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opencc-by-4.0Dec 2012View details →

Supplementary material 1 from: Virkkala R, Rajasärkkä A (2012) Preserving species populations in the boreal zone in a changing climate: contrasting trends of bird species groups in a protected area network. Nature Conservation 3: 1-20. https://doi.org/10.3897/natureconservation.3.3635

Mean densities and number of observations of species in 1981–1999 and in 2000–2009

opencc-by-4.0Oct 2017View details →

Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

Summary Uganda is endowed with a large population of goats from predominantly indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture of the exotic breed Boer is still limited. Using a medium density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six Ugandan goat breeds. Samples from five indigenous Ugandan goat breeds including Mubende (n=29), Kigezi (n=29), Small East African (n=29), Sebei (n=29) and Karamojong (n=15), and the exotic breed Boer (n=13) from different agro-ecological regions of Uganda were genotyped using the GoatSNP50 BeadChip. Analysis of genotype data revealed high levels of polymorphism with the proportion of polymorphic SNPs ranging from 0.885 in Kigezi to 0.928 in Sebei. The overall mean genetic diversity indices across breeds for HO and HE was 0.355±0.147 and 0.384±0.143 respectively. Principle components, genetic distances and ADMIXTURE analyses revealed weak population sub-structuring among the breeds. Principle components separate Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong are tightly entangled together while Mubende occupies a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. ADMIXTURE and four population test analyses further revealed gene-flow from Boer to Ugandan indigenous goat breeds and varying levels of admixture among the Ugandan indigenous breeds. Generally, moderate to high levels of genetic variability were observed in the Ugandan goat breeds. Our findings provide useful insight to devise strategies to maintain genetic diversity in local goat breeds from Uganda and to design appropriate breeding programs to exploit within breed diversity and heterozygote advantage in cross-breeding schemes.

opencc-by-4.0Nov 2017View details →

ASreml code and Data from the study "Between-population differences in the genetic and maternal components of body mass in roe deer"

This repository contains the source code (ASremL input files) and the data used to perform the QG analyses (univariate, bivariate, random regression animal models) in the study "Between-population differences in the genetic and maternal components of body mass in roe deer". Quéméré E et al.

opencc-by-4.0Jan 2018View details →

Theory dataset for "Tunable Gamma-K Valley Populations in Trilayer WSe2"

Dataset for the theoretical analysis presented in the paper "Tunable Gamma-K Valley Populations in Trilayer WSe2". Details of the contents are described in README.md.

Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity

Despite its implications for population dynamics and evolution, the relationship between genetic and phenotypic variation in wild populations remains unclear. Here, we estimated variation and plasticity in life-history traits and fitness of the annual plant Arabidopsis thaliana in two common garden experiments that differed in environmental conditions. We used up to 306 maternal inbred lines from six Iberian populations characterized by low and high genotypic (based on whole-genome sequences) and ecological (vegetation type) diversity. Low and high genotypic and ecological diversity was found in edge and core Iberian environments, respectively. Given that selection is expected to be stronger in edge environments and that ecological diversity may enhance both phenotypic variation and plasticity, we expected genotypic diversity to be positively associated with phenotypic variation and plasticity. However, maternal lines, irrespective of the genotypic and ecological diversity of their population of origin, exhibited a substantial amount of phenotypic variation and plasticity for all traits. Furthermore, all populations harbored maternal lines with canalization (robustness) or sensitivity in response to harsher environmental conditions in one of the two experiments. Overall, we conclude that the environmental attributes of each population probably determine their genotypic diversity, but all populations maintain substantial phenotypic variation and plasticity for all traits, which represents an asset to endure in changing environments.

