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Huge discordance between gene trees in a new phylogenetic study

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A friend alerts us to this Abstract:

Angiosperms represent one of the most spectacular terrestrial radiations on the planet1, but their early diversification and phylogenetic relationships remain uncertain2,3,4,5. A key reason for this impasse is the paucity of complete genomes representing early-diverging angiosperms. Here, we present high-quality, chromosomal-level genome assemblies of two aquatic species—prickly waterlily (Euryale ferox; Nymphaeales) and the rigid hornwort (Ceratophyllum demersum; Ceratophyllales)—and expand the genomic representation for key sectors of the angiosperm tree of life. We identify multiple independent polyploidization events in each of the five major clades (that is, Nymphaeales, magnoliids, monocots, Ceratophyllales and eudicots). Furthermore, our phylogenomic analyses, which spanned multiple datasets and diverse methods, confirm that Amborella and Nymphaeales are successively sister to all other angiosperms. Furthermore, these genomes help to elucidate relationships among the major subclades within Mesangiospermae, which contain about 350,000 species. In particular, the species-poor lineage Ceratophyllales is supported as sister to eudicots, and monocots and magnoliids are placed as successively sister to Ceratophyllales and eudicots. Finally, our analyses indicate that incomplete lineage sorting may account for the incongruent phylogenetic placement of magnoliids between nuclear and plastid genomes.

Yang, Y., Sun, P., Lv, L. et al. Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution. Nat. Plants (2020). https://doi.org/10.1038/s41477-020-0594-6

The paper is open access.

From the paper: “Thus, what might account for this deep phylogenetic incongruence between nuclear and plastid genomes? As multiple independent polyploidization events were identified in magnoliids, monocots, Ceratophyllales and eudicots (Fig. 1), allopolyploidization or hybridization is one probable source of genomic discordance.”

“Deep phylogenetic incongruence” sounds like journalspeak for “our current phylogenetic tree is a hot mess.”

