Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia.

Genomic diversity is a fundamental component of Earth's total biodiversity, and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution, and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy, and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.

Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads.

Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220-km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.

Population genomics and conservation management of a declining tropical rodent.

Conservation management is improved by incorporating information about the spatial distribution of population genetic diversity into planning strategies. Northern Australia is the location of some of the world's most severe ongoing declines of endemic mammal species, yet we have little genetic information from this regional mammal assemblage to inform a genetic perspective on conservation assessment and planning. We used next-generation sequencing data from remnant populations of the threatened brush-tailed rabbit-rat (Conilurus penicillatus) to compare patterns of genomic diversity and differentiation across the landscape and investigate standardised hierarchical genomic diversity metrics to better understand brush-tailed rabbit-rat population genomic structure. We found strong population structuring, with high levels of differentiation between populations (FST = 0.21-0.78). Two distinct genomic lineages between the Tiwi Islands and mainland are also present. Prioritisation analysis showed that one population in both lineages would need to be conserved to retain at least ~80% of alleles for the species. Analysis of standardised genomic diversity metrics showed that approximately half of the total diversity occurs among lineages (δ = 0.091 from grand total γ = 0.184). We suggest that a focus on conserving remnant island populations may not be appropriate for the preservation of species-level genomic diversity and adaptive potential, as these populations represent a small component of the total diversity and a narrow subset of the environmental conditions in which the species occurs. We also highlight the importance of considering both genomic and ecological differentiation between source and receiving populations when considering translocations for conservation purposes.

Exploring the internal and external wildlife gradients created by conservation fences.

Spillover effects are an expansion of conservation benefits beyond protected areas through dispersal of species that reside within. They have been well documented in marine but not terrestrial systems. To understand the effects on wildlife created by conservation fences, we explored the internal and external gradients of activity in mammal, reptile, and bird species at a conservation reserve in arid Australia that is fenced to exclude invasive rabbits (Oryctolagus cuniculus), cats (Felis catus), and foxes (Vulpes vulpes). Two methods were used: counts of animal tracks along transects on sand dunes and captures at pitfall-trapping sites. In both cases, sites were spaced at different distances from the reserve fenceline inside and outside the reserve. We recorded a range of spillover, source-sink, step, and barrier effects that combined to create a zone within and around the reserve with fence-induced species-specific wildlife gradients. Two endemic rodents but none of the 4 mammal species reintroduced to the reserve showed positive spillover effects. Barrier effects, where activity was highest close to the fence, were recorded for the feral cat and native bettong (Bettongia lesueur), species that could not breach the fence. In comparison, some reptiles and native mammal species that could permeate the fence displayed source-sink effects; that is, their activity levels were reduced close to the fence likely due to constant emigration to the side with lower density. Activity of some reptiles was lowest at sites inside the reserve and gradually increased at outside sites with distance from the fence, a gradient likely related to trophic cascades triggered by predator exclusion. Our result shows that fenced reserves can create overlapping layers of species-specific gradients related to each species' ability to permeate the fence and its varying susceptibility to threats. Managers should be aware that these gradients may extend for several kilometers either side of the fence and that not all contained species will increase in abundance. Creating wider conservation benefits may require increased fence permeability and threat reduction outside the fence.

Exploración de los gradientes de vida silvestre internos y externos creados por las vallas de conservación. Resumen Los efectos de derrame son una expansión de los beneficios de conservación más allá de las áreas protegidas a través de la dispersión de especies que residen en su interior. Han sido bien documentados en sistemas marinos, pero no terrestres. Para entender los efectos de las vallas de exclusión sobre la vida silvestre, exploramos los gradientes internos y externos de la actividad de especies de mamíferos, reptiles y aves en una reserva de conservación en la región árida de Australia que está cercada para excluir conejos invasivos (Oryctolagus cuniculus), gatos (Felis catus) y zorros (Vulpes vulpes). Se utilizaron dos métodos: conteo de huellas de animales a lo largo de transectos en dunas de arena y captura con trampas pitfall. En ambos casos, los sitios fueron espaciados a distintas distancias dentro y fuera de la valla de la reserva. Registramos una gama de efectos de derrame, fuente-sumidero, escalón y barrera que se combinaron para crear una zona dentro y alrededor de la reserva con gradientes de vida silvestre inducidos por la valla. Dos roedores endémicos, pero ninguna de 4 especies de mamíferos reintroducidas a la reserva, mostraron efectos de derrame positivos. Los efectos de barrera, donde la actividad era mayor cerca de la valla, fueron registrados para el gato feral y la rata canguro nativa (Bettongia lesueur), especies que no pudieron franquear la valla. En contraste, algunas especies de reptiles y mamíferos nativos que pudieron permear la valla mostraron efectos de fuente-sumidero; esto es, sus niveles de actividad fueron bajos cerca de la valla probablemente debido a la emigración constante hacia el lado con menor densidad. La actividad de algunos reptiles fue menor en los sitios núcleo de la reserva e incrementaron a medida que incrementó la distancia hacia afuera, un gradiente relacionado probablemente con las cascadas tróficas desencadenadas por la exclusión de depredadores. Nuestros resultados muestran que las reservas cercadas pueden crear capas sobrepuestas de gradientes específicos relacionados con la habilidad de cada especie para permear la valla y su susceptibilidad a las amenazas. Los manejadores deber ser conscientes de que esos gradientes pueden extenderse varios kilómetros a ambos lados de la valla y que no todas las especies contenidas aumentarán en abundancia. La creación de beneficios de conservación más amplios puede requerir una mayor permeabilidad de la vallas y la reducción de amenazas fuera de la reserva.

Tailoring release protocols to individual species and sites: one size does not fit all.

Reintroduction programs for threatened species often include elaborate release strategies designed to improve success, but their advantages are rarely tested scientifically. We used a set of four experiments to demonstrate that the influence of release strategies on short-term reintroduction outcomes is related to both intrinsic and extrinsic factors. We compared different reintroduction strategies for three mammal species in an arid environment where exotic mammalian predators were removed. Wild greater stick-nest rats selected vegetation shelter sites with greater structural density than captive-bred rats, travelled further from the release site and experienced lower rates of mortality. In comparison, there was no difference in mortality or movement between wild and captive-bred greater bilbies. Burrowing bettongs and greater bilbies were also subjected to immediate and delayed release strategies and whilst no difference was detected in bilbies, bettongs that were subjected to delayed releases lost less weight and took less time to establish burrows than those that were immediately released. Interspecific differences in treatment response were attributed to predation risk, the nature of the release site, and behavioural traits such as shelter investment and sociality. Our varied results highlight the inadequacies of review articles focusing on optimum release protocols due to their attempt to generalise across species and release sites. We provide an example of a predictive model to guide future release strategy experimentation that recognises the range of intrinsic and extrinsic factors influencing reintroduction outcomes. We encourage researchers to treat programs experimentally, identify individual site and species characters that may influence release strategies and record data on movements, mortality, weight dynamics, and settling times and distances. The inherent issues of small sample size and low statistical power that plague most reintroduction experiments suggests there is also a need for increased standardisation and publication of data sets to enable appropriate meta-analyses to occur.