ConR: An R package to assist large-scale multispecies preliminary conservation assessments using distribution data

Published online: 16 Dec 2017The Red List Categories and the accompanying five criteria developed by the International Union for Conservation of Nature (IUCN) provide an authoritative and comprehensive methodology to assess the conservation status of organisms. Red List criterion B, which principally uses distribution data, is the most widely used to assess conservation status, particularly of plant species. No software package has previously been available to perform large-scale multispecies calculations of the three main criterion B parameters [extent of occurrence (EOO), area of occupancy (AOO) and an estimate of the number of locations] and provide preliminary conservation assessments using an automated batch process. We developed ConR, a dedicated R package, as a rapid and efficient tool to conduct large numbers of preliminary assessments, thereby facilitating complete Red List assessment. ConR (1) calculates key geographic range parameters (AOO and EOO) and estimates the number of locations sensu IUCN needed for an assessment under criterion B; (2) uses this information in a batch process to generate preliminary assessments of multiple species; (3) summarize the parameters and preliminary assessments in a spreadsheet; and (4) provides a visualization of the results by generating maps suitable for the submission of full assessments to the IUCN Red List. ConR can be used for any living organism for which reliable georeferenced distribution data are available. As distributional data for taxa become increasingly available via large open access datasets, ConR provides a novel, timely tool to guide and accelerate the work of the conservation and taxonomic communities by enabling practitioners to conduct preliminary assessments simultaneously for hundreds or even thousands of species in an efficient and time-saving way

Open data from the third observing run of LIGO, Virgo, KAGRA, and GEO

The global network of gravitational-wave observatories now includes five detectors, namely LIGO Hanford, LIGO Livingston, Virgo, KAGRA, and GEO 600. These detectors collected data during their third observing run, O3, composed of three phases: O3a starting in 2019 April and lasting six months, O3b starting in 2019 November and lasting five months, and O3GK starting in 2020 April and lasting two weeks. In this paper we describe these data and various other science products that can be freely accessed through the Gravitational Wave Open Science Center at https://gwosc.org. The main data set, consisting of the gravitational-wave strain time series that contains the astrophysical signals, is released together with supporting data useful for their analysis and documentation, tutorials, as well as analysis software packages

A second species in the endemic New Caledonian genus Gastrolepis (Stemonuraceae) and its implications for the conservation status of high-altitude maquis vegetation : coherent application of the IUCN Red List criteria is urgently needed in New Caledonia

A new species in the previously monotypic, endemic New Caledonian genus Gastrolepis (Stemonuraceae) is described. Gastrolepis alticola differs from G. austrocaledonica by its shorter and thicker petioles, strongly coriaceous leaves with revolute margins, shorter inflorescences, and pubescent corollas. The new species is further distinguished by its ecology, occurring only in high-altitude maquis on two massifs in southern New Caledonia, Mt. Kouakoue and the Montagne des Sources. Gastrolepis alticola is assigned a preliminary conservation status of 'Endangered' using the World Conservation Union (IUCN) Red List criteria. Comparison of the IUCN threat status for the 19 species endemic to this distinctive, restricted vegetation type reveals a striking lack of consistency and underscores the need for a reassessment of the entire New Caledonian flora

Polystachya orophila (Orchidaceae, Polystachynae), a new species from tropical West Africa, and clarification on the nomenclature and taxonomy of P. microbambusa

Polystachya orophila, a new species of Orchidaceae, is described based on specimens collected during the baseline study of the Guinean Nimba Mountains for the environmental impact assessment for a proposed mining project. While material belonging to this species was mentioned as early as 1920 by Chevalier, it has historically been confused with P. microbambusa, from which it differs by its typically Polystachya-like clustered pseudobulbs, placing it in P. sect. Polystachya, whereas P. microbambusa has pseudobulbs successively growing on top of one another, forming developed and persistent stems, and is the sole representative of P. sect. Dimorphocaules. The complex taxonomic and nomenclatural history of P. microbambusa is also clarified. For both taxa we provide a morphological description as well as information on distribution, habitat, and phenology, an IUCN conservation status assessment using the Red List criteria, and a distribution map, along with a dichotomous key that also includes the most similar members of P. sect. Polystachya.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Phylogeny and circumscription of Sapindaceae revisited: molecular sequence data, morphology and biogeography support recognition of a new family, Xanthoceraceae

