New Hot Paper Comment by Timothy Y. James, and Rytas Vilgalys

Timothy Y. James, and Rytas Vilgalys answer a few questions about this month's new hot paper in the field of Plant & Animal Science.

From •>>November 2007

Field: Plant & Animal Science
Article Title: Reconstructing the early evolution of Fungi using a six-gene phylogeny
Authors: James, TY;Kauff, F;Schoch, CL;Matheny, PB;Hofstetter, V;Cox, CJ;Celio, G;Gueidan, C;Fraker, E;Miadlikowska, J;Lumbsch, HT;Rauhut, A;Reeb, V;Arnold, AE;Amtoft, A;Stajich, JE;Hosaka, K;Sung, GH;Johnson, D;O'Rourke, B;Crockett, M;Binder, M;Curtis, JM;Slot, JC;Wang, Z;Wilson, AW;Schussler, A;Longcore, JE;O'Donnell, K;Mozley-Standridge, S;Porter, D;Letcher, PM;Powell, MJ;Taylor, JW;White, MM;Griffith, GW;Davies, DR;Humber, RA;Morton, JB;Sugiyama, J;Rossman, AY;Rogers, JD;Pfister, DH;Hewitt, D;Hansen, K;Hambleton, S;Shoemaker, RA;Kohlmeyer, J;Volkmann-Kohlmeyer, B;Spotts, RA;Serdani, M;Crous, PW;Hughes, KW;Matsuura, K;Langer, E;Langer, G;Untereiner, WA;Lucking, R;Budel, B;Geiser, DM;Aptroot, A;Diederich, P;Schmitt, I;Schultz, M;Yahr, R;Hibbett, DS;Lutzoni, F;McLaughlin, DJ;Spatafora, JW;Vilgalys, R
Journal: NATURE
Volume: 443
Issue: 7113
Page: 818-822
Year: OCT 19 2006
* Duke Univ, Dept Biol, Durham, NC 27708 USA.
* Duke Univ, Dept Biol, Durham, NC 27708 USA.
* Oregon State Univ, Dept Bot & Plant Pathol, Corvallis, OR 97331 USA.
* Clark Univ, Dept Biol, Worcester, MA 01610 USA.
* Univ Minnesota, Dept Plant Biol, St Paul, MN 55108 USA.
* Field Museum Nat Hist, Chicago, IL 60605 USA.
* Fachbereich Biol, Abt Pflanzenokol & Systemat, D-67653 Kaiserslautern, Germany.
* New York Bot Garden, Inst Systemat Bot, Bronx, NY 10458 USA.
* Duke Univ, Univ Program Genet & Genom, Durham, NC 27708 USA.
* TH Darmstadt, Inst Bot, D-64287 Darmstadt, Germany.
* Univ Maine, Dept Biol Sci, Orono, ME 04469 USA.
* USDA ARS, Natl Ctr Agr Utilizat Res, Peoria, IL 61604 USA.
* Univ Georgia, Dept Plant Biol, Athens, GA 30605 USA.
* Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA.
* Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA.
* Univ Kansas, Dept Ecol & Evolutionary Biol, Lawrence, KS 66045 USA.
* Univ Wales, Inst Biol Sci, Aberystwyth SY23 3DA, Dyfed, Wales.
* Inst Grassland & Environm Res, Aberystwyth SY23 3EB, Dyfed, Wales.
* ARS, US Plant Soil & Nutr Lab, USDA, Plant Protect Res Unit, Ithaca, NY 14853 USA.
* W Virginia Univ, Div Plant & Soil Sci, Morgantown, WV 26506 USA.
* TechnoSuruga, Chiyoda Ku, Tokyo 1010052, Japan.
* ARS, Systemat Bot & Mycol Lab, USDA, Beltsville, MD 20705 USA.
* Washington State Univ, Dept Plant Pathol, Pullman, WA 99164 USA.
* Harvard Univ Hebaria, Cambridge, MA 02138 USA.
* Agr & Agri Food Canada, Biodivers Mycol & Bot, Ottawa, ON K1A 0C6, Canada.
* Univ N Carolina, Inst Marine Sci, Morehead City, NC 28557 USA.
* Oregon State Univ, Mid Columbia Agr Res & Extens Ctr, Hood River, OR 97031 USA.
* Cent Bur Schimmelcultures, Fungal Biodivers Ctr, NL-3508 AD Utrecht, Netherlands.
* Univ Tennessee, Dept Bot, Knoxville, TN 37996 USA.
* Okayama Univ, Fac Agr, Okayama 7008530, Japan.
* Univ Kassel, Inst Biol, D-34132 Kassel, Germany.
* Brandon Univ, Dept Bot, Brandon, MB R7A 6A9, Canada.
* Penn State Univ, Dept Plant Pathol, University Pk, PA 16802 USA.
* Adviesbur Bryol Lichenol, NL-3762 XK Soest, Netherlands.
* Museum Natl Hist Nat, L-2160 Luxembourg, Luxembourg.
* Univ Hamburg, Biozentrum Klein Flottbek & Bot Garten, D-22609 Hamburg, Germany.

