Archive for November, 2010

Looking out the south window, November 29. Sun touched the treetops, but it never rose high enough to shine in the window.

Sunrise 10:13; sunset 3:04, and at local solar noon (12:40 pm) the sun is a whole 3 1/2 degrees–7 times its diameter– above the horizon–which means it never gets high enough I can see it from my south windows. It does just touch the treetops. Tomorrow will be even shorter–we’re losing about 5 minutes a day, now.

At least it’s quit raining. It’s a little colder than seasonable–20 below today, with 30 below forecast for tonight, and a clear sun dog shortly after noon.  A sun dog means there are flat, hexagonal ice crystals in the air. Snow depth is a bit less than 10″. The rain early last week took it down, but we’ve had a couple of inches of snow since to bring it back up. We’ve got close to an extra inch of water in the snow pack, though.

When will it warm up? It might get up to zero by later in the week, but we may get our first 40 below of the season before that. I’ll have to post “Here Comes Ice Fog” for tomorrow’s Carol.

Bay color.

This post has been revised with new photographs here.

The base colors of horses are bay, black and chestnut, possibly with the addition of wild bay and seal brown (tan-point.) These colors are distinguished by where red and black pigment are found, both where on the whole horse and where on individual hairs. I’m going to go into more detail this time on what determines these base colors.

Red pigment in horses (more correctly, phaeomelanin) can appear brownish red to copper, sometimes approaching gold, in the absence of dilution factors. With dilution factors, it can include white, cream, tan, yellow and gold shades.

Black pigment (more correctly, eumelanin) is black in the absence of modifying genes. In horses, the genes that dilute black to blue-gray or black to chocolate brown are not known to occur, though they do occur in other species. Some dilution genes in horses do affect black, changing it to shades from sepia to dirty white or even pure white.

Black. This mare actually has a few brown hairs, but this is not unusual for blacks in summer coat–black is subject to “sunburning” of the color.

The Agouti locus is known in almost all mammals. It codes for a protein that affects more than coat color, and is complex to sequence. In general, however, more red pigment is dominant to more black pigment.

The Agouti locus is given the symbol A. Agouti alleles are A with a superscript showing the particular form of the allele. Thus Aa is the symbol for recessive black, also called non-agouti. At stands for seal brown (black with tan on the inner legs, flanks and muzzle, very hard to tell from black with the mealy gene) which is also called tan-point in some mammals. AA is the symbol for bay. A+ is the so-called wild bay, where some red pigment appears on the lower legs.

Every horse has two alleles at each locus. If one allele is dominant to the other at the same locus, that is the allele that determines the color of the horse—if the extension locus allows it to. The order of dominance at the agouti locus is wild bay is dominant to all others, bay is dominant to black and tan-point but recessive to wild bay, tan-point is dominant to black but recessive to both bays, and black is recessive to the other three alleles. This means that two recessive blacks can produce only black foals, while two wild bays can produce any color.

The agouti gene, by the way, was named for a South American rodent, the agouti. It was originally defined as controlling banded hair, seen in many wild animals. In fact, banded hair (black tips on red hairs) can be found on most bay horses, though you’ll need a magnifying glass and very good light to find it.

Chestnut paint. This particular horse appears to have the frame allele, judging from the face and lower legs.

The Extension locus is given the symbol E. The wild-type allele, E+, allows the agouti alleles to be expressed. There is also a recessive allele, Ee, which suppresses the black pigment. Not completely—a horse with two Ee alleles can still have black whiskers and may have black hairs scattered throughout the coat. But it will not have the black mane, tail and lower legs of a bay. In fact, an EeEe horse will be a chestnut, regardless of what may be at the Agouti locus.

E may also have two alleles dominant to the wild-type allele. These are dominant black ED and countershading, EB. At the E locus, alleles with more black are dominant to alleles with more red. Further, the E locus can hide what is present at the A locus. An ED horse will be black regardless of what alleles are present at the A locus, and an EeEe horse will be chestnut regardless of what is present at the A locus. The word epistatic is sometimes used to define this relationship between loci—Extension is epistatic to Agouti.

