Lecture notes

*Assume that you have a metapopulation consisting of five subpopulations with 25 individuals each. Assuming complete isolation, what is the loss of HS per generation? What happens to HT? Assuming complete panmixia, what is the loss of HT per generation? What happens to HS? *

(5*25) = 125 (1/125)= ?

*If population bottlenecks negatively impact population fitness and local adaptation positively impacts fitness, how can invasive species be successful?*

-Can be a mix from several source populations. -More individuals and more release events, the more likely it is that a spp becomes invasive -In plants, vegetative reproduction and selfing prevent inbreeding depression and loss of He

*Introduced species generally go through a founding population bottleneck. Why are introduced species often so successful if population bottlenecks are harmful?*

-Can be a mix from several source populations. -More individuals and more release events, the more likely it is that a spp becomes invasive -In plants, vegetative reproduction and selfing prevent inbreeding depression and loss of He

*Invasive species that have not had the opportunity to develop local adaptations often replace native species that we would expect to be locally adapted. Why?*

-Some spp are better competitors because they evolved in a more competitive environment -Absence of enemies: herbivores, predators -Local adaptations may only be important during extreme events like drought or flooding

*Exploited populations face 4 main issues with respect to genetics. What are they?*

1. "Unnatural" selection 2. Spatial Structure 3. Effects of releases 4. Management and recovery

*Genetic variation can either be greater or smaller in the introduced population versus the source population. Explain why.*

1. Bottleneck, so introduced spp has less genetic variation than populations in the native range 2. Admixture in introduced pops, so in the introduced population more variation than populations in the native range

*Describe 4 reasons why hybridization may act as a stimulus for invasiveness.*

1. Evolutionary novelty: hybridization can produce novel genotypes or phenotypes that do not occur in either of the parental taxa 2. Genetic variation: Increase in heterozygosity and allelic diversity may provide more opportunity for natural selection to cause adaptive change 3. Fixed heterosis: Many invasive plant species have mechanisms that can fix genotypes at single or multiple loci that demonstrate heterosis. Increased fitness via fixed heterozygosity 4. Reduction of genetic load: In small, isolated populations, deleterious alleles become fixed by drift and over time they accumulate leading to the slow erosion of fitness. Hybridization reduces genetic load.

*What are the three spatial scales of metapopulations and how do they affect genetic variation?*

1. Local Scale: Interaction of individuals during routine feeding/breeding activities 2. Metapopulation Scale: Infrequent movement of individuals from one population to another usually across unsuitable habitat 3. Species Scale: Entire geographic range of the species. Individuals usually have no chance of moving to most parts of the range

*How might you maximize genetic and ecological diversity when funding a captive population?*

1. Max the number of surviving subspp 2. Max genetic variation at the sp level 3. Max genetic variation at the susp level

*Describe four main factors that affect gene flow.*

1. Mobility: mobility of birds compared to mammals 2. Barriers to dispersal: Water bodies, mountains ranges for terrestrial spp. dry land for aquatic spp. 3. Mode of reproduction: Self-fertilizing plants don't disperse the sae distance as outcrossing plants 4. Interspecific interactions: tightly linked to one anther as prey/parasite/pollination

*What are the purposes of conservation breeding?*

1. Provide demographic & genetic support to wild populations --> Captive individuals should genetically match to wild populations 2. Establish sources for founding new populations in the wild --> Provide enough genetic variation to adapt to new environment 3. Prevent extinction of species that have no intermediate chance of survival in the wild --> Ensure sp can be maintained in captivity: propagate individuals that can reproduce in captivity

*List the three ways in which degradation affects strands of DNA. Upon what does the rate of decay depend?*

1. Reduced quantity of DNA and so it is sensitive to contamination 2. Broken strands, which reduce the length of fragments that can be amplified 3. Damage, so some mutations aren't really mutations Rate of DNA decay depends on constant temperature, temperature & humidity -Cold & Dry = good - Hot & Humid = bad

*Which three criteria have been used to define Evolutionary Significant Units?*

1. Reproductive isolation and adaptation 2. Reciprocal monophyly 3. Exchangeability of populations

*What are the 3 models that explain 3 hybrid zone persistence?*

1. Tension Zone Model: Balance between parental dispersal into hybrid zone and selection against less fit hybrids 2. Bounded Hybrid, Superiority Model: Hybrids are more fit than either parent in the hybrid zone, but less fit than parents in the parental zone 3. Mosaic Model: Similar to Bounded Hybrid Superiority Model but habitat is patchy rather than a gradient or linear. Parental and hybrid forms are each associated with a set of environmental variables.

