The details are in the genome-wide SNPs: fine scale evolution of the Malaysian weedy rice

Plant Science ◽  
2021 ◽  
pp. 110985
Author(s):  
Maggie Pui San Sudo ◽  
Rupini Yesudasan ◽  
Ting Xiang Neik ◽  
Dilipkumar Masilamany ◽  
Jayasyaliny Jayaraj ◽  
...  
Keyword(s):  
Weedy Rice ◽  
Fine Scale ◽  
Genome Wide ◽  
Scale Evolution

Fine-scale mapping in Neurospora crassa by using genome-wide knockout strains

Mycologia ◽  
2012 ◽  
Vol 104 (1) ◽  
pp. 321-323 ◽  
Author(s):  
Thomas M. Hammond ◽  
David G. Rehard ◽  
Bryant C. Harris ◽  
Patrick K.T. Shiu
Keyword(s):  
Neurospora Crassa ◽  
Fine Scale ◽  
Genome Wide ◽  
Fine Scale Mapping

scholarly journals Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

2010 ◽  
Vol 4 (7) ◽  
pp. 882-895 ◽  
Author(s):  
Arantxa Peña ◽  
Hanno Teeling ◽  
Jaime Huerta-Cepas ◽  
Fernando Santos ◽  
Pablo Yarza ◽  
...  
Keyword(s):  
Fine Scale ◽  
Ecological Differentiation ◽  
Scale Evolution

scholarly journals The genetic scenario of Mercheros: an under-represented group within the Iberian Peninsula

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
André Flores-Bello ◽  
Neus Font-Porterias ◽  
Julen Aizpurua-Iraola ◽  
Sara Duarri-Redondo ◽  
David Comas
Keyword(s):  
Iberian Peninsula ◽  
Demographic History ◽  
Ethnically Diverse ◽  
Human Populations ◽  
Minority Ethnic Group ◽  
Fine Scale ◽  
Genome Wide ◽  
Wide Range ◽  
Y Chromosome Str ◽  
Western Eurasia

Abstract Background The general picture of human genetic variation has been vastly depicted in the last years, yet many populations remain broadly understudied. In this work, we analyze for the first time the Merchero population, a Spanish minority ethnic group that has been scarcely studied and historically persecuted. Mercheros have been roughly characterised by an itinerant history, common traditional occupations, and the usage of their own language. Results Here, we examine the demographic history and genetic scenario of Mercheros, by using genome-wide array data, whole mitochondrial sequences, and Y chromosome STR markers from 25 individuals. These samples have been complemented with a wide-range of present-day populations from Western Eurasia and North Africa. Our results show that the genetic diversity of Mercheros is explained within the context of the Iberian Peninsula, evidencing a modest signal of Roma admixture. In addition, Mercheros present low genetic isolation and intrapopulation heterogeneity. Conclusions This study represents the first genetic characterisation of the Merchero population, depicting their fine-scale ancestry components and genetic scenario within the Iberian Peninsula. Since ethnicity is not only influenced by genetic ancestry but also cultural factors, other studies from multiple disciplines are needed to further explore the Merchero population. As with Mercheros, there is a considerable gap of underrepresented populations and ethnic groups in publicly available genetic data. Thus, we encourage the consideration of more ethnically diverse population panels in human genetic studies, as an attempt to improve the representation of human populations and better reconstruct their fine-scale history.

scholarly journals Broad-scale puma connectivity could restore genomic diversity to fine-scale coastal populations

2021 ◽  
Author(s):  
Kyle D Gustafson ◽  
Roderick B Gagne ◽  
Michael R Buchalski ◽  
T Winston Vickers ◽  
Seth PD Riley ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Puma Concolor ◽  
Genomic Diversity ◽  
Strong Linkage Disequilibrium ◽  
Fine Scale ◽  
High Genetic Diversity ◽  
Population Genomic ◽  
Genome Wide ◽  
Genetic Clusters

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 broadly sampled pumas. Our analyses indicated support for 4–10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the 4 genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating pumas have retained statewide genomic diversity. However, multiple lines of evidence indicated substructure, including 10 fine-scale genetic clusters, some of which exhibited allelic fixation and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at-risk populations are typically nested within a broader-scale group of interconnected populations that collectively retains high genetic diversity and heterogeneous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our broad- and fine-scale population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for fragmented population conservation management.

scholarly journals Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

2017 ◽  
Author(s):  
Meghann D Durante ◽  
Iliana B Baums
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Ex Situ ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Acropora Palmata ◽  
Single Nucleotide ◽  
Major Barrier ◽  
Genome Wide ◽  
Scale Population

The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, reveal fine-scale population structure and place the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 12 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 12 candidate loci under positive selection. Together, these results suggest that restoration of populations should use local sources and utilize existing functional variation among populations in ex situ crossing experiments to improve stress resistance of this species.

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