The hoopoe (genus: Upupa) joins the LRT

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

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

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

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

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

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

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

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

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

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

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

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

We’ll look at mousebirds tomorrow.

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

Advertisements

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

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


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

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

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

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

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

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

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

References
Shaw 1809. General Zoology 7 pt2:486

wiki/Lesser_bird-of-paradise

 

What are birds-of-paradise?

Lophorina superba
is a black and cyan male superb bird-of-paradise (BoP) with an incredible feather display during mating rituals (Figs. 1, 2).

My question is: What are birds-of-paradise?
Where do they nest in the large reptile tree (LRT, 1283 taxa)?

Wikipedia reports:
Lophorina (and all other birds-of-paradise) nests within the family Paradisaeidae within the order Passeriformes which means, close to Passer the sparrow, which nests between chickens and parrots in the LRT. One catch: Wikipedia reports: the family Paradisaeidae nests most closely with crows and jays, which are not closely related to the seed-eating chickens, sparrows and parrots in the LRT.

Figure 2. Male Lophorina niedda in various stages of its mating ritual.

Figure 2. Male Lophorina superba in various stages of its mating ritual from Scholes and Laman 2018.

Evidently the skeletons of birds-of-paradise
are not as highly prized as are the feathers. So, due to a lack of skeletal data for Lophorina
the LRT nested another bird-of-paradise, Semioptera wallacii (Fig. 3), based on skull data only, within the cuckoo clade between Menura, the lyrebird (Fig. 6), and Geococcyx, the roadrunner. Distinct from these two taxa, birds-of-paradise have shorter legs, which usually results from neotony (chicks of long-legged taxa generally have short legs).

FIgure 3. Skull of Semioptera wallacii has basic cuckoo clade features.

FIgure 3. Skull of Semioptera wallacii has basic cuckoo clade features.

Semioptera shares with Lophorina
a set of breast shields and that ventrally concave beak. Not sure yet how any other BoPs are related to one another yet. If you have access to BoP skeletons, please send the citations or images.

As we learned
earlier, few of these bird relationships (Fig. 4) match genomic studies, which have been favored in recent years over skeletal studies. For instance, using DNA Prum et al. 2015 nested the lyrebird, Menura, at the base of a clade of bowerbirds, then crows + Lophorina (BoPs), and finally thrushes and sparrows. So results are not confirmed. Adding BoP and other taxa, as they become available, will help paint a better picture of evolution here.

Figure 4. Semioptera, the bird-of-paradise, nests in the cuckoo clade between the lyrebird, Menura, and the roadrunner, Geococcyx.

Figure 4. Semioptera, the bird-of-paradise, nests in the cuckoo clade between the lyrebird, Menura, and the roadrunner, Geococcyx, not with sparrows, crows or jays (Passer, Corvus or Cyanocitta) in the LRT.

If you’ve not had your fill of dancing BoPs,
here’s a link to a YouTube video you might like:

The Darwinian thing is…
these males do not choose to act or look like they do. A long line of ancestors made that decision for them when they acted and looked that way (or thereabouts) and successfully mated with the females that, in reality, did all the choosing during these rituals.

Figure 6. The lyrebird, Menura, nests close to the one BoP in the LRT.

Figure 6. The lyrebird, Menura, nests close to the one BoP in the LRT.

References
Scholes E and Laman TG 2018. Distinctive courtship phenotype of the Vogelkop Superb Bird-of-Paradise Lophorina niedda Mayr, 1930 confirms new species status. PeerJ. 6:e4621: e4621. doi:10.7717/peerj.4621

birdsofparadiseproject.org

Neotherium: more bear than walrus in the LRT

Wikipedia reports, 
Neotherium mirum (Kellogg 1931; Middle Miocene, 12mya) is an extinct species of basal walrus.” 

By contrast,
the large reptile tree (LRT, 1281 taxa) nests Neotherium (Figs. 1, 2) with Ursus, the bear (Fig. 1), several nodes apart from the Odebenus, the walrus (Fig. 2). Since bears are also somewhat basal to the walrus, the wiki statement may be true, but a little misleading and less than direct.

Figure 2. Neotherium and the origin of bears in the LRT. Puijila is a last common ancestor.

