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Four Pristionchus species associated with two mass-occurring Parafontaria laminata populations

Natsumi Kanzaki
Natsumi Kanzaki
, 
Minami Ozawa
Minami Ozawa
, 
Yuko Ota
Yuko Ota
 and 
Yousuke Degawa
Yousuke Degawa
   | Nov 30, 2020
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Published Online: Nov 30, 2020
Page range: 1 - 10
DOI: https://doi.org/10.21307/jofnem-2020-115
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© 2020 Natsumi Kanzaki et al., published by Sciendo
This work is licensed under the Creative Commons Attribution 4.0 International License.

Figure 1:

Millipedes (Parafontaria laminata) collected for this study.
Millipedes (Parafontaria laminata) collected for this study.

Figure 2:

Phylogenetic relationships among the 54 haplotypes of four Pristionchus species found in this study. A: Unrooted tree showing the relationships among the four species; B: Phylogenetic relationships among the 47 genotypes of P. degawai. The Maximum Likelihood tree was inferred from partial sequences of the mtCOI gene. The GTR+G model was applied, and the parameters were as follows: lnL = –45,723.93825, freqA = 0.21, freqC = 0.10, freqG = 0.16, freqT = 0.43, R(a) = 3.9, R(b) = 100.0, R(c) = 15.8, R(d) = 14.0, R(e) = 100.0, R(f) = 1.0, and Shape = 0.12. Bootstrap values exceeding 50% are given on the appropriate clades. Some P. fukushimae strains did not amplify with the universal mtCOI primers (Kanzaki and Futai, 2002), probably because of a mutation in the primer region, and these strains were treated as a genotype (they do not appear in the tree). Symbols after haplotype codes indicate the haplotype found only from Nob (open circle), only from Mat (closed circle) and both Nob and Mat (arrow).
Phylogenetic relationships among the 54 haplotypes of four Pristionchus species found in this study. A: Unrooted tree showing the relationships among the four species; B: Phylogenetic relationships among the 47 genotypes of P. degawai. The Maximum Likelihood tree was inferred from partial sequences of the mtCOI gene. The GTR+G model was applied, and the parameters were as follows: lnL = –45,723.93825, freqA = 0.21, freqC = 0.10, freqG = 0.16, freqT = 0.43, R(a) = 3.9, R(b) = 100.0, R(c) = 15.8, R(d) = 14.0, R(e) = 100.0, R(f) = 1.0, and Shape = 0.12. Bootstrap values exceeding 50% are given on the appropriate clades. Some P. fukushimae strains did not amplify with the universal mtCOI primers (Kanzaki and Futai, 2002), probably because of a mutation in the primer region, and these strains were treated as a genotype (they do not appear in the tree). Symbols after haplotype codes indicate the haplotype found only from Nob (open circle), only from Mat (closed circle) and both Nob and Mat (arrow).

Figure 3:

Previous isolation record of Pristionchus spp. associated with millipedes in Japan. The collection localities for the present study are suggested by solid line box, previous record of the species mentioned in the present study are suggested by dotted line box, and Hachijojima Isl. (Carta et al., 2018) is suggested by double line box. N. Kanzaki’s unpubl. obs. is indicated with an asterisk.
Previous isolation record of Pristionchus spp. associated with millipedes in Japan. The collection localities for the present study are suggested by solid line box, previous record of the species mentioned in the present study are suggested by dotted line box, and Hachijojima Isl. (Carta et al., 2018) is suggested by double line box. N. Kanzaki’s unpubl. obs. is indicated with an asterisk.

GenBank accession numbers for the mtCOI haplotypes.

Type Species Accession number Type Species Accession number
A P. fukushimae LC589007 E4 P. degawai LC589034
B LC589008 E5 LC589035
G P. entomophagus LC589009 E6 LC589036
L P. laevicollis LC589010 E7 LC589037
M LC589011 F1 LC589038
O LC589012 F2 LC589039
C P. degawai LC589013 F3 LC589040
D1 LC589014 F4 LC589041
D2 LC589015 F5 LC589042
D3 LC589016 F6 LC589043
D4 LC589017 F7 LC589044
D5 LC589018 F8 LC589045
D6 LC589019 F9 LC589046
D7 LC589020 F10 LC589047
D8 LC589021 F11 LC589048
D9 LC589022 F12 LC589049
D10 LC589023 F13 LC589050
D11 LC589024 F14 LC589051
D12 LC589025 F15 LC589052
D13 LC589026 F16 LC589053
D14 LC589027 F17 LC589054
D15 LC589028 H LC589055
D16 LC589029 I1 LC589056
D17 LC589030 I2 LC589057
E1 LC589031 J LC589058
E2 LC589032 K LC589059
E3 LC589033 N LC589060

Isolation of Pristionchus spp. in the preliminary study.

