Unexpected persistence on habitat islands: genetic signatures reveal dispersal of a eucalypt-dependent marsupial through a hostile pine matrix

Several factors contribute to the extinction of populations in fragmented habitat but key ones include habitat loss and disruptions to connectivity. Aspects of the ecology of greater gliders (Petauroides volans), along with observations of their response to native forest clearance at a site in southeastern Australia, lead to the prediction in the 1960s that the species would not persist in the replacement exotic pine plantation. However, 35 years later, the species was observed in many remnant native vegetation patches retained within the plantation boundary, albeit at a lower occupancy rate than at matched continuous forest control sites. To determine the role of patch connectivity in persistence of P. volans in remnants, we employed 12 microsatellite markers to genotype individuals from 11 remnants, three contemporary nearby continuous native eucalypt forest sites and a sample collected during native vegetation clearance at the site in the 1960s. Patch samples retained substantially more genetic diversity than expected under an isolation model, suggesting that patches have experienced some immigration. Five putative patch immigrants--two from sampled sites 1- and 7-km distant, and three from unresolved or unsampled localities--were identified via genetic parentage and population assignment analyses. Patch populations displayed varying levels of admixture in Bayesian genetic structure analyses, with the oldest and most geographically isolated ones showing the least admixture, suggesting they have experienced relatively little immigration. Evidence of at least some immigration into patches may explain why P. volans has persisted contrary to expectation in heavily fragmented habitat.     

Rapid,pervasive genetic differentiation of urban white‐footed mouse (Peromyscus leucopus) populations in New York City

We investigated genetic diversity and structure of urban white‐footed mouse, Peromyscus leucopus, populations in New York City (NYC) using variation at 18 microsatellite loci. White‐footed mice are ‘urban adapters’ that occur at higher population densities as habitat fragments are reduced in area but have a limited ability to disperse through urbanized areas. We hypothesized that this combination of traits has produced substantial genetic structure but minimal loss of genetic variation over the last century in NYC. Allelic diversity and heterozygosity in 14 NYC populations were high, and nearly all of our NYC study sites contained genetically distinct populations of white‐footed mice as measured by pairwise F_ST, assignment tests, and Bayesian clustering analyses performed by Structure and baps . Analysis of molecular variance revealed that genetic differences between populations separated by a few kilometres are more significant than differences between prehistorically isolated landmasses (i.e. Bronx, Queens, and Manhattan). Allele size permutation tests and lack of isolation by distance indicated that mutation and migration are less important than drift as explanations for structure in urban, fragmented P. leucopus populations. Peromyscus often exhibit little genetic structure over even regional scales, prompting us to conclude that urbanization is a particularly potent driver of genetic differentiation compared to natural fragmentation.     

Population genetic structure and dispersal across a fragmented landscape in cerulean warblers (<Emphasis Type="Italic">Dendroica cerulea</Emphasis>)

Cerulean warblers (Dendroica cerulea) have experienced significant declines across their breeding range and presently exist in disjunct populations, largely because of extensive loss and fragmentation of their breeding and wintering habitat. Despite this overall decline, a recent north-eastern expansion of the breeding range has been proposed, and some researchers have suggested that the eastern Ontario population may be acting as a source population maintaining sink populations elsewhere. However, little is known about either the geographic distribution of genetic variation or dispersal in these birds. We assayed variation in five microsatellite loci and a 366 base-pair fragment of the mitochondrial control region among 154 cerulean warblers from five populations throughout the breeding range. No evidence of population genetic structure was found. Assignment tests suggested that six individuals were either inter-population migrants or descendants of recent migrants. The lack of population genetic structure is probably due to a combination of historical association and contemporary dispersal. Population decline does not appear to have reduced genetic variation yet. Overall results suggest that cerulean warblers from Ontario, Illinois, Arkansas and Tennessee should be considered a single genetic management unit for conservation.     

