XX Applied Ethology -- Lecture & Book Flashcards

Research animal

Animals that are used or intended to be used in animal experiments

Kept at a facility or another housing area for experimental animals

• “Animals shall be treated well and protected from unnecessary suffering and disease.”

• Animals are allowed to suffer in research if it is considered necessary.

Ethical permits are needed for

• Certain species

  • mammals, birds, reptiles, amphibians, fishes, cyclostomata, octopus

• Certain experiments

Not needed if

• you have the owner’s permission

• for e.g. enrichment or observational studies at zoos etc

3R

• Replace

• Reduce

• Refine

• (Respect)

• (Responsibility)

Humane end point

Predefined criteria on when to end (interrupt) the experiment

• “upper limit of suffering”

• Not equal to experimental endpoint

Sentience

Ability to obtain and interpret stimuli + has a basic ability for memory, judgment, and emotion

• Not equal to intelligence

Nocireception

• Not equal to experience of pain/suffering

• E.g. insects still react to pain/stress but we don’t know how it actually affects them

Taming vs domestication

• Taming

  • On an individual level

  • Non-inheritable process

  • Happens within a singular individual’s lifetime through habituation or conditioning

  • Purely behavioural, no genetic change to the species or population

  • Not passed down to offspring: a tame animal’s offspring is not tame from birth

  • Can apply to any species

• Domestication

  • On a population level

  • Evolutionary process across many generations

  • Heritable — genetic change is passed onto offspring whether or not they are personally ever handled by a human

  • Driven by selection

    • natural, artificial, or both

  • Only a few number of species have ever been domesticated

Taming vs tameness

• Taming is a human action

• Tameness is a behavioural trait

  • can be selected upon

Domestication requires

• Selection on tameness

• Reproductive isolation

  • A founder population breeds under human conditions not in the wild

• Multi-generational selection

  • includes unconscious selection

The three pathways to domestication

• Commensal

  • A species voluntarily enters the human niche

    • drawn by food or shelter

    • e.g. cats, dogs

• Prey

  • Managed hunting gradually becomes controlled breeding

  • e.g. cows, turkey

• Directed

  • Deliberate capture of a wild species for a specific purpose

  • e.g. horses, bees

Are some species pre-disposed for domestication?

• Pros

  • Large gregarious group

  • Non-territorial

  • Promiscuous mating system

  • Precocial young (born “functional”)

  • Generalist feeders

  • Short flight distance from humans

  • Low reactivity to novelty

• Cons

  • Family groups

  • Territorial

  • Monogamous mating system

  • Altricial young (“useless” when born)

  • Specialist feeders

  • Wariness and long flight distances

  • High sensitivity to novelty

Reasons why the wolf was an unlikely candidate for domestication

• First domesticated species of any animal or plant

• The only domesticated large carnivore

• Not instigated by human action

  • less fearful wolves were pre-adapted to exploit this new niche

Exaptation

An old trait being used in a new context

Domestication syndrome

The general alteration of morphological, physiological, and behavioural traits occurs simultaneously in domesticated animals

• e.g. floppy ears, curly tails, white pigmentation, playfulness

Domestication traits vs Improvement traits

• Domestication traits

  • Essential at the early stages of domestication

  • Generally shared across all domesticates of a species

  • Under selection during the initial stages of domestication. In animals, these traits will primarily be behavioural, e.g.

    • tameness

    • low reactivity

    • tolerance of restricted space/movement

  • Often (partly) a relaxation of natural selection, not only positive selection

• Improvement traits

  • Arose after the initial stages of domestication

  • Present in only a portion of domesticates, often fixed within particular breeds or regional populations

  • Product of later, increasingly deliberate (artificial) selection, e.g.

    • Milk yield

    • Egg number

    • Body size

    • Specific coat colours

    • Specific behaviours (e.g. herding)

Methods to quantify behavioural evolution

• Common garden

  • Raise both populations in the same environment. A difference that persists indicates genetic differentiation

• Cross-fostering

  • Allows the separation of genotype, environment, and parental effects

• Selection experiment

  • A response to selection across generations is evolved change by definition

• Note that most (if not all) domesticates have been so heavily improved that we can no longer separate domestication traits from improvement traits.

