Niveoporofomes (Basidiomycota, Fomitopsidaceae) in Tropical Africa: Niveoporofomes oboensis sp. nov. and N.widdringtoniae comb. nov., two species from Afromontane Forests

doi:10.21203/rs.3.rs-927746/v1

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Niveoporofomes (Basidiomycota, Fomitopsidaceae) in Tropical Africa: Niveoporofomes oboensis sp. nov. and N.widdringtoniae comb. nov., two species from Afromontane Forests

https://doi.org/10.21203/rs.3.rs-927746/v1

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During a survey of polypores in the montane forest of the Ôbo de São Tomé National Park, in the western African, equatorial island of São Tomé, a specimen that was, a priori, related to Fomitopsis, based on the gross morphology of the basidiome and a brown rot, showed deviating features including subglobose basidiospores with a large gutta, what pointed toward Niveoporofomes. Phylogenetic inferences based on multiple loci dataset (ITS-nLSU-nSSU-tef1-rpb2) confirmed these affinities, and Niveoporofomes oboensis is described as new. The species is compared to Fomitopsis widdringtoniae, known from southeast Africa, which is characterized also by subglobose basidiospores; hence, the new combination N. widdringtoniae is proposed. The new combination Niveoporofomes globosporus (basionym Trametes globospora) is also proposed based on phylogenetic analyses. A key to the species of Fomitopsis, Niveoporofomes, Rhodofomes, and Rhodofomitopsis in Tropical Africa is presented.

Botany

Afromontane ranges

Basidiomycota

Fomitopsis

polypores

phylogeny

taxonomy

Fomitopsidaceae, typified by Fomitopsis P. Karst., is a family of brown rot polypores, mostly spanning over temperate areas (Han et al. 2016; Justo et al. 2017). The family (also referred to as the Antrodia clade) was revised by Han et al. (2016) and Fomitopsis, as accepted by then (or sensu lato, e.g., Ryvarden and Johansen 1980), was shown to be polyphyletic. Consequently, Fomitopsis species were reclassified into several new or reinstated genera, including Fragifomes, Niveoporofomes, Rhodofomes, Rhodofomitopsis, or still Rubellofomes (Han et al. 2016).

In tropical Africa, Fomitopsis s.l. were represented by seven species (Ryvarden and Johansen 1980; Masuka and Ryvarden 1993; Mossebo and Ryvarden 1997). However, considering the current treatment of Fomitopsidaceae (Han et al. 2016), Rhodofomes and Rhodofomitopsis occur also in Tropical Africa, represented by Rhodofomes carneus (as Fomitopsis carnea (Blume & T. Nees) Imazeki, Ryvarden and Johansen 1980) and Rhodofomitopsis africana (as Fomitopsis africana Mossebo & Ryvarden, Mossebo and Ryvarden 1997).

As part of an ongoing survey of polypores (Basidiomycota) in sub-Saharan Africa (Decock and Mossebo 2001, 2002; Decock 2001, 2007, 2011a, b; Decock and Ryvarden 2002, 2015, 2020; Decock and Masuka 2003; Decock et al. 2005, 2021; Amalfi et al. 2010; Yombiyeni et al. 2011; Decock and Bitew 2012), a specimen from the African, equatorial island of São Tomé, collected at Ôbo de São Tomé National Park, was shown to belong to Niveoporofomes based on morphology and [ITS-nLSU-nSSU-tef1-α-rpb2]-based phylogenetic inferences. It is interpreted as representing a distinct, undescribed species, proposed as Niveoporofomes oboensis. This species is compared to Fomitopsis widdringtoniae Masuka & Ryvarden, known from south-eastern Africa, which has identical basidiospores (Masuka and Ryvarden 1993). A key to the species of Fomitopsis, Niveoporofomes, Rhodofomes, and Rhodofomitopsis in Tropical Africa is presented.

Niveoporofomes has been proposed to host Fomitopsis spraguei, a species that deviates from Fomitopsis pinicola and species of other related genera in having obovoid to broadly ellipsoid basidiospores with a large gutta. The genus was up to now considered monospecific (Han et al. 2016). Analyses of available ITS sequences showed that sensu Han et al. (2016), N. spraguei is not monophyletic, but encompasses several clades that could represent each a distinct species, of which N. globosporus that is proposed as a new combination.

Material and collection localities

The type specimen originated from mid-elevation forest at elev. ~1300 masl at Ôbo de São Tomé National Park in São Tomé, which vegetation is the Afromontane Equatorial rainforest (Carvalho et al. 2004). The type specimen is preserved at O, with isotypes at BR and MUCL (herbarium acronyms according to Thiers (Thiers 2016) continuously updated (http://sciweb.nybg.org/science2/IndexHerbariorum.asp).

Description

Colours are described according to Kornerup and Wanscher (Kornerup and Wanscher 1981). Sections were carefully dissected under a stereomicroscope in hot (40° C) NaOH 3% solution and later examined in NaOH 3% solution at room temperature (Decock et al. 2010). Sections were also examined in Melzer's reagent and lactic acid Cotton blue to show staining reaction. All the microscopic measurements were done in Melzer's reagent. In presenting the size range of several microscopic elements, 5% of the measurements at each end of the range are given in parentheses when relevant. In the text, the following abbreviations are used: av. = arithmetic mean, R = the ratio of length/width of basidiospores, and av_R = arithmetic mean of the ratio R.

