Taxonomy and Systematics

Summary

The video script from the Penguin Prof Channel explores the significance of taxonomy in understanding evolutionary relationships among organisms. It traces the history of biological classification from Aristotle to Carl Linnaeus, who introduced the binomial nomenclature system. The script explains the hierarchical structure of taxonomy and how it's based on various characteristics, including morphology, physiology, and molecular data. It also touches on the fluid nature of species definitions and the challenges faced by taxonomists in classifying organisms, setting the stage for a deeper dive into Darwin's work in a future video.

Takeaways

• 🌳 The script discusses the importance of taxonomy in understanding evolutionary relationships among different organisms.
• 🔍 Taxonomy helps in organizing and naming organisms, which was initially based on descriptions but later evolved into a more systematic approach.
• 📚 Aristotle was one of the first to write extensively about classifying animals, categorizing them into those with blood and those without.
• 🔡 Latin was established as the language of scholarly writing, and early names were descriptive phrases in Latin, like 'Apis pubescens' for the honeybee.
• 🔄 Carl Linnaeus introduced the binomial nomenclature, a two-part naming system consisting of a genus name and a species name, which simplified the naming process.
• 📝 The binomial nomenclature is written with the genus name capitalized and the species name in lowercase, underlined or in italics for clarity.
• 🌐 Scientific names often come from classical Latin or Greek, and sometimes are named after people or other languages, reflecting cultural and historical influences.
• 🔬 Biological naming is complex due to the need to consider multiple taxonomic characters, unlike chemical nomenclature which is based on structure.
• 🏛 Linnaeus' three-domain system categorized life into animals, plants, and minerals, which has since been updated to include three domains of life: bacteria, archaea, and eukaryotes.
• 🔄 The taxonomic hierarchy ranges from domain to kingdom, phylum, class, order, family, genus, and species, with each level representing a decreasing number of shared traits.
• 🤔 Taxonomy is not without debate; taxonomists often argue about groupings and species definitions, highlighting the dynamic nature of biological classification.

Q & A

What is the main topic of the video on the Penguin Prof Channel?

The main topic of the video is taxonomy, which is the science of naming and classifying organisms based on their evolutionary relationships.

Why is taxonomy considered important in understanding evolutionary relationships?

Taxonomy is important because it helps us organize and understand the relationships among different groups of organisms, providing insights into their evolution and shared characteristics.

Who is considered the first person to write extensively about classifying living things?

Aristotle is considered the first person to write extensively about classifying living things, dividing animals into those with blood and those he called bloodless.

What was the significance of Carl Linnaeus' 'Systema Naturae'?

Carl Linnaeus' 'Systema Naturae' was significant because it was one of the first works to use binomial nomenclature consistently, providing a systematic way to name and classify organisms.

What is binomial nomenclature and why was it introduced?

Binomial nomenclature is a system of naming species that includes a genus name and a species name. It was introduced by Linnaeus to simplify and standardize the naming of organisms, making it easier to communicate about them scientifically.

How does the binomial nomenclature differentiate between genus and species names in writing?

In binomial nomenclature, the genus name is always capitalized, while the species name is never capitalized. When written together, both names are typically underlined or in italics.

What are some sources from which scientific names for organisms are derived?

Scientific names for organisms are derived from various sources, including classical or medieval Latin, classical Greek, other languages, and sometimes even named in honor of people.

Why is the naming of organisms not as systematic as chemical nomenclature?

The naming of organisms is not as systematic as chemical nomenclature because organisms are classified based on a variety of taxonomic characters, including morphology, physiology, molecular characteristics, behavior, ecology, and geography, rather than a simple structural formula.

What is the hierarchical structure of biological classification according to the script?

The hierarchical structure of biological classification, from largest to smallest, is domain, kingdom, phylum, class, order, family, genus, and species.

How does the script describe the evolution of taxonomic systems from Linnaeus to the present?

