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141 results for “Rattus rattus”
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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Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus)
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Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities
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Data from: Global origins of invasive brown rats (Rattus norvegicus) in the Haida Gwaii archipelago
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Data from: Habitat use and seed removal by invasive rats (Rattus rattus) in disturbed and undisturbed rainforest, Puerto Rico
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In vivo differentially-expressed genes in Peromyscus leucopus, Mus musculus, and Rattus norvegicus blood in response to LPS
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Konza Prairie site, station Konza Prairie LTER watershed 001d, study of animal abundance of Rattus norvegicus in units of numberPerTransectLinePer4DayTrapSeason on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Konza Prairie (KNZ) contains animal abundance of Rattus norvegicus measurements in numberPerTransectLinePer4DayTrapSeason units and were aggregated to a yearly timescale.
Konza Prairie site, station Konza Prairie LTER watershed 004b, study of animal abundance of Rattus norvegicus in units of numberPerTransectLinePer4DayTrapSeason on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Konza Prairie (KNZ) contains animal abundance of Rattus norvegicus measurements in numberPerTransectLinePer4DayTrapSeason units and were aggregated to a yearly timescale.
Data from: Invasion genetics of a human commensal rodent: the black rat Rattus rattus in Madagascar
Studies focusing on geographical genetic patterns of commensal species and on human history complement each other, and provide proxies to trace common colonisation events. On Madagascar, the unintentional introduction and spread of the commensal species Rattus rattus by people may have left a living clue of human colonization patterns and history. In this study, we addressed this question by characterising the genetic structure of natural populations of R. rattus using both microsatellites and mitochondrial sequences, on an extensive sampling across the island. Such datasets were analysed by a combination of methods using population genetics, phylogeography and Approximate Bayesian Computation. Our results indicated two different introduction events to Madagascar from the same ancestral source of R. rattus, one in the extreme north of the island and the other further south. The latter was the source of a large spatial expansion, which may have initially started from an original point located on the southern coast. The inferred timing of introduction events – several centuries ago - is temporally congruent with the Arabian trade network in the Indian Ocean, which was flourishing from the middle of the first millennium.
Data from: Broad and flexible stable isotope niches in invasive non-native Rattus spp. in anthropogenic and natural habitats of central eastern Madagascar
Background: Rodents of the genus Rattus are among the most pervasive and successful invasive species, causing major vicissitudes in native ecological communities. A broad and flexible generalist diet has been suggested as key to the invasion success of Rattus spp. Here, we use an indirect approach to better understand foraging niche width, plasticity, and overlap within and between introduced Rattus spp. in anthropogenic habitats and natural humid forests of Madagascar. Results: Based on stable carbon and nitrogen isotope values measured in hair samples of 565 individual rodents, we found that R. rattus had an extremely wide foraging niche, encompassing the isotopic space covered by a complete endemic forest-dwelling Malagasy small mammal community. Comparisons of Bayesian standard ellipses, as well as (multivariate) mixed-modeling analyses, revealed that the stable isotope niche of R. rattus tended to change seasonally and differed between natural forests and anthropogenic habitats, indicating plasticity in feeding niches. In co-occurrence, R. rattus and R. norvegicus partitioned feeding niches. Isotopic mismatch of signatures of individual R. rattus and the habitat in which they were captured, indicate frequent dispersal movements for this species between natural forest and anthropogenic habitats. Conclusions: Since R. rattus are known to transmit a number of zoonoses, potentially affecting communities of endemic small mammals, as well as humans, these movements presumably increase transmission potential. Our results suggest that due to their generalist diet and potential movement between natural forest and anthropogenic habitats, Rattus spp. might affect native forest-dependent Malagasy rodents as competitors, predators, and disease vectors. The combination of these effects helps explain the invasion success of Rattus spp. and the detrimental effects of this genus on the endemic Malagasy rodent fauna.
Data from: Gut microflora may facilitate adaptation to anthropic habitat: a comparative study in Rattus
Anthropophilic species ('commensal' species) that are completely dependent upon anthropic habitats experience different selective pressures particularly in terms of food than their non-commensal counterparts. Using a next-generation-sequencing approach, we characterized and compared the gut microflora community of 53 commensal Rattus rattus and 59 non-commensal Rattus satarae captured in 10 locations in the Western Ghats, India. We observed that while species identity was important in characterizing the microflora communities of the two Rattus hosts, environmental factors also had a significant effect. While there was significant geographic variation in the microflora of the non-commensal R. satarae, there was no effect of geographic distance on gut microflora of the commensal R. rattus. Interestingly, host genetic distance did not significantly influence the community in either Rattus hosts. Collectively, these results indicate that a shift in habitat is likely to result in a change in the gut microflora community and imply that the gut microflora is a complex trait, influenced by various parameters in different habitats.
