Patagopteryx: it’s a hen-sized ostrich sister in the LRT

Patagopteryx deferrariisi (Late Cretaceous, 80mya; Alvarenga and Bonaparte 1992, Chiappe 1996, Chiappe 2002, MACN-N-03, 10, 11, 14 and others) was a hen-sized bird originally considered a ratite, but later (Chiappe 1996) nested it between Enantiornithes and Hesperonis. Back then Patagopteryx was one of only a few Cretaceous birds known. Here, with more included taxa, Patagopteryx nests with Struthio, the ostrich, back among the ratites.

FIgure 1. Patagopteryx compared to Struthio to scale and scaled to a similar shoulder height.

FIgure 1. Patagopteryx compared to Struthio to scale and scaled to a similar shoulder height. This Late Cretaceous taxon retained four toes and a robust tail.

Four toes are present.
As in Casaurius pedal ungual 2 is elongate. The pubis tip bends ventrally, like a boot. The anterior skull is unknown but otherwise is similar to Struthio.

Figure 2. Patagopteryx skull from Chiappe 2002 with color restoration.

Figure 2. Patagopteryx skull from Chiappe 2002 with color restoration show the skull to be very ostrich like. Note the tiny squamosal barely overlapping the quadrate, smaller than in Struthio.

Aepyornis, the elephant bird, moves over the the tinamous with this taxon addition.

Figure 3. Struthio skull with a long maxilla.

Figure 3. Struthio skull with a long maxilla.

References
Alvarenga and Bonaparte 1992.
 A new flightless land bird from the Cretaceous of Patagonia; pp. 51–64 in K. E. Campbell (ed.), Papers in Avian Paleontology, Honoring Pierce Brodkorb. Natural History Museum of Los Angeles County, Science Series 36.
Chiappe LM 1996. Early avian evolution in the southern hemisphere: Fossil record of birds in the Mesozoic of Gondwana. Memoirs of the Queensland Museum 39:533–556.
Chiappe LM 2002. Osteology of the flightless Patagopteryx deferrariisi from the late Cretaceous of Patagonia (Argentina) pp.281–316 in Mesozoic Birds, Above the Heads of Dinosaurs, Chapter: 13, Editors: Chiappe LM and Witmer LM, University of California Press.

http://www.reptileevolution.com/struthio.htm

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The origin of hummingbirds

Hummingbirds are the tiniest of living birds.
They are famous for hovering with wings beating so rapidly they essentially blur from view. Today hummingbirds live only in the New World.

Prum et al. 2015
based on DNA, nested hummingbirds with swifts and these nested with the nocturnal nightjars. That is the traditional nesting.

In the LRT 2015
based on morphology, hummingbirds nest with the extinct Eocypselus (Fig. 4, 50 mya) and the sea gull, Chroicocephalus (Figs. 1, 3; extant). Mayr 2004 reported on an Old World hummingbird, Eurotrochilus inexpectatus (Fig. 4; 30 mya), from the early Oligocene.

Elsewhere on the cladogram,
swifts nest with owls in the large reptile tree (LRT, 1129 taxa).

Figure 1. A sea gull hovering. Many birds can do this for short periods, but sea gulls are phylogenetic sisters to hummingbirds, so this is where it all began for hummers.

Figure 1. A sea gull hovering. Many birds can do this for short periods, but sea gulls are phylogenetic sisters to hummingbirds, so this is where it all began for hummers.

To be fair,
swifts also hover. And here is a sample of that on YouTube. https://www.youtube.com/watch?v=9u8YuBGQWb0
It should be noted that swifts do not feed while hovering. They speed through the air snatching insects in flight. On the other hand, gulls do hover, and here is another image of that (Fig. 2). Gulls appear to hover only in a breeze, which is often present at shorelines. Thus gulls represent the awkward origin of hummingbird hovering, which improved with faster wingbeats. a deeper sternum and a smaller size.

Figure 2. The smallest gull, Hydrocoloeus_minutus, hovering while feeding.

