A3.2 Classification and cladistics

4 reasons why classification is needed

1. easier storage and retrieval of information about species

2. identification and naming of new species

• start from obvious large groups, then narrow down to smaller sub-groups until genus and species is reached

3. predicting characteristics of species based on their groups

4. research evolutionary relationships

• species share traits if they evolved from a common ancestor

• classification system used to generate hypotheses about evolutionary origins of species

taxa vs taxon vs taxonomy

taxa: groups used to classify organisms

taxon: 1 taxonomic group

taxonomy: assigning organisms to groups

traditional taxonomic rank

domain, kingdom, phylum, class, order, family, genus, species

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problem with traditional taxonomic rank

GRADUAL divergence of species and larger groups over time → point of divergence cannot be determined objectively

• disagreements over what taxonomic rank groups of species belong to

  • some think traits are similar enough to be genus, some think traits are different enough to be family

• Fixed taxonomic ranks do not reflect the continuous, gradual nature of evolution

what makes a classification successful in reflecting evolutionary origins of species

all species in the same taxonomic group evolved from the same common ancestor

synapomorphies

shared traits among members of a taxonomic group inherited from a common ancestor

predictions that can be made for new species of bat

• has four-chambered heart

• has hair

• has mammary glands

• has placenta

• has navel

daffodil

• some types of daffodil (Narcissus species) produce galanthamine

  • drug for treatment of Alzheimer’s disease

  • a type of alkaloids

• very likely that all species from genus Narcissus evolved from a common ancestor

  • prediction: Narcissus species produce other types of alkaloids

clade

group of organisms evolved from a common ancestor

things to remember about clades

• clades includes ancestral species & species evolved from it (extinct or alive)

• species in a clade share characteristics

• all species are in more than 1 clade

  • small clades nested in larger clades

the evidence used to determine which clade to classify organisms into

• base sequence of genes

  • most accurate and objective

  • useful if species has gone extinct

• amino acid sequence of proteins

  • objective

• morphological traits

  • less objective or accurate

molecular clock

• differences in base sequence / amino acid sequence are a result of mutation

• differences accumulate over long periods of time

• assuming differences’ accumulation occur at a constant rate, the larger the number of differences in sequences the longer since they diverged from a common ancestor

a technique that uses mutation rate of molecules to estimate when 2 species diverged

factors affecting mutation rate

• mutation can be affected by

  • length of generation time

  • size of population

  • intensity of selective pressure etc

cladogram

branching diagram that represents ancestor-descendants relationships

conclusions made from observations on cladogram

• species diverged more recently → fewer differences in base or amino acid sequences → more closely related within clade

• species diverged longer time ago → more differences in base or amino acid sequences → less closely related within clade

• comparing base sequences → estimate how long ago pairs of species diverged → suggest the order in which divergence occurred

parsimony criterion

computer analysis of evolutionary relationships

• compare sequences of all species pairs

• complex calculations determine how species could have evolved with the fewest sequence changes (maximum parsimony)

  • does not prove how clade evolved but indicates the most probable pattern of divergence

terminal branch on cladogram

represent individual species or clades

nodes/branching point

represents the point at which a hypothetical ancestral species split to form two or more clades

clades linked at close node, clades connected via series of nodes

closely related vs not closely related

root of cladogram

hypothetical ancestor of all clades

assumptions in making cladogram

the smallest possible number of mutations occurred that can amount for current base or amino acid differences

what does cladistics allow scientists to do

1. Check whether a traditional classification matches evolutionary history.

2. Reclassify groups ‌that turn out not to be monophyletic.

3. Detect the convergent evolution ‍that misled earlier taxonomists.

how is cladistics used

1. Cladistics compares base sequences ‍of genes or amino acid sequences of proteins to find shared ‌derived characteristics.

2. A cladogram is then built using the principle of ‍parsimony, as covered in A3.2.5 and A3.‍2.6.

3. The cladogram is compared with the existing classification to ‌see whether it matches evolutionary history.

advantages of cladistics

1. Accuracy: groups are based on shared ancestry, ‍not superficial traits.

2. Correction of errors: reclassification removes artificial groups ‍so each taxon is monophyletic.

3. Better understanding of evolution: it ‍traces pathways of divergence and speciation.

traditional vs modern classification

traditional: 5 kingdoms of life

modern: archaea, eubacteria, eukaryota

rRNA as molecular marker

1. rRNA is found in all living organisms,‌ making it a universal molecular marker.

2. Its conserved ‌regions barely change, so it can be compared ‍across distantly related groups.

3. Its variable regions accumulate mutations ‍steadily, showing evolutionary divergence.

eubacteria vs eukaryota vs archaea

eukaryota:

• eukaryotic

• linear chromosomes

• glycerol-ESTER lipids in cell membrane

• 80S in cytoplasm and 70S in mitochondria and chloroplasts

• sometimes have cell wall

• cell wall not made of peptidoglycan

• have histone

• have introns

eubacteria:

• prokaryotic

• circular chromosomes

• glycerol-ESTER lipids in cell membrane

• 70S ribosomes

• always have cell wall

• cell wall made of peptidoglycan

• no histone

• rarely have introns

archara:

• prokaryotic

• circular chromosomes

• glycerol-ETHER lipids in cell membrane

• 70S ribosomes

• always have cell wall

• cell wall not made of peptidoglycan

• have histone

• sometimes have introns