Atheist Sex?

A shocking misrepresentation, but while we're misrepresentin' Lets have some fun... Change the title to "What the God Fearin' Cry Out During Sex" and YOU FILL IN THE CAPTIONS!

1st, the original:



Now, my modified version:



Original from My Confined Space

Is the apparent lack of human genetic diversity the result of dispersal?

Reed has an interesting repost (Chimps are Laughing at You) over on his blog - partly in response to a blog over at PZ's place that is generating alot of furor..

Basically he has a graph from a 1999 PNAS paper that looks at African hominoid genetic diversity: He presents this graph:

and says:

What is very obvious from this paper figure is how genetically homogeneous we are compared to our closest relatives. I’ve heard it stated that a single chimpanzee tribe has as much genetic diversity as is found in the entire human species. So next time you feel fit to make fun of us southerners for kissin’ cousins remember that chimps are laughing at you.

And I'll agree- there is either

1. A shit load of genetic diversity in chimps, or
2. Very little Human diversity

My question is this: Is the lack of human diversity related to our ability for long (global) distance migration? Would human diversity have looked so pitiful say 100 years ago?? Has the homogenizing effect of gene flow done this?

I bet its been a really long time since a "western chimp" bred with an "eastern chimp" and as a result, they have been on their own evolutionary trajectories for a really long time....

Anybody have a thought about this?

Maternal Behavior and Eusociality

OK, so all this DDIG writing unfortunately means that I have not been keeping up on current literature.. So, this paper: Wasp Gene Expression Supports an Evolutionary Link Between Maternal Behavior and Eusociality from the 27-Sept issue of Science was missed completely...

Before I get into the paper, I want to rant for a minute about "Next generation" sequencing. So I am a Behavioral Ecologist, and generally study behavior at the level of the population or species. For example, while reproductive behavior surely varies at the level of the individual, more interesting are the patterns of behavior that emerge at higher levels. So while whole genome scans are becoming more available, it's utility for me seems limited at best. In a nutshell- there won't be 45MB of DNA sequence data (a 454 run) in my near future...

Th's being said- the U of Illinois researchers have used 454 and the Apis genome to do something pretty cool. Here is what they did:

1. Characterize behavior of 4 different worker castes in Polistes and ID a bunch of individuals of those particular castes.
2. Wait for the Apis genome
3. ID a set of genes that are related to maternal care
4. Get the cash money for the 454 run using Polistes cDNA
5. ID those maternal care genes in Polistes using the Apis genome
6. Measured gene expression for these genes in the 4 castes
7. See which groups were similar using LD and some strange clustering analysis.

Turns out, the workers (provide sibling care) are really similar to Foundresses (provide maternal care) in their patterns of gene expression. But does that mean that maternal care and eusociality are mechanistically related?? They claim yes, and maybe I would too if I too thought that the only thing that made eusociality noteworthy and different than other things was sibling care.. There are a whole shit-load of cooperative breeders... If these genes are associated specifically with eusociality and not just care-giving, then care givers in cooperative systems should be distinct from eusocial care givers..

For me, it seems like this is another example of overstating conclusions.. I'll not deny that it is cool, and that we should be excited about this, but just because the same set of genes seem to regulate maternal care and sibling care does not mean that maternal care is so tightly linked to eusociality- especially in Polistes- a wasp genus that is not all that eusocial. Now I'd be alot more excited if this same study was done in some eusocial Hymenoptera or in mole rats, and if knockout experiments dissolved colony structure...

Basically, if sibling care = eusocialiy, then their conclusions are right on...otherwise, not so much, at least not until more work is done...

Oh hell, what the heck do I know, it got 'em into Science I guess..

____________________________________
Reference,
Toth, et. al., 2007. Wasp Gene Expression Supports an Evolutionary Link Between Maternal Behavior and Eusociality
Science. Vol. 318. no. 5849, pp. 441 - 444
DOI: 10.1126/science.1146647

Sexual vs. social behavior and MHC polymorphism

Following up on my post from a few days ago about the unexpected results looking at MHC polymorphism and mating system- It seems to me that I should make explicit the alternative hypotheses...

