Cretaceous feather taphonomy + avian molecular phylogeny and morphological characters + tetrapod diet and body temperature + Pterosphenus (giant Eocene marine snake) revised + more

[Ben Creisler]

Ben Creisler

bcre...@gmail.com

Some recent mainly non-dino papers:

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Free pdf:

Yanhong Pan, Zeming Qi, Jianfang Hu, Xiaoting Zheng & Xiaoli Wang (2024)
Bio-molecular analyses enable new insights into the taphonomy of feathers
PNAS Nexus, pgae341
doi: https://doi.org/10.1093/pnasnexus/pgae341
https://academic.oup.com/pnasnexus/advance-article/doi/10.1093/pnasnexus/pgae341/7738345


Exceptionally preserved feathers from the Mesozoic era have provided valuable insights into the early evolution of feathers and enabled colour reconstruction of extinct dinosaurs, including early birds. Mounting chemical evidence for the two key components of feathers–keratins and melanins - in fossil feathers has demonstrated that exceptional preservation can be traced down to the molecular level. However, the chemical changes that keratin and eumelanin undergo during fossilization are still not fully understood, introducing uncertainty in the identification of these two molecules in fossil feathers. To address this issue, we need to examine their taphonomic process. In this study, we analyzed the structural and chemical composition of fossil feathers from the Jehol Biota and compared them with the structural and chemical changes observed in modern feathers during the process of biodegradation and thermal degradation, as well as the structural and chemical characteristics of a Cenozoic fossil feather. Our results suggest that the taphonomic process of feathers from the Cretaceous Jehol Biota is mainly controlled by the process of thermal degradation. The Cretaceous fossil feathers studied exhibited minimal keratin preservation but retained strong melanin signals, attributed to melanin’s higher thermal stability. Low-maturity carbonaceous fossils can indeed preserve biosignals, especially signals from molecules with high resistance to thermal degradation. These findings provide new clues about the preservation potential of keratin and melanin, and serve as a reference for searching for those two biomolecules in different geological periods and environments.

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Free pdf:

Per G P Ericson FLS & Yanhua Qu (2024)
An evaluation of the usefulness of morphological characters to infer higher-level relationships in birds by mapping them to a molecular phylogeny
Biological Journal of the Linnean Society, blae070
doi: https://doi.org/10.1093/biolinnean/blae070
https://academic.oup.com/biolinnean/advance-article/doi/10.1093/biolinnean/blae070/7739876


The use of genetic data to reconstruct systematic relationships has revolutionized our understanding of avian evolution. Morphology-based classifications were often in conflict because of different opinions among scholars about the relative importance of certain phenotypes. The considerable morphological variation observed among birds was codified into phylogenetic characters by Livezey and Zusi (2006) who also scored them for 150 extinct and extant taxa. Herein we have evaluated the phylogenetic signal of 1860 of these characters by mapping them to a molecular phylogeny including 102 taxa that represent all extant birds (with the underlying assumption that this tree topology is a good estimate of the evolutionary relationships among birds). The characters fit the molecular tree with a mean consistency index (CI) of 0.38. Muscle characters are the most homoplasious (CI 0.32), while characters related to integument, feathers, intestinal, respiratory, syrinx, urogenital, nervous, and reproductive organs show a considerably better fit (mean CI 0.49). We also explored what characters may unambiguously support certain basal clades that are well-supported by molecular data. We found only a few clades (e.g. Galloanserae, Procellariimorphae) being supported by unambiguous apomorphies, while many well-established clades (e.g. Pelecaniformes, Charadriiformes, Accipitriformes, Coraciiformes) lack such support entirely.

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Free pdf:

Kristen E. Saban & John J. Wiens (2024)
Diet Evolution and Body Temperature in Tetrapods: Cool Old Carnivores and Hot Young Herbivores
Global Ecology and Biogeography e13900
doi: https://doi.org/10.1111/geb.13900
https://onlinelibrary.wiley.com/doi/10.1111/geb.13900

Free pdf:
https://www.researchgate.net/publication/383223868_Diet_Evolution_and_Body_Temperature_in_Tetrapods_Cool_Old_Carnivores_and_Hot_Young_Herbivores


Aim

Diet is a key aspect of life in animals. There have been numerous independent origins of herbivorous diet across animals, but the factors that explain these origins remain poorly understood. One potentially crucial factor is body temperature (Tb), as the gut-dwelling bacteria that help digest cellulose in many herbivores are thought to require high temperatures. However, analyses in birds, lizards and mammals found only limited evidence for higher Tb in herbivores than in carnivores. These analyses tested whether diet explains Tb evolution. Here, we focus instead on testing whether Tb helps explain the evolution of diet across tetrapods.

Location

Global.

Time Period

Past 350 million years.

Major Taxa Studied

Tetrapods.

Methods

We analysed 1712 species with matched data on diet and Tb using diverse phylogenetic methods.

