| Literature DB >> 25004106 |
Robert G Foottit1, Eric Maw1, P D N Hebert2.
Abstract
BACKGROUND: Many studies have shown the suitability of sequence variation in the 5' region of the mitochondrial cytochrome c oxidase I (COI) gene as a DNA barcode for the identification of species in a wide range of animal groups. We examined 471 species in 147 genera of Hemiptera: Auchenorrhyncha drawn from specimens in the Canadian National Collection of Insects to assess the effectiveness of DNA barcoding in this group. METHODOLOGY/PRINCIPALEntities:
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Year: 2014 PMID: 25004106 PMCID: PMC4087040 DOI: 10.1371/journal.pone.0101385
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Genera and number of barcoded species in each auchenorrhynch family group. Non-Nearctic genera are designated by an asterisk (*).
| Number of species examined/genus | 5 or more (number of species indicated) | 4 | 3 | 2 | 1 |
| Cicadidae |
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| Fulgoridae and Dictyopharinae |
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| Aphrophoridae and Cercopidae |
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| Cicadellidae |
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| Membracidae and Aetalionidae |
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often treated as a subgenus of Aphrophora.
often treated a subgenus subgenus of Gypona.
generic segregates of Stragania.
PCR primers used in this study.
| Primer Name | Primer sequence (5′-3′) | direction | Primer source |
| LepF2_t1 | M13F | F | Modified from |
| LepF1 |
| F |
|
| LepR1 |
| R |
|
| LCO1490 |
| F |
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| HCO2198 |
| R |
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| tRWF1_t1 | M13F | F |
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| tRWF2_t1 | M13F | F |
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| C_tRWF | tRWF1_t1+tRWF2_t1 | F |
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| MLepF1 |
| F | Paul Hebert |
| MLepR2 |
| R | Sean Prosser |
| C_LepFolF | LepF1+LCO1490 | F | Natalia Ivanova |
| C_LepFolR | LepR1+HCO2198 | R | Natalia Ivanova |
| MHemF |
| F |
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| MHemR |
| R |
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The same primers were used for sequencing amplicons, except that M13F was used to sequence strands primed with the M13-tailed primers.
cocktail primers: indicated primers combined.
M13F = TGTAAAACGACGGCCAG.
Summary statistics for 1150 sequences recovered from museum specimens of Auchenorhyncha.
| Fulgoridae | Cicadidae | Cercopoidea | Cicadellidae | Membracidae | total | |
| number of specimens submitted | 86 | 47 | 123 | 762 | 464 | 1482 |
| age of specimens, range (mean) in yr | 1–56 (35) | 8–56 (33) | 1–81 (24) | 1–57 (28) | 3–59 (35) | |
| success rate (seq >399 bp/specimens sampled) | 65% | 93% | 88% | 79% | 72% | 77% |
| proportion of sequences barcode compliant | 62% | 65% | 81% | 79% | 67% | 75% |
| age of specimens with sequence >399 bp | 1–56 (32) | 8–56 (34) | 1–52 (23) | 1–56 (25) | 3–59 (32) | |
| No. of specimens with sequences >399 bp | 56 | 44 | 109 | 606 | 335 | 1150 |
| >600 bp, (barcode compliant/total) | 35/35 | 27/29 | 81/85 | 470/471 | 219/221 | 837/841 |
| 500–600 bp, (barcode compliant/total) | 0 | 2/3 | 8/8 | 16/16 | 7/7 | 33/34 |
| 400––499 bp | 20 | 12 | 16 | 119 | 107 | 275 |
| no. of identified species | 30 | 41 | 32 | 231 | 137 | 471 |
| with >2 specimens | 6 | 0 | 25 | 115 | 49 | 195 |
| with 2 specimens | 10 | 2 | 4 | 60 | 34 | 110 |
| with 1 specimen | 14 | 39 | 3 | 56 | 54 | 166 |
