Sunday, May 8, 2011

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412 characters on phylogeny Pan-fossil avian

All living Sauropsida - or "reptile", as their more familiar, but inappropriate connotations loaded name - is one of the four major groups. (I could of course also choose two, six or fifteen groups, depending entirely on which way will I cut cladograms.) Is a turtle ( Testudines), snakes and other scaly hatérie ( Lepidosauria ) crocodiles (Crocodylia ) and birds (Neornithes ). Although it is completely counterintuitive fact, birds are not nejdivergentnější of these groups, but are deeply nested among the Sauropsida. Crocodiles are more closely related to birds than varanům, or perhaps leguánům mezozoickým marine reptiles. Monophyletic group consisting of birds and crocodiles called Archosauria . In addition to the two groups living there include many fossil pros: étosauři, poposauroidi rauisuchidi and from "the crocodile", pterosaurs, ornithischians, sauropodomorfové and many lines from avian theropods. The phylogenetic relationships of these groups is an issue that only palaeontologists and 80 very frustrated by years: until we could build a little more than one large polytomii where all these lines running out from a single point, without splitting the order was clear (this example illustrates Charig [1976]). Revolution brought about - what else - numerical methods to reconstruct phylogeny, or cladistics. Gauthier (1984, 1986, Gauthier & Padian 1985) during several years of fossil archosaurs zrevolucionalizoval scheme and laid the foundations still valid today, if only by given name Archosauria clear definition.
Content crocodile and avian archosaurs line shortly after the pioneering studies with a total Gauthierových stabilized. Ornitosuchidi soon as the relatives of birds moved closer to the crocodiles, which are - it seems - settled permanently. While at large scales is a phylogeny Total bird line boring (to recognize silesauridů in the last decade with her cuckolded bit), the crocodile line is different. Animals can not it deserves more attention than they receive - usually somehow lost in the shadow of dinosaurs. Systematically seeks to remedy such as Bill Parker on his blog Chinleana . Although he is defined more time (Triassic) than phylogenetically, precisely because of it, however, crocodile-line archosaurs occupies a prominent position - in this period because these animals had a dominance of dinosaurs (Brusatte et al. 2008). Readers Chinleany up some time ago to learn about the upcoming memoir phylogenetic archosaurs, unique in its scope, which stands for Sterling Nesbitt. And three days ago, this works with almost three hundred pages finally came out.
right foot pan-avian viewed from the front or from above. (A) Dimorphodon Macronyx , pterosaur, (B) Lagerpeton canarensis , lagerpetid; (C) left leg silesaurida Silesaurus opolensis (d) Heterodontosaurus tuck , ornithischians (E) Saturnalia tupiniquim , sauropodomorf; (F) Coelophysis Baur, theropods. Numbers refer to character states, the scale corresponding to 1 cm. For sources of illustrations and explanations of the characters, see the original publication. (Source: Nesbitt 2011: Figure 48)

Motto:
truth is just that, that paleontologists never have enough characters to a reliable phylogenetic analysis of its material.

T. Grim, Universe, 2009 / 4
Yes I quote this as an unprecedented example of chauvinism neontologického ripped out of context . The author pushes him into a reactionary bag had three independent approaches / disciplines: taxonomy based on morphology, molecular data point, "evolutionary taxonomy" (about the history pindání sense ginger) in contrast with cladistics and eventually paleontology, sharply defined against neontologii . The idea that the paleontologists to their phylogenetic hypothesis testing, is unimaginable Grim ("[...] can speculate sophisticated, often I may be right in principle but not its conclusions about the relationship between fossil organisms independently verify the data "). Elsewhere the same author shows how much morfologové compared molecules is wrong (why not also believe more molecules, but it has its limits - Health Marsupionta, turtles and archosaurs singers as nejbazálnější live birds), but did not for a moment thought that the paleontologists to reconstruct phylogeny can be used indirectly to molecular data (must see Lee et al. 2007) .* It Nesbittova A new study shows perfectly how absurd the claim Grimová. In their data matrix codes author 87 taxa (80 ingroup) to a total of 412 characters, which makes it by far the most comprehensive material ever published on the basal archosaurs. Sure, you also have neontologové much larger pieces, on the other hand, it was not so long ago that dealt with questions like velkoškálové phylogeny of metazoa matrix size of only a few dozen characters (Nielsen [2001] had 64 of them).

