scholarly journals Population Size, Sex and Purifying Selection: Comparative Genomics of Two Sister Taxa of the Wild Yeast Saccharomyces paradoxus

2020 ◽  
Vol 12 (9) ◽  
pp. 1636-1645
Author(s):  
Vassiliki Koufopanou ◽  
Susan Lomas ◽  
Olga Pronina ◽  
Pedro Almeida ◽  
Jose Paulo Sampaio ◽  
...  
Keyword(s):  
Population Size ◽  
Generation Time ◽  
Purifying Selection ◽  
Mitotic Cell ◽  
Mutation Accumulation ◽  
Exclusion Zone ◽  
Saccharomyces Paradoxus ◽  
Growing Period ◽  
Wild Yeast ◽  
Selection Parameters

Abstract This study uses population genomic data to estimate demographic and selection parameters in two sister lineages of the wild yeast Saccharomyces paradoxus and compare their evolution. We first estimate nucleotide and recombinational diversities in each of the two lineages to infer their population size and frequency of sex and then analyze the rate of mutation accumulation since divergence from their inferred common ancestor to estimate the generation time and efficacy of selection. We find that one of the lineages has significantly higher silent nucleotide diversity and lower linkage disequilibrium, indicating a larger population with more frequent sexual generations. The same lineage also shows shorter generation time and higher efficacy of purifying selection, the latter consistent with the finding of larger population size and more frequent sex. Similar analyses are also performed on the ancestries of individual strains within lineages and we find significant differences between strains implying variation in rates of mitotic cell divisions. Our sample includes some strains originating in the Chernobyl nuclear-accident exclusion zone, which has been subjected to high levels of radiation for nearly 30 years now. We find no evidence, however, for increased rates of mutation. Finally, there is a positive correlation between rates of mutation accumulation and length of growing period, as measured by latitude of the place of origin of strains. Our study illustrates the power of genomic analyses in estimating population and life history parameters and testing predictions based on population genetic theory.

scholarly journals The Timing and Direction of Introgression Under the Multispecies Network Coalescent

Genetics ◽  
2019 ◽  
Vol 211 (3) ◽  
pp. 1059-1073 ◽  
Author(s):  
Mark S. Hibbins ◽  
Matthew W. Hahn
Keyword(s):  
Statistical Methods ◽  
Biological Process ◽  
Genomic Data ◽  
Hybrid Speciation ◽  
Saccharomyces Paradoxus ◽  
Genomic Signatures ◽  
Wild Yeast ◽  
Other Information ◽  
Homoploid Hybrid ◽  
New Statistics

Introgression is a pervasive biological process, and many statistical methods have been developed to infer its presence from genomic data. However, many of the consequences and genomic signatures of introgression remain unexplored from a methodological standpoint. Here, we develop a model for the timing and direction of introgression based on the multispecies network coalescent, and from it suggest new approaches for testing introgression hypotheses. We suggest two new statistics, D1 and D2, which can be used in conjunction with other information to test hypotheses relating to the timing and direction of introgression, respectively. D1 may find use in evaluating cases of homoploid hybrid speciation (HHS), while D2 provides a four-taxon test for polarizing introgression. Although analytical expectations for our statistics require a number of assumptions to be met, we show how simulations can be used to test hypotheses about introgression when these assumptions are violated. We apply the D1 statistic to genomic data from the wild yeast Saccharomyces paradoxus—a proposed example of HHS—demonstrating its use as a test of this model. These methods provide new and powerful ways to address questions relating to the timing and direction of introgression.

Variations in life history parameters and their influence on rate of population increase of different pathogenic isolates of the pine wood nematode, Bursaphelenchus xylophilus

Nematology ◽  
2005 ◽  
Vol 7 (3) ◽  
pp. 459-467 ◽  
Author(s):  
Yu Wang ◽  
Kazuo Suzuki ◽  
Daisuke Sakaue ◽  
Toshihiro Yamada
Keyword(s):  
Life History ◽  
Population Size ◽  
Botrytis Cinerea ◽  
Generation Time ◽  
Bursaphelenchus Xylophilus ◽  
Egg Laying ◽  
Population Increase ◽  
Pine Wood Nematode ◽  
Life History Parameters ◽  
Pine Trees

AbstractTwo virulent isolates and two avirulent isolates of Bursaphelenchus xylophilus and one isolate of B. mucronatus were used to investigate the relationships between life history parameters, rate of population increase and virulence. The results showed that on fungal cultures of Botrytis cinerea, virulent B. xylophilus completed one generation much faster than did avirulent B. xylophilus and B. mucronatus. There was a tendency that virulent B. xylophilus isolates laid more eggs during the egg laying period than did avirulent populations. Shorter generation time and higher fecundity resulted in a higher rate of population increase. Generation time and fecundity were primary factors determining rate of population increase. Difference in rate of population increase is closely related to variation of virulence: virulent B. xylophilus increased population size at the fastest rate, avirulent B. xylophilus was slower, and B. mucronatus was slowest. It is assumed that similar variations in life history parameters and rate of population increase are also expressed in pine trees and help to explain variation of virulence in the field.

scholarly journals The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus

2006 ◽  
Vol 361 (1475) ◽  
pp. 1941-1946 ◽  
Author(s):  
Vassiliki Koufopanou ◽  
Joseph Hughes ◽  
Graham Bell ◽  
Austin Burt
Keyword(s):  
Genetic Differentiation ◽  
Population Genomics ◽  
Model Organism ◽  
Physical Distance ◽  
Saccharomyces Paradoxus ◽  
Population Genetic Differentiation ◽  
Wild Yeast ◽  
Oak Trees ◽  
Eukaryotic Microbes ◽  
Well Differentiated

