I am studying two types of Ophidiid fishes having features morphologically similar and would like to genetically classify them.
I have already investigated COI region of mtDNA, but the genetic difference is quite small (2 to 7 mutational steps between nearest and farthest haplotypes), so I am considering of conducting experiments using nuclear DNA.
However, I am not sure which genetic marker will be suitable for analysis to make a marked difference than COI.
So far, I am considering of using the RAG1 region, which has been studied in related species, or ITS, where base substitution is likely to occur because of non-coding region.
Could you tell me if there are better genetic markers that has a fast base substitution rate and is effective in clarifying interspecific or intraspecific differences?
I hope this paper may help you:
Article Frompromise to practice: Pairing non-invasive sampling with ...
Genotyping by sequencing techniques search for variants by next generation sequencing using different workflows to extract genomic information (GBS, RADseq, ddRAD, nextRAD...)
The lab I work in is conducting phylogeographic researches with SNPs obtained via nextRAD sequencing.
Here are some examples of the analysis and results you may construct with that kind of data:
Article Hybridization Between Yuccas From Baja California: Genomic a...
Article Pleistocene climatic fluctuations drive isolation and second...
Article Latitudinal divergence in a widespread amphibian: Contrastin...
Jose Alberto Lopez-Aleman
Thank you for your kind reply.
I didn't think of genotyping. I would like to use them as references.
Hi Mita,
Given your fish species are closely related as revealed by mtDNA, it is preferable to choose hyper variable regions of nuclear genome. Markers occurrs to me are microsattlites (STR) and MHC. STRs have faster mutation rates than mtDNA in animals in general. Some regions of MHC also evovled very fast due to selection. Have a look at review paper below might help.
Zhang DX, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology, 12: 563-584.
Cheng-Min Shi
Thank you for your reply.
I have read the paper you attached.
STR is a good way to find differences.
I would like to investigate if it can be applied to fish.
Please read this article, it will help you.......
Identifying genetic markers for a range of phylogenetic utility–From species to family level
Bokyung Choi, Michael D. Crisp, Lyn G. Cook, Karen Meusemann, Robert D. Edwards, Alicia Toon, Carsten Külheim https://doi.org/10.1371/journal.pone.0218995
Manzoor Ahmad
Thank you for giving me useful information.
Identifying genetic marker by myself is a nice way to find difference between related species.
Though it's challenging, I'd like to try.
Thank you.
Use rDNA primers either 16S or 18S or 28S.
Check the attached and given links.
Good Luck!!
Phylogenetic position of the family Orientocreadiidae within the superfamily Plagiorchioidea (Trematoda) based on partial 28S rDNA sequence
(https://link-springer-com.ezproxy.newcastle.edu.au/content/pdf/10.1007/s00436-017-5594-8.pdf)
A new classification for deep-sea opecoelid trematodes based on the phylogenetic position of some unusual taxa from shallow-water, herbivorous fishes off south-west Australia
(http://eds.b.ebscohost.com.ezproxy.newcastle.edu.au/eds/pdfviewer/pdfviewer?vid=1&sid=f950b9a5-fd79-4ec6-a40c-c88c60433662%40pdc-v-sessmgr05)
New digeneans (Opecoelidae) from hydrothermal vent fishes in the south eastern Pacific Ocean, including one new genus and five new species(attached)
- Badges
- Science method
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics
- Phylogenetic Analysis