Motivation vs Decision making

• Motivation

  • Readiness to act (internal state)

  • What drives the behaviour?

    • e.g. low blood glucose —> hunger motivation

• Decision making

  • Selection process

  • Should current energy level be used for something else?

    • E.g. is it safe to forage right now? Is it a better opportunity to mate right now?

Motivation may depend on

• Hormone level

• Time of day

• Season

• Age

• Sex

• Climate

Homeostasis

Maintenance of a stable state of internal physical and chemical conditions within narrow optimal ranges by living organisms.

• Maintains stability through negative feedback

Involves:

• Blood pH

• Core temperature

• Blood glucose and oxygen levels

• Potassium, calcium, and sodium concentrations

• Fluid balance

• Energy balance

Allostasis

Process by which animals actively adjust their internal state to meet predictable and unpredictable demands.

• allows for dynamic shifts in parameters to match needs to eventually return to homeostasis.

• e.g. increase in heart rate and blood pressure during physical activity, elevation in glucocorticoids before a breeding season (to be more aroused)

Why does allostasis matter in the context of motivation?

• not every rise in a hormone or a drive reflects a deficit being corrected. Some reflect anticipation of a demand.

Homeostasis vs allostasis

• Homeostasis

  • Fixed set points within a narrow range

• Allostasis

  • Dynamic set points that can adapt to changing demands

  • Can be predictive (changes before deviation from set point occurs), e.g. while watching a horror movie you anticipate a scary scene and your pulse goes up

Allostatic load

The cumulative cost of the body of allostasis

• When stressors become too often and lead to chronic stress

How to measure an animal’s motivation

• Testing its willingness to pay to gain access to a resource

  • e.g. how many obstacles it is willing to overcome in order to get to a resource, e.g. food or a new environment.

Wallowing

A behaviour where an animal rolls or lies in mud, water, or wet soil.

Displacement activity

A normal behaviour that appears out of its usual context.

• Redirected behaviour

  • The correct behaviour that is directed at the wrong object.

• Intention movements

  • Suboptimal or fractions of the correct behaviour.

• Ambivalence

  • Combination of intention movements from both conflicting motivational systems (e.g. approach and retreat)

Stereotypic behaviour

A repetitive, functionless, and often damaging behavioural pattern.

• Often response to chronic stress, frustration, or inability to perform natural behaviours.

• Not necessarily a displacement activity, but prolonged state of motivational conflict can lead to development of stereotypic behaviours as a coping mechanism

• Persists even if the animal is taken out of the situation that triggered it.

Judgment vs Decision

• Judgment

  • Acquiring and processing information to make an inference

  • Relies on ability to discriminate, categorize, assess, and recognize.

  • Can be difficult to assess, but time spent can indicate judgment.

• Decision

  • Evaluating and selecting options based on information

  • Expressed through preference and choice

  • Often more clear cut and quantifiable in behavioural tests

Things to keep in mind during preference tests:

• If the individual does not make a choice, we cannot say whether this is due to lack of judgment (no discrimination) or a choice not to act (lack of preference)

• To solve this, you can add additional measures:

  • Physiology

  • Neurology

  • More behaviours

Aposematism

Advertising defence strategy where an animal uses bright colours, bold patterns, distinctive sounds, or strong smells to warn predators that it is toxic, venomous, or tastes bad.

• Naïve predators learn to avoid this prey more quickly than cryptid defended prey.

Designing studies around motivations

• Avoid anthropomorphism

  • “worked hard for it” is not the same as motivation

• Control and report deprivation/energy state before testing (for tests involving food)

  • Note that some animals are less food motivated than others

• Watch for displacement activities being mistaken for what you are actually measuring.

