1
|
Jamonneau T, Dahruddin H, Limmon G, Sukmono T, Busson F, Nurjirana, Gani A, Patikawa J, Wuniarto E, Sauri S, Nurhaman U, Wowor D, Steinke D, Keith P, Hubert N. Jump dispersal drives the relationship between micro- and macroevolutionary dynamics in the Sicydiinae (Gobiiformes: Oxudercidae) of Sundaland and Wallacea. J Evol Biol 2024:voae017. [PMID: 38306450 DOI: 10.1093/jeb/voae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 02/04/2024]
Abstract
Insular biodiversity hotspots of Southeast Asia are remarkable for their biodiverse faunas. With a marine larval phase lasting up to several months, the freshwater fish subfamily Sicydiinae has colonized most islands of these hotspots. However, Sicydiinae diversity is still poorly understood in Southeast Asia. With the objective to estimate intraspecific genetic diversity and infer past demography, we conducted the molecular inventory of Sicydiinae species in Sundaland and Wallacea using 652 bp of the mitochondrial cytochrome oxidase I gene, species delimitation methods and Bayesian Skyline plot reconstructions. In total, 24 Molecular Operational Taxonomic Units are delimited among the 603 sequences belonging to 27 species and five genera. Two cases of discordance between morphology and mitochondrial sequence are observed suggesting ongoing speciation and/or introgression in two genera. Multiple new occurrences are reported, either for a single biodiversity hotspot or both, some of which corresponding to observations of a few individuals far from the range distribution of their conspecifics. Among the ten species or species group whose intraspecific diversity was examined, high levels of genetic diversity and past population expansion are revealed by Tajima's D tests and Bayesian Skyline Plot reconstructions. Together these results indicate that long-distance dispersal is common and suggest that most endemic species originated through founder events followed by population expansion. Patterns of sexual dimorphism and males' coloration among diverging species pair seem to point to sexual selection as an important mechanism contributing to speciation in the Sicydiinae of Sundaland and Wallacea.
Collapse
Affiliation(s)
- Tom Jamonneau
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Hadi Dahruddin
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta - Bogor Km 46, Cibinong, West Java, Indonesia
| | - Gino Limmon
- Universitas Pattimura, Maritime and Marine Science Center of Excellence, Jalan Wim Reawaru 9C, 678267 Ambon, Moluccas, Indonesia
| | - Tedjo Sukmono
- Universitas Jambi, Department of Biology, Jalan Lintas Jambi - Muara Bulian Km15, 36122 Jambi, Sumatra, Indonesia
| | - Frédéric Busson
- UMR 7208 BOREA (MNHN, CNRS, UPMC, IRD, UCBN), Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Nurjirana
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta - Bogor Km 46, Cibinong, West Java, Indonesia
| | - Abdul Gani
- Universitas Luwuk Muhammadiyah, Department of Biology, Jalan KH Ahmad Dahlan, 94712 Luwuk, Silawesi, Indonesia
| | - Jesaya Patikawa
- Universitas Pattimura, Maritime and Marine Science Center of Excellence, Jalan Wim Reawaru 9C, 678267 Ambon, Moluccas, Indonesia
| | - Erwin Wuniarto
- Universitas Luwuk Muhammadiyah, Department of Biology, Jalan KH Ahmad Dahlan, 94712 Luwuk, Silawesi, Indonesia
| | - Sopian Sauri
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta - Bogor Km 46, Cibinong, West Java, Indonesia
| | - Ujang Nurhaman
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta - Bogor Km 46, Cibinong, West Java, Indonesia
| | - Daisy Wowor
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta - Bogor Km 46, Cibinong, West Java, Indonesia
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Rd E, Guelph, ON N1G2W1, Canada
| | - Philippe Keith
- UMR 7208 BOREA (MNHN, CNRS, UPMC, IRD, UCBN), Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| |
Collapse
|
2
|
Hempel CA, Wright N, Harvie J, Hleap JS, Adamowicz S, Steinke D. Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments. Nucleic Acids Res 2022; 50:9279-9293. [PMID: 35979944 PMCID: PMC9458450 DOI: 10.1093/nar/gkac689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/05/2022] [Accepted: 07/29/2022] [Indexed: 12/24/2022] Open
Abstract
Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve the taxonomic identification of diverse microbial communities, which could allow for the incorporation of microbes into routine ecological assessments. However, these target-PCR-free techniques require more testing and optimization. In this study, we processed metagenomics and total RNA-Seq data from a commercially available microbial mock community using 672 data-processing workflows, identified the most accurate data-processing tools, and compared their microbial identification accuracy at equal and increasing sequencing depths. The accuracy of data-processing tools substantially varied among replicates. Total RNA-Seq was more accurate than metagenomics at equal sequencing depths and even at sequencing depths almost one order of magnitude lower than those of metagenomics. We show that while data-processing tools require further exploration, total RNA-Seq might be a favorable alternative to metagenomics for target-PCR-free taxonomic identifications of microbial communities and might enable a substantial reduction in sequencing costs while maintaining accuracy. This could be particularly an advantage for routine ecological assessments, which require cost-effective yet accurate methods, and might allow for the incorporation of microbes into ecological assessments.
Collapse
Affiliation(s)
- Christopher A Hempel
- To whom correspondence should be addressed. Tel: +1 519 824 4120; Fax: +1 519 824 5703;
| | - Natalie Wright
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Julia Harvie
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jose S Hleap
- SHARCNET, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Dirk Steinke
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
3
|
Milián-García Y, Hempel CA, Janke LAA, Young RG, Furukawa-Stoffer T, Ambagala A, Steinke D, Hanner RH. Mitochondrial genome sequencing, mapping, and assembly benchmarking for Culicoides species (Diptera: Ceratopogonidae). BMC Genomics 2022; 23:584. [PMID: 35962326 PMCID: PMC9375341 DOI: 10.1186/s12864-022-08743-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial genomes are the most sequenced genomes after bacterial and fungal genomic DNA. However, little information on mitogenomes is available for multiple metazoan taxa, such as Culicoides, a globally distributed, megadiverse genus containing 1,347 species. AIM Generating novel mitogenomic information from single Culicoides sonorensis and C. biguttatus specimens, comparing available mitogenome mapping and de novo assembly tools, and identifying the best performing strategy and tools for Culicoides species. RESULTS We present two novel and fully annotated mitochondrial haplotypes for two Culicoides species, C. sonorensis and C. biguttatus. We also annotated or re-annotated the only available reference mitogenome for C. sonorensis and C. arakawae. All species present a high similarity in mitogenome organization. The general gene arrangement for all Culicoides species was identical to the ancestral insect mitochondrial genome. Only short spacers were found in C. sonorensis (up to 30 bp), contrary to C. biguttatus (up to 114 bp). The mitochondrial genes ATP8, NAD2, NAD6, and LSU rRNA exhibited the highest nucleotide diversity and pairwise interspecific p genetic distance, suggesting that these genes might be suitable and complementary molecular barcodes for Culicoides identification in addition to the commonly utilized COI gene. We observed performance differences between the compared mitogenome generation strategies. The mapping strategy outperformed the de novo assembly strategy, but mapping results were partially biased in the absence of species-specific reference mitogenome. Among the utilized tools, BWA performed best for C. sonorensis while SPAdes, MEGAHIT, and MitoZ were among the best for C. biguttatus. The best-performing mitogenome annotator was MITOS2. Additionally, we were able to recover exogenous mitochondrial DNA from Bos taurus (biting midges host) from a C. biguttatus blood meal sample. CONCLUSIONS Two novel annotated mitogenome haplotypes for C. sonorensis and C. biguttatus using High-Throughput Sequencing are presented. Current results are useful as the baseline for mitogenome reconstruction of the remaining Culicoides species from single specimens to HTS and genome annotation. Mapping to a species-specific reference mitogenome generated better results for Culicoides mitochondrial genome reconstruction than de novo assembly, while de novo assembly resulted better in the absence of a closely related reference mitogenome. These results have direct implications for molecular-based identification of these vectors of human and zoonotic diseases, setting the basis for using the whole mitochondrial genome as a marker in Culicoides identification.
Collapse
Affiliation(s)
- Yoamel Milián-García
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.
| | - Christopher A Hempel
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Lauren A A Janke
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.,John H. Daniels Faculty of Architecture, Landscape, and Design, University of Toronto, 33 Willcocks Street, Toronto, ON, M5S 3B3, Canada
| | - Robert G Young
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Tara Furukawa-Stoffer
- Canadian Food Inspection Agency, National Centre for Animal Disease, 225090 Township Road 9-1, Lethbridge LaboratoryLethbridge, AB, T1J 0P3, Canada
| | - Aruna Ambagala
- National Centre for Foreign Animal Disease, 1015, Arlington Street, Winnipeg, MB, R3E 3M4, Canada
| | - Dirk Steinke
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|
4
|
Steinke D, deWaard SL, Sones JE, Ivanova NV, Prosser SWJ, Perez K, Braukmann TWA, Milton M, Zakharov EV, deWaard JR, Ratnasingham S, Hebert PDN. Message in a Bottle-Metabarcoding enables biodiversity comparisons across ecoregions. Gigascience 2022; 11:6575387. [PMID: 35482490 PMCID: PMC9049109 DOI: 10.1093/gigascience/giac040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/24/2022] [Accepted: 03/29/2022] [Indexed: 12/31/2022] Open
Abstract
Background Traditional biomonitoring approaches have delivered a basic understanding of biodiversity, but they cannot support the large-scale assessments required to manage and protect entire ecosystems. This study used DNA metabarcoding to assess spatial and temporal variation in species richness and diversity in arthropod communities from 52 protected areas spanning 3 Canadian ecoregions. Results This study revealed the presence of 26,263 arthropod species in the 3 ecoregions and indicated that at least another 3,000–5,000 await detection. Results further demonstrate that communities are more similar within than between ecoregions, even after controlling for geographical distance. Overall α-diversity declined from east to west, reflecting a gradient in habitat disturbance. Shifts in species composition were high at every site, with turnover greater than nestedness, suggesting the presence of many transient species. Conclusions Differences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric used in prior efforts to track change in arthropod communities.
Collapse
Affiliation(s)
- D Steinke
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S L deWaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - J E Sones
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - N V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - K Perez
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - T W A Braukmann
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - M Milton
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - E V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - J R deWaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - S Ratnasingham
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| | - P D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ONT N1G 2W1, Canada
| |
Collapse
|
5
|
Greenwood D, Steinke D, Martin S, Norton G, Tully MP. With a new role comes new responsibilities: interviews to explore what Emergency Department Pharmacist Practitioners know and understand about patient safeguarding. International Journal of Pharmacy Practice 2022. [DOI: 10.1093/ijpp/riac021.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Introduction
In the UK, pharmacists with additional clinical skills now work in emergency departments (1). Known as Emergency Department Pharmacist Practitioners (EDPPs), the role was developed in response to a shortage of doctors and nurses. EDPPs carry out activities typical of traditional hospital pharmacists, but also novel ‘practitioner’ activities such as examining patients. They also may act as designated care providers with overall responsibility for patients, which includes a responsibility to safeguard patients (children and vulnerable adults) from harm – as is required of other healthcare professionals who take on that role. The initial safeguarding process comprises four stages: recognition, ensuring safety, documentation and escalation. Professional competence, i.e. to safeguard patients, is underpinned by knowledge of the subject, but also the ability to apply that knowledge (2).
