Genetic estimates of immigration and emigration rates in relation to population density and forest patch area in Peromyscus leucopus

Landscape Structure Affects Metapopulation-Scale Tipping Points

AbstractEven when environments deteriorate gradually, ecosystems may shift abruptly from one state to another. Such catastrophic shifts are difficult to predict and sometimes to reverse (so-called hysteresis). While well studied in simplified contexts, we lack a general understanding of how catastrophic shifts spread in realistically spatially structured landscapes. For different types of landscape structures, including typical terrestrial modular and riverine dendritic networks, we here investigate landscape-scale stability in metapopulations whose patches can locally exhibit catastrophic shifts. We find that such metapopulations usually exhibit large-scale catastrophic shifts and hysteresis and that the properties of these shifts depend strongly on the metapopulation spatial structure and on the population dispersal rate: an intermediate dispersal rate, a low average degree, or a riverine spatial structure can largely reduce hysteresis size. Our study suggests that large-scale restoration is easier with spatially clustered restoration efforts and in populations characterized by an intermediate dispersal rate.

Variation in space and time: a long-term examination of density-dependent dispersal in a woodland rodent

Dispersal is a fundamental ecological process that can be affected by population density, yet studies report contrasting effects of density on propensity to disperse. In addition, the relationship between dispersal and density is seldom examined using densities measured at different spatial scales or over extensive time series. We used 51 years of trapping data to examine how dispersal by wild deer mice (Peromyscus maniculatus) was affected by changes in both local and regional population densities. We examined these patterns over both the entire time series and also in 10-year shifting windows to determine whether the nature and strength of the relationship changed through time. Probability of dispersal decreased with increased local and regional population density, and the negative effect of local density on dispersal was more pronounced in years with low regional densities. In addition, the strength of negative density-dependent dispersal changed through time, ranging from very strong in some decades to absent in other periods of the study. Finally, while females were less likely to disperse, female dispersal was more density-dependent than male dispersal. Our study shows that the relationship between density and dispersal is not temporally static and that investigations of density-dependent dispersal should consider both local and regional population densities.

Peromyscus transcriptomics: Understanding adaptation and gene expression plasticity within and between species of deer mice

Deer mice in the genus Peromyscus occupy nearly every terrestrial habitat in North America, and have a long history as subjects of behavioral, ecological, evolutionary, and physiological study. Recent advances in transcriptomics, the study of the complete set of RNA transcripts produced by certain cell types or under certain conditions, have contributed to the development of Peromyscus as a model system. We review the recent use of transcriptomics to investigate how natural selection and gene expression plasticity contribute to the existence of deer mice in challenging environments such as highlands, deserts, and cities across North America. Transcriptomics also holds great promise for elucidating the genetic basis of mating systems and other behaviors in Peromyscus, but has to date been underutilized for developmental biology and disease studies. Future Peromyscus studies should apply robust comparative frameworks to analyze the transcriptomics of multiple populations of the same species across varying environmental conditions, as well as multiple species that vary in traits of interest.

Landscape models for nuclear genetic diversity and genetic structure in white-footed mice (Peromyscus leucopus)

Dramatic changes in the North American landscape over the last 12 000 years have shaped the genomes of the small mammals, such as the white-footed mouse (Peromyscus leucopus), which currently inhabit the region. However, very recent interactions of populations with each other and the environment are expected to leave the most pronounced signature on rapidly evolving nuclear microsatellite loci. We analyzed landscape characteristics and microsatellite markers of P. leucopus populations along a transect from southern Ohio to northern Michigan, in order to evaluate hypotheses about the spatial distribution of genetic heterogeneity. Genetic diversity increased to the north and was best approximated by a single-variable model based on habitat availability within a 0.5-km radius of trapping sites. Interpopulation differentiation measured by clustering analysis was highly variable and not significantly related to latitude or habitat availability. Interpopulation differentiation measured as FST values and chord distance was correlated with the proportion of habitat intervening, but was best explained by agricultural distance and by latitude. The observed gradients in diversity and interpopulation differentiation were consistent with recent habitat availability being the major constraint on effective population size in this system, and contradicted the predictions of both the postglacial expansion and core-periphery hypotheses.

Urban park characteristics, genetic variation, and historical demography of white-footed mouse (Peromyscus leucopus) populations in New York City

