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.

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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.

The roadrunner (Geococcyx) has a funky, wide pelvis

You can’t tell
by looking at the skeleton in lateral view (Fig. 1), but the roadrunner pelvis (Figs. 1–3) is definitely different in dorsal and ventral view.

Figure 2. Geococcyx the roadrunner skeleton. Pelvis in several views.

Figure 1. Geococcyx the roadrunner skeleton. Pelvis in several views.

On a recent trip to the Sam Noble Museum
(Oklahoma Museum of Natural History, OMNH) in Norman, Oklahoma, I happened to look down at a roadrunner skeleton (genus: Geococcyx, Figs. 1–3) in the kid’s section. That pelvis struck me as quite odd and indeed it is, relative to other birds, other theropods and other dinosaurs. Even the road-running ostrich (genus: Struthio, Fig. 4) does not have such a wide pelvis.

Figure 1. Roadrunner (genus: Geococcyx) in dorsal view from the Sam Noble Museum in Norman OK USA.

Figure 2. Roadrunner (genus: Geococcyx) in dorsal view from the Sam Noble Museum in Norman OK USA. Image flipped left to right.

Roadrunners are ground cuckoos,
better at sprinting than flying. The heavily muscled hind limbs of roadrunners are well anchored on this laterally expanded pelvis. Truth be told: I have not, but would like to see a muscle comparison between a roadrunner and ostrich (Fig. 4)… then try to figure out why the roadrunner pelvis is so different.

Figure 2. Closeup of figure 1. with sacrum yellow and ilium green. This is a strange pelvis for a theropod or bird.

Figure 3. Closeup of figure 1. with sacrum yellow and ilium green. This is a strange pelvis for a theropod or bird.

Geococcyx californum (Lesson 1829, Wagler 1831; up to 60cm long) the extant roadrunner is a small terrestrial cuckoo/trumpeter and a basal neognath with a posteriorly rotated pedal digit 4, unrelated to parrots and toucans with a similar toe. Geococcyx nests with the cuckoo, Coccyzus and both nest with the long-legged trumpeter, Psophia.

Figure 1. Acetabulum of Struthio.

Figure 4. Acetabulum of Struthio, the ostrich, more typical of birds, theropods and dinosaurs in general.

Galliformes
(chickens, turkeys, peacocks, curassaws, also have a posterior wide pelvis. These are also active terrestrial birds.

References
Lesson RP 1828, 1829. Genera des Oiseaux u Nort de l’Amérique, et Synopsis des especes qui vivent aux Etats-Unis; par Charles-Lucien Bonaparte. Féruss. Bull. 2 sect 13:122-125.
Wagler 1831. Einige Mitheilungen über Thiere Mexicos. Oken’s Isis 24:510–535.
Zinoviev A 2007. Apparatus of bipedal locomotion of cuculiforms (Aves, Cuculiformes): Scenario of an adaptive radiation. Zoologichesky Zhurnal 86(10):1–9.

wiki/Geococcyx

SVP 2018: Cassowary casque development

You heard it here first.

Ontogenic studies by Green and Gignac 2018 report
cassowaries (genus: Casuarius, Fig. 1) develop their casque as “a midline chondrocranial element [the mesethmoid, that] grows relatively slowly and posteriad to buttresses lateral dermatocranial bones.” 

Figure 2. The cassowary skull shows the mesethmoid (yellow green) is greatly expanded from its original flat appearance in Rhea.

Figure 2. The cassowary skull shows the mesethmoid (yellow green) is greatly expanded from its original flat appearance in Rhea.

Green and Gignac 2018 conclude,
These findings suggest that cassowaries are an outlier among dinosaurs, making them poor models for cranial developmental and evolution studies outside of Palaeognathae.”

References
Green TL and Gignac PM 2018. Testing the utility of cassowaries as living models for non avian dinosaur cranial elements. SVP abstracts.

The quetzal (a trogon) enters the LRT

The Old World (particularly New Guinea)
includes several birds-of paradise, some of which we looked at earlier here. Today we’ll look at the best the New World has come up with: the resplendent quetzal (genus: Pharomachrus; Fig. 1), a member of the (formerly) enigmatic trogon family of extant birds.

