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Commensal Ecology, Urban Landscapes, and Their Influence on the Genetic Characteristics of City-dwelling Norway Rats (Rattus norvegicus)
Abstract
Movement of individuals promotes colonization of new areas, gene flow among local populations, and has implications for the spread of infectious agents and the control of pest species. Wild Norway rats (Rattus norvegicus) are common in highly urbanized areas but surprisingly little is known of their population structure. We sampled individuals from 11 locations within Baltimore, Maryland, to characterize the genetic structure and extent of gene flow between areas within the city. Clustering methods and a neighbour-joining tree based on pairwise genetic distances supported an east-west division in the inner city, and a third cluster comprised of historically more recent sites. Most individuals (approximately 95%) were assigned to their area of capture, indicating strong site fidelity. Moreover, the axial dispersal distance of rats (62 m) fell within typical alley length. Several rats were assigned to areas 2-11.5 km away, indicating some, albeit infrequent, long-distance movement within the city. Although individual movement appears to be limited (30-150 m), locations up to 1.7 km are comprised of relatives. Moderate F(ST), differentiation between identified clusters, and high allelic diversity indicate that regular gene flow, either via recruitment or migration, has prevented isolation. Therefore, ecology of commensal rodents in urban areas and life-history characteristics of Norway rats likely counteract many expected effects of isolation or founder events. An understanding of levels of connectivity of rat populations inhabiting urban areas provides information about the spatial scale at which populations of rats may spread disease, invade new areas, or be eradicated from an existing area without reinvasion.
... Among invasive species, rodents are among the most widely introduced vertebrates. Their success is associated with their high reproductive rates, short generation times and dietary plasticity; they can consume organic matter, seeds, fruits, different invertebrate and small vertebrate species, eggs and coastal resources (Miller and Webb 2001;Caut et al. 2008;Gardner-Santana et al. 2009;Clair 2011;Shiels et al. 2013;Banks and Smith 2015). Additionally, their evolutionary history is tightly linked with their commensal ecology (Blackburn et al. 2011;Siahsarvie et al. 2012;Lucaccioni et al. 2016), to such a degree that they are considered the main group introduced to oceanic islands (Pichlmueller et al. 2020). ...
... (R Core Team 2016), applying the alphascore method to determine the proportion of successful reassignment by individual in function of the number of retained PCs (black rat: 1 PC; house mouse: 8 PCs). We also performed a spatial genetic analysis with Geneland v.4.0.4 (Guillot et al. 2005), a spatial Bayesian method based in Monte Carlo Markov chains and Poisson-Voronoi tessellations to determine genetic discontinuities; 30 independent runs with 10,000,000 interactions and 100,000 of burn-in were performed, an uncertainty coordinate value of 30 m for the black rat based on its low dispersion in urban zones (Gardner-Santana et al. 2009), while for house mice we used a 20 m value considering the species' home range in cities (Dean et al. 2006). ...
... i.e. tending to return to or remain near a particular site or area, observed in females as it is more common (Gardner-Santana et al. 2009). In our study in Cozumel, the black rat showed differential ancestral migration with higher values in females, which could be associated with their social structure, where males have a strong hierarchy and control territories through which the females 'freely' roam; in fact, female dispersion is food-determined and shapes male dispersion (Hooker and Innes 1995). ...
Humans and wildlife experience complex interactions in urban ecosystems, favoring the presence of commensal species, among which invasive species are particularly successful. Rodents are the main vertebrate group introduced to oceanic islands, where the invasion process and dispersal patterns strongly influence their evolutionary and genetic patterns. We evaluated the house mouse Mus musculus and the black rat Rattus rattus on Cozumel Island, Mexico. We assessed genetic diversity and structure, connectivity, gene flow, relatedness and bottleneck signals based on microsatellite loci. Our genetic findings suggest that introduction of individuals of different geographic sources to the island promotes high allelic diversity and the effective establishment of migrants. We identified a clear genetic structure and low connectivity for the two species, tightly linked with anthropogenic and urban features. Notably, we found that the genetic structure of the house mouse sampled within the city of San Miguel Cozumel is associated with the historical human population growth pulses accompanying the urbanization of the city. At the fine-scale genetic level, the main urban drivers of connectivity of the house mouse were both the impervious land surfaces, i.e. the urban landscape, and the informal commerce across the city (a proxy of resources availability). Chances of a secondary invasion to natural environments have been relatively low, which is crucial for the endemic taxa of the island. Nonetheless, improving urban planning to regulate future expansions of San Miguel Cozumel is of the outmost importance to prevent these invasive species to disperse further.
... From reading the full text of all selected articles that met the inclusion criteria, we identified that the only metric of genetic diversity that met the requirement of being present in all studies was observed heterozygosity (Ho). Furthermore, given that we found deviations from the Hardy-Weinberg Equilibrium (HWE) in several selected studies [6,[19][20][21], Ho was precisely the most appropriate metric to use in our study, considering that the expected heterozygosity (He) assumes HWE. In addition, only nuclear markers were considered for the analyses to reduce the bias of Ho values due to mitochondrial markers' nature and avoid standardization by marker type as well. ...
... Several studies evaluating the genetic variability of species of the genus Rattus indicate that dispersal is low or very local, at the scale of cities and even neighborhoods within the same city, indicating the effect that the urban environment may have on the distribution of genetic diversity [3,6,[19][20][21]. For example, in the systematic review conducted herein, we found several studies [19][20][21] where an absence of correlation between genetic and geographic distances was presented, which can be expected when passive (e.g., human-mediated) dispersal or heterogeneity occurs on a fine scale in the urban habitat. ...
... Several studies evaluating the genetic variability of species of the genus Rattus indicate that dispersal is low or very local, at the scale of cities and even neighborhoods within the same city, indicating the effect that the urban environment may have on the distribution of genetic diversity [3,6,[19][20][21]. For example, in the systematic review conducted herein, we found several studies [19][20][21] where an absence of correlation between genetic and geographic distances was presented, which can be expected when passive (e.g., human-mediated) dispersal or heterogeneity occurs on a fine scale in the urban habitat. However, in our case, by exploring other types of correlations (e.g., population density vs. Ho; gridded poverty/deprivation value vs. Ho; travel time to cities/ports vs. Ho), we were able to identify some form of relationship (Table 1). ...
On a planet experiencing constant human population growth, it is necessary to explore the anthropogenic effects on the genetic diversity of species, and specifically invasive species. Using an analysis that integrates comparative phylogeography, urban landscape genetics, macrogenetics and a systematic review, we explore the worldwide genetic diversity of the human commensal and anthropogenic species Rattus rattus and Rattus norvegicus. Based on metadata obtained considering 35 selected studies related to observed heterozygosity, measured by nuclear molecular markers (mi-crosatellites, Single Nucleotide Polymorphisms-SNPs-, restrictition site-associated DNA sequencing-RAD-Seq-), socioeconomic and mobility anthropogenic factors were used as predictors of genetic diversity of R. rattus and R. norvegicus, using the Gini index, principal component analysis and Random Forest Regression as analysis methodology. Population density was on average the best predictor of genetic diversity in the Rattus species analyzed, indicating that the species respond in a particular way to the characteristics present in urban environments because of a combination of life history characteristics and human-mediated migration and colonization processes. To create better management and control strategies for these rodents and their associated diseases, it is necessary to fill the existing information gap in urban landscape genetics studies with more metadata repositories, with emphasis on tropical and subtropical regions of the world.
... For instance, the rare studies conducted on R. rattus all focused on West African cities with sampling covering several different districts (Niamey, Niger: Berthier et al. 2016;Franceville, Gabon: Mangombi et al. 2016;Cotonou, Benin: Badou et al. 2021). Urban R. norvegicus genetics was investigated in a few cities in North and South America (i.e., Baltimore, USA: Gardner-Santana et al. 2009;Salvador, Brazil: Kajdacsi et al. 2013;New York City, USA: Combs et al. 2018a;Salvador, Brazil;New Orleans, USA;Vancouver, Canada;and New York City, USA: Combs et al. 2018b). The only study on urban M. musculus we are aware of was conducted in Dakar, Senegal (Stragier et al. 2022), and again was conducted at the scale of the city. ...
... IBD may also result from social behaviour of rodent species. Indeed, R. norvegicus (Combs et al. 2018a, b;Gardner-Santana et al. 2009) and M. musculus (Lippens et al. 2017) are known for strong social structure and very limited active dispersal. In M. musculus in particular, home ranges of a few tens of metres in commensal habitats (Pocock et al. 2005), and effective dispersal of only few hundred meters (Lippens et al. 2017) may explain the high F ST values observed in this species (within the industrial seaport: mean F ST = 0.09 for M. musculus; 0.06 for R. norvegicus; 0.02 for R. rattus). ...
... Indeed, they may reflect the presence of physical barriers to individual dispersal. Such barriers within the urban landscape have already been evidenced for Norway rats, such as major waterways in Baltimore (Gardner-Santana et al. 2009), Salvador (Kajdacsi et al. 2013) and New Orleans (Combs et al. 2018b), roadways in Salvador and Vancouver, or resource deserts in New York City (Combs et al. 2018b). Within the APC, however, we could not identify obvious physical barriers that could explain the observed marked genetic partitions. ...
Black rat (Rattus rattus), brown rat (Rattus norvegicus), and house mouse (Mus musculus) are known to be among the most common anthropophilic rodent species in cities worldwide. These species are responsible for the destruction of domestic and industrial materials, considerable damage to food stocks as well as zoonotic pathogens circulation and transmission to humans and animals. These invasive species have disseminated in all continents following human-mediated exchanges, especially maritime transports. In particular, seaports appear as privileged rats and mice’s entry points into new regions, thus making them international regulations’ priorities for rodent surveillance and management. Yet, studies on seaport rodents are rare; in particular, investigations on their genetic structure are almost inexistent, thus precluding science-guided interventions. In order to fill such a gap, our study focused on the population genetics of R. rattus, R. norvegicus and M. musculus in the Autonomous Port of Cotonou, Benin. Nine different sites were surveyed for three years. In total, 366 R. rattus, 188 R. norvegicus and 244 M. musculus were genotyped using 18 microsatellites, 16 microsatellites and 17 microsatellites, respectively. Our results show very well-structured genetic clusters in all three species as well as limited impacts of rodent control campaigns. Using comparisons with genotypes from other European, Asian and African countries, we suggest for the first time that settlement of newly introduced individuals may be a rare event. Implications in terms of management units and control and monitoring are discussed.
... Rodent control actions are costly, and classical control protocols, relying mostly on poisoning, have proven to be quite inefficient in reducing urban rodent densities in the long term (Parsons et al., 2017;Richardson, Burak, et al., 2017). It is now recognized that the development of more efficient management strategies requires a better understanding of urban rodent evolutionary ecology (Kaylee Aileen Byers et al., 2019;Combs, Kaylee A Byers, et al., 2018;Feng and Himsworth, 2014;Makundi and Massawe, 2011;Parsons et al., 2017;Singleton, Lyn A Hinds, et al., 1999) and notably of variations in gene flow (Combs, Kaylee A Byers, et al., 2018;Combs, Puckett, et al., 2018;Gardner-Santana et al., 2009;Johnson and Munshi-South, 2017;Kajdacsi et al., 2013;Parsons et al., 2017;Richardson, Burak, et al., 2017). For instance, identifying genetic clusters can allow defining meaningful spatial units for control actions (Combs, Kaylee A Byers, et al., 2018;Kajdacsi et al., 2013;Richardson, Burak, et al., 2017). ...
... So far, population genetic studies of urban rodents have mostly focused on the brown rat (Rattus norvegicus). Several of these studies showed that gene flow occurs at a sufficient rate to limit genetic drift and that spatial genetic variation tends to be organized under isolation-by-distance (IBD) resulting from both the spatially restricted dispersal and social behavior of this species (Combs, Kaylee A Byers, et al., 2018;Combs, Puckett, et al., 2018;Gardner-Santana et al., 2009). Beyond this general trend, spatially explicit analyses have also revealed sharp genetic discontinuities at relatively small spatial scales (Combs, Puckett, et al., 2018;Richardson, Burak, et al., 2017). ...
... For the house mouse within the Cap-Vert peninsula, the analyses of the relationships between genetic estimates (punctual and pairwise) and cityscape variables showed that the duration of the period elapsed since the connection of a built-up area to the first European settlement, was the most important factor to explain the spatial genetic patterns: the shorter this period, the lower the level of allelic richness and the higher the level of genetic differentiation. These results strongly suggest that the observed gradient in genetic variation mainly reflects the historical process of colonization by the house mouse, which followed the continuous expansion of the city from the first European settlement (Gardner-Santana et al., 2009;SE Harris et al., 2016;Lourenço et al., 2017). This is consistent with the ecology of the house mouse, which is known to be strictly commensal in Senegal, i.e. confined to human buildings (Dalecky et al., 2015). ...
