Thursday, 13 December 2012

The optimization and impacts of animal breeding

Animal breeders work with two tools: selection and pairing. When animals are selected for breeding, the frequencies of alleles in that population always change. Some alleles may even be lost, or become fixed, when the allele is the only one in that population. Both of these chances lead to losing genetic material. This loss of material may go unnoticed for a long time, because following alleles in practical breeding is not feasible. To start with, there must be enough genetic variation in the population to allow for any genetic progress.

Selection intensity affects strongly to the progress of breeding. Selection intensity means the percentage of animals chosen for breeding from a particular population. The formula is i = SPP, where Sp is the selection difference. i expresses the selection difference measured in units of standard deviation from the population fenotypical mean. Let's say we select sheep based on their weight at 1 year of age. The population mean is 55 kg, and the mean of the chosen animals is 67 kg. Standard deviation is 10 kg. Then i = (67-55)/10 = 1.2. From a selection intensity table (such as this), we see that i of 1.2 means we'll select a bit less than 30 % of the animals in the population. Usually i < 1 is weak selection, and i > 2 is strong selection.The less animals we choose, the more genetic progress we get.

However, the amount of offspring per animal and inbreeding may limit our choices. To keep the population size stable, there are minimum amounts of animals which should be chosen. For cattle, the limits are 50-65 % of females and 0,5-1 % of males. For poultry, 1-2 % of females and 0,5-2 % of males is enough.

Optimizing genetic progression in breeding programmes

The values in The Formula (seen on the left) have connections to one another and to animal properties. Females have less offspring than males, some properties can be measured only from females, and they are sexually mature in different age (difference in L).  The differences can be counted for by calculating the progression as the sum of the genetic value of females and males, divided by the sum of time between generations.

Since different information sources have different weighting factors for females and males, the genetic values are calculated differently. For cattle, cows are evaluated based on their own results. Bulls are evaluated based on the results of their offspring.

Dependencies of the values in the formula are various:
  • increasing i by producing more offspring per animal increases L
  • using the results of offspring to increase rTI increases L
  • using pedigree information of lower L lowers rTI
  • increasing i by relying on individual evaluations only lowers rTI
So, to optimize ΔG, every factor must be optimized at the same time!

Pairing strategies and inbreeding

Pairing comes always after careful selection. Three pairing strategies exist: random pairing, assertative pairing and pairing based on kinship.

Random pairing means simply pairing the selected animals randomly. In this strategy, alleles inherit randomly, and the population follow H-W equilibrium (if also random selection is used).

Assertative pairing means that fenotypes of the animals are considered when pairing them. It may be positive or negative. In positive assertative pairing, the animals with the most extreme results in a trait are paired, creating offsprings with extreme results. For example, pairing large bulls with large cows or small bulls with small cows creates either very large or very small calves. Positive pairing temporarily increases genetic variation. Negative assertative pairing, or pairing different animals, is about compensating or fixing trait results. When large bulls are paired with small cows, medium-sized calves are born. However, the calvings will be extremely difficult, so it is important to choose the pairings correctly (small bulls+big cows works much better).

Pairing based on kinship is either avoiding or using inbreeding. Inbreeding means pairing animals which are closer relatives than "cousins". Inbreeding increases the amount of homozygotes, which leads to inbreeding depression. First production traits are affected: milk yield starts to decrease, amount of meat produces decreases and so on. If the inbreeding continues, resessive traits (usually illnesses) became more common, and fertility and survival traits start to decrease as well. The opposite of inbreeding depression is heterosis, which happens when two completely different lines are mated. Heterosis is strongest in the F1 generation, and it increases the amount of heterozygotes. Heterosis may lead to offspring which are better than the average of their parents, thus exceeding breeding expectations.

Note that some level of inbreeding cannot be avoided. Look far enough in any pedigree (even your own), and at some time there will be same names. This is especially true in small or new animal breeds, but works on humans as well. The blog of Discovery magazine states that 1 out of 200 men are direct descendants of the furious fighter (and lover) Genghis Khan!

Long-term impacts of animal breeding

Some of the basic questions of animal breeding is "how far can we go?". Have the cattle populations today reached their production maximum? Is there anything left to improve, and do we have enough genetic variation left? Ethically, one can ask are we doing the right thing? Are we really improving the animals, or just improving their productivity at the expense of their health?

Two extremes. Belgian Blue cows cannot live or give birth normally
due to their extreme size and double muscles. "Teacup puppies" are
very small, and have delicate health with extra risk of bone fractures.
 Genes and traits have correlations. Improving one trait may improve or worsen another trait. While we can estimate ΔG, genetic frequencies change, and mutations happen. Additive genetic variance decreases due to selection (Bulmer-effect). And, we still have only a basic understanding of geneology, with much to learn about interactions between genes and genetic regulation. Estimating the long-term effects on animal breeding is thus just guesswork.

We can try to estimate it using quantitative theories or using selection on populations with short L (mice, microbes, plants). Through genetics we can model changes in allele frequencies, thus estimating changes in heritability and genetic regression. Biology can help us to understand what we are doing to the animal: can it survive with the traits we've created for it, are they useful or harmful? Many examples from dog breeds may come to mind at this point. Due to positive assertative pairing, some breeds are genetically sick. Instead of banning the breed, though, the situation can be corrected by negative assertative breeding and pairing across
breeds. And again, developing traits has its price. Increasing animal's production increases it's need for feed and susceptibility to problems in metabolism. Reducing extreme traits reduces health risks, and pairing across breeds increases variation but decreases the level of racial purity.

Wednesday, 12 December 2012

Determining feed digestibility

When discussing animal feeds, the terms solubility and digestibility may easily be mixed or misunderstood. Solubility means the degree to which the food breaks down to smaller particles, for example how much of protein breaks into amino acids. The digestibility of a feed determines the amount that is actually absorbed by an animal and therefore the availability of nutrients for growth, reproduction etc. For example, wood, grass silage and straws have the same amount of gross energy, but due to the differences in their digestibility, only  grass silage is useful as a feed. See more terms explained from FAO's site on animal nutrition.

Digestibility of a feed must be originally determined in animal tests. When the base values from solubility and digestibility are thus gained, more tests can be done in laboratories. Lab tests are never equivalent to tests done on living animals, but on the basis of animal welfare, speed, repeatability and cost-effectiveness, they are widely used. This text will cover some basic methods of determining feed digestibility in vivo or in sacco, "in a living animal".

Before any in vivo feed studies, each animal goes through an adaptation phase. For cattle the phase may last 1-2 months, but only 3-5 days for pigs and 1-2 for poultry. During the adaptation, the animal gets used to the new feed, and estimates can be made about its palatability. If the animal will be in a collection pen or crate during the test, it will be there during the adaptation phase too, getting used to the new environment. The actual testing phase lasts from a day to a week or two, depending on the size of the animal.

Total collection

Total collection is a quantitative research method, where the animal is kept in a collection pen or cage. Collection cages used to be very tight, preventing the animal from moving more than a few inches backwards or forwards, but they have now been banned due to obvious animal welfare issues. The crates are designed so that all feces can be collected, and some percentage of it will be analysed. If the balance of nitrogen is studied, then urine will also be gathered and analysed. The animals are fed approximately 90 % of their normal feeding levels, so that there's no leftover feed. All necessary vitamin and mineral supplements are given during the test as usual.

(c) University of Helsinki
Total collection tests can also be done for animals in pasture or in group pens. To get individual results from each animal, the animals are fitted with harnesses or other means of carrying collection bags, which are emptied at least once a day. The harnesses cannot be too heavy or uncomfortable, because stress and pain would immediately affect the animal's behavior and metabolism. A typical collection method for pigs is to glue a plastic bag to its rear end, but it raises concerns of animal welfare.

