scholarly journals Genetic structure and admixture between the Posavina and Croatian Coldblood in contrast to Lipizzan horse from Croatia

2013 ◽  
Vol 58 (No. 2) ◽  
pp. 71-78 ◽  
Author(s):  
A. Galov ◽  
K. Byrne ◽  
T. Gomerčić ◽  
M. Duras ◽  
H. Arbanasić ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Allele Frequency Distribution ◽  
Ratio Test ◽  
Genetic Introgression ◽  
Population Bottlenecks ◽  
Mode Shift ◽  
Heterozygosity Excess ◽  
Distribution Mode ◽  
Distinct Genetic Group ◽  
Breeding Schemes

The Posavina and Croatian Coldblood are Croatian autochthonous horse breeds with interwoven breeding histories for which studbooks have only recently been established. The Lipizzan breed has the oldest formalized breeding and no record of recent genetic introgression from other breeds in Croatia. We analyzed the genetic structure, interbreeding, and breed characteristics by genotyping nine dinucleotide microsatellite loci for 53 Posavina, 37 Croatian Coldblood, and 33 Lipizzan horses and showed that differing breeding schemes and histories have had a strong and measurable impact on the population genetic structure within and between the three breeds. A Bayesian clustering method demonstrated that two population clusters best explain the genetic structure. Samples from the pre-defined breeds of the Posavina and Croatian Coldblood were assigned to a separate genetic cluster, while Lipizzan specimens were assigned to another distinct genetic group. Twelve samples of the Posavina/Croatian Coldblood cluster (13%) showed admixed ancestry with Lipizzan horses. A test for heterozygosity excess, allele frequency distribution mode-shift, and M-ratio test were used to detect genetic evidence of recent population bottlenecks, none of which provided evidence for bottlenecks in the Posavina and Croatian Coldblood populations. In contrast, although somewhat ambiguous, evidence suggests a genetic bottleneck in the Lipizzan population in Croatia.

scholarly journals Spatial genetic structure in the Eurasian otter (Lutra lutra) meta-population from its core range in Italy

2020 ◽  
Vol 90 (1) ◽  
pp. 70-92
Author(s):  
Maria Buglione ◽  
Simona Petrelli ◽  
Claudia Troiano ◽  
Tommaso Notomista ◽  
Antonio Petrella ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
River Basins ◽  
Lutra Lutra ◽  
Population Bottlenecks ◽  
Future Health ◽  
Eurasian Otter ◽  
Ecological Corridor ◽  
Heterozygosity Excess ◽  
Landscape Genetic

Abstract We characterized the genetic structure of the Eurasian otter (Lutra lutra) meta-population living in the core of its Italian distribution range providing results from 191 fresh spraints, collected from 24 watercourses included in Southern Italy. Furthermore, according to ecological corridors and barriers, we discuss the likely ways of movement and possible evolutionary fate of these populations. We genotyped 136 samples using 11 Lut microsatellite nuclear markers amplified from faecal dna. Microsatellites were moderately variable (Ho = 0.45; He = 0.46), with a total number of alleles and average number of alleles per locus in the meta-population of 50 and 4.54, respectively. No significant heterozygosity excess was observed in meta-population suggesting no recent population bottlenecks. Bayesian clustering discriminated a sub-structuring of the meta-population in five putative clusters, indicating that local populations are genetically differentiated: three of these seem to be identifiable with geographically defined sub-populations (from the Cilento, Agri and Basento river basins). The fourth is represented by multiple sub-populations with admixed genotype, that include genotypes from the Lao, Sinni and Abatemaco river basins, living in a landscape with the higher environmental permeability. Landscape genetic analysis could provide evidence of an unexpected ecological corridor: the seacoast, highlighted, for the first time as a new way for the dispersion of the South-Italian otters. Deepening the knowledge of these perspectives is crucial to identify solid strategies aimed at the future health of the populations of the Italian otters, by restoring dispersal corridors and managing the watercourses.

Assessment of recent bottlenecks and estimation of effective population size in the Ethiopian wild sorghum using simple sequence repeat allele diversity and mutation models

2015 ◽  
Vol 13 (3) ◽  
pp. 274-281 ◽  
Author(s):  
Asfaw Adugna ◽  
Endashaw Bekele
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Simple Sequence Repeat ◽  
Wild Relatives ◽  
Sequence Repeat ◽  
Wild Sorghum ◽  
Effective Population ◽  
Mode Shift ◽  
Heterozygosity Excess ◽  
Simple Sequence

