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In Parshat Vayeishev, the Torah records the lineage of Yehudah. Er, his eldest, is married to Tamar and then dies without offspring. The same occurs with Onan. Yehudah then has children with Tamar (whom he had thought was a prostitute). As some of the commentaries discuss Yibbum in connection to Onan's marriage and perhaps even Yehudah's act, shouldn't Er be Peretz's father, rather than Yehudah?

The verse following the mitzvah of Yibbum seems to imply that the son of the union will be associated with the deceased brother:

Devarim 25:6:

והיה הבכור אשר תלד יקום על שם אחיו המת ולא ימחה שמו מישראל

And the first child that is born shall rise up on the name of the deceased brother, and his name shall not be erased from Israel

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According to the Zohar (it is about a fifth of the way through the section read at a Brit Yitzhak, - you can see it here, the line starting with the words אבל תשכח דא כגון בר נש), the child is actually a reincarnation of the deceased brother.

The Malbim explains the story of Ovad's birth in this way:

Rus 4:16:

וַתִּקַּח נָעֳמִי אֶת-הַיֶּלֶד וַתְּשִׁתֵהוּ בְחֵיקָהּ, וַתְּהִי-לוֹ לְאֹמֶנֶת

And Naomi took the child, and laid it in her bosom, and became nurse unto it.

4:17:

וַתִּקְרֶאנָה לוֹ הַשְּׁכֵנוֹת שֵׁם לֵאמֹר, יֻלַּד-בֵּן לְנָעֳמִי

And the women her neighbours gave it a name, saying: 'There is a son born to Naomi'

(Translations from Mechon Mamre)

The Malbim (here, last line on the page) explains that this son was literally a son to Naomi, as this child was a reincarnation of her deceased son. Thus, Naomi nursed the child, as it was really her own child.

The Peleh Yo'etz, in the chapter titled Gilgul, says the same thing, with the (fascinating) addition that therefore, if a person were to know faults of the deceased, they should tell the child of the yibbum union so that he will know what faults he should work to rectify, as this child is a reincarnation of the deceased.

Thus, in either respect, Peretz was a child of Yehuda - Yehuda was the biological father, and he was also the spiritual father - the child's soul would be a reincarnation of Yehuda's deceased son, and therefore was his son on that level as well.

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There may or may not be a practice to name the child of a Yibbum after the deceased brother; however, I don't think that the child is considered to be the child of the deceased brother in any way, shape or form.

Deut. 25:6-7:

וְהָיָה הַבְּכוֹר אֲשֶׁר תֵּלֵד יָקוּם עַל שֵׁם אָחִיו הַמֵּת וְלֹא יִמָּחֶה שְׁמוֹ מִיִּשְׂרָאֵל

And it will be, that the eldest brother [who performs the levirate marriage, if] she [can] bear will succeed in the name of his deceased brother, so that his [the deceased brother's] name shall not be obliterated from Israel.

וְאִם לֹא יַחְפֹּץ הָאִישׁ לָקַחַת אֶת יְבִמְתּוֹ וְעָלְתָה יְבִמְתּוֹ הַשַּׁעְרָה אֶל הַזְּקֵנִים וְאָמְרָה מֵאֵן יְבָמִי לְהָקִים לְאָחִיו שֵׁם בְּיִשְׂרָאֵל לֹא אָבָה יַבְּמִי

But if the man does not wish to take his brother's wife, the brother's wife shall go up to the gate, to the elders, and say, "My husband's brother has refused to perpetuate his brother's name in Israel he does not wish to perform the obligation of a husband's brother with me."

Rashi there (6), citing the gemara (Yevamos 24a), says that this only means that the brother who does Yibbum gets extra inheritance, not that anything about the paternity of the child changes.

יקום על שם אחיו: זה שייבם את אשתו יטול נחלת המת בנכסי אביו

will succeed in the name of his deceased brother: [literally,“will rise in the name of his brother.”] The one who marries his wife, is to take the share of his deceased brother’s inheritance of their father’s property [in addition to his own share]. - [Yev. 24a]

Thus, I think it's pretty simple to say that the paternity of the child of Yehudah follows his biological father only -- and Yehuda's son from Tamar would be his own.

(all translations from Judaica Press, copied from Chabad.org)

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According to Gemara Sotah 10a as explained by Rashi, Tamar wasn't even related to Yehuda as a daughter in law once Er and Onan died, since she was an orphan married by her mother which is not a kiddushin Mideoraisa and when Yehuda told her she couldn't marry Shela she did Miun because she knew Yehuda never intended to marry her of to Shela (which is why she enticed Yehuda). If she would have been married by her fathe a Kiddushin deoraisa Yehuda would have been forbidden to marry Tamar as stated in Vayikra 18,15: ערות כלתך לא תגלה (do not sleep with your daughter inlaw). So Yehuda asked her if she was an erva (i.e daughter inlaw) to which Tamar responded no because she was never able to marry properly as her father was already dead and her marriage was a Kiddushei taus:

יתומה אני - והייתי קטנה והשיאוני אמי ואחיי ואין נישואין לער ואונן כלום לאסור עליו משום כלתו ואין זכות לאם ולאחים להשיא קטנה אלא האב זוכה בה

So since a father in law can't do Yibbum, Yehuda married her from scratch as she was never considered married to Er or Onan, Peretz was Yehuda's son not Er's son.

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