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We present a new database, EutherianCoP, of fossil mammals which lived globally from the Late Pleistocene to the Holocene. The database includes 13,972 fossil occurrences of 786 extant or recently extinct placental mammal species, plus 155,198 current occurrences for those of them which survived to the present. The occurrences are correlated with radiometric age information. For all species, we provide 32 different traits, inclusive of taxonomic, phenotypic, life history, biogeographic and phylogenetic information. Differently from any other compilation, the occurrences are complemented with estimates of past climatic conditions, including site-interpolated monthly and annual precipitation and temperature, leaf area index, megabiome type and net primary productivity, which are derived from transient paleo model simulations conducted with the Community Earth System Model 1.2 and the BIOME4 vegetation model. All data are further downloadable for further investigation., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

The Picrodontidae from the middle Palaeocene of North America are enigmatic placental mammals that were allied with various mammalian groups but are generally now considered to have close affinities to paromomyid and palaechthonid plesiadapiforms based on proposed dental synapomorphies. The picrodontid fossil record consists entirely of dental and gnathic remains except for one partial cranium of Zanycteris paleocenus (AMNH 17180). Here, we use µCT technology to unveil previously undocumented morphology in AMNH 17180, describe and compare the basicranial morphology of a picrodontid for the first time, and incorporate these new data into cladistic analyses. The basicranial morphology of Z. paleocenus is distinct from plesiadapiforms and shares similarities with the Palaeogene Apatemyidae and Nyctitheriidae. Results of cladistic analyses incorporating these novel data suggest picrodontids are not stem primates nor euarchontan mammals and that the proposed dental synapomorphies uniting picrodontids with plesiadapiforms and, by extension, primates evolved independently. Results highlight the need to scrutinize proposed synapomorphies of highly autapomorphic taxa with limited fossil records.

The Miocene Caragua fossil fauna in northern Chile contains a considerable number (7) of articulated partial skeletons tentatively assigned to Caraguatypotherium munozi (Notoungulata, Mesotheriidae), which presents up to 40% body size difference. Since either inter- and intra- specific wide size range has been observed in the Mesotheriidae family in general, we wanted explore the ontogenic stage signature of the sample, by carrying out the first comprehensive paleohistological description of the appendicular system in Notoungulata. Results show that: 1) they can be classified as subadults and adults, based on the presence of bone tissues typical of ceased somatic growth; 2) there is a notorious inter-skeletal variation on bone growth rates (skeletal modularity), particularly, the humerus showed a slower diameter growth and less remodelling than the femur, resulting as a better element for ontogenetic analyses; 3) marked cyclical growth is observed, characterised by fast early ontogenic continuous growth, and subsequent fast/slow stratified bone tissue layering. In general, such growth pattern suggests that C. munozi had a similar ontogenetic growth process as other modern mammals, that it should also be influenced by other sex-related, ecological and environmental factors. Likely related to the presence of rapid climatic variations, due to orogenic uplift and concomitant re-organization of the drainage processes along the western tectonic front of the Central Andes at that time., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Campos-Medina et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The genomes of eukaryotes preserve a vast diversity of ancient viruses in the form of endogenous viral elements (EVEs). Study of this genomic fossil record provides insights into the diversity, origin, and evolution of viruses across geological timescales. In particular, Mavericks have emerged as one of the oldest groups of endogenous viruses infecting vertebrates (≥419 million years [My]). They have been found in the genomes of fish, amphibians, birds, and nonavian reptiles but had been overlooked in mammals. Thus, their evolutionary history and the causes of their demise in mammals remain puzzling questions. Here, we conducted a detailed evolutionary study of two Maverick integrations found on human chromosomes 7 and 8. We performed a comparative analysis of the integrations and determined their orthology across placental mammals (Eutheria) via the syntenic arrangement of neighboring genes. The integrations were absent at the orthologous sites in the genomes of marsupials and monotremes. These observations allowed us to reconstruct a time-calibrated phylogeny and infer the age of their most recent common ancestor at 127 to 262 My. In addition, we estimate the age of the individual integrations at ~102 My, which represents the oldest nonretroviral EVEs found in the human genome. Our findings suggest that active Mavericks still existed in the ancestors of modern mammals ~172 My ago (Jurassic Period) and potentially to the end of the Early Cretaceous. We hypothesize that Mavericks could have gone extinct in mammals from the evolution of an antiviral defense system or from reduced opportunities for transmission in terrestrial hosts. IMPORTANCE The genomes of vertebrates preserve a large diversity of endogenous viral elements (remnants of ancient viruses that accumulate in host genomes over evolutionary time). Although retroviruses account for the vast majority of these elements, diverse DNA viruses have also been found and novel lineages are being described. Here, we analyzed two elements found in the human genome belonging to an ancient group of DNA viruses called Mavericks . We studied their evolutionary history, finding that the elements are shared between humans and many different species of placental mammals. These observations suggest that the elements inserted at least ~102 million years ago (Mya) in the most recent common ancestor of placentals. We further estimated the age of the viral ancestor at around 127 to 262 My. Our results provide evidence for some of the oldest viral integrations in the human genome and insights into the ancient interactions of viruses with the ancestors of modern-day mammals.

The estimation of the timing of major divergences in early mammal evolution is challenging owing to conflicting interpretations of key fossil taxa. One contentious group is Haramiyida, the earliest members of which are from the Late Triassic. Many phylogenetic analyses have placed haramiyidans in a clade with multituberculates within crown Mammalia, thus extending the minimum divergence date for the crown group deep into the Triassic. A second taxon of interest is the eutherian Juramaia from the Middle-Late Jurassic Yanliao Biota, which is morphologically very similar to eutherians from the Early Cretaceous Jehol Biota and implies a very early origin for therian mammals. Here, we apply Bayesian tip-dated phylogenetic methods to investigate these issues. Tip dating firmly rejects a monophyletic Allotheria (multituberculates and haramiyidans), which are split into three separate clades, a result not found in any previous analysis. Most notably, the Late Triassic Haramiyavia and Thomasia are separate from the Middle Jurassic euharamiyidans. We also test whether the Middle-Late Jurassic age of Juramaia is 'expected' given its known morphology by assigning an age prior without hard bounds. Strikingly, this analysis supports an Early Cretaceous age for Juramaia , but similar analyses on 12 other mammaliaforms from the Yanliao Biota return the correct, Jurassic age. Our results show that analyses incorporating stratigraphic data can produce results very different from other methods. Early mammal evolution may have involved multiple instances of convergent morphological evolution (e.g. in the dentition), and tip dating may be a method uniquely suitable to recognizing this owing to the incorporation of stratigraphic data. Our results also confirm that Juramaia is anomalous in exhibiting a much more derived morphology than expected given its age, which in turn implies very high rates of evolution at the base of therian mammals.

The phylogeny of eutherian mammals contains some of the most recalcitrant nodes in the tetrapod tree of life. We combined comprehensive taxon and character sampling to explore three of the most debated interordinal relationships among placental mammals. We performed in silico extraction of ultraconserved element loci from 72 published genomes and invitro enrichment and sequencing of ultraconserved elements from 28 additional mammals, resulting in alignments of 3,787 loci. We analyzed these data using concatenated and multispecies coalescent phylogenetic approaches, topological tests, and exploration of support among individual loci to identify the root of Eutheria and the sister groups of tree shrews (Scandentia) and horses (Perissodactyla). Individual loci provided weak, but often consistent support for topological hypotheses. Although many gene trees lacked accepted species-tree relationships, summary coalescent topologies were largely consistent with inferences from concatenation. At the root of Eutheria, we identified consistent support for a sister relationship between Xenarthra and Afrotheria (i.e., Atlantogenata). At the other nodes of interest, support was less consistent. We suggest Scandentia is the sister of Primatomorpha (Euarchonta), but we failed to reject a sister relationship between Scandentia and Glires. Similarly, we suggest Perissodactyla is sister to Cetartiodactyla (Euungulata), but a sister relationship between Perissodactyla and Chiroptera remains plausible., (© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughput sequencing data (RNA or DNA) generated for other biological studies and available in public databases. Following this procedure we addressed pending or controversial issues concerning the phylogenetic position of Dermoptera, Pholidota and Chiroptera, considering multiple and independent loci. Also for Chiroptera and Arctoidea we evaluated the relationships of the lineages that compose it. Although the maximum number of genes used is moderate (95), in some cases taxon coverage doubles that of previous related studies. Globally, all coalescent-based (STAR, MP-EST and ASTRAL) and concatenated (IQ-TREE and BEAST2) methods used for species tree reconstruction were consistent to each other and most of interrogated nodes received high statistical support., (Copyright © 2017 Elsevier Inc. All rights reserved.)

