Estimating dispersal from short distance spatial autocorrelation

Comparative epigenetic and genetic spatial structure in Mediterranean mountain plants: a multispecies study

Changes in epigenetic states can allow individuals to cope with environmental changes. If such changes are heritable, this may lead to epigenetic adaptation. Thus, it is likely that in sessile organisms such as plants, part of the spatial epigenetic variation found across individuals will reflect the environmental heterogeneity within populations. The departure of the spatial epigenetic structure from the baseline genetic variation can help in understanding the value of epigenetic regulation in species with different breadth of optimal environmental requirements. Here, we hypothesise that in plants with narrow environmental requirements, epigenetic variability should be less structured in space given the lower variability in suitable environmental conditions. We performed a multispecies study that considered seven pairs of congeneric plant species, each encompassing a narrow endemic with habitat specialisation and a widespread species. In three populations per species we used AFLP and methylation-sensitive AFLP markers to characterise the spatial genetic and epigenetic structures. Narrow endemics showed a significantly lower epigenetic than genetic differentiation between populations. Within populations, epigenetic variation was less spatially structured than genetic variation, mainly in narrow endemics. In these species, structural equation models revealed that such pattern was associated to a lack of correlation between epigenetic and genetic information. Altogether, these results show a greater decoupling of the spatial epigenetic variation from the baseline spatial genetic pattern in endemic species. These findings highlight the value of studying genetic and epigenetic spatial variation to better understand habitat specialisation in plants.

Stronger genetic differentiation among within-population genetic groups than among populations in Scots pine provides new insights into within-population genetic structuring

We investigated the presence of spatial genetic groups within forest tree populations and determined if the genetic divergence among these groups is greater than that between populations using Scots pine (Pinus sylvestris) as a model species. We genotyped 890 adult trees of Scots pine in six natural populations in Lithuania at 11 nuclear microsatellite loci. We used a Bayesian clustering approach to identify the within-population genetic groups within each of the six populations. We calculated the differentiation indexes among the genetic groups within each population and among the six populations by ignoring the genetic groups. The Bayesian clustering revealed 2 to 6 distinct genetic groups of varying size as the most likely genetic structures within populations. The genetic differentiation indexes among the genetic groups within populations were nearly tenfold greater (FST = 0.012-0.070) than those between the populations (FST = 0.003). We conclude on the existence of markedly stronger structuring of genetic variation within populations than between populations of Scots pine in large forest tracts of northern Europe. Such genetic structures serve as a contributing factor to large within population genetic diversity in northern conifers. We assume that within population mating in Scots pine is not completely random but rather is stratified into genetic clusters. Our study provides pioneering novel key insights into structuring of genetic variation within populations. Our findings have implications for examining within-population genetic diversity and genetic structure, conservation, and management of genetic resources.

Road environment characteristics and fatal crash injury during the rush and non-rush hour periods in the U.S: Model testing and cluster analysis

This study aims to assess the relationship between county-level fatal crash injuries and road environmental characteristics at all times of the day and during the rush and non-rush hour periods. We merged eleven-year (2010 - 2020) data from the Fatality Analysis Reporting System. The outcome variable was the county-level fatal crash injury counts. The predictor variables were measures of road types, junction types and work zone, and weather types. We tested the predictiveness of two nested negative binomial models and adjudged that a nested spatial negative binomial regression model outperformed the non-spatial negative binomial model. The median county crash mortality rates at all times of the day and during the rush and non-rush hour periods were 18.4, 7.7, and 10.4 per 100,000 population, respectively. Fatal crash injury rate ratios were significantly elevated on interstates and highways at all times of the day - rush and non-rush hour periods inclusive. Intersections, driveways, and ramps on highways were associated with elevated fatal crash injury rate ratios. Clusters of high fatal crash injury rates were observed in counties located in Montana, Nevada, Colorado, Kansas, New Mexico, Oklahoma, Texas, Arkansas, Mississippi, Alabama, Georgia, and Nevada. The built and natural road environment factors are associated with county-level fatal crash injuries during the rush and non-rush hour periods. Understanding the association of road environment characteristics and the cluster distribution of fatal crash injuries may inform areas in need of focused intervention.

