scholarly journals DNA Sequence Variation at the Period Locus Reveals the History of Species and Speciation Events in the Drosophila virilis Group

Genetics ◽  
1996 ◽  
Vol 144 (3) ◽  
pp. 1015-1025 ◽  
Author(s):  
Holly Hilton ◽  
Jody Hey
Keyword(s):  
Population Size ◽  
Dna Sequences ◽  
Sequence Variation ◽  
Drosophila Virilis ◽  
Geographic Pattern ◽  
Effective Population ◽  
Dna Sequence Variation ◽  
Virilis Group ◽  
History Of ◽  
Drosophila Virilis Group

Abstract The virilis phylad of the Drosophila virilis group consists of five closely related taxa: D. virilis, D. lummei, D. novamexicana, D. americana americana and D. americana texana. DNA sequences from a 2.1-kb pair portion of the period locus were generated in four to eight individuals from each of the five taxa. We found evidence of recombination and high levels of variation within species. We found no evidence of recent natural selection. Surprisingly there was no evidence of divergence between D. a. americana and D. a. texana, and they collectively appear to have had a large historical effective population size. The ranges of these two taxa overlap in a large hybrid zone that has been delineated in the eastern U.S. on the basis of the geographic pattern of a chromosomal fusion. Also surprisingly, D. novamexicana appears to consist of two distinct groups each with low population size and no gene flow between them.

scholarly journals STATISTICAL PROPERTIES OF THE NUMBER OF RECOMBINATION EVENTS IN THE HISTORY OF A SAMPLE OF DNA SEQUENCES

Genetics ◽  
1985 ◽  
Vol 111 (1) ◽  
pp. 147-164 ◽  
Author(s):  
Richard R Hudson ◽  
Norman L Kaplan
Keyword(s):  
Population Size ◽  
Dna Sequences ◽  
Recombination Rate ◽  
Statistical Properties ◽  
Neutral Model ◽  
Effective Population ◽  
History Of ◽  
Mean And Variance ◽  
The Mean ◽  
Quantities Of Interest

ABSTRACT Some statistical properties of samples of DNA sequences are studied under an infinite-site neutral model with recombination. The two quantities of interest are R, the number of recombination events in the history of a sample of sequences, and RM, the number of recombination events that can be parsimoniously inferred from a sample of sequences. Formulas are derived for the mean and variance of R. In contrast to R, RM can be determined from the sample. Since no formulas are known for the mean and variance of RM, they are estimated with Monte Carlo simulations. It is found that RM is often much less than R, therefore, the number of recombination events may be greatly under-estimated in a parsimonious reconstruction of the history of a sample. The statistic RM can be used to estimate the product of the recombination rate and the population size or, if the recombination rate is known, to estimate the population size. To illustrate this, DNA sequences from the Adh region of Drosophila melanogaster are used to estimate the effective population size of this species.

scholarly journals A phylogenetic estimator of effective population size or mutation rate.

Genetics ◽  
1994 ◽  
Vol 136 (2) ◽  
pp. 685-692 ◽  
Author(s):  
Y X Fu
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Dna Sequences ◽  
High Efficiency ◽  
Minimum Variance ◽  
Population Subdivision ◽  
Effective Population ◽  
Fisher Model ◽  
Mitochondrial Sequences

Abstract A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.

scholarly journals DNA Sequence Variation and the Recombinational Landscape in Drosophila pseudoobscura: A Study of the Second Chromosome

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 859-869 ◽  
Author(s):  
Martha T Hamblin ◽  
Charles F Aquadro
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Population Expansion ◽  
Drosophila Pseudoobscura ◽  
Effective Population ◽  
Standing Variation ◽  
Dna Sequence Polymorphism ◽  
Slightly Deleterious Mutations

