‘The Dawn of Mammals’ YouTube video illuminates systematic problems

Part of this YouTube video (see below, click to view)
pits DNA paleontolgist, Dr. Olaf Bininda-Emonds (U. Oldenburg), against bone trait paleontologist, Dr. John Wible (Carnegie Museum of Natural History) in their common and contrasting search for basal placental mammals. Both realize that DNA cladograms do not replicate bone cladograms and DNA cannot be utilized with ancient fossils.

Dr. Bininda-Emonds, used molecular clocks
in living taxa to hypothetically split marsupials from placentals about 160 mya ago (Late Jurassic).

By contrast, Dr. Wible reports (28:53),
“Our study supported the traditional view that there were no fossils living during the Cretaceous [that] were members of the placental group itself. There were only ancestors of the placentals living.” (unscripted verbatim)

The impulse for this argument
came from the discovery of Maelestes (Wible et al. 2007a,b; 28:30 on the video) from the Late Cretaceous (75 mya). Dr. Wible’s paper nested Maelestes with the pre-placental, Asiorcytes, another tree-shrew-like mammal from the Late Cretaceous. By contrast, the LRT, nests Maelestes unequivocally at the base of the tenrec/odontocete clade, well within the placental clade (Fig. 2), as we learned earlier here.

The large reptile tree
 (subset in Fig. 2) nests the first known placental mammals at the 160 mya mark, matching the DNA predictions of Dr. Bininda-Emonds et al. A long list of taxa, including Maelestes, nest in the Jurassic and Cretaceous, contra Wible et al. Only more complete taxa are tested in the LRT and dental traits are not emphasized.

Figure 2. Mesozoic time line showing the first appearances of several fossil mammals and the clades they belong to.

Figure 2. Mesozoic time line showing the first appearances of several fossil mammals and the clades they belong to. Many, if not most of the listed taxa are late survivors of earlier radiations, sometimes much earlier radiations. Monodelphis and Didelphis are extant animals that originated in the Early Jurassic at the latest. Note also the large gaps over tens of millions of years, highlighting the rarity of fossil bearing locales.

In the video Dr. Wible says, “Many modern groups, according to the molecular clock analysis, actually are, they should be, present in the Cretaceous fossil record. We can’t find them.” Actually Dr. Wible already found them, but does not recognize them for what they are. That’s a common problem in paleontology, largely due to taxon exclusion, that we’ve seen before here, here, here and here. And in dozens of other mislabeled clades, like multituberculates.

The Bininda-Edmonds et al. paper reports,
“Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic ‘fuses’ leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today’s mammals.”

The LRT agrees with the timing indicated by the DNA analysis
Placentals are indeed found in the LRT Cretaceous and Jurassic fossil record (Fig. 2). They were not recognized by traditional workers using smaller taxon lists, for what they were. The LRT minimizes taxon exclusion and so solves many paleo problems with an unbiased and wide gamut approach currently unmatched in the paleo literature. Extant birds have a similar deep time record based on a few recent finds.

Perhaps overlooked
there are currently large gaps spanning tens of millions of years, highlighting the rarity of fossil bearing locales. All Mesozoic mammals are rare.

The DNA tree
of the Bininda-Emonds team correctly splits monotremes from therians, but incorrectly nests ‘Afrotherians‘ with Xenarthrans at the base of all mammals followed by moles + shrews, bats + carnivores + hoofed mammals + whales, followed by primates and rodents. As anyone can see, this is a very mixed up order, placing small arboreal taxa in derived positions and stiff-backed elephants and in in basal nodes. This DNA analysis is not validated by the LRT.

To its credit, basal mammals in the LRT
greatly resemble their marsupial ancestors. Then derived mammals become generally larger, with derived tooth patterns, stiffer dorsal/lumbar areas and longer pregnancies with more developed (precocious) young.

Given three cladograms of placental relationships,
none of them identical, how does one choose which one is more accurate? Here’s my suggestion: look at each sister at each node and see where you best find a gradual accumulation of derived traits, without exception. And look at outgroups leading to basal members of the in group.