A placenta is defined as structural approximation of maternal and foetal tissues to perform physiological exchange. Associated processes of differentiation and the establishment of its cells take place within the extracellular matrix (ECM) that provides a rich environment of collagens, fibronectins, cytokines and other components. Placental ECM is promising for tissue regeneration purposes, because it has immune tolerance capacities that may cause only minimal rejections of transplants with immunological differences between donor and recipient. However, specific characteristics of ECM during evolution of the structurally very diverse mammalian placenta are not yet revealed. We here address the major aspects of placental types, that is non-invasive (epitheliochorial), medium (endotheliochorial)-to-high (haemochorial) invasive nature of the interhemal barrier between the foetal and maternal blood system as well as their main components of ECM with special reference to species that are commonly used as animal models for human placentation and in the potential applications for regenerative medicine., (© 2016 Blackwell Verlag GmbH.)

Mammals rely on two major pathways to transfer information between the two hemispheres of the brain: the anterior commissure and the corpus callosum. Metatheria and monotremes rely exclusively on the anterior commissure for interhemispheric transfer between the isocortices and olfactory allocortices of each side, whereas Eutheria use a combination of the anterior commissure and an additional pathway exclusive to Eutheria, the corpus callosum. Midline cross-sectional area of the anterior commissure and corpus callosum were measured in a range of mammals from all three infraclasses and plotted against brain volume to determine how midline anterior commissure area and its size relative to the corpus callosum vary with brain size and taxon. In Metatheria, the square root of anterior commissure area rises in almost direct proportion with the cube root of brain volume (i.e. the ratio of the two is relatively constant), whereas among Eutheria the ratio of the square root of anterior commissure area to the cube root of brain volume declines slightly with increasing brain size. The total of isocortical and olfactory allocortical commissure area rises more rapidly with increasing brain volume among Eutheria than among Metatheria. This means that the midline isocortical and olfactory allocortical commissural area of metatherians with large brains (about 70 ml) is only about 50% of that among eutherians with similarly sized brains. On the other hand, isocortical and olfactory allocortical commissural area is similar in Metatheria and Eutheria at brain volumes around 1 ml. Among the Eutheria, some groups make less use of the anterior commissure pathway than do others: soricomorphs, rodents and cetaceans have smaller anterior commissures for their brain size than do afrosoricids, erinaceomorphs and proboscideans. The findings suggest that use of the anterior commissural route for isocortical commissural connections may have placed limitations on interhemispheric transfer of information among the metatherians, but only when brain size reaches 50 ml or more., (Copyright © 2016 Elsevier GmbH. All rights reserved.)

In human and mouse, decidual stromal cells (DSC) are necessary for the establishment (implantation) and the maintenance of pregnancy by preventing inflammation and the immune rejection of the semi-allograft conceptus. DSC originated along the stem lineage of eutherian mammals, coincidental with the origin of invasive placentation. Surprisingly, in many eutherian lineages decidual cells are lost after the implantation phase of pregnancy, making it unlikely that DSC are necessary for the maintenance of pregnancy in these animals. In order to understand this variation, we review the literature on the fetal-maternal interface in all major eutherian clades Euarchontoglires, Laurasiatheria, Xenarthra and Afrotheria, as well as the literature about the ancestral eutherian species. We conclude that maintaining pregnancy may not be a shared derived function of DSC among all eutherian mammals. Rather, we propose that DSC originated to manage the inflammatory reaction associated with invasive implantation. We envision that this happened in a stem eutherian that had invasive placenta but still a short gestation. We further propose that extended gestation evolved independently in the major eutherian clades explaining why the major lineages of eutherian mammals differ with respect to the mechanisms maintaining pregnancy., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

The innate immune system of mammals is formed by a complex web of interacting proteins, which together constitute the first barrier of entry for infectious pathogens. Genes from the E3-ubiquitin ligase tripartite motif (TRIM) family have been shown to play an important role in the innate immune system by restricting the activity of different retrovirus species. For example, TRIM5 and TRIM22 have both been associated with HIV restriction and are regarded as crucial parts of the antiretroviral machinery of mammals. Our analyses of positive selection corroborate the great significance of these genes for some groups of mammals. However, we also show that many species lack TRIM5 and TRIM22 altogether. By analyzing a large number of mammalian genomes, here we provide the first comprehensive view of the evolution of these genes in eutherians, showcasing that the pattern of accumulation of TRIM genes has been dissimilar across mammalian orders. Our data suggest that these differences are caused by the evolutionary plasticity of the immune system of eutherians, which have adapted to use different strategies to combat retrovirus infections. Altogether, our results provide insights into the dissimilar evolution of a representative family of restriction factors, highlighting an example of adaptive and idiosyncratic evolution in the innate immune system.

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.

Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the levels of nucleotides and amino acids. The two approaches revealed contradictory phylogenetic signals, possibly due to a high level of ancestral incomplete lineage sorting. The positions of Eulipotyphla and Chiroptera as the first and second earliest divergences were consistent across the approaches. However, the phylogenetic relationships of Perissodactyla, Cetartiodactyla, and Ferae, were contradictory. While retrotransposon insertion analyses suggest a clade with Cetartiodactyla and Ferae, the exon dataset favoured Cetartiodactyla and Perissodactyla. Future analyses of hitherto unsampled laurasiatherian lineages and synergistic analyses of retrotransposon insertions, exon and conserved intron/intergenic sequences might unravel the conflicting patterns of relationships in this major mammalian clade.

Mitochondrial fatty acid oxidation (FAO) contributes to the proton motive force that drives ATP synthesis in many mammalian tissues. In eutherian (placental) mammals, brown adipose tissue (BAT) can also dissipate this proton gradient through uncoupling protein 1 (UCP1) to generate heat, but the evolutionary events underlying the emergence of BAT are unknown. An essential step in FAO is the transport of cytoplasmic long chain acyl-coenzyme A (acyl-CoA) into the mitochondrial matrix, which requires the action of carnitine palmitoyltransferase 1B (CPT1B) in striated muscle and BAT. In eutherians, the CPT1B gene is closely linked to the choline kinase beta (CHKB) gene, which is transcribed from the same DNA strand and terminates just upstream of CPT1B. CHKB is a rate-limiting enzyme in the synthesis of phosphatidylcholine (PC), a predominant mitochondrial membrane phospholipid, suggesting that the coordinated expression of CHKB and CPT1B may cooperatively enhance mitochondrial FAO. The present findings show that transcription of the eutherian CHKB and CPT1B genes is linked within a unitary epigenetic domain targeted to the CHKB gene, and that that this regulatory linkage appears to have resulted from an intergenic deletion in eutherians that significantly altered the distribution of CHKB and CPT1B expression. Informed by the timing of this event relative to the emergence of BAT, the phylogeny of CHKB-CPT1B synteny, and the insufficiency of UCP1 to account for eutherian BAT, these data support a mechanism for the emergence of BAT based on the acquisition of a novel capacity for adipocyte FAO in a background of extant UCP1.

