Author Archives: Gavin

Paper that may be of interest

Sampling for Microsatellite-Based Population Genetic Studies: 25 to 30 Individuals per Population Is Enough to Accurately Estimate Allele Frequencies

Marie L. Hale1*, Theresa M. Burg2, Tammy E. Steeves1
1 School of Biological Sciences, University of Canterbury, Christchurch, New Zealand, 2 Department of Biology, University of Lethbridge, Lethbridge, Canada

Abstract
One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is “how many individuals do I need to sample from each population?” This question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefaction based analyses). However, we argue that obtaining accurate allele frequencies and accurate estimates of diversity are much more important than detecting all of the alleles, given that very rare alleles (i.e. new mutations) are not very informative for assessing genetic diversity within a population or genetic structure among populations. Here we present a comparison of allele frequencies, expected heterozygosities and genetic distances between real and simulated populations by randomly subsampling 5–100 individuals from four empirical microsatellite genotype datasets (Formica lugubris, Sciurus vulgaris, Thalassarche melanophris, and Himantopus novaezelandiae) to create 100 replicate datasets at each sample size. Despite differences in taxon (two birds, one mammal, one insect), population size, number of loci and polymorphism across loci, the degree of differences between simulated and empirical dataset allele frequencies, expected heterozygosities and pairwise FST values were almost identical among the four datasets at each sample size. Variability in allele frequency and expected heterozygosity among replicates decreased with increasing sample size, but these decreases were minimal above sample sizes of 25 to 30. Therefore, there appears to be little benefit in sampling more than 25 to 30 individuals per population for population genetic studies based on microsatellite allele frequencies.

Accommodation needed

Does anyone have a spare room/sofa available for a few nights for a new post-doc, Takanori Shono (Taka), arriving from Japan on the 10th of September. He will require a few nights to organise some more permanent accommodation. If you have a spare room please contact Gareth Fraser (g.fraser@sheffield.ac.uk) and he will give you all the details.

Gav

Petanque

The sun is out so petanque is on. 1:00pm in the park. Be there or be rotund and unhealthy.

Petanque today (Thursday)

Since the sun has appeared and its the 1st of March we will be enjoying a game of petanque in the park. Feel free to come and join in.

Gav

Looks like Petanque time again

As the weather is suppose to warm up a bit we are going to have a game of Petanque in the park Friday 1pm. Be there or be……..!

Lunch today

Lunch is booked for 12-12:15 at Loch Fyne so we are probably best to leave at 12:00.

Cheers

Gav

Its my Birthday…

Hi all,

Since its my 40th Birthday next Wednesday I was planning on an outing to Loch Fyne for lunch on that day. There is a two course set menu for £9.95 which you can peruse by checking out this link http://www.lochfyne-restaurants.com/menus-and-wine-list/.

Please let me know by the end of the week if you are interested and I can book it (assuming you need to book)

Cheers

Gav

Gav is back

Hi all,
Just to let everybody know I am back at work so if anybody needs anything feel free to come and find me.

Cheers

Gav

Free Accomadation Available

Free accomodation is available at Virpi’s house from the 7th of December to the 10th of January.
Conditions are that you feed the fish every 2nd day and water the plants every two weeks. Staying for even part of the above period would also be useful.

Please contact Virpi if you are interested at V.Lummaa@sheffield.ac.uk

454 sequencing software

Hi all,

Managed to get Roche to give me a copy of there 454 sequencing analysis software in 32 and 64 bit including user manuals. If anyone would like to try it and install it on there computer or the super fast computer then come and see me. If not i will install it at some point ready for use.

Gav