Tis the season for top 10 lists, and since I’ve been spending much of the past several months getting caught up on the current state of evolutionary biology, I thought I’d take a stab at producing such a list.  As I did so, some rough guidelines were

  1. The list is derived first and foremost from the peer reviewed literature of 2011
  2. A secondary concern is the extent to which reports in the literature were covered in the world of science journalism.
  3. The list does not include developments regarding the popular acceptance or rejection of evolutionary science.  To do so would take it out of the realm of established science (wherein I have a few qualifications) and into the domains of theology and belief (where I do not).

Finally, I did ask a few of my friends from the world of science for a few suggestions.  That generated one surprise, which is noted below.

So here goes:

  1. Neanderthals, Denisovans, and Modern Humans.  This story has been emerging for the past few years, involving the sequencing of the Neanderthal genome by Svante Paabo and colleagues, as well as their genetic analysis of the Denisovan thumb from Siberia, showing the existence of yet another homonid species that was contemporaneous with Homo sapiens.  The two major stories that put this at the top of the list for 2011 are the demonstration by Abi-Rached et al. that immune system genes from both Neanderthal and Denisovan man have introgressed into the genome of Homo sapiens, and the demonstration of extensive gene flow from Denisovans into modern man by Reich et al.
  2. Deciphering the Cambrian.  As all students of evolutionary history know, the sudden appearance of animals with backbones (indeed all of the biletaria) in the fossil record durning the Cambrian vexed Charles Darwin (and many others) tremendously.  This year saw two fascinating new developments, as well as a reasoned synthesis of where we stand in our understanding.  First, Paterson et al. provided evidence regarding the origin of compound eyes, showing that Anomalocaris, a stem group to the Arthropods, possessed compound eyes with over 16,000 facets.  Then, in a story that has received much attention (and is the subject of another post) Huldtgren et al. argue that early Edicaran fossils thought previously  to be developing animal embryos are in fact encysting protists.  Finally, Doug Erwin and colleagues gave us an outstanding overview of where we stand vis-a-vis the fossil record and the molecular clock, and provided an intriguing hypothesis regarding the role of micro-RNA’s in bilaterian evolution.
  3. Australophithecus sebida  An unreconstructed fly geneticist like me ventures into the world of human origins at his peril.  However, Science saw fit to highlight the work of Lee Berger and colleagues, who make the case that Australopithecus sediba is in fact a lineal ancestor of Homo sapiens.  Given the norms in physical anthropology, it is safe to say that we haven’t heard the last of this.
  4. The genome of the black plague  I may have missed things from the world of microbial evolution, but this one does stand out.  By sequencing the genome of plague bacteria recovered from remains of victims from the 1300’s, Bos et al. were able to show that the causative strain lies at the base of the phylogenetic tree of modern Yersinia pestis, both confirming that bacterium’s role as the causative agent of the medieval plague and suggesting that it is indeed ancestral to all modern strains.
  5. The human brain, the genome and repetitive DNA  Those of us who were trained in another era either did not learn about mobile and/or repetitive DNA or thought about it as an annoying distraction from the real meat of genetics (Barbara McClintock’s use of the term “controlling elements” notwithstanding).  We now know better.  Mark Batzer and his associates have continued their groundbreaking work on transposable elements in primates, showing that in fact nearly 2/3 of the human genome is transposon-related, my old friend John McDonald and his colleagues have provided evidence that the insertion and deletion of transposons has played an important role in the divergence of humans and chimpanzees, and Baillie et al. showed that somatic transposition of retroposons plays an important role in normal and abnormal brain function.
  6. Fine-tuning the end-Permian mass extinction  In my mind, the end-Permian mass extinction is one of the most fascinating events in evolutionary history, right up there with the Cambrian explosion.  As Doug Erwin argued in his wonderful 2008 book, it defies simple explanation (unlike the Cretaceous/Tertiary event).  Shen et al. have now narrowed the timing of the extinction to a period of less than 200,000 years and have shown conclusively that it occurred simultaneously in the terrestrial and marine worlds.  Their data are consistent with rapid warming due to carbon and/or methane release as the primary causative factor.
  7. Have we entered the Anthropocene?  OK, this moves into the science/society realm, and as we enter an election year in the United states, its inclusion on this list may be seen by some as political.  Nevertheless, I would argue that the question of whether human alteration of the global environment has in fact propelled the Earth into a new geological era.  The Economist, hardly a bastion of liberal journalism, did a very thoughtful piece on the subject, and The Philosophical Proceedings of the Royal Society A devoted a theme issue to the subject.  For those of you teaching paleontology, what would you think of asking your students to speculate on what the geological signal of the past several thousand years might look like a million or so years in the future?
  8. Origins of feathers and birds  No list like this would be complete without at least one mention of dinosaurs.  So here goes.  The dispute rages on as to the ancestry of birds – while it was clearly reptilian, whether it was Archeopteryx or something else remains to be determined. A report from Xu et al. suggested Xiaotingia as an alternative, however Lee and Worthy disputed that claim.  And fossils in amber have revealed more about dinosaur feathers, including evidence regarding color and the evolution of their function for flight as early as the late cretaceous.  Once again, since dinosaurs are involved, I’m sure we’ll be hearing more
  9. Not your dinosaurs’ cycads  I’m not a botanist, but one thing that stuck from my time in Florida was that cycads are in fact “living fossils”, a taxon that has dwindled since its heyday in the Jurassic/Triassic period of ca. 165 million years ago.  Now Nagalingum et al. have shown that in fact the last common ancestor of living species dates to only about 12 MYA, suggesting a rediversification of the taxon beginning in the late miocene.
  10. How the penis lost its spine(Courtesy of Yoshi Tomyasu) OK, this is the one that was suggested to me by a colleague  McLean et al. turned what seemed to be a rather arcane subject, losses of regulatory sequences in humans relative to chimpanzees, when they found that one such loss was that of a sequence necessary for the formation of a penile spine.  They further demonstrated that the potential for such formation may still exist in the human genome, and they speculate that the loss is associated with increased pair bonding and paternal care in humans.  Sociobiology lives on!

Well that’s it.  Please feel free to tell me what I’ve missed (or what really doesn’t belong here).  All told, it’s been a good year.  Darwin and Wallace would be proud of their legacy.

Happy New Year!