Phylogenetic overview of the Boletineae
Introduction
The suborder Boletineae (originally considered Agaricales) as a taxonomic rank was first used by Gilbert (1931), and included both poroid and gilled species. This was a step forward in bolete taxonomy, the first time gilled species were included in a concept of a ‘bolete’. Since then, the generic and species concepts in the Boletineae have been dominated by those proposed by Singer (1986), which follows the inclusion of gilled species proposed by Gilbert (1931) and Smith & Thiers (1971). The broad outlines of the ‘modern’ Boletineae, based on multi-locus phylogenetic analyses, were presented by Binder & Hibbett (2006). The generic-level classifications of Smith & Thiers (1971) and Singer (1986) along with current genera of Boletineae are presented in Table 1. The systems of Smith & Thiers (1971) and Singer (1986) mainly used morphological characters and chemical staining reactions, e.g. the colours produced by placing KOH on the pileipellis, to define genera. Singer (1986) also incorporated the results of chemotaxonomic studies, which identified pigments responsible for colouration and staining reactions. Chemotaxonomic data (Besl et al. 1974, 1986; Besl & Bresinsky 1977, 1979, 1997; Steglich et al. 1977; Bresinsky & Besl 1978) were not available at the time of Smith and Thiers's (1971) work.
Morphological characters used to delimit genera and species in Boletineae include, but are not limited to: stipe ornamentation, pileipellis and stipitipellis structures, pore surface colour, pore depth, pore mouth diameter, staining reactions of bruised tissues, and staining reactions of different tissues (such as pileus context, stipe context, pileipellis, stipitipellis) to chemicals, typically KOH, 5 % ammonia solution, and FeSO4. An overview of the presence, absence, and states of key morphological characters of the genera of Boletineae is presented in Table 2. Chemical analysis of pigment production in the boletes has also been used as a taxonomic character and allowed the placement of species not previously thought to be closely related to the boletes, e.g. Chamonixia (Boletineae) and Coniophora (Coniophorineae), and further strengthened the separation of Suillus (Suillineae) from Boletus (Steglich et al. 1977; Besl et al. 1986; Besl & Bresinsky 1997).
Smith & Thiers (1971) placed only poroid fungi in the Boletaceae and included members of the modern Suillineae and Sclerodermatineae (Besl & Bresinsky 1997; Jarosch 2001; Binder & Bresinsky 2002a). The modern members of the Boletineae (Table 1) that are gilled, Paxillus and Phylloporus, were placed in the Paxillaceae (Smith & Thiers 1971). Singer's (1986) concept of the Boletineae is almost identical to the modern Boletales (Singer 1986; Binder & Hibbett 2006). The modern Boletineae members are distributed in the Paxillaceae and Boletaceae in Singer's (1986) classification. However, only one genus of Singer's Paxillaceae, Paxillus s.str. (not including Tapinella or Austropaxillus [Tapinellineae]), is included in the modern Boletineae (Binder & Hibbett 2006).
Smith and Thiers were more conservative than Singer when considering whether differences between morphological features warranted a separate genus (Smith & Thiers 1971; Singer 1986). This led Smith and Thiers to ‘lump’ species into larger genera than those recognized by Singer, except for the genus Leccinum (Smith & Thiers 1971; Singer 1986). Overall, Singer recognized 22 genera (not including families that have no modern representatives) of Boletineae and Smith and Thiers recognized 12 genera (including genera in the modern Boletineae that Smith and Thiers placed outside the Boletaceae), including Suillus (Table 1). However, Smith and Thiers placed Paragyrodon as a section of Suillus and stated that Gyrodon lividus was most closely related to Suillus; in fact, both Paragyrodon and G. lividus are members of the modern Boletineae (Paxillineae in Binder & Hibbett 2006) (see Table 1; Smith & Thiers 1971; Singer 1986; Binder & Hibbett 2006).
Some aspects of generic limits and inter-generic relationships in Boletineae have remained unclear. This is due, in part, to alternative interpretations of relatedness based on morphology (as well as lack of resolution in molecular studies). An example is provided by Boletus, which Smith and Thiers regarded as ‘the most distinctive genus in the family’. However, Smith and Thiers's concept of Boletus encompasses multiple genera recognized by Singer, e.g. Aureoboletus, Xerocomus, Xanthoconium (Smith & Thiers 1971; Singer 1986).
Analyses of chemical characters (pigments and colourless compounds that are produced via secondary metabolisms) have been useful for separating large groups, or genera, but overall have been unable to resolve intergeneric relationships among the Boletineae (Besl & Bresinsky 1977, 1979, 1997; Besl et al. 1986; Besl et al. 1974; Binder & Hibbett 2006; Bresinsky & Besl 1978; Steglich et al. 1977). Analyses of DNA sequences have also been informative, but the molecular studies of the last 15 y have failed to resolve generic relationships in the Boletineae and have often focused on only one or a few genera at a time (Binder & Bresinsky 2002b; Binder & Hibbett 2002; Desjardin et al. 2008, 2009; Dentinger et al. 2010; Vizzini et al. 2010; Lebel et al. 2011; Halling et al. 2012a). As more taxa have been sampled in molecular studies, it has become clear that some morphology-based generic concepts do not correspond to monophyletic groups, especially in the larger genera, such as Boletellus, Boletus, Tylopilus, Xerocomellus, and Xerocomus, but there has been no comprehensive phylogenetic analysis of all the genera of Boletineae. Instead, many studies have focused on finding limits of individual genera or placing species into genera (Binder & Besl 2000; Binder & Bresinsky 2002b; Desjardin et al. 2008, 2009, 2011; Dentinger et al. 2010; Li et al. 2011; Halling et al. 2012a, b; Hosen et al. 2012).
