Living the Scientific Life (Scientist, Interrupted)

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The first feathered dinosaur fossil found in China — Sinosauropteryx.
The feathers can be seen in the dark line running along the specimen’s back.

Image: Mick Ellison, AMNH [larger view]

ResearchBlogging.org

There is a lot of controversy among scientists regarding when modern birds first appeared. The current fossil record suggests that modern birds appeared approximately 60-65 million years ago when the other lineages of dinosaurs (along with at least half of all terrestrial animals) were extinguished by a bolide impact. However, it is possible that modern birds were around much longer than that, although corroborating fossil evidence have yet to be found.

But scientists can also rely on another way to estimate the age of lineages: molecular clocks.

It was hypthosized that the DNA replication error-rate is consistent when averaged over time, across species and over various regions of the genome, similar to the regular ticking of a clock’s hands. Thus, molecular clocks rely on measuring these small changes in DNA sequences to determine the passage of time. It is generally accepted by the scientific community that DNA sequences diverge between distinct lineages by two percent every one million years.

There are several weaknesses associated with the fossil record; it isn’t complete and it only documents morphological changes long after species have diverged. But molecular clocks also have some inherent problems. For example, different lineages accumulate genetic changes at different rates, so estimates of evolutionary time will vary depending upon the lineages that are analyzed.

Nonetheless, even when these methodological weaknesses are addressed, the rocks-versus-clocks data still reveal a huge discrepancy between the estimated time of the dinosaur-modern bird split: the fossil record suggests it occurred in the Cenozoic, while molecular clock data suggest it occurred deep within the Cretaceous, about 100 million years ago.

But several statistical methods have been developed that compensate for these different rates of molecular change across genomes, and a paper was just published that relies on these analytic methods for molecular clock data to estimate how long ago birds diverged from dinosaurs. The authors of this paper hoped that these new, more rigorous methods would generate data that narrow the discrepancies between the fossil record and the molecular data, thereby reducing the rock-clock conflict.

“What my colleagues and I did was apply all of these new methods to the problem of the origin of modern birds, with each method making different assumptions about how mutation rate changes across the [evolutionary] tree,” said University of Michigan graduate student Joseph Brown, who is first author on the paper.

Even though some discrepancies were expected because these two data sources rely on different stages of evolutionary change, the new analytic methods only strengthened the molecular clock conclusions that modern birds diverged from dinosaurs around 100 million years ago (Figure 1);

Figure 1: Different ways that fossil and molecular data date lineages.

Time intervals defined by the horizontal dashed lines and vertical arrows pertain to age estimates for the divergence between hypothetical lineages X and Y. Even with a complete fossil record and perfect molecular clock a discrepancy is expected between fossil (FA) and molecular (MA) age estimates. As diagnostic morphological characters generally evolve (TMorphology) after species divergence (TSpecies), the fossil record will always underestimate (by δDiagnostic character) the true speciation time. Genetic data, on the other hand, will overestimate speciation time (by δCoalescence), as polymorphisms present during species divergence will coalesce some time in the past (TGene; related to the ancestral species effective population size). The genuine difference between molecular and morphological divergence times will thus be δTrue MA-FA. With a less complete fossil record, the oldest known fossil is unlikely to temporally correspond precisely to the origination of a diagnostic character delimiting X and Y, further decreasing FA by δOldest fossil. Under the more realistic scenario of lineage-specific rate heterogeneity and limited taxon/character sampling, errors associated with molecular methods (δClock error) may result in overestimation or underestimation of the true speciation time, although underestimates are bounded by the fossil constraint (δFossil error). The observed discrepancy in age estimates, δRealized MA-FA, may be considerably larger than expectations (δTrue MA-FA). [larger view]

“[W]e find strong support for an ancient origin of modern bird lineages, with many extant orders and families arising in the mid-Cretaceous, consistent with previous molecular estimates,” writes Brown and his colleagues.

Not only that, but this research addresses the conflict between which scientific methods are most accurate for studying the evolution of life.

“Rather than fighting across groups, we now have the joint goal of explaining this rock-clock gap,” Brown said. “Resolution of the issue will be fertile ground for future research for a while to come.”

These new findings provide more credence to some of the recent spectacular avian fossil discoveries, such as a fragmentary fossil from a parrot and from a loon (both of which were dismissed because they are thought to be inconclusive), and further, these data predict that there are yet more modern bird fossils waiting to be unearthed by paleontologists.

This study was published in the peer-reviewed Open Access journal, BMC Biology.

Sources

Brown, J.W., Rest, J.S., García-Moreno, J., Sorenson, M.D., Mindell, D.P. (2008). Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. BMC Biology, 6(6) | doi:10.1186/1741-7007-6-6 [free PDF].

Comments

  1. #1 Rick
    February 13, 2008

    I believe that Joe Brown said also that this study did not really answer the question but, raised more questions. This discussion between Paleontologists and Evolutionary ornithologists has been going on for at least 25 years. I think that if Heilmann had the information we had today he would never have postulated as he did.

  2. #2 umkomasia
    February 14, 2008

    We do have Cretaceous birds and they are not members of modern groups. The problem is not the fossil record – it is the assumptions of the molecular clock model. Yes they have tried to improve these models, but they are beginning to look more and more like Ptolemy’s epicycles.

  3. #3 David Marjanovi?
    February 14, 2008

    None of the internal calibration points in this paper had an upper bound. I think that explains something. There are no epicycles in molecular dating; it just has to be applied right. :-)

    There are several weaknesses associated with the fossil record; it isn’t complete

    Yep, but the statistics on whether the absence of Neornithes from pre-Maastrichtian rocks is statistically significant hasn’t been done yet. (It can be done — wait for the paper…)

    and it only documents morphological changes long after species have diverged.

