Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus.

Even in the genomics era, the phylogeny of Neotropical small felids comprised in the genus Leopardus remains contentious. We used whole-genome resequencing data to construct a time-calibrated consensus phylogeny of this group, quantify phylogenomic discordance, test for interspecies introgression, and assess patterns of genetic diversity and demographic history. We infer that the Leopardus radiation started in the Early Pliocene as an initial speciation burst, followed by another in its subgenus Oncifelis during the Early Pleistocene. Our findings challenge the long-held notion that ocelot (Leopardus pardalis) and margay (L. wiedii) are sister species and instead indicate that margay is most closely related to the enigmatic Andean cat (L. jacobita), whose whole-genome data are reported here for the first time. In addition, we found that the newly sampled Andean tiger cat (L. tigrinus pardinoides) population from Colombia associates closely with Central American tiger cats (L. tigrinus oncilla). Genealogical discordance was largely attributable to incomplete lineage sorting, yet was augmented by strong gene flow between ocelot and the ancestral branch of Oncifelis, as well as between Geoffroy's cat (L. geoffroyi) and southern tiger cat (L. guttulus). Contrasting demographic trajectories have led to disparate levels of current genomic diversity, with a nearly tenfold difference in heterozygosity between Andean cat and ocelot, spanning the entire range of variability found in extant felids. Our analyses improved our understanding of the speciation history and diversity patterns in this felid radiation, and highlight the benefits to phylogenomic inference of embracing the many heterogeneous signals scattered across the genome.

Positive selection in gamete interaction proteins in Carnivora.

The absence of robust interspecific isolation barriers among pantherines, including the iconic South American jaguar (Panthera onca), led us to study molecular evolution of typically rapidly evolving reproductive proteins within this subfamily and related groups. In this study, we delved into the evolutionary forces acting on the zona pellucida (ZP) gamete interaction protein family and the sperm-oocyte fusion protein pair IZUMO1-JUNO across the Carnivora order, distinguishing between Caniformia and Feliformia suborders and anticipating few significant diversifying changes in the Pantherinae subfamily. A chromosome-resolved jaguar genome assembly facilitated coding sequences, enabling the reconstruction of protein evolutionary histories. Examining sequence variability across more than 30 Carnivora species revealed that Feliformia exhibited significantly lower diversity compared to its sister taxa, Caniformia. Molecular evolution analyses of ZP2 and ZP3, subunits directly involved in sperm-recognition, unveiled diversifying positive selection in Feliformia, Caniformia and Pantherinae, although no significant changes were linked to sperm binding. Structural cross-linking ZP subunits, ZP4 and ZP1 exhibited lower levels or complete absence of positive selection. Notably, the fusion protein IZUMO1 displayed prominent positive selection signatures and sites in basal lineages of both Caniformia and Feliformia, extending along the Caniformia subtree but absent in Pantherinae. Conversely, JUNO did not exhibit any positive selection signatures across tested lineages and clades. Eight Caniformia-specific positive selected sites in IZUMO1 were detected within two JUNO-interaction clusters. Our findings provide for the first time insights into the evolutionary trajectories of ZP proteins and the IZUMO1-JUNO gamete interaction pair within the Carnivora order.

Running, jumping, hunting, and scavenging: Functional analysis of vertebral mobility and backbone properties in carnivorans.