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.
Data from: Commensalism facilitates gene flow in mountains: a comparison between two Rattus species
Small mammal dispersal is strongly affected by geographical barriers. However, commensal small mammals may be passively transported over large distances and strong barriers by humans (often with agricultural products). This pattern should be especially apparent in topographically complex landscapes, such as mountain ranges, where valleys and/or peaks can limit dispersal of less vagile species. We predict that commensal species would have lower genetic differentiation and higher migration rates than related non-commensals in such landscapes. We contrasted population genetic differentiation in two sympatric Rattus species (R. satarae and R. rattus) in the Western Ghats mountains in southern India. We sampled rats from villages and adjacent forests in seven locations (20–640 km apart). Capture-based statistics confirmed that R. rattus is abundant in human settlements in this region, whereas R. satarae is non-commensal and found mostly in forests. Population structure analyses using ~970-bp mitochondrial control region and 17 microsatellite loci revealed higher differentiation for the non-commensal species (R. satarae F-statistics=0.420, 0.065, R. rattus F-statistics=0.195, 0.034; mitochondrial DNA, microsatellites, respectively). Genetic clustering analyses confirm that clusters in R. satarae are more distinct and less admixed than those in R. rattus. R. satarae shows higher slope for isolation-by-distance compared with R. rattus. Although mode of migration estimates do not strongly suggest higher rates in R. rattus than in R. satarae, they indicate that migration over long distances could still be higher in R. rattus. We suggest that association with humans could drive the observed pattern of differentiation in the commensal R. rattus, consequently impacting not only their dispersal abilities, but also their evolutionary trajectories.
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.
Data from: Invasion facilitates hybridization with introgression in the Rattus rattus species complex
Biological invasions result in novel species interactions, which can have significant evolutionary impacts on both native and invading taxa. One evolutionary concern with invasions is hybridization among lineages that were previously isolated, but make secondary contact in their invaded range(s). Black rats, consisting of several morphologically very similar but genetically distinct taxa that collectively have invaded six continents, are arguably the most successful mammalian invaders on the planet. We used mitochondrial cytochrome b sequences, two nuclear gene sequences (Atp5a1 and DHFR), and nine microsatellite loci to examine the distribution of three invasive black rat lineages (R. tanezumi, R. rattus I, and R. rattus IV) in the U.S. and Asia, and determine the extent of hybridization among these taxa. Our analyses revealed two mitochondrial lineages that have spread to multiple continents, including a previously undiscovered population of R. tanezumi in the southeastern U.S., whereas the third lineage (R. rattus IV) appears to be confined to Southeast Asia. Analyses of nuclear DNA (both sequences and microsatellites) suggested significant hybridization is occurring among R. tanezumi and R. rattus I in the U.S., and also suggest hybridization between R. tanezumi and R. rattus IV in Asia, although further sampling of the latter species pair in Asia is required. Furthermore, microsatellite analyses suggest unidirectional introgression from both R. rattus I and R. rattus IV into R. tanezumi. Within the U.S., introgression appears to be occurring to such a pronounced extent that we were unable to detect any nuclear genetic signal for R. tanezumi, and a similar pattern was detected in Asia.
FIGURES 27–34. Rodentanema aenigma n. gen., n in The gastrointestinal helminths of Rattus niobe (Rodentia: Muridae) with descriptions of two new genera and three new species (Nematoda) from Papua New Guinea and Papua Indonesia
FIGURES 27–34. Rodentanema aenigma n. gen., n. sp.. In all illustrations of the synlophe the dorsal aspect of the body is oriented towards the top of the page and the left side of the nematode is on the left side of the page. 27. Female, cephalic end; 28. Female, en face view; 29. Female posterior end, right lateral view; 30. Male posterior end, left lateral view, bursal rays numbered; 31. Male transverse section, mid body; 32. Female transverse section, mid body; 33. Bursa partially unrolled, left lateral and dorsal aspects, rays numbered; 34. Bursa, dorsal ray. Scale bars in µm: 27, 28, 31, 33, 34, 12.5; 29, 30, 50.; 32, 25.
