Kiwi ancestors

Worthy et al. 2013 reported:
“Until now, kiwi (Apteryx owenii, Apterygidae, Shaw 1813; Fig. 1) have had no pre-Quaternary fossil record to inform on the timing of their arrival in New Zealand or on their inter-ratite relationships.” They described two fossils (femur and quadrate) from the Early Miocene (Fig. 1; 19–16mya) which they named Proapteryx. “The new fossils indicate a markedly smaller and possibly volant bird, supporting a possible overwater dispersal origin to New Zealand of kiwi independent of moa. If the common ancestor of this early Miocene apterygid species and extant kiwi was similarly small and volant, then the phyletic dwarfing hypothesis to explain relatively small body size of kiwi compared with other ratites is incorrect.

Figure 2. Jurapteryx, Pseudocrypturus, Apteryx and Proapteryx to scale.

Figure 2. Jurapteryx, Pseudocrypturus, Apteryx and Proapteryx to scale. In lateral view it is difficult to see the width of the ventral pelvic elements. They are not as wide as the egg diameter. Note the lack of a pygostyle in all three taxa.

By contrast
the large reptile tree (LRT, 1213 taxa) nest the kiwi with Pseudocrypturus (Houde 1988; Early Eocene) apart from other ratites, as the basalmost birds with living representatives.

Apteryx owenii (Shaw 1813) The extant flightless kiwi has an elongate naris that extends to the tip of its beak. Maybe two teeth are there. Here it nests with Pseudocrypturus, but flightless traits push it toward Struthio, by convergence. in the pre-cladistic era, Calder (1978, 1984) considered the kiwi a phylogenetic dwarf derived from the larger moa, but that was invalidated by Worthy et al. 2013 and the large reptile tree.

Proapteryx micromeros (Worthy et. al. 2013) was a slender, tiny Miocene (18 mya) ancestor likely capable of flight.

Pseudocrypturus cercanaxius (Houde 1988; Early Eocene) was originally considered a northern hemisphere ancestor to ratites (like the ostrich, Struthio). Today these primitive flightless birds are chiefly restricted to the southern hemisphere. It could be that early birds did start in the South and had migrated to the North during the Paleocene (66-56 mya).

Since ratites are basal to extant birds, and Pseudocrypturus is basal to ratites (paleognaths), Pseudocrypturus is also quite similar to the ancestor of all extant birds despite its late appearance in the early Eocene. Perhaps something very much like it was one of the few survivors of the K-T extinction event.

It’s notable that Pseudocrypturus has long legs. Early ducks, like Presbyornis, and basal raptors, like Sagittarius, also had long legs. Evidence is building that this is the primitive condition for the clade of living birds arising from the K-T extinction event.

Worthy et al. nest Apteryx
within the order Casuariiformes, which includes cassowaries, emirs, and kiwi, but only in the absence of Pseudocrypturus.

The kiwi egg vs ventral pelvis issue
In most tetrapods, including humans, the egg/baby passes through the cloaca/vagina which passes through the two ischia. That was also likely the case with Archaeopteryx, because this is also the case with Gallus the chicken. In extant birds the ischia posterior tips no longer touch, but are widely separated. Going several steps further, in the kiwi the enormous egg is held in front of the pubis (Fig. 1), which is also in front of the ischia.

The following video of a kiwi laying an egg
shows the cloaca a substantial distance below the swirl that marks its tail. kiwi egg video click to play pretty much located at the tip of the long axis of the egg in figure 1 (maybe a little higher/closer to the tail).

Figure 2. Kiwi laying an egg. Click to play.

Figure 2. Kiwi laying an egg. Click to play.

In the LRT
Pseudocrypturus and Apteryx (Fig. 1) nest together and apart from the ratites. Pseudocrypturus is basal to all living birds. It probably first appeared in the Early Cretaceous. It was found in the Paleocene.

