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549 results for “species extinction”
Data from: Deconstructing an infamous extinction crisis: Survival of Partula species on Moorea and Tahiti
Eleven of eighteen Society Island Partula species endemic to the Windward Island subgroup (Moorea and Tahiti) have been extirpated by an ill-advised biological control program. The conservation status of this critically endangered tree snail radiation is of considerable import, but is clouded by taxonomic uncertainty due to the extensive lack of congruence among species designations, diagnostic morphologies and molecular markers. Using a combination of museum, captive, and remnant wild snails, we obtained the first high-resolution nuclear genomic perspective of the evolutionary relationships and survival of fourteen Windward Island Partula species, totaling 93 specimens. We analyzed ~1,607-28,194 nuclear genomic loci collected with the double digest Restriction-site Associated sequencing method. Results from phylogenomic trees, species estimation, and population assignment tests yielded monophyly of the Windward Island subgroup. Within this group, two well-supported clades encompassing five species complexes were recovered. Clade 1 was restricted to Tahiti and contained two species complexes: "P. affinis" (three species) and "P. otaheitana" (five species). Clade 2 occurred on Moorea and on Tahiti and consisted of three species complexes: one Tahitian, "P. clara/P. hyalina"; the other two, "P. taeniata" (three species) and "P. suturalis" (six species), Moorean. Our genomic results largely corroborated previous mitochondrial DNA survival estimates for Moorea and Tahiti, with all five species complexes having members surviving in captivity and/or as remnant wild populations, although the details vary in each case. Continued, proactive conservation and management may yet ensure a phylogenetically-representative survival of the fabled Partula species of Moorea and Tahiti.
Data from: Loss of animal seed dispersal increases extinction risk in a tropical tree species due to pervasive negative density dependence across life stages
Overhunting in tropical forests reduces populations of vertebrate seed dispersers. If reduced seed dispersal has a negative impact on tree population viability, overhunting could lead to altered forest structure and dynamics, including decreased biodiversity. However, empirical data showing decreased animal-dispersed tree abundance in overhunted forests contradict demographic models which predict minimal sensitivity of tree population growth rate to early life stages. One resolution to this discrepancy is that seed dispersal determines spatial aggregation, which could have demographic consequences for all life stages. We tested the impact of dispersal loss on population viability of a tropical tree species, Miliusa horsfieldii, currently dispersed by an intact community of large mammals in a Thai forest. We evaluated the effect of spatial aggregation for all tree life stages, from seeds to adult trees, and constructed simulation models to compare population viability with and without animal-mediated seed dispersal. In simulated populations, disperser loss increased spatial aggregation by fourfold, leading to increased negative density dependence across the life cycle and a 10-fold increase in the probability of extinction. Given that the majority of tree species in tropical forests are animal-dispersed, overhunting will potentially result in forests that are fundamentally different from those existing now.
Data from: Intraspecific haplotype diversity in Cherleria sedoides L. (Caryophyllaceae) is best explained by chloroplast capture from an extinct species
Cherleria sedoides, a plant species widespread in alpine areas of the major European mountain ranges and in Scotland, contains two highly divergent chloroplast haplotype groups, one widespread (WH) and one present only in some populations in the Alps (AH). We investigated whether this haplotype diversity is the result of (1) intraspecific differentiation, (2) retention of an ancestral polymorphism or (3) hybridisation. For this purpose, 106 matK sequences from throughout the Caryophyllaceae and 80 trnQ-rps16 and psbD-trnT sequences of C. sedoides (51) and other species of Cherleria (29) were used for the construction of phylogenies and haplotype networks. As the two haplotype groups were never each other's closest relatives, haplotype diversity as a result of intraspecific differentiation is unlikely. Patterns of genetic differentiation within the WH and AH groups are very different. Whereas WH shows a radial pattern typical of rapid expansion, AH is divided into two divergent subgroups each containing more variation than the WH group. This suggests that the two haplotype groups have dissimilar histories and are therefore unlikely to represent an ancestral polymorphism. Instead, we conclude that the polymorphism is best interpreted as the result of hybridisation. As the WH and AH haplotype groups fall into Cherleria, but do not group with any extant species, we conclude that the rare AH group represents the original C. sedoides, and that the WH group was captured from another, now extinct, species of Cherleria.
