nPeace
Veteran Member
The Phylogenetic Tree
This tree, like all phylogenetic trees, is a hypothesis about the relationships among organisms. It illustrates the idea that all of life is related and can be divided into three major clades, often referred to as the three domains: Archaea, Bacteria, and Eukaryota.
The tree is supported by many lines of evidence, but it is probably not flawless. Scientists constantly reevaluate hypotheses and compare them to new evidence. As scientists gather even more data, they may revise these particular hypotheses, rearranging some of the branches on the tree. For example, evidence discovered in the last 50 years suggests that birds are dinosaurs, which required adjustment to several "vertebrate twigs."
[It is evident that this is not a tree that grows normally.
It might have grown from a seed - Darwinism, and hence it's roots are evidently ideologies, imo.
There is no solid verifiable evidence that can support a watertight argument.
Speculations, assumptions, and inference, cannot establish fact.
That simply is what this science is.
It has its hypotheses, theories, etc.
This is what we expect from science - continuous study.
So from LUCA to the evolutionary tree assumptions are made, and the search for evidence continues.
Since we are on this topic...
I think it is important to mention this.]
Trees, not ladders
Several times in the past, biologists have committed themselves to the erroneous idea that life can be organized on a ladder of lower to higher organisms. This idea lies at the heart of Aristotle's Great Chain of Being
[GALLERY=media, 8613]Great_Chain_of_Being by nPeace posted Aug 1, 2018 at 3:54 PM[/GALLERY]
[This tree was removed, and replaced. Not that I am saying Aristotle's tree was accurate, but neither is this one, as it is admitted.
However, although I mentioned a seed and roots for this tree, all of its components are artificial. The tree does not take in nutrients to grow.
Human hands are responsible for its growth.]
Building the tree
Like family trees, phylogenetic trees represent patterns of ancestry. However, while families have the opportunity to record their own history as it happens, evolutionary lineages do not — species in nature do not come with pieces of paper showing their family histories. Instead, biologists must reconstruct those histories by collecting and analyzing evidence, which they use to form a hypothesis about how the organisms are related — a phylogeny.
[What exactly are patterns of ancestry?]
Example #1
African Pygmy groups show a distinctive pattern of phenotypic variation, including short stature, which is thought to reflect past adaptation to a tropical environment.
..........
Africa is thought to be the location of origin of modern humans within the past 200,000 years and the source of our dispersion across the globe within the past 100,000 years. Africa is also a region of extreme environmental, cultural, linguistic, and phenotypic diversity, and human populations living there show the highest levels of genetic diversity in the world. Yet little is known about the genetic basis of the observed phenotypic variation in Africa or how local adaptation and demography have influenced these patterns in the recent past.
..........
The term ‘Pygmy’ is applied to human populations whose adult males exhibit an average height of ∼150 cm or less, although thresholds between 140 and 160 cm have been employed. Such groups are found all over the world including Africa, Asia, and the Americas, tend to live in tropical environments, have high levels of pathogen exposure, and practice a predominantly hunting and gathering lifestyle.
[Clearly, these are obvious adaptation or changes which take place as genes are passed on.
Do you notice where these adaptations are observed? In one kind of organism. Not a gorilla an a human, but a human and a human.
More examples...
https://arxiv.org/ftp/arxiv/papers/1309/1309.5118.pdf]
To build a phylogenetic tree... biologists collect data about the characters of each organism they are interested in. Characters are heritable traits that can be compared across organisms, such as physical characteristics (morphology), genetic sequences, and behavioral traits.
In order to construct the vertebrate phylogeny, we begin by examining representatives of each lineage to learn about their basic morphology, whether or not the lineage has vertebrae, a bony skeleton, four limbs, an amniotic egg, etc.
Using shared derived characters
Our goal is to find evidence that will help us group organisms into less and less inclusive clades. Specifically, we are interested in shared derived characters. A shared character is one that two lineages have in common, and a derived character is one that evolved in the lineage leading up to a clade and that sets members of that clade apart from other individuals.
Shared derived characters can be used to group organisms into clades. For example, amphibians, turtles, lizards, snakes, crocodiles, birds and mammals all have, or historically had, four limbs. If you look at a modern snake you might not see obvious limbs, but fossils show that ancient snakes did have limbs, and some modern snakes actually do retain rudimentary limbs. Four limbs is a shared derived character inherited from a common ancestor that helps set apart this particular clade of vertebrates.
However, the presence of four limbs is not useful for determining relationships within the clade, since all lineages in the clade have that character. To determine the relationships in that clade, we would need to examine other characters that vary across the lineages in the clade.
[Don't miss the large font.]
