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Author Topic:   Lignin in red algae supports the Genesis days chronology? What about birds?
PaulK
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Posts: 13779
Joined: 01-10-2003
Member Rating: 2.3


Message 46 of 62 (827806)
02-01-2018 2:05 PM
Reply to: Message 45 by LamarkNewAge
02-01-2018 1:57 PM


Re: Birds, Reptiles, Frogs, and evolution with hybridization.
quote:

Birds seem to be in the tens of millions of years presently then (since ten times longer time to loose ability to have viable offspring)?

So 20-40 million years, which is rather less time than your “gap”.

quote:

So birds would take much longer than the present - 10 times longer than mammals 2-4 million infertility time scale - birds rate to have a genetic reproductive barrier to hybrids having viable offspring?

So INSTEAD OF 20 MILLION YEARS (or whatever it is exactly on average today), more like 50 million years back in the time of the very first birds (and the first 50 million years after the naissance)?


That doesn’t follow. After all the main point is that crocodiles evolved slowly.


This message is a reply to:
 Message 45 by LamarkNewAge, posted 02-01-2018 1:57 PM LamarkNewAge has responded

Replies to this message:
 Message 49 by LamarkNewAge, posted 02-01-2018 7:14 PM PaulK has responded

    
caffeine
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Posts: 1417
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.8


Message 47 of 62 (827807)
02-01-2018 2:22 PM
Reply to: Message 34 by LamarkNewAge
01-29-2018 6:09 PM


Re: Since 99% of what I say gets ignored (especially by PaulK):might have to be selective
The more I respond to, the more I get ignored (PaulK, especially, is setting a record for ignoring everything, then claiming that he has covered an issue).

You post an enormous amount. There are several things I can see are wrong; but often I can't grasp why; and it can often involve a lot of work to figure out where you're coming from and try to explain why I think you're wrong. When you post a quick stream of such statements I don't have the time to answer everything, on account of having a job, a family, and hobbies. I don't just sit here on EvC all day.

Some of what I ignore is just because I haven't the faintest idea what point is being made. Take the post I'm replying to; which includes a quote from the article I pointed you to discussing the definition of bird. There's no explanation why you posted it, and you seem to think it explains itself; but it doesn't. I have no idea why that's in your post, or how it's supposed to relate to the rest.

This is why I liked Phat's comment. Your interpretations of what you read are almost always different to mine. Maybe that's because you don't understand things properly, maybe that's because you understand things I don't. But either way, your cuts-and-pastes do not communicate your argument. Less pasting; more trying to explain what you think and why.

All that being said, you write

And I note that the 13 pre Theropoda features in Scansoriopteryx are still being ignored.

but that was specifically what I was trying to address with the discussion of cladistics. You can't figure out the relationships of organisms by just picking a small selection of features and considering that this settles it. Why do these 13 matter more than all the rest (or this 19, if we're including the six you mentioned shared with birds)?

You later go on to quote from Czerkas, who seemed intent on demonstrating that he was profoundly ignorant of things he must have known. I don't understand his motivations. He tells us that the description "arboreal theropod" was

an apparent contradiction in terms as according to definition, “theropods” do not climb.

But, of course, that's got nothing to do with the definition of theropod. Even back when they were originally named it never did - Marsh defined theropods as carnivorous dinosaurs.

It's even been argued by some palaeontologists that deinonychosaurs used their claws for climbing. This is almost certainly wrong, but the idea that an arboreal theropod is wrong by definition is just silly. All their saying is that this is an unusual theropod. Lots of organisms are unusual.

It's been standard for decades, of course, to define groups or organisms in terms of descent. Theropods have definitions like "Everything that shares a more recent common ancestor with sparrows than with sauropods" (loosely adapted from the definition given in the 2nd edition of The Dinosauria. Specific features or behaviours are not part of how we define clades, because of a little thing called evolution - these can change,

Czerkas goes on to briefly mention the few skeletal characters you're so excited about, and then declares

quote:
Therefore, Scansoriopteryx is more parsimoniously regarded as being a saurischian of “pre-theropod” status, instead of as a true theropod.

This here is a hypothesis. And yet, for some reason, he doesn't seem interested in testing that hypothesis. He seems to think the work is done once he's stated it.

That is, of course, deeply antithetical to the point of science. And that was why cladistics was developed in the first place - all the way back in the 1940s and 50s. The core of cladistics is a way of testing the parsimony of different evolutionary scenarios - using statistics to turn the classification of organisms from informed speculation into science.

It's come a long way since simple parsimony techniques; but for some reason the 'birds are not dinosaurs' gang still haven't reached the 1950s.

I will "ignore" your other points for now, since addressing one point properly takes time.

Edited by caffeine, : No reason given.


This message is a reply to:
 Message 34 by LamarkNewAge, posted 01-29-2018 6:09 PM LamarkNewAge has responded

Replies to this message:
 Message 57 by LamarkNewAge, posted 02-02-2018 2:18 PM caffeine has responded

  
caffeine
Member
Posts: 1417
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.8


Message 48 of 62 (827808)
02-01-2018 2:30 PM
Reply to: Message 44 by PaulK
02-01-2018 12:16 AM


Re: Birds, Reptiles, Frogs, and evolution with hybridization.
The scientists who carried out the cladistic analysis you object to our more work into “getting it right” than Feduccia.

