ZOOL319

Source and sink of blue duck

Use DNA fingerprinting. -The blue duck population on the Tongariro River is the smallest of the four rivers -the Tongariro population contains more genetic variation than the other three. -These results suggest that the Tongariro River population is a `sink' dependent upon immigration from a number of different source populations, rather than local production. - Should there be any decrease in the current level of migration into the Tongariro River, there may be a consequent decline in bird numbers

Genetic rescue of adders Madsen et al. 1999

Very few recruits of adders and pop went through a population bottleneck. So males introduced from a different location to increase genetic variation. High number of still born & deformities Attributed to low GV / inbreeding Introduced migrant individuals Genetic variation & recruitment increased. -More variation in MHC genes = better immune system. MHC genes tied in with smell, if can't smell, social structure breaks down. eg. mammals.

Fertility reduction?

With a 1 child policy and catastrophic mortality event, world population would still be at 5-10 billion by 2100.

Fragmentation and source/sink dynamics for dolphins in nz

With no movement the fate of each separate population was determined by the fishing pressure in that area. -at 5% movement, everybody goes down. Healthy pops getting sucked down by fished pops.

Guardians of Fiordland Fishing created 1995

With the goal: - 'the quality of Fiordland's marine environment and fisheries, including the wider fishery experience, be maintained or improved for future generations to enjoy' • Run by fishermen • Only one scientist on the group • No environmental representative until just before the end of the process • Not in the best interests of conservation

Index

does not directly calculate population size, but instead a parameter you hope is related to true population size (e.g. individuals counted per unit effort) (Relative Density, Occupancy).

Conservation genetics: Detecting hybridisation

e.g. Ethiopian wolf & dogs. -Genetic study found hybridisation -extinction by genetic swamping? -captive breeding to avoid hybridisation

Conservation genetics: Defining reintroduction/translocation experiments

e.g. Laysan Duck, -derived from Mallards? -ancient DNA = was widespread; identify previous range & better habitat -Want to know if it used to be widespread around Hawaii, DNA tells us it was. Cooper et al. 1996

Conservation genetics: Choosing best populations for translocation

e.g. black footed rock wallaby, -Barrow Island pop -Low GD and poor reproductive rate -Eldridge et al. 1999

Conservation genetics: Defining management units

e.g. coho salmon, -salmon return to same river to spawn -each river is genetically different -stocking rivers Small et al. 1998

Conservation genetics: Non-invasive sampling for genetic analyses

e.g. northern hairy-nosed wombat -70 exist -hard to catch = burrow dwellers -DNA samples from hair

Conservation genetics resolves population structure

e.g. red-cockaded woodpecker -population fragmentation -gene flow between isolates? -Translocation & reintroductions?

Conservation genetics: Resolving taxonomic uncertainties

e.g. tuatara, -two species in 1877 taxonomy -fully protected in 1895, but only one species identified.

Conservation genetics: wildlife forensics

e.g. whale meat in Japan 1993 - 1999 -"Legitimate" whale meat is a cover for poaching -43% of Minke meat not from "scientific" hunt -10% of meat from protected endangered spp

Conservation genetics: Understanding species biology

eg. mating systems, sexing etc.

Cas9 and rodents

make rodents only offspring male. So they breed themselves out, no need for poison.

The wolverine in Cali

o Grinnell et al (1937) described wolverine being confined to southern Sierra Nevada o Schempf & White (1977) concluded wolverine to be present throughout most of mountainous California relying mostly on anecdotal data o Schempf claimed data compiled left "no doubt" that wolverines were present where Grinnell et al thought they were absent.

The fisher in the pacific states

o Once occurred in most coniferous forests in Pacific states (Washington, Oregon, and California) o Two petitions submitted under the Endangered Species Act o First denied due to lacking reliable information o Second denied due to anecdotal occurrence data indicated fishers were distributed continuously across historical range

Biodiversity hotspots

support ~ 60% of the world's plant, bird, mammal, reptile, and amphibian species, with a very high proportion of endemic species.

Examples of deterministic and stochastic models

• A deterministic model predicts one exact outcome - e.g. The population will grow at 2% per year - The Maximum Sustainable Yield is 1000 tons of fish • A stochastic model estimates the probability of particular outcomes - e.g. Probability the population will grow at a particular rate - Probability of extinction - Probability a female will breed next year - Risk of fish population falling below 1/2 of its original size (or some other cut-off) if you take 1000 tons each yr.

What is a viable population?

• A population with at least a 95% probability of surviving 1000 years (Schaffer's original definition)• Maintains itself under average conditions AND is of sufficient size to endure relatively rare perturbations: - Flooding - Fires - Earthquakes & tsunamis - Disease outbreaks • e.g. Reed et al. 2003 study - 102 vertebrate species - Long term persistence (99% probability of persistence for 40 generations) - Requires at least 7000 breeding age adults - Plus sufficient habitat the lack of long-term studies for endangered species leads to widespread underestimation of extinction risk. The results of our simulations suggest that conservation programs, for wild populations, need to be designed to conserve habitat capable of supporting approximately 7000 adult vertebrates in order to ensure long-term persistence.

Causes of overexploitation

• Biological factors: ignorance and uncertainty • Economic factors: time discounting and capitalization • Political factors: quotas, subsidies and unemployment • Social factors: the tragedy of the commons

Solutions to Millennium Ecosystem Findings

• Create positive economic incentives - Withdraw subsidies of unsustainable fishing, farming, mining etc. - Taxes for activities with environmental costs - Address corruption, weak regulations and accountability - Think global, buy local • Increase knowledge and use existing data on improved environmental management • Choose sustainable food and other products • More info about sustainability of products • Increase energy efficiency

Stochastic elements of Hector's dolphin model

• Current population size - Mean and SD from population surveys • Future fishing effort - Mean and SD fishing effort • Entanglement rate - Mean and SD from observer programme • Maximum population growth rate - Uniform distribution 1.8 - 4.9% • Movement and number of dolphins caught - Binomial distributions

De-extinction cons (Seddon et al. 2014)

• Distracion from real issues • Uses limited funding/resources • False idea of ability to restore later • Commercial bio-tech interests • Taxonomic bias in candidates • Unknown captive care • Unknown ecological role • If captive-ethical issues • How close to original? • If to be reintroduced.....

International agreements for MPAs

• Establish representative networks of MPAs by 2012 • Global MPA target of 10% coverage by 2012 • Deadline for 10% coverage postponed to 2020 • 2016 IUCN conference: 30% coverage by 2030

Typical steps in PVA model

• Estimate population size in future years • Forecast viability through time - based on repeated "runs" of the model - with different input parameters - and/or different conservation scenarios

Pellet recruitment rate

• Estimating animal density from the pellet recruitment rate (RR): • The actual density of rabbits or hares per hectare (D) can be estimated by dividing the recruitment rate (RR) by the number of defecations per animal per day (DFR). -D=RR/DFR

To model or experiment?

• Experiments - Usually require several years - May increase risk for the animals you are studying - Small sample size may make interpretation of results difficult • Modelling -Allows rapid exploration of many variables -Defines limits of what is possible (e.g. max population growth) -Shows where research would be most helpful - Relies on assumptions about parameters and initial conditions - Relies on the model structure being appropriate - Difficult to test if the predictions of the model come true

Turner 2008, Limits to growth with 30 years of reality

• Exponential growth of human population and industrial output • Has reached the limits of sustainability • Current growth policies will lead to overshoot - Rather than approaching sustainable limits - and staying within sustainable bounds • Changes in policies could lead to sustainability - If the right social and technical changes are implemented very soon

Solutions to human pop growth

• Find more sustainable ways of living - Stable or declining human population - Reducing resource use per person - Reducing pollution per person Difficult to achieve politically... Individually: walk or cycle

GMO and transgenic organism

• GMO (or GEO) = an organism whose genetic material has been altered using genetic engineering techniques • Transgenic organisms (subset of GMOs) = organisms into which DNA inserted from a different species

In order of population size

• Genetic stochasticity e.g. Inbreeding - A problem for very small populations • Demographic stochasticity - Differences between individuals - A problem for very small - medium populations • Environmental stochasticity - Differences from year to year in survival, reproduction etc. • due to environmental changes (e.g. temperature, availability of food & shelter) - Affects all individuals - Affects all populations, even relatively large ones • Human impacts - Can affect populations of any size - Are especially high risk for small populations

Current protection measures for hectors

• Gillnets can not be used: - 0-7 nautical miles (nmi) from shore for part of North Island west coast - 0-4 nmi for east and south coasts of South Is - 0-2 nmi, for 3 months in summer, for west coast South Island • No trawling: - 0-2 nmi for east and south coasts of SI and part of North Is west coast

De-extinction method: selective back breeding

• Identify living descendant species • Selectively breed for primitive features -release them back to continue their browsing behaviour.

So how large is a viable population?

• Inbreeding - Effective population of at least 50 individuals is required to prevent inbreeding depression • Demographic stochasticity and Allee effect - Become a problem in populations smaller than 50-100 individuals • Genetic variation for adaptation to a changing environment - Needs a population of at least 500 individuals - 500 individuals has made its way into various species survival plans • Environmental stochasticity - Requires population sizes on the order of 1,000-10,000 • Habitat degradation and other impacts - Can be a problem for very large populations - Especially if the population is fragmented

Example of demographic stochasticity

• Individuals do not all produce average number of offspring • Some have no offspring, fewer than average, or more than average • In large populations - the average accurately describes the population • In small populations (e.g. 50 individuals) - individual variation in birth and death rates - can cause the population to fluctuate randomly up and down

Some of the changes needed

• Integration of ecosystem management goals - e.g. in agriculture, finance, trade and health • Increased transparency and accountability- of government and private ecosystem management • Elimination of environmentally damaging subsidies • Ecosystem restoration • Consider non-market values of ecosystems and their services in management decisions

Environmental implications of releasing GMOs

• Invasion issues • Genetic manipulation issues - Toxicity and allergenicity - Effects on population dynamics - Effects on biogeochemistry - Transfer of transgenes - Instability of genetic modification - Unintended effects - Novel selection pressure on natural enemies

Protected areas can solve marine mammal bycatch problems if....

• Large enough • In the right place • Effectively manage key threat(s) • Policing is effective • Threats are not displaced - To other dolphin habitat • No new threats are added - Mining, tidal turbines, etc.

PVA for meta populations

• Most endangered species not a single population but several smaller populations. •'Subpopulations' linked together by dispersal • Independent demography among subpopulations. • Local extinction and recolonization of habitat • Individual subpopulations can be short-lived • Can be re-established by colonization from another subpopulation -add movement to population model

Where to dump dredge spoils

• Not too close to shore • Avoid high-energy environments (current and swell) • Mud in muddy areas, sand in sandy areas, etc. • To help ensure the material stays • Use an experimental approach to finding out how mobile the spoils will be • Hydrology of this area not sufficiently well known to accurately predict this • Consider using more than one site (to avoid pollution from contaminants)

Summary of GMO

• Now >90 million ha by >10 million farmers in 21 countries • Soybean, maize, cotton, oilseed rape; herbicide tolerance dominant trait; Only maize and cotton have insect resistance • No scientific evidence that commercial cultivation of GM crops has caused environmental harm • Reduction in the use of chemical pesticides; Increase in crop yields; Increase in farmer profits

Population viability analysis

• Once data have been gathered on population size, survival, reproductive rates, threats etc. • PVA is a common way to analyse these to provide an overall assessment of risk - In a model that includes births, natural mortality, human impacts, genetics, etc. - Can be used to evaluate effectiveness of different management options and solutions - e.g. Is the most efficient way to save yellow-eyed penguins predator control (to stop chicks being eaten) or fisheries controls (to stop adults being caught in gillnets)?