Enthusiasm Nesbittovy of work gives a clear properly archosaurs blogosphere (ie the sum of archosaurs writing on blogs, but blogs written archosaurs). Mickey Mortimer, who typically Cup for fun pieces of ill-coded data matrix speaks in superlatives about the analysis . True, some errors also found , but given the extent of the amount of work is impressive. He wrote an admiring article Mike Taylor SV-POW . For comparison, Livezey & Zusi (2006, 2007), perhaps the greatest morphological examined with cladistic analysis of all time, containing 2954 characters. The authors devoted 556 pages of descriptions of methods, definitions of symbols and mapping their occurrence (Livezey & Zusi 2006), to then discuss the results of the next 95 pages (Livezey & Zusi 2007). Compared with Nesbittova analysis of more than seven times smaller number of characters occupying a total of 292 pages, while in the field of phylogenetic hypotheses proposed so far that the author has much less to discuss.
diligence Nesbitt characters defines and describes also does a great period. The same applies to a methodological basis. By example, describes the four categories of characters, he decided to omit from the matrix: characters unexplained, or explained little or lacking (nezužující the fibula and irreducibiled kalkaneum ") characters, which are difficult or even impossible to interpret (cited Gauthierův the character whose two states - 0 and 1 - description, correspond to any of taxa coded) characters, which describe the shape of the cranial window rather than the shape of bones, which are themselves; and finally, the characters, whose origins are tafonomický and does not reflect the true form of animals.

Pan-Aves, and his subklady apomorfie

What we Nesbitt (2011) says the pan-avian phylogeny? This:

Phylogeny of avian archosaurs line according to Nesbitt (2011). The results here are not so surprising, except perhaps for paraphyletic herrerasaury ( Staurikosaurus more closely related to birds than herrerasaurovi). Only two taxa, which in my analysis downright missing, Scleromochlus (I would really like to know if he had Benton [1999] his position correctly) and Guaibasaurus . It would be but to formulate an argument in favor of the inclusion of a number of other early dinosaurs ( Chindesaurus, Panphagia, Chromogisaurus , perhaps Agnosphitys and Spondylosoma ), but examine the phylogenetic position was not simply to Nebsittovy study. Perhaps her time in the matrix and substituting Andrew Cao Mickey Mortimer. (Source: Nesbitt 2011: Figure 52)

