scholarly journals Long-term balancing selection drives evolution of immunity genes in Capsella

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Daniel Koenig ◽  
Jörg Hagmann ◽  
Rachel Li ◽  
Felix Bemm ◽  
Tanja Slotte ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Balancing Selection ◽  
Protein Sequences ◽  
Population Bottleneck ◽  
Genomic Variability ◽  
Immune Systems ◽  
Immunity Genes ◽  
Evolution Of Immunity

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. By reconstructing the evolution of the disease-related locus MLO2b, we find that divergence between ancient haplotypes can be obscured by referenced based re-sequencing methods, and that trans-specific alleles can encode substantially diverged protein sequences. Our data point to long-term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

scholarly journals Long-term balancing selection drives evolution of immunity genes in Capsella

2018 ◽  
Author(s):  
Daniel Koenig ◽  
Jörg Hagmann ◽  
Rachel Li ◽  
Felix Bemm ◽  
Tanja Slotte ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Natural Selection ◽  
Balancing Selection ◽  
Population Bottleneck ◽  
Genomic Variability ◽  
Immune Systems ◽  
Immunity Genes ◽  
Evolution Of Immunity

ABSTRACTGenetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. Our data point to long term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

scholarly journals Author response: Long-term balancing selection drives evolution of immunity genes in Capsella

2019 ◽  
Author(s):  
Daniel Koenig ◽  
Jörg Hagmann ◽  
Rachel Li ◽  
Felix Bemm ◽  
Tanja Slotte ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Author Response ◽  
Immunity Genes ◽  
Evolution Of Immunity

Genetic polymorphism in Proteocephalus exiguus shown by enzyme electrophoresis

1996 ◽  
Vol 70 (4) ◽  
pp. 345-349 ◽  
Author(s):  
V. Šnábel ◽  
V. Hanzelová ◽  
S. Mattiucci ◽  
S. D'Amelio ◽  
L. Paggi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Polymorphism ◽  
Genetic Variability ◽  
Balancing Selection ◽  
Outcrossing Rate ◽  
Enzyme Electrophoresis ◽  
Factors Affecting ◽  
Hardy Weinberg Equilibrium ◽  
Coregonid Fishes

AbstractEnzyme electrophoresis has been used to examine genetic diversity in a population of Proteocephalus exiguus La Rue, 1911 (Cestoda: Proteocephalidae), parasitizing salmonid and coregonid fishes. Among 16 loci tested, three polymorphic loci (Ada, Got, Pgm-2) were found. Six different genotypes at the Got locus distributed in Hardy-Weinberg equilibrium suggest remarkable genetic flexibility of P. exiguus. Balancing selection is proposed as the mechanism maintaining genetic variation within the species. Data of genetic variability parameters (Ho = 0.064; He = 0.07; P = 0.19) and outcrossing rate (t = 0.842) of P. exiguus population have been provided. Possible factors affecting these data are discussed.

Worldwide genetic variation at the 3′ untranslated region of the HLA-G gene: balancing selection influencing genetic diversity

2013 ◽  
Vol 15 (2) ◽  
pp. 95-106 ◽  
Author(s):  
A Sabbagh ◽  
P Luisi ◽  
E C Castelli ◽  
L Gineau ◽  
D Courtin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Untranslated Region ◽  
Balancing Selection

scholarly journals Long-term balancing selection in highly dynamic mating loci generates trans-species polymorphisms in fungi

2021 ◽  
Author(s):  
David Peris ◽  
Dabao Sun Lu ◽  
Vilde Bruhn Kinneberg ◽  
Ine-Susanne Hopland Methlie ◽  
Malin Stapnes Dahl ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Phylogenetic Analyses ◽  
Chromosome 9 ◽  
Chromosome 2 ◽  
Evolutionary Forces ◽  
Evolutionary Force ◽  
Identity Threshold

Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, MATA and MATB. These loci are usually highly diverse, but with conserved domains. Previous studies have revealed that species of the genus Trichaptum (Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple inferred alleles for MATA and MATB. Here, we sequenced a total of a hundred and eighty specimens of three Trichaptum species. We characterized the chromosomal location of MATA (chromosome 2) and MATB (chromosome 9), the molecular structure of MAT regions and their allelic richness. We found multiple MAT alleles segregating in both multiple Trichaptum specimens, and the non-Trichaptum species included for comparison. Phylogenetic analyses and various nucleotide statistics suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an identity threshold of higher than 86%. The observed allelic classes could potentially generate 14,560 different mating types. The inferred allelic information mirrored the outcome of in vitro crosses, thus allowing us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating in Trichaptum loci is due to long-term balancing selection that likely promote sexual outcrossing, with limited recombination and duplication activity. Our large number of sequenced specimens highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.

scholarly journals Moderate Genetic Diversity and Demographic Reduction in the Threatened Giant Anteater, Myrmecophaga tridactyla

