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The diploid chromosomal architecture is rather interesting. For example, because of diploidy we Humans have to mate. Of course in that sense, because diploid organisms often have mate, this has led to emergence of sexual organs as novel features etc.

But, what I am interested in, is the prospect of recombination and mating being able to lead to drastically novel evolutionary traits.

For example, if a remote tribesman from the Pygmy peoples of Central Africa were to mate with an urban dweller, one theoretical example of a novel feature could emerge in the offspring are new inter-gene/protein interactions between these "never met before" sets of alleles. Recombination would then "seal the deal" by shuffling these allele sets between the maternal/paternal chromosomes, such an individual's offspring would now become a mosaic of their hybrid parent. Just imagine cross-over events occurring between two very divergent promoters of the same loci.

Questions:

  1. Could the unison of such divergent sets of alleles theoretically lead to unique phenotype and features that bear little resemblance to any features belonging to the parents?
  2. Are there any real examples of morphological/physiological features such as that I have tried to describe?
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I doubt this will cause any problems or new features coming up, since humans are pretty homogenous genetically speaking. This will probably cause some problems in the future with isolated populations. But when they can not mate anymore with each other, then a new species evolved. –  Chris Mar 22 at 8:26
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Could the unison of such divergent sets of alleles theoretically lead to unique phenotype and features that bear little resemblance to any features belonging to the parents?

Though it is possible that some unique characteristics may emerge but it is very less likely that the offspring will bear no resemblance to the parents. You start with an example of humans. In this case it is, in my opinion, very unlikely because there is not so much of genomic diversity yet that may lead to such an outcome as you ask about.

Some examples exist, such as the liger (offspring of a male lion and female tiger) that is bigger than both the species. This happens because of improper growth regulation because of interspecies differences. This could happen because the divergence between lion and tiger is much more than the intraspecific variations.

Just a speculation : perhaps the offspring of H.sapiens and H.neanderthalis could have had such a feature but it seems unlikely for the current population of H.sapiens

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