scholarly journals The WZA: A window-based method for characterizing genotype-environment association

2021 ◽  
Author(s):  
Tom R Booker ◽  
Sam Yeaman ◽  
Michael Whitlock
Keyword(s):  
Population Structure ◽  
Local Adaptation ◽  
Selection Pressure ◽  
Genetic Basis ◽  
Natural Populations ◽  
Original Study ◽  
Published Data ◽  
Heterogeneous Environments ◽  
Candidate Loci ◽  
Number Of Individuals

Genotype environment association (GEA) studies have the potential to elucidate the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the weighted-Z analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST. We analyze simulations modelling local adaptation to heterogeneous environments either using a GEA method that controls for population structure or an uncorrected approach. In the majority of cases we tested, the WZA either outperformed single-SNP based approaches or performed similarly. The WZA outperformed individual SNP approaches when the measured environment is not perfectly correlated with the true selection pressure or when a small number of individuals or demes was sampled. We apply the WZA to previously published data from lodgepole pine identified candidate loci that were not found in the original study.

scholarly journals The WZA: A window-based method for characterizing genotype-environment association

2021 ◽  
Author(s):  
Tom Booker ◽  
Sam Yeaman ◽  
Michael Whitlock
Keyword(s):  
Population Structure ◽  
Local Adaptation ◽  
Selection Pressure ◽  
Genetic Basis ◽  
Natural Populations ◽  
Original Study ◽  
Published Data ◽  
Heterogeneous Environments ◽  
Candidate Loci ◽  
Number Of Individuals

Genotype environment association (GEA) studies have the potential to elucidate the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the weighted-Z analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST. We analyze simulations modelling local adaptation to heterogeneous environments either using a GEA method that controls for population structure or an uncorrected approach. In the majority of cases we tested, the WZA either outperformed single-SNP based approaches or performed similarly. The WZA outperformed individual SNP approaches when the measured environment is not perfectly correlated with the true selection pressure or when a small number of individuals or demes was sampled. We apply the WZA to previously published data from lodgepole pine and identified candidate loci that were not found in the original study.

scholarly journals In the presence of population structure: From genomics to candidate genes underlying local adaptation

2019 ◽  
Author(s):  
Nicholas Price ◽  
Lua Lopez ◽  
Adrian E. Platts ◽  
Jesse R. Lasky ◽  
John K. McKay
Keyword(s):  
Population Structure ◽  
Flowering Time ◽  
Local Adaptation ◽  
Evolutionary Biology ◽  
Indirect Evidence ◽  
Mixed Linear Model ◽  
Functional Constraint ◽  
Heterogeneous Environments ◽  
Functional Sites ◽  
And Function

AbstractUnderstanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. Mixed linear mrsodels that identify allele associations to environment, while controlling for genome-wide variation at other loci, have emerged as the method of choice when studying local adaptation. Despite their importance, it is unclear whether this approach performs better than identifying environmentally-associated SNPs without accounting for population structure. To examine this, we first use the mixed linear model GEMMA, and simple Spearman correlations, to identify SNPs showing significant associations to climate with and without accounting for population structure. Subsequently, using Italy and Sweden populations, we compare evidence of allele frequency differentiation (FST), linkage disequilibrium (LD), fitness variation, and functional constraint, underlying these SNPs. Using a lenient cut-off for significance, we find that SNPs identified by both approaches, and SNPs uniquely identified by Spearman correlations, were enriched at sites showing genomic evidence of local adaptation and function but were limited across Quantitative Trait Loci (QTL) explaining fitness variation. SNPs uniquely identified by GEMMA, showed no direct or indirect evidence of local adaptation, and no enrichment along putative functional sites. Finally, SNPs that showed significantly high FST and LD, were enriched along fitness QTL peaks and cis-regulatory/nonsynonymous sites showing significant functional constraint. Using these SNPs, we identify genes underlying fitness QTL, and genes linking flowering time to local adaptation. These include a regulator of abscisic-acid (FLDH) and flowering time genes PIF3, FIO1, and COL5.

scholarly journals Intercontinental karyotype–environment parallelism supports a role for a chromosomal inversion in local adaptation in a seaweed fly

2018 ◽  
Vol 285 (1881) ◽  
pp. 20180519 ◽  
Author(s):  
Claire Mérot ◽  
Emma L. Berdan ◽  
Charles Babin ◽  
Eric Normandeau ◽  
Maren Wellenreuther ◽  
...  
Keyword(s):  
North America ◽  
Local Adaptation ◽  
Environmental Gradients ◽  
Balancing Selection ◽  
Chromosomal Rearrangements ◽  
Natural Populations ◽  
Inversion Polymorphism ◽  
Life History Strategies ◽  
Heterogeneous Environments ◽  
Adult Size

