Predictions of Evolution

PDF version: PredictionsofEvolution

I’m in the middle of an article on pesticides, so I thought I would revise some information I collected as part of a email debate. This is specifically around very specific predictions (of what scientists would discover) made by evolution that have been “fulfilled”. While technically not proof that evolution is true, they are strong evidence which increases the likelihood of it being a correct theory. It is only negative predictions that can really disprove a theory. And any honest theory should contain those negative predictions.

 

I want to add that the original pointers for most of these was found on other sites (especially talk.origins here and here and here). Talk origins have tons more of these predictions, I just picked the ones I found particularly interesting and fleshed them out with additional explanations and sources.

 

Jaw to Ear Transition

In 1837, C.B. Reichert (who was a Creationist, but not much choice on those pre-Darwinian days), observed that when pig fetuses were growing, there was a point at which a portion of the jawbone detaches to become the tiny bones of the middle ear, which he found quite remarkable.  Once we had a theory of evolution, one of its early predictions was that there should exist a fossil between reptiles and mammals that essentially has two separate jaws, one of which was smaller and near the ear. When fossils of early cynodonts were found, specifically the Diarthrognathus (“two-jointed jaw”), this prediction was found to be true.  This is described better by Stephen Jay Gould in his book Eight little piggies: reflections in natural history.

Trilobite Precursors

Darwin predicted that precursors to trilobites should be found in pre-Cambrian fossils, honestly acknowleding that a lack of such would be bad for the theory (Darwin 1872 [1]) . Despite what a (presumably outdated) anti-Darwin site would like to believe, precursor fossils have been found, even in the scant fossils that exist pre-Cambrian (Gon 2009 [2]). The evidence is admittedly not 100% certain, but nothing can be.

Long-tongued Moth (1862-1903)

This is one of my absolute favorites. Darwin predicted in 1862, from observation of the Madagascar Star orchid, that there should exist a species of moth with a tongue a bit less than 30 cm (specifically “between 10 and 11 inches”) (Darwin 1862 [3]). At the time, one with a tongue that long had not been discovered. However, evolution predicts a battle between the orchid and moths in an “arms race” to get/deny nectar without proper “payment” (in the form of pollination in this case). In 1903, A hawk moth with a tongue around 300 mm was discovered, from the species known as Xanthopan morgani (the one pictured below only has a 7 inch tongue, but demonstrates the point I think) (Wikipedia 2010 [4])

 

Archaeopteryx Teeth (1872-1877)

When the first Archaeopteryx (a sort of intermediary between reptiles and birds) fossils  was found, the head was not in good shape and had no teeth. Then when Ichtyhornis and Hesperornis were found in 1872, they were determined to be seabirds, but they retained teeth (Huxley 1872 [5]). The early evolutionists of the time, specifically Henry Woodward of the British Museum, predicted that that the archaeopteryx should also have had teeth since reptiles had teeth, and birds descended from them. Woodward recognized the controversy of his proposal, putting words to it:

“But, it may be urged, ‘your proposition that the Archaeopteryx had teeth is a pure assumption. Show me some evidence of a fossil bird whose head and skeleton are in juxtaposition so as to leave no reasonable doubt of their unity’)”. (Woodward 1875 [6])

But if the Archeopteryx didn’t have teeth, that was a problem for evolution.

In 1877, more intact Archaeopteryx fossils were found… with teeth. It is now accepted (even among Creationists) that the Archaeopteryx had teeth. And Archeopteryx would have had teeth whether or not we thought it should. The point is, evolutionary theory virtually demanded that it, and the prediction held out.

Antarctica, and its fossils (1893-1982)

Believe it or not, we didn’t always knows Antarctica existed. In 1893, H.O. Forbes presented a paper at the Royal Geographic Society in which he discussed his findings in the Chatham Islands. He (and other naturalists) predicted that there should have existed a large sub-tropical southern continent:

Taking these fresh facts into consideration, he marshals all the data which he considers prove a strong case for the probability of the existence of a former southern continent, and he sketches on a map of the Southern Hemisphere what he believes was the configuration of Antarctica, as he has named that vanished continent. He believes that it followed nearly what is the 2,000-fathom line, and extended northward from a circumpolar area, by broad extensions, one to join an old New Zealand continental island (including the Antipodes, the Maquarries, New Zealand, the Chatham, Lord Howe, Norfolk, the Kermadec, and the Fiji Islands); another to East Australia with Tasmania; another to the Mascarene and surrounding islands (the Lemuria of Sclater); perhaps one to South Africa, and, lastly, one to South America. The form of this continent would not interfere with the opinions expressed by many authorities in the permanence of the great ocean basins. (Editors 1893 [7]).

