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04 Jun 2024
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New generic name for a small Triassic ray-finned fish from Perledo (Italy)

A new study on the halecomorph fishes from the Triassic of Perledo (Italy) highlights important issues in Palaeoichthyology

Recommended by based on reviews by Guang-Hui Xu and 1 anonymous reviewer

Mesozoic fishes are extremely diverse. In fact, fishes are the most diverse group of vertebrates during the Mesozoic─just as during any other era. Yet, their study is severely underrepresented in comparison to other fossil groups. There are just too few palaeoichthyologists to deal with such a vast diversity of fishes. Nonetheless, thanks to the huge efforts they have made over the last few decades, we have come a long way in our understanding of Mesozoic ichthyofaunas. One of such devoted palaeoichthyologists is Dr. Adriana López-Arbarello, whose contributions have been crucial in elucidating the phylogenetic interrelationships and taxonomic diversity of Mesozoic actinopterygian fishes (e.g., López-Arbarello, 2012; López-Arbarello & Sferco, 2018; López-Arbarello & Ebert, 2023). In her most recent manuscript, Dr. López-Arbarello has joined forces with Dr. Rainer Brocke to tackle the taxonomy and systematics of the halecomorph fishes from one of the most relevant Triassic sites, the upper Ladinian Perledo locality from Italy (López-Arbarello & Brocke, 2024). 

Fossil fishes were reported for the first time from Perledo in the first half of the 19th century (Balsamo-Crivelli, 1839), and up to 30 different species were described from the locality in the subsequent decades. Unfortunately, this is one of the multiple examples of fossil collections that suffered the effects of World War II, and most of the type material was lost. As a consequence, many of those 30 species that have been described over the years are in need of a revision. Based on the study of additional material that was transferred to Germany and is housed at the Senckenberg Research Institute and Natural History Museum, López-Arbarello & Brocke (2024) confirm the presence of four different species of halecomorph fishes in Perledo, which were previously put under synonymy (Lombardo, 2001). They provide new detailed information on the anatomy of two of those species, together with their respective diagnoses. But more importantly, they carry out a thorough exercise of taxonomy, rigorously applying the International Code of Zoological Nomenclature to disentangle the intricacies in the taxonomic story of the species placed in the genus Allolepidotus. As a result, they propose the presence of the species A. ruppelii, which they propose to be the type species for that genus (instead of A. bellottii, which they transfer to the genus Eoeugnathus). They also propose a new genus for the other species originally included in Allolepidotus, A. nothosomoides. Finally, they provide a set of measurements and ratios for Pholidophorus oblongus and Pholidophorus curionii, the other two species previously put in synonymy with A. bellottii, to demonstrate their validity as different species. However, due to the loss of the type material, the authors propose that these two species remain as nomina dubia

In summary, apart from providing new detailed anatomical descriptions of two species and solving some long-standing issues with the taxonomy of the halecomorphs from the relevant Triassic Perledo locality, the paper by López-Arbarello & Rainer (2024) highlights three important topics for the study of the fossil record: 1) we should never forget that world-scale problems, such as World Wars, also affect our capacity to understand the natural world in which we live, and the whole society should be aware if this; 2) the importance of exhaustively following the International Code of Zoological Nomenclature when describing new species; and 3) we are in need of new palaeoichthyologists to, in Dr. López-Arbarello’s own words, “unveil the mysteries of those marvellous Mesozoic ichthyofaunas.”

References

Balsamo-Crivelli, G. (1839). Descrizione di un nuovo rettile fossile, della famiglia dei Paleosauri, e di due pesci fossili, trovati nel calcare nero, sopra Varenna sul lago di Como, dal nobile sig. Ludovico Trotti, con alcune riflessioni geologiche. Il politecnico repertorio mensile di studj applicati alla prosperita e coltura sociale, 1, 421–431.

Lombardo, C. (2001). Actinopterygians from the Middle Triassic of northern Italy and Canton Ticino (Switzerland): Anatomical descriptions and nomenclatural problems. Rivista Italiana di Paleontologia e Stratigrafia, 107, 345–369. https://doi.org/10.13130/2039-4942/5439

López-Arbarello, A. (2012). Phylogenetic interrelationships of ginglymodian fishes (Actinopterygii: Neopterygii). PLOS ONE, 7(7), e39370. https://doi.org/10.1371/journal.pone.0039370

López-Arbarello, A., and Brocke, R. (2024). New generic name for a small Triassic ray-finned fish from Perledo (Italy). PaleorXiv, bxmg5, ver. 4, peer-reviewed by PCI Paleo. https://doi.org/10.31233/osf.io/bxmg5

López-Arbarello, A., and Ebert, M. (2023). Taxonomic status of the caturid genera (Halecomorphi, Caturidae) and their Late Jurassic species. Royal Society Open Science, 10(1), 221318. https://doi.org/10.1098/rsos.221318

López-Arbarello, A., and Sferco, E. (2018). Neopterygian phylogeny: The merger assay. Royal Society Open Science, 5(3), 172337. https://doi.org/10.1098/rsos.172337

New generic name for a small Triassic ray-finned fish from Perledo (Italy)Adriana López-Arbarello, Rainer Brocke<p>Our new study of the species originally included in the genus <em>Allolepidotus</em> led to the taxonomic revision of the halecomorph species from the Triassic of Perledo, Italy. The morphological variation revealed by the analysis of the type ...Fossil record, Systematics, Taxonomy, Vertebrate paleontologyHugo Martín Abad2024-03-21 11:53:53 View
26 Apr 2024
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New insights on feeding habits of Kolpochoerus from the Shungura Formation (Lower Omo Valley, Ethiopia) using dental microwear texture analysis

Dental microwear texture analysis of suid teeth from the Shungura Formation of the Omo Valley, Ethiopia

Recommended by based on reviews by Daniela E. Winkler and Kari Prassack

Suidae are well-represented in Plio-Pleistocene African hominin sites and are particularly important for biochronological assessments. Their ubiquity in hominin sites combined with multiple appearances of what appears to be graminivorous adaptations in the lineage (Harris & White, 1979) suggest that they have the potential to contribute to our understanding of Plio-Pleistocene paleoenvironments. While they have been generally understudied in this respect, there has been recent focus on their diets to understand the paleoenvironments of early hominin habitats. Of particular interest is Kolpochoerus, one of the most abundant suid genera in the Plio-Pleistocene with a wide geographic distribution and diverse dental morphologies (Harris & White, 1979). 

