Search

Habitat degradation and climate change are globally acting as pivotal drivers of wildlife collapse, with mounting evidence that this erosion of biodiversity will accelerate in the following decades 1-3 . Here, we quantify the past, present and future ecological suitability of Europe for bumblebees, a threatened group of pollinators ranked among the highest contributors to crop production value in the northern hemisphere 4-8 . We demonstrate coherent declines of bumblebee populations since 1900 over most of Europe and identify future large-scale range contractions and species extirpations under all future climate and land use change scenarios. Around 38-76% of studied European bumblebee species currently classified as 'Least Concern' are projected to undergo losses of at least 30% of ecologically suitable territory by 2061-2080 compared to 2000-2014. All scenarios highlight that parts of Scandinavia will become potential refugia for European bumblebees; it is however uncertain whether these areas will remain clear of additional anthropogenic stressors not accounted for in present models. Our results underline the critical role of global change mitigation policies as effective levers to protect bumblebees from manmade transformation of the biosphere., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

The eastern Clarion Clipperton Fracture Zone (CCZ) is a heterogeneous abyssal environment harbouring relatively low abundances of highly diverse megafauna communities. Potential future mining of polymetallic nodules threatens these benthic communities and calls for detailed spatial investigation of megafauna. Based on the predicted probability of occurrence of 68 megafauna morphotypes, a seabed area extending over 62,000 km 2 was divided into three assemblages covering an eastern plain area, a deeper western plain area and an area covering both seamount and abyssal hill sites. Richness, estimated as the sum of morphotypes with a predicted probability of occurrence larger than 0.5, amounts to 15.4 of 68 morphotypes. Highest richness was predicted at seamount sites, and lowest richness in the western part of the study area. Combining the predicted probability of megafauna occurrences with bathymetric variables, two seamount habitats and two plain habitats could be defined. One of these megafauna plain habitats corresponds with contiguous nodule fields of high abundance that may be targeted for future mining, showing that prospective nodule fields have a clearly differentiated megafauna assemblage. Monitoring and management schemes, including the delineation of preservation and protection areas within contract areas, need to incorporate this geological and biological heterogeneity., (© 2022. The Author(s).)

Strigiformes are affected by a substantial decline mainly caused by habitat loss and destruction, poaching, and trapping. Moreover, the increasing trend in bird trade and the growing interest in wild-caught rather than captive-bred birds are expected to encourage illegal trade. The biomolecular investigation represents a valuable tool to track illegal trade and to explore the genetic variability to preserving biodiversity. Microsatellite loci (STRs) are the most used markers to study genetic variability. Despite the availability of species-specific microsatellite loci in Strigiformes, a unique panel permitting the description of the genetic variability across species has not been identified yet. We tested 32 highly polymorphic microsatellite markers to evaluate the reliability of a unique microsatellite panel in different species of Strigiformes and its use for conservation and forensic purposes. We included in the study 84 individuals belonging to 28 parental groups and 11 species of Strigiformes. After screening polymorphic microsatellite loci, the description of genetic variability, and the kinship assessment, we characterized a final panel of 12 microsatellite loci able to identify individuals in 9 Strigiformes species. This STR panel might support the authorities in the forensic investigation for suspected smugglers and false parental claims; moreover, it can be useful to evaluate relatedness among individuals in captive-bred populations and to implement research projects finalized to the description of the genetic variability in wild populations.

White-nose syndrome (WNS), a fungal disease that has caused catastrophic population declines of bats in eastern North America, is rapidly spreading across the continent and now threatens previously unexposed bat species in western North America. The causal agent of WNS, the fungus Pseudogymnoascus destructans, can infect many species of hibernating bats, but susceptibility to WNS varies by host species. We previously reported that certain traits of the skin microbiome, particularly yeast diversity and abundance, of bat species in eastern North America are strongly associated with resistance to WNS. Using these traits, we developed models to predict WNS susceptibility of 13 species of western North American bats. Based on models derived from yeast species diversity, only one bat species, Myotis velifer, was predicted to be WNS resistant (i.e., may develop the disease, but with low mortality rates). We also screened yeasts found on western bats for P. destructans -antagonistic properties by spore germination and growth inhibition/competition assays and found the ability of yeasts to inhibit P. destructans in vitro to be strain specific. Similar to results of inhibition assays performed with yeasts isolated from bats in eastern North America, few yeasts isolated from bats in western North America inhibited P. destructans in vitro. Continued monitoring of western bat populations will serve to validate the accuracy of the mycobiome analysis in predicting WNS susceptibility, document population and susceptibility trends, and identify additional predictors to assess the vulnerability of naive bat populations to WNS. IMPORTANCE White-nose syndrome is one of the most devastating wildlife diseases ever documented. Some bat species are resistant to or tolerant of the disease, and we previously reported that certain traits of the skin mycobiome of bat species in eastern North America are strongly associated with resistance to WNS. Predicting which western bat species will be most susceptible to WNS would be of great value for establishing conservation priorities. Based on models derived from yeast species diversity, only one bat species was predicted to be WNS resistant. High susceptibility to WNS would pose a significant conservation threat to bats in western North America.

Game birds may carry zoonotic bacteria in their intestines and transmit them to hunters through bird handling or through the handling and consumption of contaminated meat. In this study, the prevalence of foodborne bacteria was screened from game bird faeces and mallard breast meat using PCR. The sampling occurred in southern Finland from August to December during the hunting season. Isolates were characterized by multi-locus sequence typing. Mesophilic aerobic bacteria and Escherichia coli counts were used to assess the microbial contamination of mallard meat. In total, 100 woodpigeon (Columba palumbus), 101 pheasants (Phasianus colchicus), 110 mallards (Anas platyrhynchos), and 30 teals (Anas crecca) were screened during the hunting season. Additionally, 100 mallard breast meat samples were collected. Campylobacter and Listeria were commonly detected in the faeces and Listeria on mallard meat. L. monocytogenes of sequence types associated with human listeriosis were frequently found in game bird faeces and on mallard meat. Good hygiene during game bird handling, storing the game bird meat frozen, and proper heat treatment are important measures to minimize the health risk for hunters and consumers., (Copyright © 2021. Published by Elsevier Ltd.)

Rehabilitation centres help injured animals to recover and return back to the wild. This study aimed to analyse trends in intake and outcomes for the common kestrels (Falco tinnunculus) admitted into rehabilitation centres in the Czech Republic. From 2010 to 2019, a total of 12,923 kestrels were admitted to 34 rehabilitation centres with an increasing trend (rSp = 0.7697, P < 0.01) being found during the monitored period. Subadult kestrels (34.70%) and kestrels injured by power lines (26.57%) were most often admitted. Most kestrels in the rehabilitation centres died or had to be euthanized (81.66%), only 15.90% of the birds could be released back into the wild. The median length of stay in rehabilitation centres for kestrels that were subsequently released was 35 days. Considering survival rates, the most critical threat to kestrels was poisoning (100% of the cases resulted in death) but mortality of the kestrels admitted for most other reasons also exceeded 80%. Given the low success rate of the care of kestrels in rehabilitation centres and the relatively small proportion returned to the wild, it is essential to eliminate the causes leading to their admission, that is, to protect their natural habitats and to prevent unnecessary capture., (© 2021. The Author(s).)

