Problems of Small Populations and Conservation Genetics

DNA – blueprint of most life

DNA Strand Gene

Noncoding DNA “filler DNA”

ATCGACCGGCCTA

ATATATATATGGGC

ATCGACCGACCTA

ATATATATATGCGC

Gene Note that a single base pair change (letters) in a gene can change its function or render it nonfunctional, whereas changes in non-coding regions typically have much less impact

• Locus (Loci is plural) – a particular location/section of DNA on a chromosome; can be at a site that codes for something useful (genes) or at a non-coding site. • Allele is the form of sequence of DNA at a particular locus. • There are 23 human chromosomes x 2 copies = thus 2 copies of each gene at a particular locus. Within an individual, if the sequence at a given locus is identical on both chromosomes then we call this condition homozygous; if different we call this heterozygous. At the population level the terms change to monomorphic (all individuals in pop share same allele at a given locus) vs. polymorphic (individuals in pop have different alleles at some locus) • Recombination and mutation can lead to the formation of different alleles • Coding sections of DNA are “active blueprints” that make proteins and are referred to as genes (this is where your adaptive genetic variation is found) vs. non-coding (neutral genetic variation) sections of DNA

Why should we be concerned with Genetic Diversity? 1) Genetic variation is the RAW MATERIAL for future adaptation and is the basis for evolutionary flexibility and responsiveness • Rate of evolutionary change (adaptive potential) in a population = proportional to amount of available genetic diversity (Fundamental Theorem of Natural Selection);

2) Biodiversity at the genetic level is the PRIMARY level of biodiversity. Ultimately, genes (blueprints of life) regulate all biological processes on the planet. Loss of genetic diversity is analogous to loss of books from a library [of adaptation and survival] if we think of all life as a collective whole.

Species loss = Loss of Genetic Diversity

• 3) Conservation benefits from genetic research; theory can inform us of genetic structuring of populations, causes of loss of genetic diversity, phylogenetic relationships, and guide critical decision-making

Genetic Diversity: Importance!!

• Adaptive variation/genetic diversity ~ health of population • High genetic diversity (heterozygosity) usually indicative of individual fitness, and rough indicator of pop. fitness –

Note: Because some organisms are inherently not that genetically diverse to begin with, low heterozygosity can sometimes fool scientists into thinking that population(s) are not doing well. Other measures including examining population dynamics (changes in numbers over time) must be included when assessing the “health” and status of a species. See next bullet.

• Measure of Heterozygosity loss usually indicative of genetic problems and potential conservation concern! –

Note: This is often a better indicator of the genetic health of a population because the loss of adaptive potential is evident as “genetic cards” of survival vanish and are no longer “playable” if environmental change occurs.

Genetic Variation: How is it measured? •

Underlying assumption of using DNA as a tool to measure genetic variation is that there are standard rates of mutation known as “molecular clocks”

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You would expect that DNA that codes for important proteins don’t change much over time because those individuals in which it does often die before or shortly after birth. These would be considered lethal mutations. Therefore, non-lethal changes to these important proteins often occur over long periods of time at a fairly slow rate. As such, highly conserved pieces of DNA are often used to measure longer time span relationships/differences among organisms (say, thousands to millions of years apart). Mitochondrial, ribosomal, and chloroplast DNA are often used in these analyses because they code for critical organelles within cells.

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Conversely, noncoding/neutral DNA is often used to test relationships among closely related individuals or species because there is little selective pressure for changes in “junk” or non-coding DNA since it typically doesn’t code for anything useful. It tends to change rapidly, even from generation to generation. As such it’s useful for testing for genetic differences between closely related individuals (within a population, paternity tests, parental analysis, forensics, etc.). Microsatellite DNA is a type of noncoding “junk DNA” that is often used for these tests.

Linking Genetics to Conservation Note: Genetic variation, and thus adaptive potential, is important for all organisms. For conservation purposes we get particularly worried about small populations because they have fewer adaptive “cards”/genes to play when confronted with environmental change, thus increasing the risk of extinction at local, regional, or even global scales.