Comments
ET, 96: Whatever. It seems to me that you have been making bald assertions and were called on it. So I understand why you would want that to stop. What bald assertions did I make?JVL
March 3, 2020
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Whatever. It seems to me that you have been making bald assertions and were called on it. So I understand why you would want that to stop.ET
March 3, 2020
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@94 JVL
We seem to be arguing/discussing past each other. Seems like a good time to stop.
Can you? Or are you a neuronal 'puppet' with no real agency?Truthfreedom
March 3, 2020
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ET: We seem to be arguing/discussing past each other. Seems like a good time to stop.JVL
March 3, 2020
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The mainstream has thought there would be numerous transitional forms since Darwin. And yet EVERY TIME one is uncovered it is BIG news. When "Lucy" was found it was HUGE news, even though mainstream expected it. JVL said that finding evidence that supported unguided evolution wouldn't be news cuz mainstream expected it. Obviously past cases prove him wrong. And when it comes to falsifying ID- to demonstrate that unguided processes are up to the task. To date no one has been able to do that. That is something that flows from ID's hypothesis, JVL sez:
I think that’s a matter of opinion as there seems to be a lot of people who would disagree with you on that!
That alone proves that JVL doesn't understand how science works.ET
March 3, 2020
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AGAIN, the BEST evidence for macroevolution is presented on talk origins. And yet that evidence is absent a mechanism. If they had the evidence that unguided processes could do it they would have said that. And it pretty much shows that you really don’t know what you are talking about.ET
March 3, 2020
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JVL:
You think I don’t understand the science because I don’t obviously agree with you.
Nope. I say that you don't understand the science because of what you have posted.
I have read quite a lot of both sides.
Doubtful.
It’s particularly bad for ID though since it doesn’t have even close to the same amount of support in mainstream academia.
Nonsense. Unguided evolution doesn't have any evidentiary support. It can't even be tested. That means it is out of the realm of science. You may disagree but you will never support that disagreement. And I am more than OK with that.
What’s going to happen to the ID movement when some of the high profile supporters leave the field of battle?
Nothing. That movement rests on the science and evidence. And neither of those is going away.ET
March 3, 2020
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How about nihilism as the driving force behind science ? I don't think it was what eastern sages had in mind when they prescribed that we should empty our minds.Axel
March 3, 2020
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ET 62: 'IF you think that there is no design then everything we observe is due to unguided processes.'* 'Except for the fact there is no way to test that claim.'' The very nature of empirical science tests it, a priori, and finds it wanting. Surely, science itself is predicated on the immanence of design in the natural world. - hence the emergence of science, as a sort of obsessive preoccupation in christendom. *To me that initially read like a satirical jibe, but of course it's the truth - and more bizarre yet, seemingly one with which ID's infidels feel quite comfortable !Axel
March 3, 2020
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@78 Mimus
Not sure if it’s more remarkable that Jawa/PavelU’s response to posting under multiple itendities is to create a new one, or that the regulars start arguing with the new fake sock puppet…
Geez Mimus, we are al puppets of our brain chemistry. You know, billions and billions of mindless evolution blah blah blah... Or are you suggesting people can really 'choose' (at least some of) their actions? Can Jawa? Can I? Can you?Truthfreedom
March 3, 2020
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Jawa, 86: I really don’t understand what you’re trying to say with that statement. Please clarify it. Thanks. I think you think I'm evasive and vague because I haven't clearly committed to ID or anti-ID. I suspect, in your mind it's a black-and -white issue: either you are or you ain't. You wanted to play a game with me, taunting me with something I wanted to know by pulling my strings and making me dance to your tune. I haven't really done that and I suspect you're disappointed and losing interest. And I don't think you ever really intended on addressing Mimus's claim. Which, of course, makes you look 'guilty'. Maybe you're NOT posting under more than one username, but why wouldn't you assert that? And if you are posting under more than one username why would you do that? Just to prove how clever you are? To get more attention?JVL
March 2, 2020
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JVL @84: “ You want me to take a stance that you can argue with so you’re disappointed that I’ve avoided that.” I really don’t understand what you’re trying to say with that statement. Please clarify it. Thanks.jawa
March 2, 2020
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ET, 81: LoL! JVL is trying to baldly assert that which he has no right to. ET, 82: You’re not really discussing anything. You are just saying there is a disagreement. But you don’t seem to understand the science and the evidence. You think I don't understand the science because I don't obviously agree with you. Maybe you should just read the literature that IDists have written. Then do the same for the evolutionists. And wonder why Richard Dawkins had to use a telic process in order to demonstrate his concept of cumulative selection. Then wonder why all papers on the evolution of something are almost 100% speculation. Or why the long term evolutionary experiment has FAILed to produce new genes, new proteins or new protein complexes. I have read quite a lot of both sides. And I see both sides being completely entrenched and increasingly antagonistic to each other. That trench warfare isn't helping either side. It's particularly bad for ID though since it doesn't have even close to the same amount of support in mainstream academia. What's going to happen to the ID movement when some of the high profile supporters leave the field of battle?JVL
March 2, 2020
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<bJawa, 79: If you can’t take the heat of the discussion, then maybe quitting is the best thing to do. Your responses to some of the questions seem so vague that sometimes I get the impression that you are dodging the questions. Basically your answers sometimes raise more questions. It seems like a never-ending story. I can point to specific cases for illustration. However, i could keep asking until you can produce comprehensive answers. You want me to take a stance that you can argue with so you're disappointed that I've avoided that.JVL
March 2, 2020
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Mimus, 78: Not sure if it’s more remarkable that Jawa/PavelU’s response to posting under multiple itendities is to create a new one, or that the regulars start arguing with the new fake sock puppet… Which user names do you think are actually the same person and why would someone do that/JVL
March 2, 2020
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JVL:
I’m just discussing the disagreement and wondering if there is a possible resolution.
