Different placements of oviraptors and alvarezsaurids

Here are cladograms with oviraptors and/or alvarezsaurids within Euparaves.


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476167/ (Cau et al 2015)

Oviraptors within Euparaves.
Updated dataset of Brusatte et al. (2014).

http://www.nature.com/articles/nature08124.epdf?referrer_access_token=1LIOYM249T2ALXmHhUVXQtRgN0jAjWel9jnR3ZoTv0NAxxXDTxDgb7tt7vNCs5i7CDx_p1E8pIL0dPMGIw0CIZ1LRnUZIDT1a3FIDY_UW4FRwpODRDVwWg-KbK448VK63yIXiGAa_H8fA42yVK8TsNhr_ASjWKKTbM-PJCMVzpKKElR4FEstewHl9DZGaHr9&tracking_referrer=www.nature.com (2009)
Cladogram based on a subset of taxa from Xu et al 2009 study:
Both Alvarezsaurids and Oviraptors within Euparaves.

For details see here.

Cladogram based on all data except Epidexipteryx from Xu et al 2009 study.
Both Alvarezsaurids and Oviraptors within Euparaves.

http://www.nature.com/articles/nature08124.epdf?referrer_access_token=1LIOYM249T2ALXmHhUVXQtRgN0jAjWel9jnR3ZoTv0NAxxXDTxDgb7tt7vNCs5i7CDx_p1E8pIL0dPMGIw0CIZ1LRnUZIDT1a3FIDY_UW4FRwpODRDVwWg-KbK448VK63yIXiGAa_H8fA42yVK8TsNhr_ASjWKKTbM-PJCMVzpKKElR4FEstewHl9DZGaHr9&tracking_referrer=www.nature.com (2009)
Figure S7 of the Xu et al 2009 study using ALL taxa:
Alvarezsaurids within Euparaves.

http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652011000100008&lng=en&nrm=iso&tlng=en Angolin and Novas (2011)
http://www.scielo.br/img/revistas/aabc/v83n1/a08fig01m.jpg  Figure 1(B)
Alvarezsaurids within Euparaves

From Agnolín and Novas  (2013):
https://en.wikipedia.org/wiki/Scansoriopterygidae#Classification

Agnolín and Novas (2013) recovered scansoriopterygids as non-paravian maniraptorans and the sister group to Oviraptorosauria.^[11]

http://www.sciencedirect.com/science/article/pii/S0960982214010471 (Brusatte et al 2014)
Oviraptors within Euparaves. (Also see Figure S2 for more details.)
Notice that Pedopenna is included with Epidexipteryx within Euparaves.

https://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CCAQFjAAahUKEwi1-N7DrJzHAhUJkh4KHRtPAWA&url=http%3A%2F%2Fwww.ivpp.cas.cn%2Fcbw%2Fgjzdwxb%2Fxbwzxz%2F201401%2FP020140121386966325113.pdf&ei=A3bHVfXqAYmkepuehYAG&usg=AFQjCNH1PpVWciHk2GxOR_QxipkA_gqu5Q&sig2=MEwOmtQjh_PUu6OAxg9RCg&bvm=bv.99804247,d.dmo (O'Connor and Sullivan 2014)
Zhongornis and Oviraptors within Euparaves.

Euparaves

In order to talk about the origin of primitive birds it is necessary to introduce a new clade name, Euparaves.
Euparaves (node-based) definition:
"The most recent common ancestor of Epidendrosaurus ninchengensis (Scansoriopterygidae) and Passer domesticus (the house sparrow), and all descendants thereof".

Here is the stem-based definition of Euparaves:
"The most inclusive clade containing Passer domesticus (Linnaeus 1758) but not Pterorhynchus wellnhoferi."