Population genetic approaches may be used to investigate dispersal patterns of species living in highly urbanized environment in order to improve management strategies for biodiversity conservation or pest control. However, in such environment, population genetic structure may reflect both current features of the cityscape and urbanization history. This can be especially relevant when focusing on exotic commensal rodents that have been introduced in numerous primary colonial European settlements. Accounting for spatial and temporal cityscape heterogeneity to determine how past and recent demographic events may interplay to shape current population genetic structure of synanthropic rodents may provide useful insights to manage their populations. In this study, we addressed these issues by focusing on the house mouse, Mus musculus domesticus, in Dakar, Senegal, where the species may have been introduced as soon as Europeans settled in the middle of the nineteenth century. We examined genetic variation at one mitochondrial locus and 15 nuclear microsatellite markers from individuals sampled in 14 sampling sites representing different stages of urbanization history and different socio-economic environments in Dakar. We used various approaches, including model-based genetic clustering and model-free smoothing of pairwise genetic estimates. We further linked observed spatial genetic patterns to historical and current features of Dakar cityscape using random forest and Bayesian conditional autoregressive models. Results are consistent with an introduction of the house mouse at colonial time and the current genetic structure exhibits a gradient-like pattern reflecting the historical process of spatially continuous expansion of the city from the first European settlement. The genetic patterns further suggest that population dynamics of the house mouse is also driven by the spatial heterogeneity of the current cityscape, including socio-economics features, that translate in habitat quality. Our results highlight the potential importance of accounting for past demographic events to understand spatial genetic patterns of nonnative invasive commensal rodents in highly urbanized environment.
... Previous studies made in urban environment show that Rattus norvergicus present strong site fidelity and individual movements are usually limited to 30-150 m. Also, dispersal from their natal site seems to occur over short distances (Gardner-Santana et al. 2009;Byers et al. 2019). If that applies to the rat population in Paranaguá, the control measures implemented in the Port should be enough to avoid spread of new immigrants that arrive in the port. ...
... If an IAS manages to pass through the implemented control measures after its arrival in the new environment, linear features in the landscape, like roads, railways, and canals can facilitate its spread and colonization (Brown et al. 2006;Cameron and Bayne 2009). In Paranaguá a sampling collection through the city revealed a positive association of Norway rats (Rattus norvegicus) with the main roads used by trucks to access the Port area (Gatto-Almeida et al. 2020a). In this study we aimed to evaluate how effective are the control measures implemented by Paranaguá's port to prevent rats spread from the port. ...
... Our target species, R. norvegicus, is known to exhibit strong site fidelity and low frequency of long-distance dispersal (> 500 m) in urban environments, especially if food and harbourage are available (Gardner-Santana et al. 2009;Combs et al. 2018;Byers et al. 2019). Hence on the spatial scale of our sampling (6 km), assuming only self-dispersion of Norway rats, we expected to observe an IBD pattern if the control measures in port were not being effective. ...
Seaports are introduction hotspots for invasive alien species (IAS). This is especially true for rodents, which have accompanied humans around the globe since the earliest days of ocean-going voyages. The rapid spread of IAS soon after arrival in a new environment is facilitated by further human-mediated transport or landscape features, like roads. By measuring genetic diversity and structure to investigate dispersal pathways, we gained insight into the transport, spread and establishment stages of a biological invasion, leveraging the most common rodent species (R. norvegicus) in this setting. We characterized the genetic structure of three Norway rat populations along a busy industrial road used by trucks to access the Port area in Paranaguá city (Brazil). A total of 71 rats were genotyped using 11 microsatellite markers. The results revealed a pattern of gene flow contrary to the expected stepping-stone model along the linear transect, with the two furthest apart populations being clustered together. We hypothesize that the observed outcome is explained by natural dispersal along the corridor being lower than human-mediated transport. The sampled area furthest from the port is a gas station frequented by trucks which are considered the most likely mode of transportation. In terms of management strategies, we suggest more emphasis should be put on cargo surveillance to lower the risk of Norway rat dispersal, not only for biosecurity, but also for sanitary reasons, as this port is a major grain trading point.
... In fact, genetic approaches tend to reveal greater travel distances than suggested through traditional methods , although these patterns vary by location and sampling effort (Combs, Byers, et al., 2018). For example, genetic approaches have identified rat movement distances of up to 11.5 km in Baltimore, Maryland (Gardner-Santana et al., 2009), and up to 536 m in New York City although average movements are typically within 30-150 m Gardner-Santana et al., 2009). Genomicsbased approaches have also demonstrated that differences in movement can vary by sex, with males traveling further afield than females (Desvars-Larrive et al., 2017;Kajdacsi et al., 2013) in search of mates (Glass et al., 2016). ...
... In fact, genetic approaches tend to reveal greater travel distances than suggested through traditional methods , although these patterns vary by location and sampling effort (Combs, Byers, et al., 2018). For example, genetic approaches have identified rat movement distances of up to 11.5 km in Baltimore, Maryland (Gardner-Santana et al., 2009), and up to 536 m in New York City although average movements are typically within 30-150 m Gardner-Santana et al., 2009). Genomicsbased approaches have also demonstrated that differences in movement can vary by sex, with males traveling further afield than females (Desvars-Larrive et al., 2017;Kajdacsi et al., 2013) in search of mates (Glass et al., 2016). ...
... Genomicsbased approaches have also demonstrated that differences in movement can vary by sex, with males traveling further afield than females (Desvars-Larrive et al., 2017;Kajdacsi et al., 2013) in search of mates (Glass et al., 2016). And while natal dispersal of males is common in many species of mammals (Greenwood, 1980), genetic approaches have not revealed this trend in urban Norway rats (Gardner-Santana et al., 2009). Together, these findings suggest that patterns of relatedness vary over space and that genetic methods can provide valuable insight into movement events involved in pathogen spread or clustering. ...
Urban Norway rats (Rattus norvegicus) carry several pathogens transmissible to people. However, pathogen prevalence can vary across fine spatial scales (i.e., by city block). Using a population genomics approach, we sought to describe rat movement patterns across an urban landscape, and to evaluate whether these patterns align with pathogen distributions. We genotyped 605 rats from a single neighborhood in Vancouver, Canada and used 1,495 genome‐wide single nucleotide polymorphisms to identify parent‐offspring and sibling relationships using pedigree analysis. We resolved 1,246 pairs of relatives, of which only 1% of pairs were captured in different city blocks. Relatives were primarily caught within 33 meters of each other leading to a highly leptokurtic distribution of dispersal distances. Using binomial generalized linear mixed models we evaluated whether family relationships influenced rat pathogen status with the bacterial pathogens Leptospira interrogans, Bartonella tribocorum, and Clostridium difficile, and found that an individual’s pathogen status was not predicted any better by including disease status of related rats. The spatial clustering of related rats and their pathogens lends support to the hypothesis that spatially restricted movement promotes the heterogeneous patterns of pathogen prevalence evidenced in this population. Our findings also highlight the utility of evolutionary tools to understand movement and rat‐associated health risks in urban landscapes.
... Spatial modeling of small mammals has dealt with (Vaniscottea et al., 2009) and demonstrated the suitability of reducing the effect of extrapolation to map the distribution and clarify ecological processes. Currently, research on small mammals focuses on the impact of urbanization and urban fauna in America (Gardner-Santana et al., 2009;Munshi-South, Kharchenko, 2010), Asia (Hirota et al., 2004), and Europe (Baker et al., 2003). Also in the surrounding states of Slovakia, it was the work of Frynta et al. (1994) and Pelikán et al. (1983) for the Czech Republic. ...
... They have found a shift in species, a change in species composition, and their abundance due to urbanization (Alberti, Marzluff, 2004;Riem et al., 2012). The same results in the urban environment have been confirmed in America (Gardner-Santana et al., 2009;Munshi-South, Kharchenko, 2010), Asia (Hirota et al., 2004), and Europe (Baker et al., 2003;Gortat et al., 2014). We have found a decrease in the average value of species in year-on-year intervals in the rural landscape, while the number of individuals increased during 2017. ...
Changes in the structure of small mammals’ communities (Eulipotyphla, Rodentia) along urban–rural gradient indicate the environmental state of stability or instability. Since small mammals are important with regard to the transmission of diseases to man and domestic animals, therefore knowledge of their association with the landscape structure is needed in land use planning. In course of the period from 2015 to 2017, there were recorded 109 individuals belonging to 15 species at 9 study sites (3 rural, 3 suburban, and 3 urban). We recorded a decrease in the average number of species in the direction of the suburban–urban–rural gradient. The number of individuals decreased in the rural–urban–suburban gradient. Eudominant species Clethrionomys glareolus (D = 20.2%), Microtus arvalis (13.8%), and Sorex araneus (19.3%) preferred the close links between the terms of the rural landscape, while Apodemus agrarius (D = 11.9%) and Sorex minutus (D = 11.0%) preferred the close links between the terms of the urban landscape.
... In urban environments, wild rats spend their entire lives within a small area, which produces numerous genetic clusters of rat populations within a city. For example, in the city of Baltimore, USA, it was estimated that the kinship coefficient was estimated zero when two rats were separated more than 1,700 m [18]. In support of this finding, the leave-one-out test using genetic information at eight loci could correctly assign 95.3% of 277 trapped rats to one of 11 trapping areas [18]. ...
... For example, in the city of Baltimore, USA, it was estimated that the kinship coefficient was estimated zero when two rats were separated more than 1,700 m [18]. In support of this finding, the leave-one-out test using genetic information at eight loci could correctly assign 95.3% of 277 trapped rats to one of 11 trapping areas [18]. Similarly, wild rats in Vancouver, New Orleans, New York City, and Salvador exhibited statistically significant autocorrelation only within 200, 1,000, 1,000, and 2,500 m, respectively [8]. ...
Exposure to novel objects typically evokes avoidance behavior in wild animals, which is called neophobia. We previously found that wild brown rats (Rattus norvegicus) that were trapped in a park in downtown Tokyo, Japan, exhibited neophobia. We also found that this behavior was accompanied by the activation of the basolateral complex of the amygdala (BLA). Previous studies have suggested that genetic factors are the primary determinants of neophobia. Since rats in cities form populations with distinct genetic characteristics, it is reasonable to assume that wild rats caught at different locations in urban centers will exhibit different levels of neophobia. Here we assessed the intensity of neophobia in wild rats trapped at a wholesale market in Tokyo. Although we performed exactly the same experiment in which neophobia was observed in wild rats trapped at the park, the presence of novel objects did not affect the behaviors of wild rats trapped at the market. Conversely, laboratory rats showed approach and exploratory behaviors as seen in the previous study, suggesting that the experiment was performed appropriately. Compared to the laboratory rats, the lack of behavioral changes in the wild rats was accompanied by fewer Fos immunoreactive cells in the BLA. In addition, the numbers of Fos immunoreactive cells in the bed nucleus of the stria terminalis and ventromedial hypothalamus were similar between the two types of rats. The results demonstrated the existence of wild rats that were indifferent to novel objects.
... The design of such systems 60 has been successfully demonstrated in a variety of organisms, including yeast [15][16][17][18] , flies 19-26 , 61 mosquitoes [27][28][29][30] , and most recently, mice 31 . 62 Among other potential uses, gene drives can be designed to reduce or even outright 63 eliminate a target population. Such an approach could potentially rid islands of invasive rat 64 populations even where other control strategies cannot. ...
... This represents the ability of fully grown individuals to 187 potentially cover more ground than young individuals. An exponential distribution was chosen 188 because data indicates that motivated rats are capable of traveling vast distances under some 189 conditions 63,64 . An exponential distribution should mirror this behavior. ...
Invasive rodent populations pose a threat to biodiversity across the globe. When confronted with these new invaders, native species that evolved independently are often defenseless. CRISPR gene drive systems could provide a solution to this problem by spreading transgenes among invaders that induce population collapse. Such systems might be deployed even where traditional control methods are impractical or prohibitively expensive. Here, we develop a high-fidelity model of an island population of invasive rodents that includes three types of suppression gene drive systems. The individual-based model is spatially explicit and allows for overlapping generations and a fluctuating population size. Our model includes variables for drive fitness, efficiency, resistance allele formation rate, as well as a variety of ecological parameters. The computational burden of evaluating a model with such a high number of parameters presents a substantial barrier to a comprehensive understanding of its outcome space. We therefore accompany our population model with a meta-model that utilizes supervised machine learning to approximate the outcome space of the underlying model with a high degree of accuracy. This enables us to conduct an exhaustive inquiry of the population model, including variance-based sensitivity analyses using tens of millions of evaluations. Our results suggest that sufficiently capable gene drive systems have the potential to eliminate island populations of rodents under a wide range of demographic assumptions, but only if resistance can be kept to a minimal level. This study highlights the power of supervised machine learning for identifying the key parameters and processes that determine the population dynamics of a complex evolutionary system.
... This is consistent with studies investigating the size of the main activity area of Norway rats, which has been estimated to have a radius of 25-150m in urban areas [64,65]. In environmentally heterogeneous and resource-rich areas, such as Pau da Lima, the size of a rat's activity space has been found to be smaller, as shown by estimates of population density varying significantly within a city block [66] or along the length of an alley [67]. This is due to strong spatial heterogeneity in the presence of food and harbourage, availability of access routes and the presence of barriers to movement. ...
... This is due to strong spatial heterogeneity in the presence of food and harbourage, availability of access routes and the presence of barriers to movement. All of these can result in high site fidelity (a measure of how concentrated an animal's movements are around a specific site) [66] and significant variations in the abundance and activity of rats over small distances. The estimated value of ψ indicates that the spatially structured random effects are more important than the non-structured random effects in predicting rattiness. ...
