Subtle Allele Frequency Shifts Drive Climate Adaptation in Reef Coral of Northwest Australia

2020 ◽  
Author(s):  
L. Thomas ◽  
J N Underwood ◽  
N H Rose ◽  
Z L Fuller ◽  
Zoe Richards ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Climate Adaptation ◽  
Frequency Shifts ◽  
Northwest Australia

scholarly journals Polygenic adaptation: From sweeps to subtle frequency shifts

2018 ◽  
Author(s):  
Ilse Höllinger ◽  
Pleuni S Pennings ◽  
Joachim Hermisson
Keyword(s):  
Population Genetics ◽  
Allele Frequency ◽  
Mutation Rate ◽  
Quantitative Genetics ◽  
Large Set ◽  
Selective Sweeps ◽  
Genetic Redundancy ◽  
Small Frequency ◽  
Frequency Shifts ◽  
Polygenic Trait

1AbstractEvolutionary theory has produced two conflicting paradigms for the adaptation of a polygenic trait. While population genetics views adaptation as a sequence of selective sweeps at single loci underlying the trait, quantitative genetics posits a collective response, where phenotypic adaptation results from subtle allele frequency shifts at many loci. Yet, a synthesis of these views is largely missing and the population genetic factors that favor each scenario are not well understood. Here, we study the architecture of adaptation of a binary polygenic trait (such as resistance) with negative epistasis among the loci of its basis. The genetic structure of this trait allows for a full range of potential architectures of adaptation, ranging from sweeps to small frequency shifts. By combining computer simulations and a newly devised analytical framework based on Yule branching processes, we gain a detailed understanding of the adaptation dynamics for this trait. Our key analytical result is an expression for the joint distribution of mutant alleles at the end of the adaptive phase. This distribution characterizes the polygenic pattern of adaptation at the underlying genotype when phenotypic adaptation has been accomplished. We find that a single compound parameter, the population-scaled background mutation rate Θbg, explains the main differences among these patterns. For a focal locus, Θbg measures the mutation rate at all redundant loci in its genetic background that offer alternative ways for adaptation. For adaptation starting from mutation-selection-drift balance, we observe different patterns in three parameter regions. Adaptation proceeds by sweeps for small Θbg ≾ 0.1, while small polygenic allele frequency shifts require large Θbg ≿ 100. In the large intermediate regime, we observe a heterogeneous pattern of partial sweeps at several interacting loci.2Author summaryIt is still an open question how complex traits adapt to new selection pressures. While population genetics champions the search for selective sweeps, quantitative genetics proclaims adaptation via small concerted frequency shifts. To date the empirical evidence of clear sweep signals is more scarce than expected, while subtle shifts remain notoriously hard to detect. In the current study we develop a theoretical framework to predict the expected adaptive architecture of a simple polygenic trait, depending on parameters such as mutation rate, effective population size, size of the trait basis, and the available genetic variability at the onset of selection. For a population in mutation-selection-drift balance we find that adaptation proceeds via complete or partial sweeps for a large set of parameter values. We predict adaptation by small frequency shifts for two main cases. First, for traits with a large mutational target size and high levels of genetic redundancy among loci, and second if the starting frequencies of mutant alleles are more homogeneous than expected in mutation-selection-drift equilibrium, e.g. due to population structure or balancing selection.

scholarly journals Climate adaptation shaped by subtle to moderate allele frequency shifts in loblolly pine

2019 ◽  
Author(s):  
Amanda R. De La Torre ◽  
David B Neale
Keyword(s):  
Allele Frequency ◽  
Local Adaptation ◽  
Loblolly Pine ◽  
Climate Adaptation ◽  
Geographic Location ◽  
Woody Species ◽  
Climatic Variables ◽  
Whole Genome ◽  
Temperature And Precipitation ◽  
Genomic Regions

ABSTRACTUnderstanding the genomic basis of local adaptation is crucial to determine the potential of long-lived woody species to withstand changes in their natural environment. In the past, efforts to dissect the genomic architecture in gymnosperms species have been limited due to the absence of reference genomes. Recently, the genomes of some commercially important conifers, such as loblolly pine, have become available, allowing whole-genome studies of these species. In this study, we test for associations between 87k SNPs, obtained from whole-genome re-sequencing of loblolly pine individuals, and 270 environmental variables and combinations of them. We determine the geographic location of significant alleles and identify their genomic location using our newly constructed ultra-dense 26k SNP linkage map. We found that water availability is the main climatic variable shaping local adaptation of the species, and found 492 SNPs showing significant associations with climatic variables or combinations of them. Our results suggest that adaptation to climate in the species might have occurred by many changes in the allele frequency of alleles with moderate to small effect sizes, and by the smaller contribution of large effect alleles in genes related to moisture deficit, temperature and precipitation. Genomic regions of low recombination and high population differentiation harbored SNPs associated with principal components but not with individual climatic variables, suggesting climate adaptation might have evolved as a result of different selection pressures acting on groups of genes associated with an aspect of climate rather than on individual climatic variables.

scholarly journals Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes

2015 ◽  
Vol 7 (12) ◽  
pp. 3269-3285 ◽  
Author(s):  
Benjamin Hornoy ◽  
Nathalie Pavy ◽  
Sébastien Gérardi ◽  
Jean Beaulieu ◽  
Jean Bousquet
Keyword(s):  
Allele Frequency ◽  
White Spruce ◽  
Genetic Adaptation ◽  
Frequency Shifts ◽  
Functionally Diverse

scholarly journals Demographic Genetics of Brown Trout (Salmo trutta) and Estimation of Effective Population Size From Temporal Change of Allele Frequencies

