McEachran and Aschliman 2004 reported,
“all authors agree that batoids constitute a monophyletic group.”
Underwood et al. 2015 reported,
“While the monophyly of the Batoidea is not in doubt, phylogenetic relationships within the group are uncertain.”
By including a wider gamut of taxa,
the large reptile tree (LRT, 1785+ taxa, subset Fig. 1) recovers rays apart from skates and mantas apart from both. So the monophyly of the Batoidea is in doubt when more taxa are added. It is also surprising that a character list with no batoid characters is able to lump and split them, indicating the primacy and necessity of adding taxa.
Franklin et al. 2014 wrote:
“A database of 253 specimens, encompassing 60 of the 72 batoid genera, reveals that the majority of morphological variation across Batoidea is attributable to fin aspect-ratio and the chordwise location of fin apexes. Both aspect-ratio and apex location exhibit significant phylogenetic signal.”
For those who want evidence of evolution
the four cladograms offered in Underwood et al. 2015 (Fig. 2) offer little.
- They employ suprageneric taxa for outgroup taxa
- They exclude pertinent taxa (see Fig. 2) from both the in-group and out-group.
Sasko et al. 2006 published a batoid phylogeny
that included notes on swimming styles. Taxon exclusion also mars this study. As a result convergence is ignored. These authors didn’t think they were cherry-picking taxa… but they were doing exactly that. They thought they were covering ‘all the bases’. The editors and referees agreed. That’s why the LRT tests a wider gamut of taxa to minimize the possibility of this sort of taxon exclusion. Outgroups are important. Omit pertinent outgroups and nothing else goes right.
By contrast
in the LRT (subset Fig. 1, diagram Fig. 4) Holocephali (=ratfish) is a derived clade, not a basal bauplan upon which rays and skates evolved. While more rays and skates are listed in the four Underwood et al. cladograms, the LRT includes outgroup taxa back to headless chordates. Long nosed sawfish and guitarfish nest together in the LRT. Marginally toothless and filter-feeding mantas nest with similar whale sharks and kin (not found in Underwood et al. cladograms). Bottom line: prior authors assumed too much. More taxa would have helped, as shown in Fig. 2.
A key to understanding evolution
is to understand that most of the time (tunicates, starfish and kin a clear exception), simpler taxa evolve into more complex taxa by the gradual accumulation of derived traits. In vertebrates, jawless chordates appear first. Then pre-jaws appear ventrally in sturgeons. In mantas and whale sharks marginally toothless jaws migrate anteriorly. In the rest, the sensitive rostrum continues to overhang the now tooth-lined jaws. Starting with this scenario, the rest of the chondrichthyes evolves wither a shorter or longer rostrum, pectoral fins might take over propulsion (convergent with mantas), and teeth might turn into pavement stone analogs.
While we’re at it,
please note the overlooked sturgeon-like reversal displayed by the guitarfish, Rhinobatos (Figs. 4, 7), basal to skates. That tiny-extending mouth morphology (Figs. 6, 7) didn’t appear de novo. It was waiting in the sturgeon-shark-skate gene pool to return.
References
Aschliman NC, Nishida M, Miya M, Inoue JG, Rosana KM and Nayloer GJP 2012. Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea). Mol Phylogenet Evol 63(1):28-42. doi: 10.1016/j.ympev.2011.12.012. Epub 2011 Dec 22.
Franklin O, Palmer C and Dyke G 2014. Pectoral fin morphology of batoid fishes (Chondrichthyes: Batoidea): explaining phylogenetic variation with geometric morphometrics. J Morphol 275(10):1173-86. doi: 10.1002/jmor.20294. Epub 2014 May 5.
Hall KC, Hundt PJ, Swenson JD, Summers AP and Crow KD 2018. The evolution of underwater flight: The redistribution of pectoral fin rays, in manta rays and their relatives (Myliobatidae). J Morphol 279(8):1155-1170. doi: 10.1002/jmor.20837. Epub 2018 Jun 7. PMID: 29878395
Larouche O, Zelditch ML and Cloutier R 2017. Fin modules: an evolutionary perspective on appendage disparity in basal vertebrates. BMC Biol. 2017 Apr 27;15(1):32. doi: 10.1186/s12915-017-0370-x. PMID: 28449681
Martinez CM, Rohlf FJ and Frisk MG 2016. Re-evaluation of batoid pectoral morphology reveals novel patterns of diversity among major lineages. J Morphol. 277(4):482-93. doi: 10.1002/jmor.20513. Epub 2016 Feb 11. PMID: 26869186
McEachran JD, Dunn KA and Miyake T 1996. Interrelationships of the batoid fishes (Chondrichthyes: Batoidei). Pp. 63–84 in Stiassny MLJ, Parenti LR, Johnson G D eds. Interrelationships of fishes. Academic Press, San Diego.
McEachran JD and Aschliman N 2004. Phylogeny of Batoidea. Chapter 3 in: Biology of Sharks and Their Relatives, Second Edition. DOI: 10.1201/9780203491317.ch3
Pavan-Kumar A et al. 2013. Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers. Mol Biol Rep 41:447–457. doi: 10.1007/s11033-013-2879-6 PMID: 24293104.