In this study, Louail et al. (2024) present the results of the first dental microwear texture analysis (DMTA) conducted on suids from the Shungura Formation of the Omo Valley, an important Plio-Pleistocene hominin site that records an almost continuous sedimentary record from ca. 3.75 Ma to 1.0 Ma (Heinzelin 1983; McDougall et al., 2012; Kidane et al., 2014). Dental microwear is one of the main proxies in understanding diet in fossil mammals, particularly herbivores, and DMTA has been shown to be effective in differentiating inter- and intra-species dietary differences (e.g., Scott et al., 2006; 2012; Merceron et al., 2010). However, only a few studies have applied this method to extinct suids (Souron et al., 2015; Ungar et al., 2020), making this study especially pertinent for those interested in suid dietary evolution or hominin paleoecology.

In addition to examining DMT variations of Kolpochoerus specimens from Omo, Louail et al. (2024) also expanded the modern comparative data set to include larger samples of African suids with different diets from herbivores to omnivores to better interpret the fossil data. They found that DMTA distinguishes between extant suid taxa, reflecting differences in diet, indicating that DMT can be used to examine the diets of fossil suids. The results suggest that Kolpochoerus at Omo had a substantially different diet from any extant suid taxon and that although its anistropy values increased through time, they remain well below those observed in modern Phacochoerus that specializes in fibrous, abrasive plants. Based on these results, in combination with comparative and experimental DMT, enamel carbon isotopic, and morphological data, Louail et al. (2024) propose that Omo Kolpochoerus preferred short, soft and low abrasive herbaceous plants (e.g., fresh grass shoots), probably in more mesic habitats. Louail et al. (2024) note that with the wide temporal and geographic distribution of Kolpochoerus, different species and populations may have had different feeding habits as they exploited different local habitats. However, it is noteworthy that similar inferences were made at other hominin sites based on other types of dietary data (e.g., Harris & Cerling, 2002; Rannikko et al., 2017, 2020; Yang et al., 2022). If this is an indication of their habitat preferences, the wide-ranging distribution of Kolpochoerus may suggest that mesic habitats with short, soft herbaceous plants were present in various proportions at most Plio-Pleistocene hominin sites. 

References

Harris, J. M., and Cerling, T. E. (2002). Dietary adaptations of extant and Neogene African suids. Journal of Zoology, 256(1), 45–54. https://doi.org/10.1017/S0952836902000067

Harris, J. M., and White, T. D. (1979). Evolution of the Plio-Pleistocene African Suidae. Transactions of the American Philosophical Society, 69(2), 1–128. https://doi.org/10.2307/1006288

Heinzelin, J. de. (1983). The Omo Group. Archives of the International Omo Research Expedition. Volume 85. Annales du Musée Royal de l’Afrique Centrale, série 8, Sciences géologiques, Tervuren, 388 p.

Kidane, T., Brown, F. H., and Kidney, C. (2014). Magnetostratigraphy of the fossil-rich Shungura Formation, southwest Ethiopia. Journal of African Earth Sciences, 97, 207–223. https://doi.org/10.1016/j.jafrearsci.2014.05.005

Louail, M., Souron, A., Merceron, G., and Boisserie, J.-R. (2024). New insights on feeding habits of Kolpochoerus from the Shungura Formation (Lower Omo Valley, Ethiopia) using dental microwear texture analysis. PaleorXiv, dbgtp, ver. 3, peer-reviewed by PCI Paleo. https://doi.org/10.31233/osf.io/dbgtp

McDougall, I., Brown, F. H., Vasconcelos, P. M., Cohen, B. E., Thiede, D. S., and Buchanan, M. J. (2012). New single crystal 40Ar/39Ar ages improve time scale for deposition of the Omo Group, Omo–Turkana Basin, East Africa. Journal of the Geological Society, 169(2), 213–226. https://doi.org/10.1144/0016-76492010-188

Merceron, G., Escarguel, G., Angibault, J.-M., and Verheyden-Tixier, H. (2010). Can dental microwear textures record inter-individual dietary variations? PLoS ONE, 5(3), e9542. https://doi.org/10.1371/journal.pone.0009542

Rannikko, J., Adhikari, H., Karme, A., Žliobaitė, I., and Fortelius, M. (2020). The case of the grass‐eating suids in the Plio‐Pleistocene Turkana Basin: 3D dental topography in relation to diet in extant and fossil pigs. Journal of Morphology, 281(3), 348–364. https://doi.org/10.1002/jmor.21103

Rannikko, J., Žliobaitė, I., and Fortelius, M. (2017). Relative abundances and palaeoecology of four suid genera in the Turkana Basin, Kenya, during the late Miocene to Pleistocene. Palaeogeography, Palaeoclimatology, Palaeoecology, 487, 187–193. https://doi.org/10.1016/j.palaeo.2017.08.033

Scott, R. S., Teaford, M. F., and Ungar, P. S. (2012). Dental microwear texture and anthropoid diets. American Journal of Physical Anthropology, 147(4), 551–579. https://doi.org/10.1002/ajpa.22007

Scott, R. S., Ungar, P. S., Bergstrom, T. S., Brown, C. A., Childs, B. E., Teaford, M. F., and Walker, A. (2006). Dental microwear texture analysis: Technical considerations. Journal of Human Evolution, 51(4), 339–349. https://doi.org/10.1016/j.jhevol.2006.04.006

Souron, A., Merceron, G., Blondel, C., Brunetière, N., Colyn, M., Hofman-Kamińska, E., and Boisserie, J.-R. (2015). Three-dimensional dental microwear texture analysis and diet in extant Suidae (Mammalia: Cetartiodactyla). Mammalia, 79(3). https://doi.org/10.1515/mammalia-2014-0023

Ungar, P. S., Abella, E. F., Burgman, J. H. E., Lazagabaster, I. A., Scott, J. R., Delezene, L. K., Manthi, F. K., Plavcan, J. M., and Ward, C. V. (2020). Dental microwear and Pliocene paleocommunity ecology of bovids, primates, rodents, and suids at Kanapoi. Journal of Human Evolution, 140, 102315. https://doi.org/10.1016/j.jhevol.2017.03.005

Yang, D., Pisano, A., Kolasa, J., Jashashvili, T., Kibii, J., Gomez Cano, A. R., Viriot, L., Grine, F. E., and Souron, A. (2022). Why the long teeth? Morphometric analysis suggests different selective pressures on functional occlusal traits in Plio-Pleistocene African suids. Paleobiology, 48(4), 655–676. https://doi.org/10.1017/pab.2022.11

