So far we have emphasized that life
is an interesting form of chemistry.
This helps understand its role in
transforming the biosphere.
But the most obvious feature of life is the
staggering DIVERSITY of its many forms
We will examine this diversity from
the two main perspectives
1. Evolution
2. Ecology
In order to make sense of this vast diversity,
we look for ways to classify it, to simplify
Looking closer at this diversity, various patterns emerge.
One natural classification scheme is to arrange organisms
into groups that look the same. This is the approach of
traditional __________. This approach leads naturally to a
study of evolution - evolutionary relatedness and organismal
adaptation (form and function).
That is, organisms will look the same for two main reasons – they
are closely related, and/or they express similar functional “designs”
For example, butterflies, birds and bats all fly and they all
look similar because of the wings. But looking closer, there
are big differences too, so they are classified as separate
groups (there are many different kinds within each group)
Another natural classification scheme comes from noticing that
some organisms tend to live together in the same places (and not
in others) – that life is organized into natural “communities” of
diverse organisms. This leads to the study of ________, the
logic of how different organisms interact and coexist.
For example,
major ecosystem
types called
________ (deserts,
rainforests etc.)
have characteristic
organisms and are
found distributed
in different places
on the earth
3-5/3-6
And the
distribution of
_______ is
closely related
to the
distribution of
_________.
12-2
___________ – the classification of life
Both evolution and ecology are important dimensions of the
multidimensional problem of understanding biodiversity.
But before we could think about understanding, a
huge effort had to be expended in collecting and
grouping organisms into logical classes.
All human cultures have developed systems for classifying life
The system used by our culture
was established by Carolus
________ in the 1700s in Sweden.
http://www.ucmp.berkeley.edu/history/linnaeus.html
The _________ System
This system is based on the idea that life is separated into
distinct _________ that can be classified into a nested, or
hierarchical, increasingly inclusive set of groups.
Ultimately, each species is given a distinctive _______ – a
two word name referring to the species and the group to
which it belongs (this is called “binomial nomenclature”)
This is similar to our method of naming
people, family name and individual name
e.g. Jimmy Page
Leopard- Panthera pardus
Genus – Panthera
Species - pardus
Panthera onca (jaguar)
Panthera pardus (leopard)
Panthera tigris (tiger)
Panthera uncia
(snow leopard)
Panthera leo (lion)
http://home.globalcrossing.net/~brendel/index.html
The Linnaean System
Some interesting examples of species names (NY Times Feb 20 2005):
Bittium (mollusk) has a related
genus Ittibittium
Ba humbugi (snail)
Insects:
Heerz tooya
Apopyllus now
Pieza pi, Pieza rhea, Pieza
deresistans
Phthireia relativitae
For more check this out: http://home.earthlink.net/~misaak/taxonomy.html
The Linnaean System
Hierarchical classification is
totally natural for us –
although the “ideal” system
of classification can be
elusive
Music groups
English Rock Bands
Led Zeppelin
Jimmy Page
Dec. 10, 2007
The Linnaean System
The Linnaean system uses a
particular set of levels that has
been modified over time –
genus, family, order, etc.
The Tree of Life
The Linnaean system was developed before ideas about
evolution and the relatedness of all life, yet it is consistent with
that view (and inspired it) and has remained in wide use
The evolutionary view adds an historical component – that
the species we see today derive by a process of __________
(separation of one species into two over time), creating a
“family tree” of ancestral and descendant species
These relationships are usually
depicted as a branching tree, or
_________ (or “phylogenetic tree”)
The Y-axis is time – down is
longer into the past, ________
implies speciation events
The Tree of Life
The hierarchical
branch “clusters”
correspond to the
taxonomic levels
This is a “rough”
correspondence but
overall traditional
taxonomy _____ been
an excellent guide to
modern phylogenetic
reconstruction
The Tree of Life
_____________ – determining these trees for taxonomic
groups is a very active area of research. The ultimate
goal is to construct the complete family tree of life, and to
make this the basis of our taxonomic system.
You can find out the current status of this effort at
http://tolweb.org/tree/phylogeny.html
The basic idea of this approach is to classify
species by their various characteristics, or
traits, and to identify which traits are newer and which
older. Traits that are relatively older are called ________,
more recently evolved are called __________.