Genetics

Small, and/or isolated populations Increased tendency to lose genetic variation Loss of Adaptive Variation

Increased risk of extinction Reduced Ability to Maintain Biodiversity and Evolutionary Trajectories

3 Typical Measured levels of genetic diversity

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Gene Flow (Immigration)

Important Processes that Influence Genetic Variation

Mutation

Genetic Variation: Doin’ the Accounting +/• Mutation and Gene Flow (via immigration) help maintain genetic variation (gv) (heterozygosity). Mutation acts slowly to maintain gv, while gene flow via immigration can quickly increase gv

Genetic Drift

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Genetic Drift causes loss of genetic diversity; the smaller the population the faster it occurs and can have a negative impact on gv.

Mutations •

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Mutations cause changes in DNA and can be neutral, or alter gene expression. – How? Changes in single nucleotides, loss of nucleotides, deletion or insertion of nucleotide sequences, loss of pieces or entire chromosomes The ultimate source of genetic variation within an organism; –

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when measured across generations is typically a relatively slow process (although some microorganisms mutate particularly fast, and ironically some of the most lethal ones are those that have poor DNA repair mechanisms)

Mutations happen at different rates; much more common in junk DNA where little selection pressure occurs. DNA Mutations http://www.youtube.com/watch?v=efstlgoynlk

Some Mutagens (external factors that cause mutations) Viruses Chemicals UV radiation

Genetic Drift Alleles are randomly passed from parents to offspring, and typically not all individuals reproduce in a population, both of which characterize a directionless phenomenon known as genetic drift. As such, alleles can be removed from a population by genetic drift, but not replaced. Thus, over time genetic drift leads to genetic uniformity if no other forces (mutation, gene flow) act to maintain genetic variation. •

As an example think of a gumball machine that has 10 red and 90 blue pieces. It’s possible that if you randomly draw out 40 pieces (the offspring) that you would not get a red gumball. In that situation the red “allele” is lost from the 2nd generation gumball population unless a mutation occurs that would change blue to red, or unless a red gumball “immigrated” (gene flow) to the new machine.

When an allele reaches a frequency of 1 (100%) it becomes "fixed" and genetic drift no longer impacts that allele because everyone has it! A Mutational Meltdown occurs when a number of deleterious alleles get fixed into a population resulting in decreased survival of individuals that can lead to a downward spiraling of species fitness towards extinction When an allele reaches a frequency of 0 (0%) it is lost forever from a population unless recovered via mutation or reintroduced into the local gene pool from an immigrant that has the allele.

Loss of Heterozygosity from Genetic Drift • •

Genetic drift is due to chance If rare allele occurs in population (5%) then in a pop of 1000 individuals 100 copies of the gene are present (1000 x 2 copies/individual x 0.05) = 100 But in a pop of 10 individuals only 1 copy is present (10 x 2 copies/indiv x 0.05) = 1! Thus, it is much easier to lose rare (and potentially valuable) alleles to genetic drift in small pops. The proportion of original heterozygosity remaining after each generation (H) is strongly influenced by the effective population size (Ne = the number of breeding individuals). H = 1 – 1/ [2Ne] H = 1 – 1/ [2(50)] H = 1 – 1/100 = 1 – 0.01 = 0.99 (thus after one generation, this population would retain 99% of its heterozygosity) The proportion of heterozygosity remaining after t generations (Ht) decreases over time as follows in this equation using the value (0.99) from the equation above.