Carnivorans are well-known for their exceptional backbone mobility, which enables them to excel in fast running and long jumping, leading to them being among the most successful predators amongst terrestrial mammals. This study presents the first large-scale analysis of mobility throughout the presacral region of the vertebral column in carnivorans. The study covers representatives of 6 families, 24 genera and 34 species. We utilized a previously developed osteometry-based method to calculate available range of motion, quantifying all three directions of intervertebral mobility: sagittal bending (SB), lateral bending (LB), and axial rotation (AR). We observed a strong phylogenetic signal in the structural basis of the vertebral column (vertebral and joint formulae, length proportions of the backbone modules) and an insignificant phylogenetic signal in most characteristics of intervertebral mobility. This indicates that within the existing structure (stabilization of which occurred rather early in different phylogenetic lineages), intervertebral mobility in carnivorans is quite flexible. Our findings reveal that hyenas and canids, which use their jaws to seize prey, are characterized by a noticeably elongated cervical region and significantly higher SB and LB mobility of the cervical joints compared to other carnivorans. In representatives of other carnivoran families, the cervical region is very short, but the flexibility of the neck (both SB and LB) is significantly higher than that of short-necked odd-toed and even-toed ungulates. The lumbar region of the backbone in carnivorans is dorsomobile in the sagittal plane, being on average ~23° more mobile than in artiodactyls and ~38° more mobile than in perissodactyls. However, despite the general dorsomobility, only some representatives of Canidae, Felidae, and Viverridae are superior in lumbar flexibility to the most dorsomobile ungulates. The most dorsomobile artiodactyls are equal or even superior to carnivorans in their ability to engage in dorsal extension during galloping. In contrast, carnivorans are far superior to ungulates in their ability to engage ventral flexion. The cumulative SB in the lumbar region in carnivorans largely depends on the mode of running and hunting. Thus, adaptation to prolonged and enduring pursuit of prey in hyenas is accompanied by markedly reduced SB flexibility in the lumbar region. A more dorsostable run is also a characteristic of the Ursidae, and the peculiar maned wolf. Representatives of Felidae and Canidae have significantly more available SB mobility in the lumbar region. However, they fully engage it only occasionally at key moments of the hunt associated with the direct capture of the prey or when running in a straight line at maximum speed.

Alteration of the gut microbial composition of critically endangered Malayan tigers (Panthera tigris jacksoni) in captivity during enrichment phase.

BACKGROUND: Enrichment activities may influence the microbiomes of captive tigers', affecting their health, digestion, and behavior. Currently, there are few studies that address the impact of enrichment activity on tigers' health. This study aimed to determine the diversity of the gut microbiome in captive Malayan tigers at Zoo Melaka and Night Safari during the environmental enrichment phase using a metabarcoding approach. METHODS AND RESULTS: This study utilized different enrichment activities which catered for food, sensory, and cognitive enrichment. Eleven fresh fecal samples from captive Malayan tigers at Zoo Melaka and Night Safari were collected under different conditions. All samples were extracted and 16S rRNA V3-V4 region amplicon sequencing was used to characterize the gut microbiome of captive Malayan tigers subjected to various enrichment activities. Firmicutes, Actinobacteriota, and Fusobacteriota were the dominant phyla observed in the gut microbiome of captive Malayan tigers during enrichment activities. This study revealed ß-diversity significantly varied between normal and enrichment phase, however no significant differences were observed in α-diversity. This study demonstrates that environmental enrichment improves the gut microbiome of Malayan tigers because gut microbes such as Lachnoclostridium, which has anti-inflammatory effects and helps maintain homeostasis, and Romboutsia, which has a probiotic effect on the gut microbiome. CONCLUSIONS: This study provides valuable insights into the effects of enrichment activities on the gut microbiome of captive Malayan tigers, offering guidance for enhancing captive management practices aimed at promoting the health and well-being of Malayan tiger in captivity.

Neuropil Variation in the Prefrontal, Motor, and Visual Cortex of Six Felids.

INTRODUCTION: Felids have evolved a specialized suite of morphological adaptations for obligate carnivory. Although the musculoskeletal anatomy of the Felidae has been studied extensively, the comparative neuroanatomy of felids is relatively unexplored. Little is known about how variation in the cerebral anatomy of felids relates to species-specific differences in sociality, hunting strategy, or activity patterns. METHODS: We quantitatively analyzed neuropil variation in the prefrontal, primary motor, and primary visual cortices of six species of Felidae (Panthera leo, Panthera uncia, Panthera tigris, Panthera leopardus, Acinonyx jubatus, Felis sylvestris domesticus) to investigate relationships with brain size, neuronal cell parameters, and select behavioral and ecological factors. Neuropil is the dense, intricate network of axons, dendrites, and synapses in the brain, playing a critical role in information processing and communication between neurons. RESULTS: There were significant species and regional differences in neuropil proportions, with African lion, cheetah, and tiger having more neuropil in all three cortical regions in comparison to the other species. Based on regression analyses, we find that the increased neuropil fraction in the prefrontal cortex supports social and behavioral flexibility, while in the primary motor cortex, this facilitates the neural activity needed for hunting movements. Greater neuropil fraction in the primary visual cortex may contribute to visual requirements associated with diel activity patterns. CONCLUSION: These results provide a cross-species comparison of neuropil fraction variation in the Felidae, particularly the understudied Panthera, and provide evidence for convergence of the neuroanatomy of Panthera and cheetahs.

