Social inheritance of avoidances shapes the structure of animal social networks.

Social structure can have significant effects on selection, affecting both individual fitness traits and population-level processes. As such, research into its dynamics and evolution has spiked in the last decade, where theoretical and computational advances in social network analysis have increased our understanding of its ecological and inheritance underpinnings. Yet, the processes that shape the formation of structure within social networks are poorly understood and the role of social avoidances unknown. Social avoidances are an alternate of social affiliation in animal societies, which, although invisible, likely play a role in shaping animal social networks. Assuming social avoidances evolve under similar constraints as affiliative behavior, we extended a previous model of social inheritance of affiliations to investigate the impact of social inheritance of avoidances on social network structure. We modeled avoidances as relationships that individuals can copy from their mothers or from their mother's social environment and varied the degrees to which individuals inherit social affiliates and avoidances to test their combined influence on social network structure. We found that inheriting avoidances via maternal social environments made social networks less dense and more modular, thereby demonstrating how social avoidance can shape the evolution of animal social networks.

Influence of scat ageing on the gut microbiome: how old is too old?

BACKGROUND: The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus). RESULTS: We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery. CONCLUSION: We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so.

Whole-mitochondrial genomes of Nannizziopsis provide insights in evolution and detection.

Infectious fungal diseases can have devastating effects on wildlife health and a detailed understanding of the evolution of related emerging fungal pathogen along with the ability to detect them in the wild is considered indispensable for effective management strategies. Several fungi from the genera Nannizziopsis and Paranannizziopsis are emerging pathogens of reptiles and have been observed to cause disease in a wide range of taxa. Nannizziopsis barbatae has become a particularly important pathogen of Australian reptiles with an increasing number of herpetofauna being reported with cases of infection from across the country. Here, we present the mitochondrial genome sequences and phylogenetic analysis for seven species in this group of fungi uncovering new information on the evolutionary relationship of these emerging pathogens. From this analysis, we designed a species-specific qPCR assay for the rapid detection of N. barbatae and demonstrate its application in a wild urban population of a dragon lizard.

Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression.

The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some threats are well known and have clear methods of prevention (e.g., habitat loss can be reduced with stronger land-clearing control), whereas others are less easily addressed. One of the major current threats to koalas is chlamydial disease, which can have major impacts on individual survival and reproduction rates and can translate into population declines. Effective management strategies for the disease in the wild are currently lacking, and, to date, we know little about the determinants of individual susceptibility to disease. Here, we investigated the genetic basis of variation in susceptibility to chlamydia using one of the most intensively studied wild koala populations. We combined data from veterinary examinations, chlamydia testing, genetic sampling and movement monitoring. Out of our sample of 342 wild koalas, 60 were found to have chlamydia. Using genotype information on 5007 SNPs to investigate the role of genetic variation in determining disease status, we found no evidence of inbreeding depression, but a heritability of 0.11 (95% CI: 0.06-0.23) for the probability that koalas had chlamydia. Heritability of susceptibility to chlamydia could be relevant for future disease management, as it suggests adaptive potential for the population.

Selection in the city: Rapid and fine-scale evolution of urban eastern water dragons.

Oceanic archipelagos have long been treated as a Petri dish for studies of evolutionary and ecological processes. Like archipelagos, cities exhibit similar patterns and processes, such as the rapid phenotypic divergence of a species between urban and nonurban environments. However, on a local scale, cities can be highly heterogenous, where geographically close populations can experience dramatically different environmental conditions. Nevertheless, we are yet to understand the evolutionary and ecological implications for populations spread across a heterogenous cityscape. To address this, we compared neutral genetic divergence to quantitative trait divergence within three native riparian and four city park populations of an iconic urban adapter, the eastern water dragon. We demonstrated that selection is likely acting to drive divergence of snout-vent length and jaw width across native riparian populations that are geographically isolated and across city park populations that are geographically close yet isolated by urbanization. City park populations as close as 0.9 km exhibited signs of selection-driven divergence to the same extent as native riparian populations isolated by up to 114.5 km. These findings suggest that local adaptation may be occurring over exceptionally small geographic and temporal scales within a single metropolis, demonstrating that city parks can act as archipelagos for the study of rapid evolution.

