Epigenetics: why DNA might fail over great phylogenetic distance

No one doubts
that DNA is helpful within a genus to determine relationships. It’s great to use in crime scenes and to figure out where bloodlines run among extant humans and dogs. It’s when DNA is asked to determine suprageneric and superordinal relationships that disparate topologies of interrelationships arise.

Now that we have
over 910 taxa in the large reptile tree (LRT) it is worth our effort to wonder why that topology differs from the DNA topologies that have arisen lately. To be sure, ‘Why’ questions are often impossible to answer with authority until evidence comes in. At present, there is no evidence for the speculation presented below. But all hypotheses start with such “what if” and “why not” scenarios that are then tested and re-tested.

Morphological studies look at skeletons.
Every detail. That’s hard evidence. Morph studies also look at fossils. DNA studies do not. What you get in DNA studies are comparable gene sequences that no one is sure what processes or angles they are responsible for in the adult taxon.

With that out of the way,
first let’s look at two major conflicts.

Turtles

  1. The LRT derives two clades of turtles arising from two clades of miniaturized pareiasaurs. A gradual accumulation of traits is apparent here.
  2. DNA derives a single clade of turtles from somewhere within the archosauromorpha branch of the diphyletic diapsida.
  3. Combining DNA and morphology, Pappochelys and Eunotosaurus are current ancestral candidates in this scenario, with sauropterygia as the next sister taxon clade, followed by lepidosauriformes in Schoch and Sues 2016. The Eunotosaurus upper temporal fenestra is only viewed when the supratemporal is removed, and that taxon nests in the Lepidosauromorpha in the LRT.

Mammals

  1. The LRT recovers a topology in which tiny opossum-like placentals arise arise from opossum-like marsupials. Then, from a series of tiny and small Jurassic and Cretaceous mammals arise the carnivores, rodents and kin, arboreal omnivores (including primates, bats and pangolins) and basalmost tenrecs.. Only after the Cretaceous do large placentals arise, including a new clade of large herbivores beginning with the Xenarthra.
  2. DNA recovers the clade Afrotheria that according to Wikipedia,“are either currently living in Africa or of African origin: golden moles, elephant shrews (also known as sengis), tenrecs, aardvarks, hyraxes, elephants, sea cows, and several extinct clades. They share few anatomical features but many are partly or entirely African in their distribution.” Of course, the extinct clades not listed in that quote cannot be tested and are therefore speculative.

Earlier morphological reports do not match the LRT:
Springer et al. 2004 report, “Variations of this tree largely conform to the topology of ordinal relationships proposed by Novacek 1992, which evolved from the mammalian classifications of Gregory in 1910, Simpson in 1945, and McKenna in 1975. The major characteristics of this tree are that Xenarthra (e.g. armadillos, anteaters) are the most basal placental group, and that most of the remaining orders are grouped into three generally accepted clades:  Ungulata,  Archonta and Anagalida.” See Definitions below.

The molecule supporters report:
Springer et al. report, “This [morphological] topology deviates from the currently emerging molecular tree, which recognizes three novel superordinal clades: Afrotheria, Laurasiatheria, and Euarchontoglires.” See Definitions below.

Epigenetics
According to genetics.thetech.org, summarizing Ledon-Rettig et al. 2012, “The environment can cause DNA mutations, Sunlight, cigarette smoke, and radiation are all known to cause changes to our DNA.” What factors in Africa affected such a wide range of morphologies to produce similar DNA strands in the DNA clade of Afrotheria? I don’t know, but the fact that several disparate morphologies all have a single African origin according to DNA, suggests that something in the sun, air, soil or water is the uniting factor. These factors might includes African viruses, volcanic emissions and invertebrates that live in the soil, perhaps as virus carriers. I don’t know which is correct or even if this list is complete, but this would make an excellent study starting point.

