Bah bah black sheep, have you any ERVs?

More evidence that evilution is a vast, world-wide conspiracy.

Revealing the History of Sheep Domestication Using Retrovirus Integrations

Scientists from all over the world (literally, Portugal to Pakistan, Italy to Iceland, Tanzania to Texas) have used the random insertion of endogenous retroviruses, specifically, Jaagsiekte sheep retrovirus, to determine the evolutionary history of sheepies:

enJSRVs can be used as highly informative genetic markers because the presence of each endogenous retrovirus in the host genome is the result of a single integration event in a single animal and is irreversible, so populations sharing the same provirus in the same genomic location are de facto phylogenetically related.

This crew focused on finding/analyzing six ERVs in 1362 animals from 133 kinds of sheep and sheepy-like relatives. They combined the PCR tricks I wrote about earlier (except they drew their figures in MS Paint instead of Poweroint, LOL!) with sequence analysis of the ERV LTRs. The LTRs on either end of the ERV should be identical-- differences between them indicate age.

Proximal and distal LTRs of an endogenous retrovirus must be identical upon integration, but can diverge over time at the same rate as noncoding sequences (~2.3 x 10-9 to 5 x 10-9 substitutions per site per year). enJSRV-7 appears to be the oldest provirus in our samples because it displays five nucleotide (nt) substitutions between 5' and 3' LTRs (445 nt long), whereas all the other insertionally polymorphic proviruses (including enJSRV-18) have identical LTRs.

What they found matched archeological evidence, and provided support for outside hypotheses about the evolution and domestication of sheepies:

The homogeneous retrotypes (R2 only, or both R2 and R4) that we observed in the sheep of modern-day Turkey, Iran, Saudi Arabia, Syria, Israel, and Egypt, combined with available archaeological evidence, suggest that selection of domestic sheep with the desired secondary characteristics common to the modern breeds occurred first in Southwest Asia and then spread successfully into Europe and Africa, and the rest of Asia. This may provide genetic support to the theory that specialized wool production arose in Southwest Asia and then spread throughout Europe (11). The primitive breeds survived the second migrations of improved breeds from Southwest Asia by returning to a feral or semiferal state in islands without predators or by occupying inaccessible areas less prone to commercial exchanges and associated introgression. Most, if not all, of the breeds we identified as of ancient origin were already considered primitive on the basis of morphological traits such as a darker and coarser hair (instead of a whiter woolly fleece), a moulting coat, and the frequent presence of horns in females as well as males (Fig. 4).

Ancestral sheepies founded a first wave of domestication for meat-- yummy-sheep. When people started breeding them for wool as well as meat in SW Asia, the woolly yummy-sheep bounced out the yummy-only sheep in Europe. Domesticated yummy-only sheep in Europe were 'de-domesticated' back into their 'wild' state.

Also, Bible stories:

Our study also provides genetic evidence supporting the anecdotal origin of some less common sheep breeds. For example, one of the 10 populations analyzed from the British Isles, the Jacob sheep, displayed a homogeneous R2 retrotype very different from that of the other British populations and more similar to that of the southwestern Asiatic and African breeds. The origins of the Jacob are unknown. This breed owes its name to the Biblical story of Jacob who took "every speckled and spotted sheep" as a wage from his father-in-law Laban (Genesis 30:25-43; probably the first recorded use of selective breeding in livestock). Our retrotype analysis supports a direct link between the Jacob sheep and breeds in Southwest Asia or Africa rather than other British breeds. Our study also firmly links the Soay sheep with the Mediterranean and Asiatic Mouflon.

Cooooooooool!

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They are wrong because they didn't prove that Jacob used bark from the poplar tree to make the sheep spotted and striped. Geez, don't these people read the Bible?

Heh. Poweroints - that must be using strong oil paints, right? Obviously a whole lot more punch than them thar MS crippled kinds.

Mind Curmudgeon they's wid Aberdonian jeenies if yiz wair tae luik.

By BlindRobin (not verified) on 28 Apr 2009 #permalink

Like, totally awesome! you've "blinded me with science" (Sorry, Thomas Dolby on the brain tonight.)

DaveH @2 Very Cool, I never knew there were four horned sheep! Are they an actual breading population? I'll have to check that out some more when I'm not to tipsy to google.

Well, I'm toast. To the hot tub, Batman!

Cheers & Happy Monkey,
Ray

Baaa! Love the wool - but sheep aren't on my menu. I'm on an unholy crusade to replace wooly-not-yummy sheep with wooly-yummy goats. meeeeh.

By MadScientist (not verified) on 28 Apr 2009 #permalink

Remember guys, this kind of pattern is not a problem for creationists - on the contrary, but evidence for common descent by shared orthologues in different 'unrelated' species/kinds is another matter.
JSRV is also interesting because of the late restriction of XRVs by 'coopted' ERVs (SA's counter comments on MMTV noted).

Bah.

What about the cow genome? Didn't they just get a full one?

You are right, of course, cprs; scientific evidence is never a problem for creotards because their position has fuck-all to do with objective reality and everything to do with magic. Evidence is conveniently ignored.

By Wolfhound (not verified) on 29 Apr 2009 #permalink

cprs--Remember guys, this kind of pattern is not a problem for creationists...

Oh, naturally. Even though they looked in different species of sheep, theyre all really just Noahs 'sheep kind', aka 'zoology for toddlers'. Which is why you and Wee-Willy-Winky were trying so hard to 'disprove' ERVs in this thread-- Sure, humans could be just part of duh munkee kind, but you aint related to no munkee.

But dis just all be 'sheepie kind', so its all good.

You still dont know what 'orthologues' means, btw.

Another OT question for Abbie: Can you do a serious post explaining why vaccines cannot lead to ERVs?

Or if vaccines could conceivable lead to new ERVs being inserted into the human genome, (and I don't know if it is even feasible) why should we not care? Or, why is it worth it?

A live, attenuated retrovirus will never be in a vaccine because we cannot control where it inserts (retroviral insertion is random), thus cancer would always be a potential 'side-effect' of the vaccine.

That would never make it past basic safety standards of any government, ever.

Not dumb. We were going to try it with HIV-1 viruses with an accessory gene, nef, deleted-- it looked like that deletion attenuated the virus enough for it to work for a vaccine, and HIV-1 doesnt cause cancer due to the nature of its life-cycle (it only infects cells that are terminally differentiated), so we thought it would be worth a try.

However due to HIV-1s mutational capabilities, individuals that got delta-nef viruses (blood transfusions) ultimately got AIDS anyway.

However the kinds of retroviruses that make ERVs would make very bad live attenuated vaccines.

Just for the sake of argument, suppose some crazy mad scientist actually did create a doomsday virus and delivered it to the population. Let's further suppose that scientists isolate the killer virus and no criminal conspiracy evidence emerges (you know like an email saying "Boss, the death gel idea worked great! Doom Virus is ready for distribution. Love, Igor." or Condoleeza Rice saying something like "If the president says it's ok to make doom germs then it's ok to make doom germs.")

How would scientists go about discovering if the virus was designed? What kinds of design fingerprints would Dr. Evil leave on his creation, if any? If scientists weren't specifically looking for evidence of design (just focusing on what the thing was and how to cure it), what kinds of things would tip them off that it was designed? I'd ask an ID guy but then I remembered they know sweet FA about design.

Oops, meant to post my conspiracy questions in the crazy sweater guy thread. I suck at teh intarweb. I'll repost it over there.