Aim
To investigate what EDPPs know and understand about safeguarding vulnerable children and adults.
Methods
Past and current students of an ‘Advanced Specialist Training in Emergency Medicine’ programme, which delivers additional clinical skills to pharmacists, were interviewed to explore their knowledge and understanding of safeguarding. Interview questions were developed from review of relevant literature, as were four vignettes which were used to further explore participants’ understanding i.e. apply their knowledge of safeguarding to realistic scenarios. Vignettes concerned victims of: theft, sexual abuse, physical abuse and a medication error. A Social Worker reviewed the vignettes for plausibility, suggesting changes e.g. to victim characteristics. The interview schedule and vignettes were then piloted by two acute medicine pharmacists. For analysis, interview transcripts were reviewed with template analysis used to code data to four a priori themes (stages of the initial safeguarding process), and new themes that emerged throughout the process.
Results
Thirteen EDPPs were interviewed (four in 2016, and then a further nine in 2019 following delays due to competing research commitments). In addition to the four a priori themes, a further six themes were identified: scope of safeguarding; responsibility to safeguard; resources and setting; education, training and experiential learning; multidisciplinary working and communication; and culture. Overall, participants had a broad and often detailed knowledge of safeguarding. All four stages were frequently described which demonstrates EDPPs awareness of how safeguarding concerns are both recognised and responded to. Somewhat unsurprisingly, participants were generally more comfortable when responding to medicines related concerns although whether these should be reported via safeguarding or error systems is currently unclear. Several participants were more involved with the formal escalation of issues, and one participant had safeguarding issues escalated to them and had given evidence in court.
Conclusion
Although interview phases were three years apart, no thematic differences were identified between these phases and thematic saturation was also achieved. EDPPs interviewed were aware of the different types of maltreatment and the safeguarding process. Safeguarding training for pharmacists should include a focus on the importance of good inter-professional communication. Training should also include information about the types of medication error (e.g. type and severity) that require escalation via safeguarding, but these first need to be confirmed through future research.
References
(1) Greenwood D, Tully MP, Martin S, Steinke D. The description and definition of Emergency Department Pharmacist Practitioners in the United Kingdom (the ENDPAPER study). International journal of clinical pharmacy. 2019 Apr;41(2):434-44.
(2) James KL, Davies JG, Kinchin I, Patel JP, Whittlesea C. Understanding vs. competency: the case of accuracy checking dispensed medicines in pharmacy. Advances in health sciences education. 2010 Dec;15(5):735-47.
Collapse
Affiliation(s)
- D Greenwood
- School of Medicine, Anglia Ruskin University, Chelmsford, United Kingdom
- Division of Pharmacy and Optometry, University of Manchester, Manchester, United Kingdom
| | - D Steinke
- Division of Pharmacy and Optometry, University of Manchester, Manchester, United Kingdom
| | - S Martin
- School of Pharmacy and Medical Sciences, University of Bradford, Bradford, United Kingdom
| | - G Norton
- Division of Pharmacy and Optometry, University of Manchester, Manchester, United Kingdom
| | - M P Tully
- Division of Pharmacy and Optometry, University of Manchester, Manchester, United Kingdom
| |
Collapse
|
6
|
Greenwood D, Tully MP, Martin S, Steinke D. Development of the Manchester framework for the evaluation of emergency department pharmacy services. Int J Clin Pharm 2022; 44:930-938. [PMID: 35449350 PMCID: PMC9393142 DOI: 10.1007/s11096-022-01403-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Many countries, including the United Kingdom, have established Emergency Department (ED) pharmacy services where some ED pharmacists now work as practitioners. They provide both traditional pharmaceutical care and novel practitioner care i.e. clinical examination, yet their impact on quality of care is unknown. AIM To develop a framework of structures, processes and potential outcome indicators to support evaluation of the quality of ED pharmacy services in future studies. METHOD Framework components (structures, processes and potential outcome indicators) were identified in three ways: from a narrative review of relevant international literature, and separate panel meetings with ED pharmacists and then other ED healthcare professionals. Structures and processes were collated into categories developed iteratively throughout data collection, with outcome indicators collated into six domains of quality as proposed by the Institute of Medicine. These raw data were then processed e.g. outcome indicators screened for clarity i.e. those which explicitly stated what would be measured were included in the framework. RESULTS A total of 190 structures, 533 processes, and 503 outcome indicators were identified. Through data processing a total of 153 outcome indicators were included in the final framework divided into the domains safe (32), effective (50), patient centred (18), timely (24), efficient (20) and equitable (9). CONCLUSION The first framework specific to the quality evaluation ED pharmacy services, service evaluators should validate potential outcome indicators prior to their use. The minimum expected of a high-quality service should also be defined to enable interpretation of relevant measurements.
Collapse
Affiliation(s)
- D Greenwood
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, M13 9PT, Manchester, UK. .,School of Medicine, Anglia Ruskin University, Bishop Hall Lane, CM1 1SQ, Chelmsford, UK.
| | - MP Tully
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, M13 9PT Manchester, UK
| | - S Martin
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, M13 9PT Manchester, UK ,School of Pharmacy and Medical Sciences, University of Bradford, Richmond Road, BD7 1DP Bradford, UK
| | - D Steinke
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, M13 9PT Manchester, UK
| |
Collapse
|
7
|
Turunen J, Mykrä H, Elbrecht V, Steinke D, Braukmann T, Aroviita J. The power of metabarcoding: Can we improve bioassessment and biodiversity surveys of stream macroinvertebrate communities? MBMG 2021. [DOI: 10.3897/mbmg.5.68938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most stream bioassessment and biodiversity surveys are currently based on morphological identification of communities. However, DNA metabarcoding is emerging as a fast and cost-effective alternative for species identification. We compared both methods in a survey of benthic macroinvertebrate communities across 36 stream sites in northern Finland. We identified 291 taxa of which 62% were identified only by DNA metabarcoding. DNA metabarcoding produced extensive species level inventories for groups (Oligochaeta, Chironomidae, Simuliidae, Limoniidae and Limnephilidae), for which morphological identification was not feasible due to the high level of expertise needed. Metabarcoding also provided more insightful taxonomic information on the occurrence of three red-listed vulnerable or data deficient species, the discovery of two likely cryptic and potentially new species to Finland and species information of insect genera at an early larval stage that could not be separated morphologically. However, it systematically failed to reliably detect the occurrence of gastropods that were easily identified morphologically. The impact of mining on community structure could only be shown using DNA metabarcoding data which suggests that the finer taxonomic detail can improve detection of subtle impacts. Both methods generally exhibited similar strength of community-environment relationships, but DNA metabarcoding showed better performance with presence/absence data than with relative DNA sequence abundances. Our results suggest that DNA metabarcoding holds a promise for future anthropogenic impact assessments, although, in our case, the performance did not improve much from the morphological species identification. The key advantage of DNA metabarcoding lies in efficient biodiversity surveys, taxonomical studies and applications in conservation biology.
Collapse
|
8
|
Elbrecht V, Lindner A, Manerus L, Steinke D. A bright idea-metabarcoding arthropods from light fixtures. PeerJ 2021; 9:e11841. [PMID: 34395083 PMCID: PMC8320520 DOI: 10.7717/peerj.11841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022] Open
Abstract
Arthropod communities in buildings have not been extensively studied, although humans have always shared their homes with them. In this study we explored if arthropod DNA can be retrieved and metabarcoded from indoor environments through the collection of dead specimens in light fixtures to better understand what shapes arthropod diversity in our homes. Insects were collected from 45 light fixtures at the Centre for Biodiversity Genomics (CBG, Guelph, Canada), and by community scientists at 12 different residential homes in Southern Ontario. The CBG ground floor of the CBG showed the greatest arthropod diversity, especially in light fixtures that were continuously illuminated. The community scientist samples varied strongly by light fixture type, lightbulb used, time passed since lamp was last cleaned, and specimen size. In all cases, the majority of OTUs was not shared between samples even within the same building. This study demonstrates that light fixtures might be a useful resource to determine arthropod diversity in our homes, but individual samples are likely not representative of the full diversity.
Collapse
Affiliation(s)
- Vasco Elbrecht
- Department of Environmental Systems Science Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zurich, Zurich, Switzerland
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Angie Lindner
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Laura Manerus
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
9
|
Crobe V, Ferrari A, Hanner R, Leslie RW, Steinke D, Tinti F, Cariani A. Molecular Taxonomy and Diversification of Atlantic Skates (Chondrichthyes, Rajiformes): Adding More Pieces to the Puzzle of Their Evolutionary History. Life (Basel) 2021; 11:life11070596. [PMID: 34206388 PMCID: PMC8303890 DOI: 10.3390/life11070596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/19/2021] [Accepted: 06/20/2021] [Indexed: 11/16/2022] Open
Abstract
Conservation and long-term management plans of marine species need to be based upon the universally recognized key-feature of species identity. This important assignment is particularly challenging in skates (Rajiformes) in which the phenotypic similarity between some taxa and the individual variability in others, hampers accurate species identification. Here, 432 individual skate samples collected from four major ocean areas of the Atlantic were barcoded and taxonomically analysed. A BOLD project ELASMO ATL was implemented with the aim of establishing a new fully available and well curated barcode library containing both biological and molecular information. The evolutionary histories of the 38 skate taxa were estimated with two concatenated mitochondrial markers (COI and NADH2) through Maximum Likelihood and Bayesian inference. New evolutionary lineages within the genus Raja were discovered off Angola, where paleogeographic history coupled with oceanographic discontinuities could have contributed to the establishment of isolated refugia, playing a fundamental role among skates' speciation events. These data successfully resolved many taxonomic ambiguities, identified cryptic diversity within valid species and demonstrated a highly cohesive monophyletic clustering among the order, laying the background for further inference of evolutionary patterns suitable for addressing management and conservation issues.
Collapse
Affiliation(s)
- Valentina Crobe
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 240126 Bologna, Italy; (A.F.); (A.C.)
- Correspondence: (V.C.); (F.T.)
| | - Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 240126 Bologna, Italy; (A.F.); (A.C.)
| | - Robert Hanner
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Robin W. Leslie
- Department of Agriculture, Forestry and Fisheries (DAFF), Branch Fisheries Management, Cape Town 8018, South Africa;
- Department of Ichthyology and Fisheries Science (DIFS), Rhodes University, Grahamstown 6139, South Africa
| | - Dirk Steinke
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 240126 Bologna, Italy; (A.F.); (A.C.)
- Correspondence: (V.C.); (F.T.)
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 240126 Bologna, Italy; (A.F.); (A.C.)
| |
Collapse
|
10
|
Arida E, Ashari H, Dahruddin H, Fitriana YS, Hamidy A, Irham M, Kadarusman, Riyanto A, Wiantoro S, Zein MSA, Hadiaty RK, Apandi, Krey F, Kurnianingsih, Melmambessy EHP, Mulyadi, Ohee HL, Saidin, Salamuk A, Sauri S, Suparno, Supriatna N, Suruwaky AM, Laksono WT, Warikar EL, Wikanta H, Yohanita AM, Slembrouck J, Legendre M, Gaucher P, Cochet C, Delrieu-Trottin E, Thébaud C, Mila B, Fouquet A, Borisenko A, Steinke D, Hocdé R, Semiadi G, Pouyaud L, Hubert N. Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes. Mol Ecol Resour 2021; 21:2369-2387. [PMID: 33942522 DOI: 10.1111/1755-0998.13411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.
