Biodiversity and other risks of intensive and selective breeding

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Summary of
Biodiversity and other risks of
intensive and selective breeding
Ezemvelo KZN Wildlife & Scientific Authority
Intergovernmental Task Team
DEA Consultation, Pretoria, 2 December 2015
Intensive and selective breeding
Deliberate selection of and breeding for
selected animal traits, usually in controlled
• E.g. coat colour & pattern; horn & body size
• Simple inheritance, recessive genes, more predictable (e.g.
coat colour)
• Complex inheritance, Quantitative features, (e.g. horn length,
body size)
• E.g. German Shepherd hip dysplasia
Definition: Domestication
• Domestication (from Latin domesticus: "of the
home") is the process whereby a population
of living organisms is changed at the genetic
level, through generations of selective
breeding, to accentuate traits that ultimately
benefit the interests of humans.
Intensive & Selective Breeding
The wolf….
Evaluation of Biodiversity Impacts
• Spatial scale
– Area
– Processes impacted
• Number of species
– Directly
– Indirectly
• Numbers of individuals
– Directly
– Indirectly
• Likelihood
• Severity
• Permanence/
Number of species affected
(colour morphs)
Variet Names*
Black, White, Copper, Coffee
Black, Saddled, Black-backed, Grey, Black nosed, Whiteflanked
Blue wildebeest
Golden, King
White, Yellow, Copper, Skilder, Woolly, Red, Speckled,
Top Deck
White, Black, Brown, Zebra-striped
Red hartebeest
Skilder, Gold, Cardinal, Scimitar
Plains zebra
* Unlike livestock1 colour
variants not accurately described
Black x Blue Wildebeest
Black x Blue = Red; >40% black wildebeest
tested have introgressed blue wildebeest genes
Nyala x Kudu
Deliberate hybridisation
Waterbuck x Lechwe
Deliberate hybridisation
East African x southern
African Buffalo
Breeding for long horns
Blesbok x Bontebok
>40% of blesbok tested have introgressed
bontebok genes
Tsessebe x Red
Western x Southern
Deliberate hybridisation for body and horn size
Zambian x South African
Morphological differences, not supported by
genetic evidence
40% (10/26) commonly traded antelope
species have colour morphs; safe to
assume 100% eventually
69% (18/26) commonly traded antelope
have been genetically manipulated
Risks of Intensive and Selective Breeding of
• Inbreeding, Outbreeding, directional change
• Reduced heterozygosity
– Of captive stock
– Of species as a whole if conservation only happens inside PAs
• Founder effects
• Loss of rare alleles/allelic diversity
– Wildebeest simulations, agricultural examples
– Loss of adaptive potential to climate change
• Impact related to size of wild population
– e.g. roan
• Active hybridisation
– e.g. Southern x Western Roan, Waterbuck x Lechwe
Outbreeding Depression
Extrinsic mechanisms
•Alpine Ibex overhunted
in European Alps and
augmented by
translocations from
population in the Sinai
Peninsula and Turkey
•Southern ibex breed
earlier in the fall and
hybrid young were born
in the middle of alpine
Habitat loss and fragmentation
• New trend is resulting in:
– Habitat transformation
• Small enclosures, high stocking rates, trampling, loss of
habitat along fences
– Habitat fragmentation
• Additional fencing, disruption of processes of gene
flow, dispersal and migration
– Death of animals
• Pangolins, tortoises, pythons
– Does not trigger EIA process
Misuse of chemicals
• Large incidence of off-label use of agricultural remedies
– Unregistered use of anthelmintics in game feed supplements
• No control over dosage rate leading to resistance
• Avermectin type anthelmintics that are ingested pass through rapidly and
are deposited in the dung, posing a severe risk to dung beetles
• Constant dosing compromises natural immunity against endoparasites
– Unregistered use of ectoparasiticides with ‘’automatic applicators’’
• No control over dosage rate leading to resistance
• Constant dosing compromises natural immunity against symbiotic
– Translocation of hosts and/or ticks to non-endemic areas, and high
stocking rates, resulting in necessity for treatment with acaricides
• Leading to resistant strains of parasites that could have impacts
both on natural populations of game and on agriculture
• E.g. Schroder & Reilly (2013) concluded that the tick species
Rhipicephalus decoloratus became resistant to the acaricide
treatment being applied in intensive breeding camps.