Population genetic effects of urban habitat fragmentation in the perennial herb Viola pubescens (Violaceae) using ISSR markers

BACKGROUND AND AIMS: Fragmentation of natural habitats can negatively impact plant populations by leading to reduced genetic variation and increased genetic distance as populations become geographically and genetically isolated from one another. To test whether such detrimental effects occur within an urban landscape, the genetic structure of six populations of the perennial herb Viola pubescens was characterized in the metropolitan area of Greater Cincinnati in southwestern Ohio, USA. METHODS: Using three inter-simple sequence repeat (ISSR) markers, 51 loci amplified across all urban populations. For reference, four previously examined agricultural populations in central/northern Ohio and a geographically distant population in Michigan were also included in the analysis. KEY RESULTS: Urban populations retained high levels of genetic variation (percentage of polymorphic loci, P(p) = 80.7 %) with similar genetic distances among populations and an absence of unique alleles. Geographic and genetic distances were correlated with one another, and all populations grouped according to region. Individuals from urban populations clustered together and away from individuals from agricultural populations and from the Michigan population in a principle coordinates analysis. Hierarchical analysis of molecular variance (AMOVA) revealed that most of the genetic variability was partitioned within populations (69.1 %) and among groups (22.2 %) of southwestern Ohio, central/northern Ohio and Michigan groups. Mean F(st) was 0.308, indicating substantial population differentiation. CONCLUSIONS: It is concluded that urban fragmentation does not appear to impede gene flow in V. pubescens in southwestern Ohio. These results are consistent with life history traits of this species and the possibility of high insect abundance in urban habitats due to diverse floral resources and nesting sites. Combined with the cleistogamous breeding system of this species, pollinator availability in the urban matrix may buffer populations against detrimental effects of habitat fragmentation, at least in larger forest fragments. Consequently, it may be inappropriate to generalize about genetic effects of fragmentation across landscapes or even across plant species with different pollination systems.     

Isolation and characterization of microsatellite loci in Geum urbanum (Rosaceae) and their transferability within the genus Geum

Thirteen novel polymorphic microsatellite loci are presented for Geum urbanum (Rosaceae). The microsatellites will be useful tools to analyse the influence of landscape structure and land‐use intensity in agricultural landscapes on genetic diversity within and among populations of Geum urbanum. Transferability was tested in 19 other Geum species and two Waldsteinia species. In most species polymerase chain reaction (PCR) products of the expected range were obtained, therefore the markers reported here appear to be applicable across the whole genus.     

Impact of habitat fragmentation on the genetics of populations in dendritic landscapes

1. The effect of habitat fragmentation on freshwater species has been addressed using brown trout Salmo trutta L. as a model species with a dendritic population structure. 2. Microsatellite loci were employed as molecular markers. Levels of gene flow and population subdivision were determined in more than 1200 brown trout individuals inhabiting four south European rivers with contrasting patterns of fragmentation, defined by the presence of barriers. 3. The genetic units in the four rivers were restricted by artificial barriers, and gene flow among samples within each river was associated with the level of fragmentation of the river. 4. Loss of genetic diversity and dislocation of the dendritic model have been detected in fragmented rivers. These results emphasise the importance of mitigating the impact of dams by constructing passages to restore gene flow along the river, for fish and other migratory species, as well as the need for caution in relation to stocking in isolated areas to avoid problems of inbreeding.     

Variations in the diet of introduced Norway rats (Rattus norvegicus) inferred using stable isotope analysis

The presence of introduced Norway rats Rattus norvegicus has raised concerns for the fate of the large least auklet Aethia pusilla colony situated at Sirius Point, Kiska Island, Alaska. Previous studies have documented extreme interannual variation in least auklet reproductive success and potential drastic population declines, both of which have been attributed to the varying abundance of, and predation by, Norway rats. A diet study would resolve the uncertainty that remains about the role of rats in the auklet's reproductive failure and the colony's decline. Our main objectives here were to quantify the variation in diet of introduced Norway rats and assess predation on least auklets. Using stable isotope analysis we document wide variability in rat diet dependent on location and provide direct evidence that Norway rats are preferentially preying on least auklets at Sirius Point. In conclusion, we hypothesize that the observed wide variability in rat diet will contribute to the persistence of rats on Kiska long after auklets have been extirpated. The persistence of rats enabled by their foraging plasticity will increase their effects by creating ecological traps within which prospecting individuals will fall and be depredated. This has large conservation consequences as it suggests that when seabirds are extirpated recolonization by prospecting birds is virtually impossible and island ecosystems will continue to be negatively affected and altered as long as introduced predators, such as rats, remain within them.     

