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
Two important levels of diversity:
1. There are many species of organisms,
often very different from each other
-- interspecific variation

how organisms are built and how
their morphology and physiology let
them 'work' in their environments:
Structure and function
1. Within species, each individual is
different from every other individual
-- intraspecific variation
(intraspecific variation is unique about
biology, compared to chemistry or physics)

To make
Also senseabout
unique of structure and function,
biology: we
individual What is known and unknown - about diversity?
need to deal with biological diversity. There are a lot of species -- about 2 million have
organisms change within their lifetimes!
Two important levels of diversity: been described (collected, analyzed, and
1. Development, growth, maturation, formally discussed in the scientific literature)
There are many species of organisms, and
aging
they are often very different from each Described species in various groups
other -- interspecific variation Arthropods
You are not the same organism > 1,000,000 Vertebrates
Plants invertebrates
2. Within species,
that youeach individual
were 10 yearsis ago
different ~ 52,000
~ 300,000 ~ 1,000,000 insects (not arthropods)
from every other individual -- intraspecific > 350,000 beetles! ~ 150,000 4500 mammals
(or 5 minutes ago)
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)
There are huge differences in form and
function between these species.
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
Examples of intra- and interspecific commonalities:
DNA sequence difference between any two
humans is about 0.1%
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%
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 Phylogeny -- history of species formation
because of lifes evolutionary history:
Often shown as a
present
phylogenetic tree as
descent with modification from shared symbolized here:
common ancestors trunk' is the most
deeply ancestral form

time
We
organize our knowledge of diversity 'branches' are more
recent ancestors
with a hierarchical system based on
green 'leaves'
evolutionary lineages: PHYLOGENY past common ancestor
show existing species
Describes common ancestry, 'dead leaves'
like a geneology or family tree. show extinct lineages.

Phylogeny -- history of species formation Phylogeny -- history of species formation

Branch points ( )
present indicate events that present
formed new lineages
Closely related
(last shared ancestors) (recent shared
Lineages separated
ancestor)
time

time
by few branch points
are more related than Distantly related
lineages separated by (no recent shared
many branch points.
past common ancestor past common ancestor ancestor)
More similarity in closely related species More similarity in closely related species
than in distantly related species -- less time for than in distantly related species -- less time for
evolutionary change from ancestors evolutionary change from ancestors
 Phylogeny -- history of species formation Phylogeny -- history of species formation

present present
time

time
past common ancestor past common ancestor

Rotating the tree does not change its Rotating the tree does not change its
meaning in terms of patterns of relationships meaning in terms of patterns of relationships

Phylogeny -- history of species formation Phylogeny -- history of species formation

common common
ancestor ancestor

past time present time time

past present past present
Rotating any part of the tree also does not
affect meaning IF branch pattern unchanged Phylogenetic trees can be drawn in several ways
Taxonomy is the naming system indicating Taxonomy is the naming system indicating
degrees of relationship degrees of relationship
Many taxonomic levels; the most traditional are: Many taxonomic levels; the most traditional are:
Species Species lupus
Genus (genera) Genus (genera) Canis
Family Family Canids (dogs)
Order Order Carnivores
Class Class Mammals
Phylum (phyla) Phylum (phyla) Chordates
Kingdom Kingdom Animals
Domain Domain Eukaryotic organisms

Species is most restrictive category; domain is the Wolf

most inclusive (3 domains; millions of species).

