We agree with Shafer et al. [ 1 Shafer A.B.A. et al. Genomics and the challenging translation into conservation practice. Trends Ecol. Evol. 2015; 30: 78-87 Abstract Full Text Full Text PDF PubMed Scopus (331) Google Scholar ] that there is a need for well-documented case studies of the application of genomics in conservation and management as well as increased communication between academics and natural resource managers. However, we challenge Shafer et al.'s [ 1 Shafer A.B.A. et al. Genomics and the challenging translation into conservation practice. Trends Ecol. Evol. 2015; 30: 78-87 Abstract Full Text Full Text PDF PubMed Scopus (331) Google Scholar ] relatively pessimistic assertion that 'conservation genomics is far from seeing regular application'. Here we illustrate by examples that conservation practitioners utilize more genomic research than is often apparent. In addition, we highlight the work of nonacademic laboratories [government and nongovernmental organizations (NGOs)], some of which are not always well represented in peer-reviewed literature. Finally, we suggest that increased agency–academic collaboration would enhance the application of genomics to real-world conservation and help conserve biodiversity.

The letter by Garner et al. [ 1 Garner B.A. et al. Genomics in conservation: case studies and bridging the gap between data and application. Trends Ecol. Evol. 2016; 31: 81-83 Abstract Full Text Full Text PDF PubMed Scopus (114) Google Scholar ] continued an important discussion regarding the role genomics might play in conservation biology. In general, we do not see a dichotomy between our point of view [ 2 Shafer A.B.A. et al. Genomics and the challenging translation into conservation practice. Trends Ecol. Evol. 2015; 30: 78-87 Abstract Full Text Full Text PDF PubMed Scopus (322) Google Scholar ] and that put forth by Garner et al. [ 1 Garner B.A. et al. Genomics in conservation: case studies and bridging the gap between data and application. Trends Ecol. Evol. 2016; 31: 81-83 Abstract Full Text Full Text PDF PubMed Scopus (114) Google Scholar ]. At the heart of the issue is how to define an actual impact of genomics on applied conservation and find suitable ways to remove existing barriers limiting the use of genomics for managing wild populations. The promised gains of identifying adaptive loci and the genes underlying phenotypes [ 3 Allendorf F.W. et al. Genomics and the future of conservation genetics. Nat. Rev. Genet. 2010; 11: 697-709 Crossref PubMed Scopus (888) Google Scholar , 4 McMahon B.J. et al. How and why should we implement genomics into conservation?. Evol. Appl. 2014; 7: 999-1007 Crossref PubMed Scopus (126) Google Scholar ] have in most systems not yet been realized and recent empirical work further highlights the challenges [ 5 Kardos M. et al. Whole genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations. Mol. Ecol. Res. 2015; (in press) PubMed Google Scholar , 6 Burri R. et al. Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Genome Res. 2015; 25: 1656-1665 Crossref PubMed Scopus (249) Google Scholar ]. Thus, our take-home message boiled down to the application of genomics in wild populations being at an early developmental stage that is far from straightforward and far from regularly applied [ 2 Shafer A.B.A. et al. Genomics and the challenging translation into conservation practice. Trends Ecol. Evol. 2015; 30: 78-87 Abstract Full Text Full Text PDF PubMed Scopus (322) Google Scholar ].

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.