Undersampling Genomes has Biased Time and Rate Estimates Throughout the Tree of Life

Molecular Biology and Evolution
Julie Marin, S Blair Hedges

Abstract

Genomic data drive evolutionary research on the relationships and timescale of life but the genomes of most species remain poorly sampled. Phylogenetic trees can be reconstructed reliably using small data sets and the same has been assumed for the estimation of divergence time with molecular clocks. However, we show here that undersampling of molecular data results in a bias expressed as disproportionately shorter branch lengths and underestimated divergence times in the youngest nodes and branches, termed the small sample artifact. In turn, this leads to increasing speciation and diversification rates towards the present. Any evolutionary analyses derived from these biased branch lengths and speciation rates will be similarly biased. The widely used timetrees of the major species-rich studies of amphibians, birds, mammals, and squamate reptiles are all data-poor and show upswings in diversification rate, suggesting that their results were biased by undersampling. Our results show that greater sampling of genomes is needed for accurate time and rate estimation, which are basic data used in ecological and evolutionary research.

References

Jul 14, 2005·Systematic Biology·Paul O LewisKent E Holsinger
Jul 14, 2005·Systematic Biology·Ziheng Yang, Bruce Rannala
Mar 30, 2007·Nature·Olaf R P Bininda-EmondsAndy Purvis
Oct 30, 2007·Trends in Ecology & Evolution·Robert E Ricklefs
Nov 17, 2007·Bioinformatics·Luke J HarmonWendell Challenger
Dec 25, 2009·Evolution; International Journal of Organic Evolution·Daniel L Rabosky
Jun 9, 2010·Systematic Biology·Regis Debruyne, Hendrik N Poinar
Oct 12, 2010·PLoS Biology·Hélène MorlonJoshua B Plotkin
Dec 21, 2010·Bioinformatics·Klaus Peter Schliep
Mar 30, 2011·Proceedings of the National Academy of Sciences of the United States of America·Tanja Stadler
Mar 1, 2012·Molecular Biology and Evolution·Alexei J DrummondAndrew Rambaut
Nov 6, 2012·Nature·W JetzA O Mooers
Nov 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Koichiro TamuraSudhir Kumar
May 1, 2013·BMC Evolutionary Biology·R Alexander PyronJohn J Wiens
Jun 30, 2014·Molecular Biology and Evolution·Alan FilipskiSudhir Kumar
Mar 6, 2015·Molecular Biology and Evolution·S Blair HedgesSudhir Kumar
Nov 26, 2015·Evolution; International Journal of Organic Evolution·Daniel L Rabosky
Jan 30, 2016·Science Advances·Santiago Claramunt, Joel Cracraft
Aug 12, 2016·Proceedings of the National Academy of Sciences of the United States of America·Brian R MooreJohn P Huelsenbeck
May 26, 2017·Nature·Peter Uetz, Akhil Garg

❮ Previous
Next ❯

Citations

Jan 29, 2019·Molecular Biology and Evolution·Qiqing TaoSudhir Kumar
Mar 27, 2019·Proceedings of the National Academy of Sciences of the United States of America·L Francisco Henao DiazMatthew W Pennell

❮ 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.