Why are small populations at risk

• Particularly susceptible to stochasticity - Demographic - Environmental - Genetic

What is PVA?

• Population model to estimate: - Risk of extinction - Sustainable level of human impact - Effectiveness of different management options • e.g. Size of protected area needed, proportion of population that needs to be protected

Rule of thumb

• Population size - above which a population is thought to be safe - below which it faces moderate or high risk of extinction • Useful when little is known about the species •"50/500 rule" - the classic rule of thumb - based on theoretical population genetics - Ne of 50: short-term goal to prevent inbreeding - Ne of 500: long-term goal to balance genetic variation created by mutation with that lost by genetic drift. To be able to adapt to the environment. -Neglects other factors: e.g. demographic stochasticity e.g. environmental stochasticity

Mitigation of behavioural effects

• Pre-release behavioral selection • Managing the rearing environment • Transition to the release environment • Pre-release training or conditioning -run through tests -soft release

Uses of PVA

• Quantitative, repeatable measure of risk • Can use extinction probabilities to prioritise conservation actions • Like a thermometer is used as a measure of health and reponse to treatment • To prioritise species for attention • Identify risk factors and change them • Identify research priorities

Threats to PAs

• Rapid human population growth • Urbanisation • Illegal harvest and overexploitation • Habitat fragmentation and loss • Invasive species • Poor management • Climate change

Models that incorporate stochasticity...

• Recognize - population growth rate not constant through time - extinction essentially a chance event • Even populations in favourable environments may go extinct due to stochastic perturbations • 3 types of stochasticity - demographic, environmental, genetic

De-extinction method: genome engineering

• Recover and decipher ancient DNA from many specimens • Compare with nearest living relative to identify gaps and differences • Starting with the genome of the relative, splice in gene sequences to reconstruct the extinct genome • Nuclei from cell lines inserted in cell capable of forming an embryo • Implant embryo into surrogate mother (production of chimeras in birds) -re-engineer genes from wooly mammoth in to elephants so they can live in cold environments.

De-extinction method: cloning (somatic cell nuclear transfer)

• Recover intact frozen cell and remove nucleus containing DNA • Get nucleus into host species cell that has had its nucleus removed • Implant the embryo into a surrogate mother -ibex: took cells from last one. 8 years later use those cells to clone. -epigenetic effects, learning/rearing effects.

Is the population stable or declining?

• Repeated surveys - Often take many years to detect trends - More difficult for very small populations - Doesn't tell you what's causing population trends • Population model - Estimate survival & reproductive rates - Use these to calculate population growth rate - Check if model "fits" real-life situation - Compare "expected" with "observed" values

Estimation for extinction risk

• Rules of thumb based on theoretical predictions - e.g. Need population of 50 to avoid inbreeding • Empirical evidence - Experience with other species (e.g. bighorn sheep) • Deterministic models • Stochastic models • Detailed PVA models

DOC fecal pellet index guide

• Several possible measures: - Presence/absence - Total count - Recruitment rate (remove them all then see how many more come). - Point distance-nearest neighbor

What makes species vulnerable?

• Small population and/or distribution • Naturally less abundant species (e.g. predators) • Long-lived, slow-reproducing species • Live in habitats that humans like to live in • Use limited resources • Specialists

Analysing hectors dolphins using individual based models

• Still considerable overlap • dolphins and gillnets • especially dolphins and trawling

Marine reserve program objectives

• Take positive initiative to restore natural character and quality of NZ's marine environment. • Establish network of marine reserves to capture special and typical features of each part of the coast. • Enhance the profile of areas given marine reserve status. • Improve public appreciation of and facilitate education about the marine environment. • Recognise links between land and sea in establishment of marine reserves and the need to protect both.

Types of variability in very small populations

• The effects of other types of variability and uncertainty become more important - e.g. Environmental variability • Physical: e.g. temperatures, air/water currents • Biological: e.g. fluctuations in predators/prey - Catastrophes • An extreme form of environmental variation • e.g. Earthquakes, volcanic eruptions, major disease outbreaks - Parameter uncertainty • Measurement error in parameters like survival, reproduction

The issue of labeling

• The right to know what you are eating • Negative signals of "GM" label • Facilitate epidemiological studies • NZ imports 57 varieties of GM foods • No label required if GMO <1%

Comments from submissions from South East marine protection forum

• The size of each reserve is important: larger is better • Especially for long-ranging animals (e.g. seabirds, sharks, marine mammals). • Shape matters: simple shape, large volume, small surface area (edge effects). • Need a science-based approach • Social, concensus driven process has led to proposals that fail to meet NZ's objectives to: "...protect marine biodiversity by establishing a network of MPAs that is comprehensive and representative of New Zealand's marine habitats and ecosystems..." • No bulk fishing methods like gillnets & trawling within any of the MPAs • Importance of a network of marine reserves

Resolution Island hair tube work

• This study violated all assumptions of mark-recapture. • Inter-sex differences in capture. • Neophobia • Trap happy animals. • Trap shy animals. • Great difficulties in the lab. • Therefore can't identify accurately recaptures.

De-extinction pros

• Undo mistakes • Moral imperative • Counter environmental losses • Learn more • Engage public and funders • Technology aid current species • Deep ecological enrichment • Restore ecological functions • Increase biodiversity • Increase ecosystem resilience

Environmental stochasticity

• Variability associated with good and bad years for population growth • Affects all individuals in the population (of a given age) equally

wolf and caribou study using netlogo

• Wolves travel up steep slopes • Caribou avoid slopes steeper than 3 m elevation over 20 m distance.

Unsustainable ocean harvesting

•Each year humans harvest and consume >25% annual fish production of ocean upwelling regions and tropical marine shelves •Humans remove ~8% total primary productivity from aquatic ecosystems annually; global climate change could exacerbate impacts. -31% stocks overexploited; 58% fully exploited; only 11% under-exploited.

Line transect assumptions

•all individuals on transect line itself are seen •you don't disturb animal before recording it •distances / angles measured without error •sightings are independent Consequences of faulty assumptions: 1) population over- or under-estimate 2) part of population may be more mis-counted than other parts (e.g. one sex or age-class is less detectable). -Extrapolation from surveyed area(s) to total area: Are areas typical? consider randomization, stratification -Transects vary in habitat / ease of detection; extrapolation may be difficult.

Genetic identification of whale products

•dolphins sold as whale-meat: illegal •commercial sale of northern minke: illegal •hunting of humpback whale: illegal •hunting of fin whale: illegal 50% of Japanese whale products sampled were illegal.

Uses of population model

- Conservation - 'Harvest' management (e.g. fishing, hunting) - Pest control -Use PVA to compare management options

When does a population model become a PVA

- Needs to include stochasticity - Be suitable for small populations - Estimate risk (e.g. of extinction, or population decline to low levels).

Tools to help solve conservation problems

- Population Viability Analysis • Estimating (extinction) risk • Assessing effectiveness of conservation options - Conservation genetics • Genetic drift, inbreeding, biodiversity • Units of conservation, forensics

Recombinant DNA technology

- Possible to combine molecules from different sources into the one molecule with result that the abilities/phenotype/proteins of the organism are modified

To maintain quality of life

- Reduce resource use - Much more efficient use of resources • e.g. Insulate homes so you need less energy • Buy local products to reduce food (and other product) miles • Less food and other products thrown away - Greater use of renewable resources - Less polluting technologies

Advantages and disadvantages of fixed hunting mortality rate

- Safer - large margin or error not needed (as for fixed effort) - Harvester free to use any technology - Yield varies annually - Managers need to know pre-harvest N

Dunedin private gardens

-17 % native species -mainly shrubs -factors that predict plant diversity: vegetated area of the property, capital value.

HWE: No change in genetic variation

-Given assumptions 2 conclusions: Allele frequencies will not change. If allele frequencies are p and q, genotype frequencies will be p2, 2pq, and q2.

Systematic factors

-Habitat loss -Anthropogenic factors (hunting, resource competition) -Predation -Competition with invasive species -Hybridization with invasive species

Characteristics of urban ecosystems

-Highly modified -High level of heterogeneity organized along a gradient -Extreme habitat fragmentation -children that grow up in cities don't experience nature and they grow up to be voters that don't care as much about conservation.

MPA design issues

-Hikurangi marine reserve over a very large trench so wasn't a good place for fishing anyway. -lots of SA compared to volume which isn't good. Want it as simple as possible. -only a tiny bit covers the coastline. -marine reserve at punakaiki had holes in it....

Assisted colonization

-Increased assisted colonizations will create more conservation problems than it solves. It poses potentially great and incalculable risks. -The potential of these to preserve species stands in direct tension with its potential to unleash invasion by the focal species.

Protecting regions

-Limit unnecessary translocations: spreads disease, causes outbreeding depression, erodes historic (evolutionary) information. -design regional reserves: protect ecosystems in different regions. -Protect hundreds of unknown ESUs?

Concerns posed by GMOs

-Morality -Health (use of antibiotic marker genes, allergies, toxins). -Environmental risks

Conclusions: impacts of climate change

-More frequent beech seed masting -Invasive predator populations less irruptive/more chronic higher abundances -Current control strategies no longer valid -Conventional management for rats compromised -Important to include community dynamics when predicting climate change consequences. Could improve modelling: 1. Masting is modeled as an all or nothing event although there is clear variation in the extent of masting. 2. Dispersal and re-colonization by invasive species not accounted for.

Morality and animals: Immanuel Kant

-animals are not moral or reasoning creatures -but we should treat them kindly as it helps improve out internal moral function.

What about extinctions, what options

-arabian ostrich extinct 1950s. Replaced in the area by ostrich from Sudan. Ecological replacement. -Introduction of north island kokako to south island.

Why preserve species? Russow 1981

-because we are stewards or caretakers -extrinsic value to humans (potential or realised) -extrinsic value to the ecosystem -intrinsic value -aesthetic value

Regulating ecosystem service

-climate regulation -disease regulation -flood regulation -water purification

Operation nest egg: kiwi

-eggs destroyed -young kiwi can't defend themselves -5% chance of survival to adulthood Monitor adults Radio-telemetry No need to maintain birds in captivity 50% of effort! Remove eggs <10 days - 1% chance of survival c. 25 days age Too late = predation Artificial incubation Species-specific conditions

Tiritiri island takahe

-fluctuating amounts of inbreeding -robins at ulva island: increasing numbers of pairs and increase in inbreeding.

PA's should protect

-globally threatened species and viable populations of range restricted species. -large intact ecosystems with important assemblages of species. -viable representatives of every ecosystem -Need to consider: biodiversity, representativeness, connectivity, size, threats and pressures.

Examples of transgenic plants

-golden rice: has enhanced beta-carotene. Potential treatment for Vit A deficiency. -calcium carrots: double calcium content. "Super-charged" vegetables could help reduce risk of osteoporosis - one of the world's leading nutritional disorders

Invasive species modify habitat: Increased erosion

-in capetown acacia's have shallow roots so uproot frequently, increasing erosion.

Management of land sharing/sparing

-move sparing relationships to sharing -increased street tree planting -use of permeable roads and footpaths -green walls and roofs: facilitate food production, noise abatement, pollution mitigation and temp regulation.

Three directions of responses to climate change through phenotypic plasticity or evolutionary responses

-moving in space -shifting life history traits in time -changing life history traits

de novo genetic variation

-mutations but these are very rare and often harmful. -insertion= brand new protein, could be bad. -deletion = brand new protein, could be bad. -stop= no protein made.

