/sci/ - Science & Math

[Charles !DARwiN.Ixs No.4007972]

Okay, /sci/, let's try to have a discussion about phylogenetics and evolution.

I'm sure most of you have not heard about the scientific arguments regarding Archaeopteryx.

A nature paper (Xu et al., 2011) recently described Archaeopteryx as not a member of Avialae but instead as a member of the clade Deinonychosauria. This grouping was based on a parsimony analysis using a strict consensus tree.

This literally means that Archaeopteryx was not the first bird.

As expected this finding was contentious and caused caustic debate.

A later study in 2011 (Lee and Worthy, 2011) used maximum likelihood via bootstrapping and Bayesian analysis and found that Archaeopteryx was, indeed, in the clade Avialae. The analyses run found a bootstrap value of 73 and a posterior probability of 1.

I will post the phylogenies and explanations as well.
What does /sci/ think of this? Most people will object to priors adulterating the posterior in Bayesian analysis but this study also used resampling statistics as outlined by Felsenstein (1985).

Xing Xu, Hailu You, Kai Du and Fenglu Han (2011) An Archaeopteryx-like theropod from China and the origin of Avialae. Nature 475, 465–470.

Lee Michael S. Y. and Trevor H. Worthy (2011) Likelihood reinstates Archaeopteryx as a primitive bird. Biology letters 26 October 2011. doi:10.1098/rsbl.2011.0884

Felsenstein, Joseph (1985) Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution, 39(4): 783-791.

[Charles !DARwiN.Ixs No.4007994]

The phylogeny that results from a maximum parsimony analysis with strict consensus in PAUP*.

Notice that Archaeopteryx is a sister taxa in the clade Deinonychosauria.

The attached picture can be found in the supplementary materials of the Xu et al. (2011) paper.

[Charles !DARwiN.Ixs No.4008010]

The resulting phylogeny using maximum likelihood from RaxML and Bayesian analysis in MrBayes.

Notice that Archaeopteryx is found to be a member of Avialae.

The attached picture is a segment of figure 1 in the Lee and Worthy (2011) paper.

[Anonymous No.4008054]

wut

[Anonymous No.4008066]

soooo.... for those of us who don't have a degree in evolutionary biology, what are the implications of this?

[Anonymous No.4008067]

lol, I think we chased all our biologists away with that meme, interesting thread OP unfortunately I don't think I can contribute anything worthwhile to this discussion so I'll just give you a bump instead.

[Charles !DARwiN.Ixs No.4008078]

>>4008066

If the Xu et al. (2011) paper is correct then our understanding on the origin or birds is incorrect. This means our ideas on avian evolution were false.

If the Lee and Worthy (2011) paper is correct, it reaffirms the ideas already in place; that is, that Archaeopteryx is basal to the avian clade and that powered frontlimb front evolved only once.

[Anonymous No.4008108]

>>4008078
>If the Xu et al. (2011) paper is correct then our understanding on the origin or birds is incorrect. This means our ideas on avian evolution were false.
so would that hypothesis predict another more distant ancestor to all birds?

[Anonymous No.4008112]

>>4008078
>not a member of Avialae but instead as a member of the clade Deinonychosauria
I assume Aviale would be ancestors of birds and Deinonychosauria not, right?

Now how does this change our view on the evolution of birds?

[Anonymous No.4008116]

>A nature paper (Xu et al., 2011) recently described Archaeopteryx as not a member of Avialae but instead as a member of the clade Deinonychosauria.
But where exactly?
We already know now that many Deinonychosauria had bird-like features, their common ancestor could have very well been something more "bird-like", and later Dinosaurs lost those traits, as they adapted.

[Anonymous No.4008123]

How much of his genome do we have anyway?

[Anonymous No.4008137]

>>4008078
>This means our ideas on avian evolution were false.
How?

[Charles !DARwiN.Ixs No.4008146]

>>4008108

Not necessarily. It could mean that, of course, or it could mean that another lineage lead to birds at the time we hypothesized, but placed Archaeopteryx there incorrectly.

>>4008112

>I assume Aviale would be ancestors of birds and Deinonychosauria not, right?

Yes. The Deinonychosauria are very bird like dinosaurs that were a sister clade to the currently extant Aves.

>Now how does this change our view on the evolution of birds?

Archaeopteryx was placed basal in the Avialae clade, meaning it was the first bird. If moved to Deinonychosauria, Archaeopteryx is not a bird at all; all the morphological data used from it to construct flight evolution would be incorrect.

>>4008116

>But where exactly? The picture shown here >>4007994 shows the exact placement of Archaeopteryx in the Deinonychosauria. Keep in mind this is a strict consensus, meaning polytomies are rampant; exact phylogenetic positioning is not possible until more data are collected.

>We already know now that many Deinonychosauria had bird-like features, their common ancestor could have very well been something more "bird-like", and later Dinosaurs lost those traits, as they adapted.

Could be. But the analysis finding Archaeopteryx in the clade Deinonychosauria used parsimony; your hypothetical situation is not the most parsimonious answer and would be rejected by the Xu et al. (2011) analysis.

[Charles !DARwiN.Ixs No.4008164]

>>4008137

See >>4008146.

Flight evolution was categorized using morphological data from Archaeopteryx, assumung it was basal to Avialae. If Archaeopteryx is not a bird, then all data gathered from it to estimate the evolution of flight is incorrect.

>>4008123

Of Archaeopteryx there is no DNA available. Under such large periods of time, DNA is not preferable as it only has four character states (A, C, T, G) and is extremely prone to homoplasy as time progresses.

