DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species
Abstract
:1. Introduction
2. Materials and Methods
2.1. Nematode Sampling and Identification
2.2. DNA Extraction, PCR Amplification, and DNA Sequencing
2.3. Data Analysis
2.4. Phylogenetic Tree Reconstruction and DNA Taxonomy
3. Results
3.1. Morphological Identification
3.2. Amplification and Sequencing
3.3. Phylogenetic Analysis and DNA Taxonomy
4. Discussion
4.1. Diversity and Distribution of Meiofaunal Marine Nematodes in Mexico
4.2. COI Amplification
4.3. Integrative Taxonomy
4.4. Application of Species Delineation Models to Disentangle Diversity
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sites | Site ID | Lat | Long | Date of Sampling mm/yy/2011 |
---|---|---|---|---|
Cancún | A | 21.140 | −86.677 | 03/11 |
Puerto Morelos | B | 20.508 | −86.525 | 03/11 |
Cozumel (Playa Azul) | C | 20.548 | −86.929 | 03/11 |
Cozumel (Punta sur) | D | 20.291 | −86.959 | 03/11 |
Tulum | E | 20.395 | −87.315 | 03/11 |
Mahahual | F | 18.708 | −87.712 | 09/11 |
Xcalak | G | 18.2475 | −87.8944 | 09/11 |
Taxonomy | Identified Specimens (n) | Sites | Sequences (n) | |
---|---|---|---|---|
Araeolaimida | ||||
Odontophora bermudensis (Jensen & Gerlach, 1976) | 2 | D | 0 | |
Chromadorida | ||||
Actinonema sp.1 | 1 | B | 0 | |
Chromadoridae sp.1 | 1 | G | 0 | |
Chromadoridae sp.2 | 1 | E | 0 | |
Chromadorida sp.1 | 2 | F | 2 | |
Chromadorita sp.1 | 1 | D | 0 | |
Rhips sp.1 | 9 | A; B | 6 | |
Prochromadorella sp.1 | 4 | E | 0 | |
Desmodorida | ||||
Catanema sp.1 | 1 | D | 1 | |
Epsilonema sp.1 | 6 | C; E | 5 | |
Metachromadora sp.1 | 2 | F | 2 | |
Monoposthia mirabilis (Schulz, 1932) | 10 | A; B; D | 8 | |
Onyx litorale (Schulz, 1938) | 2 | D; F | 2 | |
Spirinia sp.1 | 11 | D; F; G | 9 | |
Spirinia sp.2 | 7 | G | 6 | |
Enoplida | ||||
Anticomidae sp.1 | 3 | B | 3 | |
Eurystomina sp.1 | 1 | D | 1 | |
Enoploides sp.1 | 1 | D | 1 | |
Enoploides sp.2 | 3 | C | 2 | |
Enoploides gryphus (Wieser& Hopper, 1967) | 2 | E | 2 | |
Epacanthion sp.1 | 5 | D | 0 | |
Halalaimus sp.1 | 6 | B | 2 | |
Metaparoncholaimus sp.1 | 1 | E | 0 | |
Oncholaimus sp.1 | 9 | E | 0 | |
Pontonema cf. simile (Southern, 1914) Filipjev, 1921 | 1 | E | 1 | |
Proplatycoma fleurdelis (Hope, 1988) | 10 | C; B; E | 1 | |
Monhysterida | ||||
Monhysteridae sp.1 | 1 | F | 1 | |
Xyala striata (Cobb, 1920) | 2 | D | 1 | |
Terschellingia longicaudata (de Man, 1907) | 1 | G | 0 | |
Plectida | ||||
Haliplectus bickneri (Chitwood, 1956) | 1 | B | 1 |
ALGORITHMIC APPROACHES | ||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
BIN System | mPTP Model | ABGD | ||||||||||||||||||||||||
p-value | 0.001 | |||||||||||||||||||||||||
Subst. model | K2P | JC69 | ||||||||||||||||||||||||
Prior intraspecific divergence (P) | 0.0010 | 0.0017 | 0.0028 | 0.0046 | 0.0077 | 0.129 | 0.0010 | 0.0017 | 0.0028 | 0.0046 | 0.0077 | 0.129 | ||||||||||||||
Partition | I | R | I | R | I | R | I | R | I | R | I | R | I | R | I | R | I | R | I | R | I | R | I | R | ||
EiEs | 22 | 20 | 20 | 25 | 20 | 21 | 20 | 21 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 25 | 20 | 21 | 20 | 21 | 20 | 20 | 20 | 20 | 20 | 20 |
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Martínez-Arce, A.; De Jesús-Navarrete, A.; Leasi, F. DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species. Diversity 2020, 12, 107. https://doi.org/10.3390/d12030107
Martínez-Arce A, De Jesús-Navarrete A, Leasi F. DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species. Diversity. 2020; 12(3):107. https://doi.org/10.3390/d12030107
Chicago/Turabian StyleMartínez-Arce, Arely, Alberto De Jesús-Navarrete, and Francesca Leasi. 2020. "DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species" Diversity 12, no. 3: 107. https://doi.org/10.3390/d12030107