Since the immediate wild relatives ofSorghum bicolor(L.) Moench are indigenous to Ethiopia, studying their population biology is timely for undertaking conservation measures. A study was conducted to investigate the occurrence of population bottlenecks and to estimate the long-term effective population size (Ne) in wild relatives of sorghum. For this, 40 samples of wild sorghum were collected from two remotely located populations that were allopatric to the cultivated sorghum. The presence of bottlenecks was investigated using heterozygosity excess/deficiency, mode shift and allelic diversity based on nine polymorphic simple sequence repeat (SSR) loci. We also estimated theNeof the studied populations using two different methods employing SSR mutation models. The expected heterozygosity was found to be 0.41 and 0.71 and allelic richness was 3.0 and 4.9, in Awash and Gibe populations, respectively. Neither the heterozygosity excess nor the mode-shift methods detected signatures of bottlenecks in the studied populations. The effective size of the two wild sorghum populations studied also showed no risk of population reduction in these regions of Ethiopia. Therefore, these allopatric wild sorghum populations can survive by occupying patches by the roadsides and fences, areas within abandoned farm lands, forests, etc., which shows that their wild characteristics of adaptation have been adequate for them to survive from extinction despite extensive deforestation of their habitat for modern agriculture and frequent grazing by livestock. However, this does not guarantee the survival of these species for the future andex situconservation measures or policies could help maintain their diversity.

scholarly journals The Sri Lankan paradox: high genetic diversity in Plasmodium vivax populations despite decreasing levels of malaria transmission

Parasitology ◽  
2014 ◽  
Vol 141 (7) ◽  
pp. 880-890 ◽  
Author(s):  
SHARMINI GUNAWARDENA ◽  
MARCELO U. FERREIRA ◽  
G. M. G. KAPILANANDA ◽  
DYANN F. WIRTH ◽  
NADIRA D. KARUNAWEERA
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Plasmodium Vivax ◽  
Malaria Transmission ◽  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency Distribution ◽  
Effective Population ◽  
High Genetic Diversity ◽  
Mode Shift

SUMMARYHere we examined whether the recent dramatic decline in malaria transmission in Sri Lanka led to a major bottleneck in the local Plasmodium vivax population, with a substantial decrease in the effective population size. To this end, we typed 14 highly polymorphic microsatellite markers in 185 P. vivax patient isolates collected from 13 districts in Sri Lanka over a period of 5 years (2003–2007). Overall, we found a high degree of polymorphism, with 184 unique haplotypes (12–46 alleles per locus) and average genetic diversity (expected heterozygosity) of 0·8744. Almost 69% (n = 127) isolates had multiple-clone infections (MCI). Significant spatial and temporal differentiation (FST = 0·04–0·25; P⩽0·0009) between populations was observed. The effective population size was relatively high but showed a decline from 2003–4 to 2006–7 periods (estimated as 45 661 to 22 896 or 10 513 to 7057, depending on the underlying model used). We used three approaches – namely, mode-shift in allele frequency distribution, detection of heterozygote excess and the M-ratio statistics – to test for evidence of a recent population bottleneck but only the low values of M-ratio statistics (ranging between 0·15–0·33, mean 0·26) were suggestive of such a bottleneck. The persistence of high genetic diversity and high proportion of MCI, with little change in effective population size, despite the collapse in demographic population size of P. vivax in Sri Lanka indicates the importance of maintaining stringent control and surveillance measures to prevent resurgence.

scholarly journals Grape Phylloxera Genetic Structure Reveals Root–Leaf Migration within Commercial Vineyards

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 697
Author(s):  
Jurrian Wilmink ◽  
Michael Breuer ◽  
Astrid Forneck
Keyword(s):  
Life Cycle ◽  
Genetic Structure ◽  
Genotypic Diversity ◽  
Vegetation Period ◽  
Population Bottlenecks ◽  
Grape Phylloxera ◽  
Sexual Recombination ◽  
Population Structures ◽  
Natural Infestation ◽  
Root Feeding

Depending on their life cycle, grape phylloxera (Daktulosphaira vitifoliae Fitch) leaf-feeding populations are initiated through asexually produced offspring or sexual recombination. The vine’s initial foliar larvae may originate from root-feeding phylloxera or wind-drifted foliar larvae from other habitats. Though some studies have reported phylloxera leaf-feeding in commercial vineyards, it is still unclear if they are genetically distinct from the population structure of these two sources. Using seven SSR-markers, this study analyzed the genetic structure of phylloxera populations in commercial vineyards with different natural infestation scenarios and that of single-plant insect systems that exclude infestation by wind-drifted larvae. We saw that during the vegetation period, phylloxera populations predominately go through their asexual life cycle to migrate from roots to leaves. We provided evidence that such migrations do not exclusively occur through wind-drifted foliar populations from rootstock vines in abandoned thickets, but that root populations within commercial vineyards also migrate to establish V. vinifera leaf populations. Whereas the former scenario generates foliar populations with high genotypic diversity, the latter produces population bottlenecks through founder effects or phylloxera biotype selection pressure. We finally compared these population structures with those of populations in their native habitat in North America, using four microsatellite markers.

