Brocklehurst and Field 2021: Tooth loss in birds

Brocklehurst and Field 2021 report,
“The origin of crown bird edentulism has been discussed in terms of a broad-scale selective pressure or trend toward toothlessness, although this has never been quantitatively tested. Here [Fig. 1], we find no evidence for models whereby iterative acquisitions of toothlessness among Mesozoic Avialae were driven by an overarching selective trend. Instead, our results support modularity among jaw regions underlying heterogeneous tooth loss patterns, and indicate a substantially later transition to complete crown bird edentulism than previously hypothesized (∼ 90 MYA). We show that patterns of avialan tooth loss adhere to Dollo’s law and suggest that the exclusive survival of toothless birds to the present represents lineage-specific selective pressures, irreversibility of tooth loss, and the filter of the K–Pg mass extinction.”

Never? Not true and more quantitively than in Brocklehurst and Field. According to the LRT a clade of Cretaceous toothed birds arose from a series of toothless taxa, including Megapodius (Figs. 2, 3). Brocklehurst and Field could have found this, too, but their taxon list is too small. Taxon exclusion is the #2 problem in paleontology.

Figure 1. Cladogram from Brocklehurst and Field 2021. Colors added to clades. Note the paucity of cherry-picked taxa compared to the LRT. Entire clades of extinct birds are missing here due to taxon exclusion.

When you minimize taxon exclusion,
as in the LRT (subset Fig. 2) the actual patterns of evolution start to emerge. When you cherry-pick taxa (Fig. 1), you risk missing the important nodes and steps that Brocklehurst and Field missed.

Figure 4. Subset of the LRT focusing on birds. The amber box are the toothed Cretaceous birds, descendants of toothless taxa like Megapodius.

The Brocklehurst and Field 2021 study
depends on a valid phylogenetic context, but suffers from taxon exclusion. Only one ‘Archaeopteryx‘ taxon was used. A competing online cladogram (the LRT, subset Fig. 2) finds that nine of thirteen Solnhofen birds are needed to flesh out the origins of various succeeding bird clades, each with a few Solnhofen birds at their base.

Figure 1. Click to enlarge. Toothed birds of the Cretaceous to scale.

Several toothless extant birds
that phylogenetically precede the Eogranivora to Ichthyornis and Yanornis clade (Figs. 2, 3) were excluded from this analysis. Missing taxa include Apteryx, Megapodius, and all members of the Palaeognathae, both living and extinct. Brocklehurst and Field missed a great opportunity due to taxon exclusion.

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References
Brocklehurst N and Field DJ 2021. Macroevolutionary dynamics of dentition in Mesozoic birds reveal no long-term selection towards tooth loss, ISCIENCE (2021), doi: https://doi.org/10.1016/j.isci.2021.102243.

Agnolin 2021 on Brontornis affinities (still excluding parrots and stinkbirds)

Yes, it’s massive taxon exclusion time again
as Agnolin 2021 tells us that Brontornis (Fig. 2) is a giant goose.

We’ve known since 2011
that Brontornis is closely related to Gastornis (Figs. 1, 2) the giant flightless parrot.  Derived from hoatzins first, then sparrows, then even more distantly from fowl (= chickens, pheasants, peacocks), these giant flightless, herbivorous birds have all the hallmarks (= characters) of Ara, the parrot (Fig. 1).

Unfortunately,
these taxa were excluded from Agnolin’s 2021 analysis, again.

Figure 1. Gastornis (=Diatryma) to scale with Ara the parrot (lower right).

Figure 3. Skulls of Gastornis, Brontornis and Ara, the scarlet macaw.

Agnolin 2007
also considered Brontornis a giant goose (Anseriformes).

Agnolin 2021
wrote, “After few changes in the data matrix, Brontornis results as part of a clade composed by the giant anseriforms designated by Worthy et al. 2017 as Gastornithiformes. This result is in agreement with recent proposals that excluded Brontornis from phorusrhacoid cariamiforms (where it was traditionally nested) and included it among Anseriformes.”

“Finally, the nesting of Brontornis among herbivorous giant anseriforms, together with several aspects of its mandibular morphology reinforces previous thoughts that Brontornis was herbivorous in habits.”

Fowl, sparrows, hoatzin (= stinkbirds) and parrots are all also herbivorous.

Unfortunately Agnolin 2007, 2021 supports
the hypothesis that fowl and geese are closely related in a traditional genomic clade, Galloanseriformes (= chicken + geese). The large reptile tree (LRT, 1803+ taxa; subset Fig. x) does not support that relationship. Rather fowl and geese are widely separated in the LRT where fowl are in cyan (= bright light blue, Fig. x) and geese are in pale magenta (= pinkish purple Fig. x).

