Evolution - 5.4 Cladistics Flashcards
what is a clade (understanding)
A clade is a group of organisms that have evolved from a common ancestor
- each clade consists of an ancestral organism and ALL of its evolutionary descendants
- most members of a clade will posses common characteristics (due to their shared evolutionary lineage)
What is a Cladograms (understanding)
Cladograms are tree diagrams that show the most probable sequence of divergence in clades
Evidence for a clade/species (understanding)
Evidence for which species are part of a clade can be obtained from the base sequence of a gene or the corresponding amino acid sequence of a protein
- also includes biomolecules (eg DNA/RNA/protein/cytochromes)
- also includes structural characteristics (eg wings, egg laying)
differences in species and divergence (understanding)
Sequence differences accumulate gradually so there is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor
traits throughout species (changes in them) (understanding)
Traits can be analogous or homologous
Evidence from cladistics has shown that classification of some groups based on structure did not correspond with the evolutionary origins of a group or species
cladistics definition
it is a new branch of taxonomy that classifies organisms in terms of their place in the evolutionary tree based on chated characteristic with a common ancestor
what organism will have the DNA most SIMILAR to a bird (question from page 24)
= crocodiles because they are very close (= THE DIVERGE AT THE CLOSEST POINT) and have many similar characteristics
what organism will have the DNA most DIFFERENT to a bird (question from page 24)
= sharks because they are very close (= THE DIVERGE AT THE FUREREST POINT) and do not have many similar characteristics
main groups of primates
- prosimians
- New world monkeys
- old world monkeys
- hominoids
1) apes
2) hominids
examples of hominoids (primate species make closely related to humans)
1) apes
eg. chimpanzees, gorillas, orangutans, gibbons
2) hominids
eg. humans, neanderthal, Australopithecus
relation between number of differences between 2 species and time
sequence differences accumulate gradually so there is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor
Phylogeny
==> information from this can be used to construct a phylogenetic tree (or clades) based on the genetic difference (%) between different species
” can be described as the relationship between all the organisms on Earth that have descended from a common ancestor, whether they are extinct or extant.”
= it has added to cladistics by using genetic analysis of the genomes to determine the genetic difference between species
significance of Mitochondrial (DNA (mt DNA)) in determining the genetic distance/difference of species
mitochondrial DNA (aka the Y chromosome DNA) can be used to determine the genetic distance between species
= as: all cells in our body began from the egg cell, then the mitochondrial DNA in our cells came from our MOTHER, our GRANDMOTHER etc - ie its passed down throughout the maternal ancestral line
- the mitochondrial DNA is not affected by the sperm = it mutates at a constant rate
Mitochondrial (DNA (mt DNA)) is not in bacteria and viruses so for evidence we use:
their main DNA strand
details on Cladograms (NODES)
Nodes – Each node corresponds to a hypothetical common ancestor that speciated to give rise to two (or more) daughter taxa
details on cladograms (ROOT)
Root – The initial ancestor common to all organisms within the cladogram (incoming line shows it originates from a larger clade)
details on cladograms (OUTGROUP)
Outgroup – The most distantly related species in the cladogram which functions as a point of comparison and reference group
details on cladograms (CLADES)
Clades – A common ancestor and all of its descendants (i.e. a node and all of its connected branches)
steps to constructing a cladogram (Using Structural Evidence)
https://ib.bioninja.com.au/standard-level/topic-5-evolution-and-biodi/54-cladistics/cladograms.html
- Organise selected organisms according to defined characteristics
- Sequentially order organisms according to shared characteristics to construct a cladogram
steps to constructing a cladogram ( Using Molecular Evidence)
https://ib.bioninja.com.au/standard-level/topic-5-evolution-and-biodi/54-cladistics/cladograms.html
- Select a gene or protein common to a range of selected organisms
- Copy the molecular sequence (DNA or amino acid) for each of the selected organisms
- Run a multiple alignments to compare molecular sequences (DNA or amino acid)
- Generate a phylogeny tree (cladogram) from multiple alignment data
molecular clock (concept)
Some genes or protein sequences may accumulate mutations at a relatively constant rate (e.g. 1 change per million years)
If this rate of change is reliable, scientists can calculate the time of divergence according to the number of differences
molecular clock limiting factors (3)
Different genes or proteins may change at different rates (e.g. haemoglobin mutates more rapidly than cytochrome c)
The rate of change for a particular gene may differ between different groups of organisms