*You are going to reintroduce golden-lion tamarines frm the National Zoo to Brazil. What issues would you consider?*

1. Where to release individuals? 2. How many populations to establish? 3. How many individuals to release? 4. Age & sex of individuals to release 5. Which and how many source populations to use 6. How to monitor the population after release

*Give 8 ways for which the analysis of ancient DNA is helpful to conservation. Give examples for each.*

1. aDNA allows us to look at the past (Ne, gene flow , population differentiation, levels of genetic variation) and allows us to set conservation goals. 2. Helps us decide what to protect. Validity of species can be confirmed. Ex: Long-billed reed warbler 3. Recent patterns of differentiation either the result of recent fragmentation & drift of genuine long-term differentiation. Ex: Subspecies of Sierra Nevada red fox & San Clemente loggerhead shrike 4. Conservation breeding & restoration: Can tell if populations were once connected by gene flow and can use animals from each population for breeding programs. Ex: European Common Hampster Also, reintroduction, and past range to broaden suitable habitat. Ex: Laysan Duck 5. Can be used to quantify the degree of introgression. Ex: Great Lake Wolves and Coyotes 6. Human impact. Ex: Genetic variation in wild sea trout before and after aquaculture activities 7. Population sizes. aDNA can estimate Ne prior to bottlenecks and help set conservation goals. 8. Climate change. Determine how past populations dealt with climate change (did they migrate, die, adapt). Ex: Pocked gophers in Yellowstone

*What is a metapopulation?*

A population that consists of a number of subpopulations in suitable habitat patches where the absence of individuals is determined by extinction and their presence is determined by recolonization from other subpopulations.

What are hybrid swarms?

All individuals are hybrids

*Describe two species concepts*

Biological Species Concept: reproductive isolation and isolating mechanisms Phylogenetic Species Concept: monophyly - all members of a sp. must share a common ancestor

*What type of DNA is inherited from both parents (biparental)? What types of DNA are inherited from one parent (uniparental)?*

Biparentally: Nuclear DNA Unipparentally: Organelle DNA

*Exploited populations are often supported through captive breeding. Explain how releases of captive individuals may affect the wild population genetically.*

Can cause: 1. Loss of genetic variation (Released individuals may carry pathogens that decrease the wild population's fittness and Ne) 2. Loss of local adaptations 3. Change in population composition 4. Change in population structure Genetic effects are often not monitored

*How might you measure differences in chromosomal variation?*

Centromere location Banding pattern - some regions of DNA condense more than others forming dark bands

What is genomic extinction?

Combinations of genotypes over the entire genome are lost causing loss f an evolutionary lineage

Ex situ conservation

Conservation components of biodiversity outside their natural habitat (Captive breeding, Germplasm banking, Zoos, aquaria)

How does metapopulation structure affect genetic variation?

Depends on spatial and temporal scale

How does lineage sorting influence gene trees?

Different genes sort at different rates, so you can get discrepant genealogical relationships for different types of genes

*How does natural selection influence gene trees?*

Directional selection and balancing selection can cause gene trees to differ from true species trees

*How is each subpopulation of a metapopulation linked?*

Dispersal and gene flow

*How does sampling error affect gene trees?*

Error can be caused by sampling too few or an unrepresentative set of loci. Too few or non-representative individuals are sampled for a species or too few geographical locations for a species are sampled. Gene tree will differ from true species

*What are some of the problems with captive breeding?*

Expensive, sometimes ineffective and may harm wild populations

*Explain how exploitation can lead to "unnatural selection".*

Exploitation can remove phenotypes that are favored in the wild, causing a reduction in productivity. Often selects for smaller size and earlier age at maturation.

*What type of DNA would you target, and why, if you wanted to: a) compare pollen and seed flow in a flowering plant; b) compare pollen and seed flow in a conifer species, and; c) compare male and female dispersal in a mammal species?*

For both a and b I would use both types Organelle DNA (mtDNA and cpDNA) because in flowering plants and conifers pollen and seed both are inherited uniparentally but from separate parents. For situation c I would use organelle DNA but just mtDNA and Y-chromosomes genes, and as well nuclear DNA because it is inherited maternally so the more differientation found in that sex will determine the sex-biased dispersal.

