Placement Of Mexican Amber Fossil Responsible For Extremely Old Age Estimate For Anolis

Although we’ve been focusing a lot of attention on Nicholson et al.’s new classification for anoles, Daniel Scantlebury recently called attention to the fact that this monograph also contains “a bold hypothesis of the biogeographic history of” anoles.  I’m going to focus here on only one aspect of Nicholson et al.’s biogeographic analyses – namely, their use of two remarkable amber fossils to calibrate a Bayesian relaxed clock analysis supporting the hypothesis that anole diversification dates back to the Cretaceous.

Nicholson et al.’s hypothesis that anoles first appeared more than 90 million years ago and that most major clades of anoles originated prior to 70 mybp is likely to be one of the most controversial aspects their hypothesized biogeographic scenario.  These extremely old ages are significant because they make anole diversification compatible with a scenario that has long attracted the attention of vicariance biogeographers (Rosen 1975, Savage 1982, Crother and Guyer 1996).  Under this scenario, anoles occupied an ancient volcanic arc that originated in the Pacific ~120 mybp and formed a landbridge between North and South America in the Late Cretaceous (75-70 mybp) before moving on to form the present day West Indian islands.

I have characterized the ages for anole diversification in Nicholson et al.’s biogeographic reconstruction as “controversial” and “extremely old” because they are older than the age estimates obtained by most other studies.  Hedges et al. (1992) were among the first to use molecular methods to estimate ages for terrestrial vertebrate fauna of the West Indies, and reported ages for anoles and other taxa that were far too young to be compatible with Cretaceous vicariant events and the hypothesized Greater Antillean Landbridge between North and South America.  Hedges et al. (1992) suggested instead that anoles arrived in the West Indies via over-water dispersal.  Although Crother and Guyer (1996) criticized Hedges et al.’s use of immunological data and their resulting conclusions about over-water dispersal, more recent work has tended to support Hedges et al.’s conclusions by recovering ages for anoles and other terrestrial West Indian vertebrates that are too young to be compatible with the vicariant scenario hypothesized by Savage (1982), Crother and Guyer (1996) and Nicholson et al. (2012).

Daza et al.’s (2012) cladistic analysis of fossil data, for example, includes an update of the time calibrated tree generated by Conrad (2008) from available fossil material; this tree suggests that the Polychrotidae (the possibly non-monophyletic clade that includes anoles and other putative relatives like Polychrus) split from the Hoplocercidae sometime in the Eocene (~50 mybp).   Townsend et al.’s (2011) analysis of a multi-locus molecular phylogenetic dataset for iguanian lizards that used a BEAST analysis with 18 fossil calibrations suggests a split between Anolis carolinensis and the Corytophanidae at 50-70 mybp.  Most recently, Mulcahy et al.’s (In press) analysis of a multi-locus phylogenetic dataset for squamates in BEAST that relies on 14 fossil calibrations suggests that Anolis carolinensis split from Enyalioides laticeps 25-75 mybp (penalized likelihood analyses conducted by Mucahy et al. suggest a considerably older split between these two species that dates to around 80 mybp).

Recently published trees with estimates for the age of Anolis from Daza et al. 2012, Townsend et al. 2011, and Mulcahy et al. in press.

Why is there a discrepancy between the ages for anoles reported by Nicholson et al. and other studies?  There are many possible answers to this question (e.g., sampling differences, use of alternative methodologies, etc.), but I believe it is relatively easy to isolate the cause of the relatively old age estimates reported by Nicholson et al. to a single fossil calibration.  Before discussing whether this particular calibration was appropriately deployed by Nicholson et al., I’d like to first address the more salient (and somewhat easier to answer) question of whether this lone calibration is really driving the age estimates reported by Nicholson et al.

To investigate the impact of the two fossil calibrations used by Nicholson et al. on the inferred age of anoles, we need to take a quick look at a time calibrated tree.  Because Nicholson et al.’s monograph does not include any trees where branch lengths are scaled to time, I’ve crudely generated a time calibrated tree of my own using the same dataset and program used by Nicholson et al.  In my analyses, I’ve excluded fossil calibrations in favor of a simply assigning an arbitrary age to the root of anoles.  The reason for generating this tree is to illustrate the relative temporal positions of the two nodes that are calibrated with fossils by Nicholson et al.

Time calibrated tree generated using BEAST and a similar mtDNA dataset to the one analyzed by Nicholson et al. (they differ only in that this tree lacks a handful of recently sequenced species). This tree was generated without any fossil calibration data and was merely assigned an arbitrary root age mean of 100. The colored bars indicate the relative temporal positions of the two calibrated nodes in the Nicholson et al. analysis.