The Tree of Life
This style of reasoning
is ________________
traditional taxonomy
The Tree of Life
The current explosion in tree of life research has been fueled
by our new knowledge about _________________________.
This is essentially an entirely
new and extremely precise array
of species traits from which
detailed phylogenies can be
constructed – independently of
traditional observable traits.
This independence creates a welcome check on traditional
taxonomy. So far it has mostly _________the traditional approach,
but in some cases has provided interesting new insights.
The Tree of Life
For example, traditionally reptiles and birds are
separated into different classes: Reptilia and Aves
But the genetic evidence suggests that crocodiles,
traditionally considered reptiles, are really closer to
birds than to other reptiles.
Reptilia
Aves
Naturally, there is a lot of discussion about how to sort this out
What would you suggest?
The Tree of Life
Here are some of the contenders – is your solution here?
http://www.eidnesfurs.com/index.html
How can a gene sequence be used to create a phylogenetic tree?
What is a gene sequence?
Recall: Gene expression is the protein
production machinery of a cell’s
biochemistry. Proteins are used in
various ways, but especially in the form
of enzymes, that catalyze reactions – they
regulate what reactions happen when –
that is, they control everything.
What is a protein?
- a long chain molecule, or polymer, a chain of small organic
molecules _____________ (20 different types), that when
assembled, folds itself into a 3-dimensional shape that can
catalyze a reaction.
The final protein structure is determined by the
___________ of amino acids in the protein polymer.
What controls the amino acid sequence of a protein?
The _____ molecule is
also a long chain of
simpler organic molecules
(“nucleic acids”) that
contains the protein
sequence in coded form,
using the ___________
This molecule can be copied,
keeping the sequence intact
The genetic code is not a simple one-for-one code because there are
only four different nucleic acids (A,T,G,C) to code for 20 amino acids.
It is a “triplet code” – every three nucleic acids code
for each subsequent amino acid
DNA sequence
becomes a ______
sequence
There is an
intermediate
step involving
an___sequence
The genetic code
As far as we know,
the code is pretty
_______ – could
have been different
and still work fine
Yet, ________ use the
same genetic code,
supporting idea of a
common origin of all
life
The DNA stores the sequence information for all the proteins
needed by the organism
A “gene” is a particular DNA
sequence that codes for a
particular protein
“____________” is this
conversion – protein production.
Which genes are “turned on” when
Gene expression is responsive to the
____________ (internal and external)
Since enzymes regulate
biochemistry, including gene
expression, the regulation of gene
expression is the ultimate controller
Genes are the third key ingredient, or
resource, in the recipe for life –__________
1. Energy
2. Materials
3. __________
Information encoded in the sequences of
DNA can be thought of as a kind of
knowledge, often referred to as a library
This information has accumulated over the billions of years
of life’s history on earth. It is reasonable to think of it as a
natural resource, built into the structure of living organisms.
The differences between organisms
are due to differences in their ____
Each species carries
genes that are unique
to that species
DNA sequences can be used to create phylogenies
by assuming that the more _________ the gene
sequences, the more closely related the species are
What is the logic behind this assumption?
Reptilia
Aves
1. All life arose from a single common ancestor
2. Organisms differ primarily in their ______
3. Given 1 & 2, the current diversity must have resulted
from a ___________ of the genetic makeup of organisms.
4. The diversification was one step at a time –
biochemistry is too complicated to change radically
5. The more______has elapsed since lineages
diverged, the more steps have been taken
Interestingly, these assumptions don’t require any specific
knowledge about gene function – it even applies to genes
that have no known function (silent or “junk” DNA)
Some genes have changed very little, and can help
compare very distant relatives (here a segment of rRNA)
Human
...GCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTT...
Yeast
...GCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTT...
Corn
...GCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTT...
Escherichia coli
...GCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGT...
Methanococcus sp. ...GCGGTAATACCGACGGCCCGAGTGGTAGCCACTCTTATTGGGCCT...