scholarly journals POPULATION BOTTLENECKS AND NONEQUILIBRIUM MODELS IN POPULATION GENETICS. I. ALLELE NUMBERS WHEN POPULATIONS EVOLVE FROM ZERO VARIABILITY

Genetics ◽  
1984 ◽  
Vol 108 (3) ◽  
pp. 745-763
Author(s):  
Takeo Maruyama ◽  
Paul A Fuerst
Keyword(s):  
Gene Diversity ◽  
Population Expansion ◽  
Allele Frequency Distribution ◽  
Population Bottlenecks ◽  
Rare Alleles ◽  
The Mean ◽  
Low Levels ◽  
Short Time ◽  
Initial Distributions ◽  
Sudden Population Expansion

ABSTRACT A simple numerical method was developed for the mean number and average age of alleles in a population that was initiated with no genetic variation following a sudden population expansion. The methods are used to examine the question of whether allele numbers are elevated compared with values seen in equilibrium populations having equivalent gene diversity. Excess allele numbers in expanding populations were found to be the rule. This was true whether the population began with zero variation or with low levels of variation in either of two initial distributions (initially an equilibrium allele frequency distribution or initially with loci occurring in only two classes of variation). Although the increase of alleles may persist for only a short time, when compared with the time which is required for approach to final equilibrium, the increase may be long when measured in absolute generation numbers. The pattern of increase in very rare alleles (those present only once in a sample) and the persistence of the original allele were also investigated.

Effect of SNP origin on analyses of genetic diversity in cattle

2010 ◽  
Vol 50 (8) ◽  
pp. 792 ◽  
Author(s):  
Laercio R. Porto Neto ◽  
William Barendse
Keyword(s):  
Principal Component ◽  
Ascertainment Bias ◽  
Population Substructure ◽  
Allele Frequency Distribution ◽  
Population Bottlenecks ◽  
Effective Population ◽  
Extended Haplotype ◽  
Single Nucleotide ◽  
Study Selection ◽  
Selection Gene

The methods of single nucleotide polymorphism (SNP) identification can lead to ascertainment bias, which will affect population genetic analyses based on those data. In livestock species, the methods of SNP identification through genome sequencing are likely to suffer from this ascertainment bias. In the present study, a subset of data from the Bovine HapMap Project was re-analysed to quantify the effects of ascertainment bias on a range of common analyses and statistics. Data from 189 animals of the zebu breeds Brahman, Nelore and Gir, taurine beef Angus, Limousin and Hereford and taurine dairy Holstein, Jersey and Brown Swiss were analysed. There were 141 SNPs each of Angus, Brahman and Holstein origin, giving a total of 423 SNPs organised in 141 triplets. Each triplet consisted of one SNP of each breed, separated on average by 0.75 Mb within each triplet and where triplets were separated by 14.96 Mb to ensure that each triplet was unaffected by linkage disequilibrium. The minor allele frequency distribution, estimates of the F-statistic, FST, the partitioning of variance and population substructure were relatively unaffected by breed of origin of the SNPs. Estimates of heterozygosity were significantly affected by breed of origin of the SNPs. The clustering of animals of closely related breeds varied in the principal component analyses (PCA). However, in the PCA the effect of breed of origin of 141 SNPs was similar to the effect of using different panels of 141 SNPs of all three breeds, so the differences found in the PCA may not be all due to bias by the origin of the SNPs. Based on these results, analyses that depend on FST, including signatures of selection, gene flow and effective population size are unlikely to be strongly affected by SNP origin. Analyses that partition genetic variance and some analyses of population substructure will also be largely unaffected. However, analyses that are dependent on locus heterozygosity, which can be used for studying population bottlenecks, or those that study selection using extended haplotype homozygosity may be significantly affected by breed of origin of the SNPs.

scholarly journals Description and Power Analysis of Two Tests for Detecting Recent Population Bottlenecks From Allele Frequency Data

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 2001-2014 ◽  
Author(s):  
Jean Marie Cornuet ◽  
Gordon Luikart
Keyword(s):  
Power Analysis ◽  
Statistical Tests ◽  
Population Sample ◽  
Type I ◽  
Population Bottlenecks ◽  
Infinite Allele Model ◽  
Bottleneck Detection ◽  
Size Number ◽  
Heterozygosity Excess ◽  
Allele Model

When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a heterozygosity excess are described. They require measurements of the number of alleles and heterozygosity at each of several loci from a population sample. The first test determines if the proportion of loci with heterozygosity excess is significantly larger than expected at equilibrium. The second test establishes if the average of standardized differences between observed and expected heterozygosities is significantly different from zero. Type I and II errors have been evaluated by computer simulations, varying sample size, number of loci, bottleneck size, time elapsed since the beginning of the bottleneck and level of variability of loci. These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. The usefulness of these tests for conservation biology is discussed.

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