Molecular study and phylogenetic analysis

DNA extraction, amplification and sequencing of the 5' end of the nuclear ribosomal 28S rRNA gene (region including the domains D1–D3), the ITS regions (including 5.8S), the nuclear SSU regions, partial tef1-alpha gene and the region between domains 6 and 7 of the second largest subunit of the RNA polymerase II (rpb2), were as described in Amalfi et al. (2012) and Han et al. (2016). The sequences were assembled in Geneious Pro v. 6.0.6 (Biomatters). Materials and sequences used in this study are listed in Table 1.

Table 1

List of species, collections, and sequences used in the phylogenetic analyses
Species name	Sample no.		Locality	GenBank accession numbers						References
Species name	Sample no.		Locality	ITS	nLSU	nSSU		tef1	rpb2
Antrodia juniperina	CBS 117.40		USA	DQ491416	AY515346	–		–	DQ491389	Kim et al. 2007
A.juniperina	0310 1a		USA	MG787606	MG787653	MG787782		MG787873	MG787831	Chen,Y.Y., Cui,B.K. and Dai,Y.C., Direct Submission
A. malicola	Harkonen K622		China	KU866261	–	–		KU866216	–	Spirin et al. 2016
A. malicola	X1016		China	KC595896	KC595896	–		–	–	Ortiz-Santana et al. 2013
A. malicola	Cui 9491		China	KT968824	KT968828	–		–	KT988994	Han et al. 2016
A. serialis Holotype	KHL 12010 (O)		Norway	JQ700292	JQ700292	–		–	–	Spirin et al. 2017
A. serialis Neopype	KHL 12010 (GB)		Norway	NR154676	JX109844	–		JX109898	JX109870	Binder et al 2013
Antrodia serialis	Otto Miettinen X732		Finland	JQ700271	JQ700271	–		–	–	Spirin et al. 2017
A. serialis	CBS 306.82		DQ491417	–	–		–	DQ491390	Kim et al. 2007
A. serialis	Cui 10519		China	KP715307	KP715323	KR605911		KP715337	KR610830	Han et al. 2016
A. variiformis	CBS 309.82	USA		DQ491418	AY515344		–	–	DQ491391	Kim et al. 2007
A. variiformis	JV 0809/96	USA		KT995131	KT995154		MG787766	KU052736	MG787821	Spirin et al. 2017
Buglossoporus quercinus	LY BR 2030	France		KR605799	KR605738		KR605897	KR610728	KR610818	Han et al. 2016
B. americanus	JV1707_9J	Costa Rica		MN318452	–		–	–	–	Vlasák et al. 2016
B.eucalypticola	Dai 13660	China		KR605808	KR605747		KR605906	KR610736	KR610825	Han et al. 2016
B.pulvinus	CBS 858.72	Germany		DQ491419	MH872316		DQ491446	-	DQ491392	Kim et al. 2007
Daedalea africana	O 15372	Kenya		KP171196	KP171216		KR605871	KR610704	KR610795	Han et al. 2015, 2016
D. allantoidea	Dai 13612A	China		KR605795	KR605734		KR605892	KR610723	KR610813	Han et al. 2016
D. americana	JV 0312/24.7-J	USA		KP171197	KP171217		KR605872	KR610705	KR610796	Han et al. 2015, 2016
D. dochmia	CBS 426.84	Thailand		DQ491401	AY515326		–	–	DQ491374	Kim et al. 2007
D. modesta	Cui 10151	China		KP171205	KP171227		KR605883	KR610716	KR610806	Han et al. 2015, 2016
D. radiata	Cui 8575	China		KP171210	KP171233		KR605888	KR610720	KR610811	Han et al. 2015, 2016
Fomitopsis cana	Cui 6239	China		JX435777	JX435775		KR605826	KR610661	KR610761	Li et al. 2013, Han et al. 2016
F. cana	Dai 9611	China		JX435776	JX435774		KR605825	KR610660	KR610762	Li et al. 2013, Han et al. 2016
F. durescens	Overholts 4215	USA		KF937293	KF937295		KR605835	–	–	Han et al. 2014, 2016
F. durescens	Ryvarden 910796	Venezuela		KF937292	KF937294		KR605834	KR610669	KR610766	Han et al. 2014, 2016
F. hemitephra	O 10808	Australia		KR605770	KR605709		KR605841	KR610675	–	Han et al. 2016
F. meliae	Roberts GA863	United Kingdom		KR605775	KR605714		KR605848	KR610682	–	Han et al. 2016
F. meliae	Ryvarden 16893	Unknown		KR605776	KR605715		KR605849	KR610681	KR610775	Han et al. 2016
F. mounceae	CFMR:32TT	USA		KF169621	–		–	KF178346	KF169690	Haight et al. 2018
F. mounceae	CFMR:DR-301	USA		KF169625	–		–	KF178350	KF169694	Haight et al. 2018
F. mounceae	DAOM:73999	Canada		MH086784	MH086803
F. nivosa	JV 0509/52-X	China		KR605779	KR605718		KR605853	KR610686	KR610777	Han et al. 2016
F. ochracea	CFMR:DLL-3	USA		KF169588	–		–	KF178313	KF169657	Haight et al. 2018
F. ochracea	DAOM:F3249B	Canada		MH086778	MH086797		–	–	–	Haight et al. 2018
F. ostreiformis	BCC23382	Thailand		FJ372684	FJ372706		–	–	–	Rungjindamai et al. 2008
F. palustris	Cui 7615	China		KR605780	KR605719		KR605855	KR610688	KR610779	Han et al. 2016
F. pinicola	AFTOL ID 770	Unknown		AY854083	AY684164		AY705967	AY885152	AY786056	Matheny and Hibbett, Assembling the Fungal Tree of Life, direct submission
F. pinicola	CFMR:LT:323	Estonia		KF169651	–		–	KF178376	KF169720	Haight et al. 2018
F. pinicola	Cui 10312	China		KR605781	KR605720		KR605856	KR610689	KR610780	Han et al. 2016
F. pinicola	CBS 169.31	Germany		MH855169	MH866615		–	–	–	Vu et al. 2019
F. schrenkii	FP-105881-R	USA		KF169641	–		–	KF178366	KF169710	Haight et al. 2018
F. schrenkii	CFMR:JEH-142-ss12	USA		KF169642	–		–	KF178367	KF169711	Haight et al. 2018
F. subtropica	Cui 10181	China		JQ067653	JX435773		KR605866	KR610700	KR610790	Li et al. 2013, Han et al. 2016
