Book ChapterDOI
Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations
Niko Balkenhol,Rachael Y. Dudaniec,Konstantin V. Krutovsky,Jeremy S. Johnson,David M. Cairns,Gernot Segelbacher,Kimberly A. Selkoe,Sophie von der Heyden,Ian J. Wang,Oliver Selmoni,Stéphane Joost +10 more
- pp 261-322
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TLDR
Landscape genomics is a rapidly advancing research field that combines population genomics, landscape ecology, and spatial analytical techniques to explicitly quantify the effects of environmental heterogeneity on neutral and adaptive genetic variation and underlying processes.Abstract:
Landscape genomics is a rapidly advancing research field that combines population genomics, landscape ecology, and spatial analytical techniques to explicitly quantify the effects of environmental heterogeneity on neutral and adaptive genetic variation and underlying processes. Landscape genomics has tremendous potential for addressing fundamental and applied research questions in various research fields, including ecology, evolution, and conservation biology. However, the unique combination of different scientific disciplines and analytical approaches also constitute a challenge to most researchers wishing to apply landscape genomics. Here, we present an introductory overview of important concepts and methods used in current landscape genomics. For this, we first define the field and explain basic concepts and methods to capture different hypotheses of landscape influences on neutral genetic variation. Next, we highlight established and emerging genomic tools for quantifying adaptive genetic variation in landscape genomic studies. To illustrate the covered topics and to demonstrate the potential of landscape genomics, we provide empirical examples addressing a variety of research question, i.e., the investigation of evolutionary processes driving population differentiation, the landscape genomics of range expanding species, and landscape genomic patterns in organisms of special interest, including species inhabiting aquatic and terrestrial environments. We conclude by outlining remaining challenges and future research avenues in landscape genomics.read more
Citations
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Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations : [W633]
Stéphane De Mita,Anne-Céline Thuillet,Nourollah Ahmadi,Stéphanie Manel,Joëlle Ronfort,Yves Vigouroux +5 more
TL;DR: In this article, the authors provide guidelines for the use of popular or recently developed statistical methods to detect footprints of selection, and investigate the power and robustness of eight methods to identify loci potentially under selection.
Journal ArticleDOI
The search for loci under selection: trends, biases and progress
Collin W. Ahrens,Paul D. Rymer,Adam J. Stow,Jason G. Bragg,Shannon Dillon,Kate D. L. Umbers,Rachael Y. Dudaniec +6 more
TL;DR: It is found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection and it is recommended that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure.
Journal ArticleDOI
Editorial: The Least Cost Path From Landscape Genetics to Landscape Genomics: Challenges and Opportunities to Explore NGS Data in a Spatially Explicit Context.
Samuel A. Cushman,Andrew J. Shirk,Glenn T. Howe,Melanie A. Murphy,Rodney J. Dyer,Stéphane Joost +5 more
TL;DR: The Least Cost Path From Landscape Genetics to Landscape Genomics: Challenges and Opportunities to Explore NGS Data in a Spatially Explicit Context and challenges and opportunities to explore NGS data in a spatially explicit context are outlined.
Journal ArticleDOI
Recent advances in conservation and population genomics data analysis
Sarah A. Hendricks,Eric C. Anderson,Eric C. Anderson,Tiago Antao,Louis Bernatchez,Brenna R. Forester,Brittany A. Garner,Brian K. Hand,Paul A. Hohenlohe,Martin Kardos,Ben F. Koop,Arun Sethuraman,Robin S. Waples,Gordon Luikart +13 more
TL;DR: Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents.
References
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Journal ArticleDOI
Inference of population structure using multilocus genotype data
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
Journal ArticleDOI
The value of the world's ecosystem services and natural capital
Robert Costanza,Rudolf de Groot,Stephen Farberk,Monica Grasso,Bruce Hannon,Karin E. Limburg,Shahid Naeem,José M. Paruelo,Robert Raskin,Paul Suttonkk,Marjan van den Belt +10 more
TL;DR: In this paper, the authors have estimated the current economic value of 17 ecosystem services for 16 biomes, based on published studies and a few original calculations, for the entire biosphere, the value (most of which is outside the market) is estimated to be in the range of US$16-54 trillion (10^(12)) per year, with an average of US $33 trillion per year.
Journal ArticleDOI
Local Indicators of Spatial Association—LISA
TL;DR: In this paper, a new general class of local indicators of spatial association (LISA) is proposed, which allow for the decomposition of global indicators, such as Moran's I, into the contribution of each observation.
Journal ArticleDOI
Fast model-based estimation of ancestry in unrelated individuals
TL;DR: The results show that ADMIXTURE's computational speed opens up the possibility of using a much larger set of markers in model-based ancestry estimation and that its estimates are suitable for use in correcting for population stratification in association studies.
Journal ArticleDOI
A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests
Craig D. Allen,Alison K. Macalady,Haroun Chenchouni,Dominique Bachelet,Nate G. McDowell,Michel Vennetier,Thomas Kitzberger,Andreas Rigling,David D. Breshears,Edward H. Hogg,Patrick Gonzalez,Rod Fensham,Zhen Zhang,Jorge Castro,N.A. Demidova,Jong Hwan Lim,Gillian Allard,Steven W. Running,Akkin Semerci,Neil S. Cobb +19 more
TL;DR: In this paper, the authors present the first global assessment of recent tree mortality attributed to drought and heat stress and identify key information gaps and scientific uncertainties that currently hinder our ability to predict tree mortality in response to climate change and emphasizes the need for a globally coordinated observation system.
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