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502 results for “natural populations”
Supplementary material 2 from: Molloy SW, Davis RA, Dunlop JA, van Etten EJB (2017) Applying surrogate species presences to correct sample bias in species distribution models: a case study using the Pilbara population of the Northern Quoll. Nature Conservation 18: 27-46. https://doi.org/10.3897/natureconservation.18.12235
Full readout for the MaxEnt northern quoll SDM :
Supplementary material 1 from: Molloy SW, Davis RA, Dunlop JA, van Etten EJB (2017) Applying surrogate species presences to correct sample bias in species distribution models: a case study using the Pilbara population of the Northern Quoll. Nature Conservation 18: 27-46. https://doi.org/10.3897/natureconservation.18.12235
GIS data sets used in variable assessments and map of Pilbara vegetation systems :
Supplementary material 1 from: Thomaes A, Verschelde P, Mader D, Sprecher-Uebersax E, Fremlin M, Onkelinx T, Méndez M (2017) Can we successfully monitor a population density decline of elusive invertebrates? A statistical power analysis on Lucanus cervus. In: Campanaro A, Hardersen S, Sabbatini Peverieri G, Carpaneto GМ (Eds) Monitoring of saproxylic beetles and other insects protected in the European Union. Nature Conservation 19: 1-18. https://doi.org/10.3897/natureconservation.19.11761
Figures of statistical support : Data type: statistical data
Fig. 2 in Ancyrophora gracilis L , 1892 and Actinocephalus permagnus Wellmer, 1910 (Eugregarinorida: Apicomplexa) in natural populations of ground beetles (Coleoptera, Carabidae) - hosts preferences, intensity and seasonal dynamic
Fig. 2. Mean density of Actinocephalus permagnus (AT) and Ancyrophora gracilis (AC) in relation to habitat. Circle – woodland, square – meadow, triangle – arable land
Supplementary material 4 from: Davoli F, Cozzo M, Angeli F, Groff C, Randi E (2018) Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. Nature Conservation 25: 55-75. https://doi.org/10.3897/natureconservation.25.23776
Table S1. Detailed results of the biological model (consensus and composite) :
Supplementary material 1 from: Davoli F, Cozzo M, Angeli F, Groff C, Randi E (2018) Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. Nature Conservation 25: 55-75. https://doi.org/10.3897/natureconservation.25.23776
Text S1. Parameters used for parentage analysis :
Supplementary material 3 from: Davoli F, Cozzo M, Angeli F, Groff C, Randi E (2018) Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. Nature Conservation 25: 55-75. https://doi.org/10.3897/natureconservation.25.23776
Text S3. Detailed results of LRmix STUDIO for each suspected male: Global Composite (ADO 0.55) :
Supplementary material 1 from: Hong Qu H, Wang C-J, Zhang Z-X (2018) Planning priority conservation areas under climate change for six plant species with extremely small populations in China. Nature Conservation 25: 89-106. https://doi.org/10.3897/natureconservation.25.20063
Table S1, S2; Figure S1, S2 : Explanation note:
Supplementary material 2 from: Davoli F, Cozzo M, Angeli F, Groff C, Randi E (2018) Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. Nature Conservation 25: 55-75. https://doi.org/10.3897/natureconservation.25.23776
Text S2. Detailed results of LRmix STUDIO for each suspected male: Global Consensus (ADO 0.65) :
Figure 4 from: Knoblauch A, Gander A (2019) Distribution of a residual population of the Dytiscid Graphoderus bilineatus (de Geer, 1774) in the Grande Cariçaie nature reserves, Switzerland. Alpine Entomology 3: 83-91. https://doi.org/10.3897/alpento.3.30417
Figure 4 Stations in which Graphoderusbilineatus (yellow), G.cinereus (red) and G.zonatus (blue) were captured: A) in the Motte reserve and B) in the Ostende reserve in 2018. The dotted lines represent the reserve boundaries and the grey points the sampled stations in which no Graphoderus were captured. Background picture obtained from the Swiss Federal Office of Topography swisstopo.