Let's be clear, not 'analysis'. I posted one because I found an open-access pdf which included all the supplementary material. There are many analyses including scansoriopterygids - all find them to be theropods (though admittedly most aren't really testing that); most find them close to birds.

Of course; there are innumerable studies finding birds to be deeply nested in theropods, and theropods deeply nested in dinosaurs.

As a quick aside and not a reply to you, I'm a bit lost what the point of the hybridisation discussion is supposed to be, but there was some mention of DNA. To be clear; DNA is not used to figure out the relationships of extinct organisms - we don't have any DNA from the Mesozoic. Palaeontologists need to use morphological features (for dinosaurs and their relative this usually just means bones).

Edited by caffeine, : No reason given.


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LamarkNewAge
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Posts: 1108
Joined: 12-22-2015


Message 49 of 62 (827815)
02-01-2018 7:14 PM
Reply to: Message 46 by PaulK
02-01-2018 2:05 PM


Re: Birds, Reptiles, Frogs, and evolution with hybridization.
I said:
quote:

Birds seem to be in the tens of millions of years presently then (since ten times longer time to loose ability to have viable offspring)?

PaulK said?

quote:

So 20-40 million years, which is rather less time than your “gap”.

I wonder if you can imagine that Archaeopteryx could be able to reproduce with a creature it shared a common ancestor with back around 190 million years ago.

I still haven't found the exact time period for birds loosing the ability to have viable hybrids.

This search term was put into www.google.com:

average rate birds loose viable hybrid million years millions

I got some revealing links, but haven't found the answer yet.

Here is something interesting (despite paywall issues with most journals)

quote:

Mammals evolved rapidly morphologically and physiologically and quickly lost the capacity for interspecific hybridization, although they frequently remained very similar in a biochemical respect (in structure of the proteins). Birds and amphibians, on the other hand, evolved much more slowly and retained the capacity for interspecific hybridization for a long time, even in the presence of very considerable differences in the amino acid composition and sequence of the proteins. It is suggested that the rapid morphological and functional evolution of mammals is connected with the rapid evolution of the regulatory region of their genome. On the other hand, the evolution of the structural genes (cistrons) that code peptides and proteins proceeded at the same uniform rate in different classes of vertebrates. This explains why in mammals, in contrast to amphibians and birds, often in the presence of considerable biochemical similarity, there are significant differences in morphological and functional characteristics and successful interspecific hybridization is impossible.

https://link.springer.com/article/10.1007/BF01182660


Birds and Amphibians seem similar. I'm not saying the 34 million year frog hybrid event applies to most birds, but surely some birds have - at times in earth's history - done what the frogs did.

But see 11/19/2013 hybrid discovery in this link

http://wallace.genetics.uga.edu/...cafd1/Evolution_News.html

I then was quoted by you, saying:

quote:

So birds would take much longer than the present - 10 times longer than mammals 2-4 million infertility time scale - birds rate to have a genetic reproductive barrier to hybrids having viable offspring?
So INSTEAD OF 20 MILLION YEARS (or whatever it is exactly on average today), more like 50 million years back in the time of the very first birds (and the first 50 million years after the naissance)?

You said:

quote:

That doesn’t follow. After all the main point is that crocodiles evolved slowly.

But the ability to have viable hybrids is a way to enable evolutionary events FROM OUTSIDE your own species GET SHARED by your own species. Call spreading the wealth (of rapid evolution) around.

quote:

Hybridization, the interbreeding of species, provides favorable conditions for major and rapid evolution to occur. In birds it is widespread. Approximately one in ten species is known to hybridize, and the true global incidence is likely to be much higher

http://science.sciencemag.org/content/256/5054/193


There is a spreading of genetic wealth around.

Birds as much as anything do this, even before the logistical issues are considered.

On the logistical end, flying birds really can avoid the geological isolation issues that would prevent the hybridization from happening in the first place.

Rapid evolution on the one hand, and the ability to be relatively uniform in spreading the genetic code around.

No wonder birds would look more evolved than Dinosaurs. They were.

The cladistics analysis will see birds as having more evolved features, while Dinosaurs look more archaic (except there will be fossils that complicate the picture like the one we keep talking about that Czerkas named). The relationship between the two (birds and one line of dinosaurs) clearly exists. But which one truly (and ultimately) comes from the older line?

2 mutually compatible EARLY BIRD FEATURES:

Birds evolved quickly.

Birds spread their rapidly evolving genetic code broadly and widely and it made them the most UNIFORM creatures ever to live on (or above) land.


