scholarly journals Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data

2021 ◽  
Author(s):  
Wenyang Lyu ◽  
Xiaoyang Dai ◽  
Mark Beaumont ◽  
Feng Yu ◽  
Zhangyi He
Keyword(s):  
Natural Selection ◽  
Ancient Dna ◽  
Natural Populations ◽  
Genetic Evolution ◽  
Ecological Context ◽  
Gene Migration ◽  
Monte Carlo Techniques ◽  
New Information ◽  
Statistical Approaches ◽  
Detection And Quantification

With the rapid growth of the number of sequenced ancient genomes, there has been increasing interest in using this new information to study past and present adaptation. Such an additional temporal component has the promise of providing improved power for the estimation of natural selection. Over the last decade, statistical approaches for detection and quantification of natural selection from ancient DNA (aDNA) data have been developed. However, most of the existing methods do not allow us to estimate the timing of natural selection along with its strength, which is key to understanding the evolution and persistence of organismal diversity. Additionally, most methods ignore the fact that natural populations are almost always structured. This can result in overestimation of the effect of natural selection. To address these issues, we propose a novel Bayesian framework for the inference of natural selection and gene migration from aDNA data with Markov chain Monte Carlo techniques, co-estimating both timing and strength of natural selection and gene migration. Such an advance enables us to infer drivers of natural selection and gene migration by correlating genetic evolution with potential causes such as the changes in the ecological context in which an organism has evolved. The performance of our procedure is evaluated through extensive simulations, with its utility shown with an application to ancient chicken samples.

scholarly journals Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data

2021 ◽  
Author(s):  
Wenyang Lyu ◽  
Xiaoyang Dai ◽  
Mark Beaumont ◽  
Feng Yu ◽  
Zhangyi He
Keyword(s):  
Natural Selection ◽  
Ancient Dna ◽  
Natural Populations ◽  
Genetic Evolution ◽  
Ecological Context ◽  
Gene Migration ◽  
Monte Carlo Techniques ◽  
New Information ◽  
Statistical Approaches ◽  
Detection And Quantification

With the rapid growth of the number of sequenced ancient genomes, there has been increasing interest in using this new information to study past and present adaptation. Such an additional temporal component has the promise of providing improved power for the estimation of natural selection. Over the last decade, statistical approaches for detection and quantification of natural selection from ancient DNA (aDNA) data have been developed. However, most of the existing methods do not allow us to estimate the timing of natural selection along with its strength, which is key to understanding the evolution and persistence of organismal diversity. Additionally, most methods ignore the fact that natural populations are almost always structured, which can result in overestimation of the effect of natural selection. To address these issues, we propose a novel Bayesian framework for the inference of natural selection and gene migration from aDNA data with Markov chain Monte Carlo techniques, co-estimating both timing and strength of natural selection and gene migration. Such an advance enables us to infer drivers of natural selection and gene migration by correlating genetic evolution with potential causes such as the changes in the ecological context in which an organism has evolved. The performance of our procedure is evaluated through extensive simulations, with its utility shown with an application to ancient chicken samples.

scholarly journals Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models

2016 ◽  
Author(s):  
Zhangyi He ◽  
Mark Beaumont ◽  
Feng Fu
Keyword(s):  
Population Dynamics ◽  
Life Cycle ◽  
Natural Selection ◽  
Population Regulation ◽  
Genetic Research ◽  
Natural Populations ◽  
Gene Migration ◽  
Local Selection ◽  
Fisher Model ◽  
Regulation Mechanisms

AbstractThe Wright-Fisher model and its extensions are of central importance in population genetics, and so far, they have formed the basis of most theoretical and applied population genetic research. In the present work, we explore the effect that the ordering of natural selection and population regulation in the life cycle has on the resulting population dynamics under the Wright-Fisher model, especially for the evolution of one- and two-locus systems. With weak natural selection, the details of how to order natural selection and population regulation in the life cycle do not matter in the Wright-Fisher model and its diffusion approximation. By contrast, we show that when there is strong natural selection and the population is in linkage disequilibrium, there can be appreciable differences in the resulting population dynamics under the Wright-Fisher model, depending on whether natural selection occurs before or after population regulation in the life cycle. We argue that this effect may be of significance in natural populations subject to gene migration and local selection.F.Y. supported in part by EPSRC Grant EP/I028498/1.