FIGURES 15–26. Nugininema titokis n. gen., n in The gastrointestinal helminths of Rattus niobe (Rodentia: Muridae) with descriptions of two new genera and three new species (Nematoda) from Papua New Guinea and Papua Indonesia
FIGURES 15–26. Nugininema titokis n. gen., n. sp. In all illustrations of the synlophe in transverse section the dorsal aspect of the body is oriented towards the top of the page and the left side of the nematode is on the left side of the page. Long arrow shows axis of orientation of synlophe; dorsal and ventral ridges (numbers with superscripts) numbered. 15. Male anterior end, right lateral view; 16. Male transverse section, anterior end; 17. Female transverse section, anterior end; 18. Female cephalic end; 19. Male transverse section, mid body; 20. Female transverse section, mid body; 21. Female posterior end, right lateral view; 22. Gubernaculum, ventral view; 23. Spicule tip. 24. Spicule anterior end, lateral view. 25. Female posterior end, lateral view. 26. Bursa, partially unrolled, right lateral view, rays numbered. Scale bars in µm: 15, 50; 16–21, 25, 26, 25; 22–24, 12.5.
FIGURES 35–43 in The gastrointestinal helminths of Rattus niobe (Rodentia: Muridae) with descriptions of two new genera and three new species (Nematoda) from Papua New Guinea and Papua Indonesia
FIGURES 35–43. Nippostrongylinae species: Nippostrongylinae sp. 1. 35. Female anterior end, lateral view; 36. Bursa, left and right lateral lobes partially unrolled, rays numbered; 37. Male posterior end, left lateral view, rays numbered; 38. Dorsal ray; 39. Female posterior end, left lateral view. Nippostrongylinae sp. 2. 40. Female anterior end, right lateral view; 41. Female posterior end, right lateral view; 42. Ovejector; 43. Male, transverse section mid body showing the synlophe: oriented with the presumed dorsal aspect of the body towards the top of the page and the left side of the nematode on the left of the page; dorsal and ventral ridges (numbers with superscripts) numbered. Scale bars in µm: 35, 37, 39–42, 50; 36, 25; 38, 43, 12.5.
FIGURES 1–14. Syphacia niobe n in The gastrointestinal helminths of Rattus niobe (Rodentia: Muridae) with descriptions of two new genera and three new species (Nematoda) from Papua New Guinea and Papua Indonesia
FIGURES 1–14. Syphacia niobe n.sp. 1. Female anterior end, lateral view; 2. Female, en face view; 3. Male, en face view; 4. Male, lateral view; 5. Female cephalic end, lateral view; 6. Female cephalic end, ventral view; 7. Male cephalic end, lateral view; 8. Vagina, lateral view; 9. Female mid body, transverse section. 10. Male posterior end, ventral view;11. Egg; 12. Female tail, lateral view; 13. Spicule, gubernaculum and accessory piece, lateral view. 14. Male posterior end, lateral view; Scale bars in µm: 1, 4, 100; 2, 3, 12, 50; 5, 6, 8–11, 25; 7, 14, 12.5, 13, 10.
A catalog of genes and species of the brown rat (Rattus norvegicus) gut microbiota
<p></p><h1>Dataset overview</h1><br>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.<br><br>This dataset can be used to analyze shotgun sequencing data of the brown rat gut microbiota.<h1>Data sources </h1><br>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)<br>The gene catalog of the Sprague-Dawley rat gut metagenome published by Pan et al.<br><h1>Metagenomic assembly</h1><br>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.<br>Non-redundant gene catalog<br>Genes were predicted on all contigs with Prodigal (parameters : -m -p meta ). Genes with missing start codon or shorter than 99 bp were discarded.<br>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).<br>Functionnal annotation<br>KEGG Orthologs (KOs) were assigned to genes of the final catalog with KofamScan (version 1.3.0, KEGG 107 database)<br><h1>Metagenomic Species</h1><br>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.<br>Quality control of each MGS was manually performed by visualizing heatmaps representative of the normalized gene abundance profiles.<br><h1>Taxonomic annotation of Metagenomic Species</h1><br>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).<p></p>
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