Figure 2. The smallest gull, Hydrocoloeus_minutus, hovering while feeding.

Fossils tell us
that hummingbird-sized specimens, like Eocypselus (Figs. 3, 4), lived 50 mya and probably originated much earlier. One-sixth the size of the small gull, Hydrocoloeus (Figs. 2, 3), Eocypselus had a relatively short, small beak and shorter legs, though still longer than the wings.

Figure 2. Chroicocephalus, the smaller Hydrocoloeus, the much smaller Eocypselus and the ruby-throated hummingbird, Archilochus to scale.

Figure 3. Chroicocephalus, the smaller Hydrocoloeus (the smallest living gull), the much smaller Eocypselus and the ruby-throated hummingbird, Archilochus to scale.

Of course, small size is key to hummingbird evolution.
At this point, I’m not aware of any gulls smaller than Hydrocoloeus, whether extant or in the fossil record. I would like to see a skeleton of Hydrocoloeus to see if it had a larger sternum relative to the 1.25x larger Chroicocephalus. I also wonder if it has a faster wingbeat when hovering based on its smaller size.

Figure 3. Eocypselus from 50 mya, Eurotrochilus, from 30 mya and Archilochus, the extant ruby-throated hummingbird to scale.

Figure 4. Eocypselus from 50 mya, Eurotrochilus, from 30 mya and Archilochus, the extant ruby-throated hummingbird to scale.

The fossil Eutrochilus
(Fig. 4, Mayr 2004) bridges the time gap between Eocypselus and extant hummingbirds and would appear to be a complete and fully realized hummingbird itself, living some 30 mya, while originating much earlier. Eocypselus (Fig. was not much different in size or morphology.

Old World vs. New World
So, based on Eutrochilus, hummingbirds used to be in Europe. Now they are restricted to the New World. Why? There is a long list of hummingbird eaters online here. Something killed European hummingbirds in the Old World… maybe microbes?

Vultures had a similar split.
Today we have New World vultures (like Coragyps, derived from petrels) and Old World vultures (like Torgos, derived from falcons) in the LRT. The odd exception to this hemispherical split is the dodo, Raphus, and its kin, all New World flightless vultures isolated on islands in the Old World. Then there’s a report of an Old World vulture in Miocene Nebraska (Zhang et al. 2012). Really, what’s to stop them? And what killed Old World vultures in the New World? So again, there’s another mystery in need of a good explanation.

References
Mayr G 2004. Old World fossil record of modern-type hummingbirds. Science 304:861–864,
Ksepka DT, Clarke JA, Nesbitt SJ, Kulp FB and Grande L. 2013. Fossil evidence of wing shape in a stem relative of swifts and hummingbirds (Aves, Pan-Apodiformes). Proceedings of the Royal Society B: Biological Sciences 280 (1761): 20130580. doi:10.1098/rspb.2013.0580. Supplementary materials here.
McGuire JA et al. (7 coauthors) 2014. Molecular Phylogenetics and the Diversification of Hummingbirds. Current Biology, 2014; DOI: 10.1016/j.cub.2014.03.016
Zhang Z, Feduccia A and James HF 2012. A Late Miocene Accipitrid (Aves: Accipitriformes) from Nebraska and Its Implications for the Divergence of Old World Vultures. PLoS ONE7(11): e48842. https://doi.org/10.1371/journal.pone.0048842

https://wordpress.com/post/pterosaurheresies.wordpress.com/10805
https://www.livescience.com/44593-first-hummingbird-evolutionary-tree.html

Molecules vs. morphology in bird phylogeny: Prum et al. 2015 part 3

Earlier and the day before we looked at basal euornithine taxa in two cladograms: one recovered from DNA analysis (Prum et al. 2015), and one from morphology (the large reptile tree or LRT, 1026 taxa). Today we’ll look at a few more Prum et al. clades.

Prum et al. clade 5: Gruiformes
These are the rails and cranes and kin: sun grebes (Heliornis), fluff tails (Sarothrura), water rails (Rallus), ocellated crakes (Micropygia), swamp hens (Porphyrio) all in one clade. In the other clade are the shorter trumpeters (Psophia) and limpkins (Aramus), and the taller crowned cranes (Balearica) and cranes (Grus).