So basically there are 4, not-strictly-mutually-exclusive ones that I will test.

1. MHC polymorphism is related to sexual behavior, i.e. mating system. Basically saying that relative to monogamous species, non-monogamous species are at greater risk for contracting infectious disease secondary to frequency and diversity of sexual contacts. It is this risk that nudges up "optimal'" MHC polymorphism and therefore likely enhances polymorphism.


2. MHC polymorphism is related to social behavior. Here we recognize that animals that are frequently in close contact with conspecifics are are at risk for infectious disease as a direct result of tis prolonged social contact. If social behavior is important in generating selection for MHC polymorphism, then more social species are the guys that have greater polymorphism.


3. The environment dictates polymorphism. This is the "old hat" hypothesis. I explicitly test it though using a common garden type of experiment.


4. That all these adaptive hypotheses are junk- and that teh factor most related to current polymorphism is evolutionary history- i.e. phylogeny.

So let me back up another bit and tell you that there are differences in general patterns of social behavior in the animals included in that preliminary analysis. Peromyscus californicus (monogamous) spends a significant portion of its life in close contact with it's mate, and their offspring.

P. maniculatus however, is relatively asocial and usually only contacts other animals within the context of mating.

So given this, and focusing in on the sociality hypothesis, which species will you predict to have the greater polymorphism??

I hope to be able to provide mechanistic support for this finding via collection of ectoparasites from the various species. Greater numbers of ectoparasites on social species might be considered support for the sociality hypothesis. As of right now- I don't have enough info to say...

So maybe it is that although we all think of sex as being a significant contributor to infectious disease risk- that prolonged non-sexual contact is much more risky.....

Hey- at least Im not as nerdy as bug_girl!

She got a whopping 99%!

I'd challenge somebody.. but I only know nerds (wife excluded!)

Southern California Wildfires

I'm sure that some of you have been thinking about how the SoCal fires have affected my field work. I have several sites in San Diego County- most of which are either threatened or already burned. Here is the map. The areas marker by "red plus signs" are locations where I trapped last summer.

Bummer!!! 1st the drought causing extremely low population numbers- now fire...

As you can see- there are 2 places- San Felipe Valley and Warners Pass just to the east of current fires. It's concerning to know that the wind has shifted directions and is now driving the fire east! I bet thought that thee places will not burn- as it is pretty "deserty" and almost completely lacks tall trees and dense vegetation.. We'll see...

Echo Valley was my best place- and it, like many others is dry and has dense vegetation. Let's keep out fingers crossed for this one!

Is MHC polymorphism related to mating system?

So many of you know that this question has been (is) the focus of my dissertation research. (So don't scoop me/steal the idea) Basically I recognize this:


And that because polymorphism at MHC loci is costly, then optimal MHC polymorphsim should vary from species to species, depending on their risk of contracting a pathogen. While the focus has traditionally been on the environment- I focus on something else- behavior, i.e. mating behaviors.

So the basic prediction that follows is that more promiscuous species should have more polymorphism at MHC loci. I am working with Peromyscus sp. which is a nice system for testing these types of hypotheses as there is a lot of mating systems diversity- in fact all "classical mating systems" are represented- save for polyandry/polygynandry.

In the big push for submission of a NSF-DDIG, I have been putting together a multilocus genotype for animals representing the 2 extremes- genetic monogamy and extreme promiscuity. So what does it show:



The opposite pattern relative to the prediction... 1st thought... bummer.... 2nd thought- hey maybe interesting... These are very preliminary data and suffer from low sample size.power issues....

Hopefully tomorrow I can tell you why it's interesting....

See the next installment: HERE

DNA sequencing for 10 year olds...

