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ATEEB > Conservation genetics/genomics > Flashcards

Conservation genetics/genomics Flashcards

1
Q

What does natural selection act upon

A

The phenotypes that influences the genotype/DNA

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2
Q

How is mean heterozygosity measured?

A

Over a number of regions (loci) and describes level of genetic diversity - low = bad

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3
Q

How do we find out genetic diversity?

A

Allozymes-

PCR-

RAPD-

Microsatellites-

Direct sequencing-

“Next generation sequencing”

Reduced/targeted genome sequences

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4
Q

“Next generation sequencing”

A

rather than sequence one region at a time, sequence million of regions at once on a glass slide. More errors but we get way more sequences –> 312 million per lane, 8 lanes a run. Requires computer programming skills to analyse data. Dont always need this level of sequencing to answer a q

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5
Q

Direct sequencing-

A

(Sanger sequencing). Electrophoresis of fragments 1 base pair difference. In a capillary inside a machine, scored by a computer. Relatively expensive

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6
Q

Microsatellites

A

PCR amplifies specific regions of the genome. Electrophoresis. More comparable/reproducible

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7
Q

RAPD

A

Rapid Amplification of Polymorphic DNA. PCR amplifies random areas of genome. The resulting patterns form a semi-unique profile. Used when new DNA are found/ in a system with few DNA sequences. Has been used to characterise and trace the phylogeny of diverse plants and animal species

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8
Q

PCR

A

makes copies of particular regions so we can detect them

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9
Q

Allozymes

A

alternative forms of enzymes coded by the same gene but having different amino acid sequence

  • separates forms on aragose gels
  • genes are under selection and so they are very conserved (often homozygous)
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10
Q

Are all genome sequences complete?

A

No, most aren’t at chromosomal level. We have small and large pieces of the genome, but dont know how they fit together. We annotate pieces by comparing to known genes

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11
Q

Reduced/targeted genome sequences

A

Several options for getting sequence from across the genome without sequencing whole genome. eg ‘baits’ can sequence less of the genome if you dont need the whole region

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12
Q

Compare Sanger and next generation sequencing

A

Sanger

  • more expensive
  • more accurate
  • slower
  • smaller amount of data
  • easy to analyse
  • not really feasible for eg whole genome

Next gen

  • cheaper
  • less accurate
  • faster
  • get more data
  • needs computer programming
  • now we can sequence any genome
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13
Q

Describe the nuclear genome

A

One copy inherited from each parent

3 billion base pairs

lots of independent genes

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14
Q

Describe the mitochondrial genome

A

Inherited from mother
-Smaller Ne

about 17,000 base pairs

Only a few genes for energy production

Easier and faster to sequence, especially from low quality samples (eg museum specimens, feathers)

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15
Q

What genomes do vertebrates have

A

2
Nuclear
Mitochondrial

Plants have chloroplast genome

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16
Q

What processes influence genetic diversity

A

Mutation

Recombination

Linkage disequilibrium

Genetic drift

Selection

Gene flow

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17
Q

Mutation

A

Adds genetic diversity

slow

In protein coding regions about 3 per year in humans, only inheritable

Only inheritable in sperm and eggs (usually)

In non-coding regions (midget) there are about 1.7 –> 11.8 x10-9 per base pair per year

Vertebrate mtDNA is x10 faster

Once species/population lose diversity hard to get it back and they are vulnerable for a long time

Depends where mutation occurs can be good/bad/nothing in gene. Outside of gene cannot matter/change how much of a protein is made

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18
Q

Recombination

A

Shuffles genetic diversity

In sexual organisms, in gametes during meiosis

Homologous chromosome (copies you have of same chromosome from mum and dad) overlap and sometimes exchange DNA

Resulting in new combinations of alleles not seen before

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19
Q

Linkage disequilibrium

A

Occurs when the frequency of alleles at 2 or more ? occur together more than would be expected if they were independent

The non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than what would be expected if the loci were independent and associated randomly

eg can be physically located nearby on the same chromosome and not separated by recombination
can be caused by natural selection and other processes

such regions can be referred to as “linkage blocks”

