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Tuesday, February 14, 2012

Traits vs. Genes

If you get half your genes from your mum and the other half from your dad why don't you have half your mums feature's and half of your dad's?

There is something wonderful about this simple question, and all of genetics could be used to answer it. Three points seem to be worth making.

1) Dominance. If a specific trait is conferred by a dominant allele and both parents are heterozygous, then their child can lack a trait that they share.

2) Features are not genes. Some traits (features) are affected by many genes, and many genes affect multiple traits.

3) Many traits are complex. Geneticists distinguish between simple (Mendelian) traits and complex traits. Traits can show the following sorts of genetic complexity:
epistasis (where the effect of one gene depends on other genes)
incomplete penetrance (where a specific genotype doesn't always have the usual effect)
polygenic inheritance (where multiple genes affect the trait)
genetic heterogeneity (where different genes cause the same trait in different families or populations)
phenocopy (when traits that often have a genetic basis arise without a genetic basis)

Explaining all of this in detail would require a complete course in genetics!

Hybrid Sunfish

I did a post to my blog (here) about hybrid sunfish and wanted to ask the genetic experts for some clarification. As I understand it most sunfish can hybridize. The offspring are fertile but mostly male. What I don’t understand it why I seldom see hybrid sunfish in the wild. Is the success rate lower in producing hybrid offspring? Do fish tend to avoid mating with hybrids? Maybe this isn’t a question dealing with genetics as much as fish behavior. Perhaps you have some insights or could point me in the right direction.

I’m also curious what happens when hybrids do mate. Will some of the offspring revert back to “purer” sunfish? If two Bluegill/Sunfish hybrids mate what would the expected offspring be?

There is a lot known about hybrids in general, but I don't know anything about sunfish in particular. Comments from anyone who does are welcome (but you can't be anonymous).

Sunday, February 5, 2012

Software for large groups of IBD matches.

I received the following question, which I think is excellent.

Is there any software for plotting possible/probable relationships to MRCA [most recent common ancestor] for groups of 10-1,000 cousin matches suggested by various services, e.g. 23andMe, GEDmatch, FTDNA?

It seems to me that standard genealogical services are too rigid. Once you lay down a line of possible 3rd cousins and another for 4th cousins etc, linking them to various MRCAs who are perhaps 5 or 6 away becomes a bit of a nightmare.

The cousin matches referred to are typically based on shared segments longer than some threshold (typically 5 cM.) that appear to be identical by descent (IBD). In my case, 23andMe identifies 835 relatives but I know how I am related to only two (my mother and my sister).

I will contact scientists I know who work in this field to see if there is any software that is available to, and usable by, the general (informed, curious and sophisticated) public.

If you know of software that might be useful and want to see some of this data, I can send examples from 23andMe. It lists all IBD regions longer than the threshold that are shared with the user. Someone using this tool for genealogy will typically have such data for a small number of family members, and the information about most "cousins" is typically minimal. The person who posed this question can probably files to anyone who wants to see what they look like.