New insights on feeding habits of *Kolpochoerus* from the Shungura Formation (Lower Omo Valley, Ethiopia) using dental microwear texture analysisMargot Louail, Antoine Souron, Gildas Merceron, Jean-Renaud Boisserie<p>During the Neogene and the Quaternary, African suids show dental morphological changes considered to reflect adaptations to increasing specialization on graminivorous diets, notably in the genus <em>Kolpochoerus</em>. They tend to exhibit elong...Paleoecology, Vertebrate paleontologyDenise Su2023-08-28 10:38:33 View
26 Mar 2024
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Calibrations without raw data - a response to "Seasonal calibration of the end-cretaceous Chicxulub impact event"

Questioning isotopic data from the end-Cretaceous

Recommended by based on reviews by Thomas Cullen and 1 anonymous reviewer

Being able to follow the evidence and verify results is critical if we are to be confident in the findings of a scientific study. Here, During et al. (2024) comment on DePalma et al. (2021) and provide a detailed critique of the figures and methods presented that caused them to question the veracity of the isotopic data used to support a spring-time Chicxulub impact at the end-Cretaceous. Given DePalma et al. (2021) did not include a supplemental file containing the original isotopic data, the suspicions rose to accusations of data fabrication (Price, 2022). Subsequent investigations led by DePalma’s current academic institution, The University of Manchester, concluded that the study contained instances of poor research practice that constitute research misconduct, but did not find evidence of fabrication (Price, 2023). Importantly, the overall conclusions of DePalma et al. (2021) are not questioned and both the DePalma et al. (2021) study and a study by During et al. (2022) found that the end-Cretaceous impact occurred in spring.

During et al. (2024) also propose some best practices for reporting isotopic data that can help future authors make sure the evidence underlying their conclusions are well documented. Some of these suggestions are commonly reflected in the methods sections of papers working with similar data, but they are not universally required of authors to report. Authors, research mentors, reviewers, and editors, may find this a useful set of guidelines that will help instill confidence in the science that is published.​

References

DePalma, R. A., Oleinik, A. A., Gurche, L. P., Burnham, D. A., Klingler, J. J., McKinney, C. J., Cichocki, F. P., Larson, P. L., Egerton, V. M., Wogelius, R. A., Edwards, N. P., Bergmann, U., and Manning, P. L. (2021). Seasonal calibration of the end-cretaceous Chicxulub impact event. Scientific Reports, 11(1), 23704. https://doi.org/10.1038/s41598-021-03232-9​

During, M. A. D., Smit, J., Voeten, D. F. A. E., Berruyer, C., Tafforeau, P., Sanchez, S., Stein, K. H. W., Verdegaal-Warmerdam, S. J. A., and Van Der Lubbe, J. H. J. L. (2022). The Mesozoic terminated in boreal spring. Nature, 603(7899), 91–94. https://doi.org/10.1038/s41586-022-04446-1

During, M. A. D., Voeten, D. F. A. E., and Ahlberg, P. E. (2024). Calibrations without raw data—A response to “Seasonal calibration of the end-cretaceous Chicxulub impact event.” OSF Preprints, fu7rp, ver. 5, peer-reviewed by PCI Paleo. https://doi.org/10.31219/osf.io/fu7rp​

​Price, M. (2022). Paleontologist accused of fraud in paper on dino-killing asteroid. Science, 378(6625), 1155–1157. https://doi.org/10.1126/science.adg2855

​Price, M. (2023). Dinosaur extinction researcher guilty of research misconduct. Science, 382(6676), 1225–1225. https://doi.org/10.1126/science.adn4967

Calibrations without raw data - a response to "Seasonal calibration of the end-cretaceous Chicxulub impact event"Melanie A.D. During, Dennis F.A.E. Voeten, Per E. Ahlberg<p>A recent paper by DePalma et al. reported that the season of the End-Cretaceous mass extinction was confined to spring/summer on the basis of stable isotope analyses and supplementary observations. An independent study that was concurrently und...Fossil calibration, Geochemistry, Methods, Vertebrate paleontologyChristina Belanger2023-06-22 10:43:31 View
07 Mar 2024
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An Early Miocene skeleton of Brachydiceratherium Lavocat, 1951 (Mammalia, Perissodactyla) from the Baikal area, Russia, and a revised phylogeny of Eurasian teleoceratines

A Rhino from Lake Baikal

Recommended by ORCID_LOGO based on reviews by Jérémy Tissier, Panagiotis Kampouridis and Tao Deng

As for many groups, such as equids or elephants, the number of living rhinoceros species is just a fraction of their past diversity as revealed by the fossil record. Besides being far more widespread and taxonomically diverse, rhinos also came in a greater variety of shapes and sizes. Some of these – teleoceratines, or so-called ‘hippo-like’ rhinos – had short limbs, barrel-shaped bodies, were often hornless, and might have been semi-aquatic (Prothero et al., 1989; Antoine, 2002). Teleoceratines existed from the Oligocene to the Pliocene, and have been recorded from Eurasia, Africa, and North and Central America. Despite this large temporal and spatial presence, large gaps remain in our knowledge of this group, particularly when it comes to their phylogeny and their relationships to other parts of the rhino tree (Antoine, 2002; Lu et al., 2021). Here, Sizov et al. (2024) describe an almost complete skeleton of a teleoceratine found in 2008 on an island in Lake Baikal in eastern Russia. Dating to the Early Miocene, this wonderfully preserved specimen includes the skull and limb bones, which are described and figured in detail, and which indicate assignment to Brachydiceratherium shanwangense, a species otherwise known only from Shandong in eastern China, some 2000 km to the southeast (Wang, 1965; Lu et al., 2021).

The study goes on to present a new phylogenetic analysis of the teleoceratines, the results of which have important implications for the taxonomy of fossil rhinos. Besides confirming the monophyly of Teleoceratina, the phylogeny supports the reassignment of most species previously assigned to Diaceratherium to Brachydiceratherium instead.

In a field that is increasingly dominated by analyses of metadata, Sizov et al. (2024) provide a reminder of the importance of fieldwork for the discovery of fossil remains that, sometimes by virtue of a single specimen, can significantly augment our understanding of the evolution and paleobiogeography of extinct species.

References

Antoine, P.-O. (2002). Phylogénie et évolution des Elasmotheriina (Mammalia, Rhinocerotidae). Mémoires du Muséum National d’Histoire Naturelle, 188, 1–359.

Lu, X., Cerdeño, E., Zheng, X., Wang, S., & Deng, T. (2021). The first Asian skeleton of Diaceratherium from the early Miocene Shanwang Basin (Shandong, China), and implications for its migration route. Journal of Asian Earth Sciences: X, 6, 100074. https://doi.org/10.1016/j.jaesx.2021.100074

Prothero, D. R., Guérin, C., and Manning, E. (1989). The History of the Rhinocerotoidea. In D. R. Prothero and R. M. Schoch (Eds.), The Evolution of Perissodactyls (pp. 322–340). Oxford University Press.