Here is the apomorphy-based definition of Euparaves:
possessed remiges and rectrices, that is, enlarged, stiff-shafted, closed-vaned (= barbules bearing hooked distal pennulae), pennaceous feathers arising from the distal forelimbs and tail
AND
possessed feathered wings used in flapping flight



Alvarezsaurids and oviraptors are taxa within Euparaves. They are secondarily flightless, primitive birds that descended from flying basal Euparaves.

Here is a sample of flying, basal Euparavians:
Scansoriopterygids (Temporal range: Late Jurassic, 165–156 Ma)
Anchiornis (Temporal range: Late Jurassic, 161–160.5 Ma)
Aurornis (Temporal range: Late Jurassic, 160 Ma)
Xiaotingia (Temporal range: Late Jurassic, 160 Ma)
Pedopenna (Temporal range: Middle or Late Jurassic, 164 Ma)

These require further analysis:
Eosinopteryx? (Temporal range: Late Jurassic, 160 Ma)
Zhongornis? (Temporal range: Early Cretaceous, 122 Ma)
Zhenyuanlong?
Archaeopteryx?
Microraptor?
Jeholornis?
Ornithomimosaurs?
Therizinosaurids?
Velociraptor?
Jixiangornis?


Note.
Oviraptors, Alvarezsaurids and Eudromaeosaurids are secondarily flightless, primitive birds within Euparaves.

"Indistinguishable from random"

Here is a study on how the published dinosaur cladograms compare to the stratigraphic (time) record. It is significant that there is a total lack of congruence, it is "indistinguishable from random", for Paraves.

Wills et al (2008):
http://sysbio.oxfordjournals.org/cgi/content/full/57/6/891 (Full article)
http://sysbio.oxfordjournals.org/cgi/content-nw/full/57/6/891/TBL1 (Table 1)

Evidence for the evolutionary history of most groups derives from two independent sources. The first is the distribution of phylogenetically informative characters or markers in extant and extinct taxa. The second is the stratigraphic or temporal sequence in which taxa occur as fossils. Neither source of data can be read uncritically, and both require interpretation. Phylogenies incorporate assumptions concerning rooting and models of evolution. The resulting trees are therefore inferences rather than data. Fossils require varying degrees of interpretation depending upon the nature of the material, and dates may be subject to large margins of error. For these reasons, it is often desirable to compare inferences by mapping cladograms onto stratigraphic range charts

"Over all 19 data sets, congruence was extremely high (Table 1). The average GER (Wills, 1999) for static first occurrence dates was 0.767, with the best data set being the Hadrosauridae (Horner et al., 2004; 0.956) and the worst being the Paraves (Turner et al., 2007; 0.558)."

" The least congruent data sets were the Paraves (Turner et al., 2007; GERt = 0.571), Stegosauria (Galton and Upchurch, 2004b; GERt = 0.611), Prosauropoda (Galton and Upchurch, 2004a; GERt = 0.720), and Ceratopsia (Xu et al., 2002; GERt = 0.755)."

Paraves is objectively calculated as the worst in terms of congruence. In fact, the article says that it is "indistinguishable from random". And that is because it is based on the incorrect dino-to-bird idea.

This is even worse when you consider the high congruence of dinosaurs in general:

Preliminary reanalysis of the 1,000 animal and plant “static” data sets utilized by Benton et al. (2000) and Wills (2007) yielded an average GER* of 0.688, with only 34% attaining a GER* > 0.975. This strongly suggests that the congruence of dinosaur phylogenies is better than that for a large sample of data sets across a range of other taxa.

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

????

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????????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

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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

?

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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

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??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

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??????????????????????????????????????????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????

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?????????????0??????????????????????????????????????????????????????????????????????????

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Epidendrosaurus

????????????????????????????????????????????????0100?0

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?

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?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.

From pterosaur to primitive bird

Here is a draft of the lineage from pterosaur to primitive bird (click to enlarge):

This shows the transition from pterosaur to flying primitive birds and it also shows how the alvarezsaurids and oviraptors fit in as secondarily flightless primitive birds.