Survey responses from stakeholders managing, growing, advising or assessing UK populations of Juniperus communis

Increased imports of plants and timber through global trade networks provide frequent opportunities for introduction of novel plant pathogens that can cross-over from commercial to natural environments, threatening native species and ecosystem functioning. Prevention or management of such outbreaks relies on a diversity of cross-sectoral stakeholders acting along the invasion pathway. Yet guidelines are often only produced for a small number of stakeholders, missing opportunities to consider ways to control outbreaks in other parts of the pathway. We used the infection of common juniper with the invasive pathogen Phytophthora austrocedri as a case study to explore the utility of decision tools for managing outbreaks of plant pathogens in the wider environment. We invited stakeholders who manage or monitor juniper populations or supply plants or management advice to participate in a survey exploring their awareness of, and ability to use, an existing decision tree produced by a coalition of statutory agencies augmented with new distribution maps designed by the authors. Awareness of the decision tree was low across all stakeholder groups including those planting juniper for restoration purposes. Stakeholders requested that decision tools contain greater detail about environmental conditions that increase host vulnerability to the pathogen, and clearer examples of when management practices implicated in pathogen introduction or spread should not be adopted. The results demonstrate the need to set clear objectives for the purpose of decision tools and to frame and co-produce them with many different stakeholders, including overlooked groups such as growers and advisory agents, to improve management of pathogens in the wider environment.

Data from: Maternal diet influences fecundity in a freshwater turtle undergoing population decline

Food availability determines the amount of energy animals can acquire and allocate to reproduction and other necessary functions. Female animals that are food-limited thus experience reduced energy available for reproduction. When this occurs, females may reduce frequency of reproductive events or the number or size of offspring per reproductive bout. We assessed how maternal diet affects reproductive output in adult female Murray River short-necked turtles, Emydura macquarii, from four wetlands in Victoria. We previously found that turtle diets differ in the composition of plants and animals between our study wetlands. In this study, we tested whether differences in turtle diet composition (i.e plants and animals) at these wetlands were associated with differences in clutch mass, individual egg mass, bulk egg composition, and hatching success. We found total clutch mass increased with maternal body size at each site. At sites where filamentous green algae were scarce and E. macquarii were carnivorous, females produced smaller clutches relative to body size compared to females from sites where algae were abundant, and turtles were more herbivorous. Individual egg mass, bulk egg composition, and hatching success did not differ across wetlands. Isotopic analysis revealed a significant positive relationships between the carbon and nitrogen isotopes (δ13C, δ15N) of the eggs and those of the mothers, indicating that mothers allocated ratios of carbon and nitrogen isotopes to their eggs similar to those present in their tissues. Our study suggests that at sites where females are more carnivorous due to a relative absence of algae, females produce smaller clutches but other aspects of their reproduction are not significantly impacted. The reduction in clutch size associated with differences in the availability of dietary plants and animals may have long-term consequences for E. macquarii and other freshwater turtle species that are experiencing population declines.

Figure 28 in Population ecology of Ctenolepisma (C.) udumalpetense (Insecta: Zygentoma: Lepismatidae) in a deciduous forest floor of the Trimurti Dam, Tamil Nadu, India

Figure 28. Regression of Temperature on C. (C.) udumalpetense population in third row.

Figure 21 in Population ecology of Ctenolepisma (C.) udumalpetense (Insecta: Zygentoma: Lepismatidae) in a deciduous forest floor of the Trimurti Dam, Tamil Nadu, India

Figure 21. Regression of humidity on C. (C.) udumalpetense population in first row.

Figure 20 in Population ecology of Ctenolepisma (C.) udumalpetense (Insecta: Zygentoma: Lepismatidae) in a deciduous forest floor of the Trimurti Dam, Tamil Nadu, India

Figure 20. Regression of Temperature on C. (C.) udumalpetense population in first row.

Figure 22 in Population ecology of Ctenolepisma (C.) udumalpetense (Insecta: Zygentoma: Lepismatidae) in a deciduous forest floor of the Trimurti Dam, Tamil Nadu, India

Figure 22 Regression of N (%) on C. (C.) udumalpetense population in first row.

