Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective.

Systematic Biology
Sonal SinghalDaniel L Rabosky

Abstract

Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can bu...Continue Reading

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 12, 1998·Nucleic Acids Research·S M Aljanabi, I Martinez
Apr 5, 2002·Genome Research·W James Kent
Jul 15, 2003·Systematic Biology·Michael P CummingsKatarina Winka
Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
Nov 18, 2005·Nature·Bryan G FryElazar Kochva
Feb 24, 2006·Trends in Genetics : TIG·Olivier JeffroyHervé Philippe
May 31, 2006·PLoS Genetics·James H Degnan, Noah A Rosenberg
Nov 16, 2006·PLoS Biology·Antonis Rokas, Sean B Carroll
Apr 28, 2007·Systematic Biology·Jeffrey P Townsend
Aug 19, 2007·Science·Sol KatzmanDavid Haussler
Jan 26, 2008·Science·Karen M WongJohn P Huelsenbeck
Jan 17, 2009·Evolution; International Journal of Organic Evolution·Scott V Edwards
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Dec 21, 2010·Bioinformatics·Klaus Peter Schliep
Mar 23, 2011·PLoS Biology·Hervé PhilippeDenis Baurain
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
May 19, 2012·Systematic Biology·Alan R LemmonEmily Moriarty Lemmon
Aug 22, 2012·Bioinformatics·Stephen A Smith, Brian C O'Meara
Dec 15, 2012·Science·Jonathan B LososHarry W Greene
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
May 1, 2013·BMC Evolutionary Biology·R Alexander PyronJohn J Wiens
May 10, 2013·Nature·Leonidas Salichos, Antonis Rokas
Aug 21, 2013·Ecology Letters·R Alexander Pyron, Frank T Burbrink
Oct 1, 2013·Molecular Phylogenetics and Evolution·Patrick Kück, Torsten H Struck
Oct 22, 2013·Bioinformatics·Jiajie ZhangAlexandros Stamatakis
May 1, 1951·Biological Reviews of the Cambridge Philosophical Society·A D BELLAIRS, G UNDERWOOD
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Nov 29, 2014·Current Protocols in Bioinformatics·Geraldine A Van der AuweraMark A DePristo
Mar 31, 2015·Bioinformatics·Alexey M KozlovAlexandros Stamatakis
Apr 23, 2015·Proceedings of the National Academy of Sciences of the United States of America·Nathan V WhelanKenneth M Halanych
Jun 24, 2015·Systematic Biology·Vinson P DoyleJeremy M Brown
Nov 19, 2015·Molecular Biology and Evolution·Jonathan RomiguierChristophe J Praz
Dec 2, 2015·Proceedings of the National Academy of Sciences of the United States of America·Davide PisaniGert Wörheide
Dec 8, 2015·Evolution; International Journal of Organic Evolution·Matthew W Hahn, Luay Nakhleh

❮ Previous
Next ❯

Citations

Dec 12, 2020·IScience·Thiago Schineider FachiniAnnie Schmaltz Hsiou

❮ Previous
Next ❯

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.