Results

Ancestral reconstructions indicated that tetrapods likely had a carnivorous ancestor, followed by repeated transitions to omnivory and herbivory, especially in the last 110 million years. Thus, extant herbivorous lineages in tetrapods are relatively young, in contrast to many older carnivorous lineages. They are also relatively unstable in that reversals from herbivory back to omnivory and from omnivory back to carnivory were as frequent as the origins of herbivory and omnivory. Using phylogenetic logistic regression, we support the hypothesis that higher Tb helps explain the evolution of herbivory across tetrapods and within birds, mammals, lepidosaurs and turtles. Phylogenetic path analyses suggest that Tb generally drives the evolution of herbivory, and not vice versa. Our analyses also suggest that Tb is more important for the evolution of herbivory than large body size or diurnal diel activity, which are both significant predictors of herbivory in some cases.

Main Conclusions

Our results show for the first time that Tb is a significant predictor of diet evolution among and within many major animal clades.

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Abhishek Natarajan, Sudipta Dasgupta, Nibedita Rakshit & Yogesh Kashyap (2024)
Taxonomic revision of the giant marine snake genus Pterosphenus Lucas, 1898, based on new fossil material from the middle Eocene (Bartonian) Harudi Formation of Kachchh (Kutch) Basin, India
Journal of Vertebrate Paleontology e2375332
doi: https://doi.org/10.1080/02724634.2024.2375332
https://www.tandfonline.com/doi/full/10.1080/02724634.2024.2375332


Fossil snakes of the family Palaeophiidae are primarily known from rare, isolated vertebrae, leading to a poor understanding of the intra- and inter-columnar variation within a palaeophiid species. This leads to ambiguity in the taxonomic identity of these snakes, as in the case of the Eocene-age marine snakes of the genus Pterosphenus, in which the majority of species have been described by characters of problematic taxonomic value. Here, we propose a taxonomic revision of the genus based on an articulated to semi-articulated section of the vertebral column at the anterior to mid trunk-transition of Pterosphenus schucherti discovered from the middle Eocene (Bartonian) Harudi Formation, Kachchh (Kutch) Basin. The characters that separate Pterosphenus schucherti from ‘Pterosphenus schweinfurthi’ and ‘Pterosphenus biswasi,’ viz., the height of the pterapophysis and the anterior concavity of the zygosphene, have been found to be non-diagnostic, and the latter two species have been synonymized with the type species. Additionally, we utilized 2D and 3D landmark-based geometric morphometry to determine the morphometric affinity of palaeophiids amongst the alethinophidian snakes. The body size of the snake was estimated based on extant snakes with a morphometric affinity to Palaeophiidae. The cosmopolitan distribution of Pterosphenus schucherti is modelled based on the sea surface temperature (SST) constraints of the modern cosmopolitan snake Hydrophis platurus, and the known fossil localities of the species. The present findings provide crucial insights into the global paleoecological landscape of the Eocene, and the interactions of Pterosphenus schucherti with other palaeophiid snakes as well as the other Eocene fauna.

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Free pdf:

Wolfgang Wüster, Hinrich Kaiser, Marinus S Hoogmoed, Luis M P Ceríaco, Lutz Dirksen, Christophe Dufresnes, Frank Glaw, Axel Hille, Jörn Köhler, Thore Koppetsch, Konstantin D Milto, Glenn M Shea, David Tarkhnishvili, Scott A Thomson, Miguel Vences & Wolfgang Böhme (2024)
How not to describe a species: lessons from a tangle of anacondas (Boidae: Eunectes Wagler, 1830)
Zoological Journal of the Linnean Society 201(4): zlae099
doi: https://doi.org/10.1093/zoolinnean/zlae099
https://academic.oup.com/zoolinnean/article/201/4/zlae099/7735800


A recent revision of the anacondas (Serpentes: Boidae: Eunectes), with the description of a new species of green anaconda, generated extensive publicity, but also provoked considerable controversy due to inadequacies of the evidence used and errors in nomenclature. We here use the case of this problematic publication to: (i) highlight common issues affecting species delimitations, especially an over-reliance on mitochondrial DNA data, and reiterate best practices; (ii) reanalyse the data available for anacondas to establish the true current state of knowledge and to highlight lines of further research; and (iii) analyse the nomenclatural history and status of the genus. While our analysis reveals significant morphological variation in both green and yellow anacondas, denser sampling and an analysis of informative nuclear markers are required for meaningful species delimitation in Eunectes. Tracing the history of name-bearing types establishes Trinidad as the type locality for Boa murina Linnaeus, 1758 and allows identification of the extant lectotype for the species. Finally, we emphasize the responsibility of both journals and authors to ensure that published taxonomic work meets the burden of evidence required to substantiate new species descriptions and that species are named in compliance with the rules of zoological nomenclature.

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[Gregory Paul]

The 60 year old Hopkins library has been closed for the next three plus years so the interior can be completely gutted and replaced, leaving the general public me included no longer with any access to the JHU computer system, and I therefore cannot access lots of technical journals anymore. So here are a couple of papers I could use PDFs if anyone has them. 

