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population genetics

15460 relationships annotated with this phrase. Showing first 500 of 15460.
Source entity Relationship Target entity Species
block of glycosyltransferases showed evidence of hard sweep (H12 = 0.87) Ipomoea purpurea
genetic, epigenetic and transcriptomic variation was examined in samples from 21 natural populations across three climatically distinct geographic regions Fragaria vesca
minor differences in uptake may have resulted from genetic variation among populations Amaranthus tuberculatus
frequency of gbM/unM/teM epigenomic states in the population calculated to determine relationship between frequency of genic methylation states and rate of SNPs in natural Arabidopsis thaliana population Arabidopsis thaliana
Translocated paralogs that gained teM methylation showed higher polymorphism in Arabidopsis thaliana accessions compared with their parental unM and gbM paralogs Arabidopsis thaliana
demographic processes may influence molecular composition
resampling bias of populations would predict decrease in allelic richness Viola arvensis
life-history traits shape amount and distribution of genetic diversity across a species range
third and fourth principal component axes explained < 0.4% each
K = 6 resulted in Turkish and Black Sea populations split from the Western Europe populations
linkage and linkage disequilibrium indicates the potential role of both linkage and linkage disequilibrium in maintaining the cost Ipomoea purpurea
multiple loci show evidence of ILD Ipomoea purpurea
three genic methylation classes showed significant differences in polymorphism Arabidopsis thaliana
absolute differences in the rate of SNPs and weighted methylation levels between duplicate paralogs determined as response variable Arabidopsis thaliana
inbreeding coefficient (F IS ) ranged from −0.088 to 0.2
one Romanian population was slightly differentiated from rest of the sampling
more negative Tajima's D can be caused by elevated mutation rates Arabidopsis thaliana
selection is expected to be more efficacious in larger populations
expanding populations show no increased genetic load Scots pine
ratio c / s < 10 −4 would result in hitchhiking would almost be complete Ipomoea purpurea
DNA methylation patterns of genes influence differential accumulation of sequence polymorphism in natural populations Arabidopsis thaliana
parallel changes in morphology is not consistent with drift Veronica arvensis
genetic drift would predict decrease in allelic richness Viola arvensis
pairwise F ST between populations ranged from 0.009 to 0.127
Scots pine populations have no signal of genetic load Pinus sylvestris
local regions of long-distance linkage disequilibrium and ILD might be generated by genetic drift Ipomoea purpurea
recombination should decouple cost alleles that are physically linked to resistance alleles Ipomoea purpurea
inbreeding causes increased genetic drift
reduced genetic richness in Commeny is associated with most pronounced change in morphology
wind-pollinated outcrossing species are generally expected to have weaker genetic structure
recessive and additive genetic loads were not correlated with latitude or longitude
frequency of gbM within the population showed weak negative correlation with rate of SNPs Arabidopsis thaliana
teM paralogs in unM-teM and gbM-teM pairs showed a significantly higher percentage of polymorphism in natural populations compared with the unM and gbM paralogs Arabidopsis thaliana
translocation itself doesn't increase rate of polymorphism irrespective of methylation Arabidopsis thaliana
demographic model suggests that changes at land plants, vascular plants, seed plants, and angiosperms moved lineages closer to mutation-drift equilibrium
demographic events shape amount and distribution of genetic diversity across a species range
impact of landscapes and environments on population differentiation remain scarcely studied for Scots pine Pinus sylvestris
genetic differentiation and geographic distance showed pattern of isolation by distance (IBD)
combination of concise geological history and close geographical proximity of Izu Islands has led to lower degree of genetic divergence between plant populations on islands and mainland
genetic variation among individuals in the wild is much greater than genetic variation in experimental populations
Ipomoea purpurea populations show evidence of genetic admixture Ipomoea purpurea
(anac025, NAC025, NAC25, AT1G61110) and (NFD6, AT2G20585) are physically linked on chromosome 6 to regulatory region exhibiting ILD to CYP76A2 gene on chromosome 10 Ipomoea purpurea
this study aims to highlight origin and prevalence of different alleles and haplotypes associated with the semi-leafless phenotype Pisum sativum
negative D value at avrRpv3.1 locus suggests strong deficit of heterozygous genotypes Plasmopara viticola
SNPs in exons of (AVB1, IFL, IFL1, REV, AT5G60690) could indicate low allelic frequency of exonic SNPs in the population Populus trichocarpa
summary statistics for signatures of selection calculated for each Arabidopsis thaliana gene Arabidopsis thaliana
Tajima's D affected by selection and mutation rate Arabidopsis thaliana
distinct genetic signature in extant populations includes declining genetic diversity along migration routes Pinus sylvestris
testing these hypotheses requires sufficient genetic information Pinus sylvestris
avrRpv3.1 locus is in strong Hardy-Weinberg disequilibrium Plasmopara viticola
inbreeding coefficient (F) is typically used to measure average level of inbreeding
global distribution of genome sizes in angiosperms is mainly shaped by genetic drift
logarithm method indicated 20 groups
highly differentiated region on (CHD3, CHR6, CKH2, EPP1, GYM, HRB2, LWR1, PKL, SSL2, AT2G25170) exhibited alternate alleles in resistant and susceptible populations Ipomoea purpurea
percentage of nucleotides with polymorphism within 100-bp windows calculated for each gene Arabidopsis thaliana
Jost's D index was used to assess genetic differentiation between first and last generation Brassica rapa
Goodyera similis on Kozu Island has significant gene flow to Goodyera henryi × Goodyera similis on the island Goodyera henryi; Goodyera similis
rate of SNP polymorphism showed weak but significant negative correlation with unM frequency Arabidopsis thaliana
large effective population sizes tend to make natural selection more effective natural selection
InDel4337-Del alleles in teosinte accessions have been diversified teosinte populations Zea mays subsp. parviglumis
wind-pollinated outcrossing species are generally expected to have higher genetic diversity
consecutive range expansions after contraction produce differentiation via genetic drift
testing these hypotheses requires comprehensive coverage of species distribution Pinus sylvestris
Scots pine is effectively panmictic species Pinus sylvestris