Calder WA 1978. The kiwi. Scientific American 239(1):132–142.
Calder WA 1984. Size, function and life history. 448 pp. Cambridge (Harvard U Press).
Houde PW 1986. Ostrich ancestors found in the northern hemisphere suggest new hypothesis of ratite origins. Nature 324:563–565.
Houde PW 1988. Paleognathus birds from the early Tertiary of the northern hemisphere. Publications of the Nuttall Ornithological Club 22. 147 pp.
Shaw 1813. Naturalist’s Miscellany 19:
Worthy, TH. et al. (5 coauthors) 2013. Miocene fossils show that kiwi (Apteryx, Apterygidae) are probably not phyletic dwarves. Paleornithological Research 2013, Proceedings of the 8th International Meeting of the Society of Avian Paleontology and Evolution. Retrieved 16 September 2017.

wiki/Apteryx, Kiwi


The black skimmer (Rynchops niger) enters the LRT

And it nests with
the extinct great auk (Pinguinus) in the large reptile tree (LRT, 1217 taxa). No wonder it seems so different than other living birds! It is.

Figure 1. Black skimmer (genus: Rynchops) in vivo.

Figure 1. Black skimmer (genus: Rynchops) in vivo.

These, in turn
are close to the puffin (Fratercula), which also has large keratinous extensions of the rostrum and mandible, and not one, but two mandibular fenestrae.

Figure 2. Skull of the the black skimmer (Rynchops niger) with bones colorized. Note the large keratinous extension extending the mandible.

Figure 2. Skull of the the black skimmer (Rynchops niger) with bones colorized. Note the large keratinous extension extending the mandible. Note the slight differences in the two presented skulls.

Rynchops niger (Linneaus 1758; up to 50 cm in length) is the extant black skimmer, famous for having a longer lower bill than upper. It flies low on still waters to skim for fish near the surface. Close relatives include the auk, Pinguinus and the puffin, Fratercula, all derived from skuas and petrels.

Figure 2. Pinguinus the great auk skull.

Figure 3. Pinguinus the great auk skull. This flightless extinct bird nests closest to the black skimmer in the LRT. Note the two mandibular fenestra, The curved and expanded premaxilla that extends no further posteriorly than the naris, the pinched rostrum,  the tiny ascending process of the retroarticular process, the quadratojugal that extends to the antorbital fenestra,

Prum et al. 2015
nested Rynchops with the black-headed gull (Chroicocephalus) using DNA data. They did not test the extinct Pinguinius. In the LRT, the black-headed gull nests with another clade of wading birds, beginning with the limpkin, Aramus.

Figure 1. Chroicocephalus, the black-headed sea gull in vivo and as a skeleton.

Figure 4. Chroicocephalus, the black-headed sea gull in vivo and as a skeleton. This taxon nests with hummingbirds, both derived from stilts and other wading birds like the limpikin (Aramus).



Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.



Eozygodactylus: a basal wader, not a ‘songbird’

Today: a little, long-legged bird from the Green River formation
Eozygodactylus americanus (Weidig 2010; Eocene; 53mya; FMNH PA726) Originally considered a perching songbird related to Passer (the sparrow), this long-legged, lakeshore wading bird (think: sandpiper), nests at the base of the cukoo + stork clades in the large reptile tree (LRT, 1209 taxa). Like Geococcyx (the roadrunner), pedal digit 4 is also retroverted (= zygodactyl). The right (lower) femur appears to be broken in two.

Figure 1. Eozygodactylus in situ with two lighting schemes and bones colorized.

Figure 1. Eozygodactylus in situ with two lighting schemes and bones colorized. If pterosaurs had survived the K-T event, this is where we would find them.

As a basal taxon,
Eozygodactylus was derived from the predatory bird clade, the toothed bird clade and, more distantly, Megapodius (the mound builder). Eozygodactylus has a relatively large skull and short rostrum, which might suggest a possible juvenile stage. No related adult taxa (Figs. 4, 5) have similar proportions.

Figure 2. Eozygodactylus reconstructed from figure 1.

Figure 2. Eozygodactylus reconstructed from figure 1. Not sure how deep the sternum is. Sister taxa can fly, but prefer to walk.

Closely related basal neognath birds include
long-legged screamers (genus: Chauna) at the base of the sparrow/chicken/parrot clade and long-legged stone curlews (genus: Burhinus) at the base of crows + jays + woodpeckers + swallows. By convergence, woodpeckers also have a zygodactylus pes. Apparently this trait comes and goes, without a single long zygodactyl lineage.

Figure 3. Psophia the trumpeter in vivo and skeleton.

Figure 3. Psophia the trumpeter in vivo and skeleton, a close relative of Eozygodactylus, larger and without a zygodactylus foot.

