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.

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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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.

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.

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.

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.

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

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.

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 1. Skeleton of the common house sparrow, Passer domestics.

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 2. Skull of Passer domestics in four views.

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

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 4. Skull of Ara macao with bones colored.

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 5. 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.

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.

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.

Vegavis: Late Cretaceous, but not a member of the Euornithes

Clarke et al. 2005 brought us
Vegavis iaai (MLP 93-I-3-1, MACN-PV 19.748; Late Cretaceous. 68 mya; Figs. 1, 2), a disarticulated partial fossil from Antarctica, which they considered a duck relative and the first definite member of the Euornithes (extant birds and kin) that lived before the K-T boundary.

Unfortunately
I was not able to confirm this. The large reptile tree (LRT, 1064 tax, subset fig. 5) nests Vegavis as the proximal outgroup to Yanornis and the Ornithurae.

It appears that mistakes were made
by Clarke et al. which affected their matrix scores. If I made mistakes, I’d be happy to change them when better data comes along.

Figure 1. Vegavis in situ from Clarke et al. 2005. Colors added and used to create the reconstruction in figure 2. What they thought was the other humerus is instead a tibia still linked to the femur. What they thought was a long sacrum is instead the inside of the other humerus.

Figure 1. Vegavis in situ from Clarke et al. 2005. Colors added and used to create the reconstruction in figure 2. What they thought was the other humerus is instead a tibia still linked to the femur. What they thought was a long sacrum is instead the inside of the other humerus The original scale bars did not permit a good match between plate and counter plate.

From the Clarke et al. abstract:
“Long-standing controversy surrounds the question of whether living bird lineages emerged after non-avian dinosaur extinction at the Cretaceous/Tertiary (K/T) boundary or whether these lineages coexisted with other dinosaurs and passed through this mass extinction event.” 

“Here we identify a rare, partial skeleton from the Maastrichtian of Antarctica as the first Cretaceous fossil definitively placed within the extant bird radiation. Several phylogenetic analyses supported by independent histological data indicate that a new species, Vegavis iaai, is a part of Anseriformes (waterfowl) and is most closely related to Anatidae, which includes true ducks. A minimum of five divergences within Aves before the K/T bound- ary are inferred from the placement of Vegavis; at least duck, chicken and ratite bird relatives were coextant with non-avian dinosaurs.”

 

Figure 2. Vegavis had a relatively short scapula and small deltopectoral crest on a long humerus with a shorter antebrachium. The gracile elongated proportions are crane-like. The torso may have been shorter, reducing the gap between the pelvis and scapula. The original sacrum (yellow) is identical to the distal humerus in outline. Note the metatarsal elements are not fused.

Figure 2. Vegavis had a relatively short scapula and small deltopectoral crest on a long humerus with a shorter antebrachium. The gracile elongated proportions are crane-like. The torso may have been shorter, reducing the gap between the pelvis and scapula. The original sacrum (yellow) is identical to the distal humerus in outline. Note the metatarsal elements are not fused. Gray bones are restored.

Figure x. Reconstruction of Vegavis at published size (print 300 dpi reduced to web 72 dpi).

Figure 2.5. Reconstruction of Vegavis at published size (print 300 dpi reduced to web 72 dpi).

Only a tiny reconstruction
(Fig. 2.5) was provided by Clarke et al., so a larger one is provided here (Fig. 2) and it seems to be more crane- or ratite-like than duck-like, although the Eocene duck, Presbyornis (Fig. 3) does have a stork-like morphology.

Clarke et al. conclude:
Vegavis has different proportions from Presbyornis that are closer to other extant basal anseriform species [geese, screamers). Thus, there is further support that the wader proportions and the ecology used to diagnose Presbyorntihidae are derived for that particular anseriform lineage and not ancestral avian characteristics.” Not sure why they arrived at this conclusion because Vegavis appears to have  long-legged, stork- and ratite-like proportions (Fig. 2). This is a gracile bird.

Figure 2. Presbyornis (Eocene) and Anas (extant), a basal and modern duck.

Figure 3. Presbyornis (Eocene) and Anas (extant), a basal and modern duck.

Clarke et al. nest Vegavis

and ducks with chickens, like Gallus, among basalmost Neognaths, derived from sisters to paleognath tinamous like Pseudocrypturus.