Some readers are still having a hard time realizing
that someone without direct access to fossils and without a PhD is able to recover a more highly resolved cladogram that features gradual changes between every set of sister taxa than trees published over the last ten years in the academic literature. I agree. This should not be taking place. This is not what I expected to find when I started this 7-year project. One tends to trust authority. It’s been an eye-opening journey. In nearly all tested studies overlooking relevant taxa continues to be the number one shortcoming. The LRT minimizes that issue. The number two problem is blind faith in DNA results. The number three problem is an apparent refusal to examine phylogenetic results to weed out mismatched recovered sister taxa.

The video spends also some time with Zhangheotherium,
which we looked at earlier here and here. The interviewed workers talk about the ankle spur, but as a venom injector, as in the duckbill, Ornithorhynchus, not as a membrane frame, like a calcar bone, as in bats.

The video considers Repenomamus a large Early Cretaceous mammal
but the LRT nests Repenomamus as a late-surviving synapsid pre-mammal, derived from a sister to Pachygenelus, as we learned earlier here.

PS. As touched on earlier,
many basal arboreal mammals were experimenting with gliding (e.g. Volaticotherium and Maiopatagaium), but only one clade, bats, experimented with flapping. This was, perhaps not coincidentally, during the Middle to Late Jurassic (Oxordian, 160 mya). Remember, these gliding membranes were all extensions of the infant nursery membrane found in colugos and other volatantians, not far from the basalmost placental, Monodelphis.

References
Bininda-Emonds ORP, et al., (9 co-authors) 2007. The delayed rise of present-day mammals. Nature 446(7135):507-512.
Wible JR, Rougier GW, Novacel MJ and Asher RJ 2007a. The eutherian mammal Maelestes gobiensis from the Late Cretaceous of Mongolia and the phylogeny of Cretaceous Eutheria. Bulletin of the American Museum of Natural History 327:1–123.
Wible JR, Rougier GW, Novacek MJ and Asher RJ 2007b. Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary.” Nature, 447: 1003-1006.

 

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Bird, pterosaur, dinosaur simplified chronology

Following the earlier post on non-arboreal post K-T boundary birds…

…this one pretty much speaks for itself.
Here (Fig. 1) is a chronology, very much simplified, of birds, pterosaurs and dinosaurs according to the LRT.

Figure 1. Mesozoic chronology of bird, dinosaur and pterosaur clades.

Figure 1. Mesozoic chronology of bird, dinosaur and pterosaur clades based on taxa in the LRT.

If you’re curious about any of the taxa,
in the chronology, simply use Keywords to locate them.

New Como Bluff (Latest Jurassic) pterosaurs

Bits and pieces
of new Latest Jurassic pterosaurs are coming out of aquatic deposits in western North America according to McLain and Bakker 2017. The material is 3D and not very mineralized, so it is extremely fragile.

Specimen(s) #1 – HMNS/BB 5027, 5028 and 5029
“One proximal and two distal femora match a complete femur (BYU 17214) referred to Mesadactylus. Unexpectedly, both of the BBF distal femora possess a large intercondylar pneumatopore. BYU 17214 also possesses an intercondylar pneumatopore, but it is smaller than in the BBF femora. Distal femoral pnuematicity is previously recognized only in Cretaceous azhdarchoids and pteranodontids.”

The Mesadactylus holotype and referred specimens reconstructed to match the flightless pterosaur, Sos2428.

Figure 1. The Mesadactylus holotype (Jensen and Padian 1989) nests with the North American anurognathids. Several referred specimens (Smith et al. 2004), when reconstructed nest at the base of the azhdarchidae, with Huanhepterus and the flightless pterosaur SOS 2428.  The new BYU 17214 femur is essentially identical to the femur shown here.

Earlier we looked at two specimens referred to Mesadactylus. One is an anurognathid (Fig. 1). The other is a basal azhadarchid close to Huanhepterus, not far removed from its Dorygnathus ancestors in the large pterosaur tree. Instead McLain and Bakker compare the femora with unrelated and Early Cretaceous Dsungaripterus, which convergently has a similar femur. The better match is to the basal azhdarchid, so distal femoral pneumaticity does not stray outside of this clade. By the way, it is possible that Mesadactylus was flightless.

