Mammals, rising from the ashes

Yes, placental mammals diversified after the KT boundary

The asteroid hypothesis for dinosaur extinction hit the world of paleontology like a meteor, and has been a constant source of amazement, nitpicking, and doubt since. The fossil record is patchy, so even if dinosaurs really died out at the cretaceous/tertiary (K/T) boundary formed by this impact in the geological layers, not all species would have representatives neatly recovered right below the boundary, but not above. The record would present a more sporadic view of some dying out earlier, depending on their general abundance. But over time it has become increasingly certain that the impact was indeed cataclysmic, and while some groups of dinosaurs were in decline beforehand, most gave up the ghost right at the boundary.

Example of the K/T boundary, from Starkville New Mexico. One signature is a high level of the element iridium, common in asteroids. 

Likewise for their thankful successors- the mammals- there have been long-standing disputes about when the major classes originated, especially the diversified descendents of the placental mammals- whether most of them were already present as the dinosaurs strode the earth, and what they really gained from the asteroid impact.

A couple of years ago, a thorough molecular study placed the the divergence of placental mammals into its major lineages, like bats, whales, primates, herbivores, etc, well before the K/T impact boundary, at least 100 million years ago.

An older mammalian phylogeny made from molecular evidence. Note the K/T boundary marked by the shaded boundary at ~66 million years ago, which was recently honed to just a 100,000 year window- 66.043 ± 0.043 Ma. This tree has most major lineages splitting well prior to that boundary.

But recently a paper came out that used both classical anatomical/cladistic methods and molecular methods to revise the story back to what had been thought for quite a long time- that placental mammals split into their various modern subgroups only after, but relatively soon after, the K/T impact. Within five million years, as these authors have it. At this time, there was a vast explosion of lineages that led to all the modern types we know and love, and others that went extinct. In comparison, very few major lineages separated in the last forty million years.

Unfortunately, their phylogenetic tree diagram is such an overstuffed mess as to be unpresentable. But just scrunch the one above in the horizontal scale, and you pretty much get the idea, although both groups agree that the split between marsupial and placental mammals happened much farther back- about 180 million years ago. The divergence between the two views is remarkable, and comes from the interesting fact that the molecular "clock" doesn't tick very evenly.

Molecular phylogenetics uses comparisons of protein sequences. You can have your pick over a wide spectrum of sequences, from genes like immune system components that change very quickly, (in an evolutionary sense), to others like histones or ribosomes that change very slowly. So you have your choice of clocks ticking at different speeds. With modern sequencing technology, it is relatively easy to collect data for your selected proteins from many species, and crunch then computationally to align the sequences and judge their divergence.

It is very quantitative in a way, and thus attractive over the old ways of comparing the slow change of tooth shapes over a fossil series, or skull shapes, or ear bones, or ankle bone shapes, etc. But there is a catch- that the only sequences we have are modern, so we have an enormous and perilous estimate to make when we want to translate a sequence divergence into a divergence in actual biological history. (And this isn't the only catch- there are a blizzard of possible mathematical techniques and associated theories/models available for the basic alignment comparisons and other steps, which have taken a long time to shake out.)

These estimates are calibrated using divergence times of well-understood fossils that track reasonably well to species we are familiar with in sequence terms (say, sheep and horses). But this calibration becomes rapidly more hazy as we go back in time, combining the uncertainty of the winding sequence history since divergence with the uncertainty of the fossil record. So it is easiest to stick closer to home (i.e. recent evolutionary times) and project those "calibration" clock rates back to more ancient events mathematically.

However it is apparent that evolution is not a constant process, and that especially during periods of promiscuous evolutionary radiation, sequence variation (as reified in founded linages) may speed up, causing a molecular-only analysis to cast events substantially farther back in time than they really occurred. We also know that different lineages have different evolutionary rates at non-radiating times, making simple calibration rather perilous. The only way is to put more weight on studying the fossil record, which is what these current authors seem to have done.

Characters on the skull used by the authors to compare fossil mammals for lineage membership determination- just an example of the methods used to establish relatedness among real fossils, in contrast and comparison with molecular relationships.

This issue of the wayward molecular clock applies even more strongly to the advent of eukaryotes, estimates of which range from less than 1 to 2 billion years ago. The revolutionary nature of this transition can hardly be overemphasized, generating the enormous and enormously complex eukaryotic cell out of the symbiosis of two or more bacterial cells. Many new systems arose denovo (meiosis, nuclei, intermediate filaments, goli and endoplasmic reticulum). It also involved a long gestation in evolutionary obscurity, followed by an astonishing radiation to a multitude of forms most various, including all animals.

So evolution remains a story in progress, with a fair amount of its history still shrouded in misty uncertainty, and only gradually coming into focus as more data come in and are more carefully analyzed.

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