Rosenberger LJ 2001. Pectoral fin locomotion in batoid fishes: undulation versus oscillation. J Exp Biol 204(Pt 2):379-94. PMID: 11136623
Undersood CJ et al. (6 co-authors) 2015. Development and Evolution of Dentition Pattern and Tooth Order in the Skates And Rays (Batoidea; Chondrichthyes). PLoS ONE 10(4): e0122553. doi:10.1371/journal.pone.0122553
The Pterosaur Heresies 
What did you demonstrate with this post? This is just “hot air”… nothing more.
I suggested you to read some batoid papers in order to have some clue on topics you talk about, hoping you to include batoid synapomorphies to detect their monophyly. Conversely, you just read quickly some abstracts and figure captions of these papers and use your tree just to say: “Bottom line: prior authors assumed too much” and “taxon exclusion hampers prior phylogenetic results”… WOW you now clearly demonstrated scientifically that all the other scientists were wrong! How can you pretend that your data, which do not include a single batoid character but mostly reptile characters, can detect batoid (or any other clade) relationships? How can you pretend that your relationships are more reliable than those detected by years of real morphological and molecular studies? And now you cannot use the “taxon exclusion” problem as an excuse because there are several studies including sharks, rays, and chimaeras in a single analysis, using even more taxa than you.
You probably think that the main goal in phylogenetics is to recover a single tree. This demonstrates that you have no idea on phylogenetic methods. Do bootstraps and you will see that all nodes collapse in a few big polytomies. Do some support statistics, and you will see how bad your tree is.
For the next step, I would suggest you to include also invertebrates, plants, and fungi, with no characters for them. You will probably get still a single tree. Will you consider your tree still reliable? Yes, you will probably find another absurd statement for explaining that apple tree is more closely related to tyrannosaur than is to a conifer!
You wrote: “include batoid synapomorphies to detect their monophyly.”
This is distressing to see you write this. Therein lies the risk of convergence. You can detect monophyly only by phylogenetic analysis, recovering two taxa and their last common ancestor. One can only detect monophyly by testing all candidates and recovering a tree that nests all less related taxa elsewhere. The cladogram is the only tool that enables this at present.
You wrote: “all the other scientists were wrong! ”
This is hyperbole and therefore more or less false. Only those scientists who nested holocephalians basal to batoids were wrong, according to results recovered in the LRT. When you, or they, include the taxa shown to be closer to various ‘batoids’ in the LRT, then we’ll we’ll have confirmation or refutation of the present hypothesis.
You wrote: “How can you pretend that your relationships are more reliable than those detected by years of real morphological and molecular studies?”
I report results based on a wider gamut of included taxa. As you know, molecular studies too often lead to false positives that recover dissimilar sisters. The LRT is a real morphological study. To dismiss it is to shrink from your responsibility to employ the same taxa in your own studies and report results. I should not have to tell this to you, a scientist.
You wrote:
And now you cannot use the “taxon exclusion” problem as an excuse because there are several studies including sharks, rays, and chimaeras in a single analysis, using even more taxa than you.”
I have not found them yet. Please provide one citation. Those I have found, as noted, included chimaeras as a suprageneric taxon and sharks as a suprageneric taxon. The link in the article on ‘suprageneric taxa’ will show you the danger of using suprageneric taxa. The LRT employs genera exclusively.
You wrote:
“You probably think that the main goal in phylogenetics is to recover a single tree. This demonstrates that you have no idea on phylogenetic methods. Do bootstraps and you will see that all nodes collapse in a few big polytomies.”
This is distressing to see you write this. Evidently you don’t recognize the Bootstrap scores in the LRT for every node. Virtually all nodes are robust with but a few that have scores <50. The main goal in phylogenetic analysis is to model actual evolutionary events. We do this with the concept of maximum parsimony, as you know. High scores = robust nodes.
You wrote:
"Do some support statistics, and you will see how bad your tree is."
As noted above, I have been doing Bootstrap analyses for ten years and they have shown me how bad parts of my tree were when scores were wrong. Corrections have strengthened the tree throughout. Your attempts at blackwashing a project that has great internal strength are merely showing how much you are resisting maximum parsimony. Let the software show you how relationships are modeled. Throw out your preconceptions. They are holding you back. Add taxa to your own analysis to see what happens.
You wrote: "I would suggest you to include also invertebrates, plants, and fungi, with no characters for them. You will probably get still a single tree."
At present the LRT does not produce a single tree. Adding plants and fungi as a suggestion shows you are at a breaking point. I suggest either going back to bed or back to your computer to add vertebrate taxa to confirm or refute the present hypothesis of interrelationships. That's what I'm doing today. I will be adding taxa, fixing scores, attempting to understand the vertebrate tree of life better than I know it today. Only by doing so yourself will you be able to argue from evidence, rather than outdated authority based on too few taxa. I look forward to changing the LRT when a more parsimonious solution using the same taxa or more (and showing your work with skeletons, etc.) is presented. I challenge you to be the scientist you studied to be and are paid to be.