Predator persecution
• High value animals protected at all costs
– Fencing
– Intolerance of (all) predators
– Control of species that dig under fences e.g. porcupines
• (Large?) increase in (irresponsible and illegal) use of poisons
– Predator control and prevent other species feeding on food provided
to game
– Non-selective
– Non-target – vultures, ground hornbills, baboons
– Scale difficult to document
• Endangered species impacts
– Noted as a threat to ground hornbill reintroduction programme
– Vulture deaths
– Leopard DCA permits increase
Ecosystem-level impacts
• Predator-prey evolution
– Species
– Ecosystem as a whole
• Host-parasite evolution and resistance
• Natural selection
• Breakdown of functional ecosystems and
ecosystem processes
– Fire, dispersal, gene flow
• Disinvestment in extensive (= conservation
compatible) land use
Behavioural changes
• Imprinting on colour morph
– Rapid spread of recessive genes
Animal wellbeing
• Physiological
– Springbok colouration is adaptive; white parallel to sun
(cooling), dark perpendicular to sun (warming), camouflage
– Black animals suffer more during high temperatures (Hetem
et al., 2009, 2011)
– ‘’Commodities’’ moved to hotter/colder, drier/wetter
environments than adapted to
– Buying animals without experience, land etc.
• Cancers, melanomas, cataracts in white varieties
• Behavioural
– Aggressiveness/docile
– Naive to predators
• Loss of disease resistance
– Mate choice designed to maximise immunity – MHC
• Risk to tourism and hunting industry
– Loss of support for hunting
– Loss of land for conservation
• ‘’Brand South Africa’’
Parallels from Aquaculture, Agriculture,
Parallels (1): Aquaculture
• Breeding for traits (size, growth rate), escape or
release back into systems
– E.g. Brook Charr
• suggests that current stocking practices have the potential to
significantly alter the functional genetic make-up of wild
• stocking with a domestic strain affects the genetic integrity
of wild populations (change in diversity, homogenization of
population structure, increased individual genetic
admixture) not only at neutral markers, but also at coding
– FABIEN C. LAMAZE, et al. 2012. Dynamics of introgressive
hybridization assessed by SNP population genomics of coding
genes in stocked brook charr (Salvelinus fontinalis). Molecular
Ecology 21, 2877–2895
Parallels (2a): Agriculture
• Loss of genetic diversity through selective breeding
e.g. Chinese pigs
– Haplotype diversity in randomly bred populations was significantly
greater than the selectively bred populations (h=0.732 vs. 0.425 and 0,
exact test, P≤0.0036). These findings demonstrate that selective
breeding generated low genetic diversity compared to randomly bred
pig breeds.
– Meeting some productive requirements comes at the cost of diversity.
QU Kai-Xing et al: 2011.Genetic differentiations between random and selectively breeding pig populations in
Yunnan, China . Zoological Research 32(3): 255−261
e.g. cattle, sheep & goats
– Performance improvement of industrial breeds at cost of loss of
genetic resources
• C R Biol. 2011 Mar;334(3):247-54. doi: 10.1016/j.crvi.2010.12.007. Epub 2011
Feb 1. Conservation genetics of cattle, sheep, and goats. Taberlet P et al.
– The efficiency of modern selection methods successfully increased the
production, but with a dramatic loss of genetic variability. Many
industrial breeds now suffer from inbreeding, with effective
population sizes falling below 50.
• Taberlet P. et al. 2008 . Are cattle, sheep, and goats endangered species?.Mol
Ecol. 17(1):275-84
Parallels (2b): Agriculture
• Domestic gene introgression into wild populations is a
problem throughout the world
e.g. free-living Soay sheep of St Kilda, and more modern breeds
– The haplotype carrying the domesticated light coat colour allele
was favoured by natural selection, while the haplotype
associated with the domesticated self coat pattern allele was
associated with decreased survival.
