It depends on the organism. AFLP is widely accepted as valid tool for population genetics in plants but not for animals. I don't really know why. If your organisms already has a lot of published microsats I would focus on them. But if thats not the case I would go for AFLP. AFLP is a bit tricky to optimise, but so are microsats. You would get more infomation per loci with microsats but get many more loci with AFLP. The latter is valuable if you plan to test for natural selection and local adaptation. DNA for AFLP is trickier to extract since it is sensitive to fragmentation.

Thanks, Mats!

We're worlking on animals (isopods), and we'll probably go for microsats...

I have been involved in a study of genetic change in copepodes the relied on AFLP to study genetic variation. They could perhaps be helpful.

Gardeström J, Dahl U, Kotsalainen O, Maxson A, Elfwing T, Grahn M, Bengtsson BE, Breitholtz M. 2008. Evidence of population genetic effects of long-term exposure to contaminated sediments – A multi-endpoint study with copepods. Aquatic Toxicology. 86: 426-436. [doi: 10.1016/j.aquatox.2007.12.003]

15. Gardeström J, Gorokhova E, Gilek M, Grahn M, Bengtsson BE, Breitholtz M. 2006. A multilevel approach to predict toxicity in copepod populations: Assessment of growth, genetics, and population structure. Aquatic Toxicology. 79: 41-48. [doi: 10.1016/j.aquatox.2006.05.001]

I'll have a look at these papers - thanx again!

Microsats are expensive and species-specific. You cannot switch to another species after you've dealt with the previous but will need a new panel to design, the whole work from the beginning.

AFLP is universal and can be applied to genomic DNA of any organism using the original protocol as introduced by Voss et al. (1995), even same enzymes and adapters, with no constraints for animals (e.g. Jiang X. et al. Environ Entomol. 2010:232-242). See the troubleshooting guide:

https://www.researchgate.net/publication/7872175_Use_of_amplified_fragment_length_polymorphism_(AFLP)_markers_in_surveys_of_vertebrate_diversity/file/9fcfd500ff79150e70.pdf

Mats Grahn is right about DNA extraction problems, but If you can get your isopods to the lab alive prior to DNA extraction, you can extract it undegraded from alive or -80C frozen samples.

Article Use of Amplified Fragment Length Polymorphism (AFLP) Markers...

Thanks, Yuri!

Different opinions always make things complicated - but that's why we ask colleagues, isn't it.

We will probably, anywa, first check for DNA quality upon extraction (so far, we never had any problems with this, but we never before aimed at "whole genomic DNA" but rather single genes...

AFLPs are cheaper and are typically thought of as superior to microsatellites because so many fragments can be so easily obtained and they provide a framework that is easily applicable to closely related species. In contrast, microsatellites are more difficult to develop, you will wind up with fewer perhaps hyper-variable markers, and they may not cross-amplify well in related taxa. Also, while a constraint is that AFLPs are dominant, they are really useful if your study system is one in which there is a low degree of population genetic differentiation, a case in which microsatellites are known to have lower statistical power e.g. for assignment tests. AFLPs are very useful if you are studying closely related taxa, particularly if you are interested in determining population membership/sources of migrants etc.. Do you already have DNA seq data and do they show that your species/populations aren't super variable? Are you interested in assignment? If so, maybe go with AFLPs (if Fst < 20%). You could easily get >100 fragments.

Alternatively, even though the AFLP route is cheaper and a much better cost:benefit ratio, would it be possible to use both methods given they are both working?! I'm only asking this because maybe you can find a way, and if you can do so you might benefit greatly from using both of these data types in your sampling design, given their complementary nature.

Alex's point about your question is a good one though. What is your question? What are you trying to accomplish? Good luck!

Dear all - thanks a lot, indeed, for these elaborate and valuable comments!

Our question is on the relationship between intraspecific genetic diversity (in a given population - actually, comparing different populations from distinct regions, and comparing experimentally manipulated diversity (through breeding) in lab populations) ecosystem processes and environmental stress: to this end, we want to (1) test for differences in intraspecific diversity among populations from different environments, (2) follow changes in diversity over time, and (3) correlate diversity and population-level performance...

The suitability to estimate heyerozygosity with AFLP markers has been questioned since they are dominant. But if you can assume HWE they often perform well. If you know or can guess an inbreeding coefficient you can correct for that in for instance the analysis package AFLPsurv by Wekemans. However, estimating a genome wide heterozygosity with msat is very difficult since the loci will vary a lot due to their high mutation rate and varying levels of heterozygosity at different genomic regions. With your research question I would choose AFLP or SNPs. If you have not read Markert et al. 2010 I would recommend it.

http://www.ncbi.nlm.nih.gov/m/pubmed/20609254/

Thanks, Mats - that looks like a helpful paper!

It would be great if you could have both markers in your study. They provide different patterns of information and their combination gives best answer to your research question. If you focus more on differentiation among populations, gene flow, spatial diversity patterns, etc. then AFLP could be better. This applies especially in the case you do not have SSR markers available in the literature for the species in question. SSR markers are better when you want to compare diversity levels within populations (you need equally large samples though). They have many alleles and they can easily show drift effects (bottlenecks or founder effects) and mating system parameters, as well as gene flow within populations. Due to their enorm diversity within populations, SSR markers frequently have low levels of differentiation among populations and are not suited for estimating differentiation levels. Check also the null alleles option, which can lead you to false conclusions about mating system efficiency.

Since microsatellite markers are not yet known for many species and may have a challenge to build new primers for SSR, Most people focus on developing an AFLP assay for the species, as this method does not require knowledge about species-specific marker sequences. But if know the sequence of primers, microsatellite is easier as one do one PCR cycle and gives to a certain degree good results.

234

AFLP is more specific to determine the loci of gene