Large chromosomal rearrangements are thought to facilitate adaptation to heterogeneous environments by limiting genomic recombination. Indeed, inversions have been implicated in adaptation along environmental clines and in ecotype specialization. Here, we combine classical ecological studies and population genetics to investigate an inversion polymorphism previously documented in Europe among natural populations of the seaweed fly Coelopa frigida along a latitudinal cline in North America. We test if the inversion is present in North America and polymorphic, assess which environmental conditions modulate the inversion karyotype frequencies, and document the relationship between inversion karyotype and adult size. We sampled nearly 2000 flies from 20 populations along several environmental gradients to quantify associations of inversion frequencies to heterogeneous environmental variables. Genotyping and phenotyping showed a widespread and conserved inversion polymorphism between Europe and America. Variation in inversion frequency was significantly associated with environmental factors, with parallel patterns between continents, indicating that the inversion may play a role in local adaptation. The three karyotypes of the inversion are differently favoured across micro-habitats and represent life-history strategies likely to be maintained by the collective action of several mechanisms of balancing selection. Our study adds to the mounting evidence that inversions are facilitators of adaptation and enhance within-species diversity.

scholarly journals Should I stay or should I go? The Ectodysplasin locus is associated with behavioural differences in threespine stickleback

2009 ◽  
Vol 5 (6) ◽  
pp. 788-791 ◽  
Author(s):  
Rowan D. H. Barrett ◽  
Tim H. Vines ◽  
Jason S. Bystriansky ◽  
Patricia M. Schulte
Keyword(s):  
Positive Selection ◽  
Local Adaptation ◽  
Morphological Traits ◽  
Genetic Basis ◽  
Natural Populations ◽  
Threespine Stickleback ◽  
Adaptive Divergence ◽  
Freshwater Habitats ◽  
Repeated Evolution ◽  
Freshwater Environments

Adaptive divergence may be facilitated if morphological and behavioural traits associated with local adaptation share the same genetic basis. It is therefore important to determine whether genes underlying adaptive morphological traits are associated with variation in behaviour in natural populations. Positive selection on low-armour alleles at the Ectodysplasin ( Eda ) locus in threespine stickleback has led to the repeated evolution of reduced armour, following freshwater colonization by fully armoured marine sticklebacks. This adaptive divergence in armour between marine and freshwater populations would be facilitated if the low allele conferred a behavioural preference for freshwater environments. We experimentally tested whether the low allele is associated with preference for freshwater by measuring the preference of each Eda genotype for freshwater versus saltwater after acclimation to either salinity. We found no association between the Eda low allele and preference for freshwater. Instead, the low allele was significantly associated with a reduced preference for the acclimation environment. This behaviour may facilitate the colonization of freshwater habitats from the sea, but could also hinder local adaptation by promoting migration of low alleles between marine and freshwater environments.

scholarly journals Indicator role of the ontogenetic structure of rare plant cenotic populations in the assessment of the ecological state of species under anthropogenic pressure (for example, Rindera tetraspis Pall)

2020 ◽  
Vol 222 ◽  
pp. 05003
Author(s):  
Valentina Ilyina ◽  
Anna Mitroshenkova
Keyword(s):  
Population Structure ◽  
Natural Populations ◽  
Rare Plant ◽  
Anthropogenic Pressure ◽  
Ecological State ◽  
Middle Volga Basin ◽  
Ontogenetic Structure ◽  
Dynamics Of Population ◽  
Express Methods ◽  
Number Of Individuals

The study of population structure, including ratios in different ontogenetic groups of individuals, provides unique information for the development of express methods of determining the ecological state of natural complexes. Data on population structure, dynamics of population indicators and other bioecological features allow to determine more precisely the need for protection of different species at regional and more global levels. The purpose of this research is to determine the ontogenetic structure of natural populations of rare plant species. The example of Rindera tetraspis Pall. was used to establish changes in ontogenetic structure of local populations under anthropogenic pressure on species’ habitats (on the territory of the Middle Volga basin, Russia). A decrease in the ability to self-sustain the number of individuals and aging of the population at cattle grazing and steppe fires have been revealed.

scholarly journals Karyotype-environment associations support a role for a chromosomal inversion in local adaptation in the seaweed fly Coelopa frigida

2018 ◽  
Author(s):  
Claire Mérot ◽  
Emma Berdan ◽  
Charles Babin ◽  
Eric Normandeau ◽  
Maren Wellenreuther ◽  
...  
Keyword(s):  
North America ◽  
Local Adaptation ◽  
Environmental Gradients ◽  
Balancing Selection ◽  
Natural Populations ◽  
Inversion Polymorphism ◽  
Life History Strategies ◽  
Heterogeneous Environments ◽  
Adult Size ◽  
Coelopa Frigida

AbstractLarge chromosomal rearrangements are thought to facilitate adaptation to heterogeneous environments by limiting genomic recombination. Indeed, inversions have been implicated in adaptation along environmental clines and in ecotype specialisation. Here, we combine classical ecological studies and population genetics to investigate an inversion polymorphism previously documented in Europe among natural populations of the seaweed fly Coelopa frigida along a latitudinal cline in North America. We test if the inversion is present in North America and polymorphic, assess which environmental conditions modulate the inversion karyotype frequencies, and document the relationship between inversion karyotype and adult size. We sampled nearly 2,000 flies from 20 populations along several environmental gradients to quantify associations of inversion frequencies to heterogeneous environmental variables. Genotyping and phenotyping showed a widespread and conserved inversion polymorphism between Europe and America. Variation in inversion frequency was significantly associated with environmental factors, with parallel patterns between continents, indicating that the inversion may play a role in local adaptation. The three karyotypes of the inversion are differently favoured across micro-habitats and represent life-history strategies likely maintained by the collective action of several mechanisms of balancing selection. Our study adds to the mounting evidence that inversions are facilitators of adaptation and enhance within-species diversity.