Figure 4. Subset of the LRT focusing on birds. Chongmingia is highlighted in yellow in the Scansoriopterygidae.

Taxon exclusion
will always come back to haunt/bite you (pick your own favorite cliché). Add taxa as a remedy for this malady. It works every time.

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References
Agnolin F 2007. Brontornis burmeisteri Moreno & Mercerat, un Anseriformes (Aves) gigante del Mioceno Medio de Patagonia, Argentina. Revista del Museo Argentino de Ciencias Naturales, n.s.9, 15-25.
Agnolin F 2021. Reappraisal on the Phylogenetic Relationships of the Enigmatic Flightless Bird (Brontornis burmeisteri) Moreno and Mercerat, 1891. Diversity 2021, 13, 90. https://doi.org/10.3390/d13020090
Andors AV 1992. Reappraisal of the Eocene ground bird Diatryma (Aves: Anserimorphae). Science Series Natural History Museum of Los Angeles County. 36: 109–125.
Bourdon E and Cracraft J 2011. Gastornis is a terror bird: New insights into the evolution of the cariamae (Aves, Neornithes). Society of Vertebrate Paleontology 71stAnnual Meeting Program and Abstracts, p. 75
Buffetaut E 2014. Tertiary ground birds from Patagonia (Argentina) in the Tournouër collection of the Muséum National d’Histoire Naturelle, Paris. Bulletin de la Société Géologique de France. 185(3):207–214.
Cope ED 1876. On a gigantic bird from the Eocene of New Mexico. Proceedings of the Academy of Natural Sciences of Philadelphia 28 (2): 10–11.
Hackett S et al. 2008. A phylogenetic study of birds reveals their evolutionary history. Science 320:1763–1768.
Hébert E 1855a. Note sur le tibia du Gastornis pariensis [sic] [Note on the tibia of G. parisiensis]. C. R. Hebd. Acad. Sci. Paris (in French) 40: 579–582.
Hébert E 1855b. Note sur le fémur du Gastornis parisiensis [Note on the femur of G. parisiensis]. C. R. Hebd. Acad. Sci. Paris (in French) 40: 1214–1217.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Matthew WD, Granger W and Stein W 1917. The skeleton of Diatryma, a gigantic bird from the Lower Eocene of Wyoming. Buletin of the American Museum of Natural History, 37(11): 307-354.
Mustoe GE, Tucker DS and Kemplin KL 2012. Giant Eocene bird footprints from northwest Washington, USA. Palaeontology. 55 (6): 1293–1305.
Owen R 1843. On the remains of Dinornis, an extinct gigantic struthious bird. Proceedings of the Zoological Society of London: 8–10, 144–146.
Prévost C 1855. Annonce de la découverte d’un oiseau fossile de taille gigantesque, trouvé à la partie inférieure de l’argile plastique des terrains parisiens [Announcement of the discovery of a fossil bird of gigantic size, found in the lower Argile Plastique formation of the Paris region]. C. R. Hebd. Acad. Sci. Paris (in French) 40: 554–557.
Prum RO et al. (6 co-authors) 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature doi:10.1038/nature15697
Witmer L and Rose K 1991. Biomechanics of the jaw apparatus of the gigantic Eocene bird Diatryma: Implications for diet and mode of life. Paleobiology. 17 (2): 95–120.
Worthy TH, Degrange FJ, Handley WD and Lee MSY 2017. The evolution of giant flightless birds and novel phylogenetic relationships for extinct fowl (Aves, Galloanseres). Royal Society Open Science 4: 170975. http://dx.doi.org/10.1098/rsos.170975
Wright TF, et al. (ten co-authors) 2008. A Multilocus Molecular Phylogeny of the Parrots (Psittaciformes): Support for a Gondwanan Origin during the Cretaceous. Molecular Biology and Evolution, 25 (10), 2141-2156 DOI: 10.1093/molbev/msn160.

https://pterosaurheresies.wordpress.com/2017/11/06/the-origin-of-giant-birds-gastornis-diatryma-the-giant-parrot/

https://pterosaurheresies.wordpress.com/2017/09/15/lrt-sheds-light-on-gastornis-its-a-giant-flightless-parrot/

 

Degrange 2021 revises Phorusrhacidae

From the Degrange 2021 abstract
“Phorusrhacidae, popularly known as ‘terror birds’, are the most speciose clade within the avian order Cariamiformes, with a fossil record that ranges from the Eocene to the Pleistocene. Although several species have preserved skulls, our understanding of their cranial morphology remains incomplete. Here, a comprehensive overview of the current knowledge of phorusrhacid skull anatomy is presented.”

Some phylogenetic issues here due to taxon exclusion.

Figure 1. Cariama and Sagittarius. The former is a sister to flamingoes. The latter is a sister to the terror birds in the LRT.

