https://www.youtube.com/watch?v=6_XMKmFQ_w8
https://www.youtube.com/watch?v=6_XMKmFQ_w8
On Monday, March 27, 2023 at 10:21:56 PM UTC-4, Popping Mad wrote:bass and the eagle or the sea bass and the antelope. Both have the same most recent ancestor and have the same number of shared traits?"
https://www.youtube.com/watch?v=6_XMKmFQ_w8
Thanks for posting this, Ruben. It's a very clear and very basic lecture. Still, there was someone who did not understand completely, named Shelley Lauritsen, who wrote:
"Question for this cladogram - doesn't everything to the right of the organism you are comparing have the same recent ancestor and have the same number of similar traits. Wouldn't this make each of those things equally related- for instance the sea
A few minutes ago, I answered this question, the first to do so in 4 years:highly simplified example with just four traits, but might fail in a tree where many more traits are included."
"The answer is Yes to "same recent ancestor"; this is exactly how cladists define "equally closely related," except they use the more precise designation Last Common Ancestor (LCA for short). The question "same number of shared traits" works for this
Would you not agree that the eagle and the antelope (and the crocodile,
for that matter) are equally closely related to the sea bass?
On 3/29/23 08:17, John Harshman wrote:
Would you not agree that the eagle and the antelope (and the crocodile,
for that matter) are equally closely related to the sea bass?
No - I don't think so, FWIW but I am not an expert.
I can say that Crocs and Eagles are more closely related to each other
than they are to Antelope and more closely related to Antelope than a
Bass. But I really can't say anything about how closely related the
entire group is compared to a bass, and I am not even sure what the measurement is?
Is a Croc more closely realted to a Bass and an Antelope or less or
equal? I have no idea since they are not all on the same lineage.
"having a more recent common ancestor"
On 3/30/23 14:07, John Harshman wrote:
"having a more recent common ancestor"
That is a definiton based on TIME and by that definition, that would be correct. Any species that shares the common ancestor with Bass and Tetrapods, even other fish, as all equally related by that defintion.
But that is not how we conventionally compare species in relationship to their evolution.
Evolution might speed up or slow down under different
circumstances.
In computer sciences we measure and create these graphs
baces on nodes and costs between nodes. Maybe a species or a lineage
desn't evolve much over time, and the only lineage from the LCA between Antelope and Bass DOES evolved rapidly giving rise to numerous species
over the same period of time. Now which one is more closely related to
the LCA. You are saying they have the same degree of relativity.
Look at it this way. All sharks share a LCA about 400 million tears go.
https://hoopermuseum.earthsci.carleton.ca/sharks/PMP.htm https://hoopermuseum.earthsci.carleton.ca/sharks/P1-1B.htm
Two sharks that have a LCA 400 million years old are less closely
related than placentals like a Bat and an Elephant?
Now look at Sharks, Bass, and Bats. Now Bass and Bats likely have a
that a LCA of a fish not a decendent of sharks. Call is hypetheticalfishA.
HypertheticalfishA almost certainly shares a very ancient fish LCA with sharks because sharks lineage are so ancient and we expect that LCA to
be before that node. It might even be a Placoderm
https://ucmp.berkeley.edu/education/events/carlson2.html
I'm willing to bet that there are a lot more synapomorphy between
placoderms and bats than between placoderns and bass, let alone a common dogfish regardless of the fact that they all share the same LCA.
True, but relationships are not generally judged on genetic distance.
On 3/31/23 09:13, John Harshman wrote:
True, but relationships are not generally judged on genetic distance.Hmm - well try marrying your 1st cousin in most US states...
:)
"X is more/less
closely related to Y than Z" lacks the precision implicit in the construction of a tree.
Osteichthyes, that excludes sharks.
Yes, this is in fact the conventional view. You may look more like your grandparents than your first cousin does, but you are still equally
closely related to them.
On 3/31/23 11:31, erik simpson wrote:
"X is more/less
closely related to Y than Z" lacks the precision implicit in the construction of a tree.