Taxonomy is the naming system indicating Taxonomy is the naming system indicating
degrees of relationship degrees of relationship
Many taxonomic levels; the most traditional are:
This system of taxonomic
lupus
names is
Species lupus
Genus (genera) Canis somewhat arbitrary, andCanis sometimes does not
Canids (dogs)
Family Canids (dogs) adequately represent evolutionary
Carnivores
history.
Order Carnivores
Class Mammals Mammals
Phylum (phyla) Chordates Generally a more accurate way to show
Chordates
Kingdom Animals relationships is as lineages, or clades,
Animals from a
Domain Eukaryotic organisms Eukaryotic organisms
phylogenetic tree.
A species' scientific name is a binomial: the
combination of genus and species names, e.g: A clade is a lineage grouping than includes an
wolves: Canis lupus
ancestral species and all its descendants.
people: Homo sapiens
Examples of clades Benefits of knowing evolutionary
Canid clade includes
all dogs : domestic relationships
dogs, wolves, coyotes,
foxes, jackals, etc., back
to an ancestral dog Lets us arrange our
Mustelid clade
includes all mustelids:
knowledge in a way that allows
skunks, otters, weasels,
wolverines, etc., back to
accurate predictions about
an ancestral mustelid. unstudied organisms.
Carnivore clade
includes all carnivores:
cats, dogs, weasels, This is important for 3 reasons:
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.
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.
SomeOnly a tiny fraction
examples of modelof discovered
organisms: 3. We will never be able to know
species have coli
Escherichia been carefully studied
(bacterium) everything about organisms
Most
Arabidopsis thaliana
have simply (small
been plant) in terms
described there is too much to know
ofbasic
Chaenorhabditis
morphologyelegans (nematode
(what they worm)
look like). within species, individuals differ from each
Drosophila melanogaster (fruit fly) other and change during their lives
Brachydanio
A few rerio (zebrafish)
have been examined in more detail: organisms are constantly changing (evolving)
Mus musculus
physiology, ecology, (house mouse)
behavior, etc. and going extinct

A very small number of model organisms

Therefore, our understanding of biology
have been intensively studied, and their will always be incomplete.
biology is understood in considerable detail.
But thats OK:

An example: were sure that all organisms*

If we understand evolutionary
history, we dont need complete
knowledge to make useful
generalities and predictions.
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.
Why does evolutionary change occur? First,
a definition:
Evolution = Genetic change in a
population across generations
This has several implications:
Because organisms transfer genetic information
to subsequent generations, their history is a
crucial factor in their current biology.
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 What causes genetic information to change
over generations? Four primary factors: over generations? the
probably Four primary
most factors:
important
mutation: random genetic changes source of
mutation: change,
random because
genetic changes it is
gene flow: immigration of new genes not random.
gene flow: immigration of new genes
(alleles) from other populations (alleles) from other populations
How does selection work?
random genetic drift (especially in small random genetic drift (especially in small
populations) populations)

natural selection 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:
OBSERVATION #3: All organisms have a
potential reproductive rate much higher than
the real reproductive rate.
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).
mice: a single pair could cover the Earth with
their descendants in ~ 6 years (about 30
million descendants in two years!)
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 #1: Variation exists
OBSERVATION #2: Some of it is heritable
OBSERVATION #3: Organisms can reproduce
faster than they do reproduce
INFERENCE #1: Not all young that are born
survive to reproduce; therefore there must be
competition.
much direct evidence showing high
mortality and competition
 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
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

INFERENCE #2: Because of variance in INFERENCE #3: Successful individuals will

phenotype, some individuals are better able to contribute disproportionately to the genes in the
compete (survive and reproduce). next generation.
plenty of evidence showing The next generation will have a higher
differential survival and reproduction. frequency of advantageous genes.

natural selection: 3 observations, 3 inferences: natural selection: a constant endless

loop across generations:
This is a change
OBSERVATION #2:inSome
the of
genetic structure
it is heritable
OBSERVATION #3: Organisms Genetic structure Phenotypic traits of
of the population, which can reproduce
is the
faster than they do reproduce of the population individuals: morphology,
definition of evolution. physiology, behavior
There is much#3:direct
INFERENCE evidence
Successful of this will
individuals
Change in genetic structure Natural selection
happening
contribute all the time. to the genes in the
disproportionately across generations
(= evolution)
Different survival and
The next generation will have a higher
reproduction of individuals
frequency of advantageous genes. 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.
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

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)