In the LRT
only three of the last four are presently included. Psophia nests with roadrunners and cuckoos, but close to Crex, another type of rail, all derived from basal neognaths including the birds of prey clade. Aramus nests at the base of cranes, like Grus, but also terns, sea gulls, hummingbirds, penguins, pigeons and kingfishers, which is in itself quite a mixed bag of taxa—all with a long straight bill, which is not a unique trait among neognaths.

Prum et al. clade 6: Aequorlitornithes
According to Prum et al. “The Aequorlitornithes is a novel, comprehensive clade of waterbirds, including all shorebirds, diving birds, and wading birds. Within this group, the flamingos and grebes are the sister group to shorebirds, and the sunbittern and tropicbirds are the sister group to the wading and diving birds.” This is such a big clade with 18 taxa nesting distinct from 26 others that it needs to be dissected a bit more. Like so:

Aequorlitornithes clade a1: flamingos (Phoenicopterus) and grebes (Rollandia).

In the LRT: flamingos nest with the birds of prey, like the Cariama. Grebes have not been tested, but they look a great deal like loons. In any case, yesterday we looked at the untenable match between grebes and flamingos.

Aequorlitornithes clade a2: thick-knees (Burhinus), plovers and kildeers (Charadrius), oystercatchers (Haematopus), avocets (Recurvirostra).

In the LRT: none of these taxa have been tested at present.

Aequorlitornithes clade a3: plains wanderers (Pedionomus), lily trodders (Jacana), painted snipes (Rostratula), godwits (Limosa), turnstones (Arenaria), waders (Tringa).

In the LRT: none of these taxa have been tested at present.

Aequorlitornithes clade a4: buttonquails (Turnix),  pratincoles (Glareola), murres or guillemots (Uria), sea gulls (Chrococephalus), terns (Sterna) and skimmers (Rhynchops)

In the LRT: murres nest with penguins from clade b1 (see below). Sea gulls nest with hummingbirds (we’ll look at this in more detail tomorrow) and these were sisters to storks. Basically sea gulls were short-legged neotonous storks. Hummingbirds were descendants of Eocypselus, both were tiny neotonous sea gulls with an ancient lineage.

Aequorlitornithes clade b1: sunbitterns (Eurypyga), tropicbirds (Phaethon), loons (Gavia), penguins (Spheniscus).

Figure 1. The tropic bird (genus: Phaethon) in vivo.

Figure 1. The tropic bird (genus: Phaethon) in vivo. At sunset, in silhouette, some people seeing this bird with such long slender tail feathers thought it was a basal pterosaur. 

In the LRT: sunbitterns nest with similar wading storks from clade b3 (below). Loons nest with terns from clade a4 (above). Penguins nest with murres in clade a4, but a node or two apart form loons and terns. Tropicbirds, like Phaethon (Figs. 1,2), nest with barbets and toucans in the LRT.

Figure 2. The skull of the tropic bird, Phaethon rubricauda, most closely related to the barbets in the LRT.

Figure 2. The skull of the tropic bird, Phaethon rubricauda, most closely related to the barbets in the LRT. Note the posteriorly drooping maxilla, a key trait in this clade that also includes hornbills and toucans. 

Aequorlitornithes clade b2: petrels: albatrosses (Phoebastria), storm petrels (Oceanites , Pelagodroma and Oceanodroma,) fulmars (Fulmarus), shearwaters (Puffinus), petrels (Pterodroma), and diving petrels (Pelecanoides).

In the LRT: only one tube nose, Macronectes, has so far been tested. The presence of a tube nose on the rostrum of all these taxa makes this a probable monophyletic clade.

Aequorlitornithes clade b3: storks (Ciconia) maribou storks (Leptoptilos), frigate birds (Fregata), gannets (Morus), darters or snake birds (Anhinga) cormorants (Phalcrocorax), ibises (Theristicus), tiger heron (Tigrisoma), blue herons (Ardea), bitterns (Ixobrychu), hamerkops (Scopus), shoebills (Balaeniceps) and pelicans (Pelecanus).

