Genetic Diversity and Marine
Populations
Applications of Genetics to
Conservation
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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 coadapted 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
Fin Whale
Balaenoptera physalus
Minke Whale
Balaenoptera acutorostrata
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 Salmon
Oncorhynchus 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
Winter Run
Spring Run
Fall Run
Late Fall Run
Fall Run
Spring Run
From Banks et al. 2000
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)
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
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