nejbazálnější As a representative of bird branch reveals Nesbitt (2011) pterosaurs. There is nothing surprising - when it was omitted from the analysis Scleromochlus is hard to expect anything else. For example, integrating with pterosaurs dinosauromorfy ( Ornithodira ) the author found the following synapomorfie:
  1. otherwise of the end of the neural spines of cervical vertebrae
  2. otherwise of the end of neural spines on the dorsal vertebrae
  3. second finger has a longer second Article finger than the first
  4. elongated unguál (= finger article bearing claw) on the I., II. and III. finger
  5. tibia longer than femur
  6. transverse width of distal tarzálu four nearly identical to the width of the distal 3 tarzálu
  7. Kloubící pad for metatarzál in the distal tarzálu 4 smaller than half of its lateral surface
  8. pit in front astragal (= bone ankle) reduced or absent in otvůrek
  9. Sharp anteromediální (= axis of the body and forward facing) corner astragal sharp
  10. Compact with metatarzus metatarzály II-IV, crowded after at least half its length
  11. Osteodermy missing
  12. abdominal ribs (gastralia) have between them a wide gap
(only unique characters, valid only under synapomorfie optimization ACCTRAN / Deltran omitting)
for pterosaurs (or pterosauromorfy, I used the same nomenclature as the author - however, the content is identical) found 13 unique synapomorfií while in search of their phylogenetic position, the author relied on data from the two most complete basal representatives ( Eudimorphodon and Dimorphodon ). Nesbitt (2011:238) also notes that, contrary to what Bennett (1996), which advocated as early pterosaurs archosauriformy unrelated to dinosaurs, the shared features ornitodirů confined to the hind feet and features associated with movement. It is quite natural (after all, The name Ornithodira faces S-curved neck and no legs) and it is good that this argument is losing ground under the very last legs - is haunted here since 19 century. At first argument in the style of the similarities in the hind legs are only adaptive and independently associated with acquired erect position ( history again in action) the defendant used the dinosaur origin of birds and - as aptly noted Gauthier (1986) - opened the Pandora's box in which hid the dinosaur polyfylie: when dinosaurs and the birds received similar rear legs independently of each other, why can not the same country with different groups of dinosaurs?
Next in line are lagerpetidi. The topology is not worth dealing with (you can guess from a simple listing of three known members). Nesbitt (2011:239), but it comes with an interesting finding: lagerpetidů ankle is more similar than pterosaurům dinosauriformům, could thus be lagerpetidi basal pterosauromorfy? It would be nice to align the time gap between the oldest dinosauromorfy ( Asilisaurus , anis, 245 Ma) and pterosaurs ( Faxinalipterus , normal, 215-217 Ma). Astragalus supports the hypothesis of the calcaneum fused, curved bottom surface of the second element kalkaneálního or absence of bone. Nesbittova answer is however a good response phylogenetics: but this just does not seem the most economical hypothesis, so it's either symplezimorfie or homoplazie. The only thing that could promote pterosauromorfní lagerpetidy would have been new discoveries of early pterosaurs, which would affect the polarity of the other characters.

    Co se silesauridů týče, Nesbittovým výslovným záměrem bylo otestovat, zda jde o monofyl sesterský vůči dinosaurům (Irmis et al. 2007), nebo o sérii taxonů čím dál tím blíže dinosaurům příbuzných (Ezcurra 2006). Lépe z analýzy vyšla jednoznačně první hypotéza; Nesbitt (2011) navíc demonstroval celou řadu chyb, které Ezcurrově analýze umožnily dospět ke konfliktnímu výsledku. 2 ze 3 znaků, které eucelofyzise přibližují k dinosaurům a rozbíjejí tím monofyletické silesauridy, located on the pubic bone, whose jurisdiction the eucelofyzisově holotype is in fact uncertain (Nesbitt et al. 2007). The third character is in fact present even in smaller specimens silesaura. After proper transcoding even throw Ezcurrova matrix weakly supported monophyletic silesauridy. At Nesbittově are supported by four unambiguous synapomorfiemi:
  1. Otvůrky for cranial nerve XII (hypoglossal nerve) arranged in almost perfect sagittal plane
  2. rough ridge on the anterolateral (předobočních) outer edges of the occipital bone
  3. Center 3rd to 5 cervical vertebra over the center of vertebrae from the middle of the back
  4. notch below the proximal femoral head
Positive (+ Silesauridae Dinosauria ) is supported by 13 unambiguous synapomorfiemi. A slightly more extensive example, which includes even marasucha, but not lagerpetidy (and which, unlike previous vided name - Dinosauriformes ) has a unifying character 9, all of which relate to the pelvis and hind limbs braiding:
  1. pubic bone over the bone
  2. Kloubící seating surfaces for bone and hip bone sitting on the proximal part of the pubic bones are separated by a groove or a gap between Contact
  3. pubic bone and ischium is thin and confined to the proximal edge of both elements
  4. Kloubící surfaces of the hip bone and pubic bone in the proximal part of the buttock are continuous, but divided hole
  5. ischium length clearly exceeds the length of the upper edge of the iliac
  6. corymb front (anterior / cranial trochanter) is separated from the body of the femur no cleft and its proximal edge to the body bone occupies a steep angle
  7. front (anterior) chocholíkový shelf located proximally, respectively. above the point where the thigh bone connects muscle M. caudifemoralis
  8. Proximodistálně oriented groove on the lower side (remote) parts tibia
  9. The front talus is a small forward is less salient than the height of the rear part of the bone
Nesbittova topology applied to a timeline. The definition of stratigraphic levels are taken from Gradstein et al. (2004) with several modifications. Black stripes represent the occurrence time "senior pros, then you can of white terminal taxa. Short dashed lines represent positives arising from the lower end of the Triassic, then dashed long before the advantages arising anis. Abbreviations: (PERM) Permian, (Indian) Indian, (Olen) olenek. (Source: Nesbitt 2011: Figure 58B)