Genetic and species-level biodiversity patterns are linked by demography and ecological opportunity

The processes that give rise to species richness gradients are not well understood, but may be linked to resource-based limits on the number of species a region can support. Ecological limits placed on regional species richness should also affect population demography, suggesting that these processes could also generate genetic diversity gradients. If true, we might better understand how broad-scale biodiversity patterns are formed by identifying the common causes of genetic diversity and species richness. We develop a hypothetical framework based on the consequences of regional variation in ecological limits set by resource availability and heterogeneity to simultaneously explain spatial patterns of species richness and neutral genetic diversity. Repurposing raw genotypic data spanning 38 mammal species sampled across 801 sites in North America, we show that estimates of genome-wide genetic diversity and species richness share spatial structure. Notably, species richness hotspots tend to harbor lower levels of within-species genetic variation. A structural equation model encompassing eco-evolutionary processes related to resource availability, habitat heterogeneity, and contemporary human disturbance supports the spatial patterns we detect. These results suggest broad-scale patterns of species richness and genetic diversity could both partly be caused by intraspecific demographic and evolutionary processes acting simultaneously across species.

The population genetics of urban and rural amphibians in North America

Human land transformation is one of the leading causes of vertebrate population declines. These declines are thought to be partly due to decreased connectivity and habitat loss reducing animal population sizes in disturbed habitats. With time, this can lead to declines in effective population size and genetic diversity which restrict the ability of wildlife to efficiently cope with environmental change through genetic adaptation. However, it is not well understood whether these effects generally hold across taxa. We address this question by repurposing and synthesizing raw microsatellite data from online repositories for 19 amphibian species sampled at 554 georeferenced sites in North America. For each site, we estimated gene diversity, allelic richness, effective population size, and population differentiation. Using binary urban-rural census designations, and continuous measures of human population density, the Human Footprint Index, and impervious surface cover, we tested for generalizable effects of human land use on amphibian genetic diversity. We found minimal evidence, either positive or negative, for relationships between genetic metrics and urbanization. Together with previous work on focal species that also found varying effects of urbanization on genetic composition, it seems likely that the consequences of urbanization are not easily generalizable within or across amphibian species. Questions about the genetic consequences of urbanization for amphibians should be addressed on a case-by-case basis. This contrasts with general negative effects of urbanization in mammals and consistent, but species-specific, positive and negative effects in birds.

Extreme seascape drives local recruitment and genetic divergence in brooding and spawning corals in remote north-west Australia

Management strategies designed to conserve coral reefs threatened by climate change need to incorporate knowledge of the spatial distribution of inter- and intra-specific genetic diversity. We characterized patterns of genetic diversity and connectivity using single nucleotide polymorphisms (SNPs) in two reef-building corals to explore the eco-evolutionary processes that sustain populations in north-west Australia. Our sampling focused on the unique reefs of the Kimberley; we collected the broadcast spawning coral Acropora aspera (n = 534) and the brooding coral Isopora brueggemanni (n = 612) across inter-archipelago (tens to hundreds of kilometres), inter-reef (kilometres to tens of kilometres) and within-reef (tens of metres to a few kilometres) scales. Initial analysis of A. aspera identified four highly divergent lineages that were co-occurring but morphologically similar. Subsequent population analyses focused on the most abundant and widespread lineage, Acropora asp-c. Although the overall level of geographic subdivision was greater in the brooder than in the spawner, fundamental similarities in patterns of genetic structure were evident. Most notably, limits to gene flow were observed at scales <35 kilometres. Further, we observed four discrete clusters and a semi-permeable barrier to dispersal that were geographically consistent between species. Finally, sites experiencing bigger tides were more connected to the metapopulation and had greater gene diversity than those experiencing smaller tides. Our data indicate that the inshore reefs of the Kimberley are genetically isolated from neighbouring oceanic bioregions, but occasional dispersal between inshore archipelagos is important for the redistribution of evolutionarily important genetic diversity. Additionally, these results suggest that networks of marine reserves that effectively protect reefs from local pressures should be spaced within a few tens of kilometres to conserve the existing patterns of demographic and genetic connectivity.

