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Posts Tagged ‘genetics’

Are you a fan of criticizing evolutionary psychology? Grab some popcorn, folks, because there has been some criticizing and counter-criticizing going on that you may find entertaining! In most cases, it’s actually serious, well-reasoned debate, too (as long, I assume, as you don’t read the comments). Things began with Rebecca Watson‘s talk about pop evo psych at a skeptic conference, which was…I won’t say “debunked”, but countered, by evolutionary psychologist Edward Clint. This has sparked some dialogue, primarily on Freethought Blogs, about evolutionary psychology as a whole field and about the media coverage of the science (or, often, “science”) of gender differences. I present the (interesting parts of the) conversation so far in chronological order (perhaps I’m missing some contributions from blogs I don’t regularly read, so additions in the comments are welcome; also please note that I’m interested in collecting links that discuss the science or lack thereof involved, NOT those discussing What Rebecca Watson Really Meant):

Edward Clint’s response to Watson’s talk (the latter is embedded here and at the first Almost Diamonds link below)

Justin Griffith’s take on the above

Stephanie Zvan’s rebuttal of Edward Clint’s post

Tangential to the debate per se, Zvan also documents the gleeful response from the section of the internet that reflexively detests Watson

Zvan’s counterarguments, continued

PZ Myers begins a series critiquing evo psych

Clint’s response to criticism (this, and some other posts linked within, is more about tone and whether people are misinterpreting what other people said/wrote, which I consider not popcorn-worthy because I want to read about science)

Jerry Coyne discusses the field

Part II of Myers’s critique (and apparently more parts are planned)

UPDATE:

Myers, part III

Greg Laden’s take

Shall I write up my own contribution here? Perhaps if I run out of popcorn.

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New species and weird scientific name news that has found its way to my browser over the past few months. Enjoy.

Pictures of tropical fish that will BLOW YOUR MIND. New and non-new species.

Potential cryptic species of sharks

Giant extinct turtle

Random Wikipedia browsing reveals that there is at least one species (a spider) named for Cthulhu

More cryptic species, in this case of skinks

The Taxonomic Name Resolution Service – searchable record of plant scientific names, including all documented synonyms – important for those describing new species, as well as for those trying to find historical research on species whose names have changed

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I promised more about Wolbachia, and here it is. Quick recap: Wolbachia is a type of bacteria that lives within the cells of many insects and other arthropod species.

Wolbachia has all sorts of possible effects ranging from parasitism to symbiosis. Anopheles mosquitoes, the bugs that carry malaria and thus kill hundreds of thousands of people every year, are naturally uninfected with Wolbachia, but scientists have been investigating ways to introduce Wolbachia into them so as to prevent malaria transmission. One recent study found that, in addition to suppressing malaria transmission by mosquitoes, a certain strain of Wolbachia killed many of the infected mosquitoes, but only after they had had a blood meal.

Now, the pathogen literature is not something I normally read; I stumbled across this research on a science fiction blog. This article I’ve linked to takes a rather cute approach to this study by suggesting that it could be used to kill vampires in the event that they begin to plague the human race. Commenters on that article raised the spectre of unintended side-effects of infecting people with Wolbachia. Well, commenters, here is what you (thought you) wanted to know:

Imagine you’re a Wolbachia cell. You’re inside the cell of an insect, say a mosquito. That mosquito spreads you (and your descendents) to other mosquitoes not by biting them or sneezing on them, but by reproducing: since you’re already inside the mosquito’s cells, you just get packaged into their baby-making cells. Well, not necessarily—if you’re in a male mosquito, you’re screwed, because you just won’t fit into a tiny little mosquito sperm. If you’re in a female mosquito, though, you’re in luck (that’s right, you’re maternally inherited). But you’re a clever Wolbachia and you’re thinking not just of your kids, but of your grandkids (which will all also be your clones because you’re a bacterium!). You don’t want any of your descendents to end up in male mosquitoes. What can you do to prevent this? Let’s brainstorm:

  • kill all the male offspring of the female you’re infecting
  • turn the male offspring into functional females
  • make your host into a parthenogen, i.e. make her reproduce asexually!