Testing the effectiveness of genetic monitoring using genetic non-invasive sampling.

Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling (gNIS) as a cost-effective population-wide genetic monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream genetic analyses. Here, using high-quality single nucleotide polymorphism (SNP) data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures. We found that gNIS at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled. We show that gNIS at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.

Repeatability and heritability of social reaction norms in a wild agamid lizard.

In the evolutionary transition from solitary to group living, it should be adaptive for animals to respond to the environment and choose when to socialize to reduce conflict and maximize access to resources. Due to the associated proximate mechanisms (e.g. neural network, endocrine system), it is likely that this behavior varies between individuals according to genetic and non-genetic factors. We used long-term behavioral and genetic data from a population of eastern water dragons (Intellagama lesueurii) to explore variation in plasticity of social behavior, in response to sex ratio and density. To do so, we modeled individual variation in social reaction norms, which describe individuals' mean behavior and behavioral responses to changes in their environment, and partitioned variance into genetic and non-genetic components. We found that reaction norms were repeatable over multiple years, suggesting that individuals consistently differed in their behavioral responses to changes in the social environment. Despite high repeatability of reaction norm components, trait heritability was below our limit of detection based on power analyses (h2 < 0.12), leading to very little power to detect heritability of plasticity. This was in contrast to a relatively greater amount of variance associated with environmental effects. This could suggest that mechanisms such as social learning and frequency-dependence may shape variance in reaction norms, which will be testable as the dataset grows.

Maternal effects and fitness consequences of individual variation in bottlenose dolphins' ecological niche.

The niche describes the ecological and social environment that an organism lives in, as well as the behavioural tactics used to interact with its environment. A species niche is key to both ecological and evolutionary processes, including speciation, and has therefore been a central focus in ecology. Recent evidence, however, points to considerable individual variation in a species' or population's niche use, although how this variation evolves or is maintained remains unclear. We used a large longitudinal dataset to investigate the drivers and maintenance of individual variation in bottlenose dolphins' Tursiops aduncus niche. Specifically, we (a) characterised the extent of individual differences in habitat use, (b) identified whether there were maternal effects associated with this variation and (c) investigated the relationship between habitat use and calving success, a component of reproductive fitness. By examining patterns of habitat use, we provide evidence that individual dolphins vary consistently between one another in their niche. We further show that such individual variation is driven by a strong maternal effect. Finally, habitat use and calving success were not related, suggesting that use of different habitats results in similar fitness outcomes. Niche partitioning, maintained by maternal effects, likely facilitates the coexistence of multiple ecotypes within this population.

Genome Sequence of the Fungus Nannizziopsis barbatae, an Emerging Reptile Pathogen.

Nannizziopsis barbatae is an emerging fungal pathogen capable of causing contagious dermatomycosis in reptiles. Here, we report a 31.54-Mb draft genome sequence of an isolate originating from an infected eastern water dragon in Brisbane, Australia.

Inbreeding and disease avoidance in a free-ranging koala population.

Habitat destruction and fragmentation are increasing globally, forcing surviving species into small, isolated populations. Isolated populations typically experience heightened inbreeding risk and associated inbreeding depression and population decline; although individuals in these populations may mitigate these risks through inbreeding avoidance strategies. For koalas, as dietary specialists already under threat in the northern parts of their range, increased habitat fragmentation and associated inbreeding costs are of great conservation concern. Koalas are known to display passive inbreeding avoidance through sex-biased dispersal, although population isolation will reduce dispersal pathways. We tested whether free-ranging koalas display active inbreeding avoidance behaviours. We used VHF tracking data, parentage reconstruction, and veterinary examination results to test whether free-ranging female koalas avoid mating with (a) more closely related males; and (b) males infected with sexually transmitted Chlamydia pecorum. We found no evidence that female koalas avoid mating with relatively more related available mates. In fact, as the relatedness of potential mates increases, so did inbreeding events. We also found no evidence that female koalas can avoid mating with males infected with C. pecorum. The absence of active inbreeding avoidance mechanisms in koalas is concerning from a conservation perspective, as small, isolated populations may be at even higher risk of inbreeding depression than expected. At risk koala populations may require urgent conservation interventions to augment gene flow and reduce inbreeding risks. Similarly, if koalas are not avoiding mating with individuals with chlamydial disease, populations may be at higher risk from disease than anticipated, further impacting population viability.