In the LRT: hamerkops, shoebills and pelicans also nest together. Storks nest apart from herons and also apart from hamerkops and kin. The ibises nest at the base of spoonbills and ducks, sisters to hornbills and toucans. The rest have not yet been tested.

 

 

 

 

 

Palaelodus: transitional between flamingos and grebes?

A short break from our Prum et al. 2015 series
as we take a peek at the origin of flamingos and other basal neognath birds, which we’ll look at in greater depth tomorrow in part 3.

Traditionally
flamingos, like Phoenicopterus (Fig. 1), have been difficult to nest in bird cladograms. Flamingos seem to stand alone. Bird expert Gerald Mayr 2004 quoted Sibley & Ahlquist (1990), who wrote flamingos are “among the ‘most controversial and long-standing problems’” in phylogenetic analysis.

Bird expert
Cracraft (1981) made a luke-warm suggestion for stork affinities. Other bird experts, Olson and Feduccia (1980) liked stilts and avocets as relatives. They also suggested that flamingo-like Palaelodus (Figs. 2, 3) ‘may have occupied a more duck-like swimming niche than do typical flamingos’, The Galloanseres (chickens + ducks invalid clade) was considered, perhaps based on the long-legged duck Presbyornis.

Using molecules,
Prum 2015 and others before them nested the flamingo, Phoenicopterus, with the flightless grebe, Rollandia (Fig. 1). And now (hopefully) you see what I mean when I say, DNA does not recover testable or valid relations over long phylogenetic distances.

Figure 1. The flamingo, Phoenicopterus, compared to the grebe, Rollandia. DNA says these two are more closely related than any other tested taxa. The LRT reports they are not related.

Figure 1. The flamingo, Phoenicopterus, compared to the grebe, Rollandia. DNA says these two are more closely related than any other tested taxa. The LRT reports they are not related.

Using morphology
the large reptile tree, (LRT, 1026 taxa) nests the flamingo with the similarly proportioned, hook-beaked seriema, Cariama sisters to the terrestrial birds of prey, represented today by Sagittarius, the secretary bird. Here (Fig. 2), based on a long list of shared traits, it is possible to see how flamingos could gradually arise from seriemas.

Figure 2. Which taxa share more traits? Phoenicopterus, the flamingo nests with Cariama, the seriema in the LRT, but with Gavia in the Prum et al. DNA study. Gavia nests with Thalasseus, the tern in the LRT.

Figure 2. Which taxa share more traits? Phoenicopterus, the flamingo nests with Cariama, the seriema in the LRT, but with Gavia in the Prum et al. DNA study. Gavia nests with Thalasseus, the tern in the LRT.

Mayr 2004 wrote:
“A recent molecular analysis strongly supported sister group relationship between flamingos (Phoenicopteridae) and grebes (Podicipedidae), a hypothesis which has not been suggested before. Flamingos are long-legged filter-feeders whereas grebes are morphologically quite divergent foot-propelled diving birds, and sister group relationship between these two taxa would thus provide an interesting example of evolution of different feeding strategies in birds.”

Morphologicaly,
grebes are quite similar to loons, like Gavia (Fig. 2), which nests with terns and penguins in the Prum et al. tree AND in the LRT. (Wow! That’s a rare happenstance!)

Then Mayr 2006
found a taxon that had been around awhile Palaelodus ambiguus (Figs. 3–5), that morphologically linked flamingos to grebes. Mayr reports, “Since both grebes and †Palaelodidae are aquatic birds which use their hindlimbs for propulsion, it is most parsimonious to assume that the stem species of (Pan-)Phoenicopteriformes also was an aquatic bird which used its hind limbs for propulsion in the water (Mayr 2004). Palaelodus has “derived skull features of flamingos with leg adaptations for hindlimb propulsion found in grebes.”

