Alpaca Color Genetics
There is LOTS of speculation about the genetics of alpaca color -- even in the scientific literature! Some of the basics are well agreed upon ---
As in all mammals, alpaca color is the result of two pigments:eumelanin and phaeomelanin. White is the absence of either.
A and E genes (and the alleles of those two loci) control the balance of eumelanin and phaeomelanin.
And there the commonality seems to stop. There's a huge swirl of scientific debate. Female alpacas only ever have one cria at a time, so there isn't information available on litters to help determine the genetics of individuals. Alpacas shift colors somewhat as they age (generally darkening) -- meaning the colors reported on pedigree (birth records) may contain inaccuracies. And the registry data shows that alpaca colors at the population scale don't conform to obvious Mendelian rules of simple dominance. Some genes seem to be linked (passed together most of the time), some combinations may have health effects or be lethal (there are fewer blue-eyed whites in the registry than predicted by a straightforward inheritance and around 60% of blue-eyed whites are deaf -- perhaps sometimes the 'missing' BEWs are aborted?) and some 'identical' colors can be created by several different genetic mechanisms (as in goats, white could be dominant white, recessive white or very heavy white spotting).
BUT ... I've just run across a GREAT research report - published by the Australian Government in 2011. It relies heavily on research into the chemistry of alpaca fleece (what pigments are actually in the fibers), understanding of the biochemistry of pigment production common to all mammals, DNA sequencing, and statistical analysis of the various registries. Most importantly (to me), the genetic inheritance patterns described in this paper are at core consistent with other mammals (well, at least rabbits, cavies and goats). You can read that report yourself here... http://www.alpaca.asn.au/pub/about/info/readings/docs/inheritance_white_colour.pdf Even here, though, the information isn't complete. So I've supplemented wherever I could find additional info.
The authors of the linked report describe eumelanin and phaeomelanin as being the two 'base colors' for alpacas. This is different from rabbits and cavies where 'base color' refers to the forms (black/chocolate) and dilution (blue/lilac) of eumelanin.
As in all mammals, alpaca color is the result of two pigments:eumelanin and phaeomelanin. White is the absence of either.
A and E genes (and the alleles of those two loci) control the balance of eumelanin and phaeomelanin.
And there the commonality seems to stop. There's a huge swirl of scientific debate. Female alpacas only ever have one cria at a time, so there isn't information available on litters to help determine the genetics of individuals. Alpacas shift colors somewhat as they age (generally darkening) -- meaning the colors reported on pedigree (birth records) may contain inaccuracies. And the registry data shows that alpaca colors at the population scale don't conform to obvious Mendelian rules of simple dominance. Some genes seem to be linked (passed together most of the time), some combinations may have health effects or be lethal (there are fewer blue-eyed whites in the registry than predicted by a straightforward inheritance and around 60% of blue-eyed whites are deaf -- perhaps sometimes the 'missing' BEWs are aborted?) and some 'identical' colors can be created by several different genetic mechanisms (as in goats, white could be dominant white, recessive white or very heavy white spotting).
BUT ... I've just run across a GREAT research report - published by the Australian Government in 2011. It relies heavily on research into the chemistry of alpaca fleece (what pigments are actually in the fibers), understanding of the biochemistry of pigment production common to all mammals, DNA sequencing, and statistical analysis of the various registries. Most importantly (to me), the genetic inheritance patterns described in this paper are at core consistent with other mammals (well, at least rabbits, cavies and goats). You can read that report yourself here... http://www.alpaca.asn.au/pub/about/info/readings/docs/inheritance_white_colour.pdf Even here, though, the information isn't complete. So I've supplemented wherever I could find additional info.
The authors of the linked report describe eumelanin and phaeomelanin as being the two 'base colors' for alpacas. This is different from rabbits and cavies where 'base color' refers to the forms (black/chocolate) and dilution (blue/lilac) of eumelanin.
