Gene Trees and Species Trees

| 18 Comments

One of the most compelling confirmations of the theory of evolution, in particular common descent, was the finding of close concordance between phylogenies derived on the basis of organismal biology and those inferred from molecular data. A wide array of evidence from pseudogenes, endogenous retroviruses, and functional genes generally corroborates the picture of common descent that began to be worked out in the 18th and 19th centuries mainly from comparative anatomy when even the existence of genes was unknown..

However, we know that out near the twigs, trees inferred from individual genes and species trees are not identical, and Thomas Mailund, a researcher at the Bioinformatics Research Center at the University of Aarhus in Denmark, has an excellent post on the relationship between gene trees and species trees with some great illustrations. I commend it to your attention, along with his other posts.

18 Comments

How ironic that this topic follows one about AIG.

Think about it: AIG and the DI base nearly all of their arguments on their perceived weaknesses of “Darwinism,” but rarely address their own radical differences, let alone provide independent evidence for their particular “theory.”

At the DI, the only one to offer some detail on his “theory” is Michael Behe. While he rejects “evolution” as a cause, he agrees that the “trees” - and the “biological continuum” that they imply - are real, as are their ~4 billion year chronology. Behe also stated that the Bible should not be used as a source of evidence, and indeed his conclusions from the evidence look nothing like AIG’s interpretation of Genesis or any of the common OEC interpretations.

Meanwhile AIG starts with the Bible and admits to picking and choosing only that “evidence” that fits.

Thus there are two “kinds” of debate that AIG and the DI (with Behe or other old-earther as a representative) can, and must, conduct if either is ever to have any hope that their ideas will be taken seriously by the scientific community. One concerns “what happened when,” and the other concerns whether evidence that doesn’t fit the Bible (Genesis) should be included or excluded. Both debates should be far easier that any “creation/evolution” debate, because neither party has a prior commitment to “naturalism,” which invariably makes all debates between creationism/ID and evolution degrade into a no-win debate about “naturalism.”

Yesterday I started a thread on Talk.Origins specifically for anti-evolutionists to debate their differences. So far no takers (not that I expected any). And 2 years ago I posted a “call for proposals” for any alternate explanations regarding human origins. The stipulation was that they stick to the whats, whens and hows, and test their ideas independent of any problems they may have with “Darwinism” or “naturalism.” As you might expect, no takers there too.

In case anyone wonders why I bother, I don’t expect any changes in anti-evolution activists’ behavior, but I also think that most people are sill unaware of the extent of their antics.

Have you completely lost your minds?

Another Sandefur “article” consisting of a comments-barred, adulatory link to the hyper-controversial, widely-believed-to-be-racist, and climate-change-denying site “Little Green Footballs”?

To clarify, the problems, again, are -

1) Lack of comments section, blocking any expression from those who disagree. This is particularly outrageous because LGF is also a comments-blocked site.

2) Representation of a political site as “scientifically accurate” when it’s far more likely that the site in general is scientifically uninformed and inaccurate on most issues, and when, frankly, “support for evolution” is probably nothing more than an epiphenomenon of “support for social Darwinism”.

This isn’t funny; it’s direct fuel for any creationist who seeks to muddy the waters and an absolute violation of any hypocritical claims that this isn’t a political site.

Why on earth you allow a political extremist who advocates ending all federal funding for research to use your site as a billboard for his extremist political views is beyond me.

I don’t have a lot of power here. I’m not a PT volunteer, I don’t maintain a blog that links to PT, and I also am not even a very prolific commenter.

So all I can do is express my disgust at the hypocrisy and favoritism, as well as the cowardice of those who cannot handle even collegial critique of their views.

I urge you to remove the Sandefur post, and frankly, to consider whether or not Timothy Sandefur is adding anything of value whatsoever.

Alright, deep breath, and a final conciliatory comment -

Of course it’s true that many people who hold “conservative” political views are not evolution deniers.

In short, although there is an intensely strong association between evolution denying and the American (and UK and Canadian and Australian) political right, there are some people on the right who do not deny evolution. And there are plenty of self-identified liberals or leftists who are scientifically ignorant or superstitious.

The strong association between evolution denial and the political right wing is not a one-to-one matching function.

But -

1) Timothy Sandefur is using THE WRONG METHOD to make this point. A comments-allowed, original content post would be the way to go, not a blind link to a far right web site.