Figure 3. From Mayr 2006, who wrote, "Palaelodus sp. (†Palaelodidae; uncatalogued specimen from Alliers in France in the collection of Forschungsinstitut Senckenberg). Note that the upper beak and part of the cranium in B are reconstructed."

Figure 3. From Mayr 2006, who wrote, “Palaelodus sp. (†Palaelodidae; uncatalogued specimen from
Alliers in France in the collection of Forschungsinstitut Senckenberg). Note that the upper beak and part of the cranium in B are reconstructed.”

In the LRT
stork-like Palaelodus (1.5m tall) nests with Rhynchotus, a tinamou. Like Rhynchotus, Palaelodus appears to be fully volant.

Figure x. Data used to score Palaelodus in the LRT. Note the very flamingo-like proportions, but this is a ratite.

Figure 4. Data used to score Palaelodus in the LRT. Note the very flamingo-like proportions, but this is a tall, gracile tinamou.

70 characters and 17 suprageneric taxa later, Mayr 2004 wrote:
“Previously overlooked morphological, oological and parasitological evidence is recorded which supports this hypothesis, and which makes the taxon (Podicipedidae + Phoenicopteridae) one of the best supported higher-level clades within modern birds. It is more parsimonious to assume that flamingos evolved from a highly aquatic ancestor than from a shorebird-like ancestor.” Do you see the fatal flaw here?

Figure x. From Mayr 2006, comparing the flamingo (above) to Palaelodus (middle) and the grebe (below) assuming a gradual transition of traits from grebe to flamingo.

Figure 5. From Mayr 2006, comparing the flamingo (above) to Palaelodus (middle) and the grebe (below) assuming a gradual transition of traits from grebe to flamingo that is not readily apparent because these taxa are not related to one another in the LRT.

Mayr employed 17 suprageneric taxa,
rather than generic taxa, even though his museum has a long list of bird skeletons in its collection. The Mayr 2004 cladogram is very poorly supported with most nodes failing to attain a Bootstrap score over 50. But it did nest Gavia with Phoenicopterus and grebes. Mayr also notes a parasite common to both grebes and flamingos alone among birds. Mayr did include tinamous in his analysis. So, I suppose character scoring is to blame here. Mayr’s hypothesis of relationships (Fig. 5) appears to be untenable. Many other taxa are closer to all three in morphology.

G. Mayr wrote via email upon seeing this cladogram:
“Hmm, to me the trees make little sense. If Palaelodus results within palaeognathous birds, many characters must be incorrectly scored. Furthermore, this exemplifies the pitfalls of laerge-scale cladistzic analyses.
Best wishes,
Gerald Mayr”

Unfortunately
this reply reflects the general view of PhDs. Large scale analyses, as readers know, test more possibilities, giving each taxon more opportunities to nest wherever they most parsimoniously fit.

References
Cracraft J 1981. Toward a phylogenetic classification of the recent birds of the world (Class Aves).Auk98: 681–714.
Mayr G 2004. Morphological evidence for sister group relationship between flamingos (Aves: Phoenicopteridae) and grebes (Podicipedidae). Zoological Journal of the Linnean Society. 140 (2): 157–169. doi:10.1111/j.1096-3642.2003.00094.x. ISSN 0024-4082.
Mayr G 2006. The contribution of fossils to the reconstruction of the higherlevelphylogeny of birds. Species, Phylogeny and Evolution 1 (2006):59–64.
Mayr G 2015. Cranial and vertebral morphology of the straight-billed Miocene phoenicopteriform bird Palaelodus and its evolutionary significance. Zoologischer Anzeiger – A Journal of Comparative Zoology. 254:18–26.
Milne-Edwards A 1863. Mémoire sur la distribution géologique des oiseaux fossiles et description de quelques espèces nouvelles. Annales des Sciences Naturelles (in French). 4 (20): 132–176.
Milne-Edwards, A 1867-1871. Recherches anatomiques et paleontologiques pour servir a l’histoire des oiseaux fos- siles de la France (Paris, G. Masson).
Olson SL, Feduccia A 1980a. Relationships and evolution of flamingos (Aves: Phoenicopteridae). Smithsonian Contributions to Zoology 316: 1–73.

wiki/Palaelodidae
wiki/Palaelodus
Dr. Gerald Mayr

Molecules vs. morphology in bird phylogeny: Prum et al. 2015 part 2

Yesterday we looked at the basal bird taxa in both the LRT (morphology) and Prum 2015 (molecules/DNA). Today that continues with Prum’s Neoaves.