Wikipedia reports, “The position of the trogons within the class Aves has been a long-standing mystery. They might constitute a member of the basal radiation of the order Coraciiformes (= kingfishers) or be closely related to mousebirds and owls. A variety of relations have been suggested, including the parrots, cuckoos, toucans, jacamars and puffbirds, rollers, owls and nightjars. The unique arrangement of the toes on the foot (retro digits 1+2) has led many to consider the trogons to have no close relatives, and to place them in their own order, possibly with the similarly atypical mousebirds as their closest relatives.”

Figure 1. Quetzalcoatlus (a type of trogon, genus: Pharomachrus mocinno) skeleton, skull and invivo presentation.

Figure 1. Quetzalcoatlus (a type of trogon, genus: Pharomachrus mocinno) skeleton, skull and invivo presentation. Note only two toes, 3 and 4 face anteriorly while perching. The other two wrap posteriorly.

No surprises here:
The large reptile tree (LRT, 1308 taxa) nests the quetzal Pharomachrus with the mousebird, Urocolius. We looked at the Urocolius earlier here.

Figure 1. Urocolius, the blue-napes mousebird, converges with parrots in having a reversible toe 4, the ability to feed upside-down and having a short, deep, hooked beak...plus that long parrot-like tail!

Figure 2. Urocolius, the blue-napes mousebird, converges with parrots in having a reversible toe 4, the ability to feed upside-down and having a short, deep, hooked beak…plus that long parrot-like tail!

Pharomachrus mocinno (La Llave 1832; 40cm snout-vent length +65cm tail) is the extant resplendent quetzal, a member of the trogon family of birds, here nesting with the mousebird, Urocolius. It has large eyes and an odd second toe that, along with pedal digit 1, is also retroverted for perching. This weak flyer has iridescent feathers.

References
de La Llave P 1832. Memorias sobre el quetzaltototl, género nuevo de aves. Registro Trimestre o collección de historia, literatura, ciencias y artes, por una sociedad de literatos 1: 43–49.

wiki/Pharomachrus
wiki/Resplendent quetzal

Side notes:
I’ll be doing a museum tour of the Western United States for the next 10 days or so. Following that will be 44 posts praising and/or criticizing various SVP abstracts, probably three to four times a day to keep them somewhat current.

Today I found 23 ‘pending’ comments. Though many were SPAM, others were approved and most were replied to. I apologize for overlooking these, some of which go back two years.

Best wishes and thank you for your attention.

 

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

Mousebirds (genus: Urocolius)

Yesterday we looked at the hoopoe (genus: Upupa)
famous for its head crest of elevating feathers. Today we look at its sister, the mousebird (genus: Urocolius) which has a similar feathery crest, but differs in having a short parrot-like beak, a long parrot-like tail and a rare parrot-like reversible toe 4. These nest between toucans + hornbills and barbets + tropicbirds. These birds share a deep maxilla with a relatively elevated jugal (Fig. 1).

Figure 1. Urocolius, the blue-napes mousebird, converges with parrots in having a reversible toe 4, the ability to feed upside-down and having a short, deep, hooked beak...plus that long parrot-like tail!

Figure 1. Urocolius, the blue-napes mousebird, converges with parrots in having a reversible toe 4, the ability to feed upside-down and having a short, deep, hooked beak…plus that long parrot-like tail! The pygostyle is missing from this specimen.

Urocolius macrourus (Bonaparte 1854; 10cm snout-vent length) is the extant blue-naped mousebird, a member of the Coliiformers. Note the deep maxilla compared to the jugal. It nests with the hoopoe in the large reptile tree between hornbills and barbets. An omniovore restricted to sub-Saharan Africa, mousebirds build nests. They are gregarious, acrobatic and scurry through the leaves like rodents. Reversible toe 4 is able to rotate posteriorly, as in the related toucan, Pteroglossus.

References
Bonaparte CL 1854. En Ateneo Italiano. 1854. 2: 313.
wiki/Urocolius
wiki/Mousebird