scholarly journals Evolution of the genetic architecture of local adaptations under genetic rescue is determined by mutational load and polygenicity

2020 ◽  
Author(s):  
Yulin Zhang ◽  
Aaron J. Stern ◽  
Rasmus Nielsen
Keyword(s):  
Complex Traits ◽  
Genetic Architecture ◽  
Demographic History ◽  
Purifying Selection ◽  
Mutational Load ◽  
Genetic Rescue ◽  
Effective Population ◽  
Lower Efficiency ◽  
Local Adaptations ◽  
Inbred Populations

AbstractInbred populations often suffer from heightened mutational load and decreased fitness due to lower efficiency of purifying selection at small effective population size. Genetic rescue (GR) is a tool that is studied and deployed with the aim of increasing fitness of such inbred populations. The success of GR is known to depend on certain factors that may vary between different populations, such as their demographic history and distribution of dominance effects of mutations. While we understand the effects of these factors on the evolution of overall ancestry in the inbred population after GR, it is less clear what the effect is on local adaptations and their genetic architecture. To this end, we conduct a population genetic simulation study evaluating the effect of several different factors on the efficacy of GR including trait complexity (Mendelian vs. polygenic), dominance effects, and demographic history. We find that the effect on local adaptations depends highly on the mutational load at the time of GR, which is shaped dynamically by interactions between demographic history and dominance effects of deleterious variation. While local adaptations are generally restored post-GR in the long run, in the short term they are often compromised in the process of purging deleterious variation. We also show that while local adaptations are almost always fully restored, the degree to which ancestral genetic variation comprising the trait is replaced by donor variation can vary drastically, and is especially high for complex traits. Our results provide considerations for practical GR and its effects on trait evolution.

scholarly journals An evolutionary perspective on contemporary genetic load in threatened species to inform future conservation efforts

2021 ◽  
Author(s):  
Samarth Mathur ◽  
John Tomeček ◽  
Luis Tarango-Arámbula ◽  
Robert Perez ◽  
Andrew DeWoody
Keyword(s):  
Population Genomics ◽  
Empirical Distribution ◽  
Demographic History ◽  
Genetic Load ◽  
Purifying Selection ◽  
Deleterious Mutations ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Potential Donor ◽  
Inbred Populations

In theory, genomic erosion can be reduced in fragile “recipient” populations by translocating individuals from genetically diverse “donor” populations. However, recent simulation studies have argued that such translocations can, in principle, serve as a conduit for new deleterious mutations to enter recipient populations. A reduction in evolutionary fitness is associated with a higher load of deleterious mutations and thus, a better understanding of evolutionary processes driving the empirical distribution of deleterious mutations is crucial. Here, we show that genetic load is evolutionarily dynamic in nature and that demographic history greatly influences the distribution of deleterious mutations over time. Our analyses, based on both demographically explicit simulations as well as whole genome sequences of potential donor-recipient pairs of Montezuma Quail (Cyrtonyx montezumae) populations, indicate that all populations tend to lose deleterious mutations during bottlenecks, but that genetic purging is pronounced in smaller populations with stronger bottlenecks. Despite carrying relatively fewer deleterious mutations, we demonstrate how small, isolated populations are more likely to suffer inbreeding depression as deleterious mutations that escape purging are homogenized due to drift, inbreeding, and ineffective purifying selection. We apply a population genomics framework to showcase how the phylogeography and historical demography of a given species can enlighten genetic rescue efforts. Our data suggest that small, inbred populations should benefit the most when assisted gene flow stems from genetically diverse donor populations that have the lowest proportion of deleterious mutations.

scholarly journals Evolutionary insights into plant breeding

2019 ◽  
Author(s):  
Sarah Diane Turner-Hissong ◽  
Makenzie E. Mabry ◽  
Timothy M. Beissinger ◽  
Jeffrey Ross-Ibarra ◽  
J. Chris Pires
Keyword(s):  
Plant Breeding ◽  
Complex Traits ◽  
Life Histories ◽  
Evolutionary Biology ◽  
Genetic Architecture ◽  
Demographic History ◽  
Crop Improvement ◽  
Community Resources ◽  
Crop Species ◽  
Selection Strategies

Crop domestication is a fascinating area of study, as evidenced by a multitude of recent reviews. Coupled with the increasing availability of genomic and phenomic resources in numerous crop species, insights from evolutionary biology will enable a deeper understanding of the genetic architecture and short-term evolution of complex traits, which can be used to inform selection strategies. Future advances in crop improvement will rely on the integration of population genetics with plant breeding methodology, and the development of community resources to support research in a variety of crop life histories and reproductive strategies. We highlight recent advances in the role of selective sweeps and demographic history in shaping genetic architecture, how these breakthroughs can inform selection strategies, and the application of precision gene editing to leverage these connections.

