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FIGURE 1 in Genetic diversity in two threatened species of guitarfish (Elasmobranchii: Rhinobatidae) from the Brazilian and Argentinian coasts: an alert for conservation
FIGURE 1 | Median-joining network of mtCR haplotypes for A. Pseudobatos horkelii and B. Pseudobatos percellens. Haplotypes are represented by circles with size proportional to frequency in the total sample. All hatch marks correspond to one mutation. Samples from northern Argentina (AR), Torrinha/RS (RS), Florianópolis/SC (SC), Pontal do Paraná/PR (PR), Cananéia/ SP (SP1), Mongaguá/SP (SP2), Santos/SP (SP3), Rio de Janeiro/RJ(RJ).
FIGURE 2 in Genetic diversity in two threatened species of guitarfish (Elasmobranchii: Rhinobatidae) from the Brazilian and Argentinian coasts: an alert for conservation
FIGURE 2 | Graph of the Bayesian analysis of population structure of mtCR for A. Pseudobatos horkelii and B. Pseudobatos percellens. Samples from northern Argentina (AR), Torrinha/RS (RS), Florianópolis/SC (SC), Pontal do Paraná/PR (PR), Cananéia/ SP (SP1), Mongaguá/SP (SP2), Santos/SP (SP3), Rio de Janeiro/RJ(RJ).
When resilience is not enough: 2022 extreme marine heatwave threatens climatic refugia for a habitat-forming Mediterranean octocoral
<p>Climate change is impacting ecosystems worldwide, and the Mediterranean Sea is no exception. Extreme climatic events, such as marine heat waves (MHWs), are increasing in frequency, extent, and intensity during the last decades, which has been associated with an increase in mass mortality events for multiple species. Coralligenous assemblages, where the octocoral <em>Paramuricea clavata</em> lives, are strongly affected by MHWs. The Medes Islands Marine Reserve (NW Mediterranean) was considered a climate refugia for <em>P. clavata</em>, as their populations were showing some resilience to these changing conditions. In this study, we assessed the impacts of the MHWs that occurred between 2016 and 2022 in seven shallow populations of the octocoral <em>P. clavata</em> from a Mediterranean Marine Protected Area. The years that the mortality rates increased significantly were associated with the ones with strong MHWs, 2022 being the one with higher mortalities. In 2022, with 50 MHW days, the proportion of total affected colonies was almost 70%, with a proportion of the injured surface of almost 40%, reaching levels never attained in our study site since the monitoring was started. We also found spatial variability between the monitored populations. Whereas few of them showed low levels of mortality, others lost around 75% of their biomass. The significant impacts documented here raise concerns about the future of shallow <em>P. clavata</em> populations across the Mediterranean, suggesting that the resilience of this species may not be maintained to sustain these populations face the ongoing warming trends.</p>
Fig. 2 in The herpetofauna of Honaz Mountain National Park (Denizli Province, Turkey) and threatening factors
Fig. 2. Some of the amphibian and reptilian species in the study area: (a) Bufo bufo, (b) Hyla orientalis, (c) Rana macrocnemis, (d) Testudo graeca, (e) Mediodactylus kotschyi, (f) Ablepharus kitaibellii, (g) Stellagama stellio, (h) Anatololacerta danfordi, (i) Blanus strauchi, (j) Eryx jaculus, (k) Natrix natrix, and (l) Montivipera xanthina.
Fig. 1 in The herpetofauna of Honaz Mountain National Park (Denizli Province, Turkey) and threatening factors
Fig. 1. Study area and locations of field surveys in Honaz Mountain National Park, Turkey. The coordinates and elevations of the numbered sites are given in Appendix 1.
Fig. 6 in Endemism on a threatened sky island: new and rare species of herpetofauna from Cerro Chucantí, Eastern Panama
Fig. 6. Species accumulation curves for amphibians (left) and reptiles (right) for transects in the PMF and PWF on Cerro Chucantí. obs: observed species on transects; est: estimated species if the sampling effort is doubled. Details on the transects are shown in Table 1.
Fig. 1 in Endemism on a threatened sky island: new and rare species of herpetofauna from Cerro Chucantí, Eastern Panama
Fig. 1. (A) Satellite map and (B) abstract digital map showing the trails used on Cerro Chucantí for transects in the PWF (beige, black, partly blue, and red dashed trails) and PMF (orange, dark-grey, and green dashed trails). Records of some species are also shown (see Materials and Methods for details).