Over long periods, earlier changes may be reversed by later changes, potentially confounding the accuracy of predictions
The number of differences between comparable base sequences demonstrates the DEGREE of evolutionary DIVERGENCE …. therefore
more difference = more divergence = less related
less difference = less divergence = closely related
reasons for using non-coding DNA in evidence for divergence
Non-coding DNA provides the best means of comparison as mutations will occur more readily in these sequences
reasons for using gene sequences in evidence for divergence
Gene sequences mutate at a slower rate, as changes to base sequence may potentially affect protein structure and function
reasons for using Amino acid sequences in evidence for divergence
Amino acid sequences may also be used for comparison, but will have the slowest rate of change due to codon degeneracy
However, there are 2 key limitations to using morphological (STRUCTURAL) differences as a basis for classification:
- Closely related organisms can exhibit very different structural features due to adaptive radiation (e.g. pentadactyl limb)
- Distantly related organisms can display very similar structural features due to convergent evolution
Convergent evolution =
is the independent evolution of similar features in species with distinct lineages
reasons for convergent evolution (eg the black and white moths)
- It may occur when different species occupy the same habitat and are thus subjected to the same selection pressures
- The shared conditions cause common adaptations to be selected in different species, resulting in structural similarity
homologous structures (in divergences) =
Traits that are SIMILAR because they are derived from COMMON ancestry
analogous structures (in divergence) =
Traits that are superficially SIMILAR but were derived through SEPARATE evolutionary pathways
mDNA
- Female line only
- Easy to find mutations (constant mutation rate)
- short
- cheap
nuclear DNA - divergence and cladistics
= it is found in the nucleus of cells, contains 3000 million bases, not usually used for evolutionary studies as it contains a mix of the male and female chromosomes. Can be used to understand the evolutionary relationships between populations
Y chromosome DNA - divergence and cladistics
Y chromosome contains 59 million base pairs and also accumulates more mutations than other chromosomes.
Passed from father to son, therefore, the genetic difference for different species can be determined by analysing the y chromosomes of each species
= the ancestry of the male line can be determined
Amino acid analysis - divergence and cladistics
the slowest rate of change due to codon degeneracy = mutations change at a constant rate
Homologous structure
features that are common in difference organisms because of common ancestry
- different function
- common structure
- common ancestor
Analogous structure
features in different organisms that have a similar function due to similar selection factors, but are structurally different as they do not have a common ancestry
- similar function
- differing structure
- different ancestor!
Historically - classification was based primarily on morphological differences
EXPECTATIONS:
closely related species were expected to show similar structural features, indicating common ancestry
Reclassification (UNDERSTANDING)
Evidence from cladistics has shown that classifications of some groups based on structure did not correspond with the evolutionary origins of a group or species
species more closely related than thought
using molecular evidence, scientists have discovered that many species thought to be closely related based on shared structural characteristics actually demonstrate distinct evolutionary origins
eg.
crocodiles = more closely related to birds than lizards
red panda = more closely related to raccoons than padas
Figworts!!!!
plants were placed into their own figwort family based on similarity of features
BUT recent DNA analysis of the CHLOROPLAST GENE has move some “figworts-like” plants into the Lopseed and PLantain families.
now less than 1/2 o the species remain in the figwort family
base sequence (definition)
order of bases on a DNA molecule that is used to determine a gene (and therefore similarities between gene of different organisms)
amino acid sequence
sequence that codes for proteins - that can then be compared to determine difference between organisms
morphology
study of the form of things
phylogeny
branch of biology that deals with phylogensis
phylogensis
the evolutionary development and diversification of a species or group of organisms or of a particular feature of an organism
molecular clock
hypothesis that states: DNA and protein sequences evolve at a rate that is relatively constant over time and among different organisms
term for a technique that uses the mutation rule of biomolecules to deduce the time in prehistory when 2 or more life forms diverged
reclassification
reclassification is when a species has been reinvestigated and concluded that the once believed ancestor is actually different - thus linking it instead to a different species and ancester from which it has diverged
