IB Biology A3.2 Classification & Cladistics

Summary

This video script delves into the classification of living organisms, highlighting the shift from physical characteristics to DNA and genetic sequencing. It outlines the hierarchical system starting with domains to species, emphasizing the importance of common ancestry in grouping. The script also discusses the challenges of classification, such as the boundary paradox and the use of cladograms to represent evolutionary relationships. It concludes with the impact of DNA sequencing on reclassification, exemplified by the figwort family, and the addition of domains due to RNA sequencing.

Takeaways

• 🔬 Humans have a natural inclination to classify and label living organisms, which is crucial for understanding biodiversity.
• 🌐 The classification system in biology is hierarchical, starting broad with domains and becoming more specific through kingdoms, classes, orders, families, genera, and species.
• 🔬 Early classification was based on physical characteristics, but modern methods incorporate DNA and genetic sequencing to better understand evolutionary relationships.
• 🌿 There are three domains of life: Bacteria, Archaea, and Eukarya, which were established based on RNA sequencing.
• 📚 Taxonomy is the science of classifying organisms into groups, with domain being the broadest level of classification.
• 🧬 Genetic information, specifically DNA sequences, is considered the most reliable for classifying organisms and understanding their evolutionary origins.
• 🌱 Life is dynamic, with species changing and adapting to their environments, which can complicate classification efforts.
• 🌐 A cladogram is a diagram that represents the evolutionary relationships between different species based on shared characteristics.
• 🕰 The molecular clock is a concept that uses the rate of mutations to estimate the time since two species diverged from a common ancestor.
• 🔍 DNA sequencing has revolutionized the classification of species, leading to reclassifications as new evidence emerges.
• 🔄 The process of classification is not without challenges, as it involves subjective decisions and assumptions, such as the rate of mutations for the molecular clock.

Q & A

What is the primary reason humans classify and label living organisms?

Humans classify and label living organisms to organize and manage information about them, enabling scientists and biologists to understand, record, and discuss species in a comprehensive and consistent manner.

What is the basis for the modern classification system in biology?

The modern classification system in biology is based on a hierarchical structure that groups organisms according to their traits or evolutionary origins, with a shift towards using DNA and genetic sequencing.

What are the three domains that make up the largest groups of living organisms?

The three domains that make up the largest groups of living organisms are Bacteria, Archaea, and Eukarya.

How does the hierarchical system of classification work?

The hierarchical system of classification starts broad with the domain and becomes more specific through kingdom, class, order, family, genus, and species.

What is meant by the term 'taxonomic rank'?

Taxonomic rank refers to the level of classification within the hierarchy, such as domain, kingdom, class, order, family, genus, and species.

What is the 'boundary paradox' in the context of biological classification?

The 'boundary paradox' refers to the difficulty in determining when species have diverged enough to be considered separate species or different groups within the classification system.

Why is it important for classification to reflect evolutionary origins?

Classification must reflect evolutionary origins because it allows for the sharing of traits between members of a group, enabling predictions to be made based on the classification, such as shared characteristics and adaptations.

What is a cladogram and how is it used in biological classification?

A cladogram is a branching diagram that represents the evolutionary relationships among various groupings of organisms called clades, based on shared characteristics and common ancestry.

What is the molecular clock hypothesis and how is it used in classification?

The molecular clock hypothesis is the idea that mutations occur at a consistent rate over time, allowing scientists to estimate the time since two species diverged from a common ancestor based on the differences in their DNA sequences.

How has DNA sequencing technology impacted the classification of species?

DNA sequencing technology has greatly impacted the classification of species by providing more accurate information about evolutionary relationships, leading to reclassifications and a better understanding of species' ancestry.

What is the parsimony criterion in cladogram construction?

The parsimony criterion is a method used in cladogram construction to find the simplest explanation for the evolutionary relationships among species, minimizing the number of evolutionary changes required.

Outlines

00:00

🔍 Introduction to Biological Classification

The video script begins by discussing the human inclination to organize and classify living organisms. It emphasizes the importance of a classification system in biology for consistency in describing, discussing, and naming species. The script outlines the historical shift from classifying organisms based on physical characteristics to using DNA and genetic sequencing. It introduces the hierarchical system of classification, starting with the broadest category, 'domain,' and becoming more specific through kingdom, class, order, family, genus, and species. The script also touches on the challenges of classifying organisms due to the dynamic nature of life and the process of natural selection, which can lead to species changing over time.