Social organizations

• Solitary

  • e.g. Maned wolf

• Pairs

  • e.g. Laysan Albratross

• Family groups

  • e.g. wolves

• Herds/flocks

  • e.g. Pronghorn antelope

• Complex societies

  • = eusociality

  • e.g. naked mole rat

  • highest level of social organization

  • division of labour into a caste system

    • single reproductive female (queen)

    • sterile workers

    • drones (male)

    • soldiers

  • cooperative in child care etc

Benefits to group-living

• Reduced predation risk

  • “many eyes” effect

  • confusion by blending in

• Information sharing

• More reliable access to mates

• Increased success in obtaining food

  • ability to take down larger prey

  • ability to mob larger predators off kills

• Shared rearing of offspring

• Energy conservation

  • huddling together to stay warm

Costs of group-living

• Greater conspicuousness

• Competition

  • Food sharing

  • Dominance disputes

• Spreading of diseases

• Reduced reproductive fitness

  • infidelity

  • inbreeding

  • infanticide

Pros vs Cons with Group living

Benefits to group-living

• Reduced predation risk

  • “many eyes” effect

  • confusion by blending in

• Information sharing

• More reliable access to mates

• Increased success in obtaining food

  • ability to take down larger prey

  • ability to mob larger predators off kills

• Shared rearing of offspring

• Energy conservation

  • huddling together to stay warm

Costs of group-living

• Greater conspicuousness

• Competition

  • Food sharing

  • Dominance disputes

• Spreading of diseases

• Reduced reproductive fitness

  • infidelity

  • inbreeding

  • infanticide

Techniques in group size when predators are present

• Zebra and impala aggregate into larger groups

• Wildebeest split into smaller groups

• Grant’s gazelle and giraffe show weak responses

Vigilance levels in species

• Obligate grazers that form largest herds

  • Lowest level of vigilance

• Mixed feeders with intermediate group sizes

  • Intermediate level of vigilance

• Obligatory browsing (giraffe) forming small groups

  • Highest level of vigilance

Selfish herd

Predation risk is not evenly distributed across positions within a group

• due to edge effect

• animals want to be in the middle

• social status, health, age, food motivation, reproductive status all affect an animal’s physical position in the group

Edge effect

Higher exposure to predation risk at the edge of a group

Social network analysis

• Nodes

  • represent individuals, groups, classes etc

• Edges

  • represent how two nodes relate to each other

  • can be used to describe how frequently they associate or interact

• Centrality

  • measure of an individual’s structural importance in a group based on its network position

• Degree centrality

  • based on the number of direct edges an animal has

    • animals with more edges (degree nodes) will have more influence on the individuals around it (and possibly the entire network)

• Direct edges

  • a focal individual’s immediate connections

• Indirect edges

  • connections with individuals through other individuals

• Bridges

  • individuals that connect two “populations”

What is dominance, really?

A social relationship reducing conflicts.

• Determines priority access to contested resources (food, shelter, mates)

• NOT a personality trait! Rank can change

• Only applicable WITHIN species

Establishing dominance hierarchies:

• Signals of dominance

  • Phenotype linked with dominance rank

  • Influences rank-related interactions in stable groups

  • e.g. chemical signals in social insects

• Signals of individual identity

  • unique phenotype that is learned and associated with dominance information

  • influences rank-related interactions with known individuals

  • e.g. unique whoops in hyenas

• Signals of fighting ability

  • Phenotype linked with resource holding potential, but not dominance per se

  • Influences contests with unknown individuals

  • e.g. call frequency in frogs

Why bother with cooperative breeding?

• Kin selection

• Habitat saturation/fragmentation

• Reliable food supply

• Succession for breeding opportunity

  • may breed another year and then receive help

Super normal behaviour

Preference for exaggerated versions of a normal trait.

• E.g. red beak thingy

Tinbergen’s Four Questions

1. Mechanism/Causation

            what mechanism triggers the behaviour?

            how does it work?

2. Development/Ontogeny

            how age, environment etc affects the behaviour

            how does it develop?

3. Function/Adaptive value

            current function of the behaviour/fitness

            what is it for?

4. Evolution/Phylogeny

            how did the behaviour evolve?

            which species share its behaviour? did it evolve once or multiple times?

Proximate explanations

• 1 and 2

Ultimate explanations

• 3 and 4

How to test each of Tinbergen’s questions?

