csfcbiology.wikispaces.compage+2new.docx · Web viewThere's a fish named after Frank Zappa, a crustacean genus named for Godzilla, and a fly called Dicrotendipes thanatogratus after

2.1 Biodiversity and Evolution

Classification – Page 2

Completed1. Watch the ‘Brainpop’ video on ‘What’s in a name?’

2. Read 1. ‘Why we classify living things’ and answer the following:a. What is a taxon?b. Distinguish between the terms classification and

taxonomy.c. Which scientist developed the binomial naming system?d. Describe the essential features of this system.e. Why was a universal system of naming organisms

adopted?f. Give a general definition for a species.

3. Read 2. ‘What features are used in classification?’ Watch the pbs video Using DNA as evidence of evolution.a. Natural classification is based on homology. Explain the

words in bold.b. Complete the question looking at the amino acid sequence

similarity of haemoglobin in different organisms.c. Distinguish between the terms divergent (adaptive radiation

is an example of this) and convergent evolution.d. Complete the questions on the fish and convergent

evolution.

1. WHY WE CLASSIFY LIVING THINGS.

Classification is essential to biology because there are too many different living things to sort out and compare unless they are managed into manageable categories. The scheme of classification has to be flexible, enabling newly discovered organisms to be added to the scheme where they best fit. It should also be able to accommodate fossil organisms as they are discovered, since Biologists believe that living and extinct species are related.The process of classification involves:

Classification is the grouping together of organisms based on shared characteristics. The type of classification most often employed groups organisms according to evolutionary relationships (called natural or phylogenetic classification) i.e. all the organisms in a group show a range of similarities because of a shared ancestry. Classification is hierarchical and thus as the groups get smaller the members become more closely related.

Giving every organism an agreed name Arrangement of organisms into groupings of apparently related organisms.

TAXONOMY

Taxonomists study the differences and similarities between organisms in order to place them into different groups, called taxa (sing. taxon). They also study and discuss which features should be taken into account. Organisms that share similar features are grouped together whereas organisms that are different will be placed into different groups. The whole of the living world is today organised into a hierarchy of ranked groups, which reflects evolutionary closeness between organisms. The science of classification is called ‘taxonomy’.

The basic unit of biological classification is the species. A species is a group of organisms, which have numerous features in common and are capable of interbreeding and producing viable offspring.

The binomial system of naming

The system of naming organisms using two names is called binomial nomenclature. ‘Bi’ means two; ‘nomial’ meaning name and ‘nomenclature’ refers to a system used to name things. The first name (a noun) in the binomial nomenclature system is always capitalized and it refers to the genus; the second name (an adjective) always begins with a small letter and refers to the species. Both are always written in italics when typed or underlined when written by hand. Most words used in binomial nomenclature are Latin or Greek in origin.

Closely related organisms have the same generic name (belong to the same genus); only their species name differs.

generic name + specific name(noun) (adjective)

Water buttercup = Ranunculus aqauticusCreeping buttercup = Ranunclulus repens

The system of naming organisms was consolidated and popularized by the Swedish naturalist Carolus Linnaeus. In his book Systema Naturae (The Natural World, 1735) he listed and explained the binomial system of nomenclature for species, which had been brought to him from all over the world.

One clear advantage of the binomial nomenclature system is that scientists from all over the world working in any language can share data about a species and be sure that they are conversing about the same organism. Globally we speak a range of different languages and we will have a multitude of different names for an organism. Even when we speak the language we may have regional differences in the names we give to organisms.

What’s in a name? (reading for fun!!)By Richard Conniff

In the 1750s, the Swedish botanist Carolus Linnaeus devised a system for naming species, and zoologists have been fooling around with it ever since. There's a beetle named Agra vation and a spider named Draculoides bramstokeri. There's a fish named after Frank Zappa, a crustacean genus named for Godzilla, and a fly called Dicrotendipes thanatogratus after the Grateful Dead.

At least one entomologist named a genus of bugs after his mistress. A well-known American entomologist, who was also a bigamist, named a couple of species for his two wives. Having scientific colleagues name a new species after you can be an honor or an insult, however unintended. The genus name Dyaria was coined by an amateur lepidopterist who thought he was honoring a colleague named Dyar.

