A tiny bit of knowledge is a dangerous thing

Posted 11 March 2012 by PZ Myers

Good news! The gorilla genome sequence was published in Nature last week, and adds to our body of knowledge about primate evolution. Here's the abstract:

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

I've highlighted one phrase in that abstract because, surprise surprise, creationists read the paper and that was the only thing they saw, and in either dumb incomprehension or malicious distortion, took an article titled "Insights into hominid evolution from the gorilla genome sequence" and twisted it into a bumbling mess of lies titled "Gorilla Genome Is Bad News for Evolution". They treat a phenomenon called Incomplete Lineage Sorting (ILS) as an obstacle to evolution rather than an expected outcome.

This problem is related to a biological paradigm called independent lineage sorting. To illustrate this concept among humans and primates, some segments of human DNA seem more related to gorilla DNA than chimpanzee DNA, and vice versa. This well-established fact produces different evolutionary trees for humans with various primates, depending on the DNA sequence being analyzed.
In a significant number of cases, evolutionary trees based on DNA sequences show that humans are more closely related to gorillas or orangutans than chimpanzees--again, all depending on which DNA fragment is used for the analysis. The overall outcome is that no clear path of common ancestry between humans and various primates exists, so no coherent model of primate evolution can be achieved.
The recent release of the gorilla genome spectacularly highlights this evolutionary quandary. According to the Nature study, "in 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other."

When you compare the genomic sequences of three related species, such as the human, chimp, and gorilla, you'll typically find from an average that a pattern of relatedness is revealed: humans and chimps are closer to each other than they are to gorillas, indicating a more recent divergence between humans and chimps than between humans and gorillas. However, that's an average result: if you compare them base by base, you'll find genes and regions of the chromosomes in which the gorilla sequence is more similar to the human sequence than to the chimpanzee sequence; if you looked at only that gene, you'd conclude that humans and gorillas were closer cousins, and chimpanzees were more distant.

Is ILS a problem? It complicates the analysis of sequences for sure (although it also can be used as a probe to look at evolution). But it's not a problem that calls evolution into question; to the contrary, it's an expected phenomenon.

Here's why. This diagram illustrates the simplistic, naïve expectation you might have.

The outline of the tree illustrates the average pattern of sequence similarity, with the conclusion that humans (H) and chimpanzees (C) diverged more recently than humans/chimps and gorillas (G), which diverged more recently than humans/chimps/gorillas and orangutans (O). The solid line inside the outline illustrates the history of a single gene, drawn in black to represent the ancestral state, and then drawn in blue at the time humans and chimps diverged.

This is a gene that acquired its unique differences in the two lineages at the time of the human-chimpanzee split. It fits perfectly with the average pattern.

But just ask yourself: how likely is that? There are tens of thousands of genes in each of these species. Do you really think all the differences popped into existence simultaneously, at one instant when two populations of our last common ancestor discretely and completely separated? Of course not: you'd have to be a creationist to believe in something that stupid.

Here's another possibility. Speciation wasn't instantaneous, but a matter of multiple populations existing in parallel, with changes in genes appearing in different subsets at different times, spread out over long periods of time. So sometimes a mutation unique to one extant lineage appeared long before the split, and was just sorted at the time of separation into one lineage or the other.

In this case, comparison of the gene in question would give the same qualitative answer — humans and chimps are most closely related — but a different quantitative difference in the time of divergence. But as you can see, it requires nothing weird or unexplainable or contradictory to evolutionary theory: you just have to appreciate the population nature of evolution.

We can go further: different forms of the genes can be sorted into different lineages entirely by chance.

In these cases, we have two different forms of a gene that arose in ancestral population, ancestral to humans, chimps, and gorillas. By drift, one form was lost in the gorilla lineage, but both forms continue to be found in the ancestral manpanzee population; at the time of human/chimp divergence, these gene forms were sorted into different lineages. By chance, these will show either a closer relationship between humans and gorillas or chimpanzees and gorillas.

And the likelihood of HC2, HG, and CG above are equally probable!

So the creationist argument against evolution on the basis of incomplete lineage sorting is very, very silly. The only way you would fail to see ILS is if every genetic difference between two species emerged simultaneously, in lockstep, in one grand swoop. That is, the observation of ILS contradicts creationism, not evolution.

The authors of the Nature paper were well aware of this, and even illustrated it in their first figure.

Phylogeny of the great ape family, showing the speciation of human (H), chimpanzee (C), gorilla (G) and orang-utan (O). Horizontal lines indicate speciation times within the hominine subfamily and the sequence divergence time between human and orang-utan. Interior grey lines illustrate an example of incomplete lineage sorting at a particular genetic locus--in this case (((C, G), H), O) rather than (((H, C), G), O). Below are mean nucleotide divergences between human and the other great apes from the EPO alignment.

We can measure the average genetic distance between the species (the percentages at the bottom of the figure), but we can still see individual genes (the gray line) that branched at different points in their history. This is simply not a problem for evolutionary theory; once again, the creationists rely on their proponents having a foolishly cartoonish version of evolution in their heads in order to raise a false objection.