Viewing the article, you can see that it was not just about a single bird, but actually a wide variety of species whose distribution only made sense in light of there being this continent. At this time Antarctica had been spotted, but was seen as just being ice shelves. Additionally, at this time scientists were just starting work on the idea of prior large connected continents that broke up over millions of years. In any case, Antarctica was obviously finally discovered.

One of his examples was “Marsupials – Nototherium, Diprotodon, Thylacoleo, Thylacinus in Australia ; Prothylacinus, Amphiproviverra in Patagonia.There were obviously not going to be live marsupials extent in the current Antarctica, but it stood to reason that there should be fossils from the Mesozoic era.

These were found in 1982, with Polydolops. It was a 9-foot marsupial (Woodburne 1984 [8])

No doubt you can find papers for all the other fossils that were predicted to exist.

Flying Insects with Hemocyanin (2003)

The theory of evolution held for a long time that flying insects evolved from gilled crustaceans (Burmester 1996 [9]). Those crustaceans use a protein known as hemocyanin to circulate oxygen. Evolutionary theory would hold that there should be still be remnants of that in some flying insects, but none had been found. In 2003, scientists discovered a type of stonefly (generally considered to be some of the most “primitive” of insects, which makes sense) which still had functional versions of that protein (Hagner-Holler 2004 [10]). This is discussed more fully in an article by James H. Marden where he talks about the evolution of flight in aquatic insects (Marsden 2008 [11]).

Ancestral whale with teeth and baleen (-2008)

Currently there are two types of whales: those that have teeth, and those that have baleen to filter their food. None exist currently that have both. On the assumption that all whales must have descended from a common ancestor, it was predicted that there must have existed a whale that had both teeth and baleen at the point in time when the two diverged. Even today, baleen whales start with tooth buds that disappear (evidence that the toothed whale was first).  Well,  in 2008 this transitional form was found to have existed  24-28 million years ago, when baleen whales where splitting from toothed whales (Coyne 2010 [12]).

“Junk” DNA fingerprinting

“Junk” DNA can actually be used to predict (coming from a retrovirus) whether two seemingly-unrelated animals shared a common ancestor. Or, to put it another way. When we know that two species are related, we can predict whether or not they will share certain sequences of “junk” DNA. For example, There is a particular sequence found in hippos, whales  and cows but not in humans, mice, kangaroo, elephants or horses. This would lead to conclusion that there was a common ancestor that split off and shared by hippos , whales and cows (which is true). And based on this theory, they should be able to find this  same set of “junk” DNA in deer, but not in monkeys. Incidentally, finding this particular “junk” DNA in monkeys would actually be a point against evolution, since the retro-virus that caused it came after the ancestor to primates. (Lindsay 2010 [13])

As another example, both guinea pigs and humans have a specific defect in the gene that encodes for Vitamin C processing, meaning that anything from guinea pigs up to humans should have that mutation (the math works out that that genetic divergence would have occurred approximately 20 million years ago) (Nishikimi 1988 [14]). If this exact same “typo” (of the same letters) were found outside of the primate line from guinea pigs to humans, that would be a problem for evolution.

Conclusion

As I said at the beginning, strictly speaking none of these predictions actually prove evolution to be correct. But the fact that they were able to be made, and found true, might leave you pondering how that could be if it weren’t true. Outside of evolution, there is no reason for many of them to be true, and certainly no reason to predict ahead of time for them to be true. Creationism is unable to make any predictions of this sort. Compare these with the predictions that Creationism/Intelligent Design attempts to make.


[1]Darwin, Charles. “The origin of species by natural selection”. Odhams Press Limited. 6th ed. 1872. pp338

[2]Gon III, S.M. “Origins of Trilobites”. Updated Jan 22, 2009. Accessed Nov 10, 2010. <http://www.trilobites.info/origins.htm&gt;

[3]Darwin, Charles. “On the various contrivances by which British and foreign orchids are fertilised by insects”. Harvard University. 365 pages. pp. 198

[4]Wikipedia contributors. “Xanthopan morgani.” Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 9 Nov. 2010. Web. 11 Nov. 2010.

[5]Huxley, TH. “Prof. Huxley’s lectures on the evidence as to the origin of existing vertebrate animals”. Nature. Volume 13. 1876. p.515

[6]Woodward, H. “Birds with teeth”. The Popular Science Review. 14(57). 1875. 337-350.

