Ecological restoration of degraded ecosystems has emerged as a critical tool in the fight to reverse and ameliorate the current loss of biodiversity and ecosystem services. Approaches derived from different genetic disciplines are extending the theoretical and applied frameworks on which ecological restoration is based. We performed a search of scientific articles and identified 160 articles that employed a genetic approach within a restoration context to shed light on the links between genetics and restoration. These articles were then classified on whether they examined association between genetics and fitness or the application of genetics in demographic studies, and on the way the studies informed restoration practice. Although genetic research in restoration is rapidly growing, we found that studies could make better use of the extensive toolbox developed by applied fields in genetics. Overall, 41% of reviewed studies used genetic information to evaluate or monitor restoration, and 59% provided genetic information to guide prerestoration decision-making processes. Reviewed studies suggest that restoration practitioners often overlook the importance of including genetic aspects within their restoration goals. Even though there is a genetic basis influencing the provision of ecosystem services, few studies explored this relationship. We provide a view of research gaps, future directions and challenges in the genetics of restoration.

Running title: Effects of habitat fragmentation. Abstract:A deep understanding of population structures and of the relationships among populations is fundamental to guarantee adequate management of endangered species. We used a molecular approach (12 microsatellite loci and mitochondrial DNA) to investigate these aspects in the woylie or brush-tailed bettong (Bettongia penicillata ogilbyi). Four distinct indigenous populations were identified in this study (i.e. Dryandra woodland and Tutanning nature reserve in the wheatbelt region and two discrete populations in the Upper Warren in the south-west forests of Western Australia). Additionally, previously undisclosed modern and historical connections between these units became evident, such as the historical connection between populations at 150 km distance (Dryandra and Upper Warren) and the contemporary gene flow between the two populations in Upper Warren (up to 60 km). 2Genetic attributes of the four populations were analysed and the evidence of unique genetic material in each of these populations indicated that conservation effort should aim towards the preservation of all these units. Additionally, the lower genetic diversity of the woylie population in Tutanning nature reserve prompted the need for the investigation of factors that are limiting the demographic growth of this population. This study enhances not only our knowledge about the ecology of woylies, but also the genetic consequences of habitat fragmentation and reiterates the strength and pertinence of molecular techniques in similar investigations.

1. Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within the reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/ absence of amplified sequence tags) by providing user-friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities.2. Here, we present Version 2 of dartR. In this version, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting.3. dartR provides many functions for importing, exporting and linking to other packages, to provide an easy-to-navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions.4. As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice.

The transmission of pathogens between wildlife and livestock is a globally recognised threat to the livestock industry, as well as to human and wildlife health. Wild cervids are susceptible to many diseases affecting livestock. This presents a challenge for wildlife and domestic animal disease management because the frequent use of agricultural areas by wild cervids may hamper the effectiveness of disease control strategies. Six deer species have established wild populations in Australia and are expanding in range and abundance. A comprehensive literature review of diseases impacting deer and livestock was undertaken, resulting in consideration of 38 pathogens. A qualitative risk assessment was then carried out to assess the overall risk posed by the pathogens to the livestock industry. Five diseases (bovine tuberculosis, foot and mouth disease, malignant catarrhal fever, surra, and screw‐worm fly infestation) ranked highly in our risk assessment. Of these five diseases, only one (malignant catarrhal fever) is currently present in Australia, but all five are notifiable diseases at a national level. Data on these diseases in deer are limited, especially for one of the most abundant species, the sambar deer Rusa unicolor, highlighting a further potential risk attributable to a lack of understanding of disease epidemiology. This paper provides a detailed review of the pathogens affecting both cervids and livestock in Australia, and applies a qualitative framework for assessing the risk posed by deer to the livestock industry. The qualitative framework used here could easily be adapted to assess disease risk in other contexts, making this work relevant to scientists and wildlife managers, as well as to livestock industry workers, worldwide.