05:00

🌿 Understanding Taxonomy and Evolutionary Relationships

Paragraph 2 delves into the concept of taxonomy as the process of assigning organisms to specific groups. It explains the three domains of life: Archaea, Bacteria, and Eukarya. The script discusses how classification helps scientists understand and communicate about species. It introduces the idea of 'synapomorphies,' which are traits shared among species due to common ancestry, allowing for predictions about species characteristics. The paragraph also explores how species adapt to environmental changes, leading to the formation of new species and the concept of a 'boundary paradox,' which refers to the difficulty in determining when one species splits into two. The script concludes by highlighting the importance of classifying species to reflect their evolutionary origins.

10:01

🌳 Cladograms and Genetic Evidence in Classification

Paragraph 3 focuses on cladograms, which are branching diagrams that represent the evolutionary relationships between species. It explains how cladograms are constructed based on genetic or amino acid sequences, with a preference for genetic information. The script discusses how mutations in DNA sequences accumulate over time, leading to species divergence, and how this can be used to estimate the time since two species shared a common ancestor through the concept of a 'molecular clock.' The paragraph also mentions the use of parsimony criterion in constructing cladograms, which involves identifying the smallest number of genetic changes to explain the relationships. The script concludes by noting that cladograms are based on assumptions and that DNA sequencing has revolutionized our understanding of species classification.

15:04

🧬 The Impact of DNA Sequencing on Biological Classification

The final paragraph discusses the impact of DNA sequencing on the classification of species. It mentions the reclassification of species as a result of new genetic evidence, such as the reorganization of the figwort family based on DNA evaluations. The script highlights the shift from classifying life into two broad categories (prokaryotes and eukaryotes) to three domains (Bacteria, Archaea, and Eukarya) due to the diversity found in prokaryotes. It concludes by emphasizing that our understanding of biological classification is continually evolving as new genetic information becomes available.

Keywords

💡Classification

Classification is the process of organizing living organisms into groups based on shared characteristics or common evolutionary origins. In the video, classification is discussed as a fundamental aspect of biology that allows scientists to systematically categorize and study life forms. The script mentions that biologists use a hierarchical system to classify organisms, starting from broad categories like domain and narrowing down to more specific ones like species.

💡Species

A species is a group of living organisms that can interbreed to produce fertile offspring. In the context of the video, species are the basic units of classification. The script discusses how species are named and classified according to their traits and evolutionary relationships, which is crucial for scientific communication and understanding biodiversity.

💡Hierarchical System

A hierarchical system is a method of organizing things into a structured order of categories. The video script explains that biological classification uses a hierarchical system that starts with broad groups like domains and becomes more specific with kingdoms, classes, orders, families, genera, and species. This system allows scientists to infer a lot about an organism based on the groups it belongs to.

💡Domain

Domain is the broadest category in biological classification, encompassing all life forms. The script mentions that there are three domains: Bacteria, Archaea, and Eukarya. This level of classification is significant because it reflects the most fundamental divisions among living organisms based on genetic and cellular characteristics.

💡Evolutionary Origins

Evolutionary origins refer to the common ancestry of a group of organisms. The video emphasizes the importance of classifying organisms based on their evolutionary origins, meaning that organisms within the same taxonomic group share a common ancestor. This concept is crucial for understanding the relationships between different species and predicting shared traits.

💡Genetic Sequencing

Genetic sequencing is the process of determining the precise order of nucleotides within a DNA molecule. The script discusses how genetic sequencing has become a primary tool for classifying organisms, as it provides a more accurate reflection of evolutionary relationships than physical characteristics alone. DNA sequences are used to establish how closely related different species are.

💡Cladograms

A cladogram is a branching diagram that represents the evolutionary relationships among various groups of organisms. The video script explains how cladograms are constructed based on shared characteristics and used to visualize the evolutionary history of species. Cladograms help scientists understand how different species are related and how they have diverged over time.

💡Mutations

Mutations are changes in an organism's DNA sequence. The video script mentions that mutations cause differences in DNA sequences, which accumulate over time and lead to the divergence of species. Mutations are the raw material for evolution and are used in molecular clocks to estimate the time since two species shared a common ancestor.

💡Molecular Clock

The molecular clock is a concept in evolutionary biology that assumes a constant rate of genetic mutations over time. The video explains how the molecular clock allows scientists to estimate when species diverged from a common ancestor by counting mutations in their DNA sequences. This provides a timescale for evolutionary events.

