HOFFMANN Federico's profile
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HOFFMANN Federico

  • Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, United States of America
  • Bioinformatics, Evolutionary genomics, Vertebrates
  • recommender

Recommendation:  1

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Areas of expertise
EDUCATION Texas Tech University, Ph.D. in Zoology (Robert J. Baker, advisor) 1999-2002 Universidad de la República, Uruguay, M.Sc. in Biology (Enrique P. Lessa, advisor) 1993-1998 Universidad de la República, Uruguay, B.Sc. in Biology 1989-1993 PROFESSIONAL POSITIONS Associate Professor, Department of Biochemistry, Molecular Biology Entomology and Plant Pathology, Mississippi State University. July 2017 - Assistant Professor, Department of Biochemistry, Molecular Biology Entomology and Plant Pathology, Mississippi State University. January 2011 – June 2017. Postdoctoral Fellow Storz’s Lab, School of Biological Sciences, University of Nebraska at Lincoln. Jan. 2010- Dec. 2010 Postdoctoral Fellow, Instituto Carlos Chagas - ICC – Fiocruz, Curitiba, PR, Brazil. 2008-2009 Postdoctoral Fellow in Population Biology, Storz’s Lab, School of Biological Sciences, University of Nebraska at Lincoln. November 2005-March 2008 Postdoctoral Researcher, Wood’s Lab, School of Biological Sciences, University of Nebraska at Lincoln. January 2005-October 2005 Postdoctoral Researcher, Ortí’s Lab, School of Biological Sciences, University of Nebraska at Lincoln. January 2003-February 2005 Research Assistant, Robert J. Baker’s Lab, Texas Tech University. June 1999-December 2002 Research and Teaching Assistant, Laboratorio de Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay 1997-1999.

Recommendation:  1

28 Nov 2024
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Factors influencing the accuracy and precision in dating single gene trees

Dating single gene trees in the age of phylogenomics

Recommended by based on reviews by Sishuo Wang, David Duchêne and 1 anonymous reviewer

Dating evolutionary trees is a critical task that allows us to connect biological history to ecological and geological events, helping us explore connections between environmental change and genetic innovations. The central idea behind these techniques is to link changes at the sequence level to divergence times, under the general assumption that substitutions accumulate steadily over time. So, sequences that diverged earlier are expected to be more different than sequences that diverged more recently. For a number of biological and statistical reasons, the relationship between sequence divergence and time is not linear, so it is not always the case that more divergent sequences have accumulated more substitutions than less divergent ones. In the case of organismal-level divergences, a natural approach to mitigate these challenges is to incorporate as many genes as possible into the analyses. However, this route is not available when we are focusing our interest on a single gene or a gene family. Thus, exploring how different features of single gene trees impact the accuracy and precision of divergence time estimates is of interest. In this study, Louvel and Roest Crollius (2024), select a well-studied group of mammals, primates, extract single copy genes from their genomes, and explore how different factors such as alignment size, evolutionary rate variation and discordance between the gene and species trees impact divergence time estimates. 

There are many strengths of this study. The central ones are the number of factors considered and the transparent discussion of the limitations. In this regard, the study is an elegant combination of empirical and simulated data. Some of the results match intuitive expectations. For example, the authors find that longer alignments are more informative than shorter ones, that differences in evolutionary rate among branches lead to loss in precision, and that slow-evolving genes perform worse. Intriguingly, they also find differences in performance among genes with different ontologies. The empirical data used in this study is limited to a single group, and generally considers genes that have apparently remained as single copies. Accordingly, the conclusions that can be drawn are somewhat limited, calling for future studies building on and expanding the concepts of the study by Louvel and colleagues. For example, including genes that have been lost or duplicated would be of interest because changes in gene complement are a prevalent source of variation at the genome level in mammals in general (Demuth et al. 2006), and particularly in primates (Hahn et al. 2007).

                        

References

Demuth JP, De Bie T, Stajich JE, Cristianini N, Hahn MW (2006) The evolution of mammalian gene families. PLoS One, e85. https://doi.org/10.1371/journal.pone.0000085

Hahn MW, Demuth JP, Han SG (2007) Accelerated rate of gene gain and loss in primates. Genetics, 177,1941-1949. https://doi.org/10.1534/genetics.107.080077

Louvel, G and Roest Crollius, H (2024) Factors influencing the accuracy and precision in dating single gene trees. bioRxiv, ver. 6 peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2020.08.24.264671

 

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HOFFMANN Federico

  • Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, United States of America
  • Bioinformatics, Evolutionary genomics, Vertebrates
  • recommender

Recommendation:  1

Reviews:  0

Areas of expertise
EDUCATION Texas Tech University, Ph.D. in Zoology (Robert J. Baker, advisor) 1999-2002 Universidad de la República, Uruguay, M.Sc. in Biology (Enrique P. Lessa, advisor) 1993-1998 Universidad de la República, Uruguay, B.Sc. in Biology 1989-1993 PROFESSIONAL POSITIONS Associate Professor, Department of Biochemistry, Molecular Biology Entomology and Plant Pathology, Mississippi State University. July 2017 - Assistant Professor, Department of Biochemistry, Molecular Biology Entomology and Plant Pathology, Mississippi State University. January 2011 – June 2017. Postdoctoral Fellow Storz’s Lab, School of Biological Sciences, University of Nebraska at Lincoln. Jan. 2010- Dec. 2010 Postdoctoral Fellow, Instituto Carlos Chagas - ICC – Fiocruz, Curitiba, PR, Brazil. 2008-2009 Postdoctoral Fellow in Population Biology, Storz’s Lab, School of Biological Sciences, University of Nebraska at Lincoln. November 2005-March 2008 Postdoctoral Researcher, Wood’s Lab, School of Biological Sciences, University of Nebraska at Lincoln. January 2005-October 2005 Postdoctoral Researcher, Ortí’s Lab, School of Biological Sciences, University of Nebraska at Lincoln. January 2003-February 2005 Research Assistant, Robert J. Baker’s Lab, Texas Tech University. June 1999-December 2002 Research and Teaching Assistant, Laboratorio de Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay 1997-1999.