Plasmopara viticola has large population size Plasmopara viticola
avr1 allele was second most frequent (39%) Plasmopara viticola
region on chromosome 6 shows strong signals of selection (average Md-rank-P = 6.55; average (ATGSTU24, GST, GSTU24, AT1G17170) = 0.782) Ipomoea purpurea
strong demographic bottleneck would predict decrease in allelic richness Viola arvensis
unM genes showed 0.15× higher polymorphism in natural population compared to gbM genes Arabidopsis thaliana
InDel4337-Del frequency is substantially lower in teosinte lines (16%) Zea mays subsp. parviglumis
region under selection on (ASG3, CHR10, AT2G44980) exhibited the strongest LD to other chromosomal regions under selection Ipomoea purpurea
teM frequency in the population showed moderate positive correlation with rate of SNPs Arabidopsis thaliana
Tajima's D is more negative in teM genes compared with unM and gbM genes Arabidopsis thaliana
greater polymorphism combined with a more negative Tajima's D value in teM genes consistent with expected effects of elevated mutation rates and a weaker distribution of fitness effects of new mutation Arabidopsis thaliana
Whole-genome duplicates (WGDs) had lower polymorphism compared with four different types of single-gene duplicates (SGDs) Arabidopsis thaliana
species survived in many micro-refugia scattered across current distribution would predict little decline of diversity in the north Pinus sylvestris
Spanish populations were separated from rest of the samples
limited gene flow in Arabidopsis is not able to counteract effect of drift in populations Arabidopsis thaliana
four highly differentiated regions under selection showed higher LD with one another compared with four randomly pulled, but highly differentiated regions between resistant and susceptible populations not under selection Ipomoea purpurea
multiple glycosyltransferases and cytochrome P450s under selection on (ASG3, CHR10, AT2G44980) showed high ILD with SNPs on (CHR11, AT3G06400) Ipomoea purpurea
Commeny population exhibits slight decrease in allelic richness Viola arvensis
rapid colonization from few isolated refugia is expected to leave distinct genetic signature in extant populations Pinus sylvestris
species survived in many micro-refugia scattered across current distribution would predict weak differentiation between populations Pinus sylvestris
extensive sampling of 2321 Scots pine individuals from > 200 populations aimed to assess genetic and environmental associations Pinus sylvestris
these analyses enhance understanding of how diversity correlates with geography, demography and climate adaptation Pinus sylvestris
effective population size tends to be greater than n = 10^3 flowering plants
hitchhiking would almost be complete could result in cost alleles could become fixed in populations Ipomoea purpurea
nonsyntenic SGDs such as translocated and dispersed duplicates had lower polymorphism in natural accessions compared with local SGDs: tandem and proximal Arabidopsis thaliana
population size plays a compounding role in genome composition evolution
selection shapes amount and distribution of genetic diversity across a species range
Tajima's D values were all highly negative
major changes in traits and life history across the Viridiplantae are associated with longer generation times and/or reductions in effective population size
patterns in base composition shifts that occur at key nodes in plant phylogeny are likely the result of some combination or subset of population processes
K = 2 observed clear gradient between western (Spanish) and eastern (Chinese) populations
genetic differentiation showed weak correlation with environmental distance
lack of correlation between π 0 /π 4 ratio and Tajima's D indicated no increase in genetic load in the expanding northern populations
SNPs along contig Primary_000014F were at Hardy-Weinberg equilibrium (>95%) Plasmopara viticola
inbreeding depression reduces genetic diversity of selfing populations
changes at land plants, vascular plants, seed plants, and angiosperms moved lineages away from strong natural selection and BGC
extensive gene flow is predominantly responsible for observed genetic patterns in Scots pine Scots pine
123 large populations showed pairwise nucleotide diversity (π) with average of 0.0062 differences per base pair
K = 5 resulted in Russian populations west of the Ural Mountains differentiated from the rest of the Asian populations
presence and absence genotypes on chromosomes 3 and 4 existed in strains from South America Magnaporthe oryzae
TEM genes have a higher level of polymorphism than gbM Arabidopsis thaliana
inbreeding causes fitness measures to decline
natural populations have the potential to respond quickly to environmental changes
π values, including π 0 , π 4 and the π 0 /π 4 ratio decreased slightly with increasing latitude and longitude
biotic interactions may influence population genetic structure in Scots pine Pinus sylvestris
TEM genes showed the highest rates of polymorphism Arabidopsis thaliana
Genes with a higher frequency of gbM show a lower proportion of polymorphism across the population Arabidopsis thaliana
principal component analysis evidenced population structure bias Plasmopara viticola
Disease resistance phenotypes were segregated between and within populations Arabidopsis thaliana
TEM genes showed 1.37× more polymorphism than gbM genes Arabidopsis thaliana
first two principal component axes ( (APC1, PC1, AT5G17480) and PC2) explained < 2% of the overall genetic variation
K = 12 resulted in Caucasus populations separated from Asia Minor
global F ST among the 123 large populations averaged 0.048
clonality results in reduction in genetic diversity
experiment using single genotype pairs of diploids and their neopolyploid progeny in competition is limited by lack of genetic variation among individuals
four highly differentiated regions under selection showed islands of elevated ILD in a backdrop of nearly zero genome-wide ILD Ipomoea purpurea
inbreeding depression is well-known
first principal component axis (PC1) followed rough south–north direction in west-central Europe
40 out of 42 individuals sampled from Kozu Island were classified as individuals resulting from repeated crossing among hybrids of Goodyera henryi and Goodyera similis Goodyera henryi; Goodyera similis
Disease resistance phenotypes did not follow obvious geographical or population structure patterns Arabidopsis thaliana
linkage disequilibrium pattern across (AVB1, IFL, IFL1, REV, AT5G60690) gene is likely incomplete due to possible ascertainment bias Populus trichocarpa
minor allele frequencies (MAF) hint at relative ages of mutations Populus trichocarpa
All resistant and susceptible genotypes carried (AT3G24580) Col-0 alleles Arabidopsis thaliana
30% of individuals in the Gw population carried a conserved RPP1-like Ler haplotype Arabidopsis thaliana
geography acts as major determinant of population genetic structure in S. hermonthica Striga hermonthica
