Carnivora genomic testing: Hassanin et al. 2021

From the abstract:
“The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora.”

Genomic tests too often do not and can not test fossil taxa leading to a problem with taxon exclusion. Moreover, genomic testing in deep time too often delivers false positives relative to phenomic (trait-based) traits that are designed to produce tree topologies in which all sister taxa greatly resemble one another, modeling micro-evolutionary events. Why this is so remains an unsolved problem. A phenomic cladogram (the LRT, subset Fig. x) that includes fossil taxa is found online here: http://reptileevolution.com/reptile-tree.htm

Figure 2. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Figure 1. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Talpa, the mole (Fig. 1), was excluded here, but nests within Carnivora in the phenomic analysis, the large reptile tree (LRT, 1803+ taxa, subset Fig. x).

Figure 1. Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Figure 2 Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Nandinia, the palm civet sure looks like it, but is not a basal member of Carnivora in the LRT, but a basal placental outgroup taxon to the clade Carnivora.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Figure 3. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Carnivora is the first major clade to split off
from basal Placentalia (Fig. x). Therefore, the proximal outgroup taxon, the woolly oppossum, Caluromys (Fig. 3) , should be included as the outgroup next time.

Figure 2. Subset of the LRT focusing on the Carnivora.

Figure x. Subset of the LRT focusing on the Carnivora.

By chilling contrast,
in the Hassanin et al. 2021 genomic analysis, a hoofed placental, the tapir (Tapirus), was used as the outgroup taxon. Given all other placentals for their choice of outgroup for Carnivora, why did they choose a relative of horses and rhinos? We’ve seen this sort of confused mayhem before and recently in genomic studies. Let’s all pray that the ghost of Alfred Sherwood Romer will come visit Hassanin et al. and all others who think this is a good idea.


References
Hassanin A, Veron G, Ropiquet A, Jansen van Vuuren B, Le´cu A, Goodman SM, et al. 2021. Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. PLoS ONE 16(2): e0240770. https://doi.
org/10.1371/journal.pone.0240770

New passerine genomic study not confirmed by phenomic study

Oliveros et al. 2019
produced an exhaustive DNA study from 137 passerine families, then calibrated their phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification.

Unfortunately
the large reptile tree (LRT, 1434 taxa) produced a different tree because it uses phenomic traits, not genes.

The two trees both started with birds of prey, including owls.
Then they diverged. The Oliveros team recovered 137 families of passerines arising from highly derived parrots, arising from highly derived owls.

The LRT recovered highly derived parrots arising from the more primitive hoatzin Opisthocomus, arising from the more primitive sparrow, Passer, arising from the more primitive grouse + chickens + peafowl and kin going back to Early Cretaceous Eogranivora. In the LRT owls give rise to birds of smaller prey: owlets, like Aegotheles, and swifts, like Apus, not herbivorous parrots.

Figure 1. Skeleton of the common house sparrow, Passer domestics.

Figure 1. Skeleton of the common house sparrow, Passer domestics. Note the heavy, seed-crunching beak, a precursor for the heavier see-crunching beak in parrots, not the other way around.

Among the traditional ‘passerines’ tested by the Oliveros team
are the distinctively different crows (genus Corvus) and nuthatches (genus Sitta). These clades nest apart from each other in the LRT and apart from Passer, the sparrow. In the LRT, crows and nuthatches are not Passerines, but parrots and hoatzins are passerines. Sometimes competing cladograms can be topsy-turvy like that, with similar sister taxa flipped with regard to primitive and derived. Earlier I mentioned ‘woodpeckers’, which have never been considered passerines, because woodpeckers and nuthatches are sisters in the LRT.

Robins (genus: Turdus) are considered passerines in the DNA study. They are crow relatives in the LRT. Jays (genus: Cyanocitta) and grackles (genus: Quiscalus) are crow relatives in the LRT. Neither are included in the DNA study that includes crows (genus: Corvus).

Figure 1. Several birds with zygodactyl feet (light red) and one member of the clade Zygodactylidae (red).

Figure 2. Subset of the LRT focusing on birds. This is how they are related to one another based on phenomic traits. Note the presence of Passer nesting between the chicken, Gallus and the parrot, Ara. Other purported passerines, like Turdus, Corvus and Sitta,  nest in other clades here.

