More than an academic exercise: Structuring international partnerships to build research and professional capacity for conservation impact

Toward a Global Science of Conservation Genomics: Coldspots in Genomic Resources Highlight a Need for Equitable Collaborations and Capacity Building

Advances in genomic sequencing have magnified our understanding of ecological and evolutionary mechanisms relevant to biodiversity conservation. As a result, the field of conservation genomics has grown rapidly. Genomic data can be effective in guiding conservation decisions by revealing fine-scale patterns of genetic diversity and adaptation. Adaptive potential, sometimes referred to as evolutionary potential, is particularly informative for conservation due to its inverse relationship with extinction risk. Yet, global coldspots in genomic resources impede progress toward conservation goals. We undertook a systematic literature review to characterise the global distribution of genomic resources for amphibians and reptiles relative to species richness, IUCN status, and predicted global change. We classify the scope of available genomic resources by their potential applicability to global change. Finally, we examine global patterns of collaborations in genomic studies. Our findings underscore current priorities for expanding genomic resources, especially those aimed at predicting adaptive potential to future environmental change. Our results also highlight the need for improved global collaborations in genomic research, resource sharing, and capacity building in the Global South.

rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R

The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach ( blast_seeds() ). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.

The science behind soft skills: Do's and Don'ts for early career researchers and beyond. A review paper from the EU-CardioRNA COST Action CA17129

Soft skills are the elementary management, personal, and interpersonal abilities that are vital for an individual to be efficient at workplace or in their personal life. Each work place requires different set of soft skills. Thus, in addition to scientific/technical skills that are easier to access within a short time frame, several key soft skills are essential for the success of a researcher in today's international work environment. In this paper, the trainees and trainers of the EU-CardioRNA COST Action CA17129 training school on soft skills present basic and advanced soft skills for early career researchers. Here, we particularly emphasize on the importance of transferable and presentation skills, ethics, literature reading and reviewing, research protocol and grant writing, networking, and career opportunities for researchers. All these skills are vital but are often overlooked by some scholars. We also provide tips to ace in aforementioned skills that are crucial in a day-to-day life of early and late career researchers in academia and industry.

The science behind soft skills: Do's and Don'ts for early career researchers and beyond. A review paper from the EU-CardioRNA COST Action CA17129

Soft skills are the elementary management, personal, and interpersonal abilities that are vital for an individual to be efficient at workplace or in their personal life. Each work place requires different set of soft skills. Thus, in addition to scientific/technical skills that are easier to access within a short time frame, several key soft skills are essential for the success of a researcher in today's international work environment. In this paper, the trainees and trainers of the EU-CardioRNA COST Action CA17129 training school on soft skills present basic and advanced soft skills for early career researchers. Here, we particularly emphasize on the importance of transferable and presentation skills, ethics, literature reading and reviewing, research protocol and grant writing, networking, and career opportunities for researchers. All these skills are vital but are often overlooked by some scholars. We also provide tips to ace in aforementioned skills that are crucial in a day-to-day life of early and late career researchers in academia and industry.

Assessing national-level provision of conservation capacity building: lessons learnt from a case study of Kenya

As global environmental pressures grow, the need for delivering relevant and sustainable capacity building in conservation has never been greater. Individuals, organizations and communities need the skills, knowledge and information that allow them to address environmental issues at a variety of spatial scales and in diverse contexts. Capacity is currently built through a range of activities, including tertiary education, training courses, online learning, mentoring and continuing professional development. However, a significant proportion of the current capacity-building provision is non-strategic, project-based and reactive. The conservation sector still lacks a coordinated approach to capacity building linked to broader conservation goals. Without an assessment of current capacity-building provision and future capacity needs, the delivery of capacity building in conservation will remain fundamentally ad hoc. The need for strategic conservation capacity building in sub-Saharan Africa has been identified and here we report on the first collation of online material to assess current conservation capacity provision in Kenya (the country with the greatest online capacity-building presence). We reviewed a total of 177 capacity-building initiatives delivered during 2014–2019 and recorded 55 separate metrics for each initiative. We present: (1) a broad overview of the data collation methods developed, (2) examples of data that will support strategic capacity-building strategies, and (3) the lessons learnt from this assessment.