Laboratory Information Management Systems for DNA Barcoding

Parker, Meaghan; Stones-Havas, Steven; Starger, Craig J.; Meyer, Christopher

doi:10.1007/978-1-61779-591-6_13

Cited by 11 publications

(11 citation statements)

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“…Collection data, DNA extraction, PCR settings, and sequencing results were tracked for individual samples using the software Geneious® R9 (version 9.1.5) with the plugin ‘biocode’ (version 3.0.0) [37]. Geneious® was also used to trim sequences and to calculate Neighbor-Joining (NJ) trees with bootstrap support (1,000 replicates) based on Tamura-Nei distances.…”

Section: Methodsmentioning

confidence: 99%

Community Sampling and Integrative Taxonomy Reveal New Species and Host Specificity in the Army Ant-Associated Beetle Genus Tetradonia (Coleoptera, Staphylinidae, Aleocharinae)

2016

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Army ant colonies host a diverse community of arthropod symbionts. Among the best-studied symbiont communities are those of Neotropical army ants of the genus Eciton. It is clear, however, that even in these comparatively well studied systems, a large proportion of symbiont biodiversity remains unknown. Even more striking is our lack of knowledge regarding the nature and specificity of these host-symbiont interactions. Here we surveyed the diversity and host specificity of rove beetles of the genus Tetradonia Wasmann, 1894 (Staphylinidae: Aleocharinae). Systematic community sampling of 58 colonies of the six local Eciton species at La Selva Biological Station, Costa Rica, combined with an integrative taxonomic approach, allowed us to uncover species diversity, host specificity, and co-occurrence patterns of symbionts in unprecedented detail. We used an integrative taxonomic approach combining morphological and genetic analyses, to delineate species boundaries. Mitochondrial DNA barcodes were analyzed for 362 Tetradonia specimens, and additional nuclear markers for a subset of 88 specimens. All analyses supported the presence of five Tetradonia species, including two species new to science. Host specificity is highly variable across species, ranging from generalists such as T. laticeps, which parasitizes all six local Eciton species, to specialists such as T. lizonae, which primarily parasitizes a single species, E. hamatum. Here we provide a dichotomous key along with diagnostic molecular characters for identification of Tetradonia species at La Selva Biological Station. By reliably assessing biodiversity and providing tools for species identification, we hope to set the baseline for future studies of the ecological and evolutionary dynamics in these species-rich host-symbiont networks.

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Section: Methodsmentioning

confidence: 99%

Community Sampling and Integrative Taxonomy Reveal New Species and Host Specificity in the Army Ant-Associated Beetle Genus Tetradonia (Coleoptera, Staphylinidae, Aleocharinae)

2016

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“…While the need to manually transcribe and enter sample identifiers is likely to persist, ultimately, we hope that project teams will move away from management of sample data and metadata using spreadsheets and transition toward relational databases, field information management systems (FIMS) (see, e.g., reference 10), and laboratory information management systems (LIMS) (see, e.g., reference 11). These systems benefit users by offering features, including centralized sample tracking across projects; synchronized metadata between team members in the field, the wet lab, and the bioinformatics lab; and automated backups.…”

Section: Discussionmentioning

confidence: 99%

cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies

et al. 2016

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The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta- and/or integrated analysis, sample identifiers generated with cual-id will not need to change; thus, costly and error-prone updating of data and metadata identifiers will be avoided. Further, using cual-id will ensure that transcription errors in sample identifiers do not require the discarding of otherwise-useful samples that may have been expensive to obtain. Finally, cual-id is simple to install and use and is free for all use. No centralized infrastructure is required to ensure global uniqueness, so it is feasible for any lab to get started using these identifiers within their existing infrastructure.

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“…All workflows including specimen data, extractions, PCRs and cycle sequencing were tracked using the laboratory information management system implemented in the software geneious ® (version 7.1.7) with the biocode plugin (version 2.8.0) (Parker et al . ). Sequences were aligned and trimmed in geneious ® .…”

Section: Methodsmentioning

confidence: 97%

Cryptic diversity, high host specificity and reproductive synchronization in army ant‐associated Vatesus beetles

2016

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Army ants and their arthropod symbionts represent one of the most species-rich animal associations on Earth, and constitute a fascinating example of diverse host-symbiont interaction networks. However, despite decades of research, our knowledge of army ant symbionts remains fragmentary due to taxonomic ambiguity and the inability to study army ants in the laboratory. Here, we present an integrative approach that allows us to reliably determine species boundaries, assess biodiversity, match different developmental stages and sexes, and to study the life cycles of army ant symbionts. This approach is based on a combination of community sampling, DNA barcoding, morphology and physiology. As a test case, we applied this approach to the staphylinid beetle genus Vatesus and its different Eciton army ant host species at La Selva Biological Station, Costa Rica. DNA barcoding led to the discovery of cryptic biodiversity and, in combination with extensive community sampling, revealed strict host partitioning with no overlap in host range. Using DNA barcoding, we were also able to match the larval stages of all focal Vatesus species. In combination with studies of female reproductive physiology, this allowed us to reconstruct almost the complete life cycles of the different beetle species. We show that Vatesus beetles are highly adapted to the symbiosis with army ants, in that their reproduction and larval development are synchronized with the stereotypical reproductive and behavioural cycles of their host colonies. Our approach can now be used to study army ant-symbiont communities more broadly, and to obtain novel insights into co-evolutionary and ecological dynamics in species-rich host-symbiont systems.

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Laboratory Information Management Systems for DNA Barcoding

Cited by 11 publications

References 0 publications

Community Sampling and Integrative Taxonomy Reveal New Species and Host Specificity in the Army Ant-Associated Beetle Genus Tetradonia (Coleoptera, Staphylinidae, Aleocharinae)

Community Sampling and Integrative Taxonomy Reveal New Species and Host Specificity in the Army Ant-Associated Beetle Genus Tetradonia (Coleoptera, Staphylinidae, Aleocharinae)

cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies

Cryptic diversity, high host specificity and reproductive synchronization in army ant‐associated Vatesus beetles

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