Sloth DNA results “differ substantially from morphology-based concepts”

Presslee et al. 2019
used mitochondrial DNA to assess relationships of tree sloths and their extinct relatives. “Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts.”

Figure 2. Subset of the LRT focusing on the Edentata. Armored taxa are color tinted and their branches are thicker.

Figure 2. Subset of the LRT focusing on the Edentata. Armored taxa are color tinted and their branches are thicker.

No, kidding!
The Presslee team essentially flipped the clade Edentata upside-down and twisted it around, nesting the small arboreal and ant-loving taxa at the base and the basal herbivorous giants as derived. This conclusion is based on morphological testing in the large reptile tree (LRT, 1500 taxa; subset Fig. 1)

‘Palaeoproteomics’
is the term used to describe the applications of proteomics ( the analysis of sets of proteins) to ancient materials.


The validated outgroup taxon in the LRT, Barylambda,
was not tested by Presslee’s team.

The invalid outgroup they chose, Dasypus (the armadillo)
is a derived taxon in the LRT.

Summary
This study was a waste of time and paper. Phylogenetic analysis yields false positives when invalid outgroup taxa are employed. The software does not know any better than to follow instructions. Colleagues, please don’t trust DNA. Don’t choose an outgroup taxon. Let a wider gamut study that includes 1500 candidates choose a validated one for you.


References
Presslee S et al. (19 co-authors) 2019. Palaeoproteomics resolves sloth relationships. Nature Ecology & Evolution Online access.

The pink fairy armadillo joins the LRT as a glyptodont…

…not an armadillo.
The pink daily ‘armadillo’ (genus: Chlamyphorus) nests with the much larger glyptodont, Holmesina in the large reptile tree (LRT, 1255 taxa, subset Fig. 4), not with Dasypus novemcinctus, the extant llong-nosed armadillo nesting on the other side of the aardvark Orycteropus. Another fairy armadillo (genus: Calyptophractos) is also described here.

The pink fairy armadillos
(genus: Chlamyphorus trunca) and the greater fairy armadillo (genus: Calyptophractos retusus) are little glyptodonts. This is not heretical news (Fig. 1).

Figure 3. When glyptodonts were nested with armadillos, the fairy armadillos nested with extinct glyptodonts. Cladogram from xx

Figure 1. When glyptodonts were nested with armadillos, the fairy armadillos nested with extinct glyptodonts. Cladogram from Delsuc et al. 2016, a DNA analysis. No aardvarks were tested here.

Using DNA
(both ancient and modern) Delsuc et al. 2016 nested the fairy armadillo with the extinct glyptodont, Doedicurus (Fig. 1). We already know not to trust DNA evidence in paleontology, but in this case trait analysis supports something like this arrangement of taxa. The distance is not great either way.

Figure 2. DNA analysis by Möller-Krull et al. 2007 omits fossil taxa and aardvarks and arrives at this tree topology of extant edentates.

Figure 2. DNA analysis by Möller-Krull et al. 2007 omits fossil taxa and aardvarks and arrives at this tree topology of extant edentates.

Delsuc et al. 2016 nested fairy armadillos with glyptodonts
when they attempted to nest glyptodonts within the armadillo clade using DNA, omitting other fossil taxa.  I did not see LRT outgroups in their cladogram, nor did I see the aardvark.

Figure 3. Skulls of Holmesina and Calyptophractus compared.

Figure 3. Skulls of Holmesina and Calyptophractus compared. When they are together, the similarities are obvious.

Here in the LRT Calyptophractus is a phylogenetic miniature of Holmesina, with a shorter rostrum and expanded cranium (Fig. 3), along with its much smaller size and thinner scales. In lateral view the skulls are quite alike and distinct from all other edentates.

We know that aardvarks (genus: Orycteropus) nest with edentates because all the other possibilities were offered and found to be not as parsimonious (similar). Earlier we looked at the nesting of Holmesina and the phylogenetic fact that all aardvarks, armadillos and anteaters are derived from various types of glyptodonts.

Figure 2. Subset of the LRT focusing on the Edentata. Armored taxa are color tinted and their branches are thicker.

Figure 4. Subset of the LRT focusing on the Edentata. Armored taxa are color tinted and their branches are thicker.

