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. Evolution2. Ecology

Looking closer at this diversity, various patterns emerge.

In order to make sense of this vast diversity, we look for ways to classify it, to simplify

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 organismaladaptation (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 notin 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

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.

___________ – the classification of life

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 pardusGenus – PantheraSpecies - pardus

Panthera tigris (tiger)

Panthera leo (lion)

Panthera pardus (leopard)

Panthera onca (jaguar)

http://home.globalcrossing.net/~brendel/index.html

Panthera uncia(snow leopard)

Some interesting examples of species names (NY Times Feb 20 2005):

Bittium (mollusk) has a related genus IttibittiumBa humbugi (snail)Insects:Heerz tooyaApopyllus nowPieza pi, Pieza rhea, Pieza

deresistansPhthireia relativitae

For more check this out: http://home.earthlink.net/~misaak/taxonomy.html

The Linnaean System

Jimmy Page

Led Zeppelin

English Rock Bands

Music groupsHierarchical classification is totally natural for us –although the “ideal” system of classification can be elusive

The Linnaean System

Dec. 10, 2007

The Linnaean system uses a particular set of levels that has been modified over time –genus, family, order, etc.

The Linnaean System

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 hierarchical branch “clusters”correspond to the taxonomic levels

This is a “rough”correspondence but overall traditional taxonomy _____ been an excellent guide to modern phylogeneticreconstruction

The Tree of Life

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 classifyspecies 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.

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 outWhat would you suggest?

The Tree of Life

Here are some of the contenders – is your solution here?

The Tree of Life

http://www.eidnesfurs.com/index.html

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.

How can a gene sequence be used to create a phylogenetic tree?

- 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.

What is a protein?

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 ___________

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.

This molecule can be copied, keeping the sequence intact

DNA sequence becomes a ______ sequence

There is an intermediate step involving an___sequence

It is a “triplet code” – every three nucleic acids code for each subsequent amino acid

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

“____________” is this conversion – protein production. Which genes are “turned on” when

Since enzymes regulate biochemistry, including gene expression, the regulation of gene expression is the ultimate controller

Gene expression is responsive to the ____________ (internal and external)

A “gene” is a particular DNA sequence that codes for a particular protein

Genes are the third key ingredient, or resource, in the recipe for life –__________

1. Energy2. Materials3. __________

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

3. Given 1 & 2, the current diversity must have resulted from a ___________ of the genetic makeup of organisms.

1. All life arose from a single common ancestor

2. Organisms differ primarily in their ______

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)

Human ...GCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTT...

Yeast ...GCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTT...

Corn ...GCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTT...

Escherichia coli ...GCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGT...

Methanococcus sp. ...GCGGTAATACCGACGGCCCGAGTGGTAGCCACTCTTATTGGGCCT...

Some genes have changed very little, and can help compare very distant relatives (here a segment of rRNA)

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

Diversification requires two aspects1. Speciation – division of one lineage into two2. 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

The diversity problem: Why is there more than one species?

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?

1. Physical separation

Factors that increase reproductive isolation

2. Ecological separation3. 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.

3-4/3-3

An example of a probable __________ speciation

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.

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 typesincrease variation – “creative”decrease variation – “restrictive”

Both are required for adaptive evolution

Adaptive evolution refers to changes that increase organism success, and is of central interest in understanding diversity

Creating variability – adding new genes1. _________– change in DNA sequence2. Duplication, deletion – change in number3. Introgression, conversion

Restricting variability – eliminating genes1. 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 adaptationby eliminating less fit types.

Unfinished sculpture by Michelangelo for the tomb of Pope Guilio II

While mutation and other processes create variation – it is generally a result of ______________, “undirected”change

Michelangelo's Pieta was carved in 1499, when the sculptor was 24 years old.

I saw the angel in the marble and I carved until I set him free. Michelangelo

Natural selection continually works to to improve the “______” by favoring the most effective variants

The genes of an individual are called the genotype, and the organism with all its traits is called the __________

For this to work, differences in ________of individuals must be due to differences in genes

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 - 1613Genetic Evidence for an East Asian Origin of Domestic Dogs Peter Savolainen,1* Ya-ping Zhang,2 Jing Luo,2 Joakim Lundeberg,1 Thomas Leitner3

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 geneticvariation 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 shortlyBefore that, we will look at a few features of organisms reflect uniquely “Darwinian” features

And also survey the results of this diversification