Using spatial genetics to quantify mosquito dispersal for control programs

Background

Hundreds of millions of people get a mosquito-borne disease every year and nearly one million die. Transmission of these infections is primarily tackled through the control of mosquito vectors. The accurate quantification of mosquito dispersal is critical for the design and optimization of vector control programs, yet the measurement of dispersal using traditional mark-release-recapture (MRR) methods is logistically challenging and often unrepresentative of an insect’s true behavior. Using Aedes aegypti (a major arboviral vector) as a model and two study sites in Singapore, we show how mosquito dispersal can be characterized by the spatial analyses of genetic relatedness among individuals sampled over a short time span without interruption of their natural behaviors.

Results

Using simple oviposition traps, we captured adult female Ae. aegypti across high-rise apartment blocks and genotyped them using genome-wide SNP markers. We developed a methodology that produces a dispersal kernel for distance which results from one generation of successful breeding (effective dispersal), using the distance separating full siblings and 2nd- and 3rd-degree relatives (close kin). The estimated dispersal distance kernel was exponential (Laplacian), with a mean dispersal distance (and dispersal kernel spread σ) of 45.2 m (95% CI 39.7–51.3 m), and 10% probability of a dispersal > 100 m (95% CI 92–117 m). Our genetically derived estimates matched the parametrized dispersal kernels from previous MRR experiments. If few close kin are captured, a conventional genetic isolation-by-distance analysis can be used, as it can produce σ estimates congruent with the close-kin method if effective population density is accurately estimated. Genetic patch size, estimated by spatial autocorrelation analysis, reflects the spatial extent of the dispersal kernel “tail” that influences, for example, the critical radii of release zones and the speed of Wolbachia spread in mosquito replacement programs.

Conclusions

We demonstrate that spatial genetics can provide a robust characterization of mosquito dispersal. With the decreasing cost of next-generation sequencing, the production of spatial genetic data is increasingly accessible. Given the challenges of conventional MRR methods, and the importance of quantified dispersal in operational vector control decisions, we recommend genetic-based dispersal characterization as the more desirable means of parameterization.

ResDisMapper: An r package for fine-scale mapping of resistance to dispersal

Management of biological invasions and conservation activity in the fight against habitat fragmentation both require information on how ongoing dispersal of organisms is affected by the environment. However, there are few landscape genetic computer programs that map resistance to dispersal at small spatiotemporal scales. To facilitate such analyses, we present an r package named ResDisMapper for the mapping of resistance to dispersal at small spatiotemporal scales, without the need for prior knowledge on environmental features or intensive computation. Based on the concept of isolation by distance (IBD), ResDisMapper calculates resistance using deviations of each pair of samples from the general IBD trend (IBD residuals). The IBD residuals are projected onto the studied area, which allows construction and visualization of a fine-scale map of resistance based on spatial accumulation of positive or negative IBD residuals. In this study, we tested ResDisMapper with both simulated and empirical data sets and compared its performance with two other popular landscape genetic programs. Overall, we found that ResDisMapper can map resistance with relatively high accuracy. The latest version of the package and associated documentation are available on Github (https://github.com/takfung/ResDisMapper).

Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa

Savannah elephant populations have been severely reduced and fragmented throughout its remaining range. In general, however, there is limited information regarding their genetic status, which is essential knowledge for conservation. We investigated patterns of genetic variation in savannah elephants from the Greater Kruger Biosphere, with a focus on those in previously unstudied nature reserves adjacent to Kruger National Park, using dung samples from 294 individuals and 18 microsatellites. The results of genetic structure analyses using several different methods of ordination and Bayesian clustering strongly suggest that elephants throughout the Greater Kruger National Park (GKNP) constitute a single population. No evidence of a recent genetic bottleneck was detected using three moment-based approaches and two coalescent likelihood methods. The apparent absence of a recent genetic bottleneck associated with the known early 1900s demographic bottleneck may result from a combination of rapid post-bottleneck population growth, immigration and long generation time. Point estimates of contemporary effective population size (Ne) for the GKNP were ~ 500-700, that is, at the low end of the range of Ne values that have been proposed for maintaining evolutionary potential and the current ratio of Ne to census population size (Nc) may be quite low (<0.1). This study illustrates the difficulties in assessing the impacts on Ne in populations that have suffered demographic crashes but have recovered rapidly and received gene flow, particularly in species with long generation times in which genetic time lags are longer. This work provides a starting point and baseline information for genetic monitoring of the GKNP elephants.