GSPaul

Ren, X.-X.; Wang, X.-R.; Ji, Y.-N.; Guo, Z.; Ji, Q. (2024). "The first mamenchisaurid from the Upper Jurassic Dongxing Formation of Guangxi, southernmost China". Historical Biology: An International Journal of Paleobiology: 1–14. doi:10.1080/08912963.2024.2309287

Yates, Adam M.; Matthew F. Bonnan; Johann Neveling (2011). "A new basal sauropodomorph dinosaur from the Early Jurassic of South Africa". Journal of Vertebrate Paleontology. 31 (3): 610–625.

[Ralph Molnar]

Dear Greg,

Here they are, plus the addendum

Cheers, Ralph

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[Gregory Paul]

Thanks! 

To view this discussion on the web visit https://groups.google.com/d/msgid/DinosaurMailingGroup/400407936.11554194.1724449479894%40mail.yahoo.com.

[Thomas Richard Holtz]

Are you on Tracy Ford's mailing list? Every Friday he posts new papers of the week, which at least will help with the recent material.

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Email: tho...@umd.edu         Phone: 301-405-4084
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[Gregory Paul]

Is the Marnes de la Maurine the lower or upper portion of the Marnes Rouges Inferieures Formation? 

GSPaul

[Skye McDavid]

 The Marnes Rouges Inférieures Formation ("Lower Red Marks") has 4 members of which the Marnes de La Maurine is the third counting up from the base.

This paper has further info which may be useful:

 https://doi.org/10.1016/j.cretres.2015.08.009 

On Fri, Aug 23, 2024, 8:16 PM 'Gregory Paul' via Dinosaur Mailing Group <DinosaurMa...@googlegroups.com> wrote:

Is the Marnes de la Maurine the lower or upper portion of the Marnes Rouges Inferieures Formation? 

GSPaul

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[Mickey Mortimer]

The abstract of Ericson and Qu's paper makes it sound like morphological characters map terribly on to the molecular topology of birds when it says "The characters fit the molecular tree with a mean consistency index (CI) of 0.38", but I think there some factors that deserve comment.  First, the morphological scorings are taken from Livezey and Zusi's (2006) huge analysis, which it turns out has a ton of misscorings (Mayr, 2008).  Mayr wrote "the study is flawed by incorrect or very doubtful character scorings, and unacceptable generalizations on character distribution based on unverified assumptions" and gives some hilarious examples, but that paper is only referenced once by Ericson and Qu who write Livezey and Zusi's "impact on the understanding of the higher-level relationships (orders and families) in birds did not become as prominent as hoped for (e.g. Mayr 2008)."  That doesn't hint at all to WHY Mayr didn't think it should have a large impact, and indeed one of Mayr's criticisms directly impacts consistency indices as he finds that characters will be scored for all members of an order based on a reference merely saying 'character x may be unique to this order' based on its presence in one family when none of the other families had even been checked.  So the source data isn't great to begin with.  But then looking at the supplementary info, if the same taxa are arranged in Livezey and Zusi's recovered topology, that consistency index is only 0.44, which is not that much better than the molecular tree's 0.38.  And the subcategories of characters' consistency indices don't vary much either- myology 0.31 vs. 0.36, cranial osteo 0.44 vs. 0.48, body osteo 0.32 vs. 0.39, wing osteo 0.37 vs. 0.46, leg osteo 0.37 vs. 0.47.  If these seem too low for the analysis to be trustworthy, compare Cau's (2024) similar-sized (1944 characters vs. 1860 parsimony-informative ones in Livezey and Zusi) analysis which has a consistency index of 0.17.  I'd bet the consistency index of a properly scored Livezey and Zusi matrix would be comparable, as it seems like taxa thought to be related were lazily scored the same without checking the anatomy (e.g. Mayr found "numerous other incorrect character scorings for Leptosomus in the character matrix [i.e. many characters are incorrectly assigned the same state as in Brachypteraciidae]").  Finally, it should be noted that these trees only include living taxa, so

if fossil taxa were included that support the molecular consensus (e.g. palaelodids for grebes and flamingos), that could very well raise the consistency index of the molecular topology compared to the morphological one.

Mickey Mortimer

[Gregory Paul]

Thanks! 

To view this discussion on the web visit https://groups.google.com/d/msgid/DinosaurMailingGroup/CABrjrNEDdBG2Wga%3DCjnrsdkQ_Tm9X74TuuHRjfkr99Uw7fUfqg%40mail.gmail.com.

[e w]

Hello,

As for the _Leptosomus_ scorings, I could check some of them against an actual courol specimen (in Berlin). AFAIR - it was more than 10 years ago -, L&Z completely mis-scored the forelimbs as brachypteraciid, while the hindlimbs are OK (or it was the other way around).

Possibly L&Z used a "courol" specimen that was actually was a chimera - I don't remember (I don't have L&Z at hand right now) seeing any indication that it was incomplete.


Best,

Eike Wulfmeyer

Am Sonntag, 25. August 2024 um 03:46:02 MESZ hat Mickey Mortimer <therizino...@gmail.com> Folgendes geschrieben:

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