Use of Allelic Frequencies to Describe Population Structure

1981 ◽  
Vol 38 (12) ◽  
pp. 1507-1514 ◽  
Author(s):  
Fred W. Allendorf ◽  
Stevan R. Phelps
Keyword(s):  
Reproductive Isolation ◽  
Absolute Number ◽  
Allelic Frequency ◽  
Genetic Exchange ◽  
Frequency Data ◽  
Allelic Frequencies ◽  
Population Sizes ◽  
Isozyme Loci ◽  
Electrophoretic Techniques ◽  
Degree Of Isolation

Development of electrophoretic techniques has allowed the estimation of allelic frequencies at many isozyme loci in populations of fish. The pattern of allelic frequency divergence in salmonid populations has been used to describe the pattern of genetic exchange and degree of isolation among local geographic units. Our goal is to determine how much genetic exchange among subpopulations will yield observed patterns of allelic divergence. We approach this goal using population genetics theory and a series of computer simulations.The amount of allelic divergence between subpopulations is a function of the absolute number of migrant individuals exchanged, and not the proportion of individuals exchanged. Therefore, some knowledge of population sizes is needed to estimate degree of reproductive isolation from allelic frequency data. Second, statistically significant allelic divergence will often be present even when there is substantial exchange among subpopulations. For example, significant allelic divergence was present in our simulations over 50% of the time with 20 subpopulations exchanging 50 individuals per generation. Third, allelic frequencies estimated from fry should be used with caution when drawing conclusions about the significance of allelic divergence in the reproducing adults.Key words: allelic divergence, reproductive isolation, gene flow, genetic drift, computer simulations

scholarly journals Reproductive isolation of hybrid populations driven by genetic incompatibilities

2014 ◽  
Author(s):  
Molly Schumer ◽  
Rongfeng Cui ◽  
Gil G Rosenthal ◽  
Peter Andolfatto
Keyword(s):  
Reproductive Isolation ◽  
Alternative Model ◽  
Parental Species ◽  
Small Population ◽  
Hybrid Population ◽  
Ecological Niches ◽  
Simple Consequence ◽  
Hybrid Species ◽  
Population Sizes ◽  
Adaptive Radiations

Despite its role in homogenizing populations, hybridization has also been proposed as a means to generate new species. The conceptual basis for this idea is that hybridization can result in novel phenotypes through recombination between the parental genomes, allowing a hybrid population to occupy ecological niches unavailable to parental species. A key feature of these models is that these novel phenotypes ecologically isolate hybrid populations from parental populations, precipitating speciation. Here we present an alternative model of the evolution of reproductive isolation in hybrid populations that occurs as a simple consequence of selection against incompatibilities. Unlike previous models, our model does not require small population sizes, the availability of new niches for hybrids or ecological or sexual selection on hybrid traits. We show that reproductive isolation between hybrids and parents evolves frequently and rapidly under this model, even in the presence of ongoing migration with parental species and strong selection against hybrids. Our model predicts that multiple distinct hybrid species can emerge from replicate hybrid populations formed from the same parental species, potentially generating patterns of species diversity and relatedness that mimic adaptive radiations.

scholarly journals POLYMORPHISM IN A CYCLIC PARTHENOGENETIC SPECIES: SIMOCEPHALUS SERRULATUS

Genetics ◽  
1976 ◽  
Vol 84 (3) ◽  
pp. 631-637
Author(s):  
M Yao Smith ◽  
Alex Fraser
Keyword(s):  
Seasonal Changes ◽  
Natural Populations ◽  
Genetic Homogeneity ◽  
Laboratory Population ◽  
Gametic Disequilibrium ◽  
Polymorphic Loci ◽  
Parthenogenetic Species ◽  
Apomictic Parthenogenesis ◽  
Isozyme Loci ◽  
Electrophoretic Techniques

