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174 results for “Biodiversity assessment”
Data from: Global biodiversity assessment and hyper-cryptic species complexes: more than one species of elephant in the room?
Several recent estimates of global biodiversity have concluded that the total number of species on Earth lies near the lower end of the wide range touted in previous decades. However, none of these recent estimates formally explore the real 'elephant in the room', namely, what proportion of species are taxonomically invisible to conventional assessments, and thus, as undiagnosed cryptic species, remain uncountable until revealed by multi-gene molecular assessments. Here we explore the significance and extent of so-called 'hyper-cryptic' species complexes, using the Australian freshwater fish Galaxias olidus as a proxy for any organism whose taxonomy ought to be largely finalized when compared to those in little-studied or morphologically undifferentiated groups. Our comprehensive allozyme (838 fish for 54 putative loci), mtDNA (557 fish for 605bp of cytb), and morphological (1963–3389 vouchers for 17–58 characters) assessment of this species across its broad geographic range revealed a 1500% increase in species-level biodiversity, and suggested that additional taxa may remain undiscovered. Importantly, while all 15 candidate species were morphologically diagnosable a posteriori from one another, single-gene DNA barcoding proved largely unsuccessful as an a priori method for species identification. These results lead us to draw two strong inferences of relevance to estimates of global biodiversity. First, hyper-cryptic complexes are likely to be common in many organismal groups. Second, no assessment of species numbers can be considered 'best practice' in the molecular age unless it explicitly includes estimates of the extent of cryptic and hyper-cryptic biodiversity.
Data from: Automated DNA-based plant identification for large-scale biodiversity assessment
Rapid degradation of tropical forests urges to improve our efficiency in large-scale biodiversity assessment. DNA-barcoding can assist greatly in this task, but commonly used phenetic approaches for DNA-based identifications rely on the existence of comprehensive reference databases, which are infeasible for hyperdiverse tropical ecosystems. Alternatively, phylogenetic methods are more robust to sparse taxon sampling but time-consuming, while multiple alignment of species-diagnostic, typically length-variable markers can be problematic across divergent taxa. We advocate the combination of phylogenetic and phenetic methods for taxonomic assignment of DNA-barcode sequences against incomplete reference databases such as GenBank, and we developed a pipeline to implement this approach on large-scale plant diversity projects. The pipeline workflow includes several steps: database construction and curation, query sequence clustering, sequence retrieval, distance calculation, multiple alignment and phylogenetic reconstruction. We describe the strategies used to establish these steps and the optimisation of parameters to fit the selected psbA-trnH marker. We tested the pipeline using infertile plant samples and herbivore diet sequences from the highly threatened Nicaraguan seasonally dry forest and exploiting a valuable purpose-built resource: a partial local reference database of plant psbA-trnH. The selected methodology proved efficient and reliable for high-throughput taxonomic assignment, and our results corroborate the advantage of applying 'strict' tree-based criteria to avoid false positives. The pipeline tools are distributed as the scripts suite 'BAGpipe' (pipeline for Biodiversity Assessment using GenBank data), which can be readily adjusted to the purposes of other projects and applied to sequence-based identification for any marker or taxon.
Data from: A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south-eastern Australia
Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species-level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south-eastern Australia and, in combination with their broad, naturally divided distribution and biological attributes that might limit dispersal, as well as ongoing taxonomic uncertainty, they comprise an ideal study group for assessing cryptic biodiversity. We used a multigene molecular assessment including both nuclear (51 allozyme loci; two S7 introns) and matrilineal markers (cytb) to assess species boundaries and broad genetic substructure within freshwater blackfishes. Range-wide examination demonstrates the presence of at least six candidate species across two nominal taxa, Gadopsis marmoratus and Gadopsis bispinosus. Phylogeographical patterns often aligned to purported biogeographical provinces but occasionally reflected more restricted and unexpected relationships. We highlight key issues with taxonomy, conservation, and management for a species group in a highly modified region.
Data from: Analysing biodiversity and conservation knowledge products to support regional environmental assessments
Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird & Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments.
Data from: Spectral diversity area relationships for assessing biodiversity in a wildland-agriculture matrix
Species-area relationships have long been used to assess patterns of species diversity across scales. Here this concept is extended to spectral diversity using hyperspectral data collected by NASA's Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) over western Michigan. This mixture of mesic forest and agricultural lands offers two end-points on the local-scale diversity continuum – one set of well mixed forest patches and one set of highly homogeneous agricultural patches. Using the sum of the first three principal component values and the principal components' convex hull volume, spectral diversity was compared within and among these plots and to null expectations for perfectly random and perfectly patchy landscapes. Overall the spectral diversity area relationship confirms the patterns that would be expected for this landscape, but this application suggests that this approach could be extended to less well understood landscapes and could reveal key insights about the relative importance of different drivers of community assembly, even in the absence of additional data about plant functional traits or species' identities.
FIGURE 10. Adult D in Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity ' hotspot' of southwestern Western Australia
FIGURE 10. Adult D. hebesa sp. nov. photographed in life from (A) Scaddan and (B) Mettler Lake, Western Australia (images‒B. Maryan).
FIGURE 12 in Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity ' hotspot' of southwestern Western Australia
FIGURE 12. The habitat of D. hebesa sp. nov., dense scrub heath on sandplain at Stirling Range National Park, Western Australia (image‒B. Maryan).
