The genome of a globally invasive passerine, the common myna, Acridotheres tristis.

In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (Acridotheres tristis) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.

Tracing the introduction of the invasive common myna using population genomics.

The common myna (Acridotheres tristis) is one of the most invasive bird species in the world, yet its colonisation history is only partly understood. We identified the introduction history and population structure, and quantified the genetic diversity of myna populations from the native range in India and introduced populations in New Zealand, Australia, Fiji, Hawaii, and South Africa, based on thousands of single nucleotide polymorphism markers in 814 individuals. We were able to identify the source population of mynas in several invasive locations: mynas from Fiji and Melbourne, Australia, were likely founded by individuals from a subpopulation in Maharashtra, India, while mynas in Hawaii and South Africa were likely independently founded by individuals from other localities in India. Our findings suggest that New Zealand mynas were founded by individuals from Melbourne, which, in turn, were founded by individuals from Maharashtra. We identified two genetic clusters among New Zealand mynas, divided by New Zealand's North Island's axial mountain ranges, confirming previous observations that mountains and thick forests may form barriers to myna dispersal. Our study provides a foundation for other population and invasion genomic studies and provides useful information for the management of this invasive species.

Is bin-opening in cockatoos leading to an innovation arms race with humans?

Foraging innovations can give wild animals access to human-derived food sources1. If these innovations spread, they can enable adaptive flexibility2 but also lead to human-wildlife conflicts3. Examples include crop-raiding elephants4 and long-tailed macaques that steal items from people to trade them back for food5. Behavioural responses by humans might act as a further driver on animal innovation2,6, even potentially leading to an inter-species 'innovation arms-race'7, yet this is almost entirely unexplored. Here, we report a potential case in wild, urban-living, sulphur-crested cockatoos (Cacatua galerita; henceforth cockatoos), where the socially-learnt behaviour of opening and raiding of household bins by cockatoos8 is met with increasingly effective and socially-learnt bin-protection measures by human residents.

Innovation and geographic spread of a complex foraging culture in an urban parrot.

The emergence, spread, and establishment of innovations within cultures can promote adaptive responses to anthropogenic change. We describe a putative case of the development of a cultural adaptation to urban environments: opening of household waste bins by wild sulphur-crested cockatoos. A spatial network analysis of community science reports revealed the geographic spread of bin opening from three suburbs to 44 in Sydney, Australia, by means of social learning. Analysis of 160 direct observations revealed individual styles and site-specific differences. We describe a full pathway from the spread of innovation to emergence of geographic variation, evidencing foraging cultures in parrots and indicating the existence of cultural complexity in parrots. Bin opening is directly linked to human-provided opportunities, highlighting the potential for culture to facilitate behavioral responses to anthropogenic change.

A citizen science approach reveals long-term social network structure in an urban parrot, Cacatua galerita.

Parrots are often referenced in discussions of social and cognitive complexity, yet relatively little is known of their social organization in the wild. In particular, the presence of long-lasting social ties has been highlighted as a hallmark of social complexity; however, the presence of such ties can be masked in fission-fusion systems like that exhibited by most parrot species. Social network analysis has the potential to elucidate such multi-level dynamics. While most parrot species are tropical canopy dwellers, a subset has successfully colonized urban habitats, where they are often the focus of much public interest. Our study takes advantage of this to use citizen science to collect observations of wing-tagged sulphur-crested cockatoos in central Sydney and record their social associations over multiple years. Using a specifically designed mobile phone application 'Wingtags', we collected over >27,000 citizen science reports of wing-tagged cockatoos, and built social networks from spatial-temporal co-occurrences in observations for 130 tagged birds. To validate this novel methodology, we GPS-tagged a subset of wing-tagged birds and compared networks built from both data collection methods. We then examined correlates of social network structure before exploring the temporal dynamics of network structure and social associations. Social networks constructed from GPS data and citizen science data were highly correlated, suggesting that this novel methodology is robust. Network structure exhibited little seasonal variability and was largely driven by roost site choice; however, individuals also showed a surprising degree of mixing between roosts in their foraging associations. Finally, within this larger fission-fusion system, individuals tended to maintain specific social ties for long periods of time. There was an effect of age on these temporal dynamics, with aging individuals increasing both social stability and longevity of associations. Our findings highlight the utility of citizen science to measure social networks in urban species, and add to the evidence that long-lasting social associations can persist in fission-fusion social systems such as those observed in wild sulphur-crested cockatoos.

Optimizing future biodiversity sampling by citizen scientists.

