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Using the Clan Mating System
Low-Input Breeding for Maximum Genetic Diversity
in Small Flocks


This page was originally posted to the site April 2016. I revised it August 2016 to reflect changes in my thinking about the breeding of “too-closely-related” individuals and implications for managing clan matings on the male side in the future. ~HU

Smart gardeners know that, if they save their own seed, as the seasons roll the strains of crops they grow will be more and more attuned to their specific conditions of soil, climate, and management. The same holds true for breeding our own chickens, though far too few home flocksters are breeding their own and reaping the benefits of healthier, more robust and productive birds with each passing generation. I hope this brief description of a simple mating system will convince you that breeding your own feathered stock could improve your flock—and could be a lot of fun as well.

Note that term “mating system”: We will not achieve improved strains of stock through haphazard, free-for-all matings. Many people probably assume that after all reproduction in nature is based on haphazard mating, but that is a misconception—actually many social and sexual behaviors in the wild promote matings that are not haphazard at all, but follow patterns that serve at least two critical functions. First, the gene pool of any population must remain as diverse as possible if it is to respond to challenges in its environment, whether from increased predation or disease, food scarcity or changing climate. Such changes obviously require immediate adaptations if the population is to thrive in the new circumstances. The more diverse the array of genetic combinations in the population, the greater the chance that the needed adaptations are already latent—and that their possessors will enjoy greater reproductive success and lead the way into the future. For improvement breeding, likewise, the greater the genetic diversity we maintain in the flock, the greater the chance that the traits we’re targeting—faster growth, greater disease resistance, better egg production in winter, broodiness, more docile temperament, whatever— will express in the offspring and be available for selection.

Second, a population must avoid inbreeding depression resulting from excess breeding of individuals too closely related to each other. Simplifying for brevity: Closely related individuals are more likely than unrelated ones to share the same recessive gene for a negative trait. If both the male and the female share the same recessive gene, then that trait will be expressed in the offspring. Thus indiscriminate breeding of too-closely-related individuals generation after generation has a strong tendency toward inbreeding depression—the expression of more and more negative recessive traits, leading to an increase in deformities and a decline in health, vigor, productivity, and reproductive success.

How to choose who mates whom is a complicated question, and certainly closely-related matings can be used with care to achieve particular goals (as in well managed linebreeding). The main thrust of the mating pattern, however, must be toward the prevention of inbreeding depression. In my project, I interpret “too-closely-related” as prohibiting “first degree” matings—that is, those between parent and son or daughter, and those between siblings and half-siblings.

Since breeding populations in home and farm flocks are necessarily small, it is critically important to manage matings so that, paradoxically, they more closely mimic patterns of natural mating that avoid the breeding of too-closely-related individuals while maximizing overall genetic diversity in the flock. Fortunately there are a number of breeding systems available to achieve these goals, though questions of practicality, management style, and our tolerance for record keeping will strongly influence our choice. Some flocksters adopt pedigree mating systems, and track individual breeders through their entire lives, keeping detailed records of who mates whom in every generation. There are advantages to that approach: Enhancement of particular traits can be targeted more specifically and more quickly. Even careful mating of siblings or parent-offspring is acceptable, so long as there is reasonable certainty that cock and hen do not share the same recessive gene for a flaw. On the other hand, a breeder might do away with record keeping entirely by bringing in unrelated cocks from trusted outside sources every breeding season.

I prefer to maintain a closed flock as much as possible, minimizing importation of breeding stock from elsewhere. At the same time, I do not have the patience for tracking every one of the three dozen or so breeders in my flock and every mating among them in every season. I am looking for a mating system that combines rigor with practicality, that avoids breeding individuals that are too closely related while maximizing genetic diversity within my breeding pool and reducing record keeping to an acceptable minimum. The following is a brief sketch of clan mating as I am implementing it for breeding my flock of Icelandic chickens.


Let’s assume that you start with the best stock you can find, a minimum of three pairs—three hens and three cocks. (Of course in extreme cases you might not have access to that many birds—I’ve heard of restoration projects that started with a single trio of breeders. In such a case you would make an initial breeding that will produce at least three pairs with which to begin your clan system.)

Start by separating initial breeding stock into three “clans“ (or ”lines” or ”families”). You can give your clans fanciful names if you like, or simply call them A, B, and C. If you’re going to use colored bandettes or wing bands for identification, naming clans by ID color is a good idea. Let’s assume your clans will be Red, Green, and Blue (in that order).

