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262 results for “Genetic variability”
Environmentally triggered variability in the genetic variance-covariance of herbivory resistance of an exotic plant Solidago altissima
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Data: The effects of weather variability on patterns of genetic diversity in Tasmanian bettongs
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Data from: Resident-disperser differences and genetic variability affect communities in microcosms
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A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population
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Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the Leray COI fragment
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FIGURE 2 in Genetic variability among Paralaudakia microlepis (Blanford, 1874) (Sauria: Agamidae) populations in the Iranian Plateau
FIGURE 2. Phylogenetic relationships (BI) among Paralaudakia microlepis populations based on the 707 bp ND4 gene fragment. The numbers next to the nodes refer to the bootstrap support and posterior probability (ML/PP).
Datasets of the study: "Describing variability in pig genes involved in coronavirus infections: towards a One Health perspective in conservation of animal genetic resources"
<p><strong>Dataset description</strong></p> <p>Sequencing data (*.bam files) of four pig genes (<em>ACE2</em>, <em>ANPEP</em>, <em>DPP4</em> and <em>TMPRSS2</em>)<em> </em>that can serve as receptors or protease for priming the infection of coronaviruses.</p> <p>The datasets are related to 22 European pig breeds and wild boars (Alentejana, AL; Apulo-Calabrese, AC; Basque, BA; Bísara, BI; Black Slavonian, BS; Casertana, CA; Cinta Senese, CS; Gascon, GA; Krškopolje, KR; Lithuanian Indigenous Wattle, LIW; Lithuanian White Old Type, LWOT; Majorcan Black, MB; Mora Romagnola, MR; Moravka, MO; Nero Siciliano, NS; Sarda, SA; Schwäbisch-Hällisches Schwein, SHS; Swallow-Bellied Mangalitsa, SBMA; Turopolje, TU; Italian Duroc, IDU; Italian Large White, ILW; Italian Landrace, ILA; Wild Boar, WB). This work took advantage of a study design developed within the Horizon 2020 TREASURE project.</p> <p>Each folder contains *.bam files and the related indexes *.bai. The name of the investigated breed and gene is part of the file name (e.g. ILW.ACE2.bam identifies the sequencing data related to the ACE2 gene in the Italian Large White pig breed). Details of sequencing and the bioinformatic pipeline are below reported.</p> <p><strong>Sequencing data</strong></p> <p>A total of 22 DNA pools were constructed from the European pig breeds and one DNA pool was constructed from European wild boars, including in each pool 30 or 35 individual DNA samples pooled at equimolar concentration. For the 22 DNA pools, libraries were prepared and fed into an Illumina HiSeq X Ten sequencer for paired-end sequencing, obtaining 150 bp length reads. The wild boar DNA pool was sequenced from 250 bp fragment libraries, with 100 bp long paired-end reads, on the BGISeq 500 platform, following the provider’s procedures.</p> <p><strong>Data processing</strong></p> <p>Reads that were obtained from the sequenced libraries were cleaned by removing adapter sequences and filtering out sequences presenting more than 10% unknown bases (N) and/or containing low-quality bases (Q ≤ 5) over 50% of the total sequenced bases. Then, filtered high-quality reads were mapped on the latest version of the <em>Sus scrofa</em> reference genome (Sscrofa11.1; https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.fna.gz) using the BWA-MEM algorithm v.0.7.17 and the parameters for paired-end data. Picard v.2.1.1 (https://broadinstitute.github.io/picard/) was used to remove duplicated reads. Whole sequence data are available in the EMBL-EBI European Nucleotide Archive (ENA) repository (http://www.ebi.ac.uk/ena), under the study accession PRJEB36830. </p> <p>Reads covering the four genes (ACE2: NC_010461.5:12094853-12156275; ANPEP: NC_010449.5:55346083-55378881; DPP4: NC_010457.5:68655849-68748818; TMPRSS2: NC_010455.5:204871561-204907561) were extracted with samtools v.1.7 and exported as aligned, sorted and indexed *.bam files. Gene length includes UTRs and flanking regions of 5 kbp upstream [flanking (5’-UTR)] and downstream [flanking (3’-UTR)].</p>
Data from: High levels of genetic structure and striking phenotypic variability in a sexually dimorphic suckermouth catfish from the African Highveld