Silesauridi as dinosaurs?

silesauridů internal topology can not be a surprise to anyone who has read the description last asilisaura (Nesbitt et al. 2010) - is exactly the same, with lewisuchem (= pseudolagosuchem) as nejbazálnějším representative. Interesting is when Nesbitt (2011) examines the assumption that advocated Sulej & Dzik (2007) and examined with cladistic substantiate Ferigolo & Langer (2007) - that are monofyletičtí silesauridi nejbazálnějšími ptakopánvými dinosaurs. Enforcement of this topology was worth only 11 extra steps compared nejúspornějšímu tree (with a length of 1285 steps). It's not so much, so this hypothesis would not be so quickly dismissed. The problem however is that the tapered end of the edentulous jaw, forming a "beak" similar to that of ptakopánvých is limited the derived silesauridy, while lewisucha / pseudolagosucha missing. This taxon (taxon these s?) Is, however, typical of the flat and curved back teeth carnivores. This is true even in both directions: the teeth are similar to those derived silesauridů teeth derived ptakopánvých - heterodontosauridi and Pisanosaurus , nejbazálnější ornithischians (Butler et al. 2008), the teeth are different.
Ferigolo & Langer (2007) even suggested that Silesaurus and Sacisaurus to share one of the most striking apomorfií ptakopánvých dinosaur bone předzubní (predentary - hence the name "Predentata" which had been used for ornithischians in archaic literature and Bakker). Even if this questionable assumption Nesbitt included in the analysis silesauridů position has not changed.

What defines archosaurům against other dinosaurs?

Since Thulborna (1975), virtually no challenge - and if so, no one took it seriously - that dinosaurs are a monophyletic group. At the beginning 90. years there has been a consensus on what exactly the term "dinosaur" to mean the smallest natural group, which includes both ornithischians and Saurischia. There was also consensus on the fact that this group includes herrerasaury, which had previously been challenged (Gauthier 1986, but still Fraser et al. 2002) - herrerasauři While dinosaurs were called, but should be separated before the emergence of a dichotomy ornithischians / Saurischia. The problem, he moved to what characters are dinosaurs apomorfické, or characters that distinguish it over other archosaurům, včetně jejich nejbližších příbuzných ( Marasuchus , silesauridi):
All numerical analyses provided a core set of dinosaurian synapomorphies, many of which overlapped. However, the absence of skulls and hands in the proximal outgroups of Dinosauria has prevented the optimization of many characters at Dinosauria. The new material of basal dinosauriforms, represented by both crania and postcrania, allows further testing of dinosaurian synapomorphies.

