scholarly journals An island‐hopping bird reveals how founder events shape genome‐wide divergence

2021 ◽  
Author(s):  
Ashley T. Sendell‐Price ◽  
Kristen C. Ruegg ◽  
Bruce C. Robertson ◽  
Sonya M. Clegg
Keyword(s):  
Genome Wide ◽  
Founder Events

scholarly journals Quantitative Genetics of the Maize Leaf Microbiome

2018 ◽  
Vol 2 (4) ◽  
pp. 208-224 ◽  
Author(s):  
Jason G. Wallace ◽  
Karl A. Kremling ◽  
Lynsey L. Kovar ◽  
Edward S. Buckler
Keyword(s):  
Community Diversity ◽  
Exact Nature ◽  
Multiple Traits ◽  
Exact Test ◽  
Maize Leaf ◽  
Microbiome Composition ◽  
Metabolic Functions ◽  
Genome Wide ◽  
Founder Events ◽  
Diversity Metrics

The degree to which the genotype of an organism can affect the composition of its associated microbial communities (“microbiome”) varies by organism and habitat, and in many cases is unknown. We analyzed the metabolically active bacteria of maize leaves across 300 diverse maize lines growing in a common environment. We performed comprehensive heritability analysis for 49 community diversity metrics, 380 bacterial clades, and 9,042 predicted metagenomic functions. We find that only a few bacterial clades (5) and diversity metrics (2) are significantly heritable, while a much larger number of metabolic functions (200) are. Many of these associations appear to be driven by the Methylobacteria in each sample. Among these heritable metabolic traits, Fisher’s exact test identifies significant overrepresentation of traits relating to short-chain carbon metabolism, secretion, and nitrotoluene degradation. Genome-wide association analysis identified a small number of associated loci for these heritable traits, including two that affect multiple traits. Our results indicate that while most of the maize leaf microbiome composition is driven by environmental factors and/or stochastic founder events, a subset of bacterial taxa and metabolic functions is nonetheless significantly impacted by host genetics. Additional work will be needed to identify the exact nature of these interactions and what effects they may have on their host. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

scholarly journals The promise of disease gene discovery in South Asia

2016 ◽  
Author(s):  
Nathan Nakatsuka ◽  
Priya Moorjani ◽  
Niraj Rai ◽  
Biswanath Sarkar ◽  
Arti Tandon ◽  
...  
Keyword(s):  
South Asia ◽  
Disease Burden ◽  
South Asians ◽  
Large Population ◽  
Disease Genes ◽  
Ashkenazi Jews ◽  
Disease Gene Discovery ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Founder Events

The more than 1.5 billion people who live in South Asia are correctly viewed not as a single large population, but as many small endogamous groups. We assembled genome-wide data from over 2,800 individuals from over 260 distinct South Asian groups. We identify 81 unique groups, of which 14 have estimated census sizes of more than a million, that descend from founder events more extreme than those in Ashkenazi Jews and Finns, both of which have high rates of recessive disease due to founder events. We identify multiple examples of recessive diseases in South Asia that are the result of such founder events. This study highlights an under-appreciated opportunity for reducing disease burden among South Asians through the discovery of and testing for recessive disease genes.

scholarly journals Quantitative Genetic Analysis of the Maize Leaf Microbiome

2018 ◽  
Author(s):  
Jason G. Wallace ◽  
Karl A. Kremling ◽  
Edward S. Buckler
Keyword(s):  
Community Diversity ◽  
Exact Nature ◽  
Common Environment ◽  
Operational Taxonomic Units ◽  
Metabolic Functions ◽  
Genome Wide ◽  
Significant Enrichment ◽  
Heritability Analysis ◽  
Founder Events ◽  
Diversity Metrics

AbstractThe degree to which an organism can affect its associated microbial communities (“microbiome”) varies by organism and habitat, and in many cases is unknown. We address this question by analyzing the metabolically active bacteria of the maize phyllosphere across 300 diverse maize lines growing in a common environment. We performed comprehensive heritability analysis for 49 community diversity metrics, 380 bacterial clades (individual operational taxonomic units and higher-level groupings), and 9042 predicted metagenomic functions. We find that only a few few bacterial clades (5) and diversity metrics (2) are significantly heritable, while a much larger number of metabolic functions (200) are. Many of these associations appear to be driven by the amount of Methylobacteria present in each sample, and we find significant enrichment for traits relating to short-chain carbon metabolism, secretion, and nitrotoluene degradation. Genome-wide association analysis identifies a small number of associated loci for these heritable traits, including two loci (on maize chromosomes 7 and 10) that affect a large number of traits even after correcting for correlations among traits. This work is among the most comprehensive analyses of the maize phyllosphere to date. Our results indicate that while most of the maize phyllosphere composition is driven by environmental factors and/or stochastic founder events, a subset of bacterial taxa and metabolic functions is nonetheless significantly impacted by host plant genetics. Additional work will be needed to identify the exact nature of these interactions and what effects they may have on the phenotype of host plants.