Scally A, Dutheil JY, Hillier LW et al. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175.

Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH (2009) Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach. Genetics 183: 259-274.

(Also on FtB)

48 Comments

https://me.yahoo.com/a/n2WhMtEQrvsReG10Z0oryyrwcalqfxDNMct2#93ec7 · 11 March 2012

Thanks PZ. I just read that article in Nature and was fairly sure someone would misinterpret it. You saved me the time I was going to take to go look this up to rebut it. I'll probably be hearing this argument from a relative fairly soon, and I'll be sure to point out your takeaway message that this contradicts creationism, not evolution.
--dan

DS · 11 March 2012

Once again, creationists display nothing but distortion and misrepresentation. They take clear evidence for evolution and in direct opposition to creationism and try to pretend that just the opposite is true. And these are the same guys who try to get scientific respectability by holding fake "conferences"!. Man, these guys are pathetic.

But then again, what else have they got? This is all they can really do, distort and misrepresent. All of the evidence is against them and the only people who are going to be fooled by their faulty reasoning are those who just want to believe regardless of the evidence anyway.

Here is an idea, why not let the creationists explain the evidence? Instead of letting them try to claim that his is somehow a problem for evolution, let them explain why they predicted this pattern. That should be fun, since they didn't. Let them explain why god did it this way. LEt hem explain why they aren;t the ones who did the research. Let them explain why they never bothered to do any sequencing if they are so sure the results support their position.

Reed A. Cartwright · 11 March 2012

And about 1% of our genome is most closely related to Orangutans than Gorillas and Chimps.

harold · 11 March 2012

Here is an idea, why not let the creationists explain the evidence? Instead of letting them try to claim that his is somehow a problem for evolution, let them explain why they predicted this pattern. That should be fun, since they didn’t. Let them explain why god did it this way. LEt hem explain why they aren;t the ones who did the research. Let them explain why they never bothered to do any sequencing if they are so sure the results support their position.

As I mentioned in a longer comment on another thread, ID/creationists try to do three things simultaneously, and those things sometimes interfere with one another. They try to 1) confuse the general public, 2) create a fake appearance of "doing science" at a level that is intended to fool judges, and 3) pander to and reassure the hard core ideological base (which is selectively "Biblical literalist", climate change denial, HIV/AIDS denial, sometimes cigarette/health denial, open to vaccine denial, homophobic, misogynistic, jingoistic, war-mongering, often ethnically bigoted, and typically against "social programs", but often while benefiting extensively from government programs). Of these, "3)" is the most important (because the money will dry up if they don't do it. But it interferes with the other two. Here we see a clear case of "3)", which also attempts to reach into "1)". However, the fact that this material is presented on a YEC site limits its impact on the broader general public. Misrepresentation of actual research, on religious sites, works strongly against the goal of pretending to do "neutral non-religious science".

apokryltaros · 11 March 2012

DS said: Here is an idea, why not let the creationists explain the evidence? Instead of letting them try to claim that his is somehow a problem for evolution, let them explain why they predicted this pattern. That should be fun, since they didn't. Let them explain why god did it this way. LEt hem explain why they aren;t the ones who did the research. Let them explain why they never bothered to do any sequencing if they are so sure the results support their position.

Newsflash: Creationists have already tried explaining the evidence. All they've come up with are silly, uselessly stupid ideas that won't last half a second with Occam's corpse. Things like the Ice Vapor Canopy, or Henry Morris' magic sorting flood, or Kurt Wise's navel contemplation about how the Coal Measures were formed by magic floating forests, or that all the oil and coal all used to be the Antidiluvian people who didn't survive to be fossilized, and so on. But the only reasons that anyone is given to believe these stupid thought-chimeras are that A) "I say Jesus said so," and B) "Believe me without question, or I'll sic God on you to send you to Hell." Yet, Creationists have to wonder out loud why people tend to consider them idiots.

TomS · 11 March 2012

apokryltaros said: Newsflash: Creationists have already tried explaining the evidence. All they've come up with are silly, uselessly stupid ideas ...

Even a fool, when he holdeth his peace, is counted wise: and he that shutteth his lips is esteemed a man of understanding. Proverbs 17:28 One of the reasons for the rise of "Intelligent Design". If the best than can be thought of as an "alternative to evolution" is YEC or Omphalism then it's better not to say anything about what happened and when.

Ron Okimoto · 11 March 2012

The title isn't quite apt. It isn't that they knew a little, it is that they lie a lot. Misrepresentation should not be confused with ignorance.

apokryltaros · 11 March 2012

Ron Okimoto said: The title isn't quite apt. It isn't that they knew a little, it is that they lie a lot. Misrepresentation should not be confused with ignorance.

