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Spoilers for Season 6 Episode 10 and Season 7 of Game of Thrones.

I have tagged this question also with because I am interested about eventual book details that didn't make it into the show.

I know that in the books Jon's ancestry is still a mystery, but I suppose it won't be much different from what we've seen in the show.

In the show, Jon Snow Targaryen is shown to be dark haired, while all other Targaryens are blonde-almost white.

We have seen that the colour of the hair is deemed a good indication as to which family one could belong to (see the "Baratheon" children).

Is there a good explanation of why Jon does not fit the Targaryen pattern? Or should it be considered "hand-wave" away-able because "no other Targaryen-Stark child was ever born so it is not a given that he should have Targaryen hair"?

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    Jon having Dark hair is not exactly a spoiler. – Aegon Aug 21 '17 at 8:31
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    Related: scifi.stackexchange.com/questions/134593/… – Skooba Aug 21 '17 at 11:50
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    I think there was a very good reason that the first book put so much emphasis on hair color. Sure, they were talking about the Baratheon children being illegitimate due to their blonde hair, but it sets a precedent that, in this world, if a blonde and dark haired person have a baby, it will have dark hair. So, even though he is a Targaryen, he will have Stark hair. – EvSunWoodard Aug 21 '17 at 15:03
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    The seed is weak! – CR Drost Aug 21 '17 at 15:22
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    @EvSunWoodard Rhaenys Targaryen's mother was a Baratheon, she inherited silver-gold locks of her father Prince Aemon. – Aegon Aug 21 '17 at 15:38
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Historical Half Targaryens with Non-Valyrian features

That's the case with many Half Targaryens in history.

King Daeron II married Mariah Martell. His first born son, Prince Baelor had dark hair of his mother.

Of Prince Maekar he saw no sign, but he recognized Prince Baelor at Lord Ashford's side. Sunlight flashed golden off the shoulder clasp that held his cloak and the slim coronet about his temples, but otherwise he dressed far more simply than most of the other lords. He does not look a Targaryen in truth, with that dark hair. Dunk said as much to Egg.

"It's said he favors his mother," the boy reminded him. "She was a Dornish princess."
Dunk and Egg: The Hedge Knight

Prince Baelor's own sons Valarr and Matarys had the same hair.

King Daeron's fourth son, Maekar had Targaryen silver hair. But he married a Dayne. So his first born son, Prince Daeron also had the common hair instead of the silver-gold hair of Targaryens.

Dunk chewed, swallowed, and tore off some more bread. "Why did you do it? Was it some jape, to make a fool of the stupid hedge knight?"

"No." The boy's eyes filled with tears, but he stood there manfully. "I was supposed to squire for Daeron. He's my oldest brother. I learned everything I had to learn to be a good squire, but Daeron isn't a very good knight. He didn't want to ride in the tourney, so after we left Summerhall he stole away from our escort, only instead of doubling back he went straight on toward Ashford, thinking they'd never look for us that way. It was him shaved my head. He knew my father would send men hunting us. Daeron has common hair, sort of a pale brown, nothing special, but mine is like Aerion's and my father's."
Dunk and Egg: The Hedge Knight

Similarly, Ser Harwin Strong fathered three bastard sons on Princess Rhaenyra Targaryen , all of them inherited their real father's brown hair (But supposedly their legal father was Laenor Velaryon, who didn't care about getting cuckolded).

Whatever the truth of these tales, it was soon announced that the princess was with child. Born in the waning days of 114 AC, the boy was a large, strapping lad, with brown hair, brown eyes, and a pug nose (Ser Laenor had the aquiline nose, silver-white hair, and purple eyes that bespoke his Valyrian blood). Laenor’s wish to name the child Joffrey was overruled by his father, Lord Corlys. Instead the child was given a traditional Velaryon name: Jacaerys (friends and brothers would call him Jace).
The Rogue Prince

And

Princess Rhaenyra had given birth to a second son late in the year 115 AC. The child was named Lucerys (Luke for short). Septon Eustace tells us that both Ser Laenor and Ser Harwin were at Rhaenyra’s bedside for his birth. Like his brother Jace, Luke had brown eyes and a healthy head of brown hair, rather than the silver-gilt hair of Targaryen princelings
The Rogue Prince

And

In 117 AC, on Dragonstone, Princess Rhaenyra bore yet another son. Ser Laenor was at last permitted to name a child after his fallen friend, Ser Joffrey Lonmouth. Joffrey Velaryon was as big and red-faced and healthy as his brothers, but like them he had brown hair, brown eyes, and features that some at court called common. The whispering began again. Amongst the greens, it was an article of faith that the father of Rhaenyra’s sons was not her husband Laenor, but her champion, Harwin Strong.
The Rogue Prince

Other than that, King Aegon IV sired a ripe crop of bastards. Three of them were sired on a black courtesan, named Bellenora, Narha and Balerion. Their description is not given but since Bellenora came to be known as the Black Pearl of Bravos, I suppose she was black as were her siblings. He also had Aegor Rivers, better known as Bittersteel, the founder of Golden Company, with Lady Barba Bracken. The lad had purple eyes from his father but inherited black hair of his mother.

King Aegon V married Betha Blackwood. His eldest son was a ravenhead. His physical description is not given but his illustration in TWOIAF shows that he inherited raven locks of his mother, unlike his brothers and sisters.

enter image description here

And most Recently, Prince Rhaegar's children with Elia Martell are good example. Rhaenys took after her mother and inherited her dark hair but Aegon took after his father. So among all three of Rhaegar's children, only Aegon took after him while Rhaenys and Jon took after their mothers.

Historical Half Targaryens with Valyrian features

While it can happen (Half-Targaryens taking after non-Targaryen parent), as we see evidence above, it is not something which always happens.

