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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).)

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).)

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.

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.

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.

The attire of the Tyrolean Iceman, a 5,300-year-old natural mummy from the Ötzal Italian Alps, provides a surviving example of ancient manufacturing technologies. Research into his garments has however, been limited by ambiguity surrounding their source species. Here we present a targeted enrichment and sequencing of full mitochondrial genomes sampled from his clothes and quiver, which elucidates the species of production for nine fragments. Results indicate that the majority of the samples originate from domestic ungulate species (cattle, sheep and goat), whose recovered haplogroups are now at high frequency in today's domestic populations. Intriguingly, the hat and quiver samples were produced from wild species, brown bear and roe deer respectively. Combined, these results suggest that Copper Age populations made considered choices of clothing material from both the wild and domestic populations available to them. Moreover, these results show the potential for the recovery of complete mitochondrial genomes from degraded prehistoric artefacts.

Five haplogroups have been identified in domestic sheep through global surveys of mitochondrial (mt) sequence variation, however these group classifications are often based on small fragments of the complete mtDNA sequence; partial control region or the cytochrome B gene. This study presents the complete mitogenome from representatives of each haplogroup identified in domestic sheep, plus a sample of their wild relatives. Comparison of the sequence successfully resolved the relationships between each haplogroup and provided insight into the relationship with wild sheep. The five haplogroups were characterised as branching independently, a radiation that shared a common ancestor 920,000 ± 190,000 years ago based on protein coding sequence. The utility of various mtDNA components to inform the true relationship between sheep was also examined with Bayesian, maximum likelihood and partitioned Bremmer support analyses. The control region was found to be the mtDNA component, which contributed the highest amount of support to the tree generated using the complete data set. This study provides the nucleus of a mtDNA mitogenome panel, which can be used to assess additional mitogenomes and serve as a reference set to evaluate small fragments of the mtDNA.

Plasmodium falciparum is the most prevalent and lethal of the malaria parasites infecting humans, yet the origin and evolutionary history of this important pathogen remain controversial. Here we develop a single-genome amplification strategy to identify and characterize Plasmodium spp. DNA sequences in faecal samples from wild-living apes. Among nearly 3,000 specimens collected from field sites throughout central Africa, we found Plasmodium infection in chimpanzees (Pan troglodytes) and western gorillas (Gorilla gorilla), but not in eastern gorillas (Gorilla beringei) or bonobos (Pan paniscus). Ape plasmodial infections were highly prevalent, widely distributed and almost always made up of mixed parasite species. Analysis of more than 1,100 mitochondrial, apicoplast and nuclear gene sequences from chimpanzees and gorillas revealed that 99% grouped within one of six host-specific lineages representing distinct Plasmodium species within the subgenus Laverania. One of these from western gorillas comprised parasites that were nearly identical to P. falciparum. In phylogenetic analyses of full-length mitochondrial sequences, human P. falciparum formed a monophyletic lineage within the gorilla parasite radiation. These findings indicate that P. falciparum is of gorilla origin and not of chimpanzee, bonobo or ancient human origin.

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data. Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.

In 1997, the rediscovery of Sus bucculentus in Laos was announced by Groves et al.--this wild pig species had gone unrecorded since first being described in 1892. Although the identification of the new specimen was based initially on morphology, the authors also used a 7% sequence divergence from the common Eurasian pig S. scrofa (based on their analysis of 327 base pairs of the gene encoding mitochondrial 12S ribosomal RNA) as support for the species status of S. bucculentus. Concerned about the large divergence reported for a relatively conserved gene, and the absence of the sequence in any public database, we analysed an additional tissue sample from the specimen and found only 0.6% divergence from S. scrofa. Our more extensive analysis places the sample within the S. scrofa clade, calling into question the species status of S. bucculentus and demonstrating the need for both phylogenetic and morphological evidence in defining species.

Global efforts to conserve species have been strongly influenced by the heterogeneous distribution of species diversity across the Earth. This is manifest in conservation efforts focused on diversity hotspots. The conservation of genetic diversity within an individual species is an important factor in its survival in the face of environmental changes and disease. Here we show that diversity within species is also distributed unevenly. Using simple genealogical models, we show that genetic distinctiveness has a scale-free power law distribution. This property implies that a disproportionate fraction of the diversity is concentrated in small sub-populations, even when the population is well-mixed. Small groups are of such importance to overall population diversity that even without extrinsic perturbations, there are large fluctuations in diversity owing to extinctions of these small groups. We also show that diversity can be geographically non-uniform--potentially including sharp boundaries between distantly related organisms--without extrinsic causes such as barriers to gene flow or past migration events. We obtained these results by studying the fundamental scaling properties of genealogical trees. Our theoretical results agree with field data from global samples of Pseudomonas bacteria. Contrary to previous studies, our results imply that diversity loss owing to severe extinction events is high, and focusing conservation efforts on highly distinctive groups can save much of the diversity.

Taxonomy does not deserve its reputation as an arcane science. As the following examples from ungulate taxonomy show, classification has important implications for conservation legislation.