Actually it is an apt title: they're taking a little fragment of knowledge, and spinning it into a big lie. Like the way dessert chefs take a tablespoon of sugar and spin it into a caramel sculpture.

apokryltaros · 11 March 2012

TomS said:
apokryltaros said: Newsflash: Creationists have already tried explaining the evidence. All they've come up with are silly, uselessly stupid ideas ...
Even a fool, when he holdeth his peace, is counted wise: and he that shutteth his lips is esteemed a man of understanding. Proverbs 17:28 One of the reasons for the rise of "Intelligent Design". If the best than can be thought of as an "alternative to evolution" is YEC or Omphalism then it's better not to say anything about what happened and when.

And with this, they've torn out their own heart. If the only alternatives to evolution ID proponents can bring up are silly, religiously inspired inanities, political word-lawyering or blatant science-denials, then they can not legitimately claim to be an alternative to evolution to begin with. And they know this.

Karen S. · 11 March 2012

Newsflash: Creationists have already tried explaining the evidence. All they’ve come up with are silly, uselessly stupid ideas that won’t last half a second with Occam’s corpse.

But oh my goodness, they sure can tap-dance!

Henry · 11 March 2012

"It is noteworthy that both the recent gorilla paper and Ebersberger's report utilize highly filtered data in which repetitive DNA (which comprises a significant portion of the genome) is masked and omitted, homologous (similar) regions are pre-selected, and sequence gaps are omitted. Both papers cited here explicitly state this. After this initial level of data selection, a methodology called multiple sequence alignment lines up the DNA segments between multiple organisms and the data is parsed into evolutionary trees.

Therefore, the data are always carefully prepared and selected for optimal tree development and should be full of evolution-favorable DNA sequences. Nevertheless, despite all of the data manipulation to make it more conducive to an evolutionary outcome, the picture that always emerges is a unique mosaic pattern of DNA between the various genomes being compare."

This is near the end of the ICR article.

apokryltaros · 11 March 2012

Karen S. said:
Newsflash: Creationists have already tried explaining the evidence. All they’ve come up with are silly, uselessly stupid ideas that won’t last half a second with Occam’s corpse.
But oh my goodness, they sure can tap-dance!

Yes, they do. Like how Henry is pointing out how ICR Whines For Jesus about how the researchers allegedly unfairly and deliberately skewed the data towards more evolution-friendly results.

Atheistoclast · 11 March 2012

This comment has been moved to The Bathroom Wall.

https://me.yahoo.com/a/JxVN0eQFqtmgoY7wC1cZM44ET_iAanxHQmLgYgX_Zhn8#57cad · 11 March 2012

Henry said: "It is noteworthy that both the recent gorilla paper and Ebersberger's report utilize highly filtered data in which repetitive DNA (which comprises a significant portion of the genome) is masked and omitted, homologous (similar) regions are pre-selected, and sequence gaps are omitted. Both papers cited here explicitly state this. After this initial level of data selection, a methodology called multiple sequence alignment lines up the DNA segments between multiple organisms and the data is parsed into evolutionary trees. Therefore, the data are always carefully prepared and selected for optimal tree development and should be full of evolution-favorable DNA sequences. Nevertheless, despite all of the data manipulation to make it more conducive to an evolutionary outcome, the picture that always emerges is a unique mosaic pattern of DNA between the various genomes being compare." This is near the end of the ICR article.

Or in other words, data were used according to the organizing theory of biology, and doing so indicated both the main expected pattern, and one that strongly suggests cross-breeding early on. So once again, evolution proves its crucial role in even being able to make use of data, while ID/creationism hasn't a clue how to understand the data (except by cribbing from evolution). This is, of course, a bad thing to the ignorant who wish desperately to remain so and to keep their followers in the dark. Say, creationists, why don't we find such more-closely related sequences that occurred between mice and humans, horses and cattle, or birds and humans, within the last million years or so? Could it possibly be because that such cross-breeding isn't possible now or in the recent past, while it would be expected between human ancestors and gorilla ancestors within a few million years? So, evolution wins again, and the liars for Jeebus claim otherwise. We can predict that as easily as we can predict that such "mosaic patterns" will only exist in primates within the time period within which diverging lines can still interbreed. Glen Davidson

vreejack · 11 March 2012

A simple thought experiment will illustrate this. Suppose for argument's sake the unlikely situation had occurred in which humans, chimps and gorillas all diverged at the same time from the same ancestral population. As some genes in some populations were lost through random fixation, the remaining shared genes would be roughly equally distributed between any pair of species. Some pairs of fixed genes will be common to chimps and humans, some will be common to gorillas and chimps, and some will be common to gorillas and humans in roughly equal proportions. Pushing the date of gorilla--chimp/human divergence back a few generations will not change this noticeably, but as the number of generations of the division grows, the shared gene ratios will begin to diverge. And this is what we see. Chimps and humans share more genes then either one alone shares with gorillas, but there are still genes shared exclusively between gorillas and chimps and between humans and gorillas. Anything else would actually require an explanation.

