Adding more birds to the LRT

Over the last week or so
more birds have been added to the large reptile tree (LRT, 1074 taxa, subset Fig. 1). Many are still with us. Others are recently extinct. Still others are known only from the Paleocene.

Figure 1. Subset of the LRT focusing on extant birds and their closest kin.

I was surprised to see

1. the toothed birds, Yanornis, Ichthyornis and Hesperornis nest within the clade of extant birds. That means, like Pelagornis, some sort of teeth came back.
2. the moa, DInornis and Gastornis (= Diatryma) both nest close to parrots (like Ara) and the hoatzin (Opisthocomus). Here ratites are no longer monophyletic. Wikipedia notes, “The systematics involved have been in flux.”
3. ducks, like Anas, are close to predatory birds, like Sagittarius
4. the Solnhofen bird, Jurapteryx (= Archaeopteryx) recurva nests at the base of the clade of extant birds
5. Details later.

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SVP abstracts 2017: The enigmatic New Haven Reptile

Pritchard et al. 2017
introduce the concepts of a ‘pan-archosaur’ and a ‘pan-lepidosaur’ as they describe the small, enigmatic “New Haven Reptile” (Latest Triassic; 2.5cm skull length).

From the Pritchard et al. abstract:
“The fossil record of early-diverging pan-archosaurs and pan-lepidosaurs in the Triassic is biased towards large-bodied animals (1+ meters). The Triassic Newark Supergroup of eastern North America has produced tantalizing specimens of small reptiles, hinting at high diversity on the continent. Among these is a remarkable diapsid skull (~2.5 cm length) lacking teeth and a mandible, from the Upper Triassic New Haven Arkose of Connecticut that has been referred to as one of the oldest sphenodontians from North America (referred to herein as the New Haven Reptile). 

“Following further preparation, we re-assessed the affinities of the New Haven Reptile using three-dimensional reconstruction of microCT data. The ontogenetic state of the New Haven Reptile is uncertain; despite the extensive reinforcement of the skull, the skull roof exhibits a large fontanelle between frontals and parietals. The feeding apparatus of this species is distinct from most small-bodied Triassic diapsids, with a strongly reinforced rostrum, a narrow sagittal crest on the parietals, and transverse expansion of postorbitals and jugals. The latter two conditions suggest transverse expansions of deep and superficial adductor musculature in a manner very similar to derived Rhynchosauria. This may suggest a specialized herbivorous diet similar to rhynchosaurs, although the New Haven Reptile is smaller than most modern herbivorous diapsids. 

“A phylogenetic analysis suggests that the New Haven Reptile is not a sphenodontian but an early pan-archosaur, representing a distinctive and previously unrecognized lineage. Regardless of its affinities, the New Haven Reptile differs from other small-bodied Triassic Sauria in its hypertrophied jaw musculature suggesting a greater dietary specialization in these taxa than previously understood. It underscores the importance of geographically undersampled regions in understanding the true ecomorphological diversity in the fossil record.”

So, what is the New Haven reptile?
Without seeing the fossil or the presentation, we start with what was offered:

1. a small taxon (skull = 2.5cm)
2. like a sphenodontian, diapsid temporal openings
3. lacking teeth
4. extensive reinforcement of the skull
5. large fontanelle between frontals and parietals (pineal?)
6. strongly reinforced rostrum
7. a narrow sagittal crest on the parietals
8. transverse expansion of postorbitals and jugals, like rhynchosaurs
9. hypertrophied jaw musculature

Figure 1. Priosphenodon model. Is this what the New Haven Reptile looked like? Note the dorsal fontanelle, the pineal opening that largely disappears in rhynchosaurs. 

This sounds like
Priosphenodon avelasi, (Figs. 1, 2) which is a transitional taxon more derived than sphenodontians and more primitive than rhynchosaurs. The only skull known to me is about 8cm in length, or 3x larger than the New Haven Reptile. Priosphenodon was a late-surviving Cenomian, Cretaceous taxon, more derived  than the even later-surviving extant taxon, Sphenodon.

Figure 2. Priosphenodon nests closer to rhynchosaurs than Mesosuchus does, yet it was not included in the Ezcurra et al. 2016 study.

If my guess is valid,
its no wonder that Pritchard et al. are confused. To them rhynchosaurs are not related to sphendontians. These fellow workers need to include more taxa in their analysis and a suggested list is found at the large reptile tree (LRT, 1069 taxa). 