Ht = Ht so after 3 generations (0.99)3 = 0.97 Note: This figure clearly indicates that small pops will lose genetic variation much faster than large ones as a result of genetic drift, particularly small pops that are on islands or in fragmented landscapes

Factors that Determine Effective Population Size

Effective Pop Size almost always lower than the Total Pop Size

Important Factors that Determine Ne 1. Unequal Sex Ratio – Ne = 4(Nm x Nf) / (Nm + Nf) – Ne = 4(50 x 100) / (50 + 100) = 133 2. Variation in Reproductive Output: disproportionate output of offspring (highly fecund individuals) (animal/plant examples) 3. Population Fluctuations and Bottlenecks: where pop size varies dramatically from generation to generation (e.g. butterflies, annual plants, some amphibians) – Ne = t / 1/N1 + 1/N2...1/Nt) E.g. pop of butterflies over 5 years that has 10, 20, 100, 20, and 10 breeding individuals in a given year Ne = 5 / 1/10 + 1/20 + 1/100 + 1/20 + 1/10 = 5 / (31/100) = 16.1

Bottlenecks – When a catastrophic or other event leads to only a few surviving individuals it causes a special kind of genetic drift known as the bottleneck effect, whereby genetic variation is dramatically reduced, the founders, and thus Ne is very small and it can take thousands of years to regain genetic diversity without an influx of genetically diverse individuals (e.g. cheetah) – In keeping w/ this same concept, invading/colonizing/ organisms must deal w/ a special kind of bottleneck called founder effects. Founding populations usually consist of only a handful of individuals, and thus they inherently only have a small amount of the total genetic variation of the larger population from which they came. Thus, as they reproduce the population will continue to have a relatively low amount of genetic variation.

African cheetah (Acinonyx jubatus) • Cheetahs occurred in 4 continents only 20K YA • Climate change, other factors caused extirpation of other cheetah species • jubatus survived but went through population bottleneck • Current individuals suffer from lack of genetic diversity, sharing 99% of all genes within remaining population, reflected in low survivorship, poor sperm quality or low counts, more susceptible to disease

Bottleneck Recovery •

Dependent on: – Growth rate – # Founders

Gene Flow Gene flow is the exchange of genes among populations via immigration and emigration. It is facilitated by good connectivity (landscape permeability) among populations. • The more habitat fragmentation and the more incompatible the matrix, the harder it is for individuals to move from one population to another, thus reducing gene flow. • The higher gene flow is, the less genetic variation typically is among populations. This is the case where there is good connectivity and/or organisms are highly mobile (e.g. large mammals, birds, marine fish). • Where significant habitat fragmentation occurs, wildlife managers sometimes move individuals among populations (a process called translocation) to artificially maintain gene flow.

Gene Flow

Jaguar (El tigre): Then, Now, and The Future?

With dwindling populations of many species, planning and implementation of ecological corridors help maintain gene flow and maintenance of genetic diversity

Gene Flow vs. Mutation in helping Small Populations • In large pops, mutation can compensate for loss of alleles due to genetic drift. In small (< 100 individuals) pops, mutation isn’t enough to counter genetic loss due to genetic drift. • Gene flow tends to reduce genetic differences among populations • Rule of thumb: If Nem > 1 (one migrant/generation) this rate of gene flow is sufficient to minimize loss of alleles and heterozygosity (e.g. one bear moves between population A and B every generation) Note: Gene flow is dominant force affecting genetic variation in small pops…way more important than mutation, therefore its very important to maintain connectivity among pops!

50/500 Rule • It was thought that in small pops 50 individuals were needed to prevent inbreeding and 500 were needed for sufficient mutation to offset genetic drift. • More recent studies suggest the actual number to prevent either of these conditions is much higher; ultimately several thousand individuals are usually needed to ensure long-term viability.

I. Variation among Individuals w/in Population

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Measured as Hp = mean individual heterozygosity measured at multiple loci Cheetahs of Masai Mara Game Reserve Immigration/Emigration (provides Gene Flow) Genetic Drift

Gene Pool = Allele types and relative frequencies among all individuals w/n a population

Why knowing this level of Genetic Variation is important! • Individual is the basic unit upon which natural selection acts • Where genetic problems arise (e.g. inbreeding) • Important to know genetic profile for captive breeding • Fundamental genetic unit for understanding what’s going on within and among pops since those calcs are summaries of the individuals w/n them

Population-level Genetic Variation (Genetic Variation Among Individuals) •

What do we look at? – – –

Types of alleles present, 2) relative frequency of alleles across populations Measured as mean individual heteorzygosity (Hp) at multiple loci Con Bio Geneticists focus on changes in gene frequency, including loss of alleles

Which of these populations is most genetically diverse? Least?