The A Series
The A series is one of the two genes controlling base color (red/black). Most colors can be explained by one of these four alleles. In order of dominance these are:
A = white to fawn
Ab = brown with dark points
at = black & tan (as in tan pattern rabbits - eumelanin with a phaeomelanin belly and minor phaeomelanin markings)
a = black (both warm & blue black)
A is thus likely the same allele as the 'dominant white Awht allele of goats rather than the Agouti allele of rabbits.
Ab seems to be quite different from the other mammals I've studied, but apparently is a common color-pattern for horses and this allele is similar to the gene seen there.
at is the tan pattern allele as expressed in cavies.
a is the 'recessive black' of goats, but really the same (genetically and biochemically) as the self allele in rabbits and cavies too.
In this series, A is completely dominant to at and a, and incompletely dominant to Ab. Ab is incompletely dominant over at and a.
BUT -- the basic rule we used for goats -- 'phaeomelanin wins' should still work.
Other authors split the patterns into more refined categories and assign additional A-alleles as responsible. These include splitting A into AT (solid phaeomelanin) and A+ (with minor eumelanin trim) adding Ar (red with black trim), and adding am (mahoghany).
AT > A+ > Ar > Ab > at > am > a
It is also possible that yet other relatively rare A-alleles are responsible for the black/red spotting patterns that are sometimes seen.
There are 10 possible combinations (genotypes) of the four primary alleles
AA = white to fawn
AAb = fawn/ light brown
Aat = white to fawn
Aa = white to fawn
AbAb = brown with black points (bay black)
Abat = dark brown body with black points
Aba = black brown
atat = black & tan
ata = dark brown
aa = black
Alpacas with AA, Aat or Aa genotypes will not have darker points (“points” refers to the muzzle, ears, around eyes, lower legs, sometimes tail).
Animals that are white due to AA, Aat or Aa (rather than due to one of the following genes) will have black skin under the white fiber.
A = white to fawn
Ab = brown with dark points
at = black & tan (as in tan pattern rabbits - eumelanin with a phaeomelanin belly and minor phaeomelanin markings)
a = black (both warm & blue black)
A is thus likely the same allele as the 'dominant white Awht allele of goats rather than the Agouti allele of rabbits.
Ab seems to be quite different from the other mammals I've studied, but apparently is a common color-pattern for horses and this allele is similar to the gene seen there.
at is the tan pattern allele as expressed in cavies.
a is the 'recessive black' of goats, but really the same (genetically and biochemically) as the self allele in rabbits and cavies too.
In this series, A is completely dominant to at and a, and incompletely dominant to Ab. Ab is incompletely dominant over at and a.
BUT -- the basic rule we used for goats -- 'phaeomelanin wins' should still work.
Other authors split the patterns into more refined categories and assign additional A-alleles as responsible. These include splitting A into AT (solid phaeomelanin) and A+ (with minor eumelanin trim) adding Ar (red with black trim), and adding am (mahoghany).
AT > A+ > Ar > Ab > at > am > a
It is also possible that yet other relatively rare A-alleles are responsible for the black/red spotting patterns that are sometimes seen.
There are 10 possible combinations (genotypes) of the four primary alleles
AA = white to fawn
AAb = fawn/ light brown
Aat = white to fawn
Aa = white to fawn
AbAb = brown with black points (bay black)
Abat = dark brown body with black points
Aba = black brown
atat = black & tan
ata = dark brown
aa = black
Alpacas with AA, Aat or Aa genotypes will not have darker points (“points” refers to the muzzle, ears, around eyes, lower legs, sometimes tail).
Animals that are white due to AA, Aat or Aa (rather than due to one of the following genes) will have black skin under the white fiber.
The E series
As with the goats, the Extension gene E works in opposition to the A series in that the more dominant allele is darker.
The paper cited above gives just two E alleles ...
E gives the 'normal' color
e blocks all eumelanin production.