group II A. tauschii accessions have lower level of genetic diversity Aegilops tauschii
environmental clines correlate with changes in allelic frequencies at specific candidate genes
research objectives include determining population genetic structure in S. hermonthica sampled from Eastern and Western Africa Striga hermonthica
distinct epigenomic features in unM, gbM, and teM genes associated with accumulation of polymorphism in genes at the population level Arabidopsis thaliana
genetic drift would predict decrease in genetic diversity Viola arvensis
Tajima's D showed weak correlation with longitude
low interspecific heterozygosity in hybrids indicated that significant portion of Goodyera henryi × Goodyera similis on Kozu Island are genetically admixed hybrids of later generations Goodyera henryi; Goodyera similis
positive selection results in negative Tajima's D value Hordeum vulgare
amplified fragment length polymorphism (AFLP) is used for S. hermonthica genetic diversity studies Striga hermonthica
Tajima's D test suggested that HTD1 deviated significantly from neutral expectation Oryza sativa
accessions in panel could be used for GWAS analysis Brassica juncea
linkage disequilibrium (LD) decay was estimated on the basis of pairwise r 2 measures Zea mays
genetic structure of the mapping panel is reminiscent of two populations of which it is comprised Zea mays
linkage disequilibrium (LD) was higher in rootstock-type subgroup than in food-type
population structure across multiple causal loci can produce different genotypic combinations in different geographic regions geographic regions
large effect loci may be less variable in local populations with less genetic diversity and lacking broad geographic structure local populations
highly conserved and less polymorphic nature of ESTs results in Y53 expected to show slower linkage disequilibrium decay than would be expected for outcrossing species like Striga hermonthica Striga hermonthica
broad collection of genotypes might be due to very weak kinship Brassica juncea
mutation is one of the uncertain evolutionary forces causing linkage disequilibrium decay Striga hermonthica
Random amplification of polymorphic DNA (RAPD) is used for S. hermonthica genetic diversity studies Striga hermonthica
genetic recombination rate is one of the uncertain evolutionary forces causing linkage disequilibrium decay Striga hermonthica
linkage disequilibrium (LD) analysis estimated LD as a function of physical distance Hordeum vulgare
subpopulation-specific estimates of Tajima's D included both negative and positive values with strong skew towards positive mean values Hordeum vulgare
GWAS mapping panels capture deep pools of genetic variation from natural populations
pangenomes facilitate studies on population structure
SNPs are expected to be in linkage with intergenic loci, including non-coding DNA Zea mays
WG7 gene and flanking region have lower nucleotide diversity in indica and japonica cultivars Oryza sativa
method to genotype giant NORGs showed dynamic change in distribution of giant NORGs in rice natural population Oryza sativa; Oryza glaberrima
grain width differences between (HAP1, MAGO, MEE63, AT1G02140) and (ATHAP3, ATNF-YB1, HAP3, HAP3A, NF-YB1, AT2G38880) is likely caused by population structure Oryza sativa
891,289 SNPs from resequencing population used to estimate relative kinship in population Brassica juncea
mating system is one of the uncertain evolutionary forces causing linkage disequilibrium decay Striga hermonthica
(FST, LHL3, LL1, AT1G64625) and XP-CLR (cross-population composite likelihood ratio test) showed similar results genome-wide selection analysis Oryza sativa
SNPs associated with MGR status have minor allele frequencies between 0.051 and 0.284
second model seeks to predict genotype values for genetic markers in the target interval
grain width between haplotypes within subpopulations shows no significant difference Oryza sativa
small DNA losses may overcome power of genetic drift
re-sequencing of a large number of germplasm accessions provides information on origin, domestication, and population structure
subpopulation-specific estimates of Tajima's D differed extensively among subpopulations Hordeum vulgare
genome-wide LD decay distance estimated to be >400 kb
Cucumis metuliferus has nucleotide diversity (π value) of 1.61 × 10⁻³ Cucumis metuliferus
non-synonymous mutations in R-related genes were different in two Cucumis metuliferus groups Cucumis metuliferus
low recombination causes deleterious variants to persist in population
SSR markers are widely used for genetic investigation
winter/facultative barley group has PIC of 0.17 Hordeum vulgare
primary maturity group set (MG I-VII) for DTF contained 241 alleles (128 negative plus 113 positive) on 52 loci with average DTF of 50 days Glycine max
demographic processes modulate genome-wide levels and patterns of genetic variation
Zymoseptoria tritici (Z. tritici) populations harbour genetic diversity including rare mutations Zymoseptoria tritici
two-row barley group has PIC of 0.17 Hordeum vulgare
G1–G3 are clustered together in one branch distantly separated from GS groups Glycine max; Glycine soja
rare variants tend to be more geographically restricted than common variants
co-appearance of SD1 DGWG with (HTD1, AT2G19540) 1005C is significantly higher than whole-genome random regions Oryza sativa
late maturity group set (MG VIII-IX/X) retained 201 (83.40%) DTF alleles and 197 (80.08%) DTM alleles from primary MG set Glycine max
statistical bias arising from small sample population size could be difficult to eliminate when determining linkage disequilibrium Striga hermonthica
food and rootstock types of bottle gourds were genetically diversified genetic diversity
SNP LD blocks (SNPLDBs) handles multiple allele characteristics of a natural population Glycine max
early maturity group set (MG 000-0) retained only 181 (75.10%) DTF alleles and 194 (78.86%) DTM alleles from primary MG set Glycine max
method to infer relatedness between tea accessions detected genetic signatures of 106 tea accessions Camellia sinensis
Cucumis metuliferus accessions show slower decay of linkage disequilibrium in group 2 than group 1 Cucumis metuliferus
local samples typically contain fewer polymorphic causal loci than samples collected across broader geographic ranges
WYS and GYC populations are existing DT and ET ancient populations respectively Euscaphis japonica
AMOVA analysis indicated very significant genetic differences among and within maturity groups (MGs) Glycine max
principal component analysis confirmed genetic divergence between market classes of cultivated tomato Solanum lycopersicum
pangenomes facilitate studies on genetic diversity
PCA and model-based clustering indicated weak population stratification
chromosome 2 is richest in SNPs Solanum melongena
