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[dinosaur] Fwd: Early placental mammal evolution + parrot brains + Eusthenopteron + more free non-dino papers

This post apparently to the DML did not go through. Apologies if got through for some people...

---------- Forwarded message ----------
From: Ben Creisler <bcreisler@gmail.com>
Date: Tue, Jul 3, 2018 at 2:27 PM
Subject: Early placental mammal evolution + parrot brains + Eusthenopteron + more free non-dino papers
To: dinosaur-l@usc.edu

Ben Creisler

Some recent non-dino papers with free pdfs:

Free pdf:

Matthew J. Phillips & Carmelo Fruciano (2018)
The soft explosive model of placental mammal evolution.
BMC Evolutionary Biology 18:104Â


Recent molecular dating estimates for placental mammals echo fossil inferences for an explosive interordinal diversification, but typically place this event some 10â20 million years earlier than the Paleocene fossils, among apparently more âprimitiveâ mammal faunas.


However, current models of molecular evolution do not adequately account for parallel rate changes, and result in dramatic divergence underestimates for large, long-lived mammals such as whales and hominids. Calibrating among these taxa shifts the rate model errors deeper in the tree, inflating interordinal divergence estimates. We employ simulations based on empirical rate variation, which show that this âerror-shift inflationâ can explain previous molecular dating overestimates relative to fossil inferences. Molecular dating accuracy is substantially improved in the simulations by focusing on calibrations for taxa that retain plesiomorphic life-history characteristics. Applying this strategy to the empirical data favours the soft explosive model of placental evolution, in line with traditional palaeontological interpretations â a few Cretaceous placental lineages give rise to a rapid interordinal diversification following the 66 Ma Cretaceous-Paleogene boundary mass extinction.


Our soft explosive model for the diversification of placental mammals brings into agreement previously incongruous molecular, fossil, and ancestral life history estimates, and closely aligns with a growing consensus for a similar model for bird evolution. We show that recent criticism of the soft explosive model relies on ignoring both experimental controls and statistical confidence, as well as misrepresentation, and inconsistent interpretations of morphological phylogeny. More generally, we suggest that the evolutionary properties of adaptive radiations may leave current molecular dating methods susceptible to overestimating the timing of major diversification events.


Free pdf:

Virag Sharma, Thomas Lehmann, Heiko Stuckas, Liane Funke &Â Michael Hiller (2018)
Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals.Â
PLoS Biology 16(6): e2005293.


Descent of testes from a position near the kidneys into the lower abdomen or into the scrotum is an important developmental process that occurs in all placental mammals, with the exception of five afrotherian lineages. Since soft-tissue structures like testes are not preserved in the fossil record and since key parts of the placental mammal phylogeny remain controversial, it has been debated whether testicular descent is the ancestral or derived condition in placental mammals. To resolve this debate, we used genomic data of 71 mammalian species and analyzed the evolution of two key genes (relaxin/insulin-like family peptide receptor 2 [RXFP2] and insulin-like 3 [INSL3]) that induce the development of the gubernaculum, the ligament that is crucial for testicular descent. We show that both RXFP2 and INSL3 are lost or nonfunctional exclusively in four afrotherians (tenrec, cape elephant shrew, cape golden mole, and manatee) that completely lack testicular descent. The presence of remnants of once functional orthologs of both genes in these afrotherian species shows that these gene losses happened after the split from the placental mammal ancestor. These âmolecular vestigesâ provide strong evidence that testicular descent is the ancestral condition, irrespective of persisting phylogenetic discrepancies. Furthermore, the absence of shared gene-inactivating mutations and our estimates that the loss of RXFP2 happened at different time points strongly suggest that testicular descent was lost independently in Afrotheria. Our results provide a molecular mechanism that explains the loss of testicular descent in afrotherians and, more generally, highlight how molecular vestiges can provide insights into the evolution of soft-tissue characters.

Author summary

While fossils of whales with legs demonstrate that these species evolved from legged ancestors, the ancestral state of nonfossilizing soft-tissue structures can only be indirectly inferred. This difficulty is also confounded by uncertainties in the phylogenetic relationships between the animals concerned. A prime example is the case of testicular descent, a developmental process that determines the final position of testes, which occurs in most placental mammals but is absent from several afrotherian lineages. Here, we discovered that afrotherians possess remnants of genes known to be required for testicular descent. These âmolecular vestigesâ show that testicular descent was already present in the placental ancestor and was subsequently lost in Afrotheria. Our study highlights the potential of molecular vestiges in resolving contradictory ancestral states of soft-tissue characters.


