Degutopia Posted January 12, 2006 Report Share Posted January 12, 2006 Hi all, I'm new here. I would like to know if anyone is interested in the subject of Rodentia monophyly/polyphyly, particularly the subject of possible Caviomorpha divergence, just so that I can talk about it with some other people and see what they think. Does anyone have any experience in the area of phylogeny or mitDNA sequencing? Look forward to hearing from you all! Chloewww.degutopia.co.uk[email protected] Quote Link to comment Share on other sites More sharing options...
MortenS Posted January 13, 2006 Report Share Posted January 13, 2006 I am rather interested in reconstructing phylogenies from molecular data, and do a bit on a hobby basis, although not an expert in it. Turtle 1 Quote Link to comment Share on other sites More sharing options...
Degutopia Posted January 16, 2006 Author Report Share Posted January 16, 2006 Hi there, Do you know of any of the background to the Rodentia/Caviomorpha/Lagomorpha history? There is a semi-overview on Degutopia's website (degu?-controversy menu). I just want to discuss some recent findings, really. I can post the journal refs (pubmed) if you'd like? Chloe Quote Link to comment Share on other sites More sharing options...
MortenS Posted January 16, 2006 Report Share Posted January 16, 2006 Sure, please post them. I am aware of some of the controversy, although I cannot say I am well versed in it yet. However, I am in the process of collecting mtDNA sequences (and possibly nuclear DNA sequences if I find some) from various databases so I can take a view at the data myself. Quote Link to comment Share on other sites More sharing options...
Degutopia Posted January 17, 2006 Author Report Share Posted January 17, 2006 Lovely! Basically I'm interested in this area so much because I'm the founder of a degu organisation (sub-order Caviomorpha). Briefly, Rodentia is one of the biggest orders and it's monophyly is debatable. Recently, rabbits, hares and maras (Lagomorphs) were found to diverge from Rodentia and so reclassified into their own order (Lagomorpha). DNA sequencing and other analysis on the Caviomorphs has suggested that they too may need to be reclassified, however this is under hot debate as a lot of research contradicts itself. A few papers recently have caught my attention in this area which are: Durocher, F, Sanchez, R, Ricketts, M, Labrie, Y, Laudet, V andSimard, J (2005) 'Characterization of the guinea pig 3beta-hydroxysteroid dehydrogenase/Delta5-Delta4-isomerase expressed in theadrenal gland and gonads.' J Steroid Biochem Mol Biol., 97 (3): 289-98.http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16143518&query_hl=2&itool=pubmed_docsum Frye, M and Hedges, S (1995) 'Monophyly of the order Rodentiainferred from mitochondrial DNA sequences of the genes for 12S rRNA,16S rRNA and tRNA-valine.' Mol Biol Evol., 12 (1): 168-76.http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7877492&query_hl=4&itool=pubmed_docsum 1. Durocher et al. it seems sequenced only a specific portion of DNA from the guinea pig adrenal gland, rather than using mtDNA as is more common, to determine that (according to them) there is a paraphyly of order Rodentia. What differences are there in using DNA comapred to mtDNA for sequencing? As far as I am aware, most mammals have mitochondria that has it's own unique DNA as it evolved with the organism as a symbiant- can you explain a bit more about mt DNA sequencing for phylogeny? B) 2. The more interesting paper for me is Frye and Hedges as it attempts to explain a few things. From what I gather, they think that the reason everyone's sequencing is so inconclusive when it comes to Caviomorphs is their unique insulin structure/function. Would you agree that it is possible for the Caviomorph insulin DNA coding to account for enough of a difference in sequencing to suggest Rodentia polyphyly at least in terms of the Caviomorphs, and why would this affect mtDNA?? Thanks so much for your help/thoughts on this, I really appreciate it! Chloe Quote Link to comment Share on other sites More sharing options...
MortenS Posted January 17, 2006 Report Share Posted January 17, 2006 Thanks for the articles, I will have to read them closely before I attempt an answer. The second paper looks very interesting, indeed. Quote Link to comment Share on other sites More sharing options...