Confidence intervals in molecular dating by maximum likelihood.

Molecular dating has been widely used to infer the times of past evolutionary events using molecular sequences. This paper describes three bootstrap methods to infer confidence intervals under a penalized likelihood framework. The basic idea is to use data pseudoreplicates to infer uncertainty in the branch lengths of a phylogeny reconstructed with molecular sequences. The three specific bootstrap methods are nonparametric (direct tree bootstrapping), semiparametric (rate smoothing), and parametric (Poisson simulation). Our extensive simulation study showed that the three methods perform generally well under a simple strict clock model of molecular evolution; however, the results were less positive with data simulated using an uncorrelated or a correlated relaxed clock model. Several factors impacted, possibly in interaction, the performance of the confidence intervals. Increasing the number of calibration points had a positive effect, as well as increasing the sequence length or the number of sequences although both latter effects depended on the model of evolution. A case study is presented with a molecular phylogeny of the Felidae (Mammalia: Carnivora). A comparison was made with a Bayesian analysis: the results were very close in terms of confidence intervals and there was no marked tendency for an approach to produce younger or older bounds compared to the other.

A new large pantherine and a sabre-toothed cat (Mammalia, Carnivora, Felidae) from the late Miocene hominoid-bearing Khorat sand pits, Nakhon Ratchasima Province, northeastern Thailand.

We describe two large predators from the hominoid-bearing Khorat sand pits, Nakhon Ratchasima Province, northeastern Thailand: a new genus of pantherine, Pachypanthera n. gen., represented by partial mandible and maxilla and an indeterminate sabre-toothed cat, represented by a fragment of upper canine. The morphological characters of Pachypanthera n. gen., notably the large and powerful canine, the great robustness of the mandibular body, the very deep fossa for the m. masseter, the zigzag HSB enamel pattern, indicate bone-cracking capacities. The genus is unique among Felidae as it has one of the most powerful and robust mandibles ever found. Moreover, it may be the oldest known pantherine, as other Asian pantherines are dated back to the early Pliocene. The taxa we report here are the only carnivorans known from the late Miocene of Thailand. Although the material is rather scarce, it brings new insights to the evolutionary history of Neogene mammals of Southeast Asia, in a geographic place which is partly "terra incognita."

A chromosome-scale high-contiguity genome assembly of the cheetah (Acinonyx jubatus).

The cheetah (Acinonyx jubatus, SCHREBER 1775) is a large felid and is considered the fastest land animal. Historically, it inhabited open grassland across Africa, the Arabian Peninsula, and southwestern Asia; however, only small and fragmented populations remain today. Here, we present a de novo genome assembly of the cheetah based on PacBio continuous long reads and Hi-C proximity ligation data. The final assembly (VMU_Ajub_asm_v1.0) has a total length of 2.38 Gb, of which 99.7% are anchored into the expected 19 chromosome-scale scaffolds. The contig and scaffold N50 values of 96.8 Mb and 144.4 Mb, respectively, a BUSCO completeness of 95.4% and a k-mer completeness of 98.4%, emphasize the high quality of the assembly. Furthermore, annotation of the assembly identified 23,622 genes and a repeat content of 40.4%. This new highly contiguous and chromosome-scale assembly will greatly benefit conservation and evolutionary genomic analyses and will be a valuable resource, e.g., to gain a detailed understanding of the function and diversity of immune response genes in felids.

Demodex murilegi and Demodex obliquus, two new specific skin mites from domestic cat Felis catus, with notes on parasitism.

