AP BIO REVIEW: 4-24-03

Cladistics, Taxonomy, Plants, Photosynthesis

Implications of Cladistics

Understanding Branching Diagrams

The output from a phylogenetic analysis is a hypothesis of relationship of different taxa. This hypothesis can be represented as a cladogram, a branching diagram. Cladograms* bear a lot in common with the notion of family trees. In a family tree we trace back our ancestry. For example, in the family tree on the top right, the ancestors of all the rest of the family are the initial black dot and yellow square. These ancestors give rise to three children, one of which mates and has two children. We can all trace our lineages back to one set of ancestors.

All species have ancestors* too. So, for example, sometime in the past an ancestral species (father) of Homo sapiens walked the earth. This ancestor went extinct (died), but left descendent species (children). In family trees, we can talk coherently about real ancestors. In biology, the ancestors are often gone sometimes without a trace. All we have left are the children. Reading cladograms is much like reading a family tree. Both are rich in information. Cladograms, like family trees, tell the pattern of ancestry and descent. Unlike family trees, ancestors in cladistics ideally give rise to only two descendent species. Also unlike family trees, new species form from splitting of old species. In speciation, it does not take two to tango. The formation of the two descendent species is called a splitting event. The ancestor is usually assumed to "die" after the splitting event.

In the first tree, labelled Cladogram A, notice the green dots. Each dot has a letter associated with it. The dots with letters are the nodes of the tree. The stems of the tree end with the taxa under consideration, represented by boxes. At each node a splitting event occurs. The node therefore represents the end of the ancestral taxon and the stems the species that split from the ancestor. The two taxa that split from the node are called sister taxa*. They are called sister taxa because they are like the siblings from the parent or ancestor. The sister taxa must each be more closely related to one another than to any other group because they share a close common ancestor. In the same way, you are most closely related to your siblings than to anyone else since you share common parents. Lets focus on Node C in Cladogram A. At the node, the ancestor goes extinct but leaves two siblings hypothesized to be humans and gorillas. Humans and gorillas are sister taxa and are more closely related to one another than either is to chimpanzees or baboons.

Working down the tree we come to node B. At this node the ancestor of the humans and gorillas split from the chimpanzees. Therefore the chimpanzees sister taxon is the human/gorilla ancestor. A sister taxon can be an ancestor and all its descedents. We call an ancestor plus all its descendents a clade. A cladogram shows us hypothesized clades*.

Finally we come to node A. Here, we find the splitting event that led to the baboons and the ancestor to the chimpanzees, humans and gorillas. By working our way down the cladogram we have learned the pattern of splitting. We have found out that chimpazees, humans and gorillas are more closely related to each other than to baboons. In this example, baboons are the outgroup*.

Now, how in the world did we manufacture Cladogram A? We mentioned that it was a hypothesis. What if it we chose another hypothesis like Cladogram B or Cladogram C? We would change the pattern of speciation events. In Cladogram B, humans and chimpanzees are sister taxa and in Cladogram C, chimps and gorillas are sister taxa.

Which of the three cladograms presented above is correct? None of the cladograms can be proved correct, but Cladogram B is the best supported of the three based on character data and is therefore hypothesized to best reflect the true branching pattern.

Manufacturing cladograms which show hypotheses of ancestry and descent requires that we analyze characters and find those characters that unite clades.

Continue your journey by selecting one of the topics below.

Taxonomy

Taxonomy: System of classification based upon similarities in structure.

Developed by: Linnaeus , a Swedish botanist in the 18th century. Linneaus used Latin names because they would not change over time.

Binomial Names     Genus + species   Ex: Musca + domestica "House Fly"The 5 Kingdoms: REALLY  6 NOW!!!

 

Name

Structure

Prokaryotic/
Eukaryotic

Monera (BACTERIA)

Unicellular

Prokaryotic

Protista (AMEBA)

Unicellular

Eukaryotic

Fungi

Multicellular

Eukaryotic

Heterotrophic....Ex:Mushrooms

Plants Autotrophic

Multicellular

Eukaryotic

Many Plants Perform Photosynthesis Within The Chloroplasts

Animals Heterotrophic

Multicellular

Eukaryotic

Heterotrophic
can be carnivorous, herbivorous or omnivorous.

# 6 ARCHAEBACTERIA   EX: Cyanobacteria

Unicellular 

Photosynthetic prokayotes

         

 


Archaea

Index to this page

These organisms are microscopic prokaryotes. When the first ones were discovered (in 1977), they were considered bacteria. However, when their ribosomal RNA was sequenced, it became obvious that they bore no close relationship to the bacteria and were, in fact, more closely related to the eukaryotes (including ourselves!) For a time they were referred to as archaebacteria, but now to emphasize their distinctness, we call them Archaea.