Supporting ecosystem service

-nutrient cycling -soil formation -primary production

Ecosystem services

-provisioning -supporting -regulating -cultural

Modifying influences

-remnant size -remnant shape -position in landscape -matrix habitat

Saddleback translocation

-sequential movement -loss of variation

management questions

-what are my management objectives? -will this intervention work to achieve these? -are there ways to reach this objective harming fewer animals? -reduce, reuse, recycle

When making a policy....

-what is morally relevant? -how should this be treated? -is my view justifiable or is it simply a culturally informed personal construct?

Mark-Recapture or Mark-Resight

1. Mark as many individuals as you can (or record indiv. markings) 2. "Recatch" animals. 3. Estimate proportion of population caught. 4. Estimate abundance, density.

New Zealand PA's

>17,000 protected areas covering ~32% of NZ.

What is a protected area?

A clearly defined geographical space, recognised, dedicated and managed through legal means to achieve the longterm conservation of nature with associated ecosystem services and cultural values- IUCN.

Tasmanian devil facial tumor disease

Assisted Colonization to create a disease-free population of Devils on Maria Island.

Prehistoric swan

Australian black swans flew to New Zealand at this time and then evolved into a separate species. It became large and robust.

Shiitake mushrooms

BSC= 1 species Morphology= 3 species Genetics= 4 species

Human decisions drive environmental conditions in cities

Bottom up: individual or household behaviour Top down: government level policies -socio economic factors drive urban species diversity

Kiwi chreches

Chicks are precocious Yolk 5-10 days Predator-free environments Islands Mainland islands Released to wild at 1200g - can now defend themselves. -increases survivorship of population.

Range shift of butterflies in spain

Elevation boundaries moved up by 212m due to temp increase of 1.3C.

Research approaches in reintroduction biology

Experiments: mitigating the effects of captivity. Modeling: project planning and evaluation.

Measuring fragmentation (Sewall Wright, 1969).

FST (fixation index) examines genetic divergence of sub populations. With high gene flow FST is low. With low gene flow, pops diverge and become inbred and FST increases. FST, the mean reduction in H of a subpopulation (relative to the total population) due to genetic drift among subpopulations.

How does conservation biology differ from other biological sciences?

It is a crisis discipline. Need to act before knowing all the facts. Risk assessment. Long time scale: emphasis on long term viability of ecosystems and species.

Problems with regulating services

Natural hazard regulation -more people -occupying regions exposed to extreme events -The capacity of ecosystems to buffer from extreme events has been reduced through loss of wetlands, forests, mangroves.

relationship between human population density and biodiversity loss.

Species richness & HPD - sig. +ve relationship. Threatened species richness & HPD - sig. +ve relationship. Extinctions & HPD - sig. +ve relationship. Introduced species & HPD - very strong +ve relationship. Protected/conservation areas & HPD - sig. -ve relationship.

Temporal stability of index

Survey duration and season influence the detection of introduced eastern rosella in New Zealand. More likely detected in summer and when spent 25 mins.

Shifting life history traits in time

adjusting life cycle events to match the new climatic conditions, including phenology and diurnal rhythms.

Estimate

combine count of some kind with estimate of proportion missed; obtain population estimate and (typically) confidence interval around estimate (e.g. line transects, mark-recapture estimators)- (Abundance, Density)

Conservation science

• Document and quantify conservation problems • Suggest ways to avoid and solve environmental problems • Work out environmental, social and economic costs & benefits of alternative management options - How will the environment change if we do A, B or C? - What will this environment be like in 10, 20, 50 years time? • Monitoring - State of the environment - Performance of conservation measures

Management approach

• List potential population dynamics for the species • Assess sustainable human impact for each scenario • Ensure impacts are sustainable for all of these population dynamics scenarios • Research to narrow down the list of scenarios

What's needed to protect marine mammals

• Remove gillnet and trawl fisheries • Throughout Hector's and Maui's dolphin habitat • In waters < 100 m deep, including harbours • Change to more selective, sustainable fishing methods • No need for further research, need to improve protection now

Why is genetic variation important?

"Evolutionary potential of population is proportional to amount of genetic diversity present." -Fundamental Theorem of Natural Selection (Fisher 1930). - Loss of genetic diversity limits evolutionary options & response to environmental change. Positive correlation between genetic diversity (heterozygosity) and fitness. Heterozygosity confers fitness advantage. -lots of variation means natural selection can act on it and perpetuate advantageous phenotypes to next generation.

Disease susceptibility in California Sea lions. Acevedo-Whitehouse et al (2003)

11 DNA microsatellites = estimate internal relatedness health problems identified (carcinoma, infections), plus controls (trauma, etc). inbreeding is an important factor in susceptibility to disease. -more serious health problems in highly related individuals of sea lions.

California condor Ralls et al. 2000.

14 remaining removed from wild (1987) Breed well in captivity Reintroduced into wild in 1992 Population consists of 146 individuals Inbreeding - exposed a lethal recessive -lethal dwarfism

Kaki captive management

23 birds (1970) Predation of wild nests/birds Hybridisation with Pied Stilt Mix of wild eggs & captive breeding Outdoor aviaries with adults -74 released into wild at 9 months in predator controlled areas. -avoid predation, hybridisation and genetic swamping.

Expression of deleterious mutations

All populations have rare 'deleterious' alleles Rare harmful recessives - only a problem if homozygous Some mutations have mild effects: decrease in fitness Others may be lethal Difficult to manage

ESUs in ghost bats

Australia's only carnivorous bat Roost in caves Mining & deforestation Very fragmented range MtDNA No shared haplotypes No gene flow Extinct colonies not recolonised Isolation is not recent Manage bat populations as distinct ESUs

Management unit

Basic unit of management Less strict compared with ESUs Reflects current population structure Criteria: differences at MtDNA &/or nuclear DNA Not take into account phylogenetic distinctiveness (compare with ESUs) Some refer to genetically-defined units as genetic management units (GMU)

Habitat fragmentation

Breaks up once continuous populations Produces isolated patches Reduces: overall population size and gene flow between populations.

Inbreeding depression

Consequence of inbreeding Expression of recessives in homozygotes Many recessives are deleterious or lethal Positive correlation between heterozygosity & fitness.

Summary of captive management

Crisis management Should not be first method used Part of wider conservation strategy Benefits But, many hurdles that need to be overcome

What about 500?

Far reaching implications (e.g. reserve design) Ne=500: the point that balances loss & gain of GV Given that Ne /N = 0.1, must have N of 5000 individuals! -Drift reduces variation (H) by 1/2Ne per generation. -If Ne = 500, loss of H through drift = 1/2Ne = 0.001 per gen. -Mutation increases variation (H) by roughly 0.001 per gen.

Consequences of fragmentation

Fragmentation results in genetic subdivision Diversification by genetic drift & inbreeding over time in each population

Implications: translocations

Gene flow between populations New genetic variation into an inbred population lessen inbreeding depression Which individuals to move?

Four important factors involved in GV loss

Genetic drift (greater effect in small pops.) Founder effects Demographic bottlenecks Mating between relatives (Inbreeding)

Measuring genetic variation

Genetic variation measured in individual: Level of action of natural selection Inbreeding occurs among individuals but populations/species = units of concern in most conservation Use molecular genetic techniques to measure GV and population genetic theory to interpret results

Founder effect

Group of individuals start a new population by migration. Allele frequencies are subset of origin eg. silvereyes from Tasmania to South Island NZ.

Natural pops of birds and inbreeding

Inbreeding affects reproductive success Lower hatching success when parents related Van Noordwijk & Scharloo (1981)

Fitness effects of drift

Increase of homozygotes Increases frequency of harmful alleles Deleterious recessive alleles expressed in homozygotes Can lead to inbreeding depression

Inbreeding & genetic variation

Increases the number of homozygotes Not alter allele frequencies - not a mechanism of evolution. Selfing population - complete inbreeding

Is there a minimum viable pop (MVP) size?

Limited conservation resources (trade-offs) Managers like hard goals "save them all" and "save all you can" are dissatisfying How large so loss of GV is not an extinction factor? How large to maintain evolutionary potential?

Florida panther Hedrick 1995

Low GV Inbreeding depression Sperm abnormalities & testicular problems Cardiac defects Hybridised with Texan subspecies 5 females introduced 25 progeny resulted All lack the inbred characteristics of "pure" panthers

Hector's dolphin

NZ endemic Shallow water (estuaries) N=7000 Human disturbance, chemical pollution, noise pollution, entanglement in fishing nets, prey depletion? Disjoint distribution -Fst of 0.2 or more = differentiation is high. -2 GMUs

Why detect gene flow?

NZ fur seals West Coast colonies impacted by Hoki fishery? Replenish from east? Estimate gene flow Bradshaw et al. (2000)

Skewed reproductive success

Ne = N only when offspring numbers follow a Poisson distribution with a mean of 2.0 children per parent

Lost genetic variation

Not a problem if quickly regenerated... Single locus variation (mutation rate 10-5 or 10-6 per gen) 100,000 to 10 million gen Multiple locus genetic variation (mutation rate 10-3 per gen) 100-1000 gen 2600-26,000 years in elephants. Slow breeding animals have less variation. Cannot rely on mutation in conservation's time frame -use genetic scissors to reinsert lost genetic diversity

Why is heterozygosity lost > 1/2N?

Not all individuals breed (juveniles) More males than females Difficult finding mates Better breeders than others Fluctuations in N: bottlenecks -at low N, hybridisation, individuals start breeding with closely related.

Is there a downside to mixing pops?

Outbreeding depression occurs when individuals from genetically differentiated populations mate Reduce fitness of offspring Two causes: mixing of genomes adapted to different environments (loss of locally-adapted genes) and Genetic incompatibility.

Imprinting

Phase sensitive learning Young animals acquire behaviours from parents Can imprint on other species (black robin raised with tomtits and then started hybridizing with them). Methods to avoid imprinting (use puppets)

Ne: Fluctuation in population size

Populations are not constant Disease, Flood, Drought, etc Ne is adjusted for numbers of breeders in different years -bad years more important than good years. Ne is difficult to calculate - requires good data Typically < number of breeders Use values from other species? conservative value?

Bottle neck and population growth

Priority: increase N Minimise genetic drift -bottle neck where pop goes down to 2 individuals. if you want to retain genetic diversity need to increase pop size to > 400. -loss of heterozygosity leads to inbreeding depression.

Need to manage/raise N

Remove sex ratio bias All individuals breed Equal contribution to gene pool Constant population size

Demographic bottle necks

Severe/temporary reductions of N Loss of GV depends on bottleneck size & rate of pop growth Northern Elephant seal 1 bull = 25 gallons of lamp oil 100,000's to 100 to 130,000 Little GV compared to southern elephant seals where nearly every individual is a genetic variant. -fast pop growth = recover quicker. Elephant seal recover very slowly.

What use is HWE principle?

Starting point for Population Genetic Theory Serves as a null hypothesis Indicates a genetic issue Not indicate which issue

What about Ne=50?

Sufficient to avoid inbreeding depression? Corresponds to 1% loss of GV per generation (1/2Ne) Assumes there is little inbreeding depression over 5-10 generation Little available data to test assumption at time (1978)

Franklin's 50/500 Rule

Two issues: an immediate danger of extinction via inbreeding depression a loss of variability that might restrict future evolutionary potential Ne: 50 for reproductive fitness 500 for evolutionary potential Rapidly incorporated into conservation policy Problem = not take into account catastrophes

Conservation genetics

Uses genetics to address the (man-made) loss of biodiversity and the erosion of the natural evolutionary processes that produce and maintain it.