The script describes the evolution of taxonomic systems as starting with Linnaeus' three-domain system, which was later challenged and evolved with the discovery of more species and the development of paleontology. Today, we use a three-domain system that includes prokaryotic domains and eukaryotes, reflecting a deeper understanding of organismal relationships.

What is the significance of the domesticated dog's subspecies name, Canis lupis familiares?

The subspecies name Canis lupis familiares signifies that the domesticated dog is a distinct subspecies derived from the species Canis lupus, highlighting the process of domestication and specialization.

Why do taxonomists argue about different groupings and classifications?

Taxonomists argue about different groupings and classifications because the determination of relationships and groupings is complex and involves interpretation of various characteristics and evidence, leading to different perspectives on how organisms should be classified.

Outlines

00:00

🌿 Introduction to Taxonomy and Its Importance

The video script begins by introducing the concept of taxonomy, which is the science of classifying organisms. It emphasizes the significance of taxonomy in understanding evolutionary relationships among different groups of organisms. The script explains that while taxonomy may initially seem mundane, it is crucial for comprehending the broader picture of life's diversity. The historical context of naming and classifying organisms is also provided, starting from ancient times with Aristotle's initial classifications to the more systematic approach introduced by Carl Linnaeus, who is credited with the consistent use of binomial nomenclature, a two-part naming system for organisms consisting of a genus and species name.

05:02

🔍 Evolution of Taxonomic Systems and Naming Conventions

This paragraph delves into the evolution of taxonomic systems, highlighting the shift from descriptive names in Latin to the more streamlined binomial nomenclature. It discusses the complexities of naming organisms, which can draw from classical Latin, Greek, or even local languages. The script also touches on the challenges of creating a systematic naming process in biology, as opposed to the structured nomenclature used in chemistry, due to the vast diversity and characteristics of living organisms. The paragraph further explores the various criteria used in taxonomy, such as morphology, physiology, molecular characteristics, behavior, ecology, and geography, and explains the hierarchical levels of biological classification, from domain to species.

10:05

🐾 The Taxonomic Hierarchy and Species Classification

The script continues by illustrating the taxonomic hierarchy using the example of a dog, detailing each level from domain to subspecies. It explains how organisms are categorized based on shared characteristics and how this system helps to understand the levels of relatedness among different organisms. The paragraph also acknowledges the complexities and debates among taxonomists regarding the classification of organisms, especially at the species level. It touches on historical perspectives, such as Linnaeus's view of species as immutable, and introduces the concept of species change over time, with examples of hybridization in nature.

15:09

🌴 The Dynamic Nature of Species and the Influence of Darwin

The final paragraph discusses the dynamic nature of species, challenging the previously held belief in their immutability. It references the work of Buffon and the impact of paleontology and the discovery of extinct species on the understanding of species as evolving entities. The script concludes with a mention of Charles Darwin's pivotal work on the subject, which is set to be the focus of a subsequent video. The paragraph ends with a call to action for viewers to support the channel through likes, shares, subscriptions, and social media engagement.

Keywords

💡Taxonomy

Taxonomy is the science of classification, particularly of organisms. It is the framework through which biological diversity is organized into a hierarchical structure of categories. In the video, taxonomy is central to understanding the evolutionary relationships among different groups of organisms. The script discusses how taxonomy goes beyond simple naming, emphasizing its importance in revealing deeper insights into the natural world.

💡Evolutionary Relationships

Evolutionary relationships refer to the connections between different species based on their shared ancestry and the changes that occur over time. The video script highlights how taxonomy helps in understanding these relationships by organizing organisms into a hierarchy that reflects their evolutionary history, as seen in the discussion of how humans named things important for survival and how systems for organizing life evolved.

💡Aristotle

Aristotle was an ancient Greek philosopher and scientist who made significant contributions to the field of biology, including the early systems of classifying organisms. In the script, Aristotle is mentioned as the first person to write extensively about classifying animals into those with blood and those he called bloodless, laying the groundwork for future taxonomic systems.

