scholarly journals Partial selfing eliminates inbreeding depression while maintaining genetic diversity

2017 ◽  
Author(s):  
Ivo M. Chelo ◽  
Bruno Afonso ◽  
Sara Carvalho ◽  
Ioannis Theologidis ◽  
Christine Goy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Inbreeding Depression ◽  
Experimental Evolution ◽  
Natural Populations ◽  
Ancestral Population ◽  
Origin And Evolution ◽  
C Elegans ◽  
Genome Wide ◽  
Adaptive Genetic Diversity

AbstractClassical theory on the origin and evolution of selfing and outcrossing relies on the role of inbreeding depression created by unlinked partially-deleterious recessive alleles to predict that individuals from natural populations predominantly self or outcross. Comparative data indicates, however, that maintenance of partial selfing and outcrossing at intermediate frequencies is common in nature. In part to explain the presence of mixed reproductive modes within populations, several hypotheses regarding the evolution of inbreeding depression have been put forward based on the complex interaction of linkage and identity disequilibrium among fitness loci, together with Hill-Robertson effects. We here ask what is the genetic basis of inbreeding depression so that populations with intermediate selfing rates can eliminate it while maintain potentially adaptive genetic diversity. For this, we use experimental evolution in the nematode C. elegans under partial selfing and compare it to the experimental evolution of populations evolved under exclusive selfing and predominant outcrossing. We find that the ancestral risk of extinction upon enforced inbreeding by selfing is maintained when populations evolve under predominant outcrossing, but reduced when populations evolve under partial or exclusive selfing. Analysis of genome-wide single-nucleotide polymorphism (SNP) during experimental evolution and after enforced inbreeding suggests that, under partial selfing, populations were purged of unlinked deleterious recessive alleles that segregate in the ancestral population, which in turn allowed the expression of unlinked overdominant fitness loci. Taken together, these observations indicate that populations evolving under partial selfing gain the short-term benefits of selfing, in purging deleterious recessive alleles, but also the long-term benefits of outcrossing, in maintaining genetic diversity that may important for future adaptation.

scholarly journals Gene-level quantitative trait mapping in an expandedC. elegansmultiparent experimental evolution panel

2019 ◽  
Author(s):  
Luke M. Noble ◽  
Matthew V. Rockman ◽  
Henrique Teotónio
Keyword(s):  
Experimental Evolution ◽  
Recombinant Inbred Lines ◽  
Single Gene ◽  
Ancestral Population ◽  
C Elegans ◽  
Quantitative Trait Mapping ◽  
Trait Variance ◽  
Gene Level ◽  
Evolution Experiment

ABSTRACTTheCaenorhabditis elegansmultiparental experimental evolution (CeMEE) panel is a collection of genome-sequenced, cryopreserved recombinant inbred lines useful for mapping the genetic basis and evolution of quantitative traits. We have expanded the resource with new lines and new populations, and here report updated additive and epistatic mapping simulations and the genetic and haplotypic composition of CeMEE version 2. Additive QTL explaining 3% of trait variance are detected with >80% power, and the median detection interval is around the length of a single gene on the highly recombinant chromosome arms. Although CeMEE populations are derived from a long-term evolution experiment, genetic structure is dominated by variation present in the ancestral population and is not obviously associated with phenotypic differentiation.C. elegansprovides exceptional experimental advantages for the study of phenotypic evolution.

To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations?

2008 ◽  
Vol 17 (17) ◽  
pp. 3808-3817 ◽  
Author(s):  
ÜLO VÄLI ◽  
ANNIKA EINARSSON ◽  
LISETTE WAITS ◽  
HANS ELLEGREN
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Natural Populations ◽  
Genome Wide

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

scholarly journals Spatio-temporal ecological and evolutionary dynamics in natural butterfly populations

2017 ◽  
Vol 40 ◽  
pp. 31-36
Author(s):  
Zachariah Gompert ◽  
Lauren Lucas
Keyword(s):  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Distance Sampling ◽  
Spatial And Temporal Variation ◽  
Insect Community ◽  
Long Term Study ◽  
Greater Yellowstone Area ◽  
Genome Wide ◽  
Spatio Temporal

Long term studies of wild populations indicate that natural selection can cause rapid and dramatic changes in traits, with spatial and temporal variation in the strength of selection a critical driver of genetic variation in natural populations. In 2012, we began a long term study of genome-wide molecular evolution in populations of the butterfly Lycaeides ideas in the Greater Yellowstone Area (GYA). We aimed to quantify the role of environment-dependent selection on evolution in these populations. Building on previous work, in 2017 we collected new samples, incorporated distance sampling, and surveyed the insect community at each site. We also defined the habitat boundary at anew, eleventh site. Our preliminary analyses suggest that both genetic drift and selection are important drivers in this system.   Featured photo from Figure 1 in report.

