Can We Reliably Calibrate Deep Nodes in the Tetrapod Tree? Case Studies in Deep Tetrapod Divergences

Frontiers in Genetics
Jason D PardoJason S Anderson

Abstract

Recent efforts have led to the development of extremely sophisticated methods for incorporating tree-wide data and accommodating uncertainty when estimating the temporal patterns of phylogenetic trees, but assignment of prior constraints on node age remains the most important factor. This depends largely on understanding substantive disagreements between specialists (paleontologists, geologists, and comparative anatomists), which are often opaque to phylogeneticists and molecular biologists who rely on these data as downstream users. This often leads to misunderstandings of how the uncertainty associated with node age minima arises, leading to inappropriate treatments of that uncertainty by phylogeneticists. In order to promote dialogue on this subject, we here review factors (phylogeny, preservational megabiases, spatial and temporal patterns in the tetrapod fossil record) that complicate assignment of prior node age constraints for deep divergences in the tetrapod tree, focusing on the origin of crown-group Amniota, crown-group Amphibia, and crown-group Tetrapoda. We find that node priors for amphibians and tetrapods show high phylogenetic lability and different phylogenetic treatments identifying disparate taxa as the earlie...Continue Reading

References

Jan 21, 2000·Animal Behaviour·R Mace
Feb 17, 2000·Trends in Ecology & Evolution·I Laurin de Ricqlès I
Mar 28, 2003·Nature·Ke-Qin Gao, Neil H Shubin
Dec 12, 2003·Proceedings. Biological Sciences·Marcello RutaMichael I Coates
Jan 30, 2004·Trends in Genetics : TIG·Dan Graur, William Martin
Sep 17, 2004·Systematic Biology·Michel Laurin
Nov 3, 2004·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Thomas J Near, Michael J Sanderson
Mar 30, 2005·The American Naturalist·Diego San MauroAxel Meyer
Sep 16, 2005·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Johannes Müller, Robert R Reisz
Oct 19, 2006·Molecular Biology and Evolution·Michael J Benton, Philip C J Donoghue
Oct 27, 2006·Proceedings of the National Academy of Sciences of the United States of America·Peter WardRobert A Berner
May 24, 2007·Systematic Biology·David Marjanović, Michel Laurin
Jul 27, 2007·Evolution & Development·Jesse Love HendrikseBenedikt Hallgrímsson
Jul 27, 2007·Die Naturwissenschaften·Florian WitzmannMichael W Maisch
Mar 19, 1982·Science·D M Raup, J J Sepkoski
Jan 4, 2008·The American Naturalist·James F Parham, Randall B Irmis
Jun 25, 2009·Journal of Morphology·Trond Sigurdsen, John R Bolt
Apr 20, 2010·Molecular Phylogenetics and Evolution·Diego San Mauro
May 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Lauren Cole Sallan, Michael I Coates
Jun 9, 2010·Systematic Biology·Nadia B Fröbisch, Rainer R Schoch
Jun 1, 1997·Trends in Ecology & Evolution·R R Reisz
Apr 6, 2011·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Nadia B Fröbisch, Neil H Shubin
Apr 29, 2011·Proceedings. Biological Sciences·Robert R ReiszDiane M Scott
Nov 23, 2011·Systematic Biology·James F ParhamMichael J Benton
Mar 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Timothy R SmithsonJennifer A Clack
May 1, 2013·Systematic Biology·Tanja Stadler, Ziheng Yang
Jun 10, 2014·Molecular Phylogenetics and Evolution·Sebastián DuchêneSimon Y W Ho
Jul 11, 2014·Proceedings of the National Academy of Sciences of the United States of America·Tracy A HeathTanja Stadler
Sep 17, 2014·Proceedings of the National Academy of Sciences of the United States of America·Anne-Claire ChaboureauAlain Franc
Jan 16, 2015·Proceedings. Biological Sciences·Sean P ModestoRobert R Reisz
Apr 29, 2015·PloS One·Jason S AndersonJennifer Clack
Jun 25, 2015·Nature·Rainer R Schoch, Hans-Dieter Sues
Aug 19, 2015·Cytogenetic and Genome Research·David Cannatella
Sep 4, 2015·Nature·G S BeverBhart-Anjan S Bhullar
Nov 6, 2015·Nature Communications·Juan C CisnerosRudyard W Sadleir

❮ Previous
Next ❯

Citations

Sep 7, 2021·The Anatomical Record : Advances in Integrative Anatomy and Evolutionary Biology·Rachel C GecelterNathan E Thompson

❮ Previous
Next ❯

Software Mentioned

Lethiscus

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.

© 2021 Meta ULC. All rights reserved