Sizov, A., Klementiev, A., & Antoine, P.-O. (2024). An Early Miocene skeleton of Brachydiceratherium Lavocat, 1951 (Mammalia, Perissodactyla) from the Baikal area, Russia, and a revised phylogeny of Eurasian teleoceratines. bioRxiv, 498987, ver. 6 peer-reviewed by PCI Paleo. https://doi.org/10.1101/2022.07.06.498987

Wang, B. Y. (1965). A new Miocene aceratheriine rhinoceros of Shanwang, Shandong. Vertebrata Palasiatica, 9, 109–112.

 

An Early Miocene skeleton of *Brachydiceratherium* Lavocat, 1951 (Mammalia, Perissodactyla) from the Baikal area, Russia, and a revised phylogeny of Eurasian teleoceratinesAlexander Sizov, Alexey Klementiev, Pierre-Olivier Antoine<p>Hippo-like rhinocerotids, or teleoceratines, were a conspicuous component of Holarctic Miocene mammalian faunas, but their phylogenetic relationships remain poorly known. Excavations in lower Miocene deposits of the Olkhon Island (Tagay localit...Biostratigraphy, Comparative anatomy, Fieldwork, Paleobiogeography, Paleogeography, Phylogenetics, Systematics, Vertebrate paleontologyFaysal Bibi2022-07-07 15:27:12 View
26 Oct 2023
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OH 89: A newly described ~1.8-million-year-old hominid clavicle from Olduvai Gorge

A new method for measuring clavicular curvature

Recommended by based on reviews by 2 anonymous reviewers

The evolution of the hominid clavicle has not been studied in depth by paleoanthropologists given its high morphological variability and the scarcity of complete diagnosable specimens. A nearly complete Nacholapithecus clavicle from Kenya (Senut et al. 2004) together with a fragment from Ardipithecus from the Afar region of Ethiopia (Lovejoy et al. 2009) complete our knowledge of the Miocene record. The Australopithecus collection of clavicles from Eastern and South African Plio-Pleistocene sites is slightly more abundant but mostly represented by fragmentary specimens. The number of fossil clavicles increases for the genus Homo from more recent sites and thus our potential knowledge about the shoulder evolution. 

In their new contribution, Taylor et al. (2023) present a detailed analysis of OH 89, a ~1.8-million-year-old partial hominin clavicle recovered from Olduvai Gorge (Tanzania). The work goes over previous studies which included clavicles found in the hominid fossil record. The text is accompanied by useful tables of data and a series of excellent photographs. It is a great opportunity to learn its role in the evolution of the hominid shoulder gird as clavicles are relatively poorly preserved in the fossil record compared to other long bones. The study compares the specimen OH 89 with five other hominid clavicles and a sample of 25 modern clavicles, 30 Gorilla, 31 Pan and 7 Papio. The authors propose a new methodology for measuring clavicular curvature using measurements of sternal and acromial curvature, from which an overall curvature measurement is calculated. The study of OH 89 provides good evidence about the hominid who lived 1.8 million years ago in the Olduvai Gorge region. This time period is especially relevant because it can help to understand the morphological changes that occurred between Australopithecus and the appearance of Homo. The authors conclude that OH 89 is the largest of the hominid clavicles included in the analysis. Although they are not able to assign this partial element to species level, this clavicle from Olduvai is at the larger end of the variation observed in Homo sapiens and show similarities to modern humans, especially when analysing the estimated sinusoidal curvature.

References

Lovejoy, C. O., Suwa, G., Simpson, S. W., Matternes, J. H., and White, T. D. (2009). The Great Divides: Ardipithecus ramidus peveals the postcrania of our last common ancestors with African apes. Science, 326(5949), 73–106. https://doi.org/10.1126/science.1175833

Senut, B., Nakatsukasa, M., Kunimatsu, Y., Nakano, Y., Takano, T., Tsujikawa, H., Shimizu, D., Kagaya, M., and Ishida, H. (2004). Preliminary analysis of Nacholapithecus scapula and clavicle from Nachola, Kenya. Primates, 45(2), 97–104. https://doi.org/10.1007/s10329-003-0073-5

Taylor, C., Masao, F., Njau, J. K., Songita, A. V., and Hlusko, L. J. (2023). OH 89: A newly described ∼1.8-million-year-old hominid clavicle from Olduvai Gorge. bioRxiv, 526656, ver. 6 peer-reviewed by PCI Paleo. https://doi.org/10.1101/2023.02.02.526656

OH 89: A newly described ~1.8-million-year-old hominid clavicle from Olduvai GorgeCatherine E. Taylor, Fidelis Masao, Jackson K. Njau, Agustino Venance Songita, Leslea J. Hlusko<p>Objectives: Here, we describe the morphology and geologic context of OH 89, a ~1.8-million-year-old partial hominid clavicle from Olduvai Gorge, Tanzania. We compare the morphology and clavicular curvature of OH 89 to modern humans, extant apes...Comparative anatomy, Evolutionary biology, Fossil record, Methods, Morphological evolution, Paleoanthropology, Vertebrate paleontologyNuria Garcia2023-02-08 19:45:01 View
19 Sep 2023
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PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins

An open-source pipeline to reconstruct phylogenies with paleoproteomic data

Recommended by based on reviews by Katerina Douka and 2 anonymous reviewers

One of the most recent technological advances in paleontology enables the characterization of ancient proteins, a new discipline known as palaeoproteomics (Ostrom et al., 2000; Warinner et al., 2022). Palaeoproteomics has superficial similarities with ancient DNA, as both work with ancient molecules, however the former focuses on peptides and the latter on nucleotides. While the study of ancient DNA is more established (e.g., Shapiro et al., 2019), palaeoproteomics is experiencing a rapid diversification of application, from deep time paleontology (e.g., Schroeter et al., 2022) to taxonomic identification of bone fragments (e.g., Douka et al., 2019), and determining genetic sex of ancient individuals (e.g., Lugli et al., 2022). However, as Patramanis et al. (2023) note in this manuscript, tools for analyzing protein sequence data are still in the informal stage, making the application of this methodology a challenge for many new-comers to the discipline, especially those with little bioinformatics expertise.

