https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree

Building a phylogenetic tree
AP.BIO: EVO‑3 (EU), EVO‑3.B (LO), EVO‑3.B.1 (EK), EVO‑3.C (LO),
EVO‑3.C.1 (EK), EVO‑3.C.2 (EK), EVO‑3.C.3 (EK)
Google Classroom
The logic behind phylogenetic trees. How to build a tree using data
about features that are present or absent in a group of organisms.
Key points:
Phylogenetic trees represent hypotheses about the evolutionary
relationships among a group of organisms.
A phylogenetic tree may be built using morphological (body shape),
biochemical, behavioral, or molecular features of species or other groups.
In building a tree, we organize species into nested groups based on
shared derived traits (traits different from those of the group's ancestor).
The sequences of genes or proteins can be compared among species and
used to build phylogenetic trees. Closely related species typically have
few sequence differences, while less related species tend to have more.
Introduction
We're all related—and I don't just mean us humans, though that's most
definitely true! Instead, all living things on Earth can trace their
descent back to a common ancestor. Any smaller group of species can also
trace its ancestry back to common ancestor, often a much more recent one.
Given that we can't go back in time and see how species evolved, how can
we figure out how they are related to one another? In this article,
we'll look at the basic methods and logic used to build phylogenetic
trees, or trees that represent the evolutionary history and
relationships of a group of organisms.
Overview of phylogenetic trees
In a phylogenetic tree, the species of interest are shown at the tips of
the tree's branches. The branches themselves connect up in a way that
represents the evolutionary history of the species—that is, how we think
they evolved from a common ancestor through a series of divergence
(splitting-in-two) events. At each branch point lies the most recent
common ancestor shared by all of the species descended from that branch
point. The lines of the tree represent long series of ancestors that
extend from one species to the next.

Image modified from Taxonomy and phylogeny: Figure 2, by Robert Bear et
al., CC BY 4.0
For a more detailed explanation, check out the article on phylogenetic
trees.
Even once you feel comfortable reading a phylogenetic tree, you may have
the nagging question: How do you build one of these things? In this
article, we'll take a closer look at how phylogenetic trees are constructed.
The idea behind tree construction
How do we build a phylogenetic tree? The underlying principle is
Darwin’s idea of “descent with modification.” Basically, by looking at
the pattern of modifications (novel traits) in present-day organisms, we
can figure out—or at least, make hypotheses about—their path of descent
from a common ancestor.
As an example, let's consider the phylogenetic tree below (which shows
the evolutionary history of a made-up group of mouse-like species). We
see three new traits arising at different points during the evolutionary
history of the group: a fuzzy tail, big ears, and whiskers. Each new
trait is shared by all of the species descended from the ancestor in
which the trait arose (shown by the tick marks), but absent from the
species that split off before the trait appeared.

[That tree is confusing! Can we go through step-by-step?]
When we are building phylogenetic trees, traits that arise during the
evolution of a group and differ from the traits of the ancestor of the
group are called derived traits. In our example, a fuzzy tail, big ears,
and whiskers are derived traits, while a skinny tail, small ears, and
lack of whiskers are ancestral traits. An important point is that a
derived trait may appear through either loss or gain of a feature. For
instance, if there were another change on the E lineage that resulted in
loss of a tail, taillessness would be considered a derived trait.
Derived traits shared among the species or other groups in a dataset are
key to helping us build trees. As shown above, shared derived traits
tend to form nested patterns that provide information about when
branching events occurred in the evolution of the species.
When we are building a phylogenetic tree from a dataset, our goal is to
use shared derived traits in present-day species to infer the branching
pattern of their evolutionary history. The trick, however, is that we
can’t watch our species of interest evolving and see when new traits
arose in each lineage.
Instead, we have to work backwards. That is, we have to look at our
species of interest – such as A, B, C, D, and E – and figure out which
traits are ancestral and which are derived. Then, we can use the shared
derived traits to organize the species into nested groups like the ones
shown above. A tree made in this way is a hypothesis about the
evolutionary history of the species – typically, one with the simplest
possible branching pattern that can explain their traits.