Total collection method can be used to study the effect of one feed (direct method), of basic feed + test feed (differential method), or of feeds in different amounts, for example 10, 20 and 30% of wheat (regression method). Knowing the chemical composition and dry matter (DM) content of the tested feeds is crucial.

When choosing animals for a total collection test, make sure that
  • the animals are of the same age and size
  • the feed given is processed identically every day
  • the amount of feed eaten is recorded for each individual animal
  • feces (and urine) are collected at the same intervals, often enough and without contaminating the samples
  • consider the impact of proteins and fat to the digestibility of the feed
  • use identical and accurate analyzing methods
Calculating the results
All values are g/kg DM if not stated otherwise. The formulas do not apply for regression method.

Digestibility of the feed:  
(amount of feed eaten - amount of  feces ) / amount of feed eaten
1 - (amount of  feces / amount of feed eaten) * 100

Digestibility of different nutrients (multiply with 100 to get the results in percentages):
(Nutrient content in the eaten amount of the feed - Nutrient content in the feces)
 / Nutrient content in the eaten amount of the feed
Digestibility of the feed and nutrients when using the differential method:
(amount of test feed eaten - (amount of  feces - undigested basic, non-test feed))
 / amount of test feed eaten

Marker method

Marker method can be used when total collection is not possible or feasible. Marking method includes adding a marker substance to the feed, and then analysing the amount of marker feed in the feces. This method may be conducted with the animal in a collection cage, but is also usable for grazing animal.

The marker substances used in marker method trials must be safe for the animal, travel at the same speed than the feed in the digestive tract, they can not impact the digestibility, mix well with the feed and be stabile. The marker must be detectable and measurable even in very small amounts. Markers can be either liquid or solid, and either added to the feed or insoluble parts of the feed (such as insoluble ash). Common markers used are
  • titanium oxide TiO2
  • chromium oxide Cr2O3
  • ytterbium acetate
  • litium
  • strontium
  • cobalt EDTA
  • chromium-mordanted straw (straw covered with chrome, fixed in place with a mordant)
Calculating the results
All values are g/kg DM if not stated otherwise.

Measuring the digestibility in a certain spot in the digestive tract

Fistulated horse (c) Todd Huffman
In some cases, it is important to measure how nutrients are digested in different parts of the digestive tract. This is especially true with ruminants and amino acids. Amino acids which are absorbed in the rumen are used by the rumen microbes, and the animal itself gets only the amino acids which absorb from the small intestine. Even the monogastric pigs can use only the amino acids which absorb from the small intestine, and some trials are done on horses as well.

These trials (animal tests) always need animals with a fistula and/or a cannula. The fistula is usually installed to the rumen or to the beginning/and or end of the small intestine. Sometimes the rumen fistula may be connected to the abomasum with a long tube, enabling collecting samples from the abomasum.

The idea of an animal having a hole in it, and people digging the innards of the animal through the hole is (and should be) very distressing. People who work with fistulated animals may not be the most reliable source, but they claim the fistula causes no discomfort for the animal. Permits for conducting and animal test are needed before the operation. Fistulas are always  made by experienced vets.  Sedation and local anesthetics are always used, and left to heal for two months under direct supervision and care. After healing, the fistula is painless even when used. If the animal is used to being treated (brushed, milked, petted etc), it shows no signs of pain, discomfort or fear when the fistula is opened and a sample is taken. At least fistulated cattle live their lives normally, milking, eating, calving and socializing without problems. However, health and welfare risks exist and must be minimized or removed before proceeding.

In sacco -method (ruminants only)

Fistulated cows (c) David Wilson

In an in sacco -method small nylon bags are filled with the test feed, and inserted into the rumen.  Like in the previous method, in sacco also requires fistulated cows. Being small and light, the nylon bags do not cause discomfort, or affect the rumen functions. It is an reliable way to measure the solubility of certain feeds. Insoluble fibres can be most reliably measured in sacco. The nylon bags are so tight, that no feed particles can escape from the bag or enter it. Only the rumen microbes are able to affect the feed in the bag.

After the bag is taken away from the rumen, it is washed with clean water, and then dried. Single bags are removed after a certain time, and the weight and contents are then analyzed to study the solubility of the feed. Most often bags are removed after 2,4,6,8,10,12 and 48 hours, but for insolubility tests, last samples may be taken as late as after 72 and 96 hours, or even 12 days. Determining the solubility of the tested feed is a matter of comparing the composition and weight of the feed samples before and after the in sacco test.

Apparent vs true digestibility

The digestive tract secretes several substances, which get mixed with the feed and eventually the feces. Most commonly tthey are proteins or other nitrogenous compounds. These animal-based substances, known as metabolical or endogenous secretions, must be considered when analysing digestibility. Apparent digestibility does not consider endogenous secretions, unlike true digestibility. True digestibility for proteins, amino acids and fats is always higher than apparent.

Endogenous excretions include bacteria, enzymes, endogenous peptides, amines, urea, mucus and dead cells of the digestive tract. Measuring the levels of endogenous secretion is difficult, so common factors are used to estimate them. Cattle is estimated to secrete 5 g of endogenous matter per a kilogram of eaten dry matter, while pigs and rats secrete 1 g. 

More information:

FAO: Animal nutrition
University of Florida, dept of Animal Sciences:  Digestibility
E R Ørskov: Methods of estimating nutritive value of fibrous residues

Tuesday, 11 December 2012

The value, quality and preservation of silage

Silage means forage, which is made of grass or other organic material, and has been preserved with methods based on acidity. Preservation, ensiling or silaging is the process where the spoilage of the forage is prevented by lowering it's pH either with acid or by adding anaerobic, acid-producing fermentative bacteria.

Silage, like any animal feed, has two values: a feed value and a dietary value. Feed value means the energy content and the nutrients of the feed for the animal. Feed value includes the chemical  composition, digestability and the rate of metabolisation. Dietary value is a wider concept, which includes the factors directly or indirectly affecting the metabolisation rate of the silage. These factors are the hygienic quality and the feed value of the silage, plus the animal's need for nutrients and the amount of feed it eats.

Microbial quality of silage concerns the amount of volatile fatty acids (VFA) and the pH of the feed. pH clearly over 4.2 is a sign of failed preservation, and increases the risk of the feed spoiling. pH can rise if unwanted bacteria proliferate in the silage, fermenting proteins into ammonia. VFAs and a high amount of ammonium nitrogen from the total amount of nitrogen also indicate the existence of unwanted microbes. Sometimes microbes (spores of Clostridium, yeasts, molds) can be determined from the feed directly. It is not, however, a routine analysis.

No animal eats just one type of food, but the values of the feeds no dot add up. Different feeds in a diet affect one another. For example, fats decrease the digestability of roughage, but proteins may increase it. These combined effects must be considered when planning for the indoor feeding season. The aim of feed planning is to maximise the "output response", the amount of the feed the animal can use for it's maintenance and production. Maximising the output response must be made cost-efficiently, and without endangering animal welfare and health.

There are several reasons why knowing the quality and value of the forage is important, be it silage, hay or any other feed:
  • planning a cost-effective and well balanced diet requires knowledge on the feeds
  • giving the right amount of added vitamins etc requires information on the content of the silage
  • weather conditions and preservation methods can change the quality of the silage during storage
  • dairies must be assured that the feed does not endanger the quality of the milk or any milk products made 
  • improving the silage making process is based on knowing the weaknesses and strength of the current process and products


Aspergillus-mold on a maize silage.
(c) North Dakota State University

Preservation of silage

Silage is preserved mainly by three different ways: with acid, with acid-producing bacteria or without any additives. Preservation with acid is usually the most effective method, since it lowers the pH faster than the other methods.When the pH decreases, the plants stop breathing and unwanted bacteria dies. Anaerobic preservation is vital for keeping mold and yeast away from the feed, and for promoting the growth of useful lactic acid bacteria. Low amount of moisture also helps to prevent enterobacteria and Clostridium. Silage contaminated with unwanted microbes can endanger the health of the animals and/or the people handling the feed, and affect the quality of products derived from the animal.