Unfortunately,
Degrange 2021 nests terror birds within the clade Cariamiformes, which include Cariama (Fig. 1) , the sister to Phoenicopterus, the flamingo in the large reptile tree (LRT, 1793+ taxa). By adding taxa, rather than relying on outdated tradition, Degrange should have nested phorusrhacids withe the secretary bird, Sagittarius (Fig. 1), the sister to phorusrhachids in the LRT. We looked at this taxonomic problem in September 2017. and again in November 2017.

Figure 2. Phorushacids to scale. The extant Sagittarius is in color at lower right.

According to Wikipedia,
“Molecular phylogenetic studies have shown that Cariamiformes is basal to the Falconiformes, Psittaciformes and Passeriformes” 

In the LRT Cariama and Sagittarius are basal to nearly all non-ratite birds. The above list omits galliformes (Gallus), which nest between falconiformes (Falco) and passeriformes (Passer) in the LRT.

Figure 3. Phorusrhacos to scale with Dinornis, Struthio and Homo.

Once again,
adding taxa while avoiding molecular studies and outdated traditions recovers a cladogram in which gradual evolution is demonstrated at every node.

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References
Degrange FJ 2021. A Revision of Skull Morphology In Phorusrhacidae (Aves, Cariamiformes) Journal of Vertebrate Paleontology Article: e1848855
DOI: 10.1080/02724634.2020.1848855

https://www.tandfonline.com/doi/full/10.1080/02724634.2020.1848855

 

The taller ancestors of crows to scale

Every so often it’s worthwhile to take a wider view
to appreciate the model of evolution hypothesized by the large reptile tree (LRT, 1761+ taxa) to see the patterns of microevolution it documents. Otherwise, all you have is a long list of under-appreciated taxa on a dense family tree.

Today, let’s look at the ancestry of one of the smartest birds,
(Corvus brachyrhynchos, Linneaus 1758; Fig. 1), the extant American crow.  Derived from a long list of longer-legged freshwater shorebirds, Corvus is generalized bird close to the stone curlew (Burhinus) and the grackle (Oedicnemus) and basal to robins, jays, birds of paradise and cuckoos.

Figure 1. Click to enlarge. Taxa in the LRT ancestral to crows. Each taxon represents a branch that has gone its own way since the divergent node.

Chronology
The presence of Eogranivora in the Early Cretaceous indicates that sisters to Pseudocrypturus and Crypturus (close to Megapodius) are more ancient. Seriemas, storks and corn crakes are more recent, perhaps radiating in the Late Cretaceous. Short-legged taxa are neotonous, since chicks of long-legged taxa do not have such long bills and long legs as adults. This makes birds different than pterosaurs, in which hatchlings are identical to 8x larger adults.

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References
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.

wiki/Common_grackle
wiki/Corvus
wiki/Blue_jay
wiki/Eurasian_stone-curlew

An even larger genetic study of extant birds in Nature

Feng et al. 2020 bring us
yet another genomic study of extant birds, this time with a circular cladogram so dense it makes no attempt to list the 10,135 bird taxa in this study by dozens of authors.

This was my reply on the study,
copied from the Comments section on the Nature website. The asterisk and double asterisk are how the chicken* and finch** are located on the dense cladogram (their figure 1).

“How can one test the validity of genomic studies like this one? Earlier testing by Prum et al. 2015 nested flamingoes (Phoenicopterus) with dissimilar grebes (Aechmophorus) and yardbirds/chickens (Gallus) with dissimilar geese (Anser). Three of these four are not named in the present cladogram which lists and illustrates only a few sample genera. Among these, the genomically distant separation of the phenomically similar finch**, parrot (Agapornis) and chicken* duplicate what was discovered earlier in the Prum et al. 2015 study. Genomic deep time studies too often produce false positives that separate similar taxa and lump dissimilar taxa. By comparison, phenomic studies, like the one online at: http://reptileevolution.com lump similar taxa and separate dissimilar taxa, modeling evolutionary events while including fossil taxa.

Only in phenomic (trait-based) studies can one produce a cladogram in which all related taxa document a gradual accumulation of derived traits modeling actual events. If one is concerned about convergence, adding taxa to phenomic studies overcomes that problem.

Genomic studies have lumped bats with whales (Laurasiatheria) and golden moles with elephants (Afrotheria). Workers have to wake up to the sad fact that genetic studies work in criminal investigations, but not in cladograms.”

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References
Feng et al. (dozens of co-authors) 2020. Dense sampling of bird diversity increases power of comparative genomics. Nature 587:252–257.

Chongmingia manus: separating those overlapping phalanges

Chongmingia zhengi 
(Wang et al. 2016; Aptian, Early Cretaceous; Figs. 1–3) is a basal bird preserving the limbs and not much else. Earlier in 2017 I did not make a reconstruction because so little was preserved. That is remedied here (Figs 1, 2). The new reconstruction of Chongmingia corrects several errors made by Wang et al. 2016.

