Friday, February 22, 2013

Can molecular phylogenies be trusted?

iguanian on the left with simple tongue, scleroglossan on the right with forked tongue.  Losos et al., 2012.

We live in an age in which DNA has a powerful mystique...and for good reason. The technology for sequencing DNA has revolutionized several fields, including phylogenetic systematics. Molecular phylogeny has become the de facto standard for revealing the true evolutionary relationships between organisms. Molecular phylogenies are though to be inherently more trustworthy for a couple of reasons.  For one, there is less room to argue over trait definitions when we are dealing with DNA base pairs versus morphology. ATGC is unambiguous, where as first molar length may differ based on how length is measured or the wear stage of teeth. 

Molecular phylogenies have revealed a couple of apparent truths about evolutionary relationships that we couldn't readily have guessed from the anatomy. One is that whales are more closely related to cows  than cows are to horses. Or in other words, Cetartiodactyla is natural group of organisms that includes cetaceans (whales) as well as artiodactyls (hoofed-critters with an even number of toes....i.e. cloven -hoofed animals).  This group excludes perissodactyls (hoofed-critters with an odd number of horses).  DNA tells us that Cetartiodactyla is a valid phylogenetic group, but would have been really hard to come up with from anatomy alone....just think of all the basic similarities between cows an horses that would lead you to believe they are closely related to the exclusion of Flipper.

This thing is a closer cousin to a cow than a cow is to a horse. 

Which brings me to a recent discussion by Losos and colleagues in Science about the vast and irreconcilable differences between cutting-edge molecular phylogenies and exhaustive morphological phylogenies for lizards. Based on massively detailed morphological studies, there is a great deal of evidence that iguanians are the most primitive group of lizards, distinct from scleroglossans (other lizards). The scleroglossans share a huge number of morphological shared derived traits, the most obvious of which is that scleroglossans have a forked tongue. But recent molecular data suggests that iguanians are nested high within the group of scleroglossans, implying that all of the supposedly primitive traits shared by iguanians are in fact evolutionary reversals.  This is a tough pill to swallow, because 
"the synapomorphies of scleroglossans inferred as lost by iguanians in the molecular tree come from many functionally different parts of anatomy. These traits have disparate embryological origins and growth patterns, discounting general explanations based on development. Furthermore, iguanians have diverse lifestyles, ranging from large herbivorous iguanas to ant-eating horned lizards and gliding dragons. It is hard to see how this multifaceted suite of characteristics could reflect adaptation to an overall iguanian lifestyle." Losos et al, 2012:1429
So we are left with a conundrum in which the molecular and morphological data are saying fundamentally different things...and the morphological data set appears to be as good as it gets, with great care having been taken to address the problems inherent in morphological data sets. Which do we trust?  Losos and colleagues suggest that the molecular data could well be wrong.  They argue that natural selection acts on the molecular level as well, so we have to consider the possibility that convergence/homoplasy might be obscuring true phylogenetic patterns in the molecular data. 

Their main point is that we shouldn't just accept the molecular data as the truth, without looking at all the evidence.  What do you think?

Thanks to Claud Bramblett for pointing out this article.