[7]Editors. “Antarctica: A Supposed Former Southern Continent”. Natural Science, vol. 3. July 1893. pp54-57 (summary of paper by H.O. Forbes)

[8]Woodburne MO, Zinsmeister WJ. “The First Land Mammal from Antarctica and Its Biogeographic Implications”. Journal of Paleontology. Vol. 58, No. 4 (Jul., 1984), pp. 913-948

[9]Burmester T, Scheller K. Common origin of arthropod tyrosinase, arthropod hemocyanin, insect hexamerin, and dipteran arylphorin receptor. J Mol Evol. 1996 Jun;42(6):713-28.

[10]Hagner-Holler S, Schoen A, Erker W, Marden JH, Rupprecht R, Decker H,

Burmester T. A respiratory hemocyanin from an insect. Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):871-4. Epub 2004 Jan 8.

[11]Marsden JH. “Evolution and Physiology of Flight in Aquatic Insects.” In: Aquatic Insects: challenges to populations. CABI 2008. pp230-248

[12]Coyne, JA. “Baleen whales: a lovely transitional form”.  Accessed 11/11/2010. <http://whyevolutionistrue.wordpress.com/2010/07/22/baleen-whales-a-lovely-transitional-form/&gt;

[13]Lindsay, D. “Different species with the same ‘Junk DNA’. Don Lindsay Archive. Updated 1/12/2001. Accessed 11/11/2010. <http://www.don-lindsay-archive.org/creation/dna_virus.html&gt;

[14]Nishikimi M, Koshizaka T, Ozawa T, Yagi K. Occurrence in humans and guinea

pigs of the gene related to their missing enzyme L-gulono-gamma-lactone oxidase. Arch Biochem Biophys. 1988 Dec;267(2):842-6.

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7 Responses

  1. I agree, there’s a lot of transitional species supporting the the theory of evolution, in intelligent design and creationism, it doesn’t give way for those transitional species to be incorporated anywhere in the “evolutionary tree of life”

    • The frustrating part about Creationism (and possibly the ID variant, though less so) is that any evidence one can bring to bear, they can simply fall back on “well, that’s just how God decided to make it.” Theoretically, a Designer could have made everything in a way that looks exactly like evolution, complete with transitional forms. Of course, this is a completely unsatisfactory explanation (read: it explains nothing). Even if true, it seems we may as well act is if evolution is true, since it certainly explains what we see.

  2. To date the question of proposed precursors to trilobites and other Cambrian creatures has actually become more problematic over the years, and this is in the literature. You also failed to mentioned that the specific ediacara biota which some propose to be precursors of the Cambrian phyla actually went extinct millions of years before the Cambrian radiation event.

    In spite of the popular media, no one dispute that micro evolution or what some call adaptation has taken place even amongst whales. What is disputed is macro evolution or the notion that land mammals evolved into whales, such as Pakicetus, which was first touted as an aquatic creature that swam and dived for its food. In fact today you can still find pictures of this creature portrayed as an aquatic animal with nasal apertures that look like they are slowly receding towards the top of the head as in modern whales. Subsequent fossils have proved this wrong and they are now known to be fully terrestrial with nasal apertures in the front. Even Phillip Gingerich admitted this when I emailed him a few years ago and has since published these new findings. Anatomist and biologist had and in some case still have major disagreements as to what the closest relative is to the modern whale is, including there supposed precursors, and only now are some coming to the consensus that whales are more closely related to hippos which creates a whole new set of problems geographically speaking, as well as for many other reasons to numerous to mention.

    As for Archaeopteryx we have found birds that are much older than Archy and today even some evolutionist are challenging the idea that Archy is the smoking gun we once thought.

    As for Junk DNA, we have recently discovered that what we once referred to as junk, is not junk after all. This is also in the literature and has been published in respected science journals, and not as a proposition, but as an empirical observation. Even the notion of these ERV’s being random as well as the reasoning for their position on any specific chromosomal loci of humans and chimps is also now being challenged. Not to mention the fact that of all the thousands of ERV’s, only a handful if that, appear on the same chromosomal loci between the two species. Junk DNA is a myth. Again much of these non coding protein regions once written off as junk and random in fact do code for RNA, and are extremely vital to gene regulation especially in embryology and have been found to be very specified.
    Just recently we have found that the mantra that humans and chimp DNA share a 98% similarity is also wrong. The overall differential including indels, alignable sequences and single nucleotide polymorphism is more closer to 70%.

    I can provide citations upon request.
    When you look deeper, these so call predictions are like a house of cards worded in ways to fool the uninitiated.
    I didn’t have a lot of time to edit. My apologies.

