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Biodiversity and Conservation

, Volume 21, Issue 9, pp 2269–2285 | Cite as

A clustering optimization strategy to estimate species richness of Sebacinales in the tropical Andes based on molecular sequences from distinct DNA regions

  • Sabrina D. Setaro
  • Sigisfredo Garnica
  • Paulo I. Herrera
  • Juan Pablo Suárez
  • Markus Göker
Original Paper

Abstract

Fungi are believed to be diverse in the tropics, but because many groups are only known from their DNA sequences this hampers comparative diversity studies. We investigated mycorrhizal Sebacinales (Basidiomycota) of 67 individuals of Ericaceae and Orchidaceae in a tropical mountain ecosystem in Southern Ecuador to provide a first estimate of whether these fungi are particularly diverse in the Northern Andes. We partially sequenced the internal transcribed spacer (ITS) and large subunit (LSU) regions of the nuclear ribosomal DNA and analyzed them together with all Sebacinales sequences available from GenBank. The clustering optimization technique was used to determine clustering parameters that maximize the comparability between molecular operational taxonomic units (MOTUs) obtained from the distinct loci. Sampling effort and species richness were estimated with rarefaction-accumulation curves and non-parametric estimation using Chao2 and compared between Southern Ecuador and France. Clustering optimization indicated that a 1% LSU distance threshold corresponds to the commonly used 3% dissimilarity threshold for ITS, and that a clustering algorithm close to single-linkage clustering is optimal. The resulting clusters show that about 8–9% of observed Sebacinales MOTUs occur in the study area and that most of these MOTUs are endemic (74%). The widespread MOTUs from Southern Ecuador were also found in Panama, North America and Europe. The estimation of species richness revealed unsaturated sampling of Sebacinales in general and also in our study area. Our results suggest a high diversity of Sebacinales associated with Ericaceae and Orchidaceae at the study site in Southern Ecuador, but no hotspot of Sebacinales in comparison with other areas.

Keywords

Biodiversity Ericaceae ITS LSU Molecular diversity Mycorrhizal fungi Orchids Ribosomal DNA Species richness Tropical mountain rain forest 

Abbreviations

BLAST

Basic local alignment search tool

F

Linkage fraction

ITS

Internal transcribed spacer

LSU

Large subunit (beginning of LSU to primer region LR3)

nrDNA

Nuclear ribosomal DNA

MOTU

Molecular operational taxonomic unit

MRI

Modified Rand index

NCBI

National Center for Biotechnology Information

PCR

Polymerase chain reaction

RBSF+S

Reserva Biológica San Francisco and surroundings

SSU

Small subunit

T

Threshold (distance)

Notes

Acknowledgments

We thank Jim Luteyn and Paola Pedraza for help with species identification of Neotropical Ericaceae and Michael Weiß for kindly providing Sebacinales-specific primers. We also express our gratitude to Ingrid Kottke for valuable comments and Tanja Schuster for critically revising earlier versions of this manuscript. We thank Jörg Bendix, Rüttger Rollenbeck and Christoph Reudenbach for providing a map of Ecuador. In addition, the support and assistance of the UTPL in Loja, Ecuador and members of the research group FOR 816 are highly appreciated. This project was funded by the DFG as part of the research unit FOR 816.

Supplementary material

10531_2011_205_MOESM1_ESM.tif (404 kb)
Fig. S1: Plot of modified Rand indices (MRI) observed during cluster optimization with a linkage fraction of 0.1 (TIFF 404 kb)
10531_2011_205_MOESM2_ESM.xls (340 kb)
Table S1: General information about sequences from all three data sets (XLS 341 kb)
10531_2011_205_MOESM3_ESM.xls (24 kb)
Table S2: Numbers of molecular operational taxonomic units (MOTUs) of Sebacinales obtained with distinct clustering approaches (XLS 24 kb)

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Sabrina D. Setaro
    • 1
  • Sigisfredo Garnica
    • 2
  • Paulo I. Herrera
    • 3
  • Juan Pablo Suárez
    • 3
  • Markus Göker
    • 4
  1. 1.Department of BiologyWake Forest UniversityWinston-SalemUSA
  2. 2.Institut für Evolution und Ökologie, Organismische BotanikUniversität TübingenTübingenGermany
  3. 3.Centro de Biología Celular y MolecularUniversidad Técnica Particular de LojaLojaEcuador
  4. 4.DSMZ—German Collection of Microorganisms and Cell CulturesBraunschweigGermany

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