Connection of Rhamphorhynchoid pterosaurs to primitive birds:
http://pterosaurnet.blogspot.ca/2015/10/ancestor.html

Oviraptors as secondarily flightless primitive birds:
http://pterosaurnet.blogspot.ca/2014/09/oviraptors-as-secondarily-flightless.html

Connection of Jeholornis and Oviraptors:
http://pterosaurnet.blogspot.ca/2015/10/jeholornis-and-oviraptors.html

If anyone has a comment or a question, please feel free to submit it.

Jeholornis and Oviraptors

I suggest that secondarily flightless oviraptors descended (in both senses) from a flying creature like Jeholornis. Notice the similarities in morphology, time and location.

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

Jeholornis (meaning "Jehol bird") is a genus of avialans that lived between approximately 122 and 120 million years ago during the early Cretaceous Period in China. Fossil Jeholornis were first discovered in the Jiufotang Formation in Hebei Province, China (in what was previously Rehe Province, also known as Jehol—hence the name) and additional specimens have been found in the older Yixian Formation.[1] Jeholornis had long tails and few small teeth, and were approximately the size of turkeys,[2] making them among the largest avialans known until the Late Cretaceous. Their diet included seeds of cycads, Ginkgo or similar plants. Jeholornis were relatively large, primitive avialans, with a maximum adult length of up to 80 cm (2.6 ft).[2] Their skulls were short and high, similar to other primitive avialans like Epidexipteryx and to early oviraptorosaurs like Incisivosaurus.

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

Avialae is also occasionally defined as an apomorphy-based clade (that is, one based on physical characteristics). Jacques Gauthier, who named Avialae in 1986, re-defined it in 2001 as all dinosaurs that possessed feathered wings used in flapping flight, and the birds that descended from them.[8][9]

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

Oviraptorosaurs ("egg thief lizards") are a group of feathered maniraptoran dinosaurs from the Cretaceous Period of what are now Asia and North America. They are distinct for their characteristically short, beaked, parrot-like skulls, with or without bony crests atop the head. They ranged in size from Caudipteryx, which was the size of a turkey, to the 8 metre long, 1.4 ton Gigantoraptor.[4] The group (along with all maniraptoran dinosaurs) is close to the ancestry of birds. Analyses like those of Maryanska et al (2002) and Osmólska et al. (2004) suggest that they may represent primitive flightless birds.[5][6]

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

Caudipteridae is a family of oviraptorosaurian dinosaurs known from the Early Cretaceous of China. Found in the Yixian and Jiufotang Formations, the group existed between 125-120 million years ago.

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

Protarchaeopteryx (meaning "before Archaeopteryx") is a genus of turkey-sized feathered theropod dinosaur from China.[1] Known from the Jianshangou bed of the Yixian Formation, it lived during the early Aptian age of the Early Cretaceous, approximately 124.6 million years ago.[2]

JEHOLORNIS



OVIRAPTOR

NOTE:
"Maniraptors" were either secondarily flightless avialae or secondarily flightless non-avialae paraves.
In either case, they descended from flying ancestors. They are not transitional between dinosaurs and Paraves.

Outgroups

There are many problems with the analyses of the dino to bird theory. Here is one of them:

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

Also, the use of bipedal coelurosaurian
outgroups, as in the analysis by Clark et
al. (2002), may be contributing to a potentially
misleading topology. Outgroup choice determines
the polarity of character states, including
ancestral reconstructions for entire clades (Nixon
and Carpenter 1993). In this case, using bipedal
cursors as outgroups may obscure phylogenetic
signal by wrongly treating characters indicating
flight loss as plesiomorphy.

The "maniraptors" such as oviraptors and alvarezsaurids were flightless. They lived on the ground. The question is whether their ancestor was a ground-living creature (such as a dinosaur) or whether their ancestor was a flying, primitive bird.
When a cladistic analysis uses a ground-based dinosaur (eg. allosaurus) as the outgroup it takes the flightlessness of the "maniraptors" as being inherited from a dinosaur lineage, when in fact they actually descended (in both senses) from a flying primitive bird ancestor.

