Richie Hodel awarded Florida Museum Austin Award for Research

March 29th, 2019
By Gitzendanner, Matt

Former lab member Richie Hodel was awarded the Florida Museum’s Austin Award for Research! Congrats Richie!

Toward a large-scale and deep phenological stage annotation of herbarium specimens: Case studies from temperate, tropical, and equatorial floras

March 29th, 2019
By Gitzendanner, Matt

Lorieul, T., K. D. Pearson, E. R. Ellwood, H. Goëau, J.-F. Molino, P. W. Sweeney, J. M. Yost, J. Sachs, E. Mata‐Montero, G. Nelson, P. S. Soltis, P. Bonnet, and A. Joly. 2019. Toward a large-scale and deep phenological stage annotation of herbarium specimens: Case studies from temperate, tropical, and equatorial floras. Applications in Plant Sciences 7:e01233. [View on publisher’s site]

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Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass.

February 19th, 2019
By Gitzendanner, Matt

A simplified example of how spike‐in standards can be used during read normalization to enable comparisons of expression level at different biological scales between a hypothetical diploid–polyploid pair with differing cell density. The large circles represent a unit of biomass and contain a number of cells (green squares). Beneath each circle is a depiction of how the read normalizations are calculated. Under a per transcriptome normalization, the ratio of target transcripts to the total transcriptome is compared. The per biomass normalization uses the ratio of the transcript of interest to the spike‐in transcripts. The per cell normalization also uses the ratio of the transcript of interest to spike‐in transcripts, but scales the spike‐in transcript abundance by cell density, represented here by multiplying the spike‐in abundance by the number of contributing cells. Whether the transcript of interest would be found as not differentially expressed (=) or upregulated (<) in the polyploid under each normalization is indicated (downregulated not included). DE: differential expression.

Visger, C. J., G. K.-S. Wong, Y. Zhang, P. S. Soltis, and D. E. Soltis. 2019. Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass. American Journal of Botany [View on publisher’s site]

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A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways.

February 13th, 2019
By Gitzendanner, Matt

Zhao, D., J. P. Hamilton, W. W. Bhat, S. R. Johnson, G. T. Godden, T. J. Kinser, B. Boachon, N. Dudareva, D. E. Soltis, P. S. Soltis, B. Hamberger, and C. R. Buell. 2019. A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways. Gigascience, doi: 10.1093/gigascience/giz005.

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Plastid phylogenomic insights into the evolution of Caryophyllales

February 12th, 2019
By Gitzendanner, Matt

Graphical abstract of Gang et al 2019.Yao, G., J.-J. Jin, H.-T. Li, J.-B. Yang, V. Shiva Mandala, M. Croley, R. Mostow, N. A. Douglas, M. W. Chase, M. J. M. Christenhusz, D. E. Soltis, P. S. Soltis, S. A. Smith, S. F. Brockington, M. J. Moore, T.-S. Yi, and D.-Z. Li. 2019. Plastid phylogenomic insights into the evolution of Caryophyllales. Molecular Phylogenetics and Evolution, doi: 10.1016/j.ympev.2018.12.023.

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Nuclear genomes of two magnoliids

January 10th, 2019
By Gitzendanner, Matt

Soltis, D. E., and P. S. Soltis. 2019. Nuclear genomes of two magnoliids. Nature Plants 5:6. [View on Publisher’s site]

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Biodiversity synthesis across the green branches of the tree of life.

January 10th, 2019
By Gitzendanner, Matt

Figure 1 from paper

Global resources can be spatially, taxonomically or temporally subset to serve focused needs, as shown. The top rows in the inset show needed data resources, and the bottom row shows synthetic products, such as regional assessments of evolutionary diversity that inform about community processes and conservation priorities.

Allen, J. M., R. A. Folk, P. S. Soltis, D. E. Soltis, and R. P. Guralnick. 2019. Biodiversity synthesis across the green branches of the tree of life. Nature Plants 5:11. [View on Publisher’s site]

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The Great Tree of Life

December 19th, 2018
By Gitzendanner, Matt

Cover image of The Great Tree of Life bookSoltis, D., and P. Soltis. 2018. The Great Tree of Life. Academic Press.

 

The Great Tree of Life is a concise, approachable treatment that surveys the concept of the Tree of Life, including chapters on its historical introduction and cultural connection. The Tree of Life is a metaphor used to describe the relationships between organisms, both living and extinct. It has been widely recognized that the relationship between the roughly 10 million species on earth drives the ecological system. This work covers options on how to build the tree, demonstrating its utility in drug discovery, curing disease, crop improvement, conservation biology and ecology, along with tactics on how to respond to the challenges of climate change.

This book is a key aid on the improvement of our understanding of the relationships between species, the increasing and essential awareness of biodiversity, and the power of employing modern biology to build the tree of life.

  • Provides a single reference describing the properties, history and utility of The Tree of Life
  • Introduces phylogenetics and its applications in an approachable manner
  • Written by experts on the Tree of Life
  • Includes an online companion site containing various original videos to enhance the reader’s understanding and experience

Spatial phylogenetics of Florida vascular plants: The effects of calibration and uncertainty on diversity estimates

December 19th, 2018
By Gitzendanner, Matt

Graphical abstract of Allen et al 2018

Graphical Abstract

Allen, J. M., C. C. Germain-Aubrey, N. Barve, K. M. Neubig, L. C. Majure, S. W. Laffan, B. D. Mishler, H. L. Owens, S. A. Smith, W. M. Whitten, J. R. Abbott, D. E. Soltis, R. Guralnick, and P. S. Soltis. 2018. Spatial phylogenetics of Florida vascular plants: The effects of calibration and uncertainty on diversity estimates. iScience, doi: 10.1016/j.isci.2018.12.002.

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Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China

December 19th, 2018
By Gitzendanner, Matt

Yang, T., L. Tedersoo, P. S. Soltis, D. E. Soltis, J. A. Gilbert, M. Sun, Y. Shi, H. Wang, Y. Li, J. Zhang, Z. Chen, H. Lin, Y. Zhao, C. Fu, and H. Chu. 2018. Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China. The ISME Journal. [View on publisher’s site]

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