1. E.g. measuring hormones, neural activity, or the stimuli that trigger responses.

2. Compare individuals at different developmental stages or with different early experiences.

3. Estimation of fitness.

                e.g. stotting in gazelles is an honest signal of their fitness

4. Comparing genetic expression, phylogenetic analyses etc.

Hypothesis vs Prediction

Hypothesis:

• A proposed explanation for an observed behaviour

• Should always state WHY

• Can generate multiple predictions

Predictions:

• What you would observe in your data if your hypothesis is true

• States WHAT happens

• Can be consistent with multiple hypotheses

• If prediction fails, the hypothesis is challenged

How to write a good hypothesis

Ask yourself:

• Does it state a mechanism?

• Does it explain the observation or just redescribe it?

How to write good predictions

• State what you will measure and in what direction

• Generate at least two predictions from the same hypothesis

  • If both succeed, confidence increases

  • If one is wrong, you learn specifically which part of the hypothesis don’t hold up

• Identify a prediction that discriminates between competing hypotheses

  • Kin selection predicts that related individuals call more

  • Reciprocal altruism predicts social partners call more

• State what the data will look like under the null hypothesis

How much of today’s studies can be replicated?

50%

Effect size

A metric that quantifies the size of the difference in the means of two groups or the strength of correlation between two variables. Larger effects are characterised by bigger differences in means or stronger correlations between variables.

• Standardised effect sizes (e.g. Cohen’s d) express these latter differences in units of standard deviations, and hence allow estimates from different studies to be compared directly.

α

The criterion for statistical significance, which is p < 0.05

β

The false-negative error rate

• 1 - β is the power

Power

Affected by the effect size to be detected

• Larger sample —> higher power

• Calculated through 1 - β

Researcher degree of freedom

The flexibility of choosing which data and statistical tests to use and how to interpret the results.

• May be different between researcher due to different approaches.

Problems with doing close replications

• Difficult to perform: Despite using the same sample size etc, the conditions can never be truly identical, e.g. time of day, experience etc.

• May give unjustified confidence about the generality of findings that in fact rely on one aspect of the methodology.

  • Small differences (e.g. in a male bird’s song) may actually give large differences in results, which close replications would miss.

Decline effect

When effect sizes systematically decrease in follow-up studies

• Over replications, estimates values closer to the smaller (true) value.

• The differences between groups are smaller / correlations between variables are lower than those originally reported.

p-hacking

When a non-significant result becomes significant (p < 0.05)

• Often driven by the pressure to publish “sexy papers” (positive findings) rather than data/research question

  • In order to get funding

Ways to p-hack

• Ending the data collection as soon p<0.05

  • Before pre-determined sample size

• Conducting multiple experiments but only reporting the one that worked

• Only reporting variables that are significant

  • Despite measuring multiple variables

• Removing outliers / transform data to get a significance

  • = tweaking the data

• Performing many tests without correcting for family-wise error rate

How to detect p-hacking

• A sudden peak in p-values just around 0.05

Type I errors

• due to chance

  • p significant despite H₀ being true

Type II errors

• due to lack of power, e.g. small sample size

  • p insignificant despite H₁ being true (H₀ false)

HARKing

Hypothesising after results are known

• making a coincidental finding look like a prior prediction

Why is HARKing problematic?

• Inflates false positive rates

  • p = 0.05 means that there is a 5% probability that your data appeared due to random chance

  • If you run 20 independent tests at α= 0.05 and report the best one as a “prediction”, your actual false positive rate is closer to 1 - 0.95²⁰ ≈ 64%, not 5%

• Results cannot be replicated

  • Because the results are post-hoc justified, they are unlikely to replicate in a study with new data

  • Entire research fields can be based on non-replicable results

  • Researchers will spend time and money trying to replicate findings that cannot be replicated

• Invisible in publications

  • Readers cannot detect HARKing from the published paper alone

  • Peer review cannot catch HARKing without access to study logs

Publication bias

Positive findings (p < 0.05) are far more likely to be submitted, reviewed, and published than null/negative results, regardless of scientific value.

File-drawer effect

Null results remain unpublished in researcher’s file drawers. They are not written up or published.

Funnel plot

Scatterplot used in meta-analyses to visually detect publication bias.