DNA evidence also cannot construct "true" phylogenies but can only approximate them by summing the gene trees it independently constructs. Deep coalescence would be such a problem here that most DNA studies would be hard to trust.

[Anonymous No.4008193]

What does its placement have to do with whether or not it could fly or whether birds came from it?

[Charles !DARwiN.Ixs No.4008194]

Because this topic is esoteric I can also discuss ideas in ecology, evolution and systematics.

I will also answer questions about graduate school, etc, if people seem interested in that.

[Charles !DARwiN.Ixs No.4008203]

>>4008193

In phylogenies, placement is everything. If Archaeopteryx is not basal then all modern birds did not stem from its clade and hence all data drawn from that clade is useless. We suspect it could fly as it shared many morphological features with modern birds, in a more plesiomorphic state.

[Anonymous No.4008217]

>>4008194
What's your background?

>Because this topic is esoteric

Hell, I'm doing a PhD in molecular evolution, and this is esoteric to me as well.

>most DNA studies would be hard to trust.

But you wouldn't reconstruct phylogeny based only on the genetic data, you would reconcile it with fossil data as well. would that work?

[Charles !DARwiN.Ixs No.4008251]

>>4008217

>What's your background?

I'm working on my PhD in ecology and evolutionary biology. I focus on natural selection and speciation, but systematic is a topic I am very interested in.

>But you wouldn't reconstruct phylogeny based only on the genetic data, you would reconcile it with fossil data as well. would that work?

It would work. But saying it is easier said than done. Until 2004ish or so, fossils could only be analyzed using parsimony; other methods such as maximum likelihood, jackknifing/bootstrapping, and Bayesian analysis weren't even possible.

Because DNA will exhibit homoplasy well before morphology, using it in parsimony analyses wouldn't get published when dealing that deep in the tree.

So the two couldn't even be used in conjunction until the mid 2000's. Now that they can, a large problem still stands in the way: getting DNA from the fossils, but also getting the exact same stretch of the genome from many fossils. It's near impossible.

[Anonymous No.4008256]

What is your opinion on the origin of life?

Was the planet seeded, or do you believe the process started under a case of purely random chemical reactions in the right environment?

[Anonymous No.4008263]

>>4008256
>Was the planet seeded
That's not an origin of life, that's just an excuse that places the origin elsewhere.

[Anonymous No.4008274]

>Xing Xu, Hailu You, Kai Du and Fenglu Han (2011) An Archaeopteryx-like theropod from China and the origin of Avialae. Nature 475, 465–470.

I feel I should point this out, not to start a fight or anything, but just to be thorough. The fossil that this paper was primarily based upon was independently reviewed by American scientists, one of the things they did was to do a very close analysis of the anatomy of the animal and the sediment it was found in. The team working on it had some serious questions about the fossil, because after their examinations began, they became suspicious that it was pieced together from multiple fossils. i.e.- they said it was faked. When they asked for more information from the Chinese team that lent the fossil, Chinese officials from the nearest embassy came to their lab, thanked them for their work, and confiscated the fossil and all the files they could find.

China has a history of such things in the fields of archaeology and paleontology. It is a bad idea to outright discount Chinese findings in these fields, but it's an equally bad idea to accept them at face value.

I'm not saying that the Chinese are the only ones that do this, or have done this, of course. They're not. Americans and the English have notably been the origins of some older hoaxes in these fields. The difference is that those hoaxes were exposed by countrymen of the original perpetrators, whereas this case stinks of cover-up.

Just my two cents worth.

[Charles !DARwiN.Ixs No.4008276]

>>4008256

Your two scenarios are not mutually exclusive.

Your first hypothesis (panspermia) is junk in my opinion.

First, it does nothing to answer the question of the origin of life. Panspermia simply says "well, life came from a comet or meteor". This does nothing to answer the question: all it simply does is shift the mechanical process somewhere else. If we accept panspermia, we literally just move your second hypothesis (chemical chance) to another location.

Your latter statement of chemical chance in the right environment is possible, but we need to be modest and remember that this explanation is a "how possibly" explanation; it does not demonstrate any "truth", but rather removes objections. Even with that in mind, it could still be how things actually happened.

With me saying that, I also want to state that I do not, under any circumstance, approve of appealing to the supernatural (god et al.) as an explanation for any phenomena. It is intellectually lazy to do so in my opinion.

[Charles !DARwiN.Ixs No.4008286]

>>4008274

>I feel I should point this out, not to start a fight or anything, but just to be thorough. The fossil that this paper was primarily based upon was independently reviewed by American scientists, one of the things they did was to do a very close analysis of the anatomy of the animal and the sediment it was found in. The team working on it had some serious questions about the fossil, because after their examinations began, they became suspicious that it was pieced together from multiple fossils. i.e.- they said it was faked. When they asked for more information from the Chinese team that lent the fossil, Chinese officials from the nearest embassy came to their lab, thanked them for their work, and confiscated the fossil and all the files they could find.

Do you have a source for this? I know the professor who reviewed the Xu et al. (2011) paper. I've discussed the paper with him and he never brought that up.

[Anonymous No.4008312]

>>4008286

Sadly no, but it wasn't any of the people reviewing the paper in question. The fossil that was the basis for the question was lent for independent analysis, and the team doing that research became suspicious.

Please note, I am not a biologist of any sort. I'm a physics guy. This just made science news, and it caught my eye through one of the news feeds that I subscribe to.

[Anonymous No.4008442]