Javan mongoose or small Indian mongoose–who is where?

Genetic relationships among populations of the small Indian mongoose (Urva auropunctata) introduced in Japan

The small Indian mongoose, Urva auropunctata, is one of the most notorious invasive species in the world. In Japan, the mongoose was introduced to Amami, Kyushu (Kiire region), and Okinawa Islands. Currently, an eradication program for the Amami population is proving successful. To prevent reinvasion and conserve biodiversity, it would be advantageous to investigate the origin and dispersal history of introduced mongoose populations in Japan. We determined the mitochondrial genome of a mongoose from the Okinawa population and confirmed that the systematic status of the mongoose is Urva auropunctata. We also found two haplotypes of cytochrome b in the Amami population, one of which is common among the Okinawa, Amami, and Kiire populations. Based on our microsatellite analysis, the three populations were genetically different from each other. Furthermore, with a low pairwise FST value, the Kiire population was closer to the Okinawa than the Amami population. Our results suggest that the Okinawa population could be the source of the Amami and Kiire populations. These results align with historical records of mongoose in Japan and clarify its genetic status. Our results should aid the prediction of the pathway through which a new invasion will likely occur.

Genetic structure and ecological niche segregation of Indian gray mongoose (Urva edwardsii) in Iran

Combining genetic data with ecological niche models is an effective approach for exploring climatic and nonclimatic environmental variables affecting spatial patterns of intraspecific genetic variation. Here, we adopted this combined approach to evaluate genetic structure and ecological niche of the Indian gray mongoose (Urva edwardsii) in Iran, as the most western part of the species range. Using mtDNA, we confirmed the presence of two highly differentiated clades. Then, we incorporated ensemble of small models (ESMs) using climatic and nonclimatic variables with genetic data to assess whether genetic differentiation among clades was coupled with their ecological niche. Climate niche divergence was also examined based on a principal component analysis on climatic factors only. The relative habitat suitability values predicted by the ESMs for both clades revealed their niche separation. Between-clade climate only niche comparison revealed that climate space occupied by clades is similar to some extent, but the niches that they utilize differ between the distribution ranges of clades. We found that in the absence of evidence for recent genetic exchanges, distribution models suggest the species occurs in different niches and that there are apparent areas of disconnection across the species range. The estimated divergence time between the two Iranian clades (4.9 Mya) coincides with the uplifting of the Zagros Mountains during the Early Pliocene. The Zagros mountain-building event seems to have prevented the distribution of U. edwardsii populations between the western and eastern parts of the mountains as a result of vicariance events. Our findings indicated that the two U. edwardsii genetic clades in Iran can be considered as two conservation units and can be utilized to develop habitat-specific and climate change-integrated management strategies.

First Report on Detection and Molecular Characterization of Adenoviruses in the Small Indian Mongoose (Urva auropunctata)

Using a broad-range nested PCR assay targeting the DNA-dependent DNA polymerase (pol) gene, we detected adenoviruses in 17 (20.48%) out of 83 fecal samples from small Indian mongooses (Urva auropunctata) on the Caribbean island of St. Kitts. All 17 PCR amplicons were sequenced for the partial pol gene (~300 bp, hereafter referred to as Mon sequences). Fourteen of the 17 Mon sequences shared maximum homology (98.3-99.6% and 97-98.9% nucleotide (nt) and deduced amino acid (aa) sequence identities, respectively) with that of bovine adenovirus-6 (species Bovine atadenovirus E). Mongoose-associated adenovirus Mon-39 was most closely related (absolute nt and deduced aa identities) to an atadenovirus from a tropical screech owl. Mon-66 shared maximum nt and deduced aa identities of 69% and 71.4% with those of atadenoviruses from a spur-thighed tortoise and a brown anole lizard, respectively. Phylogenetically, Mon-39 and Mon-66 clustered within clades that were predominated by atadenoviruses from reptiles, indicating a reptilian origin of these viruses. Only a single mongoose-associated adenovirus, Mon-34, was related to the genus Mastadenovirus. However, phylogenetically, Mon-34 formed an isolated branch, distinct from other mastadenoviruses. Since the fecal samples were collected from apparently healthy mongooses, we could not determine whether the mongoose-associated adenoviruses infected the host. On the other hand, the phylogenetic clustering patterns of the mongoose-associated atadenoviruses pointed more towards a dietary origin of these viruses. Although the present study was based on partial pol sequences (~90 aa), sequence identities and phylogenetic analysis suggested that Mon-34, Mon-39, and Mon-66 might represent novel adenoviruses. To our knowledge, this is the first report on the detection and molecular characterization of adenoviruses from the mongoose.