The influence of landscape structure on occurrence, abundance and genetic diversity of the common frog, Rana temporaria

Human‐caused habitat destruction and modification constitute one of the largest threats to population persistence and biodiversity, and are also suspected to be the major cause behind the global decline of amphibian populations. We assessed the potential role of agriculture‐related habitat fragmentation on population size and genetic variability in the common frog (Rana temporaria) by recording the occurrence, population density and genetic diversity in three geographically disparate regions in Sweden – each containing landscapes of high and low agricultural activity – and related these to landscape variables extracted from digital maps. We found a highly significant region‐by‐landscape interaction in occurrence, population density and genetic diversity revealing a reversed response to agriculture from south to north: while the effects of agriculture on R. temporaria populations were negative in the south, there were no effects in the central region, whereas positive effects were observed in the north. Spatial autocorrelation analyses of genetic data revealed that populations in high agricultural activity areas were more isolated than populations in low activity areas both in the southern and central regions of Sweden. Landscape diversity showed a strong positive correlation with both density and occurrence of frogs in Sweden as a whole, as well as in the southern region. Also, negative effects of roads and positive effects of ditches on genetic diversity were found in the south. Overall, these results suggest clear but regionally opposite effects of habitat structure on the population size and genetic diversity of amphibian populations. This means that the management strategy aiming to maximize the size and genetic diversity of local common frog populations, and perhaps also those of other amphibian populations, should account for regional differences in existing land‐use patterns.     

Edge effects on the prevalence and mortality factors of Phytomyza ilicis (Diptera, Agromyzidae) in a suburban woodland

Although the effects of edges on the biotas of habitat patches have been widely discussed, there have been few empirical studies of the mechanistic basis of population and community differences between patch edges and interiors. This is particularly true of differential effects of edges on species' mortalities, and on interactions in insect populations and communities. Here we examine edge-associated differences in the prevalence and mortality factors of the holly leaf-miner Phytomyza ilicis , in a suburban woodland in Sheffield, U.K. Leaf miner prevalence was higher and survivorship to adulthood lower at the woodland edge. Natural enemies and other mortality factors contributed differently to total mortality at the edge and interior. Mechanisms underlying edge effects on P. ilicis arose from the interaction between microclimate, adult movement and host-plant quality. The differential induction of species mortality found, confirms the complexity of species' responses to habitat edges and the importance of understanding the effects of edges on species interactions.     

Habitat distribution influences dispersal and fine-scale genetic population structure of eastern foxsnakes (Mintonius gloydi) across a fragmented landscape

Dispersal is a fundamental attribute of species in nature and shapes population dynamics, evolutionary trajectories and genetic variation across spatial and temporal scales. It is increasingly clear that landscape features have large impacts on dispersal patterns. Thus, understanding how individuals and species move through landscapes is essential for predicting impacts of landscape alterations. Information on dispersal patterns, however, is lacking for many taxa, particularly reptiles. Eastern foxsnakes (Mintoinus gloydi) are marsh and prairie specialists that avoid agricultural fields, but they have persisted across a fragmented region in southwestern Ontario and northern Ohio. Here, we combined habitat suitability modelling with population genetic analyses to infer how foxsnakes disperse through a habitat mosaic of natural and altered landscape features. Boundary regions between the eight genetic clusters, identified through assignment tests, were comprised of low suitability habitat (e.g. agricultural fields). Island populations were grouped into a single genetic cluster, and comparatively low F(ST) values between island and mainland populations suggest open water presents less of a barrier than nonsuitable terrestrial habitat. Isolation by resistance and least-cost path analysis produced similar results with matrices of pairwise individual genetic distance significantly more correlated to matrices of resistance values derived from habitat suitability than models with an undifferentiated landscape. Spatial autocorrelation results matched better with assignment results when incorporating resistance values rather than straight-line distances. All analyses used in our study produced similar results suggesting that habitat degradation limits dispersal for foxsnakes, which has had a strong effect on the genetic population structure across this region.     