A key requirement in studies of endemic vector-borne or zoonotic disease is an estimate of the spatial variation in vector or reservoir host abundance. For many vector species, multiple indices of abundance are available, but current approaches to choosing between or combining these indices do not fully exploit the potential inferential benefits that might accrue from modelling their joint spatial distribution. Here, we develop a class of multivariate generalized linear geostatistical models for multiple indices of abundance. We illustrate this novel methodology with a case study on Norway rats in a low-income urban Brazilian community, where rat abundance is a likely risk factor for human leptospirosis. We combine three indices of rat abundance to draw predictive inferences on a spatially continuous latent process, rattiness, that acts as a proxy for abundance. We show how to explore the association between rattiness and spatially varying environmental factors, evaluate the relative importance of each of the three contributing indices and assess the presence of residual, unexplained spatial variation, and identify rattiness hotspots. The proposed methodology is applicable more generally as a tool for understanding the role of vector or reservoir host abundance in predicting spatial variation in the risk of human disease.
... This is consistent with studies investigating the size of the main activity area of Norway rats, which has been estimated to have a radius of 25-150m in urban areas [64,65]. In environmentally heterogeneous and resource-rich areas, such as Pau da Lima, the size of a rat's activity space has been found to be smaller, as shown by estimates of population density varying significantly within a city block [66] or along the length of an alley [67]. This is due to strong spatial heterogeneity in the presence of food and harbourage, availability of access routes and the presence of barriers to movement. ...
... This is due to strong spatial heterogeneity in the presence of food and harbourage, availability of access routes and the presence of barriers to movement. All of these can result in high site fidelity (a measure of how concentrated an animal's movements are around a specific site) [66] and significant variations in the abundance and activity of rats over small distances. The estimated value of ψ indicates that the spatially structured random effects are more important than the non-structured random effects in predicting rattiness. ...
A key requirement in studies of endemic vector-borne or zoonotic disease is an estimate of the spatial variation in vector or reservoir host abundance. For many vector species, multiple indices of abundance are available, but current approaches to choosing between or combining these indices do not fully exploit the potential inferential benefits that might accrue from modelling their joint spatial distribution. Here, we develop a class of multivariate generalized linear geostatistical models for multiple indices of abundance. We illustrate this novel methodology with a case study on Nor- way rats in a low-income urban Brazilian community, where rat abundance is a likely risk-factor for human leptospirosis. We combine three indices of rat abundance to draw predictive inferences on a spatially continuous latent process, rattiness, that acts as a proxy for abundance. We show how to explore the association between rattiness and spatially varying environmental factors, evaluate the relative importance of each of the three contributing indices, assess the presence of residual, unexplained spatial variation, and identify rattiness hotspots. The proposed methodology is applicable more generally as a tool for understanding the role of vector or reservoir host abundance in predicting spatial variation in the risk of human disease.
... While these methods have been commonly used to promote movement in species of conservation concern and protect at-risk populations (Schwartz et al. 2006), they can also be implemented in efforts to remove or limit invasive pests (Russell et al. 2010, Fraser et al. 2013, Piertney et al. 2016. Several studies have used population genetics to gain insights on urban rat biology (Gardner-Santana et al. 2009, Kajdacsi et al. 2013, Combs et al. 2017), but few have described the benefits and challenges of these tools and strategies for PMPs specifically. ...
... Genetic diversity is directly influenced by the processes of gene flow and genetic drift, which increase and decrease diversity over time, respectively. While often interpreted in conjunction with population genetic structure, analysis of the spatial distribution of genetic diversity can provide insight into movement patterns to inform PMPs about recent behavioral patterns and optimal strategies for efficient pest removal (Gardner-Santana et al. 2009). ...
Effective management of rodent pests requires an ecological understanding of how they move through their environment and how those movements influence the invasion, persistence, or reinvasion of problematic colonies. Traditional methodologies used to describe rodent movement patterns, such as mark-recapture, are hindered by their time-consuming nature and limited geographic scope. As such, our understanding of how rodents interact with urban environments remains limited. Population genetic principles and tools have the capacity to greatly increase our understanding of rodent population dynamics, ecological relationships, and movements across space, but this field is often unapproachable to non-scientist pest management professionals (PMPs). In this commentary, we aim to promote collaborative and integrative rodent pest management by introducing relevant population genetic principles, providing examples of their applications in studies of urban brown rats (Rattus norvegicus), and proposing future initiatives that link scientific, private, and government entities. We reinterpret results from a 2018 study of brown rats in Vancouver, British Columbia, Canada to show how genetic relationships among individual brown rats can be used to understand the geographic distribution of genetic clusters (i.e., colonies), natural barriers to migration, and the spatial scale of dispersal. While the 2018 study originally aimed to describe patterns of population genetic structure to understand the influence of urban landscapes on rats, here we describe how these results can be exploited by PMPs to directly inform the creation of management units and decrease the likelihood of rapid post-treatment reinvasion. Further, we discuss the difficulties inherent in population genetic studies and the potential for high-quality model sites to develop generalizable strategies. Overall, we hope to expand the toolbox of PMPs, foster collaboration, and move toward more informed and sustainable management strategies.
... Food waste items included actual food items, while waste items included all waste excluding food items (e.g., plastic and paper wrappings). The variables NDVI, number of restaurants, and the presence of petting zoos were calculated within a circular buffer with a 150 m radius around each trapping location, representing the average home range of rats (Badi et al. 1992;Davis 1953;Gardner-Santana et al. 2009;Heiberg et al. 2012;Recht 1988) using QGIS version 3.16 (GIS Development Team 2022). To calculate the shortest distance between trapping sites and the nearest water body (m) in QGIS, we used a shapefile of national water bodies, which includes natural public water bodies such as rivers, canals, lakes, streams, ponds and The socio-economic variables considered in this study included: mean yearly income, human population density, and the percentage of owner-occupied houses (Table 1). ...
Urban greening has become an increasingly popular strategy to improve urban life and human health. However, there are indications that the presence and extent of urban greenness may increase the abundance of wild rats. Therefore, we investigated which environmental and socio-economic factors are associated with rat abundance, with a focus on factors related to urban greenness. We systematically trapped rats (222 Rattus norvegicus and 5 Rattus rattus) in parks and residential areas in three cities in the Netherlands. We modelled the relative abundance of rats against various environmental and socio-economic variables. In addition, we compared municipality rat complaint data with our trapping data and analysed trap success over time. We observed positive relationships between the relative abundance of rats and both greenness (NDVI) and different proxies for food resources (restaurants and petting zoos). In addition, there were more municipality rat complaints in residential areas compared to parks, while there was a higher relative abundance of rats in parks. Our findings corroborate that greenness is associated with a higher abundance of wild rats, and that municipality rat complaints may underestimate the abundance of rats in greener urban areas. This study provides new insights on factors affecting relative rat abundance in cities and can guide policy makers and city planners how to minimize rat nuisance in the greener parts of cities. By taking these potential effects of urban greenness on rat abundance into account, measures can be taken that on the one hand maintain the beneficial effects of urban greening, but at the same time reduce the carrying capacity for rats.
... Four of the samples were from Rattus norvegicus and one from Rattus tiomanicus. This finding is supported by the fact that this commensal rodent species is very common in urbanised areas as they dwell around human settlements due to their ecological and behavioural traits (Gardner-Santana et al., 2009;Palmeirim et al., 2014;Morand et al., 2015). ...
... Preference for kin has been reported in female mammals, who are mostly the philopatric sex [63]. A study on wild Norway rats living in highly urbanized areas did not show clear philopatry or sex-biased dispersal patterns [64]. Social bonds based on kin relations has been reported between mother-infant pairs but not between adults (see [65]). ...
There is growing evidence that social relationships influence individual fitness through various effects. Clarifying individual differences in social interaction patterns and determinants for such differences will lead to better understanding of sociality and its fitness consequences for animals. Behavioral traits are considered one of the determining factors of social interaction. The purpose of this study was to explore the effects of individual behavioral traits on social relationship building in laboratory rats ( Rattus norvegicus ), a highly social species. Initially, the following behavioral characteristics were measured in individuals: tameness (glove test), activity (open field test), exploration (novel object test), sociability (three-chamber test), and boldness (elevated plus maze test). We then used DeepLabCut to behaviorally track three groups of four individuals (12 total) and analyze social behaviors such as approach and avoidance behaviors. Principal component analysis based on behavioral test results detected behavioral traits interpreted as related to exploration, boldness, activity, and tameness, but not sociability. In addition, behavioral tracking results showed consistent individual differences in social behavior indices such as isolation time and partner preference. Furthermore, we found that different components were correlated with different phases of social behavior; exploration and boldness were associated with the early stages of group formation, whereas activity was associated with later stages of relationship building. From these results, we derived hypothesize that personality traits related to the physical and social environment have a larger influence in the relationship formation phase, and the behavioral trait of activity becomes important in the maintenance phase of relationships. Future studies should examine this hypothesis by testing larger group sizes and ensuring there is less bias introduced into group composition.
... D The average density of SNPs of different effects in expansion clusters and flanking regions. genetics of rats in cities have also shown evidence of limited dispersal of rats and population genetic differentiation among rats in different city regions 29 . ...
Nematodes are important parasites of people and animals, and in natural ecosystems they are a major ecological force. Strongyloides ratti is a common parasitic nematode of wild rats and we have investigated its population genetics using single-worm, whole-genome sequencing. We find that S. ratti populations in the UK consist of mixtures of mainly asexual lineages that are widely dispersed across a host population. These parasite lineages are likely very old and may have originated in Asia from where rats originated. Genes that underly the parasitic phase of the parasite’s life cycle are hyperdiverse compared with the rest of the genome, and this may allow the parasites to maximise their fitness in a diverse host population. These patterns of parasitic nematode population genetics have not been found before and may also apply to Strongyloides spp. that infect people, which will affect how we should approach their control.
... Removal of clutter around the home or relocating it least 400-500 ft (approx. 120-150 m) away can reduce numbers of rodents and other mammals from the immediate vicinity of the main dwelling (Gardner-Santana et al., 2009). Excluding wildlife living within, under and near human dwellings is important, as this reduces the likelihood that infestations will establish close to the home. ...
Triatomines (Hemiptera: Reduviidae: Triatominae), commonly called “kissing bugs”, are blood-sucking pests and
vectors of the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease (CD). Eleven species of
kissing bugs occur throughout the southern half of the USA, four of which are well known to invade human
dwellings. Certain kissing bugs in the USA are known to transmit T. cruzi to humans and other animals and their
bites can also lead to serious allergic reactions, including anaphylaxis. In Florida, the kissing bug Triatoma
sanguisuga frequently invades homes, bites residents, and has been found infected with T. cruzi, placing humans
and companion animals at risk for CD. This review outlines integrated pest management (IPM) strategies for
minimizing human exposure to T. sanguisuga and CD. A comprehensive IPM plan for kissing bugs includes
detailed inspections, removal of vertebrate host nesting areas, and kissing bug harborage, home improvements to
exclude kissing bugs from entering structures, pest removal, and judicious use of pesticides. This approach can
limit or eliminate kissing bug entry into residential structures, thereby preventing kissing bug bites, and CD
infections in humans and companion animals.
... Rat control programs therefore need to consider populations in the urban matrix and urban bushland remnants. Genetic techniques and GPS tracking could shed more light on black rat movement at the urban fringe and the degree of connectivity between urban and bushland populations of black rats to inform management (Gardner-Santana et al. 2009;Byers et al. 2019). ...
Context Small mammals may traverse the urban fringe and use both natural and anthropogenic resources. In Australia, human commensal black rats (Rattus rattus) and native long-nosed bandicoots (Perameles nasuta) are important tick hosts, which can be found persisting at the urban fringe, leading to human–wildlife conflict. Aims We aimed to (1) determine the relative activity of small mammals in yards and associations with yard attributes, (2) compare activity of black rats and long-nosed bandicoots in bushland with activity in yards and (3) determine the proportion of black rats and long-nosed bandicoots that crossed the urban fringe. We predicted that native bandicoots would be more active in bushland habitats and that black rats would be more active in yards. Methods We used camera trapping in 56 residential yards, 18 of which were paired with adjacent bushland to measure small mammal activity in the two habitats. We recorded yard attributes and examined these associations using generalised linear models. We used isodar analysis to investigate black rat preferences of bushland habitat compared with yards, and we used Rhodamine B baiting to investigate movement at the urban fringe. Key results We found that black rats were the most active small mammal in residential yards and were detected in more yards than other small mammals, followed by bandicoots. Black rat activity was greater in yards adjacent to bushland, but no other yard attributes were associated with black rat and bandicoot activity. Overall, activity tended to be higher in bushland than in yards at paired locations. Conclusions Our findings suggest residential yards likely provide high-quality resources for long-nosed bandicoots. Low rates of movement at the urban fringe (6%), and a preference for bushland at low densities suggests that black rats may be synanthropic rather than commensal, occupying an urban niche but not depending on anthropogenic resources as expected. Implications Residential properties located adjacent to bushland may be exposed to increased black rat activity in yards. Future work should consider how introduced rats may be controlled in bushland to assist urban rat control efforts and avoid non-target impacts. Residential yards are likely to be important habitat for the persistence of long-nosed bandicoots in urban environments.
... Many rodent species serve as definitive hosts for A. cantonensis and A. malaysiensis and are capable of highly promoting the distribution and intraspecific transfer of this parasite (Eamsobhana et al., 2016). The limited dispersal of rodent hosts might be expected to limit the genomic origin of their worm parasites, resulting in genetic structure over small geographical scales (Pocock et al., 2005;Gardner-Santana et al., 2009). However, data on the genetic diversity of Angiostrongylus remain scarce in invaded areas (Simões et al., 2011;Monte et al., 2012;Moreira et al., 2013;Dalton et al., 2017). ...