Specific features of long-term domestication of australian crayfish Cherax quadricarinatus in conditions of the western part of Russian Federation

2018 ◽  
Vol 194 ◽  
pp. 188-192
Author(s):  
D. I. Shokasheva
Keyword(s):  
Natural Selection ◽  
Russian Federation ◽  
Natural Populations ◽  
Cherax Quadricarinatus ◽  
Local Environments ◽  
Local Species ◽  
Adaptive Ability

Natural populations of crayfish are in depression in Russia and local species are not cultivated. In this situation, experimental cultivation of allochtonous australian crayfish Cherax quadricarinatus is conducted. This species is distinguished by high reproductive abilities and good consumer properties. It has domesticated in Russia spontaneously and produced 9–10 generations in Astrakhan Region. Certain natural selection in the process of domestication provides adaptive ability of this species to local environments and its capabil­ity to reproduce a viable progeny, so there is no doubts in good prospects of its cultivation in industrial conditions.

scholarly journals GENETIC LOAD IN NATURAL POPULATIONS: IS IT COMPATIBLE WITH THE HYPOTHESIS THAT MANY POLYMORPHISMS ARE MAINTAINED BY NATURAL SELECTION?

Genetics ◽  
1974 ◽  
Vol 77 (3) ◽  
pp. 569-589
Author(s):  
Martin L Tracey ◽  
Francisco J Ayala
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Natural Population ◽  
Natural Populations ◽  
Genetic Load ◽  
Structural Genes ◽  
Invertebrate Species ◽  
Average Proportion ◽  
Mean Fitness ◽  
The Mean

ABSTRACT Recent studies of genetically controlled enzyme variation lead to an estimation that at least 30 to 60% of the structural genes are polymorphic in natural populations of many vertebrate and invertebrate species. Some authors have argued that a substantial proportion of these polymorphisms cannot be maintained by natural selection because this would result in an unbearable genetic load. If many polymorphisms are maintained by heterotic natural selection, individuals with much greater than average proportion of homozygous loci should have very low fitness. We have measured in Drosophila melanogaster the fitness of flies homozygous for a complete chromosome relative to normal wild flies. A total of 37 chromosomes from a natural population have been tested using 92 experimental populations. The mean fitness of homozygous flies is 0.12 for second chromosomes, and 0.13 for third chromosomes. These estimates are compatible with the hypothesis that many (more than one thousand) loci are maintained by heterotic selection in natural populations of D. melanogaster.

Laboratory comparison of the relative success of Biomphalaria glabrata stocks which are susceptible and insusceptible to infection with Schistosoma mansoni

Parasitology ◽  
1983 ◽  
Vol 86 (2) ◽  
pp. 335-344 ◽  
Author(s):  
D. J. Minchella ◽  
P. T. Loverde
Keyword(s):  
Life Cycle ◽  
Natural Selection ◽  
Reproductive Success ◽  
Natural Populations ◽  
Biomphalaria Glabrata ◽  
Selective Advantage ◽  
Controlled Conditions ◽  
Plausible Answer ◽  
Major Objection ◽  
Transmit Disease