Ancestor

The ancestor of primitive birds was a rhamphorhynchoid pterosaur much like Jeholopterus or Pterorhynchus.
The earliest primitive birds were the feathered, flying creatures with long-bony-tails, such as the scansoriopterygids.

http://en.wikipedia.org/wiki/Scansoriopterygidae

The scansoriopterygids would have lived alongside synapsids such as the aquatic Castorocauda and arboreal gliding mammal Volaticotherium, the rhamphorhynchoid pterosaurs Jeholopterus and Pterorhynchus, as well as a diverse range of insect life (including mayflies and beetles) and several species of salamander.[14][15]

 http://www.ivpp.ac.cn/qt/papers/201206/P020120604508520389814.pdf

The [Epidendrosaurus] material described in this paper was collected from a new locality, Daohugou, in east Nei Mongol, northeast China, which is west of Liaoning Province. Many salamanders(Wang 2000), plants and insects (Zhang 2002)have recently been discovered from this new locality. It is notable that an anurognathid rhamphorhynchoid pterosaur [Jeholopterus] with beautiful hair [pycnofibers] covering the whole body has also been reported from this locality (Wang et al. 2002). The estimated age of the deposit at this locality is very controversial and ranges from the Middle Jurassic or the Early Cretaceous according to various authors (Wang etal. 2000; Zhang 2002); however, most workers currently regard it as being Late Jurassic.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842671/

Two other Chinese specimens were reported with integumental covering, coming from the same stratum (the Daohugou Bed) as Jeholopterus. So far we have not had the opportunity to examine this material. The first one is a small unnamed anurognathid with extensive preservation of soft tissue, including fibres that have been interpreted as protofeathers (Ji & Yuan 2002). The published pictures show that the soft tissue interpreted as protofeathers is of the same nature as the pycnofibres of Jeholopterus. 

 http://en.wikipedia.org/wiki/Pterosaur

At least some pterosaurs had hair-like filaments known as pycnofibres on the head and body, similar to, but not homologous (sharing a common structure) with, mammalian hair. Though a fuzzy "integument" (natural covering/outer coat) "was first reported in 1831" by Goldfuss,^[29] recent pterosaur finds and the technology for histological and ultraviolet examination of pterosaur specimens have provided incontrovertible proof: pterosaurs had pycnofibre coats. Pycnofibres were not true hair as seen in mammals, but a unique structure that developed a similar appearance. Although, in some cases, actinofibrils (internal structural fibres) in the wing membrane have been mistaken for pycnofibres or true hair, some fossils such as those of Sordes pilosus (which translates as "hairy demon") and Jeholopterus ninchengensis do show the unmistakable imprints of pycnofibres on the head and body, not unlike modern-day bats, another example of convergent evolution.^[21] The head-coats do not cover the pterosaur's large jaws in many of the specimens found so far.^[29]

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

Jeholopterus was a small anurognathid pterosaur from the Middle to Late Jurassic^[1] Daohugou Beds of the Tiaojishan Formation of Inner Mongolia, China , preserved with hair-like pycnofibres and skin remains.

http://link.springer.com/article/10.1360/02tb9054#page-1

We report a new and nearly completely articulated rhamphorhynchoid pterosaur, Jeholopterus ningchengensis gen. et sp. nov., with excellently preserved fibres in the wing membrane and “hairs” [pycnofibers] in the neck, body and tail regions. Many of its characteristics such as a short neck, short metacarpals and distinctively long fifth pedal digit are characteristic of rhamphorhynchoids. The new species can be further referred to the ‘strange’ short-tailed rhamphorhynchoid family Anurognathidae. It is much more complete than the other known members of the family, namely, Anurognathus from Solnhofen, Germany, Batrachognathus from Karatau, Kazakhstan, and Dendrorhynchoides from Beipiao, Liaoning Province, China. The new pterosaur also shows that the wing membrane is attached to the ankle of the hind limb. The pedal digits are webbed. Furthermore, the “hair” of Jeholopterus bears some resemblance to the hair-like integumental structures of the feathered dinosaur Sinosauropteryx although there is yet no direct evidence to argue for or against their homology.

