Next‐generation conservation genetics and biodiversity monitoring

Abstract This special issue of Evolutionary Applications consists of 10 publications investigating the use of next‐generation tools and techniques in population genetic analyses and biodiversity assessment. The special issue stems from a 2016 Next Generation Genetic Monitoring Workshop, hosted by the National Institute for Mathematical and Biological Synthesis (NIMBioS) in Tennessee, USA. The improved accessibility of next‐generation sequencing platforms has allowed molecular ecologists to rapidly produce large amounts of data. However, with the increased availability of new genomic markers and mathematical techniques, care is needed in selecting appropriate study designs, interpreting results in light of conservation concerns, and determining appropriate management actions. This special issue identifies key attributes of successful genetic data analyses in biodiversity evaluation and suggests ways to improve analyses and their application in current population and conservation genetics research.


| INTRODUC TI ON
As biodiversity loss accelerates and environmental challenges mount, there is a need for quantitative evaluation of the status and trends of intraspecific and interspecific genetic diversity of species and communities. Assessing variation in neutral and adaptive loci can identify genetic threats to populations, species, and communities (Alsos et al., 2012;Hemingway et al., 2018). Such assessments can also help to identify the precise mechanism of diversity loss (e.g., correlated with habitat fragmentation; Jump, Hunt, & Peñuelas, 2006;Vranckx, Jacquemyn, Muys, & Honnay, 2012) and which human activities most impact the genetic variation and evolutionary potential of the species (Aguilar, Quesada, Ashworth, Herrerias-Diego, & Lobo, 2008;DiBattista, 2008;Hoban et al., 2010). By monitoring genetic diversity through time, we can determine long-term impacts and assess whether interventions have met conservation targets and improved biodiversity (this issue, Flanagan, Forester, Latch, Aitken, & Hoban, 2018;Hoban et al., 2014).
Recent technological advances have enabled routine assessment of genetic diversity at the genome level (Garner et al., 2016;Narum, Buerkle, Davey, Miller, & Hohenlohe, 2013). However, as genetic datasets are becoming larger and more complex, and analyses are becoming more specialized, thoughtful project planning and application of statistical tools are increasingly needed. Inappropriate choice of study design or analysis can lead to incorrect conclusions, and thus misguided interventions (Lotterhos & Whitlock, 2015;Meirmans, 2015). Moreover, there is recognition that currently available analyses do not make full use of large genomic datasets (Lotterhos et al., 2017;Villemereuil, Frichot, Bazin, François, & Gaggiotti, 2014), and that both informatic and theoretical advances are still needed. These improvements to genetic monitoring and analyses are the focus of this special issue.
At the time of writing, the proposed Convention on Biological Diversity 2020 Aichi Biodiversity Targets is 2 years away. These targets were developed in Aichi, Japan, in 2010 and provide an overarching framework for the United Nations system and various Nations In many species, this target has not yet been met, as studies continue to document genetic erosion across many animal and plant taxa (e.g., Laikre et al., 2010;Nielsen, Gebhard, Smalla, Bones, & van Elsas, 1997;Vilà et al., 2003;Zhu et al., 2013). However, there are increasing efforts to safeguard genetic resources of wild and domesticated plants and animals in situ and ex situ (Mounce, Smith, & Brockington, 2017;O'Donnell & Sharrock, 2017 (Tittensor et al., 2014). In short, the preservation of genetic diversity in wild systems is well recognized in theory but less so in practice, partly due to a need for better-applied conservation genetics tools and guidance for implementation in management decisions.
Until approximately 2010, much of the phylogenetic, evolutionary applications, and conservation genetic analyses were conducted using PCR on between one and 20 loci, or electrophoresis on >30 allozymes. Most studies involved Sanger sequencing at a handful of nuclear markers or mitochondrial DNA loci, or fragment analysis of ~10-20 microsatellites. As we transition into the next phase of genomic analysis, individuals and populations can be assessed at 1,000s to millions of loci using next-generation sequencing (NGS).
This massively parallel high-throughput sequencing approach produces high coverage sequencing reads for many loci and samples (Andrews, Good, Miller, Luikart, & Hohenlohe, 2016 The workshop participants identified key attributes of successful data analysis in biodiversity evaluation and surveyed and critiqued existing genetic metrics to improve analyses and how they might be applied to current needs. For example, monitoring tools should be able to assess system conditions, diagnose the cause of population or diversity losses (e.g., harvest or habitat fragmentation), and predict future changes. Moreover, they should ideally be easily measured, simple to apply, readily understood by nonspecialists such as decision makers, and respond to stressors in a predictable manner (Dale & Beyeler, 2001). Due to the complexity of genomic studies, many of the customary statistical methods do not fit these criteria.
Discussion among participants exposed several areas that warrant  Ferchaud et al., 2018 andFlanagan et al., 2018). Another major advancement of our time, the development of genetic manipulation technologies in combination with gene drive systems, presents the opportunity to modify organisms in a radically new way. To date, this has been primarily applied in the control of diseases, such as producing infertile mosquitos to prevent malaria transmission (Eckhoff, Wenger, Godfray, & Burt, 2017;Gantz et al., 2015;Hammond et al., 2016). In the future, additional options will include introducing genetic variation in imperiled species to recover lost genotypes, improve diversity, reduce inbreeding, or improve resistance to specific diseases (Piaggio et al., 2017). Continued development of guidelines and experimental investigations into the feasibility and utility of these new synthetic biology-based approaches are needed (Akbari et al., 2015;Oye et al., 2014). The papers presented in this special issue form the scientific basis for many of these guidelines. It is vital that genetic information is included in the political decision-making processes aimed at halting and reversing biodiversity loss at national and global scales.
We would like to dedicate this special issue to Dr. Tim King of the US Geological Survey, Leetown Science Center. Dr. King was a renowned conservation geneticist, making key contributions to the field and promoting the application of genetic data in management decisions. His focus, detail, and thoughtful approach to science paved the way for many of us by highlighting the importance of genetic data in imperiled and invasive species management. Dr. King was also a beloved friend and mentor to many and we endeavor to carry his extraordinary legacy forward.

ACK N OWLED G EM ENTS
This work was assisted through participation in the Next

CO N FLI C TO FI NTE R E S T
None declared.