There are roughly five classes of preservatives used in silaging, and they vary by function. Some types prevent others: using strong acid to quickly decrease the pH leads to minimal production of lactic acid.
  1. Promotes fermentation
    - Lactic acid bacteria, enzymes, sugar (molasses)
  2. Prevents fermentation
    - Formic, lactic and mineral acids
    - Nitrite and sulfite salts
    - NaCl
  3. Prevents spoiling in aerobic conditions
    - Propionic acid
    - Benzoe and sorbic acid
    - Lactic acid bacteria
  4. Nutrients
    - Urea, ammonia, minerals
  5. Sorbents (used to absorb the effluent)
    - Straw and beet pulp
 Preservation method may change for silage of different types due to the different buffer capacities of feeds. Grass+legume-silage can resist the decreasing of the pH much better than barley, so different amounts of preservatives are needed. Fermentation factor describes the easiness of preservation for a type of silage. The formula is
dry matter content (%) + 8 * (sugar content/buffer capacity)
A fermentation factor over 45 predicts only a small probability for wrong types of fermentation, i.e. a well-preservable silage.


There are many forms of fermentation, based on which microbes are involved. For silage, fermentation is the process where anaerobic microbes convert sugars (glucose, fructose and saccharose) into lactic acid. The silage must also have enough sugar to maintain fermentation. If the preservation fails, unwanted microbes proliferate, causing faulty fermentation. These microbes produce VFAs, ethanol and especially ammonia, which increases the pH, spoiling the silage even further. Factors affecting the quality of fermentation and thus the whole process of ensiling are
  • chemical composition of the feed
  • microbiological content
  • time of harvest
  • weather conditions during harvest
  • technique of harvest
  • type and amount of preservatives used
  • dry matter content of the feed (wet feed needs more preservatives than pre-dried feed)
Fermentation does not only produce something, it also uses nutrients of the feed. The products of fermentation are always less useful for the animal than the original nutrients used. The level of fermentation should thus be kept optimal for ensuring the preservation of the silage, but also losing as little nutrients as possible. The fermentation in the silage ends naturally when there's enough lactic acid to keep the silage acidic. If the silage doesn't have enough sugar or it's pH is too high, the lactic acid fermentation stops and unwanted fermentation begins. The amount of sugar left in the silage can be used when estimating the level and types of fermentation.

The fermentation process.
(c) Engormix

Types of fermentation
The basic rule is that the drier the forage is, the less there's fermentation. The difference between the types of fermentation are also less apparent in dry forage.
Limited fermentation may result from using acid or other fermentation preventing preservative. pH is low, sugar content is high and there's only little fermentation end products in the silage. Proteins are scarcely dissolved, so there's little ammonia and soluble nitrogen.
Strong lactic acid fermentation occurs in well-pressed silage or when using preservatives promoting fermentation. pH is low due to high amount of lactic acid, there's only little sugar left and proteins are more dissolved than in limited fermentation. Because the fermentation is caused by lactic acid bacteria, there's not much VFAs (propionate acid, butyric acid and acetic acid).
Faulty fermentation is caused by unwanted microbes. The silage has high pH and lots of VFAs. Proteins are strongly dissolved and mostly transformed into ammonia.

Thursday, 6 December 2012

Mathematics of animal breeding

As I mentioned in the post on Basics on animal breeding, this area of animal science is full of equations and mathematical models. This text will shortly list and explain some of these equations, but it will not cover them thoroughly. For a deeper understanding of breeding math, try to get your hands on Richard Bourdon's book Understanding Animal Breeding.

Hardy-Weinberg law

Hardy-Weinberg law (H-W law for short) was formulated by two scientists at the same time, hence the name. It predicts the frequencies of genotypes in a generation based on the allele frequency. The formula is simply

p2 : 2pq : q2 

where p is the frequency of the dominant allele, and q is the frequency of the resessive allele (in other words, it's fAA: fAa : faa). H-W equilibrium is a status where both the allele frequency and the genotype frequency stay unchanged from generation to another. This can be achieved only in an "ideal population", where there's no random genetic drift, no mutation, no selection, no migration, and all males can reproduce with any female in the population (free reproduction).

Example: In a population of 1000 cows, 175 are white, 600 are spotted and the rest are black. Let's pretend that the genotype for whiteness is bb, Bb for spotted and BB for black. The genotypes hold the following alleles
white: 175 * 2 =  350 b alleles
spotted: 600  b alleles and 600 B alleles
black: 225 * 2 = 450 B alleles
Total:  950 b alleles and 1050 B alleles. Relative frequencies are 0,475 for b and 0,525 for B. Relative genotype frequencies are bb = 0,175, Bb = 0,6 and BB = 0,225.

But does this imaginary population follow the H-W equilibrium? To check that, we count what the genotype frequencies should be according to the law. Now p = 0,525 and q = 0,475. So we should have p2 : 2pq : q2 = 0,525 : 2*0,525*0,475 : 0,4752 = 0,276 : 0,5 : 0,224. Since these are NOT the same as the observed genotype frequencies (0,175 : 0,6 : 0,225), the population is NOT in H-W equilibrium.

Heritability (h2)

Heritability shows how much of the difference between animals is caused by genes. It has two forms: a narrow definition (h2) and a wide definition (H2). Of these two, animal breeding uses h2, because it does not include dominance and epistasis, which are not  inherited. The definition of heritability is

h2 = σ2A / σ2P

where σ2A denotes the variance in additive genetic impact and σ2P the variance in phenotype. So heritability in it's narrow sense shows how much of the difference between animals is caused by differences in their breeding value. It can also be though of as the animal's possibility for genetic progress. The third interpretation for heritability h2 is that it is the regression factor for the estimated breeding value (EBV) in relation to the phenotype. So the heritability value is needed when calculating the EBV.

Repeatability (r)

When calculating the EBV, we should always have several measurement results of one trait from one animal. For example, the milk yields for several lactation periods, of the amount of piglets in all of the litters of one sow. This repeatability is the correlation factor between these results, showing a linear continuation in the results for thet trait. Using repeatability one results can be combined into one when calculating the EBV. The formula for repeatability is

r = (σ2G + σ2Ep)/ σ2P

where the sum of genetic variance and permanent environmental variance is divided by the variance in phenotype.

Kinship factor fx,y

Like it's name suggests, the kinship factor has to do with relationships between two living animals. It predicts the probability that a random allele of one animal is identical by descendent (IBD) with an allele of another animal. That is to say whether that allele is inherited or not. It's important to separate IBD alleles from identical in state (IIS) alleles, where two animals have chemically identical alleles, but they're not inherited. IBD alleles are always inherited from one parent, IIS alleles are just identical but not inherited. IBS is always IIS, but not vice versa!

Kinship factor between a parent and its offspring is always 1/4. Kinship factor is 1/4 also between full sibs. The calculation formula is explained below, the example calculates the kinship between a parent and its offspring.

Additive genetic relationship ax,y

Additive genetic relationship is simply

ax,y = 2fx,y        or formally        ax,y = Cov(Ax, Ay) / σ2A

and it shows the conformity between the breeding values (BV) of two animals (x and y). It depends on the probability of common alleles (IBD), and considers only one allele. The probability that one allele of an offspring is inherited from its parent is always 50 %. The probability that full sibs have inherited the same allele (their kinship factor) is 1/4, so their additive genetic relationship is 2 * 1/4 = 1/2 or 50 %.

If the animals considered are inbred, the formula doesn't apply.

