Carnival of Evolution #20!

Welcome to Carnival of Evolution #20!
The time has come to analyse and describe the environmental samples that piled up in my inbox throughout the month, kindly donated by my esteemed colleagues. Some of the samples were clearly inorganic matter pretending to be evolution-related, and thus had to be discarded (sorry, but we are trying to stay on topic here...), but the rest of it consists of some intriguing and exciting posts organisms.

Sequence data was extracted using the Copy+Paste Protocol (CPP) devised by [citation forgotten], and then analysed in a sophisticated combination of Notepad, MS Word and Mesquite. My first analysis involved the URLs of the submissions, as they seemed to be at least somewhat conserved. Since this was my first time actually building a tree from scratch (cell biologist here), and since I'm just learning about NNJ, SPR, treelength, maximum parsimony, etc in phylo class, my data is obviously very reliable and makes sense. Clearly, I should now go ahead and reconstruct the history of life, the universe and everything. Without further ado, here are the latest Nature-worthy phylogenies:

MY FIRST PHYLOGENIES EVER! ^_^ Left: Colours mark submissions from the same blog: Yellow - Phylogenomics, Blue - Grrlscientist's blog, Green - Evolving Mind, Red - Pleiotropy. Oh and a clade I missed: (sea-slugs,hi-resolution-evolution) - Adaptive Complexity. Right: Second analysis, a consensus tree of the post 'content' sequences. See text. Blue - omg, a clade! =D With support of... 0.52. Whatever that means, exactly -- doesn't feel too comfy though.
(Blog URL 'sequences' converted to a protein character matrix (fig. S1), gaps removed and tree found via SPR searching for minimum treelength in Mesquite (Maddison WP & Maddison DR 2009)

So Bjørn Østman apparently has a paraphyletic blog. Learn something new every day...

But one gene is never enough, so I went ahead and PCR'd some of the post contents. EVOLUTION was used as primer, and the 40 letters (including gaps) following the first instance of the primer were used in the alignment matrix. No proper alignment was actually done as the data was utterly random, and the non-existant grant did not provide for any extra work. In a couple cases, no instances of EVOLUTION were found, so other primers were picked completely at random. Ignorant and unskilled parsimony-based tree reconstruction was used haphazardly, revealing a rather large clade (fig. 1, right; in blue) that clearly has long reaching scientific significance.

Post Taxonomy
Now that we have a couple utterly nonsensical curious phylogenies, we must sketch a basic taxonomy before we proceed to species descriptions. I will act as an old-fashioned traditional taxonomist and completely and utterly ignore phylogeny in my classification scheme altogether.

So, Cavalier-Smith style: (Note: not approved by ICZN/ICBN, yet)
KINGDOM Evolutionary Biology

INFRAKINGDOM Animal Evolution
SUPERPHYLUM Non-Mammalian Evolution
SUPERPHYLUM Mammalian Evolution
Microphylum Human Evolution

INFRAKINGDOM General Evolution Topics
SUBKINGDOM Genomics
SUBKINGDOM Selection
Phylum Cooperation
Phylum Group Selection
Phylum Evolvability
SUBKINGDOM Symbiosis

KINGDOM Science Communication

PHYLUM Combatting Creationism
PHYLUM Public Education of Evolution

Note: Only some of these will actually be used... I really don't care for ranked taxonomy.

And in case it's not obvious, I am not actually an evolutionary/phylogenetic/systematic biologist. I colour cell structure with GFP and stare at them all day. Also, I pour microtubule-disrupting drugs on my plants and wonder how they die so quickly. So apologies if you're a real phylogenetic biologist/taxonomist and the above made your eyes bleed =P

The Carnival
Let's now describe and analyse our 'samples'.

Since spring shall be on its way eventually soon, we've got cryptochromes and the biology of monarch butterly migration patterns. Turns out that monarchs can actually 'see' the earth's magnetic field! Speaking of which, Grrlscientist also talks about how egg predation has driven the evolution of bird migration patterns. Furthermore, it turns out that colourful feather colouration may be used as an indicator of the male Tit's ability to resist oxidative stress due to increased carotenoid uptake and secretion, in Grrlscientist's "Colourful tits produce speedier sperm". Still on the topic of birds, the Pacific Dunlin employs a weight loss strategy not for cosmetic purposes but rather to avoid predation by Peregrine Falcons, while over on the Galapagos some Darwins finches have developed an immune response to the pox virus while their neighbours on a nearby island have not.

Meanwhile over at Observations of a Nerd we've got a discussion of dog evolution, including a case of stray dogs of [my native] Moscow learning how to navigate our rather elaborate subway system! Furthermore, they've adapted well to coexist with humans, and even keep out the wilder strays from the outskirts, earning some favours from the local politicians. Another wonderful illustration of the power of natural selection! (which, we must remind ourselves, is not the only driver of evolution...) Heading over to coastal wetlands, we've got a post on Terrapin evolution and their adaptations to brackish seawater.