Joe Felsenstein · 12 March 2012

Folks, the easier way of thinking about "lineage sorting" is to go backwards in time and call it "coalescence". Suppose you have one sequence (from a single copy of a single locus) in (present-day) Human, one in Chimp, and one in Gorilla. Each copy is descended from a single copy in the previous generation, that from a single copy in the one before that, and so on backwards in time. Finally you get back to the common ancestor of Human and Chimp. In that common ancestor the two copies are in separate individuals. Now if the population size is N, there are 2N copies at this locus in that population. Each generation (going back) there is a 1/(2N) chance that the two copies come from the same copy. If there are (say) 2 million years back further to the common ancestor with gorilla, and if generation time is 20 years, and if the population size of the Human/Chimp common ancestor is 100,000, then there are 2000000/20 = 100,000 "trials", each with probability 1/(200,000).

The chance that the two copies do not coalesce in that time is thus about 0.999995, raised to the 100,000-th power. That is 0.368. So that fraction of Human/Chimp loci do not coalesce before we get back to the HCG common ancestor. Once there, and going back in time, the three copies sooner or later have two of them coalesce, then all three. So there is a further one-third of the 0.368 cases that will happen to have the H and C copies coalesce.

Thus (with these numbers) the fraction of the time that the tree of gene copies turns out to be ((H,C),G) is (1-0.368) + (1/3)(0.368) = 0.754. Of the remainder, half of the trees of gene copies will then be ((H,G),C) and half ((C,G).H), so 0.123 each. With a little more tinkering with population sizes we can get a close fit to the proportions seen from using the genome sequences.

And yes, I have been assuming here that there is no recombination within the locus, and no natural selection "sweeps" disturbing the random pattern of genetic drift. Any mutations that are occurring on these trees of gene copies are being assumed to be neutral. Note that if we think we know the divergence times of the species and also the generation times, the calculation permits us to estimate the population size of the Human/Chimp common ancestor.

The theory of coalescent trees of gene copies was worked out by John Kingman in 1982, and the extension to coalescent trees inside of species trees is due to Fumio Tajima, Naoyuki Takahata, and Masatoshi Nei in 1983-1985. It is explained in my book Inferring Phylogenies or in recent good books by John Wakeley and by Jotun Hein, Mikkel Schierup and Carsten Wiuf.

Does that help?

eric · 12 March 2012

Joe, is this the right way of thinking about it?

Say HC1 has ten genes: AAA AAAA AAA

HC splits from G. Both evolve (B denotes the "HC" evolved gene). HC: AAA AABB BBB. G: AAA GGGG GGG

H and C split. Both evolve: H: HAA AABB BBB. C: CCC AABB BBB

In this scenario, humans end up closer to gorillas than chimps in genes 2 and 3. The genera lesson is, humans and gorillas may share a more similar gene when that gene was stable after the HC-gorilla split, but then mutated in chimps after the human-chimp split.

harold · 12 March 2012

The genera lesson is, humans and gorillas may share a more similar gene when that gene was stable after the HC-gorilla split, but then mutated in chimps after the human-chimp split.

That is certainly what PZ has illustrated in the figure labeled "HC1".

Joe Felsenstein · 12 March 2012

eric said: Joe, is this the right way of thinking about it? Say HC1 has ten genes: AAA AAAA AAA HC splits from G. Both evolve (B denotes the "HC" evolved gene). HC: AAA AABB BBB. G: AAA GGGG GGG H and C split. Both evolve: H: HAA AABB BBB. C: CCC AABB BBB In this scenario, humans end up closer to gorillas than chimps in genes 2 and 3. The genera lesson is, humans and gorillas may share a more similar gene when that gene was stable after the HC-gorilla split, but then mutated in chimps after the human-chimp split.

It's not what I was talking about. You are considering each species to have one sequence at the locus. Both the coalescent and the lineage-sorting ways of thinking consider the species to be a population with 2N copies at that locus. They ask about the genealogy of those copies, which are reproducing inside the species.

John Harshman · 12 March 2012

Another common buzzphrase under which this subject is discussed would be "gene tree vs. species tree". Because there is polymorphism within species, and because polymorphisms can persist through speciation events, the true phylogeny of a section of DNA may not match the overall phylogeny of the population. We are just now beginning to see methods of phylogenetic analysis that take real discordance of history within a genome into account.

dennis.venema · 12 March 2012

Knowing well how often ILS turns up in creationist arguments, I did a piece on this for BioLogos a while ago, which some might find of use:

http://biologos.org/blog/understanding-evolution-speciation-and-incomplete-lineage-sorting

Richard B. Hoppe · 12 March 2012

dennis.venema said: Knowing well how often ILS turns up in creationist arguments, I did a piece on this for BioLogos a while ago, which some might find of use: http://biologos.org/blog/understanding-evolution-speciation-and-incomplete-lineage-sorting

I'd forgotten about that post. Thanks for the reminder.

Joe Felsenstein · 12 March 2012

Dennis's post on lineage sorting is very good.

However I continue to insist to all of you that the clearest way to think about "lineage sorting" is to turn around, look backwards in time, and think of it instead as coalescence.

John Harshman · 12 March 2012

Joe Felsenstein said: Dennis's post on lineage sorting is very good. However I continue to insist to all of you that the clearest way to think about "lineage sorting" is to turn around, look backwards in time, and think of it instead as coalescence.

