To make sense of structure and function, we need

to deal with biological diversity.

The primary focus of Biology 5B is:

The functional biology of organisms,
especially multicellular organisms
how organisms are built and how
their morphology and physiology let
them 'work' in their environments:

Structure and function

To make
senseabout
of structure
and function,
we
Also
unique
biology:
individual
need to deal with biological diversity.
organisms
change within their lifetimes!
Two important levels of diversity:

1. Development,
growth, maturation,
There are many species of organisms, and
aging
they are often very different from each
other -- interspecific variation

You are not the same organism

2. Within species,
each
individual
different
that you
were
10 yearsis ago
from every other individual -- intraspecific
(or 5 minutes ago)
variation
(intraspecific variation is unique about
biology, compared to chemistry or physics)

Two important levels of diversity:

1. There are many species of organisms,

often very different from each other

-- interspecific variation
1. Within species, each individual is

different from every other individual

-- intraspecific variation
(intraspecific variation is unique about
biology, compared to chemistry or physics)

What is known and unknown - about diversity?

There are a lot of species -- about 2 million have
been described (collected, analyzed, and
formally discussed in the scientific literature)
Described species in various groups
Arthropods
> 1,000,000

Plants
~ 300,000 ~ 1,000,000 insects
> 350,000 beetles!

invertebrates
(not arthropods)
~ 150,000

Vertebrates
~ 52,000
4500 mammals

What is known and unknown - about diversity?

Examples of intra- and interspecific commonalities:

There are a lot of species -- about 2 million have

been described (collected, analyzed, and
formally discussed in the scientific literature)

DNA sequence difference between any two

humans is about 0.1%

There are huge differences in form and

function between these species.

DNA sequence difference between humans and

chimpanzees is about 1-2%
DNA sequence difference between humans and
rodents (mice, rats, etc.) is about 12-15%

But there are also many commonalities:

DNA code; sequence similarity;
basic biochemistry; cell structure and
function, etc.

More commonalities:

all mammals have the same set of

about 23,000 protein-coding genes
all vertebrates share nearly all of the
same genes
many are also in invertebrates

The commonalities and the differences are there

because of lifes evolutionary history:

descent with modification from shared

common ancestors
Similar species (like humans and
chimpanzees) have recent common ancestors
Dissimilar species had common ancestors
much farther in the past
All species share common ancestry from very
long ago (~ 3.5 billion years ) -- origin of life

The commonalities and the differences are there

because of lifes evolutionary history:

Phylogeny -- history of species formation

Often shown as a
phylogenetic tree as
symbolized here:

present

descent with modification from shared

common ancestors
time

organize our knowledge of diversity

We
with a hierarchical system based on
evolutionary lineages: PHYLOGENY

trunk' is the most

deeply ancestral form

past

'branches' are more

recent ancestors
common ancestor

Describes common ancestry,

like a geneology or family tree.

Branch points ( )
indicate events that
formed new lineages
(last shared ancestors)

time

present

past

common ancestor

Lineages separated
by few branch points
are more related than
lineages separated by
many branch points.

More similarity in closely related species

than in distantly related species -- less time for
evolutionary change from ancestors

'dead leaves'
show extinct lineages.

Phylogeny -- history of species formation

present

Closely related
(recent shared
ancestor)

time

Phylogeny -- history of species formation

green 'leaves'
show existing species

past

common ancestor

Distantly related
(no recent shared
ancestor)

More similarity in closely related species

than in distantly related species -- less time for
evolutionary change from ancestors

Phylogeny -- history of species formation

time

present

time

present

Phylogeny -- history of species formation

past

common ancestor

Rotating the tree does not change its

meaning in terms of patterns of relationships

Phylogeny -- history of species formation

common
ancestor

past

past

common ancestor

Rotating the tree does not change its

meaning in terms of patterns of relationships

Phylogeny -- history of species formation

common
ancestor

time

present

Rotating any part of the tree also does not

affect meaning IF branch pattern unchanged

past

time

present past

time

present

Phylogenetic trees can be drawn in several ways

Taxonomy is the naming system indicating

degrees of relationship

Taxonomy is the naming system indicating

degrees of relationship

Many taxonomic levels; the most traditional are:

Many taxonomic levels; the most traditional are:

Species
Genus (genera)
Family
Order
Class
Phylum (phyla)
Kingdom
Domain

Species
Genus (genera)
Family
Order
Class
Phylum (phyla)
Kingdom
Domain

Species is most restrictive category; domain is the

most inclusive (3 domains; millions of species).

