scholarly journals Fluctuating environments maintain genetic diversity through neutral fitness effects and balancing selection

2021 ◽  
Author(s):  
Farah Abdul-Rahman ◽  
Daniel Tranchina ◽  
David Gresham
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Biology ◽  
Balancing Selection ◽  
Oscillatory Behavior ◽  
Population Diversity ◽  
Raw Material ◽  
Environmental Fluctuation ◽  
Fitness Effects ◽  
Fluctuating Environments ◽  
Static Conditions

AbstractGenetic variation is the raw material upon which selection acts. The majority of environmental conditions change over time and therefore may result in variable selective effects. How temporally fluctuating environments impact the distribution of fitness effects and in turn population diversity is an unresolved question in evolutionary biology. Here, we employed continuous culturing using chemostats to establish environments that switch periodically between different nutrient limitations and compared the dynamics of selection to static conditions. We used the pooled Saccharomyces cerevisiae haploid gene deletion collection as a synthetic model for populations comprising thousands of unique genotypes. Using barcode sequencing (barseq), we find that static environments are uniquely characterized by a small number of high fitness genotypes that rapidly dominate the population leading to dramatic decreases in genetic diversity. By contrast, fluctuating environments are enriched in genotypes with neutral fitness effects and an absence of extreme fitness genotypes contributing to the maintenance of genetic diversity. We also identified a unique class of genotypes whose frequencies oscillate sinusoidally with a period matching the environmental fluctuation. Oscillatory behavior corresponds to large differences in short term fitness that are not observed across long timescales pointing to the importance of balancing selection in maintaining genetic diversity in fluctuating environments. Our results are consistent with a high degree of environmental specificity in the distribution of fitness effects and the combined effects of reduced and balancing selection in maintaining genetic diversity in the presence of variable selection.

scholarly journals Negative frequency-dependent selection is frequently confounding

2017 ◽  
Author(s):  
Dustin Brisson
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Biology ◽  
Balancing Selection ◽  
Natural Populations ◽  
Research Progress ◽  
Selective Force ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Negative Frequency Dependent Selection ◽  
Peer Community

AbstractThis preprint has been reviewed and recommended by Peer Community in Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100024).The existence of persistent genetic variation within natural populations presents an evolutionary problem as natural selection and genetic drift tend to erode genetic diversity. Models of balancing selection were developed to account for the high and sometimes extreme levels of polymorphism found in many natural populations. Negative frequency-dependent selection may be the most powerful selective force maintaining balanced natural polymorphisms but it is also commonly misinterpreted. The aim of this review is to clarify the processes underlying negative frequency-dependent selection, describe classes of natural polymorphisms that can and cannot result from these processes, and discuss observational and experimental data that can aid in accurately identifying the processes that generated or are maintain diversity in nature. Finally, I consider the importance of accurately describing the processes affecting genetic diversity within populations as it relates to research progress.

scholarly journals Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fehintola V. Ajogbasile ◽  
Adeyemi T. Kayode ◽  
Paul E. Oluniyi ◽  
Kazeem O. Akano ◽  
Jessica N. Uwanibe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Control Strategies ◽  
Population Diversity ◽  
Parasite Population ◽  
Nested Polymerase Chain Reaction ◽  
Public Health Burden ◽  
Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

scholarly journals Genetic diversity in Australian Cedar genotypes selected by mixed models

2012 ◽  
Vol 36 (2) ◽  
pp. 171-179 ◽  
Author(s):  
Rulfe Tavares ◽  
Alexandre Pio Viana ◽  
Deborah Guerra Barroso ◽  
Antonio Teixeira do Amaral Júnior
Keyword(s):  
Genetic Diversity ◽  
Mixed Models ◽  
Forest Products ◽  
Raw Material ◽  
Morphological Data ◽  
Technical Improvement ◽  
Diameter At Breast Height ◽  
Breast Height ◽  
Toona Ciliata ◽  
Increasing Demand