They have also been called Extremophiles in recognition of the extreme environments in which they have been found:

Most of the >250 named species that have been discovered so far have been placed in two groups:

Euryarchaeota

There are three main groups:

1. Methanogens

These are found living in such anaerobic environments as

They are autotrophic; using hydrogen as a source of electrons for reducing carbon dioxide to food and giving off methane ("marsh gas", CH4) as a byproduct.

4H2 + CO2 -> CH4 + 2H2O

Two methanogens have had their complete genomes sequenced:

[View the data]

2. Halophiles

These are found in extremely saline environments such as the Great Salt Lake in the U.S. and the Dead Sea. They maintain osmotic balance with their surroundings by building up the solute concentration within their cells.

3. Thermoacidophiles

As their name suggests, these like it hot and acid (but not as hot some of the Crenarchaeota!). They are found in such places as acidic sulfur springs (e.g., in Yellowstone National Park) and undersea vents ("smokers").

Crenarchaeota

The first members of this group to be discovered like it really hot and so are called hyperthermophiles. One, Pyrolobus fumaris, lives at 113°C (the boiling point of water at sea level is 100°C).

Many like it acid as well as hot and live in acidic sulfur springs at a pH as low as 1 (the equivalent of dilute sulfuric acid). These use hydrogen as a source of electrons to reduce sulfur in order to get the energy they need to synthesize their food (from CO2).

One member of the group, Aeropyrum pernix, has had its genome completely sequenced.

Other members of this group seem to make up a large portion of the plankton in cool, marine waters. As yet, none of these has been isolated and cultivated in the laboratory.

Evolutionary Position of the Archaea  http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Archaea.html

 

The archaea have a curious mix of traits characteristic of

The table summarizes some of them.

Eukaryotic Traits

Bacterial Traits

  • single, circular chromosome
  • operons
  • no introns
  • bacterial-type membrane transport channels
  • Many metabolic processes
    • energy production
    • nitrogen-fixation
    • polysaccharide synthesis

What can we conclude from this collection of traits?

occurred after their line had diverged from the archaea.

The Origin of Life?

Their

have suggested that the archaea may be the little-changed descendants of the first forms of life on earth.

Economic Importance of the Archaea

Because they have enzymes that can function at high temperatures, considerable effort is being made to exploit the archaea for commercial processes such as providing

Archaea may also be enlisted to aid in cleaning up contaminated sites, e.g., petroleum spills.

Welcome&Next Search

17 May 2002

 

 

 

 

 

http://www.guilford.k12.ct.us/~faitschb/evolrev.html

 

Evolution review:

natural selection - facts and assumptions
darwins missing evidence
Galapagos Is. significance
source of new genes in a population
signs of evolution (evidence)
fossils
homologous structures
analogous structures
hardy weinberg theory and conditions
h-w problems
gene frequency
types of selection:

diversifying

stabilizing

directional
radiant adaptation
isolation
sympatric and allopatric speciation
punctuated equilibrium vs gradualism
Lamarck's erroneous theory
genetic drift

bottleneck effect

founder effect
species definition
gene pool
heterozygotes (hybrids)
rev. 1/9/2002

Taxonomy: Classifying Life

 

 

At least 1.7 million species of living organisms have been discovered, and the list grows longer every year (especially of insects in the tropical rain forest). How are they to be classified?

Ideally, classification should be based on homology; that is, shared characteristics that have been inherited from a common ancestor. The more recently two species have shared a common ancestor,

Until recent decades, the study of homologies was limited to

However, since the birth of molecular biology, homologies can now also be studied at the level of

Anatomical homology: an example

The figure shows the bones in the forelimbs of three mammals: human, whale, and bat (obviously not drawn to the same scale!). Although used for such different functions as throwing, swimming, and flying, the same basic structural plan is evident in them all. In each case, the bone shown in color is the radius.

Body parts are considered homologous if they have

It seems unlikely that a single pattern of bones represents the best possible structure to accomplish the functions to which these forelimbs are put. However, if we interpret the persistence of the basic pattern as evidence of inheritance from a common ancestor, we see that the various modifications are adaptations of the plan to the special needs of the organism. It tells us that evolution is opportunistic, working with materials that have been handed down by inheritance.

Embryonic Development

The embryonic development of all vertebrates shows remarkable similarities as you can see from these drawings (supplied by Open Court Publishing Company). The drawings in the top row are of the embryonic stage called the pharyngula. At this stage ("I") they all contain a:

The branchial grooves are matched on the inside by a series of paired gill pouches. In fishes, the pouches and grooves eventually meet and form the gill slits, which allow water to pass from the pharynx over the gills and out the body.