I agree. That was my first statement. The question might not even make
any sense. John is saying that the question actually can be
conventionally understood by the rules of phenology and a cladgraph.
I
disagree. A cladograph has a lot of information about the relationships between species. You can say that these two species are closely related because they share a node... a Hyrax and an Asian Elephant.
It doesn't
do much to quanity how much closer or less closer either are to a NYC
subway rat.... IMO, and I don't even know what units I can hang such a measurement on. In that context, I don't know what closely related even means... exactly.
On 3/31/23 09:13, John Harshman wrote:
Osteichthyes, that excludes sharks.
I could be wrong but perhaps sharks are Ostriethyes that lost the bone?
I was reading something like that.
I chose sharks because they have several long lived species, living
fossils, so it would better emphasis my point, and chose bats because
they recently radiated in the mamialian line and evolved and speciated quickly with a lot of diversity.
On 3/31/23 09:13, John Harshman wrote:
Yes, this is in fact the conventional view. You may look more like your
grandparents than your first cousin does, but you are still equally
closely related to them.
That is a bad example because it doesn't resolve the issue any closer.
It doesn't address something like the radiation of bird species in the
last 20K years compared to the radiation of sharks in the great white family.. whatever that family is called.
"synapomorphy between" actually refers to similarity, not distance.
On 3/31/23 09:13, John Harshman wrote:
"synapomorphy between" actually refers to similarity, not distance.
that is not computationally correct. synapomorphy represent nodes on a
map that are branching points based on the development of a novel
feature which is then inherited in a unidirection - evolution is a unidirectional graph (although that might be coming into question with
some of the genetics papers I have read of late when you resolve the
graph more closely).
I might not be an expert on evolution but I am an expert in
computational math.
I would say the more Synapomorphic nodes that exists between two species
is a truer measure of the distance between species, rather than just
time on the clock.
I wouldn't consider time at all as a factor and neither does a
cladogram. Distance is the sum of the cost between all adjecent pairs
of nodes on a path, in this case between a LCA and several different
species.
C D
| | |
/-----*----*----*---A
* LCA
\-------*-------*----B
| |
If the cost of between each node is equal (and it is not but we will
make this assumption here to simplify this arguement),
Species A is computationally more closely related to the LCA than B by
on unit.
Also - C is closer to D
which C, D, A, and B are al extanct species.
With regard to the original question, two species along a path I can
compare ... say A and C. A is more closely related to the LCA than C.
It is harder to compare A and B because they don't share the same path
and costs between nodes are not shared, or well known.
The immediate subject isn't computational math;
On 3/31/23 22:03, John Harshman wrote:
The immediate subject isn't computational math;
Actually, that is EXACTLY the subject.
On 4/1/23 7:53 AM, Popping Mad wrote:
On 3/31/23 22:03, John Harshman wrote:
The immediate subject isn't computational math;
Actually, that is EXACTLY the subject.
How so?
On Friday, March 31, 2023 at 8:07:03 AM UTC-7, Popping Mad wrote:
On 3/31/23 09:13, John Harshman wrote:
True, but relationships are not generally judged on genetic distance.Hmm - well try marrying your 1st cousin in most US states...
:)Both you and John have the advantage of me with respect to knowledge of phylogenetic tree
construction and structure, but I will stick my less-informed oar in the water anyway. "X is more/less
closely related to Y than Z" lacks the precision implicit in the construction of a tree.
It's just a sentence
in English, and as such "closely" and "related" inherit some wiggle.
The "conventional view" may look
or sound surprising or counterintuitive, but at least it's consistent.
On Saturday, April 1, 2023 at 7:29:22 PM UTC-4, John Harshman wrote:
On 4/1/23 7:53 AM, Popping Mad wrote:
On 3/31/23 22:03, John Harshman wrote:
The immediate subject isn't computational math;
Actually, that is EXACTLY the subject.
How so?
You are missing Ruben's point, just as you did way back in 2016.