comprehensive parallel analyses of soybean nuclear and cytoplasmic diversities are needed to address if there is a positive selection on soybean mitogenome Glycine max
spatial and temporal heterogeneity in population structure have different influences on persistence of new mutations and genetic variation
populations with no recent growth explain less additive genomic variance for rare alleles
ADMIXTURE analysis confirmed optimal classification of Euscaphis japonica populations (K=2) Euscaphis japonica
primary maturity group set (MG I-VII) for DTM contained 246 (117 negative plus 129 positive) alleles on 59 loci with average DTM of 127 days Glycine max
groups of germplasm within a panel may be genetically distinct due to similar pedigree history within each
neighbor-joining tree constructed based on SNP-calling showed all samples were divided into DT and ET Euscaphis japonica Euscaphis japonica
higher Tajima's D values in DT populations may be because of population bottleneck effect, population structure, and unbalanced selection Euscaphis japonica
domestic soybean accessions are grouped in three different clusters with respect to the cytoplasmic diversity Glycine max
higher θw and θπ values in DT populations indicates DT populations have rich genetic diversity Euscaphis japonica
circadian studies sampling populations have drawn attention to hierarchical structure of genetic diversity in the wild
more genetic diversity results in more loci segregating for causal variants
cases of different causal variants across geographic regions were observed more than twice as often as shared causal variants across regions Arabidopsis thaliana
distribution of genome-wide set of over 33,000 genetic variants was analysed in terms of geographic region Hordeum vulgare
S. melongena accessions clustered separately from NMS accessions Solanum melongena; Solanum insanum; Solanum incanum
trees have intermediate levels of nucleotide variation relative to other plants
recombination determines the fate of new mutations in populations
geographically restricted allele distributions causes genetic basis of a trait to vary across regions
outcrossing species demonstrates higher genetic variation within structured populations than between structured populations
Striga hermonthica class with six and four populations each appear twice but with different linkage disequilibrium values Striga hermonthica
global barley panel analysed for distribution of genetic variants with respect to geographic region or historical breeding category Hordeum vulgare
unrooted phylogenetic tree of 50 accessions constructed based on SNP information
two subgroups from PCA matched usage types (food or rootstock)
pairwise sequential Markovian coalescent analysis (PSMC) was applied to assess demographic history of Euscaphis japonica populations Euscaphis japonica
Arabidopsis thaliana exhibits genetic differentiation between populations due to environmental adaptation or demographic history Arabidopsis thaliana
identification of selective sweeps can be confounded by population structure
founder events and population bottlenecks occur locally in highly structured populations highly structured populations
most alleles are rare (i.e., at low frequency) globally
local populations are already present in nature
early and late maturity group sets (six of 13 MGs) formed from QTL-alleles inherited from primary maturity group set Glycine max
hierarchical structure of genetic diversity in the wild unveils pronounced genetic variation on a scale of metres
genomic data from 700 to 3700-year-old European oak trees showed genetic diversity and population structure persistence over time Quercus alba
herbarium collections have been used to study plants' past genetic diversity
early maturity group set for DTF retained 181 (104 plus 77) alleles with 24 negative and 36 positive in total of 60 alleles excluded Glycine max
G3 ('Bedford'-type) is one of five cytoplasmic groups in domestic soybean Glycine max
restricted geographic distribution of globally rare variants implies that each one will be more common in the region(s) where it is present locally rare variants
first model seeks to predict genotype values for genetic markers in the target interval
selfing reduces genetic diversity
18 types of mtDNAs were reported in > 1000 Japanese wild soybean plants Glycine soja
linkage disequilibrium (LD) patterns are affected by mating, selection, genetic drift, and effective population size Euscaphis japonica
mtDNA SVs identified five cytoplasmic groups or mitogenome types in domestic soybean Glycine max
identification of selective sweeps can be confounded by gene flow from wild or feral populations
Hap-7A-3 distribution in Europe showed geographic bias with higher frequency in western than eastern Europe Triticum aestivum
ADMIXTURE analysis indicated no genetic exchange between DT and ET populations Euscaphis japonica
recombination events that resulted in intron losses and that were inherited to the next generation had the chance to increase in frequency in population
polymorphism spectrum of Os03g01450 showed slight deviation from neutrality Oryza sativa
linkage disequilibrium (LD) extends short distances in diverse maize inbreds Zea mays
low LD of DT populations may be accounted for by large effective population size Euscaphis japonica
sampling from a local population produces less allelic heterogeneity than sampling broadly because exclusion of geographically restricted alleles and overall reduction in genetic diversity lead to fewer alleles per locus
stepwise duplications could then continue to segregate as hemizygous loci in populations
non-random background co-ancestry among accessions is population structure and familial relationship
single nucleotide polymorphism (SNP) markers are used for population structure analysis
principal components analysis (PCA) divided 46 accessions into two subgroups
populations that experience a bottleneck followed by recent growth explain more additive genomic variance for rare alleles
balance between influence on host fitness and transmission rate could determine frequency of eccDNA in a population
pangenomes play important roles in plant population genomics
large insertion at 987,580 was not present in any C. grandiflora sample Capsella grandiflora
effects of inbreeding depression are severe in Geranium maculatum Geranium maculatum
hypothesis that selection for market differentiation left a signature that could be detected through the analysis of genome-wide patterns of SNP variation was tested genome-wide patterns of SNP variation in cultivated tomatoes Solanum lycopersicum
Darwin's insights are often uncanny and productive for testing hypotheses about population-level studies
384 wheat cultivars from 18 European countries showed average frequency of Hap-7A-3 of 41.4% Triticum aestivum
Hap-7A-3 frequency in European cultivars ranging from 10% to 68.2% Triticum aestivum
trans-specific rather than species-specific clusters of S-RNases is a consequence of balancing selection and the longevity of alleles Prunoideae; Maloideae
