Effects of missing data on topological inference using a Total Evidence approach

Molecular Phylogenetics and Evolution
Thomas Guillerme, Natalie Cooper

Abstract

To fully understand macroevolutionary patterns and processes, we need to include both extant and extinct species in our models. This requires phylogenetic trees with both living and fossil taxa at the tips. One way to infer such phylogenies is the Total Evidence approach which uses molecular data from living taxa and morphological data from living and fossil taxa. Although the Total Evidence approach is very promising, it requires a great deal of data that can be hard to collect. Therefore this method is likely to suffer from missing data issues that may affect its ability to infer correct phylogenies. Here we use simulations to assess the effects of missing data on tree topologies inferred from Total Evidence matrices. We investigate three major factors that directly affect the completeness and the size of the morphological part of the matrix: the proportion of living taxa with no morphological data, the amount of missing data in the fossil record, and the overall number of morphological characters in the matrix. We infer phylogenies from complete matrices and from matrices with various amounts of missing data, and then compare missing data topologies to the "best" tree topology inferred using the complete matrix. We find that...Continue Reading

References

Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Mar 1, 1965·Journal of Theoretical Biology·E Zuckerkandl, L Pauling
Jun 1, 1997·Computer Applications in the Biosciences : CABIOS·A Rambaut, N C Grassly
Jul 6, 2000·Comptes rendus de l'Académie des sciences. Série III, Sciences de la vie·A HassaninS Tillier
Dec 19, 2001·American Journal of Physical Anthropology·Judith C Masters, Denis J Brothers
Feb 25, 2003·Molecular Biology and Evolution·Christophe J DouadyEmmanuel J P Douzery
May 14, 2003·Molecular Phylogenetics and Evolution·Nicolas SalaminVincent Savolainen
Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
Jun 1, 2005·Journal of Biomedical Informatics·John J Wiens
Jul 7, 2005·Journal of Molecular Evolution·Daniel E RozenRichard E Lenski
Oct 26, 2005·Systematic Biology·John J WiensTod W Reeder
May 11, 2006·PLoS Biology·Alexei J DrummondAndrew Rambaut
Jun 14, 2006·Trends in Ecology & Evolution·Jeremy B C Jackson, Douglas H Erwin
Feb 22, 2008·Trends in Ecology & Evolution·Peter B PearmanChristophe F Randin
Oct 15, 2008·Systematic Biology·Alexandros StamatakisJacques Rougemont
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Nicholas D PattengaleAlexandros Stamatakis
Jul 22, 2010·Trends in Ecology & Evolution·Tiago B Quental, Charles R Marshall
Nov 3, 2010·Trends in Ecology & Evolution·Gregory P Dietl, Karl W Flessa
Nov 9, 2010·Evolution; International Journal of Organic Evolution·Emmanuel Paradis
Jan 18, 2011·BMC Evolutionary Biology·Béatrice Roure, Hervé Philippe
Sep 1, 1996·Trends in Ecology & Evolution·Z Yang
Jun 18, 2011·Science·Michael J SandersonMike Steel
Feb 24, 2012·Systematic Biology·Fredrik RonquistJohn P Huelsenbeck
Jun 23, 2012·Systematic Biology·Fredrik RonquistAlexandr P Rasnitsyn
May 1, 2013·Systematic Biology·Tanja Stadler, Ziheng Yang
Jun 4, 2013·Trends in Ecology & Evolution·Susanne A FritzCatherine H Graham
Aug 30, 2013·Scientific Reports·Robert S Sansom, Matthew A Wills
Sep 11, 2013·Journal of Evolutionary Biology·C G SchragoA E R Soares
Apr 18, 2014·Proceedings. Biological Sciences·Kevin HealyNatalie Cooper
Aug 29, 2014·Proceedings. Biological Sciences·Robin M D Beck, Michael S Y Lee
Nov 8, 2014·Systematic Biology·Mary K Kuhner, Jon Yamato
Dec 3, 2014·Molecular Phylogenetics and Evolution·Dahiana ArcilaRicardo Betancur-R

❮ Previous
Next ❯

Citations

Nov 25, 2016·Scientific Reports·Benjamin P KearMichael Westerman
Mar 7, 2019·Proceedings. Biological Sciences·Thomas J D HallidayAnjali Goswami
Sep 26, 2017·Systematic Biology·Caroline Parins-Fukuchi
Apr 17, 2018·Royal Society Open Science·Adriana López-Arbarello, Emilia Sferco
Aug 17, 2019·Royal Society Open Science·Robert J AsherRobert J Emry
Feb 25, 2021·American Journal of Botany·Kelly K S Matsunaga, Selena Y Smith
Dec 13, 2016·Current Opinion in Insect Science·Jessica L Ware, Phillip Barden
Sep 2, 2021·Systematic Biology·Robert J Asher, Martin R Smith

❮ 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.