On 4/3/23 3:07 AM, Popping Mad wrote:
> https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree
>
>
> Building a phylogenetic tree
> AP.BIO: EVO‑3 (EU), EVO‑3.B (LO), EVO‑3.B.1 (EK), EVO‑3.C (LO),
> EVO‑3.C.1 (EK), EVO‑3.C.2 (EK), EVO‑3.C.3 (EK)
> Google Classroom
> The logic behind phylogenetic trees. How to build a tree using data
> about features that are present or absent in a group of organisms.
> Key points:
> Phylogenetic trees represent hypotheses about the evolutionary
> relationships among a group of organisms.
> A phylogenetic tree may be built using morphological (body shape),
> biochemical, behavioral, or molecular features of species or other groups.
> In building a tree, we organize species into nested groups based on
> shared derived traits (traits different from those of the group's ancestor).
> The sequences of genes or proteins can be compared among species and
> used to build phylogenetic trees. Closely related species typically have
> few sequence differences, while less related species tend to have more.
> Introduction
> We're all related—and I don't just mean us humans, though that's most
> definitely true! Instead, all living things on Earth can trace their
> descent back to a common ancestor. Any smaller group of species can also
> trace its ancestry back to common ancestor, often a much more recent one.
> Given that we can't go back in time and see how species evolved, how can
> we figure out how they are related to one another? In this article,
> we'll look at the basic methods and logic used to build phylogenetic
> trees, or trees that represent the evolutionary history and
> relationships of a group of organisms.
> Overview of phylogenetic trees
> In a phylogenetic tree, the species of interest are shown at the tips of
> the tree's branches. The branches themselves connect up in a way that
> represents the evolutionary history of the species—that is, how we think
> they evolved from a common ancestor through a series of divergence
> (splitting-in-two) events. At each branch point lies the most recent
> common ancestor shared by all of the species descended from that branch
> point. The lines of the tree represent long series of ancestors that
> extend from one species to the next.
> 
> Image modified from Taxonomy and phylogeny: Figure 2, by Robert Bear et
> al., CC BY 4.0
> For a more detailed explanation, check out the article on phylogenetic
> trees.
> Even once you feel comfortable reading a phylogenetic tree, you may have
> the nagging question: How do you build one of these things? In this
> article, we'll take a closer look at how phylogenetic trees are constructed.
> The idea behind tree construction
> How do we build a phylogenetic tree? The underlying principle is
> Darwin’s idea of “descent with modification.” Basically, by looking at
> the pattern of modifications (novel traits) in present-day organisms, we
> can figure out—or at least, make hypotheses about—their path of descent
> from a common ancestor.
> As an example, let's consider the phylogenetic tree below (which shows
> the evolutionary history of a made-up group of mouse-like species). We
> see three new traits arising at different points during the evolutionary
> history of the group: a fuzzy tail, big ears, and whiskers. Each new
> trait is shared by all of the species descended from the ancestor in
> which the trait arose (shown by the tick marks), but absent from the
> species that split off before the trait appeared.
> 
> [That tree is confusing! Can we go through step-by-step?]
> When we are building phylogenetic trees, traits that arise during the
> evolution of a group and differ from the traits of the ancestor of the
> group are called derived traits. In our example, a fuzzy tail, big ears,
> and whiskers are derived traits, while a skinny tail, small ears, and
> lack of whiskers are ancestral traits. An important point is that a
> derived trait may appear through either loss or gain of a feature. For
> instance, if there were another change on the E lineage that resulted in
> loss of a tail, taillessness would be considered a derived trait.
> Derived traits shared among the species or other groups in a dataset are
> key to helping us build trees. As shown above, shared derived traits
> tend to form nested patterns that provide information about when
> branching events occurred in the evolution of the species.
> When we are building a phylogenetic tree from a dataset, our goal is to
> use shared derived traits in present-day species to infer the branching
> pattern of their evolutionary history. The trick, however, is that we
> can’t watch our species of interest evolving and see when new traits
> arose in each lineage.
> Instead, we have to work backwards. That is, we have to look at our
> species of interest – such as A, B, C, D, and E – and figure out which
> traits are ancestral and which are derived. Then, we can use the shared
> derived traits to organize the species into nested groups like the ones
> shown above. A tree made in this way is a hypothesis about the
> evolutionary history of the species – typically, one with the simplest
> possible branching pattern that can explain their traits.