The rat lungworm Angiostrongylus cantonensis is globally known to be the cause of oeosinophilic meningitis in humans. Another congener, Angiostrongylus malaysiensis, is closely related to A. cantonensis and has been described as a potential human pathogenic parasite. These 2 worms are similar in terms of life cycle, host range and morphological and genetic information. However, there are limited studies about their genetic diversity based on the 66-kDa protein-encoding gene. The objective of this study was to explore the 66-kDa protein sequence variation of A. cantonensis and A. malaysiensis collected from Thailand. Two adult and 53 third-stage larval specimens of Angiostrongylus from 4 geographic locations in Thailand were molecularly identified using the 66-kDa protein gene. The phylogenetic trees (Bayesian inference tree and maximum-likelihood tree) showed that Angiostrongylus formed a monophyletic clade with a clear separation between A. cantonensis and A. malaysiensis. The genetic distance between A. cantonensis and A. malaysiensis varies from 0.82 to 2.86%, with a total of 16 variable sites. The analysis of genetic diversity revealed 1 and 5 new haplotypes of A. cantonensis and A. malaysiensis, respectively, and showed genetic differences between the populations of A. cantonensis and A. malaysiensis. The haplotype networks of A. cantonensis and A. malaysiensis populations in Thailand are similar to those of populations in some countries, indicating the range expansion of genomic origin between populations in different areas. In conclusion, the 66-kDa protein gene was a good genetic marker for studying genetic diversity and discriminating between A. cantonensis and A. malaysiensis.
... Some viruses are considered non-seasonal in rats (e.g., hantaviruses [11,35]), while others have demonstrated seasonal variations (e.g., for seasonal IAV [17]) in rat populations. Because urban brown rats are synanthropic and may come into contact with food supplies [5,36,37], rat-to-human transmission is likely to occur via direct or indirect contact with rat excreta (e.g., hantaviruses, HEV, encephalomyocarditis virus) or saliva (e.g., hantaviruses), via the bite of competent vector (e.g., WNV, USUV), or direct inoculation via close contact with infected animals (poxviruses). In general, much is unknown about the role of urban rats in the transmission of zoonotic viruses to humans, and studies such as this one may shed light on poorly understood aspects of viral zoonoses (e.g., precise transmission routes, seasonality, etc) [1,38,39]. ...
Urban environments represent unique ecosystems where dense human populations may come into contact with wildlife species, some of which are established or potential reservoirs for zoonotic pathogens that cause human diseases. Finding practical ways to monitor the presence and/or abundance of zoonotic pathogens is important to estimate the risk of spillover to humans in cities. As brown rats (Rattus norvegicus) are ubiquitous in urban habitats, and are hosts of several zoonotic viruses, we conducted longitudinal sampling of brown rats in Vienna, Austria, a large population center in Central Europe. We investigated rat tissues for the presence of several zoonotic viruses, including flaviviruses, hantaviruses, coronaviruses, poxviruses, hepatitis E virus, encephalomyocarditis virus, and influenza A virus. Although we found no evidence of active infections (all were negative for viral nucleic acids) among 96 rats captured between 2016 and 2018, our study supports the findings of others, suggesting that monitoring urban rats may be an efficient way to estimate the activity of zoonotic viruses in urban environments.
... The observed differences in the prevalence of Bartonella in rodents may be related to rodent species, habitats, and arthropod vector populations (Meheretu et al., 2013). Herein, all Bartonella-positive were detected from R. norvegicus, which is the predominant species of rodents captured in our study and also a synanthropic rodent species mostly found in the urban environments (Gardner-Santana et al., 2009;Kosoy and Bai, 2019). Particularly, fleas have been shown to play an extremely important role in the transmission and acquisition of Bartonella species in rodents (Silaghi et al., 2016). ...
Bartonella spp. are gram-negative bacteria that can infect a wide spectrum of mammals. Rodents are considered to be the natural reservoir of many Bartonella species that are transmitted by various blood-sucking arthropods. The close contact between rodents and humans in urban areas increased the chance of transmitting rodent-borne Bartonella to humans. Investigation of the epidemiological characteristics of Bartonella infection in rodents is of great significance for the prevention and control of human Bartonellosis. In this study, rodents were captured to monitor the prevalence of Bartonella in urban areas of Guangzhou city. Six official or candidate species of Bartonella , including two confirmed zoonotic species, were detected with an overall prevalence of 6.4% in rodents captured herein. In addition, Rattus norvegicus was the predominant host species for Bartonella infection, and B. queenslandensis was the dominant species circulating in rodents in these areas. These results provide insights into the prevalence and genetic diversity of Bartonella species circulating in rodents in the urban areas of Guangzhou, and also urged the surveillance of rodent-associated Bartonella species in these areas.
... Urbanization can result in loss of native species in many animal and plant communities (Savard et al. 2000, McKinney 2002, Lepczyk et al. 2008, Thongsripong et al. 2013, Sol et al. 2014), but is also associated with species gains through introduction of non-native species (Lepczyk et al. 2008, Francis and Chadwick 2015, Francis and Chadwick 2015, Francis and Chadwick 2017, Gaertner et al. 2017, Evans et al. 2018a, Pearse et al. 2018. High resource availability and/or low predation in urban ecosystems can further support high population growth for some organisms, including many rodent, weed, and mosquito species (Gardner-Santana et al. 2009, Hoshi et al. 2014, Johnson et al. 2015a. The presence and abundance of mosquito species in any environment is strongly influenced by environmental conditions experienced during juvenile stages (Juliano 2007). ...
Environmental conditions associated with urbanization are likely to influence the composition and abundance of mosquito (Diptera, Culicidae) assemblages through effects on juvenile stages, with important consequences for human disease risk. We present six years (2011–2016) of weekly juvenile mosquito data from distributed standardized ovitraps and evaluate how variation in impervious cover and temperature affect the composition and abundance of container-breeding mosquito species in Maryland, USA. Species richness and evenness were lowest at sites with high impervious cover (>60% in 100-m buffer). However, peak diversity was recorded at sites with intermediate impervious cover (28–35%). Four species were observed at all sites, including two recent invasives (Aedes albopictus Skuse, Ae. japonicus Theobald), an established resident (Culex pipiens L), and one native (Cx. restuans Theobald). All four are viral vectors in zoonotic or human transmission cycles. Temperature was a positive predictor of weekly larval abundance during the growing season for each species, as well as a positive predictor of rapid pupal development. Despite being observed at all sites, each species responded differently to impervious cover. Abundance of Ae. albopictus larvae was positively associated with impervious cover, emphasizing that this medically-important vector not only persists in the warmer, impervious urban landscape but is positively associated with it. Positive temperature effects in our models of larval abundance and pupae occurrence in container habitats suggest that these four vector species are likely to continue to be present and abundant in temperate cities under future temperature scenarios.
... This represents the ability of fully grown individuals to potentially cover more ground than young individuals. An exponential distribution was chosen because data indicates that motivated rats are capable of traveling vast distances under some conditions [66,67]. An exponential distribution should mirror this behavior. ...
Invasive rodent populations pose a threat to biodiversity across the globe. When confronted with these invaders, native species that evolved independently are often defenseless. CRISPR gene drive systems could provide a solution to this problem by spreading transgenes among invaders that induce population collapse, and could be deployed even where traditional control methods are impractical or prohibitively expensive. Here, we develop a high-fidelity model of an island population of invasive rodents that includes three types of suppression gene drive systems. The individual-based model is spatially explicit, allows for overlapping generations and a fluctuating population size, and includes variables for drive fitness, efficiency, resistance allele formation rate, as well as a variety of ecological parameters. The computational burden of evaluating a model with such a high number of parameters presents a substantial barrier to a comprehensive understanding of its outcome space. We therefore accompany our population model with a meta-model that utilizes supervised machine learning to approximate the outcome space of the underlying model with a high degree of accuracy. This enables us to conduct an exhaustive inquiry of the population model, including variance-based sensitivity analyses using tens of millions of evaluations. Our results suggest that sufficiently capable gene drive systems have the potential to eliminate island populations of rodents under a wide range of demographic assumptions, though only if resistance can be kept to a minimal level. This study highlights the power of supervised machine learning to identify the key parameters and processes that determine the population dynamics of a complex evolutionary system.
... Social distancing measures might have forced brown rats to forage in new areas in order to find alternative food sources because restaurants and bars closed early at night and the quantities of garbage placed curb-side decreased dramatically. Because brown rats do not travel long distances in urban areas (Combs et al. 2018;Gardner-Santana et al. 2009), rat sightings would only have increased in a limited number of wards. However, the increased sightings of brown rats did not result in rat infestations in buildings that were serious enough to prompt residents to hire pest management professionals. ...
Because rats are commensal organisms that depend on human activities for food, shifts in human behavior will have pronounced effects on local rat populations. In the spring of 2020, social distancing measures were implemented globally to curtail the spread of SARS-CoV-2. This presented a unique opportunity to obtain information regarding the immediate effects of shifts in human behavior on rat populations in a variety of countries. In response to increased sightings of rats in the USA that were reported in American media, we analyzed the changes in the number of public service calls in Tokyo, Japan. We found that the number of calls increased after the implementation of social distancing measures, suggesting that rat sightings had also increased in Tokyo. We then surveyed the changes in the business activities of pest management professionals in the USA, Canada, and Tokyo. We found that the activities were increased in 50 to 60% of the respondents from the USA and Canada. In contrast, 60 to 70% of the respondents from Tokyo answered that their activities were not changed. These results implied that, following the implementation of social distancing measures, rat infestations increased in North America, but not in Tokyo. The survey also suggested that roof rats were considered to be the predominant rodent species in Tokyo. This may account for the limited infestations in Tokyo because roof rats are more sedentary than brown rats. Taken together, our findings suggest that social distancing measures differentially affected rat populations in North America and Tokyo.
Supplementary information:
The online version contains supplementary material available at 10.1007/s10340-021-01405-z.
... However, in wild rodent populations, genetic differentiation is considered when Φ ST > 0.05 with a local distance between 5 and 10 km between analyzed populations (Peakall et al. 2003). Our results differ from the results for other wild rodent populations: Spermophilus mollis (Rodentia: Sciuridae), Rattus norvegicus (Rodentia: Muridae) (Antolin et al. 2001;Gardner-Santana et al. 2009), and P. melanophrys, from the same study sites (Mussali-Galante et al. 2013b). It has been reported that exposure to chronic environmental pollutants significantly affects the intensity and duration of evolutive forces, which play a key role in the genetic structuring of populations (Medina et al. 2007). ...
Wild animals that inhabit inside mine tailings which contain heavy metals are an excellent study model to conduct ecotoxicological studies that analyze chronic metal exposures at low doses (realistic exposures). This study was conducted in Huautla, Morelos, Mexico, in a mining district where 780,000 tons of wastes were deposited in open air. Liomys irroratus is a small mammal species that lives inside these mine tailings. A multibiomarker approach study was performed to analyze metal bioaccumulation levels (biomarker of exposure) by inductively coupled plasma mass spectrometry, DNA damage levels (biomarker of early effects) through the alkaline comet assay, and population genetic structure and diversity (biomarker of permanent effects), using seven microsatellite loci, in 75 L. irroratus individuals, from two mine tailings and one reference site. Concentrations of aluminum, copper, iron, nickel, lead, and zinc were statistically higher in the liver of exposed individuals. Significant DNA damage levels were registered in the mine tailings groups. Aluminum, lead, and nickel had the highest contribution to the genetic damage levels observed, while aluminum and nickel had the highest contribution to genetic diversity effects. A positive and significant relationship was detected between individual genetic diversity (internal relatedness) and genetic damage (DNA single-strand breaks). Genetic structure of L. irroratus populations revealed that the main source of genetic variation was located within populations. We consider that multibiomarker studies in environmental settings using sentinel species are valuable for environmental risk assessment and ecological responses in chronic exposed populations.
... The commensal rodents [Norway rats (Rattus norvegicus (Berkenhout, 1769)) and house mice (Mus musculus L. 1758)] live in close association with people and exploit human resources to survive, while peri-domestic deer mice (Peromyscus maniculatus (Wagner, 1845)) and white-footed mice (Peromyscus leucopus (Rafinesque, 1818)) utilize human spaces near their habitats (Gardner-Santana et al., 2009). Each year, contamination and consumption by rodents results in billions of dollars in losses to the food supply (Pimentel et al., 2005). ...
Rodent management programs at food distribution centers in the United States and Canada often adhere to interval-based spacing of control devices, with traps spaced 6–12 m apart on the interior perimeter, and exterior bait stations spaced 15–30 m apart. However, this design is based only on rodent foraging ranges, and does not consider the influence of rodent behavior or biology on movement patterns. Therefore, this study evaluated characteristics of food distribution centers that influence rodent behavior to determine their impact on interior trap capture and exterior bait feeding by rodents. We found that rodent interactions with control devices was not uniform in facilities, and less than half (45.2%) of all interior devices trapped at least one mouse. Rodent feeding at exterior bait stations was similarly not uniform, with 56.1% of observations representing minor feeding (one corner of bait or less consumed). Furthermore, we found that certain ecological and structural characteristics of device location were associated with higher trap capture and/or bait consumption. Results of this investigation suggest that rodent management at food distribution centers can be improved with assessment-based placement of traps and bait stations. In addition to reducing food safety threats through improved trap capture, this approach can reduce the number of devices to service and redirect service time toward pro-active inspections, rather than trap checking. Finally, device locations that are assessment-based align with the 2011 Food Safety Modernization Act that mandates preventive controls to protect human food.