As the biodiversity crisis continues, we must redouble efforts to understand and curb pressures pushing species closer to extinction. One major driver is the unsustainable trade of wildlife. Trade in internationally regulated species gains the most research attention, but this only accounts for a minority of traded species and we risk failing to appreciate the scale and impacts of unregulated legal trade. Despite being legal, trade puts pressure on wild species via direct collection, introduced pathogens, and invasive species. Smaller species-rich vertebrates, such as reptiles, fish, and amphibians, may be particularly vulnerable to trading because of gaps in regulations, small distributions, and demand of novel species. Here, we combine data from five sources: online web searches in six languages, Convention on International Trade in Endangered Species (CITES) trade database, Law Enforcement Management Information System (LEMIS) trade inventory, IUCN assessments, and a recent literature review, to characterise the global trade in amphibians, and also map use by purpose including meat, pets, medicinal, and for research. We show that 1215 species are being traded (17% of amphibian species), almost three times previous recorded numbers, 345 are threatened, and 100 Data Deficient or unassessed. Traded species origin hotspots include South America, China, and Central Africa; sources indicate 42% of amphibians are taken from the wild. Newly described species can be rapidly traded (mean time lag of 6.5 years), including threatened and unassessed species. The scale and limited regulation of the amphibian trade, paired with the triptych of connected pressures (collection, pathogens, invasive species), warrants a re-examination of the wildlife trade status quo, application of the precautionary principle in regard to wildlife trade, and a renewed push to achieve global biodiversity goals., Competing Interests: AH, BM, CS No competing interests declared, (© 2021, Hughes et al.)

The revealed prevalence of coronaviruses in wild bird populations in Poland was 4.15% and the main reservoirs were birds from orders Anseriformes and Charadriiformes , with a prevalence of 3.51% and 5.59%, respectively. Gammacoronaviruses were detected more often than deltacoronaviruses, with detection rates of 3.5% and 0.7%, respectively. Gammacoronaviruses were detected in birds belonging to six orders, including Anseriformes , Charadriiformes , Columbiformes , Galliformes , Gruiformes , and Passeriformes , indicating a relatively wide host range. Interestingly, this was the only coronavirus detected in Anseriformes (3.51%), while in Charadriiformes , the prevalence was 3.1%. The identified gammacoronaviruses belonged to the Igacovirus and Brangacovirus subgeneras. Most of these were igacoviruses and formed a common phylogenetic group with a Duck Coronavirus 2714 and two with an Avian Coronavirus/Avian Coronavirus9203, while the viruses from the pigeons formed a distinct "pigeon-like" group, not yet officially represented. The presence of deltacoronaviruses was detected in birds belonging to three orders, Charadriiformes , Galliformes , and Suliformes indicating a narrower host range. Most identified deltacoronaviruses belonged to the Buldecovirus subgenus, while only one belonged to Herdecovirus . Interestingly, the majority of buldecoviruses were identified in gulls, and they formed a distinct phylogenetic lineage not represented by any officially ratified virus species. Another separate group of buldecoviruses, also not represented by the official species, was formed by a virus identified in a common snipe. Only one identified buldecovirus (from common pheasant) formed a group with the ratified species Coronavirus HKU15. The results obtained indicate the high diversity of detected coronaviruses, and thus also the need to update their taxonomy (establishing new representative virus species). The serological studies performed revealed antibodies against an infectious bronchitis virus in the sera of white storks and mallards.

Background: Improved knowledge on vector-borne pathogens in wildlife will help determine their effect on host species at the population and individual level and whether these are affected by anthropogenic factors such as global climate change and landscape changes. Here, samples from brown hyenas (Parahyaena brunnea) from Namibia (BHNA) and spotted hyenas (Crocuta crocuta) from Namibia (SHNA) and Tanzania (SHTZ) were screened for vector-borne pathogens to assess the frequency and genetic diversity of pathogens and the effect of ecological conditions and host taxonomy on this diversity., Methods: Tissue samples from BHNA (n = 17), SHNA (n = 19) and SHTZ (n = 25) were analysed by PCRs targeting Anaplasmataceae, Rickettsia spp., piroplasms, specifically Babesia lengau-like piroplasms, Hepatozoidae and filarioids. After sequencing, maximum-likelihood phylogenetic analyses were conducted., Results: The relative frequency of Anaplasmataceae was significantly higher in BHNA (82.4%) and SHNA (100.0%) than in SHTZ (32.0%). Only Anaplasma phagocytophilum/platys-like and Anaplasma bovis-like sequences were detected. Rickettsia raoultii was found in one BHNA and three SHTZ. This is the first report of R. raoultii from sub-Saharan Africa. Babesia lengau-like piroplasms were found in 70.6% of BHNA, 88.9% of SHNA and 32.0% of SHTZ, showing higher sequence diversity than B. lengau from South African cheetahs (Acinonyx jubatus). In one SHTZ, a Babesia vogeli-like sequence was identified. Hepatozoon felis-like parasites were identified in 64.7% of BHNA, 36.8% of SHNA and 44.0% of SHTZ. Phylogenetic analysis placed the sequences outside the major H. felis cluster originating from wild and domestic felids. Filarioids were detected in 47.1% of BHNA, 47.4% of SHNA and 36.0% of SHTZ. Phylogenetic analysis revealed high genetic diversity and suggested the presence of several undescribed species. Co-infections were frequently detected in SHNA and BHNA (BHNA median 3 pathogens, range 1-4; SHNA median 3 pathogens, range 2-4) and significantly rarer in SHTZ (median 1, range 0-4, 9 individuals uninfected)., Conclusions: The frequencies of all pathogens groups were high, and except for Rickettsia, multiple species and genotypes were identified for each pathogen group. Ecological conditions explained pathogen identity and diversity better than host taxonomy.

Objectives: We investigated the diversity of the pygmy marmoset, Cebuella pygmaea, by comparing genetic, morphological and pelage traits of animals from Peru and Ecuador., Materials and Methods: We extracted DNA from museum specimen osteocrusts and from fecal samples collected from free-ranging individuals. We sequenced the mtDNA cytochrome b gene and the control region from samples collected at 13 different sites and used Bayesian inference and Maximum Likelihood to identify distinct clades. We took measurements of the crania of a subset of these specimens (n = 26) and ran a logistic regression to determine if any of the cranial measurements (n = 22) could predict a specimen's clade. In addition, we examined the pelage patterns of the museum specimens and photographs taken of free-ranging individuals and divided them into pelage types based on coloration of the underbelly., Results: We identified two divergent clades, and two distinct groups with clear geographic boundaries within one of those clades. Two measurements of the zygomatic bone perfectly predicted a given individual's mtDNA clade. We found four distinct pelage patterns in our samples, but these patterns are variable within clades and among individuals within the same population., Conclusion: These analyses indicate that the two recognized subspecies of pygmy marmoset should be elevated to the species level (C. pygmaea and C. niveiventris) based on molecular and cranial differences but not on pelage patterns. We provide evidence on the geographic limits of the two clades and identify regions where additional sampling is required to better define the geographic distribution of the two clades., (© 2021 Wiley Periodicals LLC.)

Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Mammalian orthoreoviruses (MRVs) are emerging infectious agents that may affect wild animals. MRVs are usually associated with asymptomatic or mild respiratory and enteric infections. However, severe clinical manifestations have been occasionally reported in human and animal hosts. An insight into their circulation is essential to minimize the risk of diffusion to farmed animals and possibly to humans. The aim of this study was to investigate the presence of likely zoonotic MRVs in wild ungulates. Liver samples were collected from wild boar, red deer, roe deer, and chamois. Samples originated from two areas (Sondrio and Parma provinces) in Northern Italy with different environmental characteristics. MRV detection was carried out by PCR; confirmation by sequencing and typing for MRV type 3, which has been frequently associated with disease in pigs, were carried out for positive samples. MRV prevalence was as high as 45.3% in wild boars and 40.6% in red deer in the Sondrio area, with lower prevalence in the Parma area (15.4% in wild boars). Our findings shed light on MRV occurrence and distribution in some wild species and posed the issue of their possible role as reservoir.