    • Thanks for the comment, some brief notes.
      This wasn’t intended as an in depth article about evolution, merely that when evolution is used as a model, it allows us to make predictions about the types of things will find, and that often turns out to be correct. ID/Creationism is unable to do the same, as it’s not intended as a scientific model, but more of a “The Designer/God did it, what more explanation do we need”.

      1. I feel as though you’re pasting in large parts an edited version of some other previous comment… I never made mention of the “Pakicetus”, and certainly didn’t “tout” it as anything.

      2. trilobites – lack of fossil evidence isn’t an issue for evolution, only *wrong* fossils. It’s just a big win when we find fossils.

      3. The separation between “micro” and “macro” evolution is completely artificial. What is it that you think happens when something has a series of “micro” evolution events over a period of 300 million years? I’d say that’s going to be “macro” at that point. Are you postulating some sort of “mutation credit” system that a creature burns up once they have “micro” evolved enough times?

      4. In what sense is hippos as most recent living ancestor a problem? I’d recommend the section entitled “The Hippo’s Tale” in Chapter 11 of Richard Dawkins’ excellent book _The Ancestor’s Tale_’. I’m not sure what “geographic” issues you are proposing for animals that evolved millions of years ago. I’m also confused by your “point” that “Anatomist and biologist had and in some case still have major disagreements as to what the closest relative is to the modern whale”… this is science in action. We are trying to find the most explanatory model using the given evidence. Of course there are disagreements. That’s a good thing, not bad.

      5. For junk DNA… your comments here don’t in any way refute the claim, and I’m not sure that they have much to do with my statements (see note 1.) (except for the catchphrase “junk DNA” being present). The point in the section is that there are sections of DNA that came from retro-viruses that exist in ways that follow the “evolutionary tree” exactly. We can predict in what animals we will find this stretch, and when we won’t. If it turns out that DNA section has usage, that’s great! But the predictions we’re making using them as nothing whatsoever to do with the proposed function of the DNA (or any phenotypical elements of the creature).

      6. Archeopteryx – It appears that there is some controversy as to whether or not “Protoavis” (which is what I assume you’re referring) to is a legitimate find. In any case, there’s not real need, as I understand evolution, for Archeopteryx to *be* the “transition” between birds and dinosaurs… it just happens to be a remaining fossil that is a “cousin” of the creature that was in the direct line of ascension. Recall that each animal is an animal in itself… and didn’t exist purely to be an “ancestor” to another. Consider that humans and chimps exist together… this isn’t an issue because they themselves shared a common ancestor well into the past, but that doesn’t mean that chimps aren’t helpful in telling us about *our* evolution.

      (responding to your second comment).
      7. There aren’t “logistical nightmares” because this evolution isn’t happening in a single stage. There is no time at which the animal is maladapted, or else it wouldn’t have been able to pass on its genes. The time scales are vast. Each minor mutation doesn’t suddenly make the creature vastly different from its parents. They are insanely small adaptations. There are turtles still living today that have both lung-like, and gill-like breathing apparatus. Sometimes it does cause issues, but they survive and pass on their DNA. The difficulty doesn’t confer evolutionary disadvantage. Not sure why platypuses are referenced here… they are a living modern creature. Just because they have the appearance of somehow being a “transitionary” animal doesn’t make them useful as an example.

      I would like to point out again that the point of this article wasn’t to “prove” evolution, merely to point out that it is capable of making predictions that have no reason to be true within a Creationist/ID model. I don’t have any desire to engage in a debate about whether or not this or that fossil is a “problem” for evolution, or how to explain some evolutionary trait. Frankly I’m not qualified to have that discussion, but no doubt P.Z. Meyers of Pharyngula could take you up on your more specific points.

  3. This is the first part I left out by accident.

    I don’t have time to go in to all claims but let me just critique a few things that were said.
    The article on Diarthrognathus did not seriously attempt to answer Gish’s question concerning how this creature was able to function between intermediate stages. The article never even touches on the logistical nightmare concerning the internal physiology of transitioning between a cold blooded egg laying creature to a warm blooded placental mammal that nurse her young as well as the multitude of other internal changes that would need to take place including the vast amounts of new and novel genetic and or epigenetic information needed to acquire these changes. Ever hear of the Platypuses?…..

  4. If you read carefully I never accused you of touting anything. I was speaking of Phillip Gingerich because Pak is often used when speaking of whales and evolution. Sorry if you misunderstood.