• Plots individual study effect sizes against a measure of precision (like standard error)

• If not biased:

  • Plot resembles an inverted, symmetrical funnel.

  • Larger studies at the top, smaller studies spread out equally on its sides

    • Suggests that both positive and negative results were published equally

• If biased:

  • Plot is asymmetrical

  • Small studies with negative, non-significant, or unfavourable results were unpublished (file-drawer effect)

  • Small studies with positive, statistically significant results made it to publication

Types of replication

• Close replication

  • Repeats original study with the same species, sample size, setting, and protocol

  • Rare

• Conceptual replications

  • Tests the same hypothesis with a different design

  • also called triangulation or constructive replication

Reasons why replications may give different results from the original study

• An unconsidered variable may have caused a difference in the results

  • These are called moderators.

• Individual differences in how animals react and behave.

• True-negative or false-positive result (type i and type ii errors)

  • Larger sample size gives lower false-negative error rate

  • p-value of 0.05 makes type ii error rate less than one in 20

• Random variation

Moderators

Variables that have not been considered, but is actually an important factor that gives different results in replication studies.

Standardisation fallacy

The phenomenon that over-standardisation of laboratory protocols could reduce the replicability of results.

• E.g. mice behaviour might change depending on the time of the day

  • Research team MORNING and research time NIGHT will have different results

  • If the two teams expanded their study to last the entire day, the mean of their results would be the same, yet more variable.

How to avoid inaccurate reporting in our papers

• Pre-register hypothesis, design, sample size, and analysis plan on repositories before collecting data

  • Eliminates HARKing

  • Reduces p-hacking

• Calculate minimum N needed to reliably detect an effect of the expected magnitude before starting

  • Prevents underpowered studies

• Provide raw data, analysis scripts, and methods in the paper

• Actively conduct and publish close replication studies from different labs.

• Report null results, failed conditions, and unexpected findings, not just p<0.05 outcomes.

  • Reduces file-drawer effect

Positive predictive value (PPV)

The probability that a positive research finding is a true-positive result.

• Higher power = higher PPV

Why do we like animals?

• Biophilia hypothesis

  • An innate love for nature

• Kindchensschema

  • Konrad Lorenz had a hypothesis that we are more willing to take care of creatures with large eyes, small noses, round faces etc (cuteness, in other words)

Differences between HAI, HAR, HAB?

• HAI= Human animal interaction

  • Simply interactions one may have with the deer crossing the road

  • Can be positive or negative

• HAR= Human-animal relationship

  • After a couple of interactions once you start to learn their behaviours etc.

  • May also be general and not specifically to an individual, e.g. HAR between moose and hunters (learn to avoid them), or dogs learning that vets are evil

  • Can be positive or negative

• HAB= Human-animal bond

  • Once both parts start feeling very good together

  • Can only be positive

What is needed for a relationship?

• Proximity (shared geography)

• Cognitive ability to remember/recognize individuals

• Understanding social cues (initiating, receiving, responding)

Why eye contact with dogs?

• They show us eye contact. Oxytocin is released inside us.

• We give them more love. Oxytocin is released within them.

• They show us more eye contact. The cycle continues.

Are visitors enrichment or stressors for zoo animals?

Depends on the species

• Elephants, grizzly bears, polar bears, cheetahs, servals, black-tailed prairie dogs, and cockatoos respond positively to public feedings.

  • Show more activity and less repetitive behaviours afterwards

• Flightless birds, odd/even-toed ungulates, marsupials, tuatara, and hedgehogs react negatively.

Different kinds of eyes

• Pupils

  • Can be round and expanded

    • e.g. humans, birds

    • 180 degree visual field with mostly overlap/depth perception

  • Narrow —> round

    • e.g. cats, dogs

    • Better at adjusting their size

    • Broader visual field with more narrow overlap

  • Horizontal

    • e.g. horses, goats, sheep

    • Very broad visual field (almost 360 degrees)

      • Horses still have 65-80 degree frontal overlap, just like canids.

