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opencc-zeroDec 2011View details →

Data from: Fine-scale environmental control of hybridization in oaks

Natural hybridization is attracting much interest in modern speciation and conservation biology studies, but the underlying mechanisms remain poorly understood. In particular, it is unclear why environmental changes often increase hybridization rates. To study this question, we surveyed mating events in a mixed oak stand and developed a spatially-explicit individual-based hybridization model. This model, where hybridization is frequency dependent, pollen is non-limiting and which allows immigrant pollen to compete with local pollen, takes into account species-specific pollen dispersal and sexual barriers to hybridization. The consequences of pollen limitation on hybridization were studied using another simple model. The results indicate that environmental changes could increase hybridization rates through two distinct mechanisms. First, by disrupting the spatial organisation of communities, they should decrease the proportion of conspecific pollen available for mating, thus increasing hybridization rates. Second, by decreasing the density of conspecifics, they should increase pollen limitation and thus hybridization rates, as a consequence of chance pollination predominating over deterministic pollen competition. Altogether, our results point to a need for considering hybridization events at the appropriate level of organisation and provide new insights into why hybridization rates generally increase in disturbed environments.

opencc-zeroDec 2016View details →

Data from: Fine-scale population dynamics in a marine fish species inferred from dynamic state-space models

Identifying the spatial scale of population structuring is critical for the conservation of natural populations and for drawing accurate ecological inferences. However, population studies often use spatially aggregated data to draw inferences about population trends and drivers, potentially masking ecologically relevant population sub-structure and dynamics. The goals of this study were to investigate how population dynamics models with and without spatial structure affect inferences on population trends and the identification of intrinsic drivers of population dynamics (e.g. density dependence). Specifically, we developed dynamic, age-structured, state-space models to test different hypotheses regarding the spatial structure of a population complex of coastal Atlantic cod (Gadus morhua). Data were from a 93-year survey of juvenile (age 0 and 1) cod sampled along >200 km of the Norwegian Skagerrak coast. We compared two models: one which assumes all sampled cod belong to one larger population, and a second which assumes that each fjord contains a unique population with locally determined dynamics. Using the best supported model, we then reconstructed the historical spatial and temporal dynamics of Skagerrak coastal cod. Cross-validation showed that the spatially structured model with local dynamics had better predictive ability. Furthermore, posterior predictive checks showed that a model which assumes one homogeneous population failed to capture the spatial correlation pattern present in the survey data. The spatially structured model indicated that population trends differed markedly among fjords, as did estimates of population parameters including density-dependent survival. Recent biomass was estimated to be at a near-record low all along the coast, but the finer scale model indicated that the decline occurred at different times in different regions. Warm temperatures were associated with poor recruitment, but local changes in habitat and fishing pressure may have played a role in driving local dynamics. More generally, we demonstrated how state-space models can be used to test evidence for population spatial structure based on survey time-series data. Our study shows the importance of considering spatially structured dynamics, as the inferences from such an approach can lead to a different ecological understanding of the drivers of population declines, and fundamentally different management actions to restore populations.

opencc-zeroDec 2014View details →

Data from: Fine-scale landscape genetics of the American badger (Taxidea taxus): disentangling landscape effects and sampling artifacts in a poorly understood species

Landscape genetics is a powerful tool for conservation because it identifies landscape features that are important for maintaining genetic connectivity between populations within heterogeneous landscapes. However, using landscape genetics in poorly understood species presents a number of challenges, namely, limited life history information for the focal population and spatially biased sampling. Both obstacles can reduce power in statistics, particularly in individual-based studies. In this study, we genotyped 233 American badgers in Wisconsin at 12 microsatellite loci to identify alternative statistical approaches that can be applied to poorly understood species in an individual-based framework. Badgers are protected in Wisconsin owing to an overall lack in life history information, so our study utilized partial redundancy analysis (RDA) and spatially lagged regressions to quantify how three landscape factors (Wisconsin River, Ecoregions and land cover) impacted gene flow. We also performed simulations to quantify errors created by spatially biased sampling. Statistical analyses first found that geographic distance was an important influence on gene flow, mainly driven by fine-scale positive spatial autocorrelations. After controlling for geographic distance, both RDA and regressions found that Wisconsin River and Agriculture were correlated with genetic differentiation. However, only Agriculture had an acceptable type I error rate (3–5%) to be considered biologically relevant. Collectively, this study highlights the benefits of combining robust statistics and error assessment via simulations and provides a method for hypothesis testing in individual-based landscape genetics.

opencc-by-4.0Mar 2024View details →

Contrasting reproductive traits affect the genetic diversity and fine-scale genetic structure of two sympatric and epiphytic tropical bromeliads.

