Module 3 Flashcards
What is DNA barcoding?
A way to use short standardised gene-regions to identify samples to species. A yard stick, Based on CO1 in animals (a mitochondrial gene), successrate of 96-100 % of correctly assigning samples.
Match to a database. If not in there potentially a way of identifying a new species (sort of).
Divergence rate in the CO1 gene at a sweet spot to be able to distinguish most species from each other. Easy to amplify and relatively fast evolving.
IT IS IMPORTANT TO NOTE that because there is an overlap between intra and interspecific genetic distances DNA barcodes cannot be used as the sole criterion for describing new species.
What can we do with DNA barcoding?
Identify animals at all life stages, fragments or products, stomach contents (food chain analysis), cryptic species.
Applications in food control, customs, invasive species control, disease vector. Police, agriculture, forestry, conservation, education
IT IS IMPORTANT TO NOTE that because there is an overlap between intra and interspecific genetic distances DNA barcodes cannot be used as the sole criterion for describing new species.
What are some critiques of DNA barcoding?
Can’t detect
- ancestral polymorphisms
- male-biased gene flow (mitochondrial is maternal)
- Gene flow after hybridisation
- Transfer of mtDNA loci to the nuclear genome
- Recent speciation
- Slowed rates of molecular evolution (like in corals)
What is the barcoding gap?
An underlying assumption that barcoding is based on, saying that there is a detectable gap between the genetic distance between species and the genetic distance within species.
Visualised as to normal distributions with an x axis of “genetic distance” that do NOT overlap.
IN REALITY there is an overlap between intraspecific and interspecific genetic distance, making it harder to distinguish the two.
Why is it necessary to resolve the taxonomic status of animals in wildlife management?
We have to know the tools at our disposal and the status of the things we are trying to save.
- Undiagnosed species can be left to go extinct or denied legal protection
- Incorrectly identified species can hybridize leading to outbreeding depression
- We can waste resources in populations wrongly identified as endangered or on hybrids that are not actual distinct species
- Populations that could be used to improve fitness of inbred populations can be overlooked
Causes of taxonomic uncertainty
- Morphological data is inadequate but has been widely used in the past
- Use of different species definitions means that there is no common “yardstick”
- Divergent populations part way through speciation
- Secondary contact and hybridisation
The tuatara example of taxonomic uncertainty
The tuatara are the only survivors of an ancient reptilian order and was believed to be a single species.
Studies using morphological, immunological, allozyme and mtDNA data showed that there are 3 distinct groups (ESUs), 1 of which were at risk of extinction with no legal protection and management.
After the taxonomic resolvement the three groups are now being managed independently and effectively.
The puma example from north america, taxonomic uncertainty
The puma was thought to be 8 subspecies based on morphological data, but later found out to be only 1 ESU since none were genetically distinct.
Using both microsatellites and mtDNA.
Here they were wasting resources on trying to manage 8 subspecies when really there was only one species.
Example Grey wolf, red wolf and coyotes, taxonomic uncertainty
Red wolf was found to be a hybrid between gray wolf and coyote and thus needed to be recognised as such and managed accordingly.
What is the biological species concept? (BSC)
Mayr 1963
A species is a group of interbreeding populations with unique genetic identities that are reproductively isolated from other populations.
Reproductive isolation allows species to evolve independently of other species
The foundation of many other species definitions.
Limitations:
Can’t
- Identify whether geographically isolated populations belong to the same species
- Classify species in extinct populations
- Account for asexually reproducing organisms
- Clearly define species when barriers to reproduction are incomplete (hybridisation)
THE BEST way to define species in terms of conservation is likely within an evolutionary context, i.e. a species exchanges genes and share an evolutionary trajectory
What is taxonomic inflation?
When the number of species artificially increase and increase the cost of conservation efforts
What is the best way of defining a species for conservation?
THE BEST way to define species in terms of conservation is likely within an evolutionary context, i.e. a species exchanges genes and share an evolutionary trajectory
What is an ESU?
An evolutionary significant unit is a population or group that has high genetic and ecological distinctiveness and should therefore be managed separately.
The ESU is informed by
- Life History (e.g. timing of reproduction)
- Behaviour (e.g. courtship displays)
- Morphology (e.g. colour pattern, horn shape, bill shape, flower shape etc.)