scholarly journals Reproductive Assurance Maintains Red-Flowered Plants of Lysimachia arvensis in Mediterranean Populations Despite Inbreeding Depression

2020 ◽  
Vol 11 ◽  
Author(s):  
Francisco J. Jiménez-López ◽  
Pedro L. Ortiz ◽  
María Talavera ◽  
Montserrat Arista
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Inbreeding Depression ◽  
Abiotic Factors ◽  
Natural Populations ◽  
Flower Color ◽  
Selfed Progeny ◽  
Mediterranean Populations ◽  
Mediterranean Areas ◽  
Flower Color Polymorphism

Flower color polymorphism, an infrequent but phylogenetically widespread condition in plants, is captivating because it can only be maintained under a few selective regimes but also because it can drive intra-morph assortative mating and promote speciation. Lysimachia arvensis is a polymorphic species with red or blue flowered morphs. In polymorphic populations, which are mostly Mediterranean, pollinators prefer blue-flowered plants to the red ones, and abiotic factors also favors blue-flowered plants. We hypothesize that the red morph is maintained in Mediterranean areas due to its selfing capacity. We assessed inbreeding depression in both color morphs in two Mediterranean populations and genetic diversity was studied via SSR microsatellites in 20 natural populations. Results showed that only 44–47% of selfed progeny of the red plants reached reproduction while about 72–91% of blue morph progeny did it. Between-morph genetic differentiation was high and the red morph had a lower genetic diversity and a higher inbreeding coefficient, mainly in the Mediterranean. Results suggest that selfing maintaining the red morph in Mediterranean areas despite its inbreeding depression. In addition, genetic differentiation between morphs suggests a low gene flow between them, suggesting reproductive isolation.

scholarly journals Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Ulfar Bergthorsson ◽  
Caroline J. Sheeba ◽  
Anke Konrad ◽  
Tony Belicard ◽  
Toni Beltran ◽  
...  
Keyword(s):  
Natural Selection ◽  
Transcriptional Activation ◽  
Small Rnas ◽  
Active Regions ◽  
Purifying Selection ◽  
Ancestral Population ◽  
Sequence Context ◽  
C Elegans ◽  
Population Sizes

Abstract Background Transposable elements (TEs) are an almost universal constituent of eukaryotic genomes. In animals, Piwi-interacting small RNAs (piRNAs) and repressive chromatin often play crucial roles in preventing TE transcription and thus restricting TE activity. Nevertheless, TE content varies widely across eukaryotes and the dynamics of TE activity and TE silencing across evolutionary time is poorly understood. Results Here, we used experimentally evolved populations of C. elegans to study the dynamics of TE expression over 409 generations. The experimental populations were evolved at population sizes of 1, 10 and 100 individuals to manipulate the efficiency of natural selection versus genetic drift. We demonstrate increased TE expression relative to the ancestral population, with the largest increases occurring in the smallest populations. We show that the transcriptional activation of TEs within active regions of the genome is associated with failure of piRNA-mediated silencing, whilst desilenced TEs in repressed chromatin domains retain small RNAs. Additionally, we find that the sequence context of the surrounding region influences the propensity of TEs to lose silencing through failure of small RNA-mediated silencing. Conclusions Our results show that natural selection in C. elegans is responsible for maintaining low levels of TE expression, and provide new insights into the epigenomic features responsible.

scholarly journals Genetic and species-level biodiversity patterns are linked by demography and ecological opportunity

2020 ◽  
Author(s):  
Chloé Schmidt ◽  
Stéphane Dray ◽  
Colin J. Garroway
Keyword(s):  
Genetic Diversity ◽  
Species Richness ◽  
Gene Diversity ◽  
Spatial Scales ◽  
Ecological Opportunity ◽  
Biogeographic Patterns ◽  
Genome Wide ◽  
Diversity Gradients ◽  
Low Levels

AbstractSpecies richness and genetic diversity are the two most fundamental products of evolution. Both are important conservation targets—species richness contributes to ecosystem functioning and human wellbeing, while genetic diversity allows those species to respond to changes in their environment and persist in the long-term. Biogeographic patterns of species richness are well-described, but we know little about patterns of genome-wide genetic diversity at similar spatial scales. Further, despite considerable attention to latitudinal trends in species richness, we still do not have a solid empirical understanding of the various processes that produce them, how they interact, or how they affect genetic diversity. Here we show that genome-wide genetic diversity and species richness share spatial structure, however, species richness hotspots tend to harbor low levels of within-species genetic variation. A single model encompassing eco-evolutionary processes related to environmental energy availability, niche availability, and proximity to humans explained 75% of variation in gene diversity and 90% of the variation in species richness. Our empirical model of both levels of biodiversity supports theory and demonstrates the importance of carrying capacity and ecological opportunity at individual and species levels for generating continent-wide genetic and species diversity gradients.