Density-dependent fitness, not dispersal movements, drives temporal variation in spatial genetic structure in dark-eyed juncos (Junco hyemalis)

Some studies have found that dispersal rates and distances increase with density, indicating that density-dependent dispersal likely affects spatial genetic structure. In an 11-year mark-recapture study on a passerine, the dark-eyed junco, we tested whether density affected dispersal distance and/or fine-scale spatial genetic structure. Contrary to expectations, we found no effect of predispersal density on dispersal distance or the proportion of locally produced juveniles returning to the population from which they hatched. However, even though density did not affect dispersal distance or natal return rates, we found that density still did affect spatial genetic structure. We found significant positive spatial genetic structure at low densities of (postdispersal) adults but not at high densities. In years with high postdispersal (adult) densities that also had high predispersal (juvenile) densities in the previous year, we found negative spatial genetic structure, indicating high levels of dispersal. We found that density also affected fitness of recruits, and fitness of immigrants, potentially linking these population parameters with the spatial genetic structure detected. Immigrants and recruits rarely nested in low postdispersal density years. In contrast, in years with high postdispersal density, recruits were common and immigrants had equal success to local birds, so novel genotypes diluted the gene pool and effectively eliminated positive spatial genetic structure. In relation to fine-scale spatial genetic structure, fitness of immigrants and new recruits is poorly understood compared to dispersal movements, but we conclude that it can have implications for the spatial distribution of genotypes in populations.

Deconstructing isolation-by-distance: The genomic consequences of limited dispersal

Geographically limited dispersal can shape genetic population structure and result in a correlation between genetic and geographic distance, commonly called isolation-by-distance. Despite the prevalence of isolation-by-distance in nature, to date few studies have empirically demonstrated the processes that generate this pattern, largely because few populations have direct measures of individual dispersal and pedigree information. Intensive, long-term demographic studies and exhaustive genomic surveys in the Florida Scrub-Jay (Aphelocoma coerulescens) provide an excellent opportunity to investigate the influence of dispersal on genetic structure. Here, we used a panel of genome-wide SNPs and extensive pedigree information to explore the role of limited dispersal in shaping patterns of isolation-by-distance in both sexes, and at an exceedingly fine spatial scale (within ~10 km). Isolation-by-distance patterns were stronger in male-male and male-female comparisons than in female-female comparisons, consistent with observed differences in dispersal propensity between the sexes. Using the pedigree, we demonstrated how various genealogical relationships contribute to fine-scale isolation-by-distance. Simulations using field-observed distributions of male and female natal dispersal distances showed good agreement with the distribution of geographic distances between breeding individuals of different pedigree relationship classes. Furthermore, we built coalescent simulations parameterized by the observed dispersal curve, population density, and immigration rate, and showed how incorporating these extensions to Malécot’s theory of isolation-by-distance allows us to accurately reconstruct observed sex-specific isolation-by-distance patterns in autosomal and Z-linked SNPs. Therefore, patterns of fine-scale isolation-by-distance in the Florida Scrub-Jay can be well understood as a result of limited dispersal over contemporary timescales.

Dispersal is a fundamental component of the life history of most organisms and therefore influences many biological processes. Dispersal is particularly important in creating genetic structure on the landscape. We often observe a pattern of decreased genetic relatedness between individuals as geographic distances increases, or isolation-by-distance. This pattern is particularly pronounced in organisms with extremely short dispersal distances. Despite the ubiquity of isolation-by-distance patterns in nature, there are few examples that explicitly demonstrate how limited dispersal influences spatial genetic structure. Here we investigate the processes that result in spatial genetic structure using the Florida Scrub-Jay, a bird with extremely limited dispersal behavior and extensive genome-wide data. We take advantage of the long-term monitoring of a contiguous population of Florida Scrub-Jays, which has resulted in a detailed pedigree and measurements of dispersal for hundreds of individuals. We show how limited dispersal results in close genealogical relatives living closer together geographically, which generates a strong pattern of isolation-by-distance at an extremely small spatial scale (<10 km) in just a few generations. Given the detailed dispersal, pedigree, and genomic data, we can achieve a fairly complete understanding of how dispersal shapes patterns of genetic diversity over short spatial scales.

