Genetic Diversity and Marine Populations

Applications of Genetics to Conservation

• Define the limits of populations of concern

• Measure gene flow between populations

• Identify genetically isolated populations

• Identify sub-population (deme) structure for demographic analysis (e.g. PVA)

• Quantify rate at which genetic variation is being lost

Applications of Genetics to Conservation

• Describe historical population characteristics• Used to identify parents, offspring or close

relatives– For captive breeding programs – For endangered wild populations

• Delineate cryptic and sibling species• Help with population augmentation• Assist with population restoration

Genetic Analyses

• Assume basic knowledge of population genetics– Genes, alleles, selection, drift, recombination– Allozyme vs. DNA sequence analysis

• Discuss limited details of molecular methods– Allozyme (protein) vs. DNA analysis– Effective population size– Mutation rates

Habitat Restoration

• Restoring marine habitats may involve replanting marine and coastal plants (sea grasses, salt marshes)

• Choosing the source of plants (or animals) may require matching genotypes with local ones

• Need genetic analysis of remnant plants in area as well potential source locations

Population Augmentation

• In some cases, there is a need to augment populations that are critically endangered

• This must be done with individuals that are closely related (some but not too much genetic differentiation)

• Introducing unrelated individuals will increase genetic diversity but avoiding outcrossing depression

Restoring Native Oysters

Native Olympia Oyster Ostrea lurida

Restoring Native Oysters

• Restoration of native Olympia oysters in western U.S. estuaries

• Historically an important fishery, but decimated in 1800s

• Important foundation species that increased benthic diversity and water quality

• Populations have not recovered despite no harvest for 100 years

Enhancing Native Oyster Populations

• Method for augmenting populations is to hatchery rear and outplant juvenile oysters

• Should there be mixing of breeding population within and among estuaries?– If populations are inbred, then using oysters from

elsewhere could help viability – If populations are adapted to local habitat, then using

oysters from elsewhere could be harmful (breakup co-adapted gene complexes)

• Molecular genetics will not answer this, only breeding experiments

Forensic Analysis

• Many countries have pledged to respect International Whaling Commission (IWC) agreements

• Baker and Palumbi (1994) tested whale meat for sale in Japanese markets using genetic sequencing (PCR and mtDNA)

• The wanted to determine if the Japanese were illegally selling whale meat from protected species

• They found humpback, minke and fin whale samples that were likely in illegally taken

Exploited Whales

Humpback Whale Megaptera novaeangliae

Minke WhaleBalaenoptera acutorostrata

Fin WhaleBalaenoptera physalus

Forensic Analysis

• Baker et al. (1996) also used mitochondrial DNA to test “whale meat” sold in Japan and South Korea

• Found a dolphin, a beaked whale, and a possible subspecies of Bryde’s whale

• Again showing that protected species are being sold as whale in some Asian retail markets

Comparisons of Historical Diversity

• Comparisons of current genetic diversity in endangered populations can be compared with historical samples

• Museum samples (preserved, dried) can provide estimates of genetic variation when populations were larger/widely distributed

• Comparisons of historical and recent samples can provide estimate of loss of genetic diversity

• Can provide estimate of historical population size which may inform conservation efforts

Assessing Historic Populations

• In some cases, genetic methods can be used to estimate past population sizes of endangered species

• Roman and Palumbi (2003) used genetic methods to estimate historic population sizes of three baleen whales

• Neutral genetic variation increases with population size, but current levels of genetic variation are much greater than could be maintained by present population sizes

Assessing Historic Populations

• With estimates of mutation rate and breeding population size, you can estimate how big the population must have been to create the current genetic variation

• Long term effective population size Ne(f) is related to genetic diversity Ф and mutation rate μ

• Ф = 2 Ne(f) μ

Assessing Historic Populations

• Genetic estimates suggest that population sizes historically were very large 6-20 times greater than earlier estimates

• This means that conservation targets set by IWC (Intl. Whaling Comm.) based on low historical populations are far too low

• Much longer recovery times (larger populations) would be needed before whaling could resume

Historic Whale Populations

From Roman and Palumbi 2003

Historic Whale Populations

From Roman and Palumbi 2003

Historic Whale Populations

From Roman and Palumbi 2003

Assessing Population Structure

• Assessing genetic divisions within populations of species of conservation interest among the most important areas of conservation genetics

• Determine rates of gene flow and isolation of populations is critical to species management

Population Structure

• Older protein studies used differences in allele frequencies to compare populations

• Frequencies of alleles (a,b,c,…) were calculated• Alleles were all treated as same• Now DNA sequence analysis allows determining

the phylogenetic origin of an allele– Is it rare?– Is it specific to a certain population?