This message is a reply to:
 Message 46 by PaulK, posted 02-01-2018 2:05 PM PaulK has responded

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LamarkNewAge
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Posts: 1108
Joined: 12-22-2015


Message 50 of 62 (827816)
02-01-2018 7:21 PM
Reply to: Message 48 by caffeine
02-01-2018 2:30 PM


Re: Birds, Reptiles, Frogs, and evolution with hybridization.
quote:

As a quick aside and not a reply to you, I'm a bit lost what the point of the hybridisation discussion is supposed to be, but there was some mention of DNA. To be clear; DNA is not used to figure out the relationships of extinct organisms - we don't have any DNA from the Mesozoic. Palaeontologists need to use morphological features (for dinosaurs and their relative this usually just means bones).

See this:

quote:

The demise of the dinosaurs touched off an evolutionary “big bang” that lasted 15 million years or less and gave rise to all the types of birds we see today, according to the findings from a massive research effort involving hundreds of researchers from 20 countries.

Over the course of more than four years, the Avian Phylogenomics Consortium sequenced the genomes of 45 species representing virtually every major limb of the bird world's evolutionary family tree, which takes in more than 10,000 species around the world.

Those genomes were compared using the equivalent of 400 years of supercomputer time, and organized using a new statistical method for tracing genetic connections.

The results were as overwhelming as the scale of the project: More than two dozen research papers were published online Thursday, in Science as well as Genome Biology, GigaScience and other journals. Among the findings:
•A study of genome structure suggests that the chicken is the modern-day bird that most closely resembles the dinosaurian ancestor of birds. That finding is in line with previous analyses of proteins recovered from a Tyrannosaurus rex fossil.
•The earliest common ancestor of land birds, a category that includes parrots and finches as well as hawks and eagles, appears to have been an apex predator. "This predatory trait has been lost several times," said Duke University's Erich Jarvis, one of the project's leaders.
•Genetic comparisons suggest that brain regions in songbirds are activated in a way that's similar to the patterns seen in humans — but not similar to the patterns seen in non-singing birds or non-human primates. That analysis took advantage of the Allen Human Brain Atlas.
•The process by which the ancestors of modern birds began to lose their teeth apparently started about 116 million years ago, when dinosaurs were having their heyday.
having their heyday.
•A parallel study of crocodilian genomes suggests that the earliest common ancestor of dinosaurs, crocodiles, alligators and birds — all members of a group of creatures known as archosaurs — lived around 240 million years ago. While birds were among the fastest-evolving members of the group, crocodilans were among the slowest to evolve.
•A comparative study of Adelie penguins and Emperor penguins points to genetic factors that could help explain why Adelie populations go through climate-related boom-and-bust patterns, while Emperor populations have stayed relatively stable.

The scientists behind the project say their findings shed dramatic new light on the evolutionary history of birds, but are almost certain to have broader application in biology and medicine as well.

For instance, insights into the genetic roots of birdsong could point researchers to new clues about the roots of human speech disorders as well. And the fact that bird genomes are more compact could help scientists zero in on more precise targets as they hunt for the genetic factors behind human traits.

"These make birds or chickens good models," said Guoxie Zhang of BGI-Shenzhen, one of the major partners in the genomics project.

flock of genomes

Before the Avian Phylogenomics Consortium set to work, only a few bird genomes — including the codes for chickens, turkeys and zebra finches — had been deciphered. What's more, researchers knew very little about the deep genetic connections between species.

"In the past, people have been using one, two — up to 10 or 20 genes — to try to infer species relationships over the last 100 million years or so," Jarvis said in a news release. "Our theory has been, if you take the whole genome, you would have a more accurate species tree than just one or two genes alone."

Most of the whole genomes added to the list come from the biggest subdivision of the bird world, known as the Neoaves. That's the group that takes in parrots and finches, hawks and eagles (but not ostriches or chickens).

The more genomes you have, the easier it is to see the relationships between species and figure out how and when they diverged. However, there's also a greater potential for spurious information to produce a wrongly constructed evolutionary tree. To make sure their tree was solid, the bird genetics consortium developed a method known as "statistical binning" to help avoid creating misshapen trees.

Multiple runs using different tree-building methods produced a consistent picture of the bird world's evolutionary history. "This is the biggest DNA sequence tree ever generated," Jarvis told reporters during a teleconference. "In this case, it's 30 million base pairs long."

When did bird species soar?

Technically speaking, scientists regard birds as the only species of dinosaurs to survive a mass extinction that occurred 65 million years ago. Jarvis said the genetic analysis was likely to settle a longstanding debate over whether the proliferation of bird species occurred before or after the big die-off.

"We suggest it occurred right at that time, with only a few lineages surviving mass extinction, and they giving rise to ... what we call the Passerea, Columbea and Neoaves group within the last 66 million years," Jarvis said. "And all modern orders formed from this radiation within a 10- to 15-million-year period, around 50 million years ago."

The process used to organize the evolutionary tree for birds is likely to be used in the future to take a fresh look at other branches of the overall tree of life, said Tandy Warnow, a bioengineering and computer science professor at the University of Illinois who led the computational effort.
Neither Warnow nor Jarvis was willing put a cost estimate on the effort, because the expenses were shared by so many institutions as well as funders such as the National Science Foundation and the National Institutes of Health.

"It's really hard to calculate a number, but it's a really big number," Jarvis said.

