ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

2019 ◽  
Vol 28 (10) ◽  
pp. 2594-2609 ◽  
Author(s):  
Philip Lavretsky ◽  
Jeffrey M. DaCosta ◽  
Michael D. Sorenson ◽  
Kevin G. McCracken ◽  
Jeffrey L. Peters
Keyword(s):  
Population Structure ◽  
North America ◽  
Genome Wide ◽  
Close Relatives ◽  
Genomic Regions ◽  
Wide Population

scholarly journals Genome-wide DNA Variants Identify Genetic Diversity and Population Structure of Leptosphaeria maculans in Western Canada

2020 ◽  
Author(s):  
Qilin Chen ◽  
Gary Peng ◽  
Randy Kutcher ◽  
Fengqun Yu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genome Wide Association Study ◽  
Leptosphaeria Maculans ◽  
Western Canada ◽  
Effective Management ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
Dna Variants ◽  
Genomic Regions

Abstract Background: Leptosphaeria maculans is a serious concern for canola production in Canada. For effective management, knowledge of the pathogen’s genetic variability and population structure is a prerequisite. Despite some information on race dynamics of the western Canadian L. maculans population in recent years, genetic diversity based on a large number of genome-wide DNA variants has not been investigated.Results: From 1,590 L. maculans isolates collected from 23 field sites in three provinces: Manitoba, Saskatchewan and Alberta, Canada, in the years 2007-2008 and 2012-2014, 150 representative isolates were selected and whole-genome sequenced, and 31,870 polymorphic DNA variants (SNPs and InDels) were used to study L. maculans genetic diversity and population structure. Cluster analysis showed that the genetic diversity levels and isolate groupings varied with the number and genomic regions of the variants involved; isolates collected in 2012-2014 were more genetically diverse than those collected in 2007-2008 when genome-wide variants were considered. The genome wide association study (GWAS) detected variants in egn4_Lema_T86290 (AvrLm4-7), egn4_Lema_T86300 and egn4_Lema_T86310 associated with the year of collection, but no variants was found to be associated with the province or specific location from which the isolates were collected. Population structure analysis indicated the presence of three distinct sub-populations in western Canada. While isolates from Saskatchewan were mainly of one sub-population (sub-pop1), the Alberta isolates comprised two sub-populations (sub-pop1 and sub-pop2), and all the 3 subpopulations were found in Manitoba.Conclusion: The genetic diversity of the western Canadian L. maculans population varied among provinces. It was highly admixed in Manitoba, followed by that in Alberta. The Saskatchewan population had the lowest genetic diversity. Significant genome variation between 2007-2008 and 2012-2014 occurred in the genes egn4_Lema_T86290 (AvrLm4-7), egn4_Lema_T86300 and egn4_Lema_T86310), with AvrLm4-7 becoming much more common in the L. maculans population in the later period.

scholarly journals Genome-wide population structure and evolutionary history of the Frizarta dairy sheep

animal ◽  
2017 ◽  
Vol 11 (10) ◽  
pp. 1680-1688 ◽  
Author(s):  
A. Kominakis ◽  
A.L. Hager-Theodorides ◽  
A. Saridaki ◽  
G. Antonakos ◽  
G. Tsiamis
Keyword(s):  
Population Structure ◽  
Evolutionary History ◽  
Dairy Sheep ◽  
Genome Wide ◽  
History Of ◽  
Wide Population

scholarly journals Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

2018 ◽  
Vol 49 (1) ◽  
pp. 59-70 ◽  
Author(s):  
R. B. Onzima ◽  
M. R. Upadhyay ◽  
R. Mukiibi ◽  
E. Kanis ◽  
M. A. M. Groenen ◽  
...  
Keyword(s):  
Population Structure ◽  
Admixture Analysis ◽  
Genome Wide ◽  
Wide Population

scholarly journals Evaluating the use of ABBA-BABA statistics to locate introgressed loci

