Lecture 13b: Conservation genetics 4 Flashcards
(20 cards)
Lecture outline
Managing endangered species:
Captive breeding programs:
*avoiding inbreeding depression & loss of genetic diversity
*Reintroductions
*Outbreeding depression
Managing diversity
Aim to maximise diversity.
In captive breeding programs through selective mating (using pedigree data or molecular markers).
But, must also focus on the protection of natural habitat so populations don’t become too small or fragmented in the first place.
And may need to attempt ‘genetic recovery’ of an endangered population through reintroduction.
Or make difficult decisions about what populations are most in need of investment for management and protection.
List of successful captive breeding programs
Some spp. that have been saved from
extinction by captive breeding:
— Guam rail,
— Franklin tree (North America),
— Partu/a snail (Tahiti),
— Potosi pupfish (Mexico),
— Socorro dove (Mexico),
— Pere David’s deer (China)
— European bison.
Example: Guam Rail (bird)
captive breeding resulted in successful reintroduction of Guam rail:
US military cargo ship introduced an invasive species to Guam towards the end of WWII (brown tree snake; Boiga irregularis – ate bird eggs)
21 Guam rail taken into captive breeding program in 1980s (extinct in wild by 1986) and later released in snake-free habitat on nearby Cocos and Rota.
Genetic management among meta-populations in US zoos, minimising kinship (see Haig et al. (1994) Mol. Ecol. 3, 109-119).
see: https://www.birdlife.org/worldwide/news/guam-bird-coming-back-extinction-wild
Captive breeding programs:
avoiding inbreeding depression & loss of diversity.
Impact of founder events:
1) Loss of heterozygosity through the sexual recombination of alleles that are identical by descent :
Ht = Ht-1 (1 – (1/2Ne))
2) Loss of alleles through a sampling effect
3) Distortion of allele frequencies through the chance selection of alleles
Can lead to higher frequency of alleles that are non-functional due to a mutation that affects their translation.
^ These ‘LOF’ and other deleterious alleles are harder to eliminate by purifying selection when Ne (effective population size) is small and drift is strong
So how many individuals are needed to maintain a captive population with enough diversity?
Impact of founder events: No. Of founders vs proportion of H they capture:
see 2 graphs in notes
graph 1: In this case 20-30 founders will capture most of the H in the source population - but some of the rarer alleles will still be lost
graph 2: Pr of sampling at least 1 copy of each allele vs No. founders for loci with alleles at frequencies of p=0.05 & p = 0.01 – Again, retain much with 20-30 founders, but rare alleles lost
Previous 2 graphs consider and ‘instantaneous’ effect, but remember that loss of diversity is inversely proportional to Ne
For an Ne = 10, 95% diversity remains after 1 generation, but only 65% after 10 generations: see graph 3
Avoiding inbreeding depression & loss of diversity:
See: Wright et al (2021; 10.1002/ece3.7143) used a genetic method to estimate Ne and compared it among different sized populations of woodland bats Sample size mattered (coloured boxes)
Variance in family size has an important impact on the Ne/N ratio
– ‘sweepstakes breeding’, when only a few families are successful, decreasing Ne (see Hendrick 2005, Evolution 59(7),1596–1599) e.g. fish eggs float around and many are consumed whereas one fish may therefore have no offspring a clutch of eggs from another fish could all survive and therefore more of their genes will be retained
see fig. 1 in notes:
The N./N ratio when a proportion of parents y have two progeny, there are one, 10, or 100 parents that contribute equally
in a population of 10,000 adults. The broken line indicates a N/N ratio of 0.11.
