Conservation Genetics Final

What are your methods for your project?

Field methods

Describe what DNA you extracted (mitochondrial dna)

whole or partial?

MiSeq

Describe Why that method

What are three common pathways that increase the risk of species introduction in marine ecosystems? (Compared to natural dispersal in non marine ecosystems)

Ballast water, hull fouling

•Aquarium release, seafood trade

•Aquaculture escape

True or false: the number of escapes is proportional (1 to 1 relationship) to the number of new aquaculture sites

False

What is hybridization? What is one negative consequence with an aquaculture escapee, either for the organism or for the ecosystem?

individuals from two different species or distinct genetic lineages interbreed, producing offspring that carry genetic material from both parent populations.

Dilute or erase native genotypes

Reduced fitness: hybrids may be sterile or maladapted.

Under the right conditions, lead to speciation (via reproductive isolation)

What are two reasons why hybridization was already common in the ocean before human intervention?

External fertilization = gametes released into the water → less control over mate choice

Few physical or behavioral barriers compared to terrestrial systems

Large, continuous habitats (especially in the pelagic zone) make isolation difficult

What percentage of the ocean needs to be protected by mpas? Is California currently meeting the requirement?

30% by 2030 but currently at 10%

Imagine talking to a fisherman who’s concerned about a new mpa how can you explain the potential benefits of the mpa even though it might require him to fish in different areas?

If he’s right outside the mpa there will be more fish, and allowing them to grow larger allows for more fish to be reproduced and more fish in the long run

How can genetic tools help to inform the management of mpas? Provide specific examples

Can see the species diversity and connectivity of areas through FSTs to measure gene flow, or eDNA to measure biodiversity (describe how you’d do this)

What are some external (global or regional) threats to mpas? What are some threats that occur at a local level?

Rising temps, ocean acidity, pollution

Poor management, inadequate enforcement of rules, illegal fishing

What are three criteria (besides connectivity) commonly used to select mpas? Why is connectivity one of the most critical factors?

Biogeographic representation, ecosystem extent, economic and social importance, biodiversity

Maintains gene flow

What are two main models used to evaluate connectivity among mpas? Describe one in detail

Stepping stone model- population is represented as island that connect through gene flow

Highland model

What’s the difference between parentage analysis and alignment tests in the context of evaluating population connectivity?

It evaluates a store of dna of who its direct parents are, whereas the alignment test assigns individuals to the closest population origin. We can determine how spread out the population is

What traits are commonly used to select surrogate species for MPA assessment?

Surrogate: species that are easy to sample and representative of many other organism

Invertebrates: easy to track movements, broadcast spawners can be tracked by the current, easy to collect and experiment with/study

What are the advantages and disadvantages of using a flagship species instead of a more commonly used surrogate?

Flagship species: organism that is commonly loved and public wants to protect

Easy to get public support and funding

Disadvantages: might not represent other organisms well, harder to trace and sample,

What is a species?

What is the difference between allopatric and sympatric speciation? What type of speciation is hybrid speciation and what does hybrid speciation involve?

Separated by land, not separated by land

Sympatric: two separate species create one new species

What is a cryptic species? Why is it inadequate to assume they are the same species when makin management and conservation decisions? How can you evaluate which is which?

Species that look the same but are genetically different

They may have different behaviors and needs and ecology that need different management decisions. You can evaluate which is which through genetic tests such as barcoding/ amplicon analysis

What’s a crptogenic species?

We don’t know if it’s native or not, nit enough info on its history

Are all nonnative species invasive? Why or why not?

No, because they don’t always outcompete the native plants and have negative ecological effects on the ecosystem

What are some traits that increase the likelihood that a species will become invasive?

Generalist feeding, few predators, broad environmental tolerance

What is one consequence of biological invasion that can be considered direct or indirect?

Direct: predate on another species to extinction, take over space from natives

Indirect: change ph of water, become barrier from one species to another

Briefly argue whether conservation should prioritize historical genetic integrity or evolutionary potential?

If potential for gene flow and increasing number of individuals, historical

Evolutionary potential if they are struggling and may need stronger traits to continue to survive as a species, prioritize those that have evolutionary potential

Effective population size!! If less than 50, evolutionary potential

What are three ways we can manage the risk of invasive species in aquaculture?

Physical barriers, sterile stock, rapid response protocols

What are two reasons active restoration commonly used for coral species, but not for most other marine species?

Can be reproduced asexually and there is a very low effective population size for most species, bring a lot of tourism, broadcast spawners but so few others to reproduce with

What are three main methods of active coral restoration?

Assisted gene flow, selective breeding, assisted asexual reproduction

What are two major factors that limit coral sexual reproduction in the wild?

Broadcast spawning at different times, limited reproduction and low concentrations of corals

Slide ten long question

Because it’s a low census population, meaning effective population is even lower, meaning not many are contributing to future offspring and high potential to die out

The FL govt could release at least more than 13 captive genotypes to support short term survival

Which genetic technique (micro satellites or SNPs) is better for distinguishing different coral genotypes? Describe both methods

SNPs because we can see all small differences that distinguish them

Analyzing differences in single nucleotides polymorphisms

Micro satellites: looking at short repeated regions and less reliable

Describe how assisted gene flow can result in better …

What does it indicate

What is heterozygosity and how does low heterozygosity support the need for active coral restoration?

Presence of two alleles in an organism

Low had less genetic diversity overall

Coral can be assessed….

Select for the ones with long term potential to survive, medium

How do rats lead to lowered outcomes for coral reefs?

They eat the seabirds which causes them to not poop in coral reefs, decreasing the nutrients in the reefs and less coral

What is eDNA? How can it be used to monitor impact or removing rats from coral ecosystems?

Environmental dna

Test for biodiversity of the area over time, with hopefully an increase of biodiversity with less rats

How can you use eDNA to detect a species of interest?

Taking a water sample and seeing what evidence of the species is within the sample through its eDNA

What is one way to evaluate epigenetic changes to the genome?

Methylation (turning on or off portions of a genome)

What is RADSeq and why do many researchers propose to use it in genetic studies of their species?

Restriction site (where restriction enzyme cuts), making it simpler by not looking at a WHOLE sequence

Why is collecting blue rockfish from fishermen for RNA analysis not a best practice?

RNA degrades very fast and won’t be accurate

Illumina vs Sanger sequencing

Look at whole sequences with millions of reads

Looking at one region at a time

What is qRT-PCR and how can it be used to confirm RNA results?

Do whole sample RNA sequencing and look at one region of the gene of interest, targets specific gene regions, turn RNA into cDNA

Why is it important to collect environmental data long with genetic data in ecological studies?

To see what environmental influences and conditions are affecting genetics and adaptations of organisms