Out of thin air: surveying tropical bat roosts through air sampling of eDNA

Understanding roosting behaviour is essential to bat conservation and biomonitoring, often providing the most accurate methods of assessing bat population size and health. However, roosts can be challenging to survey, e.g., physically impossible to access or presenting risks for researchers. Disturbance during monitoring can also disrupt natural bat behaviour and present material risks to the population such as disrupting hibernation cycles. One solution to this is the use of non-invasive monitoring approaches. Environmental (e)DNA has proven especially effective at detecting rare and elusive species particularly in hard-to-reach locations. It has recently been demonstrated that eDNA from vertebrates is carried in air. When collected in semi-confined spaces, this airborne eDNA can provide remarkably accurate profiles of biodiversity, even in complex tropical communities. In this study, we deploy novel airborne eDNA collection for the first time in a natural setting and use this approach to survey difficult to access potential roosts in the neotropics. Using airborne eDNA, we confirmed the presence of bats in nine out of 12 roosts. The identified species matched previous records of roost use obtained from photographic and live capture methods, thus demonstrating the utility of this approach. We also detected the presence of the white-winged vampire bat (Diaemus youngi) which had never been confirmed in the area but was long suspected based on range maps. In addition to the bats, we detected several non-bat vertebrates, including the big-eared climbing rat (Ototylomys phyllotis), which has previously been observed in and around bat roosts in our study area. We also detected eDNA from other local species known to be in the vicinity. Using airborne eDNA to detect new roosts and monitor known populations, particularly when species turnover is rapid, could maximize efficiency for surveyors while minimizing disturbance to the animals. This study presents the first applied use of airborne eDNA collection for ecological analysis moving beyond proof of concept to demonstrate a clear utility for this technology in the wild.

Safeguarding Imperiled Biodiversity and Evolutionary Processes in the Wallacea Center of Endemism

Wallacea-the meeting point between the Asian and Australian fauna-is one of the world's largest centers of endemism. Twenty-three million years of complex geological history have given rise to a living laboratory for the study of evolution and biodiversity, highly vulnerable to anthropogenic pressures. In the present article, we review the historic and contemporary processes shaping Wallacea's biodiversity and explore ways to conserve its unique ecosystems. Although remoteness has spared many Wallacean islands from the severe overexploitation that characterizes many tropical regions, industrial-scale expansion of agriculture, mining, aquaculture and fisheries is damaging terrestrial and aquatic ecosystems, denuding endemics from communities, and threatening a long-term legacy of impoverished human populations. An impending biodiversity catastrophe demands collaborative actions to improve community-based management, minimize environmental impacts, monitor threatened species, and reduce wildlife trade. Securing a positive future for Wallacea's imperiled ecosystems requires a fundamental shift away from managing marine and terrestrial realms independently.

Measuring biodiversity from DNA in the air

The crisis of declining biodiversity¹ exceeds our current ability to monitor changes in ecosystems. Rapid terrestrial biomonitoring approaches are essential to quantify the causes and consequences of global change. Environmental DNA² has revolutionized aquatic ecology,³ permitting population monitoring⁴ and remote diversity assessments matching or outperforming conventional methods of community sampling.^3-5 Despite this model, similar methods have not been widely adopted in terrestrial ecosystems. Here, we demonstrate that DNA from terrestrial animals can be filtered, amplified, and then sequenced from air samples collected in natural settings representing a powerful tool for terrestrial ecology. We collected air samples at a zoological park, where spatially confined non-native species allowed us to track DNA sources. We show that DNA can be collected from air and used to identify species and their ecological interactions. Air samples contained DNA from 25 species of mammals and birds, including 17 known terrestrial resident zoo species. We also identified food items from air sampled in enclosures and detected taxa native to the local area, including the Eurasian hedgehog, endangered in the United Kingdom. Our data demonstrate that airborne eDNA concentrates around recently inhabited areas but disperses away from sources, suggesting an ecology to airborne eDNA and the potential for sampling at a distance. Our findings demonstrate the profound potential of air as a source of DNA for global terrestrial biomonitoring.