In the spirit of democratizing the field of palaeoproteomics, Patramanis et al. (2023) developed an open-source pipeline, PaleoProPhyler released under a CC-BY license (https://github.com/johnpatramanis/Proteomic_Pipeline). Here, Patramanis et al. (2023) introduce their workflow designed to facilitate the phylogenetic analysis of ancient proteins. This pipeline is built on the methods from earlier studies probing the phylogenetic relationships of an extinct genus of rhinoceros Stephanorhinus (Cappellini et al., 2019), the large extinct ape Gigantopithecus (Welker et al., 2019), and Homo antecessor (Welker et al., 2020). PaleoProPhyler has three interacting modules that initialize, construct, and analyze an input dataset. The authors provide a demonstration of application, presenting a molecular hominid phyloproteomic tree. 

In order to run some of the analyses within the pipeline, the authors also generated the Hominid Palaeoproteomic Reference Dataset which includes 10,058 protein sequences per individual translated from publicly available whole genomes of extant hominids (orangutans, gorillas, chimpanzees, and humans) as well as some ancient genomes of Neanderthals and Denisovans. This valuable research resource is also publicly available, on Zenodo (Patramanis et al., 2022). 

Three reviewers reported positively about the development of this program, noting its importance in advancing the application of palaeoproteomics more broadly in paleontology.

References

Cappellini, E., Welker, F., Pandolfi, L., Ramos-Madrigal, J., Samodova, D., Rüther, P. L., Fotakis, A. K., Lyon, D., Moreno-Mayar, J. V., Bukhsianidze, M., Rakownikow Jersie-Christensen, R., Mackie, M., Ginolhac, A., Ferring, R., Tappen, M., Palkopoulou, E., Dickinson, M. R., Stafford, T. W., Chan, Y. L., … Willerslev, E. (2019). Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature, 574(7776), 103–107. https://doi.org/10.1038/s41586-019-1555-y

Douka, K., Brown, S., Higham, T., Pääbo, S., Derevianko, A., and Shunkov, M. (2019). FINDER project: Collagen fingerprinting (ZooMS) for the identification of new human fossils. Antiquity, 93(367), e1. https://doi.org/10.15184/aqy.2019.3 

Lugli, F., Nava, A., Sorrentino, R., Vazzana, A., Bortolini, E., Oxilia, G., Silvestrini, S., Nannini, N., Bondioli, L., Fewlass, H., Talamo, S., Bard, E., Mancini, L., Müller, W., Romandini, M., and Benazzi, S. (2022). Tracing the mobility of a Late Epigravettian (~ 13 ka) male infant from Grotte di Pradis (Northeastern Italian Prealps) at high-temporal resolution. Scientific Reports, 12(1), 8104. https://doi.org/10.1038/s41598-022-12193-6

Ostrom, P. H., Schall, M., Gandhi, H., Shen, T.-L., Hauschka, P. V., Strahler, J. R., and Gage, D. A. (2000). New strategies for characterizing ancient proteins using matrix-assisted laser desorption ionization mass spectrometry. Geochimica et Cosmochimica Acta, 64(6), 1043–1050. https://doi.org/10.1016/S0016-7037(99)00381-6

Patramanis, I., Ramos-Madrigal, J., Cappellini, E., and Racimo, F. (2022). Hominid Palaeoproteomic Reference Dataset (1.0.1) [dataset]. Zenodo. https://doi.org/10.5281/ZENODO.7333226

Patramanis, I., Ramos-Madrigal, J., Cappellini, E., and Racimo, F. (2023). PaleoProPhyler: A reproducible pipeline for phylogenetic inference using ancient proteins. BioRxiv, 519721, ver. 3 peer-reviewed by PCI Paleo. https://doi.org/10.1101/2022.12.12.519721

Schroeter, E. R., Cleland, T. P., and Schweitzer, M. H. (2022). Deep Time Paleoproteomics: Looking Forward. Journal of Proteome Research, 21(1), 9–19. https://doi.org/10.1021/acs.jproteome.1c00755

Shapiro, B., Barlow, A., Heintzman, P. D., Hofreiter, M., Paijmans, J. L. A., and Soares, A. E. R. (Eds.). (2019). Ancient DNA: Methods and Protocols (2nd ed., Vol. 1963). Humana, New York. https://doi.org/10.1007/978-1-4939-9176-1

Warinner, C., Korzow Richter, K., and Collins, M. J. (2022). Paleoproteomics. Chemical Reviews, 122(16), 13401–13446. https://doi.org/10.1021/acs.chemrev.1c00703

Welker, F., Ramos-Madrigal, J., Gutenbrunner, P., Mackie, M., Tiwary, S., Rakownikow Jersie-Christensen, R., Chiva, C., Dickinson, M. R., Kuhlwilm, M., De Manuel, M., Gelabert, P., Martinón-Torres, M., Margvelashvili, A., Arsuaga, J. L., Carbonell, E., Marques-Bonet, T., Penkman, K., Sabidó, E., Cox, J., … Cappellini, E. (2020). The dental proteome of Homo antecessor. Nature, 580(7802), 235–238. https://doi.org/10.1038/s41586-020-2153-8

Welker, F., Ramos-Madrigal, J., Kuhlwilm, M., Liao, W., Gutenbrunner, P., De Manuel, M., Samodova, D., Mackie, M., Allentoft, M. E., Bacon, A.-M., Collins, M. J., Cox, J., Lalueza-Fox, C., Olsen, J. V., Demeter, F., Wang, W., Marques-Bonet, T., and Cappellini, E. (2019). Enamel proteome shows that Gigantopithecus was an early diverging pongine. Nature, 576(7786), 262–265. https://doi.org/10.1038/s41586-019-1728-8

PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteinsIoannis Patramanis, Jazmín Ramos-Madrigal, Enrico Cappellini, Fernando Racimo<p>Ancient proteins from fossilized or semi-fossilized remains can yield phylogenetic information at broad temporal horizons, in some cases even millions of years into the past. In recent years, peptides extracted from archaic hominins and long-ex...Evolutionary biology, Paleoanthropology, Paleogenetics & Ancient DNA, PhylogeneticsLeslea Hlusko2023-02-24 13:40:12 View
13 Jul 2023
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A baenid turtle shell from the Mesaverde Formation (Campanian, Late Cretaceous) of Park County, Wyoming, USA

New baenid turtle material from the Campanian of Wyoming

Recommended by ORCID_LOGO based on reviews by Heather F. Smith and Brent Adrian

The Baenidae form a diverse extinct clade of exclusively North American paracryptodiran turtles known from the Early Cretaceous to the Eocene (Hay, 1908; Gaffney, 1972; Joyce and Lyson, 2015). Their fossil record was recently extended down to the Berriasian-Valanginian (Joyce et al. 2020), but the group probably originates in the Late Jurassic because it is usually retrieved as the sister group of Pleurosternidae in phylogenetic analyses. However, baenids only became abundant during the Late Cretaceous, when they are restricted in distribution to the western United States, Alberta and Saskatchewan (Joyce and Lyson, 2015).

