Wednesday, January 21, 2009

Misleading Mitochondria and Ancient Neopterygian Fossils

Last post we looked at the basics of ray-finned fish classification and some of the problems associated with them. Foremost among these are two rather dramatically different topologies. Morphology supports a clade called the Neopterygii which includes ginglymods, halecomorphs and teleosts whereas mitochondrial genetics support an ‘Ancient Fish Clade (AFC)’ that groups chondrosteans, ginglymods and halecomorphs to the exclusion of teleosts. Divergence dates based on the molecular clock are also dramatically older than minimal dates based on the fossil record. Hurley et al. (2007) tackle both problems with a two-pronged approach. Firstly they relook at the early ray-finned fossil record, scrutinizing it for the first appearance of derived characters diagnostic of these major groups and incorporating the data into a new cladistic analysis. Secondly they assembled a new, comprehensive molecular data set of four nuclear genes 29 species covering all the relevant clades (except the cladistians), thus is the first analysis capable of addressing the timing of the whole genome duplication event.
The tree based on the morphological data found strong support for the Neopterygii and virtually no support for the ‘Ancient Fish Clade’ at all. Indeed when the AFC topology was enforced upon an analysis that included only the living taxa the tree length grew by 80 steps (125% of the number of steps in the shortest possible tree) and found just one character that could be interpreted as a synapomorphy of this clade. Clearly the morphology doesn’t just fail to support the molecular ‘AFC’ it is strongly contradicting it. Analysis of the nuclear gene data also strongly supports the neopterygian clade over the AFC. Thus the signal for the AFC is coming from the mitochondrial genes alone. Given that this data set is so at odds with morphology, nuclear genes and the fossil record it seems likely that the source of error is the mitochondrial data. Perhaps more interesting is the morphological analysis that includes the fossils. Neopterygii continues to be strongly supported but the divergence date estimates have changed. Two fossils in particular were found to be significant: Brachydegma and Discoserra. Brachydegma from the Early Permian (285 million years) of Texas was previously regarded as a basal actinopterygian that diverged before the chondrostean-neopterygian split. However Hurley et al. found that it had a number of characteristics of Halecomorpha (that is the bowfin and its fossil relatives), such as an enlarged gular plate, a medial shelf at the front end of the maxilla, and possibly a posteriorly indented maxilla. The latter character is less secure because it depends on the interpretation of a small elliptical patch of differing ornament on the rear edge of the maxilla. If this patch is interpreted as a fused-on scale, then the maxilla does have the classic halecomorph indented maxilla (see figure below).



Brachydegma (from Hurley et al. 2007) on the left and the modern bowfin (Amia) on the right (not to scale; from Grande and Bemis 1998). Two diagnostic features of the Halecomorphi are colourised – the posteriorly indented maxilla (red) and the very large gular plate (green).

Sure enough Brachydegma comes out as the basal most member of the Halecomorphi in their analysis. As an halecomorph, Brachydegma is part of the neopterygian crown-group and pushes the origin of this clade back the Palaeozoic Era, before the big extinction event at the end of the Permian Period. The previous oldest known crown-group neopterygians were the parasemionotids (also halecomorphs) from the Early Triassic of Madagascar and Greenland. Discoserra from the Early Carboniferous (320 million years) of Montana (the famous Bear Gulch Limestone fish deposits) is a far older fish, and is not apparently a member of the neopterygian crown group but it has many of the synapomorphies of the crown-group indicating that by this early stage the neopterygian bodyplan was mostly in place. Previously Discoserra was thought to be an early cladistian.



Discoserra, from Lund 2000.

The new fossil data places the origination of the neopterygian crown group into the Paleozoic Era, long before the big Permo-Triassic mass extinction event of 251 million years, and at least 40 million years earlier than the previous oldest crown-group neopterygian and somewhat closing the gap between the molecular and palaeontological dating of the Neopterygian crown-group origination. Furthermore molecular clock dating using the nuclear gene data, rather than the mitochondrial genes yields a more recent range of dates 271-371 million years that actually ecompasses the age of Brachydegma, thus the discrepancy is more or less resolved. Once again it appears that the mitochondrial genes are giving misleading results, but why this is so is not immediately clear. No particularly ancient crown-group teleosts were recognized in this study so the fossil based minimum age for this clade is unchanged. However the new nuclear genetic data were used to estimate the divergence of the crown group. Like the estimates for the age of the neopterygian crown-group the estimates for the teleost crown-group based on nuclear genes are considerably younger than the estimates based on mitochondrial data. Thus using these new age estimates the discrepancy between molecular and palaeontological dates closes to a minimum of 30 million years.
Lastly Hurley et al. look at the timing of the whole genome duplication and how it relates to the explosive radiation of teleost fishes. The duplication event is indeed shown to be a feature of the teleost stem, as its products appear to be present in all living teleosts but are not found in the other surviving actinopterygian groups. This suggests that the duplication event most likely happened sometime in the Permian or Triassic, with the most recent possible occurrence being the Mid Jurassic, before the first appearance of crown-group teleosts in the fossil record. However the explosion in teleost diversity does not get underway until the Late Cretaceous, demonstrating a considerable lag between the duplication event and the rapid diversification event. This falsifies the hypothesis that the duplication was the direct causative agent of diversification.
In conclusion, this is a case where the morphological signal appears to have given a more reliable estimate of phylogeny than mitochondrial genes, whereas the huge discrepancy in divergence date estimates were a product of both overlooked fossil data and misleading signal based on the same unreliable genetic data.

Grande, L. and Bemis, W.E. (1998) A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy. An empirical search for interconnected patterns of natural history. Society of Vertebrate Paleontology Memoir 4: 1-690.

Hurley, I.A., Lockridge Mueller, R, Dunn, K.A.,Schmidt, Friedman, M., Ho1, R.K., Prince, V.E., Yang, Z., Thomas, M.G. and Coates, M.I. (2007)A new timescale for ray finned fish evolution. Proc. R. Soc. B 274, 489–498

Lund, R. (2000) The new actinopterygian order Guildayichthyiformes from the Lower Carboniferous of Montana (USA). Geodiversitas 22, 171-206.

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