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104 results for “genotypic variation”
Data from: Phenotypic and genotypic variation across a stable white-eye (Zosterops sp.) hybrid zone in central South Africa
The interbreeding of two species after a period of separation (secondary contact) most often results in stable areas of hybridization or tension zones characterized by selection against hybrid individuals. Three plumage forms of Zosterops meet and interbreed in central South Africa. Here we examine how phenotypic measures (biometric and plumage) and genotypic markers (mitochondrial and nuclear DNA) change through a putative hybrid zone located in the area where the ranges of the Orange River white-eye Zosterops pallidus and a subspecies of the Cape white-eye Zosterops virens capensis meet. Four of the five sequenced loci (i.e. ATP6, MUSK, GADPH and TGF-β2) showed strong divergence and differentiation between allopatric parental populations, whereas the sex-linked CHD1Z locus exhibited high homogeneity. Microsatellite data also distinguished between pure Z. pallidus and Z. v. capensis populations. Together, the nuclear data (introns and microsatellites) identified at least 12 hybrid individuals as later generation hybrids (i.e. F2 or backcrosses), and no F1 hybrids were detected. As genetic incompatibility does not appear to play a role in restricting this stable hybrid zone, it is likely that environmental conditions including biome type and edge effect are constraining hybrid zone movement.
Data from: Testing genotypic variation of an invasive plant species in response to soil disturbance and herbivory
Herbivores, competitors, and predators can inhibit biological invasions ("biotic resistance" sensu Elton 1959), while disturbance typically promotes biological invasions. Although biotic resistance and disturbance are often considered separately in the invasion literature, these two forces may be linked. One mechanism by which disturbance may facilitate biological invasions is by decreasing the effectiveness of biotic resistance. The effects of both disturbance and biotic resistance may vary across invading genotypes, and genetic variation in the invasive propagule pool may increase the likelihood that some genotypes can overcome biotic resistance or take greater advantage of disturbance. We conducted an experimental field trial in which we manipulated soil disturbance (thatch removal and loosening soil) and the presence of insect herbivores and examined their effects on the invasion success of 44 Medicago polymorpha genotypes. As expected, insecticide reduced leaf damage and increased Medicago fecundity, suggesting that insect herbivores in this system provide some biotic resistance. Soil disturbance increased Medicago fecundity, but did not alter the effectiveness of biotic resistance by insect herbivores. We found significant genetic variation in Medicago in response to disturbance, but not in response to insect herbivores. These results suggest that the ability of Medicago to invade particular habitats depends on the amount of insect herbivory, the history of disturbance in the habitat, and how the specific genotypes in the invader pool respond to these factors.
The potential for genotype-by-environment interactions to maintain genetic variation in a model legume–rhizobia mutualism
<p>The maintenance of genetic variation in mutualism-related traits is key for understanding mutualism evolution, yet the mechanisms maintaining variation remain unclear. We asked whether genotype-by-environment (G×E) interaction is a potential mechanism maintaining variation in the model legume–rhizobia system, <em>Medicago truncatula–Ensifer meliloti</em>. We planted 50 legume genotypes in a greenhouse under ambient light and shade to reflect reduced carbon availability for plants. We found an expected reduction under shaded conditions for plant performance traits, such as leaf number, aboveground and belowground biomass, and a mutualism-related trait, nodule number. We also found G×E for nodule number, with ∼83% of this interaction due to shifts in genotype fitness rank order across light environments, coupled with strong positive directional selection on nodule number regardless of light environment. Our results suggest that G×E can maintain genetic variation in a mutualism-related trait that is under consistent positive directional selection across light environments.</p>
Genotypic variation in an ecologically important parasite is associated with host species, lake, and spore size
<p>Genetic variation in parasites has important consequences for host-parasite interactions. Prior studies of the ecologically important parasite <i>Metschnikowia bicuspidata</i> have suggested low genetic variation in the species. Here, we collected <i>M. bicuspidata</i> from two host species (<i>Daphnia dentifera</i> and <i>Ceriodaphnia dubia</i>) and two regions (Michigan and Indiana, USA). Within a lake, outbreaks tended to occur in one host species but not the other. Using microsatellite markers, we identified six parasite genotypes grouped within three distinct clades, one of which was rare. Of the two main clades, one was generally associated with <i>D. dentifera,</i> with lakes in both regions containing a single genotype. The other <i>M. bicuspidata</i> clade was mainly associated with <i>C. dubia</i>, with a different genotype dominating in each region. Despite these associations, both <i>D. dentifera-</i> and <i>C. dubia</i>-associated genotypes were found infecting both hosts in lakes. However, in lab experiments, the <i>D. dentifera</i>-associated genotype infected both <i>D. dentifera</i> and <i>C. dubia</i>, but the <i>C. dubia</i>-associated genotype, which had spores that were approximately 30% smaller, did not infect <i>D. dentifera. </i>We hypothesize that variation in spore size might help explain patterns of cross-species transmission. Future studies exploring the causes and consequences of variation in spore size may help explain patterns of infection and the maintenance of genotypic diversity in this ecologically important system.</p>
Template-specific optimization of NGS genotyping pipelines reveals allele-specific variation in MHC gene expression