Uncovering biological diversity to more accurately understand diversity patterns, and ultimately the processes driving diversification, is important not only from an evolutionary perspective but also a conservation perspective. This is particularly pertinent in Africa's rivers in which overall diversity, as well as how it arose, is poorly understood in comparison with lacustrine environments. Here we investigate population divergence in the sexually dimorphic suckermouth catfish species Chiloglanis anoterus (Crass, 1960) from the African Highveld, in which we observe striking variability in exaggerated male caudal fins across its range. As this trait is likely to be indirect evidence for sexual selection by female choice, a mechanism that has been shown to increase species diversity in different taxa, we used an integrated approach to test if current diversity in this species is underestimated. Results based on phylogenetic inference, population genetics and geometric morphometrics indicate that the recognized species C. anoterus represents five distinct lineages that may be considered confirmed candidate species. We suggest that diversification in these highland catfish has been facilitated through geographical isolation in upper river catchments, and that sexual selection through female choice has probably driven variation in male caudal fin morphology. In contrast to the relatively large range size of the currently recognized species (C. anoterus), our findings highlight highly restricted ranges of the lineages identified here, indicating that these highland habitats may harbour higher levels of endemic diversity than previously thought.
Data from: Multi-objective optimization for plant germplasm collection conservation of genetic resources based on molecular variability
Germplasm collections play a significant role among strategies for conservation of diversity. It is common to select a core collection to represent the genetic diversity of a germplasm collection, in order to minimize the cost of conservation, while ensuring the maximization of genetic variation. We aimed to solve two main problems: (1) to select a set of individuals, from an in situ data set, that is genetically complementary to an existing germplasm collection, and (2) to define a core collection for a germplasm collection. We proposed a new multi-objective optimization (MOO) approach based on principles of systematic conservation planning (SCP) incorporating heterozygosity information; therefore, optimization takes genotypic diversity and variability patterns into account as well. As a case study, we used Dipteryx alata microsatellite loci information from two sources, an ex situ germplasm collection located at the Agronomy School of the Federal University of Goiás (UFG-AS), and an in situ data set composed of 642 sampled individual trees. We were able to identify within a population of several individuals, the exact accessions/samples that should be chosen in order to preserve the species diversity. We found that material from nine in situ individual trees are enough to complement the UFG-AS germplasm collection as it is, and that it is possible to define a core collection of 20 individual trees representing all studied genetic diversity. Moreover, we defined a method (a protocol) to deal with large amounts of accessions in the context of MOO. The proposed approach can be used to help constructing collections with maximal allelic richness and can also be extended to the in situ conservation. As far as we know, this is the first time that principles of SCP and the MOO approach are applied to the problem of complementing a germplasm collection and of finding a core collection for a germplasm collection.
Data from: Do pathogens reduce genetic diversity of their hosts? Variable effects of sylvatic plague in black-tailed prairie dogs
Introduced diseases can cause dramatic declines in—and even the loss of—natural populations. Extirpations may be followed by low recolonization rates, leading to inbreeding and a loss of genetic variation, with consequences on population viability. Conversely, extirpations may create vacant habitat patches that individuals from multiple source populations can colonize, potentially leading to an influx of variation. We tested these alternative hypotheses by sampling 15 colonies in a prairie dog metapopulation during 7 years that encompassed an outbreak of sylvatic plague, providing the opportunity to monitor genetic diversity before, during and after the outbreak. Analysis of nine microsatellite loci revealed that within the metapopulation, there was no change in diversity. However, within extirpated colonies, patterns varied: In half of the colonies, allelic richness after recovery was less than the preplague conditions, and in the other half, richness was greater than the preplague conditions. Finally, analysis of variation within individuals revealed that prairie dogs present in recolonized colonies had higher heterozygosity than those present before plague. We confirmed plague survivorship in six founders; these individuals had significantly higher heterozygosity than expected by chance. Collectively, our results suggest that high immigration rates can maintain genetic variation at a regional scale despite simultaneous extirpations in spatially proximate populations. Thus, virulent diseases may increase genetic diversity of host populations by creating vacant habitats that allow an influx of genetic diversity. Furthermore, even highly virulent diseases may not eliminate individuals randomly; rather, they may selectively remove the most inbred individuals.
