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ResearchBlogging.orgTHERE ARE certain niches that seem to be filled by one species or another at any time period. In my recent post on mammalian evolution, for instance, I mentioned Castorocauda, a Jurassic mammaliform that seems to have fit into the niche now occupied by beavers or otters. But occasionally we run across an animal that seems to be adapted for a unique role in its ecosystem. One of these animals is Simocyon. This is a puma-sized caniform that lived about 14 million years ago, and died out by four million years ago. Simocyon has a variety of unusual adaptations.

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I published a post yesterday on T. Ryan Gregory’s article “Understanding Evolutionary Trees”, but failed to make the connection that the T. Ryan Gregory who wrote that article is the same T. Ryan Gregory over at Genomicron! Genomicron has been on my blogroll since I started blogging seriously here, and is a must-read for anyone interested in evolution, especially the genetic aspects of it.

ResearchBlogging.orgEVOLUTIONARY TREES will show up fairly frequently here, and are also frequently misunderstood, so I will present a summary of Gregory’s excellent article “Understanding Evolutionary Trees“. I strongly suggest reading it (free full text!) because while I have shown a few of his cladograms he has many more in the paper and goes into much more detail regarding common misunderstandings about evolutionary trees. Some of these misunderstandings are related to the way we tend to think about evolution, some are due to unfamiliarity, and others are learned from obsolete presentations of the process of evolution. Even people who are familiar with evolution may need to pause once in a while and think “Is that a correct interpretation?” when looking at evolutionary trees.

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ALL SABER-TOOTH and big cat fans should step over to Tetrapod Zoology, where Darren Naish reports on the Big Cats in Britain conference. The first part of this two-part survey discusses the possible late survival of Homotherium latidens, a saber-toothed cat, as well as extinct leopards and lions. The second talks about extinct pumas in Europe and cheetahs in America, geographical distributions that we are not accustomed to for these cats.

THIS WEEK I’ve been covering some interesting instances of new gene evolution. The one I’m covering today is hard to boil down into a short title. This is a case of a new gene in hominoids as the result of retrotransposition of an aberrant mRNA transcript. Transposons showed up in the last post as well, but here they play a different role. That example involved a class II transposon, a segment of DNA that can jump around the genome. This case involves a class I transposon, a retrotransposon that transcribes itself into RNA, then copies that transcript back into DNA, and inserts it elsewhere in the genome. Here the retrotransposon accidentally retrotransposed a gene transcript instead of a retrotransposon transcript. This is not an especially rare event, but this case is unusual because the transcript itself is unusual.

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I COVERED on Monday the birth of two new genes via an intragenic inversion, today I will look at a new gene from capture of a gene from a mobile element. The product is a gene found in Old and New World monkeys and apes, but not in prosimians.

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In a narrow escape, we evaded catastrophe today when fellow blogger Xeno discovered a giant chicken egg did not contain either a mutated chick intent on razing Tokyo or a parasitic alien, but a second normal chicken egg! Sci-fi fans everywhere breathe a sigh of relief.

After my post yesterday I decided to do a few more entries on the unusual routes that have produced new genes. In the first example an intragenic inversion produced two new genes, tomorrow I will talk about a chimeric gene from capture of a gene from a mobile element, and then Thursday aberrant splicing in a fortuitous transcript of two adjacent genes followed by reverse transcription to insert the new gene into the genome. I don’t know about you, but my pulse goes up at least 5 bpm just thinking about it!

I MENTIONED BEFORE the IAD model for gene synthesis–innovation in a gene producing a new secondary function, amplification of that gene by duplication, and divergence of the gene copies. However, sometimes things can happen more suddenly. In 2002 studies of a pond snail reveal the generation of two new genes by duplication of an ancestral gene, and then a intragenic inversion converting one duplicate into two new genes!

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ORIGINALLY PEOPLE thought that the long canines of saber-toothed cats were intended to pierce the thick skin of mammoths and were used to inflict gaping wounds. However, recent modeling suggests that repeated biting of struggling prey would result in breaking the saber-cats’ teeth, and that the fangs were used in a single neck bite on pinned prey, severing major blood vessels and quickly resulting in death.1 As the other two major groups of saber-tooth carnivores, Nimravidae and Barbourofelidae, have been extinct for millions of years, we will probably have to determine their diet based upon deduction. Fortunately the saber-toothed felids have been extinct for only tens of thousands of years, which is practically yesterday! We have some evidence of their diet in a cave that served as den for Homotherium and in the bones of Smilodon preserved in the La Brea tar pits.

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IN THE PAST few years there has been some acrimony regarding the division of the protostomes into Lophotrochozoa and Ecdysozoa. This decision split the annelids and the arthropods, and placed nematodes in with the arthropods. At its first proposal support for this tree was weak, but successive discoveries have strengthened it. Now the most detailed tree yet confirms this division, and clarifies other relationships.

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