Monday, November 16, 2015

The bigger picture

Here is the bigger picture.
We can see the dinosaur branch that simply went extinct, and the pterosaur branch that leads to birds.



Here is a cladistic analysis, which confirms the placement of Oviraptors (eg. Hagryphus, Conchoraptor) and Alvarezsaurids (eg. Mononykus, Shuvuuia) within Paraves:


Here is the TNT input file, which is based on the data from:

A Jurassic ceratosaur from China helps clarify avian digital homologies (2009)
http://www.nature.com/articles/nature08124.epdf?referrer_access_token=1LIOYM249T2ALXmHhUVXQtRgN0jAjWel9jnR3ZoTv0NAxxXDTxDgb7tt7vNCs5i7CDx_p1E8pIL0dPMGIw0CIZ1LRnUZIDT1a3FIDY_UW4FRwpODRDVwWg-KbK448VK63yIXiGAa_H8fA42yVK8TsNhr_ASjWKKTbM-PJCMVzpKKElR4FEstewHl9DZGaHr9&tracking_referrer=www.nature.com

http://www.nature.com/nature/journal/v459/n7249/extref/nature08124-s1.pdf

xread
517 17

Euparkeria ???0000?0?000???00?0?00000000000000000001??00000000000?0?1000??0
??00?00?0?000?00?0000?0?0?0?0?000?0???0??00??0?0?001?0?000????????0030?01?0??000?1
0200?0?10?001?00000100000?0???0?0000?000???0???00?000?0??0??00??0010?00????????0??
???????????0?????0???0??0?00?00?????10?0????0???0???????000?0???????00??00?????00??0?
??00110010???00?0?0?0???0?0???????0?0000??0?00?????????0???0?0??0?0????0???0?0??????
?????????????????????????????????????????????????????????0??????????????????????????????
????????????????????????????????

Marasuchus
????
????????????????????????????????????????????????????????????????????????????????????
????????0000?00--0??001???0?00?0??0?????????????????????????????????????????????0?????
????00000?00?000--?00?00??1??0?0?0?00?20000?0?0??0?0??00000000000??????????0????01?
00?????10?0????????0???????000002-?00?00000000-0?000000-??00000011?4?00-20000-0?000
002?010000000000?00??00000000010000000?0000000?01??????????????????????????????????
????????????????????????????????????????????????????????????????????????????????????????
??????


Allosaurus ???0?0100101?0000?000?10?010?0??0??0????11??00000111?0??11001000?
00??010???0?00010001120?00010??001001100?0011000??011001?10?0000000000010010?1?0
00001010100102000000102000000000102120010000111000101100001001100100300000?00?
0?0110100101010000?1??10??00010110000000000000000100000??01001110000000?0000100
100000000100?1100001000011000000?000101000100011010001012?0?10000001101110?0020
00000?020000000010201111000000111200?100113100000010001110002000104?10?0010001
00000000000???????????????????????0???????????????????????

Compsognathus
0??00100
0???1010?1?0??201000?00?00??0000??000000000010???10110???000?001000??????
?0?????????????0?????1????????????00?????????????00000010010?0?000?1210?1??101001001
10200000000010??1??00?00111?00?????10001??110?023????0?00?0?00?10000010010100???1
???0001010?000000?1???????0?0000?????010100??0???0?0?1???????00?011??0100001000001
0000?0??1?????0000?1???1??0??????0??0?0001??10?0000200?000?0200??0010102??101000??
?1012?1?010113?0000000???0000?10010104?00?0110???0000??????0???????????????????????
0???????????????????????


Tyrannosaurus ???100000011101011101100000000001110010?00221000001110??1111010
0
0001?111
22?010100100103?00001000001001110?00100001101?01?010?02000000000100101
1?0110010101011010001001020000000001021200000001111?0100100001001100000310?00?
10?0?0?0001001111000001??11??00010100000001001001?00100010?1?0?01111100000?0110
10110000001010001100001000001021000?101101001200011010001012?20??0100020110100
0020000100020000000010200111000000111200?0001131002000100010100000001?0?00?101
0?0?02????????0???????????????????????0???????????????????????