Individual-level Genetic Variation Issues •

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Inbreeding – matings between related individuals, individuals have increased likelihood of inheriting alleles that are similar as a result from common decent Queen Victoria and recessive genes for hemophilia; “Blue Fugates” of Hazard, Kentucky had hereditary diaphorase deficiency and methemoglobinemia leading to bluish skin tone Information important for captive breeding programs that attempt to maximize genetic diversity; shows what can happen when pops get isolated or are too small – the chance of inheriting deleterious alleles that have fitness costs or even cause lethality increases greatly.

• Inbreeding = matings between related individuals – individuals have increased likelihood of inheriting alleles that are similar as a result from common decent; – increased likelihood of having a homozygous lethal or deleterious condition. Inbreeding Depression causes decreased fitness

Florida Panther (Puma concolor coryi) • Hunting, habitat loss caused near range-wide extirpation in southeastern U.S. • As few as 30 individuals in early 1980’s • Inbreeding effects evident; chryptochordism, aortic defects, kinked tails

Historic range

Current Range

• Intensive multi-agency monitoring effort 1981-present •

8 female Texas cougars introduced in 1995 for genetic supplementation

• Most panthers now have TX genes • Current estimates ~175 individuals • Recent studies support that hybrid cats doing well

II. Variation among Individuals among Populations (Total Genetic Variation) •

Measured as HT = total genetic variation (or mean total heterozygosity) Cheetah Pops in 4 different reserves in Kenya

HT = Hp + Dpt where Hp = Mean diversity within pops where Dpt = Mean divergence among pops Why knowing this level of Genetic Variation is important! • Provides an understanding of the total genetic diversity • Gives spatial idea where important areas of genetic diversity occur in the landscape and where conservation interest and measures can be best applied

Red-cockaded Woodpecker •

An example of how ecological characteristics of a species can dictate genetic structuring

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Federally threatened species Nest in live pine trees Because they are territorial and colonial, these birds are less mobile; HT= HP (14%) + DPT (86%)

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Gettin’ Around

Species within vagile (mobile) taxa tend to have lower genetic diversity among pops (Dpt) than those that are not very mobile.

Genetic Variation Among Population Structure Types • Panmictic – ~ contiguous single population of interbreeding individuals. Retains genetic variation well. • Metapopulations – multiple, typically smaller populations connected by occasional dispersal of individuals. Tends to lose genetic variation faster than single pop because some of the smaller units go extinct over time.

Coyote-red wolf hybridization

• Reintroduction of red wolves to Alligator NWR in 1980s • Coyotes now colonized area, genetic swamping

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Outbreeding Depression – results in a decrease in fitness when individuals are crossed from 2 different populations, subspecies, or species and the resulting offspring are sterile or have decreased fitness. Examples: Animals (diff and same species) Particularly troublesome for plants. Plants (diff species) Plants (same species) Why can this be a problem w/ species reintroductions?

While important remember that rates of loss of genetic diversity is usually slower than the time frame in which conservation actions occur!

Most Threatened/Endangered Species will lose very little genetic diversity over next century…other factors typically much more important and immediate extinction threats!

Importance of Human Food Biodiversity What are the dangers of overdependence on food monocultures? What can history teach us?