If it is something different
please send an image or publication and I will add it to the LRT.

References
Pritchard AC, Bhullar B-A S and Gauthier JA 2017. A tiny, early pan-archosaur from the Early Triassic of Connecticut and the diversity of the early saurian feeding apparatus. SVP abstracts 2017.

Study says: toothless beak + grainivory in basalmost Paleocene birds

Larson , Brown and Evans 2016 conclude:
“To explain this sudden extinction of toothed maniraptorans and the survival of Neornithes, we propose that diet may have been an extinction filter and suggest that granivory associated with an edentulous beak was a key ecological trait in the survival of some lineages.” … like birds (Euornithes).

A few days ago we looked at the most likely candidate at present to nest at the base of all extant birds, and it wasn’t a little seed-eater. Unfortunately, the Larson et al. study was done without a phylogenetic analysis based on morphology. So they don’t know what the basalmost Euornithine was or looked like. Rather they looked at tooth shapes in derived theropods… and threw a Hail Mary pass.

The authors report,
“To date, only one Maastrichtian bird has been assigned to a crown group clade based on a phylogenetic analysis [1], suggesting that crown group birds were less common than contemporary non-neornithine birds in the Cretaceous. There are also no Late Cretaceous neornithines or advanced ornithuromorphs with known cranial remains.”

Seed eaters
as basalmost Euornithine birds appears unlikely given that basalmost Euornithine birds resemble cranes and ratites. Moreover, the crown group Maastrichtian bird isn’t part of the crown group according to the LRT.

References
Larson DW, Brown CM and Evans DC 2016. Dental Disparity and Ecological Stability in Bird-like Dinosaurs prior to the End-Cretaceous Mass Extinction. Current Biology 26(10):1325–1333.

Screamers: the return of digit ‘0’

Screamers are extant birds
in the family Anhimae. They include the genera Chauna (Oken 1816; Southern screamer; up to 90 cm in length) and Anhima (Brisson 1760; horned screamer). The clade lacks uncinate processes on the ribs. but has large spurs on the metacarpus (Figs. 1, 2). The young are precocial (able to run soon after hatching). This is a rather primitive and very vocal clade.

The Anhimae clade was considered closest
to ducks (Anatidae) based on DNA, but the rostrum, as you can see (Fig. 1) lacks many duck-like traits.

By contrast,
the large reptile tree (LRT, 1065 taxa), grounded on morphology, nests Chauna at the base of the chicken, sparrow and parrot clade.

Fig. 1. Anhima skeleton and skull.

The manus of screamers is atypical
(Fig. 2) in that large spurs arise from the distal metacarpus (as a new ossification) and from the proximal metacarpus (as the return of digit ‘0’, a digit first brought to light with the Limusaurus discovery and misinterpretation). Along with the return of digit ‘0’ we also find fused vestiges of digits 4 and 5.

Fig. 2. Screameer manus showing the full expression of digit 0 at the base of the metacarpals producing a large anteriorly-directed spur. Faint vestiges of digits 4 and 5 are also present.  Note how easy color explains things by clearing segregating one bone from another, even when they fuse.

You won’t find any references to digit ‘0″
in the academic literature. That reversal in theropods and birds was first hypothesized here a few years ago, and well documented above (Fig. 2).

References
Brisson MJ 1760. Ornithologie, ou, Méthode contenant la division des oiseaux en ordres, sections, genres, especes & leurs variétés : a laquelle on a joint une description exacte de chaque espece, avec les citations des auteurs qui en ont traité, les noms quils leur ont donnés, ceux que leur ont donnés les différentes nations, & les noms vulgaires
Oken L 1816. Lehrbuch der Zoologie (or Lehrbuch der Naturgeschichte 1–3. Theil. Zoologie ; 2. Abt. Fleischthiere) Jena.

wiki/Anhima
wiki/Chauna

 

Flamingoes are taller, skinnier seriemas, according to the LRT

Figure 1. Phoenicopterus, the flamingo is closest to Cariama, the seriema, (Fig. 2) in the LRT.

When you see them together,
(Figs. 1, 2) it’s pretty obvious. Flamingoes and seriemas share a long list of traits. Oddly, in Wikipedia, both are considered ‘sole representatives’ of their respective orders. Closest representatives have wavered from storks to ibises to ducks and geese like Presbyornis, even doves!