Data from: Genetic rediscovery of an 'extinct' Galápagos giant tortoise species
Genes from recently extinct species can live on in the genomes of extant individuals of mixed ancestry. Recently, Poulakakis et al. detected genetic signatures of the giant Galápagos tortoise once endemic to Floreana Island (Chelonoidis elephantopus) within eleven hybrid individuals of otherwise pure C. becki on Volcano Wolf, Isabela Island. Movement of tortoises among islands by pirate and whaling ships was not uncommon during the 1800's, representing a likely mechanism by which individuals from Floreana were translocated to northern Isabela, despite being presumed extinct soon after Charles Darwin's historic voyage to the Galápagos Islands in 1835. These eleven hybrid individuals with C. elephantopus ancestry were thought to be the last genetic vestiges of a unique evolutionary lineage in the wild. Here we report that reproductively mature purebred tortoises of the recently 'extinct' C. elephantopus from Floreana Island are very likely still alive today, as identified and tracked through the genetic footprints' left in the genomes of very recent hybrid offspring on Volcano Wolf, Isabela Island. If found, these purebred C. elephantopus individuals could constitute core founders of a captive breeding program directed towards resurrecting this species.
Data from: Diversity patterns of native and exotic fish species suggest homogenization processes, but partly fail to highlight extinction threats
Exotic species are a major threat to biodiversity and have modified native communities worldwide. Invasion processes have been extensively studied, but studies on species richness and beta diversity patterns of exotic and native species are rare. We investigate such patterns among exotic and native fish communities in upland and lowland rivers to explore their relationship with environmental drivers. Location: Northern Italy. Exotic and native fish beta diversity patterns were investigated separately in lowland and upland sites using Local Contribution to Beta Diversity (LCBD) and Species Contribution to Beta Diversity (SCBD) analyses. To examine the main environmental variables affecting the LCBD, a Boosted Regression Trees (BRT) method was used. Community dispersion among and within stream orders was investigated with the PERMDISP test. In lowland sites, exotic species richness was higher than native species richness, especially in large rivers and drainage canals. An opposite trend was found in upland sites, where native species richness was higher than exotic species richness, especially in large rivers. No clear LCBD patterns were found along stream orders in the lowland, whereas higher stream orders in the upland showed the highest LCBD. Its patterns in upland and lowland sites were related with a number of factors, such as total suspended solids and total phosphorus. Community dispersion among stream orders did not show a relationship with environmental heterogeneity. SCBD values were positively correlated with species occupancy in the study area and native species showed higher SCBD values than exotic species only in the uplands. Main conclusions: Large rivers in the uplands are important in maintaining native fish diversity and should be protected against invasive fish. In contrast, most lowland rivers have suffered from biological homogenization. Some rare native species can show low contribution to beta diversity, but still need conservation actions due to their risk of local extinction.
FIGURE 5 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 5. Scatterplot of sheared second and third PC scores of 13 logtransformed morphometric variables of Ptychochromoides betsileanus (n = 10; triangles), P. itasy (n = 3; squares), and Ptychochromoides sp (MNHN 1907104; n = 2; circles).
FIGURE 1 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 1. Map of Madagascar indicating recent or verifiable (Lake Itasy) collection localities for members of Ptychochromoides and Oxylapia polli.
FIGURES 13 in Polygyrid land snails, Vespericola (Gastropoda: Pulmonata), 4. A new and possibly extinct species from central California, U. S. A.
FIGURES 13. Vespericola ohlone Roth, sp. nov. Holotype, SBMNH 348128, Patterson's Willows, Alameda County, California. Top, apertural, and basal views of shell. Diameter (exclusive of outer lip) 14.5 mm; scale bar = 5 mm.
FIGURE 4 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 4. Ptychochromoides betsileanus, lectotype, BMNH 1882.2.25:69, adult male, 159.6 mm SL; Madagascar: Betsileo region. Right side illustrated due to damage to left side (image reversed).
FIGURE 6 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 6. Ptychochromoides vondrozo, holotype, UMMZ 235297, adult female, 182.0 mm SL; Madagascar: Fianarantsoa Province: Ramanara River. Right side illustrated due to distortion of specimen (image reversed). Photograph by Heok Hee Ng.