Three levels of biodiversity

Genes Species Ecosystems Need to protect all 3 to conserve biodiversity

*Explain what causes genetic change in captivity. Describe how you could minimize their effect individually and jointly.*

Genetic Drift: Equalize reproductive success among individuals and maximize founder size Natural Selection: Adaption to captive conditions, reduced adaptation to wild conditions. Minimize variance in reproductive success will delay adaptation

*How could you detect hybridization using genetics?*

Genetic analyses: Loci which have different frequencies in parental taxa. Diagnostic loci are fixed/nearly fixed.

*How can genetics be applied to invasive species research?*

Genetics can be used to assess source populations, number of introduced populations, and population structure of invasive spp

What are reproductive technologies?

Genome banking Cryopreservation Artificial insemination Cloning

*Why is the metapopulation concept important in terms of on-going habitat loss and fragmentation?*

Habitat is becoming increasingly fragmented.

*What are the possible fitness consequences of hybridization? Give some examples*

Heterosis: Hybrid vigor/superority. Ex: Inbred corn lines crossed to produce high yield hybrid corn. Squinting bush brown immigrants are 20 times more successful than inbred non-immigrants Outbreeding Depression: Hybrids have decreased performance relative to parental taxa. Ex: Shell coiling different directions in snails.

High differentiation vs. low differentiation

High differentiation: Few founders fr one patch Low differentiation: Many founders from several patches

*How does introgression influence gene trees?*

Hybridization and backcrossing can cause an allele from species X to introgress into species Y. So if you only use mtDNA the species would appear more similar than they really are

What is transgressive segregation?

Hybridization produces phenotypes that are extreme or outside the range of either parental type.

*Describe what happens when introgression occurs*

If hybrids are fertile, parental forms are displaced via hybrid swarms.

*If hybrids are sterile, can introgression occur? Why? How does it affect fitness? Are there any management actions that can be taken?*

If hybrids are sterile, no introgression, but it reduces reproductive potential and decreases population growth rate. Endangered species are wasting their reproductive effort. Management actions: Remove all hybrids and non-native spp.

*Explain how a species that is spatially structured should be exploited.*

If you're harvesting a mixed population, you need to ensure that individual populations aren't extirpated. ?

*What is genetic rescue? Given an example.*

Immigrants alleviate inbreeding depression and fitness increases Example: Mustard

*What is the difference between inbreeding and genetic drift?*

Inbreeding can be eliminated in a single generation, but loss of genetic variation is longer-lasting.

*What is the best situation for a metapopulation in terms of the amount of gene flow? *

Intermediate gene flow ?

What are 2 major reasons for outbreeding depression?

Intrinsic: Genetic incompatibilities between hybridizing taxa. Extrinsic: Reduced adaptation to environmental conditions Genetic Incompatibilities: Chromosomal (Different in number/structure) Genic (Interactions between genes from different taxa)

*Why are plants and inverts better candidates for conservation breeding than large mammals?*

Inverts: They have a high probability of success for both rearing and release. Small size = little space and cost. High reproductive potential. Plants: Can be maintained as dormant seeds for many years, which can increase generation interval and reduce genetic change. Can reproduce by selfing and cloning which can reduce breeding problems.

*Why might you get differences in phylogenies that were built using different genes?*

Lineage sorting Natural selection Introgression (following hybridization) Sampling error - genes, individuals & population ?

*Explain the difference between match probability and probability of identity*

MP is the ACTUAL probability of sampling ONE individual identical to the sample in hand. MP gives the probability of sampling the individual genotype in question, that was sampled previously. PIav is the AVERAGE probability of randomly sampling TWO individuals that have the same genotype. It is for computing the average power of a set of markers.

*Explain how exploitation can affect genetic variation and Ne*

Male biased or male harvest only causes uneven sex ratios that lower Ne.

*Define hybridization*

Matings between individuals from two populations or groups of populations, which are distinguishable on the basis of one or more heritable characters. Can reduce fitness and the integrity of evolutionary lineages, therefore it can be a serious problem for endangered species.

*Why are taxonomic and population units important when making decisions about protecting biodiversity?*

Need to identify and protect suitable taxonomic and population units in order to conserve biological diversity ?