F. subtropica	Cui 10578	China		KR605787	KR605726		KR605867	KR610698	KR610791	Han et al. 2016
Fragifomes niveomarginatus	Cui 10108	China		KR605778	KR605717		KR605851	KR610684	KR610776	Han et al. 2016
F. niveomarginatus	Wei 5583	China		HQ693994	KC507175		KR605852	KR610685	–	Han and Cui 2015, Han et al. 2016
Neolentiporus maculatissimus	Rajchenberg 158	Unknown		–	AF518632		AF334921	–	AY218497	Hibbett and Binder 2002, Wang et al. 2004
Niveoporofomes globosporus comb nov Holotype	M.C. Aime 3413	Belize		KC017760	KC017762		–	–	–	Ryvarden et al. (2009)
Niveoporofomes globosporus comb nov	S-20	Mexico		KR135353	–		–	–	–	Alfonso-Corrado,C. et al. unpublished
Niveoporofomes oboensis sp nov	MUCL 53518	Sao Tome		This study	This study		This study	This study	This study	This study
Niveoporofomes spraguei	4638	France		KR605784	KR605723		KR605862	KR610696	KR610786	Han et al. 2016
N. spraguei	Cui 8969	China		KR605785	KR605724		KR605863	KR610695	KR610787	Han et al. 2016
N. spraguei	JV 0509/62	USA		KR605786	KR605725		KR605864	KR610697	KR610788	Han et al. 2016
N. spraguei	CBS 365.34	USA		DQ491406	MH867073		–	–	DQ491379	Kim et al. 2007
N. spraguei	C5	Unknown		JX434660	–		–	–	–	Chai,D.-D. direct submission
N. spraguei	Cui 8951	China		KC507164	KC507174		–	–	–	Han and Cui 2015
N. spraguei	X1430	China		KC595924	–		–	–	–	Ortiz-Santana et al. 2013
N. spraguei	KA12-1397	South Korea		KR673596	–		–	–	–	Kim et al. 2015
N. spraguei	SAT1224005	USA		KY777368	–		–	–	–	Matheny et al direct submission
N. spraguei	SAT1028304	USA		MG663257	–		–	–	–	Matheny et al direct submission
N. spraguei	CLZhao 2241	China		MH114658	–		–	–	–	Zhao,C.-L. direct submission
N. spraguei	S.D. Russell MycoMap 6609	USA		MK560112	–		–	–	–	Russell S.D. direct submission
N. spraguei	Mushroom Observer # 247114	USA		MK571181	–		–	–	–	Russell S.D. direct submission
N. spraguei	S.D. Russell MycoMap # 73	USA		MK575221	–		–	–	–	Russell S.D. direct submission
N. spraguei	S.D. Russell MycoMap # 1318	USA		MK575222	–		–	–	–	Russell S.D. direct submission
N. spraguei	S.D. Russell MycoMap # 105	USA		MK575223	–		–	–	–	Russell S.D. direct submission
Pilatoporus ibericus	O 10810	Portugal		KR605771	KR605710		KR605842	KR610676	KR610771	Han et al. 2016
P. ibericus	O 10811	Italy		KR605772	KR605711		KR605843	KR610677	KR610772	Han et al. 2016
Piptoporus betulinus	CBS 377.51	Japan		MH856908	MH86843		–	–	–	Vu et al. 2019
	CBS 378.51	Austria		DQ491423	DQ491423		–	–	–	Kim et al. 2007
P. betulinus	Dai 12665	China		KP171215	KP171238		KR605896	KR610724	KR610817	Han et al. 2015, 2016
P. betulinus	Miettinen 12388	Finland		JX109856	JX109856		–	JX109913	JX109884	Binder at al. 2013
Rhodofomes cajanderi	Cui 9879	China		KC507157	KC507167		KR605827	KR610663	KR610763	Han and Cui 2015, Han et al. 2016
R. cajanderi	Cui 9888	China		KC507156	KC507166		KR605828	KR610662	KR610764	Han and Cui 2015, Han et al. 2016
R. cajanderi	JV 0410/14a,b-J	USA		KR605768	KR605707		KR605829	KR610664	–	Han et al. 2016
R. cajanderi	CBS 142.25	USA		MH854818	–		–	–	–	Vu et al. 2019
R. carnea	Ryvarden 10118	Tanzania		KF999921	KF999925		KR605831	KR610666	–	Han and Cui 2015, Han et al. 2016
R. incarnatus	Cui 10348	China		KC844848	KC844853		KR605844	KR610679	KR610773	Han and Cui 2015, Han et al. 2016
R. rosea	JV 1110/9	Czech Republic		KR605783	KR605722		KR605861	KR610694	KR610785	Han et al. 2016
R. subfeei	Cui 9229	China		KR605789	KR605728		KR605869	KR610701	KR610793	Han et al. 2016
Rhodofomitopsis africana	MUCL 43284	Cameroon		DQ491422	–		–	–	DQ491395	Kim et al. 2007
Rh. africana	Isolate 6537	India		MG430342	–		–	–	–	Saroj,P et al. direct submission
Rh. cupreorosea	CBS 236.87	Costa Rica		DQ491400	AY515325		–	–	DQ491373	Kim et al. 2007
Rh. feei	JV 0610/K9-Kout	Mexico		KF999922	KF999926		KR605836 a	KR610673 a	–	Han and Cui 2015, Han et al. 2016
Rh. feei	Oinonen 6011906	Brazil		KC844851	KC844856		KR605837	KR610671	KR610767	Han and Cui 2015, Han et al. 2016
Rh. feei	Ryvarden 14115	Costa Rica		KF999923	KF999927		–	–	–	Han and Cui 2015
Rh. feei	Ryvarden 42928	Australia		KF999924	KF999928		KR605839	KR610672	KR610769	Han and Cui 2015, Han et al. 2016
Rh. feei	Ryvarden 37603	Venezuela		KC844850	KC844855		KR605838	KR610670	KR610768	Han and Cui 2015, Han et al. 2016
Rh. lilacinogilva	CBS 422.84	Australia		DQ491403	–		DQ491430	–	DQ491376	Kim et al. 2007
Rh. lilacinogilva	Schigel 5193	Australia		KR605773	KR605712		KR605846	KR610680	KR610774	Han et al. 2016
Rubellofomes cystidiatus	Cui 5481	China		KF937288	KF937291		KR605832	KR610667	KR610765	Han et al. 2014, 2016
Ru. cystidiatus	Yuan 6304	China		KR605769	KR605708		KR605833	KR610668	–	Han et al. 2016
Ungulidaedalea fragilis	Cui 10919	China		KF937286	KF937290		KR605840	KR610674	KR610770	Han et al. 2014, 2016