Update on the Boundaries of the Curly Birch Range

2020 ◽  
pp. 9-21
Author(s):  
L.V. Vetchinnikova ◽  
◽  
A.F. Titov ◽  
◽  
Keyword(s):  
Population Size ◽  
Natural Populations ◽  
Forest Tree ◽  
Published Data ◽  
Population Approach ◽  
Key Factors ◽  
History Of ◽  
Individual Trees ◽  
Karelian Birch

The article reports on the application of the best known principles for mapping natural populations of curly (Karelian) birch Betula pendula Roth var. carelica (Mercklin) Hämet-Ahti – one of the most appealing representatives of the forest tree flora. Relying on the synthesis and analysis of the published data amassed over nearly 100 years and the data from own full-scale studies done in the past few decades almost throughout the area where curly birch has grown naturally, it is concluded that its range outlined in the middle of the 20th century and since then hardly revised is outdated. The key factors and reasons necessitating its revision are specified. Herewith it is suggested that the range is delineated using the population approach, and the key element will be the critical population size below which the population is no longer viable in the long term. This approach implies that the boundaries of the taxon range depend on the boundaries of local populations (rather than the locations of individual trees or small clumps of trees), the size of which should not be lower than the critical value, which is supposed to be around 100–500 trees for curly birch. A schematic map of the curly birch range delineated using this approach is provided. We specially address the problem of determining the minimum population size to secure genetic diversity maintenance. The advantages of the population approach to delineating the distribution range of curly birch with regard to its biological features are highlighted. The authors argue that it enables a more accurate delineation of the range; shows the natural evolutionary history of the taxon (although it is not yet officially recognized as a species) and its range; can be relatively easily updated (e.g. depending on the scope of reintroduction); should be taken into account when working on the strategy of conservation and other actions designed to maintain and regenerate this unique representative of the forest tree flora.

scholarly journals Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa

2021 ◽  
Vol 22 (7) ◽  
pp. 3477
Author(s):  
Julia Zaborowska ◽  
Bartosz Łabiszak ◽  
Annika Perry ◽  
Stephen Cavers ◽  
Witold Wachowiak
Keyword(s):  
Population Structure ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Redox Homeostasis ◽  
Snp Markers ◽  
Regulation Of Transcription ◽  
Single Nucleotide ◽  
Homeostasis Regulation ◽  
Genomic Regions ◽  
Mountain Plants

Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.

scholarly journals POPULATION STRUCTURE AND PRODUCTION OF COPAIBA OLEORESIN BETWEEN VALLEYS AND HILLSIDES OF THE MINING AREA OFTROMBETAS RIVER - PARÁ1

2016 ◽  
Vol 40 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Jonas Gebara ◽  
Antenor Pereira Barbosa ◽  
Isabel Maria Gonçalves Azevedo ◽  
Bruno Oliva Gimenez
Keyword(s):  
Population Structure ◽  
Forest Inventory ◽  
Sustainable Management ◽  
Natural Populations ◽  
Mining Area ◽  
National Forest ◽  
The South ◽  
Potential Production ◽  
Average Value ◽  
Bauxite Ore

ABSTRACT We aimed in this work to study natural populations of copaiba (Copaifera multijuga Hayne) on the Monte Branco mountain at Porto Trombetas-PA, in order to support sustainable management and the exploitation of oleoresin from copaiba. We studied the population structure of copaiba on hillsides and valleys of the south face of Monte Branco, within Saracá Taquera National Forest, where bauxite ore was extracted in the biennium 2013-2014 by Mineração Rio do Norte (MRN). We produced a 100% forest inventory of the specie and of oleoresin extraction in order to quantify the potential production of the remaining area. The density of copaiba individuals with DBH > 30 cm was 0.33 individuals per hectare in the hillside and 0.25 individuals per hectare in the valley. Both environments presented a density of 0.28 individuals per hectare. The average copaiba oleoresin yield was 0.661±0.334 liters in the hillside and 0.765±0.280 liters in the valley. The average value of both environments together (hillside and valley) was 0.714±0.218 liters. From all individuals with DBH over 30 cm, 38 (58%) produced some amount of oleoresin, averaging 1.113±0.562 liters in the hillside, 1.329±0.448 liters in the valley and 1.190±0.355 liters in both environments together. The results show the need for planning the use of the surroundings of the study area in order to reach the required volume of copaiba to make feasible the sustainable management of oleoresin extraction in the region.

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