*Describe the differences between nuclear and organelle DNA.*

Nuclear DNA: Biparentally inherited and one copy of DNA per cell Organelle DNA: Uniparentally inherited and both versions of mtDNA and cpDNA have 1000 copies/cell. More sensitive to bottlenecks

*Describe three temporal components of biodiversity*

Past - ancient lineages Present - current patterns of diversity Future - diversity required for future adaptation

*What is a phylogenetic tree?*

Pattern and timing of branching events in evolution history

What are two groups of taxonomic classification?

Phenetics Cladistics

*Describe population-based and individual-based methods for characterizing genetic relationships*

Population-based: Dendrogram based on genetic similarity of populations. Use a clustering algorithm to group populations with similar allele frequencies. Individual-based: Identify populations by identifying genetically similar individuals first then look at relationships among populations.

What is the probability of identity?

Probability of identity: Probability of randomly sampling two individuals that have the same genotype for the loci being studied.

*What is the most important factor in predicting whether an introduced species will become established?*

Propagule: A dispersal vector - any disseminitive unit or part of an organism capable of independent growth (seed, spore, tuber, root, shoot)

*What are the pros and cons of using uniparentally inherited DNA?*

Pros: Can follow transmission of material/paternal genotypes through time, can look ad differences in dispersal, can identify hybrids Cons: Single inherited so it may not reflect the true history of the species, not representative of populations as a whole, better to use mix of markers

*What is a hybrid zone?*

Region where two spp are sympatric and hybridize to form partially fertile progeny

Short-term Ne vs. Long-term Ne

Short-term Ne is the amount of drift within local populations (related to Hs) Long-term Ne is the rate at which genetic variation is lost over 10s or 100s of generations within metapopulations (related to Ht)

*What do short-term and long-term goals address?*

Short-term goals address inbreeding in local populations and rely on gene flow from neighboring populations to maintain genetic variation. Long-term goals address the balance between loss of variation through drift and introduction of new variation through mutation in the global population

What is phenotypic pasticity?

Similar genotypes but differences in phenotype caused by environment during development

*What are three main units of conservation?*

Species Evolutionary Significant units Management units

*What is genome banking?*

Storage of gametes and embryos, seeds, tissues, and DNA.

Define introgression

The incorporation of genes from one population another through hybridization that results in fertile offspring that further hybridize and backcross to parental populations

*What is the advantage of using allelic richness over the mean number of alleles as a measure of genetic variation?*

The number of alleles is more sensitive to loss of genetic variation and doesn't take sample size into effect, allelic richness takes into account sample size, but isn't dependent.

*What is lineage sorting?*

The process of alleles becoming population-specific that occurs primarily via drift

*Bornean and Sumantran orangutans are restricted to their respective islands in Southeast Asia and differ in morphology, behavior, and a reversed chromosomal segment. Hybridization has occurred in zoos between individuals from the two populations. Why might this be a problem?*

There is a large possibility of offspring being sterile

*What's the official policy for hybrids in the US?*

There is no official policy for hybrids

*Repeated extinctions and colonizations reduce genetic variation? Explain why. *

They are often associated with population bottlenecks, which reduce Ne, increase drift, and deplete genetic variation. ?

*Information on the genetic population structure of rats on South Georgia Island has helped to plan an eradication. Explain how.*

Used genetics to look for population structure and identify isolated reproductive units. May be able to eradicate portions of a population at a time is strong genetic structure. Also may allow you to determine if an eradication has failed bc individuals were missed or if the area was recolonized.

*What is match probability?*

Using highly polymorphic markers and then compute a match probability based on allele frequencies from the reference population

*Discuss a potential problem of using phenotypic traits to study patterns of genetic variation. What type of experiment is typically used to overcome this problem?*

Variation caused by genetic and environmental differences. Need to partition total phenotypic variation into variation caused by genetic and environmental differences. The common garden experiment

*Explain how exploited populations should be managed from a genetic standpoint*

We should implement genetic monitoring programs to examine loss of variation over time. Lower rates of exploitation and/or harvest over a range of age/size classes. Harvest subpopulations individually and/or genetically monitor the contributions of subpopulations in a mixed population harvest. No-take protected areas depending on dispersal.

What is panmixia?

Where all individuals are potential partners

*Is the proportion of polymorphic loci a useful way to measure of genetic variation among populations? Why or why not?*

Yes, but it is dependent on the situation