Prum et al. 2015 clade 3: Strisores
Derived from a sister to screamers and megapodes, the clade, Strisores, includes nightjars, potoos, and arising from owlet nightjars, the apodiformes (= swifts + hummingbirds). In other words, this clade includes several aerial insect-eaters with a wide, short, hooked rostrum and the hummingbirds, which have a narrow, long, not-hooked rostrum.

The skull and skeleton of Apus apus,

Figure 2. The skull and skeleton of Apus apus, the Common Swift. Note the big eyes, like an owl, and hooked beak, like an owl.

In the LRT
(subset Fig. 4) hummingbirds arise from similar taxa with a narrow and long rostrum, like the sea gull, Chroicocephalus. By contrast, swifts and their kin arise from the birds of prey clade all with a short, hooked rostrum. Swifts, like Apus (Fig. 2) are most closely related to owls. Perhaps that is why the owlet nightjars nest with them (they have not yet been tested). Googling: owlet nightjar reveals that the skull is very much like that of the tested swift, Apus with the same big eyes, like an owl, only in swifts they eyeballs are not so exposed.

The swift clade
includes such supreme masters of the air that the feet are reduced and seldom used except for perching. That they should arise from dirt-pecking, ground-dwelling chicken-like taxa that run around and rarely take flight, does not make sense when looking for a gradual accumulation of traits. The better relationship is with falcons (some of the fastest of all flyers) and owls (some of the quietest of all flyers), as recovered using morphology.

Prum et al. clade 4: Columbaves
this clade derived from a sister to the swifts, is divided between cuckoos and their kin (turacos and bustards) and pigeons and their kin. Among the bustards, the Kori bustard (Ardeotis lori) is the largest extant flying bird native to Africa.

Figure 2. Ardeotis skull. Note the ridge at the posterior cranium. Compare to figure 3, the heron skull is similar.

Figure 2. Ardeotis skull. Note the ridge at the posterior cranium. Compare to figure 3, the heron skull is similar.

By contrast, the LRT, based on morphology,
widely separates cuckoos and pigeons. Cukoos and the Kori bustard both nest with herons. Pigeons, like Columba, nest with wrens and dippers.

Figure 4. Subset of the LRT focusing on birds.

Figure 4. Subset of the LRT focusing on birds.

A reader asked about
Pandion, the osprey. Here it nests between falcons and owls + swifts.

References
Prum et al. (6 co-authors) 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526:569–573. online

Molecules vs. morphology in bird phylogeny: Prum et al. 2015

As readers know
DNA cladograms do not match morphology cladograms, like the large reptile tree (LRT, 1124 taxa). Today we’ll be looking at some of the ‘strange bedfellows‘ that the Prum et al. 2015 DNA cladograms produced.

The LRT outgroups
include a long line of taxa extending through theropods and Jurassic birds, like Archaeopteryx), and other taxa going all the way back to Devonian tetrapods. That’s a solid out group. At every node the taxa document a gradual accumulation of traits. 76+ (the number may grow) Euornithine birds comprise the in group.

Figure 2. Basal Euornithes/horizontal. Click to enlarge.

Figure 1. Basal Euornithes. Click to enlarge this horizontal view of figure 1.

The Prum et al. cladogram employed 198 euornithine birds,
and nested the ones genetically closest to crocs at the base: Struthio, the ostrich + (Leipoa, the megapode + Chauna, the screamer).

Prum et al. chose two outgroup taxa:
Two crocodilians. No theropods were included. No Jurassic birds were included.

