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): 

http://www.bioon.com/book/biology/bioinformatics/chapter-14.pdf

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.

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

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]

Reversions

The dino to bird theory requires "remarkable" reversals. 

ANKLE:

http://www.nature.com/ncomms/2015/151113/ncomms9902/full/ncomms9902.html (2015)

The anklebone (astragalus) of dinosaurs presents a characteristic upward projection, the ‘ascending process’ (ASC). The ASC is present in modern birds, but develops a separate ossification centre, and projects from the calcaneum in most species. These differences have been argued to make it non-comparable to dinosaurs. We studied ASC development in six different orders of birds using traditional techniques and spin–disc microscopy for whole-mount immunofluorescence. Unexpectedly, we found the ASC derives from the embryonic intermedium, an ancient element of the tetrapod ankle. In some birds it comes in contact with the astragalus, and, in others, with the calcaneum. The fact that the intermedium fails to fuse early with the tibiale and develops an ossification centre is unlike any other amniotes, yet resembles basal, amphibian-grade tetrapods. The ASC originated in early dinosaurs along changes to upright posture and locomotion, revealing an intriguing combination of functional innovation and reversion in its evolution.

Also see here:

More remarkably, however, this finding reveals an unexpected evolutionary transformation in birds. In embryos of the landegg-laying animals, the amniotes (which include crocodilians, lizards, turtles, and mammals, who secondarily evolved live birth) the intermedium fuses to the anklebone shortly after it forms, disappearing as a separate element. This does not occur in the bird ankle, which develops more like their very distant relatives that still lay their eggs in water, the amphibians. Since birds clearly belong within landegg-laying animals, their ankles have somehow resurrected a long-lost developmental pathway, still retained in the amphibians of today -- a surprising case of evolutionary reversal.

WRIST:
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001957

We confirm the proximal–posterior bone is a pisiform in terms of embryonic position and its development as a sesamoid associated to a tendon. However, the pisiform is absent in bird-like dinosaurs, which are known from several articulated specimens. The combined data provide compelling evidence of a remarkable evolutionary reversal: A large, ossified pisiform re-evolved in the lineage leading to birds, after a period in which it was either absent, nonossified, or very small, consistently escaping fossil preservation.

FINGERS:
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.

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 [Bilateral Digit Reduction] 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.

There is no actual evidence for these reversals. The dino to bird theorists need to imagine they happened so the dino to bird theory does not collapse.

Unjustifiable assumptions of homology

http://www.bio.fsu.edu/James/Ornithological%20Monographs%202009.pdf

Unjustifiable assumptions of homology incorporated
into data matrices.—The most glaring example of
this problem is the coding of avian and theropod
manual, carpal, and tarsal characters as if they were homologous, despite the ambiguity of the data, and despite the assumption this coding entails that
the BMT [birds are maniraptor theropods] hypothesis is correct a priori. 

Because of the above ambiguities, these five
sets of characters [the palate, the basipterygoid process, the carpus, the manus, and the tarsus] cannot be coded for birds and theropods without unjustified assumptions of
homology. They were not included in the primary
analysis of our matrix. This decision is
understood to be especially controversial, so
we have documented our reasoning, which was
based on careful review of the anatomical evidence,
in Appendix 3.

Criticisms of the James and Pourtless study:
http://theropoddatabase.blogspot.ca/2015/01/bandit-cladogram-evaluated-james-and.html

http://dml.cmnh.org/2009Apr/msg00230.html

http://dml.cmnh.org/2009Apr/msg00236.html

http://scienceblogs.com/tetrapodzoology/2009/06/08/birds-come-first-hypothesis/#comment-12898

https://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=15&cad=rja&uact=8&ved=0CC4QFjAEOApqFQoTCPHX39mS-MgCFUxWHgod3RMGig&url=http%3A%2F%2Fwww4.ncsu.edu%2F~mhschwei%2FResearch_files%2FMakovicky___Zanno_2011_theropod_diversity_and_avian_characteristics-1.pdf&usg=AFQjCNFFUYs0N4rfq2F8aGPuSQSnEumwdw&sig2=cKMU3Gu8JjB9YDNvGjDDFQ&bvm=bv.106674449,d.cWw

James and Pourtless excluded the characteristics that are in dispute. That is impartial.
The critics object to that. The critics want things scored their way.