Nucleotide sequences were automatically aligned using the MUSCLE algorithm (Edgar 2004) with default settings. The alignment was further optimised and manually adjusted as necessary by direct examination with the software Se-Al v. 2.0a11 (University of Oxford).

Two datasets were constructed and used for further phylogenetic analyses respectively at family and genus level. A combined dataset combined nuclear ribosomal partial LSU, ITS-5.8S, and SSU, partial tef1-α, and rpb2 genes sequences from 75 collections (Online Resource 1), including the outgroup (Neolentiporus maculatissimus strain Rajchenberg 158, (Han et al. 2016)). A second dataset combined the ITS-5.8S sequences of 23 collections (Online Resource 2), including all nineteen Niveoporofomes sequences available in public databases (based on a > 95.0% sequence similarity threshold, on 22/04/2021), with Piptoporus betulinus strain (CBS 378.51) as outgroup (Han et al. 2016).

The assignment of codon positions in the protein-coding sequences was confirmed by translating nucleotide sequences into predicted amino acid sequences using Mac-Clade 4.0 (Maddison and Maddison 2005) and then compared with the annotated Fomitopsis pinicola isolate AFTOL-ID 770 sequences.

Potential ambiguously aligned segments, especially in the introns present in tef-1 and in the ITS-5.8S alignment, were detected by Gblocks v0.91b (Castresana 2000) (http://molevol.cmima.csic.es/castresana/Gblocks.html), with the following parameter settings: minimum number of sequences for a conserved position = 38 (minimum possible); minimum number of sequences for a flank position = 38 (minimum possible); maximum number of contiguous non-conserved positions = 4 bp, minimum block size = 4 bp, and gaps allowed within selected blocks in half of the sequences.

To detect the possible bias from substitution saturation and to evaluate the phylogenetic signal, we tested each partition of the combined dataset and the ITS-5.8S dataset by using Xia’s test (Xia et al. 2003; Xia and Lemey 2009), as implemented in DAMBE (Xia and Xie 2001). As the Iss.c is based on simulation results, there is a problem with more than 32 species. To circumvent this problem, DAMBE was used to randomly sample subsets of 4, 8, 16 and 32 OTUs multiple times and to perform the test for each subset to see if substitution saturation exists for these subsets of sequences. In order to confirm the results of the Xia’s method, we also plotted the raw number of transversions and transitions against Tamura-Nei genetic distances with the aid of the DAMBE package, with an asymptotic relationship indicating the presence of saturation. Models of evolution for BI were estimated using the Akaike Information Criterion (AIC) as implemented in Modeltest 3.7 (Posada and Crandall 1998). The combined dataset was subdivided into 7 data partitions: ITS, nuc-LSU, Nuc-SSU, tef1-α 1st and 2nd codon positions, tef1-α 3rd codon positions, and rpb2 1st and 2nd codon positions, and rpb2 3rd codon positions. The three introns present in tef1-α and the one present at the end of rpb2 sequences were excluded from the phylogenetic inferences because judged too ambiguous to be confidently aligned (tef1-α) or because were missing in most of the sequences (rpb2). Phylogenetic analyses were performed separately for each individual and concatenated loci using Bayesian Inference (BI) as implemented in MrBayes v3. 2 (Ronquist et al. 2011) and Maximum Likelihood (ML) as implemented in RAxML 7.2.7 (Stamatakis et al. 2008). The best-fit models for each partition were implemented as partition specific models within partitioned mixed-model analyses of the combined dataset (Table 2). All parameters were unlinked across partitions. Bayesian analyses were implemented with two independent runs, each with four simultaneous independent chains for six million generations for both combined and ITS datasets, starting from random trees and keeping one tree every 1000th generation. All trees sampled after convergence (average standard deviation of split frequencies < 0.01 and confirmed using Tracer v1.4 (Rambaut and Drummond 2007) were used to reconstruct a 50% majority-rule consensus tree (BC) and to calculate Bayesian Posterior Probabilities (BPP). BPP of each node was estimated based on the frequency at which the node was resolved amongst the sampled trees with the consensus option of 50% majority-rule (Simmons et al. 2004). A probability of 0.95 was considered significant. Maximum Likelihood (ML) searches conducted with RAxML involved 1000 replicates under the GTRGAMMAI model, with all model parameters estimated by the programme. In addition, 1000 bootstrap (ML BS) replicates were run with the same GTRGAMMAI model. We provided an additional alignment partition file to force RAxML software to search for a separate evolution model for each dataset. Clades with Maximum Likelihood bootstrap values of 75% or greater were considered supported by the data.