Figure 1. Neotherium and the origin of bears in the LRT. Puijila is a last common ancestor. The size increase is obvious.

The problem might be
taxon exclusion. There is a traditional paradigm that bears are related to raccoons and/or dogs. That is not validated in the LRT, which tests all of these candidates at once and with a long list of other tetrapod taxa. The taxa nest where they want to when give the opportunity to do so, as we’ve seen before many times.

Figure 3. Ancestral walrus taxa from Robert Boessenecker. See references below.

Figure 2. Ancestral walrus taxa from Robert Boessenecker. See references below.

References
Kellogg AR 1931. Pelagic mammals of the Temblor Formation of the Kern River region, California. Proceedings of the California Academy of Science 19(12):217-397
Kohno  N, Barnes LG and Hirota K 1994. Miocene fossil pinnipeds of the genera Prototaria and Neotherium (Carnivora; Otariidae; Imagotariinae) in the North Pacific Ocean: Evolution, relationships and distribution. The Island Arc. 3(4): 285–308. doi:10.1111/j.1440-1738.1994.tb00117.x

https://en.wikipedia.org/wiki/Neotherium

Thinking about the Crocodylomorpha…

Short one today.
The following GIF animation of 4 frames (5 seconds each) is a subset of the large reptile tree (LRT, 1280 taxa) focusing on the Crocodylomorpha and showing:

  1. Clades within Crocodylomorpha
  2. Extent of bipedality
  3. Extent of dorsal scutes
  4. Extent of elongate ulnare and radiale (synapomorphy of the clade)
FIgure 1. Subset of the LRT focusing on the Crocodylomorpha, dorsal scutes, elongate proximal carpals, bipedality and clades.

FIgure 1. Subset of the LRT focusing on the Crocodylomorpha, dorsal scutes, elongate proximal carpals, bipedality and clades. There are more taxa at the origin of this clade, fewer extant taxa here. When traits are unknown (lost due to taphonomy), colors are estimated.

Distinct from all prior smaller studies,
here the Crocodylomorpha is the sister taxon to the Dinosauria. Together these alone comprise the Archosauria. They arise from a sister to the Poposauria and these arise from basalmost Rauisuchia, a sister to Vjushkovia (not Postosuchus). The traditional clade ‘Pseudosuchia‘ is invalid (= not recovered as a monophyletic clade) under this hypothesis/cladogram.

Taxon exclusion
misinformed earlier studies of the Crocodylomorpha. Those earlier studies did not include enough pertinent taxa to recover the present hypothesis of relationships. Most prior studies included irrelevant taxa (members of the Pterosauria), which nest not with archosaurs, but within Lepidosauria.

Figure 2. The genesis of the Archosauria embodied in PVL 4597 to scale with a modern archosaur, Cyanocritta.

Figure 2. The genesis of the Archosauria embodied in PVL 4597 to scale with a modern archosaur, Cyanocritta. Dorsal scutes are shown above the dorsal vertebrae.

Phylogenetic miniaturization
occurred at the origin of the Archosauria, with duck-sized PVL 4597 (Fig. 2) at the origin of the Archosauria. Thereafter dinosaurs lost their dorsal scutes and gained feather placodes.

References
https://en.wikipedia.org/wiki/Crocodylomorpha

The walrus (genus: Odobenus) joins the LRT

No surprises here.
Odobenus, the walrus (Figs. 1, 2), nests with the seal, Phoca, in the large reptile tree (LRT, 1280 taxa). But I think you’ll see, the division between seals and walruses runs deep, perhaps with some parallel development of the flippers, fat, etc.

Figure 1. Walrus skeletons, swimming and walking, plus a view of the teeth, which barely erupt and cannot be seen in lateral view.

Figure 1. Walrus skeletons, swimming and walking, plus a view of the teeth, which barely erupt and cannot be seen in lateral view. Yes, that extra bone between the legs of the lower specimen resides in the penis.

Odobenus rasmanus (Linneaus 1758) is the extant walrus. The canines are much enlarged here. The other teeth are flat and barely erupt. The naris is elevated. The jaw joint is aligned with the bottom of the jaw and the retroarticular process is much reduced. The scapula is robust.

FIgure 2. Walrus skull with bones colorized.

