Signs of Genetic and Morphometric Population Differentiation in Small Planctivorous Seabird, Parakeet Auklet Aethia psittacula, Reinforces Linkage between Population Structure and Migratory Strategy

2021 ◽  
Vol 56 (1) ◽  
Author(s):  
Olesya Pshenichnikova ◽  
Anna Klenova ◽  
Nikolay Konyukhov ◽  
Victor Zubakin ◽  
Yuri Artukhin ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Differentiation ◽  
Migratory Strategy

scholarly journals Genome-wide genetic diversity, population structure and admixture analysis in Eritrean Indigenous Cattle

2020 ◽  
Vol 49 (6) ◽  
pp. 1083-1092
Author(s):  
S Goitom ◽  
M.G. Gicheha ◽  
F.K. Njonge ◽  
N Kiplangat
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Population Differentiation ◽  
Principal Component ◽  
Vital Role ◽  
Group Method ◽  
Indigenous Cattle ◽  
Ecological Zones ◽  
Genome Wide

Indigenous cattle play a vital role in subsistence and livelihood of pastoral producers in Eritrea. In order to optimally utilize and conserve these valuable indigenous cattle genetic resources, the need to carry out an inventory of their genetic diversity was recognized. This study assessed the genetic variability, population structure and admixture of the indigenous cattle populations (ICPs) of Eritrea using a genotype by sequencing (GBS) approach. The authors genotyped 188 animals, which were sampled from 27 cattle populations in three diverse agro-ecological zones (western lowlands, highlands and eastern lowlands). The genome-wide analysis results from this study revealed genetic diversity, population structure and admixture among the ICPs. Averages of the minor allele frequency (AF), observed heterozygosity (HO), expected heterozygosity (HE), and inbreeding coefficient (FIS) were 0.157, 0.255, 0.218, and -0.089, respectively. Nei’s genetic distance (Ds) between populations ranged from 0.24 to 0.27. Mean population differentiation (FST) ranged from 0.01 to 0.30. Analysis of molecular variance revealed high genetic variation between the populations. Principal component analysis and the distance-based unweighted pair group method and arithmetic mean analyses revealed weak substructure among the populations, separating them into three genetic clusters. However, multi-locus clustering had the lowest cross-validation error when two genetically distinct groups were modelled. This information about genetic diversity and population structure of Eritrean ICPs provided a basis for establishing their conservation and genetic improvement programmes. Keywords: genetic variability, molecular characterization, population differentiation

scholarly journals Study of genetic differences among Slovak Tsigai populations using microsatellite markers

2009 ◽  
Vol 54 (No. 10) ◽  
pp. 468-474 ◽  
Author(s):  
S. Kusza ◽  
E. Gyarmathy ◽  
J. Dubravska ◽  
I. Nagy ◽  
A. Jávor ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Mating System ◽  
Population Differentiation ◽  
Genetic Relationships ◽  
The Other ◽  
Potential Risks ◽  
Substantial Degree

In this study genetic diversity, population structure and genetic relationships of Tsigai populations in Slovakia were investigated using microsatellite markers. Altogether 195 animals from 12 populations were genotyped for 16 microsatellites. 212 alleles were detected on the loci. The number of identified alleles per locus ranged from 11 to 35. In the majority of the populations heterozygosity deficiency and potential risks of inbreeding could be determined. High values of <I>F</I><sub>ST</sub> (0.133) across all the loci revealed a substantial degree of population differentiation. The estimation of genetic distance value showed that the Slovak Vojin population was the most different from the other populations. The 12 examined populations were able to group into 4 clusters. With this result our aim is to help the Slovak sheep breeders to establish their own mating system, to avoid genetic loss and to prevent diversity of Tsigai breed in Slovakia.

scholarly journals Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jugpreet Singh ◽  
Awais Khan
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Differentiation ◽  
Selection Pressure ◽  
Fire Blight ◽  
Erwinia Amylovora ◽  
Balancing Selection ◽  
Genomic Diversity ◽  
Economic Losses ◽  
Population Structure Analysis