Table 2

Summary of data sets used for phylogenetic inferences.
Datasets
Properties	tef1 1st & 2nd	tef1 3rd	tef1 introns	rpb2 1st & 2nd	rpb2 3rd	rpb2 intron	nucSSU	nucLSU	ITS	ITS-5.8S restricted
Alignment size	244	121	208	432	216	76	83	1348	771	668
Excluded characters	-	-	208	-	-	76	-	-	369	-
Model selected	F81 + I + G	GTR + G	HKY + I + G	SYM + I + G	GTR + G	K80	GTR + I + G	GTR + I + G	GTR + I + G	GTR + G
-Likelihood score	1160.8060	2428.8706	3254.8496	2032.5619	3033.6099	237.5902	2041.7124	4516.7588	7215.0537	1653.3608
Base frequencies
FrEq. A =	0.2993	0.0343	0.2138	Equal	0.2478	Equal	0.2726	0.2697	0.2346	0.2329
FrEq. C =	0.2284	0.4948	0.2421	Equal	0.1956	Equal	0.1900	0.2032	0.1762	0.2027
FrEq. G =	0.2639	0.2981	0.2087	Equal	0.2541	Equal	0.2593	0.2780	0.2206	0.2317
FrEq. T =	0.2085	0.1728	0.3354	Equal	0.3025	Equal	0.2780	0.2491	0.3686	0.3326
Proportion of invariable sites	0.8401	-	0.0591	0.6471	-	-	0.9082	0.6094	0.2125	-
Gamma shape	0.6822	0.8036	2.2345	0.5604	2.7065	-	2.1111	0.5410	0.6111	0.2537
Test of substitution saturation
Iss	0.066	0.377	1.157	0.130	0.565	0.4635	0.020	0.292	0.169	0.0668
Iss.cSym	0.683	0.756	0.689	0.695	0.687	1.015	0.749	0.768	0.691	0.7417
P (Sym)	< 0.0001	< 0.0001	< 0.0001	< 0.0001	< 0.0001	< 0.0001	< 0.0001	< 0.0001	< 0.0001	< 0.0001
Iss.cAsym	0.359	0.499	0.372	0.367	0.633	1.067	0.444	0.479	0. 362	0.4961
P (Asym)	< 0.0001	< 0.0062	< 0.0001	< 0.0001	< 0.0436	< 0.0001	< 0.0001	< 0.0001	< 0.0001	< 0. 0001
Note: Iss: index of substitution saturation. Iss.cSym: critical value for symmetrical tree topology. Iss.cAsym: critical value for extremely assymetrical tree topology. P: probability that Iss is significantly different from the critical value (Iss.cSym or Iss.cAsym). Iss < Iss.c = no saturation, Iss > Iss.c = substantial saturation (very poor for phylogenetics)

To detect topological conflicts amongst data partitions, the nodes between the majority-rule consensus trees obtained in the ML analysis from the individual datasets were compared with the software compat.py (available at www.lutzonilab.net/downloads). Paired trees were examined for conflicts only involving nodes with ML BS > 75% (Mason-Gamer and Kellogg 1996; Reeb et al. 2004; Lutzoni et al. 2004). A conflict was assumed to be significant if two different relationships for the same set of taxa (one being monophyletic and the other not) were observed in rival trees. Sequence data and statistical analysis for each individual dataset and combined analysis are provided in Table 2.

Phylogenetic analysis

By comparing the tree topologies obtained for the individual datasets, no significant conflict involving significantly supported nodes was found using the 75% ML BP criterion; the datasets were therefore combined.

The test of substitution saturation (Table 2) showed that the observed index of substitution saturation (Iss) for the restricted ITS-5.8S dataset, the tef-1 (1st and 2nd codon positions, and 3rd codon position), rpb2 (each codon positions), nucLSU and nucSSU alignments of the combined dataset was significantly lower than the corresponding critical index substitution saturation (Iss.c), indicating that there was little saturation in our sequences (P < 0.001). On the other hand, the ITS-5.8S partition of the combined dataset, the tef-1 introns and the rpb2 intron showed sign of substitution saturation, indicating the unsuitability of these data for phylogenetic analysis. Nevertheless, reanalysing the ITS partition with DAMBE after that Gblocks retained 402 sites (51% of a total of 771 sites), the substitution saturation test revealed an Iss value that was significantly (P < 0.001) lower than the Iss.c (Table 2), indicating the suitability of this data for further phylogenetic analysis. We therefore included the ITS-5.8S partition in the combined dataset, excluding the poorly aligned positions identified by Gblocks as well as the tef-1 and the rpb2 introns partitions.