<p>Using high-throughput sequencing for precise genotyping of multi-locus gene families, such as the Major Histocompatibility Complex (MHC), remains challenging, due to the complexity of the data and difficulties in distinguishing genuine from erroneous variants. Several dedicated genotyping pipelines for data from high-throughput sequencing, such as next-generation sequencing (NGS), have been developed to tackle the ensuing risk of artificially inflated diversity. Here, we thoroughly assess three such multi-locus genotyping pipelines for NGS data, the DOC method, AmpliSAS and ACACIA, using MHC class IIβ datasets of three-spined stickleback gDNA, cDNA, and "artificial" plasmid samples with known allelic diversity. We show that genotyping of gDNA and plasmid samples at optimal pipeline parameters was highly accurate and reproducible across methods. However, for cDNA data, gDNA-optimal parameter configuration yielded decreased overall genotyping precision and consistency between pipelines. Further adjustments of key clustering parameters were required tο account for higher error rates and larger variation in sequencing depth per allele, highlighting the importance of template-specific pipeline optimization for reliable genotyping of multi-locus gene families. Through accurate paired gDNA-cDNA typing and MHC-II haplotype inference, we show that MHC-II allele-specific expression levels correlate negatively with allele number across haplotypes. Lastly, sibship-assisted cDNA-typing of MHC-I revealed novel variants linked in haplotype blocks and a higher-than-previously-reported individual MHC-I allelic diversity. In conclusion, we provide novel genotyping protocols for the three-spined stickleback MHC-I and -II genes and evaluate the performance of popular NGS-genotyping pipelines. We also show that fine-tuned genotyping of paired gDNA-cDNA samples facilitates amplification bias-corrected MHC allele expression analysis.</p>
Data from: Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges
<p>The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid-origin lineages to occupy unique environmental space relative to one (or both) parents. We document such a case of hybridization between two sedge species, <em>Carex</em> <em>nova</em> and <em>Carex</em> <em>nelsonii</em> (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (<em>C. nelsonii</em>) is at the edge of its environmental tolerance. Hybrid-origin individuals display mixed ancestry between the parental taxa – of nearly 7,000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage – approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid-origin lineage, we conducted genotype-environment association analyses on different combinations of loci – with and without excess ancestry – and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (<em>C. nelsonii</em>), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent<em>.</em></p>
Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity
<p>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 <em>Arabidopsis thaliana</em> 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.</p>
EST-SSR genotyping data from: Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: Genetic, phenotypic, and environmental insights
<p><em>Callicarpa subpubescens</em>, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Post-mating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.</p>
Fig. 1 in Among-Genotype Variation For Sediment Rejection In The Reef-Building Coral Diploastrea Heliopora (Lamarck, 1816)
Fig. 1. Location of sampling site.
Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data
<p class="MsoNormal">Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic diversity of Enset (<em>Ensete ventricosum</em>), an indigenous African relative of bananas (<em>Musa</em>) and principal starch staple for 20 million Ethiopians. Wild enset is strictly sexually outcrossing, but in cultivation is propagated clonally and associated with diversification and specialisation into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages we found significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. Development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.</p>
Data for: A predominant role of genotypic variation in both expression of sperm competition genes and paternity success in Drosophila melanogaster
<p>The study focuses on investigating the impact of both environmental and genotypic variations on the expression of sperm competition genes and relative paternity success (i.e. second male paternity; P2) in Drosophila melanogaster. To address this, the research leverages the Drosophila Genetic Reference Panel (DGRP) inbred lines and introduces manipulation of developmental population density, specifically larval density. This experimental design allows for the examination of the effects of genotype, environment, and potential genotype-environment interactions (GEI) on the expression of seminal fluid genes, namely Sex Peptide, Acp36DE, and CG9997 and sperm competitiveness. In light of the observed genotypic influence on genes' expression, a genome-wide association study (GWAS) was also conducted for Sex Peptide and Acp36DE.</p>
Data from: Phenotypic and genotypic variation across a stable white-eye (Zosterops sp.) hybrid zone in central South Africa
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Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data
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EST-SSR genotyping data from: Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: Genetic, phenotypic, and environmental insights
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Data from: Patterns of genotype variation and demographic history in Lindera glauca (Lauraceae), an apomict-containing dioecious forest tree
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Genotype-environment interaction and the maintenance of genetic variation: an empirical study of Lobelia inflata (Campanulaceae)
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Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity
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A genotype-by-sequencing dataset and identity-by-state matrix of genetic variation in Pinus radiata from 16 counties
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The potential for genotype-by-environment interactions to maintain genetic variation in a model legume–rhizobia mutualism
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Data for: A predominant role of genotypic variation in both expression of sperm competition genes and paternity success in Drosophila melanogaster
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