References
Delsuc F et al. 2016. The phylogenetic affinities of the extinct glyptodonts. Current Biology 26(4):R155–R156.
Harlan R 1825. Annals of the Lyceum of Natural History of New York 1:235.
Möller-Krull M et al. 2007. Retroposed Elements and Their Flanking Regions Resolve the Evolutionary History of Xenarthran Mammals (Armadillos, Anteaters, and Sloths). Mol. Biol. Evol. 24 (11): 2573–2582. PDF
Yarrell W 1828. On the osteology of the Chlamyphorus truncatus of Dr. Harlan microform; in a letter to N.A. Vigors. Zoological Journal 3:544–554.

AKA
Pink Fairy Armadillo, Lesser Fairy Armadillo, Lesser Pichi Ciego, Pichiciego
http://www.iucnredlist.org/details/4704/0

Greater Fairy Armadillo, Burmeister’s Armadillo, Chacoan Fairy Armadillo, Greater Pichi Ciego: http://www.iucnredlist.org/details/4703/0

wiki/Pink_fairy_armadillo

https://www.amnh.org/explore/news-blogs/research-posts/study-finds-relationship-between-glyptodonts-modern-armadillos/

https://www.forbes.com/sites/shaenamontanari/2016/02/23/ancient-dna-from-extinct-glyptodont-reveals-it-was-a-really-big-armadillo/#2cb057ae287d

Think of aardvarks and sloths as naked and hairy glyptodonts respectively

Because
that’s what they really are… aardvarks are naked and sloths are hairy glyptodonts. And, yes, that comes as a surprise, it breaks a paradigm, it spins your head around, it’s heretical… and it’s exactly where the data takes us.

The Edentata is an odd clade
in which the basalmost taxa, like Barylambda, Glyptodon and Holmesina are very large. On the other hand, terminal extant and derived taxa, like Peltephilus and Cyclopesare much smaller, just the opposite of most mammal clades (in which smaller usually lead to larger, following Cope’s Rule.)

According to Wikipedia,
“Glyptodontinae (glyptodonts or glyptodontines) are an extinct subfamily of large, heavily armored armadillos which developed in South America and spread to North America.”

In the large reptile tree (LRT, 1252 taxa) the glyptodont, Glyptodon, nests between the massive Barylambda and giant sloths, followed by smaller tree sloths and small extinct horned armadillos, like Peltephilus. On another branch (Fig. 1) another large glyptodont, Holmesina, nests between the massive Barylambda and the much smaller aardvark, Orycteropus, the armadillo, Dasypus, and the anteaters, Tamandua and Cyclopes.

Such a big-to-small phylogenetic pattern,
is known as phylogenetic miniaturization or the Lilliput Effect and is often the product of neotony (adults retaining juvenile traits, including juvenile size).

Figure 2. Holmesina, the glyptodont ancestor to aardvarks, anteaters and armadillos.

Figure 2. Holmesina, the glyptodont ancestor to aardvarks, anteaters and armadillos. Those are aardvark hands (Fig. 3), glyptodont feet.

Holmesina (Fig. 2) is added to the LRT today.
Basically it is a longer-snouted glyptodont, basal to the longer snouted above-mentioned aardvarks, armadillos and anteaters.

Following a reader comment,
(suggesting ‘taxon exclusion’ was the issue that did not unite glyptodonts with armadillos) I was looking for a transitional taxon to more closely nest glyptodonts with armadillos, rather than sloths. I did so and the tree topology did not change when Holmesina was added. Armadillos are still one taxon removed from glyptodonts, but at least now we have a glyptodont on the long-nosed clade of aardvarks, etc.. As before, aardvarks nest between glyptodonts and armadillos. Looking at all the edentate taxa in detail and overall. I think this nesting and this tree topology seem very reasonable (= it produces a gradual accumulation of derived traits at all nodes and between all taxa).

Figure 3. Orycterpus, the extant aardvark, is a living sister to Barylambda from the Paleocene.

Figure 3. Orycterpus, the extant aardvark, is a living sister to Barylambda from the Paleocene. Aardvarks traditionally nest alone, but in the LRT they are edentates without armor… or hair.

Other workers, like Fernicola, Vizcaíno and Fariña 2008,
described the phylogeny of glyptodonts by putting taxa like Holmesina at the base while omitting Barylambda. Thus such studies do not present the full picture due to taxon exclusion. Everyone seems to omit Barylambda and all the other edentate outgroups back to Devonian tetrapods… but not the LRT.

Goodbye ‘Xenarthra’. Goodbye ‘Pilosa’. Goodbye ‘Cingulata’.
According to Wikipedia, “The order Pilosa is a group of placental mammals, extant today only in the Americas. It includes the anteaters and sloths, including the extinct ground sloths, which became extinct about 10,000 years ago.” According to Wikipedia, Cingulata, part of the superorder Xenarthra, is an order of armored New World placental mammals.” In the LRT ‘Xenarthra’ (Cope 1889) is a junior synonym for ‘Pilosa’ (Flower 1883) and that is a junior synonym for Edentata (Darwin 1859).

