>> 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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