Skip to main content
Log in

Exposing hidden diversity by concordant genealogies and morphology—a study of the Lactifluus volemus (Russulales) species complex in Sikkim Himalaya (India)

  • Published:
Fungal Diversity Aims and scope Submit manuscript

Abstract

Although Sikkim belongs to one of the Global Biodiversity Hotspots, little is known about its ectomycorrhizal fungi, and even less about the main genera of Russulales, i.e. Lactarius, Lactifluus, Multifurca and Russula. Combining a multilocus genealogical and morphological study, we aimed to document the diversity within Lactifluus volemus sensu lato of Sikkim Himalaya. We compared nuclear ITS and LSU rDNA, nuclear rpb1 and rpb2 protein-coding, and mitochondrial atp6 protein-coding genealogies to determine species boundaries. Interspecific relationships were inferred from the combined dataset. Bayesian and maximum likelihood single-locus genealogies are concordant and support recognition of six species. Three of these could be identified by unique morphological characteristics and are described as new species: L. dissitus, L. leptomerus and L. versiformis.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10

Similar content being viewed by others

References

  • Acharya K, Rai M, Pradhan P (2010) Agaricales of Sikkim Himalaya: a review. Researcher 2(5):29–38

    Google Scholar 

  • Avise JC, Ball RM (1990) Principles of genealogical concordance in species concepts and biological taxonomy. In: Futuyama D, Antonovics J (eds) Evolutionary biology. Oxford University Press, New York, pp 45–67

    Google Scholar 

  • Barton NH (2011) What role does natural selection play in speciation. Philos Trans R Soc B 365:1825–1840

    Article  Google Scholar 

  • Baum D, Shaw KL (1995) Genealogical perspectives on the species problem. In: Hoch PC, Stephenson AG (eds) Experimental and molecular approaches to plant biosystematics. Missouri Botanical Garden, St. Louis, pp 289–303

    Google Scholar 

  • Beiko RG, Keith JM, Harlow TJ, Ragan MA (2006) Searching for convergence in phylogenetic Markov chain Monte Carlo. Syst Biol 55(4):553–565

    Article  PubMed  Google Scholar 

  • Berkeley MJ (1852) Decades of fungi, decades XXXIX., XL. Sikkim and Khassya Fungi. In Hooker’s Journal of Botany 4:130–142

  • Bhupathy S, Chettri B, Bauer AM (2009) Rediscovery and revalidation of Takydromus sikkimensis (Günther, 1888) (Squamata: Lacertidae) from Sikkim, India. J Herpetol 43(2):267–274

    Article  Google Scholar 

  • Blackwell M (2011) The fungi: 1, 2, 3 … 5.1 million species? Am J Bot 98(3):426–438

    Article  PubMed  Google Scholar 

  • Buyck B, Hofstetter V, Eberhardt U, Verbeken A, Kauff F (2008) Walking the thin line between Russula and Lactarius: the dilemma of Russula subsect. Ochricompactae. Fungal Diversity 28:15–40

    Google Scholar 

  • Buyck B, Hofstetter V, Verbeken A, Walleyn R (2010) Proposal to conserve Lactarius nom. cons. (Basidiomycota) with a conserved type. Taxon 59(1):295–296

    Google Scholar 

  • Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552

    Article  PubMed  CAS  Google Scholar 

  • Chettri N (2010) Cross-taxon congruence in a trekking corridor of Sikkim Himalayas: surrogate analysis for conservation planning. J Nat Conserv 18:75–88

    Article  Google Scholar 

  • Das K (2010) Russulaceae of Kumaon Himalaya: an overview. In: Mukerji KG, Manoharachary CIK (eds) Taxonomy and ecology of Indian Fungi. International Publishing House Pvt. Ltd, New Delhi, pp 171–186

    Google Scholar 

  • Das K, Van de Putte K, Buyck B (2010) New or interesting Russula from Sikkim Himalaya (India). Cryptogam Mycol 31(4):373–387

    Google Scholar 

  • Dentinger BTM, Ammirati JF, Both EE, Desjardin DE, Halling RE, Henkel TW, Moreau P-A, Nagasawa E, Soytong K, Taylor AF, Watling R, Moncalvo J-M, McLaughlin DJ (2010) Molecular phylogenetics of porcini mushrooms (Boletus section Boletus). Mol Phylogenet Evol 57:1276–1292

    Article  PubMed  CAS  Google Scholar 

  • De Ruiter PC, Neutel A-M, Moore J (2005) The balance between productivity and food web structure in soil ecosystems. In: Bardgett RD, Usher MB, Hopkins DW (eds) Biological diversity and Function in Soils, pp 139–153. Cambridge University Press. British Ecological Society

  • Dettman JR, Jacobson DJ, Taylor JW (2003) A multilocus genealogical approach to phylogenetic species recognition in the model Eukaryote Neurospora. Evolution 57(12):2703–2720