Data from: Laboratory rearing of Anopheles arabiensis: impact on genetic variability and implications for Sterile Insect Technique (SIT) based mosquito control in northern Sudan
Background: Mosquito colony populations often show significant changes in their population genetic make-up compared to the field populations that were used as founding source. Most of the changes that have been reported are indicators of depletion in the overall genetic diversity of the colony populations. The Sterile Insect Techniques programme of mosquito control that is underway in Northern Sudan uses sterilized males produced from a laboratory-maintained colony population. The genetic diversity of an advanced generation of this colony population was quantitatively assessed and compared to the field population from which the colony was derived. Methods: Anopheles arabiensis mosquito samples from the 13th generation of the colony, and from the locality that was the source of the first generation of the colony, were genotyped at 11 microsatellite loci distributed throughout the species' genome. Standard population genetic analyses were carried out to quantify and compare their population genetic make-up and diversities. Results: The colony samples showed significant reduction in the total number of alleles, the numbers of rare and private alleles, and the fractions of heterozygote individuals at all the loci. The pattern of change is consistent with the expected effect of the use of a small number of mosquitoes when the colony was established. Departure from Hardy–Weinberg equilibrium in the direction of homozygote excess was observed at some loci and attributed to the presence of null-alleles. Conclusions: This study highlights the need for broad sampling when initiating colony populations and for ongoing assessment of the population genetic make-up of colony populations. Previous assessments of survivorship, dispersive behaviour and swarm formation indicate that the inbreeding and reduced genetic variability reported in this study may not have had direct fitness consequences yet. However, noting the lessons learned in other SIT programmes about the impact of colonization on male sexual behaviour and longevity, as well as other inbreeding related adverse effects, a systematic investigation of these potential effects is recommended because they have direct impact on the ultimate success of the programme.
Data from: Genetic variability and structuring of Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia
Variation in presumably neutral genetic markers can inform us about evolvability, historical effective population sizes and phylogeographic history of contemporary populations. We studied genetic variability in 15 microsatellite loci in six native landlocked Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia, where this species is considered near threatened. We discovered that all populations were genetically highly (mean FST ≈ 0.26) differentiated and isolated from each other. Evidence was found for historical, but not for recent population size bottlenecks. Estimates of contemporary effective population size (Ne) ranged from seven to 228 and were significantly correlated with those of historical Ne but not with lake size. A census size (NC) was estimated to be approximately 300 individuals in a pond (0.14 ha), which exhibited the smallest Ne (i.e. Ne/NC = 0.02). Genetic variability in this pond and a connected lake is severely reduced, and both genetic and empirical estimates of migration rates indicate a lack of gene flow between them. Hence, albeit currently thriving, some northern Fennoscandian populations appear to be vulnerable to further loss of genetic variability and are likely to have limited capacity to adapt if selection pressures change.