💡Synapomorphies

Synapomorphies are shared derived characteristics that indicate a common evolutionary origin. In the video, synapomorphies are mentioned as traits that are used to classify organisms into the same taxonomic group because they share a common ancestor. For example, the script mentions that all mammals have a four-chambered heart, which is a synapomorphy indicating their shared evolutionary history.

💡Parsimony Criterion

The parsimony criterion is a principle used in constructing cladograms that favors the simplest explanation, requiring the fewest number of evolutionary changes. The video script discusses how software can use this criterion to analyze genetic sequences and construct cladograms that represent the most likely evolutionary relationships based on the minimal number of mutations.

Highlights

Biologists classify millions of species to ensure consistency in their description and discussion.

Classification system is crucial for organizing and managing information about life on Earth.

Organisms are classified based on traits or evolutionary origins.

Classification has transitioned from physical characteristics to DNA and genetic sequencing.

The hierarchical system of classification starts broad and becomes more specific.

The largest group in classification is the domain, followed by kingdom, class, order, family, genus, and species.

Taxonomy is the process of assigning organisms to specific groups.

There are three domains of life: bacteria, archaea, and eukarya.

Classification helps scientists understand and communicate about species.

Life is not stagnant; species change and react to their environments.

Natural selection causes species to change over time, leading to the need for reclassification.

The boundary paradox refers to the difficulty in determining when species split.

Classifications are somewhat arbitrary, especially between closely related species.

Evolutionary origins must be reflected in the classification of species.

Synapomorphies allow for predictions based on species classification.

Cladograms represent the evolutionary relationships of species based on genetic similarities.

Cladistics is the systematic placement of organisms into groups called clades based on common descent.

Genetic or amino acid sequences are the best evidence for establishing clades.

Mutations cause differences in DNA sequences, which accumulate over time.

The molecular clock estimates the time since species diverged from a common ancestor based on mutation rates.

Cladograms are branching diagrams that represent ancestor-descendant relationships.

Parsimony criterion is a tool used to produce cladograms based on genetic differences.

DNA sequencing has revolutionized species classification and led to reclassification.

The figwort family is an example of reclassification based on DNA evidence.

Life is organized into three broad domains: bacteria, archaea, and eukarya.

