scholarly journals The probability of genetic parallelism and convergence in natural populations

2012 ◽  
Vol 279 (1749) ◽  
pp. 5039-5047 ◽  
Author(s):  
Gina L. Conte ◽  
Matthew E. Arnegard ◽  
Catherine L. Peichel ◽  
Dolph Schluter
Keyword(s):  
Adaptive Evolution ◽  
Natural Populations ◽  
Small Subset ◽  
Phenotypic Traits ◽  
Phenotypic Evolution ◽  
Genomic Studies ◽  
Genetic Level ◽  
Candidate Gene Studies ◽  
Different Populations ◽  
Using Data

Genomic and genetic methods allow investigation of how frequently the same genes are used by different populations during adaptive evolution, yielding insights into the predictability of evolution at the genetic level. We estimated the probability of gene reuse in parallel and convergent phenotypic evolution in nature using data from published studies. The estimates are surprisingly high, with mean probabilities of 0.32 for genetic mapping studies and 0.55 for candidate gene studies. The probability declines with increasing age of the common ancestor of compared taxa, from about 0.8 for young nodes to 0.1–0.4 for the oldest nodes in our study. Probability of gene reuse is higher when populations begin from the same ancestor (genetic parallelism) than when they begin from divergent ancestors (genetic convergence). Our estimates are broadly consistent with genomic estimates of gene reuse during repeated adaptation to similar environments, but most genomic studies lack data on phenotypic traits affected. Frequent reuse of the same genes during repeated phenotypic evolution suggests that strong biases and constraints affect adaptive evolution, resulting in changes at a relatively small subset of available genes. Declines in the probability of gene reuse with increasing age suggest that these biases diverge with time.

scholarly journals STATISTICAL STUDIES ON PROTEIN POLYMORPHISM IN NATURAL POPULATIONS II. GENE DIFFERENTIATION BETWEEN POPULATIONS

Genetics ◽  
1978 ◽  
Vol 88 (2) ◽  
pp. 367-390
Author(s):  
Ranajit Chakraborty ◽  
Paul A Fuerst ◽  
Masatoshi Nei
Keyword(s):  
Genetic Differentiation ◽  
Natural Populations ◽  
Drift Theory ◽  
Alternative Hypotheses ◽  
Mean And Variance ◽  
Statistical Studies ◽  
Different Populations ◽  
Using Data ◽  
Almost All ◽  
Good Agreement

ABSTRACT With the aim of testing the validity of the mutation-drift hypothesis, we examined the pattern of genetic differentiation between populations by using data from Drosophila, fishes, reptiles, and mammals. The observed relationship between genetic identity and correlation of heterozygosities of different populations or species was generally in good agreement with the theoretical expectations from the mutation-drift theory, when the variation in mutation rate among loci was taken into account. In some species of Drosophila, however, the correlation was unduly high. The relationship between the mean and variance of genetic distance was also in good agreement with the theoretical prediction in almost all organisms. We noted that both the distribution of heterozygosity within species and the pattern of genetic differentiation between species can be explained by the same set of genetic parameters in each group of organisms. Alternative hypotheses for explaining these observations are discussed.

Adaptation

2016 ◽  
Author(s):  
Andrew P. Hendry
Keyword(s):  
Genetic Variation ◽  
Adaptive Evolution ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Phenotypic Change ◽  
Adaptive Landscapes ◽  
Local Environments ◽  
Short And Long Term ◽  
Different Populations

This chapter outlines how to conceptualize and predict adaptive evolution based on information about selection and genetic variation. It introduces and explains adaptive landscapes, a concept that has proven useful in guiding the understanding of evolution. The chapter also reviews empirical data to answer fundamental questions about adaptation in nature, including to what extent short- and long-term evolution is predictable, how fast is phenotypic change, to what extent is adaptation constrained by genetic variation, and how well adapted natural populations are to their local environments. Moving beyond selection and adaptation within populations, the chapter shows how eco-evolutionary dynamics will be shaped by biological diversity: that is, different populations and species have different effects on their environment.