Some regions change very fast – what would they reveal?
http://www.bact.wisc.edu/Bact303/Phylogeny
This work has led to
a detailed “big
picture” view of the
tree of life, including
the establishment of
the “Three _______”
concept
Also, much fine detailed
study of evolutionary
changes within-species
The diversity problem: Why is there more than one species?
Diversification requires two aspects
1. Speciation – division of one lineage into two
2. Differentiation of the two lineages (change in
one or both)
If this happens over and over,
you get a lot of species –
speciation itself has a kind of
exponential capacity
Part 2
Speciation
A species generally exists in multiple subgroups
distributed in space, each called a ___________
The populations will tend to stay similar if individuals can
move between them (called __________) and reproduce.
Conversely, they will have the
capacity to diverge genetically if there
is no gene flow, if they are
____________________
What kind of factors might cause reproductive isolation?
Factors that increase reproductive isolation
1. Physical separation
2. Ecological separation
3. Reproductive incompatibility, asexuality
_________ speciation - populations become separated
geographically (#1 - e.g. a river or mountain range), then
diverge. This is considered likely the most important form
of speciation.
_________ speciation – populations in the same range but
ecologically (#2) or reproductively (#3) separated diverge.
An example of a probable __________ speciation
3-4/3-3
Note that a key component of this is the
change in one or both of the separated
populations – evolution.
Evolution is defined as change in genes in a population over time.
Adaptive evolution refers to changes that increase organism
success, and is of central interest in understanding diversity
There are many genes in an organism, even more in a
population (since individuals are different) – ________
The total number of different genes in a population is
called the _______________
Causes of evolution are of 2 basic types
increase variation – “creative”
decrease variation – “restrictive”
Both are required for adaptive evolution
Creating variability – adding new genes
1. _________– change in DNA sequence
2. Duplication, deletion – change in number
3. Introgression, conversion
Restricting variability – eliminating genes
1. Random fluctuations, losses (“drift”)
2. Natural selection
_________ - Darwin proposed that in a
given environment, types that were most
suited would survive better and reproduce
more – this would tend to create adaptation
by eliminating less fit types.
While mutation and other processes
create variation – it is generally a result
of ______________, “undirected”
change
Natural selection continually works to
to improve the “______” by favoring the
most effective variants
Unfinished sculpture by Michelangelo
for the tomb of Pope Guilio II
I saw the angel in the marble and I
carved until I set him free.
Michelangelo
Michelangelo's Pieta was carved in 1499,
when the sculptor was 24 years old.
For this to work, differences in ________of individuals
must be due to differences in genes
The genes of an individual are called the genotype, and the
organism with all its traits is called the __________
Adaptation is achieved by phenotypes, but
for this to result in adaptive evolution, the
phenotypes must reflect the genotypes.
The differences must be passed on to the
offspring – called ______________
Natural selection is a powerful process that can
cause adaptive evolution by favoring a subset
of the existing heritable variation.
The more the marbles wastes, the more the statue grows.
Michelangelo
Darwin compared this
to “_______selection”
Science 22 November 2002:
Vol. 298. no. 5598, pp. 1610 - 1613
Genetic Evidence for an East Asian Origin of Domestic Dogs
1*
2
2
1
3
Peter Savolainen, Ya-ping Zhang, Jing Luo, Joakim Lundeberg, Thomas Leitner
The origin of the domestic dog from wolves has been established, but the number of
founding events, as well as where and when these occurred, is not known. To address these
questions, we examined the mitochondrial DNA (mtDNA) sequence variation among
654 domestic dogs representing all major dog populations worldwide. Although our data
indicate several maternal origins from wolf, >95% of all sequences belonged to three
phylogenetic groups universally represented at similar frequencies, suggesting a
common origin from a single gene pool for all dog populations. A larger genetic
variation in East Asia than in other regions and the pattern of phylogeographic variation
suggest an East Asian origin for the domestic dog, ~15,000 years ago.
Many examples exist of
natural populations
responding to selection
without controlled breeding
For example, evolution of
_____________________
So the basic idea that diversification can result
from speciation and adaptive divergent evolution
is plausible and consistent with observation
The question of what species are adapting to is an
ecological question we’ll take up shortly
Before that, we will look at a few features of
organisms reflect uniquely “Darwinian” features
And also survey the results of this diversification