So I was working on some sequences the other night using ClustalW, the online resource for editing and aligning sequences, when Patrick, my 10 year old come up and asked me what I was doing. He noticed all the interesting colors (as bases are colored in this program), and picked up on some of the obvious patterns.

"What's that" he asks...

Having my science brain on at the moment, I told him that these represented MHC sequences from several different rodent species, and that I was going to develop primers targeting a specific exon....

"Huh".... His predictable response came soon after.

So I started to explain that "genes made your body do things, and this gene helps you fight diseases", but apparently, he has not learned about genes in school yet, as indicated by the blank look on his face... I took a step back.

DNA is a collection of genes, and genes make your body do all the things it does.... DNA is in your cells, all of them (remember the target audience)...

Now we are starting to get some place- shocking though that he has never been introduced to this basic life science material.. He is in 5th grade now. In what grade do they introduce this stuff??

So not to relate the concept of DNA and genes back to what started it all- DNA sequence data. This was hard. I showed him a model of DNA, and pointed out the base pairing.. I explained that there were only 4 types of bases, and that certain bases only paired with certain others.. What the sequence I was working with was a list of these bases..

"So why do some animals have different lists" he asks.. We were using the enzyme amylase as an example. You know, 10 year olds like spit, and to know something about it makes you cool. Additionally, its function is pretty easy to understand, and all (most??) animals have it.. "especially what the gene from different animals makes the same thing", he adds.

Thankfully, it was bedtime, and I was able to dodge the issue of homology, convergence, mutation, drift, and stochastic processes at least for now..

Anyway- for the teachers amongst us... at what grade is DNA/genetics introduced?

Peromyscus Phylogeny

Is there anyone out there working on a genus level phylogeny of Peromyscus?? It is super annoying that a "super-tree" does not exist.... Argh... I need a tree to proceed with several of the most exciting research questions- and not being a phylogeneticist, the prospects of having to build one myself is slightly daunting..

Anyway- to the right is my feeble 1st stab at it. It is a tree using the whole cytochrome B (~1100bp), MrBayes with 5 million reps. Numbers are bootstrap values. As you can see, even with the "pretty variable" gene, there are several places where resolution is sub-optimal.

The parsimony tree showed similar, although not identical topology. The ML tree is complete, and bootstrapping has been in progress for >96 hours (argh....)

Is parasitism a cost of sociality?

Parasitism has long been thought of as a significant cost of sociality- as their transmission is typically density defendant. Basically- as the density of hosts increases (as it does in social species) so does the rate of transmission, which is parasites is equivalent to reproduction. More recently however, the ubiquity of this relationship has been challenged- mostly as studies emerge that fail to find significant correlation between the two variables.

Most recently, a short piece was published in Biology Letters by Bordes et. al., entitled "Rodent sociality and parasite diversity" Here, they put another small nail in the coffin in finding a negative relationship between parasite richness and a measure of sociality. Weird, huh...

They come up with 2 different hypotheses- I'll first give you the one I think is more plausible...

1. That social species have evolved behavioral defenses to mitigate the effect of parasites. Basically here they are thinking about allogrooming and related behaviors. I judge this to be a very likely explanation, especially as grooming is very well documented in many mammalian taxa...
2. This one is a bit more complicated, and has to do with intraspecific competition between parasite species themselves. Basically sociality creates a homogeneous environment (from the perspective of the parasite), co-infection is more likely-- at least initially. This co-infection sets the stage for competition, and thinking of the situation where one species outcompetes the other- a reduction in parasite richness might be the outcome.
   

While the study itself is neat- I think for me the take home message is this: Biology at the level of intraspecific interactions is really really complex- and while theory is great for making broad generalizations- it is absolutely true that as we continue to study specific systems many exceptions will be found to the theory driven rules.

It is exactly for this reason (I feel) that it is important to continue to study animals in the wild... Surely effects exactly like the ones here would have been missed if it were not for good field studies..