Figure 3. Reconstruction of the basal ornithuromorph bird, Archaeornithura with skull added. Feathers and ribs omitted. The length of the tail is hard to determine.

Figure 4. Reconstruction of the basal ornithuromorph bird, Archaeornithura with skull added. Feathers and ribs omitted. The length of the tail is hard to determine.

By contrast,
the LRT nests ducks higher on the tree (Fig. 5), closer to long-legged predatory birds. Here Vegavis nests with other pre-Ornithurae Cretaceous birds, like Archaeornithura (Fig. 4), most of which have teeth, unfused metatarsals and gastralia. I found gastralia on the published photo of Vegavis. Unfused metatarsals were originally illustrated. The purported fused sacrum (yellow in figs 1, 2) is the same shape as a distal humerus. It appears to be a split humerus, internal view (Fig. 6). The other split ‘humerus’ appears to be a tibia still articulating with the distal femur. Unfused sacral vertebrae are identified above. Pedal digit 5 is not absent. No scattered cervicals are longer than tall. The ischium is shorter than the pubis, which has a small pubic foot.

Apparently 
all birds with shorter limbs evolved them by neotony. Ratite, flamingo and stork juveniles have shorter legs.

Figure 5. Subset of the LRT with the addition of Vegavis as a proximal outgroup to Yanornis and the Ornithurae.

Figure 5. Subset of the LRT with the addition of Vegavis as a proximal outgroup to Yanornis and the Ornithurae.

I’m interested only
in getting things right. If you can provide better resolution images that support the original identifications, I will make changes to the data presented here. At present Vegavis is the result of a gradual accumulation of traits. It is transitional from birds with unfused sacrals and metatarsals to those with fused sacrals and metatarsals and no pedal digit 5 among several other traits.

Figure 6. Here's the purported sacrum of Vegavis with color added. This looks more like a crushed bird humerus. Higher resolution would be helpful.

Figure 6. Here’s the purported sacrum of Vegavis with color added. This matches the one good humerus. I don’t see the hallmarks of a typical fused sacrum here Note the longitudinal lines that should be transverse if this was indeed a sacrum. Of the fused sacra I have seen, fusion extends to the ilia, which are not fused to the sacrum here. Is this the dorsal view? Lateral view? Ventral view of the purported sacrum? Other unfused sacrals are identified closer to the pelvis. Higher resolution would have been helpful, but the authors did not provide it for this key identification.

If you want to see what a related bird sacrum should look like
click here for several samples.

References
Clarke, JA, Tambussi CP, Noriega JI, Erickson GM and Ketcham RA 2005. Definitive fossil evidence for the extant avian radiation in the Cretaceous. Nature 433, 305–308.

 

digimorph.org/specimens/Vegavis_iaai/
wiki/Vegavis

Gansus: an Early Cretaceous volant basal hesperornithid

Figure 1. Gansus as originally reconstructed and with corrections indicated by the fossils.

Figure 1. Gansus as originally reconstructed and with corrections indicated by the fossils. 2 frames every 5 seconds. Note the actual shape of the coracoid fossils compared to the illustrated version. Note the long pedal digit 4 and the long posterior ilium.

Gansus yumenensis (Early Cretaceous; Hou and Liu 1984, You et al. 2006) is known from several fossils, none of them complete and none of them including the skull, mandibles or anterior neck. Both You et al. and the large reptile tree (LRT, 1063 taxa) nest Gansus between Hesperornis and Ichthyornis among the Mesozoic toothed birds. The long posterior ilium and long pedal digit 4 are the first traits shared with Hesperornis, appearing some 35 million years later. 

The LRT used far fewer bird traits
than did You et al. And I never observed the fossil firsthand. Nevertheless the LRT was able to confirm the nesting of Gansus in You et. al.

References
Hou L and Liu Z 1984. A new fossil bird from Lower Cretaceous of Gansu and early evolution of birds. Sci. Sin. Ser. B. 27:1296−1302.
Li Y et al. (5 co-authors) 2011. New material of Gansus and a discussion on its habit.  Vertebrata PalAsiatica 49:435–445.
You et al. (12 co-authors) 2006.
A nearly modern amphibious bird from the Early Cretaceous of Northwestern China. Science 312:1640–1643.

wiki/Gansus