Like Yi qi, the new Ambopteryx does NOT have bat wings

Wang, O’Connor, Xu and Zhou 2019
report on another scasoriopterygid with a ‘styliform’ bone creating a bat-like wing membrane in their imaginations. They named this specimen, Ambopteryx longibrachium (Fig. 1). This would be the second such instance, in their opinion, of a bat-wing bird. You might remember the flap over the first such instance, Yi qi (Fig. 2), which turned out NOT to have as styliform bone, just a displaced ulna on one side, a displaced radius on the other.

Figure 1. Photos and black tracing from Wang et al. 2019. Colors added here. There is no styliform bone on either wing. That is a displaced ulna... again.

Figure 1. Photos and black tracing from Wang et al. 2019. Colors added here. There is no styliform bone on either wing. That is a displaced ulna… again, as the reconstruction at upper left shows.

Well… tracing the elements in color
|reveals no styliform bone. See for yourself (Fig. 1). Again the authors mistook a perfectly good ulna for the invalid and imagined ‘styliform’ bone on the left wing. Turns out Ambopteryx longibrachium has a perfectly normal radius and ulna, just like all of its sisters in the bird clade. The authors do not illustrate a styliform bone on the better articulated right wing. It should have been there, if it was there in life.

Figure x. Closeup of the Ambopteryx forelimb. Here the purported radius + ulna is only the radius after crushing with two quarters of the exposed radius crushed neatly in half giving the impression of a radius + ulna, exactly the same length and without any interosseum space, which never happens in birds.

Figure x. Closeup of the Ambopteryx forelimb. Here the purported radius + ulna is only the radius after crushing with two quarters of the exposed radius crushed neatly in half giving the impression of a radius + ulna, exactly the same length and without any interosseum space, which never happens in birds.

The authors tried to make the extraordinary and implausible ordinary
by introducing another example of their previously invalidated observations. Today’s exercise demonstrates the importance of color tracing and using those tracings, as is, to build reconstructions. Do not freehand! The present notes also demonstrate, once again, just because some discovery is published in Nature, and heralded by major publications (see below) it still might not be true.

Figure 4. Yi qi tracing of the in situ specimen using DGS method and bones rearranged, also using the DGS method, to form a standing and flying Yi qi specimen. Note the lack of a styliform element, here identified as a displaced radius and ulna.

Figure 2. Yi qi tracing of the in situ specimen using DGS method and bones rearranged, also using the DGS method, to form a standing and flying Yi qi specimen. Note the lack of a styliform element, here identified as a displaced radius and ulna.

The news media is all over this:
with gorgeous paintings and glorified reports of a mythical creature with a bird body and bat wings. Unfortunately, like the editors and referees at Nature, they, too, were bamboozled by bombast.

www.nationalgeographic.com
www.smithsonianmag.com

Lead author Wang dramatically reported,
“I was frozen when I realized that a second membranous winged dinosaur was in front of my eyes,” Wang says. The 163 million-year-old fossil confirms that Yi was not an aberration or a one-off. Together, the two species represent an alternate evolutionary path for airborne dinosaurs.”

Not an aberration or a one-off, Dr. Wang…
two similar errors based on wishful thinking and cognitive bias.


References
Wang M, O’Connor JK.; Xu X and Zhou Z 2019. A new Jurassic scansoriopterygid and the loss of membranous wings in theropod dinosaurs. Nature 569: 256–259. doi:10.1038/s41586-019-1137-z
Xu X, Zheng X-T, Sullivan C, Wang X-L, Xing l, Wang Y, Zhang X-M, O’Connor JK, Zhang F-C and Pan Y-H 2015. A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings. Nature (advance online publication)
doi:10.1038/nature14423

reptileevolution.com/scansoriopterygidae2.htm

wiki/Yi_(dinosaur)
wiki/Ambopteryx

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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: Cyanocritta) 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

Avimaia and her enormous egg

Bailleul et al. 2019 reported
on the posterior half of an Early Cretaceous enantiornithine bird from China, Avimaia schweitzerae (IVPP V25371, Figs. 1,2), including an enormous eggshell within her torso. The authors commented on the eggshell, which had not one, but several several layers, an abnormal condition, probably leading to the demise of the mother.

Phylogenetic analysis
The Bailleul et al. 2019 phylogenetic analysis nested Avimaia with eight most closely related taxa, of which only one, Cathayornis (Fig. 1), was also tested in the large reptile tree (LRT, 1425 taxa, subset Fig. 3) and likewise nested with Avimaia. Significantly, Cathayornis also has a very deep ventral pelvis capable of developing and expelling very large eggs.

Figure 1. Avimaia compared to Cathayornis to scale.