I’ve indicated the temporal position of Nicholson et al.’s two calibrations in the above figure, with the red dot and line indicating a node that is assigned a minimum age of 28 mybp and a blue dot and line indicating a node that is assigned a minimum age of 23 mybp.  Notice that the younger (i.e., closer to the tips) red node is assigned an older minimum age than the older (i.e., closer to the root) blue node.  As a result, assigning the minimum permissible age to the older blue node (23 mybp) will inevitably involve assigning the younger red node an age that is younger than its minimum age (28 mybp).  In other words, the blue node can’t actually have a date that is close to its minimum because this would violate assumptions of the red node’s calibration.  On the other hand, trees that assign the younger red node its minimum value (28 mybp) will remain compatible with the constraint on the older blue node (minimum age of 23 mybp).  Because of the fact that Nicholson et al. have placed the older calibration at the younger node, we expect that the minimum age of 28 mybp assigned to the younger red node will drive the overall tree calibration and root age while the 23 mybp calibration assigned to the blue node will have a relatively minor impact on the overall calibration.

Think about the age we’d likely recover for the root if we only used one fossil or the other.  If we used only the blue calibration, the scale of the figure above suggests that we’d likely arrive at a root age somewhere around 50 mybp.  If we used only the red calibration, however, the scale of the figure above suggests that we shouldn’t be surprised to recover root ages in excess of 100 mybp.

With this background we can return to a consideration of the two fossils used to calibrate this tree.  The first is the largely intact skeleton of a juvenile lizard from Dominican amber.  Although interpreting the phylogenetic position of this specimen was complicated by the fact that it is a juvenile from which some characters important to cladistic analyses of anole relationships could not be scored, de Queiroz et al.’s (1998) cladistic evaluation of the available data suggested that this fossil likely belonged to the clade that includes extant species of Hispaniolan trunk-crown anoles.  The Dominican amber is also well-dated and is thought to result from forests that existed 15-20 mybp (Iturralde-Vinent and MacPhee 1996).  Given this information, it seems reasonable to place this fossil calibration as a minimum age at the stem of the chlorocyanus species group, and this is exactly what Nicholson et al. have done (this fossil corresponds with the blue dot and line in the figure above).  Although we could quibble about the use of a 23 mybp estimate that seems slightly older than most of the current research on the Dominican amber would have us believe, I’m not particularly concerned about this point because, as I’ve argued above, I don’t think this fossil calibration has a big impact on the ages recovered by Nicholson et al.

The second fossil used to calibrate Nicholson et al.’s tree is from Mexican amber and includes fragmentary remains of a juvenile lizard.  Nicholson et al. rely on Lazell’s description of this fossil to place it in their phylogenetic tree.  Lazell’s description of the fossil includes informal pre-cladistic comparisons of features observable on the fossil to features of other extant anole species.  Based on these comparisons, Lazell regarded the amber fossil as most phenotypically similar to three different species, including representatives of both of the two deeply divergent anole clades that occur on the mainland (see also Jonathan Losos’s post on this fossil).  Because only one of these two clades occurs in Mexico today, and because Lazell considered only one of the Mexican species known in 1965 – limifrons – as worthy of comparison to A. electrum, Nicholson et al. assign this fossil calibration to the stem of limifrons/zeus.  I don’t want to argue that this is clearly the wrong place for this fossil.  It’s not difficult, however, to argue that its placement here is based on somewhat tenuous evidence and that a more conservative placement at the stem of other fuscoauratus-like anoles, or even at the stem of Norops, would generate a much younger estimate for the root age of anoles.

In addition to potentially placing this fossil closer to the tips of the tree than the available data can justify, Nicholson et al. also assign this node a minimum age of 28 mybp.  Lazell believed the Mexican amber fossil was “Oligocene or Miocene in age,” but most modern authorities now assign the Mexican amber to the Miocene with an age of 15-20 million years and believe that it results from the same type of trees that occurred contemporaneously on Hispaniola.  In response to a previous post on this topic, Nicholson commented “I seriously doubt there would be a significant difference between using some date [for the Mexican amber] between 15 – 20 mya, vs. 28 mya.”  It is my argument here that any such change would lead to near-commensurate changes in the ages of nodes across their tree.

Overall, it is my opinion that Nicholson et al.’s biogeographic scenario for anoles rests on two potentially flawed decisions about a single fossil calibration.  As reanalayses of Nicholson et al.’s dataset are implemented, I predict that reasonable calibration scenarios for Lazell’s Mexican fossil will produce much younger ages for the root of anoles and will challenge the vicariant scenario hypothesized in Nicholson et al.

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Rich Glor

Latest posts by Rich Glor (see all)

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