Clearest for you. I like my time to run forward, thank you very much. So why doesn't PHYLIP draw its trees upside down?

Joe Felsenstein · 12 March 2012

John Harshman said:
Joe Felsenstein said: Dennis's post on lineage sorting is very good. However I continue to insist to all of you that the clearest way to think about "lineage sorting" is to turn around, look backwards in time, and think of it instead as coalescence.
Clearest for you. I like my time to run forward, thank you very much. So why doesn't PHYLIP draw its trees upside down?

This will be the lighthearted response. The serious one will be in the next comment. PHYLIP will draw rooted trees left-to-right, or bottom-to-top. I didn't bother with the other ways. (Unrooted trees can be rotated arbitrarily, though). It reminds me of a story Walter Fitch told me. When he was first working on molecular phylogenies in 1967, he suddenly realized he didn't know whether they "grew" bottom-to-top or top-to-bottom. He was puzzled and wondered how biologists drew them. Then he remembered that they were always talking about the "descent" of species, so he drew them top-to-bottom. His tree diagrams influenced many molecular biologists to do it this way. Unfortunately for Walter, the biologists talked about the "descent' of species but drew the trees bottom-to-top, as actual plants grew.

Joe Felsenstein · 12 March 2012

When you think in terms of Lineage Sorting it is confusing. For example, think of two lineages that just separated, within a species that is ancestral to Human and Chimp. When the Human/Chimp split happens either one could go left or right. But not independently. For example they could not both go left, or both go right. You need to condition on ending up with one lineage in each descendant species, so they could go LR or RL. There need to end up being as many lineages in each species as we sampled from them.

But going backwards it is easy: you start from the sampled sequences and ask about their ancestry. As the samples are the starting point, there is no need to specially condition in drawing the coalescence events. For example, in my long post above I was able to calculate actual probabilities of various outcomes. None of the people who talked about lineage sorting did anything like that.

dennis.venema · 12 March 2012

Joe, I agree that's the simplest way to think about it, but coalescence - thinking doesn't come naturally to most people, much less folks who don't really understand speciation in the first place...

Joe Felsenstein · 12 March 2012

dennis.venema said: Joe, I agree that's the simplest way to think about it, but coalescence - thinking doesn't come naturally to most people, much less folks who don't really understand speciation in the first place...

Yes, but there's a price to pay. For example, someone thinking about lineage sorting could think that there is variability within a species, with multiple lineages, then at the speciation they randomly sort out -- maybe all go to one of the two descendants. But that's impossible, as we have samples from both descendants and some lineages must be ancestral to both. Also we couldn't have more lineages going into one of the daughter species than there are samples from it. Just whining ...

https://me.yahoo.com/a/iX7ogXAAzJTzNjXBRaGw5n0Bwpz2uulxmPduIrnhZEg-#cc736 · 15 March 2012

Perhaps joe or dennis could comment. You show that the gorilla results can be explained exclusively by incomplete lineage sorting. However, this success does not exclude other processes that might contribute to the observed phenomenon. In particular, I would like to know if hybridization could make gorillas seem closer, supposing that proto-gorillas could and did occasionally cross with manpanzees for a million or more years after proto-gorillas split off.

We now have evidence of sapiens-neanderthal crossing, and Scally and company estimate that eastern and western gorillas have had 2 million years of isolation, yet remain gorillas (can they cross?). This is about the same time-span separating gorilla from chimp offshoots in human evolution.

Resuming, could a 'lineage sorting' pattern be reinforced or mimicked by pieces of gorilla genome coming from hybridization events close up to the man-chimp bifurcation? If so, this kind of lead-off argument might be easier for the general public to understand than coalescence – admittedly more inevitable [excuse grammar] in the mathematical sense but easier for know-nothing (or dishonest) creationists to peddle as mumbo-jumbo.

Joe also mentions that the coalescence model assumes that there is no recombination and that natural selection does not act on mutations or produce selective sweeps. Are these assumptions reasonable? If the assumptions are false and recombination and natural selection are important, how does this affect the predictions of simple coalescence models?
Thanks

– W. Benson

RWard · 15 March 2012

I love this thread. Thoughtful (and civil) discourse from people who actually do science. There's a lesson to be learned by our friends from the DI and other religious organizations.

Henry J · 15 March 2012

What if gorillas and humans are still like the common ancestor in some areas in which chimpanzees evolved some differences of their own?

Thomas Mailund · 15 March 2012

https://me.yahoo.com/a/iX7ogXAAzJTzNjXBRaGw5n0Bwpz2uulxmPduIrnhZEg-#cc736 said: Perhaps joe or dennis could comment. You show that the gorilla results can be explained exclusively by incomplete lineage sorting. However, this success does not exclude other processes that might contribute to the observed phenomenon. In particular, I would like to know if hybridization could make gorillas seem closer, supposing that proto-gorillas could and did occasionally cross with manpanzees for a million or more years after proto-gorillas split off.