Nesbitt 2011:13
    Výjimečná velikost Nesbittovy matrice opět usnadnila hledání odpovědi. Autor nalezl celkem 12 unique apomorfií vided Dinosauria, 8 more under ACCTRAN mode (= one assumes the creation of the state emblem and its subsequent reversal) and 6 of the mode Deltran (= implies that the character originated several times independently, homoplasticky). Here I will once again only the first category:
  1. Exokcipitály (lateral occipital bones) do not meet the center bottom vnitrolebeční cavity. (Also, I lay in Crocodylomorpha and ( Effigia Shuvosaurus +).) *
  2. Nadspánková hole is nadspánkovým before the window
  3. čepovcem vertebrae in the front of the neck are present epipofýzy (= projections on the upper side of the vertebrae on both sides of the neural spike)
  4. deltopektorálního Peak ridge at the end of the proximal third of the humerus bone
  5. radius less than 80% bone length arm
  6. Kloubící surfaces for hip bone and pubic bone in the proximal part of the buttock are separated by a large, concave surface and nekloubícím *
  7. fourth corymb in the form of a sharp ridge
  8. fourth corymb asymmetric, where the distal edge of the body forms an angle of less bone than the proximal edge
  9. comb tibia for insertion napřimovače thigh (cnemial CREST) \u200b\u200bform an arc forward and included in the
  10. * On the back side remote end of the tibia is present pronounced proximodistálně (longitudinally) oriented ridge *
  11. Kloubící facet for fibula bone occupies less than 30% of the transverse width talus
  12. Kloubící facet for fibula bone is the calcaneus (heel bone) inside the convex
Characters marked with an asterisk were identified as dinosaur synapomorfie time.
These characters are relatively new - As indicated Nesbitt (2011:246), many previously proposed after the discovery apomorfií sielsauridů either move to a larger example, and their optimization has become problematic and ambiguous. On the other hand, most synapomorfií, proposed often in the phylogenetic-time analysis Nesbittovou was again exposed. The author himself expresses surprise that these characters do not affect or rather a fundamental change in the topology of the dinosaur, as přeskokování herrerasaurů and Eoraptor between theropods and basal plazopánvými heterodontosauridů or recognition as a very early ptakopánvých (Butler et al. 2008).

internal structure of dinosaurs

Nesbittova analysis has a good chance to make me believe in theropod herrerasaurů identity. By their words included by most characters, which Langer and Benton (2006) Drifting outside herrerasaury Eusaurischia ( Sauropodomorpha + Theropoda). In his analysis, but it is most economical to treat them as early convergence and sauropodomorfů neoteropodů. A bit more of a problem I have with teropodním Eoraptor (after all, Martinez et al. 2011 and informal feedback on the results of DML suggest a nice solution a protracted problem). And as proof that even the matrix can not be 412 characters in all believe I said herrerasaury paraphyletic. Staurikosaurus, according to her, closer to birds than to herrerasaurovi, which makes the example Herrerasauridae ( sensu Novas 1992) containing the equivalent example and Theropoda Herrerasauria it restricts itself to herrerasaura. (By the way, nice demonstration that the phylogenetic nomenclature ever have done far more harm than good.) It is interesting that the author mentions that his score almost in passing, even though it contravenes all phylogenetic analyzes the past 25 years, which are I know. I wonder if parafylie otherwise generally respected bands Nesbittových any deviation matrices: the author has the following description as tawy broke celofyzoidy (Nesbitt et al. 2009).
Celofyzoidi would probably have to smithereens in the new analysis, but know it, because of their traditional representatives are only here Dilophosaurus and Coelophysis personally. Dilophosaurus is taking these two taxa actually closer to birds, but it coincides with some analysis; are monophyletic celofyzoidy actually reveal a less extensive than usual (Smith et al. 2007). It is interesting that a large portion of the internal structure of the phylogenetic signal stretches plazopánvých tawy: Without it, I lay at the base of established polytomie sauropodomorfů, herrerasaura, and my staurikosaura ( Eorapto r + Neotheropoda ). Nesbittovy dinosaur results are still unsatisfactory in one, and poorly resolve ptakopánvých basis. Even if we leave aside the somewhat curious position within pisanosaura heterodontosauridů, analysis was still not able to determine whether a single somehow derivative ptakopánvému (skutellosaurovi, with early armored dinosaur from the group Thyreophora ) closer Eocursor , Lesothosaurus or just heterodontosauridi. Butler et al. (2008) would like their topology ( Pisanosaurus + (+ Heterodontosauridae Genasauria including lesotosaura)) believed more.