Early genetic consequences of defaunation in a large-seeded vertebrate-dispersed palm (Syagrus romanzoffiana)

Plant populations are seriously threatened by anthropogenic habitat disturbance. In particular, defaunation may disrupt plant-disperser mutualisms, thus reducing levels of seed-mediated gene flow and genetic variation in animal-dispersed plants. This may ultimately limit their adaptive potential and ability to cope with environmental change. Tropical forest remnants are typically deprived of medium to large vertebrates upon which many large-seeded plants rely for accomplishing effective seed dispersal. Our main goal was to examine the potential early genetic consequences of the loss of large vertebrates for large-seeded vertebrate-dispersed plants. We compared the genetic variation in early-stage individuals of the large-seeded palm Syagrus romanzoffiana between continuous protected forest and nearby partially defaunated fragments in the Atlantic Forest of South America. Using nine microsatellites, we found lower allelic richness and stronger fine-scale spatial genetic structure in the disturbed area. In addition, the percentage of dispersed recruits around conspecific adults was lower, although not significantly, in the disturbed area (median values: 0.0 vs 14.4%). On the other hand, no evidence of increased inbreeding or reduced pollen-mediated gene flow (selfing rate and diversity of pollen donors) was found in the disturbed area. Our findings are strongly suggestive of some early genetic consequences resulting from the limitation in contemporary gene flow via seeds, but not pollen, in defaunated areas. Plant-disperser mutualisms involving medium-large frugivores, which are seriously threatened in tropical systems, should therefore be protected to warrant the maintenance of seed-mediated gene flow and genetic diversity in large-seeded plants.

Genetic structure and signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos)

With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genetic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear single-nucleotide polymorphisms (SNPs) and a mitochondrial DNA (mtDNA) gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Using samples from Australia, Indonesia and oceanic reefs in the Indian Ocean, we established that large oceanic distances represent barriers to gene flow, whereas genetic differentiation on continental shelves follows an isolation by distance model. In Australia and Indonesia differentiation at nuclear SNPs was weak, with coral reefs acting as stepping stones maintaining connectivity across large distances. Differentiation of mtDNA was stronger, and more pronounced in females, suggesting sex-biased dispersal. Four independent tests identified a set of loci putatively under selection, indicating that grey reef sharks in eastern Australia are likely under different selective pressures to those in western Australia and Indonesia. Genetic distances averaged across all loci were uncorrelated with genetic distances calculated from outlier loci, supporting the conclusion that different processes underpin genetic divergence in these two data sets. This pattern of heterogeneous genomic differentiation, suggestive of local adaptation, has implications for the conservation of grey reef sharks; furthermore, it highlights that marine species showing little genetic differentiation at neutral loci may exhibit patterns of cryptic genetic structure driven by local selection.

Using Genealogical Mapping and Genetic Neighborhood Sizes to Quantify Dispersal Distances in the Neotropical Passerine, the Black-Capped Vireo

Dispersal is a key demographic process, ultimately responsible for genetic connectivity among populations. Despite its importance, quantifying dispersal within and between populations has proven difficult for many taxa. Even in passerines, which are among the most intensely studied, individual movement and its relation to gene flow remains poorly understood. In this study we used two parallel genetic approaches to quantify natal dispersal distances in a Neotropical migratory passerine, the black-capped vireo. First, we employed a strategy of sampling evenly across the landscape coupled with parentage assignment to map the genealogical relationships of individuals across the landscape, and estimate dispersal distances; next, we calculated Wright’s neighborhood size to estimate gene dispersal distances. We found that a high percentage of captured individuals were assigned at short distances within the natal population, and males were assigned to the natal population more often than females, confirming sex-biased dispersal. Parentage-based dispersal estimates averaged 2400m, whereas gene dispersal estimates indicated dispersal distances ranging from 1600–4200 m. Our study was successful in quantifying natal dispersal distances, linking individual movement to gene dispersal distances, while also providing a detailed look into the dispersal biology of Neotropical passerines. The high-resolution information was obtained with much reduced effort (sampling only 20% of breeding population) compared to mark-resight approaches, demonstrating the potential applicability of parentage-based approaches for quantifying dispersal in other vagile passerine species.