See my comments on a thread Ruben ("Popping Mad") began at 6:11 am EDT today:
https://groups.google.com/g/sci.bio.paleontology/c/rX_v-fcwq7s/m/3Y7nZwYrAwAJ Re: Phylogenetic Trees: The What and The Why
[EXCERPT:]
For this first post, I am skipping over how phylogenetic diversity is calculated,
and moving to an issue that has caused untold confusion down through the decades,
both in s.b.p. and in the big outside world: how closely related are two species?
This is quantified in the article by using the best weights we can assign to each edge in the tree,
and adding together the ones on the unique path through the tree from species A to species B.
This is called "the path metric" between A and B.
The article avoids defining "related" [specifically, "more closely related"] because of the way the systematists who dominate systematics define it.
Their method cannot be quantified because of its rudimentary nature.
And it is totally at odds with the quantification I gave above.
The dominant definition is the analogue of saying,
"Mitochondrial Eve is more closely related to everyone on earth today than she was
to anyone alive before she had children, including her parents and her siblings, if any."
On the other hand, look at the sentence "Species A is more closely related to species B
than it is to species C because the path metric from A to C is greater than the one from A to B."
This corresponds closely to the way we, including genealogists, use "more closely related" in everyday life.
[END OF EXCERPT]
On 4/3/23 2:20 PM, Peter Nyikos wrote:
On Saturday, April 1, 2023 at 7:29:22 PM UTC-4, John Harshman wrote:
On 4/1/23 7:53 AM, Popping Mad wrote:
On 3/31/23 22:03, John Harshman wrote:
The immediate subject isn't computational math;
Actually, that is EXACTLY the subject.
How so?
You are missing Ruben's point, just as you did way back in 2016.
What is Ruben's point, then?
See my comments on a thread Ruben ("Popping Mad") began at 6:11 am EDT today:
https://groups.google.com/g/sci.bio.paleontology/c/rX_v-fcwq7s/m/3Y7nZwYrAwAJ
Re: Phylogenetic Trees: The What and The Why
[EXCERPT:]
For this first post, I am skipping over how phylogenetic diversity is calculated,
and moving to an issue that has caused untold confusion down through the decades,
both in s.b.p. and in the big outside world: how closely related are two species?
This is quantified in the article by using the best weights we can assign to each edge in the tree,
and adding together the ones on the unique path through the tree from species A to species B.
This is called "the path metric" between A and B.
The article avoids defining "related" [specifically, "more closely related"]
because of the way the systematists who dominate systematics define it. Their method cannot be quantified because of its rudimentary nature.
And it is totally at odds with the quantification I gave above.
The dominant definition is the analogue of saying,
"Mitochondrial Eve is more closely related to everyone on earth today than she was
to anyone alive before she had children, including her parents and her siblings, if any."
On the other hand, look at the sentence "Species A is more closely related to species B
than it is to species C because the path metric from A to C is greater than the one from A to B."
This corresponds closely to the way we, including genealogists, use "more closely related" in everyday life.
[END OF EXCERPT]
What you call "path distance" is called "patristic distance" in phylogenetics.
But I wouldn't call that a measure of relatedness,
and it certainly doesn't fit the ordinary meaning, especially if evolutionary
rates differ among lineages.
The cladistic definition could be
quantified on a time-calibrated tree, i.e. one on which the ages of the ancestral nodes are estimated.
But since in general this information is
unavailable (or at least unreliable), we content ourselves with only relative ages, such that ancestral nodes are older than descendant nodes.
I reject the idea that evolutionary distances should be equated with closeness of relationship.
On Monday, April 3, 2023 at 8:25:17 PM UTC-4, John Harshman wrote:
On 4/3/23 2:20 PM, Peter Nyikos wrote:
On Saturday, April 1, 2023 at 7:29:22 PM UTC-4, John Harshman wrote:
On 4/1/23 7:53 AM, Popping Mad wrote:
On 3/31/23 22:03, John Harshman wrote:
The immediate subject isn't computational math;
Actually, that is EXACTLY the subject.
How so?