resulting data were used to assess extent of inter- and intra-chromosomal linkage disequilibrium (LD) in cultivated tomato Solanum lycopersicum
observed heterozygosity (H o ) and expected heterozygosity (H e ) showed no significant variation along longitude
gbM genes have more negative Tajima's D than unM genes Arabidopsis thaliana
WGDs showed more negative Tajima's D values than local SGDs: tandem and proximal duplicates Arabidopsis thaliana
GbM translocated paralogs had lower rates of polymorphism compared to parental gbM paralogs Arabidopsis thaliana
genetic draft is interaction of inbreeding and selection
absence of reduction in genetic diversity in other locations could be due to recent increase in inbreeding
unmethylated genes showed intermediate rates of polymorphism Arabidopsis thaliana
ancestral populations exhibit no significant differences in genetic diversity Viola arvensis
expected heterozygosity (H e ) averaged 0.277
genetic differentiation correlated strongly with geographic distance separating the populations
genetic bottlenecks result in changes in allele frequencies
selfer populations may have reduced potential response to future selective pressures
outcrossing maintains genetic diversity within populations
isolation by distance (IBD) and isolation by environment (IBE) can act independently or in concert with how genetic variation is partitioned among populations
gene-tree conflict is potentially indicative of dynamic population processes and the reassortment of ancestral polymorphisms among descendant lineages
microsatellites and isozymes indicate that N. truncata is followed by N. solandri and N. cliffortioides most closely related Nothofagus truncata; Nothofagus solandri; Nothofagus cliffortioides
reduction of genetic richness could be the product of drift and of the interaction of inbreeding and selection
25 830 SNPs showed no evidence of linkage disequilibrium
K = 10 resulted in Scottish populations were differentiated
genetically dominant nature of mapped resistance results in resistant plants heterozygous with expected ratio 1:1 Solanum berthaultii; Solanum ruiz-ceballosii
MsT–MsJR followed by with FST value of 0.15 Miscanthus sinensis
gene flow between northern and southern M. sinensis non-significantly >0 gene flow level Miscanthus sinensis
MSG42_2 was differentiated in all intra-specific taxa Miscanthus
var. transmorrisonensis was most distinctive Miscanthus sinensis
ACD6-Est-1 allele is frequent in natural populations of Arabidopsis thaliana Arabidopsis thaliana
phylogeographic framework informs accession sampling Cardamine hirsuta
analysis of molecular variance revealed most genetic variants resided within populations Miscanthus
allopatric pairs (e.g. M. floridulus in Taiwan versus mainland China, and var. condensatus versus var. transmorrisonensis) had more outliers Miscanthus
inter-specific outliers are not simply extrapolation of intra-specific ones Miscanthus
Population cluster analysis divided 612 upland cotton accessions into four groups Gossypium hirsutum
levels of variation across miRNA-encoding loci vary significantly across loci Arabidopsis thaliana
population-level analysis of nrITS haplotypes revealed predominant Canina types in all 16 accessions Rosa canina
intervals harboring genes involved in detoxification show high ILD values between intervals harboring genes involved in stress signaling and response Ipomoea purpurea
increase in selfing rate is expected to have genomic impacts on individuals and populations
recent demography of Scots pine reconstructed population history Scots pine
feems analysis identified several regions with slightly reduced gene flow
(NFD6, AT2G20585) is within 83 kb from, and thus physically linked to, and in high LD with (r2 = 0.70) the potential regulatory region under selection for glyphosate resistance on Chr6.2 Ipomoea purpurea
changes in composition might reflect important shifts between the balance of mutation and drift, and hence effective population size
K = 3 resulted in Scandinavian populations formed a new cluster
strains sampled on susceptible and resistant varieties show high genetic differentiation at avrRpv3.1 locus Plasmopara viticola; Vitis vinifera
Hap-7A-3 occurred in two zones in Chinese landraces (III at 8.7% and VII at 11.1%) Triticum aestivum
polymorphic sites in TaTEF-7A promoter region showed significant linkage disequilibrium (r2=1, P<0.001) Triticum aestivum
coefficient of genetic differentiation (QST) for xylem resistance to cavitation in Pinus pinaster is low Pinus pinaster
SSLP marker within PLANT U-BOX8 (B80, PUB8, AT4G21350) 5′ sequences that distinguishes C24 from RLD/Col-0 was used to find that the PLANT U-BOX8 (B80, PUB8, AT4G21350) RLD/Col-0 allele occurs in approximately one-third of 86 accessions tested Arabidopsis thaliana
Bd21 and Bd21-3 were most similar overall, but in some genome regions they are the most divergent Brachypodium distachyon
Bd1-1-unique SNPs result in low D-statistic Brachypodium distachyon
linkage disequilibrium (LD) is one of important signatures of natural selection
additional geographic sampling of Arabidopsis thaliana did not alter considerably previously described phylogeography of Arabidopsis thaliana Arabidopsis thaliana
genetic variation expressed for xylem resistance to cavitation within natural populations of poplars remains poorly documented in studies with limited number of genotypes per population Populus
Bd1-1 has excess of Bd1-1-unique SNPs relative to pairwise differences in genome segments Brachypodium distachyon
MsT and Mf high levels of bi-directional gene exchanges detected between gene flow Miscanthus sinensis; Miscanthus floridulus
pairwise comparisons provided reliable estimate of gene flow between focal populations Miscanthus
R. canina accessions were collected across Central and Eastern Europe Rosa canina
close proximity of cost and resistance loci (< 85 kb) supports requirement that c ≪ s is not improbable Ipomoea purpurea
InDel4337-Del frequency is only temperate lines (3%) Zea mays
high selfing rate is due to genomic constraints
Tajima's D test of z2δ10 showed non-significant Tajima's D values in individual populations
47% of North American pairs exhibit extensive haplotype sharing Arabidopsis thaliana
sparse sampling design of Triticum urartu collection cannot provide full representation of geographic structuration of Triticum urartu diversity Triticum urartu
92% of genetic variation between lineages A and B was indicative of long history of isolation with very low levels of gene flow Senecio coronatus
fewer private alleles in lines from northern Sweden than in lines from southern Sweden 18% versus 67% population divergence Arabidopsis thaliana
linkage disequilibrium characterization began systematic characterization of genome-wide polymorphism in Arabidopsis thaliana Arabidopsis thaliana