Note that I am following Sponenberg, Equine Color Genetics Third Edition, plus my own observations on hair color.

Oh, Christmas Tree (1986, to the tune of Oh Tannenbaum”)

Oh Christmas tree, Oh Christmas tree,
How green were once your branches
Oh Christmas tree, Oh Christmas tree,
How yellow now your branches
We think it’s something in the air,
But ozone? Sulfur? And from where?
Oh Christmas tree, Oh Christmas tree,
How brown are now your branches

Remember acid rain? Now it’s more insects, at least in our area. Global change?

I was going to wait til after Thanksgiving to start posting these, but the verse of this one is just too appropriate to the current weather in Alaska!

White Christmas (1986, to the tune of “White Christmas)

The sun is shining, the snow is slush,
The willow and birch trees sway.
There’s never been such a day
At Christmastime in A.K.
But it’s December the twenty-fourth
Where is the weather that should be north?

I’m hearing of a white Christmas
Just like the ones we used to know.
Where the treetops glisten, and drivers listen
To hear snowplows in the snow,
I’m hearing of a white Christmas
The jet stream’s wandering tonight,
All the east is chilly, but bright,
And the Christmas in Florida is white.

These Geoophysical Christmas Carols will be posted on Tuesdays and Thursdays for the rest of the holiday season. Enjoy! And sing along!

Snow stake around noon, November 22, 2010

I live in North Pole. Not at the North Pole, but a suburb of Fairbanks, Alaska. This time of year it’s normally dark except for a few hours around noon, and reliably below freezing.

Not this year.

It’s not only above freezing, it’s raining, and expected to keep raining through tomorrow. Of course the ground is well cold-soaked, and there are ten inches of snow on the ground, so the roads are–to put it mildly–treacherous. Like people can’t stand up, let alone cars. My paved patio has about a quarter inch of clear, wet ice. Schools are closed. A friend’s dog couldn’t stand up.

Of course it won’t get warm enough to melt anything, so we’ll have ice on the roads until it wears off (takes several weeks on the heavily traveled roads, until spring on the side roads.)

Living as I do on a gravel road, with gravel large enough to poke through most ice, I thought I could drive the tenth of a mile to the mailbox and at least check my mail. Ha! The car, an all-wheel drive with Blizzak tires, felt like it was floating all the way, and when I touched the brakes, the anti-lock system engaged at once (without slowing the car.) I didn’t even try the paved road.

I surely hope it cools off by Wednesday.

This post has been reissued with additional photographs here.

The colors of all wild animals are a tradeoff between camouflage, which hides the animal from its predators or hides the predator from its prey, and display, which involves making the animal more attractive to members of the opposite sex or more threatening to rivals of the same sex. In equines, camouflage may involve blending into the herd (as in zebras) or blending with the background (often dry grass.) Bay, black and chestnut are not very good camouflage colors, but flatter, duller shades of these colors are.

The dun gene flattens and dulls the coat color over most of the body, leaving head, lower legs, and sometimes manes and tails darker than the body. Both red and black pigments are affected. It also produces a highly variable degree of striping of the coat. In general the horse will have a dark stripe running from the mane to the base of the tail, which in some cases continues down the center of the mane (dark mane center with light edges as in the Fjord horse) and tail. (Dorsal stripes do occur on other colors, but they are rarely unbroken from mane to tail.) In addition duns often have zebra-like stripes on the legs (especially near the knees and hocks.) Less commonly, they will have spiderweb-like markings on the forehead, or a cross stripe over the wither area—a marking common in donkeys. All of these markings are grouped as primitive marks.

One early study of dun suggested that the dulling is due to a crowding of the pigment granules to one side of the hair. My own observations tentatively support this, but I am aware of no published studies—looking at individual hairs under a microscope doesn’t seem to be popular today.