Confuciusornis
011?1
?1?0000???????0???0?110???????0????1???1?00??0?????10-??0?0?10??000?????0?00001
?????????0??0?????????????1?????0?????????????00100000010?1?000?0???000?11-????1?????
2??????????????????0?????????0100???1?????0?5????0?21?-?1?????????????011?21?010?0???
??0?11114020????1111???0?11?11?002???0?1?1??????02??100?30-?1???00101????1?211011?1
1????2??1?10???0?1????????01??1??20???11?0?01?10??0?00??000?0-----------------------1?2??1
110?0???020??0-10?1?3??0000?0???11????200?1?4??0-0110???000???120?0?????????????????
??????

Jeholornis
????
??????0????????????????????????0?????????????????????????????????????????????1??0??
????????????????????????????????????10?????00?????????????????????????1?????1????????2?
???????????????????????????0?????2?????3???1???0?2?2???1???????????0???????1?????1??10
11[04]0????????1?1??????110?012?0??0??1?????????????????????????????????????1??1??????
??????????????????????????????????????????????????000?0-----------------------102??01100????
???200-000113?000000???????0003000104??0-0110??????00030000-----------------------


Shuvuuia
???0?011000010101?1010200000?000000000001100-1111-10111011001000-100000100010000
00010-??01?120000021101000100110??100010??110121000010001000001001110??0000?1??0
1??02--210011?1?2010?1121111?1110101010100??01?011?0?502??1120111211100200?11100
10?20??002000-1000000030001011-0001100???1?1?010?2-?111????2??111?000?20-2?1??0000
0?0??-?22000-01??11121?1010011??1???1121??1011122110?0000200102000?001101120-------
----------------1?2??2200?1000101211-1111?3??0200?01?0000???301?1????1-10?10?1000????01
?????????????????????????

Mononykus
?
???
????????????????????????????????????????????????????????????????????????????????????
??????????????????????100??????????1012?0???????????????????????????????????2--?1?0?1??
0????????1?11?0--?101?10101???1?011?0??????11?01?12?1????????????1??20??002000-?00?0
000300010?1-00011?1?1?1?1?0?????0??????????111??00?2????1??00?00?0??-?????0-?1????12
1?101001?101????1?1??1011??21???0000200102000?000101120-----------------------112112200?
1000101?11-1111????0200?01?0000?????1?1????1-10010?1000?????1???????????????????????
??


Gallus 0
110102
10?00??????101????????0??0000?100??0201111?000?1110-100?01?????01?00100?0??
?1??????012??101----0???????100?101??0?1??????????????????????????????????11-----1-----2-
-------11011200111111?0?10111100001101?101701110031?-???????????????001?2111103010-
10011011111010111101110011?1?1101012-00101?01???0210111?30-2--2?10031201011?211??
?1101112--11101010?110121?11???111???101110020011??01?001002--0-----------------------10
2?1121000001010200-02111210000000000000000-3--101-00?011?00?00?000----0----------------
-------


Conchoraptor
??????00
111
0?0?00??1???0?020???????1????1???111?000??12?10-?1000010??001?????000000
0?????????1??1?????????0????1??????00??11?????0212000201?0?0?000?0???101011-????1???
??2????-?????????0????????????1???01??0????????11??0??????1????????????0???????1?11?01
??0??010001??????001????????????010?1?001?1??????0210000?1100?1??20??1???010??000-0
??????11?1010?010?0????????????0????????0?0?00?00??0?0???10000-----------------------102??
1?1000?0?11110?-110113??000000?0?10?00?0010104??0-0010?0?00000?00100-------------------
----


Microraptor
0100?01000??1??????0??00????????00?0????????1??0??????????????????????0???????????????
??????????0??????????????????????????????????0?00010??????01??1??????010???1?01--210?0
000?0????2???011?????????0?100?0?1?00??014???1??10?1?1??1--1-0?1??2011?01101??0????1
??1111011???0??11???00??1100?111?11??1?1??????02011?1?21110?2001131?0?011111010?1
?????11?1111??10?0?????????0?0???01???1000010?11?01?11?010000-----------------------10???
???????0????2?0??0010????????????????????0011???????0????????????0?0-----------------------


Hagryphus
????
????????????????????????????????????????????????????????????????????????????????????
????????????????????????????????????????????????????????????????????????????????????????
????????????????????????????????????????????????????????????????????????????????????????
???????????????0?110???????????????????????????????????????????????????????????????????
??????????????????????????????????????????10000-----------------------1020001100000011010?-
0001131000000100010000?200?104-00-011010100000?00000-----------------------


Dilong
10?100
0?011
?10100110?1000?0001001010000001221000010110?0010001000000000120001?1
0010011??0?????00001001100000???1??1?100??0????????000000100001111111010101?1101?
00100102000000000????1?00??0?1?1??0100?????1?????0101????????????0????1?001????000?
??????0????01000?01??10001???????????????1?1?00000??0?10100100?0?0??11?????????0????
?0??0????11?110001?00??010001?12?201???00020111??0????0?00?0?2?0??000?1?2??1010?00
?011?2???00?1?3??0000?10?010????000?1?4??000010???000???120?????????????????????????
????????????????????????