Genetics ◽  
1996 ◽  
Vol 143 (3) ◽  
pp. 1369-1381 ◽  
Author(s):  
Per Erik Jorde ◽  
Nils Ryman
Keyword(s):  
Allele Frequency ◽  
Brown Trout ◽  
Salmo Trutta ◽  
Natural Populations ◽  
Effective Size ◽  
Effective Population ◽  
Frequency Shifts ◽  
Brown Trout Salmo Trutta ◽  
Population Sizes ◽  
Allozyme Loci

Abstract We studied temporal allele frequency shifts over 15 years and estimated the genetically effective size of four natural populations of brown trout (Salmo trutta L.) on the basis of the variation at 14 polymorphic allozyme loci. The allele frequency differences between consecutive cohorts were significant in all four populations. There were no indications of natural selection, and we conclude that random genetic drift is the most likely cause of temporal allele frequency shifts at the loci examined. Effective population sizes were estimated from observed allele frequency shifts among cohorts, taking into consideration the demographic characteristics of each population. The estimated effective sizes of the four populations range from 52 to 480 individuals, and we conclude that the effective size of natural brown trout populations may differ considerably among lakes that are similar in size and other apparent characteristics. In spite of their different effective sizes all four populations have similar levels of genetic variation (average heterozygosity) indicating that excessive loss of genetic variability has been retarded, most likely because of gene flow among neighboring populations.

scholarly journals Detection of human adaptation during the past 2,000 years

2016 ◽  
Author(s):  
Yair Field ◽  
Evan A Boyle ◽  
Natalie Telis ◽  
Ziyue Gao ◽  
Kyle J. Gaulton ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Complex Traits ◽  
Frequency Shifts ◽  
The Past ◽  
Polygenic Adaptation ◽  
Selection For ◽  
Frequency Changes ◽  
Long Timescales ◽  
Blue Eyes ◽  
New Evidence

AbstractDetection of recent natural selection is a challenging problem in population genetics, as standard methods generally integrate over long timescales. Here we introduce the Singleton Density Score (SDS), a powerful measure to infer very recent changes in allele frequencies from contemporary genome sequences. When applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past 2,000 years. We see strong signals of selection at lactase and HLA, and in favor of blond hair and blue eyes. Turning to signals of polygenic adaptation we find, remarkably, that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we report suggestive new evidence for polygenic shifts affecting many other complex traits. Our results suggest that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.

scholarly journals Temporal allele frequency change and estimation of effective size in populations with overlapping generations.

Genetics ◽  
1995 ◽  
Vol 139 (2) ◽  
pp. 1077-1090 ◽  
Author(s):  
P E Jorde ◽  
N Ryman
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Overlapping Generations ◽  
Temporal Frequency ◽  
Effective Size ◽  
Frequency Change ◽  
Effective Population ◽  
Frequency Shifts ◽  
Frequency Changes

Abstract In this paper we study the process of allele frequency change in finite populations with overlapping generations with the purpose of evaluating the possibility of estimating the effective size from observations of temporal frequency shifts of selectively neutral alleles. Focusing on allele frequency changes between successive cohorts (individuals born in particular years), we show that such changes are not determined by the effective population size alone, as they are when generations are discrete. Rather, in populations with overlapping generations, the amount of temporal allele frequency change is dependent on the age-specific survival and birth rates. Taking this phenomenon into account, we present an estimator for effective size that can be applied to populations with overlapping generations.

The Methow Beaver Project: the Challenges of an Ecosystem Services Experiment

2019 ◽  
Vol 3 (1) ◽  
pp. 1-14
Author(s):  
Philip Brick ◽  
Kent Woodruff
Keyword(s):  
Ecosystem Services ◽  
Climate Adaptation ◽  
Castor Canadensis ◽  
Water Storage ◽  
Climate Projections ◽  
High Mountain ◽  
Natural Resource Policy ◽  
Watershed Scale ◽  
Positive Role ◽  
Climate Conditions

This case explores the Methow Beaver Project (MBP), an ambitious experiment to restore beaver (Castor canadensis) to a high mountain watershed in Washington State, USA. The Pacific Northwest is already experiencing weather regimes consistent with longer term climate projections, which predict longer and drier summers and stronger and wetter winter storms. Ironically, this combination makes imperative more water storage in one of the most heavily dammed regions in the nation. Although the positive role that beaver can play in watershed enhancement has been well known for decades, no project has previously attempted to re-introduce beaver on a watershed scale with a rigorous monitoring protocol designed to document improved water storage and temperature conditions needed for human uses and aquatic species. While the MBP has demonstrated that beaver can be re-introduced on a watershed scale, it has been much more difficult to scientifically demonstrate positive changes in water retention and stream temperature, given hydrologic complexity, unprecedented fire and floods, and the fact that beaver are highly mobile. This case study can help environmental studies students and natural resource policy professionals think about the broader challenges of diffuse, ecosystem services approaches to climate adaptation. Beaver-produced watershed improvements will remain difficult to quantify and verify, and thus will likely remain less attractive to water planners than conventional storage dams. But as climate conditions put additional pressure on such infrastructure, it is worth considering how beaver might be employed to augment watershed storage capacity, even if this capacity is likely to remain at least in part inscrutable.

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