The nesting of Eozygodactylus
at the base of a basal bird clade supports the antiquity of long-legged shore birds (Figs. 4, 5) in the evolution of birds, distinct from traditional and DNA tree topologies.

Figure 1. Click to enlarge. Duck origins recovered by the LRT. Duck descendants were long-legged walkers and later waders.

Figure 4. Click to enlarge. Duck origins recovered by the LRT. Duck descendants were long-legged walkers and later waders.

Figure 2. Basal bird phylogeny based on the LRT (morphology)

Figure 5. Basal bird phylogeny based on the LRT (morphology)

Weidig I 2010. New Birds from the Lower Eocene Green River Formation, North America. Records of the Australian Museum 62:29-44.

Nat Geo: These are the dinosaurs that didn’t die.

Figure 1. Messel swift (48 mya) from the Nat Geo bird article.

Figure 1. Messel swift (48 mya) from the Nat Geo bird article.

A recent edition of National Geographic
featured an article on bird evolution by Victoria Jaggard with photographs by Robert Clark and many illustrations. Unfortunately, they relied on DNA for their cladogram, featuring an apologetic illustration of a dissimilar grebe and flamingo arising from a common stem (Fig. 2). Dissimilar taxa are never closely related in trait analysis, but DNA analysis keeps finding such pairs in birds, always with the vague hope/faith/belief that someday this will resolve itself with new transitional discoveries. According to the large reptile tree (LRT, 1206 taxa) that will never happen as both flamingos and grebes each have a long list of more similar sisters, cousins and second-cousins that intervene between these two.

Figure 2. Flamingo and grebe illustration from Nat Geo article on birds.

Figure 2. Flamingo and grebe illustration from Nat Geo article on birds.

When it comes to fossils
Nat Geo is still stuck in the stone age as they conflate all Solnhofen birds into a single genus, Archaeopteryx, no doubt following the advice of certain professional avian paleontologists resting on tradition and an unwillingness to test specimen-based taxa. In the LRT the many Solnhofen birds are a diverse assemblage, not a single genus.

Figure 3. Vegavis being chased by a dromaeosaur in the Latest Cretaceous of Antarctica. Dr. Julia Clarke considered Vegavis an early duck. The LRT nests it with tinamou-like birds.

Figure 3. Vegavis being chased by a dromaeosaur in the Latest Cretaceous of Antarctica. Dr. Julia Clarke considered Vegavis an early duck. The LRT nests Vegavis as the long-legged tinamou-like outgroup to all living birds.

Relying on the work of Dr. Julia Clarke,
Nat Geo nests the outgroup all living birds in the LRT, Vegavis (Figs, 3, 4), as a basal chicken/duck and beautifully illustrates it as a merganser-like taxon with short swimming legs (Fig. 3). In reality we don’t have the skull of Vegavis and the legs are quite long and slender (Fig. 4), like those of the most primitive of all living birds, tinamou-like taxa.

Figure 4. Vegavis skeleton (gray parts restored) compared to duck skeleton.

Figure 4. Vegavis skeleton (gray parts restored) compared to duck skeleton.

Regarding the K-T extinction-survival event, Jaggard wrote:
“Depending on whom you ask, smaller bodies, polar adaptations, seed-based diets, and even nest designs may have played roles in determining who lived and who died. Solving the mystery will almost certainly require exhaustive hunts for animals that lived even closer in time to the impact. Ongoing fieldwork in places like South America, New Zealand, and the frosty deserts of Antarctica already hint at fresh discoveries in the near future.”

Although Vegavis fossils seem to form a bottleneck for birds in the latest Cretaceous, the present diversity of later birds arises from early Cretaceous taxa, including a clade of toothed birds like Hangshanornis, basal chickens, like Eogranivora, and the appearance of highly derived birds, like basal penguins, shortly after the K-T extinction event. We also find Vegavis-like taxa in the Early Cretaceous.

Jarrard continues:
“And richer genetic clues should flood the field in the coming years. At the China National GeneBank in Shenzhen, scientists are using faster, more precise techniques to churn out drafts of entire genomes for all living bird species by 2020. Their work should help researchers not only to understand living birds but also to match useful traits in fossil animals to those in the animals’ living descendants.”

That’s unfortunate because after testing we already know
DNA does not always work with birds. Bird workers believe in DNA, hoping that someday it will produce a tree topology in which all sister taxa will look like one another, gradually blending on adjacent branches. Unfortunately, trait analysis demonstrates that day will never come. There are just too many intervening taxa.

