Population structure and landscape genetics in the endangered subterranean rodent Ctenomys porteousi (original) (raw)
Related papers
Genetica, 2020
Understanding the processes and patterns of local adaptation and migration involves an exhaustive knowledge of how landscape features and population distances shape the genetic variation at the geographical level. Ctenomys australis is an endangered subterranean rodent characterized by having a restricted geographic range immerse in a highly fragmented sand dune landscape in the Southeast of Buenos Aires province, Argentina. We use 13 microsatellite loci in a total of 194 individuals from 13 sampling sites to assess the dispersal patterns and population structure in the complete geographic range of this endemic species. Our analyses show that populations are highly structured with low rates of gene flow among them. Genetic differentiation among sampling sites was consistent with an isolation by distance pattern, however, an important fraction of the population differentiation was explained by natural barriers such as rivers and streams. Although the individuals were sampled at locations distanced from each other, we also use some landscape genetics approaches to evaluate the effects of landscape configuration on the genetic connectivity among populations. These analyses showed that the sand dune habitat availability (the most suitable habitat for the occupation of the species), was one of the main factors that explained the differentiation patterns of the different sampling sites located on both sides of the Quequén Salado River. Finally, habitat availability was directly associated with the width of the sand dune landscape in the Southeast of Buenos Aires province, finding the greatest genetic differentiation among the populations of the Northeast, where this landscape is narrower.
Landscape Ecology, 2020
Context Anthropogenic activities have detrimental impacts on natural habitats and the species inhabiting them. In particular, habitat fragmentation has a profound effect on the dynamics and structure of natural populations and the species' probability of persistence. Objectives In this study, we examined which factors determine the population structure of Ctenomys species (tuco-tucos) at a local scale, evaluating the effects of natural and anthropic barriers on population divergence. Methods We sampled tuco-tucos at 28 localities and genotyped 231 individuals at 11 microsatellite loci. Additionally, we built six spatial layers that describe the landscape inhabited by tuco-tucos, to evaluate the effects of habitat traits in the movement of individuals. We applied Bayesian clustering methods to infer the population structure, and landscape genetic tools to understand how landscape traits affect this structure. Results We detected a high degree of population structure, even at a small spatial scale. Genetic structure seems to be influenced not only by current landscape configuration but also by their recent evolution. Altitude was the main contributing factor explaining this structure, with independent populations restricted to different sandy elevations in the region. However, anthropic activities were also shown to have had a significant effect on the differentiation among populations. Conclusions The accelerated transformation process that the region is undergoing strongly conditions the dynamics of population differentiation in Ctenomys and reduces prospects of viability for the species. Our findings underscore the importance of incorporating variables that describe the temporal component of habitat changes in landscapes experiencing intense and recent transformation processes.
Spatial genetic structure of a small rodent in a heterogeneous landscape
Molecular Ecology, 2008
Gene flow in natural populations may be strongly influenced by landscape features. The integration of landscape characteristics in population genetic studies may thus improve our understanding of population functioning. In this study, we investigated the population genetic structure and gene flow pattern for the common vole, Microtus arvalis, in a heterogeneous landscape characterised by strong spatial and temporal variation. The studied area is an intensive agricultural zone of approximately 500 km 2 crossed by a motorway. We used individual-based Bayesian methods to define the number of population units and their spatial borders without prior delimitation of such units. Unexpectedly, we determined a single genetic unit that covered the entire area studied. In particular, the motorway considered as a likely barrier to dispersal was not associated with any spatial genetic discontinuity. Using computer simulations, we demonstrated that recent anthropogenic barriers to effective dispersal are difficult to detect through analysis of genetic variation for species with large effective population sizes. We observed a slight, but significant, pattern of isolation by distance over the whole study site. Spatial autocorrelation analyses detected genetic structuring on a local scale, most probably due to the social organisation of the study species. Overall, our analysis suggests intense small-scale dispersal associated with a large effective population size. High dispersal rates may be imposed by the strong spatio-temporal heterogeneity of habitat quality, which characterises intensive agroecosystems.
BMC Genetics, 2010
Background: The population genetic structure of subterranean rodent species is strongly affected by demographic (e.g. rates of dispersal and social structure) and stochastic factors (e.g. random genetic drift among subpopulations and habitat fragmentation). In particular, gene flow estimates at different spatial scales are essential to understand genetic differentiation among populations of a species living in a highly fragmented landscape. Ctenomys australis (the sand dune tuco-tuco) is a territorial subterranean rodent that inhabits a relatively secure, permanently sealed burrow system, occurring in sand dune habitats on the coastal landscape in the south-east of Buenos Aires province, Argentina. Currently, this habitat is threatened by urban development and forestry and, therefore, the survival of this endemic species is at risk. Here, we assess population genetic structure and patterns of dispersal among individuals of this species at different spatial scales using 8 polymorphic microsatellite loci. Furthermore, we evaluate the relative importance of sex and habitat configuration in modulating the dispersal patterns at these geographical scales.