2013 ◽  
Author(s):  
Simon H. Martin ◽  
John W. Davey ◽  
Chris D. Jiggins
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Ancestral Population ◽  
Whole Genome ◽  
Effective Population ◽  
Genome Data ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson?s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic f̂d, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. f̂d is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f̂d outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

scholarly journals Deciphering the genic basis of environmental adaptations by simultaneous forward and reverse genetics in Saccharomyces cerevisiae

2016 ◽  
Author(s):  
Calum J. Maclean ◽  
Brian P.H. Metzger ◽  
Jian-Rong Yang ◽  
Wei-Chin Ho ◽  
Bryan Moyers ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Population Structure ◽  
Association Mapping ◽  
Cell Biology ◽  
Reverse Genetics ◽  
Dna Barcode ◽  
Genome Wide ◽  
Environmental Adaptations ◽  
Yeast Genes ◽  
Genomic Regions

ABSTRACTThe budding yeast Saccharomyces cerevisiae is the best studied eukaryote in molecular and cell biology, but its utility for understanding the genetic basis of natural phenotypic variation is limited by the inefficiency of association mapping owing to strong and complex population structure. To facilitate association mapping, we analyzed 190 high-quality genomes of diverse strains, including 85 newly sequenced ones, to uncover yeast’s population structure that varies substantially among genomic regions. We identified 181 yeast genes that are absent from the reference genome and demonstrated their expression and role in important functions such as drug resistance. We then simultaneously measured the growth rates of over 4500 lab strains each deficient of a nonessential gene and 81 natural strains across multiple environments using unique DNA barcode present in each strain. We combined the genome-wide reverse genetic information with genome-wide association analysis to determine potential genomic regions of importance to environmental adaptations, and for a subset experimentally validated their role by reciprocal hemizygosity tests. The resources provided permit efficient and reliable association mapping in yeast and significantly enhances its value as a model for understanding the genetic mechanisms of phenotypic polymorphism and evolution.

scholarly journals Repeat-Induced Point Mutations Drive Divergence between Fusarium circinatum and Its Close Relatives

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 298 ◽  
Author(s):  
Stephanie van Wyk ◽  
Brenda D. Wingfield ◽  
Lieschen De Vos ◽  
Nicolaas A. van der Merwe ◽  
Quentin C. Santana ◽  
...  
Keyword(s):  
Defense Mechanism ◽  
Point Mutations ◽  
Fusarium Fujikuroi ◽  
Fusarium Circinatum ◽  
Chromosome Architecture ◽  
Genome Defense ◽  
Genome Wide ◽  
Fusarium Fujikuroi Species Complex ◽  
Close Relatives ◽  
Genomic Regions

The Repeat-Induced Point (RIP) mutation pathway is a fungal-specific genome defense mechanism that counteracts the deleterious effects of transposable elements. This pathway permanently mutates its target sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence of RIP in the pitch canker pathogen, Fusarium circinatum, and its close relatives in the Fusarium fujikuroi species complex (FFSC). Our results showed that the examined fungi all exhibited hallmarks of RIP, but that they differed in terms of the extent to which their genomes were affected by this pathway. RIP mutations constituted a large proportion of all the FFSC genomes, including both core and dispensable chromosomes, although the latter were generally more extensively affected by RIP. Large RIP-affected genomic regions were also much more gene sparse than the rest of the genome. Our data further showed that RIP-directed sequence diversification increased the variability between homologous regions of related species, and that RIP-affected regions can interfere with homologous recombination during meiosis, thereby contributing to post-mating segregation distortion. Taken together, these findings suggest that RIP can drive the independent divergence of chromosomes, alter chromosome architecture, and contribute to the divergence among F. circinatum and other members of this economically important group of fungi.

scholarly journals Genome-wide Population Structure Analyses of Three Minor Millets: Kodo Millet, Little Millet, and Proso Millet

2018 ◽  
Author(s):  
Matthew Johnson ◽  
Santosh Deshpande ◽  
Mani Vetriventhan ◽  
Hari D Upadhyaya ◽  
Jason G. Wallace
Keyword(s):  
Population Structure ◽  
Smallholder Farmers ◽  
Population Genetic Analysis ◽  
Proso Millet ◽  
Little Millet ◽  
Genome Wide ◽  
A Genome ◽  
Kodo Millet ◽  
Minor Millets ◽  
Wide Population

