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Fig. 7 in Lesions associated with Eucoleus sp. in the non-glandular stomach of wild urban rats (Rattus norvegicus)

Fig. 7. Spatial distribution of Norway rats (Rattus norvegicus) infected with Eucoleus sp. and/or with associated stomach pathology in the Downtown Eastside of Vancouver, Canada. There are no clusters of affected rats.

Fig. 6 in Lesions associated with Eucoleus sp. in the non-glandular stomach of wild urban rats (Rattus norvegicus)

Fig. 6. Eucoleus sp. egg collected from a female worm embedded in the non-glandular stomach mucosa of a wild, Norway rat (Rattus norvegicus). (A) Photomicrogaph of an egg taken with correct focus (B) Photomicrogaph of the same egg as in A, but taken in an elevated focus targeting the egg shell. Note the dense network of anastomosing ridges.

Fig. 4 in Lesions associated with Eucoleus sp. in the non-glandular stomach of wild urban rats (Rattus norvegicus)

Fig. 4. Female Eucoleus sp. embedded in the mucosa of non-glandular stomach of a wild, Norway rat (Rattus norvegicus). Black arrows point to the meandering nematode. Red arrows points to eggs in uterus. Blue lines indicate the width (~60 µm) of the nematode at various positions. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 5 in Lesions associated with Eucoleus sp. in the non-glandular stomach of wild urban rats (Rattus norvegicus)

Fig. 5. Tail of a male Eucoleus sp. collected from the non-glandular stomach mucosa of a wild, Norway rat (Rattus norvegicus). Note the slender long moderately sclerotized spicule (black arrow) with cuticular spine covered spicular sheath (red arrow). Blue arrow points to posteriorly directed two minute lobes of the rudimentary pseudo bursa. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2 in Lesions associated with Eucoleus sp. in the non-glandular stomach of wild urban rats (Rattus norvegicus)

Fig. 2. Cross-sections of Eucoleus sp. adults (arrows) and eggs (arrowheads) within the keratin and superficial mucosa of the esophagus in a wild Norway rat (Rattus norvegicus). Scale bar = 100 µm.

Fig. 3 in Lesions associated with Eucoleus sp. in the non-glandular stomach of wild urban rats (Rattus norvegicus)

Fig. 3. Eucoleus sp. eggs (arrow) embedded within hyperkeratosis (A) in the nonglandular stomach of a wild, Norway rat (Rattus norvegicus). There is mucosal hyperplasia (B) and subcutaneous granulocytic inflammation (‡). Scale bar = 100 µm.

Fig. 1 in Lesions associated with Eucoleus sp. in the non-glandular stomach of wild urban rats (Rattus norvegicus)

Fig. 1. Squamous papilloma (arrow) arising from the non-glandular stomach of a wild Norway rat (Rattus norvegicus) from Vancouver, Canada. Asterisk (‡) indicates the unaffected glandular stomach. Scale bar = 1 cm.

opencc-zeroDec 2017View details →

Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities

Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15,000 genome-wide SNPs. Levels of genome-wide diversity were similar across cities, but varied across neighborhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (< 500 m) due to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.

opencc-zeroOct 2022View details →

Comparative phylogeography of two commensal rat species (Rattus tanezumi and R. norvegicus) in China: Insights from mitochondiral DNA, microsatellite and RADseq

Rattus norvegicus and Rattus tanezumi are dominant species of Chinese house rats, but the colonization and demographic history of two species in China have not been thoroughly explored. Phylogenetic analyses with mitochondrial DNA including 486 individuals from 31 localities revealed that R. norvegicus is widely distributed in China, R. tanezumi is mainly distributed in southern China with currently invading northward; northeast China was the natal region of R. norvegicus, while the spread of R. tanezumi in China most likely started from the southeast coast. A total of 123 individuals from 18 localities were subjected to 2b‐RAD analyses. In the neighbor‐joining tree, individuals of R. tanezumi grouped into geographic‐specific branches, and populations from the southeast coast were ancestral groups, which confirmed the colonization route from the southeast coast to central and western China. However, individuals of R. norvegicus were generally grouped into two clusters instead of geographic‐specific branches. One cluster comprised inland populations, and another cluster included both southeast coast and inland populations, which indicated that the spread history of R. norvegicus in China was complex; in addition to on‐land colonization, shipping transportation also played a great role. ADMIXTURE and principal component analyses provided further supports for the colonization history. Demographic analyses revealed that climate changes at ~40,000 to 18,000 years ago and ~4000 years ago had led to population declines of both species; the R. norvegicus declined rapidly while the population of R. tanezumi continuously expanded since ~1500 years ago, indicating the importance of interspecies' competition in their population size changes. Our study provided a valuable framework for further investigation of phylogeography of two species in China.

publicOct 2022View details →

Comparative phylogeography of two commensal rat species (Rattus tanezumi and R. norvegicus) in China: Insights from mitochondiral DNA, microsatellite and RADseq

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publicSep 2016View details →

Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus)

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publicMay 2018View details →

Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities

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publicMar 2021View details →

Data from: Global origins of invasive brown rats (Rattus norvegicus) in the Haida Gwaii archipelago

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opencc-zeroDec 2012View details →

