Population genetics is the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation, and gene flow. It also takes into account the factors of recombination, population subdivision, and population structure. It attempts to explain such phenomena as adaptation and speciation.

• Matías Sebastián Mora

  Selection analysis to perform on intron genetic markers

  I need to perform a selection analysis on some intron genetic markers that were sequenced from several natural populations of a rodent species, but I have no idea which test(s) I would have to useI need to perform a selection analysis on some intron genetic markers that were sequenced from several natural populations of a rodent species, but I have no idea which test(s) I would have to use for this purpose. We thought that some introns could have been influenced by selection processes, but I do not have the corresponding exon sequences. Can someone help me to some helpful papers?

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    Pedro Hidalgo replied

    Hi, Perhaps this paper will be useful: Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Mol Ecol 13:969–980

    28 days ago
• Gunter Kathagen

  Which genetic marker to use for a coalescence analyses?

  For my thesis I might want to do a coalescence analyses on populations of a rare herbaceous grassland plant, but I have no idea which genetic marker(s) I would have to use. Can anyone help me orFor my thesis I might want to do a coalescence analyses on populations of a rare herbaceous grassland plant, but I have no idea which genetic marker(s) I would have to use. Can anyone help me or redirect me to some helpful papers?

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    Pairot Pramual replied

    It is easier to start with the DNA sequence marker. You could use ITS or rbc or matK genes. These sequences often use for population genetic of plants. Good luck

    Apr 17, 2012
• Flavio Oliveira Francisco

  Does anybody know how to apply Jost's D for mtDNA sequence data?

  I want to check if there is genetic differentiation among pairs of populations, and with mtDNA sequence data I am allowed to use Fst and Exact Test in Arlequin. The results are pretty contrasting andI want to check if there is genetic differentiation among pairs of populations, and with mtDNA sequence data I am allowed to use Fst and Exact Test in Arlequin. The results are pretty contrasting and I am reading some papers about the drawbacks in using Fst and hypothesis tests as a measure of differentiation. Jost's D and Hedrick's G'st are being widely used with microsatellites data. But, what would be appropriate for mtDNA data?

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    Flavio Oliveira Francisco replied

    Hi Mark. Thanks for the link. I found a similar question in this forum. And similar results as well. Using haplotypes as alleles (all in homozygosis, to use genepop input format in SMOGD), D valuesHi Mark. Thanks for the link. I found a similar question in this forum. And similar results as well. Using haplotypes as alleles (all in homozygosis, to use genepop input format in SMOGD), D values are very high, even between populations that share haplotypes. Maybe Exact Tests are more suitable for this kind of situation.

    Mar 16, 2012

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    Alexander Pudovkin replied

    Alexander Pudovkin I am interested.

    Feb 22, 2012
• Vitor Miranda

  Book about populations genetics focusing related computing methods

  Hi, I would appreciate an advice to a great book about populations genetics focusing related computing methods (median joining, bayesian, molecular clock, etc.). Could anyone help me? Thanks!

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    Vitor Miranda replied

    Hi Kornelia, hi Thierry, Thanks for the references. The second one is new for me. Cheers, Vitor

    Feb 19, 2012
• Flavio Oliveira Francisco

  Doubts about Bonferroni correction.

  I have 14 microsatellite markers and 24 populations. How do I apply Bonferroni correction in my Genepop results (HWE, LD, and genic differentiation for all pairs of population)?

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    Flavio Oliveira Francisco replied

    Hi Anahi. You are right. Arlequin uses fragment size and it is possible to run it using SMM or IAM. Now I have a lot of analyses to perform! And thanks for the papers.

    Jan 31, 2012
• Rute Brito

  Is it possible to use Structure v.2.3.3 (http://pritch.bsd.uchicago.edu/structure.html) in Windows 7?

  I had successfully used the Structure in Linux, Windows XP and Vista, but I can't make it run with Windows 7. I already went through the specialized forum at the program's website and the only hintI had successfully used the Structure in Linux, Windows XP and Vista, but I can't make it run with Windows 7. I already went through the specialized forum at the program's website and the only hint that I could relate with my case was about Java updating. Well, I updated it and even so it doesn't work. It runs the MCMC and burn in, but it crashes when it try to "Start a Job". My computer is a Core 2 Duo T6400 2.00GHz, 4GB RAM, Windows 7 Home Premium SP1 64-bit java 6 update 30. Does anyone have any suggestion? Thank you in advance!

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    Rute Brito replied

    Hi Vitor! The "troubleshoot compatibility" worked!!! Thank you very much for the powerful hint! Cheers, Rute

    Jan 31, 2012
• Vitor Aguiar

  R code for Hardy-Weinberg test for multiple allele STR loci

  Does anyone have a simple R code (without packages) to test for HWE by chi-square for multiple allele STR loci if I have an array of genotype and allele frequencies?
• Vitor Aguiar

  Hardy-Weinberg Equilibrium of STR markers using R

  Hello! May anyone help me? I'd like to know what's the best way to calculate Hardy-Weinberg Equilibrium using R. I tried the pegas package, but since I'm not familiar with programming I could notHello! May anyone help me? I'd like to know what's the best way to calculate Hardy-Weinberg Equilibrium using R. I tried the pegas package, but since I'm not familiar with programming I could not make it work yet... I'm analyzing multi allelic STR markers.

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    Bernardo Bertoni replied

    Sorry I wasn't clear. Of course you can use pegas. Also you have 'genetic' package for R (usually I use it). Arlequin is easier once you have your data formatted. You can treat them as number ofSorry I wasn't clear. Of course you can use pegas. Also you have 'genetic' package for R (usually I use it). Arlequin is easier once you have your data formatted. You can treat them as number of repeat (under stepwise mutation model) for example, if you are planning to do another kind of analysis.

