I am studying a mud snail genus called Ecrobia. For the Caspian species (Ecrobia grimmi), there is a discrepancy between dates provided by the fossil record and the molecular clock:

  • First appearance of Ecrobia grimmi in the fossil record: Middle and Upper Miocene (15.97 to 5.33 million years ago)
  • Age of Ecrobia grimmi as suggested by the molecular clock: 0.58 to 2.04 million years. The molecular clock was calibrated using an external marker-specific clock rate, and the climax of a geological event.

What could explain this discrepancy?

  • $\begingroup$ Could you give the sources for both dates? It would make finding the answer easier because afaik there are many different things that could account for discrepancies between molecular clock dates and fossil dates. For one thing, what was the molecular clock measuring exactly? Divergence from closest relative, and if so what relative was it? Age of common ancestor of extant individuals? $\endgroup$ – Oosaka Aug 16 '18 at 10:08
  • $\begingroup$ As @Oosaka said, there are many reasons that molecular dates can be discordant with fossil dates. Without actually knowing what methods you've used to generate the molecular date, we can't be much help. For example, it could be due to lineage-specific rate heterogeneity, if you have used a method which assumes a strict clock. $\endgroup$ – NatWH Aug 16 '18 at 10:58
  • $\begingroup$ The source for the fossil record is Asnafi 2010, the source for the molecular clock is my own ongoing study. The molecular clock was measuring the divergence from closest relatives; all Ecrobia spp. were included. The age of the common ancestor is ca. 15 Ma. The molecular-clock analyses were run with *BEAST. The results of the strict- and relaxed-clock analyses were similar. $\endgroup$ – Justine Vandendorpe Aug 16 '18 at 12:15

First, the example you give is unusual in that molecular dating analysis should be calibrated with fossils to set minimum ages. If Ecrobia grimmi exists in the fossil record, then no proper molecular analysis would estimate them to be younger than those fossils. There are two main causes of discrepancies between fossil and molecular dating. For fossils you never find the oldest example of a species. If a species diverged 100 million years ago, you might not find a fossil of that lineage for millions of years, meaning that fossil estimates are almost always underestimates, but they do form a baseline upon which to calibrate molecular data. The problem with molecular data is that there is no "molecular clock". Lineages, genes and individual nucleotides all change at different rates. The best you can do is plug in fossil and/or geological dates into a model that is based on other lineages. Hopefully you have calibrated dates for closely related species, and the same genes. Even then, you do not know that the lineage you are working with will follow the same rates as the model predicts. At a minimum, you need to set a minimum possible age in BEAST to 5-16 mya.

  • $\begingroup$ I cannot use fossils to calibrate the molecular clock because Ecrobia spp. are cryptic (i.e. they are morphologically indistinguishable). Therefore, I thought the discrepancies between fossil and molecular dating might be due to a misidentification of the fossils: fossils identified as Ecrobia grimmi could actually be of a different Ecrobia sp., or alternatively, of an ancestral species. What do you think about that? $\endgroup$ – Justine Vandendorpe Aug 17 '18 at 7:14
  • $\begingroup$ Fossils are the gold standard. But if you cannot trust their identity, then you were right to exclude them. But without a reliable calibration, I don't think molecular dating is worth doing at all. Better to not know at all than to "know" something that is wrong. $\endgroup$ – Karl Kjer Aug 17 '18 at 11:19
  • $\begingroup$ What do you think about using external marker-specific clock rate and/or geological events to calibrate the molecular clock? $\endgroup$ – Justine Vandendorpe Aug 21 '18 at 6:44
  • $\begingroup$ @JustineVandendorpe I think they are OK, but need to be pretty solid. For example, the formation of the isthmus of Panama is well established. Is Ecrobia marine or freshwater? $\endgroup$ – Karl Kjer Aug 21 '18 at 11:54
  • $\begingroup$ Ecrobia is a brackish genus (from 6‰ to 38‰). $\endgroup$ – Justine Vandendorpe Aug 21 '18 at 12:56

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