| no. of undetermined OTUs | 0 | 1 | 1 | 37 | 27 | 66 |
| with >2 specimens | 0 | 0 | 0 | 9 | 3 | 12 |
| with 2 specimens | 0 | 0 | 0 | 5 | 3 | 8 |
| with 1 specimen | 0 | 1 | 1 | 23 | 21 | 46 |
| intraspecific divergence | ||||||
| range (K2P) | 0–2.29 | 0–1.01 | 0–7.47 | 0–8.26 | 0–5.28 | 0–8.26 |
| mean ± se (K2P) | 0.36±0.02 | 0.50±0.25 | 0.51±0.04 | 0.55±0.002 | 0.64±0.01 | 0.56±0.03 |
| range (uncorrected) | 0–2.24 | 0–1.01 | 0–7.03 | 0–7.71 | 0–4.98 | 0–7.71. |
| mean ± se (uncorrected) | 0.36±0.02 | 0.50±0.25 | 0.50±0.04 | 54±0.002 | 0.63±0.01 | 0.55±0.03 |
| distance | ||||||
| minimum pairwise distance <1% | 10% | 26% | 37% | 28% | 19% | 25% |
| minimum distance 1 to 2% | 13% | 7% | 0% | 4% | 3% | 4% |
| minimum distance >2% | 76% | 65% | 62% | 67% | 79% | 70% |
| no. of genera | 11 | 11 | 10 | 59 | 56 | 147 |
| no. of genera with >1 species | 6 | 5 | 5 | 40 | 32 | 88 |
| interspecific divergence within genus (K2P,%) | ||||||
| range | 0.15–16.5 | 0.15–23.25 | 0–20.465 | 0–26.81 | 0–26.19 | 0–26.81 |
| mean ± se | 8.87±0.01 | 9.33±0.02 | 8.28±0.004 | 9.82±0.001 | 11.69±0.004 | 9.91±0.06 |
| inter-generic divergence within family (K2P,%) | ||||||
| range | 7.9–28.9 | 14.6–30.9 | 10.0–29.5 | 5.1–40.2 | 0.2–43.0 | 0.2–43 |
| mean ± se | 19.0±0.2 | 22.3±0.0 | 19.4±0.0 | 24.6±0.0 | 24.3±0.0 | 24.5±0.01 |
Aphrophoridae and Cercopidae.
Membracidae including Aetalionidae.
undetermined at species level, including undescribed taxa.
includes undetermined/undescribed species.
normalized for number of specimens per species.
Species with maximum intraspecific pairwise divergence (K2P) greater than 2%.
| number of specimens | K2P distance (range, %) | uncorrected distance (range, %) | |
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| 3 | 3.47–7.47 | 3.37–7.03 |
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| 3 | 0.15–2.82 | 0.15–2.76 |
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| 3 | 0–8.26 | 0–7.71 |
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| 3 | 0.15–2.18 | 0.15–2.14 |
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| 3 | 0–3.30 | 0–3.21 |
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| 3 | 0–7.72 | 0–7.21 |
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| 2 | 2.02 | 1.99 |
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| 3 | 0.15–2.02 | 0.15–1.99 |
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| 3 | 2.99–4.77 | 2.91–4.59 |
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| 2 | 2.42 | 2.37 |
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| 3 | 1.40–2.34 | 1.22–2.29 |
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| 2 | 2.02 | 1.99 |
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| 3 | 0–2.66 | 0–2.60 |
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| 3 | 3.77 | 3.67 |
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| 2 | 2.03 | 1.99 |
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| 3 | 1.00–3.14 | 1.00–3.06 |
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| 5 | 0.15–2.27 | 0.15–2.24 |
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| 2 | 2.30 | 2.26 |
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| 5 | 0.25–2.57 | 0.25–2.50 |
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| 2 | 2.04 | 2.00 |
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| 6 | 0.75–3.09 | 0.75–3.01 |
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| 6 | 2.54–5.23 | 2.49–4.98 |
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| 2 | 3.15 | 3.05 |
Groups of species with low interspecific distance (minimum pairwise K2P divergence among members of group is less than 2%).