So, once again,
when taxonomists use genomic (DNA) tests they run the risk of wasting their time when dealing with deep time taxa. Some paleo and bird workers put their faith in DNA, hoping it will recover relationships because it works well in humans. Unfortunately, too often phenomic tests are at odds with genomic tests to put  faith in genomic tests. Only phenomic (trait) tests recover cladograms that produce a gradual accumulation of traits among sister taxa, echoing deep time events. Only phenomic tests can employ fossils. Let’s not forget our fossils.

A suggestion for Oliveros et al. 2019:
test your results against your own phenomic study. If valid, both of your results will be the same. If not, one of your tests needs to be trashed.


References
Oliveros CH and 31 co-authors 2019. Earth history and the passerine superradiation.

www.pnas.org/cgi/doi/10.1073/pnas.1813206116

Molecules vs morphology in mammals: Beck and Baillie 2018

Some published thoughts
on traits vs. molecules just out in the last week.

Beck and Baillie 2018 titled their paper: 
“Improvements in the fossil record may largely resolve the conflict between morphological and molecular estimates of mammal phylogeny.” No. Just the opposite. But you can see exactly where they put their faith… not in what they can see and measure.

From the abstract (annotated):
“Morphological phylogenies of mammals continue to show major conflicts with the robust molecular consensus view of their relationships.” True.

“This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships, particularly for fossil taxa for which, in most cases, molecular data is unlikely to ever become available.” Just the opposite. Doubts should have been raised about molecular data, which can be influenced by local viruses. Only physical traits, i. e. the expression of activated molecules, resolves relationships, as the large reptile tree (LRT, 1255 taxa) attests. 

“We tested this under a hypothetical ‘best case scenario’ by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive molecular phylogeny of mammals, and then seeing what effect inclusion of these predicted ancestors had on unconstrained analyses of morphological data. We found that this resulted in topologies that are highly congruent with the molecular consensus, even when simulating the effect of incomplete fossilisation. Most strikingly, several analyses recovered monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria.” In other words, we used our imaginations to make molecule phylogenies work, rather than considering the possibility that molecular phylogenies did not work. 

“Our results suggest that, at least in principle, improvements in the fossil record may be sufficient to largely reconcile morphological and molecular phylogenies of mammals, even with current morphological character sets.” They used far too few taxa. And they used suprageneric taxa. They avoided fossil taxa. This is omitting available data. 

This is not the way science is supposed to work.
So why was this published?

References
Beck RMD and Baillie C 2018. Improvements in the fossil record may largely resolve the conflict between morphological and molecular estimates of mammal phylogeny. bioRxiv doi:10.1101/373191. First posted online July 20, 2018.

Click to access 373191.full.pdf

July 2011-July 2018: Marking 7 years of paleo-heresies.

On July 12, 2011
a new blogpost entitled, “Welcome to The Pterosaur Heresies” first appeared online. It was (and is) meant to be the newsletter for taxon additions to the large reptile tree (LRT, 1255 taxa) at ReptileEvolution.com. More complete explanations and documentation can be provided here than at ReptileEvolution.com.

Starting two days later (July 14, 2011) and for the next three days,
the several hypotheses of pterosaur origins were compared one with another.

About a week later (July 22, 2011)
a completely resolved family of pterosaurs was presented. This was the first one to include several specimens from all well-known genera and the first to include tiny Solnhofen pterosaurs, first listed by Peters 2007. Previously tiny pterosaurs had been ignored based on the false premise that they were juveniles of larger specimens. That is a disproved hypothesis that continues to make the rounds. And we said goodbye to the clade, “Pterodactyloidea” because now 4 clades are recovered that share all of the pterodactyloid-grade traits, while two others share some, but not all of those traits. Have other workers started to include tiny Solnhofen pterosaurs in their analyses? No.

On the last day of that first month (July 31, 2011)
a  phylogenetic analysis of just 235 taxa was presented that recovered a completely resolved and diphyletic Reptilia (= Amniota), with one branch, the new Lepidosauromorpha, containing turtles, pterosaurs and lepidosaurs and their many relatives. The other branch, the new Archosauromorpha, contained mammals, enaliosaurs, archosaurs and their many relatives. An amphibian-like reptile, Gephyrostegus was their last common ancestor.  Today, with more than 1000 additional taxa, the original topology from seven years ago remains unchanged. Have other workers started to include basal amphibian-like reptiles in their analyses? No.