Collapse
Affiliation(s)
- Evy Arida
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Hidayat Ashari
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Hadi Dahruddin
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Yuli Sulistya Fitriana
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Amir Hamidy
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Mohammad Irham
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Kadarusman
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Awal Riyanto
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Sigit Wiantoro
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Moch Syamsul Arifin Zein
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Renny K Hadiaty
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Apandi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Frengky Krey
- Jurusan Perikanan, Fakultas Perikanan dan Ilmu Kelautan, Universitas Papua, Jl. Gunung Salju Amban, Manokwari, Indonesia
| | - Kurnianingsih
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Edy H P Melmambessy
- Program Studi Manajemen Sumberdaya Perairan, Fakultas Pertanian, Universitas Musamus, Jl. Kamizaun Mopah Lama, Rimba Jaya, Merauke, Indonesia
| | - Mulyadi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Henderite L Ohee
- Jurusan Biologi, Fakultas MIPA, Universitas Cendrawasih, Jl. Kamp Wolker Waena Jayapura, Jayapura, Indonesia
| | - Saidin
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Ayub Salamuk
- Dinas Kelautan dan Perikanan Kabupaten Kaimana, Jl.Utarum Kampung Coa, Kaimana, Indonesia
| | - Sopian Sauri
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Suparno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Nanang Supriatna
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Amir M Suruwaky
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Wahyudi Tri Laksono
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Evie L Warikar
- Jurusan Biologi, Fakultas MIPA, Universitas Cendrawasih, Jl. Kamp Wolker Waena Jayapura, Jayapura, Indonesia
| | - Hadi Wikanta
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Aksamina M Yohanita
- Jurusan Biologi, Fakultas MIPA, Universitas Papua Jl. Gunung Salju - Amban, Manokwari, Indonesia
| | - Jacques Slembrouck
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Marc Legendre
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Philippe Gaucher
- USR LEEISA- Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens, Centre de Recherche de Montabo, cayenne, French Guiana
| | - Christophe Cochet
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | | | | | - Borja Mila
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Antoine Fouquet
- UMR 5174 EDB CNRS, Université Paul Sabatier, IRD, Toulouse, France
| | - Alex Borisenko
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dirk Steinke
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Régis Hocdé
- UMR 9190 MARBEC (IRD, UM, CNRS, IFREMER), Université de Montpellier, Montpellier, France
| | - Gono Semiadi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Laurent Pouyaud
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| |
Collapse
|
11
|
Hleap JS, Littlefair JE, Steinke D, Hebert PDN, Cristescu ME. Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes. Mol Ecol Resour 2021; 21:2190-2203. [PMID: 33905615 DOI: 10.1111/1755-0998.13407] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 03/08/2021] [Accepted: 04/19/2021] [Indexed: 01/04/2023]
Abstract
The effective use of metabarcoding in biodiversity science has brought important analytical challenges due to the need to generate accurate taxonomic assignments. The assignment of sequences to genus or species level is critical for biodiversity surveys and biomonitoring, but it is particularly challenging as researchers must select the approach that best recovers information on species composition. This study evaluates the performance and accuracy of seven methods in recovering the species composition of mock communities by using COI barcode fragments. The mock communities varied in species number and specimen abundance, while upstream molecular and bioinformatic variables were held constant, and using a set of COI fragments. We evaluated the impact of parameter optimization on the quality of the predictions. Our results indicate that BLAST top hit competes well with more complex approaches if optimized for the mock community under study. For example, the two machine learning methods that were benchmarked proved more sensitive to reference database heterogeneity and completeness than methods based on sequence similarity. The accuracy of assignments was impacted by both species and specimen counts (query compositional heterogeneity) which ultimately influence the selection of appropriate software. We urge researchers to: (i) use realistic mock communities to allow optimization of parameters, regardless of the taxonomic assignment method employed; (ii) carefully choose and curate the reference databases including completeness; and (iii) use QIIME, BLAST or LCA methods, in conjunction with parameter tuning to better assign taxonomy to diverse communities, especially when information on species diversity is lacking for the area under study.
Collapse
Affiliation(s)
- Jose S Hleap
- Department of Biology, McGill University, Montreal, QC, Canada.,SHARCNET, University of Guelph, Guelph, ON, Canada.,Fundacion SQUALUS, Cali, Colombia
| | - Joanne E Littlefair
- Department of Biology, McGill University, Montreal, QC, Canada.,Queen Mary University of London, London, UK
| | - Dirk Steinke
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | | |
Collapse
|
12
|
Steinke D, Braukmann TWA, Manerus L, Woodhouse A, Elbrecht V. Effects of Malaise trap spacing on species richness and composition of terrestrial arthropod bulk samples. MBMG 2021. [DOI: 10.3897/mbmg.5.59201] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Malaise trap is a popular device for assessing diverse terrestrial arthropod communities because it collects large samples with modest effort. A number of factors influence its collection efficiency, placement being one of them. For instance, when designing larger biotic surveys using arrays of Malaise traps we need to know the optimal distance between individual traps that maximises observable species richness and community composition. We examined the influence of spacing between Malaise traps by metabarcoding samples from two field experiments at a site in Waterloo, Ontario, Canada. For one experiment, we used two trap pairs deployed at weekly increasing distances (3 m increments from 3 to 30 m). The second experiment involved a total of 10 traps set up in a row at 3 m distance intervals for three consecutive weeks.
Results show that community similarity of samples decreases over distance between traps. The amount of species shared between trap pairs drops considerably at about 18 m trap-to-trap distance. This change can be observed across all major taxonomic groups and for two different habitat types (grassland and forest). Large numbers of OTUs found only once within samples cause rather large dissimilarity between distance pairs even at close proximity. This could be caused by a large number of transient species from adjacent habitats which arrive at the trap through passive transport, as well as capture of rare taxa, which end up in different traps by chance.
Collapse
|
13
|
Alqenae FA, Steinke D, Keers RN. Evaluating the Utilisation of a Service Designed to Enhance Care with Medicines Following Acute Hospital Discharge: A Retrospective Study. International Journal of Pharmacy Practice 2021. [DOI: 10.1093/ijpp/riab015.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Introduction
Medication safety challenges are common after hospital discharge and an important global health care improvement target [1,2]. ‘Transfers of Care Around Medicines’ (TCAM) services have been suggested as an intervention that may help address this problem, and are designed to enable the referral of patients on discharge from the hospital to a named community pharmacy in the surrounding Clinical Commissioning Group (CCG). A TCAM service was launched by a large NHS Trust in England in February 2019 to enhance medicines communication and optimisation between primary and secondary care following hospital discharge. The TCAM service is delivered through the PharmOutcomes™ platform, and the initial focus of the service was to support patients with new or existing Monitored Dosage Systems (MDS).
Aim
To evaluate the utilisation of the TCAM service in the host NHS Trust and surrounding CCG through the examination of the nature and outcome of referrals made to community pharmacy.
Method
Anonymised service delivery data of patients referred from the TCAM service via the PharmOutcomes™ platform between March 2019 – February 2020 were retrospectively examined. The data comprised important variables, including patient demographics, status and time of referrals, and referral outcomes including problems/errors identified with medications and services provided by the community pharmacy such as medicines reconciliation. Study approvals were obtained from the host NHS Trust and the Health Research Authority (HRA); the study was exempt from the University Research Ethics Committee (UREC) approval [2019-7048-10983].
Results
A total of 3,033 TCAM referrals to 67 community pharmacies were analysed. Most referrals were for patients aged 70 and above (72%, n=2,195) and 56% (n=1,713/3,033) of the referrals were for female patients. The number of referrals varied between 215 and 310 per month (median 246, Inter quartile range [IQR] 234 - 268). Most referrals (67%, 2,038/3,033) were marked as ‘completed’ by the community pharmacies, with 32.8% (n=995) left uncompleted. The rate of referral completion varied between 59 and 80% per month (median 66.4, IQR 64.5 - 70). Five (0.2%) patients were identified by community pharmacies that had adverse drug reactions (ADRs) from the cohort of 2,038 patients with completed referrals, with 45 (2%, n=45/2,038) identified as having issues that necessitated referral to the general practitioner (GP). The most common reason for referral to GP was medication changes identified from hospital, incorrect repeat prescriptions following discharge, to request a new prescription or weekly MDS, and to inform the GP that the patient has stopped taking their medication. The most common services carried out in community pharmacies following referral were reported as medicines reconciliation (47%, n=954/2,038), followed by review of information (46.7%, n=952/2,038), home delivery of medication (39%, n=798/2,038), review MDS arrangements (23.6%, n=482/2,038), commence MDS (18.6%, n=380/2,038), and pharmacy managed repeat service (12%, n=254/2,038). The main strength of this study is the inclusion of referral data that occurred over a one-year period, while the data were limited in generalisability due to inclusion of one geographical region and only patients using MDS.
Conclusion
The findings of this study may inform the ongoing development of electronic pharmacy referral systems for use at hospital discharge.
References
1. Alqenae FA, Steinke D, Keers RN. Prevalence and Nature of Medication Errors and Medication-Related Harm Following Discharge from Hospital to Community Settings: A Systematic Review. Drug safety. 2020 Mar 3:1–21.
2. World Health Organization. Global patient safety challenge: medication without harm. 2017; p. 1–16. http://apps.who.int/iris/bitstream/10665/255263/1/WHO-HIS-SDS-2017.6-eng.pdf?ua=1&ua=1 . Accessed 20 September 2020.
Collapse
Affiliation(s)
- F A Alqenae
- Centre for Pharmacoepidemiology and Drug Safety, Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Manchester, UK
| | - D Steinke
- Centre for Pharmacoepidemiology and Drug Safety, Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Manchester, UK
- Pharmacy Department, Manchester University NHS Foundation Trust, Manchester, UK
| | - R N Keers
- Centre for Pharmacoepidemiology and Drug Safety, Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Manchester, UK
- Pharmacy Department, Greater Manchester Mental Health NHS Foundation Trust, Manchester, UK
| |
Collapse
|
14
|
Baloğlu B, Chen Z, Elbrecht V, Braukmann T, MacDonald S, Steinke D. A workflow for accurate metabarcoding using nanopore MinION sequencing. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13561] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Bilgenur Baloğlu
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Zhewei Chen
- California Institute of Technology Pasadena CA USA
| | - Vasco Elbrecht
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
- Centre for Biodiversity MonitoringZoological Research Museum Alexander Koenig Bonn Germany
| | - Thomas Braukmann
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Shanna MacDonald
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
- Integrative Biology University of Guelph Guelph ON Canada
| |
Collapse
|
15
|
Delrieu‐Trottin E, Durand J, Limmon G, Sukmono T, Kadarusman, Sugeha HY, Chen W, Busson F, Borsa P, Dahruddin H, Sauri S, Fitriana Y, Zein MSA, Hocdé R, Pouyaud L, Keith P, Wowor D, Steinke D, Hanner R, Hubert N. Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods. Evol Appl 2020; 13:1451-1467. [PMID: 32684969 PMCID: PMC7359824 DOI: 10.1111/eva.12926] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/25/2022] Open
Abstract
DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.
