A new, large-bodied omnivorous bat (Noctilionoidea: Mystacinidae) reveals lost morphological and ecological diversity since the Miocene in New Zealand

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.

Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats

Although evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. In phyllostomid bats, an ecologically diverse clade that evolved plant visiting from a presumed insectivorous ancestor, the evolution of novel food detection mechanisms is suggested to be a key innovation, as plant-visiting species rely strongly on olfaction, supplementarily using echolocation. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration are coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants-a potential ecological constraint on sensory evolution.

Emerging viruses: Cross-species transmission of coronaviruses, filoviruses, henipaviruses, and rotaviruses from bats

Emerging infectious diseases, especially if caused by bat-borne viruses, significantly affect public health and the global economy. There is an urgent need to understand the mechanism of interspecies transmission, particularly to humans. Viral genetics; host factors, including polymorphisms in the receptors; and ecological, environmental, and population dynamics are major parameters to consider. Here, we describe the taxonomy, geographic distribution, and unique traits of bats associated with their importance as virus reservoirs. Then, we summarize the origin, intermediate hosts, and the current understanding of interspecies transmission of Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Nipah, Hendra, Ebola, Marburg virus, and rotaviruses. Finally, the molecular interactions of viral surface proteins with host cell receptors are examined, and a comparison of these interactions in humans, intermediate hosts, and bats is conducted. This uncovers adaptive mutations in virus spike protein that facilitate cross-species transmission and risk factors associated with the emergence of novel viruses from bats.

Foraging shifts and visual preadaptation in ecologically diverse bats

Changes in behaviour may initiate shifts to new adaptive zones, with physical adaptations for novel environments evolving later. While new mutations are commonly considered engines of adaptive change, sensory evolution enabling access to new resources might also arise from standing genetic diversity, and even gene loss. We examine the relative contribution of molecular adaptations, measured by positive and relaxed selection, acting on eye-expressed genes associated with shifts to new adaptive zones in ecologically diverse bats from the superfamily Noctilionoidea. Collectively, noctilionoids display remarkable ecological breadth, from highly divergent echolocation to flight strategies linked to specialized insectivory, the parallel evolution of diverse plant-based diets (e.g., nectar, pollen and fruit) from ancestral insectivory, and-unusually for echolocating bats-often have large, well-developed eyes. We report contrasting levels of positive selection in genes associated with the development, maintenance and scope of visual function, tracing back to the origins of noctilionoids and Phyllostomidae (the bat family with most dietary diversity), instead of during shifts to novel diets. Generalized plant visiting was not associated with exceptional molecular adaptation, and exploration of these novel niches took place in an ancestral phyllostomid genetic background. In contrast, evidence for positive selection in vision genes was found at subsequent shifts to either nectarivory or frugivory. Thus, neotropical noctilionoids that use visual cues for identifying food and roosts, as well as for orientation, were effectively preadapted, with subsequent molecular adaptations in nectar-feeding lineages and the subfamily Stenodermatinae of fig-eating bats fine-tuning pre-existing visual adaptations for specialized purposes.

Purple haze: Cryptic purple sequestrate Cortinarius in New Zealand

CORTINARIUS

is a species-rich ectomycorrhizal genus containing taxa that exhibit agaricoid or sequestrate basidiome morphologies. In New Zealand, one of the most recognizable and common Cortinarius species is the purple sequestrate fungus, C. porphyroideus. We used genome skimming of the almost 100-y-old type specimen from C. porphyroideus to obtain the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) and partial nuc rDNA 28S (28S) sequences. The phylogenetic position of C. porphyroideus was established, and we found that it represents a rarely collected species. Purple sequestrate Cortinarius comprise multiple cryptic species in several lineages. We describe four new species of Cortinarius with strong morphological similarity to C. porphyroideus: Cortinarius diaphorus, C. minorisporus, C. purpureocapitatus, and C. violaceocystidiatus. Based on molecular evidence, Thaxterogaster viola is recognized as Cortinarius violaceovolvatus var. viola. These species are associated with Nothofagus (southern beech) and have very similar morphology to C. porphyroideus but are all phylogenetically distinct based on molecular data.

Evidence for a giant parrot from the Early Miocene of New Zealand

Insular avifaunas have repeatedly spawned evolutionary novelties in the form of unusually large, often flightless species. We report fossils from the Early Miocene St Bathans Fauna of New Zealand that attests to the former existence of a giant psittaciform, which is described as a new genus and species. The fossils are two incomplete tibiotarsi from a bird with an estimated mass of 7 kg, double that of the heaviest known parrot, the kakapo Strigops habroptila. These psittaciform fossils show that parrots join the growing group of avian taxa prone to giantism in insular species, currently restricted to palaeognaths, anatids, sylviornithids, columbids, aptornithids, ciconiids, tytonids, falconids and accipitrids.