In the seven years since July 2011
hundreds of exciting and heretical discoveries have been recovered. Some of these resolve long-standing problems by simply adding taxa. Others shed new light on topics that were not thought to be problems at all by simply adding taxa. Ironically, several other workers gained worldwide acclaim for ‘discovering’ relationships that were recovered in the LRT and promoted here years earlier. Still other workers continue to criticize the LRT, claiming it should have failed some time ago, but the LRT continues to grow.

Unfortunately,
a propagandistic pall was cast on the LRT, so most workers have ignored the taxon inclusion/exclusion suggestions offered here, leaving their work open to criticism from the ever-growing authority of the LRT.

Whatever the faults of the LRT,
the specimens included here need only be included in more focused analyses using independent character lists to test them. In other words, the faults don’t have to be employed, only the suggested taxa. When that happens, confirmation of the LRT has been the typical result. Why? Because the wide gamut and sheer number of taxa minimize the possibility of taxon exclusion, the number one problem in prior, less inclusive analyses. If you have a tetrapod of unknown affinity, test it here at the LRT.

One unexpected and disappointing discovery:
DNA analysis, the standard for crime-fighting and paternity questions, has not been able to replicate the results of wider trait studies. Rather, DNA studies lose their efficacy over large phylogenetic distances when compared to the trait-oriented LRT. Worse yet for paleontology, DNA cannot be used with most fossils. Unfortunately, many paleontologists still believe in the validity of DNA studies.

Figure 2. Dr. Sean Carroll and Dr. Antonis Rokas

Figure 1. Dr. Sean Carroll and Dr. Antonis Rokas

On that note…
Quoted from EvolutionNews.org, “Finally, a study published in Science in 2005 (Rokas and Carroll 2006) tried to use genes to reconstruct the relationships of the animal phyla, but concluded that “despite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” The following year, the same authors published a scientific paper titled, “Bushes in the Tree of Life,” which offered striking conclusions. The authors acknowledge that “a large fraction of single genes produce phylogenies of poor quality,” observing that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” The paper suggests that “certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.” The paper even contends that “the recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.”

I was not aware of that 2005 paper
before a few days ago. It needs to be more widely considered.

While other blogs journalistically report on the works of others,
the Pterosaur Heresies scientifically tests the work of others. That’s what sets it apart. That’s what makes it fun, interesting and rewarding. That’s what makes it controversial. Hopefully, that’s why you’re a subscriber. If, instead, you keep waiting for the LRT to crash and burn, well, that should have happened by now, don’t you think?

This July 2018,
seven years after it was started in 2011 with 235 taxa, there are 1000+ more taxa, all gradually blended in a tree topology that has been growing organically and with virtual complete resolution (some taxa known only from mandibles and other scraps are less resolved). Still, critics keep harping on the same perceived shortcomings (too many taxa, too few traits, not enough firsthand observation, lack of expertise)—while not harping on the shortcomings of traditional studies (principally taxon exclusion) that fail to produce gradually blended (= similar) sister taxa. There has always been a double standard at play, not only here, but for new hypotheses in geology, astronomy, physics, and paleontology. It’s universal and has been at work for centuries. It used to be that religious leaders led the charge against new ideas. Now we have PhDs trying to do the same.

Even scientists are not immune from this thing we call ‘human nature.’
Dr. J Ostrom complained about it, too. It’s human nature to follow authority, to go with the majority, and to suppress contra-indicators. Facts sometimes take decades to be widely accepted, and that’s just the way it is. It’s not acceptable, but that’s the way it is.

The beauty of science is
you, yes you can perform your own analysis to confirm or refute any analysis you read about here or anywhere. If I can do it… you can do it.

Thank you for your readership.
If there are subjects/taxa you want me to cover, or issues that need resolution, let me know. I look forward each day to corresponding with each and every one of you.