FIGURE 9. Preserved holotype WAM R144237 in Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity ' hotspot' of southwestern Western Australia
FIGURE 9. Preserved holotype WAM R144237 of D. hebesa sp. nov. and head scalation in (A) dorsal and (B) lateral views.
FIGURE 8 in Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity ' hotspot' of southwestern Western Australia
FIGURE 8. Map of Australia showing distribution of the D. australis species-group and specimens examined in the DNA and allozyme analyses. Specimens examined in the morphological analysis are indicated by a symbol with a central dot.
FIGURE 2 in Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity ' hotspot' of southwestern Western Australia
FIGURE 2. Principal Coordinates Analysis of the 48 individuals surveyed in the allozyme study. The relative PCO scores have been plotted for the first and second dimensions, which individually explained 37% and 12% respectively of the total multivariate variation present in 47 dimensions. Taxon symbols as for Figure 8.
FIGURE 1 in Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity ' hotspot' of southwestern Western Australia
FIGURE 1. Maximum likelihood tree based on the combined mitochondrial (ND2 and flanking tRNAs, 16S) and nuclear genes (RAG1, MXRA5, DYNLL1, C-mos) showing relationships among the D. australis species-group, and the outgroup species D. butleri and D. concinna. This tree highlights the paraphyly of D. australis sensu lato, with respect to D. torquata, and identifies D. hebesa sp. nov. as sister taxa to a D. australis + D. torquata clade. Values indicated at branches are Bayesian posterior probabilities/ maximum likelihood bootstrap support.
FIGURE 4 in Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity ' hotspot' of southwestern Western Australia
FIGURE 4. Bivariate plot of number of ventral scales versus number of hindlimb scales in males and females of each of the southwest W.A. population of D. australis and D. hebesa sp. nov.
FIGURE 7. Adult D in Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity ' hotspot' of southwestern Western Australia
FIGURE 7. Adult D. australis photographed in life from (A) Cowell, Eyre Peninsula, South Australia, (B) 14 km NW of Coober Pedy, South Australia, (C) Buningonia Spring, Coolgardie Goldfields bioregion, Western Australia, (D) 30 km NW of Salmon Gums, Mallee bioregion, Western Australia, (E) Rat Island, Houtman Abrolhos, Western Australia, (F) 22 km WSW of Hamelin Homestead, Shark Bay and (G) Cape Range, North West Cape, Western Australia, showing the variation in body colouration and intensity of head pattern (images‒A, B, C, E, F, G: B. Maryan, D: R. Lloyd).
FIGURE 3 in Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity ' hotspot' of southwestern Western Australia
FIGURE 3. Unrooted neighbour-joining network among six species or lineages of Delma, based on the pairwise matrix of unbiased Nei's distances presented in Table 4.
FIGURE 5 in Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity ' hotspot' of southwestern Western Australia
FIGURE 5. Bivariate plot of measurements of head length versus head depth in males and females of each of the southwest W.A. population of D. australis and D. hebesa sp. nov.
FIGURE 6. Preserved holotype WAM R27359 in Molecular and morphological assessment of Delma australis Kluge (Squamata: Pygopodidae), with a description of a new species from the biodiversity ' hotspot' of southwestern Western Australia
FIGURE 6. Preserved holotype WAM R27359 of D. australis and head scalation in (A) dorsal and (B) lateral views; F = frontals, L = loreals, LL = lower labials, M = mental, O = occipital, P = parietals, PN = postnasals, PF = prefrontals, R = rostral, SP = supraciliaries, SL = supraloreals, SN = supranasals, SO = supraoculars, UL = upper labials, T = upper temporals.
FIGURE 6. Photis geniculata a in A benefit to biodiversity assessment: An Indian survey demonstrates that Cheiriphotis geniculata is a misidentification of the valid species Photis geniculata Barnard, 1935 (Crustacea: Amphipoda)
FIGURE 6. Photis geniculata a) male habitus; b) head with extended cepalic lobe, dorsal view; c) antenna 1 without accessory flagellum.
FIGURE 3 in A benefit to biodiversity assessment: An Indian survey demonstrates that Cheiriphotis geniculata is a misidentification of the valid species Photis geniculata Barnard, 1935 (Crustacea: Amphipoda)
FIGURE 3. Photis geniculata. Male habitus (3.3 mm length). Scale bar 0.3 mm for Hd; 0.1 mm for A1, A2; 0.05 mm for Lbr, Lb, Mx1, Mx2, Mxp.
FIGURE 5 in A benefit to biodiversity assessment: An Indian survey demonstrates that Cheiriphotis geniculata is a misidentification of the valid species Photis geniculata Barnard, 1935 (Crustacea: Amphipoda)
FIGURE 5. Photis geniculata. Male habitus (3.3 mm length). Scale bar 0.2 mm for P6, P7; 0.08 mm for U1, U2, U3, T.
FIGURE 4 in A benefit to biodiversity assessment: An Indian survey demonstrates that Cheiriphotis geniculata is a misidentification of the valid species Photis geniculata Barnard, 1935 (Crustacea: Amphipoda)
FIGURE 4. Photis geniculata. Male habitus (3.3 mm length). Scale bar 0.05 mm for Md; scale bar 0.2 mm for Gn 1, Gn 2 (♂), Gn 2 (♀), P3, P4, P5; scale 0.3 mm for Ep1,2,3.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.