Chromosomal Patterns of Microsatellite Variability Contrast Sharply in African and Non-African Populations of Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 160 (1) ◽  
pp. 247-256
Author(s):  
M Kauer ◽  
B Zangerl ◽  
D Dieringer ◽  
C Schlötterer
Keyword(s):  
Chromosomal Polymorphism ◽  
Background Selection ◽  
Selective Sweeps ◽  
X Chromosomes ◽  
Evolutionary Forces ◽  
Relative Contribution ◽  
African Populations ◽  
Neutral Variation ◽  
Colonization Process ◽  
The Subject

Abstract Levels of neutral variation are influenced by background selection and hitchhiking. The relative contribution of these evolutionary forces to the distribution of neutral variation is still the subject of ongoing debates. Using 133 microsatellites, we determined levels of variability on X chromosomes and autosomes in African and non-African D. melanogaster populations. In the ancestral African populations microsatellite variability was higher on X chromosomes than on autosomes. In non-African populations X-linked polymorphism is significantly more reduced than autosomal variation. In non-African populations we observed a significant positive correlation between X chromosomal polymorphism and recombination rate. These results are consistent with the interpretation that background selection shapes levels of neutral variability in the ancestral populations, while the pattern in derived populations is determined by multiple selective sweeps during the colonization process. Further research, however, is required to investigate the influence of inversion polymorphisms and unequal sex ratios.

scholarly journals A Microsatellite Variability Screen for Positive Selection Associated With the “Out of Africa” Habitat Expansion of Drosophila melanogaster

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1137-1148
Author(s):  
M O Kauer ◽  
D Dieringer ◽  
C Schlötterer
Keyword(s):  
X Chromosome ◽  
Theoretical Work ◽  
Selective Sweeps ◽  
Mapping Study ◽  
X Chromosomes ◽  
The Third ◽  
African Populations ◽  
Average Loss ◽  
Out Of Africa ◽  
Genomic Regions

Abstract We report a “hitchhiking mapping” study in D. melanogaster, which searches for genomic regions with reduced variability. The study's aim was to identify selective sweeps associated with the “out of Africa” habitat expansion. We scanned 103 microsatellites on chromosome 3 and 102 microsatellites on the X chromosome for reduced variability in non-African populations. When the chromosomes were analyzed separately, the number of loci with a significant reduction in variability only slightly exceeded the expectation under neutrality—six loci on the third chromosome and four loci on the X chromosome. However, non-African populations also have a more pronounced average loss in variability on the X chromosomes as compared to the third chromosome, which suggests the action of selection. Therefore, comparing the X chromosome to the autosome yields a higher number of significantly reduced loci. However, a more pronounced loss of variability on the X chromosome may be caused by demographic events rather than by natural selection. We therefore explored a range of demographic scenarios and found that some of these captured most, but not all aspects of our data. More theoretical work is needed to evaluate how demographic events might differentially affect X chromosomes and autosomes and to estimate the most likely scenario associated with the out of Africa expansion of D. melanogaster.

Selection on X-linked Genes During Speciation in the Drosophila athabasca Complex

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 689-703 ◽  
Author(s):  
Michael J Ford ◽  
Charles F Aquadro
Keyword(s):  
Computer Simulation ◽  
Natural Selection ◽  
Molecular Evolution ◽  
Restriction Site ◽  
Neutral Model ◽  
Background Selection ◽  
Selective Sweeps ◽  
Differential Migration ◽  
Site Survey ◽  
Low Levels

Abstract We present the results of a restriction site survey of variation at five loci in Drosophila athabasca, complimenting a previous study of the period locus. There is considerably greater differentiation between the three semispecies of D. athabasca at the period locus and two other X-linked genes (neon-transient-A and E74A) than at three autosomal genes (Xdh, Adh and RC98). Using a modification of the HKA test, which uses fixed differences between the semispecies and a test based on differences in Fst among loci, we show that the greater differentiation of the X-linked loci compared with the autosomal loci is inconsistent with a neutral model of molecular evolution. We explore several evolutionary scenarios by computer simulation, including differential migration of X and autosomal genes, very low levels of migration among the semispecies, selective sweeps, and background selection, and conclude that X-linked selective sweeps in at least two of the semispecies are the best explanation for the data. This evidence that natural selection acted on the X-chromosome suggests that another X-linked trait, mating song differences among the semispecies, may have been the target of selection.

