Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae.

The lesser short-tailed bat (Mystacina tuberculata) and the long-tailed bat (Chalinolobus tuberculatus) are Aotearoa New Zealand's only native extant terrestrial mammals and are believed to have migrated from Australia. Long-tailed bats arrived in New Zealand an estimated two million years ago and are closely related to other Australian bat species. Lesser short-tailed bats, in contrast, are the only extant species within the Mystacinidae and are estimated to have been living in isolation in New Zealand for the past 16-18 million years. Throughout this period of isolation, lesser short-tailed bats have become one of the most terrestrial bats in the world. Through a metatranscriptomic analysis of guano samples from eight locations across New Zealand, we aimed to characterise the viromes of New Zealand's bats and determine whether viruses have jumped between these species over the past two million years. High viral richness was observed among long-tailed bats with viruses spanning seven different viral families. In contrast, no bat-specific viruses were identified in lesser short-tailed bats. Both bat species harboured an abundance of likely dietary- and environment-associated viruses. We also identified alphacoronaviruses in long-tailed bat guano that had previously been identified in lesser short-tailed bats, suggesting that these viruses had jumped the species barrier after long-tailed bats migrated to New Zealand. Of note, an alphacoronavirus species discovered here possessed a complete genome of only 22,416 nucleotides with entire deletions or truncations of several non-structural proteins, thereby representing what may be the shortest genome within the Coronaviridae identified to date. Overall, this study has revealed a diverse range of novel viruses harboured by New Zealand's only native terrestrial mammals, in turn expanding our understanding of bat viral dynamics and evolution globally.

Evaluation of counting methods for monitoring populations of a cryptic alpine passerine, the rock wren (Passeriformes, Acanthisittidae, Xenicus gilviventris).

Developing and validating methods to determine trends in populations of threatened species is essential for evaluating the effectiveness of conservation interventions. For cryptic species inhabiting remote environments, this can be particularly challenging. Rock wrens, Xenicus gilviventris, are small passerines endemic to the alpine zone of southern New Zealand. They are highly vulnerable to predation by introduced mammalian predators. Establishing a robust, cost-effective monitoring tool to evaluate population trends in rock wrens is a priority for conservation of both the species and, more broadly, as part of a suite of indicators for evaluating effectiveness of management in New Zealand's alpine ecosystems. We assessed the relative accuracy and precision of three population estimation techniques (mark-resight, distance sampling and simple counts on line transects) for two populations of rock wrens in the Southern Alps over six breeding seasons (2012-2018). The performance of these population estimators was compared to known rock wren population size derived from simultaneous territory mapping. Indices of abundance derived from counts on transects were correlated with territory mapping at both study areas, and performed better than either mark-resight methods or distance sampling. Simple counts on standardised line transects are a highly cost-effective method of monitoring birds because they do not require banding a population. As such, we recommend that line transect counts using the design outlined in this paper be adopted as a standard method for long-term monitoring of rock wren populations. Although species-specific testing is required to validate use of low-cost population indices, our results may have utility for the monitoring of other cryptic passerines in relatively open habitats.

Long seed dispersal distances by an inquisitive flightless rail (Gallirallus australis) are reduced by interaction with humans.

Human presence is becoming increasingly ubiquitous, but the influence this has on the seed dispersal services performed by frugivorous animals is largely unknown. The New Zealand weka (Gallirallus australis) is an inquisitive flightless rail that frequently congregates in areas of high human use. Weka are important seed dispersers, yet the seed dispersal services they provide are still poorly understood. We estimated seed dispersal distances of weka for two plant species (Prumnopitys ferruginea and Elaeocarpus dentatus) and tested how human interaction affected these dispersal distances. We estimated weka seed dispersal distances by combining GPS data from 39 weka over three sites with weka seed retention time data in a mechanistic model. The mean seed retention times were extremely long (38-125 h). Weka were highly effective dispersers, dispersing 93-96% of seeds away from parent canopies, and 1% of seeds over 1 km. However, we found evidence of a significant human impact on the seed dispersal distances of weka, with birds occupying areas of high human use performing 34.8-40.9% shorter distances than their more remote counterparts. This represents an example of cryptic function loss, where although weka are still present in the ecosystem, their seed dispersal services are impaired by human interaction.

