A few weeks ago I happened to listen to a fascinating interview on NPR with Brian Switek, the blogger behind Laelaps, and author of Written in Stone: Evolution, the Fossil Record, and Our Place in Nature. Switek was discussing his newest book, My Beloved Brontosaurus: On the Road with Old Bones, New Science, and Our Favorite Dinosaurs. To be frank I was captivated by the discussion, and immediately purchased a copy of the book. The reason is simple: despite our current divergent interests Brian Switek began at the same place I did, with dinosaurs. Though after reading My Beloved Brontosaurus I can’t assert that my dinomania matched Switek’s, it was of the same quality. The difference is that while Switek remained true to dinosaurs, my own interests wandered into other domains. Today I am focused more upon evolutionary forces operating on the scale of thousands of years within a species, rather than geological scale transmogrifications. But every now and then I wonder about dinosaurs, and whatever happened to them over the past 20 years after my “dinosaurs years” faded into the distance.
By this time I’m sure you’ve encountered articles about the reconstructed last common ancestor of all placental mammals. Greg Mayer at Why Evolution is True has an excellent review of the implications, along with a link to a moderately skeptical piece by Anne Yoder in Science. Yoder’s piece is titled Fossils vs. Clocks, while the original paper is The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals. The results clearly support the “Explosive Model” in the figure to the left for the origination of placentals. That might prompt the thought: “isn’t this what we knew all along?”
The standard story for the last generation in the popular imagination is that a massive asteroid impact was the direct cause of the extinction of all dinosaurs (and of course a host of other groups) except the lineage which we now term birds. And yet it turns out that there is actually some debate about this, though at least in some form it seems likely that the impact is going to be important (see this Brian Switek piece for exploration of this issue, and the general opinion of the scientific literature as of now). The second aspect to focus on is timing. Contrary to the intuition of many, over the past 20 years molecular phylogenetics has inferred a very definite (on the order of tens of millions of years) pre-K-T boundary coalescence for the common ancestors of the disinct mammalian lineages. A plausible explanation for this is that these lineages diversified through allopatry, as the Mesozoic supercontinent fragmented. Morphological diversification of these mammalian lineages also may have occurred after the K-T event.
Kennewick Man produced a cottage industry of journalism ~10 years ago, thanks to the political controversy around the science. Today the stakes are different. Consider this from John Hawks, “Agriculture, population expansion and mtDNA variation”:
I am less sanguine about their results for Europe. They show a gradual period of growth associated in time with the Younger Dryas (around 12,000 years ago), which could make sense in the archaeology. But I am not convinced that the “European” haplogroups here are really European to that time depth. We know that the Neolithic and post-Neolithic saw some large-scale shifts in the frequencies of mtDNA haplogroups in Central and Western Europe. Some Upper Paleolithic Europeans probably contributed mtDNA to this later population, but I have no confidence that the proportion was great enough to accurately infer the demography of that pre-Neolithic population. (This is also a problem with the current paper in Current Anthropology by Peter Rowley-Conwy. I’ll discuss this sometime soon.)
The next frontier in reconstructing the population history of Europe will be ancient DNA. A good sample of Neolithic and pre-Neolithic whole mtDNA genomes would settle this question and allow inferences about the kind of demographic recovery Europe underwent after the Last Glacial Maximum….
An open letter to Science highlights the same issue with Native Americans, Unexamined Bodies of Evidence:
There was a reference to complex pre-Cambrian life in a book I’m reading, Kraken, and it made me double-check Wikipedia’s Cambrian explosion entry. Lacking total clarity, I decided to read a new paper which was published in Nature, Earth’s earliest non-marine eukaryotes. The Cambrian explosion is pegged to ~500 million years ago, but these data indicate a freshwater ecosystem which predates ~1 billion years before the present. Also, there was weird stuff in the discussion which startled me:
…Early eukaryotes were clearly capable of diversifying within non-marine habitats, not just in marine settings as has been generally assumed. This idea directly supports phylogenomic studies which find that the cyanobacteria evolved first in freshwater habitats and later migrated into marine settings….
