scholarly journals Hitchhiking in space: ancestry in adapting, spatially-extended populations

2016 ◽  
Author(s):  
Brent Allman ◽  
Daniel B. Weissman
Keyword(s):  
Genetic Diversity ◽  
Small Region ◽  
Genomic Region ◽  
Spatial Distance ◽  
Selective Sweeps ◽  
Spatial Region ◽  
Neutral Genetic Diversity ◽  
Spatially Extended ◽  
Neutral Mutations ◽  
Spatial Locations

AbstractSelective sweeps reduce neutral genetic diversity. In sexual populations, this “hitchhiking” effect is thought to be limited to the local genomic region of the sweeping allele. While this is true in panmictic populations, we find that in spatially-extended populations the combined effects of many unlinked sweeps can affect patterns of ancestry (and therefore neutral genetic diversity) across the whole genome. Even low rates of sweeps can be enough to skew the spatial locations of ancestors such that neutral mutations that occur in an individual living outside a small region in the center of the range have virtually no chance of fixing in the population. The fact that nearly all ancestry rapidly traces back to a small spatial region also means that relatedness between individuals falls off very slowly as a function of the spatial distance between them.

scholarly journals Genetic Diversity, Structure, and Selective Sweeps in Spinacia turkestanica Associated With the Domestication of Cultivated Spinach

2021 ◽  
Vol 12 ◽  
Author(s):  
Sanjaya Gyawali ◽  
Gehendra Bhattarai ◽  
Ainong Shi ◽  
Chris Kik ◽  
Lindsey J. du Toit
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Selective Sweep ◽  
Spinacia Oleracea ◽  
Genomic Region ◽  
Day Length ◽  
Mountain Range ◽  
Nucleotide Polymorphisms ◽  
Selective Sweeps ◽  
Genetic Diversity And Structure

Genotype-by-sequencing (GBS) was used to explore the genetic diversity and structure of Spinacia turkestanica, and the selective sweeps involved in domestication of cultivated spinach, S. oleracea, from S. turkestanica. A total 7,065 single nucleotide polymorphisms (SNPs) generated for 16 Spinacia oleracea and 76 S. turkestanica accessions placed the S. oleracea accessions in one group, Q1, and the 76 S. turkestanica accessions, which originated from Central Asia, in two distinct groups, Q2 and Q3. The Q2 group shared greater genetic identity with the S. oleracea accessions, Q1, than the Q3 S. turkestanica group. Likewise, the S. oleracea Q1 group had a smaller Fst (0.008) with the Q2 group than with the Q3 group (Fst = 0.012), and a greater gene flow (Nm = 30.13) with the Q2 group than with the Q3 group (Nm = 21.83). The Q2 accessions originated primarily from Uzbekistan while the Q3 accessions originated mostly from Tajikistan. The Zarafshan Mountain Range appears to have served as a physical barrier that largely separated members of the Q2 and Q3 groups of S. turkestanica. Accessions with admixtures of Q2 and Q3 were collected primarily from lower elevations at the southern end of the Zarafshan Mountain Range in Uzbekistan. Selective sweep regions identified at 32, 49, and 52 Mb on chromosomes 1, 2, and 3, respectively, appear to have played a vital role in the domestication of S. oleracea as they are correlated with important domestication traits, including day length sensitivity for bolting (flowering). High XP-CLR scores at the 52 Mb genomic region of chromosome three suggest that a selective sweep at this region was responsible for early differentiation of S. turkestanica into two groups in Central Asia.

scholarly journals The Effect of Mating System Differences on Nucleotide Diversity at the Phosphoglucose Isomerase Locus in the Plant Genus Leavenworthia

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 343-357 ◽  
Author(s):  
F Liu ◽  
D Charlesworth ◽  
M Kreitman
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Phosphoglucose Isomerase ◽  
Self Incompatibility ◽  
Background Selection ◽  
Selective Sweeps ◽  
Balanced Polymorphism ◽  
Neutral Genetic Diversity ◽  
Low Diversity ◽  
High Diversity

AbstractTo test the theoretical prediction that highly inbreeding populations should have low neutral genetic diversity relative to closely related outcrossing populations, we sequenced portions of the cytosolic phosphoglucose isomerase (PgiC) gene in the plant genus Leavenworthia, which includes both self-incompatible and inbreeding taxa. On the basis of sequences of intron 12 of this gene, the expected low diversity was seen in both populations of the selfers Leavenworthia uniflora and L. torulosa and in three highly inbreeding populations of L. crassa, while high diversity was found in self-incompatible L. stylosa, and moderate diversity in L. crassa populations with partial or complete self-incompatibility. In L. stylosa, the nucleotide diversity was strongly structured into three haplotypic classes, differing by several insertion/deletion sequences, with linkage disequilibrium between sequences of the three types in intron 12, but not in the adjacent regions. Differences between the three kinds of haplotypes are larger than between sequences of this gene region from different species. The haplotype divergence suggests the presence of a balanced polymorphism at this locus, possibly predating the split between L. stylosa and its two inbreeding sister taxa, L. uniflora and L. torulosa. It is therefore difficult to distinguish between different potential causes of the much lower sequence diversity at this locus in inbreeding than outcrossing populations. Selective sweeps during the evolution of these populations are possible, or background selection, or merely loss of a balanced polymorphism maintained by overdominance in the populations that evolved high selfing rates.