Epidexipteryx
??-????????????????????????????????0???????????0000???????0?0??00?????01?1???????00?0?
???????????????????????????????????????????1??00??00????1?00??????0????0??11002???011?
1???00??????????0????????0??00?0???0????14????1?20?2????1??2????????10?1?????1?1???0?
100?1002????0000????1??????????0??????????1???????0??00??????0?00102????210?0??1????
????1???????????????0?????1??01???11102????0??0?????001???????????????????????????????
?????????????0??????????????????????????????????????????????????????????????????????????
??

Epidendrosaurus
????????????????????????????????????????????????0100?0
??????1??00?????0????????????????
???????????????????????0???????????????????21000000100?1?00?10???0????????????????1???
?
????????????????????????0?00?0?0?01???13???0??10?1????10?0???1?1????1??????101?????1
?0110?2????00?0?0??1?1?110????0??0?1?????1???????0?000??????0?00??2????2?0?0??1?????
2?2?0100????0??????0???????????????1020??00??0?00??001?0-----------------------102??????0??
??????00-00?103??0?0000?0??0?000000?114?00-0000?0?00?100200?0-----------------------

Sinosauropteryx 
1000
000
001?01??0?0????00000??0?000??0?????????00??00?0???10???????0??00????0??00012
?10??????????0??????????????0??????????????????00?00?100??????????????1??101001001102
000000000????1??01?10111?10?????10?01??2?0??13??????00?0?0??1110?0111101000??????0
0010100100000?00?00???0?0000??110010100??0???0?0?101020?000?111??1??0001000011?00
0?0??1??010001??0??01??01??1??00?0?00?201101000020??00?00200??000010201221001?0?1
112?1?11010300000000???1000?10010104?00?00100?100000000100???????????????????????0
???????????????????????

Important note (not directly related to the above): 
Be aware that [cladistic analysis] programs can give different answers (trees) depending on the order in which the sequences appear in the input file. PHYLIP, PAUP and other phylogenetic software provide a ‘‘jumble’’ option that reruns the analysis with different (jumbled) input orders. If for whatever reason the tree must be computed in a single run, sequences that are suspected of being‘‘problematic’’ should be placed toward the end of the input file, to lower the probability that tree rearrangement methods will be negatively influenced by a poor initial topology stemming from any problematic sequences.

Algorithms that perform optimization tasks (such as building cladograms) can be sensitive to the order in which the input data (the list of species and their characteristics) is presented. Inputting the data in various orders can cause the same algorithm to produce different "best" cladograms. In these situations, the user should input the data in various orders and compare the results.
Using different algorithms on a single data set can sometimes yield different "best" cladograms, because each algorithm may have a unique definition of what is "best".
Because of the astronomical number of possible cladograms, algorithms cannot guarantee that the solution is the overall best solution. A nonoptimal cladogram will be selected if the program settles on a local minimum rather than the desired global minimum.[14] To help solve this problem, many cladogram algorithms use a simulated annealing approach to increase the likelihood that the selected cladogram is the optimal one.[15]

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16 comments:

  1. Dr. PterosaurNovember 18, 2015 at 6:21 AM

    A significant 2009 study:
    http://www.nature.com/articles/nature08124.epdf?referrer_access_token=1LIOYM249T2ALXmHhUVXQtRgN0jAjWel9jnR3ZoTv0NAxxXDTxDgb7tt7vNCs5i7CDx_p1E8pIL0dPMGIw0CIZ1LRnUZIDT1a3FIDY_UW4FRwpODRDVwWg-KbK448VK63yIXiGAa_H8fA42yVK8TsNhr_ASjWKKTbM-PJCMVzpKKElR4FEstewHl9DZGaHr9&tracking_referrer=www.nature.com

    ReplyDelete
  2. Dr. PterosaurNovember 20, 2015 at 5:47 PM

    Lone Star pterosaurs:
    http://www.researchgate.net/publication/259437218_Lone_Star_Pterosaurs

    ReplyDelete
  3. Dr. PterosaurNovember 24, 2015 at 3:52 PM

    2009 study:
    A Jurassic ceratosaur from China helps clarify avian digital homologies

    ReplyDelete
  4. Dr. PterosaurNovember 26, 2015 at 3:53 PM

    http://digitallibrary.amnh.org/handle/2246/6112
    In summary, Pterosauromorpha is well supported as the sister taxon to Dinosauromorpha.