Phylogeny archosaurs (AU) with an emphasis on the bird line archosaurs (C, FJ) and basal Dinosaurs (GJ). (A), Gauthier 1984, (B), Benton & Clark 1988 (C), Juul 1994, (D), Bennett 1996 (E) Serena 1991 (F) Benton 2004 (G) Novas 1996 (H) Irmis et al. 2007 (I) Ezcurra 2006 (J), Langer & Benton 2006th Taxa with further distinguishable (but unrecognized) phylogenetic structure are in bold. (Modified from Nesbitt 2011: Figure 1, Figure 2 and Figure 5)

divergence of birds and crocodiles

interesting sub-issue, which deals with Nesbitt, the timing crocodile-bird divergence. Although "[i] if they have not found any fossils at all, we can reconstruct the phylogeny as well" (Grim 2009 - how I adore the article ...), about half of the numbers reported by web timetree.org whose purpose is to use the results of molecular clock the popularization of evolution is totally out of it at first glance, the fossil record. Some works such as the basal divergence of archosaurs date until it 10 million years the dinosaurs ruled the planet (!) - Eg Hugall et al. (2007). Even before 245 million years have been the world Asilisaurus , a representative of the group has derived a total pan-avian, and Nesbittova topology requires an additional 6 knots, before we get to the first common ancestor of birds and crocodiles (the first way back when, of course). Any estimate of less than 245 million years, this becomes feasible.

Conclusion

Nesbitt study itself concludes with this:
This analysis is far from the''last word''on basal archosaur Relationships and, I hope, this work Will Encourage Other basal archosauriform workers to continue to work on the Relationships Within the clade. [...] Even though this analysis provides the largest, most Comprehensive phylogeny of basal archosaurs to date, There is a plethora of work that follow.

Nesbitt 2011:255
Indeed, Bill Parker, who is the author of the well and the analysis of knowing well in advance, on SV-POW wrote that Nesbitt was also for this gigantic study only warm-up, and that the author has a "ton of other characters" ...

potentially interesting links:

Mike Taylor on trial Nesbittově
Mickey Mortimer Nesbittově the study
Longisquama in Nesbittově matrix
Cosesaurus in Nesbittově matrix
Langobardisaurus in Nesbittově matrix


* Although this article does not aim to address the attempt to ridicule Grimův paleontological systematics, one more point deserves an answer: "Past efforts to reconstruct the phylogeny us quite clearly teaches that sebedelším gape at "signs" in a museum or on the autopsy table is impossible to know which characters are informative and which are not. "(Grim 2009) That's right - the two" buts ". 1) If it phylogenetically informative characters is such that "all available features" over "software wise, it is not what paleontologists blame, since they do the same thing. True, molecular phylogenetics software can also be used to search primary homologies (similar to what is what), while it is good morfologům only to identify the secondary (which really is a similarity phylogeny speak), but the human factor is never eliminated (rusty 2006 - ironic is it that the Grim quotes, too, without being part of this mattered). Moreover, the very first selection of characters made man always - is whether the analysis included 18S rRNA, elongation factor 1-α, or preferably both, phylogenetics (if you know) no software to tell. 2) morphological data are different from those of molecular and have their own advantages and problems. In some cases, the newsworthiness of the character decide without gazing at exhibits. It is as evident that the relationship will not tell us anything autapomorfie to become a state for only a single OTU in the analysis. Morfologové such a symbol of peace may exclude from the matrix, while the molecular data, it will not - autapomorfické nucleotide substitution does affect the results of the analysis (the infamous attraction of long branches).

Sources:

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