scholarly journals Cyto-nuclear linkage disequilibrium resulting from admixture

2020 ◽  
Author(s):  
Peter D. Fields ◽  
David E. McCauley ◽  
Douglas R. Taylor
Keyword(s):  
Linkage Disequilibrium ◽  
North American ◽  
Invasive Plant ◽  
Mitochondrial Gene ◽  
Nuclear Genome ◽  
Silene Latifolia ◽  
Nuclear Microsatellite ◽  
Using Data ◽  
European Populations ◽  
Study Species

ABSTRACTPrevious studies of North American populations of the invasive plant Silene latifolia showed significant cyto-nuclear linkage disequilibrium (CNLD) between SNP variants of a mitochondrial gene (atp1) and the most common allele at nuclear microsatellite loci. Fields et al. (2014) hypothesized that this CNLD arose partially as a consequence of admixture that occurred during the colonization of North American (NA) populations of S latifolia via seed dispersal from genetically differentiated European populations that represent a portion of the native range of this species. In order to evaluate the plausibility of the admixture hypothesis, as opposed to metapopulation processes alone, we estimated CNLD for these same loci using data collected from eastern (EEU) and western (WEU) European populations of S. latifolia known to be genetically differentiated and likely sources of the spread of the study species to North America. We show that the CNLD found previously in NA populations of S. latifolia can be attributed to admixture of the previously isolated European demes coupled with decay since that time. Our applied framework allows the separation of the forces generating and dissolving statistical associations between alleles in cytoplasmic organelles and the nuclear genome and may thus be of utility in the study of plant or animal microbiomes.

Linkage disequilibrium for DNA haplotypes near the cystic fibrosis locus in two South European populations

1989 ◽  
Vol 83 (2) ◽  
pp. 175-178 ◽  
Author(s):  
X. Estivill ◽  
P. Gasparini ◽  
G. Novelli ◽  
T. Casals ◽  
V. Nunes ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Linkage Disequilibrium ◽  
European Populations

scholarly journals The Decay of Disease Association with Declining Linkage Disequilibrium: A Fine Mapping Theorem

2016 ◽  
Author(s):  
Mehdi Maadooliat ◽  
Naveen K. Bansal ◽  
Jiblal Upadhya ◽  
Manzur R. Farazi ◽  
Zhan Ye ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Linkage Disequilibrium ◽  
Fine Mapping ◽  
Disease Model ◽  
Disease Association ◽  
Simple Relationship ◽  
Locus System ◽  
Using Data ◽  
Relationship Of ◽  
The Relationship

AbstractSeveral important and fundamental aspects of disease genetics models have yet to be described. One such property is the relationship of disease association statistics at a marker site closely linked to a disease causing site. A complete description of this two-locus system is of particular importance to experimental efforts to fine map association signals for complex diseases. Here, we present a simple relationship between disease association statistics and the decline of linkage disequilibrium from a causal site. A complete derivation of this relationship from a general disease model is shown for very large sample sizes. Quite interestingly, this relationship holds across all modes of inheritance. Extensive Monte Carlo simulations using a disease genetics model applied to chromosomes subjected to a standard model of recombination are employed to better understand the variation around this fine mapping theorem due to sampling effects. We also use this relationship to provide a framework for estimating properties of a non-interrogated causal site using data at closely linked markers. We anticipate that understanding the patterns of disease association decay with declining linkage disequilibrium from a causal site will enable more powerful fine mapping methods.

Population structure of Heterobasidion annosum from North America and Europe

1993 ◽  
Vol 71 (8) ◽  
pp. 1064-1071 ◽  
Author(s):  
William J. Otrosina ◽  
Thomas E. Chase ◽  
Fields W. Cobb Jr. ◽  
Kari Korhonen
Keyword(s):  
Population Structure ◽  
North America ◽  
North American ◽  
Forest Tree ◽  
Heterobasidion Annosum ◽  
Evolutionary Relationships ◽  
The North ◽  
Isozyme Loci ◽  
Intersterility Groups ◽  
European Populations

Isolates of Heterobasidion annosum (Fr.) Bref. representing North American S and P and European S, P, and F intersterility groups were subjected to isozyme analysis. European S, P, and F groups had more variability than the North American S and P groups in expected hterozygosity, number of alleles per locus, and percent polymorphic loci. In contrast with the North American S and P groups, the European intersterility groups could not be distinguished from each other on the basis of individual isozyme loci, although significant differences in allele frequencies exist between European S and P groups. This suggests that evolution proceeded at different rates in the intersterility groups, or intersterility barriers appeared later in the European populations relative to the North American populations of H. annosum. Changes in climate and host species associations during the Tertiary may have been a major factor in evolution of H. annosum intersterility groups. Key words: allozymes, forest tree hosts, playnological events, evolutionary relationships, Hymenomycetes, root disease.