2021 ◽  
Vol 12 ◽  
Author(s):  
Carmen Elena Barragán-Ruiz ◽  
Rosane Silva-Santos ◽  
Bruno H. Saranholi ◽  
Arnaud L. J. Desbiez ◽  
Pedro Manoel Galetti
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Western Region ◽  
Mammal Species ◽  
Genetic Population ◽  
Entire Area ◽  
Flow Restriction ◽  
Population Structuring ◽  
Recent Bottleneck

In general, large mammal species with highly specialized feeding behavior and solitary habits are expected to suffer genetic consequences from habitat loss and fragmentation. To test this hypothesis, we analyzed the genetic diversity distribution of the threatened giant anteater inhabiting a human-modified landscape. We used 10 microsatellite loci to assess the genetic diversity and population structure of 107 giant anteaters sampled in the Brazilian Central-Western region. No genetic population structuring was observed in this region suggesting no gene flow restriction within the studied area. On the other hand, the moderate level of genetic diversity (Ho = 0.54), recent bottleneck detected and inbreeding (Fis, 0.13; p ≤ 0.001) signatures suggest potential impacts on the genetic variation of this Xenarthra. Additionally, a previous demographic reduction was suggested. Thus, considering the increased human-promoted impacts across the entire area of distribution of the giant anteater, our results can illustrate the potential effects of these disturbances on the genetic variation, allowing us to request the long-term conservation of this emblematic species.

Biodiversity at the molecular genetic level: experiences from disparate macroorganisms

1994 ◽  
Vol 345 (1311) ◽  
pp. 59-64 ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Sequence Data ◽  
Molecular Genetic ◽  
Dna Sequence Data ◽  
Genetic Level ◽  
Management Policies ◽  
Term Maintenance

Genetic variation is the basis of adaptive flexibility in populations and is the ultimate evolutionary basis of much species and community-level diversity. Accordingly, the preservation and maintenance of genetic diversity has a high priority in many conservation programmes. This paper discusses how genetic diversity is measured at the molecular level, including some newer measures made possible with restriction site or DNA sequence data as well as the development of a phylogenetic approach to assessing the significance of genetic variation within a species. These measures of genetic diversity are then used to re-examine the validity of the 50/500 rule of conservation biology; a rule that states that populations should have no fewer than 50 individuals for short-term maintenance of genetic variation and no fewer than 500 individuals for long-term maintenance. Both the 50 and 500 parts of this rule are found to be invalid and frequently misleading. Instead of invoking ‘universal’ rules, conservation biologists should recognize the role of biodiversity in management policies. Not all species are the same, and we need more research and a willingness to try novel approaches rather than naively apply a ‘rule’ that has no demonstrable generality.

scholarly journals Optimal cross selection for long-term genetic gain in two-part programs with rapid recurrent genomic selection

2017 ◽  
Author(s):  
Gregor Gorjanc ◽  
R. Chris Gaynor ◽  
John M. Hickey
Keyword(s):  
Genetic Diversity ◽  
Genomic Selection ◽  
Genetic Gain ◽  
Balancing Selection ◽  
Breeding Program ◽  
Truncation Selection ◽  
Part Program ◽  
Population Improvement ◽  
Selection For

AbstractThis study evaluates optimal cross selection for balancing selection and maintenance of genetic diversity in two-part plant breeding programs with rapid recurrent genomic selection. The two-part program reorganizes a conventional breeding program into population improvement component with recurrent genomic selection to increase the mean of germplasm and product development component with standard methods to develop new lines. Rapid recurrent genomic selection has a large potential, but is challenging due to genotyping costs or genetic drift. Here we simulate a wheat breeding program for 20 years and compare optimal cross selection against truncation selection in the population improvement with one to six cycles per year. With truncation selection we crossed a small or a large number of parents. With optimal cross selection we jointly optimised selection, maintenance of genetic diversity, and cross allocation with AlphaMate program. The results show that the two-part program with optimal cross selection delivered the largest genetic gain that increased with the increasing number of cycles. With four cycles per year optimal cross selection had 78% (15%) higher long-term genetic gain than truncation selection with a small (large) number of parents. Higher genetic gain was achieved through higher efficiency of converting genetic diversity into genetic gain; optimal cross selection quadrupled (doubled) efficiency of truncation selection with a small (large) number of parents. Optimal cross selection also reduced the drop of genomic selection accuracy due to the drift between training and prediction populations. In conclusion, optimal cross-selection enables optimal management and exploitation of population improvement germplasm in two-part programs.Key messageOptimal cross selection increases long-term genetic gain of two-part programs with rapid recurrent genomic selection. It achieves this by optimising efficiency of converting genetic diversity into genetic gain through reducing the loss of genetic diversity and reducing the drop of genomic prediction accuracy with rapid cycling.

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