scholarly journals ON THE FREQUENCY OF UNDETECTABLE RECOMBINATION EVENTS

Genetics ◽  
1986 ◽  
Vol 112 (4) ◽  
pp. 923-926
Author(s):  
J Claiborne Stephens
Keyword(s):  
Population Size ◽  
Dna Sequence ◽  
Mutation Rate ◽  
Recombination Rate ◽  
Sequence Data ◽  
Recombination Rates ◽  
Dna Sequence Data ◽  
Analytical Results

ABSTRACT Simple analytical results show that many recombination events occur in such a way as to have no effect on the resultant DNA sequence. The proportion of these undetectable events depends on the population size, mutation rate and recombination rate and is quite large for reasonable values of these quantities. Efforts to estimate recombination rates and frequencies directly from DNA sequence data must, therefore, take this undetectable fraction into account.

scholarly journals Estimation of levels of gene flow from DNA sequence data.

Genetics ◽  
1992 ◽  
Vol 132 (2) ◽  
pp. 583-589 ◽  
Author(s):  
R R Hudson ◽  
M Slatkin ◽  
W P Maddison
Keyword(s):  
Gene Flow ◽  
Dna Sequence ◽  
Sequence Data ◽  
Gene Tree ◽  
Recombination Rates ◽  
Dna Sequence Data ◽  
Minimum Number ◽  
Computer Simulation Program ◽  
Infinite Sites Model ◽  
Better Than

Abstract We compare the utility of two methods for estimating the average levels of gene flow from DNA sequence data. One method is based on estimating FST from frequencies at polymorphic sites, treating each site as a separate locus. The other method is based on computing the minimum number of migration events consistent with the gene tree inferred from their sequences. We compared the performance of these two methods on data that were generated by a computer simulation program that assumed the infinite sites model of mutation and that assumed an island model of migration. We found that in general when there is no recombination, the cladistic method performed better than FST while the reverse was true for rates of recombination similar to those found in eukaryotic nuclear genes, although FST performed better for all recombination rates for very low levels of migration (Nm = 0.1).

Potential problems in estimating the male-to-female mutation rate ratio from DNA sequence data

1993 ◽  
Vol 37 (2) ◽  
pp. 160-166 ◽  
Author(s):  
Lawrence C. Shimmin ◽  
Benny Hung-Junn Chang ◽  
David Hewett-Emmett ◽  
Wen-Hsiung Li
Keyword(s):  
Dna Sequence ◽  
Mutation Rate ◽  
Rate Ratio ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Potential Problems ◽  
Male To Female

scholarly journals The Coalescent Process With Selfing

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 1185-1195 ◽  
Author(s):  
Magnus Nordborg ◽  
Peter Donnelly
Keyword(s):  
Dna Sequence ◽  
Mutation Rate ◽  
Sequence Data ◽  
Selfing Rate ◽  
Large Sample ◽  
Dna Sequence Data ◽  
True Value ◽  
Coalescent Process ◽  
Highly Sensitive ◽  
Degree Of Certainty

A method for estimating the selfing rate using DNA sequence data was recently proposed by Milligan. Unfortunately, a number of errors make interpretation of his results problematic. In the present paper we first show how the usual coalescent process can be adapted to models that include selfing, and then use this result to find moment estimators as well as the likelihood surface for the selfing rate, s, and the scaled mutation rate, θ. We conclude that, regardless of the method used, large sample sizes are necessary to estimate s with any degree of certainty, and that the estimate is always highly sensitive to recent changes in the true value.

scholarly journals DNA sonification for public engagement in bioinformatics

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Heleen Plaisier ◽  
Thomas R. Meagher ◽  
Daniel Barker
Keyword(s):  
Dna Sequence ◽  
Public Engagement ◽  
Sequence Data ◽  
Sensory Perception ◽  
Data Representation ◽  
Sequence Information ◽  
Dna Sequence Data ◽  
Public Events ◽  
Dna Base ◽  
Alternative Means

Abstract Objective Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification. Results We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education.

A new Liopeltis Fitzinger, 1843 (Squamata: Colubridae) from Pulau Tioman, Peninsular Malaysia

Zootaxa ◽  
2020 ◽  
Vol 4766 (3) ◽  
pp. 472-484
Author(s):  
HANNAH E. SOM ◽  
L. LEE GRISMER ◽  
PERRY L. JR. WOOD ◽  
EVAN S. H. QUAH ◽  
RAFE M. BROWN ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
New Species ◽  
Dna Sequence ◽  
Rare Species ◽  
Sequence Data ◽  
Peninsular Malaysia ◽  
Tropical Asia ◽  
Dna Sequence Data ◽  
A New Species ◽  
Lines Of Evidence

Liopeltis is a genus of poorly known, infrequently sampled species of colubrid snakes in tropical Asia. We collected a specimen of Liopeltis from Pulau Tioman, Peninsular Malaysia, that superficially resembled L. philippina, a rare species that is endemic to the Palawan Pleistocene Aggregate Island Complex, western Philippines. We analyzed morphological and mitochondrial DNA sequence data from the Pulau Tioman specimen and found distinct differences to L. philippina and all other congeners. On the basis of these corroborated lines of evidence, the Pulau Tioman specimen is described as a new species, L. tiomanica sp. nov. The new species occurs in sympatry with L. tricolor on Pulau Tioman, and our description of L. tiomanica sp. nov. brings the number of endemic amphibians and reptiles on Pulau Tioman to 12. 

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