Severe fragmentation is a typical fate of native remnant habitats in cities, and urban wildlife with limited dispersal ability are predicted to lose genetic variation in isolated urban patches. However, little information exists on the characteristics of urban green spaces required to conserve genetic variation. In this study, we examine whether isolation in New York City (NYC) parks results in genetic bottlenecks in white-footed mice (Peromyscus leucopus), and test the hypotheses that park size and time since isolation are associated with genetic variability using nonlinear regression and information-theoretic model selection. White-footed mice have previously been documented to exhibit male-biased dispersal, which may create disparities in genetic variation between males and females in urban parks. We use genotypes of 18 neutral microsatellite data and four different statistical tests to assess this prediction. Given that sex-biased dispersal may create disparities between population genetic patterns inferred from bi- vs. uni-parentally inherited markers, we also sequenced a 324 bp segment of the mitochondrial D-loop for independent inferences of historical demography in urban P. leucopus. We report that isolation in urban parks does not necessarily result in genetic bottlenecks; only three out of 14 populations in NYC parks exhibited a signature of a recent bottleneck at 18 neutral microsatellite loci. Mouse populations in larger urban parks, or parks that have been isolated for shorter periods of time, also do not generally contain greater genetic variation than populations in smaller parks. These results suggest that even small networks of green spaces may be sufficient to maintain the evolutionary potential of native species with certain characteristics. We also found that isolation in urban parks results in weak to nonexistent sex-biased dispersal in a species known to exhibit male-biased dispersal in less fragmented environments. In contrast to nuclear loci, mitochondrial D-loop haplotypes exhibited a mutational pattern of demographic expansion after a recent bottleneck or selective sweep. Estimates of the timing of this expansion suggest that it occurred concurrent with urbanization of NYC over the last few dozens to hundreds of years. Given the general non-neutrality of mtDNA in many systems and evidence of selection on related coding sequences in urban P. leucopus, we argue that the P. leucopus mitochondrial genome experienced recent negative selection against haplotypes not favored in isolated urban parks. In general, rapid adaptive evolution driven by urbanization, global climate change, and other human-caused factors is underappreciated by evolutionary biologists, but many more cases will likely be documented in the near future.

Genetic structure of the white-footed mouse in the context of the emergence of Lyme disease in southern Québec

The white-footed mouse (Peromyscus leucopus) has expanded its northern limit into southern Québec over the last few decades. P. leucopus is a great disperser and colonizer and is of particular interest because it is considered a primary reservoir for the spirochete bacterium that causes Lyme disease. There is no current information on the gene flow between mouse populations on the mountains and forest fragments found scattered throughout the Montérégie region in southern Québec, and whether various landscape barriers have an effect on their dispersal. We conducted a population genetics analysis on eleven P. leucopus populations using eleven microsatellite markers and showed that isolation by distance was weak, yet barriers were effective. The agricultural matrix had the least effect on gene flow, whereas highways and main rivers were effective barriers. The abundance of ticks collected from mice varied within the study area. Both ticks and mice were screened for the presence of the spirochete bacterium Borrelia burgdorferi, and we predicted areas of greater risk for Lyme disease. Merging our results with ongoing Lyme disease surveillance programs will help determine the future threat of this disease in Québec, and will contribute toward disease prevention and management strategies throughout fragmented landscapes in southern Canada.

Microsatellite genetic structure and cytonuclear discordance in naturally fragmented populations of deer mice (Peromyscus maniculatus)

The Great Lakes impose high levels of natural fragmentation on local populations of terrestrial animals in a way rarely found within continental ecosystems. Although separated by major water barriers, woodland deer mouse (Peromyscus maniculatus gracilis) populations on the islands and on the Upper Peninsula (UP) and Lower Peninsula (LP) of Michigan have previously been shown to have a mitochondrial DNA contact zone that is incongruent with the regional landscape. We analyzed 11 microsatellite loci for 16 populations of P. m. gracilis distributed across 2 peninsulas and 6 islands in northern Michigan to address the relative importance of geographical structure and inferred postglacial colonization patterns in determining the nuclear genetic structure of this species. Results showed relatively high levels of genetic structure for this species and a significant correlation between interpopulation differentiation and separation by water but little genetic structure and no isolation-by-distance within each of the 2 peninsulas. Genetic diversity was generally high on both peninsulas but lower and correlated to island size in the Beaver Island Archipelago. These results are consistent with the genetic and demographic isolation of Lower Peninsula populations, which is a matter of concern given the dramatic decline in P. m. gracilis abundance on the Lower Peninsula in recent years.

Genetic impacts of Anacapa deer mice reintroductions following rat eradication

The Anacapa deer mouse is an endemic subspecies that inhabits Anacapa Island, part of Channel Islands National Park, California. We used mitochondrial DNA cytochrome c oxidase subunit II gene (COII) and 10 microsatellite loci to evaluate the levels of genetic differentiation and variation in ~1400 Anacapa deer mice sampled before and for 4 years after a black rat (Rattus rattus) eradication campaign that included trapping, captive holding and reintroduction of deer mice. Both mitochondrial and microsatellite analyses indicated significant differentiation between Anacapa deer mice and mainland mice, and genetic variability of mainland mice was significantly higher than Anacapa mice even prior to reintroduction. Bayesian cluster analysis and Principal Coordinates Analysis indicated that East, Middle and West Anacapa mice were genetically differentiated from each other, but translocation of mice among islands resulted in the East population becoming less distinct as a result of management. Levels of heterozygosity were similar before and after management. However, numerous private alleles in the founder populations were not observed after reintroduction and shifts in allele frequencies occurred, indicating that the reintroduced populations experienced substantial genetic drift. Surprisingly, two mitochondrial haplotypes observed in an earlier study of Anacapa deer mice were lost in the 20 years prior to the rat eradication program, leaving only a single haplotype in Anacapa deer mice. This study demonstrates how genetic monitoring can help to understand the re-establishment of endemic species after the eradication of invasive species and to evaluate the effectiveness of the management strategies employed.