Fig. 2 in Endemism on a threatened sky island: new and rare species of herpetofauna from Cerro Chucantí, Eastern Panama
Fig. 2. Study area at CPNR. (A) Cerro Chucantí; (B) entrance to the reserve; (C) Camp Site 1, on 2016; (D) modern toilet at Camp Site 1; (E–F) forest above 1,300 m asl; (G) view of the secondary forest around the biological station up to the cloud forest on the ridge; (H) the field team, at 1,200 m asl from left: Madian Miranda, above Rogemif Fuentes, Orlando Gárces, below Abel Batista, and lower right Konrad Mebert.
Fig. 5. Selected reptile species found during the 2012–2016 in Endemism on a threatened sky island: new and rare species of herpetofauna from Cerro Chucantí, Eastern Panama
Fig. 5. Selected reptile species found during the 2012–2016 surveys on Cerro Chucantí. (A) Echinosaura aff. palmeri; (B) Ptychoglossus aff. plicatus; (C) Anolis aff. fuscoauratus; (D) Geophis aff. brachycephalus; (E) Corallus annulatus, highest elevation record; (F) Tantilla berguidoi, recently described and endemic (Batista et al. 2016b); (G) Bothrops asper, 1,273 m asl, highest elevation record for Panama; (H) Lachesis acrochorda juvenile, 1,011 m asl, highest elevation for this species in Panama.
Fig. 9 in Endemism on a threatened sky island: new and rare species of herpetofauna from Cerro Chucantí, Eastern Panama
Fig. 9. Relative abundance of the reptiles found during surveys from 2012–2016 in the Premontane Moist Forest (PMF) on Cerro Chucantí. * Species observed in PWF and PMF on Cerrro Chucanti, but outside a transect; ** Species of likely occurrence that have been found in similar habitat and elevations in adjacent peaks of Majé Mountains.
Fig. 10 in Endemism on a threatened sky island: new and rare species of herpetofauna from Cerro Chucantí, Eastern Panama
Fig. 10. Relative abundance of the reptiles found during surveys from 2012–2016 in the Premontane Wet Forest (PWF) on Cerro Chucantí. 1 indicates provisional identification; * Species observed in PWF and PMF on Cerrro Chucanti, but outside a transect; ** Species of likely occurrence that have been found in similar habitat and elevations in adjacent peaks of Majé Mountains.
Fig. 8 in Endemism on a threatened sky island: new and rare species of herpetofauna from Cerro Chucantí, Eastern Panama
Fig. 8. Relative abundance of amphibians found during surveys from 2012–2016 in the Premontane Wet Forest (PWF) on Cerro Chucantí. * Species observed in PWF and PMF on Cerrro Chucanti, but outside a transect.
Fig. 7 in Endemism on a threatened sky island: new and rare species of herpetofauna from Cerro Chucantí, Eastern Panama
Fig. 7. Relative abundance of amphibians found during surveys from 2012–2016 in the Premontane Moist Forest (PMF) on Cerro Chucantí. * Species observed in PWF and PMF on Cerrro Chucanti, but outside a transect; ** Species of likely occurrence that have been found in similar habitat and elevations in adjacent peaks of Majé Mountains.
Fig. 3. Selected amphibian species found during the 2012–2016 in Endemism on a threatened sky island: new and rare species of herpetofauna from Cerro Chucantí, Eastern Panama
Fig. 3. Selected amphibian species found during the 2012–2016 surveys on Cerro Chucantí. (A) Dermophis aff. glandulosus; (B) second known specimen of Bolitoglossa chucantiensis, recently described and endemic (Batista et al. 2014a); (C) Bolitoglossa aff. biseriata; (D) Oedipina aff. complex; (E) Strabomantis bufoniformis; (F) Diasporus majeensis, recently described and endemic (Batista et al. 2016a); (G) Pristimantis gaigei; (H) Pristimantis moro.
Fig. 4. Selected amphibian species found during the 2012–2016 in Endemism on a threatened sky island: new and rare species of herpetofauna from Cerro Chucantí, Eastern Panama
Fig. 4. Selected amphibian species found during the 2012–2016 surveys on Cerro Chucantí that await formal description or clarification of relationships. (A) Colostethus aff. pratti; (B) Silverstoneia sp.; (C) Pristimantis aff. latidiscus; (D) Pristimantis aff. ridens.