The journal Science is publishing a collection of papers from the Avian Phylogenomics Project. Other papers are being published in GigaScience, Genome Biology, BMC Genomics and BMC Evolutionary Biology.

https://www.nbcnews.com/...olutionary-big-bang-birds-n265996


Also I found that above typing this into www.google.com

average rate birds loose viable hybrid million years millions

There are "rocks verses clocks" debates for sure, but here is a "rock" issue and a new discovery.

http://www.sciencemag.org/...-china-reveal-dawn-modern-birds

Edited by LamarkNewAge, : No reason given.


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PaulK
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Posts: 13779
Joined: 01-10-2003
Member Rating: 2.3


Message 51 of 62 (827818)
02-02-2018 12:19 AM
Reply to: Message 49 by LamarkNewAge
02-01-2018 7:14 PM


Re: Birds, Reptiles, Frogs, and evolution with hybridization.
quote:

I wonder if you can imagine that Archaeopteryx could be able to reproduce with a creature it shared a common ancestor with back around 190 million years ago.

It’s easy to imagine things. Assuming that they are true when they are incredibly unlikely is another matter.

quote:

I still haven't found the exact time period for birds loosing the ability to have viable hybrids.

There isn’t an exact time (do you really think that an average of 2-4 million years for mammals is an “exact time” ?). But if you can multiply by 10 you already have an adequate estimate.

quote:

But the ability to have viable hybrids is a way to enable evolutionary events FROM OUTSIDE your own species GET SHARED by your own species. Call spreading the wealth (of rapid evolution) around.

That’s an assumption, and not one supported by the article. Since the article doesn’t claim that birds evolved incredibly rapidly over the period in question - the main point is that crocodiles evolved very slowly after the dinosaurs died it it doesn’t exactly seem relevant. (And is there any reason to think that crocodiles are any faster to lose the ability to hybridise ?)

quote:

No wonder birds would look more evolved than Dinosaurs. They were.

No wonder everyone thinks you are a loon. You are. That is a very silly statement.

quote:

The cladistics analysis will see birds as having more evolved features, while Dinosaurs look more archaic (except there will be fossils that complicate the picture like the one we keep talking about that Czerkas named). The relationship between the two (birds and one line of dinosaurs) clearly exists. But which one truly (and ultimately) comes from the older line?

Birds will appear more evolved than their ancestors (for obvious reasons). But that only applies to the ancestors and close relatives, not to other dinosaurs - especially those living later. However cladistic analysis clearly shows birds as descending from dinosaurs.


This message is a reply to:
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Pressie
Member
Posts: 1901
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.0


Message 52 of 62 (827824)
02-02-2018 4:58 AM
Reply to: Message 50 by LamarkNewAge
02-01-2018 7:21 PM


Re: Birds, Reptiles, Frogs, and evolution with hybridization.
LNA, you do realise that avian dinosaurs (birds) evolved millions of years before the extinction of the non-avian dinosaurs, don't you? Avian and non-avian dinosaurs lived happily together for millions of years...birds evolved before the extinction of the dinos.

Edited by Pressie, : No reason given.


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Pressie
Member
Posts: 1901
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.0


Message 53 of 62 (827825)
02-02-2018 6:43 AM
Reply to: Message 50 by LamarkNewAge
02-01-2018 7:21 PM


Re: Birds, Reptiles, Frogs, and evolution with hybridization.
I'm also not too sure that you realise that birds, dinos and mammals lived together for millions of years... Still trying to figure out what you're trying to say.
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jar
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Posts: 30151
From: Texas!!
Joined: 04-20-2004
Member Rating: 1.8


Message 54 of 62 (827826)
02-02-2018 8:11 AM
Reply to: Message 53 by Pressie
02-02-2018 6:43 AM


Re: Birds, Reptiles, Frogs, and evolution with hybridization.
Pressie writes:

I'm also not too sure that you realise that birds, dinos and mammals lived together for millions of years... Still trying to figure out what you're trying to say.

Talk about lions and tigers and bears and ohmys...

There were even reptiles and insects and garments and ancestors all around at the same time.


My Sister's Website: Rose Hill Studios     My Website: My Website

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caffeine
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Posts: 1417
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.8


Message 55 of 62 (827848)
02-02-2018 1:00 PM
Reply to: Message 50 by LamarkNewAge
02-01-2018 7:21 PM


Re: Birds, Reptiles, Frogs, and evolution with hybridization.
Also I found that above typing this into www.google.com

And it's a very interesting article, thanks. No indication of what it has to do with your argument, though.

As I said, we need less of you showing us what you read, and more of you explaining how you interpret it. Otherwise I have no idea what you're trying to say.


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caffeine
Member
Posts: 1417
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.8


Message 56 of 62 (827849)
02-02-2018 2:13 PM
Reply to: Message 49 by LamarkNewAge
02-01-2018 7:14 PM


Re: Birds, Reptiles, Frogs, and evolution with hybridization.
There's a whole lot of confusion here. I don't think your scenario of birds evolving faster through hybridisation makes sense; but we don't need to go in to that, since the conclusion you draw from it is clearly wrong:

The cladistics analysis will see birds as having more evolved features, while Dinosaurs look more archaic (except there will be fossils that complicate the picture like the one we keep talking about that Czerkas named). The relationship between the two (birds and one line of dinosaurs) clearly exists. But which one truly (and ultimately) comes from the older line?

