determining relatedness between species Flashcards
how can relatedness be determined?
- molecular homology
- phylogenetic trees
what does molecular homology look at?
- molecules
- amino acids
- molecular clocks
- dna
how is relatedness determined using molecules
Very similar proteins, chromosomes or DNA suggest a recent common ancestor (thousands, millions)
Mutations accumulate overtime and once similar DNA diverges
Occasionally mutations are not repaired before mitosis and become a part of the genome
differences in amino acid sequences
As species diverge they begin accumulating differences in amino acid sequences in proteins
More time = more differences
Due to degeneracy not all changes in nucleotides cause changes in amino acids
Even a change in amino acid may not lead to a change in phenotype
Effects of amino acid substitution depend on how biochemically similar they are- size, hydrophobicity and charge
Conservative substitution: amino acid is swapped for a biochemically similar one and does not cause a change in protein.
Semi-conservative substitution: amino acid is swapped for one with similar shape but different biochemical properties, possibly leading to change in protein structure and function.
Non-conservative substitution: substitution of a very different amino acid which leads to major changes in structure and function.
Nucleic acid comparison is more accurate than comparing the amino acid sequence and easier and cheaper now too
Amino acid differences in cytochrome c between organisms is used
Cytochrome c is part of ETC and essential to organisms’ survival
what is a molecular clock? how is it used?
Molecular clock: technique that uses the rate of the accumulation of mutations in DNA to calculate how long ago organisms diverged from one another.
States that changed in DNA and proteins are constant over time and different linages
Calibrated using evidence from fossil record
Number of DNA differences are compared to calibrate the clock with the dates of branch points
what are limitations of molecular clocks?
Assumption that genetic changes are constant
For genetic changes to occur at a constant rate, they need to be neutral and not be affected by natural selection
And DNA regions that code for phenotype are under natural selection and will change according to environment so mutations in protein-coding DNA will not be constant
Some sections of DNA (in the same organism) mutate at different rates- mutations to important genes will mutate slower than those of less important genes
Overestimate time in recent fossils
Underestimate time in old fossils
how can mitochondrial dan be used as a molecular clock?
Passed through maternal line
Mutations accumulate overtime
Does not have as good repair mechanisms as nuclear DNA so mutation rate is usually higher
Can be used as a molecular clock in relatively closely related species while nuclear DNA compares older linages
Easier to get a lot of mtDNA because cells have many mitochondria
what techniques can be used for looking at genetic differences?
dna hybridisation
sequencing dna
how does dna hybridisation work?
Heat double stranded DNA and hydrogen bonds break between complementary strands
When cooled the complementary bases match up again
If single strands from two species are mixed a hybrid double-stranded DNA is formed
steps:
Gene probes isolate a gene
Both species gene heated to split
The individual strands are mixed and allowed to cool. Hydrogen bonds form between complementary nucleotides- hybridised DNA
Reheated and how much it is lower determines how different strands are- low separation temp suggests lots of difference and few hydrogen bonds and rise versa
how can dNA sequencing be used?
DNA hybridisation only provides a degree of overall difference
Modern DNA sequencing is more accurate
The exact number of nucleotide differences
what isa phylogenetic tree? what are the features?
Phylogenetic tree: branching diagrams that depict the evolutionary relationships between different groups of organisms.
Branch from common ancestors
Use homologous features- morphological and molecular
A hypothesis (most unknown)
Grouped with similar DNA and RNA
phylology
evolutionary history of linages as the diverge from a common ancestor over time.
Linnaean system of classification
organisms are organised into a hierarchy of groups (taxa) reflecting evolutionary relationships.
taxonomy
classifying based on shared characteristics and evolutionary relationships.
limitations of comparative morphology and classification?
Divergence of species may have species classified as distantly related
Convergence of species may have them classified as closely related
Now better techniques
what is used in comparative morphology and classification?
- phylogeny
- Linnaean system of classification
- taxonomy
what is maximum parsimony?
simplest explanation is usually correct- trees that show fewest evolutionary changes to explain variation.
what are the parts of phylogenetic trees? root, branch, leaf, node, outgrip, sister taxa, clade
root: the branches extend from the root or ancestral linage.