Figure 3 from: Knoblauch A, Gander A (2019) Distribution of a residual population of the Dytiscid Graphoderus bilineatus (de Geer, 1774) in the Grande Cariçaie nature reserves, Switzerland. Alpine Entomology 3: 83-91. https://doi.org/10.3897/alpento.3.30417
Figure 3 Stations in which Graphoderusbilineatus was captured in the Motte reserve in 2014 (green) and in 2018 (yellow). The dotted lines represent the reserve boundaries and the grey points the sampled stations (2018) in which no Graphoderusbilineatus were captured. Background picture obtained from the Swiss Federal Office of Topography swisstopo.
Figure 1 from: Knoblauch A, Gander A (2019) Distribution of a residual population of the Dytiscid Graphoderus bilineatus (de Geer, 1774) in the Grande Cariçaie nature reserves, Switzerland. Alpine Entomology 3: 83-91. https://doi.org/10.3897/alpento.3.30417
Figure 1 Graphoderusbilineatus. Copyright: Yerpo [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], from Wikimedia Commons.
Figure 5 from: Knoblauch A, Gander A (2019) Distribution of a residual population of the Dytiscid Graphoderus bilineatus (de Geer, 1774) in the Grande Cariçaie nature reserves, Switzerland. Alpine Entomology 3: 83-91. https://doi.org/10.3897/alpento.3.30417
Figure 5 Principal component (PC) for habitat depth, helophyte cover and hydrophyte cover for G.bilineatus (green) and G.cinereus (blue). The first principal component (PC1) explains 59% of the variance. The first two components (PC1 and PC2) explain 81% of the total variance. While factor loads of habitat depth, helophyte cover and hydrophyte cover for PC1 are similar, helophyte cover and depth strongly negatively influence PC2. Circles represent 95% probability ellipses.
Figure 2 from: Knoblauch A, Gander A (2019) Distribution of a residual population of the Dytiscid Graphoderus bilineatus (de Geer, 1774) in the Grande Cariçaie nature reserves, Switzerland. Alpine Entomology 3: 83-91. https://doi.org/10.3897/alpento.3.30417
Figure 2 Location of the sampling stations in the Grande Cariçaie nature reserves, on the south eastern shore of Lake Neuchâtel. We sampled seven reserves in 2018 (delimited in brown polygons): 1) Grèves de Cheseaux, 2) Baie d'Yvonand, 3) Cheyres, 4) Grèves de la Corbière et de Chevroux, 5) Grèves d'Ostende et de Chevroux, 6) Grèves de la Motte and 7) Cudrefin. The orange points represent the sampled stations (N = 101 stations). Background picture obtained from the Swiss Federal Office of Topography swisstopo.
Data from: Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations
The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine-scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.
Data from: The strength of phenotypic selection in natural populations
How strong is phenotypic selection on quantitative traits in the wild? We reviewed the literature from 1984 through 1997 for studies that estimated the strength of linear and quadratic selection in terms of standardized selection gradients or differentials on natural variation in quantitative traits for field populations. We tabulated 63 published studies of 62 species that reported over 2,500 estimates of linear or quadratic selection. More than 80% of the estimates were for morphological traits; there is very little data for behavioral or physiological traits. Most published selection studies were unreplicated and had sample sizes below 135 individuals, resulting in low statistical power to detect selection of the magnitude typically reported for natural populations. The absolute values of linear selection gradients |β| were exponentially distributed with an overall median of 0.16, suggesting that strong directional selection was uncommon. The values of |β| for selection on morphological and on life-history/phenological traits were significantly different: on average, selection on morphology was stronger than selection on phenology/life history. Similarly, the values of |β| for selection via aspects of survival, fecundity, and mating success were significantly different: on average, selection on mating success was stronger than on survival. Comparisons of estimated linear selection gradients and differentials suggest that indirect components of phenotypic selection were usually modest relative to direct components. The absolute values of quadratic selection gradients |γ| were exponentially distributed with an overall median of only 0.10, suggesting that quadratic selection is typically quite weak. The distribution of γ values was symmetric about 0, providing no evidence that stabilizing selection is stronger or more common than disruptive selection in nature.