    Let me make myself clear. My criticism is not the scientific method, nor do I object to the word evolution as defined as change through time. What I object to is Neo Darwinsm /The Modern Synthesis, better known as the The theory of evolution. Some colloquially call it “molecule to man” and It is not just ID’ers and creationist who are speaking out, but even evolutionist themselves including evo devos who are now speaking out against this theory. The same theory we have been teaching as a dogma and fact for the last 80 years. We were lied to when we were told that the Modern Synthesis was a sufficient explanation, and that we just had a couple of knots to tie up as what happened during the Dover trial.

    Watch the video I posted online entitled “Will the real theory of Evolution Please Stand up” 1 through 5. Where even evo devo Stuart Newman criticizes Neo Darwinsm and along with his colleagues are trying to extend the synthesis & who has gone on record as saying “people are told to believe thing that are simply not true” or check out “Do we need a new theory of Evolution” Go to DissentfromDarwin.org or read about what happened at the Altenberg 16 summit in Austria, and look how many mainstream scientist are now publicly challenging neo Darwinism/the modern synthesis and the limitations of natural selection, NS and random mutation, RM. Understand what is meant by the assumptions of evolutionary theory. Without a cohesive theory all you have is an assortment of propositions, ideas and a macro evolutionary paradigm based on faith.

    I have to disagree. A lack of transitional fossils is an example of a failed prediction and Darwin understood this. He said that there should be a universe of transitional sequential fossils, and that if future generations did not find them then his theory would be falsified. In recent decades to get around this many Neo Darwinist have basically re classified every extinct and extant animal as a transitional form.

    Darwin was able to show that finch beaks could vary and that certain animals from certain islands had slightly different characteristics i.e. micro evolution.
    He understood that natural selection (which was not his original idea) but none the less was able to achieve these slight changes. He then imagined that given vast amounts of time these changes could account for life as we see it today through decent with modification from simpler creatures. There are many problems with this prokaryote to man macro evolution paradigm. First it require a great imagination. It would also require massive amounts of new and novel genetic information to go from prokaryote cell to a modern anything.

    Neo Darwinist try to answer this by saying that NS and RM could account for this, but mutations are errors in the genetic code. In fact each generation goes through 100+ mutation a year and most are either deleterious or neutral. Many are cause disease, cancers and ilness. After thousands of generations these errors add up and only very rarely can one find a mutation that may be beneficial but even these come with a price. See John Sanford Genetic Entropy. The Mystery of the Genome, We know through artificial selection, e.g. dog breeding etc. that phenotypical change comes from a loss of information or redistribution of preexisting informaion not a gain. There is no free lunch in nature.

    As for Whales, again according to Gingerich these supposed ancestor of whales were found in Pakistan and if they did indeed share a common ancestor with hippo that are supposed to have evolved in Africa then the time lines and geography do not match up.

    As for junk DNA, (and in this case endogenous retro viruses) ERV’s which is a type of non protein coding DNA segment which came from an ancient cross species virus and was once referred and thought of to useless junk. We now know that they are not junk and serve important roles in embryology.

    It surprises me that you said and I quote, “your comments here don’t in any way refute the claim” when the whole premise of the argument is based on the notion that we can tell common descent through ERV’s which are supposed to be random yet exist in humans in similar or specific chromosomal loci as chimps. Again, the whole argument is based on this premise.
    Below are articles concerning junk DNA and the last one deals specifically with your statement concerning common ancestry. When you have sometime you can read it.

    Oh, as for Turtles with gills, I think your referring to what some call bum gills. They’re not actually gills. Its actual referring to the turtle ass, sometimes referred to as “bum gills” well at least in some very rare turtles. It turns out some turtle can actualy drink and breath through there ass. You can read more about it here…..http://www3.interscience.wiley.com/cgi-bin/abstract/85006057/START),

    Endogenous retroviruses regulate periimplantation placental growth and differentiation.
    Dunlap KA, Palmarini M, Varela M, Burghardt RC, Hayashi K, Farmer JL, Spencer TE.
    Source
    Center for Animal Biotechnology and Genomics, Department of Animal Science, Texas A&M University, College Station, TX 77843, USA.

    Endogenous retroviruses regulate periimplantation placental growth and differentiation.
    Dunlap KA, Palmarini M, Varela M, Burghardt RC, Hayashi K, Farmer JL, Spencer TE.

    Junk’ DNA Has Important Role, Researchers Find
    ScienceDaily (May 21, 2009) — Scientists have

    National Human Genome Research Institute (Press Release), New Findings Challenge Established Views on Human Genome, June 13 2007.

    And here is the last one that deals with specific question concerning human and chimps and ERV’s and chromosomal loci.