Collapse
Affiliation(s)
- Erwan Delrieu‐Trottin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
- Museum für NaturkundeLeibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Jean‐Dominique Durand
- UMR 9190 MARBEC (IRD, UM, CNRS, IFREMER)Université de MontpellierMontpellier CedexFrance
| | - Gino Limmon
- Maritime and Marine Science Center of ExcellenceUniversitas PattimuraAmbonIndonesia
| | - Tedjo Sukmono
- Department of BiologyUniversitas JambiJambiIndonesia
| | - Kadarusman
- Politeknik Kelautan dan Perikanan SorongKota SorongIndonesia
| | - Hagi Yulia Sugeha
- Research Center for OceanographyIndonesian Institute of SciencesJakartaIndonesia
| | - Wei‐Jen Chen
- Institute of OceanographyNational Taiwan UniversityTaipeiTaiwan
| | - Frédéric Busson
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
- UMR 7208 BOREA (MNHN, CNRS, UPMC, IRD, UCBN)Muséum National d’Histoire NaturelleParis CedexFrance
| | - Philippe Borsa
- UMR 250 ENTROPIE (IRD, UR, UNC, CNRS, IFREMER), Centre IRD‐OccitanieMontpellierFrance
| | - Hadi Dahruddin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | - Sopian Sauri
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | - Yuli Fitriana
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | | | - Régis Hocdé
- UMR 9190 MARBEC (IRD, UM, CNRS, IFREMER)Université de MontpellierMontpellier CedexFrance
| | - Laurent Pouyaud
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
| | - Philippe Keith
- UMR 7208 BOREA (MNHN, CNRS, UPMC, IRD, UCBN)Muséum National d’Histoire NaturelleParis CedexFrance
| | - Daisy Wowor
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | - Dirk Steinke
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphONCanada
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Robert Hanner
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphONCanada
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
| |
Collapse
|
16
|
Wood S, Hyrich K, Verstappen S, Steinke D. AB1203 INVESTIGATING THE VIEWS OF COMMUNITY PHARMACISTS ON THEIR ROLE IN THE MANAGEMENT OF RHEUMATOID ARTHRITIS. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.4344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Medicines optimisation is essential in the long-term management of rheumatoid arthritis (RA), particularly when considering combinations of conventional synthetic disease-modifying anti-rheumatic drugs (csDMARDs). Community pharmacists are ideally placed to optimise medicines use including monitoring side effects, counselling on dose and frequency and improving medicines adherence; however, in some countries, such as the UK, there are currently no community pharmacy services that address csDMARD use and little is known about the role community pharmacists play in managing RA as a long-term condition.Objectives:The objectives of this qualitative study were to understand community pharmacists’ views of their training, knowledge and current role in the management of RA.Methods:We conducted 9 semi-structured, face-to-face or telephone interviews with community pharmacists based in the UK; all were transcribed verbatim. A topic guide, used to inform the interviews, covered four key areas: 1) knowledge and training, 2) pharmacological management 3) patients and services, 4) potential role. The transcriptions were then imported into NVivo for thematic analysis. A coding framework was developed from continual emerging themes and applied to the transcripts.Results:Five male/4 female participants, the median age was 39 years (range 27 to 42) with a median number of years qualified as a pharmacist of 12 years (range 5 to 20) were included. The participants covered a range of roles including: pharmacist non-manager, pharmacist manager, locum pharmacist, superintendent pharmacist and relief pharmacist.In assessing the current role of community pharmacists, 4 main themes were identified: (1) access to information about the patient’s condition as a barrier, (2) their lack of knowledge in the management of RA, (3) providing practical advice about taking csDMARDs, and (4) exploring the reasons for non-adherence before taking further action. In assessing the potential role of community pharmacists, a further 2 themes were identified: improving access to information about the patient’s condition before the current role can be increased and other barriers to an additional role, including time and funding.In the theme ‘access to information as a barrier’ the most common point made was about the lack of information available to pharmacists on the individual indication for medicines. Pharmacists said this posed a barrier both to current practice and their potential role. No participants suggested the potential for an additional service specifically for RA, but some suggested that current services could be expanded to include RA as a target group. Participants discussed side effect counselling and ensuring access to medicines in detail with patients, but only 2 briefly mentioned discussing the benefits of csDMARDs.Conclusion:This is the first in-depth exploration of the perspectives of community pharmacists on the management of RA in community pharmacy. This study has highlighted several important barriers both environmental and personal including time, education and resources that, if addressed, could allow community pharmacists to play a greater role in the management of RA.Disclosure of Interests:Sarah Wood: None declared, Kimme Hyrich Grant/research support from: Pfizer, UCB, BMS, Speakers bureau: Abbvie, Suzanne Verstappen Grant/research support from: BMS, Consultant of: Celltrion, Speakers bureau: Pfizer, Douglas Steinke: None declared
Collapse
|
17
|
Limmon G, Delrieu-Trottin E, Patikawa J, Rijoly F, Dahruddin H, Busson F, Steinke D, Hubert N. Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia). Ecol Evol 2020; 10:3356-3366. [PMID: 32273993 PMCID: PMC7141007 DOI: 10.1002/ece3.6128] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 01/01/2023] Open
Abstract
The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.
Collapse
Affiliation(s)
- Gino Limmon
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Erwan Delrieu-Trottin
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- Museum für Naturkunde Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der Humboldt-Universität zu Berlin Berlin Germany
| | - Jesaya Patikawa
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Frederik Rijoly
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Hadi Dahruddin
- Division of Zoology Research Center for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia
| | - Frédéric Busson
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN) Muséum National d'Histoire Naturelle Paris France
| | - Dirk Steinke
- Department of Integrative Biology Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
| |
Collapse
|
18
|
Sholihah A, Delrieu-Trottin E, Sukmono T, Dahruddin H, Risdawati R, Elvyra R, Wibowo A, Kustiati K, Busson F, Sauri S, Nurhaman U, Dounias E, Zein MSA, Fitriana Y, Utama IV, Muchlisin ZA, Agnèse JF, Hanner R, Wowor D, Steinke D, Keith P, Rüber L, Hubert N. Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes. Sci Rep 2020; 10:2818. [PMID: 32071342 PMCID: PMC7028728 DOI: 10.1038/s41598-020-59544-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/20/2020] [Indexed: 11/25/2022] Open
Abstract
Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.
Collapse
Affiliation(s)
- Arni Sholihah
- Instut Teknologi Bandung, School of Life Sciences and Technology, Bandung, Indonesia.,UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France
| | - Erwan Delrieu-Trottin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.,Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstrasse 43, Berlin, 10115, Germany
| | - Tedjo Sukmono
- Universitas Jambi, Department of Biology, Jalan Lintas Jambi - Muara Bulian Km15, 36122, Jambi, Sumatra, Indonesia
| | - Hadi Dahruddin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.,Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Renny Risdawati
- Department of Biology Education, STKIP PGRI Sumatera Barat, Jl Gunung Pangilun, Padang, 25137, Indonesia
| | - Roza Elvyra
- Universitas Riau, Department of Biology, Simpang Baru, Tampan, Pekanbaru, 28293, Indonesia
| | - Arif Wibowo
- Southeast Asian Fisheries Development Center, Inland Fisheries Resources Development and Management Department, 8 Ulu, Seberang Ulu I, Palembang, 30267, Indonesia.,Research Institute for Inland Fisheries and Fisheries extensions, Agency for Marine and Fisheries Research, Ministry of Marine Affairs and Fisheries., Jl. H.A. Bastari No. 08, Jakabaring, Palembang, 30267, Indonesia
| | - Kustiati Kustiati
- Universitas Tanjungpura, Department of Biology, Jalan Prof. Dr. H. Hadari Nawawi, Pontianak, 78124, Indonesia
| | - Frédéric Busson
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.,UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN), Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231, Paris, cedex, 05, France
| | - Sopian Sauri
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Ujang Nurhaman
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Edmond Dounias
- UMR 5175 CEFE (IRD, UM, CNRS, EPHE), 1919 route de Mende, 34293, Montpellier, cedex, 05, France
| | - Muhamad Syamsul Arifin Zein
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Yuli Fitriana
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Ilham Vemendra Utama
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | | | - Jean-François Agnèse
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France
| | - Robert Hanner
- Department of Integrative Biology, Centre for Biodiversity Genomics, 50 Stone Rd E, Guelph, ON, N1G2W1, Canada
| | - Daisy Wowor
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Dirk Steinke
- Department of Integrative Biology, Centre for Biodiversity Genomics, 50 Stone Rd E, Guelph, ON, N1G2W1, Canada
| | - Philippe Keith
- UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN), Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231, Paris, cedex, 05, France
| | - Lukas Rüber
- Naturhistorisches Museum Bern, Bernastrasse 15, Bern, 3005, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.
| |
Collapse
|
19
|
deWaard JR, Ratnasingham S, Zakharov EV, Borisenko AV, Steinke D, Telfer AC, Perez KHJ, Sones JE, Young MR, Levesque-Beaudin V, Sobel CN, Abrahamyan A, Bessonov K, Blagoev G, deWaard SL, Ho C, Ivanova NV, Layton KKS, Lu L, Manjunath R, McKeown JTA, Milton MA, Miskie R, Monkhouse N, Naik S, Nikolova N, Pentinsaari M, Prosser SWJ, Radulovici AE, Steinke C, Warne CP, Hebert PDN. A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples. Sci Data 2019; 6:308. [PMID: 31811161 PMCID: PMC6897906 DOI: 10.1038/s41597-019-0320-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/11/2019] [Indexed: 01/08/2023] Open
Abstract
The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.
Collapse
Affiliation(s)
- Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Alex V Borisenko
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Angela C Telfer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kate H J Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Monica R Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Crystal N Sobel
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Arusyak Abrahamyan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kyrylo Bessonov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Stephanie L deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kara K S Layton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Ocean Frontier Institute, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jaclyn T A McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Megan A Milton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Norm Monkhouse
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Nadya Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Connor P Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.
| |
Collapse
|
20
|
Elbrecht V, Braukmann TW, Ivanova NV, Prosser SW, Hajibabaei M, Wright M, Zakharov EV, Hebert PD, Steinke D. Validation of COI metabarcoding primers for terrestrial arthropods. PeerJ 2019; 7:e7745. [PMID: 31608170 PMCID: PMC6786254 DOI: 10.7717/peerj.7745] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/25/2019] [Indexed: 01/08/2023] Open
Abstract
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. This study tests the performance of 36 primer sets on a mock community containing 374 insect species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets were also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from both mock community and Malaise trap sample metabarcoding were used to select four primer sets for additional evaluation at different annealing temperatures (40-60 °C) using the mock community. The effect of temperature varied by primer pair but overall it only had a minor effect on taxon recovery. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrates that certain primer sets can recover most taxa in a diverse species assemblage. Thus, based our experimental set up, there is no need to employ several primer sets targeting the same gene region. We identify several suitable primer sets for arthropod metabarcoding, and specifically recommend BF3 + BR2, as it is not affected by primer slippage and provides maximal taxonomic resolution. The fwhF2 + fwhR2n primer set amplifies a shorter fragment and is therefore ideal when targeting degraded DNA (e.g., from gut contents).