Estimated North Atlantic Ne = 2,190 (sweepstake breeding?) Catch as high as >100,000 tons/year White et al. (2009) Molecular Ecology 18, 2563–2573
Diversity is being lost according to Ne
– in fish the ratio of Ne/N is not particularly large due to sweepstake breeding
Need to Maximize Ne/N: captive populations of endangered species:
Avoiding inbreeding depression & loss of diversity:
Need to maximize Ne/N: strategies:
a) equalizing family size: single family with large brood displaces other genetic lineages
b) equalizing sex ratios.
c) equalizing population size in different generations
Minimizing kinship (MK):
– calculate coefficient of relatedness (‘k’ in this example). see notes
Strategy: preferentially use individuals with low ‘mean kinship’
calculation of coefficient relatedness can be conducted using studbooks
^ keeps track of who mated and which offspring survived
e.g. Przewalski’s horse genealogy based on studbook data (see Frankham et al. Chapter 11) was used to assist selective breeding and thus reduced inbreeding depression
Studbooks example: Tawny Frogmouth
see screenshot in notes
Records show details of individuals:
where they are
where they were born
age
sex
and whether still alive
See also Tamarin study from Frankham et al Chapter 17)
Calculate coefficient of relatedness: Using Genetic Markers
Sometimes you don’t have kinship records like studbooks – in this situation you can use DNA markers to determine this:
For example using microsatellite DNA markers from which the proportion of shared alleles is used to estimate kinship
Genetic estimation of relatedness is approximate, and dependent on the number of genetic loci used, and their level of polymorphism.
See Fabiani et al 2006 figure
^ E.g. In this example for southern elephant seals (using 8 MS loci), known mother pup pairs (r = 0.5) and pairs of unrelated individuals (r = 0) show separate but overlapping distributions of r-value estimates, and the values for half-sibs (r = 0.25) overlaps both distributions.
However, more markers means better resolution, and modern sequencing methods makes this possible. In the study below by Thrasher et al. (2017) doi: http://dx.doi.org/10.1101/169144, 12 microsatellite DNA markers (MSAT) were compared with the resolution gained from 411 SNP (single nucleotide polymorphic) markers for the variegated fairy-wren.
Some species have lost so much variation that assigning kinship levels becomes quite hard, as for this example of the northern elephant seal requiring whole nuclear genomes.
See notes for how matings would be set up using MK management to minimize kinship
^ with a group of 10 founders by gen 3 - 7 out of 8 progeny are descended from 2 founders – how to avoid inbreeding?
^ The single outbred male is mated to the 4 inbred females, and the three inbred males are not used for breeding.
Avoiding inbreeding depression & loss of diversity:
Maximum avoidance of inbreeding (MAI)
Equalise family size & institute a circular mating program:
delays inbreeding for as long as possible.
–typically used with populations when no a priori info on kinship available.
–need to follow scheme precisely
–makes no allowances for problems such as mortality of offspring, incompatibility of breeding pairs, reduced fertility, etc.
Montgomery et al. (1997):
–40 replicate populations of Drosophila
–managed after founding populations using: MK, MAI and Random mating
–assessed diversity using 6 microsattelite DNA & 7 allozyme loci.
conclusion:
MK gave highest diversity measure
avoiding inbreeding helps but not much
^minimising kinship is key
Successful reintroductions
- Mauna Kea Silver-sword (Hawaii),
- Californian Condor,
- Black-footed ferret (North America),
- Arabian oryx
- Przewalski’S horse (Mongolia).
- Guam rail
Reintroductions: recessive lethal alleles often a problem in founder populations:
e.g: California condor:
Wild populations heavily hunted and these Condor (oddly) also consumed lead shot like food resulting in a bottleneck in the population
Conservation was initiated but Chondrodytrophy (lethal form of dwarfism) became a serious issue - recessive autosomal allele at about 9%, probably due to founder effect.
Ralls et al (2000) determined that elimination of the allele by selection would require preventing over 50% of 146 birds from breeding, and the impact on diversity would be too great
Program was successful in the end, though this mutation is still segregating in the population
Reintroductions: Differing selective environments:
*relative effects of inbreeding and selection:
*Reproductive fitness vs Ne due to impacts of inbreeding depression, accumulation of deleterious mutations & genetic adaptation to captivity:
see example graphs in notes
^ increased genetic adaptation to captive environment
^ transfer to wild results in inbreeding depression a loss of this
->the ideal population may be somewhere inbetween?