An Akania (Akaniaceae) inflorescence with associated pollen from the early Miocene of New Zealand

PREMISE OF THE STUDY

An Akania-like inflorescence, including flowers with in situ pollen was recovered from the remarkable Konservat-Lagerstätte lacustrine diatomite deposit at Foulden Maar, Otago indicating the presence of Akaniaceae in southern New Zealand during the early Miocene. The flowers, although slightly smaller than the sole modern Australian species, A. bidwillii, contain pollen grains that are very like that taxon. The pollen also resembles that of the monospecific sister genus Bretschneidera from Southeast Asia and India, although that taxon has flowers with very different morphology from this genus.

METHODS

The floral morphology of the fossil and in situ pollen grains were compared with flowers and pollen grains from extant species of Akaniaceae and related taxa.

KEY RESULTS

The fossil inflorescence and associated pollen are referred to a new, extinct species of Akania: Akania gibsonorum. The floral structures and pollen resemble those of the modern Australian Akania species.

CONCLUSIONS

The discovery of fossil flowers of Akania in an early Miocene lake deposit in New Zealand, coupled with earlier recognition of Akaniaceae leaves from the Paleocene epoch and wood from the Miocene epoch in South America suggests that the genus was once widespread in former Gondwana landmasses. The extinction of Akaniaceae in New Zealand and South America, and its present relictual distribution in eastern Australia, is most likely related to post-Miocene climatic cooling.

Hibernation and daily torpor in Australian and New Zealand bats: does the climate zone matter?

We aim to summarise what is known about torpor use and patterns in Australian and New Zealand (ANZ) bats from temperate, tropical/subtropical and arid/semiarid regions and to identify whether and how they differ. ANZ bats comprise ~90 species from 10 families. Members of at least nine of these are known to use torpor, but detailed knowledge is currently restricted to the pteropodids, molossids, mystacinids, and vespertilionids. In temperate areas, several species can hibernate (use a sequence of multiday torpor bouts) in trees or caves mostly during winter and continue to use short bouts of torpor for the rest of the year, including while reproducing. Subtropical vespertilionids also use multiday torpor in winter and brief bouts of torpor in summer, which permit a reduction in foraging, probably in part to avoid predators. Like temperate-zone vespertilionids they show little or no seasonal change in thermal energetics during torpor, and observed changes in torpor patterns in the wild appear largely due to temperature effects. In contrast, subtropical blossom-bats (pteropodids) exhibit more pronounced daily torpor in summer than winter related to nectar availability, and this involves a seasonal change in physiology. Even in tropical areas, vespertilionids express short bouts of torpor lasting ~5 h in winter; summer data are not available. In the arid zone, molossids and vespertilionids use torpor throughout the year, including during desert heat waves. Given the same thermal conditions, torpor bouts in desert bats are longer in summer than in winter, probably to minimise water loss. Thus, torpor in ANZ bats is used by members of all or most families over the entire region, its regional and seasonal expression is often not pronounced or as expected, and it plays a key role in energy and water balance and other crucial biological functions that enhance long-term survival by individuals.

A synthesis of ecological and evolutionary determinants of bat diversity across spatial scales

Background

Diversity patterns result from ecological to evolutionary processes operating at different spatial and temporal scales. Species trait variation determine the spatial scales at which organisms perceive the environment. Despite this knowledge, the coupling of all these factors to understand how diversity is structured is still deficient. Here, we review the role of ecological and evolutionary processes operating across different hierarchically spatial scales to shape diversity patterns of bats—the second largest mammal order and the only mammals with real flight capability.

Main body

We observed that flight development and its provision of increased dispersal ability influenced the diversification, life history, geographic distribution, and local interspecific interactions of bats, differently across multiple spatial scales. Niche packing combined with different flight, foraging and echolocation strategies and differential use of air space allowed the coexistence among bats as well as for an increased diversity supported by the environment. Considering distinct bat species distributions across space due to their functional characteristics, we assert that understanding such characteristics in Chiroptera improves the knowledge on ecological processes at different scales. We also point two main knowledge gaps that limit progress on the knowledge on scale-dependence of ecological and evolutionary processes in bats: a geographical bias, showing that research on bats is mainly done in the New World; and the lack of studies addressing the mesoscale (i.e. landscape and metacommunity scales).

Conclusions

We propose that it is essential to couple spatial scales and different zoogeographical regions along with their functional traits, to address bat diversity patterns and understand how they are distributed across the environment. Understanding how bats perceive space is a complex task: all bats can fly, but their perception of space varies with their biological traits.

Electronic supplementary material

The online version of this article (10.1186/s12898-018-0174-z) contains supplementary material, which is available to authorized users.