Quantifying koala locomotion strategies: implications for the evolution of arborealism in marsupials.

The morphology and locomotor performance of a species can determine their inherent fitness within a habitat type. Koalas have an unusual morphology for marsupials, with several key adaptations suggested to increase stability in arboreal environments. We quantified the kinematics of their movement over ground and along narrow arboreal trackways to determine the extent to which their locomotion resembled that of primates, occupying similar niches, or basal marsupials from which they evolved. On the ground, the locomotion of koalas resembled a combination of marsupial behaviours and primate-like mechanics. For example, their fastest strides were bounding type gaits with a top speed of 2.78 m s-1 (mean 1.20 m s-1), resembling marsupials, while the relatively longer stride length was reflective of primate locomotion. Speed was increased using equal modification of stride length and frequency. On narrow substrates, koalas took longer but slower strides (mean 0.42 m s-1), adopting diagonally coupled gaits including both lateral and diagonal sequence gaits, the latter being a strategy distinctive among arboreal primates. The use of diagonally coupled gaits in the arboreal environment is likely only possible because of the unique gripping hand morphology of both the fore and hind feet of koalas. These results suggest that during ground locomotion, they use marsupial-like strategies but alternate to primate-like strategies when moving amongst branches, maximising stability in these environments. The locomotion strategies of koalas provide key insights into an independent evolutionary branch for an arboreal specialist, highlighting how locomotor strategies can convergently evolve between distant lineages.

City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii).

Urbanisation is one of the most significant threats to biodiversity, due to the rapid and large-scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild non-model species remains sparse. Using an empirical replicated study system, we show that city life alters the gut microbiome and stable isotope profiling of a wild native non-model species - the eastern water dragon (Intellagama lesueurii) in Queensland, Australia. City dragons exhibit a more diverse gut microbiome than their native habitat counterparts and show gut microbial signatures of a high fat and plant rich diet. Additionally, we also show that city dragons have elevated levels of the Nitrogen-15 isotope in their blood suggesting that a city diet, which incorporates novel anthropogenic food sources, may also be richer in protein. These results highlight the role that gut microbial plasticity plays in an animals' response to human-altered landscapes.

Individual Variation in the Social Plasticity of Water Dragons.

Individuals should alter when they socially associate with conspecifics to avoid potentially costly interactions. Moreover, individuals may vary in their propensity to use information about conspecifics when making such social decisions. However, surprisingly little is known about either the determinants of or the individual variation in such "social plasticity." We show here that eastern water dragons (Intellegama lesueurii lesueurii) may simultaneously use information from different components of their social environment when deciding whether to socially associate. In particular, we found that individuals altered when they socially associated with conspecifics according to the levels of potential conflict and competition in their social environment; both sexes socially associated more at higher local density than would be expected under increased random encounters. Further, females were more likely to socially associate during the breeding season and when there were more males and/or conspecifics whom they typically avoided in their social environment. This suggests that females may seek safety in numbers when the potential for intrasexual conflict or sexual harassment is high. Using a behavioral reaction norm framework, we also provide novel evidence to show that individuals vary in the extent and direction of their social plasticity and that males varied more than females. Our study thus implies that individuals use multiple cues in their environment when deciding to socially associate and that the resulting social plasticity varies between the sexes and between individuals.

Quality and quantity of genetic relatedness data affect the analysis of social structure.

