Some recent non-dino papers:
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Free pdf:
Paul M Hime, Alan R Lemmon, Emily C Moriarty Lemmon, Elizabeth Prendini, Jeremy M Brown, Robert C Thomson, Justin D Kratovil, Brice P Noonan, R Alexander Pyron, Pedro L V Peloso, Michelle L Kortyna, J Scott Keogh, Stephen C Donnellan, Rachel Lockridge Mueller, Christopher J Raxworthy, Krushnamegh Kunte, Santiago R Ron, Sandeep Das, Nikhil Gaitonde, David M Green, Jim Labisko, Jing Che & David W Weisrock (2020)
Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life.
Systematic Biology, syaa034 (advance online publication)
doi: https://doi.org/10.1093/sysbio/syaa034
https://academic.oup.com/sysbio/article/doi/10.1093/sysbio/syaa034/5828236
Paul M Hime, Alan R Lemmon, Emily C Moriarty Lemmon, Elizabeth Prendini, Jeremy M Brown, Robert C Thomson, Justin D Kratovil, Brice P Noonan, R Alexander Pyron, Pedro L V Peloso, Michelle L Kortyna, J Scott Keogh, Stephen C Donnellan, Rachel Lockridge Mueller, Christopher J Raxworthy, Krushnamegh Kunte, Santiago R Ron, Sandeep Das, Nikhil Gaitonde, David M Green, Jim Labisko, Jing Che & David W Weisrock (2020)
Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life.
Systematic Biology, syaa034 (advance online publication)
doi: https://doi.org/10.1093/sysbio/syaa034
https://academic.oup.com/sysbio/article/doi/10.1093/sysbio/syaa034/5828236
Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree--species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.
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Free pdf:
Neal Anthwal, Jane Catherine Fenelon, Stephen D Johnston, Marilyn B Renfree & Abigail S Tucker (2020)
Transient role of the middle ear as a lower jaw support across mammals.
eLife 9: e57860
DOI: 10.7554/eLife.57860
https://elifesciences.org/articles/57860
Mammals articulate their jaws using a novel joint between the dentary and squamosal bones. In eutherian mammals, this joint forms in the embryo, supporting feeding and vocalisation from birth. In contrast, marsupials and monotremes exhibit extreme altriciality and are born before the bones of the novel mammalian jaw joint form. These mammals need to rely on other mechanisms to allow them to feed. Here we show that this vital function is carried out by the earlier developing, cartilaginous incus of the middle ear, abutting the cranial base to form a cranio-mandibular articulation. The nature of this articulation varies between monotremes and marsupials, with juvenile monotremes retaining a double articulation, similar to that of the fossil mammaliaform Morganucodon, while marsupials use a versican-rich matrix to stabilise the jaw against the cranial base. These findings provide novel insight into the evolution of mammals and the changing relationship between the jaw and ear.
News
Hints at jaw evolution found in marsupials and monotremes
A connection between ear and jaw bones in marsupials and monotremes shortly after birth provides hints at the evolution of these bones in early mammals.
Guiting Li, Huiyuan Wei, Juanjuan Bi, Xiaoyue Ding, Lili Li, Shixia Xu, Guang Yang & Wenhua Ren (2020)
Insights into Dietary Switch in Cetaceans: Evidence from Molecular Evolution of Proteinases and Lipases.