John J. Flynn (2018)
Body mass predicts isotope enrichment in herbivorous mammals.
Proceedings of the Royal Society B 285 20181020
DOI: 10.1098/rspb.2018.1020

Carbon isotopic signatures recorded in vertebrate tissues derive from ingested food and thus reflect ecologies and ecosystems. For almost two decades, most carbon isotope-based ecological interpretations of extant and extinct herbivorous mammals have used a single dietâbioapatite enrichment value (14â). Assuming this single value applies to all herbivorous mammals, from tiny monkeys to giant elephants, it overlooks potential effects of distinct physiological and metabolic processes on carbon fractionation. By analysing a never before assessed herbivorous group spanning a broad range of body massesâslothsâwe discovered considerable variation in dietâbioapatite Î13C enrichment among mammals. Statistical tests (ordinary least squares, quantile, robust regressions, Akaike information criterion model tests) document independence from phylogeny, and a previously unrecognized strong and significant correlation of Î13C enrichment with body mass for all mammalian herbivores. A single-factor body mass model outperforms all other single-factor or more complex combinatorial models evaluated, including for physiological variables (metabolic rate and body temperature proxies), and indicates that body mass alone predicts Î13C enrichment. These analyses, spanning more than 5 orders of magnitude of body sizes, yield a size-dependent prediction of isotopic enrichment across Mammalia and for distinct digestive physiologies, permitting reconstruction of foregut versus hindgut fermentation for fossils and refined mean annual palaeoprecipitation estimates based on Î13C of mammalian bioapatite.


Free pdf:

CristiÃn GutiÃrrez-IbÃÃez, Andrew N. Iwaniuk & Douglas R. Wylie (2018)
Parrots have evolved a primate-like telencephalic-midbrain-cerebellar circuit
Scientific Reports 8, Article number: 9960Â

It is widely accepted that parrots show remarkable cognitive abilities. In mammals, the evolution of complex cognitive abilities is associated with increases in the size of the telencephalon and cerebellum as well as the pontine nuclei, which connect these two regions. Parrots have relatively large telencephalons that rival those of primates, but whether there are also evolutionary changes in their telencephalon-cerebellar relay nuclei is unknown. Like mammals, birds have two brainstem pontine nuclei that project to the cerebellum and receive projections from the telencephalon. Unlike mammals, birds also have a pretectal nucleus that connects the telencephalon with the cerebellum: the medial spiriform nucleus (SpM). We found that SpM, but not the pontine nuclei, is greatly enlarged in parrots and its relative size significantly correlated with the relative size of the telencephalon across all birds. This suggests that the telencephalon-SpM-cerebellar pathway of birds may play an analogous role to cortico-ponto-cerebellar pathways of mammals in controlling fine motor skills and complex cognitive processes. We conclude that SpM is key to understanding the role of telencephalon-cerebellar pathways in the evolution of complex cognitive abilities in birds.


Free pdf:

Fredrik K. MÃrer, Sophie Sanchez, Michelle Ãlvarez-Murga, Marco Di Michiel, Franz Pfeiffer, Martin Bech & Dag W. Breiby (2018)
3D Maps of Mineral Composition and Hydroxyapatite Orientation in Fossil Bone Samples Obtained by X-ray Diffraction Computed Tomography.
Scientific Reports 8, Article number: 10052Â

Whether hydroxyapatite (HA) orientation in fossilised bone samples can be non-destructively retrieved and used to determine the arrangement of the bone matrix and the location of muscle attachments (entheses), is a question of high relevance to palaeontology, as it facilitates a detailed understanding of the (micro-)anatomy of extinct species with no damage to the precious fossil specimens. Here, we report studies of two fossil bone samples, specifically the tibia of a 300-million-year-old tetrapod, Discosauriscus austriacus, and the humerus of a 370-million-year-old lobe-finned fish, Eusthenopteron foordi, using XRD-CT â a combination of X-ray diffraction (XRD) and computed tomography (CT). Reconstructed 3D images showing the spatial mineral distributions and the local orientation of HA were obtained. For Discosauriscus austriacus, details of the muscle attachments could be discerned. For Eusthenopteron foordi, the gross details of the preferred orientation of HA were deduced using three tomographic datasets obtained with orthogonally oriented rotation axes. For both samples, the HA in the bone matrix exhibited preferred orientation, with the unit cell c-axis of the HA crystallites tending to be parallel with the bone surface. In summary, we have demonstrated that XRD-CT combined with an intuitive reconstruction procedure is becoming a powerful tool for studying palaeontological samples.