Prum 2015
nests Phoenicopterus with Rollandia, the flightless Lake Titicaca grebe (a type of diving bird) using DNA. Hackett et al. 2008 nested Phoenicopterus with Podiceps, another grebe, also using DNA.

Figure x. Cariama cristatus, the seriema in several views. Here the downturned beak of the flamingo is just beginning to turn down.

As it turns out,
the secretary bird, Sagittarius, is closer to the prehistoric ‘terror birds’ or phorushacids, than is their traditional extant representative, Cariama, the seriema. Both secretary birds and phorushracids had a high snout with a dorsal naris, among many other traits in common.

References
Hackett S et al. 2008. A phylogenetic study of birds reveals their evolutionary history. Science 320:1763–1768.
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

wiki/Flamingo

Snake origins according to DNA studies

Figure 1. Cladogram of squamates from Streicher and Wiens 2017 highlighting the origin of snakes based on DNA. Unfortunately, only the closely related taxa are correctly nested here. See figure 2 for gradual accumulations of traits in all related taxa.

 

Why would Streicher and Wiens 2017
(Fig. 1) want to do this? They can’t use fossils. They’ll never find a gradual accumulation of traits, starting from ‘snakes with legs’. And… DNA does not work over large phylogenetic distances. They put their faith in DNA. They believed they would get an answer. Their prayers were answered, but the answer does not make sense. Their cladogram cannot be verified with morphological studies (Fig. 2). Morph studies can and do use fossils and do produce a gradual accumulation of traits. Morphology is, and will always be, the gold standard of phylogenetics.

We have to stop wasting time
on methods that do not work over large phylogenetic distances. Rant. Rant. Rave. Rave.

Figure 2. Subset of the large reptile tree focusing on lepidosaurs and snakes are among the squamates.

Here’s how you know, at first glance,
how the Streicher and Wiens cladogram produces odd, mismatching sisters.

1. Derived taxa usually do not appear at the base of major clades: Dibamus, Typhlops
2. Mismatches usually do not nest close to one another: Bipes & Lacerta, Python & Typhlops, Dibamus & Sphenodon

Streicher and Wiens will never find out
that snake ancestors had legs using DNA. Those just never shows up in molecules. Their paper’s title: “Phylogenomic analyses of more than 400 nuclear loci resolve the origin of snakes among lizards families” do not resolve the origin of snakes.

Snakes arise
from near the very beginning of a rapidly diversifying Scleroglossa. The snake clade split from the gekko clade shortly after the origin of the Squamata. Derived burrowing snakes with jaws that pull prey items in appear in derived taxa, not as basal plesiomorphic forms. When basal taxa are bland and plesiomorphic, that’s a good sign that you’re doing something right.

References
StreicherJW and Wiens JJ 2017. Phylogenomic analyses of more than 400 nuclear loci resolve the origin of snakes among lizards families. Biology Letters 13: 20170393.
http://dx.doi.org/10.1098/rsbl.2017.0393

 

 

LRT sheds light on Gastornis: its a giant flightless parrot!

I left adding extant birds to the LRT for last
because I thought the phylogeny of birds was already set in stone using extant bird DNA (Hackett et al. 2008; Prum et al. 2015). Now I’m learning that, once again, DNA does not replicate morphological analyses in birds over large phylogenetic differences.

I’m learning about post K-T birds step-by-step
as I meet them, one-by-one, as usual. Some surprises are popping up. Last time we looked at the giant bird Gastornis (Fig. 1, 6), it nested with the hoatzin, or stink bird, Opisthocomus. It still does so, but now we have an intervening transitional taxon, Ara macao, the scarlet macaw (Figs. 4, 5), a brilliantly colored parrot.

Figure 1. Gastornis turns out to be a giant parrot sister in the chicken clade in the LRT.

But first….
In the last few days I added two extant birds to the LRT. The common house sparrow, Passer domesticus (Linneaus 1758; Figs. 1,2) nests between the chicken, Gallus, and the hoatzin, Opisthocomus in the large reptile tree (LRT, 1065 taxa; subset Fig. 7). This counters DNA studies (Hackett et al. 2008; Prum et al. 2015) which nested Passer in a very derived node in a very derived clade with the long-legged snake-eater, Cariama, at its base.