Adapisoriculidae, a family of primitive eutherian, insectivore-like small mammals, is known from Europe, mainland Asia, India and Africa (Morocco, Namibia) but not thus far from the New World. Previous discoveries of this family in Africa were restricted to Morocco, but in 2019 a specimen was found in early to middle Eocene freshwater limestones at Black Crow, Namibia, thereby greatly extending the geographic range of the family well to the south of all other records of the group, even taking into account the northward drift of India since the early Palaeogene. A new genus and species is described and compared in detail with other members of the family as well as with other small-bodied eutherians and placentals. Its biogeography is discussed, but the limited amount of evidence available, allied with the huge geographic and temporal gaps in its distribution, does not yield a clear picture of where the family originated and when it dispersed to other parts of the Old World. [ABSTRACT FROM AUTHOR]

We report the discovery of a new Late Cretaceous eutherian mammal, Azilestes ragei n. gen., n. sp. from the Mas-d’Azil northern Pyrenean site (France), which is among the largest known. It is only known from a broken lower jaw found in uppermost levels of the Grès de Labarre Formation (early Maastrichtian). Despite its poor preservation, it displays distinctive specialized features with respect to known Cretaceous eutherians. This includes a reduced premolar formula and shortened and robust jaw, an incipient hypolophid, and a cingular-like postcristid and hypoconulid. The phylogenetic analysis suggests indeed a possible stem relationship between Azilestes n. gen. and some clades of herbivorous Cenozoic placentals, but with weak support. Several molar features reminiscent of the Zhelestidae, especially Valentinella Tabuce, Vianey-Liaud & Garcia, 2004, support instead that Azilestes n. gen. is a basal eutherian showing early specialization in a herbivorous diet convergent with some crown placentals. Whatever the suprageneric position of Azilestes n. gen., which remains to be clarified with additional material, its discovery highlights a significant diversity of European Cretaceous eutherians in contrast to their very poor fossil record. [ABSTRACT FROM AUTHOR]

We report a new genus and species of herbivorous mammal, Pahelia mysteriosa, from the early Eocene Cambay Shale Formation, Tadkeshwar Lignite Mine, Gujarat, India. The new taxon, approximately the size of a small phenacodontid (e.g. Ectocion parvus), is represented by three mandibular fragments, the most complete of which documents nearly the entire symphysis and mandibular body plus P3–M3. Pahelia has incipiently selenolophodont molars with strong exodaenodonty, absent paraconids, weak but distinct entolophids, and prominent ectostylids. Molar size increases distally, but M3 does not develop a prominent third lobe. Premolars are simple, with prominent protoconids and short talonids but little development of other trigonid cusps. The mandibular symphysis is strongly fused, and there is an enlarged alveolus for an anterior tooth. The combination of features present in the new taxon does not closely match that of any known mammal, but there are some similarities to a diversity of ungulates from Africa, Asia, Europe and North America. Preserved morphology is insufficient to assess the affinities of the new taxon with confidence, but a link to Quettacyonidae, also endemic to the Indian subcontinent, is morphologically and biogeographically plausible. If this scenario is correct, it suggests that P. mysteriosa could be a part of the endemic mammalian fauna of India prior to its initial faunal contact with Asia. [ABSTRACT FROM AUTHOR]

Cetacean stranding records can provide vital information on species richness and diversity through space and time. Here we collate stranding records from Victoria, Australia and assess them for temporal, spatial and demographic trends. Between 1920 and 2016, 424 stranding events involving 907 individuals were recorded across 31 Cetacea species from seven families, including five new species records for the state. Seven of these events were mass strandings, and six mother and calf strandings were recorded. Importantly, 48% of the species recorded are recognised as data deficient on the IUCN Red List. The most commonly recorded taxa were Tursiops spp. (n = 146) and Delphinus delphis (common dolphins, n = 81), with the greatest taxonomic richness (n = 24) and highest incidence of stranding events documented within the Otways mesoscale bioregion. We found no seasonal stranding patterns anywhere in the state. While our findings improve understanding of the spatial and temporal patterns of cetacean diversity within Victoria, we suggest greater effort to collect demographic data at stranding events in order to better study state-wide patterns through time. We conclude with guidelines for minimum data collection standards for future strandings to maximise information capture from each event. [ABSTRACT FROM AUTHOR]

The relationship between hydrogen and oxygen stable isotopic compositions in environmental water and hair was investigated for both domestic cats (Felis catus) and dogs (Canis lupus familiaris). A strong, but different, covariance was measured between the hydrogen and oxygen stable isotopic compositions of local precipitation and hair keratin from both cats and dogs. These isotopic differences are most likely a result of the differences between the dietary and drinking water needs of cats compared to dogs. Moreover, the δ2H and δ18O values of hair from captive and wild felids and canids, such as cougars (Puma concolor), bobcats (Lynx rufus), and wolves (Canis lupus) are broadly consistent with these measurements. This evidence indicates that while the water budgets of terrestrial mammalian carnivores need to be considered in isotopic applications, it is clear that felids and canids may be placed on tissue–specific hydrogen and oxygen isotopic landscapes for ecological, provenance, or forensic studies. [ABSTRACT FROM AUTHOR]

Carnivore protoparvovirus 1 (CPPV-1) is widespread among free-living carnivores, and CPPV-1 infection may directly or indirectly impact on the population of endangered carnivore species. In this study, we used molecular screening of viral capsid protein 2 (VP2) from 2015 to 2017, to assess the prevalence of CPPV-1 infection in 9 live-trapped (LT) and 17 vehicle collision (VC)-affected free-living leopard cats (Prionailurus bengalensis chinensis). In addition, we conducted the phylogenetic analysis to evaluate the possible transmission of CPPV-1 between domestic carnivores and leopard cats. We identified the circulation of feline parvovirus and variants of canine parvovirus (CPV), including CPV-2a, CPV-2b, and CPV-2c, in the free-living leopard cat population. The partial sequences of different variants of VP2 obtained from the leopard cats were identical with those obtained from the domestic dogs and cats in Taiwan. Our result suggested that CPPV-1 was currently transmitted between domestic carnivores and leopard cats in Taiwan. A plan of conservation measures based on vaccination program for domestic carnivores, strict controls on populations of free-living dogs and cats and limiting road development only to low-risk areas for leopard cats should be encouraged. [ABSTRACT FROM AUTHOR]

Carrion resources sustain a complex and diverse community of both vertebrate and invertebrate scavengers, either obligate or facultative. However, although carrion ecology has received increasing scientific attention in recent years, our understanding of carrion partitioning in natural conditions is severely limited as most studies are restricted either to the vertebrate or the insect scavenger communities. Moreover, carnivore carcasses have been traditionally neglected as study model. Here, we provide the first data on the partitioning between vertebrate and invertebrate scavengers of medium-sized carnivore carcasses, red fox (Vulpes vulpes (Linnaeus)), in two mountainous Mediterranean areas of south-eastern Spain. Carcasses were visited by several mammalian and avian scavengers, but only one carcass was partially consumed by golden eagle Aquila chrysaetos (Linnaeus). These results provide additional support to the carnivore carrion-avoidance hypothesis, which suggests that mammalian carnivores avoid the consumption of carnivore carcasses to prevent disease transmission risk. In turn, the absence of vertebrate scavengers at carnivore carcasses enabled a diverse and well-structured successional community of insects to colonise the carcasses. The observed richness and abundance of the most frequent families was more influenced by the decomposition time than by the study area. Overall, our study encourages further research on carrion resource partitioning in natural conditions. [ABSTRACT FROM AUTHOR]

Fes1 is a conserved armadillo repeat-containing Hsp70 nucleotide exchange factor important for growth at high temperature, proteasomal protein degradation and prion propagation. Depleting or mutating Fes1 induces a stress response and causes defects in these processes that are ascribed solely to disruption of Fes1 regulation of Hsp70. Here, we find Fes1 was essential for degradation of gluconeogenic enzymes by the vacuole import and degradation (Vid) pathway and for cell wall integrity (CWI), which is crucial for growth at high temperature. Unexpectedly, Fes1 mutants defective in physical or functional interaction with Hsp70 retained activities that support Vid and CWI. Fes1 and the Fes1 mutants bound to the Vid substrate Fbp1 in vitro and captured Slt2, a signaling kinase that regulates CWI, from cell lysates. Our data show that the armadillo domain of Fes1 binds proteins other than Hsp70, that Fes1 has important Hsp70-independent roles in the cell, and that major growth defects caused by depleting Fes1 are due to loss of these functions rather than to loss of Hsp70 regulation. We uncovered diverse functions of Fes1 beyond its defined role in regulating Hsp70, which points to possible multi-functionality among its conserved counterparts in other organisms or organelles. [ABSTRACT FROM AUTHOR]