Figure 1. Avimaia compared to Cathayornis to scale. Cathayornis is the only other tested enantiornithine bird to have such a deep ventral pelvis.

A long, thin, straight, displaced bone was found
beneath the rib cage and identified as a rib by Bailleul et al. 2019. I wonder if it is instead a radius (Fig. 1) because it is not curved like a rib and it does not have an expanded medial process. The radius is vestigial. Regardless of the identify of this slender bone, Avimaia, appears to be ill-suited for flying based on her robust tibiae, short dorsal ribs  and giant egg. Cathayornis (Fig. 1) appears to be better-suited for flying, based on its chicken-like proportions.

Figure 2. Avimaia in situ. Some bones were originally mislabeled. Here the egg is reconstructed with a more traditional egg shape.

Figure 2. Avimaia in situ. Some bones were originally mislabeled. Here the egg is reconstructed with a more traditional egg shape.

Mislabeled bones
The right ‘pubis’ (Fig. 2) is the right ischium. The reidentified pubis has a pubic boot and the ischium does, not as in sister taxa. The authors failed to identify vestigial pedal digit 5.

The egg was originally reconstructed as a sphere (drawn as a circle) inside the abdomen. Here (Figs. 1, 2) the egg is reconstructed in a more traditional egg shape more likely to pass through the ischia and cloaca.

Figure 2. Subset of the LRT focusing on the clade Enantiornithes and the nesting of Avimaia as a derived taxon within that clade.

Figure 3. Subset of the LRT focusing on the clade Enantiornithes and the nesting of Avimaia as a derived taxon within that clade.

Most birds
lay more than one egg in a clutch. Another exceptional bird that develops a very large egg is the flightless kiwi (Apterypterx, Fig. 4).

Figure 2. Jurapteryx, Pseudocrypturus, Apteryx and Proapteryx to scale.

Figure 2. Jurapteryx, Pseudocrypturus, Apteryx and Proapteryx to scale.


References
Bailleul AM, et al. 2019. An Early Cretaceous enantiornithine (Aves) preserving an unlaid egg and probable medullary bone. Nature Communications. 10 (1275). doi:10.1038/s41467-019-09259-x
Pickrell, J 2019. “Unlaid egg discovered in ancient bird fossil”. Science. doi:10.1126/science.aax3954

wiki/Avimaia

New view on ‘Paravians’: Agnolin et al. 2019

Agnolin et al. 2019 produced
a new view of early bird and pre-bird relationships. They write, “We here present a review of the taxonomic composition and main anatomical characteristics of those theropod families closely related with early birds, with the aim of analyzing and discussing the main competing hypotheses pertaining to avian origins. We reject the postulated troodontid affinities of anchiornithines, and the dromaeosaurid affinities of microraptorians and unenlagiids, and instead place these groups as successive sister taxa to Avialae.”

By contrast
in the large reptile tree (LRT, 1401 taxa; subset Fig. 1) some troodontids are basal to anchiornithines, which are basal to avians. Other traditional troodontids are not basal to birds and pre-birds.

Agnolin et al. report, “Regarding character evolution, we found that: (1) the presence of an ossified sternum goes hand in hand with that of ossified uncinate processes; (2) the presence of foldable forelimbs in basal archosaurs indicates widespread distribution of this trait among reptiles, contradicting previous proposals that forelimb folding driven by propatagial and associated tendons was exclusive to the avian lineage; (3) in basal paravians and avialans (e.g., Archaeopteryx, Anchiornis) the wings are relatively large and wide, with relatively short rectricial feathers, a rounded alar contour, and a convex leading margin. These taxa exhibit restricted forelimb folding capability with respect to more derived birds, their hands being preserved at angles of flexion (with respect to the radius/ulna) of no less than 90. In more derived birds, however, the rectrices are notably elongate and the angle between the hand and forearm is much less than 90, indicating not only increased forelimb folding capability but also an increased variety of wingbeat movements during flight. Because of the strong similarities in pectoral girdle configuration between ratites and basal avialans and paravians, it is possible to infer that the main forelimb movements were similar in all these taxa, lacking the complex dorsoventral wing excursion characteristic of living neognathans.”

Unfortunately
Agnolin et al. presented a cladogram that was largely unresolved. According to the LRT that loss of resolution can be attributed to one thing: exclusion of taxa. Key taxa missing from the Agnolin et al. tree include:

  1. Compsognathus (both species)
  2. Ornitholestes
  3. The other ten or so ‘Archaeopteryx’ specimens

With the addition of these key taxa theropods (including pre-birds and birds) become completely resolved in the LRT (subset Fig. 1).

Figure 1. More taxa, updated tree, new clade names.

Figure 1. More taxa, updated tree, new clade names, from an earlier blog post.