You seem to be envisioning that cladistics finds birds to have evolved from dinosaurs because birds are 'more evolved', and so must have come later. But that's not how cladistics works. It's nothing to do with figuring out who has evolved the most - it's about looking into evolutionary changes shared between groups.

The simple idea is to take a bunch of characters; and then code a bunch of organisms for them. Simple parsimony techniques then look at the collection of coded characters; and figure out how to construct a family tree with the fewest changes of character. The key point is that this doesn't tell you that one thing is descended from another. All the organisms used in your analysis are treated as the end products - they're all sisters and cousins, not ancestors and descendants.

We see birds as being evolved from dinosaurs because they come out as nested within dinosaurs, not because they're more evolved from them. Like so:

The point here is that some dinosaurs are more closely related to birds than they are to other dinosaurs. The most recent common ancestor of two dinosaurs is, of course, a dinosaur, and it's in this sense that we see birds to be evolved from dinosaurs.

Now, if we accept your strange scenario in which birds evolve unusually quickly; the very last thing we would expect is to find birds spuriously placed within dinosaurs. In fact, the opposite is more likely. One of the best known sources of systematic errors in cladistic analysis is the problem of long-branch attraction. This is caused when you have organisms which evolve very quickly, or which have no close relatives. They are said to be on a long branch; since on the branch which separates them from their nearest relatives there will be a lot of changes of character. All these changes tend to 'overwrite' the signal of shared ancestry; and long-branched taxa tend to be spuriously drawn to the base of a tree; not to deep within it.

In a dinosaur-bird tree; a long branch would artificially pull birds towards crocodiles - not because of similarities but simply because crocodilians are also separated from dinosaurs by their own long branch. It would make it more likely that we would find the scenario (I think) you're arguing for; even if it wasn't true.

But we don't find that. Birds always come out as nested deep, deep within dinosaurs; because of all the things they share in common with theropods. And, more, the things they share with some theropods to the exclusion of other theropods.

Not sure if I explained this at all well, but too tired to try to rewrite now


This message is a reply to:
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LamarkNewAge
Member
Posts: 1108
Joined: 12-22-2015


Message 57 of 62 (827850)
02-02-2018 2:18 PM
Reply to: Message 47 by caffeine
02-01-2018 2:22 PM


Let us stay on topic. Caffeine went back to a good spot to start: post 34
This post 34 had my very first response to the cladistics issue that Caffein brought up.

I said:

quote:

The biggest problem with this cladistics issue is that ignores the fact that some creatures can maintain the ability to reproduce (and thus blend in genes) 34 million years after separating, like some frogs have done.

Early flying birds might have been part of a small number of rare types of creature that were constantly exchanging genes (reproducing) and over long distances too.

There could have been something of a conservative genetic process going on, with less genetic isolation than typically happens with diverging species. Lots of hybrids and long lasting features.

There would be LOTS of evolution going on, and speciation would have been broad (in like a million directions), but there would be lots of opportunity for older genetic types to last for a long time(with some real variation and evolution for sure) after the earlier "nascent stage(s)".

Page 14 of your PDF link said this:

....

"However, nearly every single character
that at one time was thought to make
something a ‘‘bird’’ is now known to occur
progressively earlier in theropod evolution.
Therefore, ‘‘bird’’ is a colloquial term that
lacks a meaningful taxonomic or scientific
basis as it has no precise phylogenetic meaning."


Try to understand the issue because I have been trying to avoid too much other discussion so we could stay on this one. (posts 53 and 54 seem to not have a clue what post 50 was all about, and frankly post 55 is even more of a mystery since the poster (again Caffeine) raise the issue of DNA being irrelevant.

Pay close attention to this below.

(page 20 wasn't available but 19 and 21 are very helpful)

quote:

Natural Hybridization and Evolution (Oxford Series in Ecology and Evolution) (9780195099751): Michael L. Arnold: Books.
Series: Oxford Series in Ecology and Evolution
Publisher: Oxford University Press; 1 edition (January 30, 1997)

p.19

The Phylogenetic Species Concept (PSC) defines species as “an irreducible (basal) cluster of organisms, diagnosably distinct from other such clusters, and within which there is a parental pattern of ancestry and descent” (Cracraft, 1989). Inherent in this definition is the aspect of history—evolutionary or phylogenetic history.The object of focus is the determination of the pattern of phylogenetic relationships. Applying this concept to define species and the process of speciation depends on the identification of the ancestral and derived states of particular characters. The pattern of branching within these cladograms is the basis for determining not only the boundaries of a species (i.e., irreducible clusters; Cracraft, 1989), but also the relationships among species.

