Lecture 13a: Conservation genetics 3 Flashcards
Lecture outline
*Definitions: bottleneck vs. founder events
*Impact of a Bottleneck Event
Impact of Bottleneck Size:
-Impact on quantitative characters.
-Extinction risk
*Northern elephant seal example
*Some other examples of impact
*Tracking demography over time
Bottlenecks vs founder effects
Population bottleneck:
–reduction in population size, especially transition from a large random mating population to less than about 100 individuals.
–often results from catastrophic event (natural or man made)
–A bottleneck leads to the loss of genetic variation.
Founder Event:
a small number of individuals from larger source population founding a new population
–effects similar to population bottleneck,
–But: new populations may be founded by a group of related individuals
–Whereas: individuals remaining after bottleneck typically result from ‘random sampling’.
How bottlenecks lead to loss of genetic variation:
1: sampling effect:
–rare alleles likely to be lost to the population,
–or if they survive the bottleneck, may be much more common in the post-bottleneck population.
–distorts pattern of allele frequencies
–this can be used as a `signature’ of a bottleneck event.
2: impact on diversity as expressed by the proportion of heterozygous individuals in the population.
–In a small population, the chance of combining alleles that are identical by decent increases (increasing the risk of inbreeding depression – due to deleterious allele density increase proportionally),
–Therefore, alleles go more quickly to fixation (present in all individuals) or extinction in the population.
= Loss of heterozygosity
Expectations of bottleneck impacts
- loss of rare alleles as a function of population size:
–Simulation model: large population starts with 8 alleles, 7 of which are relatively rare.
–Original allele frequencies = 0.80, 0.07,0.03,0.02, 0.02, 0.02 & 0.01
–average no. remaining alleles after 1 generation at various Ne: see simulated values in notes
- instantaneous effect on diversity:
average % genetic variance after bottlenecks of various sizes in a theoretical idealised population. - loss over time at small population size:
See graphs from Jones et al. (2012) WALKERANA, 35, 27-44
^ Top graph: Rate of decline of mean heterozygosity and allelic diversity over time for populations with different effective size.
^ Bottom graph: Variation lost randomly through genetic drift (stochastic process)
- time to regain lost variation
see (Nei 1987) :
^ Changes in average H when population goes through a bottleneck (Nei 1987)
No = bottleneck size
r = intrinsic rate of growth (logistic)
> impact if smaller r
Takes a long time to regain lost variation
Quantitative characters
Typically morphological, behavioural & other complex traits are quantitative (multiple genes contribute.) These traits are referred to as polygenic traits because more than one gene is involved in their expression.
Relationship between multiple genes encoding a single trait are additive or non-additive:
Additive:
genes make independent contributions, combined genetic variance reflects average among loci.
Non-Additive:
Dominance: genes that are preferentially expressed
Epistasis: genes controlling the expression of other genes
Bottleneck: Genetics component interacts with Environmental component -
Impact on quantitative characteristics:
*For additive effects, variation in quantitative traits may be lost following a bottleneck event
*However, for non-additive effects (epistasis or dominance): bottleneck can increase variation & fluctuating asymmetry (FA).
*Disruption of gene complexes due to inbreeding could disrupt developmental process such that more variation and FA results.
Bottleneck: Genetics component interacts with Environmental component :
Extinction risk
Demographic stochastisity: chance element to all aspects of demographic growth of a population.
e.g: there is a chance element associated with the survival of a newborn animal, chance that it will survive to reproductive age, chance that it will reproduce, a chance element associated with how many offspring it will have, etc.
2 important consequences:
1: exact same population starting out at two different times is likely to show different patterns and rates of population growth.
2: probability associated with the chance that a population will go to extinction, and this probability is greater when the population size is small.
Factors affecting impact of bottlenecks
Reproductive behaviour
* if Nm does not equal Nf
(e.g: in polygynous spp.),
then impact of bottleneck on genetic diversity will be increased.
e.g. in polygynous elephant seals:
Ne could equal 4(Nm*Nf)/(Nm+Nf)
Northern Elephant seal example
Largest phocid – highly polygynous – annual breeding
history:
*Hunted extensively for oil from ~1810 until ~1860
*Taken by collectors and hunters until 1884 when 153 were killed
*Not seen again until 1892 when 8 were found on Guadalupe and 7 were killed! Modelling suggests ~20 left.
*Protected in US & Mexico in 1922, and the population recovered
See: Hoelzel et al. (2024) Genomics of post-bottleneck recovery in the northern elephant seal.
