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.

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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.

 

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

The hoopoe (genus: Upupa) joins the LRT

And so does the mousebird, Colius.
They nest together between hornbills + toucans and barbets + tropicbirds.

Figure 1. Hoopoe (genus: Upupa) in vivo and as a skeleton.

Figure 1. Hoopoe (genus: Upupa) in vivo and as a skeleton.

First bird watchers thought the hoopoe was a kingfisher relative.
Then it was nested with barbets, which is where the large reptile tree (LRT, 1288 taxa) nests the hoopoe, famous for its head crest of mobile feathers.

Using DNA
Prum et al. 2015 nests all the barbets, hornbills, hoopoes, toucans and mousebirds together. And so does the LRT! The only difference is, Prum et al. split mousebirds off first, toucans last. The untenable outgroup for mousebirds and kin includes owls, vultures and the hoatzin in order of increasing distance.

Using skeletal traits
the outgroups for the extant taxa listed above are fossil specimens, Septencoracias and Cyrilavis. Owls nest with predator birds, nowhere near this clade.

Not well publicized,
the hoopoe skull appears to have four nostrils (Fig. 2). The anterior two are operative, while the posterior two are novel fenestrae opening dorsally.

Figure 1. Upupa skull in the three views. Pink arrows point to nares and fenestrae.

Figure 1. Upupa skull in the three views. Pink arrows point to nares and fenestrae.

Upupa epops (Linneaus 1758) is the extant hoopoe. It nests with mousebirds in the large reptile tree. According to Wikipedia: “The hoopoe has two basic requirements of its habitat: bare or lightly vegetated ground on which to forage and vertical surfaces with cavities in which to nest.”

Figure 3. Hoopoe skull superimposed on a specimen showing alignment of the nares, orbit and rostral tip. The rest is feathers.

Figure 3. Hoopoe skull superimposed on a specimen showing alignment of the nares, orbit and rostral tip. The rest is feathers.

We’ll look at mousebirds tomorrow.

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.

What are birds-of-paradise? (part 2, Paradisaea minor)

 Figure 1. Paradisaea minor skeleton somewhat matched to in vivo pose.


Figure 1. Paradisaea minor skeleton somewhat matched to in vivo pose.

Yesterday a bird-of-paradise (BoP; Semioptera) was added to the large reptile tree (LRT, 1285 taxa) based on skull material only. It nested between the lyrebird and the roadrunner (genera: Menura and Geoccocyx, respectively) within the trumpeter/cuckoo clade. Crows (genus: Corvus) are the traditional (based on DNA) sister clade.

Fortunately,
I found a BoP skeleton online (Figs. 1, 2). It belongs to Paradisaea minor (Shaw 1809), the lesser bird-of-paradise. In BoPs the legs are shorter than in sister taxa, reflecting an instance of phylogenetic miniaturization at the genesis of the clade.

Even with the semi-crappy data currently available
(note the tibia and femur flipped upside down, lack of ribs and the lo-rez image overall) the LRT was able to successfully nest the BoPs together, apart from crows and jays.

Figure 2. Skull or Paradisaea minor, the lesser bird-of-paradise.

Figure 2. Skull or Paradisaea minor, the lesser bird-of-paradise.

Let’s not forget
that trumpeters and lyrebirds are both jungle residents, as are BoPs.

References
Shaw 1809. General Zoology 7 pt2:486

wiki/Lesser_bird-of-paradise