Background: The analysis of blow microbiota has been proposed as a biomarker for respiratory health analysis in cetaceans. Yet, we lack crucial knowledge on the long-term stability of the blow microbiota and its potential changes during disease. Research in humans and mice have provided evidence that respiratory disease is accompanied by a shift in microbial communities of the airways. We investigate here the stability of the community composition of the blow microbiota for 13 captive bottlenose dolphins over eight months including both sick and healthy individuals. We used barcoded tag sequencing of the bacterial 16S rRNA gene. Four of the dolphins experienced distinct medical conditions and received systemic antimicrobial treatment during the study., Results: We showed that each dolphin harboured a unique community of zero-radius operational taxonomic units (zOTUs) that was present throughout the entire sampling period ('intra-core'). Although for most dolphins there was significant variation over time, overall the intra-core accounted for an average of 73% of relative abundance of the blow microbiota. In addition, the dolphins shared between 8 and 66 zOTUs on any of the sampling occasions ('inter-core'), accounting for a relative abundance between 17 and 41% of any dolphin's airway microbiota. The majority of the intra-core and all of the inter-core zOTUs in this study are commonly found in captive and free-ranging dolphins and have previously been reported from several different body sites. While we did not find a clear effect of microbial treatment on blow microbiota, age and sex of the dolphins did have such an effect., Conclusions: The airways of dolphins were colonized by an individual intra-core 'signature' that varied in abundance relative to more temporary bacteria. We speculate that the intra-core bacteria interact with the immune response of the respiratory tract and support its function. This study provides the first evidence of individual-specific airway microbiota in cetaceans that is stable over eight months.

Background: Birds can act as reservoirs of tick-borne pathogens and can also disperse pathogen-containing ticks to both nearby and remote localities. The aims of this study were to estimate tick infestation patterns on migratory birds and the prevalence of different Borrelia species and tick-borne encephalitis virus (TBEV) in ticks removed from birds in south-eastern Sweden., Methods: Ticks were collected from resident and migratory birds captured at the Ottenby Bird Observatory, Öland, Sweden, from March to November 2009. Ticks were molecularly identified to species, and morphologically to developmental stage, and the presence of Borrelia bacteria and TBEV was determined by quantitative real-time PCR., Results: A total of 1339 ticks in the genera Haemaphysalis, Hyalomma, and Ixodes was recorded of which I. ricinus was the most abundant species. Important tick hosts were the European robin (Erithacus rubecula), Blackbird (Turdus merula), Tree pipit (Anthus trivialis), Eurasian wren (Troglodytes troglodytes), Common redstart (Phoenicurus phoenicurus), Willow warbler (Phylloscopus trochilus), and Common whitethroat (Sylvia communis). Borrelia bacteria were detected in 25% (285/1,124) of the detached ticks available for analysis. Seven Borrelia species (B. afzelii, B. burgdorferi (s.s.), B. garinii, B. lusitaniae, B. turdi, B. valaisiana, and B. miyamotoi) were identified. B. turdi was recorded for the first time in ticks in Sweden. The number of Borrelia cells per tick ranged from 2.0 × 10 0 to 7.0 × 10 5 . B. miyamotoi-containing ticks contained a significantly higher median number of Borrelia cells than B. burgdorferi (s.l.)-containing ticks. B. garinii and B. miyamotoi were the most prevalent Borrelia species in tick larvae. Larvae of I. ricinus with B. garinii were removed from seven bird species, particularly S. communis and A. trivialis, which may suggest that the larvae had contracted the Borrelia bacteria from or via these birds. Also, a high percentage of tick larvae containing B. miyamotoi was removed from E. rubecula. All ticks were negative for TBEV., Conclusions: The results corroborate the view that the contributions of birds to human disease are substantial, particularly as blood hosts for ticks and for their short-, medium-, and long-distance dispersal. Moreover, several ground-foraging bird species appear to be important for the maintenance and dispersal of Borrelia species. The absence of TBEV in the ticks conforms to other similar studies.

Background: Piroplasms are vector-borne intracellular hemoprotozoan parasites that infect wildlife and livestock. Wildlife species are reservoir hosts to a diversity of piroplasms and play an important role in the circulation, maintenance and evolution of these parasites. The potential for likely spillover of both pathogenic and non-pathogenic piroplasm parasites from wildlife to livestock is underlined when a common ecological niche is shared in the presence of a competent vector., Method: To investigate piroplasm diversity in wildlife and the cattle population of the greater Kafue ecosystem, we utilized PCR to amplify the 18S rRNA V4 hyper-variable region and meta-barcoding strategy using the Illumina MiSeq sequencing platform and amplicon sequence variant (ASV)-based bioinformatics pipeline to generate high-resolution data that discriminate sequences down to a single nucleotide difference., Results: A parasite community of 45 ASVs corresponding to 23 species consisting of 4 genera of Babesia, Theileria, Hepatozoon and Colpodella, were identified in wildlife and the cattle population from the study area. Theileria species were detected in buffalo, impala, hartebeest, sable antelope, sitatunga, wild dog and cattle. In contrast, Babesia species were only observed in cattle and wild dog. Our results demonstrate possible spillover of these hemoprotozoan parasites from wildlife, especially buffalo, to the cattle population in the wildlife-livestock interface., Conclusion: We demonstrated that the deep amplicon sequencing of the 18S rRNA V4 hyper-variable region for wildlife was informative. Our results illustrated the diversity of piroplasma and the specificity of their hosts. They led us to speculate a possible ecological cycle including transmission from wildlife to domestic animals in the greater Kafue ecosystem. Thus, this approach may contribute to the establishment of appropriate disease control strategies in wildlife-livestock interface areas.

Background: Kissing bugs (Triatominae) are blood-feeding insects best known as the vectors of Trypanosoma cruzi, the causative agent of Chagas' disease. Considering the high epidemiological relevance of these vectors, their biology and bacterial symbiosis remains surprisingly understudied. While previous investigations revealed generally low individual complexity but high among-individual variability of the triatomine microbiomes, any consistent microbiome determinants have not yet been identified across multiple Triatominae species., Methods: To obtain a more comprehensive view of triatomine microbiomes, we investigated the host-microbiome relationship of five Triatoma species sampled from white-throated woodrat (Neotoma albigula) nests in multiple locations across the USA. We applied optimised 16S rRNA gene metabarcoding with a novel 18S rRNA gene blocking primer to a set of 170 T. cruzi-negative individuals across all six instars., Results: Triatomine gut microbiome composition is strongly influenced by three principal factors: ontogeny, species identity, and the environment. The microbiomes are characterised by significant loss in bacterial diversity throughout ontogenetic development. First instars possess the highest bacterial diversity while adult microbiomes are routinely dominated by a single taxon. Primarily, the bacterial genus Dietzia dominates late-stage nymphs and adults of T. rubida, T. protracta, and T. lecticularia but is not present in the phylogenetically more distant T. gerstaeckeri and T. sanguisuga. Species-specific microbiome composition, particularly pronounced in early instars, is further modulated by locality-specific effects. In addition, pathogenic bacteria of the genus Bartonella, acquired from the vertebrate hosts, are an abundant component of Triatoma microbiomes., Conclusion: Our study is the first to demonstrate deterministic patterns in microbiome composition among all life stages and multiple Triatoma species. We hypothesise that triatomine microbiome assemblages are produced by species- and life stage-dependent uptake of environmental bacteria and multiple indirect transmission strategies that promote bacterial transfer between individuals. Altogether, our study highlights the complexity of Triatominae symbiosis with bacteria and warrant further investigation to understand microbiome function in these important vectors. Video abstract.