Collapse
Affiliation(s)
- Vasco Elbrecht
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Natalia V. Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Sean W.J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Michael Wright
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
21
|
Braukmann TWA, Ivanova NV, Prosser SWJ, Elbrecht V, Steinke D, Ratnasingham S, de Waard JR, Sones JE, Zakharov EV, Hebert PDN. Metabarcoding a diverse arthropod mock community. Mol Ecol Resour 2019; 19:711-727. [PMID: 30779309 PMCID: PMC6850013 DOI: 10.1111/1755-0998.13008] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/13/2019] [Indexed: 12/31/2022]
Abstract
Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 species. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways. The first two protocols involved the construction of bulk DNA extracts from different body segments (Bulk Abdomen, Bulk Leg). The other protocols involved the production of DNA extracts from single legs which were then merged prior to PCR (Composite Leg) or PCR‐amplified separately (Single Leg) and then pooled. The amplicons generated by these four treatments were then sequenced on three platforms (Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5). The choice of sequencing platform did not substantially influence species recovery, although the Miseq delivered the highest sequence quality. As expected, species recovery was most efficient from the Single Leg treatment because amplicon abundance varied little among taxa. Among the three treatments where PCR occurred after pooling, the Bulk Abdomen treatment produced a more uniform read abundance than the Bulk Leg or Composite Leg treatment. Primer choice also influenced species recovery and evenness. Our results reveal how variation in protocols can have substantial impacts on perceived diversity unless sequencing coverage is sufficient to reach an asymptote.
Collapse
Affiliation(s)
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Vasco Elbrecht
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | | | - Jeremy R de Waard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
22
|
Greenwood D, Tully MP, Martin S, Steinke D. The description and definition of Emergency Department Pharmacist Practitioners in the United Kingdom (the ENDPAPER study). Int J Clin Pharm 2019; 41:434-444. [PMID: 30879216 PMCID: PMC6509098 DOI: 10.1007/s11096-019-00799-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/18/2019] [Indexed: 11/20/2022]
Abstract
Background Due to a shortage of emergency department doctors and nurses, hospitals have started to employ pharmacists who have additional clinical skills, known as Emergency Department Pharmacist Practitioners, to help deliver services. Objective To describe, compare and define the Emergency Department Pharmacist Practitioner role. Setting UK emergency departments. Method Using a purpose developed questionnaire hosted on a tablet computer, Emergency Department Pharmacist Practitioners were asked to report their contribution to patient care and the wider emergency department over 10 work days. Main outcome measure Emergency Department Pharmacist Practitioners’ work. Results Twenty Emergency Department Pharmacist Practitioners from 15 UK hospitals were recruited. Of 682 patients cared for, 4.8% (n=33) were of blue triage category (least urgent) and 4.1% (n=28) red (immediate need). Specific activities to inform patient diagnosis included clinical examinations (264/682 patients, 38.7%) and the review of investigation/test/procedure results (270, 39.6%). For treatment, EDPPs prescribed a total of 603 medicines (for administration in the ED) to 266 patients (39.0%) and performed procedures for 63 (9.2%). Eleven of the practitioners also took on the role of designated care provider (i.e. the healthcare professional with overall clinical responsibility) for at least some of their patients. From application of the care typology, all 20 practitioners carried out both ‘traditional’ and ‘practitioner’ activity and 9/20 of them sometimes provided more ‘practitioner’ than ‘traditional’ care to individual patients. Seven key role attributes were identified including how these pharmacists support patients with medical complaints and injuries of any severity and at any stage of their visit. Conclusion Emergency Department Pharmacist Practitioners combine traditional clinical pharmacy activities with more hands-on medical practise including being designated care provider. The role is versatile in that care and support provided to patients and the wider emergency department professional team is varied and therefore somewhat adaptable to situations which present.
Collapse
Affiliation(s)
- D Greenwood
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - M P Tully
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - S Martin
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - D Steinke
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| |
Collapse
|
23
|
Adamowicz SJ, Boatwright JS, Chain F, Fisher BL, Hogg ID, Leese F, Lijtmaer DA, Mwale M, Naaum AM, Pochon X, Steinke D, Wilson JJ, Wood S, Xu J, Xu S, Zhou X, van der Bank M. Trends in DNA barcoding and metabarcoding. Genome 2019; 62:v-viii. [DOI: 10.1139/gen-2019-0054] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
| | | | | | - Brian L. Fisher
- California Academy of Sciences, San Francisco, California, USA
| | - Ian D. Hogg
- Polar Knowledge Canada, Cambridge Bay, Nunavut, Canada
| | - Florian Leese
- University of Duisburg-Essen, North Rhine-Westphalia, Germany
| | - Darío A. Lijtmaer
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” – CONICET, Buenos Aires, Argentina
| | - Monica Mwale
- South African National Biodiversity Institute, National Zoological Gardens, Pretoria, Gauteng, South Africa
| | - Amanda M. Naaum
- TRU-ID Ltd., Guelph, Ontario, Canada; Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Xavier Pochon
- Cawthron Institute, Nelson, New Zealand & Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | | | | | | | - Jianping Xu
- McMaster University, Hamilton, Ontario, Canada
| | - Sen Xu
- University of Texas at Arlington, Arlington, Texas, USA
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China, 100193
| | | |
Collapse
|
24
|
Christiansen H, Dettai A, Heindler FM, Collins MA, Duhamel G, Hautecoeur M, Steinke D, Volckaert FAM, Van de Putte AP. Corrigendum: Diversity of Mesopelagic Fishes in the Southern Ocean – A Phylogeographic Perspective Using DNA Barcoding. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
25
|
KC KB, Dias GM, Veeramani A, Swanton CJ, Fraser D, Steinke D, Lee E, Wittman H, Farber JM, Dunfield K, McCann K, Anand M, Campbell M, Rooney N, Raine NE, Acker RV, Hanner R, Pascoal S, Sharif S, Benton TG, Fraser EDG. When too much isn't enough: Does current food production meet global nutritional needs? PLoS One 2018; 13:e0205683. [PMID: 30352069 PMCID: PMC6198966 DOI: 10.1371/journal.pone.0205683] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/29/2018] [Indexed: 01/19/2023] Open
Abstract
Sustainably feeding the next generation is often described as one of the most pressing “grand challenges” facing the 21st century. Generally, scholars propose addressing this problem by increasing agricultural production, investing in technology to boost yields, changing diets, or reducing food waste. In this paper, we explore whether global food production is nutritionally balanced by comparing the diet that nutritionists recommend versus global agricultural production statistics. Results show that the global agricultural system currently overproduces grains, fats, and sugars while production of fruits and vegetables and protein is not sufficient to meet the nutritional needs of the current population. Correcting this imbalance could reduce the amount of arable land used by agriculture by 51 million ha globally but would increase total land used for agriculture by 407 million ha and increase greenhouse gas emissions. For a growing population, our calculations suggest that the only way to eat a nutritionally balanced diet, save land and reduce greenhouse gas emissions is to consume and produce more fruits and vegetables as well as transition to diets higher in plant-based protein. Such a move will help protect habitats and help meet the Sustainable Development Goals.
Collapse
Affiliation(s)
- Krishna Bahadur KC
- Department of Geography, Environment and Geomatics, University of Guelph, Guelph, Canada
- * E-mail:
| | - Goretty M. Dias
- School of Environment, Enterprise and Development, University of Waterloo, Waterloo, Canada
| | - Anastasia Veeramani
- School of Environment, Enterprise and Development, University of Waterloo, Waterloo, Canada
| | | | - David Fraser
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, Canada
| | - Dirk Steinke
- Department of Integrative Biology, University of Guelph, Guelph, Canada
| | - Elizabeth Lee
- Department of Plant Agriculture, University of Guelph, Guelph, Canada
| | - Hannah Wittman
- Centre for Sustainable Food System, The University of British Columbia, Vancouver, Canada
| | - Jeffrey M. Farber
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, Canada
| | - Kari Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Kevin McCann
- Department of Integrative Biology, University of Guelph, Guelph, Canada
| | - Madhur Anand
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Malcolm Campbell
- Office of Research, University of Guelph, Guelph, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Neil Rooney
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Nigel E. Raine
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Rene Van Acker
- Department of Plant Agriculture, University of Guelph, Guelph, Canada
| | - Robert Hanner
- Department of Integrative Biology, University of Guelph, Guelph, Canada
| | - Samantha Pascoal
- Department of Geography, Environment and Geomatics, University of Guelph, Guelph, Canada
| | - Shayan Sharif
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Tim G. Benton
- School of Biology, University of Leeds, Leeds, United Kingdom
| | - Evan D. G. Fraser
- Department of Geography, Environment and Geomatics, University of Guelph, Guelph, Canada
- Arrell Food Institute, University of Guelph, Guelph, Canada
| |
Collapse
|
26
|
Merlo EM, Milligan KA, Sheets NB, Neufeld CJ, Eastham TM, Estores-Pacheco AK, Steinke D, Hebert PD, Valdés Á, Wyeth RC. Range extension for the region of sympatry between the nudibranchs Hermissenda opalescens and Hermissenda crassicornis in the northeastern Pacific. Facets (Ott) 2018. [DOI: 10.1139/facets-2017-0060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The mollusc nudibranch genus Hermissenda Bergh, 1879 was recently discovered to include three pseudocryptic species, dividing a single species H. crassicornis (sensu lato) into H. crassicornis Escholtz, 1831, H. opalescens J.G. Cooper, 1863, and H. emurai Baba, 1937. The species were distinguished by both genetic and morphological evidence, and the distribution of sampled animals suggested the three species had mostly distinct geographical ranges. Here, we report the presence of both H. crassicornis and H. opalescens in Barkley and Clayoquot Sounds, British Columbia, Canada, based on diagnostic characters and molecular data congruent with the differences described for these two species. This result extends the region of sympatry for the two species from northern California, USA, to, at least, Vancouver Island, British Columbia in 2016. Depending on how long this overlap has occurred, the possible northward expansion of H. opalescens would have implications for understanding the effects of short- or long-term environmental changes in ocean temperatures as well as complicating the interpretation of past neurobiological studies of H. crassicornis (sensu lato).
Collapse
Affiliation(s)
- Emily M. Merlo
- Bamfield Marine Sciences Centre, 100 Pachena Road, Bamfield, BC V0R 1B0, Canada
| | - Kathryn A. Milligan
- Bamfield Marine Sciences Centre, 100 Pachena Road, Bamfield, BC V0R 1B0, Canada
| | - Nola B. Sheets
- Bamfield Marine Sciences Centre, 100 Pachena Road, Bamfield, BC V0R 1B0, Canada
| | - Christopher J. Neufeld
- Bamfield Marine Sciences Centre, 100 Pachena Road, Bamfield, BC V0R 1B0, Canada
- Quest University Canada, 3200 University Boulevard, Squamish, BC V8B 0N8, Canada
| | - Tao M. Eastham
- Bamfield Marine Sciences Centre, 100 Pachena Road, Bamfield, BC V0R 1B0, Canada
| | | | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Ángel Valdés
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA 91768, USA
| | - Russell C. Wyeth
- Bamfield Marine Sciences Centre, 100 Pachena Road, Bamfield, BC V0R 1B0, Canada
- Biology Department, St Francis Xavier University, 2321 Notre Dame Avenue, Antigonish, NS B2G 2W5, Canada
| |
Collapse
|
27
|
Christiansen H, Dettai A, Heindler FM, Collins MA, Duhamel G, Hautecoeur M, Steinke D, Volckaert FAM, Van de Putte AP. Diversity of Mesopelagic Fishes in the Southern Ocean - A Phylogeographic Perspective Using DNA Barcoding. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
28
|
|
29
|
Elbrecht V, Hebert PDN, Steinke D. Slippage of degenerate primers can cause variation in amplicon length. Sci Rep 2018; 8:10999. [PMID: 30030475 PMCID: PMC6054607 DOI: 10.1038/s41598-018-29364-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/10/2018] [Indexed: 12/05/2022] Open
Abstract
It is well understood that homopolymer regions should be avoided for primer binding to prevent off-target amplification. However, in metabarcoding, it is often difficult to avoid primer degeneracy in order to maximize taxa detection. We here investigate primer binding specificity using different primer sets from several invertebrate metabarcoding studies. Our results indicate that primers frequently bound 1-2 bp upstream in taxa where a homopolymer region was present in the amplification direction. Primer binding 1 bp downstream was observed less frequently. This primer slippage leads to taxon-specific length variation in amplicons and subsequent length variation in recovered sequences. Some widely used primer sets were severely affected by this bias, while others were not. While this variation will only have small impacts on the designation of Operational Taxonomic Units (OTUs) by clustering algorithms that ignore terminal gaps, primer sets employed in metabarcoding projects should be evaluated for their sensitivity to slippage. Moreover, steps should be taken to reduce slippage by improving protocols for primer design. For example, the flanking region adjacent to the 3′ end of the primer is not considered by current primer development software although GC clamps in this position could mitigate slippage.