THE EVOLUTION OF AN INVASIVE PLANT: AN EXPERIMENTAL STUDY WITH SILENE LATIFOLIA

Ecology ◽  
2004 ◽  
Vol 85 (11) ◽  
pp. 3035-3042 ◽  
Author(s):  
Amy C. Blair ◽  
Lorne M. Wolfe
Keyword(s):  
Experimental Study ◽  
Invasive Plant ◽  
Silene Latifolia

The genes TR, Ost, ProR, and L in natural populations of Melanoplus sanguinipes

1983 ◽  
Vol 25 (2) ◽  
pp. 88-92 ◽  
Author(s):  
W. Chapco
Keyword(s):  
Lactic Acid ◽  
Linkage Disequilibrium ◽  
North American ◽  
Geographical Variation ◽  
Natural Populations ◽  
Melanoplus Sanguinipes ◽  
Lactic Acid Dehydrogenase ◽  
Acid Dehydrogenase

Several North American populations of the migratory grasshopper, Melanoplus sanguinipes (F.), were screened for variation at the loci, TR, Ost, ProR, and L; these are associated, respectively, with tibiae color, femoral stripe, pronotum color, and lactic acid dehydrogenase allozymes (LDH). The most common LDH allele, L2, is uniformly frequent over all sites; TR and Ost show considerable geographical variation, while allele, ProR, is rare or absent in all sampled areas. There is very little evidence of linkage disequilibrium between pairs of loci.

scholarly journals Chromosomal Thermal Index: a comprehensive way to integrate the thermal adaptation of Drosophila subobscura whole karyotype

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 73-78 ◽  
Author(s):  
Conxita Arenas ◽  
Goran Zivanovic ◽  
Francesc Mestres
Keyword(s):  
Global Warming ◽  
Natural Populations ◽  
Thermal Adaptation ◽  
Chromosomal Polymorphism ◽  
Thermal Index ◽  
Homologous Chromosomes ◽  
Cold Adapted ◽  
Using Data ◽  
Over Time ◽  
European Populations

Drosophila has demonstrated to be an excellent model to study the adaptation of organisms to global warming, with inversion chromosomal polymorphism having a key role in this adaptation. Here, we introduce a new index (Chromosomal Thermal Index or CTI) to quantify the thermal adaptation of a population according to its composition of “warm” and “cold” adapted inversions. This index is intuitive, has good statistical properties, and can be used to hypothesis on the effect of global warming on natural populations. We show the usefulness of CTI using data from European populations of D. subobscura, sampled in different years. Out of 15 comparisons over time, nine showed significant increase of CTI, in accordance with global warming expectations. Although large regions of the genome outside inversions contain thermal adaptation genes, our results show that the total amount of warm or cold inversions in populations seems to be directly involved in thermal adaptation, whereas the interactions between the inversions content of homologous and non-homologous chromosomes are not relevant.

Patterns and mechanisms of invasive plant impacts on North American birds: a systematic review

2017 ◽  
Vol 19 (5) ◽  
pp. 1547-1563 ◽  
Author(s):  
Scott B. Nelson ◽  
Jaime J. Coon ◽  
Courtney J. Duchardt ◽  
Jason D. Fischer ◽  
Samniqueka J. Halsey ◽  
...  
Keyword(s):  
Systematic Review ◽  
North American ◽  
Invasive Plant

scholarly journals The Contextual Essentiality of Mitochondrial Genes in Cancer

2021 ◽  
Vol 9 ◽  
Author(s):  
Luke W. Thomas ◽  
Margaret Ashcroft
Keyword(s):  
Cancer Cell ◽  
Mitochondrial Gene ◽  
Nuclear Genome ◽  
Mitochondrial Genes ◽  
Cancer Cell Proliferation ◽  
Oxygen Species ◽  
Eukaryotic Evolution ◽  
Genome Wide ◽  
Gene Level ◽  
Microenvironmental Factors

Mitochondria are key organelles in eukaryotic evolution that perform crucial roles as metabolic and cellular signaling hubs. Mitochondrial function and dysfunction are associated with a range of diseases, including cancer. Mitochondria support cancer cell proliferation through biosynthetic reactions and their role in signaling, and can also promote tumorigenesis via processes such as the production of reactive oxygen species (ROS). The advent of (nuclear) genome-wide CRISPR-Cas9 deletion screens has provided gene-level resolution of the requirement of nuclear-encoded mitochondrial genes (NEMGs) for cancer cell viability (essentiality). More recently, it has become apparent that the essentiality of NEMGs is highly dependent on the cancer cell context. In particular, key tumor microenvironmental factors such as hypoxia, and changes in nutrient (e.g., glucose) availability, significantly influence the essentiality of NEMGs. In this mini-review we will discuss recent advances in our understanding of the contribution of NEMGs to cancer from CRISPR-Cas9 deletion screens, and discuss emerging concepts surrounding the context-dependent nature of mitochondrial gene essentiality.

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