User:Dysmorodrepanis~enwiki/Sandbox6

here there be papers

General
List of birds


 * Gerald Mayr & Clarke, Julia (2003): The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters. Cladistics 19: 527–553


 * Dyke & van Tuinen (2004): The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record. Zoological Journal of the Linnean Society 141: 153–177.


 * Marcel van Tuinen & S. Blair Hedges (2004): The effect of external and internal fossil calibrations on the avian evolutionary timescale, Journal of Paleontology 78(1), 45 -- 50 (January 2004) see also here


 * Slack, Kerryn E.; Jones, Craig M.; Ando, Tatsuro; Harrison G. L. "Abby"; Fordyce R. Ewan; Arnason, Ulfur & Penny, David (2006): Early Penguin Fossils, plus Mitochondrial Genomes, Calibrate Avian Evolution. Molecular Biology and Evolution 23(6): 1144-1155. PDF fulltext Supplementary Material


 * van Tuinen et al (2006): Tempo and mode of modern bird evolution observed with large-scale taxonomic sampling. Historical Biology 18:205 - 221.
 * Probably an update/revision of the above.


 * Livezey, Bradley C. & Zusi, Richard L. (2007): Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zoological Journal of the Linnean Society 149 (1), 1–95.
 * The most massive study of morphological characters in birds to date.

Ratites

 * (AOU South American Classification Committee)
 * Haddrath O, Baker AJ. (2001): Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc Biol Sci. 268(1470): 939-45.
 * Ah, don't we just love reading things like:
 * "'The non-stationary base composition in these sequences violates the assumptions of most tree-building methods [...] The avian sequences also violate a molecular clock [...]'"
 * What they fail to address is the odd pattern of the NZ taxa. There seems some confounding factor in their molecular evolution; it is just too weird. Enough paleobiogeographical discussion for two papers. Altogether quite nice. Not very informative for the issue at hand though, rather for why it hasn't been resolved yet.

Galloanserae

 * (AOU South American Classification Committee)
 * Galloanserae: A Critical Examination (EvoWiki)
 * Zool. J. Linn. Soc. 121 pp361 (1997): A phylogenetic analysis of basal Anseriformes, the fossil Presbyornis, and the interordinal relationships of waterfowl. Plus erratum issue 124 p397.
 * Apparently basis for current view of these things.


 * Zool. J. Linn. Soc. 121 pp429 (1997): Systematic relationships of the palaeogene family Presbyornithidae (Aves: Anseriformes)
 * The last mention of the presbyornithid-phoenicopterid link before it was rather ignobly sunk it appears.


 * Michael D. Sorenson, Elen Oneal, Jaime García-Moreno, and David P. Mindell (2003): More Taxa, More Characters: The Hoatzin Problem Is Still Unresolved. Mol. Biol. Evol. 20(9): 1484–1499.
 * Methodological studies as regards monophyly of Galloanserae, Galliformes and Anseriformes, and the placement of Anseranas.

Neoaves

 * Mayr, Manegold, Johansson (2003): Monophyletic groups within 'higher land birds'- comparison of morphological and molecular data. Journal of Zoological Systematics and Evolutionary Research Vol. 41 Issue 4 Page 233


 * Fain, Matthew G. & Houde, Peter (2004): Parallel radiations in the primary clades of birds. Evolution 58(11): 2558-2573. PDF fulltext


 * Ericson PGP, Anderson CL, Britton T, Elzanowski A, Johansson US, Kallersjo M, Ohlson JI, Parsons TJ, Zuccon D, Mayr G (2006)"Diversification of Neoaves: integration of molecular sequence data and fossils" Biology Letters 2(4): 543-547
 * Sabine's Sunbird talk 23:25, 7 April 2007 (UTC)