Genetic diversity

Variation present at genes Within species: Within populations Between populations Between species

Effective population size

based on a model population of constant size in which all individuals contribute equally to the next generation Ne = "the size of an ideal population that shows the same loss of genetic diversity as the actual population" Ideal population: Equal sex ratio Equal contribution to next gen Constant N Non-overlapping gen

Mitochondrial DNA

circular 16kb, 37 genes maternally inherited no recombination - clonal allele = "haplotype" highly variable very useful! -mutates at a much faster rate

Pedigree inbreeding

inbreeding quantified by inbreeding coefficient (F): the probability that 2 alleles in an individual are identical by descent (IBD). F values range from 0 (fully outbred) to 1 (fully inbred).

Heterosis

increase in fitness of F1 progeny relative to the two parental lines also called hybrid vigor

Chatham Island black robin (Ardern and Lambert 1997)

just 5 birds in 1980 increased to >200 little genetic variation remains

What is inbreeding?

matings between relatives decreases genetic variation: increase in homozygosity, decrease in heterozygosity doesn't alter allele frequencies in population inbreeding is relative - not an absolute measure

Inbreeding: non-random mating

parents more closely related than expected at random can be worked out from pedigree data, but rarely available normally measured as deviation between observed heterozygosity (Ho) and heterozygosity expected (He) under random mating (Hardy-Weinberg equilibrium): FIS = 1 - Ho/He -So...if mating is random, Ho = He, and FIS = 0 -But...if mating is assortative, Ho < He, and FIS > 0 (up to 1) (decrease in heterozygosity)

The greenhouse effects and nature reserves

"...isolated reserve populations could not respond to changing climatic conditions within the reserve by colonizing habitat outside the reserve where the climate is suitable..." "... individuals of disappearing species may have to be transferred to new reserves [outside the current species range limit]..." • Consider: - Status of present and future ranges, i.e. are both represented in same existing reserve? - If • Only present or future ranges represented • Neither present nor future range represented • Present and future ranges represented but in separate areas - Then • Consider creation of new reserves/enhance connectivity.

MPA definition

"An area of the marine environment especially dedicated to, or achieving, through adequate protection, the maintenance and/or recovery of biological diversity at the habitat and ecosystem level in a healthy functioning state"

De-extinction

"Humans have made a huge hole in nature in the last 10,000 years... We have the ability now-and maybe the moral obligation-to repair some of the damage." Stuart Brand 2013

Diet and sex allocation

"Mothers in better condition produce more of the sex with the higher fitness return" (Trivers & Willard 1973). -kakapo, weight of mother dictates which sex she produces

New genetic variation

"New variants/combinations arise from mixing up existing genetic variation." -Rearrangement of DNA in sexual reproduction.

Elsewhere in NZ 1990-1995

- 11 marine reserves created, including - Kermadec, Pollen, Mayor, Kapiti, Long and Tonga Islands - Te Whanganui-a-Hei (Cathedral Cove) - Long Bay - Okura, West Haven - Milford Sound and the Gut (Doubtful Sound)

Status of worlds PA's

- > 100,000 terrestrial and marine PA's - ~19 million km2 (but only 3.4 of earths surface) - Most on land but only ~12% of total area.

Solutions

- Captive rearing and re-introductions - Protected areas ( e.g.marine reserves, mainland islands) - Conserving species, ecosystem processes, biodiversity - Ethics, education and public participation in ventures like Orokonui - Prioritisation and population monitoring (to test conservation effectiveness) - The threatened species strategy

A meta-analysis: corridor effectiveness

- Corridors incr. movement btwn patches by 50% c.f. patches not connected by corridors - less important for birds - distance btwn source and patch influenced movement - natural corridors better than manipulated corridors

Eating GMOs

- Food safety depend on properties, not mode of production, therefore nothing inherently risky about GM food - FDA Expert Committee - No added risk of allergic reactions posed by GM foods and no evidence of health risk - ANZFA 2002 (now Food Standards Australia New Zealand FSANZ)

Why produce transgenic plants?

- Increase yields - Decrease use of pesticides - Increase efficiency of herbicides - Improve human health, e.g. edible vaccines eliminate needles and cold storage - Remove contamination, e.g. poplar trees engineered to clean up heavy metals from contaminated soils

Hectors dolphin pop numbers by two different analysis. Paper comparing them (Slooten and Davies, 2011)

- Liz compared with NIWA (Davies et al. 2008) -Very similar results - Despite very different modelling approach - Population Viability Analysis - Compared to Bayesian fisheries model • Population size in 50 years - Past management: 5,369 vs 5,631 individuals - Zero fisheries mortality: 15,776 vs 14,379

Chance extinctions greater in species with:

- Low birth rates - Longer to recover from chance reductions in population size. - Unequal sex ratios - Can reduce birth rate

Why produce transgenic animals?

- Models for study of human disease - Products for treatment of human disease - Increased animal product yields

Advantages and disadvantages of fixed number breeding

- Safest biologically - Doesn't rely on assumption of logistic growth - Yield and seasons very variable - Constant monitoring required throughout season - Analysis of data is complex

IUCN protected area categories

- Strict Nature reserve: protection of biodiversity, access and use limited -Wilderness area: managed to preserve natural conditions, accessible but limited infrastructure. -National Park: protect ecological processes, educational and recreational opportunities. -Protected landscape: interaction between people and nature has produced character.

Predicting population decline/incline

- a deterministic model can predict population decline - but without stochasticity, time to extinction will be underestimated - a deterministic model predicts population increase - but with high stochasticity population may still go extinct

Extinction is forever

- no current technology will enable complete resurrection of an extinct species, due to unknown epigenetic, genetic, physiological, social, behavioral and other differences. -Less about species restoration and more about ecological restoration -Release into suitable areas of habitat = ecological replacement.

Recent views on conservation introductions

-"It is likely that many species will need assisted colonization." -ecological replacements offer promise for the mitigation of megaherbivore extinctions. -could be valuable restoration tool. -risk to recipient ecosystems may be too large to ever accept it as a conservation tool even if it means extinction.

Biological species concept

-"groups of actual or potentially interbreeding natural populations which are reproductively isolated from other such groups" -doesn't work when you get natural hybridisation. It's a very strict sp. concept.

Phylogenetic species concept

-"the smallest biological entities that are diagnosable and/or monophyletic" -a looser concept. Get an overestimation of taxonomic richness.

Hyvrid vigour in corn

-2 different lines of corn: the 'children' have a huge increase in fitness. Do this with translocations.

Tuatara conservation

-3 species in 19th century S. p. punctatus (Northern) S. p. western (Cook Strait) S. guntheri (N. Brother Is) -protected as one species -N. Brother highly inbred and doesn't cope with climate change. Give up trying to protect this and focus on other sub. species?

ESU synthesis

-3 widely used frameworks: 1) Isolation and adaptation 2) Reciprocal monophyly 3) Ecological & genetic exchangeability If outbreeding depression when moved into new habitat (i.e. disruption of adaptation) then NOT an ESU

Space: Poleward range shift

-84% boundaries expand northward -spp may be forced to interact with those from which they were formerly separated. -not all equally responsive. Results in shifting dominance in communities.

The global magnitude of forest fragmentation

->70% of remaining forest is within 1 km of the forest's edge -most forests in the range where human activity, altered microclimate and non forest species will continue to degrade forest ecosystems. -largest continuing expanse of remaining forest in the Amazon and Congo.

Management vs. research

-A wildlife manager manipulates systems to achieve a managemental objective rather than to find out how the system works. -a large proportion of effort is expended by managers who manipulate systems without taking advantage of the scientific opportunities. -wildlife management literature is free of failures which is a waste of info.

MSY: problems with fixed quota

-Actual density > MSY = decline to equilibrium -Actual density < MSY = decline to extinction If recruitment > than harvest, population recovers.

Red cockaded woodpecker

-Approx. 6,000 individuals -Longleaf pine forests about 80-120 years old -Preferred habitat has substantial openings maintained by recurring fires that prevent succession to hardwoods. -Nest in cavities, birds hollow out living mature longleaf pines that have had heartwood destroyed by fungal attack. Requires... -Low growth of plants among the mature pine trees. - Controlled fires to reduce forest undergrowth - But, continual logging and fire prevention caused a decline of about 10% per year

Factors determining spread

-Availability of suitable habitat (some ecosystems more resistant to invasion). -Local population dynamics -Dispersal ability of species -Anthropogenic factors (eg. possums spread around NZ by people, tried to get them going).

Population indices: detection devices

-Chew cards -Wax tags -Tracking tunnels -Camera Traps

Availability of suitable habitat

-Climatic and habitat matching of source & recipient habitats. -Degree of disturbance of recipient habitat. -Sometimes habitat and climate v different but it still does well. eg. Pinus radiatus in Cali vs. NZ.

Permeability of matrix habitat (chilean bird)

-Conducted translocation experiments to test landscape permeability -3 landscape treatments -birds have territory they always return to. -Birds released in patches surrounded by open habitat remained there longer before dispersing. -Birds released in patches surrounded by dense shrubs or linked via wooded corridors dispersed faster. -birds more reluctant to cross pastures to return to their territory.

Random factors determining establishment

-Demographic - random effects of birth, death & mating in small populations (birds being blown over to NZ from Aussy, random effects in small population). -Parametric - initial population size affects likelihood of establishing (large number of animals arriving in one place, more likely to be successful). -Catastrophic - extinction of a local population irrespective of its size & vigour (flood, volcano etc).

What determines where native bush birds are found in Dunedin?

-Density of built structures (% vegetated area) -Amount of native vegetation -Complexity of structure of vegetation -Presence of tall trees -Proximity to fragments of native vegetation -fragments in dunedin aren't very connected. The Town Belt is big but long and skinny, should be wider because edge effects dominate. Fraser's Gully lacks connection to anything and South D has nothing.

Factors determining arrival of invader

-Distance from source of colonization -Dispersal ability -Association with man - the chief predictor

Density dependence

-Don't make a model density dependent if pops are very small because the chances of them running out of food is minimal. -also depends on habitat size.

What about 50?

-Drosophila Ne =50 for 210 gen: ¼ pops extinct -House fly Ne =50 after 12 gen: inbreeding depression. -Ne = 90 after 5 gen: inbreeding depression -½ of all captive threatened mammals have N<50!!

Influence of matrix habitat

-Edge effects -Dispersal & colonization rates -Within-remnant community dynamics -Alternative habitat (galas in Aussy do well in matrix because water that's provided for stock).

Change of plants on folivorous mammals

-Foliage quality - can determine abundance of arboreal folivores. -Arboreal folivorous mammals - high mass-specific metabolic requirements - If foliage quality already low, higher CO2 levels may reduce foliage quality below minimum necessary to maintain folivore populations

Why define units for conservation?

-For legislative reasons -For conservation science recognition of unique species recognition of stocks recognition of evolutionary units recognition of management unit

Genetics and evolutionary significant units

-Genetically differentiated pops managed as separate genetic units. -ESUs based on genetic markers: mtDNA & nuclear Divergence, monophyly, allele frequency diff. -Criticism Ignores local adaptation that can occur with gene flow

Dunedin Urban study

-Global homogenisers found in highly modified areas (house sparrows, blackbirds, rock doves, starlings -New species invaded forest & matrix (blackbird, starling house sparrow -Forest species able to use matrix: grey warbler, tui, bellbird, kereru -Matrix avoiders: tomtits, robins, rifleman, brown creeper

Age structure models

-Have a column for each age class -younger and older individuals have lower survival rate. -add parameter uncertainty and environmental variability (calving interval may change year to year eg. good/bad years).

Emerging threats?