Little information is presently available on the factors promoting genetic divergence in eukaryotic microbes. We studied the spatial distribution of genetic variation in Saccharomyces paradoxus , the wild relative of Saccharomyces cerevisiae , from the scale of a few centimetres on individual oak trees to thousands of kilometres across different continents. Genealogical analysis of six loci shows that isolates from Europe form a single recombining population, and within this population genetic differentiation increases with physical distance. Between different continents, strains are more divergent and genealogically independent, indicating well-differentiated lineages that may be in the process of speciation. Such replicated populations will be useful for studies in population genomics.

scholarly journals Selection in a growing bacterial/yeast colony biases results of mutation accumulation experiments

2021 ◽  
Author(s):  
Anjali Mahilkar ◽  
Sharvari Kemkar ◽  
Supreet Saini
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Effective Population Size ◽  
Colony Growth ◽  
Mutation Accumulation ◽  
Rate Of Change ◽  
Raw Material ◽  
Effective Population ◽  
The Face ◽  
Mean Fitness

AbstractMutations provide the raw material for natural selection to act. Therefore, understanding the variety and relative frequency of different type of mutations is critical to understanding the nature of genetic diversity in a population. Mutation accumulation (MA) experiments have been used in this context to estimate parameters defining mutation rates, distribution of fitness effects (DFE), and spectrum of mutations. MA experiments performed with organisms such asDrosophilahave an effective population size of one. However, in MA experiments with bacteria and yeast, a single founder is allowed to grow to a size of a colony (~108). The effective population size in these experiments is of the order of 10. In this scenario, while it is assumed that natural selection plays a minimal role in dictating the dynamics of colony growth and therefore, the MA experiment; this effect has not been tested explicitly. In this work, we simulate colony growth and perform an MA experiment, and demonstrate that selection ensures that, in an MA experiment, fraction of all mutations that are beneficial is over represented by a factor greater than two. The DFE of beneficial and deleterious mutations are accurately captured in an MA experiment. We show that the effect of selection in a growing colony varies non-monotonically and that, in the face of natural selection dictating an MA experiment, estimates of mutation rate of an organism is not trivial. We perform experiments with 160 MA lines ofE. coli, and demonstrate that rate of change of mean fitness is a non-monotonic function of the colony size, and that selection acts differently in different sectors of a growing colony. Overall, we demonstrate that the results of MA experiments need to be revisited taking into account the action of selection in a growing colony.

scholarly journals Intra-Species Differences in Population Size shape Life History and Genome Evolution

2019 ◽  
Author(s):  
David Willemsen ◽  
Rongfeng Cui ◽  
Martin Reichard ◽  
Dario Riccardo Valenzano
Keyword(s):  
Life History ◽  
Population Size ◽  
Genetic Drift ◽  
Sex Chromosome ◽  
Purifying Selection ◽  
Life History Trait ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Annual Life Cycle ◽  
Evolutionary Forces

AbstractThe evolutionary forces shaping life history trait divergence within species are largely unknown. Killifish (oviparous Cyprinodontiformes) evolved an annual life cycle as an exceptional adaptation to life in arid savannah environments characterized by seasonal water availability. The turquoise killifish (Nothobranchius furzeri) is the shortest-lived vertebrate known to science and displays differences in lifespan among wild populations, representing an ideal natural experiment in the evolution and diversification of life history. Here, by combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among turquoise killifish populations. We generate an improved reference assembly for the turquoise killifish genome, trace the evolutionary origin of the sex chromosome, and identify genes under strong positive and purifying selection, as well as those evolving neutrally. We find that the shortest-lived turquoise killifish populations, which dwell in fragmented and isolated habitats at the outer margin of the geographical range of the species, are characterized by small effective population size and accumulate throughout the genome several small to large-effect deleterious mutations due to genetic drift. The genes most affected by drift in the shortest-lived turquoise killifish populations are involved in the WNT signalling pathway, neurodegenerative disorders, cancer and the mTOR pathway. As the populations under stronger genetic drift are the shortest-lived ones, we propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by causing the genome-wide accumulation of deleterious mutations, cumulatively contribute to the short adult lifespan in turquoise killifish populations.

scholarly journals The timing and direction of introgression under the multispecies network coalescent

2018 ◽  
Author(s):  
Mark S. Hibbins ◽  
Matthew W. Hahn
Keyword(s):  
Statistical Methods ◽  
Biological Process ◽  
Genomic Data ◽  
Hybrid Speciation ◽  
Saccharomyces Paradoxus ◽  
Genomic Signatures ◽  
Wild Yeast ◽  
Other Information ◽  
Homoploid Hybrid ◽  
New Statistics

AbstractIntrogression is a pervasive biological process, and many statistical methods have been developed to infer its presence from genomic data. However, many of the consequences and genomic signatures of introgression remain unexplored from a methodological standpoint. Here, we develop a model for the timing and direction of introgression based on the multispecies network coalescent, and from it suggest new approaches for testing introgression hypotheses. We suggest two new statistics, D1 and D2, which can be used in conjunction with other information to test hypotheses relating to the timing and direction of introgression, respectively. D1 may find use in evaluating cases of homoploid hybrid speciation, while D2 provides a four-taxon test for polarizing introgression. Although analytical expectations for our statistics require a number of assumptions to be met, we show how simulations can be used to test hypotheses about introgression when these assumptions are violated. We apply the D1 statistic to genomic data from the wild yeast Saccharomyces paradoxus, a proposed example of homoploid hybrid speciation, demonstrating its use as a test of this model. These methods provide new and powerful ways to address questions relating to the timing and direction of introgression.

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