References
Peters D 2007. The origin and radiation of the Pterosauria. Flugsaurier. The Wellnhofer Pterosaur Meeting, Munich 27
Rokas A and Carroll SB 2006. Bushes in the Tree of Life. PLoS Biology, 4(11): 1899-1904.

refined-fine-tuned-placental-mammal-family-tree/

 

An OpenLetter to the OpenWings Project

According to their website:
“The goal of the OpenWings Project (http://blog.openwings.org) is to understand the evolutionary history of and evolutionary relationships among birds.”

“One of our goals in this project is to collect genomic data from DNA samples that have an associated voucher specimen in a research collection.”

Figure 2. Newell's shearwater (Puffinus newelli) in vivo.

Figure 1 Newell’s shearwater (Puffinus newelli) in vivo. We’ll examine the skeleton of this bird in an upcoming blogpost. 

“The fundamental and missing piece of this otherwise powerful comparative biology toolkit is an accurate and complete avian phylogeny. The overarching goal of the OpenWings Project is to fill this gap by producing: a complete phylogeny for all 10,560 bird species that will provide a unifying framework for understanding the origins and maintenance of avian diversity… as well as serving as a case study of the benefits and challenges of sampling all species in a major clade.”

Suggestion #1:
Start with a dozen diverse birds. IF the genotypes and phenotypes produce identical tree topologies, double that number and test two dozen birds. IF those produce identical tree topologies, test four dozen birds. Etc. Etc. You’ll get to 10,560 at that rate in ten steps with confidence that your results have been validated at every step.

If at any point the genotypes and phenotypes don’t produce identical tree topologies, review your paradigms and hypothesis. There is something wrong if they don’t match. In my testing, birds genes do not recover the same tree topologies as bird traits. Don’t waste your time and money testing 10,560 bird genes only to find they don’t deliver the same tree topology as bird traits.

Suggestion #2:
Since no large scale genomic and phenomic studies of birds have ever matched, just study phenotypes. Then you can include fossils and you won’t have to exclude taxa critical to understanding the phylogeny of birds. Click here for a starter list of taxa.

I would have contacted the OpenWings Project directly,
but (at present) they don’t provide access except through apps (like Twitter) I don’t have or want.

We looked at another DNA analysis of birds
by Prum et al. 2015 here and here and found it matched dissimilar taxa while separating similar taxa. So beware of DNA. It can only be validated with trait analysis and too often it produces odd results needing odd explanations.

References
https://www.markmybird.org
http://blog.openwings.org/2018/04/10/introducing-the-openwings-project/
https://www.ReptileEvolution.com/reptile-tree.htm

Another DNA analysis fails to replicate LRT analysis

Earlier we talked about the failure of DNA studies to replicate or confirm morphological studies in phylogenetic analysis. A few days ago Shaffer et al. 2017 discussed turtle origins using DNA, trying to figure out when turtles diverged from archosaurs (birds + crocs) and when cryptodires diverged from pleurodires.

Figure 1. From Schaeffer et al. a graphic showing the divergence times for cryptodires and pleurodires according to their studies of molecules and morphology.

Figure 1. From Schaeffer et al. a graphic showing the divergence times for cryptodires and pleurodires according to their studies of molecules and morphology. Some titles were added for clarity. 

From the Shaffer et al. abstract
“We used our genomic data to estimate the ages of living turtle clades including a mid-late Triassic origin for crown turtles and a mid-Carboniferous split of turtles from their sister group, Archosauria. By specifically excluding several of the earliest potential crown turtle fossils and limiting the age of fossil calibration points to the unambiguous crown lineage Caribemys oxfordiensis from the Late Jurassic (Oxfordian, 163.5–157.3 Ma) we corroborate a relatively ancient age for living turtles. We also provide novel age estimates for five of the ten testudine families containing more than a single species, as well as several intrafamilial clades. Most of the diversity of crown turtles appears to date to the Paleogene, well after the Cretaceous-Paleogene mass extinction 66 mya.
By contrast 
In the large reptile tree (LRT 1042 taxa) the divergence date between soft-shell turtles (like Odontochelys) and hard-shelled domed turtles (like Meiolania or perhaps Elginia) dates back probably to, but at least to the Late Permian with Elginia. Without valid outgroups, like Elginia and Sclerosaurus, there is no way Schaeffer et al. are going to get the base of their turtle tree right. And the dominoes fall from there.
The “mid-Carboniferous split” reported by Shaffer et al. between Archosauria and turtles is more or less supported by the LRT In that analysis the Viséan (Early Carboniferous) is when we have evidence that the Lepidosauromorpha (including turtle ancestors) and Archosauromorpha (including archosaur ancestors) had split apart from its last common ancestor, Gephyrostegus at the base of the Reptilia.
But let’s be clear,
turtles are in no way related to archosaurs, except at the very base of the Reptilia.
The journal title:
‘Molecular Phylogenetics and Evolution’
 (see below) is fast becoming an oxymoron and an invalidated science except when taxa are closely related to one another. Someone please mention this to the editors. Long phylogenetic distances constantly fail to produce DNA trees that match morphology trees, as everyone acknowledges, but no one else is ready to accept at present.