Please, let’s all get back to trait analysis.
I’ve shown that it can be done. DNA, at least with regard to birds, is just not working.

Jaggard V. 2018. These are the Dinosaurs that didn’t die. Nat Geo online

New skull bones for Ichthyornis

News from co-author Bhart-Anjan Singh Bhullar:
re: premax/nasal contact:

  1. We can see the facets and
  2. We have a new specimen that shows the actual shape of the nasals, so the dotted lines aren’t really so dotted.

I learned (after initially posting this),
distinct from other Cretaceous toothed birds that Ichthyornis and Hesperornis (and by phylogenetic bracketing, Gansus and Apsaravis), the premaxilla takes up a large portion of the rostrum.

Back in the day…
Ichthyornis (Fig. 1) and Hesperornis made news for being the only known toothed birds in the mid- to late Cretaceous. These birds were otherwise of such modern aspect that it was thought the teeth were ‘the last to go’ before the advent of all the toothless birds known worldwide today.

Figure 1. Skull of Ichthyornis in 3 views from Field et al. 2018 and overall skeleton.

Figure 1. Skull of Ichthyornis in 3 views from Field et al. 2018 and overall skeleton.

there are dozens of toothed birds known from the Cretaceous.

Field et al. 2018
bring news of more Ichthyornis skull bones, with few surprises as these were predicted using phylogenetic bracketing. News that Ichthyornis brings us new insights into the development of the beak in modern birds are best applied to basal members of this clade, or go back to Megapodius and Rhynchotus, living basalmost birds.

Paleontological heresy:
The topology of the large reptile tree (LRT, 1212 taxa, subset Fig. 2) indicates the teeth found in Ichthyornis, Hesperornis and other more basal clade members like Yanornis and Longicrusavis, were either secondarily acquired, or secondarily enlarged, because tinamou-like basal members of this clade have tiny teeth and the paleognath outgroup members (actual tinamous) all lack teeth. Now, that could be by convergence with neognaths and some confuciusornithids. (Just like the putative clade ‘Pygostylia‘ is not monophyletic. The most derived members of this newly recognized toothed neognath clade, like Ichthyornis, have the largest teeth, and they are sometimes (as in Hesperornis) set in sockets.

Figure 3. Subset of the LRT focusing on early birds, including Ichthyornis.

Figure 3. Subset of the LRT focusing on early birds, including Ichthyornis.

Writing a summary/teaser of the paper,
Kevin Padian notes, “Ichthyornis is closely related to living birds, but retains many features of the earliest birds. The beak was small, had not yet evolved a bony shelf structure in the palate and was limited to the tip of the jaw. However, the probable mobility of the Ichthyornis skull seems to be more like that of living birds.” That statement is at odds with the published illustration (Fig. 1) that clearly show palatal processes on the maxilla (green). What was Padian thinking? I can’t say…

Padian also reports, “the cheek region, bounded by bones of the skull roof and the side of the skull, has characteristics that are closer to those of dinosaurs, such as the retention of a large bony chamber for the adductor muscles that close the jaw.” This is also not true as Ichthyornis has a temple region very much like that of all modern birds, lacking the bony temporal ‘cage’ that surround the jaw muscles found in dinosaurs. Again, not sure what Padian was thinking here…

Padian asks, “How did these different predatory approaches favour the same pattern of tooth reduction, which also happened independently in other early bird groups?” not realizing that sister taxa exhibit a wide variety of smaller to teeth (Juehuaornis) to larger teeth (Archaeovolans, Yanornis) and that Ichthyornis was a terminal taxon leaving no descendants. Neognaths arise from Early Cretaceous basal members of this clade (Fig. 2) with tiny teeth or no teeth at all (e.g. Megapodius and Crypturus.)

The published reconstruction
(Fig. 1) includes a hypothetical robust premaxilla/nasal contact that is not preserved in any recovered fossils. That’s why they added the dashed lines. After publication some nasals were discovered that duplicate the hypothetical dashed lines.

This heretical nesting of Ichthyornis
can be duplicated with the taxon list shown above. Let me know if not and send along your .nex file for comparison.

Field DJ et al. 2018. Complete Ichthyornis skull illuminates mosaic assembly of the avian head Nature 557:96–100.
Padian K 2018. Evolutionary insights from an ancient bird. Nature 557:336.