Population divergence of genetic (co)variance matrices in a subdivided plant species,Brassica cretica

Abstract The present study of Brassica cretica had two objectives. First, we compared estimates of population structure (Q_st) for seven phenotypic characters with the corresponding measures for allozyme markers (F_st) to evaluate the supposition that genetic drift is a major determinant of the evolutionary history of this species. Secondly, we compared the genetic (co)variance ( G ) matrices of five populations to examine whether a long history of population isolation is associated with large, consistent differences in the genetic (co)variance structure. Differences between estimates of F_st and Q_st were too small to be declared significant, indicating that stochastic processes have played a major role in the structuring of quantitative variation in this species. Comparison of populations using the common principal component (CPC) method rejected the hypothesis that the G matrices differed by a simple constant of proportionality: most of the variation involved principal component structure rather than the eigenvalues. However, there was strong evidence for proportionality in comparisons using the method of percentage reduction in mean‐square error (MSE), at least when characters with unusually high (co)variance estimates were included in the analyses. Although the CPC and MSE methods provide different, but complementary, views of G matrix variation, we urge caution in the use of proportionality as an indicator of whether genetic drift is responsible for divergence in the G matrix.     

Fragmentation and genetic differentiation among subpopulations of the endangered Hawaiian mint Haplostachys haplostachya (Lamiaceae)

Haplostachys haplostachya was at one time a prevalent species in the mid-elevation (1650–1800 m) xerophytic shrubland between Mauna Loa and Mauna Kea on Hawaii. Grazing pressure by feral ungulates, destruction of habitat from military activity, and conversion of forest to pastures have fragmented its range to small subpopulations restricted to several cinder cones and portions of the remaining shrubland. Some subpopulations are still extensive, while others are reduced to 20 or fewer individuals. Genetic analyses using random amplified polymorphic DNA (RAPD) markers demonstrate that plants in subpopulations with a large number of individuals maintain levels of genetic variation similar to the entire population, whereas plants in a small subpopulation at Pu'u Leilani (14 individuals remaining) have reduced levels of variation. Of the 122 loci identified, 54 (44%) were polymorphic. Two large populations showed variation at 45 and 49 loci, but the Pu'u Leilani plants showed variation at only 37 loci. The mean expected heterozygosity ( H ) in this subpopulation was also lower (0.137 vs. 0.163 and 0.154) and genetic differentiation ( G _ST) was higher (0.167 vs. 0.018 and 0.052) than in other subpopulations. An examination of variation indicates that although plants of the three subpopulations are genetically similar, there is evidence of genetic restructuring among the subpopulations. The impact of these results towards conservation efforts of this and other endangered species is discussed.     

Genomic analyses of the Formosan harvest mouse (Micromys minutus) and comparisons to the brown Norway rat (Rattus norvegicus) and the house mouse (Mus musculus)

The harvest mouse, Micromys minutus (MMIN), has a very wide range of distribution (from the British Isles across the Euroasian continent to Japan and Taiwan). We studied an isolated population of MMIN in Taiwan, which is at the southeastern margin of the species’ geographic distribution, and compared its genetic complement with those of the same species previously reported from other geographic locations and with two model rodent species, the house mouse (Mus musculus) and the brown Norway rat (Rattus norvegicus). The diploid number (2N) of MMIN was 68, consistent with that reported for other populations. However, variations were noted in the fundamental number (FN) and the shape and banding patterns of the individual chromosomes among populations. The FN of MMIN was estimated to be 72, including 2 bi-armed autosomes, 31 one-armed autosomes, and one pair of one-armed sex chromosomes. Here, we propose the first ideogram for MMIN. C-banding, Ag-NOR, and the locations of 18S rRNA gene sequences (MMIN chromosomes no. 10, 14, 19, 29, 31, 33, and X) mapped by fluorescence in situ hybridization (FISH) are also reported. Additionally, we compared the 18S rDNA sequences and performed cross-species X chromosome painting (FISH) for M. minutus, M. musculus, and R. norvegicus. The results indicate that both genetic elements are rather conserved across species. Thus, implications for the phylogenetic position of Micromys were limited.     

Genetic diversity through life history of Dioon edule Lindley (Zamiaceae, Cycadales)

The distribution of genetic diversity and structure for three populations of Dioon edule Lindley (Zamiaceae) at Monte Oscuro (MO), El Farallón (EF) and Rancho del Niño (RN) in Veracruz, Mexico was studied using 20 allozyme loci, considering four life history classes: seeds, seedlings, juveniles and adults. The MO population is genetically less diverse than the EF and RN populations. Total and local inbreeding differ significantly between life history classes. An increment of inbreeding among all classes was observed, and genetic differentiation among populations was higher in seeds and seedlings than in juveniles and adults. In terms of percentage of polymorphic loci, the MO seeds showed least (80%), followed by RN (95%) and EF had the highest values (100%), probably because of a reduction in effective population size and habitat fragmentation processes. In this context, the mean effective population size was 23.2 ± 11.3 for all populations. We conclude that seed cohorts in EF and RN represent a reservoir of genetic diversity within these two populations. Also, preservation of adult plants is an essential aspect to consider in management and conservation efforts for populations of Dioon edule in natural conditions.     