Abstract The fire blight pathogen, Erwinia amylovora (EA), causes significant economic losses in rosaceae fruit crops. Recent genome sequencing efforts have explored genetic variation, population structure, and virulence levels in EA strains. However, the genomic aspects of population bottlenecks and selection pressure from geographical isolation, host range, and management practices are yet unexplored. We conducted a comprehensive analysis of whole genome sequences of 41 strains to study genetic diversity, population structure, and the nature of selection affecting sub-population differentiation in EA. We detected 72,741 SNPs and 2,500 Indels, representing about six-fold more diversity than previous reports. Moreover, nonsynonymous substitutions were identified across the effector regions, suggesting a role in defining virulence of specific strains. EA plasmids had more diversity than the chromosome sequence. Population structure analysis identified three distinct sub-groups in EA strains, with North American strains displaying highest genetic diversity. A five kilobase genomic window scan showed differences in genomic diversity and selection pressure between these three sub-groups. This analysis also highlighted the role of purifying and balancing selection in shaping EA genome structure. Our analysis provides novel insights into the genomic diversity and selection forces accompanying EA population differentiation.

scholarly journals GENETIC VARIABILITY AND POPULATION DIFFERENTIATION OF OPISTHORCHIS FELINEUS (TREMATODA) FROM WEST SIBERIA RIVERS

2012 ◽  
Vol 10 (3) ◽  
pp. 10-16
Author(s):  
Oksana N Zhigileva ◽  
Daria V Zenovkina ◽  
Tatyana A Zamyatina
Keyword(s):  
Population Structure ◽  
Genetic Variability ◽  
Dna Markers ◽  
Population Differentiation ◽  
Western Siberia ◽  
West Siberia ◽  
Cyprinid Fish ◽  
Intermediate Hosts ◽  
Opisthorchis Felineus ◽  
Low Level

Genetic variability in Opisthorchis felineus from 6 Western Siberia rivers was studied using allozyme and multilocus DNA markers. Genetic subdivision of populations and the spatial genetic variability in O. felineus maritas were found to be the same when using two methods of analysis, but differed from these indices in metacercariae. Metacercariae from ide, dace and roach were not genetically different, indicating the absence of hostal subpopulations of the parasite. Low level of O. felineus genetic variability is not consistent with a pronounced population structure of intermediate hosts — Cyprinid fish.

scholarly journals Genomics of population differentiation in humpback dolphins, Sousa spp. in the Indo-Pacific Ocea

2020 ◽  
Author(s):  
Ana R Amaral ◽  
Cátia Chanfana ◽  
Brian D Smith ◽  
Rubaiyat Mansur ◽  
Tim Collins ◽  
...  
Keyword(s):  
Population Structure ◽  
Primary Productivity ◽  
Population Differentiation ◽  
Arabian Sea ◽  
Population Genomics ◽  
Sea Surface ◽  
Complex Process ◽  
African Coast ◽  
Fundamental Process ◽  
High Level

Abstract Speciation is a fundamental process in evolution and crucial to the formation of biodiversity. It is a continuous and complex process, which can involve multiple interacting barriers leading to heterogeneous genomic landscapes with various peaks of divergence among populations. In this study, we used a population genomics approach to gain insights on the speciation process and to understand the population structure within the genus Sousa across its distribution in the Indo-Pacifc region. We found 5 distinct clusters, corresponding to S. plumbea along the eastern African coast and the Arabian Sea, the Bangladesh population, S. chinensis off Thailand and S. sahulensis off Australian waters. We suggest that the high level of differentiation found, even across geographically close areas, is likely determined by different oceanographic features such as sea surface temperature and primary productivity.

scholarly journals Population structure of morphological traits in Clarkia dudleyana. I. Comparison of FST between allozymes and morphological traits.

Genetics ◽  
1995 ◽  
Vol 140 (2) ◽  
pp. 733-744
Author(s):  
R H Podolsky ◽  
T P Holtsford
Keyword(s):  
Population Structure ◽  
Population Differentiation ◽  
Morphological Traits ◽  
Allozyme Variation ◽  
True Value ◽  
Quantitative Genetic ◽  
Allozyme Loci ◽  
Two Populations ◽  
Geographic Group ◽  
Continuous Traits

Abstract Studies of genetic variation at allozyme loci, assumed to be selectively neutral, have provided valuable insights into the genetic structure of numerous populations. The degree to which population structure of allozyme variation reflects that of quantitative traits, however, is not well resolved. Here, we compare estimates of population differentiation (FST) of 11 populations for allozymes with those for nine discrete and nine continuous morphological traits. Overall, the allozymes have the lowest FST estimates, indicating relatively little population differentiation. Excepting two traits, petal width and long internode length, the continuous morphological traits have estimates similar to those from allozymes. The discrete morphological traits tend to have the highest estimates. On a single trait basis, estimates of FST for four discrete and two continuous traits are higher than those for allozymes. A more detailed (narrow-sense quantitative) genetic study of two populations suggests that these estimates of FST may underestimate the true value because of dominance. Clustering analyses show that the pattern of differentiation for the discrete morphological traits strongly reflects the geographical distribution of the populations, whereas the patterns for the continuous traits and allozymes do not. These results suggest that selection has been occurring on the discrete morphological traits, selecting toward a common optimum within each geographic group, and optima differing among geographic groups.