During the Campanian, baenids are abundant in the northern (Alberta, Montana) and southern (Texas, New Mexico, Utah) parts of their range, but in the middle part of this range they are mostly represented by poorly diagnosable shell fragments. In their new contribution, Wu et al. (2023) describe a new articulated baenid specimen from the Campanian Mesaverde Formation of Wyoming. Despite its poor preservation, they are able to confidently assign this partial shell to Neurankylus sp., hence definitively confirming the presence of baenids and Neurankylus in this formation. Incidentally, this new specimen was found in a non-fluvial depositional environment, which would also confirm the interpretation of Neurankylus as a pond turtle (Hutchinson and Archibald, 1986; Sullivan et al., 1988; Wu et al., 2023; see also comments from the second reviewer).

The study of Wu et al. (2023) also includes a detailed account of the state of the fossil when it was discovered and the subsequent extraction and preparation procedures followed by the team. This may seem excessive or out of place to some, but I agree with the authors that such information, when available, should be more commonly integrated into scientific articles describing new fossil specimens. Preparation and restoration can have a significant impact on the perceived morphology. This must be taken into account when working with fossil specimens. The chemicals or products used to treat, prepare, or consolidate the specimens are also important information for long-term curation. Therefore, it is important that such information is recorded and made available for researchers, curators, and preparators.

References

Gaffney, E. S. (1972). The systematics of the North American family Baenidae (Reptilia, Cryptodira). Bulletin of the American Museum of Natural History, 147(5), 241–320.

Hay, O. P. (1908). The Fossil Turtles of North America. Carnegie Institution of Washington, Washington, D.C. https://doi.org/10.5962/bhl.title.12500

Hutchison, J. H., and Archibald, J. D. (1986). Diversity of turtles across the Cretaceous/Tertiary boundary in Northeastern Montana. Palaeogeography, Palaeoclimatology, Palaeoecology, 55(1), 1–22. https://doi.org/10.1016/0031-0182(86)90133-1

Joyce, W. G., and Lyson, T. R. (2015). A review of the fossil record of turtles of the clade Baenidae. Bulletin of the Peabody Museum of Natural History, 56(2), 147–183. https://doi.org/10.3374/014.058.0105

Joyce, W. G., Rollot, Y., and Cifelli, R. L. (2020). A new species of baenid turtle from the Early Cretaceous Lakota Formation of South Dakota. Fossil Record, 23(1), 1–13. https://doi.org/10.5194/fr-23-1-2020

Sullivan, R. M., Lucas, S. G., Hunt, A. P., and Fritts, T. H. (1988). Color pattern on the selmacryptodiran turtle Neurankylus from the Early Paleocene (Puercan) of the San Juan Basin, New Mexico. Contributions in Science, 401, 1–9. https://doi.org/10.5962/p.241286

Wu, K. Y., Heuck, J., Varriale, F. J., and Farke, A. (2023). A baenid turtle shell from the Mesaverde Formation (Campanian, Late Cretaceous) of Park County, Wyoming, USA. PaleorXiv, uk3ac, ver. 5, peer-reviewed and recommended by Peer Community In Paleontology. https://doi.org/10.31233/osf.io/uk3ac

A baenid turtle shell from the Mesaverde Formation (Campanian, Late Cretaceous) of Park County, Wyoming, USAKa Yan Wu, Jared Heuck, Frank J. Varriale, and Andrew A. Farke<p>The Mesaverde Formation of the Wind River and Bighorn basins of Wyoming preserves a rich yet relatively unstudied terrestrial and marine faunal assemblage dating to the Campanian. To date, turtles within the formation have been represented prim...Paleobiodiversity, Paleobiogeography, Vertebrate paleontologyJérémy Anquetin2023-01-16 16:26:43 View
15 Dec 2022
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Spatio-temporal diversity of dietary preferences and stress sensibilities of early and middle Miocene Rhinocerotidae from Eurasia: impact of climate changes

New insights into the palaeoecology of Miocene Eurasian rhinocerotids based on tooth analysis

Recommended by based on reviews by Antigone Uzunidis, Christophe Mallet and Matthew Mihlbachler

Rhinocerotoidea originated in the Lower Eocene and diversified well during the Cenozoic in Eurasia, North America and Africa. This taxon encompasses a great diversity of ecologies and body proportions and masses. Within this group, the family Rhinocerotidae, which is the only one with extant representatives, appeared in the Late Eocene (Prothero & Schoch, 1989). They were well diversified during the Early and Middle Miocene, whereas they began to decline in both diversity and geographical range after the Miocene, throughout the Pliocene and Pleistocene, in conjunction with the marked climatic changes (Cerdeño, 1998). 

In Eurasian Early and Middle Miocene fossil localities, a variety of species are often associated. Therefore, it may be quite difficult to estimate how these large herbivores cohabited and whether competition for food resources is reflected in a diversity of ecological niches. The ecologies of these large mammals are rather poorly known and the detailed study of their teeth could bring new elements of answer. Indeed, if teeth carry a strong phylogenetic signal in mammals, they are also of great interest for ecological studies, and they have the additional advantage of being often numerous in the fossil record. 

Hullot et al. (2022) analysed both dental microwear texture, as an indicator of dietary preferences, and enamel hypoplasia, to identify stress sensitivity, in a large number of rhinocerotid fossil teeth from nine Neogene (Early to Middle Miocene) localities in Europe and Pakistan. Their aim was to analyse whether fossil species diversity is associated with a diversity of ecologies, and to investigate possible ecological differences between regions and time periods in relation to climate change. Their results show clear differences in time and space between and within species, and suggest that more flexible species are less vulnerable to environmental stressors. 

Very few studies focus on the palaeocology of Miocene rhinos. This study is therefore a great contribution to the understanding of the evolution of this group.

 

References

Cerdeño, E. (1998). Diversity and evolutionary trends of the Family Rhinocerotidae (Perissodactyla). Palaeogeography, Palaeoclimatology, Palaeoecology, 141, 13–34. https://doi.org/10.1016/S0031-0182(98)00003-0

Hullot, M., Merceron, G., and Antoine, P.-O. (2022). Spatio-temporal diversity of dietary preferences and stress sensibilities of early and middle Miocene Rhinocerotidae from Eurasia: Impact of climate changes. BioRxiv, 490903, ver. 4 peer-reviewed by PCI Paleo. https://doi.org/10.1101/2022.05.06.490903

Prothero, D. R., and Schoch, R. M. (1989). The evolution of perissodactyls. New York: Oxford University Press.