 * Look at the author lineup, YAY! BioLetters is not on my regular browse list; I might have browsed it but I can't remember deep reading it. Hmmmm... the pieces are coming together! I am not sure at all about Metaves (in Hoatzin I summed up why. "phylogenetic signal for Metaves, albeit this signal seems to be weak." 'Cause it's phony?), and the "higher landbirds" are not well resolved, I think there'll be some Near passerines standing out eventually.
 * Cuculidae, Musophagidae, Hoatzin, sandgrouse and possibly parrots are the best-known lineages which I'd decidedly class incerta sedis in the big scheme of things. The other popular birdie orders have all some sort of immediate neighborhood. I think it would pay to look at homoplasies molecular and morphological in the oddballs.
 * "Higher waterbirds" also not much resolved to satisfaction, taxa almost certainly misattributed btw seabird group, "pelecaniform" group, heron group, storks, penguins... Interesting that core Gruiformes are continuing to stand apart. Distinctness of Charadriiforms also gaining support.
 * It is interesting to note a few "stray" lineages, like the "weird 'gruiforms'". There are some interesting things, like seriemas and falcons (+ other raptor-birds?), hmmm, why not? But the seriema ecomorphotype is pretty generic stuff you always had in the savannas; hmmm, need to check out morph autapomorphies in seriemas as these might be telling.
 * All in all, the "higher landbird" "grass" and the orange Metaves (in part) look spurious to me, while the rest is a good bet for representing things as they were. Lots of alternative trees and probability value data would be good to have. We only see some numb suggestions, but what if there were like 15 trees with good likelihoods? (I think there might often well be, and I think that if you compare some 20 such studies, the correct one could be drawn from that data)
 * Mirandornithes and Cypselomorphae seem a good bet.
 * NW vultures, nothing solid any more by now. It is very unlikely by now that Falconiformes and "Ciconiiformes" are any close. Here, NWV -> basal "higher landbirds" well duh, no, "clearly have their affinity with other raptors", NO! "Data entirely confusing and convergence all over the place", yes. Dysmorodrepanis 22:00, 16 April 2007 (UTC)

"Gaviomorphae"
The #1 bogus "clade". Discredited as early as 1935, continues to pop up in cladistic analyses because the homoplasy is just so strong.

Charadriiformes/"charadriimorphs"
Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds

Baker AJ, Pereira SL, Paton TA. BIOLOGY LETTERS 3 (2): 205-209 APR 22 2007

Need to check how calibration was done. 3-5 lineages I would have entirely suspected. 14 sounds much, but why not? Need also to check outgroups - any pattern recovered there?

"Higher waterbirds"/"Conglomerati"
-> core S/A Ciconiiformes


 * Farris et al (1999): Frigatebirds, Tropicbirds, and Ciconiida: Excesses of Confidence Probability. Cladistics 15: 1–7


 * Mayr, Gerald (2005): Tertiary plotopterids (Aves, Plotopteridae) and a novel hypothesis on the phylogenetic relationships of penguins (Spheniscidae). Journal of Zoological Systematics 43(1): 67-71. PDF fulltext


 * Slack, K.E.; Jones, C.M.; Ando, T.; Harrison G.L.; Fordyce R.E.; Arnason, U. & Penny, D. (2006): Early Penguin Fossils, plus Mitochondrial Genomes, Calibrate Avian Evolution. Molecular Biology and Evolution 23(6): 1144-1155. PDF fulltext Supplementary Material

Mirandornithes
flamingos + grebes

Hoatzin
See there. For the record, in all bird taxa I have come across (and that's is A LOT), this is the one that comes closest to "falsifying" the theory of evolution; no satisfying phylogenetic hypothesis has been advanced in some 230 years: a burlesque critter with oversized wings it seems ill able to use, which swims (when ist is young) and crouches through the swamp forests of deepest Amazonia, equipped with a kind of rumen which causes it to belch and fart, stink horribly and taste possibly even worse, is generally useless for humans, but not in any way harmful or vicious, and even pretty fun to look at (if you're standing windwards of it). Creationists and proponents of Intelligent design: what does this tell you about your God? The article Lysergic acid diethylamide might give you some hints; or maybe it won't.

Seriously though - I think this is gonna get resolved too in due time. One good fossil from the Early Eocene and one younger than Foro is all we need.

Cypselomorphae
Caprimulgiformes + Aegotheliformes + Apodiformes

Daedalornithes = Aegotheliformes + Apodiformes

Metaves if valid. Else, relationship with "higher landbirds"?

"Higher landbirds"

 * Johansson, U.S., Parsons, T. J., Irestedt, M. & Ericson, P. G. P. 2001. Clades within the ‘higher land birds’, evaluated by nuclear DNA sequences. Journal of Zoological Systematics and Evolutionary Research 39: 37–51.


 * Mayr, G., Manegold, A. & Johansson, U. 2003. Monophyletic groups within ‘higher land birds’ – comparison of morphological andmolecular data. Journal of Zoological Systematics and Evolutionary Research 41: 233–248. Erratum JZS 42: 173–174

Passeriformes
see here. Approaching completion.