Regions of Lower Crossing Over Harbor More Rare Variants in African Populations ofDrosophila melanogaster

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 657-665 ◽  
Author(s):  
Peter Andolfatto ◽  
Molly Przeworski
Keyword(s):  
Frequency Spectrum ◽  
Nucleotide Diversity ◽  
Rare Variants ◽  
Purifying Selection ◽  
Crossing Over ◽  
Background Selection ◽  
Deleterious Mutations ◽  
African Populations ◽  
Rapid Fixation ◽  
Parameter Values

AbstractA correlation between diversity levels and rates of recombination is predicted both by models of positive selection, such as hitchhiking associated with the rapid fixation of advantageous mutations, and by models of purifying selection against strongly deleterious mutations (commonly referred to as “background selection”). With parameter values appropriate for Drosophila populations, only the first class of models predicts a marked skew in the frequency spectrum of linked neutral variants, relative to a neutral model. Here, we consider 29 loci scattered throughout the Drosophila melanogaster genome. We show that, in African populations, a summary of the frequency spectrum of polymorphic mutations is positively correlated with the meiotic rate of crossing over. This pattern is demonstrated to be unlikely under a model of background selection. Models of weakly deleterious selection are not expected to produce both the observed correlation and the extent to which nucleotide diversity is reduced in regions of low (but nonzero) recombination. Thus, of existing models, hitchhiking due to the recurrent fixation of advantageous variants is the most plausible explanation for the data.

scholarly journals Detecting recent selective sweeps while controlling for mutation rate and background selection

2015 ◽  
Vol 25 (1) ◽  
pp. 142-156 ◽  
Author(s):  
Christian D. Huber ◽  
Michael DeGiorgio ◽  
Ines Hellmann ◽  
Rasmus Nielsen
Keyword(s):  
Mutation Rate ◽  
Background Selection ◽  
Selective Sweeps

scholarly journals Kinetic aspects of calcium metabolism in lactating sheep offered herbages with different Ca concentrations and the effect of protein supplementation

1989 ◽  
Vol 61 (1) ◽  
pp. 45-58 ◽  
Author(s):  
J. S. Chrisp ◽  
A. R. Sykes ◽  
N. D. Grace
Keyword(s):  
White Clover ◽  
Calcium Metabolism ◽  
Lolium Multiflorum ◽  
Kinetic Studies ◽  
Protein Supplementation ◽  
Relative Contribution ◽  
Protein Status ◽  
Rate Of Absorption ◽  
The Subject ◽  
Protein Supply