This database contains the coordinates of individuals of Aechmea mariae-reginae and Werauhia ampla in phorophytic trees and the genotypes for 8 microsatellite loci.

opencc-zeroNov 2021View details →

Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from North Patagonia

Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. Eleginops maclovinus is a protandrous hermaphrodite species with economic importance for local communities that is currently managed as a single genetic unit. In this study, we sampled five locations distributed across a salinity cline from Northern Patagonia to investigate the genetic population structure of E. maclovinus. We use Restriction-site Associated DNA (RAD) sequencing and outlier tests to obtain 11,712 neutral, 338 adaptive loci, and 78 loci associated to environmental variables. We identified a spatial pattern of structuration with gene flow and spatial selection by environmental association. Neutral and adaptive loci showed two and three genetic groups, respectively. The effective population sizes estimated ranged from 572 to 14,454 and were influenced more by locality than salinity cline. We found loci putatively associated with salinity suggesting that salinity may act as a selective driver in E. maclovinus populations. These results suggest a complex interaction between genetic drift, geneflow, and natural selection in this area. Our findings suggest that at least two to three genetic units exist in this area, and the information should be integrated into the management of this species. We discuss the significance of these results for fishery management and suggest future directions to improve our understanding of how E. maclovinus is adapted to the dynamic waters of Northern Patagonia.

opencc-zeroDec 2021View details →

Data: Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon

Chromosomal rearrangements (e.g., inversions, fusions, and translocations) have long been associated with environmental variation in wild populations. New genomic tools provide the opportunity to examine the role of these structural variants in shaping adaptive differences within and among wild populations of non-model organisms. In Atlantic Salmon (Salmo salar), variations in chromosomal rearrangements exist across the species natural range, yet the role and importance of these structural variants in maintaining adaptive differences among wild populations remains poorly understood. We genotyped Atlantic Salmon (n = 1429) from 26 populations within a highly genetically structured region of southern Newfoundland, Canada with a 220K SNP array. Multivariate analysis, across two independent years, consistently identified variation in a structural variant (translocation between chromosomes Ssa01 and Ssa23), previously associated with evidence of trans-Atlantic secondary contact, as the dominant factor influencing population structure in the region. Redundancy analysis suggested that variation in the Ssa01/Ssa23 chromosomal translocation is strongly correlated with temperature. Our analyses suggest environmentally mediated selection acting on standing genetic variation in genomic architecture introduced through secondary contact may underpin fine-scale local adaptation in Placentia Bay, Newfoundland, Canada, a large and deep embayment, highlighting the importance of chromosomal structural variation as a driver of contemporary adaptive divergence.

opencc-zeroDec 2021View details →

Exposing wind stress as a driver of fine-scale variation in plant communities

The effects of temperature and precipitation, and the impacts of changes in these climatic conditions, on plant communities have been investigated extensively. The roles of other climatic factors are, however, comparatively poorly understood, despite potentially also strongly structuring community patterns. Wind, for example, is seldom considered when forecasting species responses to climate change, despite having direct physiological and mechanical impacts on plants. It is, therefore, important to understand the magnitude of potential impacts of changing wind conditions on plant communities, particularly given that wind patterns are shifting globally. Here, we examine the relationship between wind stress (i.e. a combination of wind exposure and wind speed) and species richness, vegetation cover and community composition using fine-scale, field-collected data from 1440 quadrats in a windy sub-Antarctic environment. Wind stress was consistently a strong predictor of all three community characteristics, even after accounting for other potentially ecophysiologically important variables, including pH, potential direct incident solar radiation, winter and summer soil temperature, soil moisture, soil depth, and rock cover. Plant species richness peaked at intermediate wind stress, and vegetation cover was highest in plots with the greatest wind stress. Community composition was also related to wind stress, and, after the influence of soil moisture and pH, had a similar strength of effect as winter soil temperature. Synthesis: Wind conditions are, therefore, clearly related to plant community characteristics in this ecosystem that experiences chronic winds. Based on these findings, wind conditions require greater attention when examining environment-community relationships, and changing wind patterns should be explicitly considered in climate change impact predictions.

opencc-zeroDec 2022View details →

Fine-scale ecological and anthropogenic variables predict the habitat use and detectability of sloth bears in the Churia habitat of east Nepal