The increasing demand for raw material for multiple uses of forest products and by-products has attracted the interest for fast growing species, such as the Australian Cedar (Toona ciliata), which presents high productive and economic potential. The present work aimed at estimating genetic diversity by DNA markers and morphological traits supported for the mixed models. The following traits were measured and genotypes were sampled randomly in different areas: diameter at breast height, height, cylindrical volume, diameter, distance between nodes and crown diameter. Twelve RAPD primers were used and generated a total of 91 marks, 82 of which were polymorphic. The high percentage of polymorphic markers, 90.10%, demonstrated that discrimination in this species is efficient, but it yet little studied, for this case we can find the extent of the genetic basis for the application of technical improvement. The assessment of genetic diversity by the UPGMA method using the binary and morphological data provided the expression of genetic dissimilarities among the accessions evaluated, optimizing the perception of this divergence. The use of mixed models was efficient to assess combined genetic diversity to optimize the selection of genotypes with divergent genetic values for diameter at breast height.

scholarly journals Genetic diversity increases food-web persistence in the face of climate warming

2020 ◽  
Author(s):  
Matthew A. Barbour ◽  
Daniel J. Kliebenstein ◽  
Jordi Bascompte
Keyword(s):  
Genetic Diversity ◽  
Food Web ◽  
Allelic Variation ◽  
Chemical Defenses ◽  
Trophic Levels ◽  
Raw Material ◽  
Ecological Communities ◽  
Warming Scenario ◽  
The Face ◽  
Loss Of Genetic Diversity

Genetic diversity provides the raw material for species to adapt and persist in the face of climate change. Yet, the extent to which these genetic effects scale at the level of ecological communities remains unclear. Here we experimentally test the effect of plant genetic diversity on the persistence of an insect food web under a current and future warming scenario. We found that plant genetic diversity increased food-web persistence by increasing the intrinsic growth rates of species across multiple trophic levels. This positive effect was robust to a 3°C warming scenario and resulted from allelic variation at two genes that control the biosynthesis of chemical defenses. Our results suggest that the ongoing loss of genetic diversity may undermine the persistence and functioning of ecosystems in a changing world.One Sentence SummaryThe loss of genetic diversity accelerates the extinction of inter-connected species from an experimental food web.

Inbreeding and loss of genetic diversity increase extinction risk

2019 ◽  
pp. 31-48
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Inbreeding Depression ◽  
Environmental Changes ◽  
Extinction Risk ◽  
Raw Material ◽  
Heterozygote Advantage ◽  
Isolated Populations ◽  
Survival And Reproduction ◽  
Loss Of Genetic Diversity ◽  
Harmful Effects

Inbreeding reduces survival and reproduction (i.e. it causes inbreeding depression), and thereby increases extinction risk. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies. Impacts of inbreeding are generally greater in species that naturally outbreed than those that inbreed, in stressful than benign environments, and for fitness than peripheral traits. Harmful effects accumulate across the life cycle, resulting in devastating effects on total fitness in outbreeding species.Species face ubiquitous environmental change and must adapt or they will go extinct. Genetic diversity is the raw material required for evolutionary adaptation. However, loss of genetic diversity is unavoidable in small isolated populations, diminishing their capacity to evolve in response to environmental changes, and thereby increasing extinction risk.

scholarly journals Molecular Typing Reveals High Genetic Diversity of Xanthomonas translucens Strains Infecting Small-Grain Cereals in Iran

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
Moein Khojasteh ◽  
S. Mohsen Taghavi ◽  
Pejman Khodaygan ◽  
Habiballah Hamzehzarghani ◽  
Gongyou Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Global Scale ◽  
Population Diversity ◽  
Bacterial Leaf Streak ◽  
High Genetic Diversity ◽  
Center Of Origin ◽  
Content Type ◽  
Xanthomonas Translucens ◽  
Insight Into