SUMMARYA method of interrupting the life-cycle of the human blood fluke Schistosoma by increasing the proportion of genetically insusceptible intermediate host snails in natural populations was first proposed nearly 25 years ago. The method assumes that insusceptible snails will be at a selective advantage over susceptible snails when the schistosome parasite is present, and therefore natural selection will act to increase the proportion of alleles for insusceptibility. A major objection to the proposed technique is ‘If insusceptible snails are at a selective advantage, then why are they not predominant in natural populations that transmit disease?’ One explanation of this paradox is that insusceptibility may be associated with a disadvantageous character or a physiological defect. This study tests this hypothesis by measuring the relative reproductive success of susceptible and insusceptible snails under controlled conditions. Results indicate that insusceptible (unsuitable) snails are negatively affected in the presence of either susceptible snails or schistosome parasites. Furthermore, in the presence of both susceptible snails and schistosome parasites, insusceptible snails are selectively disadvantaged compared to susceptible snails. These results obtained under laboratory-controlled conditions suggest a plausible answer as to why insusceptible snails are not predominant in natural populations that transmit disease.

scholarly journals Two different epigenetic pathways detected in wild three-spined sticklebacks are involved in salinity adaptation

2019 ◽  
Author(s):  
Melanie J. Heckwolf ◽  
Britta S. Meyer ◽  
Robert Häsler ◽  
Marc P. Höppner ◽  
Christophe Eizaguirre ◽  
...  
Keyword(s):  
Natural Selection ◽  
Gasterosteus Aculeatus ◽  
Natural Populations ◽  
Wild Populations ◽  
Epigenetic Marks ◽  
Transgenerational Plasticity ◽  
The Face ◽  
Adaptation Processes ◽  
Methylation Patterns ◽  
Rapid Emergence

AbstractWhile environmentally inducible epigenetic marks are discussed as one mechanism of transgenerational plasticity, environmentally stable epigenetic marks emerge randomly. When resulting in variable phenotypes, stable marks can be targets of natural selection analogous to DNA sequence-based adaptation processes. We studied both postulated pathways in natural populations of three-spined sticklebacks (Gasterosteus aculeatus) and sequenced their methylomes and genomes across a salinity cline. Consistent with local adaptation, populations showed differential methylation (pop-DMS) at genes enriched for osmoregulatory processes. In a two-generation experiment, 62% of these pop-DMS were insensitive to salinity manipulation, suggesting that they could be stable targets for natural selection. Two-thirds of the remaining inducible pop-DMS became more similar to patterns detected in wild populations from the corresponding salinity, and this pattern accentuated over consecutive generations, indicating a mechanism of adaptive transgenerational plasticity. Natural DNA methylation patterns can thus be attributed to two epigenetic pathways underlying the rapid emergence of adaptive phenotypes in the face of environmental change.

scholarly journals The population and evolutionary dynamics of bacteriophage: Why be temperate revisited

2019 ◽  
Author(s):  
Waqas Chaudhry ◽  
Nicole Vega ◽  
Adithi Govindan ◽  
Rodrigo Garcia ◽  
Esther Lee ◽  
...  
Keyword(s):  
Natural Selection ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Lytic Phage ◽  
Temperate Bacteriophage ◽  
Serial Transfer ◽  
Virulent Phage ◽  
E Coli ◽  
Resistant Refractory

AbstractBacteriophages are deemed either lytic (virulent) or temperate, respectively depending on whether their genomes are transmitted solely horizontally, or both horizontally and vertically. To elucidate the ecological and evolutionary conditions under which natural selection will favor the evolution and maintenance of lytic or temperate modes of phage replication and transmission, we use a comprehensive mathematical model of the dynamics of temperate and virulent phage in populations of bacteria sensitive and resistant to these viruses. For our numerical analysis of the properties of this model, we use parameters estimated with the temperate bacteriophage Lambda, λ, it’s clear and virulent mutants, andE. colisensitive and resistant - refractory to these phages. Using batch and serial transfer population dynamic and reconstruction experiments, we test the hypotheses generated from this theoretical analysis. Based on the results of this jointly theoretical and experimental study, we postulate the conditions under which natural selection will favor the evolution and maintenance of lytic and temperate modes of phage replication and transmission. A compelling and novel prediction thisin silico,in vitro, andin plasticostudy makes is lysogenic bacteria from natural populations will be resistant-refractory to the phage for which they are lysogenic as well as lytic phage sharing the same receptors as these temperate viruses.

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.

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