A snake with 4 legs - Tetrapodophis (meaning "four-footed snake" in Greek) is an extinct genus of snake from the Early Cretaceous of Brazil. It is one of the oldest snakes and the only known snake with four legs.
Classification
A phylogenetic analysis published alongside the original 2015 description of Tetrapodophis places it as a close relative of other early snakes such as Coniophis, Dinilysia, and Najash, but outside the crown group Serpentes, meaning that it branched off before the most recent common ancestor of all living snakes. Below is a cladogram from that analysis.
The interpretation of Tetrapodophis amplectus as an early snake and as an animal adapted to burrowing was challenged by Caldwell et al. (2016), who considered it more likely to be a dolichosaurid squamate.
Dolichosauridae (["long" lizard]) is a family of Late Cretaceous aquatic varanoid lizards closely related to the mosasaurs.
Studies that propose a close relation between snakes and mosasauroids in a group dubbed Pythonomorpha demonstrate the importance of Dolichosaurus, Coniasaurus and other Late Cretaceous marine squamates in squamate phylogeny and evolutionary history. The hypothesis suggesting that snakes, mosasaurs, aigialosaurs and dolichosaurs share a common aquatic ancestor is not universally accepted and stands in stark contrast with the previously widespread hypothesis of snakes having a fossorial origin.
[That debate can rage on until "thy kingdom come".]
Mistaken Identity? Debate Over Ancient 4-Legged Snake Heats Up
SALT LAKE CITY — A critter heralded as the first four-legged fossil snake on record may actually not be a snake, according to new research. Instead, the 120-million-year-old creature is likely a dolichosaurid, an extinct four-legged marine lizard with an elongated, snake-like body, a new analysis of the specimen finds.
"Tetrapodophis doesn't show any of those features that you would expect to see in a snake," said Michael Caldwell, a professor and chair of biological sciences at the University of Alberta in Edmonton, Canada, who is leading the new investigation into the enigmatic fossil.
Update: Controversial ‘four-legged snake’ may be ancient lizard instead
Four-legged snake fossil stuns scientists—and ignites controversy
new study challenges assumption.
The authors argue that T. amplectus was more closely related to aquatic lizards, and that these snake-like forebears evolved their long bodies for eel-like swimming.
[Speaking of assumptions...
Here we are trying to figure out things we may never know, but we are building trees, and based on what? Assumptions.]
Here I need to take a break. To be continued...
This tree, like all phylogenetic trees, is a hypothesis about the relationships among organisms. It illustrates the idea that all of life is related and can be divided into three major clades, often referred to as the three domains: Archaea, Bacteria, and Eukaryota.
The tree is supported by many lines of evidence, but it is probably not flawless. Scientists constantly reevaluate hypotheses and compare them to new evidence. As scientists gather even more data, they may revise these particular hypotheses, rearranging some of the branches on the tree. For example, evidence discovered in the last 50 years suggests that birds are dinosaurs, which required adjustment to several "vertebrate twigs."
[It is evident that this is not a tree that grows normally.
It might have grown from a seed - Darwinism, and hence it's roots are evidently ideologies, imo.
There is no solid verifiable evidence that can support a watertight argument.
Speculations, assumptions, and inference, cannot establish fact.
That simply is what this science is.
It has its hypotheses, theories, etc.
This is what we expect from science - continuous study.
So from LUCA to the evolutionary tree assumptions are made, and the search for evidence continues.
Since we are on this topic...
I think it is important to mention this.]
Trees, not ladders
Several times in the past, biologists have committed themselves to the erroneous idea that life can be organized on a ladder of lower to higher organisms. This idea lies at the heart of Aristotle's Great Chain of Being
[GALLERY=media, 8613]Great_Chain_of_Being by nPeace posted Aug 1, 2018 at 3:54 PM[/GALLERY]
[This tree was removed, and replaced. Not that I am saying Aristotle's tree was accurate, but neither is this one, as it is admitted.
However, although I mentioned a seed and roots for this tree, all of its components are artificial. The tree does not take in nutrients to grow.
Human hands are responsible for its growth.]
Building the tree
Like family trees, phylogenetic trees represent patterns of ancestry. However, while families have the opportunity to record their own history as it happens, evolutionary lineages do not — species in nature do not come with pieces of paper showing their family histories. Instead, biologists must reconstruct those histories by collecting and analyzing evidence, which they use to form a hypothesis about how the organisms are related — a phylogeny.
[What exactly are patterns of ancestry?]
Example #1
African Pygmy groups show a distinctive pattern of phenotypic variation, including short stature, which is thought to reflect past adaptation to a tropical environment.
..........