Figure 1. Chongmingia tracing from Wang et al. alongside a reconstruction of the elements.

Wang et al. did not separate
the overlapping phalanges (Fig. 2). Nor did they separate the overlapping coracoid and scapula (Fig. 1). Nor did they recognize the disarticulated manual unguals (Fig. 2). Nor did they realize the ‘extra’ toe phalanx was a displaced finger phalanx (Fig. 1 the white phalanx).

Figure 2. Wang et al. did not separate the overlapping phalanges or recognize the manus unguals, or recognize the extra toe phalanx was a displaced finger phalanx.

Chongmingia nests at the base of the scansoriopterygid clade
in the large reptile tree (LRT, 1752+ taxa subset Fig. 4). That clade includes Yi, Ambopteryx, Scansoriopteryx (Fig. 3) and other birds with a longer manual digit 3 than 2. That distinct, but not unique, morphology is nascent in Chongmingia (Fig. 3).

From the Wang et al. 2016 abstract:
“The Chinese Lower Cretaceous Jehol Group is the second oldest fossil bird-bearing deposit, only surpassed by Archaeopteryx from the German Upper Jurassic Solnhofen Limestones. Here we report a new bird, Chongmingia zhengi gen. et sp. nov., from the Jehol Biota. Phylogenetic analyses indicate that Chongmingia zhengi is basal to the dominant Mesozoic avian clades Enantiornithes and Ornithuromorpha and represents a new basal avialan lineage.”

The LRT does not support this nesting, but does place Chongmingia at a basal node, within the Scansoriopterygidae between the #12 specimen (privately owned) assigned to Archaeopteryx and Mei.

Figure 3. Ambopteryx nests midway and is phylogenetically midway between the larger Yi and the smaller Scansoriopteryx. None of these taxa have an extra long bone in the arm.

Do not overlook
the continuing fact that only three long arm bones (humerus, radius and ulna) are present in Chongmingia and other scansoriopterygid clade members (Figs. 3, 4), not four (the misidentified bat-like styliform element arising from the wrist) as other bird workers say.

Figure 4. Subset of the LRT focusing on birds. Chongmingia is highlighted in yellow in the Scansoriopterygidae.

I am still waiting for someone, anyone
to identify four long arm bones in any scansoriopterygid. So far, no one has.

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References
Wang M, Wang X, Wang Y and  Zhou Z 2016. A new basal bird from China with implications for morphological diversity in early birds. Nature Scientific Reports 6, art. 19700, 2016.

wiki/Chongmingia

New Eocene bird, Nahmavis, enters the LRT

Musser and Clarke 2020 present
a new Eocene bird, Nahmavis, (Figs. 1, 2) preserved with feathers. The forelimbs (= wings + pectoral girdles and sternum) were taphonomically lost. Originally Nahmavis was considered close to the traditional, but invalid shore bird clade Charadriformes (genus: Charadrius) and the traditional, but invalid stork clade, Gruiformes (genus: Grus). The authors report in their results section, “This analysis recovered a paraphyletic Gruiformes with respect to Charadriiformes, with Nahmavis grandei and Scandiavis mikkelseni being placed as the sister-taxa of all included Charadriiformes.”

As you’ll see
(below), such a nesting is about as general as one can get considering the wide variety of birds traditionally considered members of each clade. The Musser and Clarke gene-based cladogram bears no resemblance to the LRT.

Here
in the large reptile tree (LRT, 1752+ taxa; subset Fig. 3) Nahmavis nests with the less aquatic kory bustard (Ardeotis), a taxon not mentioned by Musser and Clarke. These two are close to an extremely aquatic taxon tested by Musser and Clarke, Heliornis (Fig. 5), which they consider a member of the Gruiformes.

Figure 1. Nahmavis fossil (FMNH PA778) overall. Images from Musser and Clarke 2020.

Traditional Charadriiformes include:
gulls, terns, plovers and other shorebirds. (murre, sandpiper, yellow legs, woodcock, skimmer, auk, phalarope, gull, jacana, oystercatcher, snipe, puffin, killdeer, wry-bill, noddy, razorbill, thick-knee, skuas, jaegers. In the LRT (Fig. 3) these taxa are scattered widely.

Traditional Gruiformes include:
limpkins, seriemas, sunbitterns cranes, finfoots, bustards, trumpeters, coots, rails and the kagu. In the LRT (Fig. 3) these taxa are scattered widely.

Figure 2. Nahmavis skull traced and reconstructed using DGS.