I should point out that this is not actually quite how it's done. There
is no need to determine derived states in advance; that determination
comes after the tree is formed and rooted. All you need to do is score
putatively homologous traits, e.g. by aligning DNA sequences. Then you
use some model of evolutionary processes (which may be as simple as
"parsimony", or the minimum number of changes, to decide which unrooted
tree best fits the data. After that you declare a root, most likely by
deciding that one taxon is the outgroup to the rest.

On Monday, April 3, 2023 at 6:07:54 AM UTC-4, Popping Mad wrote:
> https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree
>

This is quite a nice, down to earth treatment of the topic. I'm glad you
also did a thread using a professional article, and I've already replied to that
an hour and a half ago:

https://groups.google.com/g/sci.bio.paleontology/c/rX_v-fcwq7s/m/3Y7nZwYrAwAJ
Re: Phylogenetic Trees: The What and The Why

I happen to prefer doing several posts along the same thread to starting a new
thread for discussing closely related articles, but YMMV.
> Building a phylogenetic tree
> AP.BIO: EVO‑3 (EU), EVO‑3.B (LO), EVO‑3.B.1 (EK), EVO‑3.C (LO),
> EVO‑3.C.1 (EK), EVO‑3.C.2 (EK), EVO‑3.C.3 (EK)
> Google Classroom
> The logic behind phylogenetic trees. How to build a tree using data
> about features that are present or absent in a group of organisms.
> Key points:
> Phylogenetic trees represent hypotheses about the evolutionary
> relationships among a group of organisms.
> A phylogenetic tree may be built using morphological (body shape),
> biochemical, behavioral, or molecular features of species or other groups..
> In building a tree, we organize species into nested groups based on
> shared derived traits (traits different from those of the group's ancestor).
> The sequences of genes or proteins can be compared among species and
> used to build phylogenetic trees. Closely related species typically have
> few sequence differences, while less related species tend to have more.

"less related" can easily be defined by using "the path metric" between
the various pairs of species involved, as in 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 metric is formally defined in:

https://people.math.wisc.edu/~roch/research_files/review-steel-ams.pdf

I did an explanation of the path metric on a level intermediate between
the above article and the one we are reviewing here, in the post I referenced above.

> Introduction
> We're all related—and I don't just mean us humans, though that's most
> definitely true! Instead, all living things on Earth can trace their
> descent back to a common ancestor.

This is debatable; but substitute "eukaryotes" for "living things" and you
are on solid ground. If you try to include prokaryotes, you get involved
in endosymbiosis and also a possibly excessive amount of lateral genetic transfer.

> Any smaller group of species can also
> trace its ancestry back to common ancestor, often a much more recent one.
> Given that we can't go back in time and see how species evolved, how can
> we figure out how they are related to one another? In this article,
> we'll look at the basic methods and logic used to build phylogenetic
> trees, or trees that represent the evolutionary history and
> relationships of a group of organisms.

> Overview of phylogenetic trees
> In a phylogenetic tree, the species of interest are shown at the tips of
> the tree's branches.

This is in contrast to what are called "evolutionary trees," also known as Besseyan cactuses or commagrams,
which also show species at branching points.
Here is an example which puts species at all but one of the branching points:
https://en.wikipedia.org/wiki/Evolutionary_taxonomy#/media/File:DidymCactus..png

[snip of introductory material]

> How do we build a phylogenetic tree? The underlying principle is
> Darwin’s idea of “descent with modification.” Basically, by looking at
> the pattern of modifications (novel traits) in present-day organisms, we
> can figure out—or at least, make hypotheses about—their path of descent
> from a common ancestor.
[...]
> When we are building phylogenetic trees, traits that arise during the
> evolution of a group and differ from the traits of the ancestor of the
> group are called derived traits. In our example [of a made-up group of mouse species],
> a fuzzy tail, big ears, and whiskers are derived traits, while a skinny tail,
> small ears, and lack of whiskers are ancestral traits. An important point is that a
> derived trait may appear through either loss or gain of a feature. For
> instance, if there were another change on the E lineage that resulted in
> loss of a tail, taillessness would be considered a derived trait.