Dun is thought to be the wild-type gene for horses, and it is definitely dominant to non-dun. Why do we think it is the wild-type gene?

First, cave paintings Almost all show the darker head typical of dun, and some also show other primitive marks. Cave artists were limited by the available pigments, but their renditions are certainly compatible with the various types of dun.

Second, the wild horses that survived long enough to have their color recorded. These include the living Przewalski’s horse of Asia and the now extinct Tarpan of Europe, both duns.

Dun, though a dominant gene, is not that common in most horse breeds today. Why? During domestication, an occasional mutation to non-dun must have occurred. Human beings are attracted to what is different, and the earliest domesticators of the horse probably prized these intensely colored variants—to such a degree that in many horse breeds of today dun is either non-existent or very rare.

The words dun and buckskin are rather loosely used, and often treated as synonyms. Genetically, however, it is better to reserve buckskin for a bay with one cream gene at the cream locus, and dun for the whole suite of colors produced by one or two doses of the dun gene. The colors include red dun (dun on a chestnut background) various shades of tan with dark brown or black mane, tail and lower legs known as zebra dun, (dun on a bay background) and various shades of dark slate gray to silver with dark points known as grullo (dun on a black background.)

In my upcoming science fiction book, Tourist Trap, I have both wild horses assumed to be descended from some transplanted from Earth during the Pleistocene, described as striped duns, and a domestic mare, Raindrop, whose base color is grulla (feminine form of grullo.) Those striped duns are assumed to be duns of various base colors with very strong primitive marks.

I had my first #scifi book signing today, at Gulliver’s. Enjoyed talking to people and sold a few books–but we had serious snow for the first time today. Don’t know how deep the snow is, but a foot wouldn’t really surprise me–by the time I got home it was almost four and  too dark to see the snow stake! Winter is definitely icumin in.

This post has been reissued here.

Last week we discussed #palomino as if there were just two forms of the gene associated with palomino color: cream and non-cream. The whole story is a little more complex, but I’ll have to introduce some #genetic terminology to explain it.

The three new words we’ll be using are locus, allele and wild–type.

Locus means place in Latin, and it originally meant a place on a chromosome. Since genes code for proteins and are now known to be a little more complex than just the place on the chromosome, it now means the particular protein coded for.

There can be slightly different forms of a protein having the same function, and the different stretches of DNA (genes) that code for these slightly different forms are called alleles. Using this terminology, every horse has two alleles, one from each parent, at each locus (plural loci.) Last week we discussed two alleles, cream and non-cream, at the cream locus.

The complications come from the fact that there are in fact three rather than just two alleles at the cream locus. Each individual horse can have any two of these three alleles. To avoid confusion, I am also going to introduce the term wild-type for the gene assumed to be the “normal” allele at a locus in the wild ancestor of a domesticated animal. What we called “non-cream” last week is in fact the wild-type gene that gives normal full color.

(Note that the wild ancestor of the horse is not the “wild” horse of the West—these are in fact feral, descended from domesticated stock. The only true wild horse alive today is Przewalski’s horse in Asia. The Tarpan in Europe was also wild, but became extinct in the 19th century.)

Using our new terminology, the cream locus has three alleles: wild-type, cream, and pearl. Pearl was recognized quite recently, and it has a very low frequency except in a few Spanish and Portugese breeds and their derivatives. It could be considered a weaker allele than cream, as it has less diluting effect on the coat.

A horse with one wild-type allele and one pearl allele will look very much like a wild-type horse—chestnut, bay or black depending on what genes are present at other loci. A very close look will show skin slightly lighter than normal, or with small pale spots.

A horse with two pearl alleles will have the red pigment diluted only slightly more than would be expected for a horse with one cream allele and one wild-type allele. Black pigment, however, will be diluted much more than is the usual case for a horse with one cream and one wild-type allele. Thus a bay with two pearl alleles at the cream locus dilutes to tan or gold on the body with chocolate mane, tail and lower legs. A chestnut becomes virtually identical to a pumpkin-skinned palomino (technically gold champagne.) And a black becomes a grayish tan with chocolate mane, tail and lower legs. All of these colors appear very similar to those produced by a single dose of the champagne gene, which is a completely different gene at a different locus, but give very different breeding results. Luckily there is a DNA test for pearl.