Specimen(s) #2 – HMNS/BB 5032 (formerly JHU Paleon C Pt 5)
“A peculiar BBF jaw fragment shows strongly labiolingually compressed, incurved crowns with their upper half bent backwards; associated are anterior fangs. We suspect this specimen is a previously undiagnosed pterosaur.”

These toothy specimens were compared to two Early Cretaceous ornithocheirids, one Middle Jurassic dorygnathid, and one Latest Jurassic bird, Archaeopteryx. None are a good match. A better, but not perfect,match can be made to the Early Jurassic pre-ctenochasmatid, Angustinaripterus (Fig. 2) which has relatively larger posterior teeth than does any Dorygnathus specimen.

The HMNS BB 5032 specimen(s) probably belong to a new species of Angustinaripterus or its kin based on the relatively large posterior teeth not seen among most Dorygnathus specimens.

The HMNS BB 5032 specimen(s) probably belong to a new species of Angustinaripterus or its kin based on the relatively large posterior teeth not seen among most Dorygnathus specimens.

As before,
we paleontologists don’t always have to go to our ‘go to’ taxon list of familiar fossils. Expand your horizons and take a fresh look at some of the less famous taxa to make your comparisons. You’ll find a good place to start at ReptileEvolution.com

References
McLain MA and RT Bakker 2017. Pterosaur material from the uppermost Jurassic of the uppermost Morrison Formation, Breakfast Bench Facies, Como Bluff,
Wyoming, including a pterosaur with pneumatized femora.

Laquintasaura: verrrry basal ceratopsian from the Early Jurassic

Figure 2. Phytodinosauria with a focus on Stegosauria (yellow green).

Figure 1. Subset of the LRT focusing on the Phytodinosauria. Here Laqunitasaura nests at the base of the Ceratopsia.

I still hold to the hypothesis|
that a phylogenetic analysis that is able to lump and separate taxa is better than one that cannot do this. In the large reptile tree (LRT, 989 taxa), Laquintasaura venezuelae (Barrett et al. 2014; Early Jurassic, 200mya ~1m in overall length; Fig. 2) nests at the base of the ceratopsia (outside of Hexinlusaurus and Yinlong) and not far from the base of the Ornithopoda (outside of Changchunsaurus). It is very plesiomorphic and very early even for an ornithischian, let alone a ceratopsian.

Figure 1. Laquintasaura and tooth from Barrett et al. 2014. The early and plesiomorphic ornithischian has a naris shifted dorsally and other traits that nest it between the base of the onithopoda (Changchunsaurus) and the base of the ceratopidae (Hexinlusaurus).

Figure 2. Laquintasaura and tooth from Barrett et al. 2014. The early and plesiomorphic ornithischian has a naris shifted dorsally and other traits that nest it between the base of the onithopoda (Changchunsaurus) and the base of the ceratopidae (Hexinlusaurus). Compare to premaxillary teeth in figure 3.

Barrett et al. were not so sure where Laquintasaura nested
as they reported, “A strict consensus of these 2160 MPTs places Laquintasaura in an unresolved polytomy with the major ornithischian clades Heterodontosauridae, Neornithischia and Thyreophora along with other early ornithischian taxa, such as Lesothosaurus.”

The Barrett et al. diagnosis reports:
“Laquintasaura can be differentiated from other early ornithischians by the following autapomorphic combination  of dental characters: cheek tooth crowns have isosceles-shaped outlines, which are apicobasally elongate, taper apically, are mesiodistally widest immediately apical to the root/crown junction, possess coarse marginal denticles extending for the full lengths of the crown margins, and possess prominent apicobasally extending striations on their labial and lingual surfaces. Postcranial autapomorphies include: sharply inflected dorsal margin of ischium dorsal to the obturator process; femoral fibula epicondyle medially inset in posterior or ventral views; and astragalus with a deep, broad, ‘U’-shaped notch in anterior surface.”