ABSTRACT A survey of sixteen isozyme loci using electrophoretic techniques was conducted for three isolated natural populations and one laboratory population of the cyclic parthenogenetic species, Simocephalus serrulatus. The proportion of polymorphic loci (33%-60%) and the average number of heterozygous loci per individual (6%-23%) in the three natural populations were found to be comparable to those found in most sexually reproducing organisms. Detailed analyses were made for one of these populations using five polymorphic loci. The results indicated that (1) seasonal changes in genotypic frequencies took place, (2) apomictic parthenogenesis does not lead to genetic homogeneity, and (3) marked gametic disequilibrium at these five loci was present in the population, indicating that selection acted on coadapted groups of genes.

scholarly journals SPECIES COMPOSITION AND RELATIVE POPULATION SIZE OF FISHES IN THE OSTER RIVER (THE DESNA RIVER BASIN): 50 YEARS ANALYSIS

2021 ◽  
Vol 26 (1(48)) ◽  
pp. 73-88
Author(s):  
S. V. Mezhzherin ◽  
S. V. Kokodii ◽  
D. S. Lutsenko ◽  
А. О. Tsyba
Keyword(s):  
Species Composition ◽  
Population Size ◽  
Absolute Number ◽  
River Systems ◽  
Relative Population ◽  
Population Sizes ◽  
Invasion Species ◽  
Chondrostoma Nasus ◽  
Leuciscus Idus ◽  
Current Species

Inroduction. Changes in the species composition and population size of freshwater fihes are determined by deformations of the habitat in Ukraine and are characterized by a pronounced negative dynamics. Deformation of ichthyofauna is caused by extinction of a number of aboriginal fihes and emergence of alien species.Aim. To establish the current species composition and relative population size of fih species in the Oster River and the dynamics of these characteristics over a 50-yearlong period in the context of negative transformations of the ichthyofauna of the rivers of Ukraine.Results. Comparative study of the species composition and relative population size of fih species in the fih catches by small-river fihing gear in the Oster river was conducted during the period since 1971-72 till 2019. During this time considerable changes in species composition took place. The following species disappeared from the catches: Leuciscus leuciscus, Leuciscus idus, Chondrostoma nasus, Carassius carassius, Blicca bojerkna and Neogobius flviatilis, they were replaced by three invasion species (Percottus glenni, Pseudorasbora parva, Proterorhinus marmoratus). The changes in the dominant species took place, thus, in the Oster ichthyocene the species with the short life cycle started to prevail, the share of invasion species increased from 1.4 to 37%, and the share of initial marine fih among them is very low. The comparison with the river systems of the Stugna and the Lower Dnipro represents the fact that the mentioned negative tendencies are common for the whole Dnipro system, however the situation in the Lower Dnipro must be considered less critical than in the Oster and the Stugna rivers. The fact that the catches of industrial fih decreased more than 10 times in the Desna river during this period of time gives the reason to consider that the dramatic reduction of the absolute number of their populations occurred in the Oster river as well. That is why even relatively safe species (Abramis brama, Rutilus ritilus, Scardinius erythrophthalmus, Esox lucius, Perca flviatilis, Alburnus alburnus, Squalius cephalus) are in critical situation in this transformed river system.Сonclusions. In the ichthyocene of the Oster River over a 50-year period there have been signifiant changes in species composition, relative and absolute population numbers associated with the extinction and reduction of population sizes of rheophilic species and fih that are adapted to life in the flodplain. The modern Oster River is dominated by invasive and short-cycle species. The obtained tendencies in the dynamics of the ichthyofauna of the Oster River are similar to the nature of changes in other river systems of Ukraine, although they occur at a faster pace, which is characteristic of the smallest plain rivers.

scholarly journals Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array

2021 ◽  
Vol 11 ◽  
Author(s):  
Mariangela Arca ◽  
Tristan Mary-Huard ◽  
Brigitte Gouesnard ◽  
Aurélie Bérard ◽  
Cyril Bauland ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput ◽  
Large Scale ◽  
Allelic Frequency ◽  
Laboratory Equipment ◽  
Fluorescent Intensity ◽  
Allelic Frequencies ◽  
Wide Range ◽  
Young Leaves ◽  
Scale Characterization

Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains, however, poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on single-nucleotide polymorphism (SNP) Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger’s genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 simple sequence repeats using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.