Journal of Molecular Evolution 88: 521â535
DOI: https://doi.org/10.1007/s00239-020-09952-2
https://link.springer.com/article/10.1007/s00239-020-09952-2
Fossil evidence suggests that cetaceans evolved from artiodactylans. Thus, there was a major dietary change from herbivorous to carnivorous during their transition from a terrestrial to an aquatic environment. However, the molecular evolutionary mechanisms underlying this dietary switch have not been well investigated. Evidence of positive selection of digestive proteinases and lipases of cetaceans was detected: (1) For the four pancreatic proteinase families (carboxypeptidase, trypsin, chymotrypsin, and elastase) examined in this study, each family included only a single intact gene (e.g., CPA1, PRSS1, CTRC, and CELA3B) that had no ORF-disrupted or premature stop codons, whereas other members of each family had become pseudogenized. Further selective pressure analysis showed that three genes (PRSS1, CTRC, and CELA3B) were subjected to significant positive selection in cetaceans. (2) For digestive proteinases from the stomach, PGA was identified to be under positive selection. (3) Intense positive selection was also detected for the lipase gene PLRP2 in cetaceans. In addition, parallel /convergent amino acid substitutions between cetaceans and carnivores, two groups of mammals that have evolved similar feeding habits, were identified in 10 of the 12 functional genes. Although pseudogenization resulted in each family of pancreatic proteinases only retaining one intact gene copy in cetacean genomes, positive selection might have driven pancreatic proteinases, stomach proteinases, and lipases to adaptively evolve a stronger ability to digest a relatively higher proportion of proteins and lipids from animal foods. This study can provide some novel insights into the molecular mechanism of cetacean dietary changes during their transition from land to sea.
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Insights into Dietary Switch in Cetaceans: Evidence from Molecular Evolution of Proteinases and Lipases.
Journal of Molecular Evolution 88: 521â535
DOI: https://doi.org/10.1007/s00239-020-09952-2
https://link.springer.com/article/10.1007/s00239-020-09952-2
Fossil evidence suggests that cetaceans evolved from artiodactylans. Thus, there was a major dietary change from herbivorous to carnivorous during their transition from a terrestrial to an aquatic environment. However, the molecular evolutionary mechanisms underlying this dietary switch have not been well investigated. Evidence of positive selection of digestive proteinases and lipases of cetaceans was detected: (1) For the four pancreatic proteinase families (carboxypeptidase, trypsin, chymotrypsin, and elastase) examined in this study, each family included only a single intact gene (e.g., CPA1, PRSS1, CTRC, and CELA3B) that had no ORF-disrupted or premature stop codons, whereas other members of each family had become pseudogenized. Further selective pressure analysis showed that three genes (PRSS1, CTRC, and CELA3B) were subjected to significant positive selection in cetaceans. (2) For digestive proteinases from the stomach, PGA was identified to be under positive selection. (3) Intense positive selection was also detected for the lipase gene PLRP2 in cetaceans. In addition, parallel /convergent amino acid substitutions between cetaceans and carnivores, two groups of mammals that have evolved similar feeding habits, were identified in 10 of the 12 functional genes. Although pseudogenization resulted in each family of pancreatic proteinases only retaining one intact gene copy in cetacean genomes, positive selection might have driven pancreatic proteinases, stomach proteinases, and lipases to adaptively evolve a stronger ability to digest a relatively higher proportion of proteins and lipids from animal foods. This study can provide some novel insights into the molecular mechanism of cetacean dietary changes during their transition from land to sea.
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Free pdf:
Rodrigo L. Tomassini, Claudia I. Montalvo, Mariana C. Garrone, Laura Domingo, Jorge Ferigolo, Laura E. Cruz, DÃnae Sanz-PÃrez, Yolanda FernÃndez-Jalvo & Ignacio A. Cerda (2020)
Gregariousness in the giant sloth Lestodon (Xenarthra): multi-proxy approach of a bonebed from the Last Maximum Glacial of Argentine Pampas.
Scientific Reports 10, Article number: 10955
DOI: https://doi.org/10.1038/s41598-020-67863-0
https://www.nature.com/articles/s41598-020-67863-0
Free pdf:
https://www.nature.com/articles/s41598-020-67863-0.pdf
Megamammals constituted an important component in the Pleistocene faunal communities of South America. Paleobiological and paleoecological studies involving different megamammal taxa have increased significantly in the last years, but there are still several poorly-known issues of its life history. In this work, we analyze an assemblage composed of 13 individuals of different ontogenetic stages, and possibly different sex, belonging to the giant ground sloth Lestodon armatus (Xenarthra, Folivora), recovered from Playa del Barco site (Pampean Region, Argentina). A dating of 19,849 years Cal BP allows assigning this assemblage to a period of the MIS (Marine Isotope Stage) 2 related to the end of the Last Glacial Maximum. Based on multiple lines of research (e.g. taphonomy, paleopathology, osteohistology, isotopy), we interpret the origin of the assemblage and diverse paleobiological and paleoecological aspects (e.g. social behavior, ontogenetic changes, sexual dimorphism, diseases, resource and habitat use, trophic relationships) of L. armatus. Evidence suggests that the assemblage was formed by a local single event of catastrophic mortality, which affected different members of a social group. This record represents the first accurate evidence of gregariousness for this ground sloth, providing new data on a poorly-known behavior among extinct Folivora.