The recessive e-allele in alpacas then works like the allele in cavies -- ee is red to white with only phaeomelanin. Because eumelanin production is blocked, ee alpacas have pink skin. Often ee animals are described as “bright” in relation to colour by alpaca breeders.
NOT included in this paper, but speculated upon elsewhere, is the possibility that alpacas also have a dominant ED allele which results in dominant black.
The paper cited above gives just two E alleles ...
E gives the 'normal' color
e blocks all eumelanin production.
The recessive e-allele in alpacas then works like the allele in cavies -- ee is red to white with only phaeomelanin. Because eumelanin production is blocked, ee alpacas have pink skin. Often ee animals are described as “bright” in relation to colour by alpaca breeders.
NOT included in this paper, but speculated upon elsewhere, is the possibility that alpacas also have a dominant ED allele which results in dominant black.
The Rn Series
The dominant Rn allele results in roaning - and intermixing of white hairs with the base color.
rnrn gives the normal base color.
Rnrn gives roan.
Based on the statistics, it remains unclear whether RnRn gives a roan appearance or whether homozygous roan is lethal (as with cavies). If lethal, it results in early abortion (before pregnancy is confirmed) rather than in term crias with malformations (as with cavies).
Roan alpacas generally get lighter with age (in contrast to greys, below). Usually the head remains a darker color (less roaning).
rnrn gives the normal base color.
Rnrn gives roan.
Based on the statistics, it remains unclear whether RnRn gives a roan appearance or whether homozygous roan is lethal (as with cavies). If lethal, it results in early abortion (before pregnancy is confirmed) rather than in term crias with malformations (as with cavies).
Roan alpacas generally get lighter with age (in contrast to greys, below). Usually the head remains a darker color (less roaning).
The M series (classic grey)
The M gene acts on both eumelanin and phaeomelanin. It seems to be an 'incomplete' variation of roan in which the color of interspersed hairs is lightened, but not true white. The intermixing of white with the base color is usually quite even giving a uniform grey color to the fleece, though there may be 'more white' on the head and legs), . It is co-dominant with MM being lethal (as with roan cavies). The M is used as the symbol because this color is believe to be similar to merle in dogs, though it has yet to be confirmed as the same gene.
MM = embryonic lethal white (unlike with cavies, where lethal whites usually are born full term with significant malformations, lethal white alpacas abort very early - often before pregnancy is confirmed -- these animals are simply entirely 'missing' from the population where they would be expected)
Mm = grey
mm = normal
As with cavies, this type of roaning cannot be seen on a white coat and may be masked in very light colors.
Roaning on a black base results in silver grey alpacas.
Roaning on a red base results in rose grey alpacas.
Grey alpacas may darken significantly as they age -- sometimes to the point that they can no longer be distinguished from the base color.
Grey on a very pale background may appear white at birth and darken only with age.
MM = embryonic lethal white (unlike with cavies, where lethal whites usually are born full term with significant malformations, lethal white alpacas abort very early - often before pregnancy is confirmed -- these animals are simply entirely 'missing' from the population where they would be expected)
Mm = grey
mm = normal
As with cavies, this type of roaning cannot be seen on a white coat and may be masked in very light colors.
Roaning on a black base results in silver grey alpacas.
Roaning on a red base results in rose grey alpacas.
Grey alpacas may darken significantly as they age -- sometimes to the point that they can no longer be distinguished from the base color.
Grey on a very pale background may appear white at birth and darken only with age.
White Spotting Genes
Tuxedo and piebald are the two most common white-spotting patterns. It is unclear whether they are caused by different alleles of the same gene or separate genes. In both cases, white spots are dominant over solid colored. In tuxedos, the white spots are only on the extremities (head, neck and legs) -- they rarely go all the way around the neck. In piebald, the white spots can be anywhere, including the body. An individual can be both tuxedo and piebald (frequently resulting in white that DOES go all the way around the neck) -- though it is uncertain if this is S1S2 (heterozygous for two spotting alleles at the same locus) or TtPp (the result of dominant genes at two separate loci).