From the Musser and Clarke 2020 abstract:
“The stem lineage relationships and early phenotypic evolution of Charadriiformes (shorebirds) and Gruiformes (rails, cranes, and allies) remain unresolved. It is still debated whether these clades are sister-taxa.”

After testing in the LRT (subset Fig. 3) Charadrius nests only three nodes apart from Grus. Nahmavis does nest outside this clade, but so do crows and jays nesting between them. Membership in the traditional clades Charadriformes and Gruiformes need to be reconsidered in light of results recovered by the LRT.

Musser and Clarke concede in their introduction: 
“There is a lack of consensus among large-scale phylogenetic studies of Neoaves concerning the relationships of, and early phenotypic evolutionin, Charadriiformes or Gruiformes.”

Birds are difficult. Having a ready library of colorized skulls and other data helps immensely. Sometimes the cladogram tells you where the mistakes are.

Figure 3. Subset of the LRT focusing on birds. Nahmavis is highlighted in yellow. Color clades include extant taxa. This portion of the LRT is fully resolved.

Musser and Clarke 2020 abstract continues:
“New phylogenetic analyses incorporating Paleogene fossils have the potential to reveal the evolutionary connections of these two speciose and evolutionarily critical neoavian subclades. Although Gruiformes have a rich Paleogene fossil record, most of these fossils have not been robustly placed. The Paleogene fossil record of Charadriiformes is scarce and largely consists of fragmentary single elements. Only one proposed Eocene charadriiform-like taxon, Scandiavis mikkelseni of Denmark, is represented by a partial skeleton.”

Though not yet tested, Scandiavis appears to be a close match to Charadrius.

Figure 4. Kori bustard (Ardeotis) in vivo.

Musser and Clarke 2020 abstract continues:
“Here, we describe a new species from the early Eocene Green River Formation of North America comprising a partial skeleton and feather remains. Because the skeleton lacks the pectoral girdle and forelimbs as in S. mikkelseni, only features of the skull, axial skeleton, and hind limb are available to resolve the phylogenetic placement of this taxon. These anatomical subregions initially showed features seen in Charadriiformes and Gruiformes. To assess placement of this taxon, we use a matrix consisting of 693 morphological characters and 60 taxa, including S. mikkelseni and the oldest known charadriiform taxa represented by single elements. These more fragmentary records comprise two distal humeri from the earliest Eocene Naranbulag Formation of Mongolia and the early Eocene Nanjemoy Formation of Virginia.”

The LRT avoids testing fragmentary records, especially when it comes to birds. A single, fully resolved tree results using a third as many multi-state traits.

Fig. 5 The sun grebe (Heliornis) nests close to the bustard, Ardeotis, and the new Eocene taxon, Nahmavis, in the LRT.

Musser and Clarke 2020 abstract continues:
Our phylogenetic analyses recover the new taxon and S. mikkelseni alternatively as a charadriiform or as a stem-gruiform; placement is contingent upon enforced relationships for major neoavian subclades recovered by recent molecular-based phylogenies.

The LRT does not confirm this rather tentative and/or generalized phylogenetic position. Taxon exclusion may be the problem, since Ardeotis (Fig. 4) was excluded from the Musser and Clarke analysis. Deletion of Ardeotis from the LRT still nests Nahmavis with Heliornis (Fig. 5). Surprised that Musser and Clarke did not come up with the same conclusion, but then, they did not attempt a reconstruction (Fig. 1).

“Specifically, when constraint trees based on results that do not recover Charadriiformes and Gruiformes as sister-taxa are used, the new taxon and S. mikkelseni are recovered within stem Gruiformes. Both Paleogene fossil humeri are consistently recovered within crown Charadriiformes. If placement of these humeri or the new taxon as charadriiforms are correct, this may indicate that recent divergence time analyses have underestimated the crown age of another major crown avian subclade; however, more complete sampling of these taxa is necessary, especially of more complete specimens with pectoral elements.”

The LRT nests all extant birds in a single clade. That clade arises from an Early Cretaceous taxon, Archaeornithura and a Latest Cretaceous taxon, Vegavis. Several other Early and Late Cretaceous birds, many with secondarily evolved teeth (Fig. 6), nest with crown birds, so their fossil record already extends deep into the Mesozoic.

Figure 6. Click to enlarge. Toothed birds of the Cretaceous to scale.

With the addition of Nahmavis to the LRT
the bird subset of the LRT (Fig. 3) came under review. Several scores were changed. The basic tree topology remains the same. Some taxa moved around. These will be discussed in the next few days.

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References
Musser G and Clarke JA 2020. An exceptionally preserved specimen from the Green River Formation elucidates complex phenotypic evolution in Gruiformes and Charadriiformes. Frontiers in Ecology and Evolution – Paleontology https://doi.org/10.3389/fevo.2020.559929

 

 

Darwin’s finches: Mesozoic style

Originally ‘Darwin’s finches’ =
small birds from the Galápagos Islands west of Ecuador, in the Pacific Ocean.