MortenS Posted January 22, 2006 Report Share Posted January 22, 2006 Sorry that it took a while before I could get back to you, Degutopia. On to your questions. The difference between nuclear DNA and mtDNA when it comes to sequencing are a few. First of all, nuclear genomes are organized in multiple linear chromosomes, surrounded by protective proteins (such as histones), and generally many, many meganucleotides long. Also, protein-coding sequences in nuclear DNA is often broken up several parts, called exons, and inbetween these are sequenced called introns. Exons and introns have different substitution rates. Mitochondrial DNA is a whole other ball game. The genome is small, just 15-17 kilonucleotides in animal mitochondria. The mitochondria is ringformed, and contains very few genes: 13 protein coding genes, 2 rRNA coding genes, and about 22 tRNA coding genes. In addition there are a few non-coding regions, the most important ones being the D-loop regions. Mitochondria are only inherited via the maternal line, and are not subject to recombination such as nuclear genes are. Also, mitochondrial DNA has a much higher mutation rate than nuclear DNA (around 16-17 times as high). These differences between nuclear and mitochondrial DNA makes some differences when it comes to sequencing and phylogenetic reconstruction. 1. Cheaper and easier to sequence whole mitochondrial genomes.2. All animals have nearly the same gene order in mitochondria, while gene orders in nuclear chromosomes are much more changeable, due to crossing-over.3. Gene duplications happen much more rarely in mitochondrial DNA than in nuclear DNA, so all mitochondrial genes can be treated as orthologous genes, while much more investigation needs to go into the investigation of nuclear genes, since they are frequently target of gene duplication in the evolutionary history. As for mtDNA and phylogeny, aligning complete mitochondrial sequences are feasible with home computers. As an example, a set of 39 complete mitochondrial sequences took about 7 hours to align to each other on my home PC. While aligning single nuclear genes or proteins are pretty easy and rather fast, aligning multiple nuclear genomes are still very time consuming, although I expect to see great progress in computational methods for that too, as the number of completely sequenced genomes increase. As for the Frye and Hedges paper, I am not sure if that is enough to prove monophyly of Rodentia. The complete sequences of mitochondria that I analyzed (rather briefly I must add, I have probably not done all the various statistic tests required for a proper analysis) points to a paraphyletic Rodentia group. Cavia porcellus, Thryonomys sp and Myoxus forms a clade, and the murids forms another clade, which is coming out as a sister group to the lagomorphs. As for whether the cascade of changes in the insulin and blood sugar pathway can lead to changes in the mitochondria, I am sure it can. Mitochondria are dependent on blood sugar level, and any change in blood sugar level (whether up or down) will likely lead to an environment where changes in mitochondria can be positively or negatively selected. I doubt however that it is enough to cause complete mitochondrial sequences too look like they are paraphyletic, rather than monophyletic. After working with the sequences for some days now, I must say I would put the money on the paraphyly hypothesis. See attached phylogeny Quote Link to comment Share on other sites More sharing options...
Degutopia Posted January 24, 2006 Author Report Share Posted January 24, 2006 Thank you so much! That's really cleared it up for me a lot. And your analysis is most interesting- would you mind if I referenced you on our site? If you could e-mail me your reference as you would like it to appear that would be brilliant! Thanks again for your help, I'm sure I'll be back with some more things to discuss. Chloe Quote Link to comment Share on other sites More sharing options...
Degutopia Posted January 24, 2006 Author Report Share Posted January 24, 2006 Also one other thing, Where would you place Octodonts on your phylogeny tree, would they be classed with Lagomorphs or Rodents, or the sister Lagomorph clade with Cavia porcellus? Chloe Quote Link to comment Share on other sites More sharing options...
MortenS Posted January 24, 2006 Report Share Posted January 24, 2006 I did not include Octodon degus in the phylogenetic analysis, since there was no complete mtDNA sequence made from it. I would however, think that it would be classified somewhere in the clade Cavia belongs to. However, as you see there are a few branches where the bootstrap support is not a 100%, so there is still some uncertainties in the tree I presented as to the branching pattern. Quote Link to comment Share on other sites More sharing options...
Degutopia Posted January 24, 2006 Author Report Share Posted January 24, 2006 OK, thanks. Can I still reference you on the site? I think it would be useful all the same. Chloe Quote Link to comment Share on other sites More sharing options...
MortenS Posted January 24, 2006 Report Share Posted January 24, 2006 I do not mind if people get referred to this thread. Just do not make me a specialist in the process, because I am not. Quote Link to comment Share on other sites More sharing options...
MortenS Posted January 24, 2006 Report Share Posted January 24, 2006 Also, the phylogeny I made supports a paraphyletic Rodentia, but does not support a polyphyletic Rodentia, at least not with the sequences I included. As allways, things can change when you add more sequences to be analyzed. Quote Link to comment Share on other sites More sharing options...
Recommended Posts
Join the conversation
You can post now and register later. If you have an account, sign in now to post with your account.