Inbreeding coefficient Fx

Inbreeding means mating animals, which are related to one another. For example, mating full siblings or a parent and its offspring. Inbreeding coefficient indicates the probability (in percentage) that both of an animal's alleles are from the same parent (both alleles are IBD). The inbreeding coefficient of an offspring equals the kinship factor of its parents. Since ax,y = 2fx,y, fx,y must be 0,5*ax,y. Thus, the inbreeding coefficient of an offspring is also 0,5 * the additive genetic relationship between its parents.

Since inbreeding increases the risk of resessive traits and illnesses and narrows the gene pool, it is not recommended to breed animals which would have inbreeding coefficient over 10 %. 

Estimated breeding value

So let's get to the point already! Right, let's do that, and see how to calculate that magical EBV and a breeding value index.

EBV is an estimated breeding value, and it concerns only one trait. It is calculated differently based on what information we have available: one result from the animal, several results from the animal, or results from the animal and it's relatives. The same goes for the b-factor and for the accuracy (rTI). The best EBV is calculated using regression:

i- A) = b (Pi - P) 

where (Âi- A) is the index value, b is the regression factor, Pi is a mean of the animal's results and P is the population mean of those results. If we have only one result from the animal itself, b will be h2 squared. 
A common form of the formula, when using results of only one animal, is  just I = b (Pi - P), where I denotes the breeding value index. In this case, b is calculated as
b = (n * h2) / (1 + (n-1) *r)
where  n is the number of results and r is the repeatability factor. Accuracy is still counted as h2 squared.

Estimating the breeding value based on the animal's offspring looks like this:

I = 2 * b (Pi - P) where b = (p * h2) / (p-1) * h2 + 4

here p is the amount of offspring. The formula is based on the assumption that we have one result from each offspring, and all offsprings are half-sibs. In this case the accuracy depends on the h2 and amount of offspring.

Tuesday, 4 December 2012

Basics of animal breeding

Animal breeding is not just about pedigree dogs, champion cats or winning horses. Breeding aims at improving the genetic level of a certain trait in a population. First, laws, politics and regulations set the framework for animal husbandry. Second, a breeding programme is needed to establish common goals for what the breeders aim at. The programme can be about improving the genetics of the population, or about preserving the genes. What traits should be improved, and how to stress each trait in relation to the others? Third, a system is needed to store the measurable metrics of the traits which the breeders are interested in.

Breeding is based on two techniques: selection and pairing. They're not synonymous. Selection is about choosing which animals to use for breeding. Can one mate animals of different breeds? Which are the best breeds and animals in this situation and in this production environment? For example, one cow might excel in a tie-stall, but be run over in a free-stall barn. Certain cow breeds tolerate cold environments better than others, etc. Pairing happens only after the selection, when the selected animals are used for breeding.  To make these decisions, breeders need information about the animal itself, it's parents, sibs and possibly it's offspring. The gathered data is then used to answer one question: will the offspring be genetically better than their parents?

Breeding is full of equations. The foremost is simply P = G + E. But because genetics are never that simple, the equation is actually
P = µ + GA + GD + GI + Ek + Es

where P = Phenotype, everything about the animal which can be seen or measured
µ = the mean value of the trait in the population (for example, milk yield)
G = genes, where A denotes additive genetic traits, D dominance and I epistasis
E = environment, which may affect either positively, negatively or not at all to a given trait (for example, illnesses and quality of feed). Ek stands for random errors, and Es for systematic errors.

As the equation suggests, what we see in an animal is created and modified by it's genes, the mean of the population and the environment. Genetically identical animals (clones) can be very different if they are raised in different environments. Then again a genetically superior animal can produce well even if the environment is less than desirable.

Comparing animals

If we're about to select animals and then pair them, we should be able to compare animals. The selection is based on measurable information, which can be gathered and combined. For a single trait each animal can be assigned a  calculated breeding value, which changes each time more information is gathered from the animal. The more information is available, the higher the accuracy of the breeding value. The formulae for calculating the breeding value (BV) and the accuracy may vary in each country.

Since the environment cannot be calculated into the value, it must be evaluated separately for systematic or random errors. That's why the formula above has two E's (Ek and Es). Systematic errors affect the BV results systematically, i.e. always the same way. Age, gender and permanent environmental conditions are systematic errors. Young animals are smaller than adults, males cannot produce milk, females produce less offspring than males etc. Systematic errors can be predicted and must be corrected when calculating the BV to make the results for all animals comparable. Random errors are errors which cannot be corrected. They just happen, like misspelling the results or a measurement error. Factors affecting the BV are listed below.

Strengthen BV or accuracyWeaken BV or accuracy
  • Accuracy of data
  • Corrected systematic errors
  • Data from several offspring
  • Data from parents
  • Data from sibs and half sibs
  • Genomic information
  • Wide range of reference data from other animals in the population
  • Only a few results
  • Random errors
  • No data from offspring or relatives 
  • No genomic information available
  • Low heritability of a trait
  • No or only little data about the animal population

Thursday, 15 November 2012

Animal welfare in organic production

Directives and settings for organic production in Europe are set by the EU. In addition, each country has their own national laws and decrees, which detail the EU laws. Organic production is a farm management practice, which combines
  • production of high-quality food
  • respect for animals and their behavioral needs
  • eco-friendliness
  • sustainability.
Animals are essential in organic production. Growing animal feed diversifies the crop rotation, animals recycle nutrients, promote natural diversity, produce foodstuffs, create income and  tend to the landscape.

Welfare of animals in organic production

A miniature horse treated for leg deformity
(c) University of Pennsylvania
IFOAM has stated that "All management must aim for good animal health and welfare and must be governed by the physiological and basic ethological needs of the animal in question". (Basic standards for organic production and processing, 2002). Preventive health care is the key: producers select the best suitable breeds, feed them with high-quality feed, enabling them with access to outdoors and avoiding too high an animal density. There are strict regulations to the use of medicide for animals, which guarantees that animals are medicated only when needed, not "just in case". However, sick animals are and must be treated accordingly. Veterinarians may prescipt preventive medication, such as deworming. Vaccinations, Phytotherapeutical and homepathic treatments are allowed. Still, any animal must be removed from organic production if they are medicated more than three times a year (if the animal lives longer than 12 months) or more than once (for animals which live less than 12 months).

Some common breeding practices are banned in organic production. Artifial insemination (AI) is allowed, even though it is recommended that all breeding is based on natural methods. Embryo transfer is not allowed, but semen from embryo-transferred bulls may be used in AI. If an animal is bought to an organic production farm, that animal may be embryo transferred.

Allowed and banned animal handling procedures
A capable person may mark a goat, sheep, pig or a cow with ear marks, ear notching, tattooing or with an ID chip. Lambs can be castrated. Piglet canines may be rasped only if they cause problems to the sow, and the problems cannot be solved in another manner. Veterinarians are allowed to castrate goats, horses and cows, but the usage of pain killers is mandatory. Same applies for burning or removal of horns from lambs, goats and calves, and installing a nose ring to a cow or bull.

Producers are not allowed to keep animals chained, although some exceptions apply. Chaining a birthing animal is not allowed under any circumstances. Sows must be kept in groups until the end of pregnancy and during lactation: sow crates are not allowed. Birthing crates are also banned.

Usage of hormones  or other medication to increase growth, fertility or production is strictly forbidden.

(c) Sneeuberg
The feeding of cattle, sheep, horses and goats must be based on grazing. 60 % of their daily feed must be roughage, but for the first three months of a cow's lactation period this percentage can be lowered to 50 %. Rearing of anemic animals (for example for production of white veal) is banned.

Feed should be produced on the same farm they are used. 50 % of the feed for herbivore animals must  be endemic. All feed must be organically produced, but in an emergency normal feeds can be used with a special permit.

Feeding of young animals must be mainly milk from their mother or a female of the same species, until the animals are at the age of
  • 3 months (cattle and horses)
  • 8 weeks (goats)
  • 45 days (lambs)
  • 40 days (pigs).
Milk powder or other liquid feed can be used only during the 2-year transition phase to organic production, and even then only within limits.