Mammalian orthoreovirus (MRV) has been identified in humans, livestock and wild animals; this wide host range allows individual MRV to transmit into multiple species. Although several interspecies transmission and genetic reassortment events of MRVs among humans, livestock and wildlife have been reported, the genetic diversity and geographic distribution of MRVs in Africa are poorly understood. In this study, we report the first isolation and characterization of MRVs circulating in a pig population in Zambia. In our screening, MRV genomes were detected in 19.7 % (29/147) of faecal samples collected from pigs by reverse transcription PCR. Three infectious MRV strains (MRV-85, MRV-96 and MRV-117) were successfully isolated, and their complete genomes were sequenced. Recombination analyses based on the complete genome sequences of the isolated MRVs demonstrated that MRV-96 shared the S3 segment with a different MRV isolated from bats, and that the L1 and M3 segments of MRV-117 originated from bat and human MRVs, respectively. Our results suggest that the isolated MRVs emerged through genetic reassortment events with interspecies transmission. Given the lack of information regarding MRVs in Africa, further surveillance of MRVs circulating among humans, domestic animals and wildlife is required to assess potential risk for humans and animals.

New Guinea singing dogs (NGSD) are identifiable by their namesake vocalizations, which are unlike any other canid population. Their novel behaviors and potential singular origin during dog domestication make them an attractive, but elusive, subject for evolutionary and conservation study. Although once plentiful on the island of New Guinea (NG), they were presumed to currently exist only in captivity. This conclusion was based on the lack of sightings in the lowlands of the island and the concurrent expansion of European- and Asian-derived dogs. We have analyzed the first nuclear genomes from a canid population discovered during a recent expedition to the highlands of NG. The extreme altitude (>4,000 m) of the highland wild dogs' (HWD) observed range and confirmed vocalizations indicate their potential to be a wild NGSD population. Comparison of single-nucleotide polymorphism genotypes shows strong similarity between HWD and the homogeneous captive NGSD, with the HWD showing significantly higher genetic diversity. Admixture analyses and estimation of shared haplotypes with phylogenetically diverse populations also indicates the HWD is a novel population within the distinct evolutionary lineage of Oceanic canids. Taken together, these data indicate the HWD possesses a distinct potential to aid in the conservation of NGSD both in the wild and under human care., Competing Interests: Competing interest statement: E.A.O. is a coauthor with the dog10K Consortium on a 2019 review article; R.D.S. is a member of the consortium. J.K.M. heads and directs the New Guinea Highland Wild Dog Foundation, which funded the field work for the project. He personally was funded by PT Freeport Indonesia., (Copyright © 2020 the Author(s). Published by PNAS.)

Objectives: Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens., Methods: We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia., Results: We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra., Conclusions: Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines., (© 2020 Wiley Periodicals LLC.)

Toxicants such as organochlorine insecticides, lead ammunition, and veterinary drugs have caused severe wildlife poisoning, pushing the populations of several apex species to the edge of extinction. These prime cases epitomize the serious threat that wildlife poisoning poses to biodiversity. Much of the evidence on population effects of wildlife poisoning rests on assessments conducted at an individual level, from which population-level effects are inferred. Contrastingly, we demonstrate a straightforward relationship between poison-induced individual mortality and population changes in the threatened red kite ( Milvus milvus ). By linking field data of 1,075 poisoned red kites to changes in occupancy and abundance across 274 sites (10 × 10-km squares) over a 20-y time frame, we show a clear relationship between red kite poisoning and the decline of its breeding population in Spain, including local extinctions. Our results further support the species listing as endangered, after a breeding population decline of 31% to 43% in two decades of this once-abundant raptor. Given that poisoning threatens the global populations of more than 2,600 animal species worldwide, a greater understanding of its population-level effects may aid biodiversity conservation through increased regulatory control of chemical substances. Our results illustrate the great potential of long-term and large-scale on-ground monitoring to assist in this task., Competing Interests: The authors declare no competing interest.

Shiga toxin-producing Escherichia (E.) coli (STEC) pathogens are responsible for the outbreaks of serious diseases in humans, including haemolytic uraemic syndrome (HUS), bloody diarrhoea (BD) and diarrhoea (D), and they pose a significant public health concern. Wild ruminants are an important environmental reservoir of foodborne pathogens that can cause serious illnesses in humans and contaminate fresh products. There is a general scarcity of published data about wildlife as a reservoir of foodborne pathogens in Poland, which is why the potential epidemiological risk associated with red deer, roe deer and fallow deer as reservoirs of STEC/AE-STEC strains was evaluated in this study. The aim of the study was to investigate the prevalence of STEC strains in red deer (Cervus elaphus), roe deer (Capreolus capreolus) and fallow deer (Dama dama) populations in north-eastern Poland, and to evaluate the potential health risk associated with wild ruminants carrying STEC/AE-STEC strains. We examined 252 rectal swabs obtained from 134 roe deer (Capreolus capreolus), 97 red deer (Cervus elaphus) and 21 fallow deer (Dama dama) in north-eastern Poland. The samples were enriched in modified buffered peptone water. Polymerase chain reaction (PCR) assays were conducted to determine the virulence profile of stx1, stx2 and eae or aggR genes, to identify the subtypes of stx1 and stx2 genes, and to perform O and H serotyping. E. coli O157:H7 isolates were detected in the rectal swabs collected from 1/134 roe deer (0.75%) and 4/97 red deer (4.1%), and they were not detected in fallow deer (Dama dama). The remaining E. coli serogroups, namely O26, O103, O111 and O145 that belong to the "top five" non-O157 serogroups, were detected in 15/134 roe deer (11.19%), 18/97 red deer (18.56%) and 2/21 fallow deer (9.52%). STEC/AE-STEC strains were detected in 33 roe deer isolates (24.63%), 21 red deer isolates (21.65%) and 2 fallow deer isolates (9.52%). According to the most recent FAO/WHO report, stx2a and eae genes are the primary virulence traits associated with HUS, and these genes were identified in one roe deer isolate and one red deer isolate. Stx2 was the predominant stx gene, and it was detected in 78.79% of roe deer and in 71.43% of red deer isolates. The results of this study confirmed that red deer and roe deer in north-eastern Poland are carriers of STEC/AE-STEC strains that are potentially pathogenic for humans. This is the first report documenting the virulence of STEC/AE-STEC strains from wild ruminants in Poland., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Human activity has caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. We analyze 60 complete genomes of six ibex species and the domestic goat. We show that historic bottlenecks rather than the current conservation status predict levels of genome-wide variation. By analyzing the exceptionally well-characterized population bottlenecks of the once nearly extinct Alpine ibex, we find genomic evidence of concurrent purging of highly deleterious mutations but accumulation of mildly deleterious mutations. This suggests that recolonization bottlenecks induced both relaxed selection and purging, thus reshaping the landscape of deleterious mutation load. Our findings highlight that even populations of ~1000 individuals can accumulate mildly deleterious mutations. Conservation efforts should focus on preventing population declines below such levels to ensure long-term survival of species.

