| 1. |
- Zizka, Alexander, 1986, et al.
(författare)
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CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases
- 2019
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Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 10:5, s. 744-751
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Tidskriftsartikel (refereegranskat)abstract
- Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo-referencing or dating, can diminish their usefulness. Manual cleaning is time-consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records. Here, we present CoordinateCleaner, an r-package to scan datasets of species occurrence records for geo-referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo-referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio-temporal tests for fossils. We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic. All cleaning functions and the biodiversity institution database are open-source and available within the CoordinateCleaner r-package.
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| 2. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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Madagascar's extraordinary biodiversity : Evolution, distribution, and use
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 378:6623, s. 962-
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Tidskriftsartikel (refereegranskat)abstract
- Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique " living laboratory" for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth's biodiversity.
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| 3. |
- Branch, W. R., et al.
(författare)
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Description of a new flat gecko (Squamata: Gekkonidae: Afroedura) from Mount Gorongosa, Mozambique
- 2017
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Ingår i: Zootaxa. - : Magnolia Press. - 1175-5326 .- 1175-5334. ; 4324:1, s. 142-160
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Tidskriftsartikel (refereegranskat)abstract
- A new species of flat gecko, Afroedura gorongosa sp. nov., is described from Gorongosa National Park, Sofala Province, central Mozambique. The new species is morphologically similar to A. transvaalica and A. loveridgei, from both of which it is genetically distinct (15-17% divergence; 400 bp of 16S rRNA). Morphologically it can be distinguished from both species by having fewer midbody scale rows (97-101) and a higher number of precloacal pores in males (8-13). The type series was collected on the western flanks of Mount Gorongosa (900 and 1100 m a. s. l.) in comparatively cool and moist microclimates, where it is threatened by illegal deforestation. Additional material was collected as low as 212 m a. s. l. on an inselberg near Mount Gorongosa. The new discovery adds to the growing number of endemic montane reptiles discovered in Mozambique in recent years, and highlights the need for a national conservation assessment of the country's herpetofauna and continued protection of the Mount Gorongosa region.
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| 4. |
- Conradie, W., et al.
(författare)
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New species of Mongrel Frogs (Pyxicephalidae: Nothophryne) for northern Mozambique inselbergs
- 2018
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Ingår i: African Journal of Herpetology. - : Informa UK Limited. - 2156-4574 .- 2153-3660. ; 67:1, s. 61-85
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Tidskriftsartikel (refereegranskat)abstract
- Nothophryne Poynton, 1963 is a monotypic genus of frog, with the nominal species N. broadleyi found only on Mount Mulanje, in southern Malawi. Recent surveys in northern Mozambique, however, have uncovered at least four new species associated with four inselbergs (Mount Inago, Mount Namuli, Mount Ribaue and Taratibu Hills). Previous phylogenetic analyses using mitochondrial genes suggest that each mountain isolate has an endemic species of Nothophryne. Herein we provide a rediagnosis of the genus and comparative diagnoses of four new species based on new material.ZooBank urn:lsid:zoobank.org:pub:19C53BF3-BA52-4CAE-933F-5BBEE0AF0457
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| 5. |
- Daru, B. H., et al.
(författare)
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Endemism patterns are scale dependent
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Areas of endemism are important in biogeography because they capture facets of biodiversity not represented elsewhere. However, the scales at which they are relevant to research and conservation are poorly analysed. Here, we calculate weighted endemism (WE) and phylogenetic endemism (PE) separately for all birds and amphibians across the globe. We show that scale dependence is widespread for both indices and manifests across grain sizes, spatial extents and taxonomic treatments. Variations in taxonomic opinions—whether species are treated by systematic ‘lumping’ or ‘splitting’—can profoundly affect the allocation of WE hotspots. Global patterns of PE can provide insights into complex evolutionary processes but this congruence is lost at the continental to country extents. These findings are explained by environmental heterogeneity at coarser grains, and to a far lesser extent at finer resolutions. Regardless of scale, we find widespread deficits of protection for endemism hotspots. Our study presents a framework for assessing areas for conservation that are robust to assumptions on taxonomy, spatial grain and extent. © 2020, The Author(s).
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| 6. |
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| 7. |
- Farooq, Harith, 1986, et al.