... The influence of matrix is usually related to the movement of individuals between habitat patches in the landscape, where it can act as a selective barrier to gene flow (Kuefler et al 2010;Cline and Hunter 2014). Landscapes with low matrix contrast, such as those composed by agroforestry, usually promote higher functional connectivity and gene flow among small mammals populations compared to landscapes with high contrast, such as urban areas and/or highways (Banks et al. 2005;Magle et al. 2010;Gardner-Santana et al. 2009). The identification of elements that contribute to functional connectivity is essential for understanding the mechanisms that drive long-term population persistence in fragmented landscapes (Van Buskirk 2012). ...
Understanding the genetic responses of different species to the landscape attributes is essential to improve conservation actions and decision-making. However, making generalizations about such responses is not trivial, since they can be influenced by several factors. Aspects related to landscape matrix quality, for example, such as contrast and heterogeneity, may play a relevant role in the spatial-genetic structuring of populations since functional connectivity is influenced by the degree of matrix permeability. Intending to identify trends of genetic responses to habitat fragmentation and the aspects influencing these responses, we employed a meta-analytical approach to investigate the degree of genetic structuring of small mammal populations, measured through the fixation index (FST), in anthropogenic landscapes. For this, we obtained data of 28 species from 38 studies worldwide. We investigated the heterogeneity among species’ responses by focusing on the influence of matrix quality (contrast and heterogeneity), and species’ life-history traits (mean dispersal distance, generation time, and locomotor mode), controlling the influence of the marker type used in the study and the isolation by distance (IBD) among the patches habitat. We found a consistent pattern of genetic structuring of small mammal populations in anthropogenic landscapes, which present a significant genetic differentiation. Genetic structure is mostly influenced by matrix quality characteristics so that populations established in landscapes with high contrast and more heterogeneous matrices tend to be more structured. Also, populations of species with long generation time and high dispersal capacity exhibit a greater degree of genetic structure. Besides, accounting for IBD as a fixed effect was crucial to understand the variation among studies’ findings. Thus, the degree of genetic structuring of small mammal populations reflects the functional connectivity of the landscape, resulting from a balance between landscape attributes (matrix contrast and heterogeneity) and species’ life-history traits. Overall, our findings suggest that small mammals may be more susceptible to fragmentation than previously recognized, calling for special attention to this group considering their importance to maintain community structure and ecosystem functioning.
... This is a very different interpretation to that offered by Parsons et. al 2020, where the assumption of the mass movement of rats might drive an increase in genetic variation due to interbreeding between not previously connected populations 76,77 . ...
Shortly after the enactment of restrictions aimed at limiting the spread of COVID-19, local governments and public health authorities around the world reported an increased sighting of rats. We combined multi-catch rodent station data, rodent bait stations data, and rodent-related residents’ complaints data to explore the effects that social distancing and lockdown measures might have had on the rodent population within the City of Sydney, Australia. We found that rodent captures, activity, and rodent related residents’ complaints increased during the COVID-19 related lockdown period, followed by a steep decline post-lockdown. We found no changes in the geographical distribution of any of our indices of rodent abundance. We hypothesize that lockdown measures resulted in an increase in rodent activity driven by a reduction in human-derived food resources. This might have increased the mortality rate, triggering a population crash. There is a high chance that the surviving individuals might be rodenticide resistant. It is possible that the onset of COVID-19 might have disrupted commensal rodent populations, with profound implications for the future management of these ubiquitous urban indicator species.
... Within the population genetic structure of the two parapatric rat subspecies, we found relatively high genetic diversity within each of the three clusters ( Table 2). The genetic diversity levels observed here were compared with results reported for urban R. norvegicus individuals (He ranged from 0.67 to 0.78) (Gardner-Santana et al. 2009). The levels of genetic diversity were also comparable to those obtained for R. norvegicus according to fine-scale genetic structures (Abdelkrim et al. 2010;Kajdacsi et al. 2013). ...
Two parapatric Rattus norvegicus subspecies, R. n. humiliatus (RNH) and R. n. caraco (RNC), are classified according to morphological divergence and are mainly distributed in North and NE China. Here, we aimed to explore the population genetic structure, genetic boundary and gene flow in these rats using 16 microsatellite loci. Structure analysis and PCA revealed three ancestral clusters. We found that the intermediate cluster exhibited higher genetic diversity and a lower inbreeding coefficient than the other two clusters. The genetic differentiation between the three clusters was significant but weak, with a higher Fst value being observed between the clusters on both sides. The subspecies boundary inferred from microsatellite markers may indicate the existence of an admixture or hybridization area covering Liaoning, Inner Mongolia and Jilin Provinces, rather than corresponding to the administrative provincial boundaries between Liaoning and Jilin. The RNH and RNC subspecies presented moderate gene exchange and an asymmetric bidirectional gene flow pattern, with higher gene flow from the RNH subspecies to the RNC subspecies, constraining speciation. Such genetic characteristics might be explained by biological processes such as dispersal ability, mate choice and dynamic lineage boundaries.
... (QGIS Development Team, 2019). The length of the side of the squares was defined considering the rat behavior and the home range usually covered around a permanent den (Gardner-Santana et al., 2009). Initially the priority was given to areas with buildings built in 60's and 70's ("60/70 area"), perimeter area located S and SW of the old town, i.e. dating back to the period of greater asbestos production and high densities of population. ...
Based on a large body of evidence asbestos minerals have been classified as carcinogens. Despite the Italian ban on asbestos in 1992 and the subsequent remediation activities, latent sources of contamination may still represent a hazard where asbestos were particularly used. Using wild rats as sentinel animals, this study aimed at uncovering sites with the greatest potential for non-occupational exposure to asbestos in the city of Casale Monferrato (Piedmont Region, Italy), where the largest Italian manufacturing plant of asbestos-cement had been active.
During the study period (2013–2015) a total of 40 wild rats were captured from 16 sampling capture points. The lungs of wild rats have been investigated by using scanning electron microscopy (SEM) with energy dispersive spectroscopy (EDS). The SEM-EDS detected the presence of asbestos fibres (tremolite/actinolite, amosite, and chrysotile) in rats' lungs from 11 sampling points. The hypothetical rats' home-range and the observed site-specific concentration of asbestos fibres per gram of dry lung tissue were used to identify areas to be targeted by additional search of latent sources of asbestos.
In conclusion, our results showed that the use of wild rats as sentinel animals may effectively integrate the strategies currently in use to reduce the exposure to asbestos.
... Instead, most agonistic behaviours are directed against intruders from outside the colony (Blanchard et al., 1988). This might explain the comparatively low dispersal rates in wild rats (Gardner-Santana et al., 2009;Puckett et al., 2016). In general, males seem to be less socially tolerant than females (Calhoun, 1979). ...
The Norway rat has important impacts on our life. They are amongst the most used research subjects, resulting in groundbreaking advances. At the same time, wild rats live in close association with us, leading to various adverse interactions. In face of this relevance, it is surprising how little is known about their natural behaviour. While recent laboratory studies revealed their complex social skills, little is known about their social behaviour in the wild. An integration of these different scientific approaches is crucial to understand their social life, which will enable us to design more valid research paradigms, develop more effective management strategies, and to provide better welfare standards. Hence, I first summarise the literature on their natural social behaviour. Second, I provide an overview of recent developments concerning their social cognition. Third, I illustrate why an integration of these areas would be beneficial to optimise our interactions with them.
... In comparison to other mammalian species, Rattus norvegicus live and feed in closer proximity to humans. These rodents harbor and disseminate zoonotic parasites through their ectoparasites or via biological materials; therefore, they play an active and main role in the transmission of various zoonotic diseases [17,18]. Tehran as the capital of Iran is a large city in the north of the country that features a continentalin uenced Hot-summer Mediterranean climate. ...
Background: Rattus norvegicus are reservoirs of various zoonotic parasites that have become a global public health concern. Considering the distribution of Rattus norvegicus throughout Tehran, this study aims to assess the frequency of zoonotic parasites carried by commensal rodents in Tehran, Iran.
Methods: The study considered five regions (North, South, West, East, and center) of Tehran as case studies. The serological method was used for detecting antibodies against Trichomonas vaginalis , Babesia spp, and Cryptosporidium spp using a commercial qualitative rat ELISA kit. The frequency of Toxoplasma gondii was surveyed by the conventional PCR method. Furthermore, nested PCR was used to detect Giardia spp and Leishmania spp in commensal Rattus norvegicus in Tehran.
Results: Approximately, 76% of 100 Rattus norvegicus tested were infected with at least one zoonotic parasite, which demonstrates the significant frequency of parasites within the study areas. Seroreactivity against Trichomonas vaginalis , Babesia spp, and Cryptosporidium spp was detected in 5%, 0%, and 1% of Rattus norvegicus tested, respectively. Toxoplasma gondii DNA was detected in 32 out of 100 (32%) Rattus norvegicus , and Leishmania spp and Giardia spp DNA were found in 18 out of 100 (18%) and 76 out of 100 (76%) Rattus norvegicus investigated, respectively.
Conclusion: The findings indicate a wide geographical dissemination of Giardia spp, Toxoplasma gondii , and Leishmania spp DNA in Rattus norvegicus within five districts of Tehran. In contrast, other parasites such as Cryptosporidium spp infection rarely occurred in Rattus populations. No evidence for the circulation of Babesia spp was found in this study.
... This database contains three levels of land-use classification with 32 land-use classes. First, we approximated the home range of each captured rat by constructing a 200 m-radius (Gardner-Santana et al. 2009;Heiberg et al. 2012) circular buffer zone around each point of capture. Using the Intersection and the Add Geometry Attributes tools, we extracted for each buffer zone (i.e. ...
Leptospirosis is a worldwide bacterial zoonosis which incidence is expected to increase in conjunction with global change. In urban ecosystems, synanthropic rats are the key source of Leptospira infection in humans and other animals. Risk assessment and prediction of human leptospirosis require investigations of the environment associated with the bacteria and infection patterns in the reservoir hosts. The objective of this study was to address the prevalence of mixed Leptospira infection in the lungs and kidneys of brown rats captured in three sites of the city centre of Vienna, Austria, between 2016 and 2018. A total of 96 brown rats were examined for the presence of Leptospira using PCR. Occurrence of mixed Leptospira infections was explored through next-generation sequencing (NGS). A logistic regression model was built to predict the individual infection status using morphological and land-use data. Overall, the prevalence of Leptospira interrogans in the kidney was 25% but varied among sites (0–36%). We did not evidence any pulmonary nor mixed infections. Host body mass and sex were strong predictors of Leptospira carriage in the sampled rats (relative variable importance (RVI) = 0.98 and 0.89, respectively) while the presence of water affected it moderately (RVI = 0.44). Our findings demonstrate that NGS is an unbiased approach to the direct characterisation of mixed leptospiral infections that could provide further insights into the ecology of Leptospira. Future surveillance programmes should consider the use of rats as sentinels for the early detection of emerging pathogenic Leptospira in urban ecosystems.
... can lead to low genetic diversity, high levels of inbreeding, and therefore low adaptation potential (Frankham et al. 1999). However, founder and bottleneck effects acting on urban populations can be mitigated in fragmented landscapes through functional connectivity of subpopulations (Gardner-Santana et al. 2009;Munshi-South and Nagy 2014;Stillfried et al. 2017). The extent to which subpopulations can be connected depends on both the dispersal capabilities of a species and the resistance to movement presented by the landscape matrix (Bowne and Bowers 2004;Michels et al. 2001). ...
Urban expansion is creating environmental stressors through land use change, habitat fragmentation, and habitat loss. These stressors, along with a host of others, are driving precipitous declines in vertebrate taxa around the world. Amphibians, often requiring a narrow range of environmental conditions, can be especially susceptible to the stressors of environmental change. Despite habitat loss and degradation, some amphibian species continue to persist in altered urban landscapes. The red-backed salamander (Plethodon cinereus) is one such- species and in this study, we assess how habitat patch size affects population density and genetic diversity of salamander populations in and around an urban center in Ohio, United States. Further, we examined patterns of genetic differentiation and landscape connectivity to understand gene flow between populations and tested for historic demographic bottleneck effects. Populations were sampled from 9 urban forest patches ranging in size from less than 1 ha to approximately 250 ha. There was no apparent effect of contiguous habitat patch size on salamander density nor genetic diversity, but we did observe significant genetic differentiation between 97% of pairwise population comparisons. The differentiation observed was not a result of overland distance or effective distance due to landscape resistance. There was evidence of historic bottlenecks at every site. These results suggest that density is driven by within-patch heterogeneity and that genetic diversity is affected by drivers other than patch size or contemporary population density. Our study demonstrates that red-backed salamanders can persist in wooded, urban parks, but that genetic diversity remains susceptible to demographic changes.
... An introduced population with high genetic diversity but low genetic structure throughout a city suggests a recent, rapidly spreading invasion and/or high rates of movement and genetic exchange across the urban range. Patterns of high diversity and low structure are common in synurbic invasive invertebrate and rodent populations (Gardner-Santana et al. 2009;Mangombi et al. 2016;Rutkowski et al. 2017;Sherpa et al. 2018). However, the cause of this pattern varies between invasions. ...
