Phylogeny of the subgenus Eumitria in Tanzania

Figures & data

Table 1. Table of Usnea subgenus Eumitria taxa from Africa (Dodge 1956; Swinscow and Krog 1974, 1986; Krog 1994) with their main chemistry indicated by X; protocetraric acid (PRO), fumarprotocetraic acid (FUM), diffractaic acid (DIF), salazinic acid (SAL), norstictic acid (NOR), constictic acid (CON), thamnolic acid (THA), psoromic acid (PSO), triterpenoids (TRI), virensic acid (VIR).

Species	Chemistry
	PRO	FUM	DIF	SAL	NOR	CON	THA	PSO	VIR	TRI
U. antiqua Swinscow & Krog								X
U. baileyi (Stirt.) Zahlbr.			X	X	X
U. baileyi var. pinnatifida Swinsc. &Krog	X
U. baileyi var. planiuscula Swinsc. &Krog	X
U. brunnescens C.W. Dodge
U. cervicornis C.W. Dodge	X	X	X
U. congdonii Krog	X		X							X
U. cristata Mot.			X	X
U. elata Mot.			X
U. firmula (Stirt.) Mot.	X			X	X
U. liechtensteinii Steiner	X
U. pulvinulata C.W. Dodge	X		X	X	X
U. subcristata C.W. Dodge			X	X		X
U. uluguruensis Krog	X								X
U. welwitschiana Mot.	X
U. zombensis Krog							X

Figure 1. Map showing study sites in Tanzania indicated by dots.

Table 2. Species and GenBank accession numbers of sequences used in the DNA analyses. Newly produced sequences in bold.

		GenBank Accession numbers
Species	Isolation No	ITS	nuLSU	MCM7	RPB1
Lethariella cashmeriana	Obermayer 8335	DQ980014	DQ923665		DQ923690
Pleurosticta acetabulum	MAF9914	AY581087	AY578953	JX136677	EF092147
U. baileyi	Y04488A	AB051050
U. baileyi	Y4516	AB051051
U. baileyi	SGT 63	MN080251			MN080252
U. baileyi	SGT 65	MN080242	MN080261	MN097139
U. baileyi	SGT 110	MN080250	MN080264	MN097141	MN098768
U. baileyi	SGT 112	MN080249	MN080265
U. baileyi	SGT 118	MN080244	MN080266
U. baileyi	SGT 119	MN080248	MN080267
U. baileyi	SGT 120	MN080246	MN080262	MN097142	MN098771
U. baileyi	SGT 122	MN080247	MN080268
U. baileyi	SGT 156	MN080245	MN080269	MN097143	MN098772
U. baileyi	SGT 157	MN080243	MN080263
U. dasaea	Y2842	AB051056
U. dasaea	41	JQ837305	JQ837390	JQ837348
U. dasaea	81	JQ837306	JQ837391	JQ837349
U. diffracta	Y2889	AB051059
U. diffracta	Y1124	AB051057
U. florida	26	JN943538	JN939703		JN992584
U. florida	29	JN943535	JN939706		JN992581
U. longissima	Y2881	AB051643
U. longissima	Y3844	AB051648
U. pectinata	Y2989	AB051655
U. pectinata	Y04373	AB051656	AB720729	AB720731
U. pectinata	SGT86	MN080233	MN080253		MN098765
U. pectinata	SGT87	MN080241	MN080254		MN098766
U. pectinata	SGT106	MN080234
U. pectinata	SGT107	MN080240	MN080255
U. pectinata	SGT109	MN080236	MN080256	MN097140	MN098767
U. pectinata	SGT114	MN080235	MN080257		MN098769
U. pectinata	SGT115	MN080237	MN080258
U. pectinata	SGT116	MN080239	MN080259
U. pectinata	SGT117	MN080238			MN098770
U. rubicunda	Y3114	AB051659
U. rubicunda	38	JQ837316	JQ837399	JQ837358
U. rubicunda	39	JQ837317	JQ837400	JQ837359
U. subantarctica	NW165	EF179805			EF179792
U. subantarctica	NW73	EF179806			EF179794
U.sphacelata	F964(NIPR)	AB103542
U.sphacelata	F964(NIPR)	AB103543
U. subfloridana	09–02124	JN943540	JN939701		N992586
U. subfloridana	09–02128	JN943537	JN939704		N992583
U. trachycarpa	F 1174029a	DQ235496	EF116570		EF179793
U. trachycarpa	411	DQ767964			EF193058
U. trichodeoides	Y.4413	AB051672
U. trichodeoides	Y05316	AB720727	AB720728	AB720730
U. wamuthii	28	JN943536	JN939705		JN992582
U. wamuthii	34	JN943530	JN939710		JN992576

Figure 2. Consensus tree based on a Bayesian and ML analyses of concatenated ITS, nuLSU, RPB1 and MCM7 showing infrageneric clades in Usnea. The tree was rooted using two species Pleurosticta acetabulum and Lethariella cashmeriana. The two support values associated with each internal branch correspond to posterior probability (PP) and bootstrap support (bs) respectively. Branches in bold indicate a support of PP ≥ 95% and a MLbs ≥ 70%. An asterisk on a bold branch indicates that this node has a support of 100 % for both support estimates. A dash instead of a MLbs value indicates that the node of the Bayesian tree was not recovered by ML bootstrapping. Species groups (within annotation marks) are in accordance with Truong et al (2013). Eumitria is highlighted by a shaded box.

Figure 3. Consensus tree based on Bayesian and ML analyses of Eumitria species in Tanzania (ITS, nuLSU, RPB1 & MCM7). The two support values associated with each internal branch correspond to posterior probability (PP) and bootstrap support (bs) respectively. Branches in bold indicate a support of PP ≥ 95% and a MLbs ≥ 70%. An asterisk on a bold branch indicates that this node has a support of 100% for both support estimates. A dash instead of a MLbs value indicates that the node of the Bayesian tree was not recovered by ML bootstrapping. A: America, I: Indonesia, J: Japan, T: Tanzania 1: main chemical substance, 0 accessory chemical substance, x: dark brown pigmentation, big black dots: terete branch shape, triangles: alate branch shape, pentagon: ridged branch shape.

Figure 4. Usnea baileyi; (a): Usnea baileyi studied specimen (SGT 157), (b): blackish base, (c): soralia with short isidiomorphs (d): thin and shiny cortex, red subcortical pigment and tubular axis filled with loose hyphae.

Figure 5. Usnea pectinata; (a): Usnea pectinata studied specimen (SGT 114), (b): smain branch cylindrical with terete segments, (c): main branch irregular with alate segments, (d): blackish base, (e): soralia with short isidiomorphs, (e): dark brown pigmented axis of main branch with some fistulose areas in the central part of the axis.

Table 3. Comparison of U. baileyi anatomical characters. Mean (italic), standard deviation and extreme values (in parenthesis) are shown.

Anatomical characters	Japan (Ohmura 2001)	South America and the Galapagos (Truong and Clerc 2013)	Tanzania
% C	(3.3) – 4.9–6.6–8.3 – (9.2)	3.0–5.5	(4.4) – 5.7–7.0–7.8 – (8.2)
% M	(3.0) – 3.2–5.3–7.4 – (12)	1.5–3.0	(2.8) – 3.6–4.2–5.7 – (6.2)
% A	(58) – 70–76 – 82 – (86)	83.0–91.5	(70) – 78–81.79–82 – (88)
% TBA	–	67–83	(38) – 43–53.33–46 – (84)

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