Why do you think your paper is highly cited?

This paper provides a current phylogenetic hypothesis for the whole fungal kingdom based on a large number of fungal taxa and DNA sequences from multiple gene regions. Research interest in fungi is very high, in part spurred on by the complete genome sequencing of many fungal species. Having a solid phylogenetic framework is critical for comparative biology as well as in understanding the ecology and basic biology of the many novel species that are being discovered.

Does it describe a new discovery, methodology, or synthesis of knowledge?

“This paper provides a current phylogenetic hypothesis for the whole fungal kingdom based on a large number of fungal taxa and DNA sequences from multiple gene regions. Research interest in fungi is very high, in part spurred on by complete genome sequencing of many fungal species.”

The data are the culmination of the effort of a community of fungal systematists towards the goal of "Assembling the Fungal Tree of Life". As phylogenetic relationships of organisms that diverged nearly a billion years ago are very difficult to reconstruct, the fungal tree of life is a work in progress which will require continued effort to resolve difficult branches.

Would you summarize the significance of your paper in layman’s terms?

Our data support the hypothesis that fungi achieved most of their evolutionary success through diversification on dry land. Much of their diversity in form and ecology has been achieved through symbiotic relationships, often parasitic, with plants and animals. It appears that ancient fungi had spores that were aquatically dispersed, but that novel mechanisms of spore discharge have arisen—such as the aerial dispersal seen in mushrooms—as fungi radiated in terrestrial ecosystems.

How did you become involved in this research, and were there any particular problems encountered along the way?

This research spun out of a National Science Foundation research coordination network coined "Deep Hypha." World-leading taxonomic experts from this network and others contributed material for the project. One particular difficulty regarding biodiversity of fungi is that some of the phylogenetically most interesting species cannot be isolated into pure culture, making the obtaining of DNA sequences from such material very difficult.

Where do you see your research leading in the future?

The AFTOL project is continuing, with a slight shift in focus towards resolving the deepest branches in the fungal tree and a utilization of phylogenomic approaches.

Are there any social or political implications for your research?

Fungi play a critical role in natural ecosystems that must not be overlooked. The biodiversity of fungi is immense and we are barely scratching the surface. Much of the genetic diversity lies in species and lineages that we know so little about. Some of these species have only been recorded a single time within the scientific literature.

Timothy Y. James
Postdoctoral Fellow
Institute for Evolution, Genomics, and Systematics
Department of Evolutionary Biology
Uppsala, Sweden

Rytas Vilgalys
Professor
Department of Biology
Duke University
Durham, NC, USA

ESI Special Topics, November 2007
Citing URL - http://www.esi-topics.com/nhp/2007/november-07-James_Vilgalys.html