Taxonomy is the naming system indicating

degrees of relationship
Many taxonomic levels; the most traditional are:
Species
Genus (genera)
Family
Order
Class
Phylum (phyla)
Kingdom
Domain

lupus
Canis
Canids (dogs)
Carnivores
Mammals
Chordates
Animals
Eukaryotic organisms

A species' scientific name is a binomial: the

combination of genus and species names, e.g:
wolves: Canis lupus
people: Homo sapiens

lupus
Canis
Canids (dogs)
Carnivores
Mammals
Chordates
Animals
Eukaryotic organisms

Wolf

Taxonomy is the naming system indicating

degrees of relationship

This system of taxonomic

names is
lupus
Canis sometimes does not
somewhat arbitrary, and
Canids (dogs)
adequately represent
evolutionary
history.
Carnivores
Mammals

Generally a more accurate way

to show
Chordates
Animals
relationships is as lineages, or clades,
from a
Eukaryotic organisms
phylogenetic tree.
A clade is a lineage grouping than includes an
ancestral species and all its descendants.

Examples of clades
Canid clade includes
all dogs : domestic
dogs, wolves, coyotes,
foxes, jackals, etc., back
to an ancestral dog

Mustelid clade
includes all mustelids:
skunks, otters, weasels,
wolverines, etc., back to
an ancestral mustelid.

Carnivore clade
includes all carnivores:
cats, dogs, weasels,
bears, etc., back to an
ancestral carnivore.

1. Most species have not been discovered.

We know of ~ 2 million species; estimates of
the number of living species are 10-30 million.
we have discovered only 7-20% of
them -- and many will become extinct
before they can be described.
Most undiscovered species are probably
insects and other small organisms.
there have been millions of species
that are now extinct perhaps 100X more than
the number of species currently alive.

Benefits of knowing evolutionary

relationships
Lets us arrange our
knowledge in a way that allows

accurate predictions about

unstudied organisms.
This is important for 3 reasons:

2. Only a tiny fraction of discovered

species have been carefully studied
Most have simply been described in terms
of basic morphology (what they look like).
A few have been examined in more detail:
physiology, ecology, behavior, etc.
A very small number of model organisms
have been intensively studied, and their
biology is understood in considerable detail.

2.
Only
a tiny fraction
discovered
Some
examples
of modelof
organisms:
species
have coli
been
carefully studied
Escherichia
(bacterium)
Most
Arabidopsis
thaliana
(small
plant) in terms
have simply
been
described
Chaenorhabditis
(nematode
worm)
ofbasic
morphologyelegans
(what they
look like).
Drosophila melanogaster (fruit fly)
Brachydanio
rerio (zebrafish)
A few
have been examined
in more detail:
Mus musculus
mouse)
physiology,
ecology, (house
behavior,
etc.
A very small number of model organisms
have been intensively studied, and their
biology is understood in considerable detail.

If we understand evolutionary
history, we dont need complete
knowledge to make useful
generalities and predictions.

3. We will never be able to know

everything about organisms
there is too much to know
within species, individuals differ from each
other and change during their lives
organisms are constantly changing (evolving)
and going extinct

Therefore, our understanding of biology

will always be incomplete.

But thats OK:

An example: were sure that all organisms*

use DNA as the genetic material and that
the basic DNA coding scheme is the same
for all.
This has been tested on only a tiny fraction
of species, but because we understand
evolution, we can be confident it is
universally true.
* Not counting viruses -- some of which use
RNA instead of DNA

More examples:
We know a lot about the fruit fly
Drosophila melanogaster. Therefore we also
know a lot about other Drosophila, a bit less
about other kinds of flies, something about
insects in general, and a little about other
animals.
If we know about disease causality, and
treatment in mice, rats, or monkeys, we
also know a lot about the causes and
treatment of similar diseases in people.

What information is used deduce phylogenies?

Many kinds of data:

Early workers used anatomy,
physiology, embryology (development
patterns), and fossils.
More recently, biochemistry, behavior,
neuroanatomy, etc.
The latest approach is DNA sequences
(molecular phylogeny)

Remember that phylogenies are

HYPOTHESES about the history of
evolutionary change.
conceptual models that best fit the
available information
SUBJECT TO TESTING as new information
becomes available
REVISED and RETESTED if they do not fit
new data

Important point: We constantly revise

the 'tree of life' with new information, but
the types of data used for phylogeny
reconstruction -- even extremely different
ones such as fossils, embryology, and
DNA -- usually give fairly similar
answers.

This gives us confidence that

our understanding of evolutionary
history is reasonably accurate.

Our understanding of diversity is based on

evolution and lineages: descent with
modification.

Because organisms transfer genetic information

to subsequent generations, their history is a
crucial factor in their current biology.

Why does evolutionary change occur? First,

a definition:

Evolution = Genetic change in a

population across generations
This has several implications:

in organisms, the past strongly influences

the present, and the present will strongly
influence the future.

