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Disentangling the effects of geographic and ecological isolation on genetic differentiation
Populations can be genetically isolated both by geographic distance and by
differences in their ecology or environment that decrease the rate of
successful migration. Empirical studies often seek to investigate the
relationship between genetic differentiation and some ecological variable(s)
while accounting for geographic distance, but common approaches to this problem
(such as the partial Mantel test) have a number of drawbacks. In this article,
we present a Bayesian method that enables users to quantify the relative
contributions of geographic distance and ecological distance to genetic
differentiation between sampled populations or individuals. We model the allele
frequencies in a set of populations at a set of unlinked loci as spatially
correlated Gaussian processes, in which the covariance structure is a
decreasing function of both geographic and ecological distance. Parameters of
the model are estimated using a Markov chain Monte Carlo algorithm. We call
this method Bayesian Estimation of Differentiation in Alleles by Spatial
Structure and Local Ecology (BEDASSLE), and have implemented it in a
user-friendly format in the statistical platform R. We demonstrate its utility
with a simulation study and empirical applications to human and teosinte
datasets
Optimal sensor placement for classifier-based leak localization in drinking water networks
© 2016 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.This paper presents a sensor placement method for classifier-based leak localization in Water Distribution Networks. The proposed approach consists in applying a Genetic Algorithm to decide the sensors to be used by a classifier (based on the k-Nearest Neighbor approach). The sensors are placed in an optimal way maximizing the accuracy of the leak localization. The results are illustrated by means of the application to the Hanoi District Metered Area and they are compared to the ones obtained by the Exhaustive Search Algorithm. A comparison with the results of a previous optimal sensor placement method is provided as well.Postprint (author's final draft
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Does habitat stability structure intraspecific genetic diversity? It’s complicated...
Regional phylogeographic studies have long been conducted in the southeastern United States for a variety of species. With some exceptions, many of these studies focus on single species or single clades of organisms, and those considering multiple species tend to focus on deep historical breaks causing differentiation. However, in many species more recent factors may be influencing genetic diversity. To understand the roles of historic and contemporary processes in structuring genetic diversity, we reanalyzed existing genetic data from Southeast of North America using approaches gleaned from phylogeographic and landscape genetic literature that were implemented across species including AMOVAs, PCoAs, Species Distribution Modelling, and tests of isolation by distance, environment, and habitat instability. Genetic variance was significantly partitioned by ecoregions, watersheds, and across phylogeographic breaks in the majority of species. Similarly, genetic variation was significantly associated with some combination of geographic or environmental distance or habitat instability in most species. Patterns of genetic variation were largely idiosyncratic across species. While habitat instability over time is significantly correlated with genetic diversity in some species, it appears generally less important than isolation by geographic or environmental distance. Our results suggest that many factors, both historical and contemporary, impact genetic diversity within a species, and more so, that these patterns aren’t always similar in closely related species. This supports the importance of species- specific factors and cautions against assumptions that closely related species will respond to historical and contemporary forces in similar ways
The scale of population structure in Arabidopsis thaliana
The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales
Dispersal and population structure at different spatial scales in the subterranean rodent Ctenomys australis
This study was funded by grants from Consejo Nacional de Investigaciones CientÃficas y Técnicas (CONICET, PIP5838), Agencia de Promoción CientÃfica y Tecnológica de la Argentina (PICTO1-423, BID-1728/OC-AR), and the programme ECOS-Sud France/Argentina (A05B01).Background: The population genetic structure of subterranean rodent species is strongly affected by demographic (e.g. rates of dispersal and social structure) and stochastic factors (e.g. random genetic drift among subpopulations and habitat fragmentation). In particular, gene flow estimates at different spatial scales are essential to understand genetic differentiation among populations of a species living in a highly fragmented landscape. Ctenomys australis (the sand dune tuco-tuco) is a territorial subterranean rodent that inhabits a relatively secure, permanently sealed burrow system, occurring in sand dune habitats on the coastal landscape in the south-east of Buenos Aires province, Argentina. Currently, this habitat is threatened by urban development and forestry and, therefore, the survival of this endemic species is at risk. Here, we assess population genetic structure and patterns of dispersal among individuals of this species at different spatial scales using 8 polymorphic microsatellite loci. Furthermore, we evaluate the relative importance of sex and habitat configuration in modulating the dispersal patterns at these geographical scales. Results: Our results show that dispersal in C. australis is not restricted at regional spatial scales (similar to 4 km). Assignment tests revealed significant population substructure within the study area, providing support for the presence of two subpopulations from three original sampling sites. Finally, male-biased dispersal was found in the Western side of our study area, but in the Eastern side no apparent philopatric pattern was found, suggesting that in a more continuous habitat males might move longer distances than females. Conclusions: Overall, the assignment-based approaches were able to detect population substructure at fine geographical scales. Additionally, the maintenance of a significant genetic structure at regional (similar to 4 km) and small (less than 1 km) spatial scales despite apparently moderate to high levels of gene flow between local sampling sites could not be explained simply by the linear distance among them. On the whole, our results support the hypothesis that males disperse more frequently than females; however they do not provide support for strict philopatry within females.Publisher PDFPeer reviewe
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