2) The point is so obvious that it barely needs to be addressed.

3) More importantly, the American political right is currently associated with a plethora of science-denying positions - evolution denial, HIV denial, contraception evidence denial (and related denial of studies of the effect of abstinence-only education), climate change denial (and science denial on other environmental issues), and even some old hold-outs on things like denial of the relationship between smoking and disease (a staple of the American right for many years).

There must be one or two serious political conservatives who accept scientific consensus on all of these major issues (accept as current scientific consensus, that is). John Kwok? Maybe?

But they’re hard to find, and Sandefur undermines his own point by cherry picking sites that don’t deny evolution, while glossing over the fact that such sites are a far cry from scientifically enlightened.

Meanwhile, the article that this thread is actually about is excellent. I’ve said enough.

There must be one or two serious political conservatives who accept scientific consensus on all of these major issues (accept as current scientific consensus, that is). John Kwok? Maybe?

Well, this may come as a shock to some, but I’m a registered Republican, a former elected official of the local Republican party, am old enough to have voted for Barry Goldwater (a genuine conservative), and I accept the current scientific consensus on those issues. (‘Course I was also a higher ranking elected official of the Democratic Party once upon a time – a big city ward officer outranks a rural precinct officer. :)) Life has been tough for a fiscal conservative/social liberal the last couple of decades.

RBH,

The party left you too, huh?

Frank J said:

RBH,

The party left you too, huh?

I got dumped by the party for an ugly guy with a red sportscar. I thought he was a friend too, he went to my church.

Thanks, it was informative (especially for me personally, as it taught me some more complications of phylogenies) and a good read, as well as other posts on that site.

Speaking of confirmations, I was reading up on lateral gene transfer vs reduction ideas of early life when I found two intriguing pieces of extracted data.

Whatever you think of loss of traits or lineages (and the proposed LGT explanations of, say, the domains seems to me to involve loss of lines as well), the more narrow idea to look at use and putative evolution of folds (proteins) or nucleotides (RNA) seems easier to test. And Nature recently published a letter on molecular evolution in the Archaean:

Here we show that both rRNA and protein sequences analysed with advanced, realistic models of molecular evolution provide independent support for two environmental-temperature-related phases during the evolutionary history of the tree of life. In the first period, thermotolerance increased from a mesophilic LUCA to thermophilic ancestors of Bacteria and of Archaea–Eukaryota; in the second period, it decreased.

Disregarding the less uncertain aspects of time periods and ancestral environment, the data seems to indicate some sort of temperature bottleneck of 70-80 Celsius on two independent molecular thermometers. [Note that AFAIU the paper can only confirm those in Bacteria and Archaea - the figure can be subject for over-interpretation, I think.]

My eyebrows were raised when I googled around for Archaean temperatures, and found an earlier letter in Nature correlating silicon and oxygen isotope ratio thermometers, those combined data from cherts gives consistent sea water temperatures upwards to 70-80 Celsius in the Archaean! [Actually, I believe these two thermometers are rather independent as well, except derived from the same locales, see the letter.]

I’m not sure I would like to call this a compelling confirmation as much as a tentative test on such molecular methods. [When you look at both sets of data, you can imagine a lot more intriguing tentative correlations, but how to test for anything more than the usual lure, and common mistake, of a recognized pattern is beyond me.]

Which makes me ask the biological experts around here if such methods on evolution of folds (and/or protein families?) et cetera are seen as more than an interesting idea in this context?

@ harold:

I sympathize, but wasn’t the pronounced policy last time this question was discussed that the asked for commenting opportunity is provided by opening a thread at the AtBC forum?

Oops! Browser trouble made me drop a note: I believe high Archaean sea water temperatures, if real, can be explained by an, IIRC, putative early dense CO2 atmosphere trapping the initially relatively weak solar radiation.

Torbjörn Larsson, OM said:

Thanks, it was informative (especially for me personally, as it taught me some more complications of phylogenies) and a good read, as well as other posts on that site.

Don’t be afraid to let Mailund know that on his site. :)

RBH said:

Torbjörn Larsson, OM said:

Thanks, it was informative (especially for me personally, as it taught me some more complications of phylogenies) and a good read, as well as other posts on that site.

