I have read that sequence based data are not powerful for analyze isolation by distance between population. However, I want to know if is possible to analyze the effect of environmental variables as elevation, temperature or land use on the genetic differentiation between lineage or cryptic species using sequence based data as mitochondrial DNA and nuclear DNA (ITS2)?
If yes. Which metric should I use as a measure of genetic differentiation between lineage or cryptic species?
If not. I know that ITS data can have microsatellites, it is possible to use these microsatellites as a source of genetic information for landscape genetics?
selecting the markers for landscape genetics depends on the level of divergence of the putative lineages. For example, cytb of mtDNA can capture the lineages separated around 1 to 20 million years. If you need to capture the differentiation very recently, d-loop could be a better option. Microsatellite can capture the differentiation in very recent times even within a species. I used microsatellite markers for landscape genetics of mosquitofish in coastal Louisiana to understand genetic differentiation due to temperature, salinity and salt water intrusion.Article Salinity and hydrological barriers have little influence on ...
. I used cytb for understanding genetic differentiation between 1 to 2o million years.https://scholarworks.uark.edu/etd/3170/.
Thanks. I also use my self microsatellite to get information about relative recently landscape in two species of bees. But you partially answer my question, if I can use sequence based data for landscape genetic. As you seems to propose if I want to see effect of the landscape millions of years ago between lineages then sequence based data can be useful... But probably we still have to check how powerful is the marker for the specific taxa.
Hi, all boils down to scales (both spatial and time) at which you hope to see divergence. Sequence based markers generated by NGS may be very powerful - often shortcomings in low divergence in (some) loci are overcome by vast numbers of generated markers. This gives you many exciting possibilities, e.g. you can try to GWAS landscape-based parameters having a dense marker map, to see whether your landscape is in any way interacting with specific (selected) loci. Have a look at a brief summary of Landscape Genomics here: Article Navigating the Interface Between Landscape Genetics and Land...
I worked in SSR, ribosome(include ITS1,5.8S,ITS2,18S........),mitochondrion. I suggest you test it before you use the ssr which is in ITS. Because ribosomes are multiple copies(some of the copy are different), not have the advantages of the ssr in other region. There may be mixed bands.
Shilli Liu Thank for the information. do you have some publication about this?
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