Acoustic and morphological dataset of seven anuran populations of two species from highland forests in Northeastern Brazil

Highlands are of paramount importance to the study of evolution as they are frequently implicated in historical and ecological processes that generate and maintain biological diversity. In northeastern Brazil, sparse rainforest remnants are located in highlands north of the São Francisco River, generally surrounded by the dry and open landscape of the Caatinga biome. Earlier studies suggest that these forests acted as historical refuges to the rainforest fauna and flora, especially during the climatic cycles of the Pleistocene. However, it is still unclear whether populations distributed in distinct highlands experienced phenotypic differentiation as a result of adaptation to the environmental conditions of each forest remnant. In this study, we used two frog species with wide geographic distributions, Dendropsophus oliveirai, a habitat specialist which breeds in permanent ponds, and Physalaemus cuvieri, a habitat generalist which breeds in temporary and permanent lentic environments, as models to investigate the relationships between environmental variation, geographic, genetic, and body size distance with advertisement call variation among populations inhabiting different highlands. We hypothesized that call variation would be strongly influenced by local environmental conditions, as sound signals are frequently adapted to the transmission environment. Our results indicate that acoustic variation among P. cuvieri populations is strongly influenced by environmental variation and moderate by geographic distance. In D. oliveirai, the environment is also the most influential factor in acoustic variation, followed by genetic and morphological variation. Besides that, the association between environmental and geographic factors suggests an indirect effect of geographic distance on acoustic variation in both species through an environmental gradient and also in genetic traits of the habitat specialist species. We believe that selective processes and isolation possibly act together in driving interpopulational acoustic variation with habitat-specific species being more affected by the isolation in suitable habitats.

opencc-by-4.0Jan 2015View details →

Figure 5 in Assessing age, growth, and reproduction of Alburnus mossulensis and Acanthobrama marmid (Cyprinidae) populations in Karakaya Dam Lake (Turkey)

Figure 5. Age and length (FL) relationship due to age groups in A. marmid females.

opencc-by-4.0Jan 2015View details →

Figure 6 in Assessing age, growth, and reproduction of Alburnus mossulensis and Acanthobrama marmid (Cyprinidae) populations in Karakaya Dam Lake (Turkey)

Figure 6. Age and length (FL) relationship due to age groups in A. marmid males.

opencc-zeroMay 2024View details →

SNP data (DArTseq) for population genomics of Araucaria bidwillii

We took Araucaria bidwillii leaf DNA samples from a total of 31 sites and 171 samples, representing 3 sites from a northern population in the Australian Wet Tropics and 28 sites from a southern population in Southeast Queensland, Australia. SNP data was obtained from genotyping-by-sequencing platform Divesity Arrays Technology (DArTseq) and the resultant dataset has not been processed for quality control.

opencc-by-4.0Jan 2016View details →

Fig. 3 in SHORT COMMUNICATION Monitoring a population of Cruziohyla craspedopus (Funkhouser, 1957) using an artificial breeding habitat

Fig. 3. Newly metamorphosed juvenile Cruziohyla craspedopus.

opencc-zeroMay 2024View details →

Data from: Genome-wide scans reveal selection signatures and cross-population variation in South African and European beef cattle breeds