scholarly journals Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding elements

2021 ◽  
Author(s):  
David Murphy ◽  
Eyal Elyashiv ◽  
Guy Amster ◽  
Guy Sella
Keyword(s):  
Genetic Diversity ◽  
Purifying Selection ◽  
Dominant Mode ◽  
Background Selection ◽  
Selective Sweeps ◽  
Deleterious Mutations ◽  
Phylogenetic Conservation ◽  
Neutral Genetic Diversity ◽  
Polymorphism Data ◽  
Linked Selection

Analyses of genetic variation in many taxa have established that neutral genetic diversity is shaped by natural selection at linked sites. Whether the source of selection is primarily the fixation of strongly beneficial alleles (selective sweeps) or purifying selection on deleterious mutations (background selection) remains unknown, however. We address this question in humans by fitting a model of the joint effects of selective sweeps and background selection to autosomal polymorphism data from the 1000 Genomes Project. After controlling for variation in mutation rates along the genome, a model of background selection alone explains ~60% of the variance in diversity levels at the megabase scale. Adding the effects of selective sweeps driven by adaptive substitutions to the model does not improve the fit, and when both modes of selection are considered jointly, selective sweeps are estimated to have had little or no effect on linked neutral diversity. The regions under purifying selection are best predicted by phylogenetic conservation, with ~80% of the deleterious mutations affecting neutral diversity occurring in non-exonic regions. Thus, background selection is the dominant mode of linked selection in humans, with marked effects on diversity levels throughout autosomes.

scholarly journals Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1269-1278 ◽  
Author(s):  
Bernhard Haubold ◽  
Jürgen Kroymann ◽  
Andreas Ratzka ◽  
Thomas Mitchell-Olds ◽  
Thomas Wiehe
Keyword(s):  
Genetic Diversity ◽  
Arabidopsis Thaliana ◽  
Linkage Disequilibrium ◽  
Gene Conversion ◽  
Genomic Sequence ◽  
Genomic Region ◽  
Resistance To Herbivory ◽  
Linkage Disequilibria ◽  
Coalescent Simulations ◽  
The Mean

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

Is neutral genetic diversity related to quantitative variation in semen traits in bulls?

2021 ◽  
Author(s):  
Eddington Gororo ◽  
Fungayi Primrose Chatiza ◽  
Farisai Chidzwondo ◽  
Stanley Marshall Makuza
Keyword(s):  
Genetic Diversity ◽  
Quantitative Variation ◽  
Neutral Genetic Diversity

scholarly journals All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 139
Author(s):  
Marlien M. van der Merwe ◽  
Jia-Yee S. Yap ◽  
Peter D. Wilson ◽  
Helen T. Murphy ◽  
Andrew Ford
Keyword(s):  
Genetic Diversity ◽  
Allelic Variation ◽  
Germplasm Conservation ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Ex Situ ◽  
Spatial Distance ◽  
Genetic Connectivity ◽  
Conservation Genomics ◽  
Modelling Framework

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

Predicates, parts, and impermanence: a contemporary version of some central Buddhist tenets

2017 ◽  
Vol 54 (4) ◽  
pp. 475-488
Author(s):  
MATTHEW McKEEVER
Keyword(s):  
Natural Language ◽  
Recent Work ◽  
Analytic Philosophy ◽  
Buddhist Philosophy ◽  
Logical Constant ◽  
Good Sense ◽  
Buddhist Doctrine ◽  
Spatially Extended ◽  
Temporal Parts ◽  
Spatial Locations

AbstractIn this article, I argue that recent work in analytic philosophy on the semantics of names and the metaphysics of persistence supports two theses in Buddhist philosophy, namely the impermanence of objects and a corollary about how referential language works. According to this latter package of views, the various parts of what we call one object (say, King Milinda) possess no unity in and of themselves. Unity comes rather from language, in that we have terms (say, ‘King Milinda’) which stand for all the parts taken together. Objects are mind- (or rather language-)generated fictions. I think this package can be cashed out in terms of two central contemporary views. The first is that there are temporal parts: just as an object is spatially extended by having spatial parts at different spatial locations, so it is temporally extended by having temporal parts at different temporal locations. The second is that names are predicates: rather than standing for any one thing, a name stands for a range of things. The natural language term ‘Milinda’ is not akin to a logical constant, but akin to a predicate.Putting this together, I'll argue that names are predicates with temporal parts in their extension, which parts have no unity apart from falling under the same predicate. ‘Milinda’ is a predicate which has in its extension all Milinda's parts. The result is an interesting and original synthesis of plausible positions in semantics and metaphysics, which makes good sense of a central Buddhist doctrine.