The coalescence model that Joe describes is exactly what we modeled in the gorilla genome paper, of course, and doesn't take hybridization events into account. We are painfully aware that such events are likely -- especially considering recent analyses of archaic human admixture -- but we had to keep it simple. The simple model, the coalescence in an ancestral species, can explain the data, but it doesn't rule out more complex scenarios. Something we are looking at now.

We now have evidence of sapiens-neanderthal crossing, and Scally and company estimate that eastern and western gorillas have had 2 million years of isolation, yet remain gorillas (can they cross?). This is about the same time-span separating gorilla from chimp offshoots in human evolution.

It seems to me, that admixtures between separated ape species happens all the time -- we have seen it for gorillas here and for orangutans in last years orangutan genome paper -- so perhaps it should be the null model for ancestral species as well.

Resuming, could a 'lineage sorting' pattern be reinforced or mimicked by pieces of gorilla genome coming from hybridization events close up to the man-chimp bifurcation? If so, this kind of lead-off argument might be easier for the general public to understand than coalescence – admittedly more inevitable [excuse grammar] in the mathematical sense but easier for know-nothing (or dishonest) creationists to peddle as mumbo-jumbo.
Admixture events are less parsimonious than ILS, which is why we have looked at ILS for now, but admixtures might be more common than we think.
Joe also mentions that the coalescence model assumes that there is no recombination and that natural selection does not act on mutations or produce selective sweeps. Are these assumptions reasonable? If the assumptions are false and recombination and natural selection are important, how does this affect the predictions of simple coalescence models?

With no recombination, you wouldn't see this patter of course. That would imply that some genomes in the current species are really closer to other genomes from another species. It is only locally that we find ILS patterns, so recombination is essential for this modeling. For short enough genomic segments, though, it isn't a bad way of thinking about this. If the segments are short enough, and sufficiently far apart, you can think of them as independent samples in the ancestral species. This breaks down in a genome wide analysis, which is why we had to use CoalHMMs to deal with it. Selection certainly affects the patterns as well. We even mention this in the gorilla paper. There is less ILS around genes and in low recombination regions, something that fits very well with the expectation assuming selection.

Thomas Mailund · 15 March 2012

Reed A. Cartwright said: And about 1% of our genome is most closely related to Orangutans than Gorillas and Chimps.

That 1% was only comparing human, chimpanzees and orangutans. If we take gorillas into account, which we didn't last year, it will be less that. Probably half that, but we haven't done the analysis yet.

Joe Felsenstein · 15 March 2012

The last few comments are very thoughtful and I hope others will answer them -- I have to go grade my final exam right now. But first I do have to correct the numbers that appeared in my long posting on the coalescent. Mike Taylor emailed me this:

I just read through the thread on lineage sorting and the gorilla genome on Panda's Thumb. I was working through your response on coalescence and probability. I could not initially duplicate your numbers but I think I figured out why. It doesn't change your point at all, of course, but I want to be sure that I did do the math right so that I know I am following your reasoning. You state that
[quoting what I had written:] The chance that the two copies do not coalesce in that time is thus about 0.999995, raised to the 100,000-th power. That is 0.368.
However, 0.999995 raised to the 100,000th power is 0.60653. Instead, it is 0.99999 ^ 100,000 that is 0.368. If so, that should then change the next set of numbers to:
[quoting what I had written:] Thus (with these numbers) the fraction of the time that the tree of gene copies turns out to be ((H,C),G) is (1-0.368) + (1/3)(0.368) = 0.754. Of the remainder, half of the trees of gene copies will then be ((H,G),C) and half ((C,G).H), so 0.123 each.
(1-0.60653)+(1/3)*(0.60653) = 0.5956 Which should leave the two halves of the remaining gene trees as 0.20218 each. Is this correct, or did I miss something along the way?

He is quite correct: I miscalculated 0.999995 raised to the 100,000th power and as a result got the other numbers wrong too. The correct numbers for the case I gave are 0.5956 HC, 0.2022 HG, and 0.2022 CG.

Joe Felsenstein · 15 March 2012

Well, there we have it -- the two previous comments by Thomas Mailund are from one of the authors of the paper analyzing the Gorilla genome. That is as close as you will ever get to an official answer to your questions!

Thomas Mailund · 15 March 2012

Joe Felsenstein said: Well, there we have it -- the two previous comments by Thomas Mailund are from one of the authors of the paper analyzing the Gorilla genome. That is as close as you will ever get to an official answer to your questions!

Well, I'd love to elaborate as much as I can if there are questions, so we might get closer :) We are not done with this kind of analysis and for the bonobo genome there will be a lot more ILS analysis. It is under review now but a similar story is seen there. For the next step we have hundreds of genomes from all apes that we are now looking at, so we will know a lot more in a year's time or so. ILS, and different coalescence times along the genome in general, seems to give us a lot of information about ancestral species, and it is really exciting to work with. It boggles my mind that it can be interpreted as a failure of our theory of evolution, but life's too short to worry about that, I guess.

dennis.venema · 15 March 2012

It boggles my mind that it can be interpreted as a failure of our theory of evolution, but life’s too short to worry about that, I guess.

