February 28th, 2014
By Gitzendanner, Matt

The Soltis Lab

Scientists and students in the Soltis Lab are currently working with a variety of technologies to investigate mechanisms of speciation, evolutionary relationships and character evolution in flowering and land plants at all taxonomic levels. Current projects include the study of higher level phylogenetic relationships and character evolution in the angiosperms, floral evolution, the genetic and genomic consequences of polyploidy, conservation genetics of rare plants, phylogeography, and biogeography. Please explore our website for more information on our research.
Soltis_lab

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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Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum

December 19th, 2018
By Gitzendanner, Matt
Wang, Y., W. Jiang, W. Ye, C. Fu, M. A. Gitzendanner, P. S. Soltis, D. E. Soltis, and Y. Qiu. 2018. Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum. BMC Plant Biology 18:208. [View on publisher’s site]

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Terrestrial species adapted to sea dispersal: Differences in propagule dispersal of two Caribbean mangroves

December 19th, 2018
By Gitzendanner, Matt
Hodel, R. G. J., L. L. Knowles, S. F. McDaniel, A. C. Payton, J. F. Dunaway, P. S. Soltis, and D. E. Soltis. 2018. Terrestrial species adapted to sea dispersal: Differences in propagule dispersal of two Caribbean mangroves. Molecular Ecology 27:4612–4626. [View on publisher’s site]

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Research Computing accounts and storage

December 10th, 2018
By Gitzendanner, Matt

Request an Account

Once you have a Gatorlink, you can request an account on the form here: https://www.rc.ufl.edu/access/account-request/

List Pam as your sponsor.

Storage

/ufrc/soltis

  • We currently have 50TB of space
    • We will can add more storage, but /ufrc storage is $140/TB/yr, so not cheap!
  • Each user has their own directory
  • The /ufrc/soltis/share/ folder can be used for sharing, common data, etc.
  • If you have important data that you need regular access to and this should be backed up, keep it in /ufrc/soltis/share/Soltis_Backup/. This is the only location on /ufrc/soltis that is backed up in any way.

/orange/soltis

  • The /orange filesystem is somewhat slower than /ufrc, so not best for active data used in running jobs.
  • We currently have 52TB of space.
  • Each user can create their own directory.
  • This is a great place to archive data you are not actively working on.
  • It is much cheaper than /ufrc–only $25/TB/yr.
  • One copy of all raw sequence data should go in /orange/soltis/SequenceBackup.
    • This folder is backed up nightly.
  • If you have important data that you do not access regularly, you can put it in /orange/soltis/Backup_and_archive

Storage Backup

As noted above, the ONLY places that are backed up in any way are:

  • /ufrc/soltis/share/Soltis_Backup/: Use for important data that you need regular access to and this should be backed up.
  • /orange/soltis/Backup_and_archive/: Use for important data that you do not access regularly.
  • /home: Research Computing does maintain a daily snapshot of your home directory for one week. See this video for accessing your snapshots.
  • /orange/soltis/SequenceBackup: For archiving raw sequence data. Should be set to read only to minimize accidental data changes.
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