Yes, unless the whole group had a tailless ancestor somewhere down the line..
Tails go back to before vertebrates evolved, so it's only of interest if that
tailless species were a mouse, or at worst a rodent.

> Derived traits shared among the species or other groups in a dataset are
> key to helping us build trees. As shown above, shared derived traits
> tend to form nested patterns that provide information about when
> branching events occurred in the evolution of the species.
> When we are building a phylogenetic tree from a dataset, our goal is to
> use shared derived traits in present-day species to infer the branching
> pattern of their evolutionary history. The trick, however, is that we
> can’t watch our species of interest evolving and see when new traits
> arose in each lineage.
> Instead, we have to work backwards. That is, we have to look at our
> species of interest – such as A, B, C, D, and E – and figure out which
> traits are ancestral and which are derived. Then, we can use the shared
> derived traits to organize the species into nested groups like the ones
> shown above. A tree made in this way is a hypothesis about the
> evolutionary history of the species – typically, one with the simplest
> possible branching pattern that can explain their traits.

The part after the dash is the "maximum parsimony" (MP) method.
There are others, like ML and NJ, the latter being used sometimes
due to a drawback of MP:

"However, as Theorem 2 suggests, the space of trees is large and it turns out that constructing a maximum parsimony tree T∗ is in fact computationally intractable. (See e.g. Section 5.3 of the book under review for more details.) Nevertheless a natural heuristic for minimizing the parsimony score of C, which has proved useful in practice, is to perform a local search on tree space."
--https://people.math.wisc.edu/~roch/research_files/review-steel-ams.pdf

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos

On Monday, April 3, 2023 at 3:26:14 PM UTC-4, Peter Nyikos wrote:
> On Monday, April 3, 2023 at 6:07:54 AM UTC-4, Popping Mad wrote:

> > In a phylogenetic tree, the species of interest are shown at the tips of
> > the tree's branches.

> This is in contrast to what are called "evolutionary trees," also known as Besseyan cactuses or commagrams,
> which also show species at branching points.
> Here is an example which puts species at all but one of the branching points:
> https://en.wikipedia.org/wiki/Evolutionary_taxonomy#/media/File:DidymCactus.png

Correction: all but two of the branching points. They are represented by balloons
with question marks in them: one turquoise, the other white, near the top, with 1.5 also in it.

> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> University of South Carolina
> http://people.math.sc.edu/nyikos