In the other vertebrates shown here, the grooves and pouches disappear. In humans, the chief trace of their existence is the eustachian tube and auditory canal which (interrupted only by the eardrum) connect the pharynx with the outside of the head.

Recapitulation

The idea that embryonic development repeats that of one's ancestors is called recapitulation. It is often expressed as "ontogeny recapitulates phylogeny"; that is, embryonic development (ontogeny) repeats phylogeny (the genealogy of the species).

This is a distortion of the truth. It implies, for example, that early in our embryonic development we go through a fishlike stage. We do not. Rather, we pass through some (not all) of the embryonic stages that our ancestors passed through. Therefore, we find that the more distantly related two vertebrates are, the shorter the period during which they pass through similar embryonic stages (fish and human) and vice versa (fish and salamander).

We should also keep in mind that embryonic development prior to the pharyngula (stage I) may also be very different in the different groups. For example, while the pharyngulas of the human and the salamander look quite similar, their earlier development, starting with their fertilized eggs, are very different [illustration].

The idea that "ontogeny recapitulates phylogeny" was proposed over a century ago by the biologist Ernst Haeckel. He also made the drawings on which the drawings above are based. Periodically, people rediscover that in making them, he altered certain details to emphasize his theory. Though they are schematic, the story they illustrate here has stood the test of time.

Protein Sequences

Protein sequencing provides a tool for establishing homologies from which genealogies can be constructed and phylogenetic trees drawn.

Here are two examples.

Hemoglobins

Human beta chain

0

Gorilla

1

Gibbon

2

Rhesus monkey

8

Dog

15

Horse, cow

25

Mouse

27

Gray kangaroo

38

Chicken

45

Frog

67

Lamprey

125

Sea slug (a mollusk)

127

Soybean (leghemoglobin)

124

An example of molecular homology.

The numbers represent the number of amino acid differences between the beta chain of humans and the hemoglobins of the other species. In general, the number is inversely proportional to the closeness of kinship.

All the values listed are for the beta chain except for the last three, in which the distinction between alpha and beta chains does not occur.

The human beta chain contains 146 amino acid residues, as do most of the others.


Cytochrome c

Cytochrome c is part of the respiratory chain down which electrons are passed to oxygen during cellular respiration. [Discussion]

Cytochrome c is found in the mitochondria of every aerobic eukaryote - animal, plant, and protist. The amino acid sequences of many of these have been determined, and comparing them shows that they are related.

Human cytochrome c contains 104 amino acids, and 37 of these have been found at equivalent positions in every cytochrome c that has been sequenced. We assume that each of these molecules has descended from a precursor cytochrome in a primitive microbe that existed over 2 billion years ago. In other words, these molecules are homologous.

The first step in comparing cytochrome c sequences is to align them to find the maximum number of positions that have the same amino acid. Sometimes gaps are introduced to maximize the number of identities in the alignment (none was needed in this table). Gaps correct for insertions and deletions that occurred during the evolution of the molecule.

This table shows the N-terminal 22 amino acid residues of human cytochrome c with the corresponding sequences from six other organisms aligned beneath. A dash indicates that the amino acid is the same one found at that position in the human molecule. All the vertebrate cytochromes (the first four) start with glycine (Gly). The Drosophila, wheat, and yeast cytochromes have several amino acids that precede the sequence shown here (indicated by <<<). In every case, the heme group of the cytochrome is attached to Cys-14. and Cys-17 (human numbering). In addition to the two Cys residues, Gly-1, Gly-6, Phe-10, and His-18 are found at the equivalent positions in every cytochrome c that has been sequenced.

Molecular homology of cytochrome c

 

 

1

 

 

 

 

6

 

 

 

10

 

 

 

14

 

 

17

18

 

20

 

 

Human

 

Gly

Asp

Val

Glu

Lys

Gly

Lys

Lys

Ile

Phe

Ile

Met

Lys

Cys

Ser

Gln

Cys

His

Thr

Val

Glu

Lys

Pig

 

-

-

-

-

-

-

-

-

-

-

Val

Gln

-

-

Ala

-

-

-

-

-

-

-

Chicken

 

-

-

Ile

-

-

-

-

-

-

-

Val

Gln

-

-

-

-

-

-

-

-

-

-

Dogfish

 

-

-

-

-

-

-

-

-

Val

-

Val

Gln

-

-

Ala

-

-

-

-

-

-

Asn

Drosophila

<<<

-

-

-

-

-

-

-

-

Leu

 

Val

Gln

Arg

 

Ala

-

-

-

-

-

-

Ala

Wheat

<<<

-

Asn

Pro

Asp

Ala

-

Ala

-

-

-

Lys

Thr

-

-

Ala

-

-

-

-

-

Asp

Ala

Yeast

<<<

-

Ser

Ala

Lys