Filling reference libraries with diatom environmental sequences: strengths and weaknesses

Figures & data

Fig. 1. Maps of Guadeloupe (a), Martinique (b) and general location in the West Indies (c). The location of the sampling sites is marked with black dots, and the locations of the islands are marked with open circles.

Fig. 2. Phylogenetic position of Ulnaria goulardii (ASV2) in the ML tree. Bootstrap values are given for each node and the scale bar gives the number of substitutions per site. ‘*’ indicates sequences added in the phylogeny using the multifurcating constraint.

Figs 3–11. LM micrographs of Ulnaria goulardii. Figs 3–11. Acc. No. TCC1083. From site called Grande Rivière – Vieux habitants amount in Guadeloupe. Scale bar = 10 µm.

Fig. 12. Phylogenetic position Nupela boucheziae sp. nov. (ASV22) in the ML tree. Bootstrap values are given for each node and the scale bar gives the number of substitutions per site. ‘*’ indicates sequences added in the phylogeny using the multifurcating constraint.

Figs 13–53. LM micrographs of Nupela boucheziae sp. nov. Figs 13–33. Type material Acc. No. TCC1086. Figs 13–22. Valves (with raphe) and Figs. 23–33. Valves (without raphe), from site called Blanche-Pont de l'Alma in Martinique. Figs 34–42. Valves (with raphe) and Figs. 43–53 Valves (rapheless), from river Rivière Bras David in Guadeloupe, Acc. No. TCC1088 (paratype). Scale bar = 10 µm.

Figs 54–59. SEM micrographs of Nupela boucheziae sp. nov. from type material TCC1086. Figs 54–57. External valve view. Figs. 58–59 Internal valve view. Scale bars = 5 µm (54, 57–59). Scale bars = 2 µm (55, 56).

Fig. 60. Phylogenetic position Epithemia boucheziae sp. nov. (ASV38) in the ML tree. Bootstrap values are given for each node and the scale bar gives the number of substitutions per site. ‘*’ indicates sequences added in the phylogeny using the multifurcating constraint.

Figs 61–87. LM micrographs of Epithemia boucheziae sp. nov. Figs 61–87. Type material Acc. No. TCC1089. Figs 61–87. from river Rivière Bras David in Guadeloupe. Scale bar = 10 µm.

Figs 88–93. SEM micrographs of Epithemia boucheziae sp. nov. from type material TCC1089. Figs 88–91. External valve view. Figs 92–93. Internal valve view. Scale bars = 10 µm (88, 89, 92). Scale bars = 5 µm (90, 93). Scale bars = 2 µm (91).

Fig. 94. Phylogenetic position Gomphonema bourbonense (ASV11 and ASV16) in the ML tree. Bootstrap values are given for each node and the scale bar gives the number of substitutions per site. ‘*’ indicates sequences added in the phylogeny using the multifurcating constraint.

Fig. 95. Phylogenetic position of undetermined ASV (ASV5, ASV8, ASV37, ASV57, ASV150) of the Nitzchia complex in the ML tree. Bootstrap values are given for each node and the scale bar gives the number of substitutions per site. ‘*’ indicates sequences added in the phylogeny using the multifurcating constraint.

Table 1. Morphological comparison between Gomphonema bourbonense and Gomphonema designatum.

Morphological characteristics	Gomphonema bourbonense E. Reichardt	Gomphonema designatum E. Reichardt	Gomphonema bourbonense (this study)
Valve outline	Linear-elliptic to linear-lanceolate	Moderately heteropolar	Linear to linear-lanceolate
Apices	Rounded, never rostrate	Rounded to pointed	Rounded
Length	9.4–28 µm	22–45 µm	13.0–25.0 µm
Width	3.3–4.7 µm	4–5.5 µm	3.40–4.5 µm
Stria density	10.5–13/10 µm	10–12/10 µm	12–13/10 µm
Stria orientation	Parallel to slightly radiate	Strong, spaced parallel becoming radiate in larger specimen	Parallel to slightly radiate
Central area	Rectangular with 1 stigma	Poorly individualized, bordered by 2 shorter striae	Rectangular with 1 stigma

Table 2. Morphological features and measurements of Nupela boucheziae sp. nov. and similar species. n.a.: no data available.