Dietary insufficiencies have been well documented to decrease growth rates and survival (and therefore overall production) in fish aquaculture. By contrast, the effects of dietary insufficiencies on the sensory biology of cultured fish remains largely unstudied. Diets based solely on plant protein sources could have advantages over fish-based diets because of the cost and ecological effects of the latter, but plant proteins lack the amino acid taurine. Adequate levels of taurine are, however, necessary for the development of a fully functional visual system in mammals. As part of ongoing studies to determine the suitability of plant-based diets, we investigated the effects of normal and reduced taurine dietary levels on retinal anatomy and function in European sea bass (Dicentrarchus labrax). We could not demonstrate any effects of dietary taurine level on retinal anatomy, nor the functional properties of luminous sensitivity and temporal resolution (measured as flicker fusion frequency). We did, however, find an effect on spectral sensitivity. The peak of spectral sensitivity of individuals fed a 5% taurine diet was rightward shifted (i.e., towards longer wavelengths) relative to that of fish fed a 0% or 1.5% taurine diet. This difference in in spectral sensitivity was due to a relatively lower level of middle wavelength pigment (maximum absorbance .500 nm) in fish fed a 5% taurine diet. Changes in spectral sensitivity resulting from diets containing different taurine levels are unlikely to be detrimental to fish destined for market, but could be in fishes that are being reared for stock enhancement programs. [ABSTRACT FROM AUTHOR]

Camera traps are a key tool in ecological studies, and are increasingly being used to understand entire communities. However, robust inferences continue to be hampered by low detection of rare and elusive species. Attractants can be used to increase detection rates, but may also alter behaviour, and little research has evaluated short-term, localized response to the presence of attractants. We conducted three camera trap surveys in Kibale National Park, Uganda, using food baits and scent lures (“attractants”) at each camera station to entice small carnivores to pass in front of camera stations. To examine the interrelationship between scavenging and response to attractants, we also placed camera traps at five food refuse pits. We modelled the effect of attractant and duration of trap placement on the detection probability of small carnivores and selected African golden cat Caracal aurata prey items. We examine transient site response of each species, by comparing our observed likelihood of detection in each 24 h period from 1–7 d following refreshing of attractants to randomly generated capture histories. African civet Civettictis civetta, rusty-spotted genet Genetta maculata, African palm civet Nandinia binotata, and marsh mongoose Atilax paludinosus detection probabilities were highest and Weyns’s red duiker Cephalophus wenysi detection probability was lowest immediately after attractants were placed. Within 24 h after attractant was placed, rusty-spotted genet and African palm civet were more likely to be detected and African golden cat, red duiker, and blue duiker Philantomba monticola were less likely to be detected. Our results suggest that attractants can increase detection of small-bodied species and include some arboreal species in terrestrial camera trap sampling. However, attractants may also alter short-term visitation rates of some species, with potentially cascading effects on others. Community level and intraguild interaction studies should control for the potentially confounding effects of attractants on spatial activity patterns. [ABSTRACT FROM AUTHOR]

There is considerable debate regarding whether mandibular morphology in ungulates primarily reflects phylogenetic affinities or adaptation to specific diet. In an effort to help resolve this debate, we use three-dimensional finite element analysis (FEA) to assess the biomechanical performance of mandibles in eleven ungulate taxa with well-established but distinct dietary preferences. We found notable differences in the magnitude and the distribution of von Mises stress between Artiodactyla and Perissodactyla, with the latter displaying lower overall stress values. Additionally, within the order Artiodactyla the suborders Ruminantia and Tylopoda showed further distinctive stress patterns. Our data suggest that a strong phylogenetic signal can be detected in biomechanical performance of the ungulate mandible. In general, Perissodactyla have stiffer mandibles than Artiodactyla. This difference is more evident between Perissodactyla and ruminant species. Perissodactyla likely rely more heavily on thoroughly chewing their food upon initial ingestion, which demands higher bite forces and greater stress resistance, while ruminants shift comminution to a later state (rumination) where less mechanical effort is required by the jaw to obtain sufficient disintegration. We therefore suggest that ruminants can afford to chew sloppily regardless of ingesta, while hindgut fermenters cannot. Additionally, our data support a secondary degree of adaptation towards specific diet. We find that mandibular morphologies reflect the masticatory demands of specific ingesta within the orders Artiodactyla and Perissodactyla. Of particular note, stress patterns in the white rhinoceros (C. simum) look more like those of a general grazer than like other rhinoceros’ taxa. Similarly, the camelids (Tylopoda) appear to occupy an intermediate position in the stress patterns, which reflects the more ancestral ruminating system of the Tylopoda. [ABSTRACT FROM AUTHOR]

Different Biogeographic provinces and environmental factors are known to influence the dispersibility of long-ranging carnivores over the landscape. However, lack of empirical data on long-ranging carnivores may lead to erroneous decisions in formulating management plans. The Indian Grey wolf (Canis lupus pallipes) is known to be distributed in the vast areas of the Indian subcontinent. However, the actual population estimates are available only for Gujarat, Karnataka, Rajasthan and Bihar. Whereas, its distribution, population and habitat ecology is poorly known from the eastern region. Hence, this article aimed to evaluate the habitat suitability along with landscape connectivity for the species over the two major biogeographic provinces of India, i.e., Lower Gangetic Plains (7b) and Chhota Nagpur Plateau (6b). The present model with significantly higher Area under the curve (AUC) value of 0.981, indicates its accuracy in predicting the suitable habitats and identifying biological corridors by using environmental, topological and anthropogenic variables. Precipitation of the driest quarter and the precipitation of seasonality were the two best performing variables in our model, capable of explaining about 26% and 22.4% variation in the data respectively. Out of the total area i.e. 4,16,665 Km2, about 18,237 Km2 (4.37%) was found to be highly suitable area and about 3,16,803 Km2 (76.03%) areas as least suitable. The corridor analysis indicated that the habitat connectivity was highest in the border line area of the two biotic provinces located in the south-eastern zone via districts of Purba Singhbhum and Paschim Singhbhum of Jharkhand state and Bankura and West Midnapore districts of West Bengal state. Among the Protected Areas (PAs), natural corridors exist connecting the Simlipal National Park (NP)-Satkosia Wildlife Santuray (WLS), Dalma ranges of Chotta Nagpur plateau along with Badrama WLS, Khulasuni WLS and Debrigarh WLS. Differential management through landscape level planning may be helpful in securing the future of the species in the landscape. [ABSTRACT FROM AUTHOR]

Carnivores have long been used as model organisms to examine mechanisms that allow coexistence among ecologically similar species. Interactions between carnivores, including competition and predation, comprise important processes regulating local community structure and diversity. We use data from an intensive camera-trapping monitoring program across eight Neotropical forest sites to describe the patterns of spatiotemporal organization of a guild of five sympatric cat species: jaguar (Panthera onca), puma (Puma concolor), ocelot (Leopardus pardalis), jaguarundi (Herpailurus yagouaroundi) and margay (Leopardus wiedii). For the three largest cat species, we developed multi-stage occupancy models accounting for habitat characteristics (landscape complexity and prey availability) and models accounting for species interactions (occupancy estimates of potential competitor cat species). Patterns of habitat-use were best explained by prey availability, rather than habitat structure or species interactions, with no evidence of negative associations of jaguar on puma and ocelot occupancy or puma on ocelot occupancy. We further explore temporal activity patterns and overlap of all five felid species. We observed a moderate temporal overlap between jaguar, puma and ocelot, with differences in their activity peaks, whereas higher temporal partitioning was observed between jaguarundi and both ocelot and margay. Lastly, we conducted temporal overlap analysis and calculated species activity levels across study sites to explore if shifts in daily activity within species can be explained by varying levels of local competition pressure. Activity patterns of ocelots, jaguarundis and margays were similarly bimodal across sites, but pumas exhibited irregular activity patterns, most likely as a response to jaguar activity. Activity levels were similar among sites and observed differences were unrelated to competition or intraguild killing risk. Our study reveals apparent spatial and temporal partitioning for most of the species pairs analyzed, with prey abundance being more important than species interactions in governing the local occurrence and spatial distribution of Neotropical forest felids. [ABSTRACT FROM AUTHOR]