    ReplyDelete
  5. Dr. PterosaurNovember 27, 2015 at 1:09 PM

    An Archaeopteryx-like theropod from
    China and the origin of Avialae
    Xing Xu1,2, Hailu You3, Kai Du4 & Fenglu Han2
    http://www.researchgate.net/publication/51527707_An_Archaeopteryx-like_theropod_from_China_and_the_origin_of_Avialae._Nature

    http://www.nature.com/nature/journal/v475/n7357/full/nature10288.html

    (we identify the three manual digits of Xiaotingia
    and other maniraptorans as II-III-IV, rather than as I-II-III as in
    many other studies8).

    ReplyDelete
  6. Dr. PterosaurNovember 27, 2015 at 3:02 PM

    https://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwiNouie2rHJAhVF1h4KHT1mBaMQFggcMAA&url=http%3A%2F%2Fwww2.gwu.edu%2F~newsctr%2Fnewscenter%2Fresearch%2Fdinosaur%2Fclark.pdf&usg=AFQjCNFndKzJ5OberUETly0U3A8QMEei7Q&sig2=USwYNw6Ocmcz1p3vrrmiWQ&bvm=bv.108194040,d.dmo

    Theropods have traditionally been assumed to have lost manual digits from the lateral side inward,
    which differs from the bilateral reduction pattern seen in other tetrapod groups. This unusual
    reduction pattern is clearly present in basal theropods, and has also been inferred in non-avian
    tetanurans based on identification of their three digits as the medial ones of the hand (I-II-III). This
    contradicts the many developmental studies indicating II-III-IV identities for the three manual
    digits of the only extant tetanurans, the birds.

    ReplyDelete
  7. Dr. PterosaurNovember 27, 2015 at 4:47 PM

    TNT free download:

    http://www.lillo.org.ar/phylogeny/tnt/

    ReplyDelete
  8. Dr. PterosaurNovember 28, 2015 at 7:43 AM

    Can copy and paste from (2009):
    http://www2.gwu.edu/~newsctr/newscenter/research/dinosaur/clark.pdf

    ReplyDelete
  9. Dr. PterosaurNovember 28, 2015 at 7:47 AM

    http://www2.gwu.edu/~newsctr/newscenter/research/dinosaur/clark.pdf

    This implies the reduction of digit I before the divergence of the Ceratosauria and the
    Tetanurae, the appearance of some polleciform features in digit II and the acquisition of a novel
    phalangeal formula (X-2-3-4-X) early in tetanuran evolution. Both modifications are partially
    indicated by the manual morphologies of ceratosaurs and more basal theropods. Also, they are
    indirectly supported by observations in living animals that a digit will display features normally
    associated with the neighbouring medial digit if the latter fails to chondrify in early development21,
    that phalangeal counts can vary even within species29, 42 and that secondarily cartilaginous
    elements can regain their ability to ossify43.

    If BDR applies to the more inclusive Averostra, as the II-III-IV hypothesis suggests, early stages of
    tetanuran evolution must have involved loss of the already highly reduced metacarpal I, reduction
    in the length of metacarpal II, and the reappearance of additional phalanges on metacarpal IV.
    Both the I-II-III and II-III-IV hypotheses can claim a degree of support from morphological data,
    but the II-III-IV hypothesis is more parsimonious when developmental data from extant birds are
    considered.