Requirements for animal shelters

Animal shelters for cattle, goats, pigs and sheep must have good, non-slippery flooring, and a maximum of 50 % of the floor may be grated. Resting area must be on solid floor and have litter. All shelters must have windows, which cover an area equivalent to 1/20 of the floor area.

Poultry must have at least 8 hours of darkness in their lighting program, and at least 1/3 of the flooring must be solid (not grated). Broiler chickens must be reared a minimum of 81 days and turkeys for 100 days (females) or 140 days (males). In normal production broilers are slaughtered at the age of ~50 days. Each section of the henhouse may have a maximum of 4800 broilers or 3000 egg-laying hens.
(c) mother Earth news
When national laws don't state otherwise, animals must be able to go out at any time. Harsh weather conditions or low-quality ground are an exception. Maximum of 75 % of the outdoor pen may be roofed.  During the grazing seasons, goats, sheep and cattle must be allowed to pasture daily. The outdoor pen for pigs must have litter to nose and root. Poultry must be able to spend at least 1/3 of their life outdoors in an outdoor pen with at least 50 % covered in undergrowth.

How well do organic animals fare?

Feeding of animals in organic production has many limitations, but it does not appear to affect to milk yield of cows. Cattle in organic farm does not seem to have less udder or hoof problems compared to traditional production.

Broiler chickens suffer slightly less in organic production, but using slow-growing broiler breeds in organic production has clearly improved animal welfare. In some studies hens show slightly more pecking and cannibalism in organic production, perhaps due to increased light and flock size (egg-laying hens in traditional production are often in cages with 2-7 other birds). In other studies the beaviour of hens was similar in organic and traditional farms.

For pigs the results of actual welfare in organic vs traditional production are mixed. Organic pigs seem to have more joint injuries and liver parasites, but less lung sac inflammations and lung infections. They have less tail damange than traditionally reared pigs, likely due to more stimuli and lower animal density.  All in all, organic farms seem to suffer from the same welfare problems than traditional farms.

Wednesday, 14 November 2012

Behaviour and welfare of pigs

Pigs differ from other ungulates in many aspects: they give birth to many offspring at once, they are omnivorous, they build a nest, sleep for 12-14 hours straight and they prefer to rest close to other members of the pack. Pigs were originally domesticated from wild boars 9000 years ago in Turkey. Like chickens, pigs have changed in phenotype, but they still share instincts with their wild ancestors. Pigs are omnivorous: they eat vegetables, mushrooms, nuts, fruit, insects, worms, small animals and even carcasses.

Senses and social behaviour

Pigs rely strongly on their sense of smell and hearing. Sows recognize their piglets by smell, and boars smell the sows to check their heat. Voice and hearing are very important in the social behaviour of pigs. Pigs "chat" nearly constantly in quiet grunts to stay in contact with their pack. Warning signals and cries for help are high-pitched and loud. Boars sing a "love song" to attract sows, and the sow's voice signals tell the piglets when milk is available.

(c) Daily Mail. Check their article about pig slaughtering.
Pigs can't see very well. Thus their gestures are not subtle and small, but require a lot of space. For example, a dog recognizes a slight turn of the head as a calming signal. If a pig needs to calm a stronger animal, it turns away completely and then runs away for a short distance. In piggeries this is often impossible, so fights and injuries are common. Naturally pigs live in peaceful groups with stable social structure. In piggeries groups are often mixed, so the structure changes a lot and the animals have to create the "pecking order" over and over again.

Unlike many other animals, pigs are contact animals. A sow does not lick its piglets, nor do pigs lick one another. Instead, they eat in groups and sleep side by side, close together. Even mating behaviour is rather straightforward: instead of courting, the boar can just mount the sow. Sows have a standing reflex, which means that in heat it will stand still when pressure is applied to it's loins. In addition to sleeping, eating is also synchronized. Pigs wake up at sunrise, and spend most of their time nosing the ground for food. They eat for 8 hours, and sleep 12-14 hours a day.

Cleanliness: Contrary to popular belief, pigs are very tidy animals. They always separate a sleeping area from eating area and "bathroom" area. In piggeries this is not possible, and pigs are forced to sleep in their feces and eat in a dirty environment.

Skin care: Pigs have two ways for skin care: wallowing in mud and scratching themselves against walls. Wallowing in mud is not just fun, it also cools the animal on a hot day, rubs away dead skin and removes parasites.

Thermoregulation: Piglets under 3 weeks of age cannot thermoregulate, and in piggeries they depend on heat lamps. In the wild piglets live in a nest built by the sow, so they stay warm. Adult pigs have almost no fur and no sweat glands, so they can thermoregulate only by changing their behaviour.

Parturition and weaning

One or two days before giving birth, sows start to look for a place for a nest. They may wander several kilometers searching for a good spot. 6-12 hours before parturition the sow begins the actual nest building. It digs a shallow hole, and then collects branches, hay, turf and other materials, which it uses to build a nest. 1-2 hours before parturition the sow lays down on her nest. When the piglets are born, the sow lays passively. Domesticated pigs give birth to 10-15 piglets, which are born about 15 minutes from one another. After birth piglets instinctively crawl to the udder and start suckling. If a piglet doesn't get colostrum within few hours of birth, it will die. Colostrum is vital, for the piglets have no antibodies. If the sow is vaccinated before parturition, the piglets will get immunity as well.

For the first three days the piglets fight for teats, but they then develop a clear "teat order": each piglet has its own teat. This is important, because after 12 hours the sow gives milk only once every 45 minutes. It announces milk letting by grunting, and every piglet has about 10 minutes to find a teat and suckle.

(c) Keith Weller / Shutterstock
The sow stays in her nest for the first 1-2 days, after which she leaves the nest for a short time as she goes eating. On 4th - 5th day the piglets leave their nest to follow the sow, and learn to find solid food. After 10-14 days the sow and her litter leave the nest and return to the herd. If the piglets do not follow the sow at this time, she may abandon the whole litter. The sow starts weaning her litter from the first week by slowly introducing the piglets to solid food and by regulating her milk letting. Final weaning will happen when the piglets are 10-25 weeks old, depending on the availability of food.

In piggeries sows are not allowed to build nests, and they are often confined to tiny parturition crates for weeks. The crates don't allow the sow to turn around, sometimes not even to stand up. Crates are used so the sow wouldn't lie down on the piglets. Naturally the sow has an anti-crushing behaviour, but in piggeries the sow often cannot hear if a piglet screams when sat on. Studies show that parturition is faster, more piglets are born alive and the sow lets more milk when giving birth freely, compared to birthing crate. Building a having a sest also calms the sow, calms the parturition and improves the relationship beween the sow and the piglets.

Welfare of pigs

The welfare of pigs consists of several basic building blocks:
  • health
  • air quality and temperature
  • Pen structure (size of pen, flooring material)
  • availability of litter and  other stimuli
  • social environment (stable groups)
  • feeding (appropriate feed, enough space for all pigs to eat at the same time, enough roughage)
  • Attitude and skills of the caretaker
Pigs would eat for 8 hours every day. In a piggery this isn't possible, so the animals need plenty of modifiable litter and other objects which they can nose, chew, eat or otherwise modify. Straw, tree branches or hemp / sisal ropes are very good for this purpose. Problems with any of the factors of pig welfare may lead to the most serious behavioral prolem in any piggery: tail biting. Tail biting has been discussed in the entry about pig diseases.

In piggeries, pigs are moved from one department or piggery to one another several times. Each department should take into consideration the needs pigs have at that particular age.

Parturition dept: Since piglets are very sensitive, clean, dry and warm environment is vital for them. During the first few days piglets are castrated, ear-marked, given a tattoo and an iron injection, and their canines are filed. All these cause pain and risk for infections. Parturition dept must have clean space available for these operations. Flooring material is important, so the feces and urine can be cleaned, but the floor isn't too hard or cold for the piglets.