Gregariousness in the giant sloth Lestodon (Xenarthra): multi-proxy approach of a bonebed from the Last Maximum Glacial of Argentine Pampas.
Scientific Reports 10, Article number: 10955
DOI: https://doi.org/10.1038/s41598-020-67863-0
https://www.nature.com/articles/s41598-020-67863-0
Free pdf:
https://www.nature.com/articles/s41598-020-67863-0.pdf
Megamammals constituted an important component in the Pleistocene faunal communities of South America. Paleobiological and paleoecological studies involving different megamammal taxa have increased significantly in the last years, but there are still several poorly-known issues of its life history. In this work, we analyze an assemblage composed of 13 individuals of different ontogenetic stages, and possibly different sex, belonging to the giant ground sloth Lestodon armatus (Xenarthra, Folivora), recovered from Playa del Barco site (Pampean Region, Argentina). A dating of 19,849 years Cal BP allows assigning this assemblage to a period of the MIS (Marine Isotope Stage) 2 related to the end of the Last Glacial Maximum. Based on multiple lines of research (e.g. taphonomy, paleopathology, osteohistology, isotopy), we interpret the origin of the assemblage and diverse paleobiological and paleoecological aspects (e.g. social behavior, ontogenetic changes, sexual dimorphism, diseases, resource and habitat use, trophic relationships) of L. armatus. Evidence suggests that the assemblage was formed by a local single event of catastrophic mortality, which affected different members of a social group. This record represents the first accurate evidence of gregariousness for this ground sloth, providing new data on a poorly-known behavior among extinct Folivora.
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Free pdf:
P. David Polly (2020)
Ecometrics and Neogene faunal turnover: the roles of cats and hindlimb morphology in the assembly of carnivoran communities in the New World.
in Bonis L. de & Werdelin L. (eds), Memorial to StÃphane PeignÃ: Carnivores (Hyaenodonta and Carnivora) of the Cenozoic.
Geodiversitas 42 (17): 257-304.
doi: https://doi.org/10.5252/geodiversitas2020v42a17
http://sciencepress.mnhn.fr/en/periodiques/geodiversitas/42/17
Ecometrics and Neogene faunal turnover: the roles of cats and hindlimb morphology in the assembly of carnivoran communities in the New World.
in Bonis L. de & Werdelin L. (eds), Memorial to StÃphane PeignÃ: Carnivores (Hyaenodonta and Carnivora) of the Cenozoic.
Geodiversitas 42 (17): 257-304.
doi: https://doi.org/10.5252/geodiversitas2020v42a17
http://sciencepress.mnhn.fr/en/periodiques/geodiversitas/42/17
Cats possess some of the highest ankle gear ratios of any extant carnivorans, a feature that facilitates leaping and sprinting involved in ambush predation and scansorial lifestyles. In todayâs North American carnivoran communities, the high gear ratio of cats contributes to an overall high ecometric average for this trait and contributes strongly to measures of ecometric disparity at the community level. But cats were late additions to North American communities, arriving from Eurasia about 17 Ma at the end of the "cat gap". This paper uses ecometric analysis to document changes in hindlimb functional diversity in North American carnivoran communities over the last 19 million years in order to better understand the roles of trait evolution, clade turnover, and environmental change in community assembly. To accomplish this, I look at the phylogenetic history of ankle gear ratios of cats and other carnivorans, and the history of their occupation of high gear ratio niches in North American communities. The primary focus is on the Great Plains, which experienced profound changes in vegetation and climate through this period. Across all Carnivoramorpha, including a variety of extinct clades, it was found that gear ratios range from 1.08 (with extant ursids and viverrids and extinct miacids and barbourofelids, one of the three cat groups considered in this paper, having the lowest values) to 1.46 (with extant felids, herpestids, and canids having the highest values). Using the fossil record combined with phylogenetic ancestor reconstruction, it is shown that stem carnivorans and early felids had gear ratios about halfway between these extremes, consistent with a semidigitigrade or mildly digitigrade stance that was not overly specialized for either leaping or sprinting. Barbourofelids and some machairodontines evolved lower gear ratios that emphasized mechanical efficiency over advantage. When cats first entered North American communities in the Miocene they did not occupy high gear ratio niches and, in fact, occupied some of the lowest gear ratio niches during the Barstovian, Clarendonian, and Hemphillian. A major restructuring of gear ratio distributions in North American carnivoran communities occurred during the Blancan that appears to have resulted from clade sorting processes involving the selective loss of low gear ratio groups, as well as the evolution of increased gear ratios in felids and canids.