Sites of Domestication of Food Crops

http://www.cbsnews.com/stories/2008/03/20/60minutes/main395455 7.shtml (The Svelbard seed vault story; good overview of importance of food diversity and current crisis caused by global homogenization)

Learning Objectives (What we’ve covered thus far [yellow]): At the end of this course students should have a knowledge and conceptualbased understanding of the following: 1. Historical origins, ethics, and distinguishing characteristics of conservation biology. 2. Common terminology used by conservation biologists also shared by other fields such as forestry, ecology, economics, genetics, ethics, and wildlife management. 3. Definition, types, patterns, and processes that characterize and influence biological diversity. 4. Common methods to measure biodiversity at different scales. 5. Primary threats to biodiversity. 6. Common biodiversity valuation terminology and methods. 7. An introductory understanding of applied population biology, particularly as it relates to the conservation and management of small populations. 8. Common practical approaches for conserving biodiversity. 9. Key conservation laws and agreements. 10. Conservation implementation at various scales. 11. Current major conservation issues in Kentucky and beyond.

Additional Important Concepts for Understanding Small Populations

Small pops more likely to go extinct than large ones

Why? •

More rapid loss of genetic variability over time due to genetic drift and inbreeding than larger pops

Increased vulnerability to: •

Demographic stochasticity = demographic fluctuations due to random variations in birth and death

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Environmental stochasticity = environmental fluctuations (predation, competition, prey, disease, natural catastrophes)

Extinction Vortices

• Protecting Populations is key to Protecting Species • Ideal Plan for Conserving a Species = Protect as many individuals as possible within greatest possible area of high quality habitat. • Realistic Plan for a Species = How many individuals and how much and what kinds/configurations of habitat do we require to maintain species x over y amount of time with z degree of confidence. •

Example: We need at least 120 Eurasian lynx and 100,000 acres of old growth forest to sustain this population for 1000 years with a 95% degree of confidence.

Minimal Viable Population (MVP) • A quantitative assessment of how large a population needs to be for long-term survival • The smallest population size that can be predicted to have a very high chance of surviving into the foreseeable future. • Usually 99% chance survival for 1000 years despite foreseeable environmental or demographic catastrophes – - Must consider catastrophes (flood wall analogy)

• To determine MVP often need detailed demographic data (examples) and environmental assessment.

% of Population Remaining

MVP of Bighorn Sheep (Western U.S.)

Space • Home range – area within which an animal normally travels to satisfy life requisites. Ranges tend to shift seasonally to meet needs, but usually consistent over most of adult lifetime.

Home Range Estimators Different ways to estimate the size and shape of home range, and sometimes the intensity of use within it. Core Use Area

Minimum convex Polygon home range

Kernel Home range

Home Range Overlap

Amur (Siberian) tiger home range illustrating overlap (eastern Russia)

Establishing a home range (HR) • Usually animals disperse from natal range (where born and raised) to set up their own place (home range). It can be adjacent to or even overlap parents, or be hundreds of miles away. – Benefits of setting up HR close? – Benefits of setting up HR far away?

Coyote Home Ranges, Southeast KY

Minimum Viable Area (MVA) • Once you know MVP size, focus on the minimum habitat needed to support it. – Obviously must know what kind of habitat (e.g. forest, grassland), the configuration of that habitat (patch sizes), and the landscape context (e.g. does it matter what the surrounding matrix is – Can use individual home range sizes and colony sizes to estimate this area – E.g. Small mammal pops in Africa need 100-1000km2 Large mammal pops in Africa need ≥10,000km2

Simple way to calculate average home range size x MVP = MVA Note for animals with known tendencies of overlapping home ranges, you must adjust calculation.

Other factors that affect Small Pops • Stochasticity = random variation – Demographic (variation in birth and death rates across years) – Environmental (usually affects all individuals in a pop…weather, catastrophes, etc. Allee effect = the interaction of population density, pop size, and growth rates…basically the inability to find mates or to be at a critical density necessary for key behaviors or function (examples?)

Creating a Knowledge Checklist for Species Conservation •

Important Ingredients – Current Population Status (how many individuals and location) – MVP (# of individuals needed to sustain population…best to use Ne) – MVA (what kind and how much land needed to support MVP) – Habitat Availability and Quality (is there enough, is it available, and do we need to modify lands to create more?) – Population Dynamics (population growth rates; birth/death/immigration/emigration) – Threat Knowledge (Types, Relative Impacts) – Harvest/Exploitation Models (if necessary) – Public Support