Genetica, 2016
In this study we combine information from landscape characteristics, demographic inference and species distribution modelling to identify environmental factors that shape the genetic distribution of the fossorial rodent Ctenomys. We sequenced the mtDNA control region and amplified microsatellites from 27 populations distributed across the Iberá wetland ecosystem. Hierarchical Bayesian modelling was used to construct phylogenies and estimate divergence times. We developed species distribution models to determine what climatic variables and soil parameters predicted species presence by comparing the current to the historic and predicted future distribution of the species. Finally, we explore the impact of environmental variables on the genetic structure of Ctenomys based on current and past species distributions. The variables that consistently correlated with the predicted distribution of the species and explained the observed genetic differentiation among populations included the distribution of well-drained sandy soils and temperature seasonality. A core region of stable suitable habitat was identified from the Last Interglacial, which is projected to remain stable into the future. This region is also the most genetically diverse and is currently under strong anthropogenic pressure. Results reveal complex demographic dynamics, which have been in constant change in both time and space, and are likely linked to the evolution of the Paraná River. We suggest that any alteration of soil properties (climatic or anthropic) may significantly impact the availability of suitable habitat and consequently the ability of individuals to disperse. The protection of this core stable habitat is of prime importance given the increasing levels of human disturbance across this wetland system and the threat of climate change.
Habitat islands, genetic diversity, and gene flow in a Patagonian rodent
Molecular …, 1998
The effects of terrestrial habitat islands on gene flow and genetic diversity in animal populations have been predicted and discussed in theoretical terms, but empirical data are needed to test these predictions and provide an understanding of the relationships of life-history characteristics to genetics of insular species. We studied saxicolous mice (Phyllotis xanthopygus) in Patagonia to explore genetic structure, phylogeography, and gene flow in a species inhabiting natural habitat islands. Phylogeographic analyses based on mtDNA sequences revealed two haplotype clades, which presumably reflect early Pleistocene factors that temporarily separated the mice into two geographically isolated groups. The Río Chubut, which lies within a glacial drainage basin bisecting northern Patagonia, might have affected gene flow in the species. Although we anticipated isolation by distance and founder phenomena associated with habitat islands, in some habitat patches we found evidence of high local genetic diversity. The amount of divergence in the mitochondrial cytochrome b gene (≈ 3.4%) in animals at a single locality could best be explained through a combination of historical factors and metapopulation source-sink theory. Demographic shifts, dispersal, and episodic recolonization are important in the life history and genetic population structure of P. xanthopygus.
Spatial genetic structuring in a vagile species, the European wood mouse
Journal of Zoology, 2009
We examined the genetic structure of natural populations of the European wood mouse Apodemus sylvaticus at the microgeographic (o3 km) and macrogeographic (430 km) scales. Ecological and behavioural studies indicate that this species exhibits considerable dispersal relative to its home-range size. Thus, there is potential for high gene flow over larger geographic areas. As levels of population genetic structure are related to gene flow, we hypothesized that population genetic structuring at the microgeographic level should be negligible, increasing only with geographic distance. To test this, four sites were sampled within a microgeographic scale with two additional samples at the macrogeographic level. Individuals (n = 415) were screened and analysed for seven polymorphic microsatellite loci. Contrary to our hypothesis, significant levels of population structuring were detected at both scales. Comparing genetic differentiation with geographic distance suggests increasing genetic isolation with distance. However, this distance effect was non-significant being confounded by surprisingly high levels of differentiation among microgeographic samples. We attribute this pattern of genetic differentiation to the effect of habitat fragmentation, splitting large populations into components with small effective population sizes resulting in enhanced genetic drift. Our results indicate that it is incorrect to assume genetic homogeneity among populations even where there is no evidence of physical barriers and dispersal can occur freely. In the case of A. sylvaticus, it is not clear whether dispersal does not occur across habitat barriers or behavioural dispersal occurs without consequent gene flow.
Mammalian Biology
Determining the scale of genetic variation informs studies of dispersal, connectivity, and population dynamics particularly in heterogeneous landscapes. Mastomys natalensis and Mus minutoides are generalist rodents that utilize multiple habitat types within the agro-ecological landscapes of southern African savannas. To study the comparative spatial genetic structure of these species we developed 9 new microsatellites for Mus and used 14 microsatellite loci previously developed for Mastomys, to genotype rodents sampled across an agro-ecological landscape (200 km 2). Spatial genetic structure was measured using spatial autocorrelation and Moran's Eigenvector Maps analysis. In both species, non-random genetic similarity was limited to only the smallest spatial scales (<600 m), and at that scale, it was significantly greater in Mastomys than in Mus. Only a small proportion of the genetic signal across the landscape was due to spatial signal in Mastomys, and there was no spatial signal detected for Mus. The lack of spatial autocorrelation beyond the first six hundred meters for both species illustrated that they are capable of high rates of dispersal, while the observed patterns of genetic panmixia found for both species is the predicted genetic outcome for species with omnivorous habits and plastic habitat use. These findings have implications for both pest management and rodent-borne disease control.