Collapse
Affiliation(s)
- Vasco Elbrecht
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| |
Collapse
|
30
|
Elbrecht V, Vamos EE, Steinke D, Leese F. Estimating intraspecific genetic diversity from community DNA metabarcoding data. PeerJ 2018; 6:e4644. [PMID: 29666773 PMCID: PMC5896493 DOI: 10.7717/peerj.4644] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 03/28/2018] [Indexed: 12/18/2022] Open
Abstract
Background DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs), losing information on intraspecific diversity in the process. While Cytochrome c oxidase subunit I (COI) haplotype information is limited in resolving intraspecific diversity it is nevertheless often useful e.g. in a phylogeographic context, helping to formulate hypotheses on taxon distribution and dispersal. Methods This study combines sequence denoising strategies, normally applied in microbial research, with additional abundance-based filtering to extract haplotype information from freshwater macroinvertebrate metabarcoding datasets. This novel approach was added to the R package "JAMP" and can be applied to COI amplicon datasets. We tested our haplotyping method by sequencing (i) a single-species mock community composed of 31 individuals with 15 different haplotypes spanning three orders of magnitude in biomass and (ii) 18 monitoring samples each amplified with four different primer sets and two PCR replicates. Results We detected all 15 haplotypes of the single specimens in the mock community with relaxed filtering and denoising settings. However, up to 480 additional unexpected haplotypes remained in both replicates. Rigorous filtering removes most unexpected haplotypes, but also can discard expected haplotypes mainly from the small specimens. In the monitoring samples, the different primer sets detected 177-200 OTUs, each containing an average of 2.40-3.30 haplotypes per OTU. The derived intraspecific diversity data showed population structures that were consistent between replicates and similar between primer pairs but resolution depended on the primer length. A closer look at abundant taxa in the dataset revealed various population genetic patterns, e.g. the stonefly Taeniopteryx nebulosa and the caddisfly Hydropsyche pellucidula showed a distinct north-south cline with respect to haplotype distribution, while the beetle Oulimnius tuberculatus and the isopod Asellus aquaticus displayed no clear population pattern but differed in genetic diversity. Discussion We developed a strategy to infer intraspecific genetic diversity from bulk invertebrate metabarcoding data. It needs to be stressed that at this point this metabarcoding-informed haplotyping is not capable of capturing the full diversity present in such samples, due to variation in specimen size, primer bias and loss of sequence variants with low abundance. Nevertheless, for a high number of species intraspecific diversity was recovered, identifying potentially isolated populations and taxa for further more detailed phylogeographic investigation. While we are currently lacking large-scale metabarcoding datasets to fully take advantage of our new approach, metabarcoding-informed haplotyping holds great promise for biomonitoring efforts that not only seek information about species diversity but also underlying genetic diversity.
Collapse
Affiliation(s)
- Vasco Elbrecht
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, North Rhine-Westphalia, Germany.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Ecaterina Edith Vamos
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, North Rhine-Westphalia, Germany
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, North Rhine-Westphalia, Germany.,Centre for Water and Environmental Research (ZWU) Essen, University of Duisburg-Essen, Essen, North Rhine-Westphalia, Germany
| |
Collapse
|
31
|
Henter HJ, Imondi R, James K, Spencer D, Steinke D. DNA barcoding in diverse educational settings: five case studies. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0340. [PMID: 27481792 PMCID: PMC4971192 DOI: 10.1098/rstb.2015.0340] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2016] [Indexed: 11/19/2022] Open
Abstract
Despite 250 years of modern taxonomy, there remains a large biodiversity knowledge gap. Most species remain unknown to science. DNA barcoding can help address this gap and has been used in a variety of educational contexts to incorporate original research into school curricula and informal education programmes. A growing body of evidence suggests that actively conducting research increases student engagement and retention in science. We describe case studies in five different educational settings in Canada and the USA: a programme for primary and secondary school students (ages 5–18), a year-long professional development programme for secondary school teachers, projects embedding this research into courses in a post-secondary 2-year institution and a degree-granting university, and a citizen science project. We argue that these projects are successful because the scientific content is authentic and compelling, DNA barcoding is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and online tools exist that allow participants to contribute high-quality data to the international research effort. Evidence of success includes the broad adoption of these programmes and assessment results demonstrating that participants are gaining both knowledge and confidence. There are exciting opportunities for coordination among educational projects in the future. This article is part of the themed issue ‘From DNA barcodes to biomes’.
Collapse
Affiliation(s)
- Heather J Henter
- Natural Reserve System, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Karen James
- MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | | | - Dirk Steinke
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| |
Collapse
|
32
|
Leese F, Steinke D, Weigand A, Penev L. Ready for the deluge! Introducing the new Metabarcoding and Metagenomics (MBMG) journal. Metabarcoding and Metagenomics 2017. [DOI: 10.3897/mbmg.1.14791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
33
|
Steinke D, Bernard AM, Horn RL, Hilton P, Hanner R, Shivji MS. DNA analysis of traded shark fins and mobulid gill plates reveals a high proportion of species of conservation concern. Sci Rep 2017; 7:9505. [PMID: 28842669 PMCID: PMC5573315 DOI: 10.1038/s41598-017-10123-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/04/2017] [Indexed: 12/05/2022] Open
Abstract
Continuously increasing demand for plant and animal products causes unsustainable depletion of biological resources. It is estimated that one-quarter of sharks and rays are threatened worldwide and although the global fin trade is widely recognized as a major driver, demand for meat, liver oil, and gill plates also represents a significant threat. This study used DNA barcoding and 16 S rRNA sequencing as a method to identify shark and ray species from dried fins and gill plates, obtained in Canada, China, and Sri Lanka. 129 fins and gill plates were analysed and searches on BOLD produced matches to 20 species of sharks and five species of rays or – in two cases – to a species pair. Twelve of the species found are listed or have been approved for listing in 2017 in the appendices of the Convention on International Trade in Endangered Species of Fauna and Flora (CITES), including the whale shark (Rhincodon typus), which was surprisingly found among both shark fin and gill plate samples. More than half of identified species fall under the IUCN Red List categories ‘Endangered’ and ‘Vulnerable’, raising further concerns about the impacts of this trade on the sustainability of these low productivity species.
Collapse
Affiliation(s)
- Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
| | - Andrea M Bernard
- Save Our Seas Shark Research Center USA and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA.,Guy Harvey Research Institute and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA
| | - Rebekah L Horn
- Save Our Seas Shark Research Center USA and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA.,Guy Harvey Research Institute and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA
| | | | - Robert Hanner
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Mahmood S Shivji
- Save Our Seas Shark Research Center USA and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA. .,Guy Harvey Research Institute and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA.
| |
Collapse
|
34
|
Steinke D, deWaard JR, Gomon MF, Johnson JW, Larson HK, Lucanus O, Moore GI, Reader S, Ward RD. DNA barcoding the fishes of Lizard Island (Great Barrier Reef). Biodivers Data J 2017:e12409. [PMID: 28765727 PMCID: PMC5515069 DOI: 10.3897/bdj.5.e12409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/12/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- Dirk Steinke
- Centre for Biodiversity Genomics - University of Guelph, Guelph, Canada.,Department of Integrative Biology - University of Guelph, Guelph, Canada
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics - University of Guelph, Guelph, Canada
| | | | - Jeffrey W Johnson
- Queensland Museum, PO Box 3300, South Brisbane QLD 4101, Australia, Brisbane, Australia
| | - Helen K Larson
- Museum and Art Gallery of the Northern Territory, Darwin, Australia
| | | | | | | | - Robert D Ward
- CSIRO Marine and Atmospheric Research, Hobart, Australia
| |
Collapse
|
35
|
Cariani A, Messinetti S, Ferrari A, Arculeo M, Bonello JJ, Bonnici L, Cannas R, Carbonara P, Cau A, Charilaou C, El Ouamari N, Fiorentino F, Follesa MC, Garofalo G, Golani D, Guarniero I, Hanner R, Hemida F, Kada O, Lo Brutto S, Mancusi C, Morey G, Schembri PJ, Serena F, Sion L, Stagioni M, Tursi A, Vrgoc N, Steinke D, Tinti F. Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library. PLoS One 2017; 12:e0170244. [PMID: 28107413 PMCID: PMC5249125 DOI: 10.1371/journal.pone.0170244] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/30/2016] [Indexed: 11/18/2022] Open
Abstract
Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions.