The Niveoporofomes s.s ITS-5.8S dataset and the Fomitopsis s.l. combined [ITS-nLSU-nSSU-tef1-α-rpb2] data set comprised 23 and 75 taxa respectively including the outgroups and, once excluded the introns, were of 668 and 4149 sites long including gaps, respectively. Sequence data, evolutionary models and statistical analysis for each dataset are provided in Table 2. For the combined dataset the two Bayesian runs (6.000.000 generations) converged to stable likelihood values after 1.615.000 generations; therefore 4.385 stationary trees from each analysis were used to compute a 50% majority rule consensus tree in PAUP* to calculate posterior probabilities. For the ITS-5.8S dataset, the two Bayesian runs (4.000.000 generation) converged after 460.000 generations, and 3.540 stationary trees from each analysis were used to compute a 50% majority rule consensus tree in PAUP* to calculate posterior probabilities.

In the ML searches, the ITS-5.8S alignment had 154 distinct patterns with a proportion of gaps and undetermined characters of 11.95%. In the ML searches with RAxML, the combined dataset alignment had 1530 distinct patterns with a proportion of gaps and undetermined characters of 37.99%. The consensus of the BI and the Maximum Likelihood tree were nearly identical. The BI consensus trees for the combined and ITS-5.8S only datasets are presented in Figs. 1 and 2 respectively. The topologies of the trees regarding the recovery and the relative positions of the different taxa of the Fomitopsis complex were, overall, similar in all the phylogenetic inferences, and in accordance with previous published results (Ortiz-Santana et al. 2013; Han et al. 2016), at least for what concerns significantly supported branches.

The phylogenetic analyses recovered our specimen from Ôbo de São Tomé National Park in the vicinity of N. spraguei, forming a distinct branch (Fig. 1). On this basis and morphological characters, of which the

subglobose, obovoid basidiospores with a large gutta, the specimen is interpreted as representing an undescribed species proposed below as Niveoporofomes oboensis.

The collections of N. spraguei, available on GenBank, segregated into three clades (Fig. 2). The collections originating from USA and a single one from Europe clustered in a sister position to a clade that includes sequences from the holotype of Trametes globospora Ryvarden & Aime (Belize, Ryvarden et al. 2009) and two other collections from Mexico (KR135353, JX434660). The N. spraguei collections originating from Asia formed a third basal clade, suggesting that they represent a likely cryptic species.

Taxonomy

Niveoporofomes oboensis Decock, Amalfi & Ryvarden nov. sp. (MB 841205) Fig. 3.

Niveoporofomes oboensis is characterized by the combination of a pileate, slightly decurrent basidiome, a white pore surface, discolouring to brownish on bruising when fresh, 3.5–4 pores / mm, a pseudodimitic to dimitic hyphal system with hyaline clamped generative hyphae, dominated in the contextual trama by sclerified, thick-walled, septate, and clamped hyphae, with long aseptate segment and dominated in the hymenophoral trama by skeletal hyphae, and broadly obovoid to subglobose basidiospores with a large gutta, mostly 4.7–5.5 × 4.0–4.5 (–4.8) µm (ave = 5.2 × 4.3 µm).

Holotype: São Tomé, Ôbo de São Tomé National Park, on the way to Lagoa Amelia, approx. N 00°16.95’ – E 006°35.48’, elev. 1300 masl, on buttress of a living tree, Olea capensis (Oleaceae), 12 April 2011, Cony Decock, ST-11-04, Holotype in O, Isotypes in BR and MUCL (MUCL53518) (living strain ex holotype MUCL 53518).

Basidiome annual, pileate, with a slightly decurrent pore surface, corky when fresh, drying hard corky to woody; pileus solitary or imbricated with to 2 pilei superposed, broadly attached, elongated, 16–20 cm wide, projecting 8–9.5 cm, applanate in section, 1.5–2 cm thick at the base down to 0.5 at the margin; pileus surface white toward the margin, cinnamon to light brown, dark brown to black toward the base, glabrous; margin round, whitish, discolouring to brownish on bruising, drying dark greyish; pore surface plane to slightly concave, or wavy, whitish when fresh, drying whitish to pale corky; pores mostly round, 180–238 (–250) µm diam (ave 208 µm) to elliptic, 225–285 × 150–200 µm (ave 251 × 186 µm, 3.5–4 / mm; dissepiments thick, entire, 35–135 µm (ave 66 µm); context white, ivory when fresh or dry, dense and hard corky, fibrous, up to 10 mm thick at the base down to 2 mm at the margin; tube layer contrasting with the context, yellow white to orange white, pale corky, up to 13 mm high.

Hyphal system pseudodimitic (intermediate sensu Pegler 1996) to dimitic; generative hyphae in all parts hyaline, thin- to slightly thick-walled, with clamped septa, little branched, 2.0–2.5 µm diam; context dominated by sclerified, thick-walled generative hyphae, (3.5–) 4.0–5.0 (–5.5) µm (ave 4.6 µm) in the main part, negative in Melzers reagent, acyanophilous, with large, basal and intermediate clamps, with “spouting” clamps, with aseptate segments of variable length, measured from 50 µm up to 350 µm, reverting to thin-walled generative hyphae or ending in an aborted thin-walled hyphae, or occasionally in a whip-like narrow, unbranched to little branched process; mediate hyphae uncertain; hymenophoral trama dominated by skeletal hyphae, originating from a basal clamp or a short mediate hyphae, from 2.2–2.5 µm at the basal septum to 3.0–4.0 (–4.5) µm (ave 3.6 µm) in the main part, measured up to 500 µm long, very thick-walled, hyaline, ending thin-walled, negative in Melzers reagent, acyanophilous, irregularly swelling in alkali.