– Admixture has the potential to facilitate rapid evolutionary
change, as evidenced by the presence and maintenance of coat
polymorphisms in the Soay sheep population.
• Feulner PG, et al. 2013. Introgression and the fate of domesticated
genes in a wild mammal population. Mol Ecol. 16):4210-21. doi:
• Cancers and melanomas with white varieties e.g. Hereford
Parallels (3): Wing-shooting
• Mallard Ducks in America, domesticated variety
released for wing-shooting
– differences in egg production, fertility, growth rates,
and body weights linked to genetic differences
• Resulting in:
– >10% wild mallards have introgressed domestic genes
– improper timing of migration and nest initiation,
decreased broodiness leading to high rate of nest
and brood abandonment
Summary of Risks
Animal wellbeing
Habitat Loss
Habitat fragmentation
Predator persecution
Reputational (=economic)
Loss of parasite/disease
Economic (pyramid scheme)
Disruption of evolutionary
Diversion of scarce
conservation resources
Note 1:
Natural selection can’t be relied upon
• Colour morphs rare in nature, natural selection acts against
• Artificial selection, increase in frequency
• So won’t natural selection quickly remove these genes from the
population after introgression?
• Escapes will happen
• Frequency of escapes/introgression will increase
– Increase in numbers of populations
– Deliberate mixing with natural populations for hunting
– Values will drop, incentive to keep separate decreases
• Bubble bursts
• Natural selection no longer operational
– Selective pressures to remove colour morphs no longer operational e.g.
predation, climatic extremes
– Natural selection may select for domesticated traits (Saoy sheep example)
Note 2:
Can’t manage PAs and farms
• Biodiversity mandate nation wide, not just
protected areas (Public Trust)
• Insufficient numbers in PAs
• PA fences porous by design or neglect
Note 3:
Intensive and Selective Breeding is
NOT Conservation Breeding
Conservation Breeding
Intensive & Selective Breeding
Specific objective of breeding for
successful release into the wild to
conserve the species
Inbreeding and loss of
genetic diversity
Maximise diversity of founder
Maximise heterozygosity through
managed stud books
Behavioural changes
Maintain traits of wildness, adaptation
to natural environment
Breeding without specific objectives of release
(sale to other breeders, hunters), other than for
hunting shortly after release; no registered
conservation programmes with plans to release
to the wild
Selection of specific traits as a small subset of
overall gene pool
Active inbreeding
Stud books starting to be used, but to maintain
traits not diversity
Selection of docile animals
Wise to predators
No concern for maintaining/teaching predator
Evolution and
Widest possible range of alleles to
confer future adaptation potential
No concern, or active selection of a subset of
alleles coding for specific traits
Parasite and disease
Retain parasite and disease resistance so Treated so no ongoing evolution of parasite and
released animals are able to survive
disease resistance; husbandry resulting in
breeding of resistant parasites through use of
products outside of registration
Loss of resistance (MHC)
Who else is concerned?
• International Council for Game and Wildlife Management
• IUCN Antelope Specialist Group, 2015
• Species Survival Commission of IUCN
• Association of Zoos & Aquariums, 2011
• NSPCA, 2015
• Hunting clubs/associations
SA Hunters and Game Conservation Association, 2014
Boone & Crockett Club, 2015
Confederation of Hunters Associations of South Africa
Professional Hunters Association of South Africa, 2015
Safari Club International, 2015
• All Provinces
– KZN Wildlife, 2015
• Large areas of uncertainty, but important lessons from
aquaculture, agriculture and the pet trade
• What it is NOT
– Not conservation breeding
– Not contributing to conservation objectives/targets e.g. Red
List assessments
• What it IS
– Is resulting in significant long term risks to biodiversity and
possibly the economy
• What is NEEDED
– Risk averse regulatory approach (regulatory authorities to take
a risk averse approach to protect biodiversity and the broader
economy in terms of the Public Trust)
– Holistic view (direct and indirect impact)
– Research to quantify risks

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