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Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life
Phylogenomic Analysis of Spiders Reveals Nonmonophyly of Orb Weavers
Cryptic speciation of hormogastrid earthworms revealed by mitochondrial and nuclear data.
Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal
- P. Sharma, R. Fernández, Lauren A. Esposito, E. González-Santillán, L. Monod
- BiologyProceedings of the Royal Society B: Biological…
- 7 April 2015
A phylogenomic assessment to resolve scorpion phylogeny, for the first time, is applied, sampling extensive molecular sequence data from all superfamilies and examining basal relationships with up to 5025 genes, finding a robust basal topology of scorpions that is entirely at odds with traditional systematics and controverts previous understanding of scorpion evolutionary history.
Orthology: Definitions, Prediction, and Impact on Species Phylogeny Inference
This chapter introduces the fundamental concepts of orthology relationships and orthologous groups, including some non-trivial (and thus commonly misunderstood) implications, and discusses the impact of Orthology methods on species phylogeny inference.
Revisiting metazoan phylogeny with genomic sampling of all phyla
The first attempt to investigate animal relationships using genome-scale data from all phyla is presented, and matrix construction with an eye towards testing specific relationships is explored, showing that Lophotrochozoa can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets.
Sine Systemate Chaos? A Versatile Tool for Earthworm Taxonomy: Non-Destructive Imaging of Freshly Fixed and Museum Specimens Using Micro-Computed Tomography
It is demonstrated that the morphological features commonly used in earthworm taxonomy can now be analyzed without the need for dissection, whether freshly fixed or museum specimens collected more than 60 years ago are studied.
Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction
Results indicate that a high percentage of ribosomal proteins in the most complete matrices can act in concert to compromise the estimated relationships within the ingroup, and discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.
Evaluating topological conflict in centipede phylogeny using transcriptomic data sets.
The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, but accords with patterns of first appearances in the fossil record.