On 4/3/23 12:26 PM, Peter Nyikos wrote:
> On Monday, April 3, 2023 at 6:07:54 AM UTC-4, Popping Mad wrote:
>> https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/building-an-evolutionary-tree
>>
>
> This is quite a nice, down to earth treatment of the topic. I'm glad you
> also did a thread using a professional article, and I've already replied to that
> an hour and a half ago:
>
> https://groups.google.com/g/sci.bio.paleontology/c/rX_v-fcwq7s/m/3Y7nZwYrAwAJ
> Re: Phylogenetic Trees: The What and The Why
>
> I happen to prefer doing several posts along the same thread to starting a new
> thread for discussing closely related articles, but YMMV.
>
>> Building a phylogenetic tree
>> AP.BIO: EVO‑3 (EU), EVO‑3.B (LO), EVO‑3.B.1 (EK), EVO‑3.C (LO),
>> EVO‑3.C.1 (EK), EVO‑3.C.2 (EK), EVO‑3.C.3 (EK)
>> Google Classroom
>> The logic behind phylogenetic trees. How to build a tree using data
>> about features that are present or absent in a group of organisms.
>> Key points:
>> Phylogenetic trees represent hypotheses about the evolutionary
>> relationships among a group of organisms.
>> A phylogenetic tree may be built using morphological (body shape),
>> biochemical, behavioral, or molecular features of species or other groups.
>> In building a tree, we organize species into nested groups based on
>> shared derived traits (traits different from those of the group's ancestor).
>> The sequences of genes or proteins can be compared among species and
>> used to build phylogenetic trees. Closely related species typically have
>> few sequence differences, while less related species tend to have more.
>
>
> "less related" can easily be defined by using "the path metric" between
> the various pairs of species involved, as in 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 metric is formally defined in:
>
> https://people.math.wisc.edu/~roch/research_files/review-steel-ams.pdf
>
> I did an explanation of the path metric on a level intermediate between
> the above article and the one we are reviewing here, in the post I referenced above.
>
>
>> Introduction
>> We're all related—and I don't just mean us humans, though that's most
>> definitely true! Instead, all living things on Earth can trace their
>> descent back to a common ancestor.
>
> This is debatable; but substitute "eukaryotes" for "living things" and you
> are on solid ground. If you try to include prokaryotes, you get involved
> in endosymbiosis and also a possibly excessive amount of lateral genetic transfer.
>
>
>> Any smaller group of species can also
>> trace its ancestry back to common ancestor, often a much more recent one.
>> Given that we can't go back in time and see how species evolved, how can
>> we figure out how they are related to one another? In this article,
>> we'll look at the basic methods and logic used to build phylogenetic
>> trees, or trees that represent the evolutionary history and
>> relationships of a group of organisms.
>
>> Overview of phylogenetic trees
>> In a phylogenetic tree, the species of interest are shown at the tips of
>> the tree's branches.
>
> This is in contrast to what are called "evolutionary trees," also known as Besseyan cactuses or commagrams,
> which also show species at branching points.
> Here is an example which puts species at all but one of the branching points:
> https://en.wikipedia.org/wiki/Evolutionary_taxonomy#/media/File:DidymCactus.png
>
>
> [snip of introductory material]
>
>
>> How do we build a phylogenetic tree? The underlying principle is
>> Darwin’s idea of “descent with modification.” Basically, by looking at
>> the pattern of modifications (novel traits) in present-day organisms, we
>> can figure out—or at least, make hypotheses about—their path of descent
>> from a common ancestor.
> [...]
>> When we are building phylogenetic trees, traits that arise during the
>> evolution of a group and differ from the traits of the ancestor of the
>> group are called derived traits. In our example [of a made-up group of mouse species],
>> a fuzzy tail, big ears, and whiskers are derived traits, while a skinny tail,
>> small ears, and lack of whiskers are ancestral traits. An important point is that a
>> derived trait may appear through either loss or gain of a feature. For
>> instance, if there were another change on the E lineage that resulted in
>> loss of a tail, taillessness would be considered a derived trait.
>
> Yes, unless the whole group had a tailless ancestor somewhere down the line.
> Tails go back to before vertebrates evolved, so it's only of interest if that
> tailless species were a mouse, or at worst a rodent.
>
>> Derived traits shared among the species or other groups in a dataset are
>> key to helping us build trees. As shown above, shared derived traits
>> tend to form nested patterns that provide information about when
>> branching events occurred in the evolution of the species.
>> When we are building a phylogenetic tree from a dataset, our goal is to
>> use shared derived traits in present-day species to infer the branching
>> pattern of their evolutionary history. The trick, however, is that we
>> can’t watch our species of interest evolving and see when new traits
>> arose in each lineage.
>> Instead, we have to work backwards. That is, we have to look at our
>> species of interest – such as A, B, C, D, and E – and figure out which
>> traits are ancestral and which are derived. Then, we can use the shared
>> derived traits to organize the species into nested groups like the ones
>> shown above. A tree made in this way is a hypothesis about the
>> evolutionary history of the species – typically, one with the simplest
>> possible branching pattern that can explain their traits.
>
> The part after the dash is the "maximum parsimony" (MP) method.
> There are others, like ML and NJ, the latter being used sometimes
> due to a drawback of MP:
>
> "However, as Theorem 2 suggests, the space of trees is large and it turns out that constructing a maximum parsimony tree T∗ is in fact computationally intractable. (See e.g. Section 5.3 of the book under review for more details.) Nevertheless a natural heuristic for minimizing the parsimony score of C, which has proved useful in practice, is to perform a local search on tree space."
> --https://people.math.wisc.edu/~roch/research_files/review-steel-ams.pdf

That's not a difference between MP and ML. It's a feature of any method
that uses a search of possible trees, in which one evaluates some
measure of fit for a number of trees. It's only guaranteed to find the
best tree if you evaluate all possible trees. Since that's usually
prohibitive, one resorts to heuristics.