scholarly journals Runs of homozygosity in killer whale genomes provide a global record of demographic histories

2020 ◽  
Author(s):  
Rebecca Hooper ◽  
Laurent Excoffier ◽  
Karin A. Forney ◽  
M. Thomas P. Gilbert ◽  
Michael D. Martin ◽  
...  
Keyword(s):  
Native American ◽  
Killer Whale ◽  
Demographic History ◽  
Runs Of Homozygosity ◽  
High Background ◽  
Inbreeding Coefficients ◽  
Genome Wide ◽  
Founder Events ◽  
Extreme Outlier

SUMMARYRuns of homozygosity (ROH) occur when offspring receive the same ancestral haplotype from both parents, and, accordingly, reduce individual heterozygosity. Their distribution throughout the genome contains information on the probability of inbreeding mediated by mating system and population demography. Here, we investigate variation in killer whale demographic history as reflected in genome-wide heterozygosity, using a global dataset of 26 genomes. We find an overall pattern of lower heterozygosity in genomes sampled at high latitudes, with hundreds of short ROH (< 1Mbp) reflecting high background relatedness due to coalescence of haplotypes during bottlenecks associated with founder events during post-glacial range expansions. Across most of the species’ range, intermediate length ROH (1-10Mb) revealed long-term inbreeding in 22 of the 26 sampled killer whale genomes, consistent with the high social philopatry observed in all populations studied to date. Inbreeding coefficients (FROH) were comparable to those reported in other taxa with long-term low population size, such as bonobos and the Native American Karitiana of the Brazilian Amazon. The extreme outlier in this dataset, a Scottish killer whale, was homozygous over one-third of the autosomes (41.6%) with a distinct distribution of ROH length, indicating generations of inbreeding. This exceeds autozygosity in emblematic examples of long-term inbreeding, such as the Altai Neanderthal, and eastern lowland and mountain gorillas. The fate of this Scottish killer whale population, in which no calves have been born in over two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.

scholarly journals Geographically structured genetic variation in the Medicago lupulina – Ensifer mutualism

2017 ◽  
Author(s):  
Tia L. Harrison ◽  
Corlett W. Wood ◽  
Katy D. Heath ◽  
John R. Stinchcombe
Keyword(s):  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Interspecific Interactions ◽  
Genomic Structure ◽  
Interacting Species ◽  
Medicago Lupulina ◽  
Genome Wide ◽  
Introduced Range ◽  
Rhizobial Species ◽  
Founder Events

AbstractMutualisms are interspecific interactions affecting the ecology and evolution of species. Patterns of geographic variation in interacting species may play an important role in understanding how variation is maintained in mutualisms, particularly in introduced ranges. One agriculturally and ecologically important mutualism is the partnership between legume plants and rhizobia. Through characterizing and comparing the population genomic structure of the legume Medicago lupulina and two rhizobial species (Ensifer medicae and E. meliloti), we explored the spatial scale of population differentiation between interacting partners in their introduced range in North America. We found high proportions of E. meliloti in southeastern populations and high proportions of E. medicae in northwestern populations. Medicago lupulina and the Ensifer genus showed similar patterns of spatial genetic structure (isolation by distance). However, we detected no evidence of isolation by distance or population structure within either species of bacteria. Genome-wide nucleotide diversity within each of the two Ensifer species was low, suggesting limited introduction of strains, founder events, or severe bottlenecks. Our results suggest that there is potential for geographically structured coevolution between M. lupulina and the Ensifer genus, but not between M. lupulina and either Ensifer species.

Genome-wide screen in yeast to identify modulators of mutant SOD1 toxicity

2008 ◽  
Vol 35 (S 01) ◽  
Author(s):  
D Ubmann ◽  
B Göricke ◽  
L Fichtner ◽  
I Panou ◽  
G.H Braus ◽  
...  
Keyword(s):  
Mutant Sod1 ◽  
Genome Wide
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