The Demodecidae are skin and tissue parasites of mammals with high host, topical, and topographic specificity. They may cause a demodecosis, typically observed in pets and humans. Numerous mammal species have been found to have several, specific demodecids, which inhabit different microhabitats. Thus far, two species have been known from the domestic cat, namely Demodex cati Megnin, 1877 (Acariformes: Demodecidae) and D. gatoi Desch and Stewart, 1999; however, there have been indications for the presence of other demodecid mites in this host. Presently, two other species are described, D. murilegi sp. nov. associated primarily with the skin from the area of lips and nose, and D. obliquus sp. nov. associated with the skin of the lower part of the limb. They exhibit morphological discreteness in terms of qualitative traits significant for Demodecidae taxonomy. Demodex murilegi sp. nov. is larger than both known species, and D. obliquus sp. nov. is intermediate in length between them. It is likely that infection with different Demodex species may result in variable symptoms and courses of demodecosis; however, a correct identification of the species causing the parasitosis is needed to confirm this. Thus, the present study compares the taxonomic traits of four cat demodecid mites.

Many-to-one function of cat-like mandibles highlights a continuum of sabre-tooth adaptations.

Cat-like carnivorans are a textbook example of convergent evolution, with distinct morphological differences between taxa with short or elongated upper canines, the latter often being interpreted as an adaptation to bite at large angles and subdue large prey. This interpretation of the sabre-tooth condition is reinforced by a reduced taxonomic sampling in some studies, often focusing on highly derived taxa or using simplified morphological models. Moreover, most biomechanical analyses focus on biting scenarios at small gapes, ideal for modern carnivora but ill-suited to test for subduction of large prey by sabre-toothed taxa. In this contribution, we present the largest three-dimensional collection-based muscle-induced biting simulations on cat-like carnivorans by running a total of 1074 analyses on 17 different taxa at three different biting angles (30°, 60° and 90°) including both morphologies. While our results show a clear adaptation of extreme sabre-toothed taxa to bite at larger angles in terms of stress distribution, other performance variables display surprising similarities between all forms at the different angles tested, highlighting a continuous rather than bipolar spectrum of hunting methods in cat-like carnivorans and demonstrating a wide functional disparity and nuances of the sabre-tooth condition that cannot simply be characterized by specialized feeding biomechanics.

Muscular anatomy of the forelimb of tiger (Panthera tigris).

Dissection reports of large cats (family Felidae) have been published since the late 19th century. These reports generally describe the findings in words, show drawings of the dissection, and usually include some masses of muscles, but often neglect to provide muscle maps showing the precise location of bony origins and insertions. Although these early reports can be highly useful, the absence of visual depictions of muscle attachment sites makes it difficult to compare muscle origins and insertions in living taxa and especially to reconstruct muscle attachments in fossil taxa. Recently, more muscle maps have been published in the primary literature, but those for large cats are still limited. Here, we describe the muscular anatomy of the forelimb of the tiger (Panthera tigris), and compare muscle origins, insertions, and relative muscle masses to other felids to identify differences that may reflect functional adaptations. Our results reiterate the conservative nature of felid anatomy across body sizes and behavioral categories. We find that pantherines have relatively smaller shoulder muscle masses, and relatively larger muscles of the caudal brachium, pronators, and supinators than felines. The muscular anatomy of the tiger shows several modifications that may reflect an adaptation to terrestrial locomotion and a preference for large prey. These include in general a relatively large m. supraspinatus (shoulder flexion), an expanded origin for m. triceps brachii caput longum, and relatively large m. triceps brachii caput laterale (elbow extension), as well as relatively large mm. brachioradialis, abductor digiti I longus, and abductor digiti V. Muscle groups that are well developed in scansorial taxa are not well developed in the tiger, including muscles of the cranial compartment of the brachium and antebrachium, and m. anconeus. Overall, the musculature of the tiger strongly resembles that of the lion (Panthera leo), another large-bodied terrestrial large-prey specialist.

A Reference Genome Assembly of the Bobcat, Lynx rufus.

The bobcat (Lynx rufus) is a medium-sized carnivore well adapted to various environments and an indicator species for landscape connectivity. It is one of the 4 species within the extant Lynx genus in the family Felidae. Because of its broad geographic distribution and central role in food webs, the bobcat is important for conservation. Here we present a high-quality de novo genome assembly of a male bobcat located in Mendocino County, CA, as part of the California Conservation Genomics Project (CCGP). The assembly was generated using the standard CCGP pipeline from a combination of Omni-C and HiFi technologies. The primary assembly comprises 76 scaffolds spanning 2.4 Gb, represented by a scaffold N50 of 142 Mb, a contig N50 of 66.2 Mb, and a BUSCO completeness score of 95.90%. The bobcat genome will be an important resource for the effective management and conservation of this species and comparative genomics exploration.

Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis).

In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the offspring of a domestic cat (Felis catus) x Asian leopard cat (Prionailurus bengalensis) cross, with PacBio long sequence reads and used Illumina sequence reads from the parents to phase >99.9% of the reads into the 2 species' haplotypes. De novo assembly of the phased reads produced highly continuous haploid genome assemblies for the domestic cat and Asian leopard cat, with contig N50 statistics exceeding 83 Mb for both genomes. Whole-genome alignments reveal the Felis and Prionailurus genomes are colinear, and the cytogenetic differences between the homologous F1 and E4 chromosomes represent a case of centromere repositioning in the absence of a chromosomal inversion. Both assemblies offer significant improvements over the previous domestic cat reference genome, with a 100% increase in contiguity and the capture of the vast majority of chromosome arms in 1 or 2 large contigs. We further demonstrated that comparably accurate F1 haplotype phasing can be achieved with members of the same species when one or both parents of the trio are not available. These novel genome resources will empower studies of feline precision medicine, adaptation, and speciation.

Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi.

The Puma lineage within the family Felidae consists of 3 species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of 2 species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome sequence. The assembled genome contains a series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of cheetah and puma, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. We assessed the assembled sequence of the jaguarundi genome using BUSCO, aligned reads of the sequenced individual and another published female jaguarundi to the assembled genome, annotated protein-coding genes, repeats, genomic variants and their effects with respect to the protein-coding genes, and analyzed differences of the 2 jaguarundis from the reference mitochondrial genome. The jaguarundi genome assembly and its annotation were compared in quality, variants, and features to the previously reported genome assemblies of puma and cheetah. Computational analyzes used in the study were implemented in transparent and reproducible way to allow their further reuse and modification.

Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species.

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of postspeciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here, we tested the validity of this assumption with a phylogenomic analysis of 27 species of the cat family, assessing local effects of recombination rate on species tree inference and divergence time estimation across their genomes. We found that the prevailing phylogenetic signal within the autosomes is not always representative of the most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within regions of low recombination, and notably enriched within large X chromosome recombination cold spots that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ∼40%. We conclude that existing phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic architecture of phylogenetic signal relative to recombination rate and its interplay with historical hybridization.

Savannah roars: The vocal anatomy and the impressive rutting calls of male impala (Aepyceros melampus) - highlighting the acoustic correlates of a mobile larynx.

A retractable larynx and adaptations of the vocal folds in the males of several polygynous ruminants serve for the production of rutting calls that acoustically announce larger than actual body size to both rival males and potential female mates. Here, such features of the vocal tract and of the sound source are documented in another species. We investigated the vocal anatomy and laryngeal mobility including its acoustical effects during the rutting vocal display of free-ranging male impala (Aepyceros melampus melampus) in Namibia. Male impala produced bouts of rutting calls (consisting of oral roars and interspersed explosive nasal snorts) in a low-stretch posture while guarding a rutting territory or harem. For the duration of the roars, male impala retracted the larynx from its high resting position to a low mid-neck position involving an extensible pharynx and a resilient connection between the hyoid apparatus and the larynx. Maximal larynx retraction was 108 mm based on estimates in video single frames. This was in good concordance with 91-mm vocal tract elongation calculated on the basis of differences in formant dispersion between roar portions produced with the larynx still ascended and those produced with maximally retracted larynx. Judged by their morphological traits, the larynx-retracting muscles of male impala are homologous to those of other larynx-retracting ruminants. In contrast, the large and massive vocal keels are evolutionary novelties arising by fusion and linear arrangement of the arytenoid cartilage and the canonical vocal fold. These bulky and histologically complex vocal keels produced a low fundamental frequency of 50 Hz. Impala is another ruminant species in which the males are capable of larynx retraction. In addition, male impala vocal folds are spectacularly specialized compared with domestic bovids, allowing the production of impressive, low-frequency roaring vocalizations as a significant part of their rutting behaviour. Our study expands knowledge on the evolutionary variation of vocal fold morphology in mammals, suggesting that the structure of the mammalian sound source is not always human-like and should be considered in acoustic analysis and modelling.

