Friday, January 30, 2009

Gibbon vs. tiger cubs


My top 20 most important fossil sites

I have made my decision. I've basically gone for (what I believe is) a good mix of age, geography and recency of discovery/time of greatest interest. In chronological order, oldest first.

1. Ediacara Hills, Australia
  • Geologic period and biota named after them
  • Amongst earliest unequivocal evidence of multicellular life
  • True affinity of the frond-like taxa still disputed (possible early animals or something altogether unique)
2. Doushantuo, China
  • Precambrian sediments that include embryos of earliest animals
  • Astonishing preservation (embryos have perhaps the lowest preservation potential of any living thing!) at very important and poorly understood point in animal evolution
3. Burgess Shale, Canada
  • Most famous of several Cambrian lagerstatte (sites of exceptional fossil preservation)
  • Soft-bodied preservation of diverse taxa
  • Important window on the early diversification of animal life
4. Soom Shale, South Africa
  • Ordovician age, perhaps the period when biodiversity increased most rapidly
  • Important site for early vertebrate evolution with soft tissue preservation of the conodont animal as well as various arthropods
5. Herefordshire lagerstatte, UK
  • Unique form of preservation: fossils have to be destroyed to reveal their affinity (successive slices are ground away and a picture taken leading to a exquisite 3D reconstructions)
  • Some of the rarest fossils known from here (e.g. one of only 4 sea spiders known from last 500 million years)
  • Only real lagerstatte from whole of Silurian
  • Exact location a secret
6. Rhynie Chert, Scotland
  • Volcanic preservation of Devonian lake biota
  • Predates vertebrate colonisation of land and is one of the earliest terrestrial ecosystems preserved
  • Plants, fungi and terrestrial invertebrate fossils
7. Gogo Formation, Australia
  • Fantastic 3D preservation of reef fossils
  • Particularly important site for fish, with muscles and nerves preserved in microscopic detail
8. Mazon Creek, USA
  • Carboniferous age
  • Preserves both land and sea floras and faunas as casts
  • Extremely diverse (hundreds of species known)
9. Joggins, Canada
  • Preserves forests of ‘coal age’ (Carboniferous) in situ
  • UNESCO world heritage site
10. Karoo, South Africa
  • One of the longest periods of continuous sedimentation (Permian through Triassic)
  • Spans largest ever mass extinction (“When Life Nearly Died”)
  • Famous for showing step-like evolution of mammals
11. Jurassic Coast, UK
  • Historically important to founding of palaeontology and geology
  • Abundant marine fossils of Jurassic age (e.g. ammonites, belemnites)
  • Marine reptiles also found here most famously by Victorian collector Mary Anning
12. Solnhofen, Germany
  • Late Jurassic age
  • Lagoonal deposit with very rare fossils
  • Forever associated with most iconic fossil of all: Archaeopteryx
13. Morrison Formation, USA
  • Late Jurassic age
  • Abundant dinosaurs (Allosaurus – most completely known carnivorous dinosaur, Stegosaurus and various iconic sauropods)
  • Historically of interest in ‘bone wars’ between Cope and Marsh
  • Still important field site at present day
14. Jehol, China
  • Fantastically diverse terrestrial biota of Early Cretaceous age
  • Includes almost all known feathered dinosaurs, which have proved instrumental in closing the morphological gap between dinosaurs and birds
  • Many other rare finds include: gliding lizards, two-headed reptile, early birds
15. Santana, Brazil
  • Early Cretaceous inland sea deposits
  • Includes fish, many pterosaurs (a very rare fossil elsewhere), insects, turtles, plants and various invertebrates
16. Green River, USA
  • Eocene age
  • Extremely rich preservation of fossil fish: literally millions of specimens
  • Consequently rare acts are preserved, e.g.:
    • One fish preserved midway through eating (swallowing) another
    • A stingray giving (live) birth
17. Messel Pit, Germany
  • Eocene age
  • Diverse terrestrial biota
  • UNESCO world heritage site
18. Dominican Amber, Dominican Republic
  • Oligocene to Miocene age
  • Dominican amber, unlike Baltic amber, is clear and so fossil inclusions are more easily seen
  • Insects and spiders common, but a lizard has also been found
  • ‘As is’ preservation as tree sap has unique bacteria-killing property that means even the bacteria present inside the individual prior to death are unable to effect decay
19. Fossil Hominid Sites of N.W. South Africa (Sterkfontein, Swartkrans, Kromdraai, and environs)
  • Various fossil hominid sites spanning over 2 million years of human evolution
  • Includes fossils (Australopithecus africanus) as well as evidence of cave dwelling, fire domestication etc.
  • UNESCO world heritage site
20. La Brea Tar Pits, USA
  • 40,000 to 25,000 years old
  • Fossils preserved in tar pits many of which are still bubbling up out of the ground
  • Many, many fossils of dire wolfs, sabre-tooth cats etc.
  • Specimens from here in many museums around world (if you’ve seen a sabre-tooth cat it is almost certainly from here)
  • Located close to downtown LA!