Colored Spots (aka Apaloosa)
The genetics of the Apaloosa spotting is not well understood. Most commonly these appear as colored spots on a white animal, though sometimes on greys or other light colors. It does not appear to be related to the moon-spotting of goats. It may be similar to Apaloosa spotting in horses (which is controlled by two genes).
Blue-Eyed White
Another characteristic of uncertain genetics. More than one genetic mechanism may be responsible. Approximately 60% of blue-eyed white alpacas are deaf -- it is unclear whether deafness is due to one genotype while the non-deaf BEW is due to another.
BEWs almost always come from two white-spotted parents - most commonly from two tuxedo greys. BEWs are most common in animals that have both grey and tuxedo in their backgrounds - so some interaction of these genes (or unknown genes linked to them) are suspected. BEWs can have small colored spots and skin that is either pink or dark, so it does not appear to be a form of leucistic albinism. Some alpacas have eyes that are partially blue and/or are born with blue-eyes that darken with age. It is unclear whether these latter types of blue eyes are related to the pure blue-eyed version.
BEWs almost always come from two white-spotted parents - most commonly from two tuxedo greys. BEWs are most common in animals that have both grey and tuxedo in their backgrounds - so some interaction of these genes (or unknown genes linked to them) are suspected. BEWs can have small colored spots and skin that is either pink or dark, so it does not appear to be a form of leucistic albinism. Some alpacas have eyes that are partially blue and/or are born with blue-eyes that darken with age. It is unclear whether these latter types of blue eyes are related to the pure blue-eyed version.
White alpacas
From the above, white alpacas can result from AA ee
AA E-
Aat
Aa ee
Aa E-
Extensive roaning or greying of a pale base color (including light bays)
Extreme Piebald or Extreme Tux/ piebald
BEW
Minimal spot appaloosa
There also appear to be at least three additional recessive alleles (possibly 3 separate genes) that can result in recessive white. None of these are true genetic albinos (no pink eyes) or leucistic (blue eyed) albinos.
The data from melanin testing revealed that most alpacas called white still have a measurable amount of melanin (phaeomelanin) in their fibre, and are essentially a very dilute fawn.
AA E-
Aat
Aa ee
Aa E-
Extensive roaning or greying of a pale base color (including light bays)
Extreme Piebald or Extreme Tux/ piebald
BEW
Minimal spot appaloosa
There also appear to be at least three additional recessive alleles (possibly 3 separate genes) that can result in recessive white. None of these are true genetic albinos (no pink eyes) or leucistic (blue eyed) albinos.
The data from melanin testing revealed that most alpacas called white still have a measurable amount of melanin (phaeomelanin) in their fibre, and are essentially a very dilute fawn.
Rufus factor?
I have yet to see even one article describing the variations in phaeomelanin color in alpacas as a rufus factor. Those papers which do attempt to describe the relationship between red, fawn and white generally observe an inheritance pattern markedly different from the 'additive series' resulting in a 'bell curve' (crossing two intermediates returning the whole range of color with intermediate most common, but the extremes possible) that has been described for rabbits, cavies and goats as 'rufus factors'. Instead, the general rule for alpacas seems to be that normally mixing two shades will result in the LIGHTER of the two colors. Thus crossing 'phaeomelanin white' to 'phaeomelanin red' will usually result in white, rather than an intermediate fawn. Breeding two fawns seems to always result in fawn (of the lighter parent's shade) and not to return the spectrum. Dark reds are produced only from (genetic) red to red crosses (possibly masked by aa black, ED black, or one of the non-phaeomelanin whites).
Our alpacas
We have 3 suri alpacas...
Storm is our dominant male. Except for some curl in his topknot and on his lower legs, his coat doesn't go into ringlets as a typical suri (which he supposedly is), but isn't huyacaya fluff either. Instead, his coat is a smooth silk texture. Storm's pedigree includes a huycaya grandparent, so he may be heterozygous suri/huyacaya.