Intensive piggery, a "hog lot"(c) Wikipedia
Weaning dept: High-quality and clean water and feed are important to young pigs, who still have no stomach acids to kill any bacteria they ingest. Stable groups and temperature are needed, and stimuli help the pigs to relieve stress and pass the time.

Meat pig farm: For adult pigs, stable groups and enough space are important. They must be able to sleep together and eat together, have separate areas for eating, sleeping and defecating/urinating, and they need space for social behaviour. Stimuli are also important. Temperature can vary more than in previous departments.

Department for pregnant sows: Like the meat pig farm, but pregnant sows need even more space than meat pigs.

Tuesday, 13 November 2012

Behaviour and welfare of poultry

A red junglefowl male. (c) James Warwick
Modern chicken was domesticated from the red junglefowl, gallus gallus, approximatey 8000 years ago. The junglefowl lived in a flock in the protection of a thick undergrowth. Even though breeding has increased the growth and egg-laying capacity of modern chickens, they still share many behaviours and needs with their ancestor.

Flock and social behaviour

Naturaly, chickens form flocks of 20 chickens and 1-3 roosters. Flock size can vary from 5 to 30 chickens. The rooster tends to his chickens, ensuring their safety and mating with them every night during the egg-laying season. Young birds live on the edges of the flock. Even though chickens rest tightly side by side, during daytime they keep some distance between each others.

Chicken flocks have a rather strict social order, where the oldest and largest birds with the largest comb (the red thing on the top of a chicken's head is called a comb) dominate. Young chicks begin finding their place in the pecking order at the age of 6-8 weeks, and the order is all settled in 1-2 weeks. Chickens can recognize only up to 80 other members of the flock. When the flock size is larger, like in most henhouses, the pecking order is never stable. Fights are common in such circumstances. Roosters have a calming effect on flocks of chickens. Some producers keep roosters in their henhouse just to keep the peace.

Senses and daily schedule

Chickens have an excellent eyesight, and they can see 330º around them. In the dark chickens can barely see, so they climb up to roost or trees to spend the night, safe from predators. However, chickens can see UV-light, and in fact recognize one another by sight. Roosting during the night is a strong need for chickens, and the roost must be about 1,5 metres from the ground. The most dominating birds fly to the top, while other birds settle close together to the lower branches. In a henhouse, where the light program is controlled, "night" has to come slowly after a period of "twilight". This serves as a warning to the chickens, and they can make their way to the roost while they still can see. The roosts actually also help young chickens to develop 3D visualisation, if they are allowed to roost when very young. Chickens allowed roosting later in life never learn to use them, and have poor 3D visualisation.

After a night's rest the chickens wake up at sunrise, and lay eggs. After laying an egg the chickens eat, and would spend 90 % of the day searching for food. In midday the birds rest and bathe in sand, and afternoon is dedicated for tending to their feathers and mating. Right before night time chickens eat as much as possible, storing energy for the night. Chickens' diet consists of seeds, green feed, insects, worms, larvae and even mice. Chickens prefer to search for their food by pecking at litter or ground, instead of eating for a full bowl. 

Dust bathing. (c) The Daily Dish
Bathing is an important need for chickens. Chickens bathe in dust every other day, throwing sand on their back and flapping their wings. Sand helps to keep parasites away from the bird's skin, and keeps the feathers healthy. Chickens bathe also in sunlight, opening their wings and sometimes laying down on their backs. The reason or benefits of sunbathing are still unknown. Like other birds, chickens also arrange their feathers and stroke them with their beaks, spreading the fat from their skin to the feathers. This nsures the feathers' insulating capacity.


Egg-laying hens in henhouses are bought from breeding farms, where fast-growing but infertile hybrids are created for production use. These animals simply lay eggs until they are culled and the meat is either destroyed or used as animal feed. Naturally, a chicken would lay eggs once a year, during springtime. The chicken leaves the herd to build a nest. She walks to her nest each morning, lays one fertilized egg, and returns to mate with the rooster in the afternoon. Egg-laying stops when she sees about 10 eggs in her nest. She will then incubate the eggs, occasionally turning them around, for 21 days.
(c) Quaker Anne

The chicks recognize their mother from her sound right after hatching. Their yolk sac has enough nutrition for two days, after which they need to start picking food on their own. The mother teaches the chicks where to find food. Chicks develop fast: they run at the age of 2 days and fly short distances at the age of 10 days. For the first three weeks the chicks cannot thermoregulate well, and must sleep under their mother's wings. At 1,5 months of age they already sleep on roosts. Until three months of age the chicks stay with their mother. After that the chicken drives male chicks off to another flock or to the borders of the current flock.

Production environment creates behavioural problems

Chickens in modern henhouses live either in small cages or in flocks of tens of thousands of birds. They rarely have any litter to peck, and their food is served from a bowl. Roosts are rare, and often too low. Bathing behaviour is often impossible due to lack of space and bathing material. If chickens are not allowed to roost or to search for their food, they will get frustrated and stressed. This leads to disruptive behaviour, which can be very serious. Frustrated chickens often peck one another, tearing away feathers and causing wounds. Chickens are omnivorous, so seeing blood excites them to peck on the target even more, possibly killing the victim even if it is a chicken of the same flock. Cannibalism among production chickens is not rare, but it is abnormal.

In production henhouses, the eggs are collected daily. The visual stimuli of "enough eggs in the nest" never occurs, and the chickens continue to lay eggs indefinitely. Their metabolism is thus under heavy stress: it is meant to create 15 eggs a year instead of 300. To meet the production requirements, the chickens are fed heavily, so they may grow too fast. Fast growth combined with small cramped spaces (cages) causes leg injuries and weak muscle strength.

When chickens are reared on floor  instead of cages they have better chance of exercise, bathing and searching for food. Flock sizes are often huge, so fights, cannibalism, feather pecking and injuries are more common than in cages. Free movement may also increase the risk of sickness. Individua chickens are more difficut to check when they're on the floor

How to reduce disruptive behaviour?
  • Using red light prevents the chickens from seeing blood, thus decreasing their instinct to peck an already injured bird.
  • Dimming the lights
  • Observing the birds more closely, and removing those who peck others
  • Most importantly: allowing the animals access to roosts, bathing material and to search for food

Broiler production

Packed chickens. (c) Antaryamin's blog
 Broilers are hybrid birds reared on floor in flocks of tens of thousands. They are bred to grow incredibly fast and to become large, so each animal would produce the maximum amount of meat. A broiler lives only five weeks. It is sold from the commercial breeded as an egg or small chick to the broiler farm. Because their fast growth and cramped space, leg injuries, heart and circulatory problems are very common. Many broilers die suddenly of heart failure, and are simply removed from the poultry house. When the birds are five weeks old, they are gathered to crates using a "hoover", a chicken catcher. Gathering and transporting the animals often leads to immensely painful broken legs and wings in addition to stress and fear.

Chickens breeding broiler-breed chicks are also bred to grow as fast as the broilers. However, such a fast growth would kill the animal before it's able to reproduce, so the broiler dams are fed only 30 % of what they would need. At the age of 39 days, a freely fed broiler chicked weighs 2,2 kilos, but a broiler dam on limited feeding weighs only 615 grams. The dams are constantly hungry and frustrated, so they fight often during feeding time, and drink water excessively to ease their hunger. Elevated stress levels have been measured. Stereotypical behaviour and pecking are common due to high stress.

45 days: The life and death of a Broiler Chicken is a short 12-minute video of how broilers are reared. Warning: may disturb sensitive viewers:

Sunday, 11 November 2012

Behaviour and welfare of cattle

Estimating the welfare of an animal starts with knowing what is normal for this species and individual. Based on this knowledge we can notice changes in the behaviour, and study the possible welfare problems causing the change. So what behaviour is normal for cattle?