• Both phylogenetic information as well as allele frequency information is used

Population Structure Within Species

• Avise (1992) compared genetic structure of mitochondrial DNA in 18 species from Florida including fish, birds, reptiles, inverts

• In all 18 spp. they found distinct differences in populations from the Gulf vs. the Atlantic

• Clear case for restricted gene flow• Showed distinct biotic realms, but also made

strong case for conserving these are distinct units

Humpback Whales

• Humpback whales (Megapter novaeangliae) show hierarchical structure both within and between oceans

• Populations that spend summers off central California were very different than those spending winters off Hawaii

• Mitochondrial DNA methods showed distinctions between populations

Humpback Whales

• However, another method (RFLP analysis of introns) did not show that the Hawaii and California populations were distinct

• Several reasons why this might be the case– Mitochondrial methods only work for females (maternally

inherited) so maybe males migrate and females don’t– Mitochondrial loci are much more subject to genetic drift than – Nuclear loci take about 4 times longer for drift to have same

effect

• Both methods did agree that North Atlantic and Antarctic populations do differ from north Pacific populations

Discriminating Chinook Salmon Runs

• Ocean-going chinook salmon as anadromous and return to rivers to spawn

• CA populations returning to the Sacramento-San Joaquin River system occur in four spawning runs– Fall run (Oct-Dec)– Late-fall run (Jan-Apr)– Winter run (Apr-Aug) – Spring run (Aug-Oct)

Chinook SalmonOncorhynchus tshawytscha

Chinook Salmon Life History

Discriminating Chinook Salmon Runs

• Microsatellite alleles are used to determine whether winter run chinook can be distinguished from other runs

• Microsatellite alleles are repeated sequences (e.g. CACACACA) that can vary in size (different numbers of repeats)

• Microsatellite variation can be used to distinguish closely related populations within a species such as salmon runs

Discriminating Chinook Salmon Runs

• Banks et al. (2000) used microsatellites (10 loci) to see if they could distinguish the four runs of salmon in the Central valley

• They found that winter run was very distinct and they could also distinguish fall and late fall runs

• Spring runs turned out to be clearly distinguished but two separate runs (Butte Creek very different from Mill and Deer Creek

From Banks et al. 2000

From Banks et al. 2000

Winter Run

Spring Run

Fall Run

Spring Run

Fall Run

Late Fall Run

Captive Breeding Programs

• For highly endangered populations, captive breeding programs may be needed

• Winter run chinook salmon in Sacramento River is the focus of a captive breeding program

• Mature fish brought into lab and spawned• Goal in small population is to breed individuals

with low relatedness (increase genetic diversity)• DNA fingerprinting can be used to group

individuals and the most dissimilar chosen for breeding pairs

Morphological vs. Genetic Similarity

• Key issue is that morphology (shape/size) doesn’t match up with genetic differences

• Organisms that are morphologically or otherwise ecologically distinct may be identical genetically

• Organisms that are distinct genetically may be nearly identical morphologically

Sibling and Cryptic Species

• Species that are similar morphologically but genetically distinct are sibling species

• Sibling species that are not discovered are known as cryptic species (they become siblings once determined)

• The oceans are believed to be full of groups of cryptic sibling species

• This complicates the task of conservation of these groups

A Cryptic Invasion

• Bay mussels have been a focal species for intertidal ecology for decades

• Many studies on the west coast have studied competition between California mussels (Mytilus californianus) and Bay mussels (Mytilus edulis)

A Cryptic Invasion• Geller 1999 and colleagues showed that

Bay mussels that had been identified for decades as Mytilus edulis were really two other mussels

• They also found that historically the northern mussel Mytilus trossulus had been present in southern California

• It had been completely displaced by a cryptic invasion of Mytilus galloprovicialis

MusselsMytilus edulis

Cryptic Coral Species

• High levels of genetic diversity among many coral species

• Knowlton et al. (1992) found that Monastrea annularis, a important and abundant shallow water coral was found to be actually 3 spp.

• This “species” had been studied closely for decades and have been used to assess historical climate change

Cryptic Coral Species

Cryptic Coral Species

Cryptic Coral Symbionts

• Organisms with associates such as corals with zooxanthellae (symbiotic algal cells) may be also be genetically distinct

• Rowan et al. (1997) found that not only are the zooxanthellae of the closely related Monastrea different, but the symbionts on different parts of the coral head are very different genetically

Cryptic Coral Symbionts

From Rowan et al. 1997

Cryptic Coral Symbionts

From Rowan et al. 1997

Conclusions

• Genetics are an important tool for marine conservation

• It is essential for defining populations and species as well a tool for historical reconstruction

• Together with demographic analysis, these tools help form the basis of conservation management in the sea