Most previous molecular studies used the nuclear large subunit (nuc-lsu), which has been shown to have little resolving power in the Boletineae when used in isolation (Binder & Hibbett 2006). Continued use of nuc-lsu maintains compatibility between studies and allows placement of species into genera or cryptic forms into a family (e.g. truffle-like species), but additional loci are needed to resolve higher-level relationships in Boletineae (Binder & Besl 2000; Binder & Bresinsky 2002b; Peintner et al. 2003; Binder & Hibbett 2006; Desjardin et al. 2008, 2009; Drehmel et al. 2008; Binder et al. 2010; Dentinger et al. 2010; Vizzini et al. 2010; Lebel et al. 2011; Li et al. 2011; Halling et al. 2012a, b). Here, we present a broad phylogenetic analysis of all the major genera of the Boletineae, using three genes: nuclear large subunit ribosomal RNA (nuc-lsu), translation elongation factor 1-alpha (tef1), and DNA directed RNA polymerase II largest subunit (RPB1). Tef1 and RPB1 were chosen based on the potential they have been shown to have to resolve genera in the Boletineae in previous studies (Binder et al. 2010; Dentinger et al. 2010; Li et al. 2011; Halling et al. 2012a, b; Hosen et al. 2012). The goal of the present study was to develop a phylogenetic framework to guide further exemplar-based sampling and an eventual generic-level reclassification of the Boletineae.
Section snippets
Materials and methods
Taxon sampling—A taxon sampling scheme was designed based on a preliminary analysis of 457 nuc-lsu sequences representing 40 genera and 247 species (Binder & Hibbett 2006), including 42 unnamed species. The nuc-lsu sequences were aligned manually using the PAUP editor and analyzed in the RAxML Blackbox server using the default settings with maximum likelihood (ML) optimization (http://phylobench.vital-it.ch/raxml-bb/; Stamatakis et al. 2008; Swofford 2002). Based on the resulting phylogenetic
DNA extractions, PCR and sequencing
Tef1, RPB1, and nuc-lsu had 68 %, 42 %, and 100 % success rate for sequencing respectively. The low success rate for RPB1 amplification is probably due to primer mismatches.
Alignment and phylogenetic analysis
See Table 3 for technical output of the nuc-lsu, tef1, and RPB1 ML core and extended analyses, the core and extended MP analyses, and the constrained analysis. Following single-gene analyses to assess conflict, the core nuc-lsu, tef1, and RPB1 alignments were merged, as were the extended nuc-lsu, tef1, and RPB1 datasets. The
Taxonomy
Boletus separans Peck, Bull. Buffalo Soc. Nat. Sci. 1: 59.(1873).
Synonyms: Boletus edulis spp. separans (Peck) Singer, Amer. Midl. Nat. 37: 26 (1947).
B. edulis f. separans (Peck) Vassilkov, BekyiGrib: 15 (1966).
Xanthoconium separans (Peck) Halling & Both, Bull. Buffalo Soc, Nat. Sci. 36: 240 (1998).
TYPE: New York. Greenbush, August 1872, C.H. Peck (NYS).
MycoBank #: 226550.
Boletus subalpinus (Trappe & Thiers) M. Nuhn, Manfr. Binder, A. F. S. Taylor, Halling, Hibbett, comb. nov.
Basionym:
Overview of phylogenetic relationships in Boletineae
In both the three-gene core and extended datasets, the Boletineae and Boletaceae are upheld with maximum supported values in all analyses (BS = 100 %, MP = 100 %, PP = 1.0, reported as [BS/MP/PP] hereafter), but the backbone of the Boletaceae remains poorly resolved. Nonetheless, there are eleven strongly support, named clades shared in both the three-gene core and extended, and an additional seven supported, named clades in the three-gene extended (see Figs 1 and 2 for clades; clades 1–11 are
Conclusions
The analyses presented here identify clades containing the type species for the following genera: Aureoboletus, Boletus, Chalciporus, Hemileccinum, Leccinellum, Leccinum, Paxillus, Royoungia, Strobilomyces, Tylopilus, Xerocomellus, and Xerocomus. The type species of Buchwaldoboletus, Gyrodon, Notholepiota, Phylloporus, Paragyrodon, Pseudoboletus, Spongiforma, and Xanthoconium have also been sampled. Three new, strongly supported lineages within the Boletineae were recovered: the anaxoboletus,
Acknowledgements
This work has been supported by grants from the National Science Foundation, including award DEB-1020421 to REH, DSH and MB. We thank the many collaborators who provided specimens and DNA, including Ernst Both and PB Matheny who provided gDNA for Boletus semigastroideus. We would like to thank Duccio Migliorini for preparing the interactions between Buchwaldoboletus lignicola and Phaeolus schweinitzii. Alfredo Justo provided helpful comments on the manuscript. We thank the two anonymous
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These authors contributed equally to the work.