In genetics and evolutionary biology, the concept of selection signatures is used to describe specific patterns in the genome that are associated with the process of natural selection. These selection signatures provide insights into how evolutionary forces have shaped a population over time.In this study, a total of 96 samples were collected in several farms from four different cattle breeds, namely South African indigenous Nguni (n = 28) and Bonsmara (n = 21), Scottish Angus (n = 22), and Swedish Simmental (n = 25). Genotyped samples were subjected to quality control, and a total of 105,675 SNPs from 78 individuals remained for further analysis. Genomic signatures of positive selection within each breed were identified using the Integrated Haplotype Score (iHS) method, and cross-population comparison analysis using cross-population extended haplotype homozygosity ( XP-EHH), relative extended haplotype homozygosity (Rsb), and fixation index (Fst) methods, to assess the genetic differences between breeds. The results from the iHS method revealed selection signatures in two genomic regions for Bonsmara, six for Simmental, four for Nguni, and one for Angus cattle. Ten regions were found to be under selection, with BTA 12 being shared between Nguni and Bonsmara. Comparisons across populations using Rsb, and Fst methods performed better and revealed the most specific genomic regions that varied in selection between breeds. Gene annotation analyses linked candidate genes to several Quantitative Trait Loci (QTL). For example, in Simmental cattle's FAM110B gene was linked to carcass weight and body confirmation score. Bonsmara showed fewer candidate genes, such as CDK8 and FLT1, whereas Angus had none on BTA 18. Nguni identified potential genes such as CRB1, PLAG2GA, and VASH2, with CDK8 shared by Bonsmara and Nguni on BTA 12. Further cross-population studies revealed candidate genes associated with certain traits, genes including as PLCXD3, FAM149B1, and GRIK2 for Bonsmara versus Nguni, and SLIT2 and TSPAN9 for Simmental vs Angus. The study also emphasised gene related to meat quality, reproduction, health, illnesses, fertility, and body conformation score. Gene interaction study with the STRING database revealed a network of 63 candidate genes, demonstrating the structure of genetic connections, some biological processes. The study found that iHS performed well in population analysis with Nguni cattle, having exhibited the highest number of signatures across the genome, and significant signatures were also seen in comparisons between Nguni and Bonsmara using the Fst and Rsb methods. Furthermore, the study discovered that a bigger number of genes were connected with various traits, including sperm count and insemination per conception, sensitivity to bovine respiratory disease, and ease of calving. This genomic analysis underlined the relevance of the genetic relying which distinguishes distinct breeds. This understanding has the potential to significantly enhance selective breeding and increase desirable traits in cattle herds. This genomic analysis underlined the significance of the genetic basis for breed-specific traits. This understanding has the potential to drastically improve selective breeding and increase desirable traits in cattle herds.

opencc-zeroMay 2024View details →

Data from: Small but connected islands can maintain populations and genetic diversity under climate change

In response to the striking effects of environmental change, conservation strategies often include the identification of conservation areas that can effectively maintain vulnerable species. Consequently, identifying system-specific conditions that maintain the demographic and genetic viability of species of conservation concern is essential. Connectivity plays a critical role in the persistence of populations. Islands have been model systems to understand connectivity and metapopulation processes and have emerged as particularly favorable targets for conservation. While islands can be isolated from mainland disturbances, it is unknown what degree of isolation is necessary to avoid unfavorable changes but remain sufficiently connected to maintain population viability. To test this question, we explored connectivity within the Apostle Islands, an archipelago of 22 islands within Lake Superior, by comparing historical and contemporary trends in ice bridge connectivity and by simulating the effect of reduced connectivity within this system. We developed a demographically informed individual-based model to explicitly test the role of connectivity to influence the persistence and genetic diversity of American marten (Martes americana), a forest carnivore at risk across its southern range boundary. We found that genetic diversity was resilient to moderate changes in ice cover, but a complete loss of connectivity resulted in rapid genetic erosion. Despite genetic erosion, populations persisted as long as nominal connectivity occurred between islands. Our work suggests that connectivity will decline, but martens would be resilient to moderate changes, and, in the short term, the Apostle Islands can act as a refuge along this species' southern range boundary. Identifying thresholds in connectivity that maintain populations but allow for isolation from disturbance will be necessary to identify suitable areas for species conservation across space and time.

opencc-by-4.0May 2024View details →

Dataset belonging to SNF project: Use of physiologically based pharmacokinetic modelling to simulate dosing requirements of long-acting intramuscular antiretroviral drugs in special populations and to manage drug-drug interactions

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