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.

Advertisements

Happy Thanksgiving! A turkey joins the LRT.

When the turkey 
(genus: Meleagris gallopavo, Linneaus 1758; Fig. 1) is added to the large reptile tree (LRT, 1328 taxa) it nests at the base of the clade of chickens + peacocks + Eogranivora and more derived taxa that include sparrows, stink birds and parrots.

Many other bird cladograms
nest ducks with chickens creating the bogus clade: ‘Galloanserae.’ That is beyond logic given the gradual accumulation of traits documented in the LRT that widely separate ducks (water birds) from chickens (yard birds).

Worse yet,
the putative clade ‘Anseriformes‘ nests screamers with ducks.

Worse yet
Wikipedia reports, “The Anseriformes and the Galliformes (pheasants, etc.) are the most primitive neognathous birds, and should follow ratites and tinamous in bird classification systems. Together they belong to the Galloanserae.” In the LRT there are several clades of neognathus birds more primitive than the Galliformes.

Figure 1. The turkey (genus: Meleagris) in vivo, standing skeleton and skull.

Figure 1. The turkey (genus: Meleagris) in vivo, standing skeleton and skull.

Interestingly,
the genus (Eogranivora) goes back to the Early Cretaceous. So the turkey is even more primitive. Turkey ancestors split from the rest of the chicken/sparrow/parrot clade closer to the Jurassic/Cretaceous boundary. That ancestor probably had the long running legs of extant ground-loving birds, like Fulica, the coot, and Megapodius the scrub fowl. No doubt the early turkey was leaner and more athletic than today’s big-breasted, highly-evolved and tasty Thanksgiving centerpieces.

Figure 2. Subset of the LRT focusing on the chicken/sparrow/parrot clade.

Figure 2. Subset of the LRT focusing on the chicken/sparrow/parrot clade. Meleagris is today’s turkey. Note that many other bird cladograms nest ducks with chickens. That is beyond logic.

The turkey’s species name, ‘gallopavo’ literally means:
“chicken-peacock”… which sort of makes sense! Just look at those tail feathers!

The sharp spur at mid-medial-metatarsus
could be a pedal digit zero. A related taxon, Eogranivora, appears to have a small pedal digit zero (Fig. 3). Or not.  Hard to tell. We’ve seen manual digit zero on screamers (Anhima), the basal oviraptorid, Limusaurus and other taxa.

Figure 3. Eogranivora metatarsus with overlooked pedal digit zero identified and enlarged.

Figure 3. Eogranivora metatarsus with overlooked pedal digit zero identified and enlarged (see inset). It is hard to see, appears at the edge of a crack and could be an illusion the color of bone. Confirmation or refutation is needed here. We’re seeing the inside of most of the bones here.

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/Turkey_(bird)

The strange skull of the violet turaco (genus: Macrophaga violate)

Figure 1. The violet turaco (genus: Musophaga) with its skull and a related skeleton.

Figure 1. The violet turaco (genus: Musophaga) with its skull and a related skeleton. Note the expanded nasals rimmed by prefrontals. The spectacular color and jungle habitat are clues that turacos are in the same family as birds of paradise.

Musophaga violacea (Isert 1788; 48 cm long) is the extant violet turaco, originally considered a near-passerine. Here it nests with the trumpeter (genus: Psophia, Fig. 2). In Musophaga the legs and sternum are shorter. The pelvis is deeper and the tail is more robust.

Figure 3. Psophia the trumpeter in vivo and skeleton.

Figure 2. Psophia the trumpeter in vivo and skeleton.

References
Isert 1788. Kurze Beschreibung und Abbildung einiger Vögel aus Guinea. – Schriften der Berlinischen Gesellschaft Naturforschender Freunde 9: 16-20

SVP 2018: Two Yi qi abstracts still see a ‘styliform’ bone

Yi qi is the infamous scansoriopterygid
preserved in a scattered fashion (Fig. 1) in which some workers mistakenly identify a new long bone, the styliform, arising from the wrist that no other tetrapod has. Earlier one bone was identified as a displaced ulna. The other, straighter bone is a displaced and equally crushed radius. There is no such bone as a ‘styliform’.

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 1. 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.

