scholarly journals Distinct evolutionary strategies of human leucocyte antigen loci in pathogen-rich environments

2012 ◽  
Vol 367 (1590) ◽  
pp. 830-839 ◽  
Author(s):  
Alicia Sanchez-Mazas ◽  
Jean-François Lemaître ◽  
Mathias Currat
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Human Leucocyte Antigen ◽  
Balancing Selection ◽  
Allelic Diversity ◽  
Hla Class I ◽  
Significant Negative Correlation ◽  
Evolutionary Strategies ◽  
Hla Genes ◽  
Geographical Distances

Human leucocyte antigen (HLA) loci have a complex evolution where both stochastic (e.g. genetic drift) and deterministic (natural selection) forces are involved. Owing to their extraordinary level of polymorphism, HLA genes are useful markers for reconstructing human settlement history. However, HLA variation often deviates significantly from neutral expectations towards an excess of genetic diversity. Because HLA molecules play a crucial role in immunity, this observation is generally explained by pathogen-driven-balancing selection (PDBS). In this study, we investigate the PDBS model by analysing HLA allelic diversity on a large database of 535 populations in relation to pathogen richness. Our results confirm that geographical distances are excellent predictors of HLA genetic differentiation worldwide. We also find a significant positive correlation between genetic diversity and pathogen richness at two HLA class I loci (HLA-A and -B), as predicted by PDBS, and a significant negative correlation at one HLA class II locus (HLA-DQB1). Although these effects are weak, as shown by a loss of significance when populations submitted to rapid genetic drift are removed from the analysis, the inverse relationship between genetic diversity and pathogen richness at different loci indicates that HLA genes have adopted distinct evolutionary strategies to provide immune protection in pathogen-rich environments.

Spatial and temporal genetic diversity of the Texas kangaroo rat, Dipodomys elator (Rodentia: Heteromyidae)

2019 ◽  
Vol 100 (4) ◽  
pp. 1169-1181 ◽  
Author(s):  
Russell S Pfau ◽  
Jim R Goetze ◽  
Robert E Martin ◽  
Kenneth G Matocha ◽  
Allan D Nelson
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
Allelic Diversity ◽  
Effective Population ◽  
Kangaroo Rat ◽  
Time Periods ◽  
Mtdna Diversity ◽  
Using Data

Abstract The Texas kangaroo rat (Dipodomys elator) is listed as a threatened species in Texas because of its scarcity and small geographic range. We assessed patterns of genetic diversity in D. elator that could affect extinction risk or influence management decisions. Specific objectives included: 1) document levels of genetic diversity, 2) document the degree and patterns of genetic divergence among localities, and 3) compare levels of genetic diversity between different time periods at the same locality. Portions of the mitochondrial genome (mtDNA; control region, cytochrome c oxidase subunit I, and cytochrome b) were sequenced and nuclear microsatellites were examined. Low mtDNA diversity was observed, which could be explained by an historical, species-wide genetic bottleneck. In contrast, microsatellites exhibited ample variation, and analyses were conducted using data from 11 loci and four populations (designated Quanah, Iowa Park, Vernon, and Harrold). Allelic diversity and heterozygosity were similar between populations and temporal samples. Estimates of effective population size (Ne) ranged from 5 to 856, depending on method and population, with Iowa Park showing consistently lower values than Quanah. All methods addressing population structure indicated that the Iowa Park population was divergent from the others, with Vernon and Harrold showing a somewhat intermediate relationship but with a closer affiliation with Quanah than Iowa Park, despite their closer proximity to Iowa Park. This pattern did not conform to isolation by distance, thus genetic drift appears to have played a greater role than gene flow in establishing genetic structure. There was much less difference between temporal samples compared to geographic samples, indicating that genetic drift has had only minimal impacts in shifting allelic frequencies over the time periods examined (17–36 years).

scholarly journals Population structure in the MHC region

2021 ◽  
Author(s):  
Andre S Marostica ◽  
Kelly Nunes ◽  
Erick C Castelli ◽  
Nayara SB Silva ◽  
Bruce Weir ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bone Marrow ◽  
Population Structure ◽  
Balancing Selection ◽  
African Ancestry ◽  
Human Diversity ◽  
Hla Alleles ◽  
Hla Genes ◽  
Geographic Regions ◽  
Genomic Regions

