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In general, for dioecious species, a large portion of the genome passed from parents to offspring of both sexes - in mammals the X-chromosomes and autosomes are passed from a mother to both daughters and sons, and autosomes from the father to both sons and daughters. Only the small amount of genes present in the Y-chromosome and mitochondria are inherited solely within one sex.

Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory? What is the most sex-limited genome known to researchers?

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In birds and reptiles females are the heterogametic sex with allosome configuration ZW. However it has been reported that a homogametic WW female boa was born by parthenogenesis. So it means that although W is shorter than Z, it can still support life. So I guess that ZW system in general exchanges more sex-limited genetic material than XY system.

Platypus has 5 pairs of sex chromosomes. See here. This can qualify as the top case of sex-limited transmission.

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The new mexico whiptail reproduces purely through parthenogenesis. The species itself originates as a hybrid of two other species of whiptail, but the hybridization can't make fertile males. The females can reproduce through parthenogenesis so that's how the species continues to exist. So 100% of the genome is passed mother to daughter for many generations, very few new mexico whiptails are made through a fresh hybridization of the parental species.

http://en.wikipedia.org/wiki/Cnemidophorus_neomexicanus

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Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory?

Here are a bunch of cases and specific examples that may interest you

  • There is a species of ants where both genders evolve to be able to reproduce by parthenogenesis (which means that males might be call females as well). In this species, the two genders mate together to create workers that do not reproduce! Therefore, when you look at the phylogenetic tree you can see that males and females are on two totally separate branches as there is reproductive isolation between the sexes in terms of fertile offspring. There is an article by L. Keller on the subject.

  • In the amazon molly, there are no males. But it is interesting because females need sperm to start the development of their ovules although they don't even use the genetic material of the sperm. Therefore, the amazon mollies need to find mates in sister species. In consequence, they imitate the females of the other species. There is a recent article from Hanna Kokko that investigate with a mathematical model how such system may be able (not cause the extinction of the amazon molly or of the sister species).

  • Sex-specific segregation distorter. Nasonia sp. may be an interesting case study

  • Haplo-diploidy. In ants for example, sons receive genetic material from their mother only. They are haploid.

  • if the rate of sexual reproduction is different from 1 then, females are responsible for more than half of the inherited genes in the next generation.

I apologize for the lack of references $\ddot \smile$

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