    Jan 23, 2012
• Andre Aberer

  Computational Challenges in Population Genetics

  Dear all, what are in your opinion the major computational bottlenecks in population genetics? I am Bioinformatician and am searching for methods that are algorithmically challenging toDear all, what are in your opinion the major computational bottlenecks in population genetics? I am Bioinformatician and am searching for methods that are algorithmically challenging to optimize/parallelize. To put it differently: for which tools/programs that you use would it be advantageous, if greater datasets could be computed on a multi-core cluster? Cheers, Andre

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    Miguel Navascués replied

    I agree with Peter that we should not sacrifice the advances on population genetic inference under complex models. In many cases, I think it will be more interesting to analyse a subset of loci withI agree with Peter that we should not sacrifice the advances on population genetic inference under complex models. In many cases, I think it will be more interesting to analyse a subset of loci with current methods (MCMC/ABC) than "calculate FST scores for their genomic data". My point was that it will be a good research topic for those with a mathematical mind (not me) to explore alternatives to MCMC and ABC for the estimation or approximation of likelihood. These alternatives could be more computationally efficient or more effective for taking into account the linkage among markers. Some alternatives have been already proposed based on PAC-likelihood and Hidden Markov Models (NB: I do not fully understand those methods, but what I have read seems promising). Some advances might be done also for improving MCMC and ABC approaches in a more fundamental way that just doing the same thing faster. In any case, if any new method arises is likely to be implemented in a simple model at the begining; I do not think that would be "falling back to dark ages of population genetics" if the method has potential to be further developed into more complex models (which takes time, as Peter knows better than I do). From Peter's comment it seems that, even if nobody finds a faster way to do MCMC/ABC or faster alternatives, we could always wait for faster computers, because populations genomics is just population genetics "but with many more loci". I am not sure of this. It is not "just many more loci" but linkage among markers will be significant, while in population genetic studies usually the markers are independent. I have not followed the progress to incorporate recombination in MCMC analysis but I think it is still not very advanced (any feedback on this? it would be great to be wrong on this :) ) and regarding ABC, recombination increases simulation time enormously (well, I guess this really can be solved with faster computers...). Last, I would like to point out that model-based statistics might not be always the most appropriate or effective way to analyse our data (either "genetic" or "genomic"). It depends on the purpose of the analsys and on our study organism. For instace, partially clonal diploids (with high clonality rate) will have a coalescent completely different from the one implemented on most (all?) MCMC-based software and coalescent simulators. Another case can be that the purpose of our analysis is just descriptive, Fst scores and other summary statistics migth be useful to describe the genetic diversity of the studied species. Also, clustering algorithms based on PCA and related methods seem to lead to very similar results as model-based clustering methods (i.e. STRUCTURE, etc) in much less time, so they might be preferable for genomic data.

    Jan 19, 2012
• jagat krishna Shrestha

  Have anyone used POPGENE software in population genetics of plants?? Can it be used even if the sample no. of each population is 5??

  In case of vulnerable plants??
• Wei Lun Ng

  How to estimate genetic diversity of polyploid species?

  Hi all, I’m trying to assess the genetic diversity in several populations of a plant species believed to be threatened. However, I recently found out that the species may be a polyploid (hexaploidHi all, I’m trying to assess the genetic diversity in several populations of a plant species believed to be threatened. However, I recently found out that the species may be a polyploid (hexaploid or 12-ploid) through a comparison of the number of chromosomes present in this species and other closely-related species. The question now is: How to estimate the genetic diversity in my samples using DNA sequence data? To start, how is it even possible, technically speaking, to identify and fish out all the possible alleles/haplotypes? The possible problems that I could think of now are: 1. If cloning were to be done for every sample, at what point should I stop hoping to find new haplotypes? (It would probably be easier if we were to find 6 or 12 different haplotypes in every case given its possible ploidy level; but what if there were, for eg. only 3 haplotypes? How do we infer the frequencies of each haplotype in each individual?) 2. How many clones should I sequence in order to find all the possible haplotypes in one individual? Too few and I may miss some haplotypes; too many and I may find similar copies of chimeric sequences (recombination of plasmids during bacteria culturing) which will then be treated as a true haplotype. I’m new to such a situation and I hope someone could enlighten me on this, or maybe point me to an article with a similar study. Would really appreciate it :)) Thank you!

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    Wei Lun Ng replied

    Hi, thank you very much for the recommendation. I shall take a look at the article and come back to you once there is any development. Once again, thank you! :)

    Sep 9, 2011
• Vasulu TS

  The recent discovery of Siberian Hominin and mtDNA diversity

  The latest paper in Nature (by J Krause et al., March 2010 -doi:10.1038/nature08976) describes the mtDNA variation of Siberian Hominin, supposed to be about 30-40 thousands years ago, based on theThe latest paper in Nature (by J Krause et al., March 2010 -doi:10.1038/nature08976) describes the mtDNA variation of Siberian Hominin, supposed to be about 30-40 thousands years ago, based on the geostrata callibration showed surprising mismatch with the current population samples, samples from Neanderthal and the tree diagram shows the Siberian sample deviating away from the rest of the samples compared. For more information please get on to the on line version of the paper: nature:doi:10.1038/nature08976 I invite comments and discussion on this recent issue, which has a surprising impact of our understanding of the human evolutioanary forms known to us so far.