Species	Valve outline	Apices	Valve margins	Central area	Raphe	Axial area	Stria orientation	Length (µm)	Width (µm)	Areola density (in 10 µm)	Stria density (in 10 µm)	Ref.
Nupela boucheziae sp. nov.	Elliptical-lanceolate	Rounded to sub-rostrate	Convex	Small to very small, round to elliptical	Thread like and almost straight, incomplete on one valve, reduced to small helictoglossa, ‘ghost’ full raphe	Narrow on both valves	Radial to parallel towards the ends	7.0–15	4–4.5	ca. 50	30–40	1
Nupela praecipuoides	Lanceolate	Slightly protracted to subrostrate	Convex	Rounded	One valve with long raphe slits, other valve araphid	Raphid valve - linear and narrow. Araphid valve - lanceolate, smooth or with irregular depressions	Radial to parallel at the apices	9.0–21.5	4.0–5.5	35–39	36–38	2
Nupela praecipua	Broadly lanceolate	Obtuse ends	Convex	Unmarked	Filiform. Slightly curved. One valve with complete other with rudimentary raphe	Wide, with irregular boundaries	Radial throughout valve, slightly convergent at the apices	8–13.5	4–5	35–43	30–39	3, 4
Nupela chilensis	Linear-elliptic	Cuneiform narrowed, bluntly rounded	Convex	Quite big and roundish, well defined	Filiform on both valves	Narrower to very broad, lanceolate, widening towards the middle		16–26	5–7	n.a.	32	5, 6
Nupela difficilis	Lanceolate	Subrostrate	Strongly convex	Asymmetric, unilaterally reaching valve margin	One valve with long raphe slits. Other valve with shorter raphe slits	Lanceolate	Transapical, slightly radiate	8.8–14.8	4.1–5.9	48–50	40	2
Nupela decipiens	Lanceolate	Narrowly rostrate to subrostrate	Convex to parallel in middle	Raphid valve - broadly rounded. Araphid - broadly lanceolate, not reaching valve margin	One valve with long raphe slits and other valve araphid	Raphid valve-lanceolate. Araphid valve - broadly lanceolate, externally ornamented with irregular depressions	Transapical radiate.	8.9–18.5	4.1–5.9	52	36–40	6, 7
Nupela neglecta	Lanceolate to elliptical-lanceolate	Slightly protracted	One valvae convex to parallel in middle. Other slightly concave or slightly asymmetrical in apical and transapical planes	Small, round or elliptical	One valve - long raphe slits. Other valve - distinctly shorter raphe slits. Widely separated central endings	Linear-lanceolate	Radiate, becoming parallel or slightly convergent near the poles	3–15	2.6–4.5	n.a.	40–48	8,9
Nupela jahninae-reginae	Elliptical-lanceolate to lanceolate	Obtuse, slightly protracted	Convex to slightly parallel in middle	Wide, linear- elliptic	Filiform on both valves, one shorter than other	Linear, narrow	Radiate to convergent at apices	9–14	3–4	n.a.	ca. 50	10

1: This study

2: Tremarin et al. 2015.

3: Reichardt 1988.

4: Rumrich et al. 2000.

5: Krasske 1939.

6: Lange-Bertalot & Moser 1994.

7: Potapova 2013.

8: Reimer 1966.

9: Potapova et al. 2003.

10: Rumrich et al. 2000.

Table 3. Morphological features and measurements of Epithemia boucheziae sp. nov. and similar species. n.a.: no data available.

Species	Valve outline	Apices	Valve margins	Raphe	Striae	Length (µm)	Width (µm)	Costa density (in 10 µm)	Stria density (in 10 µm)	Stria number between two costae	Ref
Epithemia boucheziae sp. nov.	Semi-elliptical	Rounded, slightly curved	Dorsal edge, clearly convex, ventral edge slightly concave	Proximal raphe ends almost straight, slightly expanded-drop shaped. Terminal raphe ends curved to same side of valve	Uniseriate	18–23.0	5.5–7.0	3–4	16–18	4–6	1
Rhopalodia michelorum Krammer	Strongly dorsi-ventral	Quite distinct, narrow, protracted, frequently capitate and bent ventrally	Dorsal convex and ventral nearly straight	Proximal raphe ends curved to the same side	Single rows of areola	17–50	6–10	1.5-2.8	19–24	>8	2
Rhopalodia gibberula (Ehrenberg) O. Müller	Linear-elliptical to broad-elliptical	Broadly rounded to truncate	Dorsal side strongly convex, ventral side strongly concave in large forms, in smaller cells less curved	Proximal raphe ends with fissure in central portion	The areolae are provided with tube-like processes and bordered by C-shaped foramina	25–100	5–12	3–10	12–19	2–8	3, 4
Rhopalodia gibberula (Ehrenberg) O. Müller	Lanceolate to linear-elliptic, retracted in middle	Narrow, protracted, usually capitate and bent ventrally	Dorsal side convex, ventral side less curved, parallel to slightly concave	Proximal raphe ends with fissure in central portion	n.a.	30–33.5	7–8	6–7	20–28	n.a.	5
Rhopalodia gibberula var. miniuens O. Müller	Elliptical, semicircular	Protracted and bent ventrally	Dorsal side very strongly convex, ventral side straight	n.a.	n.a.	26.5	10	5–6	18–20	n.a.	5
Rhopalodia gibberula var. succincta (Brebisson) Fricke	Linear-elliptical	Broadly rounded slightly curved	Dorsal convex and ventral nearly straight	n.a.	n.a.	21–22	5–6	4–5	17–21	n.a.	5
Rhopalodia gibberula var. Van Heurckii O. Müller	Linear-elliptical, retracted in the middle	Narrow, prolonged and bent ventrally	Dorsal convex and ventral concave to straight	n.a.	n.a.	40–45	9.5	4	18–20	n.a.	5
Rhopalodia musculus (Kutzing) O. Müller	Semi-elliptic	Narrowly rounded	Dorsal strongly convex and ventral side concave	Proximally, raphe slits bend ventrally ending in round central pores	Uniseriate	12–80	10–16	3–5	15–20	2–4	6
Rhopalodia acuminata Krammer	Sickle-shaped	Acutely rounded and narrow	Strongly convex dorsally and weakly concave ventrally	n.a.	Uniseriate becoming multiseriate	22–112	7.5–11	4–6	16–19	n.a.	6, 7
Rhopalodia brebissonii Krammer	Broad-elliptical	Protracted and ventrally bent	Strongly convex dorsal margin, straight or slightly concave ventral margin	Almost straight	Double rows of puncta on both sides of raphe canal; single on rest of valve	15–40	5–8.5	3.5–6	17–22	2–5	6

1: This study.

2: Krammer K. 1988.

3: Ehrenberg C.G. 1843.

4: Lange-Bertalot H., Krammer K. 1987.

5: Bourrelly P. & Manguin E. 1952.

6: Krammer K. & H. Lange-Bertalot 1988.

7: Lange-Bertalot H. & Krammer K. 1987.

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