Usually
highly derived taxa with atypical traits nest at derived nodes, not basal nodes. Passer is the dictionary definition of a very typical, not highly derived bird.

Figure 2. Skeleton of the common house sparrow, Passer domestics.

 

So far,
the chicken/Gallus clade is primarily composed of herbivores/ grain/ seed eaters with a few insects and lizards thrown in. Since Gastornis appeared in the late Paleocene/early Eocene, that means sparrows, chickens and hoatzins also must have been part of this earliest radiation of Neognathae after the K-T extinction event.

Figure 3. Skull of Passer domestics in four views.

The scarlet macaw,
Ara macao (Linneaus 1758, Figs. 3, 4) nests between Opisthocomus, the hoatzin and Gastornis (formerly Diatryma, Fig. 1), the giant Eocene herbivore formerly considered a predator of little Eocene 3-toed horses. Gastornis shares a remarkably long list of odd bird traits with Ara, including the separation of its orbit from its temporal fenestrae (Fig. 5). Wikipedia reports Gastornis originally was allied with cranes, but recent studies nest Gastornis with geese. Neither are as good a match for Gastornis, from head to toe (and palate, Figs. 5, 6), as parrots using the LRT as our guide.

Figure 4. Skeleton of Ara macao, the scarlet macaw. Note the skeleton has pedal digits 3 and 4 switched.

Most of the skull elements in Ara are fused,
but the mandible, palatine and quadrate rotate beneath the skull like a parallelogram to lift the beak. Witmer and Rose 1991 compared the skull of Gastornis ( = Diatryma) with that of the parrot Amazona in their study of jaw mechanics, without making the phylogenetic connection.

Witmer and Rose 1991 reported,
“The morphology of the last group, parrots and finches, is similar to that of Diatryma.” They all nest together in the LRT. They also report, “Although the craniofacial hinge is not completely preserved in any known specimen, we suggest that Diatryma, like large parrots, probably had a diarthrodial craniofacial articulation.”

Figure 5. Skull of Ara macao with bones colored.

The first reconstructed palate of Gastornis
(Fig. 6) compares well with that of Ara macao (Fig. 5), including the massive palatine bones, the long slender pterygoids, the wide jugals and indented quadratojugals.

Figure 6. GIF movie, 4 frames of the palate of Gastronis/Diatryma uncrushed to match the uncrushed mandibles. Note the clear resemblance to the palate of the parrot, Ara macao in figure 4.

I know a lot of time and treasure
have gone into past DNA studies, but they do not and can not include extinct taxa. They do not replicate tree topologies when the phylogenetic distances are great. So they do not and can not produce gradual accumulations of derived traits to help us learn about bird evolution. It just doesn’t work on so many levels! So let’s keep DNA studies restricted to smaller clade studies.

Figure 7. Subset of the LRT showing the nesting of Passer and Ara, newly added taxa.

Odd nestings
occur with DNA studies when phylogenetic distances are great:

1. The plant-eating hoatzin nests at the base of the raptorial eagles, vultures and owls
2. Raptorial seriemas and falcons nest with seed-eating parrots and passerines
3. The nearly identical secretary bird, Sagittarius, and seriema, Cariama, nest far apart

Reasonable nestings
occur in DNA studies when phylogenetic distance are not great.

1. The chicken. Gallus, nests with the ostrich, Struthio, and the tinamou, Crypturellius.
2. The loon, Gavia, nests with the penguin, Spheniscus.

And you’ll only know the phylogenetic distances are great
after morphological studies – with fossils.

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
Andors AV 1992. Reappraisal of the Eocene ground bird Diatryma (Aves: Anserimorphae). Science Series Natural History Museum of Los Angeles County. 36: 109–125.
Hackett S et al. 2008. A phylogenetic study of birds reveals their evolutionary history. Science 320:1763–1768.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Mustoe GE, Tucker DS and Kemplin KL 2012. Giant Eocene bird footprints from northwest Washington, USA. Palaeontology. 55 (6): 1293–1305.
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.

wiki/Gastornis
wiki/Sparrow
wiki/Scarlet_macaw

Click here for a video of a hatching and growing Hyacinth Macaw from Andy Hoo. Excellent. 100 days to fledge.
Reminds us that dinos are naked, not scaly. And they need parents to survive.