Small populations tend to have large linkage blocks, makes it difficult to figure out exactly which gene is beneficial or harmful

20
Q

Genetic drift

A

Changes in the frequency of alleles by random chance

some alleles may disappear –> dear genetic diversity

Sometimes a single allele becomes carrier by all individuals not due to environment or reproductive success

Major mechanism by which genetic drift is lost in small populations and by which deleterious alleles can become fixed

21
Q

Selection

A

Natural - traits that increase likelihood of survival survival , reproduce

  • Phenotype selected changes underlying allele frequency
  • strength of selection and amount f change depends on environment and reproductive success

Selective sweeps and hitch-hiking- when a beneficial mutation occurs it increases reproductive success such that a large number of all individuals possess that mutation and the allele becomes fixed

  • unless recombination breaks it up, genes nearby beneficial mutations become fixed as well
  • loss of genetic diversity due to positive selection
  • alleles on neighbouring gene “hitchhike” along- these alleles may even be weakly deleterious
22
Q

Gene flow

A

Sometimes called migration. Individuals disperse into another population, breeds and reproduces
- genes enter population

Because usually not all populations breed this is a transfer from one population to another

Fst measures population differentiation
1= very high
0= same pop, total interbreeding

Hybridisation of individual of different species mate

Admixture of individuals of different species mate and produce viable offspring (genes cross over both ways)

Introgression= directional admixture- genes from one species into another but not vice versa

23
Q

What is the effective population size

A

The number of individuals that provide genes to the next generation

24
Q

Why should genomics and genetics be used in conservation?

A

Genetics can provide info we dont already know such as how related two individuals are

Genomics provides up with more data at a higher resolution to more accurately answer questions

Could use genomics to identify adaptive genes and target them for conservation (best examples are related to identifying individuals susceptible/resistant to genes)

Use genetics/genomics to identify populations that are especially vulnerable and require management (eg identifying pops with especially low genetic diversity)

  • monitor disease and pathogen load
  • monitor pops before and after translocations of individuals

Provide best info for reintroduction programmes so can choose the best individual for breeding- genetic rescue

Important to modernise conservation with new techniques should use new methods if better than old

Cases where genomics has been helpful

  • FishPopTrace- tracking fish populations for management
  • Identifying hybrid individuals vs pure for conservation such as scottish wildcats, in an article they said “have all the characteristics of a scottish wild cat,” but no genetic testing yet in CB

Costs may be high now but welcome down in future as new tech develops - won’t need to rely on experts as much to interpret data

When combined with ancient DNA- prehuman baselines can be estimated

Author Shafer et al proposed genomic info should be used broadly for relevant management tools eg determine if there are 3 vs 500 migrants per generation

25
Q

Why shouldn’t genetics/genomics be used in conservation

A

For now, currently used genetic methods provide enough info, genomics doesn’t provide large enough improvements in prevision to warrant extra effort

Genomics methods not designed directly for conservation so will never be 100% applicable –> using it could change this

Genomics is still a relatively new field an dreuqires interpretation, if we get it wrong could be conservation disaster

Expensive- could use the money to protect habitats

Requires experts to run the studies and interpret results - they info produced can be difficult for politicians and conservation managers to understand

Difficult to identify adaptive loci because false positives and false negatives and interactions between genes
- eg californian condor and dwarfism, still haven’t found cause?

Gaps between academics and practitioners, because of the publish or perish culture there is little incentive for academics to fully engage in conservation

Funding for genomics studies is related to scientific advancement, not much funding specifically for conservation applications; difficult to change governmental funding systems

Some populations that are small are much more likely to go extinct from stochastic factors eg a storm, than genetics so may be a waste of time

Few examples where genomics has been successfully used in conservation

Some examples here genetics and genomics didn’t help prevent extinctions
- northern spotted owl, red-cockaded woodpecker __> maybe in certain areas
They got an estimate of the size but didn’t account for demographics or consider habitat occupancy so decline
May be referring to the 500 pairs of NSO?