The PSC can be traced back at least to Hennig (1966) because his work is the basis for the modern phylogenetic approach. He argued that species must be of monophyletic origin. Thus, they cannot arise from heterospecific hybridization because such an origin would be necessarily polyphyletic. Cracraft (1989) illustrated this view by stating that "in the majority of cases,, phylogenetic species will be demonstrably monophyletic; they will never be nonmonophyletic, except through error. Hennig recognized that “special complications would arise if new species could also arise to a noteworthy extent by hybridization between species.” The complications of such events were, however, discounted by arguing that “in all cases in which a 'polyphyletic origin of species' has been recognized, the species involved were so closely related that they could just as well be considered races of one species” (Hennig, 1966). The production of fertile offspring and close phylogenetic relationships were thus considered evidence that the hybridizing forms were conspecific. This same view was stated by Nixon and Wheeler (1990):"With the strictest application
....
p.21

1966), but more from the operational argument that species are monophyletic. In any case, the adoption of this framework has resulted in similar constraints on the sort of questions that can (or will) be addressed concerning the process of natural hybridization. Put another way, it is unlikely that an evolutionary biologist will pursue a set of questions that address a nonexistent or trivial aspect of a process. For example, the most common theoretical framework (Barton and Hewitt, 1985) for studies of natural hybridization has an assumption of hybrid unfitness. Adoption of these models has had a profound effect on which aspects of natural hybridization have been examined and which conclusions have been drawn. The view that hybridization is costly (in terms of the fitness of hybridizing individuals; e.g., Mayr, 1963) has also contributed to a dismissal of any possibility that introgressive hybridization (i.e., introgression; Anderson and Hubricht, 1938) may lead to adaptive evolution, but this has not always been the case. Past studies have considered the possibility that introgression can lead to such adaptive evolution (Anderson and Stebbins, 1954; Lewontin and Birch, 1966). The dismissal of introgression as an important evolutionary phenomenon once again follows directly from the acceptance of a particular species concept.
The BSC, RSC, and CSC view hybridization events as maladaptive or reflective of "bad" species (i.e., incomplete speciation). The PSC views reticulate evolution as being inconsequential or impossible at least with regard to the formation of new species. The problem with this is not that such a viewpoint leads to inactivity in research, but rather that certain questions (e.g., Does introgression never, infrequently, or often lead to adaptive evolution?) are rarely if ever addressed.

I have argued that the four species concepts discussed in this chapter lead to the dismissal of certain important outcomes of natural hybridization, either from definitional constraints or from underlying points of view.However, if it is true, for example, that a large proportion of plant species have resulted from allopolyploid events (Grant, 1981; Ehrlich and Wilson, 1991; Whitham et al., 1991), it is in some ways unimportant whether the hybridizing taxa be referred to as species, semispecies, races, and so on. From this standpoint the species concepts do not limit our studying of natural hybridization. Likewise, the process of introgression is widespread (Arnold, 1992; Rieseberg and Wendel, 1993) and can be studied regardless of assumptions concerning the taxonomic placement of hybridizing taxa. However, it is of extreme importance that we do not
let definitions (e.g., species must be of monophyletic origin) or assumptions that follow directly from those definitions (e.g., hybrids possess lower fitness) limit investigations into the evolutionary importance of the process of natural hybridization.


Breakthroughs are happening

Here is an example of something never before seen: an example of this happening in a marine mammal.

quote:

Hybrid Speciation in a Marine Mammal: The Clymene Dolphin (Stenella clymene)
Ana R. Amaral , Gretchen Lovewell, Maria M. Coelho, George Amato, Howard C. Rosenbaum
Published: January 8, 2014https://doi.org/10.1371/journal.pone.0083645

Abstract
Natural hybridization may result in the exchange of genetic material between divergent lineages and even the formation of new taxa. Many of the Neo-Darwinian architects argued that, particularly for animal clades, natural hybridization was maladaptive. Recent evidence, however, has falsified this hypothesis, instead indicating that this process may lead to increased biodiversity through the formation of new species. Although such cases of hybrid speciation have been described in plants, fish and insects, they are considered exceptionally rare in mammals. Here we present evidence for a marine mammal, Stenella clymene, arising through natural hybridization. We found phylogenetic discordance between mitochondrial and nuclear markers, which, coupled with a pattern of transgressive segregation seen in the morphometric variation of some characters, support a case of hybrid speciation. S. clymene is currently genetically differentiated from its putative parental species, Stenella coerueloalba and Stenella longisrostris, although low levels of introgressive hybridization may be occurring. Although non-reticulate forms of evolution, such as incomplete lineage sorting, could explain our genetic results, we consider that the genetic and morphological evidence taken together argue more convincingly towards a case of hybrid speciation. We anticipate that our study will bring attention to this important aspect of reticulate evolution in non-model mammal species. The study of speciation through hybridization is an excellent opportunity to understand the mechanisms leading to speciation in the context of gene flow.

http://journals.plos.org/plosone/article?id=10.1371/journ...


(Yes the entire article can be accessed)

I feel that this is as economical as I can do to help this issue get understood.

(if the post 50 DNA issue didn't get anything but the confused responses that followed, then perhaps this won't work either, but I predict it will work and the air will be clearer)

quote:

Botanists recognize the importance of introgressive hybridization in evolution. Our results ... indicate that zoologists must do the same

(Dowling and DeMarais, 1993)


Edited by LamarkNewAge, : No reason given.