The increased incidence of antibiotic-resistant Enterobacteriaceae is a public health problem worldwide. The aim of this study was to analyze the potential role of wild birds, given their capacity of migrating over long distances, in the spreading of carbapenemase, extended-spectrum β-lactamase (ESBL), and acquired-AmpC beta-lactamase-producing Enterobacteriaceae in the environment. Fecal and pellet samples were recovered from 150 wild birds in seven Tunisian regions and were inoculated in MacConkey-agar plates for Enterobacteriaceae recovery (one isolate/animal). Ninety-nine isolates were obtained and acquired resistance mechanisms were characterized in the five detected imipenem-resistant and/or cefotaxime-resistant isolates, by PCR and sequencing. The following ESBL, carbapenemase, and acquired-AmpC beta-lactamase genes were detected: bla CTX-M-15 (two Escherichia fergusonii and one Klebsiella oxytoca isolates), bla KPC-2 (one K. oxytoca), bla KPC-3 (one E. fergusonii), bla ACT-36 , and bla ACC-2 (two K. oxytoca, four E. fergusonii, and two E. coli). The IncFIIs, IncF, IncFIB, IncK, IncP, and IncX replicons were detected among these beta-lactamase Enterobacteriaceae producers. The bla KPC-2 , tetA, sul3, qnrB, and cmlA determinants were co-transferred by conjugation from K. oxytoca strain to E. coli J153, in association with IncK and IncF replicons. Our results support the implication of wild birds as a biological vector for carbapenemase, ESBL, and acquired-AmpC-producing Enterobacteriaceae.

Role of avian hosts in shaping persistence, evolution, and dispersal of global low pathogenic avian influenza virus (LPAIV) H9N2 remains uncertain. Under Bayesian Markov Chain Monte Carlo framework, we used the discrete trait analysis (DTA) to reconstruct host and location switches in the evolutionary history of global H9N2 given hemagglutinin gene sequences from 18 countries/regions between 1976 and 2018. We employed generalized linear models (GLMs) to inform virus migration rates by empirical predictors. Global H9N2 isolates were mostly sampled from domestic Phasianidae in low- and middle-income countries with poor bio-security. Anatidae was inferred as the ancestral source from which the virus spread to domestic waterfowl, and later to domestic Phasianidae who have become the dominant host to sustain the virus, especially in Asia. Poultry trade was a well-supported driver to H9N2 spread across countries/regions. Strict bio-security and separation between wild and domestic poultry can be used to mitigate virus spread., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: The Tehuacán-Cuicatlán Valley is a region of outstanding biocultural diversity, harboring eight indigenous ethnic groups and a remarkable biodiversity in a territory 10,000 km 2 extent. Ethnobotanical studies of the region are among the most complete in Mexico; contrarily, ethnozoological studies are still limited. But information on both flora and fauna use and management is relevant for understanding local cultural and ecological issues, and for planning integral strategies of biodiversity conservation. Our study focused on analyzing knowledge and use of animals and their relationship with faunistic management by the Cuicatec, an ancient human culture whose distribution is restricted to the region. We hypothesized that wild animals still have significant contributions to diet, medicine, and spiritual life of the Cuicatec people. In addition, we expected to find a gradient of interactions, from simple gathering and hunting to communitarian regulations of use, specialized management techniques and care, nurturing, and domestication of animals. Such gradient of management interactions would be influenced proportionally with cultural and economic values, viability maintenance, and scarcity of animals., Methods: Our study was carried out in San Lorenzo Pápalo, Oaxaca. We conducted surveys and semi-structured and open interviews to people to document the Cuicatec nomenclature, classification, use, and management of fauna, as well as their perceptions about abundance, risks of disappearance, and availability of wild animals. We used images of animal species reported for the area as communication stimuli for confirming their local presence. Also, we recorded skins and skulls used as trophies and ornamental objects, pawprints, and excretes. Through free listing, we identified the most meaningful species of different animal groups. Whenever possible, we evaluated amounts of animals obtained from the wild, and for some species, we compared this information with data on their distribution and abundance evaluated through ecological sampling, to explore indicators on their sustainable use., Results: The Cuicatec name all animals through the term i-ti and classify them in several groups of vertebrates, arthropods, and mollusks, some of them coinciding with the formal taxonomy and some others based on their social-cultural role. The most meaningful animals are 23 species of edible organisms, outstandingly the chicatana ants (Atta mexicana) and the cuetla Lepidoptera larvae (Arsenura armida), the lizard Sceloporus grammicus, and among the mammals some squirrels (Sciurus spp.), badgers (Nasua narica), and deer (Odocoileus virginianus). Some species were reported to be used for medicinal purposes, among them opossum (Didelphis spp.) and macaws (Ara militaris), used to ease childbirths, but this use almost disappeared. Local perception of availability of animal resources is associated to forest conservation. Regulations for protecting forests and the most used animal species were recorded; the rules are mainly associated to hunting and gathering seasons, respecting females of vertebrate species, and permits for gathering and hunting given by local authorities. Nurturing of animals was recorded in bird and mammal species, but in no case, their breeding was achieved., Conclusions: Animals are important elements of the Cuicatec culture and subsistence, complementing their diet based on agricultural products. Animals used as medicine were still reported but substituted by modern medicine. There is a consensus about the need to conserve forests to ensure the maintenance of animals, which are valued as part of nature, the beauty of their territory, and culture. Communitarian regulations are the main ways for conserving fauna, but local techniques of animal management may help in designing conservation strategies.

A simple method based on direct sampling analysis, coupled with a time of flight mass spectrometer, was developed to discriminate between wild and farmed sea bream on the basis of the docosahexaenoic and arachidonic fatty acid ratio. Good precision in repeatability and reproducibility (relative standard deviation < 15%) was obtained. The fatty acid ratios of the two types of fish were statistically significant (Student's t < 0.001). The use of a simple, rapid, and cost-effective tool could aid in the detection of commercial fish fraud, increase the number of controlled samples, and strengthen control along the entire commercial chain.

Wildlife trade is a multibillion dollar industry that is driving species toward extinction. Of >31,500 terrestrial bird, mammal, amphibian, and squamate reptile species, ~18% ( N = 5579) are traded globally. Trade is strongly phylogenetically conserved, and the hotspots of this trade are concentrated in the biologically diverse tropics. Using different assessment approaches, we predict that, owing to their phylogenetic replacement and trait similarity to currently traded species, future trade will affect up to 3196 additional species-totaling 8775 species at risk of extinction from trade. Our assessment underscores the need for a strategic plan to combat trade with policies that are proactive rather than reactive, which is especially important because species can quickly transition from being safe to being endangered as humans continue to harvest and trade across the tree of life., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses (Picobirnaviridae and Reoviridae), single-stranded RNA viruses (Astroviridae, Caliciviridae, Picornaviridae), a retro-transcribing DNA virus (Hepadnaviridae), and a single-stranded DNA virus (Parvoviridae). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity (host sharing) and heterogeneity (host specificity). Virome connectivity was apparent in two well described multi-host virus species -avian coronavirus and influenza A virus- and a novel Rotavirus species that were shared among some Anseriform species, while virome heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes, as well as differences in viral abundance and alpha diversity among species. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.