Hymenium: basidia clavate to slightly pear-shaped, clamped at the basal septum, with four sterigmata; basidioles clavate to slightly pear-shaped, clamped at the basal septum, 16–20 × 6.5–8 µm; cystidioles very few, with a basal clamps, slightly ventricose, bottle-shaped, ~ 17 × 6.0 µm; basidiospores subglobose, broadly obovoid, hyaline, thin-walled, smooth, most with a large oil drop (best seen in fresh specimen), (4.5–) 4.7–5.5 (–5.7) × 4.0–4.5 (–4.8) µm (ave = 5.2 × 4.3 µm), R = 1.1–1.3 (ave R = 1.2).

Physiology (type of rot)

brown rot;

Ecology (substrate, host, habitat)

on buttress of a living tree, Olea capensis (Oleaceae), Afromontane Equatorial rainforest.

Distribution. Known from the type locality, Ôbo de São Tomé National Park, São Tomé.

Phylogenetic affinities

the sole known phylogenetic relative are, hitherto, N. spraguei and T. globospora.

Niveoporofomes was segregated from Fomitopsis based on the subglobose to globose basidiospores, which are elliptic in Fomitopsis s.s. and related genera. Multilocus phylogenetic analyses confirmed that N. spraguei and F. pinicola were not monophyletic.

The hyphal system of Niveoporofomes was described as dimitic with “frequently branched” skeletal hyphae (Han et al. 2017). This description is of uncertain interpretation. To characterize skeletal hyphae as “frequently branched” is intrinsically contradictory; skeletal hyphae are, by definition, unbranched, but for the sparingly branched mediate hyphae (Corner 1932). Ryvarden and Melo (Ryvarden and Melo 2014) described the hyphal system as trimitic, with generative, skeletal, and binding hyphae. Rivoire (Rivoire 2020) provided a more accurate description of the hyphal system, dominated both in the context and the hymenophoral trama by thick-walled [sclerified] generative hyphae, with scarce “skeletal” and “binding” hyphae.

Niveoporofomes oboensis and N. spraguei share the hyphal system, as described by Rivoire (2020), the subglobose, obovoid basidiospores, and a brown rot. Multilocus phylogenetic inference also confirmed their closed affinities. Niveoporofomes oboensis differs from N. spraguei by a basidiome margin and pore surface tinting brownish when bruised in fresh conditions. These two species also have a disjoint autecology and distribution. The autecology of N. oboensis, including the host relationships, habitat, and distribution is known for the type specimen only; it was found on buttresses of Olea capensis at Ôbo de São Tomé National Park, in Afromontane Equatorial rainforest (White 1986; Carvalho et al. 2004), whereas N. spraguei grows mostly on Quercus and Castanea in Northern temperate areas (Gilbertson and Ryvarden 1993; Ryvarden and Gilbertson 1994; Ryvarden and Melo 2014; Rivoire 2020).

In tropical Africa, F. widdringtoniae (Masuka and Ryvarden 1993) is the closest morphological relative of N. oboensis. The species was described growing on Widdringtonia nodiflora (L.) Powrie, a South-eastern African, endemic Gymnosperm (Cupressaceae). It is known so far from Malawi only, but may follow its host southernly. It is characterized also by globose basidiospores (Masuka and Ryvarden 1993), what points toward Niveoporofomes rather than Fomitopsis s.s. Its phylogenetic affinities are unknown, but on the basis of the basidiospores shape and size, and a brown rot, we propose the new combination Niveoporofomes widdringtoniae (Masuka & Ryvarden) Decock & Ryvarden, comb. nov., MB839610 (basionym F. widdringtoniae Masuka & Ryvarden, Mycol. Helv. 5(2):145, 1993, MB359440).

Niveoporofomes oboensis differs from N. widdringtoniae in basidiome size (up to 20 cm wide vs up to 5 cm wide), 3.5–4 vs 7–8 pores / mm, slightly larger basidiospores 4.7–5.5 (–5.7) × 4.0–4.5 µm, averaging 5.2 × 4.3 µm vs 4.5-5 µm in diam, on average < 5 µm, and likely in host and distribution range.

Fomitopsis s.l. was represented in Tropical Africa by seven species, F. africana, F. carneus, F. rhodophaea (Lev.) Imazeki, F. scutellata (Schwein.) Bondartsev & Singer, F. supina (Sw.) Ryvarden, F. widdringtoniae, and F. zuluensis (Wakef.) Ryvarden (Ryvarden 1972; Ryvarden and Johansen 1980; Masuka and Ryvarden 1993; Mossebo and Ryvarden 1997). Currently, F. zuluensis would be the sole Fomitopsis s.s. recognized still in Tropical Africa, but its phylogenetic affinities are unknown for the time being. Fomitopsis africana and F. carnea are nowadays accepted in Rhodofomitopsis (R. africana) and Rhodofomes (R. carneus) (Han et al. 2016), whereas F. widdringtoniae is here accepted in Niveoporofomes, a genus now represented by two species in Tropical Africa.