Edited by LamarkNewAge, : No reason given.


This message is a reply to:
 Message 47 by caffeine, posted 02-01-2018 2:22 PM caffeine has responded

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 Message 58 by caffeine, posted 02-02-2018 2:39 PM LamarkNewAge has responded

    
caffeine
Member
Posts: 1417
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.8


Message 58 of 62 (827851)
02-02-2018 2:39 PM
Reply to: Message 57 by LamarkNewAge
02-02-2018 2:18 PM


Re: Let us stay on topic. Caffeine went back to a good spot to start: post 34
I'm starting to wonder if this is a windup, but I'm willing to give you the benefit of the doubt.

Pay close attention to this below.

Okay. I did. I agree with Arnold. Somewhere on these forums there's a post from me explaining why I think the Biological Species Concept is a minority view almost never employed by taxonomists in the real world. I think I used the example of persistent gene flow from baboons into geladas.

The next step would be for you to explain why you wanted me to read this, and why you think the existence of hybridisation is relevant to your argument.


This message is a reply to:
 Message 57 by LamarkNewAge, posted 02-02-2018 2:18 PM LamarkNewAge has responded

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LamarkNewAge
Member
Posts: 1108
Joined: 12-22-2015


Message 59 of 62 (827866)
02-02-2018 9:28 PM
Reply to: Message 58 by caffeine
02-02-2018 2:39 PM


Re: Let us stay on topic. Caffeine went back to a good spot to start: post 34
quote:

Okay. I did. I agree with Arnold.

The next step would be for you to explain why you wanted me to read this, and why you think the existence of hybridisation is relevant to your argument.


It has to do with the INTROGRESSIVE HYBRIDIZATION issue, which is mixing in with a hybrid of parental species (like say a parental specie - with archaic characters - that came from 10 million years before the split of offspring branches).

I see it as a parallel to the Scansoriopteryx issue.

(I also see this as an explanation for how dinosaurs ended up with features that birds had. They got the features from birds)

quote:

Animal Evolution: Genomes, Fossils, and Trees
edited by Maximilian J. Telford, D. Timothy J. Littlewood

p. 108

if lineage splitting events succeed each other rapidly, there may not be enough time for distinctive features to evolve that can be used to group descendant species

....

pp.108-110

if newly evolved lineages have not yet evolved complete intrinsic isolating mechanisms, extensive introgressive hybridization may occur, even of morphologically distinct species (Wiens et al., 2006). Although extensive gene exchange between morphologically distinct species is considered rare (Coyne and Orr, 2004), this could scramble any original phylogenetic signal (Clark et al., 1996; Chan and Levin, 2005)

....

p.110

Causes in this category also relate to the power of natural selection or shared internal constraints to produce extensive convergent evolution, and parallelisms (non-random non-phylogenetic signal) that may lead to the false inference of monophyletic taxa. This can be an important problem for both morphological and molecular phylogenetic analysis (Waegele and Mayer, 2007)

....

The above causes can affect phylogenetic analyses of both fossil and extant taxa at any taxonomic level and independent of the type of evidence used.


Then mixture issues.

quote:

Depending on the traits considered, introgressive hybridization may lead to morphological convergence of parental populations if the underlying divergent genes behave neutrally and readily introgress upon secondary contact (Grant & Grant, 2002). A simple dilution of the parental phenotypic differences whereby hybrids display intermediate phenotypes compared to the two parental species is often observed in the populations located near the center of a hybrid zone (Mayr, 1963). Indeed, additive traits determined by quantitative traits loci (QTLs) with directional effects (with each QTL having an effect in one parental population but not in the other) should appear intermediate in hybrids compared to their parental populations (Albertson & Kocher, 2005; Rieseberg & Willis, 2007). Nevertheless, transgressive hybrid phenotypes that exceed the range of parental phenotypic variation have also been reported, in particular in the context of hybrid zones (Rieseberg, Archer, & Wayne, 1999; Rieseberg, Widmer, Arntz, & Burke, 2003). This phenomenon, referred to as transgressive segregation (Bell & Travis, 2005; Rieseberg, Archer et al., 1999; Stelkens, Schmid, Selz, & Seehausen, 2009), may be attributed on the contrary to traits encoded by QTLs with antagonistic effects in each parental population (Rieseberg, Archer et al., 1999).

Alternatively, morphological differences between species can persist despite genetic introgression if they are themselves involved in reproductive isolation, or if the genes that control them are tightly linked with genomic regions involved in reproductive isolation (Harrison & Larson, 2014). In this case, a link between morphological trait variation and individual fitness is expected (Arnold & Hodges, 1995). Some incompatible genotypic combinations may be eliminated, thereby preventing hybrids to reach the full range of phenotypic variation that could be potentially generated by recombining the parental genomes.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330901/


This all can explain the early bird situation and the relation to dinosaurs.

Here is a journal article that seems highly relevant and cutting edge?