Chemical structures of oligosaccharides in milks of the American black bear (Ursus americanus americanus) and cheetah (Acinonyx jubatus).

The milk oligosaccharides were studied for two species of the Carnivora: the American black bear (Ursus americanus, family Ursidae, Caniformia), and the cheetah, (Acinonyx jubatus, family Felidae, Feliformia). Lactose was the most dominant saccharide in cheetah milk, while this was a minor saccharide and milk oligosaccharides predominated over lactose in American black bear milk. The structures of 8 neutral saccharides from American black bear milk were found to be Gal(ß1-4)Glc (lactose), Fuc(α1-2)Gal(ß1-4)Glc (2'-fucosyllactose), Gal(α1-3)Gal(ß1-4)Glc (isoglobotriose), Gal(α1-3)[Fuc(α1-2)]Gal(ß1-4)Glc (B-tetrasaccharide), Gal(α1-3)[Fuc(α1-2)]Gal(ß1-4)[Fuc(α1-3)]Glc (B-pentasaccharide), Fuc(α1-2)Gal(ß1-4)[Fuc(α1-3)]GlcNAc(ß1-3)Gal(ß1-4)Glc (difucosyl lacto-N-neotetraose), Gal(α1-3)Gal(ß1-4)[Fuc(α1-3)]GlcNAc(ß1-3)Gal(ß1-4)Glc (monogalactosyl monofucosyl lacto-N-neotetraose) and Gal(α1-3)Gal(ß1-4)GlcNAc(ß1-3)Gal(ß1-4)Glc (Galili pentasaccharide). Structures of 5 acidic saccharides were also identified in black bear milk: Neu5Ac(α2-3)Gal(ß1-4)Glc (3'-sialyllactose), Neu5Ac(α2-6)Gal(ß1-4)GlcNAc(ß1-3)[Fuc(α1-2)Gal(ß1-4)GlcNAc(ß1-6)]Gal(ß1-4)Glc (monosialyl monofucosyl lacto-N-neohexaose), Neu5Ac(α2-6)Gal(ß1-4)GlcNAc(ß1-3)[Gal(α1-3)Gal(ß1-4)GlcNAc(ß1-6)]Gal(ß1-4)Glc (monosialyl monogalactosyl lacto-N-neohexaose), Neu5Ac(α2-6)Gal(ß1-4)GlcNAc(ß1-3){Gal(α1-3)Gal(ß1-4)[Fuc(α1-3)]GlcNAc(ß1-6)}Gal(ß1-4)Glc (monosialyl monogalactosyl monofucosyl lacto-N-neohexaose), and Neu5Ac(α2-6)Gal(ß1-4)GlcNAc(ß1-3){Gal(α1-3)[Fuc(α1-2)]Gal(ß1-4)[Fuc(α1-3)]GlcNAc(ß1-6)}Gal(ß1-4)Glc (monosialyl monogalactosyl difucosyl lacto-N-neohexaose). A notable feature of some of these milk oligosaccharides is the presence of B-antigen (Gal(α1-3)[Fuc(α1-2)]Gal), α-Gal epitope (Gal(α1-3)Gal(ß1-4)Glc(NAc)) and Lewis x (Gal(ß1-4)[Fuc(α1-3)]GlcNAc) structures within oligosaccharides. By comparison to American black bear milk, cheetah milk had a much smaller array of oligosaccharides. Two cheetah milks contained Gal(α1-3)Gal(ß1-4)Glc (isoglobotriose), while another cheetah milk did not, but contained Gal(ß1-6)Gal(ß1-4)Glc (6'-galactosyllactose) and Gal(ß1-3)Gal(ß1-4)Glc (3'-galactosyllactose). Two cheetah milks contained Gal(ß1-4)GlcNAc(ß1-3)[Gal(ß1-4)GlcNAc(ß1-6)]Gal(ß1-4)Glc (lacto-N-neohexaose), and one cheetah milk contained Gal(ß1-4)Glc-3'-O-sulfate. Neu5Ac(α2-8)Neu5Ac(α2-3)Gal(ß1-4)Glc (disialyllactose) was the only sialyl oligosaccharide identified in cheetah milk. The heterogeneity of milk oligosaccharides was found between both species with respect of the presence/absence of B-antigen and Lewis x. The variety of milk oligosaccharides was much greater in the American black bear than in the cheetah. The ratio of milk oligosaccharides-to-lactose was lower in cheetah (1:1-1:2) than American black bear (21:1) which is likely a reflection of the requirement for a dietary supply of N-acetyl neuraminic acid (sialic acid), in altricial ursids compared to more precocial felids, given the role of these oligosaccharides in the synthesis of brain gangliosides and the polysialic chains on neural cell adhesion.