Spatio-temporal diversity of dietary preferences and stress sensibilities of early and middle Miocene Rhinocerotidae from Eurasia: impact of climate changesManon Hullot, Gildas Merceron, Pierre-Olivier Antoine<p>Major climatic and ecological changes are documented in terrestrial ecosystems during the Miocene epoch. The Rhinocerotidae are a very interesting clade to investigate the impact of these changes on ecology, as they are abundant and diverse in ...Paleobiodiversity, Paleobiology, Paleoecology, Paleopathology, Vertebrate paleontologyAlexandra Houssaye2022-05-09 09:33:30 View
25 Oct 2022
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Morphometric changes in two Late Cretaceous calcareous nannofossil lineages support diversification fueled by long-term climate change

Insights into mechanisms of coccolithophore speciation: How useful is cell size in delineating species?

Recommended by ORCID_LOGO based on reviews by Andrej Spiridonov and 1 anonymous reviewer

Calcareous plankton gives us perhaps the most complete record of microevolutionary changes in the fossil record (e.g. Tong et al., 2018; Weinkauf et al., 2019), but this opportunity is not exploited enough, as it requires meticulous work in documenting assemblage-level variation through time. Especially in organisms such as coccolithophores, understanding the meaning of secular trends in morphology warrants an understanding of the functional biology and ecology of these organisms. Razmjooei and Thibault (2022) achieve this in their painstaking analysis of two coccolithophore lineages, Cribrosphaerella ehrenbergii and Microrhabdulus, in the Late Cretaceous of Iran. They propose two episodes of morphological change. The first one, starting around 76 Ma in the late Campanian, is marked by a sudden shift towards larger sizes of C. ehrenbergii and the appearance of a new species M. zagrosensis from M. undulatus. The second episode around 69 Ma (Maastrichtian) is inferred from a gradual size increase and morphological changes leading to probably anagenetic speciation of M. sinuosus n.sp.

The study remarkably analyzed the entire distributions of coccolith length and rod width, rather than focusing on summary statistics (De Baets et al., in press). This is important, because the range of variation determines the taxon’s evolvability with respect to the considered trait (Love et al., 2022). As the authors discuss, cell size in photosymbiotic unicellular organisms is not subject to the same constraints that will be familiar to researchers working e.g. on mammals (Niklas, 1994; Payne et al., 2009; Smith et al., 2016). Furthermore, temporal changes in size alone cannot be interpreted as evolutionary without knowledge of phenotypic plasticity and environmental clines present in the basin (Aloisi, 2015). The more important is that this study cross-tests size changes with other morphological parameters to examine whether their covariation supports inferred speciation events. The article addresses as well the effects of varying sedimentation rates (Hohmann, 2021) by, somewhat implicitly, correcting for the stratophenetic trend using an age-depth model and accounting for a hiatus. Such multifaceted approach as applied in this work is fundamental to unlock the dynamics of speciation offered by the microfossil record. 

The study highlights also the link between shifts in size and diversity. Klug et al. (2015) have previously demonstrated that these two variables are related, as higher diversity is more likely to lead to extreme values of morphological traits, but this study suggests that the relationship is more intertwined: environmentally-driven rise in morphological variability (and thus in size) can lead to diversification. It is a fantastic illustration of the complexity of morphological evolution that, if it can be evaluated in terms of mechanisms, provides an insight into the dynamics of speciation.

 

References

Aloisi, G. (2015). Covariation of metabolic rates and cell size in coccolithophores. Biogeosciences, 12(15), 4665–4692. doi: 10.5194/bg-12-4665-2015

De Baets, K., Jarochowska, E., Buchwald, S. Z., Klug, C., and Korn, D. (In Press). Lithology controls ammonoid size distribution. Palaios.

Hohmann, N. (2021). Incorporating information on varying sedimentation rates into palaeontological analyses. PALAIOS, 36(2), 53–67. doi: 10.2110/palo.2020.038

Klug, C., De Baets, K., Kröger, B., Bell, M. A., Korn, D., and Payne, J. L. (2015). Normal giants? Temporal and latitudinal shifts of Palaeozoic marine invertebrate gigantism and global change. Lethaia, 48(2), 267–288. doi: 10.1111/let.12104

Love, A. C., Grabowski, M., Houle, D., Liow, L. H., Porto, A., Tsuboi, M., Voje, K.L., and Hunt, G. (2022). Evolvability in the fossil record. Paleobiology, 48(2), 186–209. doi: 10.1017/pab.2021.36

Niklas, K. J. (1994). Plant allometry: The scaling of form and process. Chicago: University of Chicago Press.

Payne, J. L., Boyer, A. G., Brown, J. H., Finnegan, S., Kowalewski, M., Krause, R. A., Lyons, S.K., McClain, C.R., McShea, D.W., Novack-Gottshall, P.M., Smith, F.A., Stempien, J.A., and Wang, S. C. (2009). Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity. Proceedings of the National Academy of Sciences, 106(1), 24–27. doi: 10.1073/pnas.0806314106

Razmjooei, M. J., and Thibault, N. (2022). Morphometric changes in two Late Cretaceous calcareous nannofossil lineages support diversification fueled by long-term climate change. PaleorXiv, nfyc9, ver. 4, peer-reviewed by PCI Paleo. doi: 10.31233/osf.io/nfyc9

Smith, F. A., Payne, J. L., Heim, N. A., Balk, M. A., Finnegan, S., Kowalewski, M., Lyons, S.K., McClain, C.R., McShea, D.W., Novack-Gottshall, P.M., Anich, P.S., and Wang, S. C. (2016). Body size evolution across the Geozoic. Annual Review of Earth and Planetary Sciences, 44(1), 523–553. doi: 10.1146/annurev-earth-060115-012147

Tong, S., Gao, K., and Hutchins, D. A. (2018). Adaptive evolution in the coccolithophore Gephyrocapsa oceanica following 1,000 generations of selection under elevated CO2. Global Change Biology, 24(7), 3055–3064. doi: 10.1111/gcb.14065

Weinkauf, M. F. G., Bonitz, F. G. W., Martini, R., and Kučera, M. (2019). An extinction event in planktonic Foraminifera preceded by stabilizing selection. PLOS ONE, 14(10), e0223490. doi: 10.1371/journal.pone.0223490