References
Darwin C 1859. On the origin of species.
Fernicola JC, Vizcaíno SF and Fariña RA 2008.
The evolution of armored xenarthrans and a phylogeny of the glyptodonts. Chapter 7 in: The Biology of the Xenarthra, Eds: Vizcaíno SF and Loughry WJ. University Press of Florida.
Gaudin TJ and Croft DA 2015. Paleogene Xenarthra and the evolution of South American mammals. Journal of Mammalogy 96 (4): 622–634. https://doi.org/10.1093/jmammal/gyv073

http://www.finedictionary.com/Edentata.html

 

 

 

 

What is Fruitafossor? A basal echidna from Colorado

Updated March 23, 2021
with revised scoring that moved Fruitafossor, an edentate-mimic, to a basal relationship with Cifelliodon (Early Cretaceous) and Tachyglossus (extant), two echidnas. Luo and Wible 2005 tested Tachyglossus, but did not know about Cifelliodon, published in 2018.

Fruitafossor
was a Late Jurassic fossorial digger with universally acknowledged xenarthran (edentate) traits including a long lumbar area that included xenarthran (interlocked) vertebrae. For reasons unknown Luo and Wible 2005 did not test Fruitafossor against another fossorial xenarthran, Peltephilus. Rather the authors compared their digger to an arboreal sloth, Bradypus, among several other taxa, including distinctly different anteaters and armadillos.

Figure 1. Scapula of Fruitafossor compared to several candidate sisters. Luo and Wible made things a bit more difficult by presenting left and right scapulae. Here they are all left scapulae for ready comparison. There is no doubt that the Fruitafossor scapula looks more like that of Ornithorhynchus.

ºªº Figure 1. Scapula of Fruitafossor compared to several candidate sisters. Luo and Wible made things a bit more difficult by presenting left and right scapulae. In frame 2 they are all left scapulae for ready comparison. There is no doubt that the Fruitafossor scapula was illustrated to look more like that of Ornithorhynchus. Unfortunately the photo data (Fig. 2) does not clearly support that shape. That shape is so important, it needed to be better documented.

Luo and Wible 2005
brought us a small, mostly articulated, rather crushed and incomplete Late Jurassic mammal with simple blunt teeth and digging forelimbs. Fruitafossor windscheffeli (Figs. 1–6) is best represented by a CT scan (Figs. 2–4) and original drawings (Figs. 5, 6) created by Luo and Wible.

Figure 2. Fruitafossor in situ from Digimorph.org and used with permission and here colorized to an uncertain extent.

Figure 2. Fruitafossor in situ from Digimorph.org and used with permission and here colorized to an uncertain extent. All those little white dots could be scattered osteoderms.

The original analysis
nested Fruitafossor between extremely tiny Hadrocodium + Shuotherium and the pre-mammal, Gobiconodon, in a tree topology that does not resemble the topology of the large reptile tree (LRT, 1048 taxa then, 1818+ taxa now). The authors noted Fruitafossor is “not a eutherian, let alone a xenarthran” despite noting Fruitafossor had tubular molars and xenarthran intervertebral articulations, traits otherwise found only in xenarthrans.

Earlier
the LRT nested Fruitafossor with the horned, armored digging ‘armadillo’ more closely related to BradypusPeltephilus. Reconsideration of several traits now nests Fruitafossor with the echindas Cifelliodon and Tachyglossus.

Luo and Wible compared
Fruitafossor to the arboreal and extant Bradypus, but not to the fossorial and extinct Peltephilius.

Figure 5. Several drawings from Zhou and Wible that one must trust for accuracy. The verification data is too fuzzy to validate.

Figure 3. Several drawings from Luo and Wible that one must trust for accuracy. The verification data is too fuzzy to validate. As in other xenarthrans, the ilia actually form a pair of horizontal plates on either side of the long fused and eroded sacrals. Four fingers is a trait shared with Peltephilus. Imagine that rib cage wider and not so deep.

The retention of the coracoid
in Fruitafossor is a trait found in pre-Therian mammals. Comparisons to echidnas were previously overlooked, but are presently more parsimonious, down to the sprawling limbs. Early Cretaceous Cifelliodon retains derived tubular teeth, precursors to the toothless condition found in extant Tachyglossus. Loss of manual digit 5 in Fruitafossor could be due to taphonomy since the skeleton is somewhat scattered (Fig. 2).