A novel understanding of global DNA methylation in bobcat (Lynx rufus).

Epigenetic mechanisms may provide a novel prospective of bobcat (Lynx rufus) adaptation to habitat loss/fragmentation. Previous research has focused on bobcat behavior and genetics, but epigenetics has not been studied in bobcat. The aim of this study was to determine the quantity of global DNA methylation in the liver of 30 bobcats. DNA was extracted from liver samples obtained from the Vermont Fish and Wildlife Department. The percent of global DNA methylation was quantified and calculated using the MethylFlashTM Methylated DNA 5-mC Quantification Kit from Epigentek (Farmingdale, NY, USA). Age, sex, and carcass weight data were collected at sampling and analyzed with percent of global DNA methylation. Global DNA methylation was found to range from 0.46% to 2.76%. Age ranged from <1 to 12 years old and weight ranged from 3.18 to 13.61 kg. Further analysis of differential methylation may provide insight into novel means of bobcat conservation within different regions of Vermont. These results reinforce the need for genome-wide epigenetic studies in conservation biology.

Environmental management of two of the world's most endangered marine and terrestrial predators: Vaquita and cheetah.

Two of the world most endangered marine and terrestrial species are at the brink of extinction. The vaquita (Phocoena sinus) is the smallest existing cetacean and the population has declined to barely 22 individuals now remaining in Mexico's Gulf of California. With the ongoing decline, it is likely to go extinct within few years. The primary threat to this species has been mortality as a result of by-catch from gillnet fishing as well as environmental toxic chemicals and disturbance. This has called for the need to establish a National Park within the Gulf of California to expand essential habitat and provide the critical ecosystem protection for vaquita to thrive and multiply, given that proper conservation enforcement and management of the park are accomplished. In the terrestrial environment, the cheetah (Acinonyx jubatus) is reduced to a low number worldwide with the Iran subpopulation currently listed as Critically Endangered and the Indian subpopulation already extinct. There is a need for conservation efforts due to habitat loss, but also an indication of the conspicuous threat of illegal trade and trafficking from Africa and Arab countries in the Middle East. Funds have also been set up to provide refuges for the cheetah by working directly with farmers and landowners, which is a critical movement in adaptive management. These are the potential options for the preservation and possibly the expansion of the overall vaquita and cheetah populations.

Feline Morbillivirus Infection Associated With Tubulointerstitial Nephritis in Black Leopards (Panthera pardus).

Feline morbillivirus (FeMV) is an emerging RNA virus in the Paramyxoviridae family that was recently discovered in domestic cats (Felis catus). To date, 2 genotypes (FeMV-1 and FeMV-2) have been detected in cats from various countries, and FeMV-1 is recognized as a pathogen associated with nephritis. However, information regarding the pathological roles and potential transmission to other felids is limited. In this article, we describe the identification of FeMV in 2 black leopards (Panthera pardus) in Thailand that showed severe azotemia and tubulointerstitial nephritis. Molecular analysis of the partial coding sequence of the L gene revealed that these leopard FeMV strains were genetically close to the FeMV-1 isolate from domestic Thai cats. Immunohistochemistry and immunofluorescence analyses using polyclonal IgG antibodies against the FeMV matrix (M) protein showed FeMV-M antigen in renal tubular epithelial cells. These analyses also showed infiltrating lymphocytes in the renal parenchymal lesions and in the cytoplasm of lymphoid cells residing in the spleen, suggesting viral tropism and a possible pathological role. These findings are the first evidence that indicates that the black leopard could be a possible host for FeMV infection. As for other cats, the role of FeMV as a potential cause of renal disease remains to be established. The pathogenesis of FeMV infection in black leopards, or in other wild felids, through a viral transmission mechanism warrants further investigation.