scholarly journals Deciphering the genetic diversity of landraces with high-throughput SNP genotyping of DNA bulks: methodology and application to the maize 50k array

2020 ◽  
Author(s):  
Mariangela Arca ◽  
Tristan Mary-Huard ◽  
Brigitte Gouesnard ◽  
Aurélie Bérard ◽  
Cyril Bauland ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput ◽  
Large Scale ◽  
Allelic Frequency ◽  
Laboratory Equipment ◽  
Fluorescent Intensity ◽  
Allelic Frequencies ◽  
Wide Range ◽  
Young Leaves ◽  
Scale Characterization

ABSTRACTGenebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains however poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on SNP Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger’s genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 SSRs using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.

Allozyme Variation of Great Lakes Alewife, Alosa pseudoharengus: Genetic Differentiation and Affinities of a Recent Invader

1992 ◽  
Vol 49 (9) ◽  
pp. 1770-1777 ◽  
Author(s):  
Peter E. Ihssen ◽  
G. William Martin ◽  
David W. Rodgers
Keyword(s):  
New York ◽  
Great Lakes ◽  
Allozyme Variation ◽  
Allelic Frequency ◽  
Starch Gel Electrophoresis ◽  
Alosa Pseudoharengus ◽  
Allelic Frequencies ◽  
Cayuga Lake ◽  
Finger Lakes ◽  
Allozyme Loci

Allelic frequencies for six polymorphic allozyme loci (27 loci examined), as determined by starch-gel electrophoresis, were not significantly different for alewife, Alosa pseudoharengus, among the Great Lakes (Ontario, Erie, Huron, and Michigan). Alewife from one of the Finger Lakes (Cayuga Lake) had allelic frequencies similar to Great Lakes alewife, and the alleles of Great Lakes alewife form a subset of those found in Cayuga Lake. In contrast, Maritime Canada populations (Gaspereau, Miramichi, and St. John rivers) were distinct from each other and from the Great Lakes and Cayuga Lake populations. Highly significant allelic frequency differences were observed among the Maritime populations and between the Maritime populations and the Great Lakes or Cayuga Lake populations. Fifteen alleles were not shared between the Great Lakes and the Maritime populations. We concluded from these results that Great Lakes alewife and Cayuga Lake alewife form a contiguous stock and that Great Lakes alewife are a recent invader that probably originated from the Hudson–Mohawk rivers via the Erie Canal and the New York Finger Lakes rather than the previously suggested alternative origin from the Canadian Maritimes via the St. Lawrence River.

Genetic Differentiation of Subpopulations of Sockeye Salmon (Oncorhynchus nerka) Within Lakes of Alaska, British Columbia, and Kamchatka, Russia

1994 ◽  
Vol 51 (S1) ◽  
pp. 147-157 ◽  
Author(s):  
Nataly V. Varnavskaya ◽  
Chris C. Wood ◽  
Rebecca J. Everett ◽  
Richard L. Wilmot ◽  
Vladimir S. Varnavsky ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
The United States ◽  
Allelic Frequency ◽  
Significant Heterogeneity ◽  
Frequency Data ◽  
Spawning Habitat ◽  
Lake Systems ◽  
Spawning Sites

Genetic differentiation among subpopulations of sockeye salmon (Oncorhynchus nerka) was investigated within nine intensively sampled lake systems located throughout the species' range using allozyme allelic frequency data collected by researchers in Canada, Russia, and the United States. Allelic frequencies at up to nine highly polymorphic loci were used to examine genetic diversity among 163 samples collected from 68 distinct spawning sites and to identify subpopulation structure within lakes. Significant heterogeneity was detected among sites within all lakes. The greatest differentiation was evident among subpopulations exhibiting different run timing (earlier vs. later) or utilizing different spawning habitat (tributary vs. littoral). These findings indicate that sockeye home precisely to natal streams, not just to lake systems, and underscore the importance of conserving individual spawning sites within sockeye populations.