ABSTRACT This study provides a phylogeographic insight into the population diversity of Xanthomonas translucens strains causing bacterial leaf streak disease of small-grain cereals in Iran. Among the 65 bacterial strains isolated from wheat, barley, and gramineous weeds in eight Iranian provinces, multilocus sequence analysis and typing (MLSA and MLST) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD), identified 57 strains as X. translucens pv. undulosa, while eight strains were identified as X. translucens pv. translucens. Although the pathogenicity patterns on oat and ryegrass weed species varied among the strains, all X. translucens pv. undulosa strains were pathogenic on barley, Harding’s grass, rye (except for XtKm35) and wheat, and all X. translucens pv. translucens strains were pathogenic on barley and Harding’s grass, while none of the latter group was pathogenic on rye or wheat (except for XtKm18). MLST using the 65 strains isolated in Iran, as well as the sequences of the four genes from 112 strains of worldwide origin retrieved from the GenBank database, revealed higher genetic diversity (i.e., haplotype frequency, haplotype diversity, and percentage of polymorphic sites) among the Iranian population of X. translucens than among the North American strains of the pathogen. High genetic diversity of the BLS pathogen in Iran was in congruence with the fact that the Iranian Plateau is considered the center of origin of cultivated wheat. However, further studies using larger collections of strains are warranted to precisely elucidate the global population diversity and center of origin of the pathogen. IMPORTANCE Bacterial leaf streak (BLS) of small-grain cereals (i.e., wheat and barley) is one of the economically important diseases of gramineous crops worldwide. The disease occurs in many countries across the globe, with particular importance in regions characterized by high levels of precipitation. Two genetically distinct xanthomonads—namely, Xanthomonas translucens pv. undulosa and X. translucens pv. translucens—have been reported to cause BLS disease on small-grain cereals. As seed-borne pathogens, the causal agents are included in the A2 list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Despite its global distribution and high economic importance, the population structure, genetic diversity, and phylogeography of X. translucens remain undetermined. This study, using MLSA and MLST, provides a global-scale phylogeography of X. translucens strains infecting small-grain cereals. Based on the diversity parameters, neutrality indices, and population structure, we observe higher genetic diversity of the BLS pathogen in Iran, which is geographically close to the center of origin of common wheat, than has so far been observed in other areas of the world, including North America. The results obtained in this study provide a novel insight into the genetic diversity and population structure of the BLS pathogen of small-grain cereals on a global scale.

scholarly journals Genomics of sorghum local adaptation to a parasitic plant

2020 ◽  
Vol 117 (8) ◽  
pp. 4243-4251 ◽  
Author(s):  
Emily S. Bellis ◽  
Elizabeth A. Kelly ◽  
Claire M. Lorts ◽  
Huirong Gao ◽  
Victoria L. DeLeo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Adaptation ◽  
Species Interactions ◽  
Balancing Selection ◽  
Control Plant ◽  
Farming Systems ◽  
Striga Hermonthica ◽  
Loss Of Function ◽  
Trade Offs ◽  
Genome Wide

Host–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 trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, 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 that 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.

scholarly journals Disentangling Population History and Character Evolution among Hybridizing Lineages

2020 ◽  
Vol 37 (5) ◽  
pp. 1295-1305 ◽  
Author(s):  
Sean P Mullen ◽  
Nicholas W VanKuren ◽  
Wei Zhang ◽  
Sumitha Nallu ◽  
Evan B Kristiansen ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Balancing Selection ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Character Evolution ◽  
Population History ◽  
Lineage Sorting ◽  
Evolutionary Origins ◽  
Whole Genome Resequencing

Abstract Understanding the origin and maintenance of adaptive phenotypic novelty is a central goal of evolutionary biology. However, both hybridization and incomplete lineage sorting can lead to genealogical discordance between the regions of the genome underlying adaptive traits and the remainder of the genome, decoupling inferences about character evolution from population history. Here, to disentangle these effects, we investigated the evolutionary origins and maintenance of Batesian mimicry between North American admiral butterflies (Limenitis arthemis) and their chemically defended model (Battus philenor) using a combination of de novo genome sequencing, whole-genome resequencing, and statistical introgression mapping. Our results suggest that balancing selection, arising from geographic variation in the presence or absence of the unpalatable model, has maintained two deeply divergent color patterning haplotypes that have been repeatedly sieved among distinct mimetic and nonmimetic lineages of Limenitis via introgressive hybridization.