Data from: Persistence of an extreme male-biased adult sex ratio in a natural population of polyandrous bird
In a number of insects, fishes and birds the conventional sex roles are reversed: males are the main care provider whereas females focus on matings. The reversal of typical sex roles is an evolutionary puzzle, because it challenges the foundations of sex roles, sexual selection and parental investment theory. Recent theoretical models predict that biased parental care may be a response to biased adult sex ratios (ASRs). However, estimating ASR is challenging in natural populations, because males and females often have different detectabilities. Here we use demographic modelling with field data from 2101 individuals, including 579 molecularly sexed offspring, to provide evidence that ASR is strongly male-biased in a polyandrous bird with male-biased care. The model predicts 6.1 times more adult males than females (ASR = 0.860, proportion of males) in the Kentish plover Charadrius alexandrinus. The extreme male-bias is consistent between years, and concordant with experimental results showing strongly biased mating opportunity toward females. Based on these results we conjecture that parental sex role reversal may occur in populations that exhibit extreme male-biased ASR.
Data from: Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping by sequencing data from natural populations
Whole genome duplications have occurred in the recent ancestors of many plants, fish, and amphibians, resulting in a pervasiveness of paralogous loci and the potential for both disomic and tetrasomic inheritance in the same genome. Paralogs can be difficult to reliably genotype and are often excluded from genotyping-by-sequencing (GBS) analyses; however, removal requires paralogs to be identified which is difficult without a reference genome. We present a method for identifying paralogs in natural populations by combining two properties of duplicated loci: 1) the expected frequency of heterozygotes exceeds that for singleton loci, and 2) within heterozygotes, observed read ratios for each allele in GBS data will deviate from the 1:1 expected for singleton (diploid) loci. These deviations are often not apparent within individuals, particularly when sequence coverage is low; but, we postulated that summing allele reads for each locus over all heterozygous individuals in a population would provide sufficient power to detect deviations at those loci. We identified paralogous loci in three species: Chinook salmon (Oncorhynchus tshawytscha) which retains regions with ongoing residual tetrasomy on eight chromosome arms following a recent whole genome duplication, mountain barberry (Berberis alpina) which has a large proportion of paralogs that arose through an unknown mechanism, and dusky parrotfish (Scarus niger) which has largely re-diploidized following an ancient whole genome duplication. Importantly, this approach only requires the genotype and allele-specific read counts for each individual, information which is readily obtained from most GBS analysis pipelines.
Data from: Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size
In vitro and in vivo evolution experiments on Escherichia coli revealed several principles of bacterial adaptation. However, few data are available in the literature describing the behavior of E. coli in its natural environment. We attempted here to study the evolution in the human gut of a commensal dominant E. coli clone ED1a belonging to B2 phylogroup, through a longitudinal genomic study. We sequenced 24 isolates sampled at three different time points within a healthy individual over almost a year. We computed amutation rate of 6.90x10-7 per base per year of the chromosome for E. coli ED1a in healthy human gut. We observed a very limited genomic diversity, and could not detect any evidence of selection contrary to what is observed in experimental evolution over similar length of time. We therefore suggest that ED1a being well adapted to the healthy human gut evolves mostly neutrally with a low effective population size (Ne ≈ 500 – 1700).
Supplementary material 1 from: Ramírez-Albores JE, Richardson DM, Stefenon VM, Bizama GA, Pérez-Suárez M, Badano EI (2021) A global assessment of the potential distribution of naturalized and planted populations of the ornamental alien tree Schinus molle. NeoBiota 68: 105-126. https://doi.org/10.3897/neobiota.68.68572
Table S1
ScienceDex guides
Understand access before you commit
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.