scholarly journals Genetic Differentiation Within and Between Two Habitats

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 397-407 ◽  
Author(s):  
François Rousset
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Population Differentiation ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Host Races ◽  
Wide Range ◽  
Parameter Values ◽  
Ecological Types ◽  
F Statistics

Abstract We investigate the usefulness of analyses of population differentiation between different ecological types, such as host races of parasites or sources and sink habitats. To that aim, we formulate a model of population structure involving two classes of subpopulations found in sympatry. Extensions of previous results for Wright's F-statistics in island and isolation-by-distance models of dispersal are given. It is then shown that source and sinks cannot in general be distinguished by F-statistics nor by their gene diversities. The excess differentiation between two partially isolated classes with respect to differentiation within classes is shown to decrease with distance, and for a wide range of parameter values it should be difficult to detect. In the same circumstances little differentiation will be observed in “hierarchical analyses between pools of samples from each habitat, and differences between levels of differentiation within each habitat will only reflect differences between levels of gene diversity within each habitat. Exceptions will indicate strong isolation between the different classes or habitat-related divergent selection.

scholarly journals Genome-wide patterns of local adaptation in Drosophila melanogaster: adding intra European variability to the map

2018 ◽  
Author(s):  
Lidia Mateo ◽  
Gabriel E. Rech ◽  
Josefa González
Keyword(s):  
Drosophila Melanogaster ◽  
Population Structure ◽  
Local Adaptation ◽  
Population Differentiation ◽  
Nucleotide Polymorphisms ◽  
Low Levels ◽  
Spatially Varying ◽  
Spatially Varying Selection ◽  
Two Populations ◽  
European Populations

ABSTRACTSignatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. In Drosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, populations in these two continents showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection is challenging when analyzing these populations. European populations could be a suitable system to identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden), and Castellana Grotte, (Southern Italy). We found low levels of population structure and no evidence of recent African admixture in these two populations. We thus look for patterns of spatially varying selection affecting individual genes and gene sets. Besides single nucleotide polymorphisms, we also investigate the role of transposable elements in local adaptation. We concluded that European populations are a good dataset to identify loci under spatially varying selection. The analysis of the two populations sequenced in this work in the context of all the available D. melanogaster data allowed us to pinpoint genes and biological processes relevant for local adaptation. Identifying and analyzing populations with low levels of population structure and admixture should help to disentangle selective from non-selective forces underlying patterns of population differentiation in other species as well.

scholarly journals Weak population structure in the ant Formica fusca

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5024 ◽  
Author(s):  
Helena Johansson ◽  
Perttu Seppä ◽  
Heikki Helanterä ◽  
Kalevi Trontti ◽  
Liselotte Sundström
Keyword(s):  
Population Structure ◽  
Population Differentiation ◽  
Isolation By Distance ◽  
Population Substructure ◽  
Microsatellite Data ◽  
High Dispersal ◽  
Formica Fusca ◽  
Haplotype Data ◽  
Dna Microsatellite ◽  
Mtdna Haplotype

Dispersal is a fundamental trait of a species’ biology. High dispersal results in weakly structured or even panmictic populations over large areas, whereas weak dispersal enables population differentiation and strong spatial structuring. We report on the genetic population structure in the polygyne ant Formica fusca and the relative contribution of the dispersing males and females to this. We sampled 12 localities across a ∼35 km2 study area in Finland and generated mitochondrial DNA (mtDNA) haplotype data and microsatellite data. First, we assessed queen dispersal by estimating population differentiation from mtDNA haplotype data. Second, we analysed nuclear DNA microsatellite data to determine overall population genetic substructure in the study area with principal components analysis, Bayesian clustering, hierarchical F statistics and testing for evidence of isolation-by-distance. Third, we directly compared genetic differentiation estimates from maternally inherited mtDNA and bi-parentally inherited DNA microsatellites to test for sex-bias in dispersal. Our results showed no significant spatial structure or isolation by distance in neither mtDNA nor DNA microsatellite data, suggesting high dispersal of both sexes across the study area. However, mitochondrial differentiation was weaker (Fst-mt = 0.0047) than nuclear differentiation (Fst-nuc = 0.027), which translates into a sixfold larger female migration rate compared to that of males. We conclude that the weak population substructure reflects high dispersal in both sexes, and it is consistent with F. fusca as a pioneer species exploiting unstable habitats in successional boreal forests.

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