    PubMed  Google Scholar 

  • Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214

    Article  PubMed  Google Scholar 

  • Fries EM (1821) Systema mycologicum 1:69. Uppsala. Sweden

  • Frøslev TG, Matheny PB, Hibbett DS (2005) Lower level relationships in the mushroom genus Cortinarius (Basidiomycota, Agaricales): a comparison of RPB1, RPB2, and ITS phylogenies. Mol Phylogenet Evol 37:602–618

    Article  PubMed  Google Scholar 

  • Garnica S, Weiss M, Oertel B, Ammirati J, Oberwinkler F (2009) Phylogenetic relationships in Cortinarius, section Calochroi, inferred from nuclear DNA sequences. BMC Evol Biol 9:1

    Article  PubMed  Google Scholar 

  • Gazis R, Rehner S, Chaverri P (2011) Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences. Mol Ecol 20:3001–3013

    Article  PubMed  Google Scholar 

  • Giachini AJ, Hosaka K, Nouhra E, Spatafora J, Trappe JM (2010) Phylogenetic relationships of the Gomphales based on nuc-25S-rDNA, mit-12S-rDNA, and mit-atp6-DNA combined sequences. Fungal Biol 114(2–3):224–234

    Article  PubMed  CAS  Google Scholar 

  • Gianinazzi S, Gollotte A, Binet M-N, van Tuinen D, Redecker D, Wipf D (2010) Agroecology: the key role of arbuscular mycorrhizas in ecosystem services. Mycorrhiza 20:519–530

    Article  PubMed  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp 41:95–98

    CAS  Google Scholar 

  • Halling RE, Osmundson TW, Neves M-A (2008) Pacific boletes: implications for biogeographic relationships. Mycol Res 112:437–447

    Article  PubMed  CAS  Google Scholar 

  • Hesler LR, Smith AH (1979) North American species of Lactarius. Univ. Michigan Press, Ann Arbor

    Google Scholar 

  • Kardol P, Wardle DA (2010) How understanding aboveground-belowground linkages can assist restoration ecology. Trends Ecol Evol 25(11):670–679

    Article  PubMed  Google Scholar 

  • Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9(4):286–298

    Article  PubMed  CAS  Google Scholar 

  • Kauserud H, Stensrud O, Decock C, Shalchian-Tabrizi K, Schumacher T (2006) Multiple gene genealogies and AFLPs suggest cryptic speciation and long-distance dispersal in the basidiomycete Serpula himantioides (Boletales). Mol Ecol 15(2):421–431

    Article  PubMed  CAS  Google Scholar 

  • Knowlton N (1993) Sibling species in the sea. Annu Rev Ecol Syst 24:189–216

    Article  Google Scholar 

  • Kornerup A, Wanscher JH (1978) Methuen handbook of colour, 3rd edn. Methuen, London

    Google Scholar 

  • Kretzer AM, Bruns TD (1999) Use of atp6 in fungal phylogenetics: an example from the Boletales. Mol Phylogenet Evol 13(3):483–492

    Article  PubMed  CAS  Google Scholar 

  • Le HT (2007) Biodiversity of the genus Lactarius (Basidiomycota) in northern Thailand. PhD dissertation. Chiang Mai University

  • Le HT, Nuytinck J, Verbeken A, Lumyong S, Desjardin DE (2007) Lactarius in Northern Thailand: 1. Lactarius subgenus Piperites. Fungal Divers 102:281–291

    Google Scholar 

  • Leake JR, Johnson D, Donnelly DP, Boddy L, Read DJ (2005) Is diversity of mycorrhizal fungi important for ecosystem functioning? In: Bardgett RD, Usher MB, Hopkins DW (eds) Biological diversity and function in soils, pp 216–235. Cambridge University Press. British Ecological Society

  • Lemmon AR, Moriarty EC (2004) The importance of proper model assumptions in Bayesian phylogenetics. Syst Biol 53:265–277

    Article  PubMed  Google Scholar 

  • Loreau M, Naeem S, Inchausti P, Bengtsson J, Grime JP, Hector A, Hooper DU, Huston MA, Raffaelli D, Schmid B, Tilman D, Wardle DA (2001) Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294(5543):804–808

    Article  PubMed  CAS  Google Scholar 

  • Maron JL, Marler M, Klironomos JN, Cleveland CC (2011) Soil fungal pathogens and the relationship between plant diversity and productivity. Ecol Lett 14:36–41

    Article  PubMed  Google Scholar 

  • Matheny PB (2005) Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales). Mol Phylogenet Evol 35:1–20

    Article  PubMed  CAS  Google Scholar 

  • Matheny PB, Liu YJ, Ammirati JF, Hall BD (2002) Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). Am J Bot 89(4):688–698

    Article  PubMed  CAS  Google Scholar 

  • Mittermeier RA, Gil PR, Hoffman M, Pilgrim J, Brooks T, Mittermeier CG, Lamoreaux J, Da-Fonseca GAB (2005) Hotspots revisited. Earth’s biologically richest and most endangered terrestrial ecoregions. Conservation International, Arlington