FIGURE 1 in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 1. Holotype female of Philautus pardus, 32.1 mm SVL, BMNH 1947.2.7.96. A. Dorsal view. B. Ventral view.
FIGURE 4 in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 4. Holotype female of Philautus maia, 44.6 mm SVL, BMNH 76.3.21.18. A. Illustration of eggs carried on venter in Günther (1876). B. Ventral view, showing depressions made by eggs. C. Lateral view, showing speckled pattern.
FIGURE 3. A in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 3. A. Factor scores (no rotation) of principal components analysis of mensural data of Philautus pardus (square), P. viridis (rhombus), P. stuarti (star), and P. variabilis (circle) (females represented by open symbols, males by solid symbols). B. Canonical variables plot of discriminant function analysis of sizeadjusted residuals (the 95% confidence ellipses are centered on the centroid of each species).
FIGURE 2 in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 2. Holotype female of Philautus pardus, 32.1 mm SVL, BMNH 1947.2.7.96. A. Lateral view of head. B. Dorsal view of head. C. Left hand. D. Left foot. E. Diagrammatic representation of leftfoot webbing. Scale bars = 1 mm.
FIGURE 5 in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 5. Holotype female of Philautus maia, 44.6 mm SVL, BMNH 76.3.21.18. A. Lateral aspect of head. B. Thigh, showing reticulated pattern. C. Left hand. D. Left foot. E. Diagrammatic representation of leftfoot webbing. Scale bars = 1 mm.
FIGURE 6. A in New species amongst Sri Lanka's extinct shrub frogs (Amphibia: Rhacophoridae: Philautus)
FIGURE 6. A. Factor scores (no rotation) of principal components analysis of mensural data of P. m a i a (square), P. reticulatus (circle), P. lunatus (rhombus) and P. papillosus (star) (females represented by open symbols, males by solid symbols). B. Canonical variables plot of discriminant function analysis of sizeadjusted residuals (the 95% confidence ellipse is centered on the centroid).
FIGURES 1–4. 1–3 Spatiator martensi n in Spatiator martensi n. sp., a second species of the extinct spider family Spatiatoridae in Eocene Baltic amber (Araneae)
FIGURES 1–4. 1–3 Spatiator martensi n. sp., ♂ holotype in Baltic amber; 1 outline of the body, lateral aspect. Reconstruction from dorsal and oblique aspects. Only a single eye is drawn; 2–3 right pedipalpus, dorsal and ventral aspect. Normal (thin) setae are not drawn. 4 Spatiator praeceps Petrunkevitch 1942, ♂, in Baltic amber, ventral aspect of the right pedipalpus. C = conductor, E = embolus, M = emulsion, S = sperm duct. Scales: 1, 1.0 mm; 2–4, 0.2 mm.
FIGURE 5. Spatiator martensi n in Spatiator martensi n. sp., a second species of the extinct spider family Spatiatoridae in Eocene Baltic amber (Araneae)
FIGURE 5. Spatiator martensi n. sp. (Spatiatoridae), fossil ♂ in Baltic amber, dorsal aspect. Body length 4.3 mm.
FIGURE 15 in A taxonomic revision of Atelopus pachydermus, and description of two new (extinct?) species of Atelopus from Ecuador (Anura: Bufonidae)
FIGURE 15. Manus (A) and pes (B), in ventral view, of female Atelopus onorei from Río Chipla, Provincia Azuay (QCAZ 1868). The arrow designates the Sesamoid I. Stippled areas are bone; cartilage shown in dark gray. Broken line indicates missing phalanx. Scale = 2 mm.
FIGURE 14 in A taxonomic revision of Atelopus pachydermus, and description of two new (extinct?) species of Atelopus from Ecuador (Anura: Bufonidae)
FIGURE 14. Skeletal features of female Atelopus onorei from Río Chipla, Provincia Azuay (QCAZ 1868). (A) ventral view of hyobranchium, (B) dorsal view of vertebral column and pelvic girdle, and (C) ventral view of pectoral girdle. Scale = 5 mm.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.