In his 1972 "The apportionment of human diversity", Richard Lewontin showed that, when averaged over loci, genetic diversity is predominantly attributable to differences among individuals within populations. However, selection on specific genes and genomic regions can alter the apportionment of diversity. We examine genetic diversity at the HLA loci, located within the MHC region. HLA genes code for proteins that are critical to adaptive immunity and are well-documented targets of balancing selection. The SNPs within HLA genes show strong signatures of balancing selection on large timescales and are broadly shared among populations, with low FST values. However, when we analyze haplotypes defined by these SNPs (i.e., which define "HLA alleles"), we find marked differences in frequencies between geographic regions. These differences are not reflected in the FST values because of the extreme polymorphism at HLA loci, illustrating challenges in interpreting FST. Differences in the frequency of HLA alleles among geographic regions are relevant to bone-marrow transplantation, which requires genetic identity at HLA loci between patient and donor. We explore the case of Brazil's bone-marrow registry, where a deficit of enrolled volunteers with African ancestry reduces the chance of finding donors for individuals with an MHC region of African ancestry.

scholarly journals Genetic Diversity of C4 Photosynthesis Pathway Genes in Sorghum bicolor (L.)

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 806
Author(s):  
Yongfu Tao ◽  
Barbara George-Jaeggli ◽  
Marie Bouteillé-Pallas ◽  
Shuaishuai Tai ◽  
Alan Cruickshank ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Gene Family ◽  
C4 Photosynthesis ◽  
Balancing Selection ◽  
Regulatory Protein ◽  
Allelic Diversity ◽  
Gene Families ◽  
Photosynthetic Pathway ◽  
Sorghum Bicolor L

C4 photosynthesis has evolved in over 60 different plant taxa and is an excellent example of convergent evolution. Plants using the C4 photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C3 and C4 species have elucidated the genetic diversity underpinning the C4 photosynthetic pathway, no previous studies have described the genetic diversity of the genes involved in this pathway within a C4 crop species. Enhanced understanding of the allelic diversity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Here, we present the first genetic diversity survey of 8 known C4 gene families in an important C4 crop, Sorghum bicolor (L.) Moench, using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide diversity of C4 gene families varied more than 20-fold from the NADP-malate dehydrogenase (MDH) gene family (θπ = 0.2 × 10−3) to the pyruvate orthophosphate dikinase (PPDK) gene family (θπ = 5.21 × 10−3). Genetic diversity of C4 genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C4 photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C4 PPDK and carbonic anhydrase (CA) genes, and balancing selection signals on C4 PPDK-regulatory protein (RP) and phosphoenolpyruvate carboxylase (PEPC) genes. Allelic distribution of these C4 genes was consistent with selection signals detected. A better understanding of the genetic diversity of C4 pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.

scholarly journals Modeling minimum viable population size with multiple genetic problems of small populations

2021 ◽  
Author(s):  
Peter Nabutanyi ◽  
Meike J. Wittmann
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Genetic Drift ◽  
Balancing Selection ◽  
Fixed Number ◽  
Allele Frequency Distribution ◽  
Small Populations ◽  
Ecological Processes ◽  
Viable Population ◽  
Minimum Viable Population

An important goal for conservation is to define minimum viable population (MVP) sizes for long-term persistence. Although many MVP size estimates focus on ecological processes, with increasing evidence for the role of genetic problems in population extinction, conservation practitioners have also increasingly started to incorporate inbreeding depression (ID). However, small populations also face other genetic problems such as mutation accumulation (MA) and loss of genetic diversity through genetic drift that are usually factored into population viability assessments only via verbal arguments. Comprehensive quantitative theory on interacting genetic problems is missing. Here we develop eco-evolutionary quantitative models that track both population size and levels of genetic diversity. Our models assume a biallelic multilocus genome whose loci can be under either a single or interacting genetic forces. In addition to mutation-selection-drift balance (for loci facing ID and MA), we include three forms of balancing selection (for loci where variation is lost through genetic drift). We define MVP size as the lowest population size that avoids an eco-evolutionary extinction vortex after a time sufficient for an equilibrium allele frequency distribution to establish. Our results show that MVP size decreases rapidly with increasing mutation rates for populations whose genomes are only under balancing selection, while for genomes under mutation-selection-drift balance, the MVP size increases rapidly. MVP sizes also increase rapidly with increasing number of loci under the same or different selection mechanisms until a point is reached at which even arbitrarily large populations cannot survive anymore. In the case of fixed number of loci under selection, interaction of genetic problems did not necessarily increase MVP sizes. To further enhance our understanding about interaction of genetic problems, there is need for more empirical studies to reveal how different genetic processes interact in the genome.