scholarly journals Counterbalancing the time-dependence effect on the Human Mitochondrial DNA Molecular Clock

2019 ◽  
Author(s):  
vicente M Cabrera
Keyword(s):  
Mitochondrial Dna ◽  
Time Dependence ◽  
Molecular Clock ◽  
Demographic History ◽  
Neutral Theory ◽  
Purifying Selection ◽  
Time Dependency ◽  
Effective Population ◽  
Modern Humans ◽  
Human Mitochondrial Dna

Abstract Background The molecular clock is the most important genetic tool to estimate evolutionary timescales. However, the detection of a time dependency effect on the mutation rate estimates is complicating its application. It has been suggested that demographic processes could be the main cause of this confounding effect. In the present study I propose a new algorithm to estimate the coalescent age of phylogenetically related sequences, taking into account the observed time dependency effect on the molecular rate detected by others.Results Applying this method to real human mitochondrial DNA trees, with shallow and deep topologies, I have obtained significantly older molecular ages for the main events of human evolution than in previous estimates. These ages are in close agreement with the most recent archaeological and paleontological records that are in favor of an emergence of early anatomically modern humans in Africa at 315 ± 34 thousand years ago and the presence of recent modern humans out of Africa as early as 174 ± 48 thousand years ago. Furthermore, in the implementation process, we demonstrated that in a population with fluctuating sizes, the probability of fixation of a new neutral mutant depends on the effective population size which is more in accordance with the fact that, under the neutral theory of molecular evolution, the fate of a molecular mutation is mainly determined by random drift.Conclusions I suggest that the demographic history of populations has a more decisive effect than purifying selection and/or mutational saturation on the time dependence effect observed for the substitution rate.

scholarly journals Recent demography drives changes in linked selection across the maize genome

2015 ◽  
Author(s):  
Timothy M. Beissinger ◽  
Li Wang ◽  
Kate Crosby ◽  
Arun Durvasula ◽  
Matthew B. Hufford ◽  
...  
Keyword(s):  
Population Size ◽  
Demographic History ◽  
Purifying Selection ◽  
Rapid Expansion ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Effective Population ◽  
The Impact ◽  
Linked Selection

AbstractGenetic diversity is shaped by the interaction of drift and selection, but the details of this interaction are not well understood. The impact of genetic drift in a population is largely determined by its demographic history, typically summarized by its long-term effective population size (Ne). Rapidly changing population demographics complicate this relationship, however. To better understand how changing demography impacts selection, we used whole-genome sequencing data to investigate patterns of linked selection in domesticated and wild maize (teosinte). We produce the first whole-genome estimate of the demography of maize domestication, showing that maize was reduced to approximately 5% the population size of teosinte before it experienced rapid expansion post-domestication to population sizes much larger than its ancestor. Evaluation of patterns of nucleotide diversity in and near genes shows little evidence of selection on beneficial amino acid substitutions, and that the domestication bottleneck led to a decline in the efficiency of purifying selection in maize. Young alleles, however, show evidence of much stronger purifying selection in maize, reflecting the much larger effective size of present day populations. Our results demonstrate that recent demographic change — a hallmark of many species including both humans and crops — can have immediate and wide-ranging impacts on diversity that conflict with would-be expectations based on Ne alone.

scholarly journals The demographic history and mutational load of African hunter-gatherers and farmers

2017 ◽  
Author(s):  
Marie Lopez ◽  
Athanasios Kousathanas ◽  
Hélène Quach ◽  
Christine Harmant ◽  
Patrick Mouguiama-Daouda ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Demographic History ◽  
Purifying Selection ◽  
Human Populations ◽  
Mutational Load ◽  
Sequencing Data ◽  
Hunter Gatherers ◽  
African Populations ◽  
The Impact

AbstractThe distribution of deleterious genetic variation across human populations is a key issue in evolutionary biology and medical genetics. However, the impact of different modes of subsistence on recent changes in population size, patterns of gene flow, and deleterious mutational load remains unclear. Here, we report high-coverage exome sequencing data from various populations of rainforest hunter-gatherers and farmers from central Africa. We find that the recent demographic histories of hunter-gatherers and farmers differed considerably, with population collapses for hunter-gatherers and expansions for farmers, accompanied by increased gene flow. We show that purifying selection against deleterious alleles is of similar efficiency across African populations, in contrast with Europeans where we detect weaker purifying selection. Furthermore, the per-individual mutation load of rainforest hunter-gatherers is similar to that of farmers, under both additive and recessive models. Our results indicate that differences in the cultural practices and demographic regimes of African populations have not resulted in large differences in mutational burden, and highlight the beneficial role of gene flow in reshaping the distribution of deleterious genetic variation across human populations.