Genetically related highly pathogenic avian influenza viruses (HPAIVs) of H5N6 subtype caused outbreaks simultaneously in East Asia and Europe-geographically distinct regions-during winter 2017-2018. This situation prompted us to consider whether the application of phylogeographic analysis to a particular gene segment of AIVs could provide clues for understanding how AIV had been disseminated across the continent. Here, the N6 NA genes of influenza viruses isolated across the world were subjected to phylogeographic analysis to illustrate the inter- and intracontinental dissemination of AIVs. Those isolated in East Asia during winter and in Mongolia/Siberia during summer were comingled within particular clades of the phylogeographic tree. For AIVs in one clade, their dissemination in eastern Eurasia extended from Yakutia, Russia, in the north to East Asia in the south. AIVs in western Asia, Europe, and Mongolia were also comingled within other clades, indicating that Mongolia/Siberia plays an important role in the dissemination of AIVs across the Eurasian continent. Mongolia/Siberia may therefore have played a role in the simultaneous outbreaks of H5N6 HPAIVs in Europe and East Asia during the winter of 2017-2018. In addition to the long-distance intracontinental disseminations described above, intercontinental disseminations of AIVs between Eurasia and Africa and between Eurasia and North America were also observed. Integrating these results and known migration flyways suggested that the migration of wild birds and the overlap of flyways, such as that observed in Mongolia/Siberia and along the Alaskan Peninsula, contributed to the long-distance intra- and intercontinental dissemination of AIVs. These findings highlight the importance of understanding the movement of migratory birds and the dynamics of AIVs in breeding areas-especially where several migration flyways overlap-in forecasting outbreaks caused by HPAIVs., Competing Interests: The authors have declared that no competing interests exist.

Although signal characteristics and sensory systems are predicted to co-evolve according to environmental constraints, this hypothesis has not been tested for acoustic signalling across a wide range of species, or any mammal sensory modality. Here we use phylogenetic comparative techniques to show that mammal vocal characteristics and hearing sensitivity have co-evolved to utilise higher frequencies in forest environments - opposite to the general prediction that lower frequencies should be favoured in acoustically cluttered habitats. We also reveal an evolutionary trade-off between high frequency hearing sensitivity and the production of calls with high frequency acoustic energy that suggests forest mammals further optimise vocal communication according to their high frequency hearing sensitivity. Our results provide clear evidence of adaptive signal and sensory system coevolution. They also emphasize how constraints imposed by the signalling environment can jointly shape vocal signal structure and auditory systems, potentially driving acoustic diversity and reproductive isolation.

The implementation of intelligent software to identify and classify objects and individuals in visual fields is a technology of growing importance to operatives in many fields, including wildlife conservation and management. To non-experts, the methods can be abstruse and the results mystifying. Here, in the context of applying cutting edge methods to classify wildlife species from camera-trap data, we shed light on the methods themselves and types of features these methods extract to make efficient identifications and reliable classifications. The current state of the art is to employ convolutional neural networks (CNN) encoded within deep-learning algorithms. We outline these methods and present results obtained in training a CNN to classify 20 African wildlife species with an overall accuracy of 87.5% from a dataset containing 111,467 images. We demonstrate the application of a gradient-weighted class-activation-mapping (Grad-CAM) procedure to extract the most salient pixels in the final convolution layer. We show that these pixels highlight features in particular images that in some cases are similar to those used to train humans to identify these species. Further, we used mutual information methods to identify the neurons in the final convolution layer that consistently respond most strongly across a set of images of one particular species. We then interpret the features in the image where the strongest responses occur, and present dataset biases that were revealed by these extracted features. We also used hierarchical clustering of feature vectors (i.e., the state of the final fully-connected layer in the CNN) associated with each image to produce a visual similarity dendrogram of identified species. Finally, we evaluated the relative unfamiliarity of images that were not part of the training set when these images were one of the 20 species "known" to our CNN in contrast to images of the species that were "unknown" to our CNN.

Background: In recent years, tracing of alimentary produce of animal origin has become increasingly important, for economic, food safety and ecological reasons. The tambaqui, Colossoma macropomum, is the native fish most farmed in Brazil. The reliable identification of the origin of tambaquis (wild or farmed) offered for sale to the general public has become necessary to satisfy regulatory norms and uphold consumer confidence. Molecular methods based on the analysis of DNA sequences have often been used to evaluate the potential for tracing farmed fish, given their reliability and precision., Results: Full likelihood and Bayesian approaches proved to be the most efficient for the identification, respectively, of individuals and populations for most of the fish sampled from seven hatcheries and one wild stock. The exclusion method and genetic distances were the least effective approaches for the identification of individuals and populations. The Bayesian method identified correctly more than 99% of the fry from most stocks, except those of the Santarém hatchery and River Amazon wild stock, which presented the best results for individual identification., Conclusions: The identification of populations was effective for most hatcheries, although the identification of individuals from most stocks was hampered by the reduced genetic variability. © 2018 Society of Chemical Industry., (© 2018 Society of Chemical Industry.)

Animal populations adopting a commensal way of life, e. g. house mice in buildings and stores, are subject to different selection pressures than those living in a non-commensal environment. This may radically influence their behaviour. This study investigated the effects of a commensal way of life on exploratory behaviour in mice. The focal population was non-commensal Mus musculus musculus from Northern Iran. To assess the effect of commensal way of life on exploratory behaviour, it was compared with commensal M. m. musculus from the Czech Republic and to assess the effect of subspecies, it was compared to non-commensal M. m. domesticus from Eastern Syria. We compared their behaviour in five tests of exploratory behaviour and boldness: an open field test with 1) free exploration and 2) forced exploration, 3) hole-board test, 4) test of vertical activity and 5) elevated plus maze. We detected a significant effect of population on behaviour in all five tests. M. m. domesticus was generally bolder and more active than M. m. musculus. Commensal mice were characterized by a higher level of vertical activity (climbing, rearing, jumping). These results suggest that the specific selection pressures of the commensal lifestyle select mice for higher affinity towards elevated places., (Copyright © 2018 Elsevier B.V. All rights reserved.)

The Thoroughbred horse breed was developed primarily for racing, and has a significant contribution to the qualitative improvement of many other horse breeds. Despite the importance of Thoroughbred racehorses in historical, cultural, and economical viewpoints, there was no temporal and spatial dynamics of them using the mitogenome sequences. To explore this topic, the complete mitochondrial genome sequences of 14 Thoroughbreds and two Przewalski's horses were determined. These sequences were analyzed together along with 151 previously published horse mitochondrial genomes from a range of breeds across the globe using a Bayesian coalescent approach as well as Bayesian inference and maximum likelihood methods. The racing horses were revealed to have multiple maternal origins and to be closely related to horses from one Asian, two Middle Eastern, and five European breeds. Thoroughbred horse breed was not directly related to the Przewalski's horse which has been regarded as the closest taxon to the all domestic horses and the only true wild horse species left in the world. Our phylogenomic analyses also supported that there was no apparent correlation between geographic origin or breed and the evolution of global horses. The most recent common ancestor of the Thoroughbreds lived approximately 8,100-111,500 years ago, which was significantly younger than the most recent common ancestor of modern horses (0.7286 My). Bayesian skyline plot revealed that the population expansion of modern horses, including Thoroughbreds, occurred approximately 5,500-11,000 years ago, which coincide with the start of domestication. This is the first phylogenomic study on the Thoroughbred racehorse in association with its spatio-temporal dynamics. The database and genetic history information of Thoroughbred mitogenomes obtained from the present study provide useful information for future horse improvement projects, as well as for the study of horse genomics, conservation, and in association with its geographical distribution., Competing Interests: The authors have declared that no competing interests exist.

