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Mammals under pressure: presence data for assessing extinction of endemic, threatened, and mammals subject to use, in Colombia
<p>This is the first dataset that provides a complete compilation of mammal records based on camera traps, human observations, and specimens deposited in biological collections in Colombia. We compiled a dataset with unpublished information, including 97,943 records corresponding to 136 species, of which 38 are endemic, 92 are identified as species subject to use by humans in the literature, and 33 are categorized either as Data Deficient or threatened according to international or unofficial national assessments. The information comes from 31 out of 32 departments of Colombia and constitutes relevant input for future distribution and conservation assessments. Most records (n=96,417, 98.44%) come from non-invasive sampling methods such as camera traps. However, we highlight the contribution of museum specimens (n= 1,332), especially for small and medium-sized species, many of them with restricted distributions in the country. This dataset constitutes a joint collaborative and interinstitutional effort that serves as the basis for cooperative work to comprehensively assess the current conservation status of all mammal species in Colombia.</p>
FIGURE 2 in Extinction risk or lack of sampling in a threatened species: Genetic structure and environmental suitability of the neotropical frog Pristimantis penelopus (Anura: Craugastoridae)
FIGURE 2: (Left) Maximum clade credibility tree depicting the phylogenetic position of Pristimantis penelopus within the P. ridens series. Numbers on nodes indicate posterior probabilities. Numbers below nodes represent nodal support using the ultrafast bootstrap (see methods). Asterisks indicate nodal support above 95% in both Bayesian and ML methods. (Right) Haplotype network based on 460 bp of the COI region. Numbers of mutational steps are shown on the lines connecting haplotypes. Colors refer to geographic locations shown in Figure 1.
FIGURE 4 in Extinction risk or lack of sampling in a threatened species: Genetic structure and environmental suitability of the neotropical frog Pristimantis penelopus (Anura: Craugastoridae)
FIGURE 4: Potential distribution of Pristimantis penelopus based on ecological niche modeling (red). Yellow dots represents occurrence localities used to calibrate the model. See main text for details.
FIGURE 1 in Extinction risk or lack of sampling in a threatened species: Genetic structure and environmental suitability of the neotropical frog Pristimantis penelopus (Anura: Craugastoridae)
FIGURE 1: Geographic sampling of Pristimantis penelopus. Colored circles indicate sequenced specimens. Different colors represent the populations used in the genetic analysis (see Figure 2 for color codes).
FIGURE 3 in Extinction risk or lack of sampling in a threatened species: Genetic structure and environmental suitability of the neotropical frog Pristimantis penelopus (Anura: Craugastoridae)
FIGURE 3: Phenotypic variation of Pristimantis penelopus across its distribution. Localitites are shown in Appendix 1.
Fig. 5 in Trophic strategy of Atlantirivulus riograndensis (Cyprinodontiformes: Rivulidae), a non-annual rivulid threatened by extinction, in a perennial environment, Brazil)
Fig. 5. Seasonal distribution of Atlantirivulus riograndensis by frequency of standard length (SL). Individuals collected at the Banhado dos Pachecos wildlife refuge, Viamão, Rio Grande do Sul, Brazil, in 2012.
Fig. 3 in Trophic strategy of Atlantirivulus riograndensis (Cyprinodontiformes: Rivulidae), a non-annual rivulid threatened by extinction, in a perennial environment, Brazil)
Fig. 3. Index of stomach fullness in relation to standard length. Ontogenetic analysis of the Atlantirivulus riograndensis feeding intensity by sex, collected the Banhado dos Pachecos wildlife refuge, in the city of Viamão, Rio Grande do Sul, Brazil, in 2012.
Fig. 2 in Trophic strategy of Atlantirivulus riograndensis (Cyprinodontiformes: Rivulidae), a non-annual rivulid threatened by extinction, in a perennial environment, Brazil)
Fig. 2. Sampling area of Atlantirivulus riograndensis. Evidence of seasonal modification of landscape at the collection point at Banhado dos Pachecos wildlife refuge, Viamão, Rio Grande do Sul, Brazil, during the year 2012 (a) Summer in March; Autumn in (b) May and (c) in June; (d) Winter in September; Spring in (e) October and (f) November.
Fig. 1 in Trophic strategy of Atlantirivulus riograndensis (Cyprinodontiformes: Rivulidae), a non-annual rivulid threatened by extinction, in a perennial environment, Brazil)
Fig. 1. Geographic location of the capture area of Atlantirivulus riograndensis. Geographical representation of South America, especially (a) Brazilian territory, (b) the state of Rio Grande do Sul and (c) Banhado dos Pachecos wildlife refuge in the city of Viamão, sampling area of Atlantirivulus riograndensis in 2012.