The advent of online data aggregator infrastructures has facilitated the accumulation of Digital Accessible Knowledge (DAK) about biodiversity. Despite the vast amount of freely available data records, their usefulness for research depends on completeness of each body of data regarding their spatial, temporal and taxonomic coverage. In this paper, we assess the completeness of DAK about terrestrial mammals distributed across the Iberian Peninsula. We compiled a dataset with all records about mammals occurring in the Iberian Peninsula available in the Global Biodiversity Information Facility and in the national atlases from Portugal and Spain. After cleaning the dataset of errors as well as records lacking collection dates or not determined to species level, we assigned all occurrences to a 10-km grid. We assessed inventory completeness by calculating the ratio between observed and expected richness (based on the Chao2 richness index) in each grid cell and classified cells as well-sampled or under-sampled. We evaluated survey coverage of well-sampled cells along four environmental gradients and temporal coverage. Out of 796,283 retrieved records, quality issues led us to remove 616,141 records unfit for this use. The main reason for discarding records was missing collection dates. Only 25.95% cells contained enough records to robustly estimate completeness. The DAK about terrestrial mammals from the Iberian Peninsula was low, and spatially and temporally biased. Out of 5,874 cells holding data, only 620 (9.95%) were classified as well-sampled. Moreover, well-sampled cells were geographically aggregated and reached inventory completeness over the same temporal range. Despite the increasing availability of DAK, its usefulness is still compromised by quality issues and gaps in data. Future work should therefore focus on increasing data quality, in addition to mobilizing unpublished data. [ABSTRACT FROM AUTHOR]

G protein–coupled receptors (GPCRs) play an important role in physiology and disease and represent the most productive drug targets. Orphan GPCRs, with their endogenous ligands unknown, were considered a source of drug targets and consequently attract great interest to identify their endogenous cognate ligands for deorphanization. However, a contrary view to the ubiquitous existence of endogenous ligands for every GPCR is that there might be a significant overlooked fraction of orphan GPCRs that function constitutively in a ligand-independent manner only. Here, we investigated the evolution of the bombesin receptor–ligand family in vertebrates in which one member—bombesin receptor subtype-3 (BRS3)—is a potential orphan GPCR. With analysis of 17 vertebrate BRS3 structures and 10 vertebrate BRS3 functional data, our results demonstrated that nonplacental vertebrate BRS3 still connects to the original ligands—neuromedin B (NMB) and gastrin-releasing peptide (GRP)—because of adaptive evolution, with significantly changed protein structure, especially in three altered key residues (Q127R, P205S, and R294H) originally involved in ligand binding/activation, whereas the placental mammalian BRS3 lost the binding affinity to NMB/GRP and constitutively activates Gs/Gq/G12 signaling in a ligand-independent manner. Moreover, the N terminus of placental mammalian BRS3 underwent positive selection, exhibiting significant structural differences compared to nonplacental vertebrate BRS3, and this domain plays an important role in constitutive activity of placental mammalian BRS3. In conclusion, constitutively active BRS3 is a genuinely orphan GPCR in placental mammals, including human. To our knowledge, this study identified the first example that might represent a new group of genuinely orphan GPCRs that will never be deorphanized by the discovery of a natural ligand and provided new perspectives in addition to the current ligand-driven GPCR deorphanization. [ABSTRACT FROM AUTHOR]

There is a need for novel mechanical devices for dispatching poultry on farm following the introduction of EU Regulation (EC) no. 1099/2009 On the Protection of Animals at the Time of Killing. We examined three novel mechanical killing devices: Modified Armadillo, Modified Rabbit Zinger, a novel mechanical cervical dislocation device; and traditional manual cervical dislocation. The four killing methods were tested on 230 chickens across four batches. We measured behavioural, electroencephalogram and post-mortem outcomes in anesthetized laying hens and broilers at two life stages (juveniles and adults/slaughter age). Graeco Latin-Square designs systematically randomized killing treatment, bird type, age and kill order. All birds were lightly anaesthetized immediately prior to the killing treatment with inhalation of Sevoflurane. The novel mechanical cervical dislocation method had the highest kill success rate (single application attempt only, with no signs of recovery) of a mechanical method (96%). The Modified Armadillo was the least reliable with 49% kill success. Spectral analysis of electroencephalogram signals at 2 s intervals for successfully killed birds only revealed progressive decreases in median frequency alongside increases in total power. Later, total power decreased as the birds exhibited isoelectric electroencephalogram signal. Latencies to pre-defined spectral ranges associated with unconsciousness showed that birds subjected to manual and novel mechanical cervical dislocation achieved these states sooner than birds subjected to the modified Armadillo. Nevertheless all methods exhibited short latencies (<4 s). The Modified Rabbit Zinger had the shortest duration of reflex persistence for nictitating membrane, pupillary and rhythmic breathing post method application. Of the methods tested, the novel mechanical cervical dislocation device is the most promising mechanical method for killing poultry on-farm based on a range of behavioural, electroencephalogram and anatomical parameters. This device has the potential to fulfil the current need for a mechanical alternative to manual cervical dislocation. [ABSTRACT FROM AUTHOR]

Across the Mediterranean, conservation programmes often operate concomitantly with hunting interests within game-lands. Carnivore guilds lie at the interface between contrasting management goals, being simultaneously fundamental components of ecosystems and targets of predator control to reduce predation on game species. Here, we evaluate the composition and spatial structure of a mesocarnivore community in a protected area of Southeast Portugal, with high economic investment in conservation and significant hunting activity. Between June and August 2015, we deployed 77 camera-traps across a ~80 km2 area. We report on interspecific disparities in mesocarnivore occupancy and associated environmental determinants. Contrasting occupancy states suggest an unbalanced community, biased towards the widespread occurrence of the red fox Vulpes vulpes () compared to other species (stone marten Martes foina, European badger Meles meles, Egyptian mongoose Herpestes ichneumon, common genet Genetta genetta, and Eurasian otter Lutra lutra) exhibiting spatially-restricted occupancy patterns (). The feral cat Felis silvestris catus was the exception () and, together with the stone marten, exhibited a positive association with human settlements. These findings are consistent with theoretical predictions on how mesocarnivore communities are shaped by the effects of non-selective predator control, paradoxically favouring species with higher population growth rates and dispersal abilities, such as the red fox. Our results reinforce the need to understand the role of predator control as a community structuring agent with potential unintended effects, while exposing issues hindering such attempts, namely non-selective illegal killing or biased/concealed information on legal control measures. [ABSTRACT FROM AUTHOR]

There is evidence that in southern US, leprosy is a zoonosis infecting wild Dasypus novemcinctus armadillos but the extent of this finding is unknown. This ecological study investigated leprosy in rural communities and in wild armadillos from the Brazilian Amazon. The study area was the Mamiá Lake of Coari municipality, Amazonas State, Northern region, a hyper endemic leprosy area where residents live on subsistence farming, fishing and armadillo hunting and its meat intake are frequent. The leprosy survey was conducted in sixteen communities by a visiting team of specialists. Local partakers provided wild armadillos to investigate M. leprae infection. Volunteers had complete dermato-neurological examination by a dermatologist with expertise in leprosy diagnosis, suspect skin lesions were biopsied for histopathology (Hematoxylin-eosin/HE, Fite-Faraco/FF staining); slit skin smears were collected. Armadillos’ tissue fragments (skins, spleens, livers, lymph nodes, adrenal glands, others) were prepared for histopathology (HE/FF) and for M. leprae repetitive element-RLEP-qPCR. Among 176 volunteers, six new indeterminate leprosy cases were identified (incidence = 3.4%). Suspect skin sections and slit skin smears were negative for bacilli. Twelve wild D. novemcinctus were investigated (48 specimens/96 slides) and histopathological features of M. leprae infection were not found, except for one skin presenting unspecific inflammatory infiltrate suggestive of indeterminate leprosy. Possible traumatic neuroma, granuloma with epithelioid and Langhans cells, foreign-body granuloma were also identified. Granulomatous/non-granulomatous dermatitides were periodic-acid-Schiff/PAS negative for fungus. M. leprae-RLEP-qPCR was negative in all armadillos’ tissues; no bacillus was found in histopathology. Our survey in rural communities confirmed the high endemicity for leprosy while one armadillo was compatible with paucibacillary M. leprae infection. At least in the highly endemic rural area of Coari, in the Brazilian Amazon region where infectious sources from untreated multibacillary leprosy are abundant, M. leprae infected armadillos may not represent a major source of infection nor a significant public health concern. [ABSTRACT FROM AUTHOR]

