Next-generation genomics technology, Conservation and Extinction

Transcription

1 Next-generation genomics technology, Conservation and Extinction Oliver A. Ryder San Diego Zoo s Institute for Conservation Research

2 Genome 10K Frozen Zoo living somatic cells collection 7,500 individuals 131 families 700 taxa 7,100 mammals 88 families 580 taxa 100 reptiles 30 taxa 270 birds 100 taxa 1 amphibian 1 taxon 1 fish 1 taxon

3 New Scientist 23 January, 2009 Sabre-toothed tiger (Smilodon fatalis) Extinct: ~10,000 years ago Suitable surrogate: 3/5 Neanderthal (Homo neanderthalensis) Extinct: ~25,000 years ago DNA preservation: 1/5 Suitable surrogate: 5/5 Short-faced bear (Arctodus simus) Extinct: ~11,000 years ago Suitable surrogate: 2/5 Tasmanian tiger (Thylacinus cynocephalus) Extinct: 1936 DNA preservation: 4/5 Glyptodon (Doedicurus clavicaudatus) Extinct: ~11,000 years ago DNA preservation: 2/5 Woolly rhinoceros (Coelodonta antiquitatis) Extinct: ~10,000 years ago DNA preservation: 4/5 Suitable surrogate: 5/5 Dodo (Raphus cucullatus) Extinct: ~AD 1690 DNA preservation: 1/5 Suitable surrogate: 3/5 Giant ground sloth (Megatherium americanum) Extinct: ~8000 years ago DNA preservation: 2/5 Moa (Dinornis robustus) Suitable surrogate: 2/5 Irish Elk( Megaloceros giganteus) Extinct: ~7700 years ago Suitable surrogate: 2/5 Giant beaver (Castoroides ohioensis) Extinct: ~10,000 years ago DNA preservation: 2/5 Gorilla (Gorilla gorilla) Extinct: Almost DNA preservation: 5/5 Suitable surrogate: 5/5

4 Conservation Genomics Potential applications of genome sequencing studies that contribute to the conservation of endangered species broadly include:! animal health immune function and regulation; disease diagnosis; characterizing and mapping genetic risk factors in small populations, including genetic diseases - H5N1 avian influenza!population assessments, monitoring and management recent evolutionary history bottlenecks, selective sweeps. phylogeography inference of spatial partitioning of genetic diversity over time and bias in geographic patterns of male- vs. femalemediated gene flow.! reproductive biology, enhancement of reproduction and healthy offspring identification of genes that regulate events in the reproductive cycle - light cycle, olfactory and auditory stimuli; genes affecting implantation) imprinting of genes expressed in placentation and embryogenesis! identifying genes involved in adaptations dietary specializations; tolerance of environmental and/or dietary toxins; sensory modalities; morphological adaptations; mitigating environmental stresses; language acquisition; consciousness

5 When the last living thing has died on account of us, how poetical it would be if Earth could say, in a voice floating up perhaps from the floor of the Grand Canyon, It is done. People did not like it here. Kurt Vonnegut Po ouli

6 The Frozen Zoo Mission of the Frozen Zoo >7,500 accessionsfibroblast Over 6,500 accessions cultures To help preserve the legacy of life on Earth for future generations by establishing and maintaining genetic resources in support of worldwide efforts in research and conservation. Provides difficult to obtain but crucial resources for comparative and conservation genomics

7 How do we choose to invest our efforts? It might matter to the Future.

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9 Comparative genomics Identify functional elements of the human genome Open new doors to understanding evolution, development, and life history of species Identify genes, genetic basis of adaptations, host-pathogen co-evolution Analyze genetic variation and mutational processes Conservation Genomics Using all these insights, develop insightful approaches to!maximizing the potential success of gene pool conservation!efforts efforts.

10 Chicken genome project enables other avian genome projects California condor genomic studies: - showcase of application of genomic mapping methods for!!!!!!!!!!!!!!!!endangered species conservation efforts - segregating autosomal locus causing lethal chondrodystrophy can, in principle, be identified and a carrier test developed Michael Romanov, et al.

11 Identification of sex in California condors

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13 Available technology Gene pool management program Frozen Zoo Resources Species Survival Plan Carrying capacity Founder Genome Equivalents benefit Population management goals Cells of genetically valuable animals available Cloning rationale: Exploration of current opportunities in application of cloning technology in support of gene pool conservation efforts!? Reproductive physiology Ova - surrogates Neonatal husbandry Behavior

14 Banteng, Bos javanicus Studbook # 391, born 1974 at San Diego Zoo; transferred to SDWAP 1978; Died 1980 at San Diego Wild Animal Park Somatic cell nuclear transfer Cloning of a male banteng, Bos javanicus A genetically valuable male cell culture established 1976 clone delivered 4/1/2003

15 New Scientist 23 January, 2009 Sabre-toothed tiger (Smilodon fatalis) Extinct: ~10,000 years ago Suitable surrogate: 3/5 Neanderthal (Homo neanderthalensis) Extinct: ~25,000 years ago DNA preservation: 1/5 Suitable surrogate: 5/5 Short-faced bear (Arctodus simus) Extinct: ~11,000 years ago Suitable surrogate: 2/5 Tasmanian tiger (Thylacinus cynocephalus) Extinct: 1936 DNA preservation: 4/5 Glyptodon (Doedicurus clavicaudatus) Extinct: ~11,000 years ago DNA preservation: 2/5 Woolly rhinoceros (Coelodonta antiquitatis) Extinct: ~10,000 years ago DNA preservation: 4/5 Suitable surrogate: 5/5 Dodo (Raphus cucullatus) Extinct: ~AD 1690 DNA preservation: 1/5 Suitable surrogate: 3/5 Giant ground sloth (Megatherium americanum) Extinct: ~8000 years ago DNA preservation: 2/5 Moa (Dinornis robustus) Suitable surrogate: 2/5 Irish Elk( Megaloceros giganteus) Extinct: ~7700 years ago Suitable surrogate: 2/5 Giant beaver (Castoroides ohioensis) Extinct: ~10,000 years ago DNA preservation: 2/5 Gorilla (Gorilla gorilla) Extinct: Almost DNA preservation: 5/5 Suitable surrogate: 5/5