You might have good reasons for assigning your initial stock to their clans. You might know from the source of your stock that some of your breeders are closely related, and assign them so as to put as much “distance” between them in the first mating as possible. Those with more experience selecting breeders might match one with a particular strength to offset a weakness in the same trait in its partner. But do note that it’s okay if your initial clan assignment is entirely arbitrary. In the future, determining who mates whom will be rigorously determined, but if you have no idea how to assign your initial breeders by clan, just do so randomly.


The first breeding season is simple: Isolate your breeders so that matings are strictly controlled to occur within the same clan—Red cock to Red hen, Green cock to Green hen, Blue cock to Blue hen.


When the chicks hatch, assign them to the clan of their mother, most easily by toe-punching the chicks. In this first hatch, the assignment by clan color seems pretty obvious, since both sire (father) and dam (mother) are of the same clan. But that won’t be true in future breedings, so it is worth emphasizing: Assign all chicks, cockerels and pullets, to the clan of their mother.


Starting with the next breeding season, avoid breeding cock to hen within the same clan. Instead, again practicing strict isolation of breeding groups, ensure that cocks mate hens “in the next clan over”: Red cocks mate Green hens, Green cocks mate Blue hens, Blue cocks mate Red hens. (If you visualize the pattern in three dimensions you might see a spiral, and indeed clan mating is sometimes called “spiral mating.”)


Now we see the importance of assigning chicks to the clan of their mother. In this case the progeny of Red dams have Blue sires, hatches from Green hens have Red sires, etc. But all chicks take the clan of their mother, and remain in it for life.


In all future breeding seasons continue the same pattern, with cocks invariably mating hens of “the next clan over.” As long as you follow this scheme, there will never be a mating between siblings or half-siblings in your flock, and genetic diversity will remain as great as it can possibly be, at least without tracking individual pedigrees in much greater detail. (Note that, if cocks are retained for more than one breeding season, it is possible an older cock could breed his daughter from the previous year. Such father-daughter matings are impossible if cocks are used for one breeding season only.)


The above is merely a brief sketch of the basic concept of clan mating. How you might implement the system in practice could vary considerably. For example, I like to have more than one male in each clan, as insurance against loss to a predator or other disaster that would make it impossible to breed in one clan. In the past I kept in each clan one mature cock and one cockerel, so that each male gave service for two breeding seasons before being culled. Since realizing that breeding a cock a second season makes father-daughter matings possible, however, I plan after future breeding seasons to replace both breeding males in each clan with cockerels from the current year’s hatch. Following that practice, father-daughter matings will be impossible, however many years I continue breeding individual hens.

Three is the minimum number of clans for this mating system, but you could have more if you can manage them. Even with three clans, I will be able to maintain a closed flock for a long time (twenty years or more) before needing to bring in “new blood” from elsewhere. I’ve heard that with a five-clan system that period stretches out to close to a century.

But as for bringing in good additional stock from a trusted breeder elsewhere, there is no problem with doing so at any time, either a single cock or a group of hens and cocks. In this case, simply assign the new birds among the existing clans. Again, you might have good reason to assign to one clan rather than another, or the assignment might be arbitrary, but once assigned a new bird will never change to a different clan.

Practicing clan mating does not eliminate the need for rigorous culling as a key to improvement breeding—ideally we should keep only one or two breeders out of ten chicks hatched. It may be impossible to achieve numbers like that in small breeding flocks, but it is good to remember that Nature is a ruthless culler, and we should follow her lead. There are a couple of important caveats, however. Especially in the early breeding seasons, breeding for maximum genetic depth may have to take precedence over selecting for best possible quality in breeders. For example, in the initial seasons breeding my Icelandics, in order to keep a large enough pool of breeders I’m still having to accept minor flaws (a slight wryness of tail, a bit of malformation of eggs laid) which in future seasons I will cull much more stringently against. But in any breeder selection in the future, there could well be a case where, say, I’ve already selected my finest Red cockerel for the Red clan, and find that the remaining Red cockerel is clearly superior to any of the Green cockerels available for the Green clan. It might be frustrating and counterintuitive to cull the superior cockerel, but for the sake of maintaining the integrity of the clan system and the genetic diversity it supports, in that season I will have to select the less desirable Green cockerel. Rigorous culling is still essential for improvement breeding, but selection occurs within the individual clans rather than in the flock as a unit.

Practicalities may dictate clan mating choices. If you can accommodate only two breeding groups per breeding season, you could simply leave out the other breeding in a given year—Green to Blue, say—and make that mating in the next season, when Blue to Red is the mating that will have to “sit one out.” And if you really can’t maintain more than one breeding group but like the core concept of clan mating? If there are fellow enthusiasts for your chosen breed close by, you could each maintain one of the needed clans. When breeding time comes, swap breeder cocks and then share hatching eggs as appropriate to your joint clan mating system.