The rapid expansion of urban land across the globe presents new and numerous opportunities for invasive species to spread and flourish. Ecologists historically rejected urban ecosystems as important environments for ecology and evolution research but are beginning to recognize the importance of these systems in shaping the biology of invasion. Urbanization can aid the introduction, establishment, and spread of invaders, and these processes have substantial consequences on native species and ecosystems. Therefore, it is valuable to understand how urban areas influence populations at all stages in the invasion process. Population genetic tools are essential to explore the driving forces of invasive species dispersal, connectivity, and adaptation within cities. In this review, we synthesize current research about the influence of urban landscapes on invasion genetics dynamics. We conclude that urban areas are not only points of entry for many invasive species, they also facilitate population establishment, are pools for genetic diversity, and provide corridors for further spread both within and out of cities. We recommend the continued use of genetic studies to inform invasive species management and to understand the underlying ecological and evolutionary processes governing successful invasion.
... . an uncertain "group" containing unaffiliated species whose phylogenetic history has not yet been established extensive systems of tunnels and passages in riverbanks and open spaces, where they live and breed (Barnett, 2005). Like most mammals, rats are characterized by female philopatry and male dispersal ( Gardner-Santana et al., 2009). Rats choose their habitats based on the availability of shelter, food and water (Orgain and Schein, 1953). ...
The Norway rat, from an obnoxious pest to a laboratory pet Abstract The laboratory rat was the first mammal domesticated for research purposes. It is descended from wild Norway rats, Rattus norvegicus, which despite their name likely originated in Asia. Exceptionally adaptable, these rodents now inhabit almost all environments on Earth, especially near human settlements where they are often seen as pests. The laboratory rat thrives in captivity, and its domestication has produced many inbred and outbred lines that are used for different purposes, including medical trials and behavioral studies. Differences between wild Norway rats and their laboratory counterparts were first noted in the early 20 th century and led some researchers to later question its value as a model organism. While these views are probably unjustified, the advanced domestication of the laboratory rat does suggest that resuming studies of wild rats could benefit the wider research community.
Leptospirosis (caused by pathogenic bacteria in the genus Leptospira) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, such as rats, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus, is an important reservoir of leptospirosis in urban settings. We investigated leptospirosis among brown rats in Boston, Massachusetts and hypothesized that rat dispersal in this urban setting influences the movement, persistence, and diversity of Leptospira. We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016-2022); 59 rats representing 12 of 17 sites were positive for Leptospira. We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira isolates obtained from frozen and fresh tissue from some of the 59 Leptospira-positive rat kidneys. When isolates were not obtained, we attempted Leptospira genomic DNA capture and enrichment, which yielded 14 additional Leptospira genomes from rats. We also generated an enriched Leptospira genome from a 2018 human case in Boston. We found evidence of high genetic structure and limited dispersal among rat populations that is likely influenced by major roads and/or other unknown dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats, with specific clades tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and movement of leptospirosis in this urban rat community is driven by rat dispersal. Finally, our genomic analyses of the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other urban settings.
Rodents serve as the main carriers for leptospirosis disease. Home range and habitat usage are part of the ecological study, which was less explored in disease ecology. In this study, Rattus norvegicus (RN), Rattus rattus complex (RR), and Sundamys muelleri (SM) were chosen due to their high prevalence with pathogenic Leptospira. Three pairs of each species were tracked from urban, semi-urban, and forested areas. The rats were fitted with a transmitter radio-collar and tracked with a portable telemetry receiver consisting of a 3-element Yagi antenna and located using standard methods of ground-based triangulation. Home range and core area were higher in the forest species (SM) than urban species (RN and RR). RN roaming and nesting areas were restricted inside houses and sewers, which is similar to RR roaming outside houses but nesting in houses. SM shows more expansive roaming areas in the forest but occasionally visits dump sites. Food resources, primarily from leftovers and dumping sites, were found to be the main factor in the viability of these species. The information on the movement ecology of rats could give accurate and valuable data on the population control, by targeting the specific areas occupied by the rats.
International trade has been favouring the dissemination of a wide suite of invasive alien species. Upstream prevention through the monitoring of entry points is identified as an appropriate strategy to achieve control of bioinvasions and their consequences. Maritime transportation has been responsible for the introduction worldwide of exotic rodents that are major pests for crops and food stocks as well as reservoirs of many zoonotic pathogens. In order to limit further dissemination, the International Health Regulation constrains decisions makers and socio‐economic stakeholders to manage ship‐mediated import/export of rodents within seaports.
Unfortunately, eco‐evolutionary insights into rodent introduction events that could guide preventive actions in seaports are very scarce. In order to bridge this gap, we here describe the results of a 3 year‐long survey of small mammals conducted in the Port of Cotonou, Benin.
Our aim was to assess the spatiotemporal distribution, diversity and relative abundance of invasive and native rodents.
960 small mammal individuals were captured in nine within‐seaport sites. We found (i) a marked predominance of invasive species (84% of the individuals belonging to Mus musculus , Rattus rattus , R. norvegicus ), (ii) with native species (i.e. Mastomys natalensis and the shrew Crocidura olivieri ) essentially restricted to peripheral non‐industrial areas, as well as (iii) a fine‐scale spatial segregation stable over time between the invasive Norway rats and house mice on the one hand, and the black rats and shrews on the other hand.
Furthermore, trapping before and after two successive rodent control campaigns indicates that they were ineffective and that subsequent rodent recolonisation occurred 6–12 months following intervention.
Synthesis and applications . Our results are discussed in terms of ecological processes at play (e.g. interspecific interactions) and operational recommendations (e.g. assessment of proper eradication units, environmental modifications).
For mammals that originate in the cold north, adapting to warmer environments is crucial for southwards invasion. The brown rat (Rattus norvegicus) originated in Northeast China and has become a global pest. R. n. humiliatus (RNH) spread from the northeast, where R. n. caraco (RNC) lives, to North China and diverged to form a subspecies. Genomic analyses revealed that subspecies differentiation was promoted by temperature but impeded by gene flow and that genes related to fatty acid metabolism were under the strongest selection. Transcriptome analyses revealed downregulated hepatic genes related to fatty acid metabolism and upregulated those related to pheromones in RNH vs. RNC. Similar patterns were observed in relation to cold/warm acclimation. RNH preferred mates with stronger
pheromone signals intra-populationally and more genetic divergence inter-populationally. We concluded that RNH experienced reduced fat utilization and increased pheromone-mediated sexual selection during its invasion from the cold north to warm south.
Humans and wildlife experience complex interactions in urban ecosystems, favoring the presence of commensal species, among which invasive species are particularly successful. Rodents are the main vertebrate group introduced to oceanic islands, where the invasion process and dispersal patterns strongly influence their evolutionary and genetic patterns. We evaluated the house mouse Mus musculus and the black rat Rattus rattus on Cozumel island, Mexico. We assessed genetic diversity and structure, connectivity, gene flow, relatedness and bottleneck signals based on microsatellite loci. Our findings show that the constant introduction of individuals of different origins to the island promotes high allelic diversity and the effective establishment of migrants. We identified a clear genetic structure and low connectivity for the two species, tightly linked with anthropogenic and urban features. Moreover, we found M. musculus has a particularly restricted distribution within the city of San Miguel Cozumel, whilst its genetic structure is associated with the historical human population growth pulses accompanying the urbanization of the city. At the fine-scale genetic level, the main urban drivers of connectivity of the house mouse were both the impervious land surfaces, i.e. the urban landscape, and the informal commerce across the city (a proxy of resources availability). Chances of a secondary invasion to natural environments have been relatively low, which is crucial for the endemic taxa of the island. Nonetheless, improving urban planning to regulate future expansions of San Miguel Cozumel is of the outmost importance in order to prevent these invasive species to disperse further.
The value of PTEN in tumors has long been appreciated including colorectal cancer (CRC). It is a negative regulator of the PI3K/AKT/mTOR signaling pathway that is known to be actuated in human cancers. However, PTEN-regulated modulation of the main pathway components in different rat ecosystems is unknown. The results demonstrated the negative transcriptional correlation between Pten and Mtor and Akt genes in rats living in an urban or rural habitat. The downregulation of Pten in colon epithelium led to the upregulation of Mtor and Akt genes, possessing risk in terms of CRC for urban rats. However, for rural rats this condition was vice versa, emphasizing that rural habitat can be protective in terms of CRC. The study is valuable for the identification of the link between cancer susceptibility and urban/rural environments. Furthermore, the cytotoxic effects of urbanization in rat populations were determined by detecting chromosomal aberrations. Due to the expansion of industrial and agricultural activities of the growing human population, the rapid vanishing of natural habitats is inevitable. Being also “messengers” of environmental pollution, the disclosure of health-affecting cellular processes in different habitats of rats living in close proximities to humans will contribute to environmental policies and human wellness.
Mammals have a symbiotic relationship with various microorganisms called microbiota throughout their lives. These microorganisms are known to affect the host’s physiology, health, and even mental balance. The development of the gut microbiota is regulated by a complex interaction between host and environmental factors, including diet and lifestyle. Herein, it is aimed to elucidate the differences in the gut microbiota of rats living in urban and rural habitats. The taxonomic changes in the gut microbiota of wild rats belonging to Rattus rattus species caught from urban and rural areas of Western Anatolian (Bilecik province) were examined comparatively by 16S rRNA next-generation sequencing technique. Laboratory rats were used as reference animals. The alpha diversities were found lower in the rural rats with respect to the urban rats, whereas the highest alpha diversity was calculated for laboratory rats. The lower Firmicutes to Bacteroidetes ratios (F/B ratio) were accounted for both rural and laboratory rats compared with urban rats. The Proteobacteria to Actinobacteria ratio (P/A ratio) was lower for rural rats, but higher for laboratory rats, compared with urban rats. The heatmap analyses of taxonomic units in the microbiota of each group demonstrated distinct patterns at the species and genus levels. The study provided metagenomic data on the gut microbiota of rats residing in urban and rural habitats, offering a different perspective on future environmental biomonitoring studies.
Environmental modifications generate interface environments in which Leptospira spp. transmission may be affected. In order to identify and analyze eco-environmental variables associated with potential reservoirs of Leptospira spp. in the Reserva Ecológica Costanera Sur (RECS) (Buenos Aires, Argentina) and adjacent urbanized areas, a stratified and proportionate transect line convenience sampling was carried out. A total of 170 mammals of 11 species were captured and analyzed for the presence of Leptospira spp. by serology, culture and PCR. In conserved areas, Didelphis albiventris and Deltamys kempi were mostly recorded, while Oligoryzomys flavescens was also found in degraded areas, and Rattus norvegicus was only found in degraded areas. Leptospira spp. were not detected in wild mammals. One dog without a responsible keeper tested positive by serology. The environmental conditions of the RECS suggest a poor ecosystem for Rattus, demonstrating the importance of the conservation of natural areas in urban environments.
Las modificaciones ambientales generan entornos de interfaz en los que la transmisión de Leptospira spp. puede verse afectada. Con el objetivo de identificar y analizar variables ecoambientales asociadas a potenciales reservorios de Leptospira spp. en la Reserva Ecológica Costanera Sur (RECS) (Buenos Aires, Argentina) y áreas urbanizadas contiguas, se realizó un muestreo por conveniencia en líneas transectas, estratificado y proporcionado. Fueron capturados 170 mamíferos de 11 especies y se analizó la presencia de Leptospira spp. por serología, cultivo y PCR. En áreas conservadas, se registraron mayormente Didelphis albiventris y Deltamys kempi, mientras que el Oligoryzomys flavescens también fue hallado en áreas degradadas, y la Rattus norvegicus solo fue encontrada en áreas degradadas. No se detectó Leptospira spp. en los mamíferos silvestres. Un perro sin tenedor responsable resultó positivo por ser0ología. Las condiciones ambientales de la RECS sugieren un ecosistema poco propicio para Rattus, evidenciando la importancia de la conservación de áreas naturales en entornos urbanos.
Common medical problems diagnosed and treated in individual companion exotic mammals are relevant in a herd-health setting. Many of these problems are often associated with poor husbandry and/or inappropriate nutrition. Rabbits, ferrets, chinchillas, and rodents have been domesticated alongside humans and an understanding of their ethology gives veterinarians a base knowledge in making recommendations for animals in their care. This article briefly reviews the ethology and husbandry in such species, but detailed needs are beyond the scope of this article.
Bartonella species are recognized globally as emerging zoonotic pathogens. Small mammals such as rodents and shrews are implicated as major natural reservoirs for these microbial agents. Nevertheless, in several tropical countries, like India, the diversity of Bartonella in small mammals remain unexplored and limited information exists on the natural transmission cycles (reservoirs and vectors) of these bacteria. Using a multi-locus sequencing approach, we investigated the prevalence, haplotype diversity, and phylogenetic affinities of Bartonella in small mammals and their associated mites in a mixed-use landscape in the biodiverse Western Ghats in southern India. We sampled 141 individual small mammals belonging to eight species. Bartonella was detected in five of the eight species, including three previously unknown hosts. We observed high interspecies variability of Bartonella prevalence in the host community. However, the overall prevalence (52.5%) and haplotype diversity (0.9) was high for the individuals tested. Of the seven lineages of Bartonella identified in our samples, five lineages were phylogenetically related to putative zoonotic species– B . tribocorum , B . queenslandensis , and B . elizabethae . Haplotypes identified from mites were identical to those identified from their host species. This indicates that these Bartonella species may be zoonotic, but further work is necessary to confirm whether these are pathogenic and pose a threat to humans. Taken together, these results emphasize the presence of hitherto unexplored diversity of Bartonella in wild and synanthropic small mammals in mixed-use landscapes. The study also highlights the necessity to assess the risk of spillover to humans and other incidental hosts.