References
Agnolin FL et al. (4 co-authors) 2019. Paravian phylogeny and the dinosaur-bird transition: an overview. Frontiers in Earth Science 6:252.
doi: 10.3389/feart.2018.00252

Eofringillirostrum: a tiny Eocene crake, not a finch

Ksepka, Grande and Mayr 2019
describe two Early Eocene congeneric bird species. Eofringillirostrum parvulum (Fig. 1) is from Germany, 47mya. Eofringillirostrum boudreauxi from Wyoming, 52mya.

Figure 1. Eofringillirostrum in situ at full scale at 72 dpi and closeups of the skull in situ with DGS tracing and reconstructed. Note the slender vomer (purple).

Figure 1. Eofringillirostrum in situ at full scale at 72 dpi and closeups of the skull in situ with DGS tracing and reconstructed. Note the slender vomer (purple) and the added detail gleaned with DGS compared to the original tracing in figure 2.

Eofringillirostrum boudreauxi, E. parvulum (Ksepka, Grande and Mayr 2019; IRSNB Av 128a+bFMNH PA 793; early Eocene; < 10cm long with feathers) was originally considered a finch and a relative of Pumiliornis, a wren-sized Middle Eocene spoonbill. Here Eofringillirostrum nests as a phylogenetically miniaturized corn crake (below). The rail, Crex, is ancestral to chickens, sparrows, moas and parrots, so Eofringillirostrum probably had a Cretaceous origin. A distinctly long fourth toe  was considered capable of being reversed, but no sister taxa with a similar long toe ever reverse it for perching until, many nodes later, parrots appear.

Figure 1. Much enlarged Eofringillirostrum with original tracing and DGS colors. The crest of the sternum, originally overlooked, is just barely ossified here.

Figure 1. Much enlarged Eofringillirostrum with original tracing and DGS colors. The crest of the sternum, originally overlooked, is just barely ossified here.

Corn crake are not ‘perching birds’. 
As we learned earlier, taxa formerly considered members of Passeriformes are a much smaller list in the LRT. Birds capable of perching arise in several clades by convergence.

The corn crake is omnivorous but mainly feeds on invertebrates, the occasional small frog or mammal, and plant material including grass seed and cereal grain. It is not a perching bird, but prefers grasslands.

Figure 4. The extant corn crake (Crex) is a living relative of the giant elephant bird.

Figure 4. The extant corn crake (Crex) is a living relative of the tiny Eocene Eofringillirostrum.

According to the LRT,
Eofringillirostrum is not a finch, not a seed eater and not a ‘perching bird’ (in the classic sense, but likely evolved perching by convergence) according to phylogenetic analysis and phylogenetic bracketing.)

Figure 5. Skull of Crex most closely resembles that of the new Crex sister, Eofingillirostrum.

Figure 5. Skull of Crex most closely resembles that of the new Crex sister, Eofingillirostrum.

References
Ksepka DT, Grande L and Mayr G 2019. Oldest Finch-Beaked Birds Reveal Parallel Ecological Radiation in the Earliest Evolution of Passerines. Current Biology 29, 1–7.

sciencedaily.com

Again: Zygodactyl-footed birds are not monophyletic

Earlier I glazed over the word ‘extinct.’
Zygodactylidae is a clade of extinct birds, not including any extant birds with zygodactyl feet. Hence the confusion. Here’s the author’s diagnosis verbatim: “Zygodactylidae is primarily characterized by a zygodactyl conformation of the pedal phalanges—possessing a retroverted fourth toe and associated accessory trochlea on the distal end of the tarsometatarsus.” They also report, The results of that analysis provided further justification for a sister-taxon relationship between Passeriformes and Zygodactylidae.” That is not supported by the LRT. Rather tested members of the Zygodactylidae arise near roadrunners (genus: Geoccocyx, the cuckoo clade), not near sparrows, barbets, and woodpeckers. This was a poorly named clade. Moreover it is likely a junior synonym and a paraphyletic clade. 

A new paper by Hieronymus, Waugh and Clarke 2019,
supports the hypothesis that extinct zygodactylid birds (Zygodactylidae, Brodkorb 1971) are monophyletic. Extant zygodactyl-style birds rotate pedal digit 4 posteriorly. Such birds include parrots, roadrunners, woodpeckers, barbets and several fossil taxa. Among these, only parrots are related to sparrows (genus: Passer).

Using one or a dozen traits to determine a clade
is “Pulling a Larry Martin“. You don’t want to do that. You get false positives, like dorsal fins on whales, fish and ichthyosaurs.

Only a comprehensive (wide gamut) phylogenetic analysis
can determine the relationships of any and all taxa. The large reptile tree (LRT, 1373 taxa) nests each of these zygodactyl-footed birds in a separate clade. So that’s four convergent occurrences of this trait (Fig. 1).