I had no access to the fossil(s).
And I had to trust the drawing produced by Barrett et al. (Fig. 1) for my data. Contra the Barrett et all. analysis, there was no loss of resolution with Laquintasaura in the LRT.

Figure 2. The skull of Yinlong a basal certatopsian.

Figure 3 The skull of Yinlong a basal certatopsian. Those premaxillary teeth are quite similar to those figure in Barrett et al. for Laquintasaura. Note the dorsal naris, horizontal ventral premaxilla.

References
Barrett PM, Butler RJ, Mundil R, Scheyer TM, Irmis RB, Sánchez-Villagra MR. 2014. A palaeoequatorial ornithischian and new constraints on early dinosaur diversification. Proceedings of the Royal Society B 281:20141147. http://dx.doi.org/10.1098/rspb.2014.1147

Jurassic birds took off from the ground – SVP abstracts 2016

Everyone knows:
Ground up hypothesis – 

implies and includes flapping, always has. Birds flap, always have, at least since the elongation and locking down of the coracoid in ancestral troodontids.

Trees down hypothesis –
has always implied gliding. Gliders don’t flap, never have.

But
baby birds dropping out of trees always flap. It’s what they do. But that fact is often ignored in bird origin videos.

And, as everyone knows by now…
young birds with pre-violant wings flap them like crazy when climbing bipedally — even vertical tree trunks… also something several animated bird origin videos ignore, perhaps because of one glaring opposite extant example: the young wet hoatzin that struggles to climb with all four limbs.

With that preamble…Habib et al. 2016 provide us
a hypothesis on the origin of bird flight that appears to ignore trees and experimental work with pre-volant birds and goes straight to take-off from flat ground. Is that okay?

From the abstract:
“Many small non-avian theropods possessed well-developed feathered forelimbs, but questions remain of when powered flight evolved and whether it occured more than once within Maniraptora. Here, using a first principles modeling approach, we explore these questions and attempt to determine in which taxa takeoff and powered flight was possible. Takeoff is here defined as a combination of both the hindlimb driving the ballistic launch phase, and the wing-based propulsion (climb out). [1]

“Microraptor, Rahonavis, [2] and all avian specimens generated sufficient velocity during leaping or running for takeoff. We re-ran our analysis factoring in life history changes that can alter the flight capability in extant avians, such as egg retention and molting, to examine how these would influence take off capacity. Of the two, molting shows the most significant effects.

“When these results are coupled with work detailing the lack of arboreal features among non-avian maniraptorans and early birds, they support the hypothesis that birds achieved flight without a gliding intermediary step, something perhaps unique among volant tetrapod clades.” [3] [4] [5]

Figure 2. Cosesaurus running and flapping - slow.

Figure 1. Cosesaurus running and flapping – slow.

Notes

  1. Interesting that Habib et al. ignore the presence of trees, which are key to Dial’s hypothesis (updated in Heers et al. 2016)  and opts to go straight from ground to air. That kind of ignores key work, doesn’t it? You might recall that Dr. Habib became famous as the author of the infamous but popular forelimb quad launch hypothesis for pterosaurs.
  2.  Microraptor and Rahonavis are NOT in the lineage of birds in the LRT, but both show how widespread long feathered wings were in Theropoda. The former has elongate coracoids by convergence. The latter does not preserve coracoids, fingers or feathers, but does have the long forearm that might imply bird-like proportions for missing bones… or not.
  3. Apparently Habib et al. assume that pterosaurs and bats originated as gliders when present largely ignored evidence indicates exactly the opposite. Cosesaurus (Fig. 1) was a pterosaur precursor with elongate coracoids, unable to fly, but able to flap. Bats rarely glide, so it is unlikely that they did so primitively. Lacking coracoids, bats employ elongate clavicles to anchor flight muscles.
  4. Okay, so remember the preamble (above) about gliding and trees. When Habib et al. bring up ‘a gliding intermediary step‘, they are implying the presence of trees (high places) in competing and validated-by-experiment hypotheses for the origin of bird flight  — which they are ignoring. They also ignore the fact that baby birds don’t glide when they fall out of trees. They flap like their lives depend upon it. I find those omissions odd, but its not the first time pertinent work has been ignored in paleontology.
  5. In the LRT Xiaotingia (Fig. 2) is the most primitive bird-like troodontid to have elongate coracoids and so may have been the first flapper in the lineage.
Figure 1. Xiaotingia with new pectoral interpretation. See figure 3 for new tracing.