Free pdf:

David T. Ledesma & Simon G. Scarpetta (2018)
The skull of the gerrhonotine lizard Elgaria panamintina (Squamata: Anguidae)
PLoS ONE 13(6): e0199584.

We provide the first description of the skull, osteoderms, and hyoid apparatus of the poorly known alligator lizard Elgaria panamintina, and compare the cranial osteology of that species to the widespread and well-studied taxon Elgaria multicarinata. Patterns of morphological variation resulting from ontogenetic transformations and pathology are discussed. We employed x-ray computed tomography (CT) scans to examine two adult specimens of Elgaria panamintina and two adult specimens of Elgaria multicarinata, in addition to examining multiple traditionally prepared skeletal specimens of the latter species. CT scans provide simultaneous study of both articulated and disarticulated elements, allowing us to describe and document the morphology of the skull with exceptional precision and detail. The description of the skull of Elgaria panamintina serves as a generalization for all Elgaria; here we provide the first complete description of the skull of this genus for future uses in morphological and phylogenetic studies of both extant species and fossils.


Free pdf:

Eusthenopteron jenkinsi sp. nov.

Jason P. Downs, Edward B. Daeschler, Alison M. Long and Neil H. Shubin (2018)
Eusthenopteron jenkinsi sp. nov. (Sarcopterygii, Tristichopteridae) from the Upper Devonian of Nunavut, Canada, and a Review of Eusthenopteron Taxonomy.
Breviora 562 :1-24

Free pdf link:

New material from the Upper Devonian (Frasnian) Fram Formation of Ellesmere Island, Nunavut, Canada, represents a new large-bodied species of Eusthenopteron. The complete and well-preserved nature of the fossil material enables a description of anatomy that is otherwise poorly represented in most Eusthenopteron species; this includes braincase (ethmosphenoid and otic-occipital), scapulocoracoid, and pectoral fin. The new species is distinguished from other Eusthenopteron species by its large body size, pitted rather than tuberculated dermal cranial ornament, a distinct caudolateral margin of the vomer, an unossified basicranium, and a horizontally oriented hyomandibula. A large sample size and decades of detailed study of Eusthenopteron foordi have resulted in an important anatomical understanding of that species, but a lack of autapomorphies has complicated efforts to diagnose the grouping Eusthenopteron. We review the taxonomic history of Eusthenopteron and provide a new diagnosis that relies on a combination of discrete features that are commonly preserved and unaffected by specimen quality.


Free pdf:

Dapedium ballei sp. nov.

Erin E. Maxwell & Adriana LÃpez-Arbarello (2018)
A new species of the deep-bodied actinopterygian Dapedium from the Middle Jurassic (Aalenian) of southwestern Germany.

Dapedium is one of the most abundant and diverse genera of ganoid fishes from the Early Jurassic fossil lagerstÃtte of Europe. In spite of its abundance, however, its timing of extinction is poorly constrained, with the youngest described material being Early Jurassic in age. We describe new diagnostic and relatively complete material of a large species of Dapedium (standard length estimated at 50 cm) from the Middle Jurassic (earliest Aalenian) Opalinuston Formation of Baden-WÃrttemberg, Germany. The Aalenian material represents a distinct species, D. ballei sp. nov., differing from Early Jurassic species in a unique combination of characters pertaining to the shape of the dermal skull elements, pectoral fin position, and scale shape and ornamentation. However, although D. ballei sp. nov. exhibits a unique combination of characters, there are no autapomorphies with which to distinguish it from the Toarcian species of Dapedium. Dapedium ballei represents the geologically youngest species of Dapedium, extending the range of this genus into the Middle Jurassic. The Opalinuston Formation fills an important gap in the marine vertebrate fossil record, and finds from this horizon have the potential to greatly improve our understanding of evolutionary dynamics over this period of faunal transition.