Next‐generation conservation genetics and biodiversity monitoring

Hunter, Margaret E.; Hoban, Sean; Bruford, Michael William; Segelbacher, Gernot; Bernatchez, Louis

doi:10.1111/eva.12661

Cited by 50 publications

(35 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In fact, many applications require cost-effective high-throughput genotype data for specific study organisms and goals, but do not have high-quality reference genomes or other a priori genomic information. This scenario is particularly common in conservation research (Hunter, Hoban, Bruford, Segelbacher, & Bernatchez, 2018) and monitoring of wide-ranging, long-lived species such as marine turtles, where samples often need to be compared across regions, continents and generations, such as fisheries bycatch DPS assignment and genetic capture-recapture studies (Komoroske et al, 2017;Shamblin et al, 2017;Stewart et al, 2016).…”

mentioning

confidence: 99%

A versatile Rapture (RAD‐Capture) platform for genotyping marine turtles

Komoroske

Miller

O’Rourke

et al. 2019

Molecular Ecology Resources

View full text Add to dashboard Cite

Advances in high‐throughput sequencing (HTS) technologies coupled with increased interdisciplinary collaboration are rapidly expanding capacity in the scope and scale of wildlife genetic studies. While existing HTS methods can be directly applied to address some evolutionary and ecological questions, certain research goals necessitate tailoring methods to specific study organisms, such as high‐throughput genotyping of the same loci that are comparable over large spatial and temporal scales. These needs are particularly common for studies of highly mobile species of conservation concern like marine turtles, where life history traits, limited financial resources and other constraints require affordable, adaptable methods for HTS genotyping to meet a variety of study goals. Here, we present a versatile marine turtle HTS targeted enrichment platform adapted from the recently developed Rapture (RAD‐Capture) method specifically designed to meet these research needs. Our results demonstrate consistent enrichment of targeted regions throughout the genome and discovery of candidate variants in all species examined for use in various conservation genetics applications. Accurate species identification confirmed the ability of our platform to genotype over 1,000 multiplexed samples and identified areas for future methodological improvement such as optimization for low initial concentration samples. Finally, analyses within green turtles supported the ability of this platform to identify informative SNPs for stock structure, population assignment and other applications over a broad geographic range of interest to management. This platform provides an additional tool for marine turtle genetic studies and broadens capacity for future large‐scale initiatives such as collaborative global marine turtle genetic databases.

show abstract

mentioning

confidence: 99%

A versatile Rapture (RAD‐Capture) platform for genotyping marine turtles

Komoroske

Miller

O’Rourke

et al. 2019

Molecular Ecology Resources

View full text Add to dashboard Cite

show abstract

“…Its applications can address questions that have long been studied using previous tools (e.g., effective population size, population structure, phylogeography and demography) [5]. The use of novel tools and statistical tests now allows previously inaccessible issues to be addressed, such as physical mapping of adaptive variations and of molecular variants that underlie genotype fitness and relevant phenotypic variations throughout the genome [6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Current State and Perspectives in Population Genomics of the Common Bean

Cortinovis

Frascarelli

Vittori

et al. 2020

Plants

View full text Add to dashboard Cite

Population genomics integrates advances in sequencing technologies, bioinformatics tools, statistical methods and software into research on evolutionary and population genetics. Its application has provided novel approaches that have significantly advanced our understanding of new and long-standing questions in evolutionary processes. This has allowed the disentangling of locus-specific effects from genome-wide effects and has shed light on the genomic basis of fitness, local adaptation and phenotypes. “-Omics” tools have provided a comprehensive genome-wide view of the action of evolution. The specific features of the Phaseolus genus have made it a unique example for the study of crop evolution. The well-documented history of multiple domestications in Phaseolus vulgaris L. (common bean) and its further adaptation to different environments have provided the opportunity to investigate evolutionary issues, such as convergent evolution in the same species across different domestication events. Moreover, the availability of the P. vulgaris reference genome now allows adaptive variations to be easily mapped across the entire genome. Here, we provide an overview of the most significant outcomes obtained in common bean through the use of different computational tools for analysis of population genomics data.

show abstract

“…Genetic technology serves a crucial role in ecology and conservation research programs today (Cino & Ettore, 2018;Haig et al, 2015;Hunter, Hoban, Bruford, Segelbacher, & Bernatchez, 2018). As it becomes increasingly affordable and portable, many applications once restricted to a laboratory can now be conducted directly in the field.…”

Section: Introductionmentioning

confidence: 99%

“…Third, should fieldwork occur away from one's home country, a scientist must learn to work with people of different cultures and backgrounds, since successful field research invariably depends on access to their knowledge and collaboration in the use of their field sites. The fourth and final area of training, we believe, should be in molecular laboratory techniques and sequence analysis, given its power to address modern challenges in the conservation of wildlife and natural habitats (Cino & Ettore, 2018;Haig et al, 2015;Hunter et al, 2018). These are the areas of expertise that will maximize the abilities of the next generation of conservationists to be successful in shifting physical and political landscapes.…”

Section: Introductionmentioning

confidence: 99%

Genomics in the jungle: using portable sequencing as a teaching tool in field courses

Watsa

Pomerantz

et al. 2019

Preprint

View full text Add to dashboard Cite

Genetic research is a rapidly evolving field of study that is increasingly being utilized as a tool for wildlife conservation. However, researchers and science educators in remote areas can often find it difficult to access the latest genetic technologies, often due to a combination of high costs, bulky equipment, and lack of infrastructure. Recent technological innovations are resulting in portable, low-cost instruments that enable next-generation sequencing in remote environments, offering new opportunities to generate a more widespread network of trained conservation scientists, particularly within regions of high biodiversity. What is currently lacking are formalized educational efforts to teach participants in biodiverse areas with hands-on training in molecular biology and real-time DNA sequencing techniques. To address this challenge, we report the design and summarized feedback/outcomes of a conservation genetics field course, called 'Genomics in the Jungle', that took place at a field research station in the Amazon rainforest of southeastern Peru. The program was established by a small US-based NGO, Field Projects International, and facilitated by a local eco-tourism company in Peru, Inkaterra. We utilized portable sequencing technologies from Oxford Nanopore Technologies, and in-kind support from the manufacturers MiniPCR, MiniOne Systems, Promega, and New England Biolabs. Participants included a mix of non-Peruvian students and local/regional students, some of which had no prior exposure to a genetics laboratory. Overall, we maintain that portable sequencing technology is democratizing scientific research and conservation efforts, and is a major step forward for science educators and conservationists.

show abstract

Next‐generation conservation genetics and biodiversity monitoring

Cited by 50 publications

References 52 publications

A versatile Rapture (RAD‐Capture) platform for genotyping marine turtles

A versatile Rapture (RAD‐Capture) platform for genotyping marine turtles

Current State and Perspectives in Population Genomics of the Common Bean

Genomics in the jungle: using portable sequencing as a teaching tool in field courses

Contact Info

Product

Resources

About