Currently I am looking at divergence between some recently separated wild insect populations (*Beast says divergence ~40 to 10 ka). I'd really like to get a handle on just how different they are as a % divergence, but I have no idea how to do this for hundreds of loci and individuals. Sure, if I had a handful of loci I'd run them through DNAsp or something, but that's not really practical given the size of the dataset. Any ideas?
I don't really know the answer. As Tyler says, you could write scripts to run all the data to get the answer. But I am wondering if the answer is likely to be of much use to you. With human data, we have quite an abundance of similar data because humans are very interested in human evolution. The complete genomes of many individual humans from many populations have now been done, and we have even larger data sets from the "SNP on a Chip" methods that don't really sequence the whole genome but look at known polymorphic sites. We also have genomes of Neanderthal individuals and genomes of Denisova individuals plus genomes of chimpanzees and gorillas. There are not many DNA base changes in between humans and chimpanzees, let alone between human populations so the answer on diversity for most loci is zero percent (100% identity) but there are some major differences between chimpanzees and humans of course. A lot of the major genetic changes are changes in number and positions of Alu repeats, number and positions of endogenous retroviruses and other mobile elements. There are also chromosomal fusions and other changes which will not register as any difference in % identity between loci.
Why not do a simple neighbor doing tree and save the pairwise matrix. this can be done in PAUP, Mega, seaview, etc.
Fastphylo and/or PAUP should be able to do this on the command line if you are comfortable working in linux.
You can use Arlequin software to calculate gene diversity between your samples using transition, transversion and Indel
I just discovered the PYLUCE (pronounced Phy Loo Cee) software and it seems to do exactly what you want. It does not give the names of each of of the loci it compares but it searches complete genomes of dozens to hundreds of species or isolates and aligned conserved regions that it finds in the genomes. A few papers have been published now using complete genome data from mammals, insects, lizards and snakes, etc.
http://faircloth-lab.org/research/
Is the batch mode of DNAsp not good enough?
In my hands, it can analyse several thousands faster files in less than an hour...
- Badges
- Science topic
- Similar topics
- Biological Science
- Kinesiology
- Running