The potential for bizarre and jokey nomenclature is almost unlimited. A Smithsonian researcher estimates that there are 30 million species on earth, almost all of them insects in need of names.

What features are used in classification?The quickest way to classify organisms would be to do so according to obvious visual similarities. For example birds and insects could be classified together because they have wings. However, upon closer inspection it can be seen that classifying these together is superficial as they are built from different tissues and have different origins in terms of their development. Structures that have similar functions but differ in their basic structure are called analogous structures. A classification based on analogous structures would be referred to as an artificial classification.

Conversely a natural classification system is based on homologous structures, these are structures that are thought to reflect evolutionary relationships. A classification based upon evolutionary relationships is called phylogenetic.

Analogous structures Homologous structuresResemble each other in function Are similar in position and development

but not necessarily functionDiffer in their structure Are similar in basic structureIllustrate only superficial similarities Similar due to common ancestry

e.g. the wings of birds and insects e.g. the limbs of vertebrates, which appear to be modifications of an ancestral five-fingered pentadactyl limb

The system of naming organisms was consolidated and popularized by the Swedish naturalist Carolus Linnaeus. In his book Systema Naturae (The Natural World, 1735) he listed and explained the binomial system of nomenclature for species, which had been brought to him from all over the world.

Today similarities and difference in the biochemistry of organisms, as well as structural features have become important in taxonomy. The composition of nucleic acids and cell proteins indicates a degree of relatedness between organisms, arguably more precisely than structural features. Organisms, which have a closer evolutionary relationship, show fewer differences in the composition of specific nucleic acids and cell proteins that they possess.

DNA and protein analysis can reduce the mistakes made due to convergent evolution (the tendency of unrelated organisms to acquire similar structures).

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,the more homologies they share, andthe more similar these homologies are.

Until recent decades, the study of homologies was limited toanatomical structures (comparative anatomy e.g. pentadactyl limb)pattern of embryonic development.

With advances in molecular biology studies of DNA, proteins and immunological responses can be used to give evidence for classifying organisms. Biochemical methods have helped to prevent mistakes in classification, which have been made due to morphological convergence.

What is convergence?

Protein Sequencing

Sequencing the amino acids within shared protein and looking for differences can provide evidence for how closely organisms are related to a common ancestor.

Two examples of proteins that have been extensively studied include haemoglobin and cytochrome c (a protein that forms part of the electron transport chain in mitochondria that electrons are passed down during aerobic respiration.

Why might cytochrome C prove to be amore useful protein to compare than haemoglobin?

The β chain of haemoglobin, which is built from 146 amino acids, shows variation in the sequence of amino acids in different species that share this molecule. The longer it is since two different species diverged from a common ancestor, the more likely it is that differences will have arisen.

Table 1 summarises the similarities and differences in haemoglobin between 8 species

The top number in each cell is the number of positions on the molecule where the two species have identical amino acids. The lower number is the % of positions with identical amino acids.Complete the table (look at the information on the next 2 pages) by filling in the blank cells. First, count the number of positions where the two species have identical amino acids. Second, calculate the % similarity using the formula below:

% Similarity = 100 X number of identical positions / 147Compare your calculations with you peers. Why do you think that computers are almost always used to construct these comparison tables?

Comparing Proteins Using Immunological Techniques

Explain this technique:

This example below is given in your textbook when comparing human proteins.

DNA base sequences

Over time DNA changes due to errors in copying (mutations). If the error occurs in a sex cell it could be passed onto the next generation. Often these mutations make no difference to the observable characteristics of a species but they can cause the species to very slowly change due to the action of natural selection.The DNA changes gradually over thousands of years and we can use computers to compare the base sequences of DNA in different organisms. The more differences we find the more it is suggested that the organisms are not so closely related and the longer it is since they had a common ancestor.

By studying the sequence of bases we can see where single differences in the code have occurred and how they have been passed on through evolution.

Comparison of DNA base sequences is used to elucidate relationships between organisms.

Traditional taxonomic methods such as comparative anatomy (bones, teeth etc.) placed humans on a separate evolutionary branch and grouped all the other apes together in one family (Pongidae).

However, evidence from studying DNA shows that humans are more closely related to chimpanzees and gorillas than to orangutans. And that chimpanzees (and Bonobo) are closer in terms of an evolutionary ancestor than gorillas.

