Temporal Sequences

Temporal Sequences

Maggie Koopman and Erik Hoffmann

Time is on my side

Now!

First hard parts

First multicellular

First eukaryotes

First life!

The beginning!

1.5 billion years

1.0

2.0

3.0

4.0

0.0

The Outcrop

Sometimes you have a lot to work with...

The Outcrop

...and sometimes you don’t!

The Outcrop

Dooley et al., 2004

No crystalline rocks

• No absolute dating • Imprecise age calibration

2 meters = 10 yrs or 10 million?

The Outcrop

Dooley et al., 2004

Unconformities

• Stratigraphic gaps caused by non-deposition or erosion

• The bigger the time window, the bigger and more frequent the gaps will be

The Outcrop

Dooley et al., 2004

Cover

• Prevents examination• vegetation• loose sediment/soil• snow/ice/permafrost

The (so-so) Outcrop

Modified from Tibert et al., 2003.

100 km

2.5 M

aConstant Motion

No Outcrop!

• Resolution depends on depositional rates– High rates allow high resolution– Low rates allow low resolution– Negative rates erase the record

• Not all environments are created equal!

Schindel, 1982

Dooley et al., 2004

Gingerich, 1983

Limitations• Preservable hard parts only!

• Morphological change only!

Limitations cont. • Can’t detect fine changes.• Small directional changes followed by

reversals show up as variability within the population

Geary et al., 2002

• Long periods (relative to species durations) of morphological stasis coupled with brief periods of very rapid morphological change

• Stasis does NOT mean nothing is happening• Changes in soft parts

• Changes in tolerances/behaviors

• Small directional morphological change followed by doubling back

Punctuated Equilibrium

• Lineage (size, hard parts, frequency)

• Location (range, availability)

• Temporal resolution ((sub)stage level)

• Character sets

• Usefulness/Interest

Biases

Does the fossil record need to be complete?

Can we work around the gaps?

Can we derive viable sequences from a spotty record?

Quality of the fossil record through time

M. J. Benton, M. A. Wills and R. Hitchin

• Offers evidence that the fossil record provides uniformly good documentation of past life.

What does this paper do?

• Assesses the congruence between stratigraphy and phylogeny.

• Valid techniques for comparing large samples of cladograms to try to estimate variations in congruence between the fossil record for different groups of organisms and for different habitats

• RCI (relative completeness index)

• GER (gap ratio index)

• SCI (stratigraphic consistency index)

The Congruence Metrics

Depend on branching point estimates and calc. Of ghost ranges

Stratigraphic consistency index(Huelsenbeck 1994)

• Fit of the record to the tree= proportion of the nodes that are stratigraphically consistent.

•Significance of the fit= generate a null distribution for SCI under the hyp. That the statigraphic fit is not better than expected at random.

Figure 2

• Hypothesis 1: congruence is better than random (bars to the left)

• Alternative hypothesis: congruence is worse than expected from a random model: direct conflict between data (bars to the right)

Fig 1 a/b Benton et al 1999

RCI SCI

What causes poor matching of age and clade data? Bias in the metric

• Difference in quality of trees

• Difference in quality of fossil record

• Stratigraphic problems

• Taxonomy

• Sampling density

Molecular Clock Divergence Estimates and the Fossil Record of Cetartiodactyla

Jessica M. TheodorJ. Paleontology 78 (1), 2004, p 39-44

Why this paper?

• Ties molecular clocks to the fossil record

• Introduces cetaceans and hippopotamids

Molecular Clocks vs. the Fossil Record• Artiodactyla/Cetacea split – 60 Ma

– Earliest fossil whales 53.5 Ma

– Earliest fossil artiodactyls 55 Ma

• Odontocete/Mysticete split – 34-35 Ma– Rare at 34 Ma, good record ~30 Ma

• Hippopotamid/Cetacean split– Earliest fossil whales 53.5 Ma

– Earliest fossil hippos 15.6-15.8 Ma

» Anthracotheres - ~43 Ma

• New study using one mitochondrial and one nuclear gene sequence

Boisserie et al., 2005

Take home messages

• The fossil record is necessary to calibrate molecular clocks (and refute the bad ones)

• The fossil record fills gaps in phylogenetic trees, allowing us to confirm evolutionary sequences

ReferencesBenton, M.J., M.A. Wills, and R. Hitchin 2000, Nature. 403, 534-537Benton, M.J. 2001, Proceedings of the Royal Society of London B. 268, 2123-2130Boisserie, J.-R., F. Lihoreau, and M. Brunet 2005, Proceedings of the National Academy of Science 102

(5), 1537-1541Dooley Jr., A.C., N.C. Fraser, and Z.-X. Luo 2004, Journal of Vertebrate Paleontology. 24 (2), 453-463Geary, D.H., A.W. Staley, P. Muller, and I. Magyar 2002, Paleobiology. 28 (2), 208-221Gingerich, P.D. 1983, Science. 222, 159-161Gingerich, P.D. 1984, Science. 226, 995-996Gingerich, P.D. 2002, Cetacean EvolutionGould, S.J. 1984, Science. 226, 994-995Huelsenbeck, J.P. 1994, Paleobiology. 20 (4), 470-483Koch, C.F. 1978, Paleobiology. 4 (3), 367-372Levinton, J., L. Dubb, and G.A. Wray 2004, Journal of Paleontology. 78 (1), 31-38Lihoreau, F., and J.-R. Boisserie 2004, Journal of Vertebrate Paleontology 24 (Supp. 3), 83ARose, K. 2001, Science. 293, 2216-2217Schindel, D. 1982, Paleobiology. 8 (4), 340-353Schopf, T.J.M. 1982, Evolution. 36 (6), 1144-1157Theodor, J.M. 2004, Journal of Paleontology. 78 (1), 39-44Tibert, N.E., R.M. Leckie, J.G. Eaton, J.I. Kirkland, J.-P Colin, E.L. Leithold, and M.E. McCormick

2003, in Olson, H.C. and R.M. Leckie, eds., Micropaleontologic Proxies for Sea-Level Change and Stratigraphic Discontinuities: SEPM Special Publication No. 75, 263-299

Wills, M.A. 1999, Systematic Biology. 48 (3), 559-58