- Environment (e.g. habitat type, climate)
- Geography (e.g. vast distances, physical barriers)
- Molecular genetics (e.g. alleles frequencies, genetic distance, phylogepgraphy, discordance between divergence at candidate “adaptive” genes and neutral markers)
What are the three widely used frameworks for resolving taxonomic status?
- Reproductive isolation and adaptation (Waples 1991)
- Reciprocal monophyly (Moritz 1994)
- Exchangeability of populations -> genetic/ecological and recent/historical (Crandall et a. 2000)
What are other names for “clades”?
Natural group
Monophyletic group
All the tips and all the ancestors of the tips.
What is a paraphyletic group
Not a natural group, like fish. If the fish clade was to be considered monophyletic every terrestrial vertebrate would have to also be fish.
What does the length of branches mean in a phylogram?
Can indicate the rate of change of the DNA in a phylogram. The longer the branch the higher the level of change.
A phylogram shows more than just relationships (which is called a phylogeny)
What is a chronogram?
Also known as a timetree or as ultrametric.
A chart that shows absolute time in Mya based on fossil data to calibrate the data so we can infer when divergence events happened.
What is the root in a rooted tree?
Most recent common ancestor of the entire tree, indicates the ancestral lineage, the starting point of the tree.
What are the steps to building a molecular phylogeny?
- Gather/generate DNA data
- Sequence alignment
- Substitution model
- Phylogenetic analysis
- TADA Phylogeny
What does it mean if characters are homologous?
They are similar by descent
Also known as synapomorphies
E.g. comparison of structures in the limbs of humans, dogs, horses, bats, birds and seals
Can be used to reconstruct a systematic hierarchy of shared characters. These can be predictive of genomic differences.
In the DNA sequence alignment we distinguish homologies from analogies. Bad alignments lead to bad trees and interpretations.
What does it mean if characteristics are analogous?
They are similar but have evolved independently
What is essentially the point of DNA sequence alignment?
To distinguish between analogies and homologies
i.e. characteristics that look similar but aren’t due to common descent and characters that actually is due to common descent
The example of the Quagga, homology
An effort to revive an extinct species through selective breeding.
The last Quagga died in Amsterdam zoo in 1883, now scientists have set out to “revive” the Quagga by selective breeding of zebras to create animals with the same colouration.
Problem: The outcome is not a new species. It’s just a fancy looking zebra. If you perform a genetic analysis you find that the new “Quagga” is more related to zebras than to the ancestral Quagga.
What is an autoapomorphy?
Singletons, changes in the sequence of one species that can’t help understand relationships, but they can help understand the rate of change
How do distance based (Algorithmic) phylogenetic methods work?
They use a measure of similarity to group different OTU’s together and then pair those individual groups to each other to form a hierarchy.
Are fast and computationally easy
Reduce character states down to distances
Assumes a constant rate of change/evolution
Based on “Observed Distance” (“p”)
MAY NOT REFLECT THE “ACTUAL GENETIC DISTANCE” “d”
BLAST uses this approach
Often a good first approximation of the data
Name some distance methods in phylogenetics
Within Clustering algorithm:
1. UPGMA - Unweighted Pair Group Methods with Arithmetric Means (Clustering OTUs then clusters those new groups)
- Neighbour Joining, NJ, Shortest tree - Sequentially finds pairs of neighbours connected by a single node, aims to reduce the overall length of a tree
Within optimality criterion:
3. Minimum Evolution, ME, Shortest branch length - Reconstructs the tree with the shortest branch length, minimum distance
What is the relationship between observed distance, p, and actual genetic distance, d?
The observed distance can underestimate the true distance, especially when the degree of divergence is high (e.g. old splits)
Multiple substitutions accumulate and sequences become random/saturated
What is the difference in change rate between the 1st and 2nd codon position when compared to the 3rd?
The 3rd codon position has less impact on the outcome of mutations (it often doesn’t change the amino acid) and therefore it changes faster than the 1st and 2nd codon positions and should be treated differently when modelling evolutionary change
What are the differences in the change rates of purines (A and G, two rings) and pyrimidines (C and T)?
Transitions between the same type of nucleic acid are more frequent
Transversions between different kinds are less frequent