    Many molecular biologists like to say that, but they overlook the fact that the autapomorphies (innovations) of a group cannot appear after the group has started to diverge! This argument may explain why no Cretaceous paleognaths have been found yet, but it doesn’t explain why no clear neognaths other than the admittedly derived anseriform Vegavis have turned up in the K yet.

    the dinosaur-modern bird split:

    the molecular clock conclusions that modern birds diverged from dinosaurs around 100 million years ago

    No. The — IMHO miscalibrated — molecular conclusion is that the modern birds (Palaeognathae and Neognathae, to be precise) diverged from each other 100 Ma ago.

    The divergence between birds and… let’s say deinonychosaurs must have happened at the very least 55 million years earlier, and nobody disputes that.

    You see, there are plenty of birds in the Cretaceous (and Archaeopteryx in the Jurassic, if it isn’t actually, say, a troodontid). It just so happens that none so far is a modern bird (Neornithes), with the notable exception of Vegavis which shows that a minimum of 5 modern bird lineages has crossed the K-Pg boundary.

    a fragmentary fossil from a parrot and from a loon (both of which were dismissed because they are thought to be inconclusive)

    The fragmentary lower jaw was attributed to a lory. That’s really pushing it. Stem-group (“non-modern”) parrots without the typical parrot beak are known from the middle Eocene, and modern parrots, of which the lories are one part, turn up later still. I’m not saying it’s not a lory — I’m saying it’s really improbable.

    The supposed loon skull consists of lots of tiny fragments that were glued together and amount to maybe half a skull. In the original description, only a reconstruction of the complete skull was published… Using this animal as a calibration point for dating the origin of modern birds (published in the Journal of Paleontology in January 2004) put that date into the Precambrian. That’s called reductio ad absurdum.

    In sum, yes, the fossil record of birds in general is not very good (though we haven’t quantified that yet). Yes, a few surprises may well yet be unearthed. But molecular dating without upper bounds to the calibration points doesn’t show that.

  4. #4 David Marjanovi?
    February 14, 2008

    (To clarify, the paper I just told you to wait for won’t use birds as its example.)

    This argument may explain why no Cretaceous paleognaths have been found yet, but it doesn’t explain why no clear neognaths other than the admittedly derived anseriform Vegavis have turned up in the K yet.

    That’s true, but it’s not what I wanted to say: it doesn’t explain why no members of Neornithes (“modern birds” — Palaeognathae + Neognathae) other than V. have turned up in the K yet. :-]

  5. #5 Chris Noto
    February 16, 2008

    Two points I would like to make:

    First: At least the gross topology of the trees match! How often have the inferred relationships between groups in fossil-based and DNA-based studies matched perfectly? Granted there are only a very small number of nodes to contend with here and maybe the lower-level relationships are different between the trees, but the fact that they are recovering similar topologies is important I think.

    Second: Let us not forget that many genetic differences can accrue between lineages before significant morphological differentiation occurs. Although at this scale it may be a moot point. As a paleontologist I am not surprised by the temporal gap between the trees. We usually expect that groups diverged some millions of years before they reliably show up in the record and birds, built like they are, are notoriously hard to fossilize (as previously noted). Also fossilization will depend on what environments the early representatives of these groups were living in. The record may simply not exist.

  6. #6 David Marjanović
    February 17, 2008

    First: At least the gross topology of the trees match!

    The paper didn’t do any morphological phylogenetic analysis, only a molecular one.

    In the very basics, just about all morphological and molecular trees have matched for years: Neornithes composed of Palaeo- and Neognathae, Neognathae composed of Gallanseres + Neoaves, Gallanseres composed of Galliformes and Anseriformes. Within Neoaves, all molecular analyses and all of the few morphological analyses contradict each other, and all are poorly resolved.

    What’s more, there is only one good morphological bird analysis (Livezey & Zusi 2007). Despite having monstrous numbers of taxa and characters, it gets several suspicious results (for example grebes and loons together, even though both molecular and a morphological analysis have recently agreed on finding grebes and flamingos as sister-groups); the reason seems to be the almost complete lack of fossils in the analysis by Livezey & Zusi. The ability to use fossils is the one big potential advantage morphological analyses have over molecular ones… I hope someone will plug a few dozen fossils in sometime soon!

    The record may simply not exist.

    But the point is that a bird record, although it is bad, does exist. We have reasonable numbers of birds, including a few half-complete skeletons, from the end-Cretaceous of Argentina and Mongolia — but not one of them belongs to Neornithes (even though a partial wing from Argentina, called Limenavis, is considered the sister-group of Neornithes). France has yielded a few fragments, some of which may or may not belong to Neornithes, while the others belong to Enantiornithes like most Cretaceous birds do. The only known bird fossil from the (end-)Cretaceous of Belgium so far is the youngest known bird tooth. In the North American record, all of the fragments that can be securely identified don’t belong to Neornithes either…

    Sure, something is hiding (as shown by Vegavis), but it cannot be very much. We would have noticed by now.

  7. #7 Chris Noto
    February 18, 2008

    The ability to use fossils is the one big potential advantage morphological analyses have over molecular ones… I hope someone will plug a few dozen fossils in sometime soon!

    I couldn’t agree more. The fossil record is still relevant in studies of evolutionary relationships–DNA alone can’t always resolve the relationships. Combining both methods is probably our best bet of resolving these problems. However, much more needs to be done in order to convince molecular phylogeneticists that fossils do indeed matter. Coming from and EEB department, the attitude about the utility of fossils in modern evolutionary studies can be quite dismissive.

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