Naturally cattle would form nuclear herds of one bull and its cows, which are all related to the bull. The bull guards its herd and mates with cows in heat. All bovines are prey, not predators, so they constantly watch around and are easy to scare. Domesticated animals scare less easily, but they still have the instinct to "run first and think later". Ruminating is well suited for living amongst predators in open spaces: the animal eats very fast, just gathering food to it's rumen, before it hides away in a calm place where it can ruminate for several hours.


All bovines have a wide visual area, and just by slightly turning their heads they can see directly behind them. However, their sight is not very good. They distinguish movement far away very well, but have difficulty seeing what's close in front. Strong contrasts are also difficult for the cow to understand, so they tend to avoid them. Some farmers keep their animals in a pasture surrounded only with a white line on the ground! Since the white is so strong against the green grass, the cattle stays away from it (of course, in fright they would run over it and learn that it's only a drawn line). Indoors cows may avoid grates on the floor and shadowy corners, because they cannot see what it is. To see what's low infront of it, cattle must stop and "zoom" with their eyes, adjusting their lenses to see near.

Cattle have a good sense of smell, and an excellent sense of hearing. They recognize their offspring, each others and their caretakers mostly from their smell. The bulls can also easily smell the approaching heat of the cows. Studies show that bulls can detect cow heats much better than humans, which is why some farmers keep a bull on their farm just to detect even the silent heats. The range of sounds heard by cattle is much wider than what humans can hear. Especially high sounds (which humans can't even hear!), often generated by AC or milking robots, can frighten cattle.


Cows leave their herd right before calving. In farms the animals should be taken to calving pens, where they can be alone. When the calf has been born, the mother eats the fetal membranes to remove all signs of the newborn. It then licks the calf. By licking, the mother immediately learns to recognize her young, and also refreshens the calf and assists its breathing. Cow's tongue coarse, so it also dries the calf's skin from the fetal liquids.

A heathy calf is on its feet an hour after birth, and poking it's mother to find the udder. Young cows may not allow the calf to suckle at first, so it's vital to make sure the calf gets colostrum within few hours of its birth! Otherwise the calf does not get the antibodies it needs. Sometimes just small amount of colostrum milked from the mother and fed to the calf can get an apathetic, weak calf to get up and find the udder.

A video of a cow licking its newborn, and the quest to find the udder.

In the wild, the cow would hide the calf for the first days. Only after four days it would lead the calf to the herd. The reason for the wait is that the calf does not become bonded with its mother immediately. To make sure the calf will recognize its mom, the mom has to stay separate from the herd. In farms, calves are usually separated from their moms within a day from birth. The result is often a distressed cow and a sligtly confused calf, but within a few days both have adapted and act normally again.
See Stookey's article for more information about maternal behaviour of cows.

Behaviour of calves
Calves grow in groups, since naturally cows give birth roughly at the same time of the year. In groups the calves learn to know each others, they develop relationships and learn to behave like cattle by playing. Calves play most in the age of 2-3 months. Playing develops their muscles and keeps them healthy physically and mentally.  If the calf is not separated from its mom, it will suckle for 10-15 minutes 4-6 times a day, totalling up to 10-12 litres of milk.  Suckiling is not just a way to get food. When the calf pokes the cow's udder, the cow's body releases oxytocin. Oxytocin releases milk and acts as a mood enhancer. The calf's body releases oxytocin and gastric hormones once it suckles, relaxing the calf and enhancing its digestion.

In farms, calves are handled very unnaturally. They are weaned too soon, and often fed only twice a day. They may get sick, not grow well, have digestive problems and suck the ears, tails or penises of other calves. Calves have a very strong need to suckle. This need must be filled by providing them with dummy teats and/or feeding them from teat buckets 4-6 times a day for 10-15 minutes.

The cow will wean its calf slowly after 8-12 months. Bull calves will be driven away to their own group, but cows can stay in the nuclear group.

Eating, exercise and resting

Adult cows have a need to chew their food and to ruminate. If they are fed with too much grain or not enough roughage, they will become frustrated. Frustrated cows and bulls may roll or loll their tongues. Since cattle eats at the same time, they must all be able to do so even in a barn. There has to be enough space to eat, no need to stretch and reach to get the feed, and enough feed for everyone so that even the most timid animals get to eat.

Cattle may not look like a very sporting species, but when grazing, they walk up to 3 kilometers daily. The need to exercise builds up in a few days, causing disruptive behaviour and frustration. They must be able to move freely. Free movement also enables them to care for their fur and to socialize with other animals. Cattle must lick and scratch their skin to keep it clean and healthy. Licking other animals also stabilizes the group. Cows and bulls are large animals, and need space just to rise and lay down. Many barns have too short stalls, so the animals have problems with the most basic movements.

Cattle rests for 10-13 hours a day, of which only 4 hours is sleep. Even then they sleep only about 15 minutes at a time. Resting and laying down comfortably is vital for udder health and hoof health, and it improves blood flow to the udder, feet and womb. Laying down is also a way to thermoregulate. Cows usually lay down when they ruminate, so if they cannot lay down comfortably, they ruminate less and thus produce less.

Handling of cattle

Based on the knowledge of what's natural for cattle, it is easy to understand that calm behavior the key for good animal husbandry. Shouting, kicking and beating the animals is not ony illegal, but also very counterproductive. Scared animals are difficult to handle and produce less than relaxed animals. Cattle are prey animals: they need time to adapt to new environment, must be able to stay with the herd and are cautious of anything new. Always announce your presence when approaching cattle, and avoid approaching them directly from the front or back. Wearing the same work clothes will help them to learn to recognize you. Talking quietly, petting and calm scratching of the animal are appreciated - you may even get a cow licking you back, caring for you as if you were a member of the herd!

Wednesday, 7 November 2012

Estimating and measuring animal welfare

Research in animal welfare is based on the assumption that animals have needs and intresses, which must be respected. Animal and its needs have intrinsic value. Research is focused on how the animal feels and adapts to its environment - what we think is best for the animal isn't what counts, but what the animal itself wants.

Why should we research animal welfare? Today, humans subject animals to heavy stress in unnatural environments. Contrary to what marketing wants us to think, agriculture is industrial and harsh. Animals are kept in herds/packs of tens of thousands, they are bred to grow fast and produce much. The relationship between consumers and farm animals has changed - it's common to over- or underestimate the mental abilities of animals, either treating them as machines or as humans. Laws govern much of agriculture, but the laws must be based on knowledge about animal welfare. Ethical reasons for animal welfare research are obvious, but a well-kept animal also produces more, gives higher quality products and  needs less costly vet services.

Measuring animal welfare

Measuring animal welfare is based on deep knowledge on what is normal for a healthy animal in it's natural surroundings. Any changes to its natural activities may indicate a problem with welfare. Thus the behaviour of an animal presents many "measurements":
  • Time budget: how much time does the animal spend eating, foraging, sleeping etc per day? Welfare may be decreased if the animal no longer sleeps well or doesn't rest as much as it used to.
  • Postures: Pain and confined spaces may cause animals to change their normal postures or movements. Long-term physiological problems may arise if normal movement is not possible.
  • Abnormal behaviour: disruptive or stereotypical behaviour indicates clearly that the animal is not well. It may be stressed, bored or has some other difficulty adapting to its environment.
  • Fighting: Naturally animal packs are rather calm, fights are normal only on mating time. In farms animals cannot form natural packs, which may lead to extensive fighting between animals.
  • Preferences of the animal
Before the measurements listed above can be considered, one needs to know what is normal. For example, pigs with litter and stimuli in their pen spend 1 % in harmful social behaviour, while pigs without litter fought each others nearly 10 % of their time. Pigs with litter also nose the ground almost 30 % if their time, 25 % more than pigs without litter.