AbstractMillets are a diverse group of small-seeded grains that are rich in nutrients but have received relatively little advanced plant breeding research. Millets are important to smallholder farmers in Africa and Asia because of their short growing season, good stress tolerance, and high nutritional content. To advance the study and use of these species, we present a genome-wide marker datasets and population structure analyses for three minor millets: kodo millet (Paspalum scrobiculatum), little millet (Panicum sumatrense), and proso millet (Panicum miliaceum). We generated genome-wide marker data sets for 190 accessions of each species with genotyping-by-sequencing (GBS). After filtering, we retained between 161 and 165 accessions of each species, with 3461, 2245, and 1882 single-nucleotide polymorphisms (SNPs) for kodo, proso, and little millet, respectively. Population genetic analysis revealed 7 putative subpopulations of kodo millet and 8 each of proso millet and little millet. To confirm the accuracy of this genetic data, we used public phenotype data on a subset of these accessions to estimate the heritability of various agronomically relevant phenotypes. Heritability values largely agree with the prior expectation for each phenotype, indicating that these SNPs provide an accurate genome-wide sample of genetic variation. These data represent one of first genome-wide population genetics analyses, and the most extensive, in these species and the first genomic analyses of any sort for little millet and kodo millet. These data will be a valuable resource for researchers and breeders trying to improve these crops for smallholder farmers.

scholarly journals The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection

2017 ◽  
Author(s):  
Saioa López ◽  
Mark G. Thomas ◽  
Lucy van Dorp ◽  
Naser Ansari-Pour ◽  
Sarah Stewart ◽  
...  
Keyword(s):  
Population Structure ◽  
Historical Records ◽  
Genome Wide ◽  
Mitochondrial Data ◽  
The World ◽  
Rich Information ◽  
Second Millennium Bce ◽  
The Rich ◽  
Genomic Regions ◽  
Iranian Populations

AbstractZoroastrianism is one of the oldest extant religions in the world, originating in Persia (present-day Iran) during the second millennium BCE. Historical records indicate that migrants from Persia brought Zoroastrianism to India, but there is debate over the timing of these migrations. Here we present novel genome-wide autosomal, Y-chromosome and mitochondrial data from Iranian and Indian Zoroastrians and neighbouring modern-day Indian and Iranian populations to conduct the first genome-wide genetic analysis in these groups. Using powerful haplotype-based techniques, we show that Zoroastrians in Iran and India show increased genetic homogeneity relative to other sampled groups in their respective countries, consistent with their current practices of endogamy. Despite this, we show that Indian Zoroastrians (Parsis) intermixed with local groups sometime after their arrival in India, dating this mixture to 690-1390 CE and providing strong evidence that the migrating group was largely comprised of Zoroastrian males. By exploiting the rich information in DNA from ancient human remains, we also highlight admixture in the ancestors of Iranian Zoroastrians dated to 570 BCE-746 CE, older than admixture seen in any other sampled Iranian group, consistent with a long-standing isolation of Zoroastrians from outside groups. Finally, we report genomic regions showing signatures of positive selection in present-day Zoroastrians that might correlate to the prevalence of particular diseases amongst these communities.

scholarly journals Genome‐Wide Population Structure Analyses of Three Minor Millets: Kodo Millet, Little Millet, and Proso Millet

2019 ◽  
Vol 12 (3) ◽  
pp. 190021 ◽  
Author(s):  
Matthew Johnson ◽  
Santosh Deshpande ◽  
Mani Vetriventhan ◽  
Hari D. Upadhyaya ◽  
Jason G. Wallace
Keyword(s):  
Population Structure ◽  
Proso Millet ◽  
Little Millet ◽  
Genome Wide ◽  
Kodo Millet ◽  
Minor Millets ◽  
Wide Population
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