Data from: Low temperature reveals genetic variability against male-killing Spiroplasma in Drosophila melanogaster natural populations
Spiroplasma endosymbionts are maternally inherited microorganisms which infect many arthropod species. In some Drosophila species, it acts as a reproductive manipulator, spreading in populations by killing the sons of infected mothers. Distinct Drosophila melanogaster populations from Brazil exhibit variable male-killing Spiroplasma prevalences. In this study, we investigated the presence of variability for the male-killing phenotype among Drosophila and/or Spiroplasma strains and verified if it correlates with the endosymbiont prevalence in natural populations. For that, we analyzed the male-killing expression when Spiroplasma strains from different populations were transferred to a standard D. melanogaster line (Canton-S) and when a common Spiroplasma strain was transferred to different wild-caught D. melanogaster lines, both at optimal and challenging temperatures for the bacteria. No variation was observed in the male-killing phenotype induced by different Spiroplasma strains. No phenotypic variability among fly lines was detected at optimal temperature (23 °C), as well. Conversely, significant variation in the male-killing expression was revealed among D. melanogaster lines at 18.5 °C, probably caused by imperfect transmission of the endosymbiont. Distinct lines differed in their average sex ratios as well as in the pattern of male-killing expression as the infected females aged. Greater variation occurred among lines from one locality, although there was no clear correlation between the male-killing intensity and the endosymbiont prevalence in each population. Imperfect transmission or male killing may also occur in the field, thus helping to explain the low or intermediate prevalences reported in nature. We discuss the implications of our results for the dynamics of male-killing Spiroplasma in natural populations.
Data from: Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes
Mounting evidence of climatic effects on riverine environments, and adaptive responses of fishes has elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multi-test association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified 9 and 22 candidate loci (respectively) commonly associated with precipitation or temperature variables, and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species.
Data from: Genetic variation in variability: phenotypic variability of fledging weight and its evolution in a songbird population
Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation that within-family variance can be heritable. For offspring traits, such as birth weight, this implies that within-family variance in traits can vary among families and can thus be shaped by natural selection. Empirical evidence for this in wild populations is however lacking. We investigated whether within-family variance in fledging weight is heritable in a wild great tit (Parus major) population and whether these differences are associated with fitness. We found significant evidence for genetic variance in within-family variance. The genetic coefficient of variation (GCV) was 0.18 and 0.25, when considering fledging weight a parental or offspring trait, respectively. We found a significant quadratic relationship between within-family variance and fitness: families with low or high within-family variance had lower fitness than families with intermediate within-family variance. Our results show that within-family variance can respond to selection and provides evidence for stabilizing selection on within-family variance.
FIGURE 3 in Genetic and morphological variability among the populations assigned to the genus Tropiocolotes Peters, 1880 (Squamata: Gekkonidae) in south Iran
FIGURE 3. Bayesian inference phylogenetic tree of Tropiocolotes populations in southern Iran using two mtDNA genes (COI and 16S). Tropiocolotes steudneri sensu stricto from Egypt was used as the outgroup. Numbers next to the nodes are the MP and ML bootstrap values and BI posterior probabilities (MP/ML/BI).
FIGURE 1 in Genetic and morphological variability among the populations assigned to the genus Tropiocolotes Peters, 1880 (Squamata: Gekkonidae) in south Iran
FIGURE 1. Map of southern Iran showing sampling localities for the populations of Tropicolates. Blue circles denote T. naybandensis and red circles denote Tropiocolotes cf. steudneri. The type locality of T. naybandensis is marked with a star.
FIGURE 2 in Genetic and morphological variability among the populations assigned to the genus Tropiocolotes Peters, 1880 (Squamata: Gekkonidae) in south Iran
FIGURE 2. Ordination of principal component 1 (PC1) against principal component 2 (PC2) for differentiated characters of the genus Tropiocolotes in southern Iran.
Fig. 1 in Genetic Variability ofDigitonthophagus gazella(F.) (Coleoptera: Scarabaeidae) from Vieques, Puerto Rico and South Africa
Fig. 1. Genetic variation of two populations of Digitonthophagus gazella as indicated by the number of markers scored plotted against coefficient of variation values. A high number of markers decrease the coefficient of variation. More than 93% of genetic variation is encompassed by the markers used.
Fig. 3 in Morphological and genetic variability of Cotesia tibialis species complex (Hymenoptera: Braconidae: Microgastrinae)
Fig. 3. Comparison of centroid size of fore wings. (A) between two seasonal forms, (B) between 14 morphotypes.
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