1. Two experiments are described in which kinetic aspects of calcium metabolism were studied in housed lactating sheep consuming different fresh herbage species. The importance of protein supply was also investigated.2. In Expt. 1, two groups (n 4) were offered, ad lib., a freshly cut ryegrass (Lolium perenne L.)-white clover (Trifolium repens L.) pasture containing 5·48 g Ca/kg dry matter (DM). One group was supplemented daily with 100 g protected casein. A third group (n 4) was offered, ad lib., freshly cut oats-Tama ryegass (Lolium multiflorum L.) herbage which had a lower Ca content of 3·07 g Ca/kg DM. Stable Ca and nitrogen balances were carried out during the first 7 weeks of lactation. At this stage 180 μCi45Ca were administered for Ca kinetic studies.3. In Expt 2, eight sheep were offered, ad lib., a fresh ryegrass–white clover pasture, and paired on the basis of their udder size. One member of each pair was supplemented daily with 100 g casein via the abomasum and the amount of milk removed was equalized between pairs. Ca and N balances (12 d) and Ca kinetic studies (280 μCi 45Ca) were carried out during weeks 2 and 5 of lactation.4. Rate of absorption of Ca increased, while rate of Ca secretion in milk and resorption from bone decreased as lactation progressed. Ca balances changed from negative to positive as lactation progressed in sheep offered ryegrass–white clover, but, while improving, were always negative in sheep offered oats–Tama ryegrass. Protein supplementation increased (18%) milk production of the ewes in Expt 1 and their retention of N in Expt 2.5. The proportion of utilized Ca derived from the diet, as opposed to the skeleton, tended to increase as a result of protein supplementation.6. Availability of Ca from ryegrass–white clover ranged from 0.19 to 0.32, even though only 50% of the net Ca requirement was derived from the diet. Availability of Ca from the oats–Tama ryegrass diet was similar, though in this case less than 20% of the net Ca requirement was derived from the diet. It was concluded that availability of Ca from forage diets may be lower than previously anticipated.7. Faecal endogenous loss ranged from 16 to 40 mg Ca/kg body-weight per d, and was similar on both diets.8. These and other findings are used to discuss more fully the subject of Ca nutrition in sheep, in particular, the implications of the strong homeostatic control of Ca absorption and the influence of protein status on the relative contribution of the diet and the skeleton in meeting the net Ca requirement of the ewe during lactation.

Muscles versus bones: catfishes as a case study for a discussion on the relative contribution of myological and osteological features in phylogenetic reconstructions

2004 ◽  
Vol 54 (4) ◽  
pp. 373-391 ◽  
Author(s):  
Rui Diogo
Keyword(s):  
Morphological Variation ◽  
Phylogenetic Trees ◽  
High Reliability ◽  
Phylogenetic Analyses ◽  
Data Sets ◽  
Large Set ◽  
Relative Contribution ◽  
Phylogenetic Reconstructions ◽  
The Subject

AbstractThe levels of homoplasy and phylogenetic reliability of different types of data sets have since long intrigued evolutionary scientists. This paper provides, to the author's knowledge, the first assessment of the relative contribution of a large set of myological and osteological characters in simultaneous phylogenetic analyses. The biological taxon used as a case study for this comparison was the highly diverse and cosmopolitan teleost Siluriformes (catfishes) which, with 34 families, about 437 genera and more than 2700 species, represents about one third of all freshwater fishes and one of the most diverse vertebrate groups. Such a direct comparison of the relative contribution of these two types of data sets has the advantage that the homoplasy levels and the phylogenetic trees being compared refer to the same group and, more importantly, to the very same terminal taxa. The overall analysis of the results presented in this work seems to indicate that: (1) osteological structures display a greater morphological variation than myological ones; (2) this difference (which is very likely overenhanced by the fact that the phylogenetic variation of osteological structures has historically been the subject of many more studies and descriptions than myological ones) is particularly notable in small taxa, such as genera or species; (3) myological characters provide, however, a high proportion of informative characters for disclosing the relationships between larger taxa, and, thus, for disclosing the phylogeny of the higher clades in which these taxa are included. These results raise some puzzling, general questions. For instance, what are the reasons for the seemingly greater morphological variation of osteological structures? And why is this greater morphological variation of osteological structures in relation to myological structures particularly pronounced in low ranking taxa? Does natural selection eventually act, in certain cases, more on bones than on muscles? Is the development of myological structures eventually more constrained than that of osteological features? What explains the apparently high reliability of muscular characters to disclose the higher-level phylogeny of higher taxa? More direct comparisons, either of other major groups of teleosts or of vertebrates in general, are clearly needed to infer if the patterns found in the direct comparison of this work correspond to a more general phylogenetic pattern, or instead refer to a particular situation found in the order Siluriformes.

scholarly journals The Effect of Mating System Differences on Nucleotide Diversity at the Phosphoglucose Isomerase Locus in the Plant Genus Leavenworthia