Genetic rescue by augmenting gene flow

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Inbreeding Coefficient ◽  
Outbreeding Depression ◽  
Genetic Rescue ◽  
Evolutionary Potential ◽  
Beneficial Effects ◽  
The Difference ◽  
Inbred Populations ◽  
Harmful Effects

Inbreeding is reduced and genetic diversity enhanced when a small isolated inbred population is crossed to another unrelated population. Crossing can have beneficial or harmful effects on fitness, but beneficial effects predominate, and the risks of harmful ones (outbreeding depression) can be predicted and avoided. For crosses with a low risk of outbreeding depression, there are large and consistent benefits on fitness that persist across generations in outbreeding species. Benefits are greater in species that naturally outbreed than those that inbreed, and increase with the difference in inbreeding coefficient between crossed and inbred populations in mothers and zygotes. However, benefits are similar across invertebrates, vertebrates and plants. There are also important benefits for evolutionary potential of crossing between populations.

scholarly journals Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

scholarly journals Low effective population size and high spatial genetic structure of black poplar populations from the Oder valley in Poland

2021 ◽  
Vol 78 (2) ◽  
Author(s):  
Błażej Wójkiewicz ◽  
Andrzewj Lewandowski ◽  
Weronika B. Żukowska ◽  
Monika Litkowiec ◽  
Witold Wachowiak
Keyword(s):  
Genetic Structure ◽  
Genetic Resources ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Demographic History ◽  
River Valley ◽  
Ex Situ ◽  
Effective Population ◽  
Black Poplar

Abstract Context Black poplar (Populus nigra L.) is a keystone species of European riparian ecosystems that has been negatively impacted by riverside urbanization for centuries. Consequently, it has become an endangered tree species in many European countries. The establishment of a suitable rescue plan of the remaining black poplar forest stands requires a preliminary knowledge about the distribution of genetic variation among species populations. However, for some parts of the P. nigra distribution in Europe, the genetic resources and demographic history remain poorly recognized. Aims Here, we present the first study on identifying and characterizing the genetic resources of black poplar from the Oder valley in Poland. This study (1) assessed the genetic variability and effective population size of populations and (2) examined whether gene flow is limited by distance or there is a single migrant pool along the studied river system. Methods A total of 582 poplar trees derived from nine black poplar populations were investigated with nuclear microsatellite markers. Results (1) The allelic richness and heterozygosity level were high and comparable between populations. (2) The genetic structure of the studied poplar stands was not homogenous. (3) The signatures of past bottlenecks were detected. Conclusion Our study (1) provides evidence for genetic substructuring of natural black poplar populations from the studied river catchment, which is not a frequent phenomenon reported for this species in Europe, and (2) indicates which poplar stands may serve as new genetic conservation units (GCUs) of this species in Europe. Key message The genetic resources of black poplar in the Oder River valley are still substantial compared to those reported for rivers in Western Europe. On the other hand, clear signals of isolation by distance and genetic erosion reflected in small effective population sizes and high spatial genetic structure of the analyzed populations were detected. Based on these findings, we recommend the in situ and ex situ conservation strategies for conserving and restoring the genetic resources of black poplar populations in this strongly transformed by human river valley ecosystem.

scholarly journals Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture

2016 ◽  
Vol 283 (1835) ◽  
pp. 20160569 ◽  
Author(s):  
M. E. Goddard ◽  
K. E. Kemper ◽  
I. M. MacLeod ◽  
A. J. Chamberlain ◽  
B. J. Hayes
Keyword(s):  
Complex Traits ◽  
Genetic Architecture ◽  
Quantitative Traits ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Crop Breeding ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Phenotype Identification

Complex or quantitative traits are important in medicine, agriculture and evolution, yet, until recently, few of the polymorphisms that cause variation in these traits were known. Genome-wide association studies (GWAS), based on the ability to assay thousands of single nucleotide polymorphisms (SNPs), have revolutionized our understanding of the genetics of complex traits. We advocate the analysis of GWAS data by a statistical method that fits all SNP effects simultaneously, assuming that these effects are drawn from a prior distribution. We illustrate how this method can be used to predict future phenotypes, to map and identify the causal mutations, and to study the genetic architecture of complex traits. The genetic architecture of complex traits is even more complex than previously thought: in almost every trait studied there are thousands of polymorphisms that explain genetic variation. Methods of predicting future phenotypes, collectively known as genomic selection or genomic prediction, have been widely adopted in livestock and crop breeding, leading to increased rates of genetic improvement.

Sign in / Sign up

Export Citation Format

Share Document