Fig. 4 in Trophic strategy of Atlantirivulus riograndensis (Cyprinodontiformes: Rivulidae), a non-annual rivulid threatened by extinction, in a perennial environment, Brazil)
Fig. 4. Canonical Correspondence Analysis (CCA) of food composition of Atlantirivulus riograndensis representing the importance of seasonal and ontogenetic variables, with p <0:05, according to the length of arrows associated with each vector. Individuals collected at the Banado dos Pachecos wildlife refuge, Viamão, Rio Grande do Sul, Brazil, in 2012. A: ≤ 21.6 mm Standard length; B: Standard length from 21.7 to 32.6 mm; C: Standard length ≥ 32.7 mm.
Mitigating the extinction risk of globally threatened and endemic mountainous Orthoptera species: Parnassiana parnassica and Oropodisma parnassica
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Data from: Climate change predicts Quaternary extinctions and extant genetic diversity in a threatened Australian lizard
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Extreme weather affects colonization-extinction dynamics and the persistence of a threatened butterfly
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Fig. 2 in Conservation status and bio-ecology of Brycon orbignyanus (Characiformes: Bryconidae), an endemic fish species from the Paraná River basin (Brazil) threatened with extinction
Fig. 2. Abundance (captures per unit of effort – CPUE) of Brycon orbignyanus observed in the Upper Paraná River floodplain in different years (1986 to 1988, 1992 to 1994 and 2000 to 2010) and subsystems (Paraná, Baía and Ivinhema).
Fig. 4 in Conservation status and bio-ecology of Brycon orbignyanus (Characiformes: Bryconidae), an endemic fish species from the Paraná River basin (Brazil) threatened with extinction
Fig. 4. Ontogenetic variations in the diet of Brycon orbignyanus in the Upper Paraná River floodplain. FI = fish; AI = aquatic invertebrates; TI = terrestrial invertebrates; TP = terrestrial plants; AP = aquatic plants.
Fig. 1 in Conservation status and bio-ecology of Brycon orbignyanus (Characiformes: Bryconidae), an endemic fish species from the Paraná River basin (Brazil) threatened with extinction
Fig. 1. The locations of reservoirs from which the Brycon orbignyanus occurrence was evaluated and sites sampled throughout the Upper Paraná River floodplain (the Paraná, Baía and Ivinhema River subsystems).
Fig. 3 in Conservation status and bio-ecology of Brycon orbignyanus (Characiformes: Bryconidae), an endemic fish species from the Paraná River basin (Brazil) threatened with extinction
Fig. 3. Relationships between YOY abundance (CPUE) of Brycon orbignyanus and hydrological attributes observed in the Paraná and Ivinhema subsystems. a. Interrupted flood duration (days) (> 4.5 m Paraná River and> 2.75 m Ivinhema River), b. Uninterrupted flood duration (days).
Data from: Distribution models predict climate-related range alteration or extinction of eleven threatened tropical rainforest trees in the Western Ghats
<p>This dataset contains information related to species occurence data and species distribution modeling (SDM) analysisr of eleven threatened tree species. Occurrences are compiled from extensive field surveys in the Anamalai Hills along with data from the Global Biodiversity Information Facility (GBIF.org) and earlier work done within the southern Western Ghats, India.</p> <p>References:<br>Page, N. V., & Shanker, K. (2020). Climatic stability drives latitudinal trends in range size and richness of woody plants in the Western Ghats, India. PLOS ONE, 15(7), e0235733. https://doi.org/10.1371/journal.pone.0235733</p> <p>GBIF.org (2022) GBIF Occurrence Download, 2 August 2022. DOI:10.15468/dl.gnvuxj</p> <p><br>AUTHOR #1<br>1. Name: A.P. Madhavan<br>2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India<br>3. Email address: madhavan@ncf-india.org<br>4. ORCID: https://orcid.org/0009-0009-2754-8256</p> <p>AUTHOR #2<br>1. Name: Kshama Bhat<br>2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India<br>3. Email address: kshama@ncf-india.org<br>4. ORCID: ORCID: https://orcid.org/0000-0002-6190-2687</p> <p>AUTHOR #3<br>1. Name: Srinivasan Kasinathan<br>2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India<br>3. Email address: srini@ncf-india.org<br>4. ORCID: https://orcid.org/0000-0001-7323-6653</p> <p>AUTHOR #4<br>1. Name: Divya Mudappa <br>2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India<br>3. Email address: divya@ncf-india.org <br>4. ORCID: https://orcid.org/0000-0001-9708-4826</p> <p>AUTHOR #5<br>1. Name: Navendu Page<br>2. Work Address: Wildlife Institute of India, Post Box No. 18, Chandrabani, Dehradun, Uttarakhand 248001, India<br>3. Email address: navendu.page@gmail.com<br>4. ORCID: ORCID: https://orcid.org/0000-0002-9413-7571</p> <p>AUTHOR #6<br>1. Name: T. R. Shankar Raman <br>2. Work Address: Nature Conservation Foundation, 1311, 12th A Main, Vijayanagar 1st Stage, Mysuru 570017, Karnataka, India<br>3. Email address: trsr@ncf-india.org <br>4. ORCID: https://orcid.org/0000-0002-1347-3953</p> <p>Keywords: tropical rainforest, climate change, tree distributions, species distribution models, range shifts, Western Ghats</p> <p><br>Geographic Coverage:<br>1. Location/Study Area: Southern Western Ghats Montane Rain Forests, Southern Western Ghats Moist Deciduous Forests, India<br>2. GPS coordinates: SWG (73.95° – 80.33° E, 8.06° – 13.11°N) </p> <p>Temporal coverage<br>Starts: 2020-08-01<br>Ends: 2024-03-28</p> <p>Besides this README.txt file, the dataset includes three comma-delimited text files (csv); two R scripts, and 1 kml file of surveyed trails.