Avian trichomonosis is a widespread disease in columbids and other birds, caused by ingestion of the unicellular flagellate Trichomonas gallinae which proliferate primarily in the upper respiratory tracts. Studies using genetic analyses have determined some highly pathogenic lineages in birds, but the prevalence and distribution of potentially pathogenic and non-pathogenic T. gallinae lineages in wild birds is still not well known. We examined 440 oral swab samples of 35 bird species collected between 2015 and 2017 in Hesse, central Germany, for Trichomonas spp. infection and for determining the genetic lineages. Of these birds, 152 individuals were caught in the wild and 288 individuals were admitted from the wild to a veterinary clinic. The overall Trichomonas spp. prevalence was 35.6%. We observed significant differences between bird orders, with the highest prevalence in owls (58%) and columbids (50%), while other orders had slightly lower prevalences, with 36% in Accipitriformes, 28% in Falconiformes and 28% in Passeriformes. Among 71 successfully sequenced samples, we found 13 different haplotypes, including two previously described common lineages A/B (20 samples) and C/V/N (36 samples). The lineage A/B has been described as pathogenic, causing lesions and mortality in columbids, raptors and finches. This lineage was found in 11 of the 35 species, including columbids (feral pigeon, woodpigeon, stock dove), passerines (greenfinch, chaffinch, blackbird) and raptors (common kestrel, sparrowhawk, red kite, peregrine falcon and common buzzard). One new lineage (R) was found in a sample of a chaffinch. In conclusion, we found that the prevalence of Trichomonas spp. infection in wild birds was high overall, and the potentially pathogenic lineage A/B was widespread. Our findings are worrying, as epidemic outbreaks of trichomonosis have already been observed in Germany in several years and can have severe negative effects on bird populations. This disease may add to the multiple pressures that birds face in areas under high land-use intensity., Competing Interests: The authors have declared that no competing interests exist.

Microsporidia comprises a diverse group of obligate intracellular parasites that infect a broad range of invertebrates and vertebrates. Among Microsporidia, Enterocytozoon bieneusi is the most frequently detected species in humans and animals worldwide bringing into question the possible role of animal reservoirs in the epidemiology of this pathogen. Although E. bieneusi is an emerging zoonotic pathogen able to infect many domestic and wild mammals that could act as reservoir of infection for humans and other animals, only few studies have documented its occurrence in wild carnivores. To determine the occurrence of E. bieneusi in wild carnivores, we examined 190 wild carnivores collected from different locations in Spain. Twenty-five fecal samples (13.2%) from three host species (European badger, beech marten, and red fox) were E. bieneusi-positive by PCR. Nucleotide sequence analysis of the ITS region revealed a high degree of genetic diversity with a total of eight distinct genotypes including four known (PtEbIX, S5, S9, and WildBoar3) and four novel (EbCar1-EbCar4) genotypes identified. Phylogenetic analysis showed that the four novel genotypes (EbCar1-EbCar4), S5, S9, and WildBoar3 clustered within the previously designated zoonotic Group 1. Our results demonstrate that human-pathogenic genotypes are present in wild carnivores, corroborating their potential role as a source of human infection and environmental contamination., (© 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists.)

Compensation programs are used globally to increase tolerance for and help offset economic loss caused by large carnivores. Compensation program funding comes from a variety of sources, and in Wyoming and Idaho, USA and Alberta, Canada this includes revenue from hunting and fishing license sales. We review the patterns of livestock depredation and compensation costs of Alberta's predator-compensation program, and compare Alberta's program to compensation programs in neighboring Canadian and American jurisdictions. Current compensation costs in Alberta are well below historic levels, but have been rapidly increasing in recent years due to an increase in depredation events coupled with increased cattle prices. That increase has caused push back from Alberta's hunting and fishing community that finances the compensation program, although less than 3.6% of Alberta's license levy dollars are used for predator compensation. Hunting effort in Alberta is highest on the same privately owned lands with livestock depredation problems, suggesting that private lands support habitats for hunted ungulate species as well as carnivores. Although compensation programs do not prevent depredation events themselves, compensation programs effectively can support the maintenance of wildlife habitats on private lands.

Introduction: Serological surveys are important to assess the health status of wild animals. In this study, antibodies against Leptospira spp, causal agents of leptospirosis, were detected in free-living marsupials in the State of Pará, Brazil., Methods: Nineteen blood samples collected from marsupials in the municipalities of Peixe-Boi, Viseu, and Castanhal were subjected to microscopic agglutination tests., Results: In total, 36.8% (7/19) of samples were positive, and two exhibited co-agglutination. The most frequent serovars were Icterohaemorrhagiae (60%; 3/5), Panama (20%; 1/5), and Nupezo (20%; 1/5)., Conclusions: Anti-Leptospira spp antibodies currently circulate in free-living marsupials in Northeastern Pará.

Understanding the processes driving parasite assemblages is particularly important in the context of zoonotic infectious diseases. Leptospirosis is a widespread zoonotic bacterial infection caused by pathogenic species of the genus Leptospira. Despite a wide range of animal hosts, information is still lacking on the factors shaping Leptospira diversity in wild animal communities, especially in regions, such as tropical insular ecosystems, with high host species richness and complex biogeographical patterns. Using a large dataset (34 mammal species) and a multilocus approach at a regional scale, we analyzed the role of both host species diversity and geography in Leptospira genetic diversity in terrestrial small mammals (rodents, tenrecs, and shrews) and bats from 10 different islands/countries in the western Indian Ocean (WIO) and neighboring Africa. At least four Leptospira spp. (L. interrogans, L. borgpetersenii, L. kirschneri, and L. mayottensis) and several yet-unidentified genetic clades contributed to a remarkable regional Leptospira diversity, which was generally related to the local occurrence of the host species rather than the geography. In addition, the genetic structure patterns varied between Leptospira spp., suggesting different evolutionary histories in the region, which might reflect both in situ diversification of native mammals (for L. borgpetersenii) and the more recent introduction of non-native host species (for L. interrogans). Our data also suggested that host shifts occurred between bats and rodents, but further investigations are needed to determine how host ecology may influence these events.

Psittacine birds have been identified as reservoirs of diarrheagenic Escherichia coli, a subset of pathogens associated with mortality of children in tropical countries. The role of other orders of birds as source of infection is unclear. The aim of this study was to perform the molecular diagnosis of infection with diarrheagenic E. coli in 10 different orders of captive wild birds in the state of São Paulo, Brazil. Fecal samples were analyzed from 516 birds belonging to 10 orders: Accipitriformes, Anseriformes, Columbiformes, Falconiformes, Galliformes, Passeriformes, Pelecaniformes, Piciformes, Psittaciformes and Strigiformes. After isolation, 401 E. coli strains were subjected to multiplex PCR system with amplification of genes eae and bfp (EPEC), stx1 and stx2 for STEC. The results of these tests revealed 23/401 (5.74%) positive strains for eae gene, 16/401 positive strains for the bfp gene (3.99%) and 3/401 positive for stx2 gene (0.75%) distributed among the orders of Psittaciformes, Strigiformes and Columbiformes. None of strains were positive for stx1 gene. These data reveal the infection by STEC, typical and atypical EPEC in captive birds. The frequency of these pathotypes is low and restricted to few orders, but the data suggest the potential public health risk that these birds represent as reservoirs of diarrheagenic E. coli., (Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.)

Noninvasively collected samples are a common source of DNA in wildlife genetic studies. Currently, single nucleotide polymorphism (SNP) genotyping using microfluidic arrays is emerging as an easy-to-use and cost-effective methodology. Here we assessed the performance of microfluidic SNP arrays in genotyping noninvasive samples from grey wolves, European wildcats and brown bears, and we compared results with traditional microsatellite genotyping. We successfully SNP-genotyped 87%, 80% and 97% of the wolf, cat and bear samples, respectively. Genotype recovery was higher based on SNPs, while both marker types identified the same individuals and provided almost identical estimates of pairwise differentiation. We found that samples for which all SNP loci were scored had no disagreements across the three replicates (except one locus in a wolf sample). Thus, we argue that call rate (amplification success) can be used as a proxy for genotype quality, allowing the reduction of replication effort when call rate is high. Furthermore, we used cycle threshold values of real-time PCR to guide the choice of protocols for SNP amplification. Finally, we provide general guidelines for successful SNP genotyping of degraded DNA using microfluidic technology.