Morphometric changes in two Late Cretaceous calcareous nannofossil lineages support diversification fueled by long-term climate changeMohammad Javad Razmjooei, Nicolas Thibault<p>Morphometric changes have been investigated in the two groups of calcareous nannofossils, <em>Cribrosphaerella ehrenbergii</em> and <em>Microrhabdulus undosus</em> across the Campanian to Maastrichtian of the Zagros Basin of Iran. Results revea...Biostratigraphy, Evolutionary theory, Fossil record, Microfossils, Micropaleontology, Morphological evolution, Morphometrics, Nanofossils, Paleobiodiversity, Paleobiology, Paleoceanography, Paleoclimatology, Paleoecology, Paleoenvironments, TaxonomyEmilia Jarochowska2020-08-29 12:23:51 View
01 Oct 2021
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Ammonoid taxonomy with supervised and unsupervised machine learning algorithms

Performance of machine-learning approaches in identifying ammonoid species based on conch properties

Recommended by based on reviews by Jérémie Bardin and 1 anonymous reviewer

There are less and less experts on taxonomy of particular groups particularly among early career paleontologists and (paleo)biologists – this also includes ammonoid cephalopods. Techniques cannot replace this taxonomic expertise (Engel et al. 2021) but machine learning approaches can make taxonomy more efficient, reproducible as well as passing it over more sustainable. Initially ammonoid taxonomy was a black box with small differences sometimes sufficient to erect different species as well as really idiosyncratic groupings of superficially similar specimens (see De Baets et al. 2015 for a review). In the meantime, scientists have embraced more quantitative assessments of conch shape and morphology more generally (see Klug et al. 2015 for a more recent review). The approaches still rely on important but time-intensive collection work and seeing through daisy chains of more or less accessible papers and monographs without really knowing how these approaches perform (other than expert opinion). In addition, younger scientists are usually trained by more experienced scientists, but this practice is becoming more and more difficult which makes it difficult to resolve the taxonomic gap. This relates to the fact that less and less experienced researchers with this kind of expertise get employed as well as graduate students or postdocs choosing different research or job avenues after their initial training effectively leading to a leaky pipeline and taxonomic impediment.

Robust taxonomy and stratigraphy is the basis for all other studies we do as paleontologists/paleobiologists so Foxon (2021) represents the first step to use supervised and unsupervised machine-learning approaches and test their efficiency on ammonoid conch properties. This pilot study demonstrates that machine learning approaches can be reasonably accurate (60-70%) in identifying ammonoid species (Foxon, 2021) – at least similar to that in other mollusk taxa (e.g., Klinkenbuß et al. 2020) - and might also be interesting to assist in cases where more traditional methods are not feasible. Novel approaches might even allow to further approve the accuracy as has been demonstrated for other research objects like pollen (Romero et al. 2020). Further applying of machine learning approaches on larger datasets and additional morphological features (e.g., suture line) are now necessary in order to test and improve the robustness of these approaches for ammonoids as well as test their performance more broadly within paleontology.

 

References

De Baets K, Bert D, Hoffmann R, Monnet C, Yacobucci M, and Klug C (2015). Ammonoid intraspecific variability. In: Ammonoid Paleobiology: From anatomy to ecology. Ed. by Klug C, Korn D, De Baets K, Kruta I, and Mapes R. Vol. 43. Topics in Geobiology. Dordrecht: Springer, pp. 359–426.

Engel MS, Ceríaco LMP, Daniel GM, Dellapé PM, Löbl I, Marinov M, Reis RE, Young MT, Dubois A, Agarwal I, Lehmann A. P, Alvarado M, Alvarez N, Andreone F, Araujo-Vieira K, Ascher JS, Baêta D, Baldo D, Bandeira SA, Barden P, Barrasso DA, Bendifallah L, Bockmann FA, Böhme W, Borkent A, Brandão CRF, Busack SD, Bybee SM, Channing A, Chatzimanolis S, Christenhusz MJM, Crisci JV, D’elía G, Da Costa LM, Davis SR, De Lucena CAS, Deuve T, Fernandes Elizalde S, Faivovich J, Farooq H, Ferguson AW, Gippoliti S, Gonçalves FMP, Gonzalez VH, Greenbaum E, Hinojosa-Díaz IA, Ineich I, Jiang J, Kahono S, Kury AB, Lucinda PHF, Lynch JD, Malécot V, Marques MP, Marris JWM, Mckellar RC, Mendes LF, Nihei SS, Nishikawa K, Ohler A, Orrico VGD, Ota H, Paiva J, Parrinha D, Pauwels OSG, Pereyra MO, Pestana LB, Pinheiro PDP, Prendini L, Prokop J, Rasmussen C, Rödel MO, Rodrigues MT, Rodríguez SM, Salatnaya H, Sampaio Í, Sánchez-García A, Shebl MA, Santos BS, Solórzano-Kraemer MM, Sousa ACA, Stoev P, Teta P, Trape JF, Dos Santos CVD, Vasudevan K, Vink CJ, Vogel G, Wagner P, Wappler T, Ware JL, Wedmann S, and Zacharie CK (2021). The taxonomic impediment: a shortage of taxonomists, not the lack of technical approaches. Zoological Journal of the Linnean Society 193, 381–387. doi: 10. 1093/zoolinnean/zlab072

Foxon F (2021). Ammonoid taxonomy with supervised and unsupervised machine learning algorithms. PaleorXiv ewkx9, ver. 3, peer-reviewed by PCI Paleo. doi: 10.31233/osf.io/ewkx9

Klinkenbuß D, Metz O, Reichert J, Hauffe T, Neubauer TA, Wesselingh FP, and Wilke T (2020). Performance of 3D morphological methods in the machine learning assisted classification of closely related fossil bivalve species of the genus Dreissena. Malacologia 63, 95. doi: 10.4002/040.063.0109

Klug C, Korn D, Landman NH, Tanabe K, De Baets K, and Naglik C (2015). Ammonoid conchs. In: Ammonoid Paleobiology: From anatomy to ecology. Ed. by Klug C, Korn D, De Baets K, Kruta I, and Mapes RH. Vol. 43. Dordrecht: Springer, pp. 3–24.

Romero IC, Kong S, Fowlkes CC, Jaramillo C, Urban MA, Oboh-Ikuenobe F, D’Apolito C, and Punyasena SW (2020). Improving the taxonomy of fossil pollen using convolutional neural networks and superresolution microscopy. Proceedings of the National Academy of Sciences 117, 28496–28505. doi: 10.1073/pnas.2007324117

Ammonoid taxonomy with supervised and unsupervised machine learning algorithmsFloe Foxon<p>Ammonoid identification is crucial to biostratigraphy, systematic palaeontology, and evolutionary biology, but may prove difficult when shell features and sutures are poorly preserved. This necessitates novel approaches to ammonoid taxonomy. Th...Invertebrate paleontology, TaxonomyKenneth De Baets Jérémie Bardin2021-01-06 11:48:35 View