Overall, there are two types of methods to estimate animal welfare: resource-based (input) methods and animal-based methods.

Resource-based methods
Even when given plenty of space,
calves prefer to stay close to one another.

Resource-based methods measure the environment of the animal, estimating the risk to bad welfare. Size of a pen, quality of feed, number of sick animals and air quality are examples of resource-based measures. Each target is easy to score, and the measurements are repeatable and clearly measurable. A well-known resource-based method is ANI, or the Animal Needs Index by H. Bartussek. ANI is divided into five categories, which all have several measurable objects. The categories are
  1. Locomotion (freedom of movement)
  2. Social Interaction
  3. Flooring
  4. Light and air
  5. Stockmanship
The farm receives points in each of these categories depending on the results. The sum of the scores in all categories is the ANI-index, ranging between -9 and 45.5 in the ANI for cattle. The higher the score, the better the welfare. Details of ANI for cattle can be found from Bartussek's homepage.

Animal-based methods
Animal-based methods focus on the animal, not it's environment. Measurements in animal-based methods are difficult and non-repeatable, since the results are affected by every factor in the animal's environment (temperature, time, hunger, people in the farm, noises...). They provide information of the animal on the time of the study. One animal-based method is the Welfare Quality®, created in an EU-funded poject in 2004-2009. WQ evaluation takes up to 4-7 hours, during which the farm is estimated in 12 criteria in four principles: Good feeding, good housing, good health and appropriate behaviour.


Tuesday, 6 November 2012

What is animal welfare?

There are several explanations and definitions about what welfare is.Hurnik's theory states that welfare is a feature of the animal itself. Animal welfare is based on needs:  the ability to fulfill these needs sets the level of welfare. The animal must be able to fulfill its needs which support life (hunger, thirst, reproduction), health and comfort.  Broom's theory is based on adaptation: animal welfare is low, if the animal has conscious or unconscious problems coping with its environment. Sickness, fertility problems and pain are some indications of adaptation problems.  Moberg's theory concerns stress, which is caused by the animal's inability to maintain bodily balance with the environment. The animal may be chained so that it cannot clean itself or move away if it feels hot or cold. According to Moberg, welfare suffers if the stress is strong and continuous, or if the animal's attempts at adaptation are ineffective. In a feeling-based theory by Duncan and Petherick welfare depends only on mental needs. If the animal feels it has fulfilled its needs, its welfare is good. Sickness or injury do not thus decrease welfare, if they don't bother the animal itself. Health-based theories place physical health as the indicator for welfare. Welfare is decreased only when there are pathological changes, and the biological functions of the animal are transformed in some way.

Finally, a common and wide-spread "theory" is based on freedom. In 1993, the Farm Animal Welfare Council (FAWC) published Five Freedoms:
  1. Freedom from Hunger and Thirst - by ready access to fresh water and a diet to maintain full health and vigour.
  2. Freedom from Discomfort - by providing an appropriate environment including shelter and a comfortable resting area.
  3. Freedom from Pain, Injury or Disease - by prevention or rapid diagnosis and treatment.
  4. Freedom to Express Normal Behaviour - by providing sufficient space, proper facilities and company of the animal's own kind.
  5. Freedom from Fear and Distress - by ensuring conditions and treatment which avoid mental suffering.
These five freedoms clearly indicate that welfare is both physical and mental, and it is based on how the animal feels. Several factors affect welfare and one another. Food, water, environment, caretaker, health, behaviour and animal breeding are all equally important. Welfare cannot be turned on or off, and it cannot be simply measured. Consider this: animals cannot speak any more than new born human babies. How would you go about ensuring a baby's welfare?

Animal rights vs animal welfare comparison from, originally from Animal Rights Fund newsletter:


Farm animal welfare council FAWC
Companion animal welfare council CAWC

Monday, 5 November 2012

Animal welfare: what is ethology?

(c) Gary Larson
Ethology is the systematic science of studying animal behaviour. Applied ethology focuses on the behaviour of those animals, with which humans interact with, or which are useful to humans. Only by understanding animal behaviour we can
  • treat the animal correctly
  • understand and increase animal welfare
  • collaborate with the animal
  • learn more, thus increasing our motivation to treat the animal well
  • understand and interpret the animal
Studying one animal or one animal species is not enough, however. Each species have their own needs and behaviour. Through domestication we have changed how many animals look, but most of their behaviour is still the same it was thousands of years ago.


Domestication means "becoming genetically tame" - through selection, humans have caused permanent genetic changes when taming the animals. For example, dogs were domesticated around 15 000 years ago. Humans tamed dogs, worked together with them, and started to breed dogs for different purposes. Humans selected which dogs were bred, and took their dogs with them to new areas. With selective breeding humans were able to create different dog types, and eventually breeds.

Domesticated animals have several traits which drastically decrease their ability to survive in the wild. They become less alert and less fearful, and their escape range is smaller. Animals used for production (such as goats, cows, chickens, pigs) produce and grow much more than is natural for them. Many domesticated animals also have "unnatural" appearances or body structure, such as bright white color, long and luxurious fur or hindered movements. Domesticated animals are also less defensive of their offspring and more playful even as adults.Their life span has also increased due to living in "ideal conditions", where food, healthcare and shelter are always available. 

While domestication changes animals permanently, only domesticated species can survive and even thrive in the modern world together with us humans.

Motivation and needs

They both have the same needs, but only one can fulfill them.
(c) birthofanewearth-blog and
With every action, an animal tries to fulfill a need. Whether it will or will not do so depends on its motivation. Motivation is affected by external and internal factors: weather, food, social environment, hunger, thirst, hormonal balance and pain. For example, wild sows build nests before parturition (giving birth to piglets). It has a biological need to care for its offspring. Hormonal changes motivate the animal to build a nest, so it acts to fill this need. The building behaviour and seeing the finished nest decrease the sow's motivation for nest building. It has fulfilled a need.  Domesticated sows in piggeries have this same, very strong need for nest building, but no possibility to fill it. This creates an incredible amount of stress for the animal, even though it could be easily prevented by providing sows with nesting material (hay, straw, dry peat) a few days before parturition.

Unfilled needs lead to behaviour problems. Behaviour, which deviates for what is natural for the animal, is a behaviour problem. It may even be harmful for the animal or to the herd. Behaviour problems are not the same as disruptive behaviour, although in the common language these two are often mixed. A dog which barks when left alone shows disruptive behavior, but a dog chewing its own paws to relieve stress shows a behaviour problem. Behaviour problems are the animal's way to adapt to it's environment and to the stress it causes. Given no litter, pigs tend to relieve their stress by chewing on bars and the tails of other animals. To battle boredom, cows may loll or roll their tongues. If this behaviour is prevented, the animal tries desperately to find new ways to relieve the increased stress.

Factors affecting behaviour

Animal behaviour is formed by
  1. inborn characteristics (a newborn instinctively crawls to the udder)
  2. inherited inclinations (bird songs)
  3. learned behaviour (using a water bowl or feeder)
Reflexes are inborn characteristics, which need no conscious processing. It is an "automatic" response to a certain stimulus. Frightened animals often escape or defend themselves first, and then think afterwards. It would be essential for their survival in the wild.

Instincts are inborn characteristics which need no learning. Unlike reflexes, instincts involve conscious processing. They are often linked to basic needs: animals know instinctively what to eat or how to attract a mate.

Imprinting creates bonds between animals, animals and humans and animals and their environment. Imprinting is most effective after birth, when the mother and its offspring are imprinted to one another, creating a life-long bond. Without imprinting, moms do not recognize their offspring, and may even try to kill them.


Applied ethology:
E-learning: Ethology e-courses by Cambridge University
A short video on pig domestication: Youtube
Lorenz motivation model, often used in ethology