ability to detect footprints of selection depends greatly on sample composition and size Arabidopsis thaliana
two additional four-sample analyses with outgroup Arabidopsis lyrata produced similar patterns Arabidopsis thaliana; Arabidopsis lyrata
out-crossers have generally greater diversity than selfers
reduced recombination in the S-locus region means that a mutation at a modifier locus tightly linked to the self-incompatibility recognition genes is likely to have a significant impact on the distribution of S haplotypes in natural populations Arabidopsis thaliana
6 of 26 reliably genotyped SNPs in the promoter, one SNP in the first intron (990,275) and one of the large insertions (at 987,145) C. rubella-like alleles were virtually absent from C. grandiflora Capsella grandiflora; Capsella rubella
phylogenetic analysis revealed that majority of accessions containing the 20-bp indel originated from wild or ornamental peach groups Prunus persica
genetic divergence for some loci may exceed neutral expectations neutral expectations Miscanthus
distributions of fixation index (FST) values showed positive skewness and excess kurtosis statistical distribution Miscanthus
pairwise ima 2 analyses were performed because three-population comparisons did not reach convergence Miscanthus
resistant parents heterozygous at resistance locus results in F1-population segregates 1:1 for pathogen recognition Solanum berthaultii; Solanum ruiz-ceballosii
AMOVA analysis revealed that 30% of variation was between individuals within populations Cardamine hirsuta
extent of gene flow and allopatric intra-specific pair (MfT–MfC) gene flow level Miscanthus floridulus
Fu and Li tests are more sensitive than Tajima's D
KP hyperaccumulators grouped with non-accumulator serpentine populations in lineage A Senecio coronatus
genetic diversity decreased from YRR (π = 0.402 × 10−3) to USA region (π = 0.173 × 10−3) in upland cotton populations Gossypium hirsutum
genome-wide polymorphism data provides more powerful test of hypothesis that selfing lineages experience accumulation of deleterious mutations Capsella rubella
significant negative results of Fu and Li D * & F * in three populations confirmed existence of selection signals
Hap-4 showed highest frequency (85.26%) Glycine max
among-population variation in Ni hyperaccumulators has been reported in A. bertoloni Alyssum bertoloni
Within lineage A, most pairwise population ΦPT values were not significant at P < 0.05 and suggested gene flow was occurring Senecio coronatus
pattern of genetic diversity in Triticum urartu is consistent with isolation by distance model Triticum urartu
phenotypic variation is matched by significant genetic differentiation Senecio coronatus
apomictic plants can be analyzed with mixture model
population differentiation was little among four breeding periods Gossypium hirsutum
Tajima's D values of NNR and S3 showed substantially more positive values than other geographical distributions and breeding periods Gossypium hirsutum
genome-wide consequences of founder event and shift to selfing range to genome-wide decline in the efficacy of natural selection on amino acid polymorphisms Capsella rubella
effective barrier to migration due to non-equilibrium history of drift after divergence is illustrated by African elephant example Loxodonta africana
clustering on basis of genome-wide polymorphism revealed four major groups corresponding to A. thaliana, A. halleri, A. lyrata and A. arenosa Arabidopsis thaliana; Arabidopsis halleri; Arabidopsis lyrata; Arabidopsis arenosa
absence of positive or balancing selection at the RCO-A locus is consistent with the absence of common variants affecting leaf shape Capsella grandiflora
pairwise relative kinship of all samples and four main subgroups was small Brassica juncea
population bottleneck contributes to statistical bias in linkage disequilibrium determination Striga hermonthica
population genetic structure is one of the uncertain evolutionary forces causing linkage disequilibrium decay Striga hermonthica
linkage disequilibrium in C. grandiflora decays within a few hundred base pairs Capsella grandiflora
interchromosomal linkage disequilibrium (ILD) has been identified in other systems for ecologically relevant traits
regulatory regions show high ILD values between resistance alleles Ipomoea purpurea
TeM paralogs in unM-teM pairs showed significantly more negative Tajima's D values compared with its unM paralog Arabidopsis thaliana
unM translocated paralogs showed a slightly higher rate of polymorphism Arabidopsis thaliana
range-wide population genetic analyses conducted on 2321 trees from 202 populations Scots pine
extensive sampling of 2321 Scots pine individuals from > 200 populations aimed to assess impact of geography, ecological conditions and gene flow on spatial patterns Pinus sylvestris
Bruxaux et al. quantified genetic variation across 123 population clusters identified from 211 natural pine stands Pinus sylvestris
gene flow from Goodyera similis on Kozu Island to Goodyera henryi × Goodyera similis has proportion of migrants per generation of 0.091 Goodyera henryi; Goodyera similis
linkage disequilibrium (LD) estimated as r² (squared Pearson correlation coefficient) Brassica juncea
isozyme markers is used for S. hermonthica genetic diversity studies Striga hermonthica
local adaptation arises when genetic divergence of populations
InDel4337-Del frequency is higher in tropical inbred lines (26%) Zea mays
genotyping was essential to deflect alternative explanations such as genetic drift owing to severe population bottlenecks Veronica arvensis
inbreeding coefficient (F IS ) values were slightly elevated in northern Norway
inbreeding coefficient (F IS ) values were slightly elevated in isolated populations
tess3r did not identify a specific number of clusters that best explained genetic diversity in the population
STRUCTURE analysis demonstrated that insular ecotype contains genetic components from both Goodyera henryi and Goodyera similis Goodyera henryi; Goodyera similis
effective population size defines fate of genetic variation in populations
population-level variation carries information that can infer fine-scale characteristics of recombination based on population's natural history
epigenome-mediated polymorphism biases observed at whole-genome scales similar to duplicate paralogs that diverge in their epigenomic states also show comparable differences in polymorphism Arabidopsis thaliana
absence of reduction in genetic diversity in other locations could be due to very limited effect of genetic drift
Tajima's D showed no correlation with latitude
coalescence models tested demographic changes in three geographically distant populations found in China, Spain, and Norway Pinus sylvestris
population structure required to account for pairwise sequence divergence of several percent at individual loci must be far older than most recent glaciation Arabidopsis thaliana