    Endogenous retroviruses (ERVs) as evidence for common ancestry. (Part 1)

    I find ERVs the most compelling argument for common ancestry, so I got a little interested in viruses (and rightly so, these suckers are associated with many instances of cancers).

    The theory goes something like this:
    About 8% of the human genome mass consists of sequences of retroviral origin and it is thought that in the evolutionary past, exogenous retroviruses formed proviruses in the genomes of germ cells of ancestral primate species [1, 2]. Some of the proviruses are thought to have been fixed (through germ-line integration) in the population and were inherited as stable genomic components named ERVs.
    New ERVs may arise within genomes by at least four different mechanisms:
1) Horizontal transmission: Infection and integration via an exogenous source virus
2) Replication using LINE machinery
3) Duplication of chromosomal loci during chromosome rearrangement events
4) Retrotransposition from a pre-existing endogenous retrovirus (Experimental proof?)
    There are different strategies to determine evolutionary ages of ERV families and ERV proviral loci.
    A) BLAST the hell out of them. When extensive genomic sequence data information is available, BLAST software can be used to determine whether a specific ERV sequence (FASTA format) is present in various species of interest. This NCBI site is probably the best.
    B) If extensive sequence data information is not available, a probe specific for a particular ERV family can be used in Southern blot and PCR experiments to detect homologous sequences in other species.
    C) Estimates of evolutionary ages of particular ERV family proviral sequences can be determined by sequence divergence from the family’s consensus sequence. A considerable amount of sequence data is required in order to calculate the consensus sequence.
    D) Approximate integration times of proviruses can theoretically be calculated by assuming that both proviral LTRs are identical in sequence at time of provirus formation. Thus, without purifying selection both LTR sequences are expected to undergo random mutations over time, and the amount of sequence divergence, in combination with previously determined mutation rates for non-coding DNA, can serve to calculate the approximate integration times of proviruses.

    So, according to theory and based on comparative analyses of orthologous genomic sequence and sequence divergence of flanking LTR elements between chimpanzees and humans, the last major genomic infection of the human lineage is estimated to have occurred before the divergence of the Old World and New World monkey lineages (25-35 million years ago=mya) [[1]]. Flockerzi et al. (2005) are of the opinion that the +-139 proviruses present in the human genome were formed before the evolutionary split of New World and Old World primates, +-55 million years ago [[2]]. The phylogenetic tree paints the following picture (Figure 1): The Old world monkeys (OWM) split from the New world monkeys (NWM) +-35mya. The Human-Chimp-Gorilla-Orangutan lineage split from that of the rhesus macaque lineage after the last major genomic infection (+-25mya). Then the Human-Chimp-Gorilla lineage split from the Orangutan lineage (+-12mya), and then the Human-Chimp lineage split from the Gorilla lineage (+-7mya), and finally Humans and Chimps diverged +-6mya [[3]].

    Figure 1: Current accepted phylogenetic tree of primates.

    The chimpanzee genome contains at least 42 families of ERVs (CERV or PtERV Pt = Pan troglodytes = Chimpanzee) and of the 42 families of chimpanzee endogenous retroviruses 40 were found to have orthologues in the human genome [3]. The human endogenous retrovirus database, HERVd, currently lists, in total, 350 HERV and LTR families [3]. This, however can be misleading as members of the same family may not have orthologues (meaning homologous sequences not flanked by the same genes) and this is then interpreted as being integrated after the split of the species as a result of retrotransposition. However, retroviral retrotransposition of a HERV sequence, in general, is still awaiting experimental proof.
    CERV families are grouped into three major classes [3].
Class I: Contains elements related to the gammaretroviruses (Families 1-29)
Class II: Contains elements that are related to betaretroviruses (Families 30-39)
Class III: Contains elements that are distantly related to spumaviruses. (Families 40-42)

    Class I CERV elements display considerable variation in their tRNA binding sites, even within families. Estimates of the age of full length class I CERV elements ranges from 0.8 to 82.9 million years. Class I CERV families, CERV 1, CERV 2 and CERV 3 (on y-chromosome) (HERVS71) are most likely inserted after the chimpanzee-human divergence (about 6 mya) [3]. Human ERV-Ks have a lysine tRNA binding site and class II CERVs are orthologous to human HERV-K elements [3]. All class III CERV families have orthologues in humans. CERV 40 elements have a serine tRNA binding site while CERV 42 elements have a leucine tRNA binding site. Class III CERV elements are the oldest group of endogenous retroviruses in the chimpanzee genome. The estimated age of these elements ranges from 30 to 145 MY [3].