Detection and Complete Genome Analysis of Circoviruses and Cycloviruses in the Small Indian Mongoose (Urva auropunctata): Identification of Novel Species

Fecal samples from 76 of 83 apparently healthy small Indian mongooses (Urva auropunctata) were PCR positive with circovirus/cyclovirus pan-rep (replicase gene) primers. In this case, 30 samples yielded high quality partial rep sequences (~400 bp), of which 26 sequences shared maximum homology with cycloviruses from an arthropod, bats, humans or a sheep. Three sequences exhibited maximum identities with a bat circovirus, whilst a single sequence could not be assigned to either genus. Using inverse nested PCRs, the complete genomes of mongoose associated circoviruses (Mon-1, -29 and -66) and cycloviruses (Mon-20, -24, -32, -58, -60 and -62) were determined. Mon-1, -20, -24, -29, -32 and -66 shared <80% maximum genome-wide pairwise nucleotide sequence identities with circoviruses/cycloviruses from other animals/sources, and were assigned to novel circovirus, or cyclovirus species. Mon-58, -60 and -62 shared maximum pairwise identities of 79.90–80.20% with human and bat cycloviruses, which were borderline to the cut-off identity value for assigning novel cycloviral species. Despite high genetic diversity, the mongoose associated circoviruses/cycloviruses retained the various features that are conserved among members of the family Circoviridae, such as presence of the putative origin of replication (ori) in the 5′-intergenic region, conserved motifs in the putative replication-associated protein and an arginine rich region in the amino terminus of the putative capsid protein. Since only fecal samples were tested, and mongooses are polyphagous predators, we could not determine whether the mongoose associated circoviruses/cycloviruses were of dietary origin, or actually infected the host. To our knowledge, this is the first report on detection and complete genome analysis of circoviruses/cycloviruses in the small Indian mongoose, warranting further studies in other species of mongooses.

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 21 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

The globally invasive small Indian mongoose Urva auropunctata is likely to spread with climate change

Invasive alien species represent one of the major factors of global loss of biodiversity and disruption of natural ecosystems. The small Indian mongoose, Urva auropunctata, is considered one of the wild carnivore species with the greatest negative impact on global biodiversity. Understanding of the factors underpinning the species' distribution and potential dispersion in a context of climate change thus appears crucial in the conservation of native ecosystems. Here we modelled the current and future climatically favourable areas for the small Indian mongoose using Ecological Niche Modelling based on data sets filtrated in environmental spaces. Projections from these models show extensive current favourable geographical areas, covering continental and insular regions within tropical and sub-tropical latitudes. Moreover, predictions for 2050 reveal that climate change is likely to expand current favourable areas north of the current favourable spaces, particularly in Eastern Europe. This climate-induced expansion is particularly worrisome given that the species is already spreading in the Balkan region. Our projections suggest that it is very likely that the small Indian mongoose will have an increasing influence on ecosystems and biodiversity in Europe by 2050.

Detection and Molecular Characterization of Picobirnaviruses (PBVs) in the Mongoose: Identification of a Novel PBV Using an Alternative Genetic Code

We report high rates of detection (35.36%, 29/82) of genogroup-I (GI) picobirnaviruses (PBVs) in non-diarrheic fecal samples from the small Indian mongoose (Urva auropunctata). In addition, we identified a novel PBV-like RNA-dependent RNA polymerase (RdRp) gene sequence that uses an alternative mitochondrial genetic code (that of mold or invertebrate) for translation. The complete/nearly complete gene segment-2/RdRp gene sequences of seven mongoose PBV GI strains and the novel PBV-like strain were obtained by combining a modified non-specific primer-based amplification method with conventional RT-PCRs, facilitated by the inclusion of a new primer targeting the 3′-untranslated region (UTR) of PBV gene segment-2. The mongoose PBV and PBV-like strains retained the various features that are conserved in gene segment-2/RdRps of other PBVs. However, high genetic diversity was observed among the mongoose PBVs within and between host species. This is the first report on detection of PBVs in the mongoose. Molecular characterization of the PBV and PBV-like strains from a new animal species provided important insights into the various features and complex diversity of PBV gene segment-2/putative RdRps. The presence of the prokaryotic ribosomal binding site in the mongoose PBV genomes, and analysis of the novel PBV-like RdRp gene sequence that uses an alternative mitochondrial genetic code (especially that of mold) for translation corroborated recent speculations that PBVs may actually infect prokaryotic or fungal host cells.