Cities are uniquely complex systems regulated by interactions and feedbacks between natural and social processes. Characteristics of human society – including culture, economics, technology, and politics – underlie social patterns and activity, creating a heterogeneous environment that can influence and be influenced by both ecological and evolutionary processes. Increasing interest in urban ecology and evolutionary biology has coincided with growing interest in eco‐evolutionary dynamics, which encompasses the interactions and reciprocal feedbacks between evolution and ecology. Research on both urban evolutionary biology and eco‐evolutionary dynamics frequently focuses on contemporary evolution of species that have potentially substantial ecological – and even social – significance. Still, little research fully integrates urban evolutionary biology and eco‐evolutionary dynamics, and rarely do researchers in either of these fields fully consider the role of human social patterns and processes. Because cities are fundamentally regulated by human activities, are inherently interconnected, and are frequently undergoing social and economic transformation, they represent an opportunity for ecologists and evolutionary biologists to study urban “socio‐eco‐evolutionary dynamics.” Through this new framework, we encourage researchers of urban ecology and evolution to fully integrate human social drivers and feedbacks to increase understanding and conservation of ecosystems, their functions, and their contributions to people within and outside cities.
In recent decades Madagascar has experienced significant habitat loss and modification, with minimal understanding of how human land use practices have impacted the evolution of its flora and fauna. In light of ongoing and intensifying anthropogenic pressures, we seek new insight into mechanisms driving genetic variability on this island, using a Critically Endangered lemur species, the black-and-white ruffed lemur (Varecia variegata), as a test case. Here, we examine the relative influence of natural and anthropogenic landscape features that we predict will impose barriers to dispersal and promote genetic structuring across the species range. Using circuit theory, we model functional connectivity among 18 sampling localities using population-based genetic distance (FST). We optimized resistance surfaces using genetic algorithms and assessed their performance using maximum-likelihood population-effects mixed models. The best supported resistance model was a composite surface that included two anthropogenic features, habitat cover and distance to villages, suggesting that rapid land cover modification by humans has driven change in the genetic structure of wild lemurs. Primary conservation priority should be placed on mitigating further forest loss and connecting regions identified as having low dispersal potential to prevent further loss of genetic diversity and promote the survival of other moist forest specialists.
Correspondance : chapuimp@supagro.inra.fr
We use population genetics theory and computer simulations to demonstrate that population bottlenecks cause a characteristic mode-shift distortion in the distribution of allele frequencies at selectively neutral loci. Bottlenecks cause alleles at low frequency (< 0.1) to become less abundant than alleles in one or more intermediate allele frequency class (e.g., 0.1-0.2). This distortion is transient and likely to be detectable for only a few dozen generations. Consequently only recent bottlenecks are likely to be detected by tests for distortions in distributions of allele frequencies. We illustrate and evaluate a qualitative graphical method for detecting a bottleneck-induced distortion of allele frequency distributions. The simple novel method requires no information on historical population sizes or levels of genetic variation; it requires only samples of 5 to 20 polymorphic loci and approximately 30 individuals. The graphical method often differentiates between empirical datasets from bottlenecked and nonbottlenecked natural populations. Computer simulations show that the graphical method is likely (P > .80) to detect an allele frequency distortion after a bottleneck of < or = 20 breeding individuals when 8 to 10 polymorphic microsatellite loci are analyzed.
To evaluate whether the abundance of coyotes Canis latrans was influenced by the availability of anthropogenic foods in a humanized landscape, we compared three neighboring areas (hereafter referred to as NA, CA, and SA) under contrasting human pressures within the Santa Monica Mountains of California, USA. We quantified the use of anthropogenic foods by coyotes and assessed local densities within these three regions. Overall, 761 coyote feces were analyzed; identified food items were categorized into 11 food types (7 native and 4 anthropogenic). Though small mammals (lagomorphs and rodents) were the main prey of coyotes in all areas and seasons, log-linear modeling of multiway contingency tables indicates that consumption of anthropogenic foods by coyotes varied significantly throughout study areas. Thus, in the most humanized area (CA; 24% of this region is residential habitat), anthropogenic foods (trash, livestock, domestic fruit) comprised seasonally between 14 and 25% of total items in coyote diets, whereas in the least humanized area (NA; 2% residential) anthropogenic foods only comprised seasonally between 0 and 3% of items. Coyote density, estimated by foot-hold trapping surveys and by genotyping feces, was also highly variable between areas. The heavily human-impacted CA area had the highest coyote density (2.4-3.0 ind. km-2), whereas coyote density was significantly lower (0.3-0.4 ind. km-2) in the least humanized area (NA). In the third region (SA; 10% residential), with an intermediate level of human pressure, both importance of anthropogenic foods in coyote diet (4-6%) and coyote density (1.6-2.0 ind. km-2) were intermediate compared to the other regions. Our data suggest that subsidization by anthropogenic foods augments coyote densities and alters their diets in the Santa Monica Mountains, California. We include data from literature to show that anthropogenic foods are used by omnivorous mammals throughout the world. Surprisingly, however, the potential effects of allochthonous inputs on such species are not well-understood. Thus, further research on this phenomenon in humanized landscapes is needed.
Dominance relations between the adult males were stable and organised in a near-linear hierarchy. Dyadic interactions not fitting the social hierarchy, as well as challenges by subordinates and overt aggression by dominants were rare (<5%) and principally occurred between animals of similar social rank. The correlates of social status within the colony show, for the first time in adult small mammals, that despite the significant role of body weight on the probability of winning contests, age was the most reliable indicator of adult dominance, with the higher ranking males being older but not necessarily heavier. Age also explained the outcome of 85% of agonistic encounters between dyads, compared with 65% for weights. The proximate mechanisms of age-related dominance fit better the "previous outcome' hypothesis than the alternative "fighting skill' or "site dominance' hypotheses. The stability of dominance relations and the role of age, which in stable groups is equivalent with time spent in the colony, suggest that rats remain dominant over individuals that they have beaten in the past, long after initial body weight asymmetries have disappeared. The functional significance of the acceptance of subordinate social status is consistent with the fact that dominant individuals generally could not monopolize food resouces or mates. -from Authors
Chromosome aberration frequency in relation to population dynamics and demographic parameters was studied for six years in
a bank vole population in the Middle Urals. The frequencies of structural chromosome aberrations, chromatid gaps, aneuploidy,
and polyploidy in males and females and in animals of different ages did not differ significantly. In the breeding period,
the frequencies of structural aberrations and changes in chromosome number increased in the somatic cells of voles. Highly
significant differences between the levels of chromosome instability in different years manifested a tendency toward a negative
correlation with population size.
Geneland is a computer package that allows to make use of georeferenced individual multilocus genotypes for the inference of the number of populations and of the spatial location of genetic discontinuities between those populations. Main assumptions of the method are: (i) the number of populations is unknown and all values are considered a priori equally likely, (ii) populations are spread over areas given by a union of some polygons of unknown location in the spatial domain, (iii) Hardy–Weinberg equilibrium is assumed within each population and (iv) allele frequencies in each population are unknown and treated as random variable either following the so-called Dirichlet model or Falush model. Different algorithms implemented in Geneland to perform inferences are first briefly presented. Then major running steps and outputs (i.e. histogram of number of populations and map of posterior probabilities of population membership) are illustrated from the analysis of a simulated data set, which was also produced by Geneland.
Traditional methods for characterizing genetic differentiation among populations rely on a priori grouping of individuals. Bayesian clustering methods avoid this limitation by using linkage and Hardy–Weinberg disequilibrium to decompose a sample of individuals into genetically distinct groups. There are several software programs available for Bayesian clustering analyses, all of which describe a decrease in the ability to detect distinct clusters as levels of genetic differentiation among populations decrease. However, no study has yet compared the performance of such methods at low levels of population differentiation, which may be common in species where populations have experienced recent separation or high levels of gene flow. We used simulated data to evaluate the performance of three Bayesian clustering software programs, PARTITION, STRUCTURE, and BAPS, at levels of population differentiation below F
ST=0.1. PARTITION was unable to correctly identify the number of subpopulations until levels of F
ST reached around 0.09. Both STRUCTURE and BAPS performed very well at low levels of population differentiation, and were able to correctly identify the number of subpopulations at F
ST around 0.03. The average proportion of an individual’s genome assigned to its true population of origin increased with increasing F
ST for both programs, reaching over 92% at an F
ST of 0.05. The average number of misassignments (assignments to the incorrect subpopulation) continued to decrease as F
ST increased, and when F
ST was 0.05, fewer than 3% of individuals were misassigned using either program. Both STRUCTURE and BAPS worked extremely well for inferring the number of clusters when clusters were not well-differentiated (F
ST=0.02–0.03), but our results suggest that F
ST must be at least 0.05 to reach an assignment accuracy of greater than 97%.
I studied the proximal factors influencing dispersal from the natal site in two free-living populations of Belding's ground squirrels (Spermophilus beldingi) in the Sierra Nevada of California. I tested 10 hypotheses, each suggesting a different social, ecological, or ontogenetic factor as a proximal cause of natal dispersal in this species. Using discriminant analysis I also examined effects on dispersal of several independent variables concurrently. Data from marking and live-trapping studies over three field seasons (1979-1981) failed to support hypotheses suggesting resource shortage, ectoparasite load, social facilitation, conspecific aggression, or avoidance by conspecifics as proximal causes of natal dispersal in S. beldingi. Furthermore, dispersal is apparently not caused by changes in juveniles' response thresholds to conspecific aggression or by juveniles' attempts to avoid members of their family units, nearest neighbors, or other members of their local populations. My data supported an @'ontogenetic switch@' hypothesis that suggests natal dispersal by male S. beldingi is triggered by attainment of a particular body mass or body composition, or some combination of these two variables. Other data indicated that this ontogenetic switch initiates not only dispersal behavior per se, but also a larger syndrome o behaviors that appear to be functionally related to dispersal. Specifically, this syndrome involves changes in exploration, responses to frightening stimuli, and locomotor behavior exhibited by dispersers. I discuss possible relationships among variables operating at different proximal levels (sensu Tinbergen) to cause natal dispersal in S. beldingi and other mammals. I conclude that a complex suite of variables probably operates at genetic, physiological, and socioecological levels to proximally cause natal dispersal in each species. The ultimate (evolutionary) hypotheses most consistent with my data from S. beldingi are that dispersal: (1) reduces nuclear family incest, (2) optimizes inbreeding, and (3) improves access to mates.
The quality of the habitat patch in which individuals reside may influence demographic processes, thus affecting social organization. We manipulated the risk of predation and food availability to test the hypothesis that high patch quality decreased the propensity to disperse, increased the likelihood of social units becoming groups, and increased overall group size in prairie voles (Microtus ochrogaster). Prairie voles are socially monogamous, at least in part of their range, and they display varied social organization within a population, including groups (containing a breeding pair and at least 1 additional adult of either sex), male–female pairs, and single females. Our results indicated that the likelihood of dispersal from high-quality patches was significantly less than from lowquality patches. Dispersers also were significantly more likely to settle in similar or higher quality patches than the ones in which they were originally released. These patterns were primarily due to the dispersal of young males. Although the proportion of social units that were groups appeared to decrease with lower patch quality, the difference in social organization among patch types was not statistically significant. The total number of founding voles and founding males per social unit residing in the highest quality patches at the end of the study were significantly greater than in the lowest quality patches. Thus, under the conditions of our experiment, patch quality affected dispersal and group size but not the tendency to form groups.
The genetic structure of reservoir populations is a key characteristic in understanding the persistence of infectious diseases in natural systems. In the Highlands of Madagascar, where plague has persisted since 1920, the black rat, Rattus rattus (L., 1758), is the sole species acting as a reservoir of the disease. Ecological surveys have shown a clear correlation between the locations of the plague-persistence area in Madagascar (above 800 m elevation) and the distribution area of one endemic plague vector, the flea Synopsyllus fonquerniei, which is found exclusively on rats living outdoors. This clear habitat segregation has led to the suggestion that R. rattus populations in the central highlands are divided into indoor- and outdoor-dwelling populations. Using eight microsatellite markers, we analysed the genetic structure of R. rattus populations living within a human plague focus in relation to habitat and geographic distance. We found that habitat by itself was not a structuring factor, unlike geographic distance. Nevertheless, the significant genotypic differentiation of R. rattus populations that was found at a fine spatial scale might relate to differences in population dynamics between rats in indoor and outdoor habitats.
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.
The effect of female philopatry on the apportionment of gene diversity within a population is evaluated. Even with random mate selection, the apportionment of gene diversity within and among social lineages (groups of related females) is inherently different than in classically defined demic groups. Considerable excess heterozygosity occurs within lineages without substantial changes in total or population heterozygosity. The proportion of genetic variance among lineages within the population was dependent on the lineage size and the number of male breeders per lineage. The greatest genetic differentiation among lineages was evident when there was one polygynous male breeding within a lineage of philopatric females, a common breeding tactic in mammalian social systems. The fixation indices depicting the genetic structure of the population were found to attain constant values after the first few generations despite the continuous loss of gene diversity within the population by genetic drift. Additionally, the change of gene correlations within individuals relative to the change within the population attains a state of dynamic equilibrium, as do the changes of gene correlations within lineages relative to the total and within individuals relative to within lineages. Comparisons of coancestries and fixation indices for philopatric versus randomly dispersing females indicate that philopatry and polygyny have probably not evolved independently and that promotion of gene correlations among adults rather than offspring has been of primary importance.
