Spatial detection of outlier loci with Moran eigenvector maps

2017 ◽  
Vol 17 (6) ◽  
pp. 1122-1135 ◽  
Author(s):  
Helene H. Wagner ◽  
Mariana Chávez-Pesqueira ◽  
Brenna R. Forester
Keyword(s):  
Outlier Loci ◽  
Spatial Detection ◽  
Moran Eigenvector Maps

scholarly journals The BOLD correlates of the visual P1 and N1 in single-trial analysis of simultaneous EEG-fMRI recordings during a spatial detection task

NeuroImage ◽  
2011 ◽  
Vol 54 (2) ◽  
pp. 824-835 ◽  
Author(s):  
N. Novitskiy ◽  
J.R. Ramautar ◽  
K. Vanderperren ◽  
M. De Vos ◽  
M. Mennes ◽  
...  
Keyword(s):  
Detection Task ◽  
Single Trial ◽  
Single Trial Analysis ◽  
Trial Analysis ◽  
Spatial Detection

scholarly journals Using neutral and outlier loci to uncover the genetic structure of 'Mytilus galloprovincialis' populations from the eastern Adriatic coast using population genetic and seascape genetic approaches

2021 ◽  
Author(s):  
◽  
Joanna Szondy Hamilton
Keyword(s):  
Genetic Structure ◽  
Mytilus Galloprovincialis ◽  
Blue Mussel ◽  
Strong Association ◽  
Outlier Locus ◽  
Outlier Loci ◽  
Adriatic Coast ◽  
Low Levels ◽  
Polymorphic Microsatellite ◽  
Highly Correlated

<p>The genetic variation of the Mediterranean blue mussel, Mytilus galloprovincialis from the eastern coastline of the Adriatic Sea was investigated using polymorphic microsatellite markers. In total, 843 individuals were sampled from 18 populations representing a variety of coastal environments in Croatia, Bosnia-Herzegovina, Montenegro and Albania. Neutral loci revealed low levels of genetic structure in this continuously distributed species, while one outlier locus, MGE7, which may be under selection, provided strong evidence of genetic structure. The distribution of one of the alleles of this locus, MGE7²⁴³, was significantly correlated with latitude. A genetic seascape analysis using 9 environmental and 3 geospatial variables revealed a strong association between MGE7²⁴³ and three highly correlated environmental variables, maximum sea surface temperature, minimum salinity and maximum chlorophyll-a. This association was maintained for homozygous genotypes for the MGE7²⁴³ allele, but not for heterozygotes, providing further evidence that the locus MGE7 may be under selection or closely linked to a gene under selection. These findings highlight how previously unrecognised genetic structure can be identified through the use of genetic seascape approaches.</p>

scholarly journals Can We Compare Effect Size of Spatial Genetic Structure Between Studies and Species Using Moran Eigenvector Maps?

2021 ◽  
Vol 9 ◽  
Author(s):  
Celia Hein ◽  
Hossam E. Abdel Moniem ◽  
Helene H. Wagner
Keyword(s):  
Genetic Structure ◽  
Effect Size ◽  
Stationary Process ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Meta Analysis ◽  
Empirical Studies ◽  
Sampling Locations ◽  
Number Of Individuals ◽  
Moran Eigenvector Maps

As the field of landscape genetics is progressing toward comparative empirical studies and meta-analysis, it is important to know how best to compare the strength of spatial genetic structure between studies and species. Moran’s Eigenvector Maps are a promising method that does not make an assumption of isolation-by-distance in a homogeneous environment but can discern cryptic structure that may result from multiple processes operating in heterogeneous landscapes. MEMgene uses spatial filters from Moran’s Eigenvector Maps as predictor variables to explain variation in a genetic distance matrix, and it returns adjusted R2 as a measure of the amount of genetic variation that is spatially structured. However, it is unclear whether, and under which conditions, this value can be used to compare the degree of spatial genetic structure (effect size) between studies. This study addresses the fundamental question of comparability at two levels: between independent studies (meta-analysis mode) and between species sampled at the same locations (comparative mode). We used published datasets containing 9,900 haploid, biallelic, neutral loci simulated on a quasi-continuous, square landscape under four demographic scenarios (island model, isolation-by-distance, expansion from one or two refugia). We varied the genetic resolution (number of individuals and loci) and the number of random sampling locations. We considered two measures of effect size, the MEMgene adjusted R2 and multivariate Moran’s I, which is related to Moran’s Eigenvector Maps. Both metrics were highly sensitive to the number of locations, even when using standardized effect sizes, SES, and the number of individuals sampled per location, but not to the number of loci. In comparative mode, using the same Moran Eigenvector Maps for all species, even those with missing values at some sampling locations, reduced bias due to the number of locations under isolation-by-distance (stationary process) but increased it under expansion from one or two refugia (non-stationary process). More robust measures of effect size need to be developed before the strength of spatial genetic structure can be accurately compared, either in a meta-analysis of independent empirical studies or within a comparative, multispecies landscape genetic study.