scholarly journals Balancing Selection at Closely Linked, Overdominant Loci in a Finite Population

Genetics ◽  
2000 ◽  
Vol 154 (3) ◽  
pp. 1367-1378 ◽  
Author(s):  
Montgomery Slatkin
Keyword(s):  
Linkage Disequilibrium ◽  
Mhc Class Ii ◽  
Genetic Drift ◽  
Balancing Selection ◽  
Allelic Diversity ◽  
Analytic Theory ◽  
Descriptive Statistics ◽  
Strong Linkage Disequilibrium ◽  
Strong Linkage ◽  
Infinite Alleles Model

Abstract High levels of allelic diversity and strong linkage disequilibrium are found in the major histocompatibility (MHC) system in humans and other vertebrates. This article proposes several descriptive statistics that quantify the extent and pattern of strong linkage disequilibrium between pairs of highly polymorphic loci. It also develops an approximate analytic theory incorporating the effects of balancing selection, mutation, recombination, and genetic drift at two closely linked loci and compares the theoretical predictions with published surveys of the MHC class II loci, DQA1 and DQB1, in humans and nonhuman primates. The descriptive statistics proposed include the fraction of complementary haplotypes (haplotypes with D″ = 1), the fraction of excess haplotypes, and the numbers of alleles at each locus in complementary haplotypes with one or more alleles at the other locus. The model assumes the infinite alleles model of mutation and the symmetric overdominance model of selection. Analytic approximations in some cases are obtained in the strong selection, weak mutation (SSWM) limit introduced by J. Gillespie. The predictions of the approximate analysis are confirmed by simulation. Both the analytic theory and simulations show that relatively few haplotypes will be found when selection is strong and recombination is weak relative to genetic drift. The model can reproduce many of the observed patterns at DQA1 and DQB1 provided that the recombination rate is assumed to be very small.

scholarly journals Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

2019 ◽  
Author(s):  
Yongfu Tao ◽  
Barbara George-Jaeggli ◽  
Marie Bouteille-Pallas ◽  
Shuaishuai Tai ◽  
Alan Cruickshank ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Gene Family ◽  
Sequence Data ◽  
Allelic Variation ◽  
Balancing Selection ◽  
Allelic Diversity ◽  
Gene Families ◽  
Photosynthetic Pathway ◽  
Sorghum Bicolor L

Abstract Background C 4 photosynthesis has evolved in over 60 different plant taxa and is an excellent example of convergent evolution. Plants using the C 4 photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C 3 and C 4 species have elucidated the genetic diversity underpinning the C 4 photosynthetic pathway, no previous studies have described the genetic diversity of the genes involved in this pathway within a C 4 crop species. Enhanced understanding of the allelic diversity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Results Here, we present the first genetic diversity survey of 8 known C 4 gene families in an important C 4 crop, Sorghum bicolor (L.) Moench using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide diversity of C 4 gene families varied more than 20-fold from the NADP-MDH gene family (θπ =0.2×10 -3 ) to the PPDK gene family (θπ = 5.21×10 -3 ). Genetic diversity of C 4 genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C 4 photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C 4 PPDK and CA genes, and balancing selection signals on C 4 PPDK-RP and PEPC genes. Allelic distribution of these C 4 genes was consistent with selection signals detected. Conclusions Domestication of sorghum has reshaped diversity of C 4 pathway. A better understanding of the genetic diversity of this pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.

scholarly journals Improved Characterization of Balancing Selection Genome Wide and a Detailed Look at HLA Genes

2021 ◽  
Author(s):  
Tristan J Hayeck ◽  
Timothy L. Mosbruger ◽  
Jonathan P Bradfield ◽  
Adam G Gleason ◽  
George Damianos ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Allelic Diversity ◽  
Exon 2 ◽  
Multiple Alleles ◽  
Bayesian Techniques ◽  
Hla Genes ◽  
Genome Wide ◽  
Evolutionary Simulation ◽  
Critical Regions