scholarly journals Population genetic analysis of the Plasmodium falciparum circumsporozoite protein in two distinct ecological regions in Ghana

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Elikplim A. Amegashie ◽  
Lucas Amenga-Etego ◽  
Courage Adobor ◽  
Peter Ogoti ◽  
Kevin Mbogo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Sequence Data ◽  
Balancing Selection ◽  
Population Expansion ◽  
Circumsporozoite Protein ◽  
Cape Coast ◽  
Population Genetic Analysis ◽  
Coastal Belt ◽  
Tajima’S D

Abstract Background Extensive genetic diversity in the Plasmodium falciparum circumsporozoite protein (PfCSP) is a major contributing factor to the moderate efficacy of the RTS,S/AS01 vaccine. The transmission intensity and rates of recombination within and between populations influence the extent of its genetic diversity. Understanding the extent and dynamics of PfCSP genetic diversity in different transmission settings will help to interpret the results of current RTS,S efficacy and Phase IV implementation trials conducted within and between populations in malaria-endemic areas such as Ghana. Methods Pfcsp sequences were retrieved from the Illumina-generated paired-end short-read sequences of 101 and 131 malaria samples from children aged 6–59 months presenting with clinical malaria at health facilities in Cape Coast (in the coastal belt) and Navrongo (Guinea savannah region), respectively, in Ghana. The sequences were mapped onto the 3D7 reference strain genome to yield high-quality genome-wide coding sequence data. Following data filtering and quality checks to remove missing data, 220 sequences were retained and analysed for the allele frequency spectrum, genetic diversity both within the host and between populations and signatures of selection. Population genetics tools were used to determine the extent and dynamics of Pfcsp diversity in P. falciparum from the two geographically distinct locations in Ghana. Results Pfcsp showed extensive diversity at the two sites, with the higher transmission site, Navrongo, exhibiting higher within-host and population-level diversity. The vaccine strain C-terminal epitope of Pfcsp was found in only 5.9% and 45.7% of the Navrongo and Cape Coast sequences, respectively. Between 1 and 6 amino acid variations were observed in the TH2R and TH3R epitope regions of PfCSP. Tajima’s D was negatively skewed, especially for the population from Cape Coast, given the expected historical population expansion. In contrast, a positive Tajima’s D was observed for the Navrongo P. falciparum population, consistent with balancing selection acting on the immuno-dominant TH2R and TH3R vaccine epitopes. Conclusion The low frequencies of the Pfcsp vaccine haplotype in the analysed populations indicate a need for additional molecular and immuno-epidemiological studies with broader temporal and geographic sampling in endemic populations targeted for RTS,S application. These results have implications for the efficacy of the vaccine in Ghana and will inform the choice of alleles to be included in future multivalent or chimeric vaccines.

scholarly journals Forward from the crossroads of ecology and evolution

2011 ◽  
Vol 366 (1569) ◽  
pp. 1322-1328 ◽  
Author(s):  
Jennifer K. Rowntree ◽  
David M. Shuker ◽  
Richard F. Preziosi
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Biology ◽  
Research Literature ◽  
Community Genetics ◽  
Theoretical Development ◽  
Ecological Community ◽  
Special Issue ◽  
Community Genetic ◽  
Genetics Research ◽  
Literature Reviews

Community genetics is a synthesis of community ecology and evolutionary biology. It examines how genetic variation within a species affects interactions among species to change ecological community structure and diversity. The use of community genetics approaches has greatly expanded in recent years and the evidence for ecological effects of genetic diversity is growing. The goal of current community genetics research is to determine the circumstances in which, and the mechanisms by which community genetic effects occur and is the focus of the papers in this special issue. We bring a new group of researchers into the community genetics fold. Using a mixture of empirical research, literature reviews and theoretical development, we introduce novel concepts and methods that we hope will enable us to develop community genetics into the future.

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