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[dinosaur] Neoaves phylogeny generated from ultraconserved elements + Rhinochelys from France






Ben Creisler
bcreisler@gmail.com


Recent non-dino items:

Princess S. Gilbert, Jing Wu, Margaret W. Simon, Janet S. Sinsheimer & Michael E. Alfaro (2018)
Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements.
Molecular Phylogenetics and Evolution (advance online publication)
doi: https://doi.org/10.1016/j.ympev.2018.03.033
https://www.sciencedirect.com/science/article/pii/S1055790317308539


Highlights

Filtering Ultraconserved Elements (UCEs) for sites with the highest phylogenetic signal to noise ratio produces datasets that are able recover relationships that would otherwise require intronic and exonic data in birds.

Filtering UCEs results in UCE-only phylogenetic reconstructions that support the Columbea+ Passerea sister relationship, Phaethontimorphae + Aequornithia sister relationship, the Eucavitaves clade.

Filtering UCEs for sites with the highest signal to noise ratio can lead to increases in node support for some clades supported by Total Evidenced datasets (i.e the Pelecanidae + Ardeidae sister relationship, and the Otidiformes + Musophagiformes sister relationship) and decreases in node support for some clades supported by Total Evidenced datasets (i.e. the Hoatzin + Cursorimorphae clade and the Columbea clade)

Our automated site filtering approach which uses signal to noise estimates (Townsend et al. 2012) is applicable to large genome-wide studies that seek to resolve difficult phylogenetic questions.


Abstract



Despite genome scale analyses, high-level relationships among Neoaves birds remain contentious. The placements of the Neoaves superorders are notoriously difficult to resolve because they involve deep splits followed by short internodes. Using our approach, we investigate whether filtering UCE loci on their phylogenetic signal to noise ratio helps to resolve key nodes in the Neoaves tree of life. We find that our analysis of data sets filtered for high signal to noise ratio results in topologies that are inconsistent with unfiltered results but that are congruent with whole-genome analyses. These relationships include the Columbea + Passerea sister relationship and the Phaethontimorphae + Aequornithia sister relationship. We also find increased statistical support for more recent nodes (i.e. the Pelecanidae + Ardeidae sister relationship, the Eucavitaves clade, and the Otidiformes + Musophagiformes sister relationship). We also find instances where support is reduced for well-established clades, possibly due to the removal of sites with moderate signal-to-noise ratio. Our results suggest that filtering on the basis of signal to noise ratio is a useful tool for resolving problematic splits in phylogenomic data sets.


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Free pdf:


Isaure Scavezzoni & Valentin Fischer (2018)
Rhinochelys amaberti Moret (1935), a protostegid turtle from the Early Cretaceous of France.Â
PeerJ 6:e4594
doi: https://doi.org/10.7717/peerj.4594
https://peerj.com/articles/4594/



Modern marine turtles (chelonioids) are the remnants of an ancient radiation that roots in the Cretaceous. The oldest members of that radiation are first recorded from the Early Cretaceous and a series of species are known from the Albian-Cenomanian interval, many of which have been allocated to the widespread but poorly defined genus Rhinochelys, possibly concealing the diversity and the evolution of early marine turtles. In order to better understand the radiation of chelonioids, we redescribe the holotype and assess the taxonomy of Rhinochelys amaberti Moret (1935) (UJF-ID.11167) from the Late Albian (Stoliczkaia dispar Zone) of the Vallon de la Fauge (IsÃre, France). We also make preliminary assessments of the phylogenetic relationships of Chelonioidea using two updated datasets that widely sample Cretaceous taxa, especially Rhinochelys. Rhinochelys amaberti is a valid taxon that is supported by eight autapomorphies; an emended diagnosisis proposed. Our phylogenetic analyses suggest that Rhinochelys could be polyphyletic, but constraining it as a monophyletic entity does not produce trees that are significantly less parsimonious. Moreover, support values and stratigraphic congruence indexes are fairly low for the recovered typologies, suggesting that missing data still strongly affect our understanding of the Cretaceous diversification of sea turtles.


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Free pdf:

Lin Zhang, Kun Guo, Guang-Zheng Zhang, Long-Hui Lin & Xiang Ji (2018)
Evolutionary transitions in body plan and reproductive mode alter maintenance metabolism in squamates.
BMC Evolutionary Biology 18:45Â
DOI: https://doi.org/10.1186/s12862-018-1166-5
https://link.springer.com/article/10.1186/s12862-018-1166-5

Background

Energy (resources) acquired by animals should be allocated towards competing demands, maintenance, growth, reproduction and fat storage. Reproduction has the second lowest priority in energy allocation and only is allowed after meeting the energetic demands for maintenance and growth. This hierarchical allocation of energy suggests the hypothesis that species or taxa with high maintenance costs would be less likely to invest more energy in reproduction or to evolve an energetically more expensive mode of reproduction. Here, we used data on standard metabolic rate so far reported for 196 species of squamates to test this hypothesis.

Results

We found that maintenance costs were lower in snakes than in lizards, and that the costs were lower in viviparous species than in oviparous species. As snakes generally invest more energy per reproductive episode than lizards, and viviparity is an energetically more expensive mode of reproduction than oviparity, our results are consistent with the hypothesis tested.

Conclusion

The transition from lizard-like to snake-like body form and the transition from oviparity to viviparity are major evolutionary transitions in vertebrates, which likely alter many aspects of biology of the organisms involved. Our study is the first to demonstrate that evolutionary transitions in body plan and reproductive mode alter maintenance metabolism in squamates.