ABSTRACT 1
Dececchi, Habib and Larsson 2018 imagine
how Yi qi could fly with that bogus styliform and only one bone in each antenbrachium. They erroneously report that among the three vertebrates with the power of flight, only one, birds (in their words: ‘paravian theropods’) “Only in this last group do we have enough of a dataset that we can begin to address the question of what is sufficient to allow flight and did it evolve more than once within the group.”

Correction.
We’ve known how pterosaurs developed wings since Peters 2000. (See how Dr. Chris Bennett’s threat has come true? “You won’t get published. And if you do get published, you won’t get cited.”)

Figure 3. Scansoriopterygidae includes two Solnhofen birds traditionally labeled Archaeopteryx, but clearly distinct genera. Note, none of these taxa have a styliform bone, as originally figured in Yi qi.

Figure 2. Scansoriopterygidae includes two Solnhofen birds traditionally labeled Archaeopteryx, but clearly distinct genera. Note, none of these taxa have a styliform bone, as originally figured in Yi qi.

The origin of bats was recovered
within the last ten years at ReptileEvolution.com and here in a four part series ending here.

Over and over this team fails
to understand what they are working with. Dececchi TA, Habib M and Larsson HC 2018 report, “Yi is different from other winged and potential volant pennaraptorans because it built its primary wing structure using a skin based membrane, as opposed to the feathered flight structure seen in birds.” This is a simple misinterpretation. Dececchi, Habib and Larsson will be more or less embarrassed when they look for the displaced antebrachia and reality dawns on them.

Moreover, due to taxon exclusion
Dececchi et al. had no idea that Yi qi and the scanoriopterygidae nest within Aves (Fig. 2), the bird clade that excludes Oviraptor and Deinonychus and includes Archaeopteryx and Passer in the large reptile tree.

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

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

ABSTRACT 2
Roy et al. 2018
also studied the soft tissue anatomy of Yi qi (Fig. 1). These authors acknowledge, “The
strange membranous wings of this animal are highly disparate from the feathered wings of
avian theropods.” They report, “In this study, all previously identified textured membrane
patches exhibited negligible fluorescence under LSF. However, for the first time, LSF
revealed multiple patches of orange-coloured suspected soft tissue around the cranial bones as well as an ungual sheath. These results appear to have two alternative explanations that deserve further investigation:

  1. differential, chemical replacement of the soft and hard
    tissues of the fossil
  2. the reported membrane patches are poorly preserved clumped
    filamentous feathers.” 

Roy et al. concluded, “The radiale angle and angle of wing abduction of Yi qi, when compared with orientations of the styliform element proposed in bat, pterosaur, maniraptoran and frog models, indicate that the maniraptoran wing model was least restrictive to bird-like folding of the wings and was probably the most likely
configuration for Yi qi.”

Distinct from most birds,
scansoriopterygids like Yi qi have a longer manual digit 3 than 2.

References
Dececchi TA, Habib M and Larsson HC 2018. Flights of fancy: modeling powered flight versus gliding in the bizarre theropod Yi qi and its bearing on the question of the origins of flight across Pennaraptora. SVP abstracts.
Peters D 2000b. A Redescription of Four Prolacertiform Genera and Implications for Pterosaur Phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106 (3): 293–336.
Roy A, Pittman M, Kaye TG, Wang X, Xu X and Zheng X 2018. Further investigation of the soft-tissue anatomy and wing configuration of the ‘bat-winged’ pennaraptoran dinosaur Yi qi. SVP abstracts.

Pennaraptora = Oviraptor, Deinonychus, Passer, their last common ancestor and all descendants. In the LRT that clade also includes Compsognathus, T-rex, Struthiomimus and other small to giant theropods and Aorum is a sister to the last common ancestor.

Jinguofortis perplexus: not so perplexing after all

Figure 1. Jinguofortis perplexus in situ with interpretive drawing from Wang, Stidham and Zhou 2018.

Figure 1. Jinguofortis perplexus in situ with interpretive drawing from Wang, Stidham and Zhou 2018. Red lines are added over the fibula and digit 5.

Jinguofortis perplexes (Wang, Stidham and Zhou 2018; Early Cretaceous, 127 mya; IVPP V24194; Figs. 1-3) was described as “an unusual mosaic of bird and dinosaur features”. In the large reptile tree (LRT, 1297 taxa) it nests within the toothed bird clade (Odontornithes) of Neognathae alongside Longicrusavis. Jinguofortis has a fused scapulocoraocid, distinct from sister taxa. Although it has a pygostyle, no fan of tail feathers was preserved, even though wing feathers were preserved.