This aspect of biology is very unlike many

other sciences
(example: the past history of a molecule or
its atoms has no influence on its chemistry)

The mechanisms of evolutionary change

The mechanisms of evolutionary change

What causes genetic information to change

over generations? Four primary factors:

What causes genetic information to change

over
generations? the
Four
primary
factors:
probably
most
important

mutation: random genetic changes

mutation:
random
genetic
changes
source of
change,
because

gene flow: immigration of new genes

(alleles) from other populations

gene flow: immigration of new genes

(alleles) from other populations

random genetic drift (especially in small

populations)

random genetic drift (especially in small

populations)

natural selection

it is

not random.

How does selection work?

natural selection

How does natural selection cause evolution?

The details are hugely complex:
many genes
interactions between genes
environmental effects
gene environment interactions
numerous other factors
BUT THE BASIC PRINCIPLE IS VERY
SIMPLE.
Can be summarized in three observations and
three inferences.

natural selection: 3 observations, 3 inferences:

natural selection: 3 observations, 3 inferences:

OBSERVATION #1: Variation exists in all
biological traits. Obvious from even casual
observation.

OBSERVATION #2: Some of this variation is

heritable: encoded in the DNA. Easy to verify.
variation in traits (morphology, physiology, etc.) is
partially due to variation in genes.
variation in genes (genetic variation) comes from
mutation; new combinations of genes arise
quickly from sex.

natural selection: 3 observations, 3 inferences:

OBSERVATION #3: All organisms have a

potential reproductive rate much higher than
the real reproductive rate.

OBSERVATION #1: Variation exists

OBSERVATION #2: Some of it is heritable
OBSERVATION #3: Organisms can reproduce
faster than they do reproduce

elephants: Darwin calculated that one pair

would have more than a million offspring in 750
years if all offspring survived and reproduced
(a bit faster for people).

INFERENCE #1: Not all young that are born

survive to reproduce; therefore there must be
competition.

mice: a single pair could cover the Earth with

their descendants in ~ 6 years (about 30
million descendants in two years!)

much direct evidence showing high

mortality and competition

natural selection: 3 observations, 3 inferences:

natural selection: 3 observations, 3 inferences:

OBSERVATION #1: Variation exists

OBSERVATION #2: Some of it is heritable
OBSERVATION #3: Organisms can reproduce
faster than they do reproduce

OBSERVATION #1: Variation exists

OBSERVATION #2: Some of it is heritable
OBSERVATION #3: Organisms can reproduce
faster than they do reproduce

INFERENCE #2: Because of variance in

phenotype, some individuals are better able to
compete (survive and reproduce).

INFERENCE #3: Successful individuals will

contribute disproportionately to the genes in the
next generation.

plenty of evidence showing

differential survival and reproduction.

natural selection: 3 observations, 3 inferences:

This is a change
the of
genetic
structure
OBSERVATION
#2:inSome
it is heritable
OBSERVATION
#3: Organisms
reproduce
of the population,
which can
is the
faster than they do reproduce

definition of evolution.

There is much#3:direct
evidence
of this will
INFERENCE
Successful
individuals
happening
all the time. to the genes in the
contribute
disproportionately
The next generation will have a higher
frequency of advantageous genes.

The next generation will have a higher

frequency of advantageous genes.

natural selection: a constant endless

loop across generations:
Genetic structure
of the population

Phenotypic traits of
individuals: morphology,
physiology, behavior

Change in genetic structure Natural selection

across generations
(= evolution)

Different survival and

reproduction of individuals
with different genes

Things to remember about evolution:

its both random (mutation, recombination,
environmental events, etc.) and non-random
(selection).
its NOT GOAL-ORIENTED! Organisms
dont decide to evolve something. Selection
responds to existing conditions, and to the
organisms history as coded in the genes.
The currency of selection is NOT survival
per se. What really matters in evolution is
REPRODUCTIVE SUCCESS.

MAKE SURE YOU UNDERSTAND:

inter- and intra-specific diversity (importance of diversity for
evolution).
extent of knowledge about diversity
basic commonalities among organisms (DNA, cell structure, etc.)
phylogenies based on evolutionary history; phylogenetic trees (branch
points, species relatedness)
taxonomic naming conventions, binomials, clades
importance of understanding evolutionary history (phylogeny) for
generalizing, and for making predictions about unstudied organisms
fundamental definition of evolution
causes of evolution (mutation, gene flow, etc.)
how natural selection works (3 observations, 3 inferences)

Things to remember about evolution:

It can be fast, and small differences have a big
effect over time:
Example: consider a mutation in 1% of
individuals that gives 1% better fitness.
In 500 generations it will be in 60% of the
population
In 1000 generations it will be in 99.5% of
the population
A mutation with a 5% advantage is in 99%
of the population in 200 generations