scholarly journals Historical contingency shapes adaptive radiation in Antarctic fishes

2018 ◽  
Author(s):  
Jacob M. Daane ◽  
Alex Dornburg ◽  
Patrick Smits ◽  
Daniel J. MacGuigan ◽  
M. Brent Hawkins ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Adaptive Radiation ◽  
Natural Populations ◽  
Phenotypic Traits ◽  
Historical Contingency ◽  
Antarctic Notothenioids ◽  
Important Variation ◽  
Adaptive Radiations ◽  
The Stability ◽  
The Antarctic

AbstractAdaptive radiation illustrates the links between ecological opportunity, natural selection, and the generation of biodiversity (1). Central to adaptive radiation is the association between a diversifying lineage and the evolution of key traits that facilitate the utilization of novel environments or resources (2, 3). However, is not clear whether adaptive evolution or historical contingency is more important for the origin of key phenotypic traits in adaptive radiation (4, 5). Here we use targeted sequencing of >250,000 loci across 46 species to examine hypotheses concerning the origin and diversification of key traits in the adaptive radiation of Antarctic notothenioid fishes. Contrary to expectations of adaptive evolution, we show that notothenioids experienced a punctuated burst of genomic diversification and evolved key skeletal modifications before the onset of polar conditions in the Southern Ocean. We show that diversifying selection in pathways associated with human skeletal dysplasias facilitates ecologically important variation in buoyancy among Antarctic notothenioid species, and demonstrate the sufficiency of altered trip11, col1a2 and col1a1 function in zebrafish (Danio rerio) to phenocopy skeletal reduction in Antarctic notothenioids. Rather than adaptation being driven by the cooling of the Antarctic (6), our results highlight the role of exaptation and historical contingency in shaping the adaptive radiation of notothenioids. Understanding the historical and environmental context for the origin of key traits in adaptive radiations provides context in forecasting the effects of climate change on the stability and evolvability of natural populations.

scholarly journals Distinct characteristics of genes associated with phenome-wide variation in maize (Zea mays)

2019 ◽  
Author(s):  
Zhikai Liang ◽  
Yumou Qiu ◽  
James C. Schnable
Keyword(s):  
Natural Populations ◽  
Purifying Selection ◽  
Forward Genetics ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Functional Variation ◽  
Maize Diversity ◽  
Genome Wide ◽  
Gene Models ◽  
Using Data

ABSTRACTNaturally occurring functionally variable alleles in specific genes within a population allows the identification of which genes are involved in the determination of which phenotypes. The omnigenetic model proposes that essentially all genes which are expressed in relevant contexts likely play some role in determining phenotypic outcomes. Here, we develop an approach to identify genes where natural functional variation plays a role in shaping many phenotypic traits simultaneously. We demonstrate that this approach identifies a distinct set of genes relative to conventional genome wide association using data for 260 traits scored a maize diversity panel, and the genes identified using this approach are more likely to be independently validated than genes identified by convetional genome wide association. Genes identified by the new approach share a number of features with a gold standard set of genes characterized through forward genetics which separate them from both genes identified by conventional genome wide association and the overall population of annotated gene models. These features include evidence of significantly stronger purifying selection, positional conservation across the genomes of related species, greater length, and a scarcity of presence absence variation for these loci in natural populations. Genes identified by phenome-wide analyses also showed much stronger signals of GO enrichment and purification than genes identified by conventional genome wide association. Overall these findings are consistent with large subset of annotated gene models – despite support from transcriptional and homology evidence – being unlikely to play any role in determining organismal phenotypes.

scholarly journals Independent evolution towards larger body size in the distinctive Faroe Island mice

2021 ◽  
Author(s):  
Ricardo Wilches ◽  
William H Beluch ◽  
Ellen McConnell ◽  
Diethard Tautz ◽  
Yingguang Frank Chan
Keyword(s):  
Body Size ◽  
Meta Analysis ◽  
Small Body ◽  
Laboratory Mouse ◽  
Large Body ◽  
Natural Populations ◽  
Size Variation ◽  
Phenotypic Traits ◽  
Island Population ◽  
Multiple Loci