Don’t be afraid to let Mailund know that on his site. :)

Hey, I saw it here ;-)

Thanks!

I also agree that the article was excellent; in fact I bookmarked it for future reference.

Torbjorn -

Despite your kind words to the author, I can’t resist commenting that you also changed the subject slightly, as prokaryotes and LGT are only mildly related to great ape/hominid relationships :).

harold said:

I also agree that the article was excellent; in fact I bookmarked it for future reference.

In that case, you might also enjoy a few more posts on the topic I am working on. Not quite the different topologies issues in this post, but related to it.

I’ve just posted the first of two posts on the coalescence process and its consequences when we compare two genomes. It is a bit more technical than the species trees vs gene trees post, but I hope you will enjoy it anyway.

I will probably also consider how it changes the topologies along the genomes, but I am still working on figuring out the mathematics of this for my own research, so it might take a week or two.

Thomas Mailund said:

I’ve just posted the first of two posts on the coalescence process and its consequences when we compare two genomes. It is a bit more technical than the species trees vs gene trees post, but I hope you will enjoy it anyway.

Ups, forgot to include a link. Here it is: On segment lengths, going back in time, in the coalescence process. Part 1: The ancestry of a single species

Thomas,

Excellent articles, though I need to review a lot of math to truly appreciate them, especially the second article. But the graphics are excellent. A simplified version for high school biology might be ideal for a critical analysis (e.g. “what data would be required to support a different conclusion?”). It would also show that anti-evolution activists do not advocate a real critical analysis, only a phony one, specifically “designed” to promote unreasonable doubt.

Thomas Mailund -

Thanks very much for your contributions and for drawing my attention to all of this.

By a funny coincidence, for completely different reasons, I’ve been reviewing my old Probability book.

Although I was mainly a neuroscience type as an undergraduate, population genetics (which this reminds me of, except following alleles instead of sequences of individual nucleotides, of course) was one of my favorite courses. I believe I took it because it filled a requirement and was scheduled at a convenient time, but it ended up being a great choice.

It’s my impression that when evolution is looked at in a quantitative way, it does a great deal to eliminate the emotional biases that result from anthropomorphising it.

Frank J said:

Thomas,

Excellent articles, though I need to review a lot of math to truly appreciate them, especially the second article. But the graphics are excellent. A simplified version for high school biology might be ideal for a critical analysis (e.g. “what data would be required to support a different conclusion?”).

Yeah, I know the second one gets a bit more mathematical than the first one. The figures in the first one just explains the situations where incomplete lineage sorting can occur (but also that branch lengths are expected to differ along the genome). The second post quantifies this in a way that can be used to infer properties about the underlying population genetics. That is, in its nature, more mathematical, of course.

As for answering the question about how the data can lead to different conclusions, I think the mathematics is necessary, though. Not that the math cannot be simplified, of course. I do that when I give a talk on the subject, but to properly analyse data I fear some heavy math might be necessary to fully test the model…

Frank J said:

But the graphics are excellent. A simplified version for high school biology might be ideal for a critical analysis

I would actually really love to do some animations to explain the process, but unfortunately I do not have the skills for that :(

harold said:

Thomas Mailund -

Thanks very much for your contributions and for drawing my attention to all of this.

By a funny coincidence, for completely different reasons, I’ve been reviewing my old Probability book.

Although I was mainly a neuroscience type as an undergraduate, population genetics (which this reminds me of, except following alleles instead of sequences of individual nucleotides, of course) was one of my favorite courses. I believe I took it because it filled a requirement and was scheduled at a convenient time, but it ended up being a great choice.

It’s my impression that when evolution is looked at in a quantitative way, it does a great deal to eliminate the emotional biases that result from anthropomorphising it.

My background in all this is purely mathematical. I have a PhD in computer science and a minor in mathematics, but for biology I have little more than high school training. It is all self taught after I started working with bioinformatics (where I started out only doing algorithms and leaving the modelling to the biologists).

So essentially I start out with the mathematical modelling and worry little about the biology until I get to the data analysis part. There, of course, some model checking is needed to see how well the model fits the data, but whether the modelling is biologically interesting I leave to the biologists to decide :)

About this Entry

This page contains a single entry by Richard B. Hoppe published on February 21, 2009 12:26 AM.

I want AIG creationists on my jury! was the previous entry in this blog.

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