I know what you mean, but such is the reality of trying to communicate these types of results to a community greatly suspicious of science in general, and of evolution in particular (read: evangelical Christians). I do think we are seeing improvement, though. Ten years ago accepting evolution was exceedingly rare in evangelical circles. Now it is not uncommon for folks in the pew to accept it, and we're seeing more and more pastors coming around to the notion. They are still the minority, but they're there. It's like a selective sweep - these things take some time...

Thomas Mailund · 15 March 2012

dennis.venema said:
Ten years ago accepting evolution was exceedingly rare in evangelical circles. Now it is not uncommon for folks in the pew to accept it, and we're seeing more and more pastors coming around to the notion. They are still the minority, but they're there. It's like a selective sweep - these things take some time...

I can count on one hand the number of religions people I have ever known, so there is a cultural aspect here :) I don't think I really understand the religious aspects of this, nor do I particularly care to. If you want to discuss the science, I am always happy to do so, but I really can't be bothered to discuss the evidence for or against Santa or the Easter Bunny.

Joe Felsenstein · 15 March 2012

Thomas, Dennis Venema was originally writing at a site aimed primarily at evangelical Christians and was expressing his frustration that the Discovery Institute was misrepresenting the lineage-sorting issue as a failure of evolutionary explanations. No one was expecting you to deal with any issues of religion here.

Thomas Mailund · 15 March 2012

Joe Felsenstein said: Thomas, Dennis Venema was originally writing at a site aimed primarily at evangelical Christians and was expressing his frustration that the Discovery Institute was misrepresenting the lineage-sorting issue as a failure of evolutionary explanations. No one was expecting you to deal with any issues of religion here.

Oh, I understood that, and I'm sorry if I gave the impression that I was complaining about having to or anything. I was just trying to say that the whole religion discussing is something that is a bit alien to me since I never have to deal with it in my own life. I understand that there is a major difference between scandinavia and the US in this regard, and I admire those people who participate in these discussions. I would personally find it too frustrating, I am sure.

dennis.venema · 15 March 2012

Yes, it's an interesting American and to a lesser extent, Canadian issue that I'm sure is pretty much unheard of in Scandinavia.

Contra Coyne, et al, I do think headway is being made, though, if slowly. My approach over the last few months has just been to try teach basic evolutionary concepts to Christians, little bit by little bit. Feedback I get seems to suggest it is working. Ten years ago there wasn't an identifiable position/organization that was overtly evangelical and accepted evolution. Nowadays BioLogos will often get invitations to present alongside YECs and OECs as another "acceptable Christian position" on origins. That's real progress, in my mind.

Atheistoclast · 16 March 2012

This comment has been moved to The Bathroom Wall.

Just Bob · 16 March 2012

Atheistoclast said:
This comment has been moved to The Bathroom Wall.

Praise the lord!

snaxalotl · 28 March 2012

luskin is apparently (but without being usefully cited) insisting that the scientific position depends on arbitrary amounts of interbreeding after the split:
http://www.focusonlinecommunities.com/blogs/trueu/2012/03/28/luskin-responds-to-a-trueu-facebook-reader-on-ape-human-evolution

also, if i might raise a question: PZ lists mechanisms that cause ILS, but the one that seems obvious to me is where a mutation occurs in the chimp line after the HC split, but humans and gorillas retain their ancestral form. does this not contribute to the 30%, and if not why not?

Robert Kraus · 18 April 2012

What a nice thread of comments! I didn't know this site and got a kick from a colleague to have a look. I reply specifically to the matters arising from potential hybridisation. Just recently we have publsihed a paper in which we introduce the idea of a "persistence time analysis framework" (BMC Evol Biol 2012, 12:45; currently available there as pre-publication PDF), in which one can determine if a certain amount of shared polymorphisms between species may be due to retaining ancestral polymorphisms, or if it can only be explained by (ongoing) inter-specific gene flow. Therefore, one would need population data on polymorphisms. And also, the assumption is that the genetic markers behave neutrally. If this is established the retention of ancestral polymorphisms is a function of divergence time, effective pop size, and initial allele frequnecy. In our study we scored several duck species at hundreds of SNP markers and found that the amount of SNP sharing is higher than expected under a simple model species isolation without gene flow. I have to admit that the framework is currently rather sktechy and not yet formally formulated in mathematical terms. I hope we can achieve the neccessary closer connection to theoretical population genetics in the future. However, from our empirical observation my guess is that it will be a useful way of looking at speciation and divergence also in this example. A rate of 30% of genome sharing is quite substantial. To distinguish the ILS or coalescent way of looking at it from the potential impact that (ongoing) hybridisation may have it will be extremely useful to look at shared polymorphism from population genomic data in a persistence time analysis framework.

