Innovative Bayesian and parsimony phylogeny of dung beetles (coleoptera, scarabaeidae, scarabaeinae) enhanced by ontology-based partitioning of morphological characters

PloS One
S Tarasov, François Génier

Abstract

Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characte...Continue Reading

References

Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
Feb 18, 2004·Systematic Biology·Johan A A NylanderJosé Luis Nieves-Aldrey
Sep 3, 2005·Evolution; International Journal of Organic Evolution·Douglas J EmlenClifford W Cunningham
Jul 28, 2007·Molecular Phylogenetics and Evolution·Michael T MonaghanAlfried P Vogler
Apr 22, 2008·Molecular Phylogenetics and Evolution·Helena WirtaIlkka Hanski
Apr 27, 2010·Molecular Phylogenetics and Evolution·Catherine L Sole, Clarke H Scholtz
Aug 25, 2010·Molecular Phylogenetics and Evolution·Helena WirtaIlkka Hanski
Dec 29, 2010·Systematic Biology·Wangang XieMing-Hui Chen
Jan 7, 2011·PloS One·Matthew J YoderAndrew R Deans
Sep 6, 2011·Molecular Biology and Evolution·Bruce RannalaZiheng Yang
Feb 24, 2012·Systematic Biology·Fredrik RonquistJohn P Huelsenbeck
Dec 15, 2012·Science·Jonathan B LososHarry W Greene
Aug 13, 2013·PloS One·Jürgen DönitzGregor Bucher
Nov 7, 2013·Systematic Biology·Paul O LewisLynn Kuo
Aug 8, 2014·Proceedings. Biological Sciences·Dirk AhrensAlfried P Vogler

❮ Previous
Next ❯

Citations

Dec 1, 2017·PloS One·Lily Johanna Toro SegoviaJhon Carlos Castaño Osorio
Mar 5, 2019·Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology·Claudia ToccoMarcus Byrne
Dec 24, 2020·Applied and Environmental Microbiology·Kathryn M EbertDavid J Merritt
Aug 14, 2021·Genetics and Molecular Biology·Catarine Aragone de Albuquerque MelloRita de Cássia de Moura

❮ Previous
Next ❯

Methods Mentioned

BETA
dissecting
dissection

Software Mentioned

WinClada
Tracer
R
APE
Google Scholar
MrBayes
R script
TNT script
Adobe Illustrator

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.