North and South American alfalfa cultivars clustering in agreement with migration and cultivation history of alfalfa Medicago sativa
2968 comparisons with kinship coefficients greater than 0.92 involved 381 female lines Oryza sativa
outcrossing populations allow recessive mutations to be selected for only when they are revealed to be homozygotes and accumulated to high frequency Zea mays ssp. mays
nucleotide diversity analysis provides assessment of narrow genetic base within chickpea cultivars Cicer arietinum
84 SNPs had 44 polymorphic SNPs in entire dataset Cardamine hirsuta
(FST, LHL3, LL1, AT1G64625) value indicated strong population differentiation Cardamine hirsuta
result of paternal transmission in Rosa agrestis is in line with microsatellite data showing paternal alleles not in two copies in Rosa canina Rosa agrestis; Rosa canina
spatially varying selection along environmental gradients is expected to generate gene frequency clines at associated loci Pinus sylvestris
inbreeding causes reduced effective population sizes
rapid colonization from few isolated refugia scenario would predict lower genetic diversity in northern populations of Scots pine Pinus sylvestris
p.Ser55* mutation is observed in strains of both mating types Fulvia fulva
gbM genes showed the lowest rates of polymorphism Arabidopsis thaliana
DNA methylation difference examined for effect on rate of polymorphism between duplicate pairs Arabidopsis thaliana
shifts in base composition bias can be linked with crucial evolutionary parameters as generation time and population size
genotyping-by-sequencing used to analyze genetic structure in Scots pine Scots pine
consecutive range expansions after contraction may carry only a portion of the diversity from the source population reduced genetic diversity in expanding populations
principal component analysis (PCA) observed pattern congruent with geographic distribution
second principal component axis (PC2) followed more west–east direction for northern European, Russian and Asian populations
clustering analysis did not recover clear optimal number of clusters (K)
five other avr alleles represented 8% of population with frequency varying from 0.5% to 3% Plasmopara viticola
avrRpv3.1 locus has high genetic differentiation ( (FST, LHL3, LL1, AT1G64625) = 0.58) Plasmopara viticola
hybrids between Goodyera henryi and Goodyera similis on Kozu Island had interspecific heterozygosity below 0.3 Goodyera henryi; Goodyera similis
Ipomoea purpurea populations show low genetic differentiation Ipomoea purpurea
reductions in equilibrium GC might reflect shrinking effective population sizes or increased generation times
possible demographic changes might interact with selection to produce changes in equilibrium composition
inbreeding causes homozygosity
Avr9B mutations are restricted to strains of particular mating type Fulvia fulva
Scots pine populations have near absence of inbreeding Pinus sylvestris
hybrids between Goodyera henryi and Goodyera similis on Kozu Island had only two samples with hybrid index below 0.25 Goodyera henryi; Goodyera similis
TEM genes showed 1.06× more polymorphism than unM genes Arabidopsis thaliana
inbreeding coefficient (F IS ) values showed general tendency for marginally higher values at high latitudes
tess3r results were very similar to ones obtained with NGSadmix
high selfing rate could have negative effect on long-term maintenance of populations
recombination rate (c) much lower than selection coefficient (s) would prevent complete decoupling of cost alleles from resistance alleles Ipomoea purpurea
lack of differences in Tajima's D in other pairs consistent with interactive effects of selection and mutation rate differences Arabidopsis thaliana
gbM-gbM, teM-teM, and unM-unM translocated paralogs examined for polymorphism rate changes in Arabidopsis thaliana
Scots pine displays high and uniform genetic diversity across entire range Scots pine
global F ST measures genetic differentiation in Scots pine Scots pine
Spanish and Chinese populations were slightly differentiated from rest of the sampling
native ranges have more deterministic distribution of genotypes
Avr allele was most frequent (53%) Plasmopara viticola
absence of association between SNPs in the RCO-A locus and leaf margin dissection in C. grandiflora together with the largely fixed phenotypic difference between the species argues that the C. rubella high-lobing allele was not captured from common standing variation in C. grandiflora Capsella grandiflora; Capsella rubella
No genetic variation at (AT3G24580) was found between Hpa Gw-resistant (Gw-30, Gw-31, Gw-112, Gw-127, and Gw-144) and -susceptible (Gw-16, Gw-50, Gw-107, Gw-148, and Gw-167) genotypes Arabidopsis thaliana
several comparative studies have shown lower levels of genetic isolation in wind-pollinated than in related insect-pollinated species
simple sequence repeats (SSRs) together with expressed sequence tags (EST-SSR) is used for S. hermonthica genetic diversity studies Striga hermonthica
linkage disequilibrium (r2) calculated between long-distance and interchromosomal SNPs that showed the most extreme level of differentiation and selection Ipomoea purpurea
climatic selection, geographic distance and demographic history contribute to spatial variation in allele frequencies
microsatellites and isozymes indicate that N. fusca is the most genetically distinct Nothofagus fusca
polygenic local adaptation can generate linkage disequilibrium Ipomoea purpurea
patterns in gene–tree conflict can be explored through population dynamics such as ILS and introgression
changes in magnitude of trait evolution can be due to genetic drift
changes in magnitude of trait evolution can be due to differences in selective pressures among localities
absence of reduction in genetic diversity in other locations could be due to large enough population size
Scots pine populations have low genetic differentiation with global F ST of 0.048 Pinus sylvestris
Structure analysis under Δ K method assigned individuals to two genetic clusters Goodyera henryi; Goodyera similis
hybrids between Goodyera henryi and Goodyera similis on Kozu Island displayed intermediate values for hybrid index Goodyera henryi; Goodyera similis
highly differentiated region containing seed development genes is linked to other regions under selection that harbor resistance alleles Ipomoea purpurea
DNA methylation divergence in CG, CHG, and CHH contexts shows significant main effects and significant interactions between the variables, except for three-way interaction absolute differences in the rate of polymorphism between duplicate paralogs Arabidopsis thaliana
genome-wide patterns of genetic diversity across species range remain scarcely studied for Scots pine Pinus sylvestris
Evanno method indicated that two groups explained the genetic diversity best
(anac025, NAC025, NAC25, AT1G61110) and (NFD6, AT2G20585) are physically linked on chromosome 6 to regions under selection containing serine–threonine kinase genes Ipomoea purpurea