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 343-357 ◽  
Author(s):  
F Liu ◽  
D Charlesworth ◽  
M Kreitman
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Phosphoglucose Isomerase ◽  
Self Incompatibility ◽  
Background Selection ◽  
Selective Sweeps ◽  
Balanced Polymorphism ◽  
Neutral Genetic Diversity ◽  
Low Diversity ◽  
High Diversity

AbstractTo test the theoretical prediction that highly inbreeding populations should have low neutral genetic diversity relative to closely related outcrossing populations, we sequenced portions of the cytosolic phosphoglucose isomerase (PgiC) gene in the plant genus Leavenworthia, which includes both self-incompatible and inbreeding taxa. On the basis of sequences of intron 12 of this gene, the expected low diversity was seen in both populations of the selfers Leavenworthia uniflora and L. torulosa and in three highly inbreeding populations of L. crassa, while high diversity was found in self-incompatible L. stylosa, and moderate diversity in L. crassa populations with partial or complete self-incompatibility. In L. stylosa, the nucleotide diversity was strongly structured into three haplotypic classes, differing by several insertion/deletion sequences, with linkage disequilibrium between sequences of the three types in intron 12, but not in the adjacent regions. Differences between the three kinds of haplotypes are larger than between sequences of this gene region from different species. The haplotype divergence suggests the presence of a balanced polymorphism at this locus, possibly predating the split between L. stylosa and its two inbreeding sister taxa, L. uniflora and L. torulosa. It is therefore difficult to distinguish between different potential causes of the much lower sequence diversity at this locus in inbreeding than outcrossing populations. Selective sweeps during the evolution of these populations are possible, or background selection, or merely loss of a balanced polymorphism maintained by overdominance in the populations that evolved high selfing rates.

scholarly journals Female-limited X-chromosome evolution effects on male pre- and post-copulatory success

2021 ◽  
Vol 17 (3) ◽  
Author(s):  
Yesbol Manat ◽  
Katrine K. Lund-Hansen ◽  
Georgios Katsianis ◽  
Jessica K. Abbott
Keyword(s):  
X Chromosome ◽  
Sexual Conflict ◽  
X Chromosomes ◽  
Intralocus Sexual Conflict ◽  
Relative Contribution ◽  
Counter Selection ◽  
Evolution Experiment ◽  
X Chromosome Evolution ◽  
Shared Alleles ◽  
Copulatory Success

Intralocus sexual conflict arises when the expression of shared alleles at a single locus generates opposite fitness effects in each sex (i.e. sexually antagonistic alleles), preventing each sex from reaching its sex-specific optimum. Despite its importance to reproductive success, the relative contribution of intralocus sexual conflict to male pre- and post-copulatory success is not well-understood. Here, we used a female-limited X-chromosome (FLX) evolution experiment in Drosophila melanogaster to limit the inheritance of the X-chromosome to the matriline, eliminating possible counter-selection in males and allowing the X-chromosome to accumulate female-benefit alleles. After more than 100 generations of FLX evolution, we studied the effect of the evolved X-chromosome on male attractiveness and sperm competitiveness. We found a non-significant increase in attractiveness and decrease in sperm offence ability in males expressing the evolved X-chromosomes, but a significant increase in their ability to avoid displacement by other males' sperm. This is consistent with a trade-off between these traits, perhaps mediated by differences in body size, causing a small net reduction in overall male fitness in the FLX lines. These results indicate that the X-chromosome in D. melanogaster is subject to selection via intralocus sexual conflict in males.

scholarly journals Predictive regression modeling with MEG/EEG: from source power to signals and cognitive states

2019 ◽  
Author(s):  
David Sabbagh ◽  
Pierre Ablin ◽  
Gaël Varoquaux ◽  
Alexandre Gramfort ◽  
Denis A. Engemann
Keyword(s):  
Ground Truth ◽  
Spatial Filtering ◽  
Supervised Machine Learning ◽  
Brain Dynamics ◽  
Source Power ◽  
Relative Contribution ◽  
Cognitive States ◽  
The Subject ◽  
Eeg Recordings ◽  
Generative Mechanisms