Data from: Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil

Throughout the developing world, urban centres with sprawling slum settlements are rapidly expanding and invading previously forested ecosystems. Slum communities are characterized by untended refuse, open sewers and overgrown vegetation, which promote rodent infestation. Norway rats (Rattus norvegicus) are reservoirs for epidemic transmission of many zoonotic pathogens of public health importance. Understanding the population ecology of R. norvegicus is essential to formulate effective rodent control strategies, as this knowledge aids estimation of the temporal stability and spatial connectivity of populations. We screened for genetic variation, characterized the population genetic structure and evaluated the extent and patterns of gene flow in the urban landscape using 17 microsatellite loci in 146 rats from nine sites in the city of Salvador, Brazil. These sites were divided between three neighbourhoods within the city spaced an average of 2.7 km apart. Surprisingly, we detected very little relatedness among animals trapped at the same site and found high levels of genetic diversity, as well as structuring across small geographical distances. Most FST comparisons among sites were statistically significant, including sites <400 m apart. Bayesian analyses grouped the samples in three genetic clusters, each associated with distinct sampling sites from different neighbourhoods or valleys within neighbourhoods. These data indicate the existence of complex genetic structure in R. norvegicus in Salvador, linked to the heterogeneous urban landscape. Future rodent control measures need to take into account the spatial and temporal linkage of rat populations in Salvador, as revealed by genetic data, to develop informed eradication strategies.

opencc-zeroDec 2014View details →

Data from: Resolving patterns of population genetic and phylogeographic structure to inform control and eradication initiatives for brown rats Rattus norvegicus on South Georgia

The control and eradication of invasive species is a common management strategy to protect or restore native biodiversity. On South Georgia in the Southern Ocean, the brown rat Rattus norvegicus was brought onto the island with the onset of whaling and sealing activity in the 1800s and has had a significant detrimental impact on key bird species of conservation concern. Efforts to eradicate rats from South Georgia using poisoned bait are ongoing. Despite the South Georgia rat eradication programme being the geographically largest and most ambitious eradication initiative to date, its success is facilitated by the potential that rat populations are effectively isolated by glacial barriers. This allows for localized eradication effort at manageable scales, leading to sequential eradication of individual populations with minimal risk of incursion from neighbouring areas. Here, we use the levels of population genetic divergence estimated from 299 single nucleotide polymorphism (SNP) loci and DNA sequence variation across 993 base pairs of the mitochondrial DNA cytochrome B locus to examine whether rat populations from nine glacially isolated areas on South Georgia are genetically distinct and so can be treated as independent eradication units. Bayesian clustering of individuals based on SNP similarity identified seven different genetic groups, which were confirmed using analyses based on pairwise genetic distance estimates and ordination of individuals using principal coordinate analysis. From a management perspective, these seven groups represent individual targets in baiting operations. Two mtDNA haplotypes were resolved across South Georgia, with a distinct geographical separation between the north-western and south-eastern populations. Approximate Bayesian computation (ABC) was used to identify that this divergence was a consequence of two separate historical colonization events. Synthesis and applications. We illustrate that molecular markers are a valuable tool in species management and pest eradication given that the spatial distribution of genetic diversity can: (i) identify demographically and genetically independent populations on which local eradication effort can be focussed, (ii) distinguish between incomplete eradication and immigration in situations where individuals remain after eradication has been attempted and (iii) identify the source of migrants when dispersal occurs over large spatial scales.

zenodo32/100

A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota

<h1>Dataset overview</h1> We built a catalog of 5.9M genes found in the brown rat gut microbiota. Co-abundant genes were binned in 1627 Metagenomic Species for which we provide taxonomic labels. This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.<h1>Data sources </h1> Rat fecal (and milk) samples characterized by shotgun metagenomic sequencing during the Mamiprooffi project. Sequencing data will be submitted soon on the European Nucleotide Archive (Bioproject PRJEB57230) The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al. <h1>Metagenomic assembly</h1> Metagenomic assembly was performed on the Mamiprooffi samples (Data Source 1) with SPAdes (parameters: --iontorrent --careful). Contigs of less than 1500 bp or successfully aligned on the rat genome (Rnor_6.0) were removed. Non-redundant gene catalog Genes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded. Then, partial and complete genes were separately clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0 ). Finally, these two non-redundant gene sets were merged with the previously published catalog (Data Source 2) using cd-hit-est-2d by considering at first complete genes (contact us for futher details). Functionnal annotation KEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database) <h1>Metagenomic Species</h1> Using the Meteor software suite, reads from samples in Bioprojects PRJEB57230 and PRJEB22973 were mapped against the final non redundant catalog to build a raw gene abundance table (5.9 million genes quantified in 370 samples). This table was submitted to MSPminer and Canopy. A total of 1627 clusters of co-abundant genes or MetaGenomic Species (MGS) were discovered. Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles. <h1>Taxonomic annotation of Metagenomic Species</h1> MGS taxonomic annotation was performed by aligning all core and accessory genes against the GTDB r214 representative genomes using blastn [4] (version 2.10.1, task = megablast, word_size = 16). The 20 best hits for each gene were kept. A species-level assignment was given if > 50% of the genes matched a GTDB representative genome with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MGS were assigned to a higher taxonomic levels (genus to superkingdom) if more than 50% of their genes had the same annotation.<h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB22973 and PRJEB57230 (cohort used in catalogue assembly) and PRNJNA609596 (independent cohort not used in assembly).

opencc-zeroDec 2022View details →

publicDec 2015View details →

Data from: Multiple paternity in the Norway rat, Rattus norvegicus, from urban slums in Salvador, Brazil

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publicNov 2016View details →

Data from: Resolving patterns of population genetic and phylogeographic structure to inform control and eradication initiatives for brown rats Rattus norvegicus on South Georgia

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