Whatever the altering factor is, I wonder if it was also responsible for reversing a perfectly good set of placental genitals to form a primitive cloaca in Madagascar tenrecs and hedgehogs.

That turtle DNA is closest to bird and croc DNA makes me wonder if there is something in the water, because that is the only factor all three might have in common. They certainly don’t share any obvious traits to the exclusion of all other extinct and extant candidates. This ‘something in the water’ could have been reacting with the DNA of turtles and archosaurs since the Permian. Again, this could be a very tough, but interesting study because we will never find turtles nesting with birds or crocs based on morphology that is not convoluted (i.e. to produce a temporal fenestra by removing a bone).

Bottom line: 
Any hypothesis of tetrapod interrelationships has to produce a series of generic taxa that demonstrate a gradual accumulation of traits. If one hypothesis does so with the aid of long ghost lineages, that’s an issue. The LRT does not have long ghost lineages uniting clades. So, let’s try not to accept imaginary scenarios when skeletal evidence produces more parsimonious ancestral and related candidates.

References
Asher RJ, Bennett N and Lehmann T 2009. The new framework for understanding placental mammal evolution”. BioEssays. 31 (8): 853–864.
Ledón-Rettig CC, Richards CL and Martin LB 2012. Epigenetics for behavioral ecologists. Behavioral Ecology. doi:10.1093/beheco/ars145
Sánchez‐Villagra MR, Narita Y and Kuratani S 2007. Thoracolumbar vertebral number: The first skeletal synapomorphy for afrotherian mammals. Systematics and Biodiversity. 5 (1): 1–7.
Seiffert Erik R 2007. A new estimate of afrotherian phylogeny based on simultaneous analysis of genomic, morphological, and fossil evidence. BMC Evolutionary Biology 7(1): 224.
Schoch RR and Sues H-D 2016. The diapsid origin of turtles. Zoology (advance online publication) doi:10.1016/j.zool.2016.01.004
http: // www.sciencedirect.com/science/article/pii/S0944200616300046?np=y
Springer, MS, Stanhope MJ, Madsen O and de Jong WW 2004. Molecules consolidate the placental mammal tree. Trends in Ecology and Evolution 19(8):430–438.
Tabuce R, Marivaux L, Adaci M, Bensalah M, Hartenberger J-L, Mahboubi M, Mebrouk F, Tafforeau P and Jaeger J-J 2007. “Early Tertiary mammals from North Africa reinforce the molecular Afrotheria clade”. Proceedings of the Royal Society B: Biological Sciences. 274(1614): 1159–1166.

Definitions
Afrotheria: the molecular superordinal hypothesis that includes the orders Proboscidea (elephants), Sirenia (manatees and dugongs), Hyracoidea (hyraxes), Tubulidentata (aardvarks), Afrosoricida (golden moles and tenrecs) and Macroscelidea (elephant shrews).
Anagalida: the morphology-based superordinal hypothesis that includes Rodentia (e.g. rats, mice and guinea pigs), Lagomorpha (rabbits, hares and pikas) and Macroscelidea (elephant shrews).
Archonta: the morphology-based superordinal hypothesis that includes Chiroptera (bats), Dermoptera (flying lemurs), Primates (e.g. humans, apes and monkeys) and Scandentia (tree shrews).
Euarchontoglires: the molecular superordinal hypothesis that includes the orders Rodentia (e.g. rats, mice and guinea pigs), Lagomorpha (rabbits, hares and pikas), Scandenta (tree shrews), Dermoptera (flying lemurs) and Primates (e.g. humans, apes and monkeys).
Laurasiatheria: the molecular superordinal hypothesis that includes the orders Eulipotyphla (hedgehogs, moles and shrews), Chiroptera (bats), Perissodac- tyla (horses, tapirs, and rhinos), Cetartiodactyla (e.g. camels, pigs, cows, hippos, whales and porpoises), Carnivora (e.g. dogs, bears and cats) and Pholidota (pangolins).

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