According to Wikipedia:
The term “Darwin’s finches” was first applied by Percy Lowe in 1936, and popularised in 1947 by David Lack in his book Darwin’s Finches. The most important differences between species are in the size and shape of their beaks, which are highly adapted to different food sources.”

For today’s post, metaphorically speaking, ‘Darwin’s finches’ =
“several variations on a last common ancestor restricted to a small geographic area.”

Similar Mesozoic variations
on a last common ancestor restricted to a small geographic area are also documented in the large reptile tree (LRT) and the large pterosaur tree (LPT). Here (Figs. 1–8), other than Late Cretaceous Pteranodon (Fig. 1), and Middle Jurassic Darwinopterus (Fig. 8), the others (Figs. 2–7), are all known from the Late Jurassic Solnhofen Formation, a lagerstätte representing an archipelago or series of islands, much like today’s Galápagos Islands.

Here
(Figs. 1–8) pictures of closely related taxa tell the story of their own evolution much better than any long-winded explanation. No two are alike. Arrows indicate phylogenetic order.

If you want to know more,
click on each of the images below. When taken to the large image pages at ReptileEvolution.com a small link at the top of each page will take you to one of the species pictured therein. Other links to related taxa are posted on each species’ page.

Pteranodon

Figure 1. The DMNH specimen is in color, nesting between the short crest KS specimen and the long crest AMNH specimen. If you see a female in this diagram, let me know. No two are alike.

Rhamphorhynchus

Figure 2. Rhamphorhynchus specimens to scale. The Lauer Collection specimen would precede the Limhoff specimen on the second row. No two are alike, but the Vienna specimen is a juvenile of the larger n81 specimen to its right.

Dorygnathus

Figure 3. Click to enlarge. The descendants of Sordes in the Dorygnathus clade and their two clades of pterodactyloid-grade descendants. No two are alike.

Germanodactylus

Figure 4. Click to enlarge. Germanodactylus and kin. No two are alike.

Pterodactylus

Figure 5. Click to enlarge. The Pterodactylus lineage (in white) and mislabeled specimens formerly attributed to this “wastebasket” genus (in color boxes). No two are alike.

Scaphognathus

Figure 6. Click to enlarge. Only the left three taxa have been identified as Scaphognathus species. Other tiny unnamed specimens are transitional taxa to Pterodactylus or Germanodactylus leading to larger, later taxa. No two are alike.

Archaeopteryx (some of these Solnhofen birds have been renamed)

Figure 7. Several Solnhofen birds, including Archaeopteryx, compared to Ostromia to scale. No two are alike.

Darwinopterus

Figure 8. Darwinopterus specimens and a few outgroup taxa. None of these are basal to any pterodactyloid-grade clades. No two are alike. The female (upper right) is associates with an egg.

Unfortunately,
PhDs and other paleo workers who traditionally refuse to trace and reconstruct ‘to scale’ skeletons of taxa under study never get to discover results like these that are only revealed from producing ‘to scale’ graphics like these (Figs. 1–8). Subtleties come through here, en masse, that are lost when looking at individual skeletons in situ one at a time, especially through a microscope, where you don’t get to see ‘the big picture’. Some workers consider such graphics pseudoscience and crankery.

As a result, no other workers
understand or accept the four origins of the pterodactyloid grade arising from phylogenetic miniaturized transitional taxa (Figs. 3, 6) because they omit pertinent tiny and congeneric taxa. Likewise, workers do not yet understand nor accept the radiation of several bird clades having their genesis in Solnhofen basalmost birds. Workers don’t see ‘the big picture’ because of these taxon exclusions.

Rather, too many workers
try to compile a list of specific traits that differentiate one taxon from another. Here we call that, “Pulling a Larry Martin” because it only sometimes leads to greater understanding. The problem is unrelated taxa too often share those same traits by convergence. Here, reconstructions and a confident nesting in the LRT automatically encompass and include ALL the subtle irregularities between taxa that ‘trait seekers’ traditionally overlook.

References

wiki/Darwin’s_finches

Shedding new light (literally!) on Jianianhualong: Li et al. 2020

Li et al. 2020 used various frequencies of light
and spectroscope technology on the holotype bones and feathers of Jianianhualong (Figs. 1, 2; Early Cretaceous, Xu et al. 2020, DLXH 1218) to identify specific elements in the matrix and specimen.

From the abstract:
“Here, we carried out a large-area micro-X-Ray fluorescence (micro-XRF) analysis on the holotypic specimen of Jianianhualong tengi via a Brucker M6 Jetstream mobile XRF scanner.”

Figure 1a. Jianianhualong, Serikornis and Jurapteryx to scale.