Crocs don’t have feathers.
Their forelimbs are not transformed into wings. Morphologically crocs are not good outgroups for euornithine birds, but, when using DNA, there are no better taxa living today. Unfortunately they do not provide a readily visible gradual accumulation of traits. For those we have pertinent taxa recovered by the LRT (Figs. 1, 2).

Figure 1. Basal euornithes to scale as recovered by the LRT.

Figure 2. Basal euornithes to scale as recovered by the LRT. Basal birds, for the most part, were long-legged forms. Short forms arrive easily by way of neotony as bird hatchlings have short legs. Yanornis is Early Cretaceous.

LRT Clades 1 and 2: Tinamous and Ratites
In the LRT the first clade includes an early Eocene tinamou-like bird, Pseudocrypturus + Apteryx, the kiwi. In the next clade mid-sized tinamous are basal to giant ratites – and all other extant birds.

Prum et al. Clade 1: Ratites and Tinamous
In the Prum et al. cladogram, the giant derived ostrich splits off first, then the smaller rhea, then the even smaller kiwi (Fig. 1), then the giant cassowary and giant emu. These last two are sisters to the clade of tinamous and all members of the Palaeognathae in the DNA study. In the Prum et al. tree, the ostrich is basal to all known ratites – and all other extant birds.

This may strike you as odd.
Generally basal taxa are average to small in size (Fig. 1) and without unusual traits, but the opposite is the case in the Prum et al. cladogram.

LRT Clade 3: Toothed Birds
The next clade in the LRT includes extinct toothed birds, a clade that, perforce, has to be ignored by the Prum et al. DNA study and, for that matter, has little bearing on extant bird evolution. This clade came and went without affecting the living birds. The presence of teeth are a secondary appearance, an atavism in this clade. The basalmost taxon, Changzuiornis, had tiny teeth and most closely resembled the long-snouted, long-legged outgroup tinamous. Later toothed birds had larger teeth, shorter legs and the most derived toothed bird, Hesperornis, had vestigial wings.

Teeth in birds,
whether true teeth with dentine and enamel, or false teeth made of bone or keratin also reappear most obviously in ducks, flamingoes and Pelagornis, the giant petrel. Less obviously tiny bill projections can be found in several other bird bills on close examination.

Prum et al. Clade 2: Neognathae + Galloanseriformes
In the Prum et al cladogram the first neognath clade includes megapodes and chickens on one branch and screamers and ducks in the other. In the LRT megapodes are indeed close to chickens, but ducks are far removed from screamers. Importantly, neither screamers nor megapodes are skeletally similar to the ostrich, their proximal outgroup in Prum et al.

LRT Clade 4: Birds of Prey
Generally tinamous are infrequent flyers and so are basal members of the next clade in the LRT, the long-legged, hooked beak predators, Cariama and Sagittarius. The latter gives rise to short-legged aerial predators like Pandion (ospreys),  Falco (falcons) + Targas (Old World vultures) and Tyto (owls) + Apus (swifts).

Figure 2. Which taxa share more traits? Phoenicopterus, the flamingo nests with Cariama, the seriema in the LRT, but with Gavia in the Prum et al. DNA study. Gavia nests with Thalasseus, the tern in the LRT.

Figure 3. Which taxa share more traits? Phoenicopterus, the flamingo nests with Cariama, the seriema in the LRT, but with Gavia in the Prum et al. DNA study. Gavia nests with Thalasseus, the tern in the LRT.

Phoenicopterus, the derived flamingo is a frequent flyer, but eats while standing with a strongly hooked beak and nests with the similarly gracile basal Cariama. In summary, and heretically, swifts and flamingos nest with birds of prey in the LRT. Prum et al. nest flamingos with short-limbed, straight-billed grebes, like Gavia, and all other shorebirds (Fig. 3). The LRT nests Gavia with short-limbed, straight-billed terns and only a few other shorebirds.

More later.
It’s a big subject.