    Two CERV families have no human orthologues; CERV 1 and CERV 2. CERV 1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome and they have a proline tRNA primer binding site [3]. Phylogenetic analysis of the LTRs from full-length elements of CERV 1 revealed at least two subfamilies with the estimated ages of the each subfamily being 5 MY (subfamily 1) and 7.8 MY (subfamily 2), suggesting that subfamily 2 was present in the lineage prior to the time chimpanzees and humans diverged from a common ancestor [3]. Because no orthologues of CERV 1 was found in the human genome, Polavarapu et al. (2006) concluded that it could be due to variation accumulated during the viral transfer or due to an inter-element recombination or conversion event subsequent to integration [3]. However no historical evidence for this was provided other than the assumption that humans and chimpanzees are supposed to have a common ancestor about 6mya. Ebersberger et al. (2007) showed that 35% of human genes contain at least parts, which evolved human specific already in the progenitor species of humans, chimpanzees, and gorillas and emphasized on the possibility that human and gorillas had a common ancestor and gorillas and chimpanzees had a common ancestor (Figure 2) [[4]]. Therefore, no tangible evidence was provided to explain why these ad hoc explanations do not apply to other phylogenetic analyses of the LTRs from full-length elements, or to confirm that the variation of the LTRs from full-length elements of CERV 1 was indeed accumulated as a result of viral transfer or inter-element recombination or conversion events subsequent to integration.

    Figure 2: Possible phylogenetic tree suggested by Ebersberger et al (2007) [4].
    In an interesting study conducted by Kaiser et al. (2007), it was shown that the human, chimpanzee and Sooty mangabeys’ TRIM5alpha (tripartite motif-containing 5 alpha) gene was able to restrict an MLV/CERV1 chimeric virus and the TRIM5alpha gene from the Gorilla, Orangutan, Gibbon, Baboon and African Green Monkeys was unable to efficiently restrict the MLV/CERV1 chimeric virus [[5]]. A TRIM5alpha capable of efficient restriction of both PtERV1 and HIV-1 was not found in any of the tested primates [5].

    It was also found that the R332Q mutation in human TRIM5alpha improved the ability of human TRIM5alpha to restrict the HIV-1 virus [5]. The authors suggested that the R332 TRIM5alpha was present in the common ancestor of humans and chimpanzees and that the R332Q mutation was fixed in our common ancestor, or that the human and chimp lineages independently fixed R332 after the species diverged at different intervals, both likely, however no positive evidence that it was the case was presented other than the assumption that humans and chimpanzees had a common ancestor (why not gorillas?) [5].

    Phylogenetic analysis of LTRs from full-length elements revealed that CERV 2 elements group into at least four subfamilies and estimated ages of two of the more abundant subfamilies were 21.9 MY and 14.1 MY, respectively [3]. Again, because no orthologues to the CERV 2 family is present in the human genome, it was assumed that the CERV 2 family of ERVs integrated after the human-chimpanzee split. Again, no tangible evidence was provided to confirm this. Also, CERV 2 elements are present in chimpanzee, bonobo and gorilla (non-orthologous) but absent in human, orangutan, old world monkeys, new world monkeys and prosimians and identical to the distribution of CERV 1 elements [3].

    Because it is assumed that CERV 1 and 2 integrated from an exogenous source into the chimpanzee genome after the human-chimpanzee split, it is assumed that it integrated about 6mya or less. There are two ways of explaining the presence of CERV 1 and 2 elements in chimpanzees, bonobos and gorillas and the absence of these elements in humans, orangutans, old world monkeys, new world monkeys and prosimians.
1) Geographical isolation
2) Biological susceptibility (E.g. Trim5alpha)

    From table 1 it can be seen that the molecular basis for the presence of CERV1 and 2 in the chimpanzees is unclear and can only be explained by one of two scenarios (from Kaiser et al (2007) [5].
1) The R332 TRIM5alpha (able to restrict MLV/CERV1) was present in the common ancestor of humans and chimpanzees and that the R332Q mutation was fixed in our common ancestor
2) The human and chimp lineages independently fixed R332 after the species diverged at different intervals.
Positive evidence is needed to confirm either.

    Also, from table 1 it can be seen that the molecular basis for the absence of CERV1 and 2 like elements in the orangutans and gibbons is unclear. However, they are geographically separated from chimpanzees and might not have been exposed to these elements. But macaque species are geographically diverse and their native habitats do overlap that of orangutans and gibbons, making it possible that CERV 1 retroviral elements where introduced to orangutans and gibbons in the past. Therefore the geographical basis for the absence of CERV 1 and 2 in orangutans and gibbons become less than satisfactory.