If a horse has one pearl allele and one cream allele, the resulting color will be cream, usually slightly darker than the cream resulting from two cream alleles. In particular the eyes are generally blue or amber, and darker than those of cream horses with two cream alleles.

As I mentioned before, there are a number of different ways of diluting horse color, and when two or more at different loci are combined some very odd colors can result and it may not even be possible to tell what genes are present—or what colors can be produced—without DNA testing.

Next week I’ll consider linebacked dun—one of the few horse genes where the wild-type allele is rare today in many breeds.

(If anyone has photos I could use to illustrate some of these horse coat colors, I would really appreciate them.)

Palomino genetics

This post has been updated with new photographs here.

A palomino is, ideally, a horse the color of a new-minted gold coin with a white mane and tail. At one time, breeders tried to get them to breed true, and there are still breed registries based on palomino color. But two dark-skinned palominos, mated together, will produce only about half palomino foals, and many of them will not be the pure gold with white manes and tails wanted. Why?

Palominpo horse. Note that the eyes and the skin on the muzzle remain dark.

Palomino is an example of what is sometimes called over-dominance or partial dominance. The color is due to a dilution gene, cream or cremillo, acting on a chestnut background. A single dose of cream will dilute red pigment to golden yellow, while having very little effect on black pigment—thus the dark skin. A double dose will further dilute the red to a pale cream hard to tell from white, and black to a shade that varies from a slightly dirty white to pale gray.

All horses, in fact all mammals, have two copies of each gene, one from the father and the other from the mother. If the basic color of the horse is chestnut and the horse has a cream gene from one parent and a non-cream gene from the other, the result will be a palomino. If one parent is a cremillo (the result of a double dose of cream acting on chestnut) and the other is chestnut all of their foals will be palomino. But if both parents are palominos, about a quarter of their foals will get the non-cream gene from both parents and will be chestnut, a quarter will get the cream gene from both parents and will be cremillos, and half will get one of each kind of gene and be palominos.

Cremillos are popular with some horse owners today, but at one time they were considered very undesirable by palomino breeders. They have pink skins and blue eyes, and they may be more subject to sunburn than horses with dark skin and eyes. They are not, however, albinos or due to any form of the albino gene. The cream gene has been found and sequenced, and a DNA test for cream is available.

Palominos don’t necessarily have a clear gold body color, or white manes and tails. Remember chestnuts have varying amounts of black hair sprinkled through the coat, and these black hairs will remain and become even more conspicuous if the red of the coat is lightened to gold. Further, chestnuts often have manes that are self-colored or even darker than their bodies. These characteristics will carry over into the dilute animals, and it is not unusual to find palominos with considerable black shading or dappling, and black hair mixed into their manes and tails.

What happens if the cream gene is combined with a base color other than chestnut?

One dose of cream on bay gives a buckskin, with a yellow body and black mane, tail, and lower legs. A double dose of cream gives a perlino, a cream horse with mane, tail and lower legs very slightly darker than the body, blue eyes and pink skin.

A single dose of cream on black may be missed entirely, and the horse just called black. Some blacks with a single dose of cream are slightly lighter than normal, and are called smoky. With a double dose of the cream gene, a black becomes a smoky cream, again with blue eyes and pink skin.

Although the darkest variants of cremillo, perlino and smoky cream can be distinguished from each other, the lighter variants are very difficult to tell apart. Often they are just called cream, the distinction becoming important only if they are bred.

I emphasized palominos with black skin because it turns out that gold horses with lighter skin (sometimes called pumpkin skin) are due to a completely different gene, champagne. I’ll talk about this later.

If you want to read some very basic information about genetics, especially genetics of coat color, have a look at


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