Figure 2. Jinguofortis perplexus reconstruction based on drawings in Wang, Stidham and Zhou 2018.

Figure 2. Jinguofortis perplexus reconstruction based on drawings in Wang, Stidham and Zhou 2018.

Phylogenetically, the authors report:
Jinguofortis is resolved as the sister to Chongmingia (another bird known from fewer bones but also having a fused scapulocoracoid), and they form the out group to Sapeornis and Ornithothoraces.” 

The authors erected a new clade,
Jinguofortisidae within the clade Pygostylia. Several theropods and bird clades developed pygostyles by convergence, but this was not known to the authors due to taxon exclusion (see below). The authors reported, “the earliest evidence of reduction in manual digits among birds.” Note that all the phalanges in manual digit 3 are missing except the ungual.

Figure 3. Jinguofortis skull in situ and reconstructed using DGS

Figure 3. Jinguofortis skull in situ and reconstructed using DGS. Many of the skull bones are mere strips, making identification difficult, except, perhaps by comparison to sisters, like Longicrusavis (Fig. 4).

The LRT does not confirm this nesting.
What they identified as the quadrate, is here identified as the quadratojugal. What they identified as a splenial is here identified as a hyoid. The authors employed only one Solnhofen bird (= Archaeopteryx) in their phylogenetic analysis. They should have used more as we talked about earlier here. When that happens enanthiornithine, confusiornithine, sapeornithine birds all have Late Jurassic origins and that changes the tree topology they presented in their SuppData.

Figure 2. It's always valuable to see what the taxon looks like with scale bars. This is a tiny specimen, but rather completely known.

Figure 4. This is Longicrusavis, a coeval sister in the LRT to the newly described Jinguofortis.

Employing more Solnhofen birds in phylogenetic analysis
is getting to be the key concept in repairing traditional bird tree topologies. If I can do it (Fig. 5), anyone can. It may surprise them to find the Odontornithes nesting with the Neognathae.

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

Figure 5. Bird origins from several months ago. Although many birds have been added since then, the tree topology shown here has not changed. Updated LRT is posted.

References
Wang M, Stidham TA and Zhou Z 2018. A new clade of basal Early Cretaceous pygostylian birds and developmental plasticity of the avian shoulder girdle. PNAS https://doi.org/10.1073/pnas.1812176115

NatGeo Jinguofortis

The Zygodactylidae revisited: Smith, DeBee and Clarke 2018

According to Smith, DeBee and Clarke 2018
“Zygodactylidae are an extinct lineage of perching birds characterized by distinct morphologies of the foot and wing elements.”

According to the LRT
(large reptile tree, 1137 taxa) zygodactyly (digits 1 and 4 retroverted) appeared several times by convergence in four unrelated bird clades, including toucansparrots, roadrunners and woodpeckers.

“Although the clade has a complex taxonomic history, current hypotheses place Zygodactylidae as the sister taxon to Passeriformes (i.e., songbirds).”

Earlier we learned that Eozygodactylus (Fig.1) nests with Geococcyx, the roadrunner. Among living zygodactylus birds, only parrots, like Ara, are close to the sparrow, Passer.

“Given the rather sparse fossil record of early passeriforms, the description of zygodactylid taxa is important for inferring potentially ancestral states in the largest radiation of living birds (i.e., the ~6,000 species of extant passeriforms).”

Actually
taxa related to Passer include only Passer at this point in the LRT. Other traditional passeriformes nest elsewhere.

“Despite the exceptional preservation of many specimens and considerable species diversity in Zygodactylidae, the relationships among species have not been previously evaluated in a phylogenetic context.”

Even so, 
the LRT has exposed a problem of taxon exclusion here.

“Herein, we …provide the first hypothesis of the species-level relationships among zygodactylids. The monophyly of Zygodactylidae is supported in these new analyses.”

Figure 2. Eozygodactylus reconstructed from figure 1.

Figure 2. Eozygodactylus reconstructed from figure 1. This represents  only one of four clades with a retroverted digit 4.