Introduction of mammalian seed predators and the loss of an endemic flightless bird impair seed dispersal of the New Zealand tree Elaeocarpus dentatus.

Understanding the mutualistic services provided by species is critical when considering both the consequences of their loss or the benefits of their reintroduction. Like many other Pacific islands, New Zealand seed dispersal networks have been changed by both significant losses of large frugivorous birds and the introduction of invasive mammals. These changes are particularly concerning when important dispersers remain unidentified. We tested the impact of frugivore declines and invasive seed predators on seed dispersal for an endemic tree, hinau Elaeocarpus dentatus, by comparing seed dispersal and predation rates on the mainland of New Zealand with offshore sanctuary islands with higher bird and lower mammal numbers. We used cameras and seed traps to measure predation and dispersal from the ground and canopy, respectively. We found that canopy fruit handling rates (an index of dispersal quantity) were poor even on island sanctuaries (only 14% of seeds captured below parent trees on islands had passed through a bird), which suggests that hinau may be adapted for ground-based dispersal by flightless birds. Ground-based dispersal of hinau was low on the New Zealand mainland compared to sanctuary islands (4% of seeds dispersed on the mainland vs. 76% dispersed on islands), due to low frugivore numbers. A flightless endemic rail (Gallirallus australis) conducted the majority of ground-based fruit removal on islands. Despite being threatened, this rail is controversial in restoration projects because of its predatory impacts on native fauna. Our study demonstrates the importance of testing which species perform important mutualistic services, rather than simply relying on logical assumptions.

Cost-benefit analysis of acoustic recorders as a solution to sampling challenges experienced monitoring cryptic species.

The inferences that can be made from any study are limited by the quality of the sampling design. By bad luck, when monitoring species that are difficult to detect (cryptic), sampling designs become dictated by what is feasible rather than what is desired. We calibrated and conducted a cost-benefit analysis of four acoustic recorder options that were being considered as potential solutions to several sampling restrictions experienced while monitoring the Australasian bittern, a cryptic wetland bird. Such sampling restrictions are commonly experienced while monitoring many different endangered species, particularly those that are cryptic. The recorder options included mono and stereo devices, with two sound file processing options (visual and audible analysis). Recording devices provided call-count data similar to those collected by field observers but at a fraction of the cost, which meant that "idealistic" sampling regimes, previously thought to be too expensive, became feasible for bitterns. Our study is one of the few to assess the monetary value of recording devices in the context of data quality, allowing trade-offs (and potential solutions) commonly experienced while monitoring cryptic endangered species to be shown and compared more clearly. The ability to overcome challenges of monitoring cryptic species in this way increases research possibilities for data deficient species and is applicable to any species with similar monitoring challenges.

Mysterious Mystacina: how the New Zealand short-tailed bat (Mystacina tuberculata) locates insect prey.

The New Zealand short-tailed bat Mystacina tuberculata evolved in the absence of terrestrial mammals and initially with few potential predators. Unusual among bats, it is well adapted for the capture of prey on the ground. Bats from Fiordland, New Zealand had relatively low wing loadings and aspect ratios adapted for flight in cluttered habitats. We predicted that M. tuberculata would locate prey in air (uncluttered space) by echolocation. Echolocation call sequences associated with prey capture (terminal buzzes) were heard in the field, and bats detected and localized prey suspended on fishing line by echolocation in a flight cage. The bats emitted brief, multiharmonic echolocation calls at low duty cycle during search phase, and 64% of calls contained most energy in the fundamental harmonic. Approach- and terminal-phase calls were also broadband and multiharmonic. We predicted that bats would not use echolocation to locate prey hidden on the ground in leaf litter (cluttered space). Bats seemed unable to locate hidden prey precisely from the air and instead hunted for such prey while crawling. Echolocation calls were emitted at a low repetition rate on the ground, suggesting that here echolocation was used for orientation and not for prey detection. We experimentally removed cues available to the bats and showed that bats located mealworms in leaf litter by listening for prey-generated noises and possibly by olfaction.