FIgure 2. Walrus skull with bones colorized.

Walruses eat bivalve mollusk scraped from the sea floor bottom. 
According to Wikipedia, “The walrus’s body shape shares features with both sea lions (eared seals: Otariidae) and seals (true seals: Phocidae). As with otariids, it can turn its rear flippers forward and move on all fours; however, its swimming technique is more like that of true seals, relying less on flippers and more on sinuous whole body movements.[4] Also like phocids, it lacks external ears.” Earlier the LRT recovered separate terrestrial ancestors for seals and sea lions.

Figure 3. Ancestral walrus taxa from Robert Boessenecker. See references below.

Figure 3. Ancestral walrus taxa to scale from Boessenecker. 2014. Compare Neotherium to Puijila in figure 4. Neotherium nests closer to bears.

Neotherium (Fig. 3)
shares a long list of traits with Puijila, which was originally hailed as a last common ancestor for seals, sea lions and walruses (Fig. 4). In the LRT Pujilia is not basal to sea lions. In the LRT Neotherium nests with Ursus, the bear, not with Odobenus, the walrus.

What are the giant canines used for?
According to Wikipedia, “Tusks are slightly longer and thicker among males, which use them for fighting, dominance and display; the strongest males with the largest tusks typically dominate social groups.  Tusks are also used to form and maintain holes in the ice and aid the walrus in climbing out of water onto ice. Analyses of abrasion patterns on the tusks indicate they are dragged through the sediment while the upper edge of the snout is used for digging.”

You can think of walruses
as aquatic bears or aquatic stylinodontids (Fig. 4). Ursus and Neotherium are sisters to the last common ancestor (LCA) of walruses and stylinodontids with Puijila the LCA of bears and walruses.

Figure 4. Ursus maritimus compared to ancestral and related taxa, Mustela, Puijila and Stylinodon. Seeing them together makes comparisons easier.

Figure 4. Ursus maritimus compared to ancestral and related taxa, Mustela, Puijila and Stylinodon. Seeing them together makes comparisons easier.

Figure 5. Puijila nests down the line from the walrus, a trait you can see it its profile and general morphology. Compare to Neotherium in figure 4.

Figure 5. Puijila nests down the line from the walrus, a trait you can see it its profile and general morphology. Compare to Neotherium in figure 4.

References
Boessenecker R 2014. The evolutionary history of walruses, parts1–5:

  1. http://coastalpaleo.blogspot.com/2014/08/the-evolutionary-history-of-walruses.html
  2. http://coastalpaleo.blogspot.com/2014/08/the-evolutionary-history-of-walruses_26.html
  3. http://coastalpaleo.blogspot.com/2014/09/the-evolutionary-history-of-walruses.html
  4. http://coastalpaleo.blogspot.com/2014/09/
  5. http://coastalpaleo.blogspot.com/2014/11/the-evolutionary-history-of-walruses.html

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

wiki/Walrus

Kapes: a new procolophonid with long cheeks

Zaher, Coram and Benton 2018
bring us a new procolophonid, Kapes bentoni, with long cheek bones (Fig. 1).

Figure 1. Kapes bentoni. Perserved parts are in gray.

Figure 1. Kapes bentoni. Perserved parts are in gray.

Unfortunately,
Zaher, Coram and Benton have no idea how their included taxa are related to one another because they exclude so many pertinent taxa (Fig. 2), as determined by the large reptile tree (LRT, 1280 taxa). Infamously, Dr. Benton purposefully deleted taxa in prior works. Not sure why that was also done here.

Figure 2. Cladogram from Zaher, Coram and Benton excluding so many pertinent taxa present in the LRT that the phylogenetic order is here reversed.

Figure 2. Cladogram from Zaher, Coram and Benton excluding so many pertinent taxa present in the LRT that the phylogenetic order is here reversed.

Workers don’t have to believe
the hypothesis of relationships proposed by the LRT, but it would profit them to at least include the pertinent taxa shown revealed by the LRT.

References
Zaher M, Coram RA and Benton MJ 2018. The Middle Triassic procolophonid Kapes bentoni: computed tomography of the skull and skeleton. Papers in Palaeontology 2018:1–28. doi: 10.1002/spp2.1232