-Health-associated demands on green space -Digital mimicry -Scattered cremains -Toxoplasma: pet cats as a reservoir for wildlife disease -Uptake of LED night time lighting -Solar cities as ecological traps -Self-healing concrete -Energy-efficient housing -Drones

Hardy-Weinberg Equilibrium

-How should allele frequencies vary across generations? Assumes an ideal population: Infinite population size No selection No mutation No migration No chance events (drift) Random mating Non overlapping generations

How to promote biodiversity in an urban environment?

-Improve quality of remnants -Improve connectivity of remnants -Safeguard linkages with source populations -Control invasives -Improve quality of matrix -Education / awareness

Biotic changes in microhabitat

-Increased light - faster plant growth -Increased wind - plant mortality -Changes in distribution of plants - physiological tolerances (weedy plants that grow in high light have an advantage). -Changes in density/activity of animals -Changes in species interactions

Management scenarios for rats

-Large increase in different masting scenarios. 1. Unmanaged: rat abundance very high. 2. Possum ground control for TB (95% reduction in possums): rat abundance just as high. 3. Conventional arial control every 10 years: decrease in abundance 4. Optimistic low cost, arial control every 3 years: no rats left. 5. Conservative low cost, arial control every 3 years: very low numbers.

Modern invasions differ in three ways?

-Magnitude -Spatial scale -propagule size

Goals

-Manage 600 species by 2030 -enhance 150 populations by 2025 -Incorporate Te Ao Maori -Support research

Climate change and invasive mammals in NZ

-Mast events provide a pulsed food resource for these species, with subsequent impacts on native fauna through predation, and competition for food resources, and on vegetation through herbivory and reduced ecosystem services such as pollination and seed dispersal. -Beech seed masting drives highly irruptive invasive mammal community -Invasive predators = stoats, rats, mice, possums -masting happens more frequently due to climate change (linked to high summer temps). Going to get more rats.

Guidelines for landscape management

-Maximise area/perimeter ratios -Protect forest edges (want fragments that are round). -Minimize harshness of matrix -Provide for connectivity -Plan for climate change!

Typical sequence of events in the exploitation of a natural resource

-New resource discovered -Economic demand increases -Profits encourage new players - stocks decline -Demand outstrips supply - prices rise -Technological improvement - efficiency increases -Quotas applied and competition increases -Non-viable operations sustained by subsidies

Genetic effects of hybridisation

-New species! Plants: evening primrose -Species extinction = genetic swamping Brown teal & Mallards

Climate change and habitat fragmentation for Acadian flycatcher

-Overall productivity much greater in highly forested landscapes -Increased temps greatly reduced productivity in highly forested landscapes to values typical of least forested landscapes -Higher temps may alter activity patterns of some predators; e.g. snakes -High temps may influence abundance/behaviour of alternative prey

Rights based arguments

-Regan argues we have rights because we are subject to a life -others argue it is because we are members of a moral community -the golden rule

Random factors

-Sex ratios -Individual deaths -Litter sizes -Fires -Floods -Drought -Disease

Stoat abundances

-Small increases in different masting conditions -Small increases under optimistic & conservative approaches c.f. unmanaged scenario. -This system is strongly bottom-up driven, with mast seeding events providing a pulsed input of resources, resulting in pulses mice and rats and then a lagged numerical response by a top predator (stoats). -Models show that climate change will exacerbate invasive species impacts on native biodiversity and ecosystem function. -Increased frequency of masting will lead to stoats and rat and mice populations becoming less irruptive and being maintained at higher abundances in this forest type: so previously acute periodic impacts will become a chronic problem. In this case the current strategy of targeting pest control to periods of acute impact will no longer be valid.

Reliability of anecdotal data?

-Standardized survey reveal fishers being restricted to southwestern Oregon and disjunct areas in California. o Anecdotal data resulted in an overestimation of population size and occurrence resulting in petition being rejected. o Delayed the initiation of conservation actions by at least a decade!

Conservation/Utilization debate

-Strict preservation: utilization seldom sustainable, has single species focus, need to restrict human activities. -Use it or lose it:

Actual distribution of wolverine

-Survey efforts initiated in 1980s o Used cameras, bait stations, helicopter surveys o Aubrey et al. (2007) conducted detailed analysis of historical patterns. o Considered both historical records and current distribution of suitable habitat. o Concluded wolverines most likely never occupied North Coast regions. o Schwartz et al. (2007) support this with genetic analyses.

Ethical argument

-The problem with this is that the ethical basis of these arguments is never stated nor justified and the facts are where the discussion in. -thus we often can't understand the other persons point of view -we need to debate the hidden premises which actually look at mortality -X is morally relevant. The way to deal with X is to do Y.

DNA barcoding

-Uses COI gene -not up to interpretation or user differences -use genetic differences to tell between species -falls apart when you have species that hybridise -the barcode is only one gene, don't want to base everything off one gene

Representative regions

-WWF devised system called "Global 200 Ecoregions" to select priority regions for protection. -Ecoregion= large are containing a distinct assemblage of species and environmental conditions. -142 terrestrial ecoregions -all hotspots contain at least one ecoregion. -most contain endemic bird area • 60% of Global Ecoregions and 78% of EBAs overlap with hotspots.

Packaged PVA's

-Wider access to non-modelers -Reduced chance of programming errors -Standardisation • "Packaged" PVAs often difficult to modify for a specific species or situation • Tend to ignore demography • Survival, reproduction, sex ratio etc. • Over-emphasize population genetics • Usually do not include parameter uncertainty • Allow PVAs to be done with little understanding of the model or its assumptions

How do you define a species?

-a group of organisms with common morphology -a group of organisms that can breed and produce fertile offspring -a group of genetically similar organisms.

Darwin's fox

-a subspecies of chilean fox? Localised to Chiloé Island Morphologically distinct Listed as threatened in 1987 -In 1990, found a population on the mainland. Co-exists with other Chilean foxes without interbreeding A species under the biological species concept Mate recognition species concept also a species Also under the phylogenetic species concept

General impact of urbanisation on birds

-across different cities you get similar fauna because it's the urban exploiter birds that do well in cities. Community structure: favours a few - selects against most. Low species richness. High biomass. High degree of homogenisation. Populations: Less productive (don't raise the same number of chicks because there's less food).

Cultural ecosystem service

-aesthetic -spiritual -educational -recreational

Denialism

-arises when uncertainty on impacts is confounded by differences in values. -it attempts to manufacture uncertainty in the scientific consensus on an otherwise undisputed topic - leads to journalists presenting contrarian alternatives as a balanced analysis, ignoring the weight of evidence heavily in favour of the science.

Virtue ethics

-aristotle -intentions are the important part -if you try to kill everyone but end up saving the word... It's your intentions that matter. -virtues are universal

Benefits of captive management

-avoids immediate threats -rapid increased pop size: avoid prolonged bottle necks and limits genetic drift/loss of genetic variation. -restocking -reintroductions: avoids harvesting pressure on wild source populations.

Deep ecology

-based on a holistic rather than individualistic view -a relational, total field image -recognizes that humans are formed by their relationships -without the relationship that exists among humans and between humans and nature, humans would become different things.

ecological replacement vs. assisted colonization

-both conservation introductions If the aim of the release is to: Avoid population extinction of focal species at any scale = colonization. 2. Perform an ecological function lost by extinction of an original form = Ecological replacement

"effective migrants"

-brown rats, males are the dispersive sex. Social constraints. -Nm>10 migrants to abate differentiation

Contamination of GE crops

-can they be kept separate? -Natural spread of seeds and pollen carries risk of growth of "volunteers" and persistence of GE plants as (herbicide resistant) feral individuals (weeds in future crops) - Also spread of seed and pollen mean increased risk of: • Impacts on non-target species (Monarchs and Bt) • Gene flow to wild relatives

Breeders in small populations

-cannot avoid relatives (unless kin recognition) -go to fixation much quicker (become homozygotes).

Lack of experience

-captive born vs. wild born carnivores -wild survive better -in pheasants, captive born and reared had lower survival.

Anti-predator behaviour: whooping crane

-captive rear forage the same as wild born. But parent bred birds are a much tighter group: predator avoidance strategy.

Cats in urban areas

-cats are the worst predators in town because they're in very high numbers. -1,346 birds per yr/ km2

Amazonian forest fragments

-cattle ranching and farming has produced landscapes dominated by small and irregularly shaped forest fragments: these are vulnerable to edge effects, fires, disrupted forest hydrology etc. -fragment size is vital: species richness declines with area for lots of taxa -fragment size also influences rate of species loss: small fragments lose species quicker.

Zebra mussels in Great lakes

-cause decline in native clam and mussel populations -compete with other invertebrates and young fish for plankton -industries pay millions of dollars to clean structures clogged by mussels.

Types of wild harvest

-commercial -recreational -subsistence -cultural -oceanic fisheries -trophy hunting -african bush meat

PAs and Biodiversity hotspots

-concept identified by Norman Myers in 1988 -hotspots hold high numbers of endemic species -must contain 1,500+ endemic vascular plants -must have 30% or less of original vegetation -25 hotspots identified initially

Development of inappropriate behaviours

-condors raised in buildings so when set free they fly towards buildings (excessive tameness and curiosity). Feed their chicks wrong food- screws instead of bones.

Environmental ethics

-considers the moral relationship of human beings with the natural environment. -includes the value and moral status of the environment. -and its nonhuman contents

Environmental variability

-constant environment -moderate environmental variability -catastrophes -the more variability, the more risk: applies to environmental variability, demographic stochasticity and any other variability.

Red palm mites in America and Asia

-damage coconut palms -brought in by tourists on trinkets made from coconut palm leaves. -also by dispersal from wind

Big horn sheep population (Berger, 1990)

-demographic and weather data spanning up to 70 years for 122 bighorn sheep. (1) 100 percent of the populations with fewer than 50 individuals went extinct within 50 years (2) populations with greater than 100 individuals persisted for up to 70 years (3) the rapid loss of populations was not likely to be caused by food shortages, severe weather, predation, or interspecific competition

Edge effects

-depend on quality of matrix -can be detectable up to 600m -impact depends on shape of remnant

Initial fragments

-different allele frequencies by chance -variation in allele frequencies relates to pop size. -variance in frequency of allele p, = pq/2N

Dispersal ability and Fst

-differentiation is related to gene flow -expect dispersal ability to impact on differentiation -strong negative correlation between ability and Fst. -Species that don't disperse much (big horn sheep), you can get quite large differences in Fst over short geographical regions. -whereas for species that do disperse (bears, wolves), you don't get much change in Fst over short or large geographic distances.

Just get rid of recessive alleles

-difficult to remove (carriers) To remove entirely would remove > ½ the population Impractical to remove the allele Inbreeding depression caused by deleterious recessives of small effect Cumulative effect = Genetic Load Cannot be easily removed by purging

Argue about facts to back up their argument

-does it kill possums -does it kill birds -does it kill more or less birds than would occur by predation without 1080.

Deep water horizon oil spill

-dolphins exposed through contact, inhalation, prey. - dolphins in poor condition (25% underweight) - lung disease, including bronchitis - lost pregnancies - tooth loss - inflammation - compromised adrenal function - altered metabolism

Advantages and disadvantages of fixed effort

-easy to control -doesn't require monitoring of N -safer -yield varies annually -incentive for technological innovation

High matrix harshness

-edge gets eaten away because little regeneration. eg. in urban areas.

Population indices: physical evidence

-faecal pellet counts -sign of browse -bowers -tracks -burrow entrance -nest

Provisioning ecosystem service

-fuel -freshwater -wood -fuel

Why do we need marine reserves?

-global fish catch is declining -decreases in trophic level

Invasive species modify habitat: fire enhancement

-grass species invaded Hawaii, so fires become more frequent and hotter.