| K2P distance (range, %) | separation criteria | |
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| 0.25 | |
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| 0.15–0.48 | |
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| 0.15 | |
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| 0.48 | |
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| 0.16 | |
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| 0.55–1.4 | |
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| 0.55 | |
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| 1.4 | |
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| 0.75 | |
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| 1.99 | |
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| 0–1.81 | |
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| 0–0.31 | |
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| 0–1.71 | |
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| 0.46–0.75 | |
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| 0–1.26 | male genitalia; color pattern |
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| 0 | size, color |
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| 1.55 | |
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| 0.75 | |
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| 0–0.15 | male genitalia |
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| 0–0.5 | male and female genitalia |
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| 0.5–1.77 | |
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| 0–1.01 | |
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| geographic ssp. | |
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| 0.15–1.87 | |
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| 0.15–0.77 | |
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| 1.51–1.87 | |
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| 1.51 | |
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| 0–0.93 | biology |
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| 0–0.62 | geographic ssp. |
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| 0.15–0.97 | geographic ssp. |
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| 1.86 | |
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| 0.15–0.62 | color, size |
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| 0.62–1.39 | |
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| 0.33–0.99 | geographic ssp. |
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| 1.51–1.77 | |
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| 0 | |
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| 0.31–1.86 | geographic ssp. |
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| 1.39–1.84 | |
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| 0 | biology, size |
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| 0.62–0.85 | |
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| 0–3.29 | wing venation, colour, biology, male genitalia |
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| 0.93–1.99 | |
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| 1.08–1.96 | |
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| 0.31–1.87 | wing venation, colour, biology, male genitalia |
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| 1.71 | |
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| 1.71 | |
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| 0.15–0.46 | character displacement in size; hosts differ |
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| 0.15–0.92 | geographic ssp. |
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| 0.15–0.62 | geographic ssp. |
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| 0.93 | |
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| 0.46 | |
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| 0–1.55 | |
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| 0.31–0.77 | |
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| 0.31–0.67 | hosts |
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| 1.51–2.27 | hosts |
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| 0.47–1.24 | |
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| 1.27 | |
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| 1.68–2.34 | |
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| 0–1.39 | |
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| 1.26 | |
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| 0–1.77 | |
|
| 0–1.70 |
*Gyponana acia grp = G. acia/cacuminal/extenda/mali/parallela/pingua/praelonga/quebecensis/salsa/serpent/striata. Within the acia group: max intraspecific distance = 2.42%; mean between species distance = 1.14%.
Species belonging to genera represented by more than one species for which nearest neighbor is in a different genus.
| species>nearest neighbor | minimum divergence (%) |
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| 16% |
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| 14% |
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| 10% |
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| 8% |
|
| |
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| 14% |
|
| 11% |
|
| 15% |
|
| 10% |
|
| 13% |
|
| 14% |
|
| 13% |
|
| 13% |
|
| 10% |
|
| 14% |
|
| 10% |
|
| 10% |
|
| 13% |
|
| 13% |
|
| 10% |
|
| |
|
| 8% |
|
| 9% |
|
| 5% |
|
| 5% |
|
| 12% |
|
| 8% |
|
| 8% |
|
| 19% |
|
| 9% |
|
| 17% |
|
| ∼0% |
|
| 9% |
|
| 7% |
|
| 12% |
|
| 7% |
|
| ∼0% |
|
| 8% |
|
| 1% |
|
| 19% |
|
| 13% |
|
| 12% |
|
| 2% |
|
| 1% |
|
| 17% |
|
| 5% |
|
| 7% |
|
| 9% |
|
| 9% |
|
| 13% |
K2P divergence value rounded to nearest one percent.