IB Biology A3.2 Classification & Cladistics
Summary
TLDRThis 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
- ๐ฌ Humans have a natural inclination to classify and label living organisms, which is crucial for understanding biodiversity.
- ๐ The classification system in biology is hierarchical, starting broad with domains and becoming more specific through kingdoms, classes, orders, families, genera, and species.
- ๐ฌ Early classification was based on physical characteristics, but modern methods incorporate DNA and genetic sequencing to better understand evolutionary relationships.
- ๐ฟ There are three domains of life: Bacteria, Archaea, and Eukarya, which were established based on RNA sequencing.
- ๐ Taxonomy is the science of classifying organisms into groups, with domain being the broadest level of classification.
- ๐งฌ Genetic information, specifically DNA sequences, is considered the most reliable for classifying organisms and understanding their evolutionary origins.
- ๐ฑ Life is dynamic, with species changing and adapting to their environments, which can complicate classification efforts.
- ๐ A cladogram is a diagram that represents the evolutionary relationships between different species based on shared characteristics.
- ๐ฐ The molecular clock is a concept that uses the rate of mutations to estimate the time since two species diverged from a common ancestor.
- ๐ DNA sequencing has revolutionized the classification of species, leading to reclassifications as new evidence emerges.
- ๐ 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
๐ 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.
๐ฟ 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.
๐ณ 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.
๐งฌ 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.
Mindmap
Keywords
๐กClassification
๐กSpecies
๐กHierarchical System
๐กDomain
๐กEvolutionary Origins
๐กGenetic Sequencing
๐กCladograms
๐กMutations
๐กMolecular Clock
๐กSynapomorphies
๐กParsimony Criterion
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
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