Thursday, January 29, 2009

If you go down to the grasslands today...

A friend pointed me at this recently. I guess it's pretty old, but still pretty amazing!

Saturday, January 24, 2009

The 20 most important fossil sites

As part of my consulting job with Dorling Kindersley I have been asked to compile a list of the top 20 most important fossil sites and was hoping that my small, but extremely intelligent, readership might want to contribute. (Not that I'm trying to get you to do my job for me mind.)

Here is a few starters for you:

  • Jehol
  • Solnhofen
  • Burgess Shale
  • Chengjiang
  • Hell Creek
  • Patagonia
  • Isle of Wight
  • Soom Shale
  • Karoo
  • Doushantuo
  • Rhynie Chert
  • Gogo Formation
  • Mazon Creek
  • Joggins
  • Santana
  • Green River
  • Dominican Amber
  • La Brea

I make that 18. Of course I could always just steal Wikipedia's lagerstätte list, but there are far more than 20, and does something have to be a lagerstätte to be important?

All comments greatly appreciated.

Wednesday, January 21, 2009

Thursday, January 08, 2009

Dating phylogenetic trees of fossils

A problem I have encountered repeatedly in my PhD is that the way palaeontologists date their phylogenetic trees means lots of branches represent zero million years. In fact, at every single bifurcation one branch is always zero million years in length. This fact is somewhat hidden graphically as published trees drawn against stratigraphy (like this one) usually include some additional default length so that individual branching events can easily be seen. In reality, with branch lengths appropriately scaled, they look more like this:

Phylogeny with branch lengths scaled to time and taxon names removed

So why does this matter? Well the primary reason (as far as I am concerned) is that this screws up the standard calculation of evolutionary rates. (A rate being some change over time; with a denominator of zero the result is infinity.) A secondary problem, then, is that zero-length branches simply aren't realistic.

How to get around this? Well early authors (notably Karl Derstler and Peter Forey) independently went for the simplest option - simply add something to the divisor in each case, 1 million years, 2 million years etc. This may be fine in some cases, but for large phylogenies this divisor can end up pushing branching events really far back in time. (In one example I worked on, lungfish appeared back in the Precambrian.) Not so good.

The best method I am aware of was developed in a paper by my colleague Marcello Ruta and co-authors. They argued the best approach was for zero-length branches to 'share' some time with a preceding branch of positive length. Furthermore, they argued that the proportion of sharing should be linked to the number of character changes on each branch. This essentially assumes an underlying model of equal-rates of character change and hence is biased to what would normally be the null hypothesis.

The Ruta et al. approach was adopted by us in our Science paper, but with a slight modification. As we were using a manual implementation we (by which I mean Steve) used a simpler approach whereby the shared time was split up equally.

Recently I have returned to this problem and have now constructed R code to automate the process. Here is what the above tree looks like using the equal sharing method:

And here is what it looks like using the Ruta et al. method:

For the rate calculations (and the group) you will have to wait for the paper.

About Me

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Currently I am founding member, president elect and entire membership of SWEMP (the Society of Wonky-Eyed Macroevolutionary Palaeobiologists). In my spare time I get paid to do research on very dead organisms and think about the really big questions in life, such as: What is the ultimate nature of reality? Why is there no room for free will in science? and What are the implications of having a wardrobe that consists entirely of hotpants?