Figure 1. Early Cretaceous Cifelliodon is ancestral to the living echidna, Tachyglossus according to the LRT. The lack of teeth here led to toothlessness in living echidnas. The skull of Tachyglossus is largely fused together, lacks teeth and retains only a tiny lateral temporal fenestra (because the jaws don't move much in this anteater. Compared to Cifelliodon the braincase is greatly expanded, the lateral arches are expanded and the two elements fuse, unlike most mammals.

Figure 4. Early Cretaceous Cifelliodon is ancestral to the living echidna, Tachyglossus according to the LRT. The lack of teeth here led to toothlessness in living echidnas. The skull of Tachyglossus is largely fused together, lacks teeth and retains only a tiny lateral temporal fenestra (because the jaws don’t move much in this anteater. Compared to Cifelliodon the braincase is greatly expanded, the lateral arches are expanded and the two elements fuse, unlike most mammals.

Figure 3. Tachyglossus skeleton, manus and x-rays. Note the perforated pelvis.

Figure 5. Tachyglossus skeleton, manus and x-rays. Note the perforated pelvis.

Fruitafossor windscheffeli
(Luo and Wible 2005; Late Jurassic) was originally considered a digging basal mammal based on the shape of the scapula and sprawling forelimbs. Here Fruitafossor nests as a basal echidna from Colorado, prior to tooth loss. The teeth are blunt, as in xenarthrans, and the four fingers (perhaps five originally) have broad, digging claws with short phalanges. The torso was wider than deep with a long lumbar area that included xenarthran (interlocked) vertebrae. The skeleton was µCT scanned (see above).


References
Luo Z-X and Wible JR 2005. A late Jurassic digging mammal and early mammal diversification. Science 308:103–107.

wiki/Fruitafossor

Glyptodonts: Armored sloths, not giant armadillos.

Today three taxa were added
to the large reptile tree (now 720 taxa, subset Fig. 1):

  1. Bradypus (three-toed sloth)
  2. Dasypus (armadillo)
  3. Glyptotherium (glyptodont)

Wikipedia reports, “Glyptodonts are an extinct subfamily of large, heavily armored armadillos. Unfortunately, Glyptotherium the glyptodont nests with Bradypus, the sloth in the large reptile tree – and, as you’ll see… for good reason.

Figure 1. Mammals with a few edentates added. Here glyptodonts nest with sloths, rather than armadillos, contra traditional studies.

Figure 1. Mammals with a few xenarthans added. Here glyptodonts nest with sloths, rather than armadillos, contra traditional studies.

Bradypus is the long-legged arboreal tree-hanging sloth
with fewer toes. Just imagine where the short-legged ground sloth will nest. This hypothesis of edentate relationships runs counter to tradition, but one look at the skulls (Figs. 1, 2) and you’ll wonder why this hasn’t been noticed before.

Figure 2. Bradypus skull from Digimorph.org, used with permission, colors added to select bones.

Figure 2. Bradypus skull from Digimorph.org, used with permission, colors added to select bones. Compare to the glyptodont skull in figure 3. Darker images bring out lighter details.

Both the sloth and the glyptodont
have deep, narrow, flat-topped skulls with a deep ventral process of the jugal and a very short rostrum. These traits, along with a long list of others, split armadillos + aardvarks from sloths + glyptodonts.

Figure 3. Glyptodon skull with select bones colorized. Compare to the sloth in figure 2 and the armadillo in figure 4.

Figure 3. Glyptodon skull with select bones colorized. Compare to the sloth in figure 2 and the armadillo in figure 4.

Here armadillos nest with
aardvarks, like Orycteropus, a clade that was once accepted under the clade Xenartha. According to Wikipedia, xenarthans have extra vertebral articulations, the lowest metabolic rates among therians, the ischium and sacrum are fused and males have internal testicles. Pangolins were once considered xenarthans, but here nest with basal primates.

Figure 4. Skull of the armadillo Dasypus from Digimorph.org, used with permission. and select bones colorized.

Figure 4. Skull of the armadillo Dasypus from Digimorph.org, used with permission. and select bones colorized.

 

Note the nesting of 
whales (Maiacetus) + tenrecs (Hemicentetes), another clade without external testicles. As a scientist, I’m pleased to discover these interrelationships, but a little surprised that no one has seen this before. If you that has happened already, I will be glad to promote those papers here.

Placental mammals
are showing a basal split between carnivores and other insectivore / herbivore placentals (eutherians).