Figure 2. Xiaotingia with new pectoral interpretation.

References
Habib M, Dececchi A, Dufaault D and Larsson HC 2016. Up, up and away: terrestrial launching in theropods. Abstract from the 2016 meeting of the Society of Vertebrate Paleontology.
Heers AM, Baier DB, Jackson BE & Dial  KP 2016. 
Flapping before Flight: High Resolution, Three-Dimensional Skeletal Kinematics of Wings and Legs during Avian Development. PLoS ONE 11(4): e0153446. doi:10.1371/journal.pone.0153446
http: // journals.plos.org/plosone/article?id=10.1371/journal.pone.0153446

YouTube video showing birds running up tree trunks while flapping with nonviolent wings

ScienceNews online promo.

The first Jurassic feather – SVP abstract 2016

Pittman et al. 2016
describe a new way of looking at fossils, with laser stimulated fluorescence. I can’t show you what attendees saw at SVP as it is awaiting publication, but other examples can be seen here online. This image from Tom Kaye (Fig. 1) was bumped by me with Photoshop to increase contrast and perhaps reveal a wee bit more detail.

Figure 1. Archaeopteryx feather from T. Kaye. Second image is Photoshop contrast bump created here.

Figure 1. Archaeopteryx feather from T. Kaye. Second image is Photoshop contrast bump created here. Pittman et al. laser stimulated fluorescence imagery was shown at SVP and is awaiting publication. 

From the Pittman et al. 2016 abstract
“The single feather initial holotype of Archaeopteryx lithographica is one of the world’s most iconic fossils, but contains a 150 year old mystery. The specimen’s 1862 description by Hermann von Meyer shows that the calamus is 15 mm long and 1 mm wide. However, the calamus is no longer visible on the fossil, and there is no record of when or how it disappeared. The specimen is a rare example of a lone Archaeopteryx feather, giving access to its entire morphology, as opposed to only parts of it in the overlapping feathers of articulated specimens. This makes it an important addition to the anatomical record of Archaeopteryx and basal birds more generally. After 150 years, laser stimulated fluorescence has recovered the calamus as a chemical signature in the matrix and reveals preparation marks where the original surface details have been obliterated. The feather has recently been imaged by others under UV light as well as with X-rays at the Stanford Linear Accelerator Center, with no reports of the existence of the calamus. This demonstrates the capability of laser stimulated fluorescence to visualize important data outside the range of current methodologies. The feather has at different times, been cited as a primary, secondary and covert, and has even been suggested to belong to another taxon. With the new calamus data in hand, the morphology of the feather was examined within the framework of modern feather anatomy. The percentage of calamus length to overall feather length, when plotted against a histogram of 30 phylogenetically and ecologically diverse modern birds, comes out in the middle of the range, placing it in the flight feather regime. The most recent identification of the feather as a primary dorsal covert can be discounted because the rachis is in line with the calamus rather than curving upwind of the calamus centre line. The curvature of the rachis is also too pronounced to function as a primary or tail feather. If the feather is scaled as a secondary in the wing of Archaeopteryx, only five feathers fit the reconstruction along the ulna, rather than the 9-13 that have been estimated for this taxon and the 7-14 that are found in modern birds. These inferences suggest that the isolated feather is fundamentally inconsistent with those of Archaeopteryx and is instead a secondary of another early bird taxon or potentially even a feather of a non-avialan pennaraptoran theropod.”

Kaye’s work with fossil imaging
has revealed many interesting and otherwise invisible traits. Let’s call this one more ‘feather in his cap.’