Fomitopsis rhodophaea, F. scutellata, and F. supina belong to the white rot genera Neofomitella (Li et al. 2014b), Datroniella (Li et al. 2014a), and Fomitella (Li et al. 2014b), respectively. They are members of the core polyporoid clade (white rot species, Justo et al. 2017) and not of the Antrodia clade (brown rot species).

Brown rot polypores are little diversified in Tropical Africa. They are mostly found inhabiting highland forest ecosystems of Eastern Africa or the Albertine rift, and in the case of N. oboensis, a mountain area of western Insular Africa. The notable exception is R. africana that was originally described from lowland in Cameroon, on an African non-native host (Eucalyptus).

Key to the species of Fomitopsis, Niveoporofomes, Rhodofomitopsis, and Rhodofomes found in sub-Saharan, continental and insular Africa.

Context and pore surface distinctly pinkish (when fresh)…………………………………………………. 2

1’ Context and pore surface white, ochraceous, beige, to golden brown…………………………………….. 3

2 Pores 3–4 per mm; pileus dark brown; basidiospores cylindrical to navicular …..Rhodofomitopsis africana

Known hitherto from the lowland rain forest of Cameroon.

2’ Pores 5–7 per mm; pileus almost black; basidiospores cylindrical to allantoid………Rhodofomes carneus

Known from East Africa.

3 Pileus with a reddish to black cuticle; basidiospores elliptic 8–10 µm long………….Fomitopsis zuluensis

Known hitherto from South Africa.

3’ Pileus without cuticle; basidiospores subglobose, obovoid, ≤ 6 µm diam in the longest dimension…….4

4 Pileus white, light to dark brown from the base, bruising greenish; known from Olea capensis (Oleaceae)

…………………………………………………………………………………… Niveoporofomes oboensis

Known hitherto from highlands of São Tomé.

4’ Pileus whitish with some greyish to dirty brown spots; known from Widdringtonia (Cupressaceae)………

…………………………………………………………………………….Niveoporofomes widdringtoniae

Known hitherto from the highlands of Malawi.

Notes on N. spraguei. Niveoporofomes spraguei, as currently accepted (Gilbertson and Ryvarden 1986; Ryvarden and Melo 2014; Han et al. 2016; Rivoire 2020), is a pan-temperate taxon in the Northern hemisphere, growing on various angiosperms, mostly Quercus and Castanea, both in Europe and North America (Gilbertson and Ryvarden 1986, Ryvarden and Melo 2014, Rivoire 2020).

The phylogenetic analyses based on ITS sequences available at GenBank separated specimens of N. spraguei into three clades; an East Asian (China and South Korea) clade, a North American / European clade, and a third, Mesoamerican clade, in an intermediate position, that comprises specimens originating from Mexico and Belize (Fig. 2). The North American / European clade should correspond to N. spraguei s.s., in which case, the East Asian clade could represent a distinct taxon. The Mesoamerican clade includes the type of Trametes globospora, a species that deviates from all other species of Trametes in having globose basidiospores, 4.5–6 µm diam (Ryvarden et al. 2009). Basidiospores are elliptic in all other species of Trametes. The new combination Niveoporofomes globosporus (Ryvarden & Aime) Decock, Amalfi & Ryvarden comb. nov. (MB839611) is proposed (basionym Trametes globospora Ryvarden & Aime, Synopsis Fungorum 26: 28, 2009, MB509818).

Ethics approval and Consent to participate: Not applicable

Consent for publication: All authors are aware and agree with the submission of this manuscript.

Availability of data and materials: Scientific data concerning DNA sequences and DNA data sets are made as supplementary materials (Online Resource 1 and 2), the type specimen of Niveoporofomes oboensis sp. nov. is preserved at O, with isotypes at BR and MUCL (herbarium acronyms according to Thiers 2016)

Competing interests: The authors declare that they have no conflict of interest.

Funding information: Funding was provided to Cony Decock by Belgian State – Belgian Federal Science Policy (BELSPO), through the BCCM program; to Mario Amalfi by the Fédération Wallonie-Bruxelles and Botanic Garden Meise; funding was provided to Cony Decock by the FNRS through a FRFC project (FRFC # 2.4515.06).

Code availability: Not applicable

Authors' contributions: Mario Amalfi and Cony Decock contributed to the study conception and design. Material collections were performed by Cony Decock. Mario Amalfi produced the sequences and conducted the phylogenetic analyses. The first draft of the manuscript was written by Cony Decock and Mario Amalfi, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Acknowledgments: The authors warmly thank the Ministério de Plano e Desenvolvimento, Direcção de Agricultura e Pescas de São Tomé for granting permits to collect in the Obô de São Tomé National Park, and the staff of the Park, and Faustino Oliveira, director of the botanical garden at Bom Sucesso, for the help offered during the collecting trip in April 2011. Mr. Bastien Loloum, Zuntabawe Lda, is warmly thanks also for the logistic aspects of the collecting trip. Cony Decock gratefully acknowledges the financial support received from the Belgian State – Belgian Federal Science Policy and the Fonds de la Recherche Fondamentale Collective (FRFC # 2.4515.06 and FRFC # 2.4.544.10.F). Mario Amalfi gratefully acknowledges the financial support received from Meise Botanic Garden and the Fédération Wallonie-Bruxelles.

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Niveoporofomes (Basidiomycota, Fomitopsidaceae) in Tropical Africa: Niveoporofomes oboensis sp. nov. and N.widdringtoniae comb. nov., two species from Afromontane Forests

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