scholarly journals Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0232436
Author(s):  
Christos Dadousis ◽  
Francesca Cecchi ◽  
Michela Ablondi ◽  
Maria Chiara Fabbri ◽  
Alessandra Stella ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cross Validation ◽  
Small Region ◽  
Economic Factors ◽  
Admixture Analysis ◽  
Goat Breed ◽  
Runs Of Homozygosity ◽  
Genomic Inbreeding ◽  
Assignment Success ◽  
Integrated Study

The objective of this study was to investigate the genetic diversity of the Garfagnina (GRF) goat, a breed that currently risks extinction. For this purpose, 48 goats were genotyped with the Illumina CaprineSNP50 BeadChip and analyzed together with 214 goats belonging to 9 other Italian breeds (~25 goats/breed), whose genotypes were available from the AdaptMap project [Argentata (ARG), Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of breed traceability via discriminant analysis on principal components (DAPC) based on cross-validation. ROH analyses was used to assess the genetic diversity of GRF, while admixture and DAPC to evaluate its relationship to the other breeds. For GRF, common ROH (more than 45% in GRF samples) was detected on CHR 12 at, roughly 50.25–50.94Mbp (ARS1 assembly), which spans the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area of common ROH was also present in DIT, while a broader region (~49.25–51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis revealed a small region of common ancestry from GRF shared by BIO, VSS, ARG and CCG breeds. The DAPC model yielded 100% assignment success for GRF. Overall, our results support the identification of GRF as a distinct native Italian goat breed. This work can contribute to planning conservation programmes to save GRF from extinction and will improve the understanding of the socio-agro-economic factors related with the farming of GRF.

scholarly journals A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes within Vibrio cholerae infected patients

2020 ◽  
Author(s):  
Inès Levade ◽  
Ashraful I. Khan ◽  
Fahima Chowdhury ◽  
Stephen B. Calderwood ◽  
Edward T. Ryan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Vibrio Cholerae ◽  
Genome Sequencing ◽  
Asymptomatic Infection ◽  
Whole Genome ◽  
Metagenomic Sequencing ◽  
Asymptomatic Carriers ◽  
Adaptive Mutations ◽  
Neutral Mutations

ABSTRACTVibrio cholerae can cause a range of symptoms in infected patients, ranging from severe diarrhea to asymptomatic infection. Previous studies using whole genome sequencing (WGS) of multiple bacterial isolates per patient have shown that Vibrio cholerae can evolve a modest amount of genetic diversity during symptomatic infection. Little is known about V. cholerae genetic diversity within asymptomatic infected patients. To achieve increased resolution in the detection of Vibrio cholerae diversity within individual infections, we applied culture-based population genomics and metagenomics to a cohort of symptomatic and asymptomatic cholera patients. While the metagenomic approach allowed us to detect more mutations in symptomatic patients compared to the culture-based approach, WGS of isolates was still necessary to detect V. cholerae diversity in asymptomatic carriers, likely due to their low Vibrio cholerae load. We found that symptomatic and asymptomatic patients contain similar levels of within-patient diversity, and discovered V. cholerae hypermutators in some patients. While hypermutators appeared to generate mostly selectively neutral mutations, non-mutators showed signs of convergent mutation across multiple patients, suggesting V. cholerae adaptation within hosts. Our results highlight the power of metagenomics combined with isolate sequencing to characterize within-patient diversity in acute V. cholerae infection and asymptomatic infection, while providing evidence for hypermutator phenotypes within cholera patients.IMPORTANCEPathogen evolution within patients can impact phenotypes such as drug resistance and virulence, potentially affecting clinical outcomes. V. cholerae infection can result in life-threatening diarrheal disease, or asymptomatic infection. Here we describe whole-genome sequencing of V. cholerae isolates and culture-free metagenomic sequencing from stool of symptomatic cholera patients and asymptomatic carriers. Despite the acuteness of cholera infections, we found evidence for adaptive mutations in the V. cholerae genome that occur independently and repeatedly within multiple symptomatic patients. We also identified V. cholerae hypermutator phenotypes within 6 out of 14 patients, which appear to generate mainly neutral or deleterious mutations. Our work sets the stage for future studies of the role of hypermutators and within-patient evolution in explaining the variation from asymptomatic carriage to symptomatic cholera.

Sign in / Sign up

Export Citation Format

Share Document