scholarly journals A complex multi-locus, multi-allelic genetic architecture underlying the long-term selection-response in the Virginia body weight line of chickens

2017 ◽  
Author(s):  
Yanjun Zan ◽  
Zheya Sheng ◽  
Lars Rönnegård ◽  
Christa F. Honaker ◽  
Paul B. Siegel ◽  
...  
Keyword(s):  
Body Weight ◽  
Additive Genetic Variance ◽  
Natural Populations ◽  
Selection Response ◽  
Multiple Alleles ◽  
Term Selection ◽  
Selection Responses ◽  
Genome Wide ◽  
Genetic Mechanisms

AbstractThe ability of a population to adapt to changes in their living conditions, whether in nature or captivity, often depends on polymorphisms in multiple genes across the genome. In-depth studies of such polygenic adaptations are difficult in natural populations, but can be approached using the resources provided by artificial selection experiments. Here, we dissect the genetic mechanisms involved in long-term selection responses of the Virginia chicken lines, populations that after 40 generations of divergent selection for 56-day body weight display a nine-fold difference in the selected trait. In the F15 generation of an intercross between the divergent lines, 20 loci explained more than 60% of the additive genetic variance for the selected trait. We focused particularly on seven major QTL and found that only two fine-mapped to single, bi-allelic loci; the other five contained linked loci, multiple alleles or were epistatic. This detailed dissection of the polygenic adaptations in the Virginia lines provides a deeper understanding of genome-wide mechanisms involved in the long-term selection responses. The results illustrate that long-term selection responses, even from populations with a limited genetic diversity, can be polygenic and influenced by a range of genetic mechanisms.

scholarly journals Genomics of sorghum local adaptation to a parasitic plant

2019 ◽  
Author(s):  
Emily S. Bellis ◽  
Elizabeth A. Kelly ◽  
Claire M. Lorts ◽  
Huirong Gao ◽  
Victoria L. DeLeo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Adaptation ◽  
Striga Hermonthica ◽  
Wild Plant ◽  
Parasitic Weed ◽  
Genome Wide ◽  
Staple Crop ◽  
Term Maintenance ◽  
Maintenance Of Diversity

ABSTRACTHost-parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential tradeoffs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and belowground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with tradeoffs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR-Cas9 edited sorghum further indicate the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.SIGNIFICANCE STATEMENTUnderstanding co-evolution in crop-parasite systems is critical to management of myriad pests and pathogens confronting modern agriculture. In contrast to wild plant communities, parasites in agricultural ecosystems are usually expected to gain the upper hand in co-evolutionary ‘arms races’ due to limited genetic diversity of host crops in cultivation. Here, we develop a framework to characterize associations between genome variants in global landraces (traditional varieties) of the staple crop sorghum with the distribution of the devastating parasitic weed Striga hermonthica. We find long-term maintenance of diversity in genes related to parasite resistance, highlighting an important role of host adaptation for co-evolutionary dynamics in smallholder agroecosystems.

scholarly journals The Dynamics of Adaptive Genetic Diversity During the Early Stages of Clonal Evolution

2017 ◽  
Author(s):  
Jamie R. Blundell ◽  
Katja Schwartz ◽  
Danielle Francois ◽  
Daniel S. Fisher ◽  
Gavin Sherlock ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mathematical Modelling ◽  
Experimental Evolution ◽  
General Feature ◽  
Clonal Evolution ◽  
Cell Populations ◽  
Fitness Effects ◽  
Microbial Infections ◽  
Adaptive Genetic Diversity ◽  
Lineage Tracking

The dynamics of genetic diversity in large clonally-evolving cell populations are poorly understood, despite having implications for the treatment of cancer and microbial infections. Here, we combine barcode lineage tracking, sequencing of adaptive clones, and mathematical modelling of mutational dynamics to understand diversity changes during experimental evolution. We find that, despite differences in beneficial mutational mechanisms and fitness effects between two environments, early adaptive genetic diversity increases predictably, driven by the expansion of many single-mutant lineages. However, a crash in diversity follows, caused by highly-fit double-mutants fed from exponentially growing single-mutants, a process closely related to the classic Luria-Delbruck experiment. The diversity crash is likely to be a general feature of clonal evolution, however its timing and magnitude is stochastic and depends on the population size, the distribution of beneficial fitness effects, and patterns of epistasis.

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