It offers a solution (often the best way to see an admission of a problem is when an actual solution is proposed) but only using molecular data. Doesn't help with the fossils.

quote:

Molecular Phylogenetics and Evolution

Volume 64, Issue 1, July 2012, Pages 243-253

Species tree of a recent radiation: The subfamily Delphininae (Cetacea, Mammalia)

Author links open overlay panel Ana R. Amaral a, b, Jennifer A. Jackson c, Luciana M. Möller d, Luciano B. Beheregaray b, d, M. Manuela Coelho a
Show more
https://doi.org/10.1016/j.ympev.2012.04.004

Abstract

Lineages undergoing rapid radiations provide exceptional opportunities for studying speciation and adaptation, but also represent a challenge for molecular systematics because retention of ancestral polymorphisms and the occurrence of hybridization can obscure relationships among lineages. Dolphins in the subfamily Delphininae are one such case. Non-monophyly, rapid speciation events, and discordance between morphological and molecular characters have made the inference of phylogenetic relationships within this subfamily very difficult. Here we approach this problem by applying multiple methods intended to estimate species trees using a multi-gene dataset for the Delphininae (Sousa, Sotalia, Stenella, Tursiops, Delphinus and Lagenodelphis). Incongruent gene trees obtained indicate that incomplete lineage sorting and possibly hybridization are confounding the inference of species history in this group. Nonetheless, using coalescent-based methods, we have been able to extract an underlying species-tree signal from divergent histories of independent genes. This is the first time a molecular study provides support for such relationships. This study further illustrates how methods of species-tree inference can be very sensitive both to the characteristics of the dataset and the evolutionary processes affecting the evolution of the group under study.

Graphical abstract

https://www.sciencedirect.com/...ticle/pii/S105579031200142X


A birds that dates from 160 million to 120 million years ago will surely have mostly newer features.

But there can be a mix of (say 13?) old with the (mostly) new.

Do Dinosaurs (from 230 million to 150 million years ago) have features of birds, and do those features seem to morphologically predate birds?

Yes, the characters seem older.

But an outlier like Scansoriopteryx shows that an older (than 230 million years ago)bird line could have predated the dinosaurs.

Hybridization can be an explanation for the strange fossil.

Could all birds get a cladistic analysis that indicates that they descended from Theropod Dinosaurs (from 165 million to 150 million years ago)when they NOT ONLY DID NOT but in fact actually split from the line 230 million years ago?

The best explanation is that they were the original parents of the Theropod line 230-250 million years ago.

The Theropod line split off rapidly from the birds, and there were uniform features, and successive hybridization (between the two) happened periodically which gave certain "early characters" to early Theropoda, but which soon vanished in both birds and Theropoda. But fossils show (a small few)early Theropoda to have old (and to be obsolete very early) features, while no bird fossils were found to show that they had the features.

There would be a general trend to wash away most older features (when older style or archaic hybrids mixed with the younger ones), while the certain early features did not go away (but were underrepresented or totally absent in the older fossils and only appeared later in the fossil record).

Scansoriopteryx had some features that never were passed down the Theropoda or bird line.

Other features were passed down both.

Questions should be asked about the 230 million year ago to 165 million year ago window.

How much hybridization was going on between birds and dinosaurs?

How reasonable is it to see cladistics analysis that presents existing fossil birds as having many features that a large number of Theropod dinosaurs seemed to have gradually developed from 230 million to 165 million years ago, while birds are proposed (by me) to be the parent specie from 230 million years ago?

How many characters could be realistically retained by birds for 65 million years from 230 to 165 million years ago? (perhaps modern bird morphological characters from the last 50-100 million years can be a clue)

Requirements for the theory to work:

An early (pre theropod bird) RAPID radiation around 250 million to 230 million years ago event is a must for the theory to work.

Hybridization and cross fertilization seems especially relevant to me.

Bird morphological evolution happening faster than the Theropoda is required to partly explain the character features.

(Im sure there will be charges of improbabilities and methodological errors)


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 Message 58 by caffeine, posted 02-02-2018 2:39 PM caffeine has not yet responded

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 Message 60 by LamarkNewAge, posted 02-03-2018 12:56 AM LamarkNewAge has not yet responded

    
LamarkNewAge
Member
Posts: 1108
Joined: 12-22-2015


Message 60 of 62 (827868)
02-03-2018 12:56 AM
Reply to: Message 59 by LamarkNewAge
02-02-2018 9:28 PM


Found PDF of the groundbreaking molecular study.
I just think this might be relevant to birds especially.

a bunch of studies here:

http://www.cell.com/...ology-evolution/references/S0169-5347(04)00004-7

I can't find this spider journal article I was looking for. It was talking about morphological bias and other issues.

I would be happy to hear comments about this overall issue (or any thoughts on articles), if anybody knows anything about it.

www.google.com

INTROGRESSIVE HYBRIDIZATION spider morphological bias

www.bing.com

INTROGRESSIVE HYBRIDIZATION morphological bias spider radiation

I welcome any person's knowledge into this discussion.

Edited by LamarkNewAge, : No reason given.


This message is a reply to:
 Message 59 by LamarkNewAge, posted 02-02-2018 9:28 PM LamarkNewAge has not yet responded

Replies to this message:
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