Balancing selection occurs when different evolutionary pressures impact the fitness of multiple alleles, resulting in increased allelic diversity in the population. A new statistical method was developed to test for selection, improving inference by using efficient Bayesian techniques to test for density and strength of linkage disequilibrium. Evolutionary simulation studies showed that the method consistently outperformed existing methods. Using this methodology, we tested for novel signals of balancing selection genome wide in 500 samples from phased trios. Several novel signals of selection appeared in CYP2A7, GPC6, and CNR2 across multiple ancestries. Additionally, tests in SIRPA demonstrate dramatically strong selection signal, significantly higher than previously observed. Well-known signals around olfactory genes and the MHC, containing HLA genes associated with the immune response, also demonstrated strong signatures of selection. So, utilizing data from the 17th IHIW, a follow up analysis was then performed by leveraging over seven thousand HLA typed samples by NGS; in contrast, the genome wide scan did not include a detailed characterization of the HLA genes. The strongest signals observed in the IHIW samples were in DQA1 and DQB1 in or around exon 2, the portion of the gene responsible for antigen presentation and most likely to be under environmental and evolutionary pressure. Our new statistical approach and analysis suggest novel evolutionary pressure in new regions and additionally highlight the importance of improved sequencing and characterization of variation across the extended MHC and other critical regions.

scholarly journals Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)

2019 ◽  
Author(s):  
Yongfu Tao ◽  
Barbara George-Jaeggli ◽  
Marie Bouteille-Pallas ◽  
Shuaishuai Tai ◽  
Alan Cruickshank ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Gene Family ◽  
C4 Photosynthesis ◽  
Allelic Variation ◽  
Balancing Selection ◽  
Allelic Diversity ◽  
Gene Families ◽  
Photosynthetic Pathway ◽  
Sorghum Bicolor L

Abstract Background C4 photosynthesis has evolved in over 60 different plant taxa and is an excellent example of convergent evolution. Plants using the C4 photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C3 and C4 species have elucidated the genetic diversity underpinning the C4 photosynthetic pathway, no previous studies have described the genetic diversity of the genes involved in this pathway within a C4 crop species. Enhanced understanding of the allelic diversity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Results Here, we present the first genetic diversity survey of 8 known C4 gene families in an important C4 crop, Sorghum bicolor (L.) Moench using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide diversity of C4 gene families varied more than 20-fold from the NADP-MDH gene family (θπ =0.2×10-3) to the PPDK gene family (θπ = 5.21×10-3). Genetic diversity of C4 genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C4 photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C4 PPDK and CA genes, and balancing selection signals on C4 PPDK-RP and PEPC genes. Allelic distribution of these C4 genes was consistent with selection signals detected.Conclusions Domestication of sorghum has reshaped diversity of C4 pathway. A better understanding of the genetic diversity of this pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.

scholarly journals Balancing selection, genetic drift, and human‐mediated introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout

2021 ◽  
Author(s):  
Lorenzo Talarico ◽  
Silvio Marta ◽  
Anna Rita Rossi ◽  
Simone Crescenzo ◽  
Gerardo Petrosino ◽  
...  
Keyword(s):  
Functional Diversity ◽  
Genetic Drift ◽  
Brown Trout ◽  
Balancing Selection

scholarly journals Allelic diversity in populations of Solanum lycocarpum A. St.-Hil (Solanaceae) in a protected area and a disturbed environment

2011 ◽  
Vol 25 (4) ◽  
pp. 937-940 ◽  
Author(s):  
Tânia Maria de Moura ◽  
Alexandre Magno Sebbenn ◽  
Karina Martins ◽  
Maria Andreia Moreno ◽  
Giancarlo Conde Xavier Oliveira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Protected Areas ◽  
Allelic Diversity ◽  
Rare Allele ◽  
Conservation Unit ◽  
Long Distance ◽  
Disturbed Area ◽  
Disturbed Areas ◽  
Pasture Area ◽  
Two Populations

This study aimed to compare the genetic diversity of populations of Solanum lycocarpum A.St.-Hil between natural and human disturbed environments, with the assumption that protected areas have greater genetic diversity than disturbed areas. For this study, two populations were sampled in Goiás State, Brazil. One was located in a conservation unit, Serra de Caldas Novas State Park, in the Caldas Novas municipality. The other was located in a pasture area in the municipality of Morrinhos. The two populations are 41 km apart. We sampled 60 individuals from each population, which were genotyped with five microsatellite loci (SSR). The highest number of alleles was recorded in the population of the conservation unit, where we found 11 exclusive and five rare alleles. In the disturbed area, we recorded only three exclusive alleles and one rare allele. Although we did not observe significant inbreeding in these populations, genetic divergence between them was high (G ST (Hedrick)=0.147 =0.147) for a species with long distance seed dispersal. The results corroborate the hypothesis that the population in the less disturbed area harbors greater allelic diversity. They also confirm the effectiveness of using protected areas to preserve the genetic diversity of the species.

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