Taphonomic analyses of bone-surface modifications can provide key insights into past biotic involvement with animal remains, as well as elucidate the context(s) of other biostratinomic (pre-burial) processes, diagenesis, excavation, preparation and storage. Such analyses, however, first require researchers to rigorously disambiguate between continuums of damage morphologies prior to attributing individual marks to specific actors and effectors (e.g., carnivore tooth, stone tool cutting edge, etc.). To date, a number of bone-modifying agents have been identified, and criteria for identifying their traces have been published. Relatively little research, however, has focused on bone-surface modifications imparted during specimen preparation. Herein we report that air scribes, small pneumatic tools commonly used for preparation in museum contexts, can generate unintentional marks that may mimic surficial modification caused by carnivores. To aid investigators in assessing the hypothesis that a mark in question is derived from air-scribe preparation activities, we provide high-resolution, detailed morphological information imaged with scanning electron microscopy (SEM). The main diagnostic characteristic of air-scribe damage is the occurrence of sequential, variously spaced, sub-millimeter scallop-like stepped bone removals. This morphology can resemble damage imparted by carnivore teeth. In contrast to marks produced by trampling, stone tools and carnivores, however, no continuous internal features, such as linear microstriations, were observed within grooves produced by the air scribe. Thus, the presence of such features can be used to disprove an air-scribe origin. A culmination of the morphological criteria presented herein, cross-cutting relationships with other surficial features (e.g., diagenetic discoloration, weathering textures), the position of occurrence, and an overall contextual framework for the assemblage is suggested for accurate identification of such traces. The ability to recognize or disprove air-scribe damage will allow researchers to confidently proceed with interpreting past biological and sedimentological interactions with animal remains. [ABSTRACT FROM AUTHOR]

Leprosy is an infectious disease caused by Mycobacterium leprae and frequently resulting in irreversible deformities and disabilities. Ticks play an important role in infectious disease transmission due to their low host specificity, worldwide distribution, and the biological ability to support transovarial transmission of a wide spectrum of pathogens, including viruses, bacteria and protozoa. To investigate a possible role for ticks as vectors of leprosy, we assessed transovarial transmission of M. leprae in artificially-fed adult female Amblyomma sculptum ticks, and infection and growth of M. leprae in tick cell lines. Our results revealed M. leprae RNA and antigens persisting in the midgut and present in the ovaries of adult female A. sculptum at least 2 days after oral infection, and present in their progeny (eggs and larvae), which demonstrates the occurrence of transovarial transmission of this pathogen. Infected tick larvae were able to inoculate viable bacilli during blood-feeding on a rabbit. Moreover, following inoculation with M. leprae, the Ixodes scapularis embryo-derived tick cell line IDE8 supported a detectable increase in the number of bacilli for at least 20 days, presenting a doubling time of approximately 12 days. As far as we know, this is the first in vitro cellular system able to promote growth of M. leprae. Finally, we successfully transformed a clinical M. leprae isolate by inserting the reporter plasmid pCHERRY3; transformed bacteria infected and grew in IDE8 cells over a 2-month period. Taken together, our data not only support the hypothesis that ticks may have the potential to act as a reservoir and/or vector of leprosy, but also suggest the feasibility of technological development of tick cell lines as a tool for large-scale production of M. leprae bacteria, as well as describing for the first time a method for their transformation. [ABSTRACT FROM AUTHOR]

Long recognized as a threat to wildlife, livestock grazing in protected areas has the potential to undermine conservation goals, via competition, habitat degradation, human-carnivore conflict and disruption of predator-prey relationships. In the Strictly Protected Area Zorkul in Tajikistan (Zorkul Reserve), grazing is commonplace despite official prohibition, with potentially detrimental effects on local fauna, in particular, snow leopard Panthera uncia, wolf Canis lupus, brown bear Ursus arctos, argali sheep Ovis ammon, Asiatic ibex Capra sibirica, and long-tailed marmot Marmota caudata. To understand the impacts of grazing and associated human pastoralism on the large mammal community in Zorkul Reserve we used data from camera traps to build models of ungulate and carnivore site use intensity, and we investigated carnivore summer diets using microscopic scat analysis. While sample sizes limited our inference for several species, we found that site use of the most common ungulate, argali, decreased with proximity to herder’s camps, indicating possible displacement into sub-optimal habitats. However, no such pattern was present in carnivore site use. For wolf and snow leopard, the most frequently encountered prey items were argali and marmot, while bear depended almost exclusively on marmot. While current pastoralist practices in the reserve may not be incompatible with wildlife presence, our findings suggest that pastoralism may negatively impact ungulates by displacing them from otherwise suitable habitats, with unknown fitness consequences for ungulates or the predators that depend upon them. Managing Zorkul Reserve and other actively grazed protected areas to meet potentially competing demands of local pastoralist communities and conservation will require careful consideration of such interactions to minimize the risk of cascading negative impacts on wildlife. [ABSTRACT FROM AUTHOR]

This paper presents the histological characterisation of a selection of worked bone artefacts from Middle Stone Age layers at Sibudu cave, South Africa. Histographic rendering is achieved using high-resolution Computed Tomography, which is non-destructive and facilitates three-dimensional histologic analysis. Excellent congruency in image quality was achieved with previous studies using this method. The results show that most of the artefact fragments contain mostly primary lamellar tissue, which is the bone tissue best adapted to withstand impact stresses. This indicates that bone with greater elastic properties was chosen. Histological characterisation allows the identification of animal taxa. Based on the sample analysed in this paper, Perissodactyla bone was used predominantly in the older layers at the site. Artiodactyla are represented throughout but appear far more frequently in the later (post-Howiesons Poort onwards) layers. Some of the Artiodactyla specimens have high proportions of Haversian tissue, reducing elasticity. The higher percentages of Haversian tissue in the post-Howiesons Poort artefacts relative to Holocene examples from southern Africa suggests that people may have started experimenting with bone from different animal taxa at this time and had not yet learned to eliminate the mechanically weaker secondary tissue. Apart from mechanical considerations, possible cultural constraints governing raw material selection is also explored. [ABSTRACT FROM AUTHOR]

Information regarding species’ status at a regional scale is instrumental for effective conservation planning. Some regions of southwestern Europe, such as Portugal, albeit included in the Mediterranean biodiversity hotspot, lack a detailed assessment of the distribution patterns of several taxonomic groups, such as carnivores. Moreover, information is scattered, often unreliable and biased towards some species or regions. This study aimed at reviewing the existing knowledge on mammalian terrestrial carnivores in Portugal, to analyse research trends, update the species checklist and assess their historical and current distribution patterns. We conducted a comprehensive review of 755 scientific studies to analyse several publication metrics and compiled 20,189 presence records of all mammalian terrestrial carnivores occurring in Portugal since historical times to evaluate their distribution patterns. Carnivore research in Portugal began in the 18th century, with a recent boost in the mid-1990s, and has been biased towards certain research topics and regionally threatened species. There are 15 extant species in Portugal, with nine occurring across the country, six showing a more limited range, as well as one additional species currently locally extinct (Ursus arctos). Over the last decades, the distribution ranges of seven species apparently remained stable, two expanded, two contracted, and three showed unclear trends. The presence of a new invasive carnivore, the raccoon (Procyon lotor), is also documented here. This study illustrates the relevance of a comprehensive analysis of non-systematic data to assess the historic and current status of mammalian terrestrial carnivores at a national level, and to identify knowledge gaps and research priorities. [ABSTRACT FROM AUTHOR]

The gastrointestinal microbiome is known to play a critical role in animal health but has been relatively poorly characterized in commercial mink, an obligate carnivore. Whether the microbiota can be manipulated in mink to improve pelt quality, health, and well-being is unknown. The objectives of this study were to characterize the fecal microbiota of commercial mink, and to evaluate potential changes due to year (2014 vs 2015), life stage (adult female vs weaned kit), season (summer vs winter), and between Canadian farms. Pooled fecal samples were collected from adult females and weaned kits in the summers of 2014 (n = 173) and 2015 (n = 168), and from females in the winter of 2016 (n = 39), a time when females undergo marked calorie restriction, from 49 mink farms in Ontario. Bacterial DNA was extracted and the V4 region of the 16S rRNA gene was amplified. Approximately 22 million sequences were identified following quality control filtering. A total of 31 bacterial phyla were identified; however, only 3 comprised >1% of the total sequences identified, with Firmicutes and Proteobacteria together comprising 95% of the total sequences. Comparisons were made by life stage, season and year; no differences were found in the relative abundance of any taxa between samples collected from adult females and weaned kits from the same year and the greatest number of differences at each taxonomic level were noted between 2014 and 2015. Significantly more operational taxonomic units (OTUs) were found in 2014 than 2015 or 2016 (p<0.05) and samples from 2014 were more even, but less diverse than in 2015 (p = 0.002 and 0.001, respectively). There were significant differences in community population and structure by year and season (all p-values <0.001). The predominant phyla and genera at the farm level were similar from year to year. Together, these indicate that mink environment, season, and time are important factors in the stability of gastrointestinal microbiota, once mink reach maturity. [ABSTRACT FROM AUTHOR]