Matsubara Lake population Nobeyama population
Individual number Gender Nematode species Individual number Gender Nematode species
Mat_1 M P. degawai Nob_1 F P. degawai
Mat_2 F P. degawai Nob_2 M P. degawai, P. laevicollis
Mat_3 M P. degawai Nob_3 M P. degawai
Mat_4 F P. degawai Nob_4 M P. degawai
Mat_5 F P. degawai Nob_5 M P. degawai
Mat_6 M P. degawai Nob_6 M P. degawai
Mat_7 F P. degawai Nob_7 F P. degawai, P. laevicollis
Mat_8 F P. degawai Nob_8 F P. degawai
Mat_9 F P. degawai Nob_9 M P. degawai
Mat_10 F P. degawai Nob_10 F P. degawai
Mat_11 F P. degawai Nob_11 F P. degawai
Mat_12 F P. degawai Nob_12 F P. degawai, P. laevicollis
Mat_13 F P. degawai Nob_13 F P. degawai
Mat_14 F P. degawai Nob_14 M P. degawai
Mat_15 F P. degawai Nob_15 F P. degawai
Mat_16 F P. fukushimae Nob_16 F P. degawai
Mat_17 F P. fukushimae Nob_17 M P. degawai
Mat_18 M P. degawai Nob_18 M P. degawai
Mat_19 F P. degawai Nob_19 F P. laevicollis
Mat_20 F P. degawai Nob_20 F P. degawai
Mat_21 M P. degawai Nob_21 M P. degawai
Mat_22 M P. degawai Nob_22 M P. degawai
Mat_23 F P. degawai Nob_23 F P. degawai
Mat_24 F P. degawai Nob_24 M P. degawai
Mat_25 F P. degawai Nob_25 F P. laevicollis
Mat_26 F P. degawai Nob_26 F P. laevicollis
Mat_27 F P. degawai Nob_27 F P. laevicollis
Mat_28 M P. degawai Nob_28 M P. laevicollis
Mat_29 M P. degawai Nob_29 M P. degawai
Mat_30 F P. degawai Nob_30 M P. degawai
Mat_31 M P. degawai Nob_31 F P. laevicollis
Mat_32 F P. degawai Nob_32 M P. degawai
Mat_33 F P. degawai Nob_33 M P. laevicollis
Nob_34 F P. laevicollis
Nob_35 F P. degawai
Nob_36 F P. degawai
Nob_37 F P. degawai
Nob_38 M P. degawai

Mitochondrial cytochrome oxidase subunit I haplotypes isolated in the extensive study.

Matsubara Lake population Nobeyama population
Individual number Gender Haplotype Individual number Gender Nematode species
Mat101 M D1, D3, D12, F8, N Nob101 F F11, La, Ma
Mat102 F D1, D2, F17 Nob102 M D8, F2, Oa
Mat103 M D3, D5, F1, F14, F15 Nob103 M F2, D14
Mat104 F D1, D8, D16 Nob104 M D8, D14, F2
Mat105 F D1, D12, F1 Nob105 M D8, D14
Mat106 M C, D1, D6, D16 Nob106 M D8, F2, F6, E3, E6
Mat107 F D3, D8, D17 Nob107 F D8
Mat108 F D1, D5, D6, F15, K Nob108 F D14, F12, F13
Mat109 F D5, D8, D13, E1, E6, F1, K Nob109 M D1, E6, E7, La
Mat110 F D2, D3, D12, F1, K, Xa Nob110 F F2, E4
Mat111 F D1, D2, D11, E6, F2, F12 Nob111 F D8, D14
Mat112 F D1, D3, D7, F1, F8 Nob112 F E1, I1
Mat113 F D1, D3, D6, D12, F3 Nob113 F D1, F4, F5, I2
Mat114 F D3, D9, E6, F1, F2, F9, K, Ga Nob114 M D1, F6, D8
Mat115 F D1, D2, D3, D6, D13, F1, F7, F14 Nob115 F F6
Mat116 F D1, F1, F10 Nob116 F D1, D8, D14
Mat117 F D1, D6, D11, F8 Nob117 M F2, F12
Mat118 M D1, D2, D3, D4, D5, D6, D12 Nob118 M D1, D11, E1, E5
Mat119 F D1, D2, D3, F2, H Nob119 F D1, D3, D10, E2, J, Oa
Mat120 F D1, D2, D7, E6, F3 Nob120 F D15, Ma
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