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Mammal evolution analyses using molecules

Tuesday, November 22, 2016 10:09
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Now that
the large reptile tree (LRT) has grown to encompass a large gamut of mammals based on shared morphological traits, it’s time to compare it with prior studies based on molecules. Some scientists say that molecular studies that do not include fossil taxa should take precedence over morphological studies that do include fossils. Some studies combine extant DNA and extinct morphological data. In any case, it is important that all pertinent taxa are included and that unrelated taxa are excluded — and that suprageneric taxa are avoided. And finally, stand back and check your work to make sure it makes sense (more on that below).

The base of the Placentalia in the LRT
begins with small, omnivorous. plesiomorphic Monodelphis. This taxon gives rise to a number of small fur balls, all similar in size and shape, but differing subtly and nesting at the bases of more diverse and derived clades. In succession the following clades split off: Carnivora (includes moles), Glires, arboreal mammals, tenrecs/odontocetes, edentates and finally the large herbivores splitting mesonychids, desmostylians and mysticetes from elephants, sirenians and ungulates. This study provides a gradual accumulation of traits from small plesiomorphic generalists to large derived specialists and includes extinct taxa. Importantly, the basalmost taxon is very much like a basal marsupial — as it should be!

By comparison
Meredith 2011
 – begins with Afrotheria (elephants/ sirenians/ elephant shrews/ tenrecs/ golden moles) + edentates, arboreals (sans bats)/ Glires, and finally moles/shrews/hedgehogs + pangolins/carnivores + bats + artiodactyls (including hippos + whales).  This study does not provide a gradual accumulation of traits from small plesiomorphic generalists to large highly derived specialists and does not include extinct taxa. The basalmost taxa are not close to any marsupials in appearance.

Margulies et al. 2007 – essentially repeat this topology. This study has the same problem.

Tree of Life project 1995 – begins with edentates + pangolins, then Glires + arboreals + insectivores + (carnivores + creodonts) + artiodactyls and whales +  aardvarks, + perissodactyls + hyracoids + tethytheres (elephants, embrithopods, desmostylians and sirenians).. This study has the same problem.

Song et al. 2015 – begins with edentates + elephants/ tenrecs, insectivores + bats + ungulates + carnivores + other ungulates + whales, Glires, tree shrews, primates. This study has the same problem.

In a condescending tone
Asher, Bennett and Lehmann 2009 added their research to the topic of mammal phylogeny. Note how often these authors use the word ‘believe’ with regard to the best efforts of prior scientists, none of whom put faith ahead of evidence.

“In the not so distant past, there was a lot of uncertainty regarding how clades of living mammals were interrelated. Many mammalian systematists believed that sengis (Macroscelididae or ‘elephant shrews’) were closely related to rabbits and rodents, that pangolins (Pholidota) were ‘edentates’ along with anteaters, or that tenrecs (Tenrecidae) and golden moles (Chrysochloridae) were ‘insectivorans’ along with shrews and hedgehogs. Some believed that hyraxes (Procaviidae) were part of the Perissodactyla, and others thought that bats were so close to primates that the non-echolocating ones actually were primates, or at least close enough to make Chiroptera paraphyletic. In contrast, the consensus today on each of these issues is not only quite different, but also resolved with a substantial level of confidence. Questions regarding character evolution among living mammals now have the decisive advantage of a relatively well-resolved tree.”

Asher, Bennett and Lehmann 2009 – begin with a basal split between Atlantogenata (edentates + elephants + elephant shrews) and Boreoeutheria (primates/ rodents + insectivores + carnivores + bats + ungulates (including whales). This study has the same problem(s). And I, for one, have no ‘substantial level of confidence’ in its results. A ‘relatively well-resolved tree’ that does not provide a series of taxa with gradually accumulating derived traits is no match for a completely resolved tree topology that does provide that gradual accumulation. Let’s keep our thinking caps on. 

Does anyone else see
that in each of these studies, bats and ungulates nest as closely related? That the highly specialized edentates and elephants nest basal to the little furry opossum-like omnivores? The LRT does not have these problems. And yes, I’m picking the low-hanging fruit, but those kinds of problems are your clue that it is best to ditch DNA for major clade interrelationships (but keep DNA for congeneric and criminal studies) and stick to morphology when you create your own tree topology). That way you can visually check your results! Stand back from your cladogram before you publish it and see if all nodes and branches form a continuous and logical sequence with only gradual changes apparent between sister taxa. And that basal taxa look like outgroup taxa. That’s why I show my work.

When it comes to whales
Geisler et al. 2011 – nested fossil and extant odontocetes and mysticetes arising from Zygorhiza. and Georgiacetus, two archaeocetes. The toothed taxa, Janjucetus, Mammalodon and Aetiocetus were nested as basal mysticetes. This study appears to be accurate when it comes to extant whales. But this team assumed whales were monophyletic and thus haven them a common ancestor with fins and flukes. By contrast the LRT found toothed whales arising from toothed tenrecs and baleen whales arising from desmostylians, all of which have a long diastema (toothless region of the jawline) and dorsal nares.

Asher RJ, Bennett N and Lehmann T 2009. The new framework for understanding placental mammal evolution. BioEssays 31:853–864.
Geisler JH, McGowen MR, Yang G and Gatesy J 2011. A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea. BMC Evolutionary Biology 11:112.
Margulies EH et al. 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
Meredith RW et al. 2011. Impacts of the Cretaceous terrestrial revolution and KPg Extinction on Mammal Diversification. Scence  334(6055):521-524.
Song S, Liu L, Edwards SV and Wu S 2015. Resolving conflict in eutherian mammal phylogeny using phylogenomics and multi species coalescent model. PNAS 109(37)14942-14947.


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