Figure 1b. Jianianhualong tengi in situ. This is the largest among the early birds, a fact overlooked by the Xu et al. 2017. Think of Jianianhualong as a giant Archaeopteryx!

From the abstract:
“Jianianhualong tengi is a key taxon for understanding the evolution of pennaceous feathers as well as troodontid theropods, and it is known by only the holotype, which was recovered from the Lower Cretaceous Yixian Formation of western Liaoning, China.” 

What they didn’t do is to rerun their phylogenetic analysis with more taxa (Fig. 2).

What they didn’t do is to create a reconstruction, perhaps using DGS to precisely trace and segregate the bones to rebuild the skeleton (Figs. 1, 3, 4).

Figure x. Subset of the LRT focusing on birds and their ancestors. Jianianhualong nests within Aves (five taxa from the bottom).

By contrast,
in the large reptile tree (LRT, 1730+ taxa) Jianianhualong nests within Aves (five taxa from the bottom of Fig. 2) even though it was clearly not volant due to its much larger size and smaller forelimbs. Close relatives include Archaeopteryx (= Jurapteryx) recurva (= Eichstätt specimen, Fig. 3) and the privately held #11 specimen of Archaeopteryx.

The authors think Jianianhualong is a troodontid.
According to Wikipedia, “A number of characteristics allow Jianianhualong to be identified as a member of the Troodontidae. These include:

1. the long forward-projecting branch and flange of the lacrimal bone; [✓]
2. the foramina on the nasal bone; [?]
3. the smooth transition between the eye socket and the backward-projecting branch of the frontal bone; [✓]
4. the ridge on the forward-projecting branch of the jugal bone; [✓]
5. the triangular dentary bearing a widening groove; [✓]
6. the robust forward-projecting branch of the surangular bone; [✓]
7. the relatively large number of unevenly-distributed teeth; [✓]
8. the flattened chevrons with blunt forward projections and bifurcated backward projections; [✓]
9. and the broad and flat “pubic apron” formed by the pubic bones.” [?]

Figure 2. The Eichstätt specimen, Jurapteryx recurva, nests with the living ostrich, Struthio, presently in the LRT.

Professor Larry Martin would be so proud!
Why? Because the Wikipedia author (above) is using a list of traits to support an hypothesis of interrelationships rather than using a cladogram to support that hypothesis.  Checkmarks [✓] indicate traits Jurapteryx shares. Question marks [?] indicate traits not shown in Jianianhualong or Jurapteryx. Or did I miss something?

The problem is,
various authors add taxa to the Troodontidae that don’t belong there in the LRT, as we learned earlier here. The LRT; subset Fig. x) recovers Jiaianhualong as the largest known member of the Sapeornis/Jurapteryx clade of birds. Several flightless birds are in this clade. These could be confused with troodontids for that reason. In the LRT the clade Troodontidae include Sinornithoides + Sauronithoides their LCA and all derived taxa. None of these are direct bird ancestors.

Getting back to chemistry
“The bone in Jianianhualong is, as expected rich in calcium and phosphorus, corresponding mineralogically to apatite. The regions where feather remains can be observed show an enrichment and correlation pattern of several elements including manganese, titanium, nickel and copper.”

FIgure 3. GIF animation of the skull of Jianianhualong showing original tracing in line art and colorized bones (DGS) used to create a reconstruction (Fig. 3).

Jianianhualong is a troodontid-like bird,
not a bird-like troodontid. Note the odd scapula shape, like that in Sapeornis. Note the retrovered pedal digit 1, showing this taxon was derived from perching birds. The tall naris and long tibia are autapomorphies.

Xu et al. 2014 made a headline out of
the asymmetric feathers found with Jianianhualong. In the present context, Jianianhualong is derived from volant ancestors. So asymmetry is expected, not exceptional. This is the earliest known large flightless bird, not an example of the invalid hypothesis of ‘mosaic’ evolution.

Figure 4. Reconstruction of the skull of Jianianhualong based on DGS tracings in figure 2.

Liaoningventor curriei (Shen et al. 2017; DNHM D3012; Early Cretaceous) was also originally described as a non-avian troodontid, but nests with Jianianhualong as a flightless bird.

