Genomics and the challenging translation into conservation practice

•There are few examples of genomic data being used in conservation biology. •Many uncertainties accompany genomic analyses and interpretations. •We discuss how best to deal with these uncertainties in a conservation setting. •We outline why uptake has been difficult for practitioners and offer a solution. The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners. The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners. a region of the genome under selection that encodes a phenotype (or is closely linked to a causative locus) with fitness consequences in a particular environment. the process of delineating and assigning function to genetic sequences. the loss of genetic diversity at neutrally evolving sites that are linked to sites under purifying selection. genes putatively underlying variation in a certain phenotype. a retrospective population genetics framework that traces genetic variants of a locus to the most recent common ancestor. Used to infer demographic parameters of population histories. uses genetic markers to help conserve biodiversity and manage species and populations. Traditional genetic markers include allozymes, microsatellites, and targeted gene sequences. uses genome-wide information to help conserve biodiversity and manage species and populations. Genomic data is derived from high-throughput sequencing technology. Relevant examples are whole genome resequencing and targeted approaches like exome sequencing, GBS, SNP genotyping, and transcriptome sequencing. a population genetics convention describing the number of breeding individuals in an ideal population that would lose genetic variation at the same rate as the observed population. DNA found in environmental samples (e.g., water, soil) that can be used in genetic or genomic analysis. This contrasts with traditional approaches that target a specific organism or tissue. the loss of genetic variants due to random sampling from one generation to the next. the process of ordering and orienting sequencing into a contiguous consensus sequence of the genome. the sequencing of a repeatable subset of the genome seeded by restriction enzyme recognition sites. Restriction site-associated DNA sequencing (RAD-seq) is another commonly used term. particular combinations of alleles at collinear positions along a stretch of DNA. the increase of genomic segments in identity by descent due to mating between closely related individuals. Results in an increase in homozygosity, potentially revealing detrimental recessive alleles with negative fitness consequences. the non-random association of alleles at two or more loci. homologous DNA sequence descended from a shared common ancestor. a region of the genome that, based on user-defined criteria (often extreme population differentiation), deviates from the rest of the entire genome. the process of genetic exchange between homologous chromosomes, often resulting in a new combination of alleles. the set of all RNA molecules transcribed from a DNA template.