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Just a quick round-up of some links. On the same day I wrote about Gerobatrachus hottoni PZ Myers at Pharyngula also posted regarding the transitional amphibian, including a beautiful photograph of the fossil. I also logged in a few days ago to find to my surprise that my recent post on the non-necessity for mice of some genes that are required in humans was included in the Gene Genie blog carnival. This blog carnival covers human genetics, usually focusing on the field of medicine. Medicine is another interest of mine (I skim New England Journal of Medicine and The Lancet weekly), but since this blog is focusing on evolutionary biology I haven’t covered medicine much here, and it hadn’t occurred to me that post would meet inclusion in Gene Genie! You can read the current Gene Genie at Highlight Health. I also read the medicine-themed blogs Denialism and Respectful Insolence, so check those out if medicine interests you.

I checked in on Nature earlier, since a new issue comes out tomorrow, and find that there’s an article combining two favorite topics of mine—malaria and sex ratios. I can only read the abstract from home, so I hope the suspense doesn’t keep me up too late. I anticipate that paper will show up on my blog shortly.


ResearchBlogging.orgA PAPER PUBLISHED recently in Nature details the discovery of a common ancestor of salamanders and frogs, Gerobatrachus hottoni, by Anderson and coworkers. This creature had a salamander-like build, but has a broadened skull like frogs. A variety of traits were studied to determine this organism’s relationships, such as the teeth, various skull bones, presacral spine, and otic notch. Its position in the early Permian places the frog/salamander divergence in the Middle Permian, about 270-260 million years ago. Of course this find is interesting, but I was perhaps more interested by the phylogenetic tree that they composed including this new species.

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ResearchBlogging.orgANIMAL MODELS are widely used in medical research, sometimes in testing new drugs for safety before human trials, other times as model systems for human diseases. Like all mammals, humans and mice share most of their genes, and maintain high sequence similarity. These factors suggest that many of these genes should share the same role. A new study in Proceedings of that National Academy of Sciences examines this hypothesis.

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I HAD PLANNED on covering the article on the platypus genome that came out in Nature last week, but since then this paper has been discussed in detail on Pharyngula and Adaptive Complexity and I think further discussion would be moot. I did notice while reading the paper that the unfortunate description of certain platypus genes as “reptilian” cropped up frequently. Although the authors noted that the sauropsids and synapsids are amniotes, they never mentioned that platypus genes shared with reptiles are actually basal amniote genes. Although their phylogenetic tree shows synapsids and sauropsids clearly diverging from a common amniote ancestor, they do not seem to realize referring to these ancestral amniote genes as “reptilian” suggests evolution of the platypus (and thus all synapsids) from reptiles instead of from a non-reptilian amniote.

However, today I want to talk about the platypus’ sex chromosomes. Platypuses, like the therians, have genetic sex determination. They have an XX/XY system in which males (XY) are the heterogametic sex. Many reptiles have environmental sex determination, with sex determined by factors such as incubation temperature during embryonic development. However, some reptiles and all birds have a ZW/ZZ sex determination system, with females (ZW) as the heterogametic sex.

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LET’S SUPPOSE that we are interested in studying the evolution of the squamates, the snakes and lizards. We know that if we track down the evolutionary tree of the squamates we find that they are lepidosauromorphs, and a sister group to the archosauromorphs. Ah-hah! The archosauromorphs diverged before the evolution of the lizards, so living archosauromorphs must preserve ancestral traits, we think. So we go forth and find an archosauromorph and sequence its genome. There are multiple species from which to choose, but we grab the closest one—the European starling. Since this is an archosauromorph and early diverging compared to the snakes and lizards that must mean that it is “primitive”.

Does this seem odd to you?

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We’ve had a blitz of platypus genome papers this week, with a brand new article on the platypus genome sequence in Nature and several papers on specific aspects of this genome showing up in Genome Research. I hope to cover a couple of these in the next week. It’s been a while since my last update because I’ve been very busy, but I’ll take a look at the platypus genome paper itself tomorrow and hopefully follow-up Sunday or Monday with some of the information from Genome Research.

Of course this discovery has led to more bad reporting, and from reading the news outlet articles it looks like the scientists involved are contributing to some of it! Some of the things they are saying are not wrong, but possibly misleading. I’ll go into that a little bit tomorrow. For now let’s say I keep seeing the word “primitive”, and the New York Times refers to monotremes as “offshoots of the main mammalian lineage”. Well, I personally think the placentals and marsupials are branches off that most noble main mammalian lineage, the sadly extinct multituberculates.

ResearchBlogging.orgTHE MICROVIRUSES are positive-strand DNA viruses with very small genomes, typified by ΦX174 with 5,400 base pairs and nine genes. Cramming this many genes into that short a sequence requires overlapping reading frames, with gene B contained inside gene A, and gene E contained inside gene D.1 These nested genes are frame-shifted compared to the gene that contains them.

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