We are currently in the midst of Earth's sixth extinction event, and measuring biodiversity trends in space and time is essential for prioritizing limited resources for conservation. At the same time, the scope of the necessary biodiversity monitoring is overwhelming funding for professional scientific monitoring. In response, scientists are increasingly using citizen science data to monitor biodiversity. But citizen science data are 'noisy', with redundancies and gaps arising from unstructured human behaviours in space and time. We ask whether the information content of these data can be maximized for the express purpose of trend estimation. We develop and execute a novel framework which assigns every citizen science sampling event a marginal value, derived from the importance of an observation to our understanding of overall population trends. We then make this framework predictive, estimating the expected marginal value of future biodiversity observations. We find that past observations are useful in forecasting where high-value observations will occur in the future. Interestingly, we find high value in both 'hotspots', which are frequently sampled locations, and 'coldspots', which are areas far from recent sampling, suggesting that an optimal sampling regime balances 'hotspot' sampling with a spread across the landscape.

Improving big citizen science data: Moving beyond haphazard sampling.

Citizen science is mainstream: millions of people contribute data to a growing array of citizen science projects annually, forming massive datasets that will drive research for years to come. Many citizen science projects implement a "leaderboard" framework, ranking the contributions based on number of records or species, encouraging further participation. But is every data point equally "valuable?" Citizen scientists collect data with distinct spatial and temporal biases, leading to unfortunate gaps and redundancies, which create statistical and informational problems for downstream analyses. Up to this point, the haphazard structure of the data has been seen as an unfortunate but unchangeable aspect of citizen science data. However, we argue here that this issue can actually be addressed: we provide a very simple, tractable framework that could be adapted by broadscale citizen science projects to allow citizen scientists to optimize the marginal value of their efforts, increasing the overall collective knowledge.

Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates.

Metabolic processes in eukaryotic cells depend on interactions between mitochondrial and nuclear gene products (mitonuclear interactions). These interactions could have a direct role in population divergence. Here, we study mitonuclear co-evolution in a widespread bird that experienced population divergence followed by bidirectional mitochondrial introgression into different nuclear backgrounds. Using >60,000 single nucleotide polymorphisms, we quantify patterns of nuclear genetic differentiation between populations that occupy areas with different climates and harbour deeply divergent mitochondrial lineages despite ongoing nuclear gene flow. We find that strong genetic differentiation and sequence divergence in a region of ~15.4 megabases on chromosome 1A mirror the geographic pattern of mitochondrial DNA divergence. This result is seen in two different transects representing populations with different nuclear backgrounds. The chromosome 1A region is enriched for genes performing mitochondrial functions (N-mt genes). Molecular signatures of selective sweeps in this region alongside those in the mitochondrial genome suggest a history of adaptive mitonuclear co-introgression. Moreover, evidence for large linkage disequilibrium blocks in this genomic region suggests that low recombination could facilitate functional interactions between co-evolved nuclear alleles. Our results are consistent with mitonuclear co-evolution as an important mechanism for population divergence and local adaptation.

Short-term response of a declining woodland bird assemblage to the removal of a despotic competitor.

Interspecific aggression by the noisy miner (Manorina melanocephala), a highly despotic species, is homogenizing woodland avifaunas across eastern Australia. Although a native species, the noisy miner's aggressive exclusion of small birds is a Key Threatening Process under national law. Large-scale removal of noisy miners has been proposed as a management response to this threat following increases in miner presence due to anthropogenic land use practices. We tested this proposal by experimentally removing noisy miners from eucalypt woodland remnants (16-49 ha), assigned randomly as control (n = 12) or treatment (miner removal) sites (n = 12). Standardized bird surveys were conducted before and after removal, and generalized linear mixed models were used to investigate the effect of miner removal on bird assemblage metrics. Despite removing 3552 noisy miners in three sessions of systematic shooting, densities of noisy miners remained similarly high in treatment and control sites, even just 14 days after their removal. However, there was evidence of an increase in richness and abundance of small birds in treatment sites compared to controls-an effect we only expected to see if noisy miner densities were drastically reduced. We suggest that miner removal may have reduced the ability of the recolonizing miners to aggressively exclude small birds, even without substantially reducing miner densities, due to the breakdown of social structures that are central to the species' despotic behaviour. However, this effect on small birds is unlikely to persist in the long term. Synthesis and applications: Despite evidence from other studies that direct removal of noisy miners can result in rapid and sustained conservation benefit for bird communities at small scales, our findings cast doubt on the potential to scale-up this management approach. The circumstances under which direct control of noisy miners can be achieved remain unresolved.