Thomas Mailund said:
https://me.yahoo.com/a/iX7ogXAAzJTzNjXBRaGw5n0Bwpz2uulxmPduIrnhZEg-#cc736 said: Perhaps joe or dennis could comment. You show that the gorilla results can be explained exclusively by incomplete lineage sorting. However, this success does not exclude other processes that might contribute to the observed phenomenon. In particular, I would like to know if hybridization could make gorillas seem closer, supposing that proto-gorillas could and did occasionally cross with manpanzees for a million or more years after proto-gorillas split off.
The coalescence model that Joe describes is exactly what we modeled in the gorilla genome paper, of course, and doesn't take hybridization events into account. We are painfully aware that such events are likely -- especially considering recent analyses of archaic human admixture -- but we had to keep it simple. The simple model, the coalescence in an ancestral species, can explain the data, but it doesn't rule out more complex scenarios. Something we are looking at now.
We now have evidence of sapiens-neanderthal crossing, and Scally and company estimate that eastern and western gorillas have had 2 million years of isolation, yet remain gorillas (can they cross?). This is about the same time-span separating gorilla from chimp offshoots in human evolution.
It seems to me, that admixtures between separated ape species happens all the time -- we have seen it for gorillas here and for orangutans in last years orangutan genome paper -- so perhaps it should be the null model for ancestral species as well.
Resuming, could a 'lineage sorting' pattern be reinforced or mimicked by pieces of gorilla genome coming from hybridization events close up to the man-chimp bifurcation? If so, this kind of lead-off argument might be easier for the general public to understand than coalescence – admittedly more inevitable [excuse grammar] in the mathematical sense but easier for know-nothing (or dishonest) creationists to peddle as mumbo-jumbo.
Admixture events are less parsimonious than ILS, which is why we have looked at ILS for now, but admixtures might be more common than we think.
Joe also mentions that the coalescence model assumes that there is no recombination and that natural selection does not act on mutations or produce selective sweeps. Are these assumptions reasonable? If the assumptions are false and recombination and natural selection are important, how does this affect the predictions of simple coalescence models?
With no recombination, you wouldn't see this patter of course. That would imply that some genomes in the current species are really closer to other genomes from another species. It is only locally that we find ILS patterns, so recombination is essential for this modeling. For short enough genomic segments, though, it isn't a bad way of thinking about this. If the segments are short enough, and sufficiently far apart, you can think of them as independent samples in the ancestral species. This breaks down in a genome wide analysis, which is why we had to use CoalHMMs to deal with it. Selection certainly affects the patterns as well. We even mention this in the gorilla paper. There is less ILS around genes and in low recombination regions, something that fits very well with the expectation assuming selection.

seif abdel aziz 12 · 2 May 2012

Seif Ahmed Abdel Aziz

Personally i think that the above about evolution is not true because simply they have not yet been proven. my opinion is that no one should try to guess that something happened, and then use it as a true theory. People have to always back up their evidence. fossil records do not show or prove that evolution took place. Fossil records only show a slight change in the way somethings looks. I think that all the fossils that we find look kind of different because they change shape overtime due to the pressure that they are put through under ground. Fossil dating also goes against evolution and not with it because we see that organisms slightly change shape because if what they go through starting from when they die to the time we find them. For example we may find a persons fossil that was thousands of years old that does not have any change at all which shows that evolution doesn't happen that effectively and because evolution is not that strong than i think that it might have never happened at all. Natural selection is the process in which organisms gain certain characteristics when adapting to their environment so that they could have a better chance of survival. Natural selection does not prove evolution as a whole because natural selection is that some bears might gain stronger teeth over time because they feed on flesh, another is that lions may become faster in speed because they always have to run to hunt down a prey, but at the end natural selection does not mean that an animal or an organism becomes something else over time it just means that they have gained better characteristics.Organism classification is also a factor that people try to use a lot so that they could prove evolution. What i have to say to these people is that i do no think that organism classification has to do any thing with evolution. The things or the environment that is around the organism does not change they way it looks it just changes the way it lives.I think that fossil hominids change because they are underground for a long time. when we look at fossil hominids we don't see the change that humans were monkeys for example we just see a 1 in bigger skull which might be something normal that can even happen today because not all people look like each other. we also cant use fossil hominids to predict a lot because we did not yet find these much fossil hominids to use as a source of how people or organisms used to look like. That shows that fossil hominids are not that much of good evidence to prove evolution.Finally what makes me disagree on the concept of evolution is that i think people should not only believe in science and biology books but they also have to believe in religion books. Biology books have proved many things correct which is why people believe a lot in these books but also religion books like the Quran and the bible proved a lot of things that were correct so why believe in the science books only and not in the religious books?????!!!!

co · 2 May 2012

seif abdel aziz 12 said: Biology books have proved many things correct [...]

Everything: Ur doin it rong.

Dave Luckett · 2 May 2012

self abdel aziz 12 says Finally what makes me disagree on the concept of evolution is that i think people should not only believe in science and biology books but they also have to believe in religion books.

Yeah, we know you think they should have to. It's called "theocracy". Over here in the west, we pulled ourselves out of it by slow degrees, starting about five hundred years ago. Guess what. We're not going back.