Guess what! Wolbachia can do all of the above! SF writers, have at it.

Hughes, G., Koga, R., Xue, P., Fukatsu, T., & Rasgon, J. (2011). Wolbachia Infections Are Virulent and Inhibit the Human Malaria Parasite Plasmodium Falciparum in Anopheles Gambiae PLoS Pathogens, 7 (5) DOI: 10.1371/journal.ppat.1002043

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ResearchBlogging.orgThe search for new species brings scientists to places as near as their lab bench and as distant as the Antarctic. They may be looking for traces of species long extinct or sightings of contemporary rarities. But one new study has found evidence for the existence of an unknown organism by looking at the DNA of another species.

Drosophila quinaria, a type of fruit fly, is well known to scientists. But in the course of studying its DNA, and the prevalence of a parasitic bacterium, researchers found evidence that, sometime in the past, D. quinaria hybridized with another fruit fly species unknown to science.

This evidence comes from a comparison of nuclear and mitonchondrial DNA. Here’s where I need to back up and explain some background genetics:

Mitochondria are the parts of the cell that produce,┬áin an intricate series of chemical reactions, the energy needed for all our biological functions. They are fascinating structures for many reasons, but particularly because they contain their own DNA (usually abbreviated as mtDNA). What you probably think of as the human genome—two copies of each chromosome (apart from the sex chromosomes), one inherited from from each parent—lives in a part of the cell called the nucleus. mtDNA comes in a single copy and is only inherited from the mother, largely because egg cells are so much bigger than sperm and thus contribute all of the non-nuclear component of the cell.

Mitochondrial DNA has another interesting property: it doesn’t recombine. That is, if two mutations arise in the same mitochondrial genome, they’ll stay together in their descendents, while two mutations in the same nuclear genome won’t necessarily both end up in the offspring. This makes it easier to trace the evolutionary history of a mitochondrial genome than of an entire nuclear genome.

Back to the fruit flies: researchers found two main types of mtDNA in Drosophila quinaria. This is not particularly unusual. What was unexpected was just how different the two mtDNA types were. Not only were they as different as one might expect when looking at two different, though related, species, they were just as different from all of D. quinaria‘s closest relatives (data were unavailable for a handful of rare species). Despite this huge gulf, all the flies, regardless of mtDNA type, had similar nuclear DNA, indicating that they are indeed members of the same species.

What could be the cause of this pattern? It’s not unheard of for hybridization—ancient or recent—to allow a species to pick up the mitochondrial genome of another. But the fact that the mystery mtDNA was not particularly closely related to that of any known fruit flies suggests that the species D. quinaria hybridized with is either undiscovered or no longer existent.

Strange, no? It’s about to get stranger. What allowed the mtDNA of another species to creep into D. quinaria‘s genome and stay there? It may well have been a versatile bacterium called Wolbachia. This bug lives inside the cells of many insects and their ilk, with variable and sometimes sinister effects (more on which another day). Since it lives inside cells, but not in the nucleus, it is transmitted across generations just like mitochondria. Some, but not all, populations of D. quinaria host Wolbachia, and one of the populations in this study actually has a mix of infected and uninfected flies. And lo and behold, whether an individual fly has Wolbachia predicts almost perfectly which mtDNA group it belongs to (the single exception could mean that the occasional fly is “cured” of its infection). Wolbachia sometimes helps protect its host from viral infections, so maybe D. quinaria acquired it by hybridization (not at all unusual among flies), along with some mtDNA, and kept it because of these effects.

This fascinating study is probably not grounds for describing a new species, but if the unknown Drosophila is not extinct, we’ll be able to recognize it, and we’ll have an exciting new system for studying hybridization, the effects of Wolbachia, and possibly the genetics of speciation.