Genomics hasn’t been necessary in other case- florida panther population saved by translocation using genetic info only

Small population paradigm- all very good and well to say this small population has low genetic diversity but doesn’t tell u practically how to fix it (declining pop para)

26
Q

Evolution is an important response to recent climate change

A

Evidence that genetic adapt have occurred even though it has been found in a small population (so far) that doesn’t mean it is unimportant

As tech advances we may gain better ways of collecting data and detecting genetic adaptation

While there is environmental variation over short time scales, there is a clear overall trajectory of global CC which will provide sufficiently strong selection to drive adaptation

There are some limits to phenotypic plasticity and at some point evolution must happen or extinction

Phenotypic plasticity itself can evolve

Evolution can occur rapidly and on the same time scale as CC

27
Q

Evolution is not an important response to recent climate change

A

Lack of appropriate evidence and methodological issues

  • data doesn’t support conclusions
  • timescales of studies impropriate
  • evolution takes time, may be too soon to detect it

Environmental variation too quick and variable for genetic adaptation to occur

Difficult to prove global CC is the cause

Phenotypic plasticity more likely and there s strong evidence to support it - 87% phenotypic plasticity, 13% genetic adaptation –> plasticity is more important than adaptation ?

Migration more likely and we have evidence for this

Extinction may occur before genetic adaptation

Small populations have higher genetic drift and less able to respond to selection even when strong

Even if strong support for 1 species doesn’t mean its relevant to others

28
Q

Compare a traditional genetic study to a more modern one

A

Lukas et al 2004- traditional
Sequenced MHC locus and assessed genetic variation at 9 microsateliite loci
MHC variation similar between western and mountain gorillas
Slightly reduced genetic diversity in mountain though

Compared to

Xu et al (2015) Next generation sequencing
Sequenced 4 gorilla subspecies
2 Eastern subspecies that had experienced prolonged population declined, had low genetic diversity and more deleterious alleles
- Mountain gorillas further recent decline, extensive inbreeding, purging of deleterious alleles

Note: genome sequences are rarely complete, especially for non humans. DNA exists as a continuous sequence on chromosomes. Genome sequencing

  • randomly breaks DNA into small enough sequencws
  • assembly- using computers to try and overlap short sequence
  • Contigs- overlapping regions (short)
  • Scaffold- attempt to place the contains where they are meant to go

So it often has trouble with repetitive DNA, duplicated genes, etc

29
Q

What is quantitative genetics

A

Relates to how genes make the phenotypes that selection can act on

  • some traits are due to a single gene with large effects - eg eye colour in drosophila
  • most traits vary continuously and are controlled by many genes with small effects –> quantitative
  • many can be influenced by both the environment and genetics
30
Q

Pleiotropy

A

When one gene is involved in two genotype

31
Q

Epistasis

A

Interactions between genes

32
Q

What is the breeders equation?

A

R=h^2S

R= change in mean of trait
h= heritability
S= selection differential (difference in selected mean vs the mean of the base population)

If heritability is low then no response eg low overall genetic diversity or low genetic diversity for the species trait

If selection is too strong then too many individuals die and population declines to extinction. It’s important to understand when species will adapt to the environment.

33
Q

Why is it unlikely that advancements in bird breeding data s is an evolutionary (genetic) response?

A

The strength of selection required (ie number of selective deaths)to cause the change would not be sustainable even for large populations

34
Q

What conditions must be fulfilled to prove an evolutionary (genetic) response is occuring

A

Demonstrate that the trait of interest in under selection

Demonstrate that selection likely caused by/linked to CC/change factor

Demonstrate a genetic change in the trait

35
Q

Why might it be difficult to demonstrate an evolutionary response to CC?

A

Phenotypes are often caused by the interaction of multiple genes

If two different populations sampled local adaptations could seem like evidence of a genetic change?

36
Q

What did the author observe regarding the relationship between selected and observed traits?