Humans challenge the phenotypic, genetic, and cultural makeup of species by affecting the fitness landscapes on which they evolve. Recent studies show that cities might play a major role in contemporary evolution by accelerating phenotypic changes in wildlife, including animals, plants, fungi, and other organisms. Many studies of ecoevolutionary change have focused on anthropogenic drivers, but none of these studies has specifically examined the role that urbanization plays in ecoevolution or explicitly examined its mechanisms. This paper presents evidence on the mechanisms linking urban development patterns to rapid evolutionary changes for species that play important functional roles in communities and ecosystems. Through a metaanalysis of experimental and observational studies reporting more than 1,600 phenotypic changes in species across multiple regions, we ask whether we can discriminate an urban signature of phenotypic change beyond the established natural baselines and other anthropogenic signals. We then assess the relative impact of five types of urban disturbances including habitat modifications, biotic interactions, habitat heterogeneity, novel disturbances, and social interactions. Our study shows a clear urban signal; rates of phenotypic change are greater in urbanizing systems compared with natural and nonurban anthropogenic systems. By explicitly linking urban development to traits that affect ecosystem function, we can map potential ecoevolutionary implications of emerging patterns of urban agglomerations and uncover insights for maintaining key ecosystem functions upon which the sustainability of human well-being depends., Competing Interests: The authors declare no conflict of interest.

Background: There are few studies of careful examination of wildlife casualties in Wildlife Rehabilitation Centers. These studies are essential for detecting menaces to wild species and providing objective criteria about cost-benefit of treatments in those centers. The release rate is considered the main outcome indicator, but other parameters such as length of stay at the center and a cost-benefit index expressed as number of released animals per euro and day, could be used as reliable estimators of the rehabilitation costs., Methodology: A retrospective study based on 54772 admissions recorded from 1995-2013 in the database of the Wildlife Rehabilitation Center of Torreferrussa (Catalonia, NW Spain) assessed the morbidity, outcomes and cost-benefits of the rehabilitation practices., Results: Three hundred and two species were included: 232 birds (n = 48633), 37 mammals (n = 3293), 20 reptiles (n = 2705) and 13 amphibians (n = 141). The most frequent causes of admission were: 39.8% confiscation of protected species (89.4% passerines), 31.8% orphaned young animals (35.3% swifts, 21.7% diurnal raptors and owls) and 17.4% trauma casualties (46.7% raptors and owls). The highest proportion of releases was found in the captivity confiscation category [87.4% passerines (median time of stay: 12 days)], followed by the orphaned category [78% owls (66 days), 76.5% diurnal birds of prey (43 days), 75.6% hedgehogs (49 days), 52.7% swifts (19 days) and 52% bats (55 days)]. For the trauma group, 46.8% of releases were hedgehogs (44 days) and 25.6% owls (103 days). As regards the cost-benefit index, the trauma casualties and infectious diseases had the worse values with 1.3 and 1.4 released animals/euro/day respectively, and were particularly low in raptors, waders, marine birds and chiroptera. On the contrary, captivity (4.6) and misplacement (4.1) had the best index, particulary in amphibian, reptiles and passerines., Conclusions/significance: Cost-benefit studies including the release rate, the time of stay at the center and the cost-benefit index should be implemented for improving management efficiency of the Wildlife Rehabilitation Centers.

Although DNA barcoding is an efficient tool for species identification, however, its efficiency is uncertain for samples having degraded DNA and incomplete isolation/amplification of COI gene fragment (>500 bp). DNA mini-barcoding is a solution to this problem because small DNA fragment of COI genes is used for species identification. Twelve highly processed, chemically treated and finished animal skin (coats, tanned skins) and fur (mufflers) samples, received from the Sindh Wildlife Department, Pakistan, were subjected to DNA mini-barcoding. Eight mufflers belonged to Vulpes vulpes, one coat to Ursus thibetanus, one tanned skin to Lutra sumatrana, and one muffler to Vulpes sp. Origin of only one coat sample remained unidentified, success rate of 92% indicative of the fact that the mini barcoding technique can be used as a substitute of conventional barcoding where full length barcode (∼650 bp Folmer region) cannot be generated.

On large geographical scales, changes in animal population distribution and abundance are driven by environmental change due to climatic and anthropogenic processes. However, so far, little is known about population dynamics on a regional scale. We have investigated 92 archaeological horse remains from nine sites mainly adjacent to the Swiss Jura Mountains dating from c. 41,000-5,000 years BP. The time frame includes major environmental turning points such as the Last Glacial Maximum (LGM), followed by steppe vegetation, afforestation and initial re-opening of the landscape by human agricultural activities. To investigate matrilinear population dynamics, we assembled 240 base pairs of the mitochondrial d-loop. FST values indicate large genetic differentiation of the horse populations that were present during and directly after the LGM. After the retreat of the ice, a highly diverse population expanded as demonstrated by significantly negative results for Tajima's D, Fu's FS and mismatch analyses. At the same time, a different development took place in Asia where populations declined after the LGM. This first comprehensive investigation of wild horse remains on a regional scale reveals a discontinuous colonisation of succeeding populations, a pattern that diverges from the larger Eurasian trend.

Obtaining reliable estimates of the structure of carnivore communities is of paramount importance because of their ecological roles, ecosystem services and impact on biodiversity conservation, but they are still scarce. This information is key for carnivore management: to build support for and acceptance of management decisions and policies it is crucial that those decisions are based on robust and high quality information. Here, we combined camera and live-trapping surveys, as well as telemetry data, with spatially-explicit Bayesian models to show the usefulness of an integrated multi-method and multi-model approach to monitor carnivore community structures. Our methods account for imperfect detection and effectively deal with species with non-recognizable individuals. In our Mediterranean study system, the terrestrial carnivore community was dominated by red foxes (0.410 individuals/km 2 ); Egyptian mongooses, feral cats and stone martens were similarly abundant (0.252, 0.249 and 0.240 individuals/km 2 , respectively), whereas badgers and common genets were the least common (0.130 and 0.087 individuals/km 2 , respectively). The precision of density estimates improved by incorporating multiple covariates, device operation, and accounting for the removal of individuals. The approach presented here has substantial implications for decision-making since it allows, for instance, the evaluation, in a standard and comparable way, of community responses to interventions.

Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, evolutionary studies, and systems genetics. Here, we report the whole-genome sequencing of two wild-derived mouse inbred strains, LEWES/EiJ and ZALENDE/EiJ, of Mus musculus domesticus origin. These two inbred strains were selected based on their geographic origin, karyotype, and use in ongoing research. We generated 14× and 18× coverage sequence, respectively, and discovered over 1.1 million novel variants, most of which are private to one of these strains. This report expands the number of wild-derived inbred genomes in the Mus genus from six to eight. The sequence variation can be accessed via an online query tool; variant calls (VCF format) and alignments (BAM format) are available for download from a dedicated ftp site. Finally, the sequencing data have also been stored in a lossless, compressed, and indexed format using the multi-string Burrows-Wheeler transform. All data can be used without restriction., (Copyright © 2016 Morgan et al.)