Invasive species modify habitat: decreased erosion

-grasses bind dunes into less dynamic structures

Advantages and disadvantages of fixed quota

-guaranteed annual yield -simple to administer -assumes stock size response deterministic -large margin of error needed

Early reintroductions

-had very low success rates -increasing numbers of restorations -alot of reintroductions in oceania -focus efforts on mammals and birds -emerging discipline of reintroduction biology

Population indices: dead stuff

-harvest records (game species) -incidental take (squid in fishing nets) -road-kills (snakes on roads) -strandings (marine mammals)

NZ in the middle of major extinction event

-high endemism -island gigantism & flightlessness -3 native mammals -31 species of feral exotic mammals - >40% of all land birds extinct - >29% of all birds threatened -one cat wiped out stephen islands wren

Environment/suffering?

-how can we measure and compare ecological value with individual suffering? -are there thresholds of harm that are unacceptabe? -is more harm to an individual justifiable for greater ecological outcomes?

Conservation translocation

-human mediated movement of living organisms from one area with release in another for some conservation benefit. -Introduction: movement outside indigenous range -Reinforcement: build up existing populations eg. kaki (black stilt). -Reintroduction: intentional movement of an organism into a part of indigenous range from which it has disappeared. eg. reintroduced saddle back south island.

Examples of assortative mating

-humans choose a mate from same ethnic group (in US: African, Hispanic, Jewish, Anglo-saxon, Amish). -13-year cicadas choose mates with similar song and similar abdominal colour. Simon et al (2000). -lake sticklebacks: benthic fish mate with benthic fish; limnetic fish mate with limnetic fish, based on body size. McKinnon & Rundle (2002).

Hybridisation

-hybrids can have reduced fitness levels Cross between distinct lines Artificial (male horse x female donkey) Natural (kaki x pied stilt) Reduced fitness of progeny

Hidden moral premises

-if it doesn't kill to many birds its okay (killing is morally bad but the important thing is the greater good for the environment). -if the animals don't suffer its okay (suffering of animals is morally relevant and needs to be minimised). -you have no right to kill them its not their fault (killing animals is morally wrong).

Skewed sex ratio

-if you have a small number of individuals doing most of the breeding, you'll have a smaller pop size. eg. Kakapo have 3:1 ratio of males.

Degree of fragmentation

-increasing fragmentation = smaller pop sizes. -inbreeding and inbreeding depression increases -increased loss of GV by genetic drift -loss of heterozygozity increases with fragment number and smaller N.

Tom Regan: The case for animal rights 1983

-individuals of an endangered species are no more or less worthy of moral consideration than non-endangered species. -so killing a rat to save a kakapo is not justified.

Genetic modification

-insertion or deletion of genes -from other organisms (horizontal gene transfer)

Peter Singer: Animal liberation 1975

-interests of sentient animals should be given equal moral consideration and their capacity to suffer must be considered.

Invasive species modify habitat: increased biotic disturbance

-invasive earthworms in North America changed hardwood forests by eating the leaf litter layer, reducing cover and richness of herbaceous plants and increasing dominance of grasses. This also leads to decrease in ovenbirds. -crocs lay eggs in sandy areas and they have temp dependent sex determination. Plant invaded nesting areas, making cool temps and thus a bias towards female and eggs not developing properly.

Do invasive species cause problems in urban areas?

-invasive species can establish in urban area. Alien birds spread weedy plants. Weeds fruit at different times so provide a food source when natives aren't fruiting.

Questions?

-is there a difference in which poisons are alright to use when we eradicate islands compared to control? -is it morally right to kill thousands of rats in order to protect endangered snails. Or kill deer to protect a plant? -if money goes back into conservation, is killing a rare species justified? -is saving species out of their ecological context worthwhile? Do species have intrinsic value?

A high profile count with problems: US census

-it is biased low and the bias differs by group. Minority populations much more likely to be missed. Proposal: link standard census data with estimate of how many people missed by standard census! 1) Do normal count, plus normal follow-up of non-respondents 2) Pick a subset of population (housing units) and count everyone present on a given day (estimate 1) * (estimate 2) / number people counted by both methods =Lincoln-Peterson mark-recapture statistic!

Is the spread of 1080 ethical?

-it's good for the environment, so yes. -if it doesn't kill to many birds its okay -if the animals don't suffer its okay -possums aren't native so they dont matter -you have no right to kill them its not their fault -it kills deer and i like to hunt deer so no

Decline in target species may affect ecosystems how?

-keystone species and trophic cascade -by-catch -habitat change

Genetic variation and population size

-large populations have more GV

Ecosystem effects of shark declines in ocean

-large predatory sharks decline due to fishing and netting. -marine mammals and sea turtles decline due to bycatch. -skates and rays increase in abundance. -invertebrates and teleost fish decrease

Inference in reintroduction biology

-largely inductive inference -focus on easily measured aspects -need to draw on general theory

Genetic engineering in the past

-limited to related species -genes that are already present. -very slow

Utilitarianism

-lives are best when they experience max satisfaction and min suffering (moral principal of hedenism). -therefore, any creature capable of suffering is morally relevant. -the total suffering of all animals should be minimized over time (consequentialist argument). -For a utilitarian an action is judged right when the balance of good vs. bad consequences outweighs that of any alternative action. -this is the basis for the ethical analysis of costs and benefits used by animal ethics commitees.

Inadequacies of individual based ethics

-make no moral claim on species or environment -claims made of duties and rights require interests, and species as a whole dont have interests. -ethical frameworks are needed for the question of how we treat the environment as a whole -these can be combined with individual based rights.

Spotted owl

-management plans suggested maintaining 500 pairs to maintain enough genetic variability for populations to survive. -3,000 Pairs spread over milions of acres. -Fragmented habitat in three states (USA) -Home ranges: 1-3 square miles of conifer forest -All populations declining at 7.5-10% per yr -At that rate only 15 pairs of owls would remain in 50 years. Need way more than 500. -decline due to increased competition with barred owl which is more aggressive and more edge tolerant. -juveniles unable to find territories and mates with fragmented habitat.

Level of gene flow

-migration reduces effects of fragmentation (homogenises allele frequencies). -Sewall Wright: one migrant per generation = prevent differentiation.

Pre release conditioning

-migratory lessons for whooping cranes -ferrets moved to large enclosures with prairie holes, then released close to prairie dog colonies (Biggins et al. 1999).

Silver eyes and DNA barcoding

-mitochondrial DNA gives v different result from nuclear so need to be careful with this.

Individual based models

-more suitable for small, endangered pops.

Undesired consequences of captive management

-nature vs nurture -some things are innate -others are learnt (wallabe hadn't learnt any predator avoidance strategies).

Weaknesses

-no indication of how much funding to be allocated -not clear which species are left out and why -at risk species not included -vision does not give effect to purpose -Underlying causes of habitat loss and environmental degradation ignored.

Sex ratio bias (Faust and Thompson, 2000)

-north american zoo, spectacled bear -mother produce the offspring of the sex that most increases her own fitness. For polygynous species, this means that females in superior condition should bias offspring production toward the sex with greater variation in lifetime reproductive success, which is typically males. Captive mammal populations are generally kept in good nutritional condition and thus might be expected to have birth sex ratios biased toward males. Sex allocation theory also predicts that when competition reduces reproductive success of the mother, she should bias offspring toward whichever sex disperses.

Morality and animals: Rene Descartes

-only things with souls are morally relevant -animals are automata that may act like they are in pain or enjoying themselves but this is just programming. -only humans are morally relevant

Animal liberation/welfare causing environmental harm

-people protest killing grey squirrel so now red squirrel is going extinct. -american mink farmed in Europe and some escaped. American mink kills native mink. Animal rights people released minks from farms.

Conservation of endangered blue duck

-permanently increase the residual water flow to improve feeding areas. -North and South Is. populations diverged long time ago with v little gene flow. Translocation not suggested. Grosser et al. 2017.

Self changes in plant

-physiology, productivity and growth. -under different warming temps-plants gain advantages/disadvantages over eachother. -higher CO2 = plants produce tissue with less nutrients. Herbivores have to eat more to get enough. -leaf toughness increased

Key assumptions behind sustainable harvest models

-populations of organisms are renewable resources. -populations of organisms don't grow indefinitely

Captive management

-practiced for centuries -Pete Scot and Gerald Durell -Last resort? -Or targeted management technique: captive rearing, captive breeding.

Multi species model

-predators as a second fishing fleet -compared to first model that didn't include predators, this model produced a smaller estimate of MSY for fisherman.

Genetic information, an answer?

-provides an objective methodology -genetic variation can be useful at 4 taxonomic levles -differentiation between species -between populations -between individuals within a population (mating systems) -variation within individuals (measure inbreeding in zoos).

Abiotic changes in microhabitat

-radiation fluxes (at the edge, more radiation reflecting back, affects micro organisms in soil, affects nutrients). -wind (turbulence of air influences evapotranspiration). -water flux

Captive rearing

-raising done in captivity -use of wild pairs as source of eggs/offspring -common in bird recovery programs -captive rear kakapo chicks. Dont want them to imprint on humans so teach them species specific behavious. -operation nest egg (kiwi, blue duck)

Demographic stochasticity

-random variation among individuals - Each individual has a probability of surviving or reproducing - Expect more variability in a small population

Allele frequencies

-randomise due to genetic drift, even if identical at start. -divergence continues until fixation (increases with time, increases faster in small pops).

Partnership for biodiversity conservation

-re(engage) people with nature -enhance conservation management of species and habitats -wise non-consumptive use of wildlife resources -research informed species and habitat restoration and management.

Shallow ecology

-shallow ecology is commited to the fight against pollution and resource depletion -Naess argues that this is an anthropocentric approach with the primary objective of protecting the health and affluence of the people in developed countries. -shallow ecology is like treating the symptoms not the cause.

Population indices: I heard or saw them

-sightings -point counts (song birds) -call volume (insects, frogs) -questionnaires -individuals per sweep net (invertebrates, tadpoles)

Size and connectivity

-single large reserve better than several small ones -current focus on reducing effects of habitat fragmentation by: protecting the elements of concern. Seeking as large a representative area as possible. Enhancing connectivity between areas.

Drawbacks of captive management

-small pop size in captivity -must manage breeding to: maintain genetic diversity, avoid inbreeding. -disease and health checks

Fst and population size

-smaller population sizes diverge faster

Species level issues

-species is often important practically and politically (eg. fish stocks). -Conservation priorities are influenced by which taxa are recognised as legitimate species. -The recognition of "species" is not always clear and will be influenced by the species concept employed.

Time: Phenological changes in birds migration

-species that advanced their spring migration survived better than those that didn't. Affected by temp cues. -other examples: birds breeding earlier in Europe and USA, breeding of amphibians and evolution of squirrels. Squirrels over 4 gens started breeding earlier to time young with high food availability.

Genetic drift

-stochastic loss of genetic diversity random change in allele frequencies Due to finite N Sampling variation in the production of zygotes -genetic drift acts on individuals that go through the bottle neck. -bottlenecks and founder effect accelerate drift.

Habitat fragmentation at a global scale

-study that draws from the worlds largest and longest running fragmentation experiments -manipulate apspects of fragmentation while controlling for others so provide a powerful way to disentangle cause and effect. -multiple biomes, 5 continents, 35 years.

Life history strategies: mechanisms of change through global warming

-survival -recruitment -phenological -colouration -behaviour -range

Shags

-the two lineages of Stewart Island shag represent two separate species -Stewart Island shag, comprises two regional groups (Otago and Foveaux Strait) that show consistent differences in relative frequencies between pied and bronze plumages, the extent of carunculation, body size, and breeding season. -Previous genetic research on modern and historical specimens utilizing mitochondrial DNA has also shown that the Otago and Foveaux lineages may not be sister taxa; instead, in several analyses the Otago lineage is sister to the endemic Chatham Island shag.