References
Pittman M, Kaye TG, Schwarz D, Pei R and Xu X 2016. 150 year old Archaeopteryx mystery solved. Abstract from the 2016 meeting of the Society of Vertebrate Paleontology.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125923

What is Orientognathus? Nesting via description, not observation

Orientognathus chaoyngensis (Lü et al. 2015) is a new Late Jurassic rhamphorhynchoid pterosaur known at present from a series of comparative descriptions. No illustration or photograph of the incomplete(?) material is yet known (at least to me at present).

Given these limitations, let’s see how close we can nest this new enigma.

Data provided:

  1. toothless tip of dentary, slightly pointed
  2. mc4/humerus ratio = 0.38
  3. ulna < each individual wing phalanx
  4. tibia subequal to femur
  5. deltopectoral crest more developed than in Qinlongopterus
  6. anterior teeth stouter and longer than in Pterorhynchus
  7. teeth are straight and longer than in Jianchangnathus
  8. pteroid/humerus ratio = 0.21; pteroid has expanded distal end
  9. larger than other rhamphorhynchine pterosaurs from Late Jurassic NE China (measurements not indicated).

Evidently there is not much known of this specimen:
jaw tips and teeth, a pteroid, a humerus, an ulna, a metacarpal 4, a complete (?) wing (doubtful because the phalanx ratios are not compared to one another) and a femur are all that are mentioned here.

Step one: tibia = femur:
In almost all pterosaurs the tibia is longer than the femur. Just a few specimens have this odd sub equal ratio, so that winnows down the long list of pterosaurs to a short list of possible candidates (left me know if I overlooked any other candidates). You can click the name to view the reconstruction.

  1. Rhamphorhynchus gemmingi? MYE 13 (von Meyer 1859, No. 75 in the Wellnhofer 1975 catalog)
  2. Scaphognathus ( 2 specimens)
  3. St/Ei I (JME 1)

Step two: ulna < each individual wing phalanx
That trait removes both specimens of Scaphognathus and the St/Ei (JME 1) specimen, leaving only one candidate.

Step three: A closer look at Rhamphorhynchus MYE 13 (Fig. 1).

  1. Toothless tip of dentary, slightly pointed: Yes.
  2. mc4/humerus ratio = 0.38  No. = 0.50, but then MYE 13 has a relatively shorter humerus than most Rhamphorhynchus specimens.
  3. ulna < each individual wing phalanx Yes
  4. tibia subequal to femur  Yes
  5. deltopectoral crest more developed than in Qinlongopterus Yes
  6. anterior teeth stouter and longer than in Pterorhynchus Yes
  7. teeth are straight and longer than in Jianchangnathus Yes
  8. pteroid/humerus ratio = 0.21 (but is the pteroid complete?); No. In MYE 13 the ratio is 0.66, but, as above, the humerus is atypically short  AND pteroid has expanded distal end  Yes
  9. Larger than other rhamphorhynchine pterosaurs from Late Jurassic NE China
    Maybe. Wing fingers in Rhamphorhynchus specimens are relatively larger than are those in other Late Jurassic pterosaurs, so if only a wing is known it could belong to a relatively smaller skull and torso. Otherwise the mid-sized specimens listed above (except tiny Qinlongopterus) are all about the same size. 
Figure 1. The MYE 13 specimen of Rhamphorhynchus (n75 in the Wellnhofer 1975 catalog is currently the closest match to the Orientognathus description.

Figure 1. The MYE 13 specimen of Rhamphorhynchus (n75 in the Wellnhofer 1975 catalog is currently the closest match to the Orientognathus description.

So, we’ll test these hypotheses
when the images become available, hopefully with scale bars. Then we’ll do a comparison.

References
Lü J-C, Pu H-Y, Xu L, Wei X-F, Chang H-L and Kundrát M 2015. A new rhamphorhynchoid pterosaur (Pterosauria) from Jurassic deposits of Liaoning Province, China. Zootaxa 3911 (1): 119–129.  http://dx.doi.org/10.11646/zootaxa.3911.1.7