Eocene swift: Parargornis

Earlier we looked at
Eocypselus, an Eocene bird taxon originally considered basal to hummingbirds and swifts. The large reptile tree (LRT, 1205 taxa) nested Eocypselus with the hummingbird, Archilochus, far from the swift, Apus, which nested with falcons, owls and other hook-beaked predatory birds.

Today we look at
Parargornis (Mayr 2003; Eocene; Figs. 1–3), which nests with Apus in the LRT, far from hummingbirds and far from Eocypselus.

Figure 1. Parargornis fossil from the Messel pits in various views.

Figure 1. Parargornis fossil from the Messel pits in various views.

Mayr 2003 reported,
“Most recent authors consider the Trochilidae (hummingbirds) to be the closest extant relatives of swifts and both taxa are usually united in a single order Apodiformes (e.g. del Hoyo et al. 1999). Monophyly of swifts and hummingbirds is not only supported by derived morphological characters, but also by biochemical and molecular analyses (Kitto & Wilson 1966; Cracraft 1981; Sibley & Ahlquist 1990; Johansson et al. 2001; Mayr 2002). A recent phylogenetic analysis by Mayr (2002) provided strong evidence that the Aegothelidae (owlet nightjars) are the sister taxon of the Apodiformes.”

One of the reasons
why owlet nightjars nest close to swifts is because owls nest close to swifts in the LRT. Owlets appear to be (but have not yet been tested) transitional taxa linking owls to swifts. The hook bill of all predatory birds is not like the long straight bill of hummingbirds, which the LRT nests with certain sea gulls, far from swifts, among tested taxa.

Figure 2. Parargornis forelimb and hindlimb. One toe is broken and reconstructed here.

Figure 2. Parargornis forelimb and hindlimb. Toe two is broken and reconstructed here. Look for the ungual on top of distal metatarsal 2, courtesy of DGS.

Feathers were found with Parargornis
(Fig. 3) and more appear to be buried in the matrix forming an indistinct halo around the skeleton.

Figure 4. Parargornis feathers and feather halo.

Figure 3. Parargornis feathers and feather halo.

Mayr G 2003. A new Eocene swift-like birds with a peculiar feathering. Ibis 145:382–391.

An OpenLetter to the OpenWings Project

According to their website:
“The goal of the OpenWings Project ( is to understand the evolutionary history of and evolutionary relationships among birds.”

“One of our goals in this project is to collect genomic data from DNA samples that have an associated voucher specimen in a research collection.”

Figure 2. Newell's shearwater (Puffinus newelli) in vivo.

Figure 1 Newell’s shearwater (Puffinus newelli) in vivo. We’ll examine the skeleton of this bird in an upcoming blogpost. 

“The fundamental and missing piece of this otherwise powerful comparative biology toolkit is an accurate and complete avian phylogeny. The overarching goal of the OpenWings Project is to fill this gap by producing: a complete phylogeny for all 10,560 bird species that will provide a unifying framework for understanding the origins and maintenance of avian diversity… as well as serving as a case study of the benefits and challenges of sampling all species in a major clade.”

Suggestion #1:
Start with a dozen diverse birds. IF the genotypes and phenotypes produce identical tree topologies, double that number and test two dozen birds. IF those produce identical tree topologies, test four dozen birds. Etc. Etc. You’ll get to 10,560 at that rate in ten steps with confidence that your results have been validated at every step.

If at any point the genotypes and phenotypes don’t produce identical tree topologies, review your paradigms and hypothesis. There is something wrong if they don’t match. In my testing, birds genes do not recover the same tree topologies as bird traits. Don’t waste your time and money testing 10,560 bird genes only to find they don’t deliver the same tree topology as bird traits.

Suggestion #2:
Since no large scale genomic and phenomic studies of birds have ever matched, just study phenotypes. Then you can include fossils and you won’t have to exclude taxa critical to understanding the phylogeny of birds. Click here for a starter list of taxa.

I would have contacted the OpenWings Project directly,
but (at present) they don’t provide access except through apps (like Twitter) I don’t have or want.

We looked at another DNA analysis of birds
by Prum et al. 2015 here and here and found it matched dissimilar taxa while separating similar taxa. So beware of DNA. It can only be validated with trait analysis and too often it produces odd results needing odd explanations.