    ReplyDelete
  10. Dr. PterosaurDecember 4, 2015 at 7:30 AM

    http://www.nature.com/articles/nature08124.epdf?referrer_access_token=1LIOYM249T2ALXmHhUVXQtRgN0jAjWel9jnR3ZoTv0NAxxXDTxDgb7tt7vNCs5i7CDx_p1E8pIL0dPMGIw0CIZ1LRnUZIDT1a3FIDY_UW4FRwpODRDVwWg-KbK448VK63yIXiGAa_H8fA42yVK8TsNhr_ASjWKKTbM-PJCMVzpKKElR4FEstewHl9DZGaHr9&tracking_referrer=www.nature.com

    Based on this study, the most parsimonious alignment is for the four digits of ceratosaurs to be I-II-III-IV and the three (and sometimes four) digits of all Tetanurae to be II-III-IV(V). Accepting such a topological shift at the base of Tetanura requires that the positional homology of the three digits of tetanurans is II-III-IV(-V), as suggested by Wagner and Gauthier34. Because the four digits of ceratosaurs are therefore most parsimoniously interpreted as I-II-III-IV, the small lateral metacarpal ossification of Guanlong35, Sinraptor36, and Coelurus represents the re-ossification of metacarpal V after it is lost at the base of Ceratosauria. The poor phylogenetic resolution for basal tetanurans in our study precludes us from hypothesizing whether this re-ossification event occurred once or more than once in the evolution of Theropoda. Likewise, the fourth metacarpal, which is reduced in primitive theropods and bears an unknown number of phalanges in Ceratosauria, re-acquires at least three phalanges in Tetanurans.

    ReplyDelete
  11. Dr. PterosaurDecember 4, 2015 at 11:18 AM

    From 2009 study:
    Scansoriopterygidae (grouped with Avialae for correspondence matrix construction)

    ReplyDelete
  12. Dr. PterosaurDecember 4, 2015 at 4:09 PM

    Reference to I-II-II preferred by most dinosaur workers
    A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers
    Fucheng Zhang1, Zhonghe Zhou1, Xing Xu1, Xiaolin Wang1 & Corwin Sullivan1

    http://www.nature.com/articles/nature14423.epdf?referrer_access_token=aXP0rMThuriYuvLDytsEU9RgN0jAjWel9jnR3ZoTv0PSoBPtAJS-K6Ofmq0_6wDOhsGY0rj_zJ_eQ8W9B9wsxLSCf2nbgU8Z-z5IJJQdfB_oT5rHGSjgUyjywdd61kg7z3GhdN-kkEBzDhZufuyKopWSgg-qEOLwE4c30ePqEJaqrjmI76uW5HZhMvNHypY7KJVZOa4ZNNYps69ieswFrXO4wDINm3UKCLxElIB4H4o%3D&tracking_referrer=www.nature.com

    ReplyDelete
  13. Dr. PterosaurDecember 4, 2015 at 6:25 PM

    http://www.brooklyn.cuny.edu/bc/ahp/CLAS/CLAS.Clad.html
    Evolutionary Systematics

    ReplyDelete
  14. Dr. PterosaurDecember 8, 2015 at 6:57 AM

    Helpful information:

    Node-based:
    Pennaraptora is a clade defined as the most recent common ancestor of Oviraptor philoceratops, Deinonychus antirrhopus, and Passer domesticus (the house sparrow), and all descendants thereof, by Foth et al., 2014.[1]

    Stem-based:
    The ancestral paravian is a hypothetical animal; the first common ancestor of birds, dromaeosaurids, and troodontids which was not also ancestral to oviraptorosaurs.



    A node-based definition could read: "the last common ancestor of A and B, and all descendants of that ancestor". Thus, the entire line below the junction of A and B does not belong to the clade to which the name with this definition refers.

    A branch-based definition, often called a stem-based definition, could read: "the first ancestor of A which is not also an ancestor of C, and all descendants of that ancestor". Thus, the entire line below the junction of A and B (other than the bottommost point) does belong to the clade to which the name with this definition refers.



    In biology, the most recent common ancestor (MRCA) of any set of organisms is the most recent individual from which all organisms in a group are directly descended.

    The term MRCA is usually used to describe a common ancestor of individuals within a species. It can also be used to describe a common ancestor between species. To avoid confusion, last common ancestor (LCA) or the equivalent term concestor is sometimes used in place of MRCA when discussing ancestry between species.

    ReplyDelete
  15. Dr. PterosaurDecember 8, 2015 at 9:14 AM

    A good analysis of node based and stem based definitions:
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989695/

    ReplyDelete
  16. Dr. PterosaurSeptember 25, 2016 at 7:55 AM

    http://www.nature.com/nature/journal/v459/n7249/extref/nature08124-s1.pdf

    ReplyDelete

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