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

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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

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.