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[dinosaur] Mesosaurid swim tracks + preserving bird fossils + conflicting phylogenetic trees for birds





Ben Creisler
bcreisler@gmail.com


Some recent non-dino papers... (I've been blocked trying to send items today, so this is an experiment...)


Rafael C. Silva and  Fernando Fernando Sedor (2017)
Mesosaurid Swim Tracks
Frontiers in Ecology and Evolution (advance publication)
doi: 10.3389/fevo.2017.00022
http://journal.frontiersin.org/article/10.3389/fevo.2017.00022/abstract

Despite subaqueous fossils tracks of tetrapods being quite common in the fossil record, few studies discuss their classification and morphofunctional interpretation. Despite their simple morphology, some important information about the trackmakers can be retrieved from these footprints. Subaqueous tracks were found in Brazil in the Irati Formation (Cisuralian, Permian), Paraná Basin, and described as Mesosaurichnium natans, related to Mesosauridae. The tracks were produced in a shallow marine environment, whose substrate contained crustacean shells forming a thin layer. The mesosaurids produced tracks by swimming close to the bottom. The propulsion was provided by undulatory moves of the long tail, mainly for faster swimming. The feet could act as accessory and slower propellants, but provided more maneuverability.


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Joseph E. Peterson, Melissa E. Lenczewski,  Steven R. Clawson and  Jonathan P. Warnock (2017)
Role of sediment size and biostratinomy on the development of biofilms in recent avian vertebrate remains.
Frontiers in Earth Science (advance publication)
doi: 10.3389/feart.2017.00030
http://journal.frontiersin.org/journal/earth-science/section/paleontology


Microscopic soft tissues have been identified in fossil vertebrate remains collected from various lithologies. However, the diagenetic mechanisms to preserve such tissues have remained elusive. While previous studies have described infiltration of biofilms in Haversian and Volkmann’s canals, biostratinomic alteration (e.g., trampling), and iron derived from hemoglobin as playing roles in the preservation processes, the influence of sediment texture has not previously been investigated. This study uses a Kolmogorov Smirnov Goodness-of-Fit test to explore the influence of biostratinomic variability and burial media against the infiltration of biofilms in bone samples. Controlled columns of sediment with bone samples were used to simulate burial and subsequent groundwater flow. Sediments used in this study include clay-, silt-, and sand-sized particles modeled after various fluvial facies commonly associated with fossil vertebrates. Extant limb bone samples obtained from Gallus gallus domesticus (Domestic Chicken) buried in clay-rich sediment exhibit heavy biofilm infiltration, while bones buried in sands and silts exhibit moderate levels. Crushed bones exhibit significantly lower biofilm infiltration than whole bone samples. Strong interactions between biostratinomic alteration and sediment size are also identified with respect to biofilm development. Sediments modeling crevasse splay deposits exhibit considerable variability; whole-bone crevasse splay samples exhibit higher frequencies of high-level biofilm infiltration, and crushed-bone samples in modeled crevasse splay deposits display relatively high frequencies of low-level biofilm infiltration. These results suggest that sediment size, depositional setting, and biostratinomic condition play key roles in biofilm infiltration in vertebrate remains, and may influence soft tissue preservation in fossil vertebrates.

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Sushma Reddy,  Rebecca T. Kimball,  Akanksha Pandey,  Peter A. Hosner, Michael J. Braun,  Shannon J. Hackett,  Kin-Lan Han , John Harshman, Christopher J. Huddleston,  Sarah Kingston,  Ben D. Marks,  Kathleen J. Miglia, William S. Moore,  Frederick H. Sheldon,  Christopher C. Witt,  Tamaki Yuri, Edward L. Braun (2017)
Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling
Systematic Biologyl syx041. 
DOI: https://doi.org/10.1093/sysbio/syx041
https://academic.oup.com/sysbio/article-abstract/doi/10.1093/sysbio/syx041/3091102/Why-do-phylogenomic-data-sets-yield-conflicting



Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic datasets can also result in conflicting estimates of phylogeny. Here we use the early divergences in Neoaves, the largest clade of extant birds, as a ‘model system’ to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [~42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters (~0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more ‘biologically-realistic’ models is likely to be critical for efforts to reconstruct the tree of life.