Molecular diet analysis of the marine fish-eating bat (Myotis vivesi) and potential mercury exposure

Mercury is a toxic element acquired by animals through feeding which can accumulate within food chains through biomagnification. This possesses particular risks to higher trophic levels and may unduly impact marine foraging species or individuals. The fish-eating bat (Myotis vivesi Menegaux, 1901) inhabits islands in the Gulf of California and can act as a predator in the marine environment. A predominantly marine diet and a high trophic position increase the risk of mercury exposure owing to increased bioaccumulation. Using molecular techniques to reconstruct diet, we show that M. vivesi regularly feeds on small fishes and crustaceans, particularly on the Californian anchovy (Engraulis mordax Girard, 1854) and a krill species (Nyctiphanes simplex Hansen, 1911). Additionally, we identify significant interannual variation in diet composition within this population, but measured levels of total mercury in faecal samples were not related to dietary diversity or trophic level.

Dung beetles as samplers of mammals in Malaysian Borneo-a test of high throughput metabarcoding of iDNA

Invertebrate-derived DNA (iDNA) sampling in biodiversity surveys is becoming increasingly widespread, with most terrestrial studies relying on DNA derived from the gut contents of blood-feeding invertebrates, such as leeches and mosquitoes. Dung beetles (superfamily Scarabaeoidea) primarily feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps, are globally distributed, and occur in a wide range of habitats. To build on the few existing studies demonstrating the potential of dung beetles as sources of mammalian DNA, we subjected the large-bodied, Bornean dung beetle (Catharsius renaudpauliani) to a controlled feeding experiment. We analysed DNA from gut contents at different times after feeding using qPCR techniques. Here, we first describe the window of DNA persistence within a dung beetle digestive tract. We found that the ability to successfully amplify cattle DNA decayed over relatively short time periods, with DNA copy number decreasing by two orders of magnitude in just 6 h. In addition, we sampled communities of dung beetles from a lowland tropical rainforest in Sabah, Malaysia, in order to test whether it is possible to identify vertebrate sequences from dung beetle iDNA. We sequenced both the gut contents from large dung beetle species, as well as whole communities of smaller beetles. We successfully identified six mammalian species from our samples, including the bearded pig (Sus barbatus) and the sambar deer (Rusa unicolor)—both vulnerable species on the IUCN red list. Our results represent the first use of dung beetle iDNA to sample Southeast Asian vertebrate fauna, and highlight the potential for dung beetle iDNA to be used in future biodiversity monitoring surveys.

Exploratory analysis reveals arthropod consumption in 10 lemur species using DNA metabarcoding

Arthropods (insects, spiders, etc.) can fulfill major nutritional requirements for primates, particularly in terms of proteins, fats, vitamins, and minerals. Yet, for many primate species we know very little about the frequency and importance of arthropod consumption. Traditional methods for arthropod prey identification, such as behavioral observations and fecal dissections, offer limited taxonomic resolution and, as a result, underestimate true diversity. Metabarcoding arthropod DNA from primate fecal samples provides a promising but underused alternative. Here, we inventoried arthropod prey diversity in wild lemurs by sequencing two regions of the CO1 gene. Samples were collected opportunistically from 10 species of lemurs inhabiting three national parks in southern Madagascar using a combination of focal animal follows and live trapping. In total, we detected arthropod DNA in 98 of the 170 fecal samples analyzed. Although all lemur species included in these analyses showed evidence of arthropod consumption, those within the family Cheirogaleidae appeared to consume the highest frequency and diversity of arthropods. To our knowledge, this study presents the first evidence of arthropod consumption in Phaner pallescens, Avahi peyrierasi, and Propithecus verreauxi, and identifies 32 families of arthropods as probable food items that have not been published as lemur dietary items to date. Our study emphasizes the importance of arthropods as a nutritional source and the role DNA metabarcoding can play in elucidating an animal's diet.