Branch: evolutionary path from a common ancestor.
Leaf: the end of each branch.
Node: where two branches diverge (last common ancestor).
Outgroup: shows how those in the in-group relate to those more distantly related. Branched off longest ago.
Sister taxa: pairs grouped together that are the most closely related relative to the other taxa in the tree.
Most recently diverged/most closely related branch off most recently.
Clade: a section of the tree which includes the ancestor and all descendants.
how are taxa grouped in trees?
Monophyletic:
Clade
Based on evolutionary biology
Paraphyletic groups:
Include common ancestor and only some descendants
Not taxonomically accurate
Describe subsets of evolutionary groups (eg. How birds are not included as dinosaurs)
Polyphyletic groups:
Multiple descendants but not the common ancestor
Rare
May group on basis or shared characteristics
what are the different types of trees?
Cladograms: are unscaled
Phylograms: scaled
Rooted trees
Hypothesis a common ancestor
Includes an outgroup
Polytomies
Nodes with more organ two descendant linages (like a rake)
Not enough info to determine which order divergence occurred or rapid speciation occurred
Unrooted trees
Indicate relationship between leaf nodes
No common ancestor
Can be scaled
rapid evolution
Fossil record has suggested its not always slow
Adaptive radiation
Result of changes to master regulatory genes
what are master genes? how do they work?
Master regulatory genes: control the development of embryonic stem cells into different cell types that will result in the structures of an organism.
Few of them
Essential for correct embryonic development
Affect downstream structural genes directly or by controlling other regulatory genes
Can switch other genes on or off
Mutations in it cause major phenotypic changes and give rise to new species quickly
We share them with other animals
Most changes are fatal
changes in rate and timing
heterochrony
what is heterochrony and how does it work?
Heterochrony: master regulatory genes changing time/rate of expression of structural genes.
Can change timing of embryonic development and can lead to structural changes
Bats have long fingers due to gene for that growth being sped up whilst growth of other aspects was unchanged
changes in spatial pattern?
hox genes
what are hox genes and what do they affect?
Hox genes: a type of homeotic gene that is an example of MRG affecting the spatial expression of other genes.
Determine the body plan along the head-to-tail axis during embryonic development.
Determines structures that will be formed in a position.
Direct groups of of embryonic cells to grow into a head etc.
A mutation can result in structures being in the wrong place.
Code for transcription factors that specify how different structures will be arranged- act by regulating the expression of other RG or structural genes and thus cause embryonic cells to differentiate
Highly conserved across organisms that are very distant in evolutionary terms
Required for basic functions and mutations can cause non-viable forms
how do master genes result in evolution?
Single mutations in master genes allow many new phenotypes to develop in a short time.
cichlid fish in East Africa
Enormous diversity
Africa has greatest number of species
In Africa they are found in lakes and streams surrounding Lake Tanganyika
Fish from this lake have been periodically isolated and exposed to different selection pressured leading to rapid diversification of the species (adaptive radiation)
In different regions they are similar on feeding adaptions despite being isolated from each other
Responded to selection pressures the same way
Jaw change occurred after separated and still similar
Considered unlikely that the same mutations would occur in the same structural genes
More likely that a few mutations occurred in the MRG affecting rate and timing in the isolated groups
Later found that BMP4 was a heterochronic MRG controlling jaw phenotype was in all fish
Lots BMP4 = heavy jaws
Less BMP4 = slender jaws
With same selection pressures in different locations, they evolved similar jaws when BMP4 mutated
Galapagos islands
All finches with slight variation
Developed beaks suited to their selection pressures
roles of bmp4 and CaM in beak formation
MRG BMP4 is involved in beak development
Controls rate
Lots = large beaks
Less = slender beaks
CaM is a master gene that regulates production of calcium-binding protein calmodulin (regulates activity of transcription enzymes, binding to them and changing the rate at which other genes are expressed)
Lots = long beaks