Kinship plays a fundamental role in the evolution of social systems and is considered a key driver of group living. To understand the role of kinship in the formation and maintenance of social bonds, accurate measures of genetic relatedness are critical. Genotype-by-sequencing technologies are rapidly advancing the accuracy and precision of genetic relatedness estimates for wild populations. The ability to assign kinship from genetic data varies depending on a species' or population's mating system and pattern of dispersal, and empirical data from longitudinal studies are crucial to validate these methods. We use data from a long-term behavioural study of a polygynandrous, bisexually philopatric marine mammal to measure accuracy and precision of parentage and genetic relatedness estimation against a known partial pedigree. We show that with moderate but obtainable sample sizes of approximately 4,235 SNPs and 272 individuals, highly accurate parentage assignments and genetic relatedness coefficients can be obtained. Additionally, we subsample our data to quantify how data availability affects relatedness estimation and kinship assignment. Lastly, we conduct a social network analysis to investigate the extent to which accuracy and precision of relatedness estimation improve statistical power to detect an effect of relatedness on social structure. Our results provide practical guidance for minimum sample sizes and sequencing depth for future studies, as well as thresholds for post hoc interpretation of previous analyses.

Developing noninvasive methodologies to assess koala population health through detecting Chlamydia from scats.

Wildlife diseases are a recognized driver of global biodiversity loss, have substantial economic impacts, and are increasingly becoming a threat to human health. Disease surveillance is critical but remains difficult in the wild due to the substantial costs and potential biases associated with most disease detection methods. Noninvasive scat surveys have been proposed as a health monitoring methodology to overcome some of these limitations. Here, we use the known threat of Chlamydia disease to the iconic, yet vulnerable, koala Phascolarctos cinereus to compare three methods for Chlamydia detection in scats: multiplex quantitative PCR, next generation sequencing, and a detection dog specifically trained on scats from Chlamydia-infected koalas. All three methods demonstrated 100% specificity, while sensitivity was variable. Of particular interest is the variable sensitivity of these diagnostic tests to detect sick individuals (i.e., not only infection as confirmed by Chlamydia-positive swabs, but with observable clinical signs of the disease); for koalas with urogenital tract disease signs, sensitivity was 78% with quantitative PCR, 50% with next generation genotyping and 100% with the detection dog method. This may be due to molecular methods having to rely on high-quality DNA whereas the dog most likely detects volatile organic compounds. The most appropriate diagnostic test will vary with disease prevalence and the specific aims of disease surveillance. Acknowledging that detection dogs might not be easily accessible to all, the future development of affordable and portable "artificial noses" to detect diseases from scats in the field might enable cost-effective, rapid and large-scale disease surveillance.

Fresh is best: Accurate SNP genotyping from koala scats.

Maintaining genetic diversity is a crucial component in conserving threatened species. For the iconic Australian koala, there is little genetic information on wild populations that is not either skewed by biased sampling methods (e.g., sampling effort skewed toward urban areas) or of limited usefulness due to low numbers of microsatellites used. The ability to genotype DNA extracted from koala scats using next-generation sequencing technology will not only help resolve location sample bias but also improve the accuracy and scope of genetic analyses (e.g., neutral vs. adaptive genetic diversity, inbreeding, and effective population size). Here, we present the successful SNP genotyping (1272 SNP loci) of koala DNA extracted from scat, using a proprietary DArTseq™ protocol. We compare genotype results from two-day-old scat DNA and 14-day-old scat DNA to a blood DNA template, to test accuracy of scat genotyping. We find that DNA from fresher scat results in fewer loci with missing information than DNA from older scat; however, 14-day-old scat can still provide useful genetic information, depending on the research question. We also find that a subset of 209 conserved loci can accurately identify individual koalas, even from older scat samples. In addition, we find that DNA sequences identified from scat samples through the DArTseq™ process can provide genetic identification of koala diet species, bacterial and viral pathogens, and parasitic organisms.

A framework for the identification of long-term social avoidance in longitudinal datasets.