UDP-glycosyltransferase (UGT) catalyzes the transfer of glycosyl groups (e.g., glucuronic acid) to exogenous or endogenous chemicals and plays an important role in conjugation reactions. In vertebrates, UGT genes are divided into 5 families: UGT1, UGT2, UGT3, UGT5, and UGT8. Among these UGT enzymes, UGT1 and UGT2 enzymes are known to be important xenobiotic metabolizing enzymes in mammals. However, little is known about UGT1 and UGT2 genes in avian species. In this study, we therefore aimed to classify avian UGT1 and UGT2 genes based on their evolutionary relationships. We also investigated the association between UGT molecular evolution and ecological factors, specifically feeding habits, habitat, and migration. By examining the genomes of 43 avian species with differing ecology, we showed that avian UGT1E genes are divided into 6 groups and UGT2 genes into 3 groups. Correlations between UGT gene count and ecological factors suggested that the number of UGT1E genes is decreasing in carnivorous species. Estimates of selection pressure also support the hypothesis that diet influenced avian UGT1E gene evolution, similar to mammalian UGT1A and UGT2B genes. [ABSTRACT FROM AUTHOR]

Studies on paleopathological alterations in fossil vertebrates, including damages caused by infections and ectoparasites, are important because they are potential sources of paleoecological information. Analyzing exoskeleton material (isolated osteoderms, carapace and caudal tube fragments) from fossil cingulates of the Brazilian Quaternary Megafauna, we identified damages that were attributed to attacks by fleas and dermic infections. The former were compatible with alterations produced by one species of flea of the genus Tunga, which generates well-delimited circular perforations with a patterned distribution along the carapace; the latter were attributable to pathogenic microorganisms, likely bacteria or fungi that removed the ornamentation of osteoderms and, in certain cases, generated craters or pittings. Certain bone alterations observed in this study represent the first record of flea attack and pitting in two species of large glyptodonts (Panochthus and Glyptotherium) and in a non-glyptodontid large cingulate (Pachyarmatherium) from the Quaternary of the Brazilian Intertropical Region. These new occurrences widen the geographic distribution of those diseases during the Cenozoic and provide more evidence for the co-evolutionary interaction between cingulates and parasites registered to date only for a small number of other extinct and extant species. [ABSTRACT FROM AUTHOR]

Understanding large carnivore occurrence patterns in anthropogenic landscapes adjacent to protected areas is central to developing actions for species conservation in an increasingly human-dominated world. Among large carnivores, leopards (Panthera pardus) are the most widely distributed felid. Leopards occupying anthropogenic landscapes frequently come into conflict with humans, which often results in leopard mortality. Leopards’ use of anthropogenic landscapes, and their frequent involvement with conflict, make them an insightful species for understanding the determinants of carnivore occurrence across human-dominated habitats. We evaluated the spatial variation in leopard site use across a multiple-use landscape in Tanzania’s Ruaha landscape. Our study region encompassed i) Ruaha National Park, where human activities were restricted and sport hunting was prohibited; ii) the Pawaga-Idodi Wildlife Management Area, where wildlife sport hunting, wildlife poaching, and illegal pastoralism all occurred at relatively low levels; and iii) surrounding village lands where carnivores and other wildlife were frequently exposed to human-carnivore conflict related-killings and agricultural habitat conversion and development. We investigated leopard occurrence across the study region via an extensive camera trapping network. We estimated site use as a function of environmental (i.e. habitat and anthropogenic) variables using occupancy models within a Bayesian framework. We observed a steady decline in leopard site use with downgrading protected area status from the national park to the Wildlife Management Area and village lands. Our findings suggest that human-related activities such as increased livestock presence and proximity to human households exerted stronger influence than prey availability on leopard site use, and were the major limiting factors of leopard distribution across the gradient of human pressure, especially in the village lands outside Ruaha National Park. Overall, our study provides valuable information about the determinants of spatial distribution of leopards in human-dominated landscapes that can help inform conservation strategies in the borderlands adjacent to protected areas. [ABSTRACT FROM AUTHOR]

This paper proposes a global approach for the multi-view registration of unordered range scans. Our method starts with the pair-wise registration, where multi-scale descriptor is selected for feature point and the propagation of feature correspondence is accordingly accelerated. Subsequently, we design an effective rule to judge the reliability of these pair-wise registration results. According to the judgment of reliability, we propose a model fusion method, which can utilize reliable results of pair-wise registration to augment the model shape. Finally, multi-view registration can be achieved by operating the pair-wise registration, reliability judgment, and model fusion alternately. The proposed approach can be applied to scene reconstruction and robot mapping. Experimental results conducted on public datasets show that the proposed approach can automatically achieve multi-view registration of unordered range scans. Compared with other related approaches, the proposed approach has superior performances in accuracy and effectiveness. [ABSTRACT FROM AUTHOR]

The retinal rod pathway, featuring dedicated rod bipolar cells (RBCs) and AII amacrine cells, has been intensely studied in placental mammals. Here, we analyzed the rod pathway in a nocturnal marsupial, the South American opossum Monodelphis domestica to elucidate whether marsupials have a similar rod pathway. The retina was dominated by rods with densities of 338,000–413,000/mm². Immunohistochemistry for the RBC-specific marker protein kinase Cα (PKCα) and the AII cell marker calretinin revealed the presence of both cell types with their typical morphology. This is the first demonstration of RBCs in a marsupial and of the integration of RBCs and AII cells in the rod signaling pathway. Electron microscopy showed invaginating synaptic contacts of the PKCα-immunoreactive bipolar cells with rods; light microscopic co-immunolabeling for the synaptic ribbon marker CtBP2 confirmed dominant rod contacts. The RBC axon terminals were mostly located in the innermost stratum S5 of the inner plexiform layer (IPL), but had additional side branches and synaptic varicosities in strata S3 and S4, with S3-S5 belonging to the presumed functional ON sublayer of the IPL, as shown by immunolabeling for the ON bipolar cell marker Gγ13. Triple-immunolabeling for PKCα, calretinin and CtBP2 demonstrated RBC synapses onto AII cells. These features conform to the pattern seen in placental mammals, indicating a basically similar rod pathway in M. domestica. The density range of RBCs was 9,900–16,600/mm2, that of AII cells was 1,500–3,260/mm2. The numerical convergence (density ratio) of 146–156 rods to 4.7–6.0 RBCs to 1 AII cell is within the broad range found among placental mammals. For comparison, we collected data for the Australian nocturnal dunnart Sminthopsis crassicaudata, and found it to be similar to M. domestica, with rod-contacting PKCα-immunoreactive bipolar cells that had axon terminals also stratifying in IPL strata S3-S5. [ABSTRACT FROM AUTHOR]

Because overall cranial morphology-biomechanics linkage in carnivorans is significantly influenced by both feeding and non-feeding ecological variables, whole-skull mechanical performance measures may be less sensitive to feeding ecology than regional characteristics within the skull. The temporomandibular joint could be one regional characteristic that is highly sensitive to feeding ecology considering that this joint is used in prey capture, food processing, and experiences compressive loading during mastication. Through 3D model construction, 3D printing, and compression tests, morphological and mechanical performance measures were determined for the temporomandibular joint trabecular bone structure of 40 species representative of the phylogenetic and ecology diversity of Carnivora. Remarkably, the results indicate that relative fill volume, relative structural complexity, elastic modulus, and relative maximum compressive strength of trabecular bone structure are not significantly related to phylogeny or ecology. The results reveal that morphological and mechanical performance attributes of trabecular bone structure are primarily influenced by body size, and that positive centroid size allometry and positive body mass allometry are present for structural complexity. The lack of feeding ecological signal in dorso-ventral compressive loading of temporomandibular joint models indicates that carnivoran temporomandibular joint trabecular structures may not undergo significant differential remodeling as an evolutionary response to different mechanically demanding feeding tasks. [ABSTRACT FROM AUTHOR]