Transcripts

over the last few videos we have looked

at what makes up life how life is

organize the different types of cells

that we find in living organisms whether

they be single or multi-cell and now we

want to turn our attention to how do we

organize and classify life as humans we

really like to organize and label

different living things uh and all

things for that matter and so in this

video we want to look at how do we uh

within biology actually classify and

distinguish living organisms from one

another

biologists have classified millions of

different species and in order to ensure

that there is consistency and how those

species are described and discussed and

even named it's really important to have

a classification system and as we talked

about in our previous video Carl andas

began this process of establishing

species names and now we want to turn

our attention to the classification and

this is the idea of placing organisms in

groups according to their traits or

evolutionary origins and previously ly

in the past this was done primarily

based off of physical external

characteristics that could be observed

or internal characteristics with

dissection and now it's begun to

transition more to the use of DNA uh and

and genetic sequencing in order to

establish relationships in

classification and so how we classify

organisms is a hierarchical system where

we start really Broad and get more and

more specific as we move down these list

of criteria uh this enables us to know

lots of information about a particular

speci species or or organism based off

of the groups that it belongs to and So

currently the largest group is domain

it's the broadest group today and then

we become more and more specific and

it's essential that species are

organized in order for information and

recording and grouping to be manageable

for all life on the planet for

scientists and for biologists to be able

to understand and have comprehensive and

similar conversations about the same

species at the same time and so we'll

look at how our species classified

taxonomy is the act of assigning an

organism to a particular group and as

just mentioned domain is the broadest

level of grouping and there's three

level uh three types of domains the Ari

bacteria and UK carots and those three

domains are where we find different

living organisms and then as we progress

down the levels of organiz uh of

organization of life we become more and

more specific so from domain we get more

specific by Kingdom

class order family genus and then

species uh and it's difficult to agree

on assignments of grouping of taxonic

rank uh for example should a trait be

based off of the on on the genus or the

family and it's sometimes difficult to

classify uh organisms to a particular

group or to a particular species because

life is not stagnant as the environment

changes we see species change and react

to their environments it's one of the

the characteristics of living things as

a response to stimuli and so life

responds to changes in the environment

and this can cause species to change

over time through the process of natural

selection and as species obtain greater

differences over time uh beginning with

genetic differences which can translate

to physical characteristics that we can

actually observe

eventually those organisms those life

will need to be separated into different

groups whether it be a Genus uh or than

family Etc the time at when these

separations should happen is subjective

it's not easy to determine it um and and

this is what we call a boundary Paradox

we don't exactly know when species split

and become two and so it makes it really

challenging for biologists to sometimes

determine one species from another if

they're really closely related and we'll

talk about how uh we can do this a

little bit later on in this video and so

as a result of this the rankings the the

classification is are somewhat arbitrary

um the distinguishing between really

closely species from one another there

may not always be agreement amongst

biologists and scientists one thing that

biologists do definitely agree upon is

that classification of of species must

mirror their evolutionary origins and so

what this means is that each taxonic

group uh would have the same common

ancestor and so organisms evolved from a

common ancestor in the same taxonic

group they should be placed in the same

group together they should be uh grouped

together and so biologists agree on this

and it allows for uh the sharing of

traits between members of a different

group um because they share those traits

it allows predictions to be made based

off of the classification and this is

called

synapomorphies uh the ability to make

predictions based off of a species uh

classification and for example bats um

bats typically live in environments that

are difficult to get to and often times

are difficult to discover or or study

the species and so new species are often

discovered and because bats belong to

particular groups and families and and

uh the species belong to these different

groups assumptions can be made about uh

new bats that are discovered uh because

they're part of these same groups and so

we could assume that they have a four

chambered Hearts they have hair they

give life birth placenta they have

maming glands Etc all because they're of

the same grouping and also because they

belong to to mammals and those are all

characteristics of mammals a second

example would be found in daffodils a

plant uh all members of this group

produce alkaloid compounds and

oftentimes those can be used for drugs

and for different treatment methods and

so new discoveries of those particular

species the assumptions could be made

that they also produce alkaloids because

they're part of the same grouping and so

this is all possible because of

evolutionary relationships and the

grouping of species based off off of

their similarities and the indication of

them having a common ancestor and so be

being related to one another because

they share a common ancestor species

change over time as the environment

changes this causes species to also

change uh they adapt to the the change

environment or they can go extinct and

sometimes species that are really

successful we see Branch off into many

different groups and so then an ancestor

of all of these different groups of

species can have many species that all

derived from the ancestor

and we can see this because they have

shared characteristics and so to

organize this to view this uh we can

create a cogram and specifically a CLA

is a group of organisms evolved from a

common ancestor that includes all of the

species alive today as well as the

ancestral species that are now extinct

so it's all of the species alive today

as well as the ancestral species that

are now extinct and so then cladistics

is the approach to systematically

placing organisms into groups group

called clades based primarily on common

descent and so in the image here we can

see an example of one um and we'll talk

about how to make one also in our video

here clades can be large or small birds

are a very successful group of organisms

there's about 10,000 species in the clay

that would uh make up birds uh the tree

Ginko bboa is The Only Living member of

its clay um and so they can be massive

or they can be just individual species

the best evidence that we have for

organizing uh and establishing clades is

based off of genetic or amino acid

sequences much less desirable is the use

of physical characteristics external

characteristics um the the genetic

information is is the best and so

because we did not always have the

access to genetic information without