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Free pdf:
David E. Fastovsky, Marisol Montellano-Ballesteros, Henry C. Fricke, Jahandar Ramezani, Kaori Tsukui, Gregory P. Wilson, Paul Hall, Rene Hernandez-Rivera & Geraldo Alvarez (2020)
Paleoenvironments, taphonomy, and stable isotopic content of the terrestrial, fossil-vertebrate-bearing sequence of the El Disecado Member, El Gallo Formation, Upper Cretaceous, Baja California, MÃxico.Â
Geosphere (advance online publication)
doi: https://doi.org/10.1130/GES02207.1
https://pubs.geoscienceworld.org/gsa/geosphere/article/doi/10.1130/GES02207.1/587778/Paleoenvironments-taphonomy-and-stable-isotopic
Paleoenvironments, taphonomy, and stable isotopic content of the terrestrial, fossil-vertebrate-bearing sequence of the El Disecado Member, El Gallo Formation, Upper Cretaceous, Baja California, MÃxico.Â
Geosphere (advance online publication)
doi: https://doi.org/10.1130/GES02207.1
https://pubs.geoscienceworld.org/gsa/geosphere/article/doi/10.1130/GES02207.1/587778/Paleoenvironments-taphonomy-and-stable-isotopic
The Late Campanian (Late Cretaceous), upper part of the El Disecado Member, El Gallo Formation, Baja California, MÃxico, preserves a rich fossil assemblage of microvertebrates and macrovertebrates, silicified logs, macroscopic plant remains, and pollen that was likely deposited as the distal part of a subaerial fan. The unit was episodic and high energy, with its salient features deriving from active river channels and sheet, debris-flow deposits. Landscape stability is indicated by the presence of compound paleosol horizons, containing Fe2O3 mottling in B horizons, cutans, and calcium carbonate concretions. All of these features indicate wet/dry cyclicity in subsurface horizons, likely attributable to such cyclicity in the climate. Drainage was largely to the north and to a lesser extent, the west, however, some current flow to the south and east is preserved which, in conjunction with the proximal location of marginal marine deposits, suggest the influence of tides in this setting.
The fossil vertebrates preserved in this part of the El Disecado Member are almost exclusively allochthonous, preserved as disarticulated isolated clasts in hydraulic equivalence in the braided fluvial system. A relatively diverse microvertebrate assemblage is preserved, the largest components of which are first, dinosaurs, and second, turtles. Non-tetrapod fossils are relatively uncommon, perhaps reflecting an absence of permanent standing water in this depositional setting.
Here we report a high-precision U-Pb date of 74.706 + 0.028 Ma (2Ï internal uncertainty), obtained from zircons in an airfall tuff. The tuff is located low within the sequence studied, therefore, most of the sedimentology and fossils reported here are slightly younger. This date, which improves upon previously published 40Ar/39Ar geochronology, ultimately allows for comparison of these El Gallo faunas and environments with coeval ones globally.
Primary stable isotopic nodules associated with roots in the paleosols of the terrestrial porÂtion of the El Disecado Member are compared with ratios from similar sources from coeval northern and eastern localities in North America. Distinctive latitudinal gradients are observed in both Î13C and Î18O, reflecting the unique southern and western, coastal geographic position of this locality. These differences are best explained by differences in the floras that populated the northern and eastÂern localities, relative to the southern and western floras reported here.
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