A

Matches between expectations and obsverations may be false

Gene flow of individuals adapted to other environments can mask the signals of local adaption

The environment can cause changes in genetic phenotypes without underlying genetic changes

37
Q

How do metagenomics and met barcoding differ from genetics and genomics

A

Typical genetics and genomic studies take a tissue sample from an individual and sequence few loci or the partial whole genome

Metab and metag sample a community eg water/soil, skin swab. The samples are heterogenous and composed of many species

38
Q

Metabarcoding

A
  1. conduct PCR using ‘universal’ primers to target a species gene. No primer is truly universal, always some bias
  2. (Prior to next generation sequencing, had to clone and sanger sequence each sample = a lot of work for relatively low resolution) With next generation sequencing just sequence everything directly, skip cloning and other step
  3. Some genetic varaibiltyi exists in each diet item/spp so need to cluster sequences into what we assume to be spp. (eg assume 3% or less sequence divergence amount spp belonging same taxon) –> Operational Taxnomic Unit
  4. Compare representative OTU sequence to database to discover it taxonomy
    - BOLD database has >4 million sequences of arthropods from around the world

Targeting a specific genetic sequence via PCR limits what you can learn, but it also means you can compare your sequence to large databases of sequences from specimens with known taxonomy deposited by other researchers. Museums often barcode their specimens and deposit the sequences in the databases.

  1. Sampling
  2. Bulk DNA extraction and PCR amplification
  3. Pyrosequencing (next gen?)
  4. OTU clustering
  5. Species identification by matching OTU
    https: //www.youtube.com/watch?v=HeHVneOdO00
39
Q

Why is metabarcoding good

A

Can understand what organisms are in an area eg in a water sample. Used to use keys to understand what organisms by the way they looked. But these keys were often based on adults phenotype so we couldn’t always tell what was present, also hard to tell for micro-organisms what they are
Sampling method that used to be employed could only really identify species at medium to high densities. In the case of invasive species we want to know they’re present before they cause an issue

Get vastly more species identified as present than traditional techniques

40
Q

OTU

A

Operational Taxonomic Unit

So computer can separate samples out by divergence. Tend to have a threshold like 3%, so if the samples are 2% different then they are sample spp

However, if you are looking at very variable regions with species can come up as different OTUs. So picking a 3% divergence for everything may not be appropriate- also may under estimate for some closely related species. High level of variation may be overestimate.

41
Q

Why is metabarcoding bad

A

OTU issues

Also may have like 1 read of a species- could be rare fo could be an artefact (not really there) “singletons”

42
Q

Metagenomics

A

No PCR -> potential for less bias
- No cloning

Shot-gun sequence directly = sequence everything present

Uses

  1. DNA- identify biodiversity, analyse genomes of taxa present
  2. RNA- east genes are being expressed. Tells us about functions of members of the community

Assemble genomes and transcripts (ie genes expressed) for all species/individuals in the mixture -> computationally difficult

Further analyses: to identify biodiversity, compare DNA sequence to database. Identify genes and function.

43
Q

Compare metagenomics to metabarcoding

A

Metagenomics

  1. Broader scope- biodiversity identification and function of organisms
  2. Unhelpful data? Repetitive DNA, fewer comparative sequences in database
  3. Difficulty assembling mixtures of genomes
  4. No PCR bias- but still bias in sample prep

Metabarcoding

  1. more limited scope
  2. Taxa sequenced to region available in databases
  3. Less costly
  4. PCR bias- no primer is universal, may not recover all diversity present, multiple primers, about diversity not function?
44
Q

What methods did Roggenbuck et al (2014) use in the vulture paper?

A

Metabarcoding- to compare bacterial species in food, on face, and in hindgut between captive and wild vulture species -> they didn’t need to know the function of the bacteria in this section

Metagenomic- did it for one turkey vulture to confirm the findings they got from metabarcoding
- primary metabarcoding bc wanted to know diversity

45
Q

Roggenbuck et al (2014) tried to convince us of what in the vulture paper?

A
  1. Facial bacterial community is more diverse than the gut. Likely because extremely selection (harsh) gut environment
  2. Fusobacteria and clostrida (toxic to other organisms) predominate in the vulture gut
  3. Gut bacterial community likely derived originally from their diet, which they access through sticking their head inside dead animals
  4. ‘strong adaptation of vultures and their bacteria to their food source, exemplifying a specialised host-microbial alliance’

More stuff online, think about how you could support findings

ATEEB (5 decks)

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