Ecological Genomics and Conservation Biology

Deborah L. Rogers Center for Natural Lands Management Genetic Resources Conservation Program Fallbrook, CA University of California The (relative) complexity of understanding genetic diversity of species

Trait Animals

Location of DNA Nucleus, Nucleus, chloroplasts, mitochondria mitochondria Chromosome size Redwood Human (examples) 31,600 Mb 3,000 Mb Ploidy Often > diploid Typically diploid

Mode of Varied Typically sexual reproduction Transmission Varied Biparental, genetics maternal Hybridization More common Less common 3. The Promise of Genomics: Linking phenotype with genotype

• Phenotypic traits • Allozymes • (DNA) Fragment-based methods

• (DNA) Sequence-based Candidate methods genes, SNPs 3. The Promise of Genomics: Linking phenotype with genotype

• Leveraged genetic discovery in ‘noncommercial species’ through gene resequencing (e.g., from genes identified in model or commercial organisms) • Screen for diversity within gene sequences (SNPs—Single Nucleotide Polymorphisms) • Allows direct diversity comparisons within and among species because orthology of genes can be determined • Increasingly high-throughput (many genes, many individuals) and affordable • Can link ‘candidate genes’ with fast molecular techniques (From: Kansas State University website) 4. Critical Genetic Information Needs in Conservation and Restoration Genetics

If Ecological Genomics is the answer, what are the questions? I. Defining Units for Conservation and Management

Location A B C

Lineages Environment Adaptations ? I. Defining units for conservation and management: Conservation priorities

Biodiversity Hotspots: Conservation International www.conservation.org II. Basis of invasiveness: comparative genomics

Invasive Pinus radiata in native pampass grasslands (preserves) in Argentina

Photo: S. Zalba II. Basis of invasiveness: comparative genomics

Camissonia cheiranthifolia in GGNRA • Two subspecies in California • The non-local subspecies – C.c. suffruticosa – introduced in 1982 to restore coastal dunes • Cross-breeding with native subspecies – C.c. cheiranthifolia –is evident • Both introduced plants and hybrids have invasive qualities Photo: S.Fritzke Ecological Genomics

• Which genes are most important for how organisms respond to the environment? • What is the genetic basis for ecological responses to the environment? • What are the genetic and regulatory mechanisms involved in organismal responses to environmental change? • What is the ecological context necessary to understand gene expression within organisms? Ecological Genomics and Conservation Biology

1. Trends in Conservation Biology 2. The challenge of providing genetic information 3. The promise of Genomics 4. Critical genetic information needs in conservation and restoration 5. Application of genomic information 1. Trends in Conservation Biology

• Origins in 1970s • Discipline expansion • Broadening of species focus • MVPs, preserve design, inbreeding forensics, metapopulation dynamics, species interactions Genetic Conservation and Restoration

• Tracking natural • recovery processes • Restoration projects • Loss of diversity (genetic erosion) • Forensics • Hybridizations • Genetic contamination • Selecting in situ genetic reserves • Sampling for ex situ conservation • Baseline data for recognizing future perturbations Biodiversity: Increasing recognition of genetic diversity

• Listing species at sub-specific levels • Species interactions: importance of genetic diversity Genetic Diversity and Species Interactions

“Conserving genetic diversity is more than a species issue … it is an important community issue … nearly 60% of arthropod diversity could be accounted for by genetic diversity in cottonwood stands … MVP concept may be inadequate for describing the genetic diversity needed in a producer to maintain species diversity in the dependent community … conserving genetic diversity in dominant plant species may be just as important as conserving genetic diversity in rare and endangered species.” Whitham et al. 2003, Wimp et al. 2004.

(Photo from G. Allan) 2. The Challenge of Providing Genetic Information: the ‘Great Divide’

Molecular/allozyme Quantitative genetics • Traits expressed as • Traits that have a ‘presence/absence’ or continuous distribution of different alleles values or phenotypes • Influenced by several or • Measured in allele many genes frequencies and • Experimental design and distributions analysis separates • Single-locus (typically) ‘environmental’ effects • Typically reflect neutral from ‘genetic’ effects genetic variation • May reflect adaptive genetic variation Relationship between molecular and genetically based phenotypic variation

between molecular and phenotypic variation

Reed and Frankham 2001 III: Restoration genetics IV. Endangered species reintroduction and management

• Fragments of natural range • Disturbed or created environments • Prediction of response is critical Tree Species on the Federal (US) Endangered Species List (www.fws.gov)

Species Common name Listing date Status

Cupressus abramsiana Santa Cruz cypress 1987 E goveniana Gowen cypress 1996 T ssp. goveniana Torreya taxifolia Florida torreya 1984 E Betula uber Virginia round- 1978 T leaf birch Chioanthus pygmaeus Pygmy fringe tree 1987 E Juglans jamaicensis West Indian 1997 E walnut Prunus geniculata Scrub plum 1987 E Quercus hinckleyi Hinckley’s oak 1988 T V. Hybridization: Between native and introduced populations (e.g., restoration, landscaping, agricultural); distinguishing desirable (e.g., ‘genetic rescue’) from undesirable (e.g., outbreeding depression) hybridization. Particularly important with polyploid species (intraspecific hybridization among various cytotypes).

Inbreeding and Outbreeding Depression as a Function of Distance

inbreeding outbreeding depression depression

Fitness of Progeny Fitness (Photo: G. Allan)

Genetic Distance between Parents/Populations (After Kaye 2001) VI. Early warning of serious decline of species 5. Application of Genomic Information: Clients and Impact Currencies: • Prevention of species extinction • Assistance in species recovery, prevention of ‘listing’ • Increased adaptive potential of restored areas (land area) • Reduced costs of repeated restoration efforts

US Recovery plans for listed species: Average cost of recovery: $15.9 million

Decurrent False Aster (Boltonia decurrents) Federally threatened. Photo: Native Plants Database http://plants.usda.gov/ 5. Application of Genomic Information: Clients a) Government:

National Park System (US)

• 390 parks, totaling 84 million acres; budget of $2.4 billion (FY2005) • 400,000 acres to be restored • Many more to be revegetated post-fire (5-10,000 acres/yr)

NPS policies direct that parks use the most appropriate genetic and ecological organisms when conducting ecological restorations 5. Application of Genomic Information: Clients b) NGO, Private