scholarly journals EXAMINATION OF ALLELIC VARIATION AT THE HEXOKINASE LOCI OF DROSOPHILA PSEUDOOBSCURA AND D. PERSIMILIS BY DIFFERENT METHODS

Genetics ◽  
1977 ◽  
Vol 87 (4) ◽  
pp. 743-761
Author(s):  
Andrew T Beckenbach ◽  
Satya Prakash
Keyword(s):  
Genetic Variation ◽  
Allelic Variation ◽  
Balancing Selection ◽  
Heat Stability ◽  
Relative Activity ◽  
Allelic Frequency ◽  
Drosophila Pseudoobscura ◽  
Urea Denaturation ◽  
Thiol Reagent ◽  
Electrophoretic Techniques

ABSTRACT Recently a number of electrophoretic techniques have been applied to reveal the presence of additional genetic variation among the electrophoretic mobility classes of the highly polymorphic xanthine dehydrogenase (XDH) and esterase-5 (est-5) loci. We examined the hexokinase loci of Drosophila pseudoobscura and D. persimilis using a variety of techniques to determine whether further allelic variation could be revealed for these much less polymorphic loci and to analyze the nature of the known variation at the hexokinase-1 (hex-1) locus. The following studies were conducted: 135 strains of the two species from six localities were examined with buffer pH ranging from 5.5 to 10.0; 40 strains of D. pseudoobscura and 9 strains of D. persimilis from Mather were studied using starch gel concentrations ranging from 8.5 to 15.5% and were examined for differences in heat stability and reactivity to the thiol reagent p CMSA; strains were also tested for susceptibility to urea denaturation and differences in relative activities. Major findings of the work are: (1) No additional allelic variation could be detected at any of the hexokinase loci by applying these techniques. The finding of abundant hidden genetic variation in XDH and est-5 does not extend to all enzyme loci. (2) Evidence from studies using p CMSA indicates that the hex-1 alleles 0.6, 0.8, 1.0 and 1.2 of the two species form a series of unit charge steps. Since the 0.94 allele of D. persimilis has mobility intermediate between 0.8 and 1.0, it is argued that routine electrophoretic techniques are sensitive to at least some conservative amino acid substitutions. (3) Strong correlations were found at the hex-1locus between low allelic frequency, reduced relative activity and reduced stability to heat and urea denaturation. Since the three sibling species, D. pseudoobscura, D. persimilis and D. miranda, all appear to share a common high frequency allele (1.0) at that locus, these findings are taken as evidence that the observed allelic frequencies are a result of directional selection and mutation, rather than any form of balancing selection.

scholarly journals Human-driven genetic differentiation in a managed red deer population

2021 ◽  
Vol 67 (2) ◽  
Author(s):  
Gerald Reiner ◽  
C. Klein ◽  
M. Lang ◽  
H. Willems
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Red Deer ◽  
Young Male ◽  
Genetic Exchange ◽  
Genetic Connectivity ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Population Sizes ◽  
Populated Region

AbstractNineteen red deer areas in a densely populated region with a huge network of fenced motorways and the division into administrative management units (AMUs) with restricted ecological connectivity were investigated. In the season 2018/2019, a total of 1291 red deer samples (on average 68 per area) were collected and genotyped using 16 microsatellite markers. The results show a clear genetic differentiation between most of the AMUs. Fourteen AMUs may be combined into four regions with a considerable internal genetic exchange. Five areas were largely isolated or showed only a limited gene flow with neighbouring areas. Ten of the 19 AMUs had an effective population size below 100. Effective population sizes greater than 500–1000, required to maintain the evolutionary potential and a long-term adaptation potential, were not achieved by any of the studied AMUs, even when AMUs with an appreciable genetic exchange were aggregated. Substantial genetic differentiation between areas can be associated with the presence of landscape barriers hindering gene flow, but also with the maintenance of ‘red deer–free’ areas. Efforts to sustainably preserve the genetic diversity of the entire region should therefore focus on measures ensuring genetic connectivity. Opportunities for this goal arise from the establishment of game bridges over motorways and from the protection of young male stags migrating through the statutory ‘red deer–free’ areas.

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