Once widespread throughout the tropical forests of the Indian Subcontinent, the sloth bears have suffered a rapid range collapse and local extirpations in the recent decades. A significant portion of their current distribution range is situated outside of the protected areas (PAs). These unprotected sloth bear populations are under tremendous human pressures, but little is known about the patterns and determinants of their occurrence in most of these regions. The situation is more prevalent in Nepal where virtually no systematic information is available for sloth bears living outside of the PAs. We undertook a sign survey-based single-season occupancy study intending to overcome this information gap for the sloth bear populations residing in the Trijuga forest of southeast Nepal. Sloth bear sign detection histories and field-based covariates data were collected between 2nd October to 3rd December 2020 at the 74 randomly chosen 4-km^2 grid cells using a varying number of 400m long transects in each grid cell. From our results, the model-averaged estimate of site use probability (ψ ± SE) was estimated to be 0.432 ± 0.039, which is a 13% increase from the naïve estimate (0.297) not accounting for imperfect detections of sloth bear signs. The presence of termite mound and the distance to the nearest water source were the most important variables affecting the habitat use probability of sloth bears. The average site-level detectability (p ± SE) of sloth bear signs was estimated to be 0.195 ± 0.003 and was significantly determined by the index of human disturbances. We recommend considering the importance of fine-scale ecological and anthropogenic factors in predicting the sloth bear-habitat relationships across their range in the Churia habitat of Nepal, and more specifically in the unprotected areas.

FIGURE 6 in Fine-scale diversity in Rhodocybe mellea (Entolomataceae, Basidiomycota), with a description of a new variety and notes on sclerotia formation in Rhodocybe

FIGURE 6. Genetic transitive graph based on a dataset of nrITS sequences from R. mellea complex using the Hamming distance (cutoff point = 100). Each point is labelled with the specimen voucher and its location, while the lines are numbered with Hamming distance values.

FIGURE 4 in Fine-scale diversity in Rhodocybe mellea (Entolomataceae, Basidiomycota), with a description of a new variety and notes on sclerotia formation in Rhodocybe

FIGURE 4. Rhodocybe mellea var. depressa microscopic features (holotype UFRN-Fungos 3386). a Basidiospores. b Basidia and sclerobasidia. c Pseudocystidia. d Pileipellis: suprapellis structure and terminal hyphae. Scale bars: 5 μm. Drawings by A.G.S. Silva-Filho.

FIGURE 5 in Fine-scale diversity in Rhodocybe mellea (Entolomataceae, Basidiomycota), with a description of a new variety and notes on sclerotia formation in Rhodocybe

FIGURE 5. Comparison of pairwise genetic distances within R. mellea complex (n = 5) and between other Rhodocybe s. str. species based on nrITS sequences (n = 7). In the first graph, sequences from the R. mellea complex are represented by the abbreviation of the name of its country of origin: Dom Rep = Dominican Republic, CR = Costa Rica, BR = Brazil, BLZ = Belize.

FIGURE 3 in Fine-scale diversity in Rhodocybe mellea (Entolomataceae, Basidiomycota), with a description of a new variety and notes on sclerotia formation in Rhodocybe

FIGURE 3. Rhodocybe mellea var. depressa microscopic features (holotype UFRN-Fungos 3386). a From L–R: Sclerobasidia, basidia and pseudocystidia. b Basidiospores. c Sclerobasidia. d Pileipellis. a, b and d: in KOH 5%; c: stained in Congo Red. Scale bars: 5 μm. Photos by M.D. Xavier.

FIGURE 2 in Fine-scale diversity in Rhodocybe mellea (Entolomataceae, Basidiomycota), with a description of a new variety and notes on sclerotia formation in Rhodocybe

FIGURE 2. Photographs of the habitat and fresh basidiomata of Rhodocybe mellea var. depressa (holotype UFRN-Fungos 3386). a Basidiomata. b Coastal Tableland, Savanna vegetation. Scale bars: 10 mm. Photos by J.O. Sousa and F. Wartchow.

FIGURE 1 in Fine-scale diversity in Rhodocybe mellea (Entolomataceae, Basidiomycota), with a description of a new variety and notes on sclerotia formation in Rhodocybe

FIGURE 1. ML phylogeny based on combined nrITS and nrLSU sequences of Entolomataceae. Rhodocybe mellea var. depressa is indicated in blue. The names in red are sequences from Central and South America. For each sequence the current name and specimen voucher are provided. Thickened branches indicate those with maximum ML bootstrap values and Bayesian posterior probability (100 % BS / 1.0 BPM). Bootstrap values and posterior probabilities are indicated only if they exceed 80 % BS / 0.95 BPM. The scale bar represents the expected number of nucleotide changes per site.

opencc-by-4.0May 2024View details →

The derived data in manuscript Oblique impact adjacent to Chang'E-5 landing site: Fine-scale analysis and implication on the provenance of returned samples

This website contains the derived data in the manuscript Oblique impact adjacent to Chang’E-5 landing site: Fine-scale analysis and implication on the provenance of returned samples by Wenhui Wu, Zhaopeng Chen, Xin Ren, Dawei Liu, Xingguo Zeng, Yuan Chen, Wangli Chen, Wei Yan, Bin Liu,Xiaoxia Zhang, Jianjun Liu for Journal of Geophysical Research: Planets

opencc-by-4.0Sep 2024View details →

Spring vegetation dynamics drive sex-specific migration propensity and fine-scale green-up tracking in Alpine ibex