being able to sequence DNA uh much of

our organization of of species into

different clades through clog Glam grams

excuse me has changed uh pretty

significantly because

um before DNA we couldn't look the

ability to sequence DNA we couldn't

really look at and examine the the

sequence and so uh reclassification has

had to happen for many different clades

uh based off of this DN DNA evidence

species are part of multiple clades that

become more and more specific so we can

have a broad group that becomes more and

more specific based off of those genetic

characteristics and similarities uh and

so members of species can be part of

multiple clades because of this what

then causes these differences in DNA or

amino sequences it's ultimately

mutations mutations cause differences in

the DNA and these accumulate gradually

over time uh the longer the species pers

persists the more mutations are going to

take place and so assuming that this has

somewhat of a consistent rate we can use

this rate to estimate the time since the

Divergence of two species from a common

ancestor and this is an idea called the

molecular clock uh that we can estimate

how long ago species separated or

diverged from a common ancestor based

off of this consistent rate of mutations

it only does provide an estimate it's

based on an assumption of a constant

rate uh it's not a number that we can

necessarily go back and actually measure

or have a a specific value for it's an

assumption based off of this constant

rate and so for example humans and

chimpanzees uh at a mutation rate of 10

the9th per year humans split from uh

their most living U most closely living

relative chimpanzees about 4 and a half

million years ago and chimpanzees and

bonabo Bonos split about uh uh 1 million

years ago and that's based off of this

Assumption of the constant rate of

mutations the most recent human ancestor

lived probably about 150,000 years ago

so chimpanzees and humans while we have

a lot of DNA in common uh the vast

majority of our DNA is is similar um the

two species split from a common ancestor

a long time ago about 4 and a half

million years ago within examining DNA

sequences and how they've changed uh and

looking at clades and cladograms uh the

website ncbi has um some tools to be

able to compare sequences and we will do

this in my class with students if you're

not in my class I would recommend that

you spend some time practicing this and

doing this to construct and analyze

cladograms on your own a cladogram is a

branching diagram that represents

ancestor and descendant relationships

and these relationships as we visualize

in a cogram uh is based off of

differences in the base uh DNA based

sequences or amino acid sequences and so

more recent common ancestor is going to

suggest that there's more similarity in

those genetic bases uh and when we

compared sequences we can also then

indicate the length of time from

separation from a common ancestor like

what we just discussed with humans and

chimpanzees uh and so now we're going to

talk about how to actually make these

and interpret these analyze these when

doing this it's also possible to have

the software uh identify the smallest

number of sequence changes as building

the the cogram so in constructing it the

software can analyze the sequences to

look at what would be the smallest

number of changes to uh genetic changes

to make that that sequence work and this

is called parsimony

Criterion uh and it's a tool that we

canuse used to try to produce clogs

based off of the the genetic differences

so here we have some very basic clogs to

be able to use as talking points to

understand what we're actually looking

at and what it's showing uh cladograms

have a number of branches and this would

be based off of the different species or

the genetic sequences that we're looking

at the terminal branches represent the

uh individual clayes um and they may or

may not be subdivided nodes within a

cogram are the branching point points

usually two branches uh but can also

sometimes be three or more that uh

radiate out from a node uh it's also the

hypothetical points that the ancestral

species split to form two or more clayes

and so that that node would represent

the common ancestor and then two

different species originated from that

uh two Clays linked by a node are

relatively closely related so ancestor

two Branch out from that those two that

Branch out from that node are going to

be pretty closely related but have some

differences between them the root within

a common um within a cogram is the

common ancestor of all of the clades

within that

cogram and cladograms can also include

numbers sometimes to indicate the

differences in DNA sequences or if

they're drawn to scale can also

represent time typically we don't see

them uh at least the ones that we'll

analyze representing time but it is also

a possibility the branching patterns

then are meant to match the fogy

philogyny The evolutionary origins of

the species and should represent that

and lastly cladograms are based on

assumptions it's based off of um going

back to the molecular clock and our

assumptions of mutations it's not exact

proof it's using the best evidence that

we have to try to draw some conclusions

and help us understand but again they

are not definitive proof since the 1990s

when DNA sequencing uh has become more

and more common and cheaper and faster

uh our use of DNA sequencing to evaluate

species and their evolutionary

relationships has really changed and

improved and this has led to some

reclassification of species because of

this new technology most classification

of species is um follows the pathway of

evolution uh but if not all the

organisms within a clay share a common

ancestor then that results in

reclassification it's it's necessary

because traditionally initially

classification was based off of the

physical characteristics internal

external that could be observed and a

good example of this is seen in the

figart family um the DNA evaluation of

different species that belong to this

family indicated that they did not all

share a common ancestor and so this then

indicated that there need to be some

reclassification initially the family

was the eighth largest of angiosperm

which are flowering plants uh after

examining the DNA sequences sequences it

was found that five groups of the

species needed to be reclassified into a

different family um either previously

existing or newly created and now that

figart family is only the 36th largest

and so this was all based off of new

evidence new information from DNA

sequencing and so this has really

changed our ability to compare uh

species and the relationships to one

another as we talked about at the

beginning of this video life is

organized organized into three broad

domains uh this has not always

necessarily been the case originally um

life was organized starting at the

Kingdom level and was based off of

procaryotes ukar bacteria and then um

our plant animal fungi um this has

changed and we've added the category of

domains and that was based off of uh

examining the RNA genetic sequencing for

procaryotes and really when doing so

finding that there were two separate

groups um that were diverse enough that

a third domain had to be added and so

now we have the three domains of

bacteria our Ki and UK carots and this

was all because of examination of the

RNA sequencing the the the procaryotes

uh formerly procaryotes were so diverse

that that group needed to be split into

two um and so now we have bacteria and

archi and then also UK carots for our

three domains that make up life and so

this is how we classify living things uh

as we'll continue to discuss throughout

the course