You are missing Ruben's point, just as you did way back in 2016.
What is Ruben's point, then?
It would be best if he were to state it in his own words. However, I can say this much:
if "patristic distance" does not involve computational math, then you are wrong
about it being the same thing as "path metric."
See my comments on a thread Ruben ("Popping Mad") began at 6:11 am EDT today:
https://groups.google.com/g/sci.bio.paleontology/c/rX_v-fcwq7s/m/3Y7nZwYrAwAJ
Re: Phylogenetic Trees: The What and The Why
[EXCERPT:]
For this first post, I am skipping over how phylogenetic diversity is calculated,
and moving to an issue that has caused untold confusion down through the decades,
both in s.b.p. and in the big outside world: how closely related are two species?
This is quantified in the article by using the best weights we can assign to each edge in the tree,
and adding together the ones on the unique path through the tree from species A to species B.
This is called "the path metric" between A and B.
The article avoids defining "related" [specifically, "more closely related"]
because of the way the systematists who dominate systematics define it.
Their method cannot be quantified because of its rudimentary nature.
And it is totally at odds with the quantification I gave above.
The dominant definition is the analogue of saying,
"Mitochondrial Eve is more closely related to everyone on earth today than she was
to anyone alive before she had children, including her parents and her siblings, if any."
On the other hand, look at the sentence "Species A is more closely related to species B
than it is to species C because the path metric from A to C is greater than the one from A to B."
This corresponds closely to the way we, including genealogists, use "more closely related" in everyday life.
[END OF EXCERPT]
What you call "path distance" is called "patristic distance" in
phylogenetics.
Are you sure these designate the same thing? Ruben linked the following review
article, which I was using for "path metric," and it is quite computational.
https://people.math.wisc.edu/~roch/research_files/review-steel-ams.pdf
It's a review of the following book (for want of a better word): Phylogeny—discrete and random processes in evolution1 by Mike Steel, CBMS-NSF Regional Conference Series in Applied Mathematics, 89, Society for Industrial and Applied Mathematics (SIAM), Philadelphia, PA, 2016. xvi+293 pp
By the way, the review does not use the word "patristic" anywhere:
But I wouldn't call that a measure of relatedness,
That's because you are locked in to the definition of "relatledness" which triumphed
during the cladist wars. The famous cow - lungfish -salmon cladist victory could have been avoided if someone who was well clued into vertebrate paleontology
and its evolutionary trees had been given a hearing during that debate.
and it certainly doesn't fit the ordinary meaning, especially if evolutionary
rates differ among lineages.
The ordinary meaning accommodates cases where a sequence of four successive generations
starting with one couple occurs in the same amount of time as a sequence of two generations
comes from another couple.
Perhaps you forgot, also, that one extended family could remain at the same level wrt class or income or influence
for many generations while another improves dramatically and while a third goes to pot.
Different rates of evolution, y'see.
The cladistic definition could be
quantified on a time-calibrated tree, i.e. one on which the ages of the
ancestral nodes are estimated.
This would not work very well in the two kinds of everyday examples I gave. Time calibration would not shed much light on the social dynamics involved.
But since in general this information is
unavailable (or at least unreliable), we content ourselves with only
relative ages, such that ancestral nodes are older than descendant nodes.
Looks like you are using a concept that uses only extant organisms
and ignores fossils.
I reject the idea that evolutionary distances should be equated with
closeness of relationship.
But the one that depends only on the topology should be, in your opinion. Why,
What, besides your loyalty to the dominant group of systematics, accounts for this?
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of South Carolina at Columbia
http://people.math.sc.edu/nyikos
QUOTE OF THE DAY
Why has not anyone seen that fossils alone gave birth to a theory about the formation of the earth, that without them, no one would have ever dreamed that there were successive epochs in the formation of the globe.