    Google Scholar 

  • Montoya L, Bandala VM, Guzmán G (1996) New and interesting species of Lactarius from Mexico including scanning electron microscope observations. Mycotaxon 57:411–424

    Google Scholar 

  • Nuytinck J, Verbeken A (2005) Morphology and taxonomy of the European species in Lactarius sect. Deliciosi (Russulales). Mycotaxon 92:125–168

    Google Scholar 

  • Nylander JAA (2004) MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University

  • Pringle A, Baker DM, Platt JL, Wares JP, Latgé JP, Taylor JW (2005) Cryptic speciation in the cosmopolitan and clonal human pathogenic fungus Aspergillus fumigatus. Evolution 59(9):1886–1899

    PubMed  CAS  Google Scholar 

  • Robinson CH, Pryce Miller EJ, Deacon LJ (2005) Biodiversity of saprotrophic fungi in relation to their function: do fungi obey the rules? In: Bardgett RD, Usher MB, Hopkins DW (eds) Biological diversity and function in soils, pp 189–215. Cambridge University Press. British Ecological Society

  • Robison MM, Chiang B, Horgen PA (2001) A phylogeny of the genus Agaricus based on mitochondrial atp6 sequences. Mycologia 93:30–37

    Article  CAS  Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  PubMed  CAS  Google Scholar 

  • Shimono Y, Hiroi M, Iwase K, Takamatsu S (2007) Molecular phylogeny of Lactarius volemus and its allies inferred from the nucleotide sequences of nuclear large subunit rDNA. Mycoscience 48:152–159

    Article  CAS  Google Scholar 

  • Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690

    Article  PubMed  CAS  Google Scholar 

  • Stubbe D, Nuytinck J, Verbeken A (2010) Critical assessment of the Lactarius gerardii species complex (Russulales). Fungal Biol 114:271–283

    Article  PubMed  CAS  Google Scholar 

  • Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:31–32

    Article  Google Scholar 

  • Van de Putte K, Nuytinck J, Stubbe D, Le HT, Verbeken A (2010) Lactarius volemus sensu lato (Russulales) from northern Thailand: morphological and phylogenetic species concepts explored. Fungal Divers 45:99–130

    Article  Google Scholar 

  • van der Heijden MGA, Horton TR (2009) Socialism in soil? The importance of mycorrhizal fungal networks for facilitation in natural ecosystems. J Ecol 97:1139–1150

    Article  Google Scholar 

  • Vellinga EC (1988) Glossary. In: Bas C, Kuyper TW, Noordeloos ME, Vellinga EC (eds) Flora Agaricina Neerlandica vol 1. AA Balkema, Rotterdam, pp 54–64

    Google Scholar 

  • Verbeken A (1998) Studies in tropical African Lactarius species. 5. A synopsis of the subgenus Lactifluus (Burl.) Hesler and A.H. Sm. Emend. Mycotaxon 66:363–386

    Google Scholar 

  • Verbruggen H, De Clerck O, Kooistra W, Coppejans E (2005) Molecular and morphometric data pinpoint species boundaries in Halimeda section Rhipsalis (Bryopsidales, Chlorophyta). J Phycol 41:606–621

    Article  CAS  Google Scholar 

  • Wang XH (2007) Type studies of Lactarius species published from China. Mycologia 99(2):253–268

    Article  PubMed  Google Scholar 

  • Xia X, Xie Z (2001) DAMBE: data analysis in molecular biology and evolution. J Hered 92:371–373

    Article  PubMed  CAS  Google Scholar 

  • Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. PNAS 107(20):9264–9269

    Article  PubMed  CAS  Google Scholar 

  • Zamin TJ, Baillie JEM, Miller RM, Rodriguez JP, Ardid A, Collen B (2010) National red listing beyond the 2010 target. Conserv Biol 24(4):1012–1020

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

The first author is supported by the “Bijzonder Onderzoeksfonds Ghent University” (BOF). The survey in Sikkim Himalaya was financially supported by the Research Foundation Flanders (FWO). We would like to express our gratitude to all who helped during the fieldwork: Sundar K. Rai, Pema Bhutia and his family. Help rendered by the Forest Department of Sikkim is also duly acknowledged. We would like to thank Heroen Verbruggen for providing the script for calculating MrBayes burn-in values and convergence times and the comments on the MrBayes analyses. Kenneth Bauters, Heroen Verbruggen and the UGent Helpdesk DICT are thanked for their help with the use of the High Performance Computer. The National Botanical Garden of Belgium is thanked for the use of the scanning electron microscope and in particular Myriam de Haan for taking the photographs. We also wish to thank two anonymous reviewers for their comments on the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Kobeke Van de Putte.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 2568 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Van de Putte, K., Nuytinck, J., Das, K. et al. Exposing hidden diversity by concordant genealogies and morphology—a study of the Lactifluus volemus (Russulales) species complex in Sikkim Himalaya (India). Fungal Diversity 55, 171–194 (2012). https://doi.org/10.1007/s13225-012-0162-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13225-012-0162-0

Keywords

Navigation