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

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

References
Brodkorb P 1971.Catalogue of fossil birds: part 4 (Columbiformes through Piciformes) Bulletin of the Florida State Museum, Biological Sciences. 1971;15:163–266.
Hieronymous TL, Waugh DA and Clarke JA 2019. 
A new zygodactylid species indicates the persistence of stem passerines into the early Oligocene in North America. BMC Evolutionary Biology (2019) 19:3 https://doi.org/10.1186/s12862-018-1319-6
Smith NA, DeBee AM and Clarke JA 2018. Systematics and phylogeny of the Zygodactylidae (Aves, Neognathae) with description of a new species from the early Eocene of Wyoming, USA. PeerJ. 2018; 6: e4950.

False positives in an LRT subset lacking fossil taxa

I think you’ll find this phylogenetic experiment both
gut-wrenching and extremely illuminating. While reading this, keep in mind the importance of having/recovering the correct outgroup for every clade and every node. That can only be ascertained by including a wide gamut of taxa—including fossils. Adding taxa brings you closer and closer to echoing actual events in deep time while minimizing the negative effects of not including relevant/pertinent taxa.

Today you’ll see
what excluding fossil taxa (Fig. 1) will do to an established nearly fully resolved cladogram, the large reptile tree (LRT, 1318 taxa). Earlier we’ve subdivided the LRT before, when there were fewer taxa in total. Here we delete all fossil taxa (except Gephyrostegus, a basal amniote used to anchor the cladogram because PAUP designates the first taxon the outgroup).

PAUP recovers 250+ trees
on 264 (~20%) undeleted extant taxa.

  1. Overall lepidosaurs, turtles, birds and mammals nest within their respective clades.
  2. Overall lepidosaurs nest with archosaurs and turtles with mammals, contra the LRT, which splits turtles + lepidosaurs and mammals + archosaurs as a basal amniote dichotomy.
  3. Overall mammals are not the first clade to split from the others, contra traditional studies. All pre-mammal amniotes in the LRT are extinct.
  4. Within lepidosaurs, the highly derived horned lizards and chameleons are basal taxa, contra the LRT, which nests Iguana as a basal squamate.
  5. Within lepidosaurs, geckos no longer nest with snakes, contra the LRT.
  6. Crocodiles nest with kiwis, as in the LRT, but it is still amazing that PAUP recovered this over such a large phylogenetic distance.
  7. Within aves, so few taxa are fossils in the LRT that the tree topology is very close to the original.
  8. Within mammals marsupials no longer nest between monotremes and placentals
  9. …and because of this carnivores split off next.
  10. Contra the LRT, hippos are derived from the cat and dog clade, all derived from weasels.
  11. Within mammals odontocetes no longer nest with tenrecs.
  12. Within mammals mysticetes nest with odontocetes, no longer nest with hippos.
  13. Contra the LRT, whales are derived from manatees and elephants.
Figure 1. Subset of the LRT focusing on Amniota (=Reptilia) with all fossil taxa deleted. Gephyrostegus, a Westphalian fossil is included as the outgroup.

Figure 1. Subset of the LRT focusing on Amniota (=Reptilia) with all fossil taxa deleted. Gephyrostegus, a Westphalian fossil is included as the outgroup.

BTW,
here are the results based on using the basal fish, Cheirolepis, as an outgroup:

    1. The caecilian, Dermophis, nests as the basalmost tetrapod.
    2. Followed by the frog and salamander.
    3. Squamates branch off next with legless lizards and burrowing snakes at a basalmost node. Terrestrial snakes are derived from burrowing snakes. Gekkos split next followed by varanids and skinks. Another clade begins with the tegu and Lacerta, followed by iguanids. Sphenodon nests between the horned lizards, Moloch and Phyrnosoma + the chameleon.
    4. Turtles split off next with the soft-shell turtle, Trionyx, at the base.
    5. One clade of mammals split off next with echidnas first, then elephant shrews and tenrecs, followed by a clade including the pangolin, seals and other basal carnivores. Cats and dogs split off next followed by hippos, then artiodactyls, perissodactyls, the hyrax, elephants, manatees, mysticetes and odontocetes.
    6. Another clade of mammals include edentates, followed by tree shrews and glires, followed by (colugos + bats) + primates, followed by another clade of basal carnivores, followed by marsupials.
    7. The final clade is Crocodylus + extant birds, which are not well resolved and split apart into two major clades with some subclades maintaining their topology while other clades split apart. So the archosaurs nest together.

This test emphasizes the need for the inclusion of fossil taxa in order to recover a gradual accumulation of traits at all nodes, which takes us closer to actual evolutionary patterns in deep time.