Improving the application of Important Plant Areas to conserve threatened habitats: a case study of Uganda
<p><strong>This data set relates to the publication: Richards, S. L., Kalema, J., Ojelel, S., Williams, J., & Darbyshire, I. (2024). Improving the application of Important Plant Areas to conserve threatened habitats: A case study of Uganda. Conservation Science and Practice, e13246. https://doi.org/10.1111/csp2.13246<br></strong></p> <p><strong>Abstract:</strong></p> <p>Important Plant Areas (IPAs) are a successful method of identifying priority areas for plant conservation. Assessment of IPAs, however, often relies on criteria related to species, while incorporation of habitats has been less consistent. Using Uganda as a case study, we test the application of the threatened habitat criterion – criterion C. We identified nationally threatened habitats using Red List of Ecosystems criteria and assess, for the first time, how differing application of thresholds under IPA criterion C can influence IPA network outcomes. Eleven threatened habitats were identified, with declines switching from predominantly forest to savanna after the mid-20<sup>th</sup> century. Significantly, we found current IPA guidance on use of criterion C needlessly limits the number of sites that qualify as IPAs. The “five best sites” IPA threshold is reserved for countries where quantitative data is unavailable, however, the application of the relevant numerical thresholds (site contains ≥10% of national resource or site is among the best quality examples required to collectively prioritisie up to 20% of the national resource) to quantitative data largely generated fewer than five IPAs, comparably limiting conservation opportunities identified. We recommend, therefore, that the “five best” threshold is available for application on both qualitative and quantitative data. This will bolster the value of IPAs in conserving and restoring threatened and ecologically important habitats under the Kunming-Montreal Global Biodiversity Framework.</p> <p><strong>Dataset:</strong></p> <p>Within this dataset is a shapefile of the estimated extent of threatened habitats in Uganda. Each polygon represents a single "site" for each threatened habitat, with methodology for site identification given in the manuscript. Feature area and percentage national resource are given for each site, enabling users to identify those that trigger the different IPA criterion C thresholds.</p> <p><strong>In this study, we have preliminarily identified the threatened habitats and IPAs for Uganda. However, it is important to seek the expertise and views of stakeholders, consider other IPA criteria met and any complementarity between sites when identifying IPAs. In addition, ground-truthing or more localised data could validate the threat status of a vegetation type as well as identifying which sites are best to conserve these habitats. </strong></p>
Data and source code for: Recent adaptation in a threatened salmonid revealed by museum genomics
<p>Steelhead/rainbow trout (Oncorhynchus mykiss) is an imperiled salmonid with two main life history strategies: migrate to the ocean or remain in freshwater. Domesticated hatchery forms of this species have been stocked into almost all California waterbodies, possibly resulting in introgression into natural populations and altered population structure. </p> <p>We compared whole-genome sequence data from contemporary populations against a set of museum population samples of steelhead from the same locations that were collected prior to most hatchery stocking. </p> <p>We observed minimal introgression and few steelhead-hatchery trout hybrids despite a century of extensive stocking. Our historical data show signals of introgression with a sister species and indications of an early hatchery facility. Finally, we found that migration-associated haplotypes have become less frequent over time, a likely adaptation to decreased opportunities for migration. Since contemporary migration-associated haplotype frequencies have been used to guide species management, we consider this to be a rare example of shifting baseline syndrome that has been validated with historical data. </p> <p>We suggest cautious optimism that a century of hatchery stocking has had minimal impact on California steelhead population genetic structure, but we note that continued shifts in life history may lead to further declines in the ocean-going form of the species. </p>
Figure 1 in Phylogenetic placement of a recently discovered population of the threatened alpine she-oak skink Cyclodomorphus praealtus (Squamata: Scincidae) in Victoria
Figure 1: Elevation map of the mainland Australian alpine region indicating the five major populations of Cyclodomorphus praealtus, including the new location of Wellington Plains. Elevation is indicated by light, mid and dark grey areas at 500 m intervals, with highest elevations at or above 1500 m above sea level. Adapted from fig. 1; Koumoundouros et al. (2009).
Figure 3 in Phylogenetic placement of a recently discovered population of the threatened alpine she-oak skink Cyclodomorphus praealtus (Squamata: Scincidae) in Victoria
Figure 3: Population structure of Victorian Cyclodomorphus praealtus according to ND4 mitochondrial haplotype network. Black indicates individuals from Lankey Plain, dark grey indicates those from Mt Hotham, white indicates those from Bogong High Plains and diagonal stripes indicate those from Wellington Plains. The network structure indicates 3 haplogroups (i, ii and iii) within Victoria. Each circle represents a unique haplotype, with the circle size indicative of frequency and sample sizes within each circle. Empty circles represent missing haplotypes and differ by one base pair from the closest haplotype.
Figure 2 in Phylogenetic placement of a recently discovered population of the threatened alpine she-oak skink Cyclodomorphus praealtus (Squamata: Scincidae) in Victoria
Figure 2: A Bayesian consensus tree of the mtDNA ND4 sequences, depicting the relationship between unique haplotypes at each locality (Bogong High Plains, Lankey Plain, Mt Hotham, Wellington Plains and Kosciuszko National Park) for Cyclodomorphus praealtus. Bayesian posterior probabilities are shown at major nodes.
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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)
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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.