Captive breeding programs
Impact of captivity on comparative fitness of fruit flies (Drosophila melanogaster)
Gilligan & Frankham (2003) Conservation Genetics 4:189-197
Experiment:
1) flies with a noticeable marker (white eyes) were reared under ‘benign’ conditions
2) After different numbers of generations, captive flies were mixed with wild type flies, and a ‘competitive index’ computed as the ratio of wild-type to hybrid flies born.
Results:
1) After 87 generations the fitness of flies in the captive environment increased by a factor of 3.33.
2) Effect started to level off at about 30 generations.
Example in the wild: hatchery vs wild salmon
Wild Salmonid
Lower survival egg to smolt
Higher survival smolt to adult
Efficient forager
Lower aggression
Lower social density
Higher territorial fidelity
Disperse in migration
Bottom habitat preference
Flee from predators
More variable shape
Brighter color
Larger kype
Smaller eggs
Fewer eggs
Higher breeding success
Hatchery Salmonid
Higher survival egg to smolt
Lower survival smolt to adult
Inefficient forager
Higher aggression
Higher social density
Lower territorial fidelity
Congregate in migration
Surface habitat preference
Approach predators
Less variable shape
Duller color
Smaller kype
Larger eggs
More eggs
Lower breeding success
HYBRIDISATION IS QUICK TO OCCUR:
see:
Hindar, K., Fleming, I.A., McGinnity, P. and Diserud, O., 2006. Genetic and ecological effects of salmon farming on wild salmon: modelling from experimental results. ICES Journal of Marine Science, 63(7), pp.1234–1247. https://doi.org/10.1016/j.icesjms.2006.04.025
HYBRIDISATION HAS NEGATIVE IMPACT ON WILD STOCK SURVIVAL
See:
Coral San Román et al. (2025) compared proportion of salmon
hybrids and population size, and found that when the proportion
of hybrids was high, the population size was smaller.
Outbreeding depression
2 main causes (see Essay 6A in Meffe &Carroll)
1: co-adaptation:
when local population evolves a genome that is internally balanced with respect to reproductive fitness.
e.g. owl monkey (Aotus trivirgatus)
local populations have differing chromosomal structure.
^captive breeding attempts failed until pairs from same geographic population were mated (de Boer 1982). Populations now considered different species by some.
e.g.stickleback spawning probability reduced when different types mated – outbreeding depression Peichel et al 2001
- local adaptation:
when local populations adapt to local environments.
e.g. Ibex (Capra ibex) (Greig 1979)
* became extinct in Tatra mountains (Czechoslovakia) through overhunting.
* successful translocations were from Austria, which has similar environment.
* BUT: later introduction from Turkey, where climate is much warmer.
→hybrids rutted in early autumn NOT winter (as native Tatra population did)
→ kids born in February - coldest month of the year
→ extinction.
E.g. Pika
Meek et al. (2022) describe local climate adaptation in pikas in the US.
^hypothetical hybrid would be less adapted to either surrounding
Summary
1) Founder events lead to loss of diversity, distortion of allele frequencies & potential inbreeding depression. Aim for at least 20 individuals in founder population.
2) Managing diversity means getting the most out of genetic diversity available in captive population by maximizing Ne/N.
strategies include:
a) Equalizing family size, sex ratios & population sizes in different generations.
b) Minimizing kinship (MK)
c) Maximum avoidance of inbreeding (MAI)
3) Reintroductions
a) Expression of recessive lethal alleles (e.g. California condor Chondrodytrophy).
b) Differing selective environments - captive environment may release selective pressure for traits that are deleterious in the wild.
c) Outbreeding depression - 2 main causes (coadaptation & local adaptation).
