CERVs! Crocodile ERVs (not chimpanzee!)

Uh oh. VIRAL NOMENCLATURE WAR!!!

CERV vs CERV!!!

Chimpanzee vs Crocodile!!!

Its gonna be a THROWDOWN!!!

... Or we can just read a neat open-access article about ERVs in crocodiles :)

Strong purifying selection in endogenous retroviruses in the saltwater crocodile (Crocodylus porosus) in the Northern Territory of Australia

Specifically, Crocodylus porosu, saltwater crocodiles, one of the many terrifying creatures that inhabits Australia.

They used PCR to fish around the genomes of 47 crocs from all over Northern Australia for the gag-pol portion of some ERVs.  They successfully got sequences from all the animals, more from the group CERV2 (spumavirus-related. really! those are oddballs) than CERV1 (gammaretroviruses).

They got 227 sequences, 176 of which were novel DNA CERV sequences. And, unsurprisingly, these sequences appeared to be undergoing 'purifying selection', aka 'negative selection'.  Aint nobody wants ERVs in their genome, so the ones that *are* there, are decaying via nonsense mutations/stop codons/etc.  CERV2s are probably older than CERV1s, as the stops and such were more conserved in the CERV2 group.  While they might not code for functional CERVs (they did not sequence entire ERV genomes to determine whether the entire sequences were present and absent lethal mutations), they think that the CERV1s might be young enough that they are still replicating/reinserting as ERVs ('reinfecting' their host cell without ever leaving their host cell), rather than exogenous agents.

An unexpectedly interesting part of this paper:

Furthermore, studies into the nucleotide substitution rate of crocodilian nuclear and mitochondrial sequences suggest that this is much lower in crocodilians than in most other vertebrates [24-27]. Thus, degenerate ERV sequences are likely to accumulate changes at a slower rate in crocodilians than most other vertebrate species, leading to a low level of host lineage specific evolution, as well as low levels of lineage differentiation.

Ha! Crocodiles have a low genomic and mitochondrial mutation rate than we are accustomed to, which means that their ERVs would not mutate as much either! People who study CERVs need to be careful of how they calculate things-- crocodiles molecular clocks are... slow.  HA!

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Too bad other things about crocodiles aren't slow. I would not have wanted to collect those tissue samples!

By JustaTech (not verified) on 12 Dec 2012 #permalink

Any thoughts on why mutation rates are slower in crocodiles?.

btw, I live in Australia and I'm not terrifying.

JustaTech-- With monkeys, we just follow them around and steal their poops. Less dangerous, more creepy. :-D

Gerry-- No clue! Looking at their references, it doesnt look like it has been investigated biochemically, but the molecular biologists have had to use the fossil record to recalibrate their clocks. An avenue for further research!

@GerryC, although this paper claims that the crocodiles evolve slower than other vertebrates, the paper they cite:

Eo SH, DeWoody JA: Evolutionary rates of mitochondrial genomes correspond to
diversification rates and to contemporary species richness in birds and reptiles. Proc R
Soc Lond B Biol Sci 2010, 277:3587–3592.

shows that snakes evolve fast in comparison to other vertebrates, but the crocodiles are rather normal in their rate of mitochondrial evolution.

By Brian Foley (not verified) on 15 Dec 2012 #permalink