💡Binomial Nomenclature

Binomial nomenclature is a system of naming species that was popularized by Carl Linnaeus, where each species is given a two-part name: the genus name and the specific epithet. The video explains that this system simplifies the naming process and provides a clear way to identify organisms, as exemplified by the script's mention of Apis mellifera for the honeybee.

💡Carl Linnaeus

Carl Linnaeus was a Swedish botanist, zoologist, and physician who formalized the modern system of binomial nomenclature. The video script describes Linnaeus's work as pivotal in taxonomy, particularly through his publication of 'Systema Naturae,' which organized a vast number of species into a coherent system.

💡Genus and Species

In biological classification, 'genus' and 'species' are two key hierarchical ranks. The genus is a category that groups species that are closely related, while the species is the most specific rank, indicating a particular organism. The video script explains that in binomial nomenclature, the genus name is always capitalized, and the species name is not, as seen in examples like Canis lupus for the gray wolf.

💡Morphologic Characters

Morphologic characters refer to the physical characteristics or shapes of organisms, which are used in taxonomy to classify and distinguish between different species. The video script mentions that these characters, including the developmental forms of organisms, are essential criteria for naming and classifying organisms within the taxonomic hierarchy.

💡Phylogeny

Phylogeny is the study of the evolutionary relationships among groups of organisms. It involves the construction of phylogenetic trees that depict these relationships. The video script discusses how taxonomic names are based on various characters to determine phylogeny, indicating how organisms are related to one another through shared traits and ancestry.

💡Three-Domain System

The three-domain system is a classification system that divides all living organisms into three domains: Bacteria, Archaea, and Eukarya. The video script explains that this system is used to organize levels of relatedness among organisms, with each domain representing a distinct branch of life with unique characteristics.

💡Hybrids

Hybrids are offspring resulting from the mating of two different species or varieties. The video script uses the example of finches in the Galapagos Islands to illustrate how hybrids can result from species adapting to different environments and how their characteristics, such as beak shape, can change over time, challenging the idea of fixed species.

💡Charles Darwin

Charles Darwin was a naturalist and geologist, best known for his contributions to the science of evolution. His work laid the foundation for the theory of natural selection. The video script mentions Darwin in the context of his studies on finches and how his research was pivotal in understanding the mutability of species and the process of evolution.

Highlights

The video discusses the importance of taxonomy in understanding evolutionary relationships among different organisms.

Aristotle's early classification system divided animals into those with blood and those without.

Pliny the Elder contributed significantly with 160 volumes on the classification of living things.

Latin was established as the language of scholarly writing for naming organisms.

Carl Linnaeus introduced the binomial nomenclature, simplifying the naming of species.

Binomial nomenclature consists of a genus name and a species name, always capitalized and italicized.

Scientific names often have origins in classical Latin or Greek, and can also be named after people.

Some species are named in honor of modern figures, such as the trilobite named after Mick Jagger.

Many scientific names incorporate words from various languages, reflecting diverse cultural influences.

Biological naming does not have a systematic approach like IUPAC names in chemistry due to the complexity of organisms.

Taxonomy considers multiple characteristics including morphology, physiology, molecular traits, behavior, ecology, and geography.

Linnaeus' three-domain system categorized life into animals, plants, and minerals.

The modern three-domain system classifies life into bacteria, archaea, and eukaryotes.

Taxonomic hierarchies range from domain to kingdom, phylum, class, order, family, genus, and species.

The domesticated dog is an example of how species can have subspecies classifications.

As you move up the taxonomic hierarchy, the number of shared traits decreases, but the group size increases.

Taxonomists often debate classifications, and species level is the most contentious.

Le comte de Buffon challenged the immutability of species and contributed to the field of biogeography.

The discovery of extinct species in the fossil record and the concept of hybridization have shown species are not fixed entities.

Charles Darwin's work on finches in the Galapagos Islands demonstrated species evolution through adaptation.

Transcripts

>> 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.

Thank you so much for visiting the Penguin Prof Channel.

Please support by clicking those buttons, like, share, subscribe,

visit on Facebook, follow on Twitter.

Good luck.