AbstractPredicting biomedical outcomes from Magnetoencephalography and Electroencephalography (M/EEG) is central to applications like decoding, brain-computer-interfaces (BCI) or biomarker development and is facilitated by supervised machine learning. Yet most of the literature is concerned with classification of outcomes defined at the event-level. Here, we focus on predicting continuous outcomes from M/EEG signal defined at the subject-level, and analyze about 600 MEG recordings from Cam-CAN dataset and about 1000 EEG recordings from TUH dataset. Considering different generative mechanisms for M/EEG signals and the biomedical outcome, we propose statistically-consistent predictive models that avoid source-reconstruction based on the covariance as representation. Our mathematical analysis and ground truth simulations demonstrated that consistent function approximation can be obtained with supervised spatial filtering or by embedding with Riemannian geometry. Additional simulations revealed that Riemannian methods were more robust to model violations, in particular geometric distortions induced by individual anatomy. To estimate the relative contribution of brain dynamics and anatomy to prediction performance, we propose a novel model inspection procedure based on biophysical forward modeling. Applied to prediction of outcomes at the subject-level, the analysis revealed that the Riemannian model better exploited anatomical information while sensitivity to brain dynamics was similar across methods. We then probed the robustness of the models across different data cleaning options. Environmental denoising was globally important but Riemannian models were strikingly robust and continued performing well even without preprocessing. Our results suggest each method has its niche: supervised spatial filtering is practical for event-level prediction while the Riemannian model may enable simple end-to-end learning.

scholarly journals Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome

2018 ◽  
Author(s):  
Tom R. Booker ◽  
Peter D. Keightley
Keyword(s):  
House Mouse ◽  
Nucleotide Diversity ◽  
Mouse Genome ◽  
Parameter Estimates ◽  
Background Selection ◽  
Selective Sweeps ◽  
Functional Elements ◽  
Protein Coding ◽  
Wild Mice ◽  
Protein Coding Genes

AbstractA major goal of population genetics has been to determine the extent to which selection at linked sites influences patterns of neutral nucleotide diversity in the genome. Multiple lines of evidence suggest that diversity is influenced by both positive and negative selection. For example, in many species there are troughs in diversity surrounding functional genomic elements, consistent with the action of either background selection (BGS) or selective sweeps. In this study, we investigated the causes of the diversity troughs that are observed in the wild house mouse genome. Using the unfolded site frequency spectrum (uSFS), we estimated the strength and frequencies of deleterious and advantageous mutations occurring in different functional elements in the genome. We then used these estimates to parameterize forward-in-time simulations of chromosomes, using realistic distributions of functional elements and recombination rate variation in order to determine if selection at linked sites can explain the observed patterns of nucleotide diversity. The simulations suggest that BGS alone cannot explain the dips in diversity around either exons or conserved non-coding elements (CNEs). A combination of BGS and selective sweeps, however, can explain the troughs in diversity around CNEs. This is not the case for protein-coding exons, where observed dips in diversity cannot be explained by parameter estimates obtained from the uSFS. We discuss the extent to which our results provide evidence of sweeps playing a role in shaping patterns of nucleotide diversity and the limitations of using the uSFS for obtaining inferences of the frequency and effects of advantageous mutations.Author SummaryWe present a study examining the causes of variation in nucleotide diversity across the mouse genome. The status of mice as a model organism in the life sciences makes them an excellent model system for studying molecular evolution in mammals. In our study, we analyse how natural selection acting on new mutations can affect levels of nucleotide diversity through the processes of background selection and selective sweeps. To perform our analyses, we first estimated the rate and strengths of selected mutations from a sample of wild mice and then use our estimates in realistic population genetic simulations. Analysing simulations, we find that both harmful and beneficial mutations are required to explain patterns of nucleotide diversity in regions of the genome close to gene regulatory elements. For protein-coding genes, however, our approach is not able to fully explain observed patterns and we think that this is because there are strongly advantageous mutations that occur in protein-coding genes that we were not able to detect.

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