scholarly journals Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

2020 ◽  
Author(s):  
Erica Nielsen ◽  
Romina Henriques ◽  
Maria Beger ◽  
Robert Toonen ◽  
Sophie von der Heyden
Keyword(s):  
Global Change ◽  
Outlier Detection ◽  
Genomic Variation ◽  
Sea Surface ◽  
Environmental Drivers ◽  
Comparative Approach ◽  
Evolutionary Potential ◽  
Environmental Selection ◽  
Outlier Loci ◽  
Isolation By Environment

Abstract Background: As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). Results: Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. Conclusion: The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

scholarly journals Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

2020 ◽  
Author(s):  
Erica Nielsen ◽  
Romina Henriques ◽  
Maria Beger ◽  
Robert Toonen ◽  
Sophie von der Heyden
Keyword(s):  
Global Change ◽  
Outlier Detection ◽  
Genomic Variation ◽  
Sea Surface ◽  
Environmental Drivers ◽  
Comparative Approach ◽  
Evolutionary Potential ◽  
Environmental Selection ◽  
Outlier Loci ◽  
Isolation By Environment

Abstract Background: As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare the dominant environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin ( Parechinus angulosus ), Common shore crab ( Cyclograpsus punctatu s), and Granular limpet ( Scutellastra granularis ). Results: Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus . Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus , but not for C. punctatus . Conclusion: The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses better predict evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

Spatial Detection of the Shafts of Fractured Femur for Image-Guided Robotic Surgery*

2021 ◽  
Author(s):  
Marzieh S. Saeedi-Hosseiny ◽  
Fayez Alruwaili ◽  
Akash S. Patel ◽  
Sean McMillan ◽  
Iulian I. Iordachita ◽  
...  
Keyword(s):  
Robotic Surgery ◽  
Image Guided ◽  
Spatial Detection

Genetic population structure and tools for the management of European sprat (Sprattus sprattus)

2020 ◽  
Vol 77 (6) ◽  
pp. 2134-2143
Author(s):  
Niall J McKeown ◽  
Piera Carpi ◽  
Joana F Silva ◽  
Amy J E Healey ◽  
Paul W Shaw ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Population Connectivity ◽  
Ne Atlantic ◽  
Genetic Population ◽  
Sprattus Sprattus ◽  
Population Average ◽  
Outlier Loci ◽  
Baltic Population ◽  
Assisted Management ◽  
Mixed Stock

Abstract This study used RAD-seq-derived SNPs to explore population connectivity, local adaptation, and individual assignment in European sprat (Sprattus sprattus) and inform the alignment of management units with biological processes. FST, clustering, and outlier analyses support a genetically cohesive population spanning the Celtic Sea-English Channel-North Sea-Kattegat (NE Atlantic) region. The lack of structure among the NE Atlantic samples indicates connectivity across current management boundaries. However, the assumption of demographic panmixia is cautioned against unless verified by a multidisciplinary approach. The data confirm high genetic divergence of a Baltic population (average FST vs. NE Atlantic samples = 0.051) with signatures compatible with local adaptation in the form of outlier loci, some of which are shown to occur within exonic regions. The outliers permit diagnostic assignment of individuals between the NE Atlantic and Baltic populations and thus represent a “reduced panel” of markers for monitoring a potential mixed stock fishery within the western Baltic. Overall, this study provides information that may help refine spatial management boundaries of sprat and resources for genetic-assisted management.

scholarly journals Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2504 ◽  
Author(s):  
Katarzyna Bilska ◽  
Monika Szczecińska
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Conservation Genetics ◽  
Ssr Markers ◽  
Full Range ◽  
Mantel Test ◽  
Evolutionary Potential ◽  
Functional Variation ◽  
Genetics Research ◽  
Outlier Loci

BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation inPulsatilla patenspopulations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations ofP. patensand threeP. patenspopulations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific toP. patensand three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He= 0.609,He= 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parametersFSTand ΦPTfor SSR (20%) and ΦPTfor ISJ (21%) markers was similar. Analysis conducted in theStructureprogram divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations ofP. patensfor ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

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