinuosa Lannuzel, Gâteblé & Jian Wang ter, sp. nov. is endemic to New Caledonia and the other, L. sublyrata (Cass.) A.R.Bean & Jian Wang ter occurs there and in many other countries from the region. Both are fully described and illustrated. An identification key is provided, as are notes on the distribution (including maps), habitat, phenology and conservation status. The generic placement of the new species is also discussed

FIGURE 7 in Three new species threatened by mining activity in New Caledonia

FIGURE 7. Drawing of Tristaniopsis planidisca. A—Flowering branches; B—Abaxial (left) and adaxial (right) sides of the leaf; C—Detail of the fine pubescence and a bracteole on inflorescence axis; D—Inflorescences with flowers and young fruits; E—Old infrutescence with opened fruits; F—Flower; G—Immature fruit. Illustrator: Ramon L.Published as part of Bruy, David, Lannuzel, Guillaume, Gâteblé, Gildas & Munzinger, Jérôme, 2023, Three new species threatened by mining activity in New Caledonia, pp. 228-240 in Phytotaxa 578 (3) on page 237, DOI: 10.11646/phytotaxa.578.3.2, http://zenodo.org/record/752309

Lagenophora (Asteraceae, Astereae) in New Caledonia

The genus Lagenophora Cass. is taxonomically revised for New Caledonia with two species recognised. Lagenophora sinuosa Lannuzel, Gâteblé & Jian Wang ter, sp. nov. is endemic to New Caledonia and the other, L. sublyrata (Cass.) A.R.Bean & Jian Wang ter occurs there and in many other countries from the region. Both are fully described and illustrated. An identification key is provided, as are notes on the distribution (including maps), habitat, phenology and conservation status. The generic placement of the new species is also discussed

restoptr: an R package for ecological restoration planning

International audienceEcological restoration is essential to curb the decline of biodiversity and ecosystems worldwide. Since the resources available for restoration are limited, restoration efforts must be cost-effective to achieve conservation outcomes. Although decision support tools are available to aid in the design of protected areas, little progress has been made to provide such tools for restoration efforts. Here, we introduce the restoptr R package, a decision support tool designed to identify priority areas for ecological restoration. It uses constraint programming – an artificial intelligence technique – to identify optimal plans given ecological and socio-economic constraints. Critically, it can identify strategic locations to enhance connectivity and reduce fragmentation across a broader landscape using complex landscape metrics. We illustrate its usage with a case study in New Caledonia. By applying this tool, we identified priority areas for restoration that could reverse forest fragmentation induced by mining activities in a specific area. We also found that relatively small investments could deliver large returns to restore connectivity. The restoptr R package is a free and open-source decision support tool available on the Comprehensive R Archive Network (https://cran.r-project.org/package=restoptr