The influence of the food size,distance and food site on food carrying behavior in rats (Rattus norvegicus)

The behavior to foods in rats (Rattus norvegicus) was investigated in a seminatural enclosure and in a straight alley in the laboratory. In both situations, the size of food (0.045-, 1-, and 3-g pellets were used in the enclosure and 0.045-, 0.2-, 1-, and 3-g pellets in the alley) and distance between food sites and nest site (1.8, 3.6, 5.4, and 7.2 m in the enclosure and 2, 4, and 6 m in the alley) were varied. In both situations, when food was presented in only 1 place, the food carrying behavior increased as the size of food increased from 0.045 to 1-g. One and three g pellets were always carried, regardless of the distance to nest. On the other hand, when multiple food sites were presented in the alley, rats were more likely to carry small pellet from the further food site, whereas large pellet was always carried and were not influenced by the distance. The behavior to foods in the enclosure, however, was not influenced in either food site condition. This might be due to the difference in familiarity to the environment and anxiety from perceived predation risk.     

Temporal Distribution and Weather Correlates of Norway Rat (Rattus norvegicus) Infestations in the City of Madrid, Spain

Urban Norway rats are challenging pests, posing significant health and economic threats. Implementing ecologically based integrated rodent management (EBIRM) programmes relies primarily on the understanding of ecological relationships between rodents and their environments, with emphasis on the processes influencing rodent populations in the target ecosystem. We investigated the temporal distribution of urban Norway rat infestations in Madrid, Spain, and tested for the association of such infestations with temperature, relative humidity and precipitation by fitting a multivariate Poisson generalized linear model to a 3-year (2006–2008) daily time series of 4,689 Norway rat sightings. Norway rat infestations showed a marked seasonality, peaking in the summer. Most Norway rat sightings were reported on Mondays. Minimum temperature and relative humidity were positively associated with Norway rat infestation, whereas the association with precipitation was negative. The time series was adequately explained by the model. We identified previously unrecognized time periods that are more prone to Norway rat infestation than others and generated hypotheses about the association between weather, human outdoor activity, resource availability, rodent activity and population size. This provided local authorities engaged in preserving urban ecosystem health with basic research information to predict future rodent outbreaks and support the implementation of EBIRM programmes in urban areas.     

Life-history and habitat features influence the within-river genetic structure of Atlantic salmon

Defining populations and identifying ecological and life-history characteristics affecting genetic structure is important for understanding species biology and hence, for managing threatened or endangered species or populations. In this study, populations of the world's largest indigenous Atlantic salmon (Salmo salar) stock were first inferred using model-based clustering methods, following which life-history and habitat variables best predicting the genetic diversity of populations were identified. This study revealed that natal homing of Atlantic salmon within the Teno River system is accurate at least to the tributary level. Generally, defining populations by main tributaries was observed to be a reasonable approach in this large river system, whereas in the mainstem of the river, the number of inferred populations was fewer than the number of distinct sampling sites. Mainstem and headwater populations were genetically more diverse and less diverged, while each tributary fostered a distinct population with high genetic differentiation and lower genetic diversity. Population structure and variation in genetic diversity among populations were poorly explained by geographical distance. In contrast, age-structure, as estimated by the proportion of multisea-winter spawners, was the most predictive variable in explaining the variation in the genetic diversity of the populations. This observation, being in agreement with theoretical predictions, emphasizes the essence of large multisea-winter females in maintaining the genetic diversity of populations. In addition, the unique genetic diversity of populations, as estimated by private allele richness, was affected by the ease of accessibility of a site, with more difficult to access sites having lower unique genetic diversity. Our results show that despite this species' high capacity for migration, tributaries foster relatively closed populations with little gene flow which will be important to consider when developing management strategies for the system.