King Aegon V married Betha Blackwood, all of their children were your typical Targaryens except the eldest Prince Duncan the Small, Prince of Dragonflies (See above).

King Daeron II's all children were Typical Targaryens except Baelor Breakspear.

King Maekar's all children were typical Targaryen except Daeron Targaryen.

Princess Rhaenyra's mother was an Arryn (although Lady Aemma Arryn herself was a half Targaryen and cousin to her husband), but she was typical Targaryen. Rhaenra's half siblings Aegon II, Aemond, Daeron and Helaena were all typical Targaryens as well despite having a Hightower (Although Alicent Hightower's hair color is not mentioned) for their mother.

Case of Jon and Arya

So it shouldn't be surprising that when Rhaegar (Silver Gold hair) married Lyanna (Brown hair), their child was born with Brown hair as Silver-Gold is a recessive gene, while Brown is dominant.

Jon had the brown hair of Starks, which he inherited from his mother. Arya inherited the same from her father.

It would have been easier if Arya had been a bastard, like their half brother Jon. She even looked like Jon, with the long face and brown hair of the Starks, and nothing of their lady mother in her face or her coloring.
AGOT: Sansa I

They both also had the Grey eyes of Starks. While everyone wondered who was Jon's mother who left nothing of her in him, It was actually his father who left nothing of him in Jon.

Conclusion

In any case, Jon had a good enough chance of getting Targaryen outlook but his mother's genes won and he was born lucky, looking like a Stark, making it feasible for Eddard to lie. Otherwise explaining a Valyrian looking bastard would have been really hard. Would have gone something like this:

Robert: Say Eddard, how did you sire a Valyrian looking bastard?

Ned: I went to Lys.

Robert: When? You never had the time to go to Lys.

Ned: Okay you got me. I had an affair with Queen Rhaella.

Robert: Rhaella? Hmm I don't see the timeline match but she was with child when she fled. But her Child was Daenerys Stormborn.

Ned: She's my daughter too. Jon's twin.

Robert: GODDAMMIT NED! TELL THE TRUTH!


Further Reading

  1. Why didn't Eddard tell Catelyn about Jon's true parentage?
  2. Is there any tangible proof of Jon's parentage?
  3. Timeline of Lyanna's elopement with Rhaegar
  4. Will Jon still be a bastard?
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    This is one of the reasons House Targaryen favors inbreeding too, to keep their recessive genes (or whatever the equivalent in Westerosi evolutionary biology is) pure. – tobiasvl Aug 21 '17 at 9:07
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    @tobiasvl To keep the bloodline pure yes, but is it to retain their physical features or to avoid diluting whatever magic flows in their blood? I think they do it protect the magic, rather than physical features. – Aegon Aug 21 '17 at 9:10
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    @JohnBell No he did lie. He told that to Lady Stark and everyone else. He called him son in front of whole north, by Catelyn's memoirs. – Aegon Aug 21 '17 at 11:48
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    Just a nitpick: From my understanding, Brynden Rivers aka Bloodraven was albino, and that is the reason for his white (not silver gold) hair and red (not purple) eyes. So, well, he is an exception. – Jean Hominal Aug 22 '17 at 11:42
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    @JeanHominal Ashara Dayne plan is a sound one, After all Ned never denied it, giving impression to many that she must have been the mother. The fact that she was also pregnant around the same time would have helped. There are fair haired people in Dorne (Stony Dornishmen), Daynes are one of them. Keeping Jon's hair dyed is not such a sound plan. Varys had spies in Winterfell after all. Word would have gotten out, children talk, ALOT – Aegon Aug 22 '17 at 12:00
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Jon Snow's mother, Lyanna Stark is a Notherner and has dark hair. And this gene is dominant as Jon Arryn said. "The seed is strong", implies that a parent with dark hair will probably have a son with dark hair.

The same question here.

From the books, Targaryen ancestors had dark hair : Baelor (killed in a tournament in the novel The Hedge Knight) for example.

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    Well, the Baratheon seed is strong. I wouldn't go as far and imply that Jon Arryn's research went into actual genetic research. He just followed the familiy bush of Baratheons, not all of black haired people. – user1129682 Aug 22 '17 at 8:39
  • @user1129682 I think he just skimmed over the Baratheon Tree and read about only marriages between Lannisters and Baratheon. If he had gone through all Baratheon marriages, he would have found marriage of Prince Aemon (Son of King Jaehaerys I Targaryen) and Lady Jocelyn Baratheon (Daughter of Lord Robar Baratheon), their only daughter Rhaenys had silver-gold hair, right on the top – Aegon Aug 22 '17 at 8:42
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    @user1129682 It does. If Black haired Jocelyn gave birth to Silver Gold haired Rhaenys, it shouldn't be surprising that Cersei gave birth to three blondes. But Rhaenys was the only child of that marriage. Cersei had three. The suspicious thing wasn't them being blonde. The suspicious thing was that none of them had Black hair. It was circumstantial evidence at best. It is my personal theory that Seed is strong was a reference to Laenor Velaryon being cuckolded by Ser Harwin Strong. The seed was Strong, not Velaryon. – Aegon Aug 22 '17 at 8:48
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    @user1129682 It was a big meme which unleashed the bloodiest civil war of Westerosi history, resulting in effective extinction of dragons and near-extinction of House Targaryen, As Aegon II fought his sister Rhaenyra because no bastard Strong could ever be allowed to take the throne. But I think canon sources suggest that the phrase has more to do with genetics as Bebs said, But I like my theory :D – Aegon Aug 22 '17 at 8:59
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    @Aegon me too :D – user1129682 Aug 22 '17 at 9:01

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