4.3- Classification and Evolution (copy)

what is taxonomy

the practice of biological classification

why is classification required

• allows us to arrange species into groups based on evolutionary origins and relationships

• no overlap between groups→ each group called a taxon

• makes it easier to understand and remember organisms

the hierarchal classification system

• domain

• kingdom

• phylum

• class

• order

• family

• genus

• species

the binomial naming system

• universal way of identifying species

• uses genus and species

• italicised/underlined and

• capital letter for Genus but not for species

three domains

• bacteria

• archaea

• eukarya

archaea

• often extremophiles

• prokaryotes

• different structure to bacteria

• DNA transcription more similar to that of eukaryotes

bacteria

• prokaryotes

• divide by binary fission

eukarya

• eukaryotes

• divide by mitosis

• can reproduce sexually or asexually

differences between bacteria and archaea

Feature	Bacteria	Archaea
Membrane Lipids	unbranched hydrocarbon chains ester bonded to glycerol	branched hydrocarbon chains ether bonded to glycerol
rRNA		base sequences more similar to rRNA of eukarya
Cell Wall Composition	peptidoglycan	don’t contain peptidoglycan

the five kingdoms

• highest rank of classification before three domains were introduced

• prokaryota

• Protoctista

• fungi

• plantae

• animalia

prokaryota

• bacteria and blue-green (photosynthetic) bacteria

• unicellular

• divide by binary fission

• no nucleus

• blue-green bacteria are autotrophic

• most bacteria re heterotrophic

Protoctista

• eukaryotic

• unicellular or a group of similar cells

• protozoa cells are similar to animal cells

• algae cells are similar to plant cells

fungi

• heterotrophic/ saprotrophic

• can be unicellular e.g. yeast

• some have long threads called hyphae which form mycelium network

• some release spores that allow them to reproduce

plantae

• multicellular eukaryotes

• autotrophs

• have complex body forms→ branching systems above and below ground

animalia

• multicellular eukaryotes

• heterotrophs

what is phylogeny

• evolutionary history of organisms

• show evolutionary relationships between taxa

sequence data used in phylogeny

• DNA

• mRNA

• Amino Acids

DNA analysis and comparison

• DNA extracted from nuclei of cells of an organism

• base sequence obtained from extracted DNA

• compared to that of other organisms to determine evolutionary relationships:

  • more similar base sequence= more closely related= more recent common ancestor

immunology in phylogeny

• albumin protein found in many species and is commonly used for experiments

  1. pure albumin samples extracted from blood of multiple species

  2. each sample injected into a different rabbit

  3. rabbit produces antibodies for specific type of albumin

  4. antibodies extracted and mixed with different albumin samples

  5. ppt from each mixed sample is weighed:

     • greater weight of ppt= greater complementarity between antibody and albumin

the work of Wallace and Darwin

• Wallace collected specimens from south east Asia and South America

• Darwin made several key observations:

  • not all offspring of an organism survive

  • populations of organisms fluctuate but not significantly

  • populations of the same species of organisms show variation between individuals

  • offspring inherit characteristics from their parents

• wrote theory of evolution by natural selection

evidence for evolution by natural selection

• fossils

• molecular evidence

fossils

• preserved remains of organisms or features left by organisms

• fossils tell us that environments and organisms living in them have changed significantly over millions of years

• fossils can be dated using carbon dating, so can be put into a sequence from oldest to youngest to see how organisms have changed through evolution

• show similarities between extinct species, ancestral species and present day species

• provides evidence for gradual change from simple life forms to complex life forms

molecular evidence for evolution by natural selection

• DNA found in nucleus of cells can be sequenced and used to provide evidence of evolutionary relationships and how genetic code has changed as they have evolved

• differences between nucleotide sequences in genes of species provides information:

  • more similar sequence= more closely related= species have separated more recently

phylogenetic trees

• show relationships between species

• closer to end= more recent common ancestor

variation

• differences that exist between organisms

• can be:

  • genetic→ variation in genes

  • phenotypic→ variation in characteristics expressed

types of genetic variation

• interspecific

• intraspecific

interspecific variation

• variation between species

• useful in identifying different species

• species that look v. similar can have forms of phenotypic variation that helps differentiate them

• other species will have have slightly different niches that help distinguish between them

• in cases where phenotypes are too similar, genotypes can be used to help identify them

intraspecific variation

• variation within individuals of the same species

• variation observed in phenotypes can be due to qualitative or quantitative differences

discontinuous variation

• Caused by qualitative differences:

  • discrete and distinguishable categories e.g. blood groups

continuous variation

• caused by quantitative differences:

  • range of values exist between two extremes e.g. height, mass

causes of variation

• genetic factors

• environmental factors

causes of discontinuous variation

• occurs due to genetic factors- no environmental factors

• different genes have diff effects on phenotypes

• different alleles have large effect on phenotype

• e.g. if earlobes are attached or free

causes of continuous variation

• interaction between genetics and environment

• genetic:

  • different alleles have small effect on phenotype

  • different genes can have same effect on phenotype

• environmental factors:

  • length of sunlight hours

  • supply of nutrients

  • water availability

  • temp. range

  • oxygen levels

adaptation

• features enabling organisms to survive in the conditions of their habitat

• caused due to environmental factors giving rise to selection pressures→ natural selection

• natural selection will select for favourable alleles that produce adaptations→ organisms with these adaptations will be more likely to survive and reproduce

types of adaptation

• anatomical

• physiological

• behavioural

anatomical adaptations

• structural or physical features

• e.g. white fur of polar bear providing camouflage

physiological adaptations

• biological processes within the organism

• e.g. mosquitos produce chemicals so stop blood clotting

behavioural adaptations

• the way an organism behaves

• e.g. cold blooded reptiles bask in the sun

convergent evolution

• species that do not share recent common ancestor can show high levels of similarity

• occurs when two habitats are very similar→ organisms have similar adaptations

the process of natural selection

1. selection pressure exist in the environment due to environmental factors

2. random mutations produce new alleles of a gene

3. the new allele may benefit possessor, so there will be an increased chance of survival and increased reproductive success

4. advantageous allele is passed onto next generation

5. over several generations, new allele will increase in frequency in population

antibiotic resistance

1. within a bacterial population, there is variation caused by mutations

2. mutation causes some bacteria to become resistant to antibiotic

3. when population die, resistant bacteria do not die

4. resistant bacteria can reproduce with less competition from non-resistant bacteria

5. genes for antibiotic resistance are passed on w greater frequency to next generation

6. over time, whole pop. becomes resistant

how do bacteria inherit antibiotic resistance

• vertical transmission

• horizontal transmission

vertical transmission

• bacteria reproduce asexually through binary fission

• if one bacterium contains mutant gene, all of its descendants will carry antibiotic resistant gene

• enables antibiotic resistance to spread within a population

horizontal transmission

• plasmids contain antibiotic-resistant genes

• plasmids frequently transferred between bacteria

• occurs during conjugation:

  • tube forms between two bacteria to allow for exchange of DNA

• bacteria containing mutant gene that gives antibiotic resistance can pass this gene on to other bacteria

• enables antibiotic resistance to spread within or between populations

how to reduce cases of antibiotic resistance

• only prescribe antibiotics when absolutely necessary→ not used in non-serious cases

• ensure patients complete courses of antibiotics so all bacteria killed

• only using antibiotics for bacterial infections

• use highly specific antibiotics rather than wide spectrum antibiotics

• rotate which antibiotics are used

• hold some antibiotics back as a last resort

• more investment into researching new antibiotics

selective agent

any environmental factor that influences the survival of a particular species and therefore drives natural selection in that species

consequences of antibiotic resistance

• research into new antibiotics is time consuming and expensive

• some strains of bacteria are resistant to multiple antibiotics→ infections are difficult to treat

• can give rise to superbugs e.g. MRSA

• commonly prescribed antibiotics are becoming less effective

• bacteria can develop multiple resistance→ resistant to multiple antibiotics

consequences of pesticide resistance and how to reduce effects

• consequences:

  • less food security as crops can still be ruined

• mitigation:

  • use combination of pesticides

  • use sparingly or in rotation

  • using other forms of pest control e.g. biological control, genetic modification

Student’s t-test

• used to determine if there is a significant difference between mean values of a particular variable across two populations

• conditions:

  • data must be continuous and normally distributed

  • variances should be equal

  • samples must be independant

conducting a t-test

1. state null hypothesis→ assumes no significant difference between the means

2. calculate test statistic using t-test formula

3. calculate degrees of freedom:

   • n₁+n₂ -2
     

4. compare test statistic against critical value:

   • if t statistic>critical value, reject null hyp

   • if t statistic< critical value, accept null hyp

spearman’s rank correlation coefficient

• used to measure strength and direction of association between two continuous variables that are not normally distributed

calculating spearman’s rank correlation

1. convert raw data values into ranks from smallest to largest value

2. if two values are the same, give them an average rank

3. calculate spearman’s rho

4. compare ρ to a critical value to determine significance of correlation:

   • close to +1= strong positive correlation

   • close to -1= strong negative correlation

   • close to 0= no correlation