Rain drives foraging decisions of an urban exploiter.

Foraging decisions tend to drive individuals toward maximising energetic gains within a patchy environment. This study aims to determine the extent to which rainfall, and associated changes in food availability, can explain foraging decisions within a patchy urbanised landscape, using the Australian white ibis as a model species. Ibis density, food consumption rates and food abundance (both natural and anthropogenic) were recorded during dry and wet weather within urban parks in Sydney, Australia. Rainfall influenced ibis density in these urban parks. Of the four parks assessed, the site with the highest level of anthropogenic food and the lowest abundance of natural food (earthworms), irrespective of weather, was observed to have three times the density of ibis. Rainfall significantly increased the rate of earthworm consumption as well as their relative availability in all sites. Overall, these density and consumption measures indicate that anthropogenic derived foods, mainly from direct feeding by people, explain the apparent distribution of ibis across urban parks. However, there was evidence of prey-switching when the availability of natural foods increased following rainfall, perhaps reflecting selection of particular nutrients.

Housing shortages in urban regions: aggressive interactions at tree hollows in forest remnants.

Urbanisation typically results in a reduction of hollow-bearing trees and an increase in the density of particularly species, potentially resulting in an increased level of competition as cavity-nesting species compete for a limited resource. To improve understanding of hollow usage between urban cavity-nesting species in Australia, particularly parrots, we investigated how the hollow-using assemblage, visitation rate, diversity and number of interactions varied between hollows within urban remnant forest and continuous forest. Motion-activated video cameras were installed, via roped access to the canopy, and hollow usage was monitored at 61 hollows over a two-year period. Tree hollows within urban remnants had a significantly different assemblage of visitors to those in continuous forest as well as a higher rate of visitation than hollows within continuous forest, with the rainbow lorikeet making significantly more visitations than any other taxa. Hollows within urban remnants were characterised by significantly higher usage rates and significantly more aggressive interactions than hollows within continuous forest, with parrots responsible for almost all interactions. Within urban remnants, high rates of hollow visitation and both interspecific and intraspecific interactions observed at tree hollows suggest the number of available optimal hollows may be limiting. Understanding the usage of urban remnant hollows by wildlife, as well as the role of parrots as a potential flagship for the conservation of tree-hollows, is vital to prevent a decrease in the diversity of urban fauna, particularly as other less competitive species risk being outcompeted by abundant native species.

Rapid characterization of mitochondrial genome rearrangements in Australian songbirds using next-generation sequencing technology.

Using next-generation sequencing technology, we describe the complete mitochondrial genomes for 5 Australian passerine birds (Epthianura albifrons, Petroica phoenicea, Petroica goodenovii, Petroica boodang, and Eopsaltria australis). We successfully assemble each mitogenome de novo using just 1/8th of a Roche GL FSX 454 pyrosequencing plate. From the assembled mitogenomes, we identify 2 different mitochondrial gene arrangements in the region spanning 5'-3' from Cytochrome B to 12s RNA. These gene arrangements represent 2 of the 4 known avian mitochondrial gene arrangements. Our results, together with other previously described avian mitogenomes, highlight that certain mitochondrial rearrangements appear to have arisen multiple times.

Behavioural adaptation of a bird from transient wetland specialist to an urban resident.

Dramatic population increases of the native white ibis in urban areas have resulted in their classification as a nuisance species. In response to community and industry complaints, land managers have attempted to deter the growing population by destroying ibis nests and eggs over the last twenty years. However, our understanding of ibis ecology is poor and a question of particular importance for management is whether ibis show sufficient site fidelity to justify site-level management of nuisance populations. Ibis in non-urban areas have been observed to be highly transient and capable of moving hundreds of kilometres. In urban areas the population has been observed to vary seasonally, but at some sites ibis are always observed and are thought to be behaving as residents. To measure the level of site fidelity, we colour banded 93 adult ibis at an urban park and conducted 3-day surveys each fortnight over one year, then each quarter over four years. From the quarterly data, the first year resighting rate was 89% for females (n = 59) and 76% for males (n = 34); this decreased to 41% of females and 21% of males in the fourth year. Ibis are known to be highly mobile, and 70% of females and 77% of males were observed at additional sites within the surrounding region (up to 50 km distant). Our results indicate that a large proportion of ibis have chosen residency over transience both within the study site and across the broader urban region. Consequently the establishment of refuge breeding habitat should be a priority localised management may be effective at particular sites, but it is likely to have an impact across the broader population.