Connectivity in grey reef sharks (Carcharhinus amblyrhynchos) determined using empirical and simulated genetic data

Grey reef sharks (Carcharhinus amblyrhynchos) can be one of the numerically dominant high order predators on pristine coral reefs, yet their numbers have declined even in the highly regulated Australian Great Barrier Reef (GBR) Marine Park. Knowledge of both large scale and fine scale genetic connectivity of grey reef sharks is essential for their effective management, but no genetic data are yet available. We investigated grey reef shark genetic structure in the GBR across a 1200 km latitudinal gradient, comparing empirical data with models simulating different levels of migration. The empirical data did not reveal any genetic structuring along the entire latitudinal gradient sampled, suggesting regular widespread dispersal and gene flow of the species throughout most of the GBR. Our simulated datasets indicate that even with substantial migrations (up to 25% of individuals migrating between neighboring reefs) both large scale genetic structure and genotypic spatial autocorrelation at the reef scale were maintained. We suggest that present migration rates therefore exceed this level. These findings have important implications regarding the effectiveness of networks of spatially discontinuous Marine Protected Areas to protect reef sharks.

Spatial heterogeneity as a genetic mixing mechanism in highly philopatric colonial seabirds

How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of understanding intra-colonial dispersal and genetic mixing mechanisms in order to better estimate species-wide gene flows and population dynamics.

Isolation-by-distance in landscapes: considerations for landscape genetics

In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, FST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain geographical distance beyond which no correlation is detectable anymore (case-IV pattern). We investigated if landscape configuration influenced the rate at which a case-IV pattern changed to a case-I pattern. We also determined at what interdeme distance the highest correlation was measured between genetic differentiation and geographic distance and whether this distance corresponded to the maximum migration distance. We set up a population genetic simulation study and assessed the development of IBD patterns for several habitat configurations and maximum migration distances. We show that the rate and likelihood of the transition of case-IV to case-I FST-distance relationships was strongly influenced by habitat configuration and maximum migration distance. We also found that the maximum correlation between genetic differentiation and geographic distance was not related to the maximum migration distance and was measured across all deme pairs in a case-I pattern and, for a case-IV pattern, at the distance where the FST-distance curve flattens out. We argue that in landscape genetics, separate analyses should be performed to either assess IBD or the landscape effects on gene flow.

The influence of habitat structure on genetic differentiation in red fox populations in north-eastern Poland

The red fox (Vulpes vulpes) has the widest global distribution among terrestrial carnivore species, occupying most of the Northern Hemisphere in its native range. Because it carries diseases that can be transmitted to humans and domestic animals, it is important to gather information about their movements and dispersal in their natural habitat but it is difficult to do so at a broad scale with trapping and telemetry. In this study, we have described the genetic diversity and structure of red fox populations in six areas of north-eastern Poland, based on samples collected from 2002–2003. We tested 22 microsatellite loci isolated from the dog and the red fox genome to select a panel of nine polymorphic loci suitable for this study. Genetic differentiation between the six studied populations was low to moderate and analysis in Structure revealed a panmictic population in the region. Spatial autocorrelation among all individuals showed a pattern of decreasing relatedness with increasing distance and this was not significantly negative until 93 km, indicating a pattern of isolation-by-distance over a large area. However, there was no correlation between genetic distance and either Euclidean distance or least-cost path distance at the population level. There was a significant relationship between genetic distance and the proportion of large forests and water along the Euclidean distances. These types of habitats may influence dispersal paths taken by red foxes, which is useful information in terms of wildlife disease management.

Application of large-scale parentage analysis for investigating natal dispersal in highly vagile vertebrates: a case study of American black bears (Ursus americanus)