Collapse
Affiliation(s)
- Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Silvia Messinetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Marco Arculeo
- Department STEBICEF, University of Palermo, Palermo, Italy
| | | | | | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | | | - Alessandro Cau
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Charis Charilaou
- Department of Fisheries and Marine Research, Ministry of Agriculture, Rural Development and Environment, Nicosia, Republic of Cyprus
| | - Najib El Ouamari
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | - Fabio Fiorentino
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | | | - Germana Garofalo
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | - Daniel Golani
- Department of Evolution, Systematics and Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilaria Guarniero
- Department DIMEVET, University of Bologna, Ozzano dell'Emilia, Italy
| | - Robert Hanner
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Farid Hemida
- Ecole Nationale Superieure des Sciences de la Mer et d'Amenagement du Littoral, Campus Universitaire de Dely Ibrahim, Alger, Algeria
| | - Omar Kada
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | | | - Cecilia Mancusi
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | | | | | - Fabrizio Serena
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | - Letizia Sion
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Marco Stagioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Angelo Tursi
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Nedo Vrgoc
- Institute of Oceanography and Fisheries, Split, Croatia
| | - Dirk Steinke
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| |
Collapse
|
36
|
Page TJ, Steinke D. No homology means there can be no analyses; a comment on Jose & Harikrishnan. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:220-221. [PMID: 28024422 DOI: 10.1080/24701394.2016.1267159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Timothy J Page
- a Australian Rivers Institute, Griffith University , Nathan , QLD , Australia.,b Water Planning Ecology, Queensland Dept. of Science , Information Technology and Innovation , Dutton Park , QLD , Australia
| | - Dirk Steinke
- c Biodiversity Institute of Ontario, University of Guelph , Guelph , ON , Canada
| |
Collapse
|
37
|
Leese F, Altermatt F, Bouchez A, Ekrem T, Hering D, Meissner K, Mergen P, Pawlowski J, Piggott J, Rimet F, Steinke D, Taberlet P, Weigand A, Abarenkov K, Beja P, Bervoets L, Björnsdóttir S, Boets P, Boggero A, Bones A, Borja Á, Bruce K, Bursić V, Carlsson J, Čiampor F, Čiamporová-Zatovičová Z, Coissac E, Costa F, Costache M, Creer S, Csabai Z, Deiner K, DelValls Á, Drakare S, Duarte S, Eleršek T, Fazi S, Fišer C, Flot JF, Fonseca V, Fontaneto D, Grabowski M, Graf W, Guðbrandsson J, Hellström M, Hershkovitz Y, Hollingsworth P, Japoshvili B, Jones J, Kahlert M, Kalamujic Stroil B, Kasapidis P, Kelly M, Kelly-Quinn M, Keskin E, Kõljalg U, Ljubešić Z, Maček I, Mächler E, Mahon A, Marečková M, Mejdandzic M, Mircheva G, Montagna M, Moritz C, Mulk V, Naumoski A, Navodaru I, Padisák J, Pálsson S, Panksep K, Penev L, Petrusek A, Pfannkuchen M, Primmer C, Rinkevich B, Rotter A, Schmidt-Kloiber A, Segurado P, Speksnijder A, Stoev P, Strand M, Šulčius S, Sundberg P, Traugott M, Tsigenopoulos C, Turon X, Valentini A, van der Hoorn B, Várbíró G, Vasquez Hadjilyra M, Viguri J, Vitonytė I, Vogler A, Vrålstad T, Wägele W, Wenne R, Winding A, Woodward G, Zegura B, Zimmermann J. DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. RIO 2016. [DOI: 10.3897/rio.2.e11321] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
38
|
Adamowicz SJ, Chain FJJ, Clare EL, Deiner K, Dincă V, Elías-Gutiérrez M, Hausmann A, Hogg ID, Kekkonen M, Lijtmaer DA, Naaum A, Steinke D, Valdez-Moreno M, Van der Bank M, Wilson JJ, Xu J. From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference. Genome 2016; 59:v-ix. [PMID: 27829307 DOI: 10.1139/gen-2016-0195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Sarah J Adamowicz
- a Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Frédéric J J Chain
- b Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, QC H3A 1B1, Canada
| | - Elizabeth L Clare
- c School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, U.K
| | - Kristy Deiner
- d Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall A406A, 215 Tower Rd., Ithaca, NY 14850, USA
| | - Vlad Dincă
- e Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain
| | - Manuel Elías-Gutiérrez
- f El Colegio de la Frontera Sur, Av. Centenario Km 5.5, Chetumal, Quintana Roo 77014, Mexico
| | - Axel Hausmann
- g SNSB - Zoologische Staatssammlung München, Münchhausenstr. 21, D-81247 Munich, Germany
| | - Ian D Hogg
- h Centre for Biodiversity and Ecology Research, Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton, New Zealand
| | - Mari Kekkonen
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Darío A Lijtmaer
- j División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina
| | - Amanda Naaum
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Dirk Steinke
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Martha Valdez-Moreno
- f El Colegio de la Frontera Sur, Av. Centenario Km 5.5, Chetumal, Quintana Roo 77014, Mexico
| | - Michelle Van der Bank
- k African Centre for DNA Barcoding, University of Johannesburg, PO Box 524, APK Campus, 2006 Johannesburg, South Africa
| | - John-James Wilson
- l Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jianping Xu
- m Department of Biology, McMaster University, 12809 Main St. West, Hamilton, ON L8S 4K1, Canada
| |
Collapse
|
39
|
Adamowicz SJ, Chain FJJ, Clare EL, Deiner K, Dincă V, Elías-Gutiérrez M, Hausmann A, Hogg ID, Kekkonen M, Lijtmaer DA, Naaum A, Steinke D, Valdez-Moreno M, Van der Bank M, Wilson JJ, Xu J. From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference. Genome 2016; 59:v-ix. [PMID: 27611699 DOI: 10.1139/gen-2016-0159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Sarah J Adamowicz
- a Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Frédéric J J Chain
- b Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, QC H3A 1B1, Canada
| | - Elizabeth L Clare
- c School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, U.K
| | - Kristy Deiner
- d Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall A406A, 215 Tower Rd., Ithaca, NY 14850, USA
| | - Vlad Dincă
- e Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain
| | - Manuel Elías-Gutiérrez
- f El Colegio de la Frontera Sur, Av. Centenario Km 5.5, Chetumal, Quintana Roo 77014, Mexico
| | - Axel Hausmann
- g SNSB - Zoologische Staatssammlung München, Münchhausenstr. 21, D-81247 Munich, Germany
| | - Ian D Hogg
- h Centre for Biodiversity and Ecology Research, Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton, New Zealand
| | - Mari Kekkonen
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Darío A Lijtmaer
- j División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina
| | - Amanda Naaum
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Dirk Steinke
- i Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Martha Valdez-Moreno
- f El Colegio de la Frontera Sur, Av. Centenario Km 5.5, Chetumal, Quintana Roo 77014, Mexico
| | - Michelle Van der Bank
- k African Centre for DNA Barcoding, University of Johannesburg, PO Box 524, APK Campus, 2006 Johannesburg, South Africa
| | - John-James Wilson
- l Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jianping Xu
- m Department of Biology, McMaster University, 12809 Main St. West, Hamilton, ON L8S 4K1, Canada
| |
Collapse
|
40
|
Abstract
The early life-history stages of fishes are poorly known, impeding acquisition of the identifications needed to monitor larval recruitment and year-class strength. A comprehensive database of COI sequences, linked to authoritatively identified voucher specimens, promises to change this situation, representing a significant advance for fisheries science. Barcode records were obtained from 2526 early larvae and pelagic eggs of fishes collected on the inshore shelf within 5 km of the KwaZulu-Natal coast, about 50 km south of Durban, South Africa. Barcodes were also obtained from 3215 adults, representing 946 South African fish species. Using the COI reference library on BOLD based on adults, 89% of the immature fishes could be identified to a species level; they represented 450 species. Most of the uncertain sequences could be assigned to a genus, family, or order; only 92 specimens (4%) were unassigned. Accumulation curves based on inference of phylogenetic diversity indicate near-completeness of the collecting effort. The entire set of adult and larval fishes included 1006 species, representing 43% of all fish species known from South African waters. However, this total included 189 species not previously recorded from this region. The fact that almost 90% of the immatures gained a species identification demonstrates the power and completeness of the DNA barcode reference library for fishes generated during the 10 years of FishBOL.
Collapse
Affiliation(s)
- Dirk Steinke
- a Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Allan D Connell
- b South African Institute of Aquatic Biodiversity, Private Bag 1015, Grahamstown, South Africa 6140
| | - Paul D N Hebert
- a Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
41
|
Xavier JC, Ferreira S, Tavares S, Santos N, Mieiro CL, Trathan PN, Lourenço S, Martinho F, Steinke D, Seco J, Pereira E, Pardal M, Cherel Y. The significance of cephalopod beaks in marine ecology studies: Can we use beaks for DNA analyses and mercury contamination assessment? Mar Pollut Bull 2016; 103:220-226. [PMID: 26723473 DOI: 10.1016/j.marpolbul.2015.12.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 12/11/2015] [Accepted: 12/17/2015] [Indexed: 06/05/2023]
Abstract
Cephalopod beaks found in the diet of predators have been a major source of scientific information. In this study, we evaluated the usefulness of DNA and contaminants analysis (total mercury - T-Hg) in cephalopod beaks in order to assess their applicability as tools in marine ecology studies. We concluded that, when applying DNA techniques to cephalopod beaks from Antarctic squid species, when using flesh attached to those beaks, it was possible to obtain DNA and to successfully identify cephalopod species; DNA was not found on the beaks themselves. This study also showed that it is possible to obtain information on T-Hg concentrations in beaks: the T-Hg concentrations found in the beaks were 6 to 46 times lower than in the flesh of the same cephalopod species. More research on the relationships of mercury concentrations in cephalopod beaks (and other tissues), intra- and inter-specifically, are needed in the future.
Collapse
Affiliation(s)
- José Carlos Xavier
- MARE - Marine and Environmental Sciences Centre, Departamento das Ciências da Vida, Universidade de Coimbra, 3001-401 Coimbra, Portugal; British Antarctic Survey, NERC, High Cross, Madingley Road, CB3 0ET Cambridge, UK.
| | - Sónia Ferreira
- Department of Health and Education, Institute of Education and Citizenship, 3770-033 Mamarrosa, Portugal
| | - Sílvia Tavares
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Nuno Santos
- Department of Health and Education, Institute of Education and Citizenship, 3770-033 Mamarrosa, Portugal
| | - Cláudia Leopoldina Mieiro
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; CESAM and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Phil N Trathan
- British Antarctic Survey, NERC, High Cross, Madingley Road, CB3 0ET Cambridge, UK
| | - Sílvia Lourenço
- MARE - Marine and Environmental Sciences Centre, Departamento das Ciências da Vida, Universidade de Coimbra, 3001-401 Coimbra, Portugal
| | - Filipe Martinho
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Dirk Steinke
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G2W1, Canada
| | - José Seco
- CESAM and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; School of Biology, University of St Andrews, Scotland, UK
| | - Eduarda Pereira
- CESAM and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Miguel Pardal
- Centre for Functional Ecology - CFE, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé, UMR 7372 du CNRS-Université de La Rochelle, 79360 Villiers-en-Bois, France
| |
Collapse
|
42
|
Abstract
The accumulation of DNA barcode sequences will provide an increasingly useful and comprehensive library for species identification and discovery of marine metazoans. Here we present a summary of protocols designed to obtain DNA barcodes of marine metazoans from diverse phyla.
Collapse
Affiliation(s)
- Dirk Steinke
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1.
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
| |
Collapse
|
43
|
Abstract
DNA barcoding—the sequencing of short, standardized DNA regions for specimen identification and species discovery—has promised to facilitate rapid access to biodiversity knowledge by diverse users. Here, we advance our opinion that increased global participation in genetics research is beneficial, both to scientists and for science, and explore the premise that DNA barcoding can help to democratize participation in genetics research. We examine publication patterns (2003–2014) in the DNA barcoding literature and compare trends with those in the broader, related domain of genomics. While genomics is the older and much larger field, the number of nations contributing to the published literature is similar between disciplines. Meanwhile, DNA barcoding exhibits a higher pace of growth in the number of publications as well as greater evenness among nations in their proportional contribution to total authorships. This exploration revealed DNA barcoding to be a highly international discipline, with growing participation by researchers in especially biodiverse nations. We briefly consider several of the challenges that may hinder further participation in genetics research, including access to training and molecular facilities as well as policy relating to the movement of genetic resources.
Collapse
Affiliation(s)
- Sarah J. Adamowicz
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Dirk Steinke
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
44
|
Raupach MJ, Barco A, Steinke D, Beermann J, Laakmann S, Mohrbeck I, Neumann H, Kihara TC, Pointner K, Radulovici A, Segelken-Voigt A, Wesse C, Knebelsberger T. The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions. PLoS One 2015; 10:e0139421. [PMID: 26417993 PMCID: PMC4587929 DOI: 10.1371/journal.pone.0139421] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/14/2015] [Indexed: 12/02/2022] Open
Abstract
During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort & Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequences.