Animal sociality is of significant interest to evolutionary and behavioural ecologists, with efforts focused on the patterns, causes and fitness outcomes of social preference. However, individual social patterns are the consequence of both attraction to (preference for) and avoidance of conspecifics. Despite this, social avoidance has received far less attention than social preference. Here, we detail the necessary steps to generate a spatially explicit, iterative null model which can be used to identify non-random social avoidance in longitudinal studies of social animals. We specifically identify and detail parameters which will influence the validity of the model. To test the usability of this model, we applied it to two longitudinal studies of social animals (Eastern water dragons (Intellegama lesueurii) and bottlenose dolphins (Tursiops aduncus)) to identify the presence of social avoidances. Using this model allowed us to identify the presence of social avoidances in both species. We hope that the framework presented here inspires interest in addressing this critical gap in our understanding of animal sociality, in turn allowing for a more holistic understanding of social interactions, relationships and structure.

Genomic DNA variation confirmed Seriola lalandi comprises three different populations in the Pacific, but with recent divergence.

Captive breeding programs and aquaculture production have commenced worldwide for the globally distributed yellowtail kingfish (Seriola lalandi), and captive bred fingerlings are being shipped from the Southern Hemisphere to be farmed in the Northern Hemisphere. It was recently proposed that Pacific S. lalandi comprise at least three distinct species that diverged more than 2 million years ago. Here, we tested the hypothesis of different "species" in the Pacific using novel genomic data (namely single nucleotide polymorphisms and diversity array technology markers), as well as mtDNA and DNA microsatellite variation. These new data support the hypothesis of population subdivision between the Northeast Pacific, Northwest Pacific and South Pacific, and genetic divergence indicates restriction to the gene flow between hemispheres. However, our estimates of maximum mtDNA and nuclear DNA divergences of 2.43% and 0.67%, respectively, were within the ranges more commonly observed for populations within species than species within genera. Accordingly our data support the more traditional view that S. lalandi in the Pacific comprises three distinct populations rather than the subdivisions into several species.

Archipelagos of the Anthropocene: rapid and extensive differentiation of native terrestrial vertebrates in a single metropolis.

Some of the best evidence for rapid evolutionary change comes from studies of archipelagos and oceanic islands. City parks are analogous systems as they create geographically isolated green spaces that differ in size, structure and complexity. Very little, however, is known about whether city parks within a single urban centre drive selection and result in the diversification of native species. Here, we provide evidence for the rapid genetic and morphological differentiation of a native lizard (Intellagama lesueurii) at four geographically close yet unconnected parks within one city. Year of establishment of each city park varied from 1855 (oldest) to 2001 (youngest) equating to a generation time range of 32 to three generations. Genetic divergence among city park populations was large despite the small pairwise geographic distances (<5 km) and found to be two to three times higher for microsatellites and three to 33 times higher for mtDNA relative to nonurban populations. Patterns of morphological differentiation were also found to be most extensive among the four city park populations. In contrast to nonurban populations, city park populations showed significant differentiation in relative body size, relative head and limb morphology and relative forelimb and hindlimb length. Crucially, we show that these patterns of differentiation are unlikely to have been caused by founder events and/or drift alone. Our results suggest that city park 'archipelagos' could represent theatres for rapid evolution that may, in time, favour adaptive diversification.

Polyandry in dragon lizards: inbred paternal genotypes sire fewer offspring.

Multiple mating in female animals is something of a paradox because it can either be risky (e.g., higher probability of disease transmission, social costs) or provide substantial fitness benefits (e.g., genetic bet hedging whereby the likelihood of reproductive failure is lowered). The genetic relatedness of parental units, particularly in lizards, has rarely been studied in the wild. Here, we examined levels of multiple paternity in Australia's largest agamid lizard, the eastern water dragon (Intellagama lesueurii), and determined whether male reproductive success is best explained by its heterozygosity coefficient or the extent to which it is related to the mother. Female polyandry was the norm: 2/22 clutches (9.2%) were sired by three or more fathers, 17/22 (77.2%) were sired by two fathers, and only 3/22 (13.6%) clutches were sired by one father. Moreover, we reconstructed the paternal genotypes for 18 known mother-offspring clutches and found no evidence that females were favoring less related males or that less related males had higher fitness. However, males with greater heterozygosity sired more offspring. While the postcopulatory mechanisms underlying this pattern are not understood, female water dragons likely represent another example of reproduction through cryptic means (sperm selection/sperm competition) in a lizard, and through which they may ameliorate the effects of male-driven precopulatory sexual selection.