References
Shaffer HB, McCartney-Melstad E, Near TJ, Mount GG and Spinks PQ 2017. Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines). Molecular Phylogenetics and Evolution 115: 7–15. doi: https://doi.org/10.1016/j.ympev.2017.07.006

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).

Mammal evolution analyses using molecules

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. Sus (pig), Bos (cattle) and hippopotamidae (hippos) were outgroup taxa. 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.

References
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.

Things I didn’t know about phylogenetic analyses based on DNA molecules.

In my never ending quest to understand reptile phylogeny
I was fortunate to read Scotland et al. (2003) and Jenner (2004). Thankfully the latter rebutted the former. Scotland et al. are all plant scientists, so bear in mind, they deal with far fewer ‘moving parts’ in the taxa they study.

Scott et al. (2004) wrote: “We present the view that rigorous and critical anatomical studies of fewer morphological characters, in the context of molecular phylogenies, is a more fruitful approach to integrating the strengths of morphological data with those of sequence data. This approach is preferable to compiling larger data matrices of increasingly ambiguous and problematic morphological characters.

“In conclusion, problems surrounding character coding of morphological data reduce the number of unambiguous morphological characters for analysis. The crucial issue for morphology is that the already small number of morphological characters is further compromised by ambiguous homology assessment.

“DNA is much simpler. There is no ambiguity that the unit of comparison is the nucleotide and that adenine, guanine, cytosine, and thymine represent different versions of the same entity.
 
“Hillis and Wiens (2000) stated that dense taxon sampling is the greatest advantage of morphological data, citing recent simulation studies demonstrating the importance of taxon sampling for accurate phylogeny estimates (Hillis, 1996, 1998; Graybeal, 1998). For example, in one simulation study, Graybeal (1998) demonstrated that under some conditions phylogenetic accuracy was improved as the number of taxa increased, but not when more characters were added.”
There it is!. That’s what I’ve been saying!
Here’s the main problem with too few characters
according to Scotland et al. 2003):

“Another important issue relative to increased taxon sampling, in the context of morphological data, relates to the potential decreased number of unambiguous charactersas more taxa are added to a study. Characters that were discrete [in smaller studies] are no longer discrete when additional taxa were added.”
What the large reptile tree tells us:
Discrete characters are fine (they were Larry Martin’s favorite subject). But they’re not important in the scheme of things. What is important, as we’ve always heard, is the suite of characters present in each taxon. Let’s face it, sister taxa share all the characters that lump them together, except for the few that split them apart. And that happens again and again at every one of the 415 nodes in the large reptile tree.

A raft of clarity from Jenner 2004.
Jenner argued against Scotland et al. (2003) like this: “Scotland et al. (2003) evaluated the role of morphology in phylogeny reconstruction, and concluded that morphological evidence offers no hope to resolve phylogeny at any taxonomic level. Consequently, they advocated a very restricted role for morphology in phylogenetics, mainly by mapping selected morphological characters onto molecular phylogenies. I critically examined the scientific basis for the arguments of Scotland et al. (2003), and found them to be unconvincing.”