# Data and srcipts used to perform analyses presented in the manuscript: "Spring vegetation dynamics drive sex-specific migration propensity and fine-scale green-up tracking in Alpine ibex"

opencc-by-4.0Oct 2024View details →

Pathogen-induced alterations in fine-scale movement behaviour predict impaired reproductive success

This R-Project contains the following code files (in folder R): 01_movement_data_cleaning: Code to clean the raw ATLAS tracking data 02_nestbox_data_cleaning: Code to clean nest box control sheets 03_pathogen_data_cleaning: Code to clean the laboratory results for blood parasites PCRs 04_ctmm_models: Code to prepare data, applying continuous time movement models (incl. model selection) on movement data. Moreover, track reconstruction is performed 05_Neural_Network: Code to perform Neural Networks for classification of behavioural states 06_behavioural classification_analyses: Code to analyse Neural Network output 07_HSF: Code for Habitat Selection Functions (HSF) 08_ISSF: : Code for integrated Step Selection Functions (iSSF) 09_breeding_success_HSF: Multivariate model to perform on HSF estimates 10_breeding_success_ISSF: Multivariate model to perform on iSSF estimates This repository contains the following data files (in folder data-raw) : Nestboxes_2021: Nest box monitoring sheets 2021 Nestboxes_2022: Nest box monitoring sheets 2022 Nestboxes_2023: Nest box monitoring sheets 2023 Starlings_ring: Starling ringing data pathogen_data: Blood parasite infection data

opencc-zeroDec 2013View details →

Data from: Phylogeography of var gene repertoires reveals fine-scale geospatial clustering of Plasmodium falciparum populations in a highly endemic area

Plasmodium falciparum malaria is a major global health problem that is being targeted for progressive elimination. Knowledge of local disease transmission patterns in endemic countries is critical to these elimination efforts. To investigate fine-scale patterns of malaria transmission, we have compared repertoires of rapidly evolving var genes in a highly endemic area. A total of 3680 high quality DBLα sequences were obtained from 68 P. falciparum isolates from ten villages spread over two distinct catchment areas on the north coast of Papua New Guinea (PNG). Modeling of the extent of var gene diversity in the two parasite populations predicts more than twice as many var gene alleles circulating within each catchment (Mugil=906; Wosera=1094) than previously recognized in PNG (Amele=369). In addition, there were limited levels of var gene sharing between populations, consistent with local parasite population structure. Phylogeographic analyses demonstrate that while neutrally evolving microsatellite markers identified population structure only at the catchment level, var gene repertoires reveal further fine-scale geospatial clustering of parasite isolates. The clustering of parasite isolates by village in Mugil, but not in Wosera was consistent with the physical and cultural isolation of the human populations in the two catchments. The study highlights the micro-heterogeneity of P. falciparum transmission in highly endemic areas and demonstrates the potential of var genes as markers of local patterns of parasite population structure.

opencc-zeroDec 2017View details →

Data from: Fine-scale temporal analysis of genotype-dependent mortality at settlement in the Pacific oyster Crassostrea gigas

Settlement and metamorphosis mark a critical transition in the life cycle of marine invertebrates, during which substantial mortality occurs in both field and laboratory settings. Previous pair-crossing experiments with the Pacific oyster Crassostrea gigas have revealed significant selective or genotype-dependent mortality around the metamorphic transition, but the fine-scale nature and timing of this mortality is not known, particularly whether it occurs before, during or after metamorphosis. In this laboratory study, microsatellite marker segregation ratios were followed daily throughout the settlement and metamorphosis of an F2 cross of the Pacific oyster to examine the fine-scale patterns of genotype dependent mortality at this transition and whether settlement timing (early vs. late) might be under genetic control and affect inference of genotype dependent mortality. Settlement occurred over nine days (day 18 to day 27 post-fertilization) with 68% of individuals settling either early (day 19) or late (day 24). Tracking the survival of spat for 40 days after initial settlement revealed almost no mortality and thus no appreciable genetic mortality. Temporal genetic analysis revealed that 3/11 loci exhibited genotype dependent mortality around the metamorphic transition, one of which (Cg205) was followed throughout settlement and metamorphosis. Alternative temporal patterns of strong selection against each homozygous genotype at Cg205 revealed possible defects in both the competency pathway (inability to initiate metamorphosis) and the morphogenesis pathway (mortality during the metamorphic transition). Quantitative trait locus (QTL) mapping of settlement timing identified three individual and one epistatic QTL with significant genetic effects on this trait (29% of the variance explained in total); however, two of these loci were linked to markers exhibiting selective mortality at metamorphosis, potentially confounding their apparent association with settlement timing. Overall, the results of this study highlight the complex nature of mortality and behavior during settlement and metamorphosis in oysters and suggest that endogenous sources of mortality at settlement may play an important role in the recruitment dynamics of oysters and possibly other broadcast spawning marine invertebrates.