Cyanobacteria are the ubiquitous blue-green algae which were’t familiar with. New Scientist has some quotes from paleontologists who seem to think that this paper is credible. There’s a good and a bad to this. The good, I’ll have to read up on this area which I’m so fuzzy about in terms of details. The bad is that it slices my finite time pie even more.
I was thinking a bit about H. floresiensis today. Probably my thoughts were triggered by John Hawks’ post on the propensity for paleontologists to be “splitters,” naming new finds as species when they’re not. The issue with H. floresiensis is a little more cut & dried: if they weren’t a separate species they were obviously pathological. The original paper on the Flores hobbits came out in 2004. Is it too much to ask for a little clarity here six years on? Carl Zimmer has covered this story in depth before, so perhaps he’ll have some insights or inside sources who can shed some light at some point in the near future. John Hawks was sure that the specimens were pathological in the early days, but he hasn’t said much for a bit now. And from what I hear there are new controversies about “Ardi”. I was at a talk years ago where Tim White played up the importance of fossils as the final word, as opposed to the more indirect inferential methods of statistical genetics, but this is getting ridiculous. After the Neandertal admixture paper and the Denisova hominin, genomic inferences are looking pretty good. I assume there’s more coming in the near future (though Svante Pääbo may have kidnapped family members of people working in his lab to gain leverage, so word probably won’t start leaking until a few weeks before the paper breaks). Ötzi the Iceman is going to have his genome published next year.
With all that as preamble, here’s a new paper, Post-Cranial Skeletons of Hypothyroid Cretins Show a Similar Anatomical Mosaic as Homo floresiensis. It’s in PLoS ONE, so read it yourself. Does anyone care? I don’t know enough about about anatomy and osteology to make well-informed judgments about these sorts of things, so to the experts I absolutely defer. But frankly some of the experts strike me jokers. Here’s the problem: I don’t know who the jokers are!
I just went back and reread some of the press when the hobbit finds were revealed. New member of the human family tree! Evolution rewritten! And so forth. If H. floresiensis turns out to be pathological, I don’t know what to think about paleontology. More honestly, I might start slotting the discipline in with social psychology or macroeconomic modeling.
Though I don’t blog about the topic with the breadth and depth of individuals such as Brian Switek or Darren Naish I do take some interest in natural history. This is the domain which was my original focus as a child when it came to science, and I continue to observe it from afar with great fondness. General questions, such as the role of contingency and necessity in the arc of evolution, are obviously the sort of issue which natural history can be brought to bear upon. But I also have a fascination with specific, often anomalous details. For example, the Monito del Monte of Chile is generally held to be more closely related to the marsupials of Australia than those of the New World. It is the only extant member of the order Microbiotheria, and its connection to Australian marsupials is one of those surprises which go to show you why science is done in the field, and not just theorized from your a priori beliefs. It’s why you play the game, and don’t simply allow the handicapping professionals to decide wins and losses.
A new paper in PLoS Biology explores the phylogenetic relationship of Australian and New World marsupials through a more robust genomically focused technique. Though the method has a “in silico” spin, the basics seem to be grounded in cladistics. Look for derived characters which can indicate monophyly. Monophyly simply means that all of a set of organisms descend from one common ancestor. So, famously, the class of reptiles is not monophyletic. Some of the descendants of the common ancestors of all reptiles are not included within the class, birds. Earlier generations of taxonomists tended to classify organisms based on their characters, and the set of characters which they chose for reptiles included groups, such as crocodiles and tortoises, which were genetically very distant (when compared to crocodiles and birds). Though anatomically informative, these sorts of taxonomic classifications misled one as to evolutionary history. Not a minor matter. Ergo, the rise of cladistic techniques which replaced intuition with a more formal hypothetico-deductive framework. Because of its generality as a method naturally you can substitute genetic loci for morphological character traits, and so you get papers such as the one below.