eDNAir: proof of concept that animal DNA can be collected from air sampling

Environmental DNA (eDNA) is one of the fastest developing tools for species biomonitoring and ecological research. However, despite substantial interest from research, commercial and regulatory sectors, it has remained primarily a tool for aquatic systems with a small amount of work in substances such as soil, snow and rain. Here we demonstrate that eDNA can be collected from air and used to identify mammals. Our proof of concept successfully demonstrated that eDNA sampled from air contained mixed templates which reflect the species known to be present within a confined space and that this material can be accessed using existing sampling methods. We anticipate this demonstration will initiate a much larger research programme in terrestrial airDNA sampling and that this may rapidly advance biomonitoring approaches. Lastly, we outline these and potential related applications we expect to benefit from this development.

Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats

The application of metabarcoding to environmental and invertebrate‐derived DNA (eDNA and iDNA) is a new and increasingly applied method for monitoring biodiversity across a diverse range of habitats. This approach is particularly promising for sampling in the biodiverse humid tropics, where rapid land‐use change for agriculture means there is a growing need to understand the conservation value of the remaining mosaic and degraded landscapes. Here we use iDNA from blood‐feeding leeches (Haemadipsa picta) to assess differences in mammalian diversity across a gradient of forest degradation in Sabah, Malaysian Borneo. We screened 557 individual leeches for mammal DNA by targeting fragments of the 16S rRNA gene and detected 14 mammalian genera. We recorded lower mammal diversity in the most heavily degraded forest compared to higher quality twice logged forest. Although the accumulation curves of diversity estimates were comparable across these habitat types, diversity was higher in twice logged forest, with more taxa of conservation concern. In addition, our analysis revealed differences between the community recorded in the heavily logged forest and that of the twice logged forest. By revealing differences in mammal diversity across a human‐modified tropical landscape, our study demonstrates the value of iDNA as a noninvasive biomonitoring approach in conservation assessments.

Using metabarcoding to compare the suitability of two blood-feeding leech species for sampling mammalian diversity in North Borneo

The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. To address these questions, we collected spatially matched samples of two congeneric leech species Haemadipsa picta and Haemadipsa sumatrana from lowland rainforest in Borneo. For each species, we pooled ~500 leeches into batches of 10 individuals, performed PCR to target a section of the mammalian 16S rRNA locus and undertook sequencing of amplicon libraries using an Illumina MiSeq. In total, we identified sequences from 14 mammalian genera, spanning nine families and five orders. We found greater numbers of detections, and higher diversity of OTUs, in H. picta compared with H. sumatrana, with rodents only present in the former leech species. However, comparison of samples from across the landscape revealed no significant difference in mammal community composition between the leech species. We therefore suggest that H. picta is the more suitable iDNA sampler in this degraded Bornean forest. We conclude that the choice of invertebrate sampler can influence the detectability of different mammal groups and that this should be accounted for when designing iDNA studies.

muO-conotoxin MrVIB selectively blocks Nav1.8 sensory neuron specific sodium channels and chronic pain behavior without motor deficits

The tetrodotoxin-resistant voltage-gated sodium channel (VGSC) Na(v)1.8 is expressed predominantly by damage-sensing primary afferent nerves and is important for the development and maintenance of persistent pain states. Here we demonstrate that muO-conotoxin MrVIB from Conus marmoreus displays substantial selectivity for Na(v)1.8 and inhibits pain behavior in models of persistent pain. In rat sensory neurons, submicromolar concentrations of MrVIB blocked tetrodotoxin-resistant current characteristic of Na(v)1.8 but not Na(v)1.9 or tetrodotoxin-sensitive VGSC currents. MrVIB blocked human Na(v)1.8 expressed in Xenopus oocytes with selectivity at least 10-fold greater than other VGSCs. In neuropathic and chronic inflammatory pain models, allodynia and hyperalgesia were both reduced by intrathecal infusion of MrVIB (0.03-3 nmol), whereas motor side effects occurred only at 30-fold higher doses. In contrast, the nonselective VGSC blocker lignocaine displayed no selectivity for allodynia and hyperalgesia versus motor side effects. The actions of MrVIB reveal that VGSC antagonists displaying selectivity toward Na(v)1.8 can alleviate chronic pain behavior with a greater therapeutic index than nonselective antagonists.

