>> Hello and welcome to
the Penguin Prof Channel.
This is the Tree of Life.
Based on some molecular data,
this is the origin of all life
on Earth and this is
where we sit on this tree.
Now, look at all these names.
This video is about
taxonomy, naming stuff.
Taxonomy at the outset
doesn't seem super exciting.
I mean, coming up
with names, really?
But it is actually
really important
to help us understand a
lot more interesting things
about evolutionary relationships
among different taxa,
or different groups
of organisms.
Humans have been naming things
since the very beginning,
since we were first
able to communicate.
Certainly, we named things
that were important to us,
like what to eat and things
that we had to run away from.
You know, don't eat
these poisonous plants,
that kind of thing.
Probably stayed at about that
level for countless thousands
of years and then people
started coming up with systems
for organizing living
things on Earth.
And the first person
to write extensively
about this was Aristotle.
He said to understand anything,
you have to classify it
according to its parts,
and he classified all animals
into one of two groups,
either those with blood or
those he called bloodless.
His work was followed
by many, many others,
including Pliny the Elder
who wrote 160 volumes
on this subject.
In those days, names were
really more descriptions.
They were always
written in Latin.
Latin was established early
on as the language
of scholarly writing.
And the honeybee was given
this name, Apis pubescens,
thorace subgriseo, abdomine
fusco, pedibus posticus glabis,
untrinque margine ciliatus,
which means hairy bee,
underside of the thorax gray,
abdomen striped, feet positioned
to the rear smooth,
with outer areas
on both sides having fine hairs.
Though clumsy, obviously
this naming system worked
for many years because
scientists didn't
yet realize how many living
things they were going
to have to name.
But there was an era of great
discovery and soon, many,
many organisms came under
the eyes of scientists
and they realized a new system
was absolutely essential.
Onto the scene comes Carl
Linnaeus, a Swedish biologist
who had his first foray
into taxonomy in 1735
and a relatively small
volume about plants,
it was only 12 pages long.
But he followed this up
with "Systema Naturae."
The 10th edition,
published in 1758,
included 4,400 animal species
and 7,700 plant species.
Now, Linnaeus was
not the first person
to use this particular
naming system
that we now called
binomial nomenclature,
but he was the first person
to use it consistently
in a way that made sense.
So the honeybee became
Apis mellifera.
Oh, what a relief.
The house sparrow,
Passer domesticus.
The gray wolf, Canis lupis.
The common ostrich,
Struthio camelus.
And the mouse, Mus musculus.
So this binomial
nomenclature, bi means two
and nomial means name,
comes from the fact
that there is going to be a
genus name and a species name,
and these two words will combine
to form what we call
the scientific name.
Now, sometimes the genus name
and the species name
are the same word,
as in the case of the black rat.
How you tell the two different
names apart in that case has
to do with the fact that genus
names are always capitalized
and species names are
never capitalized.
And when you write them
together, the genus
and species name should be
either underlined or in italics.
You might wonder where these
names come from because some
of them are downright strange.
Many of them come from
classical or medieval Latin,
including the name
that we gave ourselves
in this classification
system, the name Home sapiens,
which means, basically,
wise man.
Many names come from
classical Greek.
You may know the rhododendrons.
In Greek, rhodos means rose
and dendron means tree.
This is the national
flower of Nepal.
There are over 1,000 species
of rhododendrons,
interestingly enough.
Most of them are shrubs;
very few of them are trees.
Can't win them all.
Many scientific names
are named for people.
This magnolia is named for
not one, but two people.
Magnolia campbellii, named
for a French botanist
and a lover of plants and tea.
This is an extinct
creature called a trilobite,
and if you look at the
name, you might think, hey,
that looks kind of familiar.
Yes, it was named in
honor of Mick Jagger.
What does that mean when you've
got an extinct trilobite named
after you?
Yeah. Okay.
Here's a cool stock
jellyfish, and from the name,
you can probably
guess where it's from.
A lot of scientific names come
from other languages other
than Latin and Greek,
like this one.
This comes from two Greek roots,
actually, meaning red wood,
because it does have red wood,
but the species name, coca,
is a Quechua word,
and coca is famous
for a particular
product that humans use.
And at this point, you might
be thinking, gosh, you know,
is there some sort
of more organized way
of coming up with these names?
You know, kind of like the
IUPAC names in chemistry.
By the way, this is the
structure and name of cocaine,
yes, which is from the coca
plant that I showed you earlier.
Unfortunately, biological
creatures are not as simple
as naming things based
on a three-dimensional
structure like this.
So we do not have a system
like the chemists have,
unfortunately, for
naming organisms.
Biological creatures
are named based on many,
many taxonomic characters,
and this is how we're going
to determine phylogeny, or
relatedness, between taxa
or between different groups.
So this is what our
names are based on.
Morphologic characters,
so morphology means shape.
Right? And that's going to
include not only the shape
of the adult, but also
things like embryology,
the developmental forms.
We name things based
on physiology.
We name things based on
molecular characteristics.
This, obviously, is a fairly
modern one that Linnaeus
and his peers certainly
did not have.
Behavioral characteristics,
as well as ecological
characteristics.
And geographic characteristics.
So we don't have a way to
name things like chemists do
because we take all of these
things into consideration
when coming up with names.
So how do these systems work
and what are the levels
of the hierarchies?
Well, Linnaeus came up
with a three-domain system.
He classified everything as
being either alive, which he put
in animals or plants,
or not alive,
which he put the
kingdom of minerals.
He had then six classes of
animals, and I listed these
because many of these groups
are still in use today.
So I just thought that
was worth mentioning.
Linnaeus got a lot
of this stuff right.
This is where it
kind of fell apart.