References
Prum et al. (6 co-authors) 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526:569–573. online

Laurin and Piñeiro 2017 ‘reassess’ mesosaurs

This paper came with much anticipation
following discussions several years ago with one of the authors (GHP) about mesosaurs (Fig. 2) and their relationship to pachypleurosaurs and thalattosaurs (Fig. 2) in the LRT. Unfortunately only 17 terminal taxa (many suprageneric) were employed by Laurin and Piñeiro 2017 (vs. the 1122 taxa in the large reptile tree, LRT).

Unfortunately,
pachypleurosaurs and thalattosaurs were not among the 17 taxa employed by Laurin and Piñeiro. That makes this study worthless with regard to mesosaur interrelations. Very unfortunate.

From the Laurin and Piñeiro methods:|
“We started from the matrix of Laurin and Reisz (1995), given that this was the matrix that we knew best, that we had confidence in the accuracy of the anatomical scoring, and that we were confident that we could apply the revised scores in a manner coherent with the original scoring.” 

Figure 2. Unfortunately pachypleurosaurs and thalattosaurs are omitted from this cladogram.

Figure 1. Unfortunately pachypleurosaurs and thalattosaurs are omitted from this cladogram from Laurin and Piñeiro 2017. I don’t know of any aquatic basal synapsids or basal captor hinds. Does anyone?

The authors
nested mesosaurs between Synapsida and Captorhinidae (Fig. 1). Neither suprageneric clade include basal members that in any way resemble mesosaurs.

A sampling of mesosaur sister taxa
as recovered by the LRT is shown here (Fig. 2). I challenge the authors to find better sister taxa among the Synapsida or the Captorhinidae.

Figure 2. Click to enlarge. The origin of ichthyosaurs and thalattosaurs from basal diapsids and basal mesosaurs. Relationships are rather apparent when seen in this context.

Figure 2. The origin of ichthyosaurs and thalattosaurs from basal diapsids and basal mesosaurs. Relationships are rather apparent when seen in this context. Chronology is a little mixed up based on earlier radiations and the rarity of fossil formation.

A gradual accumulation of traits
is what we’re all looking for in a cladogram. If you don’t find that using your inclusion set, expand your inclusion set until you do.

Professors Laurin and Reisz
are at the top of the list of professional paleontologists, and have been at the top for decades. Unfortunately they’re holding on to an invalid hypothesis. There is no monophyletic clade ‘Parareptilia.’ Included members don’t look alike and simple expansion of the dataset splits them to other parts of the reptile family tree.

If you find yourself working with top workers
in the field and the results don’t make sense, you may be obligated to follow their lead. That seems to happen all too often. You’ll make more sensible discoveries if you keep a modicum of independence, or complete independence. And you’ll avoid the professional embarrassment of being criticized online instead of being hailed and complimented for ‘finally putting it all together’. This was an opportunity lost, no matter how much detail and data was provided.

This paper was edited by
Holly Woodward (Oklahoma State University) and reviewed by Michael S. Lee (South Australian Museum) and Juliana Sterli (Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina). It’s almost unheard of to see editors and reviewers listed near the titles of papers, btw. More often they are thanked in the Acknowledgements section.

On the plus side
I’m happy to see Piñeiro included a mesosaur skull with every bone colored (Fig. 3). That’s the way to do it nowadays. And if you’re into mesosaurs, this paper does provide a great deal of data about mesosaurs.

Figure 3. Mesosaur skull with bones colored by Laurin and Piñeiro 2017, modified from Piñeiro et al. 2012b.

Figure 3. Mesosaur skull with bones colored by Laurin and Piñeiro 2017, modified from Piñeiro et al. 2012.

References
Laurin M and Piñeiro GH 2017. A reassessment of the taxonomic position of mesosaurs, and a surprising phylogeny of early amniotes. Frontiers in Earth Science, 02 November 2017: 13 pp.  https://doi.org/10.3389/feart.2017.00088
Piñeiro G, Ferigolo J, Ramos A and Laurin M 2012. Cranial morphology of the Early Permian mesosaurid *Mesosaurus tenuidens* and the evolution of the lower temporal fenestration reassessed. Comptes Rendus Palevol. 11(5):379-391.