    The TRIM5alpha genes among macaques vary in their ability to restrict HIV-1 infection [7]. Kaiser et al (2007) did not find any TRIM5alpha genes in primates that are capable of efficient restriction of both PtERV1 and HIV-1 [5]. Therefore the molecular basis for the presence of CERV1 and 2 elements in Pig tailed macaques is also unclear because the TRIM5alpha is unable to restrict HIV-1 (therefore can possibly restrict CERV1, although needs to be confirmed).

    Geographical evidence will only come from the sparse fossil record and the biological susceptibility factors are unable to explain many incidences of CERV1 and 2 distributions in primates (Table 1).
    Inconsistencies do exist with phylogenetic analyses and are often explained by ad hoc arguments without positive evidence.

    References

    [1] Yohn CT, Jiang Z, McGrath SD, Hayden KE, Khaitovich P et al. Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biol. 2005 Apr;3(4):e110.
    [2] Flockerzi A, Burkhardt S, Schempp W, Meese E, Mayer J.Human endogenous retrovirus HERV-K14 families: status, variants, evolution, and mobilization of other cellular sequences. J Virol. 2005 Mar;79(5):2941-9.
    [3] Polavarapu N, Bowen NJ, McDonald JF. Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biol. 2006;7(6):R51.
    [4] Ebersberger I, Galgoczy P, Taudien S, Taenzer S, Platzer M, von Haeseler A. Mapping human genetic ancestry. Mol Biol Evol. 2007 Oct;24(10):2266-76.
    [5] Kaiser SM, Malik HS, Emerman M. Restriction of an extinct retrovirus by the human TRIM5alpha antiviral protein. Science. 2007 Jun 22;316(5832):1756-8.

    [6] Yohn CT, Jiang Z, McGrath SD, Hayden KE, Khaitovich P, Johnson ME, et al. Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biol. 2005 Apr;3(4):e110.
    [7] Brennan G, Kozyrev Y, Kodama T, Hu SL. Novel TRIM5 isoforms expressed by Macaca nemestrina. J Virol. 2007 Nov;81(22):12210-7.

    The sheer number of ERVs:  
            In this light it is interesting to note that over 30,000 different ERVs are known within human genome. 37,43 The range of the total human genome occupied by ERV sequences is anywhere from 1% to 8% – depending upon the reference (with more recent references favoring 8% or greater).  The same range is true for the chimp genome as well.41   In fact, more recent work suggests a 45% ERV origin for the human genome at large (Mindell and Meyer 2001) and 50% for mammalian species in general ( Link ). In any case, of these tens of thousands of recognizable ERVs, only seven are currently known to infect both humans and chimps at identical locations within the separate genomes ( Link ).  Isn’t it interesting that out of 30,000 ERVs only 7 of them are known to have inserted at the same site in humans and chimps? – What are the odds given the known preference of many ERVs for fairly specific hot spot insertions?  Yet, this is the argument for ERVs being evidence of common descent as per Talk.Origins:
     
    Inconsistent phylogenies:

            Another interesting aspect of ERVs is that they do not always show the expected evolutionary pattern of “inheritance”.  According to the proposed phylogenetic tree (shown to the right) chimps are closer to humans than to gorillas.  Given this scenario, gorillas and chimps would only be expected to share an ERV if this same ERV were also present in humans. However there are some ERVs that don’t seem to fit this pattern. For example, the K family of ERVs (HERV-K provirus) is present in chimps and gorillas, but not in humans.40  Also, portions of ERVs known as CERV 2 and CERV 1 elements are present in chimpanzee, bonobo and gorilla (non-orthologous) but are absent in human, orangutan, old world monkeys, new world monkeys.39  
            The usual explanation for such findings, of course, is that humans lost this or that particular ERV along the way. Of course, this post-hoc argument could be used to explain any aberrancy.  Given that there are only 7 known ERVs that are shared, among tens of thousands, it is somewhat problematic that there are at least a few that are known to contradict the predicted phylogeny.  It is also interesting that an entire human population could loose an ERV that is preserved in both chimps and gorillas.  This would require yet another extreme population bottleneck to explain.
            There are also other even more problematic phylogenetic inconsistencies with ERVs:

  5. Maybe I did get carried away. Again my apologies. PZ is a mean spirited person who often resorts to name calling and has such a juvenile attitude, but I believe I have debated others who even though are less known, are just as knowledgeable. Take care. Again didn’t mean to bust your balls.

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