He classified insects and
then vermes, and that's a term
that is not in use anymore.
He called these basically
soft-bodied creatures
with tentacles.
So, you know, the
nudibranchs and the corals
and the sea anemones
would be examples
of what Linnaeus called vermes.
And, of course, we do not
classify those together
in one group.
But Linnaeus really influenced
all of the work to come,
the idea that we would build
hierarchies of similarities
to determine different
categories
and levels of relatedness.
So 1866, this was a phylogenetic
tree attempting to show,
you know, who was related
to whom and where all
of the ancestors were.
We use the same ideas today.
Some of them are very obvious.
So for example, a penguin
and a sparrow should
obviously be grouped together
because they share a
lot of characteristics.
They have beaks, they
have feathers, et cetera.
So we classify them together.
They are more similar than
either of the two groups are
to herring, for example.
But if you want to compare these
three organisms to something
like a mushroom, then you
would want to put the herring
in with the penguin
and the sparrow
because those three
organisms are all animals
and the mushroom is not.
It is a fungus.
So we group things based
on levels of similarities.
Today, we have a
three-domain system.
It's not the same as
Linnaeus' three-domain system,
but these two domains
are both prokaryotic.
So we have the true bacteria,
you may see those as eubacteria,
and the areka [phonetic]
or the ancient bacteria.
They are the oldest living
things on the planet.
And then, the third
domain are the eukaryotes.
Those are organisms that have
a nucleus, other organelles,
and gained multicellularity,
although they are not
all multicellular.
This is the way that we
organize levels of relatedness,
going from the domain to the
kingdom, phylum, class, order,
family, genus, species.
There's lots of different
mnemonics
to help you to remember that.
Botanists don't use
the word phylum.
They use the word
division instead.
So we're going to
use as an example
to show you the way
this organization --
taxonomic system works
we're going to use the dog.
So the domain eukaryote
that the dog is in,
it shares with all other
living things on the planet
with the exception
of the bacteria.
So all eukaryotic
organisms are in this domain.
The kingdom the dog is in
is the kingdom animalia.
These are mostly multicellular
heterotrophic organisms.
So now, we've excluded
things like plants and fungi
and proteasts [phonetic].
But all animals are
in this kingdom.
The phylum that the dog
is in is called chordata
and the chordates
have a notochord,
which is a supportive structure
for a dorsal nerve chord,
that's a nerve that
runs down the back,
and pharyngeal gill slits,
and we share this phylum
along with the dog.
The class is the last level
that we share with the dog.
We are, like dogs, mammals.
We have sweat glands
and we produce milk
for our offspring via
mammary glands, of course.
That's what the class
is named for.
The order that the dog
is in is carnivora.
These are mostly
meat-eating animals.
So as you can see now,
we are not in the
same order as the dog.
The family is canidae.
This family includes wolves,
foxes, coyotes, and jackals.
These are what most people
would consider dog-like animals.
The genus is Canis; dogs,
wolves, coyotes, and jackals.
And the species, which
now includes only dogs
and wolves, Canis lupus.
And because we have domesticated
the dog, it gets a third level,
as many organisms do,
we call a subspecies,
Canis lupis familiares,
the domesticated dog.
So what you should notice
is that as you go up,
you have a decrease in
the number of traits
that individuals have in
common with other members
of their group, but
you have more
and more individuals
in each group.
So consequently, as you go down,
you have less and less relatives
in each category,
but you have more
and more in common with them.
So I know this is all
presented very clear and clean
and it looks like all these
categories are super organized.
But you know what?
It's not true.
Taxonomists argue constantly
about the different groupings
and who should be put where, and
the most confusing group of all,
believe it or not, is
at the species level.
And this has really
always been the base.
Even in the past, before
the age of enlightenment,
scientists could see
that there were problems.
Linnaeus could certainly see it.
He and his peers talked about
where species came from and how
to properly define them.
He treated species as immutable.
That means that they were
not capable or susceptible
to change, and this came
from the Bible and, you know,
Noah's Ark, and Noah arrives
on Mount Ararat and all
of these animals disembark
and the flood waters recede
and everybody populates
the Earth.
And that was the popular
thinking of the day.
A French naturalist named Le
comte de Buffon was really one
of the first people to vocally
question some of these ideas
about the immutability
of species.
He was interested in
looking at fossil mammals;
that was kind of a new thing.
He loved especially
elephants and mammoths.
Mammoths are, of
course, extinct.
This one is in a museum in LA.
And he also had issues
with how old the Earth was.
He disagreed with the
Biblical age of the Earth.
He didn't understand how
organisms could cross
inhospitable barriers to
reach suitable environments.
And, in addition, he traveled a
lot and he found different kinds
of animals and plants
in similar environments
that were completely
isolated from one another.
And this is now called
Buffon's Law.
It's the first principle
of biogeography.
The Age of Enlightenment came,
the development of paleontology,
the discovery of more and more
species in the fossil record,
which are extinct today, really
challenged this very static view
of nature, which had persisted
since Aristotle's time.
And now, of course, we know that
species are not fixed entities,
that they change, and we can see
this in lots of examples, birds,
especially, like
seagulls, these crows.
Individuals of different
species will mate
and produce fertile offspring,
and we call the products
hybrids.
And, of course, most notably,
the finches in the
Galapagos Islands,
which have been traced
back to a common ancestor
from the South American
continent.
And as the finches moved
out into different islands,
they were able to
exploit and specialize
on different food items
and their beaks changed
over time as a result.
And, of course, this work
was done by Charles Darwin,
and his work is so pivotal and
his story is so interesting
that it's going to have to be
the subject of the next video.
As always, I hope
that was helpful.
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