His pedigree reads bay black, black and white. But except for a patch on each cheek, his coat shows no sign of fading/sunburn (as would be typical of the bay-black). The only white is on his face. Storm's parent's are dark brown (dam) and medium brown (sire) - so his color/pattern cannot be dominant. With no white-spotting mentioned in his pedigree for his parents, I assume the white-spotted pattern on his face is due to a recessive gene. True black (with and without white and/or brown) accounts for 2 grandparents (1 maternal and 1 paternal), 2 great-grandparents, and 1 great-great grandparent. This inheritance pattern suggests aa black. Interestingly, the 'bay black' (red brown) cheek patches are reminiscent of the 'red cheek' pattern of goats -- causing me to wonder if this allele (Arc) may be possible in alpacas.
A little online searching -- Storm's dam Benita (listed as Dark Brown) has a red brown (phaeomelanin?) tummy and cheeks - very clearly black tan (at-). Given that her cheeks have the red color as well, she could be the source of the allele if Arc is responsible. Unfortunately, I wasn't able to find photos for Gdam Nosey's Chelsea (true black, white and medium brown) or GGSire NWA Ltd El Suri (true black and white) or GGGSire NWA Ltd L.F. Rothschild (true black and white). It would be very interesting to see how those color/patterns matched to Storm. Storm's sire CLF Peruvian MacGyver's Image is a very uniform medium brown -- likely Aba. I did find a photo of his GDam Juliett's Panda -- she is true black and white with her neck fully white (far more white than Storm). Storm has just two white alpacas in his pedigree -- GGSire Peruvian Bruxo and GGDam Julieta - it is possible that Storm carries a recessive white (e or other) from one of them.
Best guess ... Storm is Arca or aa with a recessive gene for white spotting and he may carry recessive white (e or other).
His pedigree reads bay black, black and white. But except for a patch on each cheek, his coat shows no sign of fading/sunburn (as would be typical of the bay-black). The only white is on his face. Storm's parent's are dark brown (dam) and medium brown (sire) - so his color/pattern cannot be dominant. With no white-spotting mentioned in his pedigree for his parents, I assume the white-spotted pattern on his face is due to a recessive gene. True black (with and without white and/or brown) accounts for 2 grandparents (1 maternal and 1 paternal), 2 great-grandparents, and 1 great-great grandparent. This inheritance pattern suggests aa black. Interestingly, the 'bay black' (red brown) cheek patches are reminiscent of the 'red cheek' pattern of goats -- causing me to wonder if this allele (Arc) may be possible in alpacas.
A little online searching -- Storm's dam Benita (listed as Dark Brown) has a red brown (phaeomelanin?) tummy and cheeks - very clearly black tan (at-). Given that her cheeks have the red color as well, she could be the source of the allele if Arc is responsible. Unfortunately, I wasn't able to find photos for Gdam Nosey's Chelsea (true black, white and medium brown) or GGSire NWA Ltd El Suri (true black and white) or GGGSire NWA Ltd L.F. Rothschild (true black and white). It would be very interesting to see how those color/patterns matched to Storm. Storm's sire CLF Peruvian MacGyver's Image is a very uniform medium brown -- likely Aba. I did find a photo of his GDam Juliett's Panda -- she is true black and white with her neck fully white (far more white than Storm). Storm has just two white alpacas in his pedigree -- GGSire Peruvian Bruxo and GGDam Julieta - it is possible that Storm carries a recessive white (e or other) from one of them.
Best guess ... Storm is Arca or aa with a recessive gene for white spotting and he may carry recessive white (e or other).
Thomas is a slightly younger male and very submissive to Storm, yet the two are inseparable, with either becoming very stressed when separated (well except for when Storm is visiting a girl -- then he doesn't care, it's just Thomas who is stressed). Thomas is a classic fawn, with cream on his nose and belly (pedigree reads dark fawn, medium fawn and white). Thomas is a suri whose coat forms ringlets and he has a translucent look to his fiber.