Novel omega-conotoxins from Conus catus discriminate among neuronal calcium channel subtypes

omega-Conotoxins selective for N-type calcium channels are useful in the management of severe pain. In an attempt to expand the therapeutic potential of this class, four new omega-conotoxins (CVIA-D) have been discovered in the venom of the piscivorous cone snail, Conus catus, using assay-guided fractionation and gene cloning. Compared with other omega-conotoxins, CVID has a novel loop 4 sequence and the highest selectivity for N-type over P/Q-type calcium channels in radioligand binding assays. CVIA-D also inhibited contractions of electrically stimulated rat vas deferens. In electrophysiological studies, omega-conotoxins CVID and MVIIA had similar potencies to inhibit current through central (alpha(1B-d)) and peripheral (alpha(1B-b)) splice variants of the rat N-type calcium channels when coexpressed with rat beta(3) in Xenopus oocytes. However, the potency of CVID and MVIIA increased when alpha(1B-d) and alpha(1B-b) were expressed in the absence of rat beta(3), an effect most pronounced for CVID at alpha(1B-d) (up to 540-fold) and least pronounced for MVIIA at alpha(1B-d) (3-fold). The novel selectivity of CVID may have therapeutic implications. (1)H NMR studies reveal that CVID possesses a combination of unique structural features, including two hydrogen bonds that stabilize loop 2 and place loop 2 proximal to loop 4, creating a globular surface that is rigid and well defined.

Classification of the southern African sanga and east African shorthorned zebu

Humped African cattle, which are differentiated into zebu and sanga types, have traditionally been classified as Bos indicus. This paper discusses existing evidence and presents new evidence supporting the classification of southern African sangas as Bos taurus and East African zebus as 'taurindicus'. Classification is based on karyotype, frequencies of DNA markers and protein polymorphisms. The Boran, an East African zebu, has an acrocentric Y chromosome typical of Bos indicus. The southern African sanga breeds have a submetacentric Y chromosome typical of Bos taurus. Frequencies of four DNA markers support the hypothesis that the Tuli, a southern African sanga, had taurine ancestors and the Boran had both taurine and indicine ancestors. Frequencies for several protein polymorphisms strongly suggest that southern African sangas have more in common with taurine than with indicine breeds, while East African zebus are an admixture of African taurine and Asian indicine breeds.

Microsatellite mapping of a gene affecting horn development in Bos taurus

The presence or absence of horns in Bos taurus is thought to be under the genetic control of the autosomal polled locus, characterized by two alleles: P dominant over p, and causing the polled or hornless phenotype. We have demonstrated genetic linkage between the polled locus and two microsatellite markers, GMPOLL-1 and GMPOLL-2, and have assigned the corresponding linkage group to bovine chromosome 1. This confirms the existence of the postulated polled locus and the hypothesized inheritance pattern. It will allow marker assisted selection for the polledness trait in breeding programs and is a first step towards positional cloning and molecular study of a gene that has been subjected to both natural and artificial selection.

Human satellite-III DNA: an example of a "macrosatellite" polymorphism

Human satellite III DNA contains a complex polymorphism, which appears to be TaqI-specific. Its likely cause is a two-step point mutation in the pentameric repeat TTCCA, typical of satellite III. Hybridization of the satellite-III sequence-related probe that demonstrates this polymorphism is directly attributable to clusters of "pure" pentameric TTCCA repeats in the genome. The sites of such repeats include the 3.4-kb fragment specific to the Y chromosome and a limited number of autosomes. The polymorphism arises from the latter and is likely to include chromosomes containing so-called K domain satellite III sequences found, for example, in chromosomes 9 and 15. Segregation of the polymorphic fragments appears to follow orthodox genetics.

Hypervariable lengths of human DNA associated with a human satellite III sequence found in the 3.4kb Y-specific fragment

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