We have a critical discussion of brain size vs. body mass, the evolution of the two, and why one must be careful to note whether the brain size decreased along with body size (retaining proportion), or on its own. The story of Homo florensiensis and brain size evolution depends on which H.erectus ancestor it descended from. In another post on human evolution, we have a discussion about human uniqueness and whether rank insubordination may be something we're particularly good at.

What do the unicellular Hacrobian Hatena and the multicellular photosynthetic sea slug have in common? They are both partners in crime, engaging in kleptoplasty (plastid theft from algae). Furthermore, the sea slug has been found to acquire some plastid genes through lateral gene transfer through viruses! Speaking of genetic evolution, turns out the Y chromosome has a much higher evolutionary rate than other human chromosomes, and David Winter ponders why that may be. Now that we have the tools to fairly cheaply trace evolution and variation on the level of genes, there's been work done on stickleback skeletal evolution showing how they have on several separate occasions happened upon very similar genetic solutions to pelvic reduction.

Another major event recently has been the publication of the first batch of Genomic Encyclopedia of Bacteria and Archaea(GEBA) genomes, featuring a rather awesome tree. Then, we have an interview by Jonathan Eisen of several cichlid researchers about behind-the-scenespublication stories of their research.

Bjørn has found a couple interesting group selection lectures, alluding that perhaps the controversy around it is far too hyped up. (personally, I've avoided the topic altogether because of how polarised it is...) We also have altruism and helpful chimps, suggesting that helping out upon request may well not be limited to humans. We also have a couple posts on the subject of evolvability -- bacteria 'hedging bets'; and mutational robustness not necessarily being a hinderance to the organism's ability to adapt to changing environments, but in fact may even help promote it.

Lastly, we've got some posts on communicating evolution and fighting creationists. Quite shockingly, Texas is still fighting reason and good sense. Who'dathunk? And how can creationists get so fixated on evolution when developmental biology is similarly complex and 'unlikely', as Bjørn points out. All is not well in undergraduate education (I can testify...), and we need to note the frustrations resulting from some major issues with the way it's run, including underfunding and worst of all, students who are ill-prepared from highschool and generally not too curious about topics like evolution (failed by their past education), discussed by an instructor about to approach an into biol course (good luck!).

Sadly, even some proponents of our own side are guilty of miscommunication and outright errors. Dawkins can get so caught up in being defensive about evolution that he misuses words like 'proof' and 'fact', being a little too emphatic for good scientific taste. Evolution is not a 'fact', it's currently the best explanation we have for explaining, well, all of biology, and I'd argue the only framework currently seriously worth considering, by far. Fundamentalists have the facts and certainty, we've given up such luxuries in pursuit of better understanding.

Luckily, we have protists to the rescue. A JEM paper by Mark Farmer and Andrea Habura points out how thoroughly wrong some of the protist-related anti-evolution 'proofs' are. Furthermore, protists have are a wonderland of good examples for supporting and teaching evolution -- unicellular organisms are easier to analyse in large sample sizes, easier to illustrate some points with, and also more familiar to our eukaryotic biases than bacteria. Not to mention really hawt and sexy. To quote something I wrote elsewhere: 'not only should protists be used to ward off some creationist claims, but also to teach biology undergrads, and to promote public interest in biology overall. Sure cancer has its place, but I, perhaps naively, believe that at least some of the public has a latent, untapped fascination with just how weird biology can be. Creationists are far from the first of our concerns -- adressing misinformed biology students and the scientifically-curious public should be a top priority!'

Since you're currently standing on protistophile territory, I'd like to welcome those of you who have sadly been deprived of the wonderful world that is concealed within ~99% of eukaryotic diversity. Furthermore, I think it would be effective to approach some of the aforementioned problems (creationists, but much more importantly, undergrad biology students) by employing some of those wonderful stories, rather than ignoring them for the sake of memorising the insulin pathway MAP kinase cascades. I believe protists (and prokaryotes; basically, a thorough appreciation of diversity) can not only teach a lot about evolution and organismal biology, but also stretch the limits of our wildest imaginations. And that is my main purpose here, which I hope to at least somewhat attain from time to time, despite still just learning about both science writing and protistology (and the rest). All life is wonderful, and it is truly a shame that we tend to ignore the vast majority of it.


In case there's any glaring blatant errors, or if I completely misrepresented your post -- it's 4.30am, I'm getting tired, and stuff happens. But please let me know anyway!

The next Carnival of Evolution (#21) will be hosted on Mauka to Makai; you should go check it out to get ready for the next open season on evolution blogging! Speaking of open season, it's never too early to submit your February posts to the next Carnival of Evolution using this form. Take care and hope to see you around again!

Supplementary Data
Fig S1:

Submitted posts' URL sequences. So pretty!