Mycobacterium leprae (M. leprae) is a human pathogen and the causative agent for leprosy, a chronic disease characterized by lesions of the skin and peripheral nerve damage. Zoonotic transmission of M. leprae to humans by nine-banded armadillos (Dasypus novemcinctus) has been shown to occur in the southern United States, mainly in Texas, Louisiana, and Florida. Nine-banded armadillos are also common in South America, and residents living in some areas in Brazil hunt and kill armadillos as a dietary source of protein. This study examines the extent of M. leprae infection in wild armadillos and whether these New World mammals may be a natural reservoir for leprosy transmission in Brazil, similar to the situation in the southern states of the U.S. The presence of the M. leprae-specific repetitive sequence RLEP was detected by PCR amplification in purified DNA extracted from armadillo spleen and liver tissue samples. A positive RLEP signal was confirmed in 62% of the armadillos (10/16), indicating high rates of infection with M. leprae. Immunohistochemistry of sections of infected armadillo spleens revealed mycobacterial DNA and cell wall constituents in situ detected by SYBR Gold and auramine/rhodamine staining techniques, respectively. The M. leprae-specific antigen, phenolic glycolipid I (PGL-I) was detected in spleen sections using a rabbit polyclonal antibody specific for PGL-I. Anti-PGL-I titers were assessed by ELISA in sera from 146 inhabitants of Belterra, a hyperendemic city located in western Pará state in Brazil. A positive anti-PGL-I titer is a known biomarker for M. leprae infection in both humans and armadillos. Individuals who consumed armadillo meat most frequently (more than once per month) showed a significantly higher anti-PGL-I titer than those who did not eat or ate less frequently than once per month. Armadillos infected with M. leprae represent a potential environmental reservoir. Consequently, people who hunt, kill, or process or eat armadillo meat are at a higher risk for infection with M. leprae from these animals. [ABSTRACT FROM AUTHOR]

Descent of testes from a position near the kidneys into the lower abdomen or into the scrotum is an important developmental process that occurs in all placental mammals, with the exception of five afrotherian lineages. Since soft-tissue structures like testes are not preserved in the fossil record and since key parts of the placental mammal phylogeny remain controversial, it has been debated whether testicular descent is the ancestral or derived condition in placental mammals. To resolve this debate, we used genomic data of 71 mammalian species and analyzed the evolution of two key genes (relaxin/insulin-like family peptide receptor 2 [RXFP2] and insulin-like 3 [INSL3]) that induce the development of the gubernaculum, the ligament that is crucial for testicular descent. We show that both RXFP2 and INSL3 are lost or nonfunctional exclusively in four afrotherians (tenrec, cape elephant shrew, cape golden mole, and manatee) that completely lack testicular descent. The presence of remnants of once functional orthologs of both genes in these afrotherian species shows that these gene losses happened after the split from the placental mammal ancestor. These “molecular vestiges” provide strong evidence that testicular descent is the ancestral condition, irrespective of persisting phylogenetic discrepancies. Furthermore, the absence of shared gene-inactivating mutations and our estimates that the loss of RXFP2 happened at different time points strongly suggest that testicular descent was lost independently in Afrotheria. Our results provide a molecular mechanism that explains the loss of testicular descent in afrotherians and, more generally, highlight how molecular vestiges can provide insights into the evolution of soft-tissue characters. [ABSTRACT FROM AUTHOR]

Globally there are many examples of synanthropic carnivores exploiting growth in urbanisation. As carnivores can come into conflict with humans and are potential vectors of zoonotic disease, assessing densities in suburban areas and identifying factors that influence them are necessary to aid management and mitigation. However, fragmented, privately owned land restricts the use of conventional carnivore surveying techniques in these areas, requiring development of novel methods. We present a method that combines questionnaire distribution to residents with field surveys and GIS, to determine relative density of two urban carnivores in England, Great Britain. We determined the density of: red fox (Vulpes vulpes) social groups in 14, approximately 1km2 suburban areas in 8 different towns and cities; and Eurasian badger (Meles meles) social groups in three suburban areas of one city. Average relative fox group density (FGD) was 3.72 km-2, which was double the estimates for cities with resident foxes in the 1980’s. Density was comparable to an alternative estimate derived from trapping and GPS-tracking, indicating the validity of the method. However, FGD did not correlate with a national dataset based on fox sightings, indicating unreliability of the national data to determine actual densities or to extrapolate a national population estimate. Using species-specific clustering units that reflect social organisation, the method was additionally applied to suburban badgers to derive relative badger group density (BGD) for one city (Brighton, 2.41 km-2). We demonstrate that citizen science approaches can effectively obtain data to assess suburban carnivore density, however publicly derived national data sets need to be locally validated before extrapolations can be undertaken. The method we present for assessing densities of foxes and badgers in British towns and cities is also adaptable to other urban carnivores elsewhere. However this transferability is contingent on species traits meeting particular criteria, and on resident responsiveness. [ABSTRACT FROM AUTHOR]

Background: One of the classic approaches in environmental economics is the environmental Kuznets curve, which predicts that when a national economy grows from low to medium levels, threats to biodiversity conservation increase, but they decrease when the economy moves from medium to high. We evaluated this approach by examining how population densities of the brown bear (Ursus arctos), gray wolf (Canis lupus), and Eurasian lynx (Lynx lynx) were related to the national economy in 24 European countries. Methodology/Principal findings: We used forest proportions, the existence of a compensation system, and country group (former socialist countries, Nordic countries, other countries) as covariates in a linear model with the first- and the second-order polynomial terms of per capita gross domestic product (GDP). Country group was treated as a random factor, but remained insignificant and was ignored. All models concerning brown bear and wolf provided evidence that population densities decreased with increasing GDP, but densities of lynx were virtually independent of GDP. Models for the wolf explained >80% of the variation in densities, without a difference between the models with all independent variables and the model with only GDP. For the bear, the model with GDP alone accounted for 10%, and all three variables 33%, of the variation in densities. Conclusions: Wolves exhibit a higher capacity for dispersal and reproduction than bear or lynx, but still exists at the lowest densities in wealthy European countries. We are aware that several other factors, not available for our models, influenced large carnivore densities. Based on the pronounced differences among large carnivore species in their countrywide relationships between densities and GDP, and a strikingly high relationship for the gray wolf, we suggest that our results reflected differences in political history and public acceptance of these species among countries. The compensation paid for the damages caused by the carnivores is not a key to higher carnivore densities, but might be necessity for the presence of large carnivores to be accepted in countries with high GDP. [ABSTRACT FROM AUTHOR]

Understanding the factors that influence the presence and distribution of carnivores in human-dominated agricultural landscapes is one of the main challenges for biodiversity conservation, especially in landscapes where setting aside large protected areas is not feasible. Habitat use models of carnivore communities in rubber plantations are lacking despite the critical roles carnivores play in structuring ecosystems and the increasing expansion of rubber plantations. We investigated the habitat use of a mammalian carnivore community within a 4,200-ha rubber plantation/forest landscape in Bahia, Brazil. We placed two different brands of camera traps in a 90-site grid. We used a multispecies occupancy model to determine the probabilities of habitat use by each species and the effect of different brands of camera traps on their detection probabilities. Species showed significant differences in habitat use with domestic dogs (Canis familiaris) and crab-eating foxes (Cerdocyon thous) having higher probabilities of using rubber groves and coatis (Nasua nasua) having a higher probability of using forest. The moderate level of captures and low detection probabilities (≤ 0.1) of tayras (Eira barbara) and wildcats (Leopardus spp.) precluded a precise estimation of habitat use probabilities using the multispecies occupancy model. The different brands of camera traps had a significant effect on the detection probability of all species. Given that the carnivore community has persisted in this 70-year-old landscape, the results show the potential of rubber/forest landscapes to provide for the long-term conservation of carnivore communities in the Atlantic forest, especially in mosaics with 30–40% forest cover and guard patrolling systems. The results also provide insights for mitigating the impact of rubber production on biodiversity. [ABSTRACT FROM AUTHOR]