I'm doing a study on mammal colonization timeline in one of the Islands in Tanzania by using mitochondria DNA sequences. Is there a specific analysis which can do that?
Your answers will be helpfull.
Some more specific would help identify potential solutions for your question. Are you just looking to date divergence times based on a molecular clock using the mitochondrial data? I think the most comprehensive and widely used program to do that is BEAST, which has modules to both construct the phylogeny and date the divergence times.
Do you want to test explicit hypotheses about divergence times and potential scenarios? If so, there are a variety of coalescent-based programs that can do that. Again I think BEAST is one, but there are others. Maybe check out fastsimcoal and DIYABC for different approaches. Hopefully this gives you a place to start.
Thank you very much Justin H. Bohling for your answer. My basic question is that, there are hippos in one of the Island in Tanzania and we don't know where they come from and when they colinized the island. Therefore, I want to understand when they colonized that island by using mtNDA sequences. I'm not clear about which analysis is suitable to achive that objective.
Hope that added a little explanation
Identifying the population of origin should be pretty straight-forward: generate haplotypes from a variety of potential source populations and then construct a haplotype network. Specific colonization patterns can also be tested using a coalescent approach: something like DIYABC or fastsimcoal can let you test specific hypotheses.
For the timeline, I would again suggest using something like BEAST with a molecular clock to try and date the colonization. Do you have a ballpark estimate for how long these hippos have been on that island? If it is too recent, I don't know if a single mitochondrial haplotype will provide the resolution you need. For example, if all the hippos on the island have a haplotype identical to a mainland population, there really is no point in trying to estimate divergence times.
- Badges
- Science method