Abstract Most phenotypic traits in nature involve the collective action of many genes. Traits that evolve repeatedly are particularly useful for understanding how selection may act on changing trait values. In mice, large body size has evolved repeatedly on islands and under artificial selection in the laboratory. Identifying the loci and genes involved in this process may shed light on the evolution of complex, polygenic traits. Here, we have mapped the genetic basis of body size variation by making a genetic cross between mice from the Faroe Islands, which are among the largest and most distinctive natural populations of mice in the world, and a laboratory mouse strain selected for small body size, SM/J. Using this F2 intercross of 841 animals, we have identified 111 loci controlling various aspects of body size, weight and growth hormone levels. By comparing against other studies, including the use of a joint meta-analysis, we found that the loci involved in the evolution of large size in the Faroese mice were largely independent from those of a different island population or other laboratory strains. We hypothesize that colonization bottleneck, historical hybridization, or the redundancy between multiple loci have resulted in the Faroese mice achieving an outwardly similar phenotype through a distinct evolutionary path.

scholarly journals Inversion polymorphism in some natural populations of Drosophila pseudoobscura from central Mexico

Genetika ◽  
2007 ◽  
Vol 39 (3) ◽  
pp. 343-354 ◽  
Author(s):  
Víctor Salceda ◽  
Judith Guzmán ◽  
Olga Olvera
Keyword(s):  
Relative Frequency ◽  
Polytene Chromosomes ◽  
Natural Populations ◽  
Chromosomal Polymorphism ◽  
Drosophila Pseudoobscura ◽  
Central Mexico ◽  
The Third ◽  
Grand Total ◽  
Different Populations ◽  
Single Larva

Samples of D. pseudoobscura were taken in seventeen localities in Central Mexico inside the parallels 18o - 20o N, with the purpose of determine the chromosomal polymorphism in the third of the different populations of this species. From each captured female a single larva of its offspring was taken, its salivary glands extracted and stained with a solution of aceto orcein to observe the polytene chromosomes. From these smears the corresponding karyotype of each larva was determined, keeping a record of them. With the information gathered the relative frequency of each one of the fourteen different inversions found was calculated. A grand total of 1894 third chromosomes were analyzed. The fourteen different inversions found are equivalent to a 34.1 % of the total chromosomal variation of the species. The most abundant inversions found were: TL 50.6 %, CU 27.2 5, SC 9.1 % and EP 5.5 %; the remaining ten inversions detected are in general grounds rare ones with variable relative frequencies depending on the locality. Analysis of the predominant inversions for each population was done. The presence of West-East gradients is reported, even if in cases not so well defined, since as one moves in a particular direction the ups and downs in relative frequency for the alternating pairs TL-CU; TL-SC in the western populations and TL-CU in the eastern ones were observed. The assignment of each population to a particular race was also done, and such a way we were able to recognize three different races coexisting in the area of study.

scholarly journals Perspectives from animal demography on incorporating evolutionary mechanism into plant population dynamics

2018 ◽  
Author(s):  
Maria Paniw
Keyword(s):  
Environmental Change ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Population Level ◽  
Plant Population ◽  
Future Research ◽  
Phenotypic Traits ◽  
Plant Population Dynamics ◽  
Future Research Agenda ◽  
Powerful Approach

AbstractWith a growing number of long-term, individual-based data on natural populations available, it has become increasingly evident that environmental change affects populations through complex, simultaneously occurring demographic and evolutionary processes. Analyses of population-level responses to environmental change must therefore integrate demography and evolution into one coherent framework. Integral projection models (IPMs), which can relate genetic and phenotypic traits to demographic and population-level processes, offer a powerful approach for such integration. However, a rather artificial divide exists in how plant and animal population ecologists use IPMs. Here, I argue for the integration of the two sub-disciplines, particularly focusing on how plant ecologists can diversify their toolset to investigate selection pressures and eco-evolutionary dynamics in plant population models. I provide an overview of approaches that have applied IPMs for eco-evolutionary studies and discuss a potential future research agenda for plant population ecologists. Given an impending extinction crisis, a holistic look at the interacting processes mediating population persistence under environmental change is urgently needed.