As defined by the authors,
“Zygodactylidae Brodkorb, 1971 is an extinct, comparatively species-rich clade of enigmatic birds that possess derived morphological features associated with a perching habitus (Mayr, 2008, 2009, 2015). 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 (Olson & Feduccia, 1979).”

The authors chose woodpeckers (Piciformes) as the outgroup.
The unrelated basal barbet/toucan, Cyrilavis, nests at the first dichotomy along with the unrelated Nestor, the parrot. If you are starting to sense yet another case of taxon exclusion, then we are thinking along the same lines.

On the plus side, Botelho et al. 2014 reported
the zygodactyl foot evolved independently in different extant bird taxa.

References
Botelho JF, Smith-Paredes D, Nuñez-Leon D, Soto-Acuña and Vargas AO 2014. The developmental origin of zygodactyl feet and its possible loss in the evolution of Passeriformes.  Proceedings Biological Sciences 281(1788):20140765. doi: 10.1098/rspb.2014.0765.
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 6:e4950 doi: https://doi.org/10.7717/peerj.4950

The sand grouse (genus: Pterocles) revisited

The spark for this blogpost:
A PH reader considered the nesting of the sandgrouse Pterocles with the horned screamer, Anhima, a mismatch. And it is a mismatch in terms of size, color, feet, legs, etc. The thing is… in the LRT, where only skeletal traits are tested, no other tested taxon nested closer to Anhima than Pterocles.

Figure 1. Anhima adult and chick compared to Pterocles adults

Figure 1. Anhima adult and chick compared to Pterocles adults

Earlier I only had skull data (Fig. 4) for the genus Pterocles (Figs. 1–3) and with that heretically nested Pteroclesthe sand grouse, with Anhima, the screamer (Fig. 2). Sand grouse have traditionally been nested with pigeons and chickens, or between pigeons and chickens (Shufeldt 1901), which are not related to one another in the large reptile tree (LRT, 1236 taxa).

Figure 1. Skeleton of Pterocles, the extant sand grouse. Note the 'calcaneal' tubers and manual digit zero, along with the very tiny clavicle/furcula (green).

Figure 2. Skeleton of Pterocles orientalis arenarius, the extant black-bellied sand grouse. Note the ‘calcaneal’ tubers and manual digit zero, along with the very tiny clavicle/furcula (green). This is a different species than the skull shown in figure 3, hence the different mandible ventral margin shape and other differences.

Pterocles is phylogenetically miniaturized
compared to its larger sister, Anhima, the horned screamer (Fig. 2). Even so, and despite the much larger sternum and much smaller feet, Pterocles retains a digit zero process that also includes a spike in Anhima. Both taxa have a large ‘calcaneal heel’ behind the distal tibia, rare to absent in other birds. In Pterocles pedal digit 1 does not reach the substrate and the furcula is much smaller. Both share more traits with each other than with any other taxa among the 1236 taxa in the LRT.

In this case, at least,
the addition of the post-cranial data changed nothing in the LRT tree topology. It would have been less ‘trouble’ to have Pterocles nest with pigeons, or chickens, but a good scientist reports results, no matter how they differ from tradition.

FIgure 2. The larger Anhima compared to its smaller sister, Pterocles.

FIgure 3. The larger Anhima compared to its smaller sister, Pterocles. Note the digit zero spur on the manus along with the ‘calcaneal tuber’ behind the distal tibia.

Back in 1901
Shufeldt reported, “the sand grouse constitute a small assemblage of forms, related on one hand to the gallinaceous (chicken-like) birds, and on the other to the pigeons.” The two clades are not related to one another in the LRT. And that statement was made before the invention of the airplane, computer and PAUP.

Figure 1. Pterocles, the chestnut-bellied sandgrouse is not related to pigeons, despite convergent appearances, but more closely related to the screamer, Anhima.

Figure 4. Pterocles, the chestnut-bellied sandgrouse is not related to pigeons, despite convergent appearances, but more closely related to the screamer, Anhima.

The Fulica, Anhima, Petrolcles clade
is a basal one, probably extending back to the Early Cretaceous. It is a sister clade to the chicken/sparrow/parrot clade, far from the New World vulture/pigeon clade.

References
Shufeldt RW 1901. On the systematic position of the sand grouse (Pterocles: Syrrhaptes). The American Naturalist 35 (409):11–16.