DNA Hybridisation

DNA sequencing is expensive and time consuming and only small length of DNA can be studied and compared in detail. Another method called DNA hybridisation compares whole DNA molecules from different species.

The double helix structure of DNA is held together by hydrogen bonds that form between the complimentary base pairs.

In DNA hybridisation a hybrid DNA molecule is made from one strand of DNA from one species joined to another DNA strand from another species. Where the bases line up to form pairs, hydrogen bonds will form. So the more the strands match, the more bonds will have formed.

The general rule is that the closer two species are the greater the number of hydrogen bonds formed, so the more strongly the 2 strands are held together.

If we heat single species DNA it will need to be heated to about 70-80 degrees Celsius before enough energy is provided to break the bonds.

In hybrid DNA less energy is needed to separate the strands because there are fewer hydrogen bonds. (Around 1 degree lower for every 1% difference in bases)

The table below shows data obtained from a study of the DNA of humans, chimpanzees, gorillas and orangutans.

1. Which species DNA is most similar to human DNA?

2. If human DNA split at 94 degrees what temperature would you expect the human/gorilla hybrid stand to split at?

Species from which hybrid was produced Difference between the temperature at which human DNA strands separated and hybrid DNA strands

separated

Human: Chimpanzee 1.6

Human: Gorilla 2.3

Human: Orangutan 3.6

DNA genetic fingerprinting (DNA profiling)

This technique can also be used to look for evolutionary relationships between organisms.

Outline of the technique:

DNA is cut using a restriction enzyme.(Restriction enzymes cut at specific recognition sites)

This will cut DNA into different length fragments.(Fragment lengths may vary as different organisms may have evolved different VNTR {variable number tandem repeats}

The fragments will be different sizes and the fragments can be separated according to their size using a technique called gel electrophoresis.

Banding patterns then can then be compared. The more banding patterns that are shared the closer the organisms probably are in terms of their common evolutionary ancestor.

PHYLOGENY

Phylogenists study how closely different species are related and build evolutionary trees to show those relations. The more closely two species are related, the closer they appear together on the evolutionary tree.

Who is the thrush more closely related to? Explain your answer

Summary:

Classification :

Grouping organisms based on their evolutionary relationships

Taxonomy – branch of Biology concerned with naming and classifying life forms

Looks at:

physical features

biochemical features (DNA ‘genetic fingerprinting’ and enzyme studies)

Is dynamic and changes

with expanding knowledge about organisms

with differences of opinion about whether morphology or genetics are more central for the basis of classification

Ways:

Binomial Nomenclature - Two part name (Genus & species names in italics or underlines if written) ex: Panthera tigris

Hierarchical Classification –ranks groups in ascending order from large to small groups - Seven Taxonomic Categories (Kingdom, Phylum, Class, Order Family, Genus, Species)

Phylogenetic - study of the evolutionary relationship between organisms -usually uses a phylogenetic tree diagram with the oldest species at the base and more recent ones on the branches

Ex: simple phylogenetic tree (shows evolutionary relationship)

Ex: cladogram (similar but based on common traits) (often both terms are used interchangeably)

Mammals Turtles Lizards and Crocodiles Birds Snakes

Phylogenetic Tree

Closely related species:

recognised by:

their similar morphology (eg: the homology of the pentadactyl limb in the four classes of terrestrial vertebrates)

Biochemical methods

Looks at the proportion of genes or proteins shared between species to estimate relatedness (uses a process called gel electrophoresis that shows bands on a gel which can be looked at to see if they have the same proteins/genes)

Biochemical methods can reduce the mistakes made in classification due to convergent evolution.

Homologous V. Analogous:

Homology - traits inherited by two different organisms from a common ancestor

Analogy - similarity due to convergent evolution, not common ancestry Homologous:

Ex: pentadactyl limbs

Analogous- organisms evolve a similar characteristic independently of one another. This often occurs because both lineages face similar environmental challenges and selective pressures.

Ex: Wings in birds and insects Fins in sharks and dolphins

Simple observation tells us that these limbs are probably not homologous because they have such different structure

Sharks Dolphins

skeleton made of cartilage

use gills to get oxygen from the water in which they swim

don't nurse their young

don't have hair

skeleton made of bone

go to the surface and breathe atmospheric air in through their blowholes

do nurse their young

do have hair — they are born with hair around their "noses"