DYER, K., BURKE, C., & JAENIKE, J. (2011). Wolbachia-mediated persistence of mtDNA from a potentially extinct species Molecular Ecology DOI: 10.1111/j.1365-294X.2011.05128.x

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ResearchBlogging.org
The title of this post is a reference to this paper (only the first page is available for free, but only the first two paragraphs are relevent) and to a Stephen Jay Gould essay. Both address the question of whether the group of animals corresponding to a colloquial name is actually an evolutionary entity, a monophyletic group—meaning they are all the descendents of a single common ancestor, and all the descendents of that ancestor are included in the group. As you’ll soon see, the answer in the case of beavers is yes.

The question of where in the family tree of rodents the two extant beaver species should be placed has been an open question for some time. A recent paper in PLoS ONE sheds further light on the answer. By comparing the complete mitochondrial* genomes of both North American (Castor canadensis) and Eurasian (Castor fiber) beavers to those of other rodents, the authors determined that

  • beavers are a monophyletic group within the “mouse-related” rodents
  • of the other species used to build the evolutionary tree, beavers are most closely related to a type of flying squirrel called the scaly-tailed squirrel (genus Anomalurus)
  • the rodents may or may not be monophyletic; the glires (rodents plus lagomorphs, i.e. rabbits and their kin) are

Having complete mitochondrial genomes allowed the authors to do some other interesting things. First, they were able to calculate the substitution rate—how many base pairs of DNA are likely to mutate, by chance, every million years. This rate could be considered a proxy for the rate of evolutionary change in the species as a whole. Conversely, if we know this rate for some species, we can use it to estimate the age of other related species. This study found that in beavers, the substitution rate is much lower than in other rodents, possibly because they’re much longer lived. (Think about it: all rodents might have the same substitution rate per generation, but if beavers live much longer, they’ll have fewer generations in a given time period and thus fewer total substitutions than a shorter lived species. It would be interesting to see if the substitution rate is also low in the capybara, the largest living rodent.)

With substitution rates for many different kinds of rodents, the authors were also able to date the origin of the rodent order (with the assumption that they’re monophyletic). The data, 67 million years ago, fits rather nicely among other published estimates of the age of rodents and conveniently falls right around the great extinction at the end of the Cretaceous—i.e. the end of the dinosaurs. It’s only a correlation, but it’s fun to think of the end of the dinosaurs allowing rodents—the most speciose group of mammals—to take over the world.

Finally, the authors note that the closest living relative of the beavers is still not known. Although they’re most closely related to Anomalurus in this study, there was no complete mitochondrial genome available for the pocket gophers and kangaroo rats, which have also been proposed as close relatives of the beaver. And, of course, the fossil beavers—there are quite a few, including some truly massive species—aren’t represented in this study. Still, it seems likely that they will fall on the same branch of the evolutionary tree of their similar-looking (but much smaller!) modern relatives.

*The mitochondria are parts of cells that generate energy from food. They have their own DNA, separate from the 46 chromosomes that we more commonly call the human genome. The mitochondrial genome has some interesting properties, including the fact that it’s only transmitted matrilineally.
Horn, S., Durka, W., Wolf, R., Ermala, A., Stubbe, A., Stubbe, M., & Hofreiter, M. (2011). Mitochondrial Genomes Reveal Slow Rates of Molecular Evolution and the Timing of Speciation in Beavers (Castor), One of the Largest Rodent Species PLoS ONE, 6 (1) DOI: 10.1371/journal.pone.0014622

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I started this blog in part to get myself to write more in a setting that’s different from scientific writing I do nearly every day (or try to). This month, I’m going to try my hand at research blogging. I hope to write at least four posts reporting on peer-reviewed research in ecology, genetics, and/or evolutionary biology published recently in open-access journals.

First up, a short and sweet study of the genetics of asexual reproduction. It attracted my attention because I’m currently TAing a basic genetics course, and I had been telling my students how rarely anyone does classical breeding experiments anymore!

(more…)

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