Background and aims Recent studies have adopted a broad definition of Sapindaceae that includes taxa traditionally placed in Aceraceae and Hippocastanaceae, achieving monophyly but yielding a family difficult to characterize and for which no obvious morphological synapomorphy exists. This expanded circumscription was necessitated by the finding that the monotypic, temperate Asian genus Xanthoceras, historically placed in Sapindaceae tribe Harpullieae, is basal within the group. Here we seek to clarify the relationships of Xanthoceras based on phylogenetic analyses using a dataset encompassing nearly 3/4 of sapindaceous genera, comparing the results with information from morphology and biogeography, in particular with respect to the other taxa placed in Harpullieae. We then re-examine the appropriateness of maintaining the current broad, morphologically heterogeneous definition of Sapindaceae and explore the advantages of an alternative family circumscription. Methods Using 243 samples representing 104 of the 142 currently recognized genera of Sapindaceae s. lat. (including all in Harpullieae), sequence data were analyzed for nuclear (ITS) and plastid (matK, rpoB, trnD-trnT, trnK-matK, trnL-trnF and trnS-trnG) markers, adopting the methodology of a recent family-wide study, performing single-gene and total evidence analyses based on maximum likelihood (ML) and maximum parsimony (MP) criteria, and applying heuristic searches developed for large datasets, viz, a new strategy implemented in RAxML (for ML) and the parsimony ratchet (for MP). Bootstrap analyses were performed for each method to test for congruence between markers. Key results Our findings support earlier suggestions that Harpullieae are polyphyletic: Xanthoceras is confirmed as sister to all other sampled taxa of Sapindaceae s. lat.; the remaining members belong to three other clades within Sapindaceae s. lat., two of which correspond respectively to the groups traditionally treated as Aceraceae and Hippocastanaceae, together forming a clade sister to the largely tropical Sapindaceae s. str., which is monophyletic and morphologically coherent provided Xanthoceras is excluded. Conclusion To overcome the difficulties of a broadly circumscribed Sapindaceae, we resurrect the historically recognized temperate families Aceraceae and Hippocastanaceae, and describe a new family, Xanthoceraceae, thus adopting a monophyletic and easily characterized circumscription of Sapindaceae nearly identical to that used for over a century

Vegetation dynamics in a corridor between protected areas after slash-and-burn cultivation in south-eastern Madagascar

Slash-and-burn cultivation is a major cause of deforestation in Madagascar, and abandonment leads to the secondary vegetation dynamics, i.e. colonization by herbaceous vegetation, shrubs and trees. The study was conducted in south-eastern Madagascar in a steep transition zone along an altitudinal and a sharp precipitation gradient between a high altitude rainforest and a lowland dry tropical forest. The restoration of gaps created by abandoned fields in this narrow, winding corridor could be essential to maintain connectivity between two areas (areas 1 and 2) of Andohahela National Park. Prior to implementing restoration, baseline ecological information is needed on the reference ecosystem and vegetation resilience must be studied to identify restoration needs. This study aims to (1) assess whether cultivation practices (irrigated rice vs. cassava, maize and sweet potato) influence vegetation dynamics after abandonment; (2) study vegetation dynamics and soils over time since abandonment, and (3) compare secondary forest vegetation and soils with those of mature forest patches. Surveys of vegetation and soil were conducted in 26 secondary forest patches abandoned from 3 to >25 years (synchronic approach) and in 19 adjacent mature forest patches (controls). No relationship between age of abandonment and vegetation species richness, composition or structure was found, but clear differences were detected between secondary and mature forest patches. Secondary forests are not colonized by species from mature forests, but instead their vegetation dynamics appear to lead to the establishment of thorny thickets dominated by Mimosa delicatula, which is absent from the mature forest