There is. Tell those in the unguided camp to put up or shut up. Tell them to address the evidence and science or get out of the way.
Is it not possible to discuss the discussion and not be assumed to be on one side or the other?
You're not really discussing anything. You are just saying there is a disagreement. But you don't seem to understand the science and the evidence. Maybe you should just read the literature that IDists have written. Then do the same for the evolutionists. And wonder why Richard Dawkins had to use a telic process in order to demonstrate his concept of cumulative selection. Then wonder why all papers on the evolution of something are almost 100% speculation. Or why the long term evolutionary experiment has FAILed to produce new genes, new proteins or new protein complexes.ET
March 2, 2020
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LoL! JVL is trying to baldly assert that which he has no right to.ET
March 2, 2020
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Jawa
If you can’t take the heat of the discussion, then maybe quitting is the best thing to do.
With respect, JVL is trying to have a discussion with ET. One is being honest, civil and logical. The other is ET.Ed George
March 2, 2020
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JVL @77: “Maybe I should just quit.” If you can’t take the heat of the discussion, then maybe quitting is the best thing to do. Your responses to some of the questions seem so vague that sometimes I get the impression that you are dodging the questions. Basically your answers sometimes raise more questions. It seems like a never-ending story. I can point to specific cases for illustration. However, i could keep asking until you can produce comprehensive answers. But at this point I have to logout so that another avatar can login. :)jawa
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Not sure if it's more remarkable that Jawa/PavelU's response to posting under multiple itendities is to create a new one, or that the regulars start arguing with the new fake sock puppet... In any case, doesn't say a whole lot of good stuff about the vitality of this site or the ID movement...Mimus
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ET, 75: Except they won’t tell you. We have to. It hasn't been hidden. It just hasn't been promoted by the non-design crowd. Duh. But you have baldly asserted more than that. I don't think so. Look, the BEST evidence for macroevolution is presented on talk origins. And yet that evidence is absent a mechanism. If they had the evidence that unguided processes could do it they would have said that. And it pretty much shows that you really don’t know what you are talking about. Sigh. I'm not making an argument. I'm just discussing the disagreement and wondering if there is a possible resolution. Is it not possible to discuss the discussion and not be assumed to be on one side or the other? I understand your feeling of being discriminated against but is that a reason to label someone who is trying to understand the situation? Maybe I should just quit.JVL
March 2, 2020
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Asauber, 74: “But others disagree” is not an argument. It’s a deflection that could be made about anything and everything if you don’t like something. Nothing is beyond dispute, I guess. It’s a variant of the Argument Sketch, not an argument. Correct. I'm not making an argument. I am just discussing a situation and wondering if there is a resolution.JVL
March 2, 2020
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JVL:
It hasn’t been buried in that it is still accessible and easy to find.
Except they won't tell you. We have to.
Again, there are dissenting views.
I know. I am getting at the reason for it.
There is a disagreement.
Duh. But you have baldly asserted more than that. And yes, people disagree for personal reasons. Look, the BEST evidence for macroevolution is presented on talk origins. And yet that evidence is absent a mechanism. If they had the evidence that unguided processes could do it they would have said that. And it pretty much shows that you really don't know what you are talking about.ET
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JVL, "But others disagree" is not an argument. It's a deflection that could be made about anything and everything if you don't like something. Nothing is beyond dispute, I guess. It's a variant of the Argument Sketch, not an argument. Andrewasauber
March 2, 2020
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ET, 70: And you are very wrong. It would definitely be Nobel worthy and very big news. Okay. You don’t speak for any scientist. You definitely don’t speak for the majority. Scientists know better than to assume what has to be demonstrated. But they are very vocal when their assumptions are shown to be true. I can only give my impressions, which might be incorrect. Clearly it has. No one has taken it on to show that unguided processes can indeed come up with 3 or more cumulative effect mutations. No one wants to. No one cares. It hasn't been buried in that it is still accessible and easy to find. The only thing that is clear is that people will deny the science and evidence. Again, there are dissenting views. You haven’t pointed out anything. You have just made unsupported assertions. There is a disagreement. Nature can produce what the laws of nature allow. And there isn’t anything in those laws that allows for nature to produce coding systems from the ground up, literally. People can disagree with that. But they do so for personal reasons only. I hear you. But others disagree. That is just the case.JVL
March 2, 2020
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Truthfreedom, 69: So if I told you ‘you’ are an ‘illusion’: what would you think? I would think you were wrong.JVL
March 2, 2020
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JVL:
Again, I am just pointing out the gulf.
Again, I am just pointing out the facts. And we know what the crux of the matter is.ET
March 2, 2020
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JVL:
I was trying to explain why demonstrating unguided processes are capable would not be big news.
And you are very wrong. It would definitely be Nobel worthy and very big news.
It’s because that’s been the assumption of the majority of scientists so there would be no need to celebrate it.
You don't speak for any scientist. You definitely don't speak for the majority. Scientists know better than to assume what has to be demonstrated. But they are very vocal when their assumptions are shown to be true.
It’s not been buried, clearly.
Clearly it has. No one has taken it on to show that unguided processes can indeed come up with 3 or more cumulative effect mutations. No one wants to. No one cares.
Again, there is a dispute, that is clear.
The only thing that is clear is that people will deny the science and evidence.
I’m merely pointing out that a lot of scientists do not accept the design inference.
You haven't pointed out anything. You have just made unsupported assertions. Nature can produce what the laws of nature allow. And there isn't anything in those laws that allows for nature to produce coding systems from the ground up, literally. People can disagree with that. But they do so for personal reasons only.ET
March 2, 2020
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@68 JVL
Sure feels like I am. Descarte and all that.
So if I told you 'you' are an 'illusion': what would you think?Truthfreedom
March 2, 2020
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Truthfreedom, 67: But you surely can make inferences. Are you a consciouss being or are you not? Sure feels like I am. Descarte and all that.JVL
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