Africa is thought to be the location of origin of modern humans within the past 200,000 years and the source of our dispersion across the globe within the past 100,000 years. Africa is also a region of extreme environmental, cultural, linguistic, and phenotypic diversity, and human populations living there show the highest levels of genetic diversity in the world. Yet little is known about the genetic basis of the observed phenotypic variation in Africa or how local adaptation and demography have influenced these patterns in the recent past.
..........
The term ‘Pygmy’ is applied to human populations whose adult males exhibit an average height of ∼150 cm or less, although thresholds between 140 and 160 cm have been employed. Such groups are found all over the world including Africa, Asia, and the Americas, tend to live in tropical environments, have high levels of pathogen exposure, and practice a predominantly hunting and gathering lifestyle.
[Clearly, these are obvious adaptation or changes which take place as genes are passed on.
Do you notice where these adaptations are observed? In one kind of organism. Not a gorilla an a human, but a human and a human.
More examples...
https://arxiv.org/ftp/arxiv/papers/1309/1309.5118.pdf]
To build a phylogenetic tree... biologists collect data about the characters of each organism they are interested in. Characters are heritable traits that can be compared across organisms, such as physical characteristics (morphology), genetic sequences, and behavioral traits.
In order to construct the vertebrate phylogeny, we begin by examining representatives of each lineage to learn about their basic morphology, whether or not the lineage has vertebrae, a bony skeleton, four limbs, an amniotic egg, etc.
Using shared derived characters
Our goal is to find evidence that will help us group organisms into less and less inclusive clades. Specifically, we are interested in shared derived characters. A shared character is one that two lineages have in common, and a derived character is one that evolved in the lineage leading up to a clade and that sets members of that clade apart from other individuals.
Shared derived characters can be used to group organisms into clades. For example, amphibians, turtles, lizards, snakes, crocodiles, birds and mammals all have, or historically had, four limbs. If you look at a modern snake you might not see obvious limbs, but fossils show that ancient snakes did have limbs, and some modern snakes actually do retain rudimentary limbs. Four limbs is a shared derived character inherited from a common ancestor that helps set apart this particular clade of vertebrates.
However, the presence of four limbs is not useful for determining relationships within the clade, since all lineages in the clade have that character. To determine the relationships in that clade, we would need to examine other characters that vary across the lineages in the clade.
[Don't miss the large font.]
A snake with 4 legs - Tetrapodophis (meaning "four-footed snake" in Greek) is an extinct genus of snake from the Early Cretaceous of Brazil. It is one of the oldest snakes and the only known snake with four legs.
Classification
A phylogenetic analysis published alongside the original 2015 description of Tetrapodophis places it as a close relative of other early snakes such as Coniophis, Dinilysia, and Najash, but outside the crown group Serpentes, meaning that it branched off before the most recent common ancestor of all living snakes. Below is a cladogram from that analysis.
The interpretation of Tetrapodophis amplectus as an early snake and as an animal adapted to burrowing was challenged by Caldwell et al. (2016), who considered it more likely to be a dolichosaurid squamate.
Dolichosauridae (["long" lizard]) is a family of Late Cretaceous aquatic varanoid lizards closely related to the mosasaurs.
Studies that propose a close relation between snakes and mosasauroids in a group dubbed Pythonomorpha demonstrate the importance of Dolichosaurus, Coniasaurus and other Late Cretaceous marine squamates in squamate phylogeny and evolutionary history. The hypothesis suggesting that snakes, mosasaurs, aigialosaurs and dolichosaurs share a common aquatic ancestor is not universally accepted and stands in stark contrast with the previously widespread hypothesis of snakes having a fossorial origin.
[That debate can rage on until "thy kingdom come".]
Mistaken Identity? Debate Over Ancient 4-Legged Snake Heats Up
SALT LAKE CITY — A critter heralded as the first four-legged fossil snake on record may actually not be a snake, according to new research. Instead, the 120-million-year-old creature is likely a dolichosaurid, an extinct four-legged marine lizard with an elongated, snake-like body, a new analysis of the specimen finds.
"Tetrapodophis doesn't show any of those features that you would expect to see in a snake," said Michael Caldwell, a professor and chair of biological sciences at the University of Alberta in Edmonton, Canada, who is leading the new investigation into the enigmatic fossil.
Update: Controversial ‘four-legged snake’ may be ancient lizard instead
Four-legged snake fossil stuns scientists—and ignites controversy
new study challenges assumption.
The authors argue that T. amplectus was more closely related to aquatic lizards, and that these snake-like forebears evolved their long bodies for eel-like swimming.
[Speaking of assumptions...
Here we are trying to figure out things we may never know, but we are building trees, and based on what? Assumptions.]
Here I need to take a break. To be continued...
Last edited:
