[Kryptid (OP)]

I'll represent a simplified genome of a hypothetical organism as A-B-B'-C-D-E-F, where each letter represents a gene. In the case of the B' gene, that is actually a duplication of the B gene. Let's say that this is a new mutation that didn't exist before. Therefore, this organism's genome is one gene longer than the other members of its species. So what happens when it tries to sexually reproduce?

All potential mates therefore have a genome of A-B-C-D-E-F. How can the mutant's DNA properly align itself with that of its mate in order to from a viable zygote? The A gene from the mutant can pair with the A gene of its mate just fine, and B can pair with B. But what happens at B'? Wouldn't the presence of B' throw off the genetic alignment such that each gene from the mutant is paired with the wrong gene from its mate in the resulting zygote? Wouldn't there be an unpaired F gene at the end?

Given that single mutations like this don't typically make organisms sterile, there must be some way that biology can successfully keep alignments between DNA strands of dissimilar length. Any idea how this is accomplished?

[RD]

Professor Myers explains that here ... http://scienceblogs.com/pharyngula/2008/04/21/basics-how-can-chromosome-numb/

Rather than double-B, he went with double-D ...

[Kryptid (OP)]

That was an enjoyable read and did explain how chromosomal duplication happens (which I also did not know the mechanism behind). However, it didn't address the situation that I was interested in (which didn't involve changing chromosome numbers): how do genomes from two different parents successfully align when they have different numbers of genes in order to produce viable offspring?

If the father has a duplication of B, then the mother will be lacking an allele at one of those B loci (either B or B').  So the offspring will only be getting that extra B from the father. Would that simply mean that the offspring is haploid at that particular locus or what? Is that viable? How does the cell "know" which B from the father that the mother's B allele should align with? Does that mean that the diploid offspring will simply have two genomes of unequal length? What happens when that offspring performs genetic recombination with one of its chromosomes being longer than the other? Surely that can't make it sterile, because evolution requires that mutations which increase DNA length to have occurred in the past.

[evan_au]

how do genomes from two different parents successfully align when they have different numbers of genes in order to produce viable offspring?

I think the potential problem here has been raised one generation too early.

The mother and father each contribute one copy of each chromosome. These both* float around independently in the cell nucleus, producing RNAs (and ultimately, proteins). If the extra B' didn't produce any adverse effect in the parent, then it probably won't affect the child either. This baby will grow up to produce a healthy adult.

The potential problem may occur in this (now) adult, when they produces sperm or egg cells via meiosis. This does require the chromosomes from father and mother to roughly line up, to halve the number of chromosomes. During this process, a chromosome crossover can occur at some point along the chromosome. This means that one of the daughter cells could end up with both B and B', or just a B (or even 2B+B', or no Bs at all).

However, there are not very many crossovers in a given chromosome, so perfect alignment is not required. And the occasional addition or deletion of gene is not always fatal. It may mean slightly lower fertility for this adult with B+B'.

*There is an exception in girls, where one of the X chromosomes is deactivated and stored in a Barr body.

[Kryptid (OP)]

Taking these comments (and the link) into consideration, I think I now have an idea about how species can end up gaining more genes over time. Here it goes:

(1) An individual gains a new gene in one of its chromosomes via mutation.

(2) During genetic recombination and meiosis, some of the resulting sperm may end up losing some important genes (or doubling up on other genes) due to the mismatch caused by the presence of the extra gene, but other sperm will not have that problem since there is an element of chance involved as to which genes recombine.

(3) Those sperm which don't undergo a troublesome recombination event can still carry the mutation and potentially fertilize an egg.

(4) The mutant chromosome from the father is inherited alongside the corresponding normal chromosome from the mother. This causes no problem for the offspring's ability to survive.

(5) When this first offspring undergoes genetic recombination and meiosis to form its own sperm, it can end up with reduced fertility just as was the case for its father, but still has the potential to reproduce anyway.

(6) Either by chance (or by selection, if the extra gene mutates to gain a new function in the mean time), the extra gene spreads throughout the population. Eventually, two individuals mate which each have the extra gene. This can result in offspring which don't have any recombination problems during meiosis (since both chromosomes are now equal in length again).

(7) Since these individuals that are homozygous for the new mutation don't have reduce fertility, they can be expected to do better than the heterozygotes and either become a new species or to eventually have their new mutation fixed in the existing population (either due to chance or by having some real survival advantage over the variants with the normal number of genes).

Do I have that right?

[evan_au]

That's a pretty good summary.

This can result in offspring which don't have any recombination problems during meiosis (since both chromosomes are now equal in length again).

There is an implication here that if the chromosomes from both parents have exactly the same length, then they won't have any problems with crossovers.

I think the converse is defensible: if the chromosomes from both parents have very different lengths, then they are very likely to have problems with crossovers.

But crossovers happen all the time (I worked it out once, and I vaguely recall that it averaged about 1 crossover per chromosome). And these crossovers frequently drop out (or duplicate) a non-coding section, a control region, or even part of an active gene. This is so common that it is unlikely that all of the genes line up exactly in both parents. So if the crossover occurs in the middle of an important region, it is quite likely to cause a small deletion or insertion in one copy of the gene.

If this gene is vital to cell survival, the resulting embryo probably won't survive a week; by this time it needs to have grown and divided many times.
If this gene is vital to survival of the organism, the resulting fetus probably won't survive the first trimester; by this time it needs a functioning circulatory system to distribute nutrients and oxygen.

See: https://en.wikipedia.org/wiki/Deletion_(genetics)