Collapse
Affiliation(s)
- Michael J. Raupach
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
- * E-mail:
| | - Andrea Barco
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Dirk Steinke
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jan Beermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Schleswig-Holstein, Germany
| | - Silke Laakmann
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Inga Mohrbeck
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Hermann Neumann
- Department for Marine Research, Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Terue C. Kihara
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Karin Pointner
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Adriana Radulovici
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Alexandra Segelken-Voigt
- Animal Biodiversity and Evolutionary Biology, Institute for Biology and Environmental Sciences, V. School of Mathematics and Science, Carl von Ossietzky University Oldenburg, Oldenburg, Niedersachsen, Germany
| | - Christina Wesse
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Thomas Knebelsberger
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| |
Collapse
|
45
|
Telfer AC, Young MR, Quinn J, Perez K, Sobel CN, Sones JE, Levesque-Beaudin V, Derbyshire R, Fernandez-Triana J, Rougerie R, Thevanayagam A, Boskovic A, Borisenko AV, Cadel A, Brown A, Pages A, Castillo AH, Nicolai A, Glenn Mockford BM, Bukowski B, Wilson B, Trojahn B, Lacroix CA, Brimblecombe C, Hay C, Ho C, Steinke C, Warne CP, Garrido Cortes C, Engelking D, Wright D, Lijtmaer DA, Gascoigne D, Hernandez Martich D, Morningstar D, Neumann D, Steinke D, Marco DeBruin DD, Dobias D, Sears E, Richard E, Damstra E, Zakharov EV, Laberge F, Collins GE, Blagoev GA, Grainge G, Ansell G, Meredith G, Hogg I, McKeown J, Topan J, Bracey J, Guenther J, Sills-Gilligan J, Addesi J, Persi J, Layton KKS, D'Souza K, Dorji K, Grundy K, Nghidinwa K, Ronnenberg K, Lee KM, Xie L, Lu L, Penev L, Gonzalez M, Rosati ME, Kekkonen M, Kuzmina M, Iskandar M, Mutanen M, Fatahi M, Pentinsaari M, Bauman M, Nikolova N, Ivanova NV, Jones N, Weerasuriya N, Monkhouse N, Lavinia PD, Jannetta P, Hanisch PE, McMullin RT, Ojeda Flores R, Mouttet R, Vender R, Labbee RN, Forsyth R, Lauder R, Dickson R, Kroft R, Miller SE, MacDonald S, Panthi S, Pedersen S, Sobek-Swant S, Naik S, Lipinskaya T, Eagalle T, Decaëns T, Kosuth T, Braukmann T, Woodcock T, Roslin T, Zammit T, Campbell V, Dinca V, Peneva V, Hebert PDN, deWaard JR. Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve. Biodivers Data J 2015; 3:e6313. [PMID: 26379469 PMCID: PMC4568406 DOI: 10.3897/bdj.3.e6313] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Comprehensive biotic surveys, or 'all taxon biodiversity inventories' (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada. NEW INFORMATION The existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies - a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is more than a comprehensive biotic inventory - it is also a rich dataset of fine-scale occurrence and sequence data, all archived and cross-linked in the major biodiversity data repositories. This model of rapid generation and dissemination of essential biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially be employed for evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011-2020.
Collapse
Affiliation(s)
| | | | - Jenna Quinn
- rare Charitable Research Reserve, Cambridge, Canada
| | - Kate Perez
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | | | | | | | | | | | | | - Alex Cadel
- University of Waterloo, Waterloo, Canada
| | | | - Anais Pages
- Université de Montpellier, Montpellier, France
| | | | | | | | - Belén Bukowski
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Bill Wilson
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | | | | | - Christmas Ho
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | | | | | - Dario A Lijtmaer
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - David Gascoigne
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | - Dirk Neumann
- SNSB, Zoologische Staatssammlung Muenchen, Munich, Germany
| | - Dirk Steinke
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | | | - Emily Damstra
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | | | | | - Gerrie Grainge
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | - Ian Hogg
- University of Waikato, Hamilton, New Zealand
| | | | - Janet Topan
- Biodiversity Institute of Ontario, Guelph, Canada
| | - Jason Bracey
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Jerry Guenther
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | - Joshua Persi
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | - Kevin Grundy
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Kirsti Nghidinwa
- Ministry of Environment and Tourism in Namibia, Windhoek, Namibia
| | | | | | - Linxi Xie
- The University of Western Ontario, London, Canada
| | - Liuqiong Lu
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | - Mailyn Gonzalez
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Margaret E Rosati
- Smithsonian National Museum of Natural History, Washington, United States of America
| | | | | | | | | | | | | | - Miriam Bauman
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | | | | | | | | | | | - Pablo D Lavinia
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | | | - Priscila E Hanisch
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | | | | | - Raphaëlle Mouttet
- ANSES, Laboratoire de la Santé des Végétaux, Montferrier sur Lez, France
| | - Reid Vender
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | | - Ross Dickson
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Ruth Kroft
- rare Charitable Research Reserve (Affiliate of), Cambridge, Canada
| | - Scott E Miller
- Smithsonian National Museum of Natural History, Washington, United States of America
| | | | - Sishir Panthi
- Ministry of Forests and Soil Conservation, Kathmandu, Nepal
| | | | | | - Suresh Naik
- Biodiversity Institute of Ontario, Guelph, Canada
| | - Tatsiana Lipinskaya
- Scientific and Practical Center for Bioresources, National Academy of Sciences of Belarus, Minsk, Belarus
| | | | - Thibaud Decaëns
- Université de Montpellier Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France
| | | | | | - Tom Woodcock
- rare Charitable Research Reserve, Cambridge, Canada
| | - Tomas Roslin
- University of Helsinki, Helsinki, Finland
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tony Zammit
- Grand River Conservation Authority, Cambridge, Canada
| | | | - Vlad Dinca
- Biodiversity Institute of Ontario, Guelph, Canada
| | | | | | | |
Collapse
|
46
|
Serrao NR, Steinke D, Hanner RH. Calibrating snakehead diversity with DNA barcodes: expanding taxonomic coverage to enable identification of potential and established invasive species. PLoS One 2014; 9:e99546. [PMID: 24915194 PMCID: PMC4051700 DOI: 10.1371/journal.pone.0099546] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 05/15/2014] [Indexed: 11/19/2022] Open
Abstract
Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species) and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius) are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway analysis.
Collapse
Affiliation(s)
- Natasha R. Serrao
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Robert H. Hanner
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
47
|
Woodcock TS, Boyle EE, Roughley RE, Kevan PG, Labbee RN, Smith ABT, Goulet H, Steinke D, Adamowicz SJ. The diversity and biogeography of the Coleoptera of Churchill: insights from DNA barcoding. BMC Ecol 2013; 13:40. [PMID: 24164967 PMCID: PMC3819705 DOI: 10.1186/1472-6785-13-40] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/16/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coleoptera is the most diverse order of insects (>300,000 described species), but its richness diminishes at increasing latitudes (e.g., ca. 7400 species recorded in Canada), particularly of phytophagous and detritivorous species. However, incomplete sampling of northern habitats and a lack of taxonomic study of some families limits our understanding of biodiversity patterns in the Coleoptera. We conducted an intensive biodiversity survey from 2006-2010 at Churchill, Manitoba, Canada in order to quantify beetle species diversity in this model region, and to prepare a barcode library of beetles for sub-arctic biodiversity and ecological research. We employed DNA barcoding to provide estimates of provisional species diversity, including for families currently lacking taxonomic expertise, and to examine the guild structure, habitat distribution, and biogeography of beetles in the Churchill region. RESULTS We obtained DNA barcodes from 3203 specimens representing 302 species or provisional species (the latter quantitatively defined on the basis of Molecular Operational Taxonomic Units, MOTUs) in 31 families of Coleoptera. Of the 184 taxa identified to the level of a Linnaean species name, 170 (92.4%) corresponded to a single MOTU, four (2.2%) represented closely related sibling species pairs within a single MOTU, and ten (5.4%) were divided into two or more MOTUs suggestive of cryptic species. The most diverse families were the Dytiscidae (63 spp.), Staphylinidae (54 spp.), and Carabidae (52 spp.), although the accumulation curve for Staphylinidae suggests that considerable additional diversity remains to be sampled in this family. Most of the species present are predatory, with phytophagous, mycophagous, and saprophagous guilds being represented by fewer species. Most named species of Carabidae and Dytiscidae showed a significant bias toward open habitats (wet or dry). Forest habitats, particularly dry boreal forest, although limited in extent in the region, were undersampled. CONCLUSIONS We present an updated species list for this region as well as a species-level DNA barcode reference library. This resource will facilitate future work, such as biomonitoring and the study of the ecology and distribution of larvae.
Collapse
Affiliation(s)
- Thomas S Woodcock
- School of Environmental Science, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| | - Elizabeth E Boyle
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| | - Robert E Roughley
- Department of Entomology, University of Manitoba, Winnipeg, MB, Canada
| | - Peter G Kevan
- School of Environmental Science, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| | - Renee N Labbee
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| | - Andrew B T Smith
- Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, ON, Canada
| | - Henri Goulet
- Canadian National Collection, 960 Carling Ave., Ottawa, ON, Canada
| | - Dirk Steinke
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| | - Sarah J Adamowicz
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada
| |
Collapse
|
48
|
Thornton J, Tait S, Steinke D, Ashcroft D, Elliot N. P093 Determining Pharmacist Awareness And Implementation Of The Nice Medicines Adherence Guideline. BMJ Qual Saf 2013. [DOI: 10.1136/bmjqs-2013-002293.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
49
|
O’Hara TD, Smith PJ, Mills VS, Smirnov I, Steinke D. Biogeographical and phylogeographical relationships of the bathyal ophiuroid fauna of the Macquarie Ridge, Southern Ocean. Polar Biol 2012. [DOI: 10.1007/s00300-012-1261-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
50
|
Knox MA, Hogg ID, Pilditch CA, Lörz AN, Hebert PDN, Steinke D. Mitochondrial DNA (COI) analyses reveal that amphipod diversity is associated with environmental heterogeneity in deep-sea habitats. Mol Ecol 2012; 21:4885-97. [DOI: 10.1111/j.1365-294x.2012.05729.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 06/01/2012] [Accepted: 06/06/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew A. Knox
- Department of Biological Sciences; University of Waikato; Private Bag 3105; Hamilton; New Zealand
| | - Ian D. Hogg
- Department of Biological Sciences; University of Waikato; Private Bag 3105; Hamilton; New Zealand
| | - Conrad A. Pilditch
- Department of Biological Sciences; University of Waikato; Private Bag 3105; Hamilton; New Zealand
| | - Anne-Nina Lörz
- National Institute of Water and Atmospheric Research (NIWA) Ltd; Private Bag 14901; Wellington; New Zealand
| | - Paul D. N. Hebert
- Biodiversity Institute of Ontario; University of Guelph; 50 Stone Road East; Guelph; ON; N1G 2W1; Canada
| | - Dirk Steinke
- Biodiversity Institute of Ontario; University of Guelph; 50 Stone Road East; Guelph; ON; N1G 2W1; Canada
| |
Collapse
|