Lady Gabriella is our 'matriarch' - well at least she thinks she is. She came with a cria (who we lost to complications of barberpole worm) and she was an EXTREMELY protective mother. Gabi is a suri and completely white with dark eyes. Her skin is pink. Gabi is bred to Storm (he jumped our fence to get to her the first day here).
Gabi's parents were medium brown (sire) and light fawn (dam). So she must be a 'recessive white' genotype, possibly ee.
Storm's dam, Benita, is Gabi's grandmother. This is a 6% inbreeding coefficient for the current Storm x Gabi breeding. This is closer than we would like for alpacas. Storm has been gelded to prevent a recurrence, but we will keep our fingers crossed for our first cria.
We guessed Benita as atArc or ata (same hidden gene as Storm's dominant -- black with the red cheek patches). Her daughter, Gabi's mother (Benita's Bambi) was a fawn with a dark fawn sire. Bambi is likely A- and hiding at, Arc or a from her mother (Benita). If Gabi does have pink skin, she shouldn't be A, and instead likely got at, Arc or a from her mother (Bambi). Gabi's sire - Oro's Peruvian Orion - is a uniform medium brown - likely Ab-. His sire (Cool Fire) was similar, and Cool Fire's parents were fawn. Orion's dam, Peruvian Nube De Oro, was a white Peruvian import - no information is available on her ancestors, so she could be carrying any A-series genes. Best guess is that Gabi is carrying an Ab allele from her father. Seven of Gabi's ancestors had color+white but neither of her parents did. Possible she is carrying a recessive white-spotting gene.
So my best guess for Gabi is that she is Ab(at/Arc/a) ee.
Gabi x Storm -- highest probability seems to favor a re-creation of Benita's dark brown (at) pattern or a more uniform dark brown (Ab). White markings are possible. ...Sadly, the fireworks on July 4th threw Gabi into early labor. Her cria was premature, unable to stand, and lived only a few hours. He was white. His eyes were cloudy, beyond what our local llama expert considered normal for a premature at that stage. Had he lived, we think he may have been blind.
Gabi's parents were medium brown (sire) and light fawn (dam). So she must be a 'recessive white' genotype, possibly ee.
Storm's dam, Benita, is Gabi's grandmother. This is a 6% inbreeding coefficient for the current Storm x Gabi breeding. This is closer than we would like for alpacas. Storm has been gelded to prevent a recurrence, but we will keep our fingers crossed for our first cria.
We guessed Benita as atArc or ata (same hidden gene as Storm's dominant -- black with the red cheek patches). Her daughter, Gabi's mother (Benita's Bambi) was a fawn with a dark fawn sire. Bambi is likely A- and hiding at, Arc or a from her mother (Benita). If Gabi does have pink skin, she shouldn't be A, and instead likely got at, Arc or a from her mother (Bambi). Gabi's sire - Oro's Peruvian Orion - is a uniform medium brown - likely Ab-. His sire (Cool Fire) was similar, and Cool Fire's parents were fawn. Orion's dam, Peruvian Nube De Oro, was a white Peruvian import - no information is available on her ancestors, so she could be carrying any A-series genes. Best guess is that Gabi is carrying an Ab allele from her father. Seven of Gabi's ancestors had color+white but neither of her parents did. Possible she is carrying a recessive white-spotting gene.
So my best guess for Gabi is that she is Ab(at/Arc/a) ee.
Gabi x Storm -- highest probability seems to favor a re-creation of Benita's dark brown (at) pattern or a more uniform dark brown (Ab). White markings are possible. ...Sadly, the fireworks on July 4th threw Gabi into early labor. Her cria was premature, unable to stand, and lived only a few hours. He was white. His eyes were cloudy, beyond what our local llama expert considered normal for a premature at that stage. Had he lived, we think he may have been blind.