(författare)
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A call for improving the Key Biodiversity Areas framework
- 2023
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Ingår i: Perspectives in Ecology and Conservation. - : Elsevier BV. - 2530-0644. ; 21:1, s. 85-91
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Tidskriftsartikel (refereegranskat)abstract
- Eight percent of all land surface has been designated as "Key Biodiversity Areas" (KBAs). Since these areas were established based on two percent of all terrestrial species estimated to exist, we ask what would happen if we used all species on Earth to identify additional KBAs. We explore this question at a global scale by using data from 64,110 species of animals and plants to identify how many areas could qualify as KBAs under current criteria. We find that between 26% and 68% of the world's terrestrial areas can be classified as KBAs, depending on the spatial resolution. The total area from potential KBAs increases drastically as more species are assessed, suggesting that if all species were included, all land surface could eventually meet the biological requirements for becoming a KBA. KBAs are intended to be areas that are both of biological importance and manageable, but since they lack a data-driven ranking system, the current framework largely sidesteps the biological component. We, therefore, make an urgent call for stricter criteria in the KBA methodology or alternative methodologies that allow for biologically robust area prioritization, help secure evidence-based investments, and support progress toward the targets under the new Global Biodiversity Framework.(c) 2023 Associacao Brasileira de Ciencia Ecol ogica e Conservacao. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/ ).
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| 8. |
- Farooq, Harith, 1986, et al.
(författare)
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Can we identify european snakes by color patterns?
- 2021
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Ingår i: Salamandra. - 0036-3375. ; 57:4, s. 520-528
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Tidskriftsartikel (refereegranskat)abstract
- We investigated to what extent European snakes can be identified by using their color, pattern and location. We coded these criteria for all 84 snake species of Europe, including European Russia, Ukraine, and Turkey as their eastern border. Brown and blotched snakes are most common, followed by dark (brown, black) and uniformly colored species. Some highly variable species can have a dozen or more color patterns. However, in 96% of localities (grid cells) these three criteria are sufficient to narrow down the number of possible species to no more than 10, and in most cases proper identification is possible with a few photos for comparison. Given that about two dozen European vipers (and a few other species) are venomous, accurately identifying snakes is also of medical importance. In addition to identifying snakes, we provide color and pattern data for future phylogenetic and for future phylogenetic and ecological studies. © 2021 Deutsche Gesellschaft für Herpetologie und Terrarienkunde.
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| 9. |
- Farooq, Harith, 1986, et al.
(författare)
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Identifying Australian snakes by color patterns
- 2020
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Ingår i: Vertebrate Zoology. - 1864-5755. ; 70:3, s. 473-482
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Tidskriftsartikel (refereegranskat)abstract
- We investigated if Australian snakes can be identified by using their color, pattern, size and location. We coded these criteria for the 185 terrestrial snake species of Australia (excluding 37 species of sea snakes from our analysis). Uniformly brown snakes are most common, followed by banded and blotched species. Some highly variable species can have dozens of color patterns. For most localities these four criteria are sufficient to narrow down the number of possible species to fewer than 21 species and in most cases accurate identification is possible with a few photos for comparison. Given that most Australian snakes are venomous, accurately identifying snakes is also of medical importance. In addition to identifying snakes, colors and patterns provide useful data for phylogenetic and ecological studies. © 2020 Senckenbergische Naturforschende Gesellschaft. All rights reserved.
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| 10. |
- Farooq, Harith, 1986, et al.
(författare)
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Mapping Africa's Biodiversity: More of the Same Is Just Not Good Enough
- 2021
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 70:3, s. 623-633
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Tidskriftsartikel (refereegranskat)abstract
- Species distribution data are fundamental to the understanding of biodiversity patterns and processes. Yet, such data are strongly affected by sampling biases, mostly related to site accessibility. The understanding of these biases is therefore crucial in systematics, biogeography, and conservation. Here we present a novel approach for quantifying sampling effort and its impact on biodiversity knowledge, focusing on Africa. In contrast to previous studies assessing sampling completeness (percentage of species recorded in relation to predicted), we investigate whether the lack of knowledge of a site attracts scientists to visit these areas and collect samples of species. We then estimate the time required to sample 90% of the continent under a Weibull distributed biodiversity sampling rate and the number of sampling events required to record 50% of the species. Using linear and spatial regression models, we show that previous sampling has been strongly influencing the resampling of areas, attracting repeated visits. This bias has existed for over two centuries, has increased in recent decades, and is most pronounced among mammals. It may take between 172 and 274 years, depending on the group, to achieve at least one sampling event per grid cell in the entire continent. Just one visit will, however, not be enough: in order to record 50% of the current diversity, it will require at least 12 sampling events for amphibians, 13 for mammals, and 27 for birds. Our results demonstrate the importance of sampling areas that lack primary biodiversity data and the urgency with which this needs to be done. Current practice is insufficient to adequately classify and map African biodiversity; it can lead to incorrect conclusions being drawn from biogeographic analyses and can result in misleading and self-reinforcing conservation priorities.
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