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References
Li J, et al. (8 co-authors 2020. Micro-XRF study of the troodontid dinosaur Jianianhualong tengi reveals new biological and taphonomical signals. bioRxiv 2020.09.07.285833 (preprint) PDF doi: https://doi.org/10.1101/2020.09.07.285833
https://www.biorxiv.org/content/10.1101/2020.09.07.285833v1
Shen C-Z, Zhao B, Gao C-L, Lü J-C and Kundrat 2017. A New Troodontid Dinosaur (Liaoningvenator curriei gen. et sp. nov.) from the Early Cretaceous Yixian Formation in Western Liaoning Province. Acta Geoscientica Sinica 38(3):359-371.
Xu X, Currie P, Pittman M, Xing L, Meng QW-J, Lü J-C, Hu D and Yu C-Y 2017. Mosaic evolution in an asymmetrically feathered troodontid dinosaur with transitional features. Nature Communications DOI: 10.1038/ncomms14972.

wiki/Sapeornis
wiki/Jianianhualong
wiki/Liaoningvenator

“Pulling a Larry Martin” with basal bird pectorals and hands

This is a cautionary tale
The following blog reminds all workers to score the entire specimen if possible, and to score as many more-or-less-complete specimens as possible. Why?

It is of vital importance to use as much data as possible
when scoring each taxon in a phylogenetic analysis to remove any trace of attraction by convergence that happens when just using bits and pieces of cherry-picked taxa.

From Pittman et al. 2020,
“Generally during early avian evolution, the furcula, coracoid, and sternum become more craniocaudally elongate, while the manual digits become reduced and fusion between the metacarpals increases.” 

Not true. In a valid phylogenetic context (Figs. 1–3), like the wide gamut large reptile tree (LRT, 1729+ taxa; subsets Figs. 2, 3), some taxa developed birdy traits quickly while others dawdled or reversed. In this way some bones demonstrated convergence with other less related clades. With this in mind, start with a valid unbiased topology, then let the taxa tell their own story. Avoid the temptation of an easy diagram. Do the necessary work.

Figure 1. Avian furcula aviation from Pittman et al. 2020 and repaired based on LRT results. Let your software decide based on the whole specimen. Convergence is rampant as you can see here.

Due to taxon exclusion
Pittman et al. mixed up the order of the pectoral girdles + hands of basal birds (Fig. 1), hoping to tell the story they wanted to tell: gradual evolution. Not only did they skip about a dozen pertinent taxa, they got the order wrong by eyeballing a few traits on cherry-picked taxa.

With more taxa, as in the LRT,
(Figs. 2, 3) the girdles and limbs are phylogenetically re-ordered here (Fig. 1, layer 2 with colors). If Pittman et al. wanted to show gradual evolution, they needed to first establish a valid tree topology by adding more taxa. Instead, by cherry-picking certain traits to show gradual evolution, Pittman et al. were “Pulling a Larry Martin“, putting individual traits on cherry-picked taxa ahead of an entire suite of traits and a wide gamut of taxa.

Figure 2. Subset of the LRT focusing on Pennaraptora 2014 = Tyrannoraptora 1999 = Coelurosauria 1914. Here Khaan and Velociraptor substitute for Oviraptor and Deinonychus.

Figure 3. Subset of the LRT focusing on bird origins. Crown birds and toothed birds are highlighted. Figure 2 is slightly more up-to-date, but includes fewer extant birds.

When the phylogenetic order is corrected
based on unbiased results recovered by the LRT (subsets Figs. 2, 3), what seemed to Pittman et al. a gradual transitional series is here revealed to be an example or two of convergence. Note the similarly elongate coracoids on the enantiornithine Parabohaiornis and the unrelated ornithurine, Yanornis (Fig. 1`), derived from an Early Cretaceous sister to a living taxon, Megapodius.

Time after time paleontologists cherry-pick taxa.
That has to stop. Add more taxa and let the software decide the tree topology. Similarly, don’t rely on parts alone (Fig. 1) to illustrate hypotheses, unless they represent taxa already nesting together based on all of their parts and a wide gamut of taxa. Body parts, like hands and girdles, can converge, as they do here.

Figure 4. Mammal tooth evolution alongside odontocete tooth evolution, reversing the earlier addition of cusps.

On a similar note, basal mammal workers
have put too much reliance on tooth traits. Unfortunately, sometimes that’s all they have. If so, what should they do? They should build a tree topology based on complete or more nearly complete specimens. THEN fit it in those tooth and mandible taxa once the tree topology is established in a broader sense, as in the LRT. Earlier (Fig. 4) you saw how odontocete and archaeocete traits brilliantly document a step-by-step reversal to a simple cone shape, like those of basal pelycosaurs. The addition, subtraction and modification of tooth cusps in mammals occurred much more widely than shown by this one example.

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References
Pittman M, O’Connor J, Field DJ, Turner AH, Ma W, Makovicky P and Xu X 2020. Pennaraptoran Systematics. Chapter 1 from Pittman M and Xu X eds. 2020. Pennaraptoran theropod dinosaurs. Past progress and new Frontiers. Bulletin of the American Museum of Natural History 440; 353pp. 58 figures, 46 tables.

https://pterosaurheresies.wordpress.com/2020/08/23/pennaraptora-avoid-this-junior-synonym/