Empirical landscape genetic comparison of single nucleotide polymorphisms and microsatellites in three arid-zone mammals with high dispersal capacity.

Landscape genetics is increasingly transitioning away from microsatellites, with single nucleotide polymorphisms (SNPs) providing increased resolution for detecting patterns of spatial-genetic structure. This is particularly pertinent for research in arid-zone mammals due to challenges associated with unique life history traits, such as boom-bust population dynamics and long-distance dispersal capacities. Here, we provide a case study comparing SNPs versus microsatellites for testing three explicit landscape genetic hypotheses (isolation-by-distance, isolation-by-barrier, and isolation-by-resistance) in a suite of small, arid-zone mammals in the Pilbara region of Western Australia. Using clustering algorithms, Mantel tests, and linear mixed effects models, we compare functional connectivity between genetic marker types and across species, including one marsupial, Ningaui timealeyi, and two native rodents, Pseudomys chapmani and P. hermannsburgensis. SNPs resolved subtle genetic structuring not detected by microsatellites, particularly for N. timealeyi where two genetic clusters were identified. Furthermore, stronger signatures of isolation-by-distance and isolation-by-resistance were detected when using SNPs, and model selection based on SNPs tended to identify more complex resistance surfaces (i.e., composite surfaces of multiple environmental layers) in the best-performing models. While we found limited evidence for physical barriers to dispersal across the Pilbara for all species, we found that topography, substrate, and soil moisture were the main environmental drivers shaping functional connectivity. Our study demonstrates that new analytical and genetic tools can provide novel ecological insights into arid landscapes, with potential application to conservation management through identifying dispersal corridors to mediate the impacts of ongoing habitat fragmentation in the region.

Linking life history to landscape for threatened species conservation in a multiuse region.

Landscape-scale conservation that considers metapopulation dynamics will be essential for preventing declines of species facing multiple threats to their survival. Toward this end, we developed a novel approach that combines occurrence records, spatial-environmental data, and genetic information to model habitat, connectivity, and patterns of genetic structure and link spatial attributes to underlying ecological mechanisms. Using the threatened northern quoll (Dasyurus hallucatus) as a case study, we applied this approach to address the need for conservation decision-making tools that promote resilient metapopulations of this threatened species in the Pilbara, Western Australia, a multiuse landscape that is a hotspot for biodiversity and mining. Habitat and connectivity were predicted by different landscape characteristics. Whereas habitat suitability was overwhelmingly driven by terrain ruggedness, dispersal was facilitated by proximity to watercourses. Although there is limited evidence for major physical barriers in the Pilbara, areas with high silt and clay content (i.e., alluvial and hardpan plains) showed high resistance to dispersal. Climate subtlety shaped distributions and patterns of genetic turnover, suggesting the potential for local adaptation. By understanding these spatial-environmental associations and linking them to life-history and metapopulation dynamics, we highlight opportunities to provide targeted species management. To support this, we have created habitat, connectivity, and genetic uniqueness maps for conservation decision-making in the region. These tools have the potential to provide a more holistic approach to conservation in multiuse landscapes globally.

La conservación a nivel del paisaje que incluye las dinámicas metapoblacionales será esencial para prevenir la declinación de especies con múltiples amenazas a su supervivencia. Enfocados en este fin, desarrollamos una estrategia novedosa que combina los registros presenciales, datos espacio-ambientales e información genética para modelar la conectividad de hábitat y los patrones de estructura genética y conectar los atributos espaciales con los mecanismos ecológicos subyacentes. Usamos al cuol del norte (Dasyurus hallucatus) como estudio de caso para aplicar esta estrategia y abordar la necesidad de herramientas de decisión en la conservación que promuevan metapoblaciones resilientes de esta especie en la Pilbara de Australia Occidental, un paisaje multiusos que es un punto caliente para la biodiversidad y la minería. Diferentes características del paisaje pronosticaron la conectividad y el hábitat. Mientras que la escabrosidad del terreno causó enormemente la idoneidad del hábitat, la dispersión estuvo propiciada por la proximidad a los cauces. Aunque hay evidencias limitadas de barreras físicas importantes en la Pilbara, las áreas con un contenido elevado de limo y arcilla (es decir, planicies aluviales y de alio) mostraron una gran resistencia a la dispersión. La matización climática determinó la distribución y los patrones del recambio genético, lo que sugiere un potencial para la adaptación local. Si entendemos estas asociaciones espacio-ambientales y las conectamos con las dinámicas metapoblacionales y de historia de vida, podemos resaltar las oportunidades para proporcionar un manejo focalizado de la especie. Para respaldar esto hemos creado mapas de hábitat, conectividad y singularidad genética para las decisiones de conservación en la región. Estas herramientas tienen el potencial de proporcionar una estrategia más holística para la conservación en los paisajes multiusos de todo el mundo.

Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible.

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity-one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species' adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.

The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers.

For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens-hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine-scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex-biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine-scale genetic structure.

Fine-scale refuges can buffer demographic and genetic processes against short-term climatic variation and disturbance: a 22-year case study of an arboreal marsupial.

Ecological disturbance and climate are key drivers of temporal dynamics in the demography and genetic diversity of natural populations. Microscale refuges are known to buffer species' persistence against environmental change, but the effects of such refuges on demographic and genetic patterns in response to short-term environmental variation are poorly understood. We quantified demographic and genetic responses of mountain brushtail possums (Trichosurus cunninghami) to rainfall variability (1992-2013) and to a major wildfire. We hypothesized that there would be underlying differences in demographic and genetic processes between an unburnt mesic refuge and a topographically exposed zone that was burnt in 2009. Fire caused a 2-year decrease in survival in the burnt zone, but the population grew after the fire due to immigration, leading to increased expected heterozygosity. We documented a fire-related behavioural shift, where the rate of movement by individuals in the unburnt refuge to the burnt zone decreased after fire. Irrespective of the fire, there were long-term differences in demographic and genetic parameters between the mesic/unburnt refuge and the nonmesic/burnt zone. Survival was high and unaffected by rainfall in the refuge, but lower and rainfall-dependent in the nonmesic zone. Net movement of individuals was directional, from the mesic refuge to the nonmesic zone, suggesting fine-scale source-sink dynamics. There were higher expected heterozygosity (HE ) and temporal genetic stability in the refuge, but lower HE and marked temporal genetic structure in the exposed habitat, consistent with reduced generational overlap caused by elevated mortality and immigration. Thus, fine-scale refuges can mediate the short-term demographic and genetic effects of climate and ecological disturbance.

Models of systemic lupus erythematosus: development of autoimmunity following peptide immunizations of noninbred pedigreed rabbits.

Reported in this study are the initial results from studies to develop rabbit models of systemic lupus erythematosus (SLE) by immunizations using two distinct peptides on branched polylysine backbones (multiple Ag peptide)-peptides. Eleven rabbits received a peptide from the Sm B/B' spliceosomal complex previously shown to be immunogenic in rabbits, and 13 rabbits received a peptide from the rabbit N-methyl-d-aspartate receptor NR2b. All 24 animals in different generations of pedigreed, noninbred rabbits produced peptide-specific responses. Anti-nuclear autoantibody responses, including anti-dsDNA, were seen in 17 of 24 rabbits. To date, two rabbits have been observed to have seizure-like events and a third nystagmus. A model for eliciting development of SLE in genetically related yet heterogeneous rabbits may more closely resemble development of human SLE than do some models in inbred mice. Through selective breeding, it may also ultimately provide additional information about the genetics and etiology of SLE and serve as a model for assessing new treatment options.