    • Additional “white fingers” that stick out/forwards of the eye to block sunlight (the shade from this can be visible)

  • “Dots”

    • Very small dots turning into covering the entire iris (basically)

    • e.g. gecko, tarsier

Mammal eye

• Cornea

• Lens

• Iris

• Ciliary muscle

• Zonule

How does the mammalian eye work?

Ciliary muscle is a “circle” around the iris, “attached” through the zonule.

• When the ciliary muscle contracts, the zonule become relaxed and the lens becomes rounded to focus on close objects

• When the ciliary muscle relaxes, the zonule taut and flattens the lens to focus on more distant objects

Fish eye

• Spherical Gradient Lens

  • (Lens doesn’t change in shape ?)

• (Retractor/Protractor Lens in some species)

Reptile eye

• Bony ossicle

• Brucke’s muscle

Bird eye

• Bony ossicle

• Brucke’s muscle

• Crampton’s muscle

How do reptile/avian eyes work?

Active changing of the lens, actively pressing to change the shape

In birds, you have the additional Crampton’s muscle to change the size of the cornea

• Diving birds also use it as a surface for water (?)

Amphibian eye

• Protractor lentis

How does light reach the retina?

Light must go through all layers of cells before reaching the photoreceptors

• Light might “change”/reflect throughout this journey

Cones vs rods

Cones see colours and are more “angular” in shape ( > )

Rods are bigger and more light sensitive, have more pigment, and are rod shaped ( ニI )

Explain eyesight (?)

Light must go through all layers of cells before reaching the photoreceptors

• Light might “change”/reflect throughout this journey

When light is absorbed, there is a hyperpolarization

• (not depolarisation as in other processes)

• In the relaxed state, you have a lot of neurotransmitters. When light is absorbed, you get less neurotransmitters.

• “It is only the outer segment that is light sensitive, A larger outer segment can absorb more light

Ganglion cells

Ganglion cells are the last step before the signals are sent to the brain.

• When densely packed, there are less photoreceptors

• = think of them as pixels. When they are smaller (and more) we can see finer details

• Packed areas of ganglion cells is called the fovea

Fovea

Where the ganglion cells are the most packed

• in humans, this area only consists of cones (not rods)

• Horses, wolves, hares etc have rods as well in their fovea

• Most birds have 2 fovea in each eye (other species only have 1)

Correlation between domestication and vision in dogs ?

• Dogs with more “wolf-shaped” nose have a broader area of ganglion cells

• In pugs (and other dogs with flatter noses), they have a very small but very “good”/Intense? spot — just like humans    

  • This spot is called “area centralis”

• Similar pattern in horses

Spatial resolution

• Measure of how closely lines can be resolved in an image

  • (e.g. black-white stripes. One black-white is one cycle. Measured as “cycles per degree (at a certain distance)”)

    • dvs how many degrees could one’s eye detect?

• Is sacrificed in dim light

  • Spatial resolution becomes worse in darker environments

Temporal resolution

• “shutter time”

• Photoreceptors can only code information up to a certain temporal frequency

• Cones are generally better than rods to discriminate fast movements.

• Imagine a fan:

  • With short shutter time, you can see each individual blade

  • With long shutter time, you see it all as a blur

• Sacrificed in dim light

Explain how color vision works

• Colour requires two or more cone types

• The reflected light from a surface enters the cones and the brain considers which type of cone absorbed the most amount of light, compare them, and then the brain makes us perceive a certain colour based on the cones that absorbed the light.

• An absorbed photon has no “identity”, it’s just what cone absorbed it

  • Colour is just a hallucination

Ancestral cone photopigments

Most animals have the four ancestral cone photopigments

As mammals, we lost two of these four due to the nocturnal history from the dinosaur ages and whatnot

• Primates have created a new third one 30 million years ago (unrelated to the four ancestral ones) to experience red colour

Neutral point

Dichromatic visioned mammals have a so-called “neutral point” where they cannot discriminate grey shades from a green-blue shade at 480nm.

Ways to improve night vision in dim light

• Enlarge pupils

• Enlarge eyes

• Short focal length

  • Shorter distance = less “disturbance” —> clearer image

• Summation in space and time

  • Can extend visual range down to intensities 100 000 dimmer than provided by optics itself