Isolation

-time since isolation (when fragment created it has the most species it ever will, then some are lost). -distance from other remnants -connectivity (some pops too small. Depends on connectivity between fragments). -Trapdoor spider: long lived so hang around even though conditions aren't good.

Effects of current dredging in Otago Harbour

-to allow access to larger cargo ships -smother organisms on sea floor -changes in fish communities -direct effects to marine mammals (noise, physical) -indirect effects (reduced food) -toxins in dredge spoils

Importance of diet

-too fatty = extra weight which increases predation risk

Bt crops and monarch butterflies

-toxin from soil put into corn to make them insect repellent. -pollen from corn lands on milkweed which butterflies eat. -this reduces caterpillar survival and kills butterflies. -current hybrids in use have low toxicity, low dispersal and negligible impact on monarch butterfly populations (Sears et al. 2001)

Limited resources for conservation

-trade offs: do we save all of them? -managers like hard goals: want to save a species/subspecies. Save them all or save all you can are dissatisfying.

Gene flow

-transfer of genetic material between populations resulting from movements of individuals or gametes.

Animal personality

-unconscious selection of breeders -select less stressed and aggressive individuals. -good for captivity but not in wild -hawaiin crow-captivity has bred all antipredator traits out of them.

Lake Eacham Rainbow fish

-unplanned save! Lake Eacham National Park introduced predatory fish Illegal collecting for aquariums

Lack foraging skills

-use of role models -teaching foraging skills: takahe use snow tussock during winter. Not taught to use snow tussock Poor survival of captive raised Now expose chicks to snow tussock

Rearing environment

-use puppets so they don't imprint on humans (Takahe chicks or wattle cranes) -no difference between hand reared and parent reared whooping cranes. -parents raise them in large enclosures (Shrikes) -species specific

Increasing reliability of evidence

-visual observation of organism sign -visual or auditory observation -diagnostic track impressions -diagnostic recorded audio -photo or video showing diagnostic characteristics -diagnostic dna evidence -live or dead specimen

1989 consultation about southern coast marine reserves

-want reserve at nuggets because its diverse with high productivity. Two water currents meeting so complex area with wide ranging depth contour. -Marine reserve with no take and around it a buffer zone with a little take. Made iwi more inclined to have reserve at nuggets.

Types of captive management

-wild to wild translocation (Hihi) -captive rearing (Kaki) -captive breeding (Houbara bustard) -any period of captivity carries risk that future viability will be compromised. -the longer time in captivity the greater the risk

Protection for crayfish

-with total protection you get increase in both sizes of crayfish. -with partial protection not much happens but its better than none.

How many MPA in NZ?

-would have 30% protection if you count benthic protection areas and the kermadecs. -only bottom trawling prohibited in BPAs. Other fishing is allowed. -About 7% Protection around mainland NZ if you count marine mammal sanctuaries. -marine mammal sanctuaries exclude gillnets and trawling only. -marine reserves only ~1% around mainland.

Two key questions to ask about abundance indices

1) Does variation in index reliably measure change in abundance? 2) Does the design allow reasonable power to detect trends in abundance?

And some additional considerations when using indices in population studies

1) is index stable in time? 2) is index stable through space? (habitats and regions?) 3) is index proportional to true abundance? (saturation at high abundance? skipping at low abundance?)

Three steps to a successful invasion

1. Arrival/introduction 2. Establishment (depends on interaction with invaded ecosystem). 3. Spread/integration (characteristics of invaded ecosystem and of the invader determine how widespread it will become).

Creating a hybrid wooly mammoth

1. DNA extracted from frozen mammoth specimens 2. DNA spliced with skin cells from modern asian elephants. 3. skin cells reprogrammed to become stem cells and added to egg from asian elephant 4. eggs stimulated to turn into embryos 5. embryos grown in artificial womb

Techniques of genetic engineering

1. Isolation • Restriction enzymes • PCR 2. Combination • Antibiotic resistance marker 3. Insertion • Inject bacterial plasmids • Fire in DNA-coated gold particles - CRISPR

Assumptions of this simple Lincoln-Peterson estimator

1. No marks are lost 2. Population is "Closed"—no deaths, births, immigration, or emigration during estimation 3. Animals have equal catchability -Relaxing Assumptions: program CAPTURE--can model unequal catchability in time; among animals; or after trapping (trap-shy vs. trap-happy). -Relaxing Assumptions: program CAPTURE--allow open population, estimate emigration/death and births/immigration.

Why monitor?

1. Provides information on the status of wildlife populations before deciding on the appropriate course of action. 2. Evaluates the effectiveness of management actions relative to stated objectives. 3. Provides feedback for adaptive management. 4. Justifies management action (or inaction) to stakeholders.

Roles of conservation genetics

1. Reducing extinction risk by minimizing inbreeding and loss of GD e.g. flightless Guam rail, introduced brown tree snake during WWII 80,000 (1960s) to 21 birds. captive management. 2. Identifying populations of concern e.g. Wollemi Pines. Rediscovered in a gorge in Blue Mountains no GD at 100 loci. Susceptible to common die-back fungus.

LINE TRANSECTS (estimators via counts and distances)

1. Travel transect. Record all individuals seen, distance d, and angle θ. 2. Transform all data into perpendicular distances from transect. 3. Create histogram of n sightings x distance from transect; fit detection curve. 4. Calculate proportion of animals seen at each distance. 5. Estimate population size and density.

Types of population models

1. Whole population treated as one number (Population size next year = Population size this year + Births - Deaths). 2. Age structured model 3. Individual based model Features that can be added to any of the models above • Density dependence • Stochasticity • More than one population • More than one species

Editing a gene using CRISPR/CAS9 technique

1. scientists create a genetic sequence called a guide RNA that matches to the piece of DNA they want to modify. 2. This sequence is added to a cell along with a protein called Cas9, which acts like a piece of scissors that cut DNA. 3. the guide RNA hones in on the target DNA and Cas9 cuts it out. 4. Now another piece of DNA is swapped into the place of the old DNA and enzymes repair the cuts.

5 points to deep ecology

1. the flourishing of human and non-human life has intrinsic value. The value of non-human life is independent of the usefulness these may have for human purposes. 2. richness and diversity of life forms are values in themselves and contribute to the flourishing of human and non-human life. 3. Humans have no rights to reduce this richness and diversity except to satisfy vital needs. 4. Human interference with the non human world is excessive and rapidly worsening. 5. The flourishing of humans is compatible with decrease of the human pop.

Reliability of occurence data depend on:

1.) Reliability of each record 2.) Rarity of the species As species become more rare, proportion of false positives will increase. Suggested solution: Use a gradient of evidence standards that are related to species rarity

Hectors dolphin protected areas

1988: first protected area created: gillnet ban in most of sanctuary around the Banks peninsula. 2003: Two protected areas (green) with gillnet ban and restrictions on use of trawl nets. IUCN Recommendation 142 from 2012: Dolphin-safe fishing methods throughout NZ dolphin habitat, as recommended by IUCN and other international experts. Then they might begin to recover.

Implications for conservation: biodiversity hotspots and TWAs

1995-2000: the annual human population growth rate for hotspots was 38%: higher than the global rate. 2010: 23% of the human population living in hotspots and TWAs. Much of the Earth's terrestrial biodiversity & endemicity is concentrated in areas of high threat.

New Zealand ecosanctuaries and mainland islands

>70 NZ sanctuaries -42 community led

Extrinsic factors

Anthropocentric -we shouldn't destroy the rainforest because there may be cures for cancer. -warning of environmental damage -ecosystem function and adaptation -valuing nature makes us more morally creamy. Ecocentric -ecosystem function/linkage -Kokako ecologically irrelevant so no point trying to save it? -figurehead status of endangered species

Why are species successful invaders?

Ants introduced to Cali in 1980's Successful competitors for food, not aggressive but very abundant. Massive colonies with multiple queens. In argentina they behave differently, live in small groups with 1 queen. Bottle neck when invading cali so genetically different and left behind a parasite.

De-extinction defined

Any attempt to create some proxy of an extinct species or subspecies through any technique, including methods such as selective back breeding, somatic cell nuclear transfer, and genome engineering .

The changing environment

Arabian endemic passarines stranded in high altitude islands. Golden Bowerbird: queensland mountain endemic. Unable to spread across hot lowlands to colonise cooler southern areas. (Thomas 2011).

Birds and vegetation

Areas with structurally simple vegetation/ less vegetated area = mainly exotic species, dominance by a few species, bush natives - <10% total count. Areas with structurally complex vegetation / more vegetated area = native bush birds - 24-32% total count.

Wildlife counts

Assumption: you can count every individual. Consequences of faulty assumption: 1) population underestimate (typically) 2) part of population may be more under-counted than other parts. (e.g. one sex or age-class is less detectable). Extrapolation from surveyed area(s) to total area: are areas typical? consider randomization, stratification.

A meta‐analysis of factors determining intra‐urban biodiversity variation

Beninde et al. 2015 -Design variables: Area and habitat richness have sig. positive effect. -Management variables: Managed, has a sig. positive effect. -Biotic variables: Herb density, cover, structure, and shrub and tree structure and cover, and vegetation structure all have sig. positive effects. -Abiotic variables: water cover has a sig. positive effect. -Landscape features: corridors and % green area have sig. positive effects. -increasing the area of habitat patches and creating a network of corridors is the most important strategy to maintain high levels of urban biodiversity.

Absence of appropriate behaviours

Birds may lose or fail to acquire the appropriate range of behaviors: eg. thick billed parrot • Locomotor skills • Spatial orientation • Recognition of natural foods • Responses to predators

Measuring Fst

Can determine using genetic markers FST = (HT - HS) / HT HS, mean expected heterozygosity across all population fragments. HT, expected heterozygosity for total population. FST ranges: 0 (no differentiation) 1 (complete differentiation) -Fst = measure of how genetically different one population is from another.

Tipping points

Can we predict future conservation outcomes if we don't know where the tipping points are? • Human impact often does not cause gradual ecological change - But non-linear, sudden changes or 'tipping points' - It's easier to 'fall of the cliff' than it is to 'climb back up' • How does this change the way we should manage human impacts?

Snowshoe hares as lynx food

Canada lynx were federally listed as Threatened in the US (2000). -'lynx foraging habitat' protected precommercial thinning, fire, harvests managed for lynx and hares. BUT WHERE ARE THERE ENOUGH HARES TO SUPPORT LYNX?? -harvest records? -snow-tracks? -fecal pellets? -sightings? -browse damage?

New zealands first marine reserve

Cape Rodney - Okakari Point 1975 -Dr. Bill Ballantine was the pioneer of marine reserve protection in NZ and around the world.

Predator recognition training

Captive birds show less appropriate responses to predators than wild or parent reared birds. Therefore anti-predator behaviour can be learned. -Barubatu released into wild and didn't know about predators. Used hand reared fox to teach them about predators. Higher survival of birds that had been scared by the fox in captivity (Van Heezik et al. 1999).

Changing life history traits

Change physiology to cope with new climates. Plastic phenotype, micro-evolutionary change.

Problems of synchrony in pied flycatchers

Changes in phenology help keep species in sync with abiotic factors but they can be disruptive by causing asynchrony with predators/prey/plant systems. -have two weeks to breed, lay egg so when it hatches, conincides with peak caterpillar abundance. Speed up by spending less time at stop over points during migration.