http://dinosaur-museum.org/featheredinosaurs/rhamphorhynchoid.pdf

A new rhamphorhynchoid [Pterorhynchus] is described with a headcrest that is unprecedented among the long-tailed pterosaurs. The preservation of the headcrest presents significant implications regarding the physical appearance and aerodynamics of all pterosaurs. Also, "hair-like" integumentary structures of this pterosaur are shown to be complex multi-strand structures which presents evidence on the origin of feathers and the possibility of a remarkably early ancestral relationship between pterosaurs and birds.

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

Pterorhynchus was a genus of rhamphorhynchid "rhamphorhynchoid" pterosaur from the Middle or Late Jurassic-age Daohugou Formation[1] of Inner Mongolia,China.

This type specimen consists of an articulated, nearly complete skeleton with remains of the integument. These included the wing membrane, hair-like structures, a long version of the vane found at the end of "rhamphorhynchoid" tails, and a head crest with both a low bony base and a large keratin extension; the latter feature is unusual in "rhamphorhynchoids" (i.e. basal pterosaurs), the fossils of which do not often show head crests.

The hairs (pycnofibers) were originally described as pinnate, with many strands arising from a single base (calamus), and seen as corresponding to the hypothetical Stage II in the evolution of feathers.

http://en.wikipedia.org/wiki/Yi_%28dinosaur%29

The only known Yi qi fossil was found in rocks assigned to the Tiaojishan Formation, dating to the Callovian-Oxfordian age of the Middle-Late Jurassic,[1] dated to between 165 and 153 million years ago.[3] This is the same formation (and around the same age) as the other known scansoriopterygids Epidexipteryx and Scansoriopteryx.

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

Darwinopterus (meaning "Darwin's wing") is a genus of pterosaur, discovered in China and named after biologist Charles Darwin. Between 30 and 40 fossil specimens have been identified,[1] all collected from the Tiaojishan Formation, which dates to the middle Jurassic period, 161-160.5 Ma ago.[2] The type species, D. modularis, was described in February 2010.[3] D. modularis was the first known pterosaur to display features of both long-tailed ('rhamphorhynchoid') and short-tailed (pterodactyloid) pterosaurs, and was described as a transitional fossil between the two groups.[4] Two additional species, D. linglongtaensis and D. robustodens, were described from the same fossil beds in December 2010 and June 2011, respectively.[5][6]

Darwinopterus, like its closest relatives, is characterized by its unique combination of basal and derived pterosaurian features. While it had a long tail and other features characteristic of the 'rhamphorhynchoids', it also had distinct pterodactyloid features, such as long vertebrae in the neck and a single skull opening in front of the eyes, the
nasoantorbital fenestra (in most 'rhamphorhynchoids', the antorbital fenestra and the nasal opening are separate).[5]

http://digitallibrary.amnh.org/handle/2246/6352
Turner et al 2012.

For reference:

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

The Rhamphorhynchoidea forms one of the two suborders of pterosaurs and represent an evolutionary grade of primitive members of this group of flying reptiles. This suborder is paraphyletic in relation to the Pterodactyloidea, which arose from within the Rhamphorhynchoidea, not from a more distant common ancestor.

Suborder: Rhamphorhynchoidea Plieninger, 1901
Included groups
Anurognathidae Campylognathoididae Dimorphodontidae Eopterosauria Rhamphorhynchidae

JEHOLOPTERUS



PTERORHYNCHUS

SCANSORIOPTERYGIDAE