—Georges Cuvier
On Monday, April 3, 2023 at 8:25:17 PM UTC-4, John Harshman wrote:
On 4/3/23 2:20 PM, Peter Nyikos wrote:
On Saturday, April 1, 2023 at 7:29:22 PM UTC-4, John Harshman wrote:
On 4/1/23 7:53 AM, Popping Mad wrote:
On 3/31/23 22:03, John Harshman wrote:
The immediate subject isn't computational math;
Actually, that is EXACTLY the subject.
How so?
You are missing Ruben's point, just as you did way back in 2016.
What is Ruben's point, then?
It would be best if he were to state it in his own words. However, I can say this much:
if "patristic distance" does not involve computational math, then you are wrong
about it being the same thing as "path metric."
See my comments on a thread Ruben ("Popping Mad") began at 6:11 am EDT today:
https://groups.google.com/g/sci.bio.paleontology/c/rX_v-fcwq7s/m/3Y7nZwYrAwAJ
Re: Phylogenetic Trees: The What and The Why
[EXCERPT:]
For this first post, I am skipping over how phylogenetic diversity is calculated,
and moving to an issue that has caused untold confusion down through the decades,
both in s.b.p. and in the big outside world: how closely related are two species?
This is quantified in the article by using the best weights we can assign to each edge in the tree,
and adding together the ones on the unique path through the tree from species A to species B.
This is called "the path metric" between A and B.
The article avoids defining "related" [specifically, "more closely related"]
because of the way the systematists who dominate systematics define it.
Their method cannot be quantified because of its rudimentary nature.
And it is totally at odds with the quantification I gave above.
The dominant definition is the analogue of saying,
"Mitochondrial Eve is more closely related to everyone on earth today than she was
to anyone alive before she had children, including her parents and her siblings, if any."
On the other hand, look at the sentence "Species A is more closely related to species B
than it is to species C because the path metric from A to C is greater than the one from A to B."
This corresponds closely to the way we, including genealogists, use "more closely related" in everyday life.
[END OF EXCERPT]
What you call "path distance" is called "patristic distance" in
phylogenetics.
Are you sure these designate the same thing? Ruben linked the following review
article, which I was using for "path metric," and it is quite computational.
https://people.math.wisc.edu/~roch/research_files/review-steel-ams.pdf
It's a review of the following book (for want of a better word): Phylogeny—discrete and random processes in evolution1 by Mike Steel, CBMS-NSF Regional Conference Series in Applied Mathematics, 89, Society for Industrial and Applied Mathematics (SIAM), Philadelphia, PA, 2016. xvi+293 pp
By the way, the review does not use the word "patristic" anywhere:
But I wouldn't call that a measure of relatedness,
That's because you are locked in to the definition of "relatledness" which triumphed
during the cladist wars. The famous cow - lungfish -salmon cladist victory could have been avoided if someone who was well clued into vertebrate paleontology
and its evolutionary trees had been given a hearing during that debate.
and it certainly doesn't fit the ordinary meaning, especially if evolutionary
rates differ among lineages.
The ordinary meaning accommodates cases where a sequence of four successive generations
starting with one couple occurs in the same amount of time as a sequence of two generations
comes from another couple.
Perhaps you forgot, also, that one extended family could remain at the same level wrt class or income or influence
for many generations while another improves dramatically and while a third goes to pot.
Different rates of evolution, y'see.
The cladistic definition could be
quantified on a time-calibrated tree, i.e. one on which the ages of the
ancestral nodes are estimated.
This would not work very well in the two kinds of everyday examples I gave. Time calibration would not shed much light on the social dynamics involved.
But since in general this information is
unavailable (or at least unreliable), we content ourselves with only
relative ages, such that ancestral nodes are older than descendant nodes.
Looks like you are using a concept that uses only extant organisms
and ignores fossils.
I reject the idea that evolutionary distances should be equated with
closeness of relationship.
But the one that depends only on the topology should be, in your opinion. Why,
What, besides your loyalty to the dominant group of systematics, accounts for this?
Why has not anyone seen that fossils alone gave birth to a theory about the formation of the earth, that without them, no one would have ever dreamed that there were successive epochs in the formation of the globe.
—Georges Cuvier
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