Abstract The relationship between rates of recombination and DNA sequence polymorphism was analyzed for the second chromosome of Drosophila pseudoobscura. We constructed integrated genetic and physical maps of this chromosome using molecular markers at 10 loci spanning most of its physical length. The total length of the map was 128.2 cM, almost twice that of the homologous chromosome arm (3R) in D. melanogaster. There appears to be very little centromeric suppression of recombination, and rates of recombination are quite uniform across most of the chromosome. Levels of sequence variation (θW, based on the number of segregating sites) at seven loci (tropomyosin 1, Rhodopsin 3, Rhodopsin 1, bicoid, Xanthine dehydrogenase, Myosin light chain 1, and ribosomal protein 49) varied from 0.0036 to 0.0167. Generally consistent with earlier studies, the average estimate of θW at total sites is 1.5-fold higher than that in D. melanogaster, while average θW at silent sites is almost 3-fold higher. These estimates of variation were analyzed in the context of a background selection model under the same parameters of mutation rate and selection as have been proposed for D. melanogaster. It is likely that a significant fraction of the higher level of sequence variation in D. pseudoobscura can be explained by differences in regional rates of recombination rather than a larger species-level effective population size. However, the distribution of variation among synonymous, nonsynonymous, and noncoding sites appears to be quite different between the species, making direct comparisons of neutral variation, and hence inferences about effective population size, difficult. Tajima’s D statistics for 6 out of the 7 loci surveyed are negative, suggesting that D. pseudoobscura may have experienced a rapid population expansion in the recent past or, alternatively, that slightly deleterious mutations constitute an important component of standing variation in this species.

Sequence variation and evolution of nuclear DNA in man and the primates

1981 ◽  
Vol 292 (1057) ◽  
pp. 133-142 ◽  
Keyword(s):  
Dna Sequence ◽  
Sequence Variation ◽  
Nuclear Dna ◽  
Sequence Divergence ◽  
Gene Arrangement ◽  
Human Populations ◽  
Genetic Changes ◽  
Detailed Structural Analysis ◽  
Dna Sequence Variation ◽  
History Of

Recent advances in nucleic acid technology have facilitated the detection and detailed structural analysis of a wide variety of genes in higher organisms, including those in man. This in turn has opened the way to an examination of the evolution of structural genes and their surrounding and intervening sequences. In a study of the evolution of haemoglobin genes and neighbouring sequences in man and the primates, we have investigated gene arrangement and DNA sequence divergence both within and between species ranging from Old World monkeys to man. This analysis is beginning to reveal the evolutionary constraints that have acted on this region of the genome during primate evolution. Furthermore, DNA sequence variation, both within and between species, provides, in principle, a novel and powerful method for determining inter-specific phylogenetic distances and also for analysing the structure of present-day human populations. Application of this new branch of molecular biology to other areas of the human genome should prove important in unravelling the history of genetic changes that have occurred during the evolution of man.

scholarly journals Recombination Gives a New Insight in the Effective Population Size and the History of the Old World Human Populations

2011 ◽  
Vol 29 (1) ◽  
pp. 25-30 ◽  
Author(s):  
Marta Melé ◽  
Asif Javed ◽  
Marc Pybus ◽  
Pierre Zalloua ◽  
Marc Haber ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Human Populations ◽  
Effective Population ◽  
Old World ◽  
History Of

scholarly journals Mobile elements reveal small population size in the ancient ancestors of Homo sapiens

2010 ◽  
Vol 107 (5) ◽  
pp. 2147-2152 ◽  
Author(s):  
Chad D. Huff ◽  
Jinchuan Xing ◽  
Alan R. Rogers ◽  
David Witherspoon ◽  
Lynn B. Jorde
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Dna Sequences ◽  
Mobile Element ◽  
Small Population ◽  
Mobile Elements ◽  
Population History ◽  
Recent Common Ancestor ◽  
Demographic Model ◽  
Effective Population

The genealogies of different genetic loci vary in depth. The deeper the genealogy, the greater the chance that it will include a rare event, such as the insertion of a mobile element. Therefore, the genealogy of a region that contains a mobile element is on average older than that of the rest of the genome. In a simple demographic model, the expected time to most recent common ancestor (TMRCA) is doubled if a rare insertion is present. We test this expectation by examining single nucleotide polymorphisms around polymorphic Alu insertions from two completely sequenced human genomes. The estimated TMRCA for regions containing a polymorphic insertion is two times larger than the genomic average (P < <10−30), as predicted. Because genealogies that contain polymorphic mobile elements are old, they are shaped largely by the forces of ancient population history and are insensitive to recent demographic events, such as bottlenecks and expansions. Remarkably, the information in just two human DNA sequences provides substantial information about ancient human population size. By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000. This result implies an unusually small population for a species spread across the entire Old World, particularly in light of the effective population sizes of chimpanzees (21,000) and gorillas (25,000), which each inhabit only one part of a single continent.

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