decreased genetic diversity may result in reduced potential response to future selective pressures
extensive sampling of 2321 Scots pine individuals from > 200 populations aimed to assess whether expanding populations harbor high genetic load Pinus sylvestris
Ipomoea purpurea populations show recent genetic connectivity Ipomoea purpurea
genes that showed loss-of-function (LOF) mutations including missense and nonsense mutations in natural accessions of Arabidopsis thaliana show that frequency of LOF mutations showed weak positive correlation with frequency of teM across the population Arabidopsis thaliana
InDel4337-Ref alleles in teosinte accessions have been diversified teosinte populations Zea mays subsp. parviglumis
inbreeding coefficient (F IS ) averaged 0.059
Rates of sequence variability in natural populations influenced by both mutation rate and natural selection Arabidopsis thaliana
K = 4 resulted in component for Western Europe populations appeared
π 0 /π 4 ratio showed no correlation with Tajima's D
Whole-genome duplicates (WGDs) had lower polymorphism Arabidopsis thaliana
migration rate from Goodyera henryi × Goodyera similis to Goodyera similis has 95% credible interval overlapping with zero, indicating no significant gene flow Goodyera henryi; Goodyera similis
distinct genetic signature in extant populations includes genetic lineages that track their recent ancestry Pinus sylvestris
observed heterozygosity (H o ) and expected heterozygosity (H e ) showed small decrease at high latitudes
Scots pine has relatively low levels of genetic variation across its entire range Pinus sylvestris
teM parental paralogs switched to unM translocated paralogs showed lower rates of polymorphism Arabidopsis thaliana
major population crash could generate nonadaptive genetic differentiation via genetic drift Veronica arvensis
third and fourth principal component axes separated Scottish and Turkish/Black Sea populations
range expansions can lead to more stochastic distribution of genotypes in non-native ranges
single-nucleotide polymorphisms in the promoter of PaFTL2 have clinal variation in allele frequency Picea abies
more negative Tajima's D values in TeM paralogs consistent with elevated mutation rate or differences in the distribution of fitness effects between these genes Arabidopsis thaliana
scarcity of genome-wide patterns and landscape impact studies hinders recovery of evolutionary history and genetic signature of local adaptation Pinus sylvestris
Tajima's D with longitude showed higher values in Asia
UMAP analysis confirmed very low level of structure in the data
cultivar comparison and population-based studies examining associations between metabolites and/or transcripts may be confounded with population structure
hybrid index and interspecific heterozygosity estimates from introgress was consistent with results from phylogenetic and Structure analyses Goodyera henryi; Goodyera similis
population differentiation analysis (F ST) showed differentiation degree between three tetraploid alfalfa subpopulations was high Medicago sativa
OutcrossSeq method will also be robust for populations of insects and fishes with numerous progeny
DNA polymorphisms of multiple sweet orange cultivars should improve analysis of genome heterozygosity of sweet orange Citrus sinensis
non-significant Wilcoxon's signed-rank test suggests no evidence of recent population bottleneck Striga hermonthica
phenotypic sex ratios in natural populations were quantified as proxy for effective population size
alternate allele at ch09_70173370 is most abundant in S. pimpinellifolium accessions from Ecuador Solanum pimpinellifolium
geographic and environmental distances showed weak correlation between them
outcrossing reduces inbreeding
levels of genetic variation similar across species and populations in Miscanthus species complex Miscanthus
southern M. sinensis (MsT) and populations of M. floridulus (Mf) MsT closest to MfC with FST value of 0.09 Miscanthus sinensis; Miscanthus floridulus
taxa at different elevations displaying altitudinal cline of condensatus → glaber → formosanus → transmorrisonensis Miscanthus sinensis
extent of gene flow followed by allopatric inter-specific pair (MsT–MfC) gene flow level Miscanthus sinensis; Miscanthus floridulus
Solanum berthaultii population segregates for single dominant R gene Rpi-ber2 Solanum berthaultii
genetic variation in C. hirsuta is structured geographically Cardamine hirsuta
11 additional non-sequenced lines showed these polymorphisms distributed broadly among B. distachyon populations Brachypodium distachyon
LD statistic r2 calculated to distinguish outliers from background genes Miscanthus
GmGA2ox16-Hap1 allele present at frequency of 71.17% in landraces to 78.10% in improved cultivars Glycine max
Tibet population has significantly lower nucleotide diversity than Yunnan population Citrus medica
taf4b-1 is rare mutation that likely arose in South-West Ireland Arabidopsis thaliana
populations in refugial areas diverge by drift and/or local adaptation
Mf and MsT lowest differentiation at species level with FST value of 0.08 Miscanthus floridulus; Miscanthus sinensis
Bayesian-based structure program used to examine population structure in Miscanthus species complex Miscanthus
MsT and Mf M values estimated at 1.17 × 10^-6 from Mf to MsT migration rate Miscanthus sinensis; Miscanthus floridulus
389 genes represents 6.6% of genes affected by LOF variants Glycine max; Glycine soja
EM algorithm is implemented to estimate outcrossing rate
48,518 high-quality SNPs were identified in 4,225 genes Capsella grandiflora; Capsella rubella
SNPs segregating in both species had lowest nonsynonymous-to-synonymous ratio (0.22) Capsella grandiflora; Capsella rubella
analysis of molecular variance revealed very few variants resided among populations within species genetic variants Miscanthus
differentiation between (E12A11, MFT, AT1G18100) and MfC only detected using SSRS Miscanthus floridulus
MsJR to (E12A11, MFT, AT1G18100) significant uni-directional introgression detected from introgression Miscanthus sinensis; Miscanthus floridulus
Group 3 could be further divided into three subgroups highly correlated with subspecies geographic distribution Medicago sativa
confounding effects of background loci may be genome-wide due to linkage disequilibrium
SNPs segregated in both species Capsella grandiflora; Capsella rubella
deletion or absence alleles were more likely to be major alleles Arabidopsis thaliana
core germplasms acquired from specimens distributed over six continents Medicago sativa
(E12A11, MFT, AT1G18100) assigned to independent cluster at K ≥ 6 genetic cluster Miscanthus floridulus
Mf and MsJR M values estimated at 3.36 × 10^-9 from Mf to MsJR migration rate Miscanthus floridulus; Miscanthus sinensis
only a few outlier genes displayed significant LD within populations Miscanthus