Space: Poleward shift of plants and caribou

Climate change - more shrubs - absorb more sun - feedback effect, create warmer environment - lichens dies - caribu decrease - humans use caribu so impacted.

Synthetic biology

Construction of new biological parts, devices and systems, and the redesign of existing natural biological systems for useful purposes - Kent Redford Selectively altering the genes of organisms to make them do things that they wouldn't do in their untouched state - George Church

Deterministic vs. stochastic models

Deterministic models used to be commonly used in wildlife and fisheries. • Provide simple predictions • Not very realistic • Not suitable for estimating extinction risk • Definitely not appropriate for small populations • Stochastic models now most common - for endangered and "harvested" species - a model would be called a Population Viability Analysis only if it's a stochastic model

Public response to reserve at nuggets

Did not want any marine reserve at Nugget: •Ngai Tahu •Commercial fishers •Some recreational fishers Wanted a larger marine reserve: •Forest and Bird •Maruia Society •Public

Metapopulations

Differ from other structures -regular extinctions and recolonisations -genetic drift, founder events, inbreeding -different levels of gene flow -source/sink dynamic

Moving in space

Dispersing to areas with suitable habitat or changing location on a microhabitat scale.

Pros and cons of GM plants and animals

Enhanced Vit A in golden rice - was criticised for needing 9kg of cooked rice. But: latest versions deliver Vit A in only 60g of cooked rice Herman-Lactoferrine present in small amounts but extraction from milk feasible and safe. Calcium Carrot- have to eat 1.5 kg carrots per day to obtain required dose Super Bananas- Enhanced Vit A in GM banana to address deficiencies in Uganda. GMO Cassava-Enhanced and virus resistant; to be tested in Africa in 2018.

Gormely et al. 2012

First evidence that marine mammal sanctuaries work. • Analysed 21 years of Photo-ID data • Bayesian mark-recapture model • 90% probability that survival has improved • 5.4% increase in survival rate (CI 4.1 - 6.8) • Population trend improved from 0.935 to 0.995 Probability of population recovery: 7% before sanctuary, 41% after.

Setting up a stochastic model

For each model "run": -select mean values for max pop growth, fishing effort, entanglement rate to represent parameter uncertainty. Each year: use that mean to set up a distribution (e.g. normal) randomly select max pop growth, fishing effort for each year, from that normal distribution to represent environmental stochasticity. • Repeat until the year 2050 • Repeat for 5000 runs of the model

Planned crisis management

Guam rail-21 birds, now 135. California condor-14 birds now >300. Now very inbred because of captive management. -captive breeding for animals that go extinct in the wild. -some cant be released back into wild because diseases or loss of predator behaviours.

Saving earths species: a rough guide

Half earth project. -biologist E.O Wilson has proposed setting aside half of the earths habitat to preserve ~84% of all species.

Tipping point

Harder to go back after a tipping point. Want to know where the tipping point is and want to stay away from that.

Standardised camera trapping

Have camera looking down so all look at the same amount of space.

Examples of transgenic animals

Herman the Bull- genetically modified bull with human gene built into genetic code at an early embryonic stage so milk from female descendants contains human protein lactoferrine, used as medicine. In 2009 Japanese scientists produce the first transgenic primate. Transgenic goats-Feb 2009 US FDA approves 1st human drug produced by a transgenic animal: Genetically modified goats that produce Atryn in milk.

Drones for seabird counts

Hodgson et al. 2016 Precision wildlife monitoring using unmanned aerial vehicles.

Threats

Human population growth, habitat fragmentation, over-exploitation, invasive species, climate change, genetically modified organisms

Effectiveness of current protection & IWC recommendation for dolphins

IWC recommendation 4x the current protection. -much higher probability of population increase for IWC option.

Population fragmentation

Impact depends on: Number & size of pop fragments Spatial pattern of new populations Distance between populations Dispersal ability of species Environment between fragments Time since fragmented

Endemic bird areas

Important bird areas: areas with high diversity so worthy of protection.

Allee effect

In very small populations, the growth rate drops - e.g. individuals fail to find a mate - groups too small for successful foraging or predator defense. Adding environmental variability into a model increases risk. Risk also goes up as human impact increases. Allee effect has stronger impact. Synergystic feedback between allee and environmental. Make eachother worse.

Models of structure

Island model: unrealistic, equal migration and N. Meta populations: realistic? Cycles of founder events and extinctions. Inbreeding greatest and fitness lowest of all population structures.

Extinction rates of birds as a function of population size, over 80-year period

Jones and Diamond 1976. -10 breeding pairs - about 30% went extinct -100 pairs - 10% went extinct -1000+ pairs - none went extinct

Pellet counts as index of abundance of snowshoe hares

Krebs et al. 2001 Index tested >20 years of data; seems reliable in time

What number of pellets is enough to support lynx?

Mills et al. 2005 Previous literature on lynx said ~0.5 hares/hectare was enough. Can pellet counts tell us when a stand is >0.5 hares or <0.5 hares? 1. Low number of pellets, <0.6 average per plot, means <0.3 hares. 2. High number of pellets, >1.6 average per plot, means >0.7 hares. 3. BUT, between 0.6 and 1.6 pellets, relationship TOO NOISY— can't tell for sure how many hares are there.

Reintroduction specialist group

Mission: to combat loss of biodiversity by using re-introductions as a restoration tool. Indigenous range = known or inferred distribution generated from historical records or physical evidence of the species' occurrence.

Current biodiversity loss compared to previous

Modern rates of vertebrate extinctions are much higher. Increased sharply over the past 200yrs corresponding with industrial society.

Completely isolated fragments

Most severe form of fragmentation Short term: Small pops homozygous & inbreeding depression Greater allele diversity Long term: Extinction greater in frag pops Greater diversity in large population

Uncertainty and change in reintroductions

New threats, e.g. introduced predators. Environmental change, e.g. climate change. eg. mohua

Second proposal for Nugget Point Marine Reserve - 2002

Ngai Tahu Land Claims Settlement 1998 meant that Ngai Tahu were more positive about marine protection • Biodiversity strategy (2000) identified marine protection as priority, with the aim of achieving 10% of NZ's marine area by 2010 • But: Opponents now much better organised • Ministry of Fisheries starting to take control of the process • Commercial fishers argued that marine reserves and Mataitai 'impact on their ability to access fish'

Nugget point and kaikoura

Nugget: good design but pink should surround blue Kaikoura: bad cause only tiny bit on shore. No scientists on board.

Population size of hectors dolphins by 2050 (Slooten and Dawson 2010)

Past management: pop very small All fishing effort from protected areas is removed from the fishery: pop a bit higher. Half of the fishing effort is displaced to unprotected areas: pop a bit higher. All displaced, plus trawling and recreational bycatch is included: pop lowest. Zero fisheries mortality: Pop high!

Relationship between HPD and bird species richness in Aussy

Primary productivity was the main factor driving spatial congruence between bird species richness and HPD. The proportion of conservation land was an important mediating factor in areas of high HPD. Conclusion: humans prefer to live in productive ecosystems that also support high biodiversity

Critical evaluation of database records: predicting the distribution of sasquatch

Probable misidentifications o Bigfoot ENM based on repository of sightings and auditory detections (n=551) and footprint measurements (n=95)

New Zealand's threatened species strategy

Purpose -plan to halt the decline in our threatened species and restore them to healthy pops. Vision -to safeguard our vulnerable, threatened species.

Threatened status of Hector's dolphins

Rate of pop decline over three years: -93% for North island pop -74% for the species as a whole IUCN criteria: Critically Endangered ≥ 80% decline over 3 generations Endangered ≥ 50% Vulnerable ≥ 30%

Shrinking farmland

Renwick et al. 2013 Policy reform and agricultural land abandonment in the EU. -for the first time, more land being left to return to nature than is being cleared for agriculture.

Natural hybridisation (lynx and bobcat)

Schwartz et al. 2004. -hybridization is an under-appreciated factor that potentially limits the distribution and recovery of lynx. If the F1 hybrids are always sterile, the threat to the lynx population is from lost recruitment opportunities. - the production of fertile F1 hybrids may eventually lead to hybrid swarms.

Pros and cons to predator proof fences NZ

Scofield et al. 2011. •Captive breeding and release? • Just an expensive zoo? • Worth it for the educational benefits? • What about the trade-off's? -small expensive zoos surrounded by degraded habitat that will never be able to sustain the animal and plant species contained within the fence.

Land sparing vs. land sharing

Scott et al. 2015 -looked at: carbon storage, water infiltration, human well-being, agricultural production, pollination, pest control, noise reduction, air purification and temp regulation. -ecosystem services better under land sparing -land sharing better for human health -modelling shows that urban ecosystems function less well when there are fewer large parks. To benefit people and nature cities should include large parks and some land sharing is necessary.

House sparrow decline

Shaw et al. 2008. -Declines in UK & Europe -Remaining colonies biased towards deprived areas Affluent areas undergone more change: - more off-road parking - paving - shrubs predominantly ornamental - fewer nesting sites - loss of green space greater

Isolated pops = islands. Eldridge et al. 1999

Similar to oceanic islands: inbred, lower genetic diversity & > extinction risk compared to mainland Black-footed rock wallaby: Fewer alleles per microsatellite locus & most fixed Inbreeding depression (reduced fecundity) on barrow island.

Remnant size

Small populations vulnerable - -Demographic stochasticity -Environmental stochasticity -Deterministic threats -Loss of genetic variation

Terminator and traitor technology

Terminator allows production of 1st generation crops with sterile seeds: protect patents and prevent escape of GE traits - Addition of genes to crop - Activation of terminator process - Farmers plant seeds, grow plants and harvest mature, but sterile seeds. - Traitor (Trait Specific Genetic Use Restriction) • Requires yearly application of a chemical to reactivate engineered traits • Requires farmers to pay yearly

Why can alien species succeed in environments to which they have had no opportunity to adapt to?

Tested two hypotheses: 1. Exotic species are superior competitors 2. Exotic species can opportunistically exploit ecological opportunities derived from human activities. -sparrows increase with people, they're opportunistic.

Ecological replacements of megaherbivores Griffiths et al. 2013

The extinction of large herbivores, often keystone species, can dramatically modify plant communities and may prevent an ecosystem returning to its previous state and threaten native biodiversity. Aldabran and Madagascan tortoises are functionally and taxonomically similar to the extinct mauritian giant tortoise. They were introduced to Mauritius to control the non-native plants that were threatening persistence of native species.

The golden rule

The golden rule should be applied to species? -it works for individuals but maybe not for groups. -a species doesn't want to be alive, the individual does.

Translocation spectrum

The release is intentional -> the goal is to improve status or restore natural ecosystem functions or processes -> Conservation Translocation. Release in indigenous range -> Population restoration. Conspecifics present in release area -> Reinforcement.

Edge effects in Great Tit

Tits breeding at the edge of the woodland: - bred at a higher density - bred later - lay smaller clutches with larger eggs - had lower nest success due to incr. predation - Edge effects persistent > 500m from edge; therefore, edge effects omnipresent in woodlands of <80 ha. -Territories of poorer quality at the edge so they invest more in their eggs to give chicks a better chance.

IUCN critera for endangered species

Tried to come up with criteria that would fit any plant or animal species. • Critically endangered - Population size < 50 mature individuals - Extent of occurrence <100 km2 - Population decline of ≥90% over 10 yrs or 3 generations - Extinction probability ≥50% over 10 yrs / 3 generations • Endangered - Population size < 250 mature individuals - Extent of occurrence <5000 km2 - Population decline of ≥70% over 10 yrs or 3 generations - Extinction probability ≥20% over 10 yrs / 3 generations