scholarly journals Population-scale long-read sequencing uncovers transposable elements contributing to gene expression variation and associated with adaptive signatures in Drosophila melanogaster

2021 ◽  
Author(s):  
Gabriel Rech ◽  
Santiago Radio ◽  
Sara Guirao-Rico ◽  
Laura Aguilera ◽  
Vivien Horvath ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Transposable Elements ◽  
Natural Populations ◽  
Gene Expression Variation ◽  
High Quality ◽  
Expression Variation ◽  
Climatic Regions ◽  
Genomic Studies ◽  
Reference Genomes

High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generated 32 high-quality reference genomes for the well-known model species D. melanogaster and focused on the identification and analysis of transposable element variation as they are the most common type of structural variant. We showed that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identified hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.

scholarly journals Fluctuating selection: the perpetual renewal of adaptation in variable environments

2010 ◽  
Vol 365 (1537) ◽  
pp. 87-97 ◽  
Author(s):  
Graham Bell
Keyword(s):  
Natural Selection ◽  
Evolutionary Biology ◽  
Natural Populations ◽  
Phenotypic Variance ◽  
Weak Selection ◽  
Fluctuating Selection ◽  
Environmental Variance ◽  
Strong Selection ◽  
Genomic Studies ◽  
Over Time

Darwin insisted that evolutionary change occurs very slowly over long periods of time, and this gradualist view was accepted by his supporters and incorporated into the infinitesimal model of quantitative genetics developed by R. A. Fisher and others. It dominated the first century of evolutionary biology, but has been challenged in more recent years both by field surveys demonstrating strong selection in natural populations and by quantitative trait loci and genomic studies, indicating that adaptation is often attributable to mutations in a few genes. The prevalence of strong selection seems inconsistent, however, with the high heritability often observed in natural populations, and with the claim that the amount of morphological change in contemporary and fossil lineages is independent of elapsed time. I argue that these discrepancies are resolved by realistic accounts of environmental and evolutionary changes. First, the physical and biotic environment varies on all time-scales, leading to an indefinite increase in environmental variance over time. Secondly, the intensity and direction of natural selection are also likely to fluctuate over time, leading to an indefinite increase in phenotypic variance in any given evolving lineage. Finally, detailed long-term studies of selection in natural populations demonstrate that selection often changes in direction. I conclude that the traditional gradualist scheme of weak selection acting on polygenic variation should be supplemented by the view that adaptation is often based on oligogenic variation exposed to commonplace, strong, fluctuating natural selection.

Complex Traits in Natural Populations

2020 ◽  
pp. 263-290
Author(s):  
Daniel L. Hartl
Keyword(s):  
Complex Traits ◽  
Population Genomics ◽  
Association Studies ◽  
Natural Populations ◽  
Complex Diseases ◽  
Stabilizing Selection ◽  
Phenotypic Evolution ◽  
Genetic Changes ◽  
Number Of Genes ◽  
Almost All

This chapter could as well be titled “Population Genomics,” although many aspects of population genomics are integrated throughout the other chapters. It includes estimates of mutational variance and standing variance, phenotypic evolution under directional selection as measured by the linear selection gradient, and phenotypic evolution under stabilizing selection. It explores the strengths and limitations of genome-wide association studies of quantitative trait loci (QTLs) and expression (eQTLs) to detect genetic influencing complex traits in natural populations and genetic risk factors for complex diseases such as heart disease or diabetes. The number of genes affecting complex traits is considered, as well as evidence bearing on the issue of whether complex diseases are primarily affected by a very large number of genes, almost all of small effect, and how this bears on direct-to-consumer and over-the-counter genetic testing. The population genomics of adaptation is considered, including drug resistance, domestication, and local selection versus gene flow. The chapter concludes with the population genomics of speciation as illustrated by reinforcement of mating barriers, the reproducibility of phenotypic and genetic changes, and the accumulation of genetic incompatibilities.

Sign in / Sign up

Export Citation Format

Share Document