This is most enlightening from Jenner 2004:
“Nucleotides are characters of relatively low complexity, and the character state space for nucleotides is much more restricted than for morphology. In certain circumstances this creates a considerable danger that the same nucleotide has evolved independently in the same position, and this realization has been an incentive to develop models of evolution that estimate the probability that the same nucleotides at a site are historically identical, and to explore the value of more complex molecular characters. In contrast, morphology generally presents a richer space of more complex characters, which allows a more fine-grained comparison of potential homology, and this may help explain why in certain cases morphology may be qualitatively superior to molecules when considered per character.

“Scotland et al. (2014, 541) claim that these problems of “subjectivity and interpretation” are absent from molecular data, because “areas of ambiguity [in sequence alignment] can be excluded.” As recent research shows, to choose this way of least resistance may be thoroughly misleading, and this short statement seriously underplays the degree of subjectivity and interpretation asocial ted with molecular phylogenetics.”

Jenner then discussed more than a decade of 18S rDNA studies that suggested bird/mammal affinities, which, of course, was in conflict with morphological studies and other molecular data. Jenner continued:

“After the 18S data was analysed in various different ways by different workers, they concluded that this was an example of different molecules giving significantly different estimates of phylogeny. However, a recent study by Xia et al. (2003) convincingly showed that the conflict between 18S data and the traditional and other molecular data was an artifact attributable to two main factors: misalignment of sequences, and inappropriate estimation of base frequency parameters.

“Crucial to the resolution of this paradox was the incorporation in the molecular data set of those regions of the 18S molecule that were most variable, and most difficult to align unambiguously. This study clearly showed that restricting the data set to only the least unambiguous sites might produce a thoroughly misleading phylogeny. The problem that ‘different workers will perceive and define characters in different ways’ is therefore certainly not limited to morphological data.”

Ater reading Jenner (2004), you won’t wonder about DNA studies anymore. They’re not perfect and may never be. They don’t work for fossil taxa (you knew that already) and they often come up with bizarre results.

References
Graybeal A 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Systematic Biology 48:9-17.
Hillis DM 1996. Inferring complex phylogenies. Nature 383:140- 141.
Hillis DM 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
Hillis DM and Wiens JJ 2000. Molecules versus morphology in systematics. Pp 1-19 in Phylogenetic analysis of morphological data (J. J. Wiens, ed.). Smithsonian Institution Press, Washington, D.C.
Jenner RA 2004. Value of morphological phylogenetics. Accepting Partnership by Submission? Morphological Phylogenetics in a Molecular Millennium. Systematic Biology 53333-359.
Scotland RW, Olmstead RG and  Bennett JR 2003. Phylogeny Reconstruction: The Role of Morphology. Systematic Biology 52:539-548.
Xia X, Xie Z and Kjer KM 2003. 18S ribosomal RNA and tetrapod phylogeny. Systematic Biology 52:283-295.

When DNA analyses return untenable results

Sometimes DNA and RNA provide great insight into phylogenetic relationships.

Other times… not so much.

Ultimately molecule analyses have to be supported by morphological studies that enable us to see the gradual accumulation of traits in lineages. If we can’t see those gradual evolutionary changes, then we must assume there are agents in the DNA that are obfuscating relationships, rather than illuminating relationships.

Two cases in point:

Hedges & Poling (1999) argued that Sphenodon was more closely related to archosaurs than to squamates. This would require independent acquisition of a wide range of specialized features and takes no account of the fossil histories of the groups in question, according to Evans (2003).

Wiens et al., (2012) produced a molecule study of extant taxa that rearranged prior squamate trees, nesting Dibamus and gekkos at the base while nesting Anguimorpha and Iguania as derived sister clades. For those who don’t know Dibamus too well, it has no legs and a very odd skull morphology. In the large reptile tree it nests with other legless scincomorphs, with which it shares a long list of character traits.

Unfortunately these DNA studies, like ALL DNA studies, ignore fossil taxa.

But we need them.

On the other side of the coin recent work by Losos on extant anoles in the Carribbean seems to have turned up some interesting and viable results.

Not sure where to draw the line. Be careful out there.

References
Evans SE 2003. At the feet of the dinosaurs: the early history and radiation of lizards. Biological Reviews 78:513–551.
Hedges SB and Poling LL 1999. A molecular phylogeny of reptiles. Science 283, 998–1001.
Wiens JJ, et al. 2012. Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biology Letters. 2012 8, doi: 10.1098/rsbl.2012.0703.