Nature Ecology & Evolution. 8, pages 686-694
^ bottle neck led to reduced genetic diversity
^ in-breeding increased after bottle neck as did homozygosity
^more inbred female seals were less successful at weaning young
^ more inbred male seals had less functional sperm and fathered less pups
measuring success in no. of copulations vs percent of paternity in harem
Importance of reproductive behaviour – polygyny:
simulated diversity after bottlenecks of varying sizes & duration:
–for a hypothetical monogamous elephant seal. –even very small bottlenecks don’t explain observed loss of diversity
–for polygynous elephant seal –Observed loss of diversity now consistent with bottleneck of 20 seals or fewer
^polygyny has a major impact on allele heterozygosity
Quantitative characteristics of fitness include skull symmetry
^ post bottleneck event an increase in symmetry fluctuation in skulls is observed in Elephant seal population (a sign of low fitness)
Norwegian reindeer example
Two small herds (7 (Husvic) & 10 (Barff) deer) purchased by whalers and deposited one each on either side of glaciers on South Georgia ~100 years ago
(Lovatt & Hoelzel, 2014. Evol. Biol. 41, 240-250)
^ Ex norwegian colonials shipped two reindeer herds to husvik and barff
^ the two herds can’t mix due to dividing range
Diversity was reduced in colonial herds
fluctuating assymetry increased after bottleneck compared to herds in Norway
Bottlenecks decrease diversity and distort allele frequencies, so that founder populations often represent novel genetic diversity compared to the source, even when considerable diversity remains.
Phenotypes also affected. Not in an adaptive way - random
Compare phenotypic problems with other species: Cheetahs
Evidence for Genetic Uniformity In Cheetahs & observed physiological correlates:
Methods indicating reduced genetic variation
–1. Allozymes - 52 loci
–2. Two-dimensional PAGE -155 loci
–3. Increased skeletal FA
–4. Allogenic skin graft accepted
–5. MHC-RFLPs (6 restriction enzymes)
–6. mtDNA -RFLPs
–7. Microsatellite loci
–8. Lowest whole genome diversity among 11 species
Modelling based on the coalescent (more on this soon)
O’Brien et al. (1983) Science 221:459-462; O’Brien et al. (1996) in Avise et al. Conservation Genetics; case histories from nature. Chapman & Hall, pg.50-74; Dobrynin et al. (2015) Genome Biol. 16, 277
Population split and then a bottleneck at beginning of holocene
Physiological correlates
–1. Diminished sperm count
–2. Elevated frequency of morphological abnormalities in sperm development (c.70%)
–3. Low fecundity in captive breeding attempts
–4. Captive population is not self-sustaining
–5. Relatively high incidence (c.30%) juvenile mortality even among unrelated parents
–6. Increased population vulnerability to infectious disease, notably feline infectious peritonitis
Compare phenotypic problems with other species: Lions
Correlation of genetic variation & reproductive parmeters in 3 Lion Populations:
See chart in notes
^ Serengeti largest pop, smaller group in nogorongoro and gir is the smallest pop
^ we can observe this through abnormalities and lack of heterozygosity
Track demography of a population to assess conservation strategies: using the coalescent approach to track demographic history
Track population expansion or contraction in the context of natural patterns of environmental change
Track response to anthropogenic impacts (hunting, pollution, habitat loss or fragmentation, etc.)
Every generation there’s a 1/2Ne chance of coalescence
The expected coalescence interval time (μk) can be calculated as: E(μk) = 4Ne/ k(k-1)
^ Coalescent events can be used to estimate effective past population size
Skyline plots
Skyline Plots: dependent on coalescent methodology and are a 2-step
process:
1) estimate a genealogy from sequence data,
2) estimate the population history based on the genealogy.
Ne is estimated from the coalescent intervals as follows:
Ni = gamma i(i-1)/2
where i denotes the number of lineages in a given coalescent interval.
The method has been refined and developed so that the very course estimations possible from the initial ‘classical’ version have now been considerably improved.
The details of these refinements are reviewed in:
Ho SYW & Shapiro E (2011) Skyline-plot methods for estimating demographic history from nucleotide sequences. Mol. Ecol. Res. 11, 423–434
Using coalescence + ancient DNA to track demographic history
Ancient DNA provides a better representation of historical coalescent points, and thereby permits good inference about changing population size (Ne) over time.
See: deBruyn, M., Hoelzel, A.R., Carvalho, G.R. & Hofreiter, M. 2011. Faunal histories from Holocene ancient DNA. TREE 26, 405-413
See figures in notes
allows us to identify population crashes and potentially determine their cause
^ e.g. Bison decline was prior to human settlement which was prev. Assumed the cause
Summary
1) When a large outcrossing population is drastically reduced in size, the resulting inbreeding can lead to inbreeding depression through the expression of recessive genes as homozygotes.
2) Lost diversity means fewer evolutionary options in a changing environment.
3) Diversity is lost both through the reduction of heterozygosity & the loss of alleles. Can have direct impact on fitness.
4) The severity of the impact of a bottleneck event is proportional to the bottleneck’s size & duration, & diversity is regained very slowly through mutation (or more quickly through immigration).
5) Quantitative characters may respond to inbreeding by showing an increase in variation & asymmetry, but such changes are unlikely to be adaptive.
6) Genetic data can be used to assess past population demography using coalescent methods, and compared with known past events to help predict future impact.