While the concept of effective population size is of obvious applicability to many questions in population genetics and conservation biology, its utility has suffered due to a lack of agreement among its various formulations. Often, mathematical formulations for effective sizes apply restrictive assumptions that limit their applicability. Herein, expressions for effective sizes of populations that account for mating tactics, biases in sex ratios, and differential dispersal rates (among other parameters) are developed. Of primary interest is the influence of multiple paternity on the maintenance of genetic variation in a population. In addition to the standard inbreeding and variance effective sizes, intragroup (coancestral) and intergroup effective sizes also are developed. Expressions for effective sizes are developed for the beginning of nonrandom gene exchanges (initial effective sizes), the transition of gene correlations (instantaneous effective sizes), and the steady-state (asymptotic effective size). Results indicate that systems of mating that incorporate more than one male mate per female increase all effective sizes above those expected from polygyny and monogamy. Instantaneous and asymptotic sizes can be expressed relative to the fixation indices. The parameters presented herein can be utilized in models of effective sizes for the study of evolutionary biology and conservation genetics.
When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a heterozygosity excess are described. They require measurements of the number of alleles and heterozygosity at each of several loci from a population sample. The first test determines if the proportion of loci with heterozygosity excess is significantly larger than expected at equilibrium. The second test establishes if the average of standardized differences between observed and expected heterozygosities is significantly different from zero. Type I and II errors have been evaluated by computer simulations, varying sample size, number of loci, bottleneck size, time elapsed since the beginning of the bottleneck and level of variability of loci. These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. The usefulness of these tests for conservation biology is discussed.
Analyses of fine-scale and macrogeographic genetic structure in plant populations provide an initial indication of how gene flow, natural selection, and genetic drift may collectively influence the distribution of genetic variation. The objective of our study is to evaluate the spatial dispersion of alleles within and among subpopulations of a tropical shrub, Psychotria officinalis (Rubiaceae), in a lowland wet forest in Costa Rica. This insect-pollinated, self-incompatible understory plant is dispersed primarily by birds, some species of which drop the seeds immediately while others transport seeds away from the parent plant. Thus, pollination should promote gene flow while at least one type of seed dispersal agent might restrict gene flow. Sampling from five subpopulations in undisturbed wet forest at Estación Biologíca La Selva, Costa Rica, we used electrophoretically detected isozyme markers to examine the spatial scale of genetic structure. Our goals are: 1) describe genetic diversity of each of the five subpopulations of Psychotria officinalis sampled within a contiguous wet tropical forest; 2) evaluate fine-scale genetic structure of adults of P. officinalis within a single 2.25-ha mapped plot; and 3) estimate genetic structure of P. officinalis using data from five subpopulations located up to 2 km apart. Using estimates of coancestry, statistical analyses reveal significant positive genetic correlations between individuals on a scale of 5 m but no significant genetic relatedness beyond that interplant distance within the studied subpopulation. Multilocus estimates of genetic differentiation among subpopulations were low, but significant (Fst = 0.095). Significant Fst estimates were largely attributable to a single locus (Lap-2). Thus, multilocus estimates of Fst may be influenced by microgeographic selection. If true, then the observed levels of IBD may be overestimates.
A new method is described for estimating genetic relatedness from genetic markers such as protein polymorphisms. It is based on Grafen's (1985) relatedness coefficient and is most easily interpreted in terms of identity by descent rather than as a genetic regression. It has several advantages over methods currently in use: it eliminates a downward bias for small sample sizes; it improves estimation of relatedness for subsets of population samples; and it allows estimation of relatedness for a single group or for a single pair of individuals. Individual estimates of relatedness tend to be highly variable but, in aggregate, can still be very useful as data for nonparametric tests. Such tests allow testing for differences in relatedness between two samples or for correlating individual relatedness values with another variable.
A knowledge of the effective size of a population (Ne ) is important in understanding its current and future evolutionary potential. Unfortunately, the effective size of a hierarchically structured population is not, in general, equal to the sum of its parts. In particular, the inbreeding structure has a major influence on Ne . Here I link Ne to Wright's hierarchical measures of inbreeding, FIS and FST , for an island-structured population (or metapopulation) of size NT . The influence of FST depends strongly on the degree to which island productivity is regulated. In the absence of local regulation (the interdemic model), interdemic genetic drift reduces Ne . When such drift is combined with local inbreeding under otherwise ideal conditions, the effects of FIS and FST are identical: increasing inbreeding either within or between islands reduces Ne , with Ne = NT /[(1 + FIS )(1 + FST ) - 2FIS FST ]. However, if islands are all equally productive because of local density regulation (the traditional island model), then Ne = NT /[(1 + FIS )(1 -FST )] and the effect of FST is reversed. Under the interdemic model, random variation in the habitat quality (and hence productivity) of islands act to markedly decrease Ne . This variation has no effect under the island model because, by definition, all islands are equally productive. Even when no permanent island structure exists, spatial differences in habitat quality can significantly increase the overall variance in reproductive success of both males and females and hence lower Ne . Each of these basic results holds when other nonideal factors are added to the model. These factors, deviations from a 1:1 sex ratio, greater than Poisson variance in female reproductive success, and variation in male mating success due to polygynous mating systems, all act to lower Ne . The effects of male and female variance on Ne have important differences because only females affect island productivity. Finally, it is noted that to use these relationships, FIS and FST must be estimated according to Wright's definition (and corrected to have a zero expectation under the null model). A commonly used partitioning (θ, θg ) can be biased if either island size or the number of islands is small.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
1.
Urban and rural populations of animals can differ in their behaviour, both in order to meet their
ecological requirements and due to the constraints imposed by different environments. The study
of urban populations can therefore offer useful insights into the behavioural flexibility of a species as
a whole, as well as indicating how the species in question adapts to a specifically urban environment.
2.
The genetic structure of a population can provide information about social structure and
movement patterns that is difficult to obtain by other means. Using non-invasively collected hair
samples, we estimated the population size of Eurasian badgers
Meles meles
in the city of Brighton,
England, and calculated population-specific parameters of genetic variability and sex-specific rates
of outbreeding and dispersal.
3.
Population density was high in the context of badger densities reported throughout their range.
This was due to a high density of social groups rather than large numbers of individuals per group.
4.
The allelic richness of the population was low compared with other British populations. However,
the rate of extra-group paternity and the relatively frequent (mainly temporary) intergroup movements
suggest that, on a local scale, the population was outbred. Although members of both sexes visited
other groups, there was a trend for more females to make intergroup movements.
5.
The results reveal that urban badgers can achieve high densities and suggest that while some
population parameters are similar between urban and rural populations, the frequency of intergroup
movements is higher among urban badgers. In a wider context, these results demonstrate the
ability of non-invasive genetic sampling to provide information about the population density, social
structure and behaviour of urban wildlife.
Microsatellite markers are routinely used to investigate the genetic structuring of natural populations. The knowledge of how genetic variation is partitioned among populations may have important implications not only in evolutionary biology and ecology, but also in conservation biology. Hence, reliable estimates of population differentiation are crucial to understand the connectivity among populations and represent important tools to develop conservation strategies. The estimation of differentiation is c from Wright's FST and/or Slatkin's RST, an FST -analogue assuming a stepwise mutation model. Both these statistics have their drawbacks. Furthermore, there is no clear consensus over their relative accuracy. In this review, we first discuss the consequences of different temporal and spatial sampling strategies on differentiation estimation. Then, we move to statistical problems directly associated with the estimation of population structuring itself, with particular emphasis on the effects of high mutation rates and mutation patterns of microsatellite loci. Finally, we discuss the biological interpretation of population structuring estimates.
A new method is described for estimating genetic relatedness from genetic markers such as protein polymorphisms. It is based on Grafen's (1985) relatedness coefficient and is most easily interpreted in terms of identity by descent rather than as a genetic regression. It has several advantages over methods currently in use: it eliminates a downward bias for small sample sizes; it improves estimation of relatedness for subsets of population samples; and it allows estimation of relatedness for a single group or for a single pair of individuals. Individual estimates of relatedness tend to be highly variable but, in aggregate, can still be very useful as data for nonparametric tests. Such tests allow testing for differences in relatedness between two samples or for correlating individual relatedness values with another variable.
(1) Radio-tracking techniques were used to study movements of rats on arable land. The mean range length for ten female rats was 340 m and for seven male rats 660 m. (2) Movement occurred primarily along hedgerows which provided cover, but several individuals occasionally crossed open ground, covering distances of up to 500 m without approaching cover. Most of the movements observed were between homesites and known food sources up to 500 m away. (3) Although the rats frequently changed their homesites, there was no noticeable tendency to move them towards recognized food sources in the area; changes of homesite were apparently random occurrences or were related to encounters with other rats. Males and females changed their homesites on average once every 7 and 14 days respectively. (4) The rats studied became active soon after sunset but generally did not move away from their homes until about one hour later. Peak activity occurred 4-5 h after sunset. Six of the twenty-one rats studied were active at times during daylight and one was predominantly diurnal. (5) Eleven rats with transmitters died during the experiment including five that were killed by predators. (6) The failure of outdoor rats to become established in farm buildings, despite apparent food shortage in the fields, is attributed to antagonism from rats already resident in the buildings.
A knowledge of the effective size of a population (Ne) is important in understanding its current and future evolutionary potential. Unfortunately, the effective size of a hierarchically structured population is not, in general, equal to the sum of its parts. In particular, the inbreeding structure has a major influence on Ne. Here I link Ne to Wright's hierarchical measures of inbreeding, FIS and FST, for an island-structured population (or metapopulation) of size NT. The influence of FST depends strongly on the degree to which island productivity is regulated. In the absence of local regulation (the interdemic model), interdemic genetic drift reduces Ne. When such drift is combined with local inbreeding under otherwise ideal conditions, the effects of FIS and FST are identical: increasing inbreeding either within or between islands reduces Ne, with Ne = NT/[(1 + FIS)(1 + FST) - 2FISFST]. However, if islands are all equally productive because of local density regulation (the traditional island model), then Ne = NT/[(1 + FIS)(1 - FST)] and the effect of FST is reversed. Under the interdemic model, random variation in the habitat quality (and hence productivity) of islands act to markedly decrease Ne. This variation has no effect under the island model because, by definition, all islands are equally productive. Even when no permanent island structure exists, spatial differences in habitat quality can significantly increase the overall variance in reproductive success of both males and females and hence lower Ne. Each of these basic results holds when other nonideal factors are added to the model. These factors, deviations from a 1:1 sex ratio, greater than Poisson variance in female reproductive success, and variation in male mating success due to polygynous mating systems, all act to lower Ne. The effects of male and female variance on Ne have important differences because only females affect island productivity. Finally, it is noted that to use these relationships, FIS and FST must be estimated according to Wright's definition (and corrected to have a zero expectation under the null model). A commonly used partitioning (θ, θg) can be biased if either island size or the number of islands is small.
Abstract On the basis of simulated data, this study compares the relative performances of the Bayesian clustering computer programsstructure,geneland,geneclustand a new program namedtess. While these four programs can detect population genetic structure from multilocus genotypes, only the last three ones include simultaneous analysis from geographical data. The programs are compared with respect to their abilities to infer the number of populations, to estimate membership probabilities, and to detect genetic discontinuities and clinal variation. The results suggest that combining analyses usingtessandstructureoffers a convenient way to address inference of spatial population structure.
Habitat fragmentation may have significant consequences for population genetic structure because geographic distance and physical barriers may impede gene flow. In this study, we investigated whether habitat fragmentation affects fine-scale genetic structure of populations of the white-footed mouse (Peromyscus leucopus). We studied 27 populations of P. leucopus, 17 in continuous forest and 10 in isolated woodlots. Populations were trapped in pairs that were either 500 or 2000 m apart. We estimated genetic variation at eight P. leucopus specific microsatellite DNA loci. We discovered significant genetic variation within all populations, but no significant differences in numbers of alleles or heterozygosity between populations. For given population pairs, we found significant genetic differentiation even at very short distances, based on multilocus FST estimates. The amount of genetic differentiation between population pairs was similar in the two habitats. Distance had a marginal effect on genetic differentiation when comparing paired populations separated by 2000 m with those separated by 500 m. However, at a larger geographic scale, there was no evidence of isolation by distance. This study confirms that microsatellite-based studies have the potential to detect interpopulation differentiation at an extremely local scale, and suggests that habitat fragmentation has surprisingly few effects on P. leucopus genetic structure.
Research on populations of rats (Rattus norvegicus) in Baltimore beginning in 1943 suggested the hypothesis that aggressive behavior could regulate the numbers in a city block where food and shelter were adequate. A program of experiments using wild rats or laboratory mice justified publication of the aggressive behavior hypothesis in 1949. Continued research by Davis, Calhoun, Christian and graduate students showed that the number of rats in a city block returned towards an asymptote after a reduction in number, and that the introduction of alien rats was followed by a decline. Communication about the level of population was achieved by signals (visual, olfactory, auditory and tactile) that determined social status. Rates of reproduction declined and rates of mortality increased as the population increased. Various physiological mechanisms were explored but the mechanisms of communication were little studied before 1955.