</p> <p>CSV files with the data in columns as explained below:</p> <p>1) Focal_Tree_Dat.csv</p> <p>Comp: Number identifier<br>FT_ID: Unique tree no for each individual<br>Focal_tree: Scientific name of species<br>Date: Date of occurrence observation<br>Place: Area/locality description<br>Trail: Unique trail ID<br>Waypoint: Waypoint number <br>Time: Time in hh:mm format <br>Location: Specific description of occurrence locality <br>Latitude: Latitude in decimal degrees N <br>Longitude: Longitude in decimal degrees E <br>Elevation: Elevation in metres <br>Slope: Cateory of slope <br>ID_Notes: Notes on identification<br>Phenophase: Phenophase expression at the time of observation <br>GBH: Girth at breast height in centimetres (comma separated list of numbers in case of multi-stemmed trees) <br>Tree_ht: Tree height in metres<br>Canopy_ht: Maximimum height of the surrounding canopy in metres<br>Substrate: Soil substrate composition<br>Invasives: Name of invasive species (if present) <br>Stature: Vegetation strata position <br>Relatively: Stature of focal individual relative to other surrounding individuals <br>Deadwood: Description of deadwood on the tree <br>Damage: Description of damage on the bole <br>Shape: Description of tree canopy shape<br>Closure: Canopy closure at focal tree <br>Seedlings: Number of conspecific seedlings present in 5 m radius of focal tree <br>Saplings: Number of conspecific saplings present in 5 m radius of focal tree<br>Trees: Number of conspecific trees present in 5 m radius of focal tree<br>Remarks: Remarks </p> <p>2) Ffspecies.csv</p> <p>Source: Source of occurrence <br>ID: State/location of occurrence<br>Region: Biogeographic region of occurrence <br>decimalLatitude: Latitude in decimal degrees N<br>decimalLongitude: Longitude in decimal degrees E<br>species: Scientific name of species</p> <p>4) ft_surveys.csv</p> <p>Date: Date of survey of sample trail<br>Prot_type: Category indicating whether protected area or fragment <br>Place: Area/locality description<br>Route_description: Specific landmark description of trail<br>Trail: Unique trail ID <br>Trail_distance: Tracked distance of trail in km <br>Corrected_trail_distance: Corrected distance of trail in km<br>Track_filename_kml: File name of gps track<br>Sample_collected: Name of species if sample collected <br>Observers: Name of observers <br>Remarks: Remarks</p> <p>ANALYSES SCRIPTS<br>flexsdm_script.R<br>Script containing the analysis of all maxent distribution modeling and associated analysis</p> <p>Franklinia_density.Rmd<br>Script of density and abundance related analysis</p> <p> </p>
Projected climate change threatens significant range contraction of Cochemiea halei (Cactaceae), an island endemic, serpentine adapted plant species at risk of extinction
<p>Threats faced by narrowly distributed endemic plant species in the face of the Earth's sixth mass extinction and climate change exposure are especially severe for taxa on islands. We investigated the current and projected distribution and range changes of Cochemiea halei, an island endemic cactus. This taxon is of conservation concern, currently listed as vulnerable on the International Union for the Conservation of Nature Red List and as a species of special concern under Mexican federal law.</p> <p>The goals of this study are to 1). identify the correlations between climate variables and current suitable habitat for C. halei; 2). determine if the species is a serpentine endemic or has a facultative relationship with ultramafic soils; 3). predict range changes of the species based on climate change scenarios.</p> <p>Location: The island archipelago in Bahía Magdalena on the Pacific coast, Baja California Sur, Mexico.</p> <p>Main conclusions: The occurrence of the species is found to be strongly correlated with ultramafic soils. The most important climate predictor for habitat suitability is annual temperature range. The species is predicted to undergo range contractions from 21% to 53%, depending on the severity and duration of exposure to climate change. The broader implications for a wide range of narrowly adapted, threatened and endemic plant species indicate an urgent need for threat assessment based on habitat suitability and climate change modeling.</p>
Projected climate change threatens significant range contraction of Cochemiea halei (Cactaceae), an island endemic, serpentine adapted plant species at risk of extinction
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