Understanding the factors that affect dispersal is a fundamental question in ecology and conservation biology, particularly as populations are faced with increasing anthropogenic impacts. Here we collected georeferenced genetic samples (n = 2,540) from three generations of black bears (Ursus americanus) harvested in a large (47,739 km²), geographically isolated population and used parentage analysis to identify mother-offspring dyads (n = 337). We quantified the effects of sex, age, habitat type and suitability, and local harvest density at the natal and settlement sites on the probability of natal dispersal, and on dispersal distances. Dispersal was male-biased (76% of males dispersed) but a small proportion (21%) of females also dispersed, and female dispersal distances (mean ± SE  =  48.9±7.7 km) were comparable to male dispersal distances (59.0±3.2 km). Dispersal probabilities and dispersal distances were greatest for bears in areas with high habitat suitability and low harvest density. The inverse relationship between dispersal and harvest density in black bears suggests that 1) intensive harvest promotes restricted dispersal, or 2) high black bear population density decreases the propensity to disperse. Multigenerational genetic data collected over large landscape scales can be a powerful means of characterizing dispersal patterns and causal associations with demographic and landscape features in wild populations of elusive and wide-ranging species.

European invasion of North American Pinus strobus at large and fine scales: high genetic diversity and fine-scale genetic clustering over time in the adventive range

BACKGROUND

North American Pinus strobus is a highly invasive tree species in Central Europe. Using ten polymorphic microsatellite loci we compared various aspects of the large-scale genetic diversity of individuals from 30 sites in the native distribution range with those from 30 sites in the European adventive distribution range. To investigate the ascertained pattern of genetic diversity of this intercontinental comparison further, we surveyed fine-scale genetic diversity patterns and changes over time within four highly invasive populations in the adventive range.

RESULTS

Our data show that at the large scale the genetic diversity found within the relatively small adventive range in Central Europe, surprisingly, equals the diversity found within the sampled area in the native range, which is about thirty times larger. Bayesian assignment grouped individuals into two genetic clusters separating North American native populations from the European, non-native populations, without any strong genetic structure shown over either range. In the case of the fine scale, our comparison of genetic diversity parameters among the localities and age classes yielded no evidence of genetic diversity increase over time. We found that SGS differed across age classes within the populations under study. Old trees in general completely lacked any SGS, which increased over time and reached its maximum in the sapling stage.

CONCLUSIONS

Based on (1) the absence of difference in genetic diversity between the native and adventive ranges, together with the lack of structure in the native range, and (2) the lack of any evidence of any temporal increase in genetic diversity at four highly invasive populations in the adventive range, we conclude that population amalgamation probably first happened in the native range, prior to introduction. In such case, there would have been no need for multiple introductions from previously isolated populations, but only several introductions from genetically diverse populations.

Range-wide population genetic structure of the Caribbean sea fan coral, Gorgonia ventalina

The population structure of benthic marine organisms is of central relevance to the conservation and management of these often threatened species, as well as to the accurate understanding of their ecological and evolutionary dynamics. A growing body of evidence suggests that marine populations can be structured over short distances despite theoretically high dispersal potential. Yet the proposed mechanisms governing this structure vary, and existing empirical population genetic evidence is of insufficient taxonomic and geographic scope to allow for strong general inferences. Here, we describe the range-wide population genetic structure of an ecologically important Caribbean octocoral, Gorgonia ventalina. Genetic differentiation was positively correlated with geographic distance and negatively correlated with oceanographically modelled dispersal probability throughout the range. Although we observed admixture across hundreds of kilometres, estimated dispersal was low, and populations were differentiated across distances <2 km. These results suggest that populations of G. ventalina may be evolutionarily coupled via gene flow but are largely demographically independent. Observed patterns of differentiation corroborate biogeographic breaks found in other taxa (e.g. an east/west divide near Puerto Rico), and also identify population divides not discussed in previous studies (e.g. the Yucatan Channel). High genotypic diversity and absence of clonemates indicate that sex is the primary reproductive mode for G. ventalina. A comparative analysis of the population structure of G. ventalina and its dinoflagellate symbiont, Symbiodinium, indicates that the dispersal of these symbiotic partners is not coupled, and symbiont transmission occurs horizontally.

Genetic spatial autocorrelation can readily detect sex-biased dispersal

Sex-biased dispersal is expected to generate differences in the fine-scale genetic structure of males and females. Therefore, spatial analyses of multilocus genotypes may offer a powerful approach for detecting sex-biased dispersal in natural populations. However, the effects of sex-biased dispersal on fine-scale genetic structure have not been explored. We used simulations and multilocus spatial autocorrelation analysis to investigate how sex-biased dispersal influences fine-scale genetic structure. We evaluated three statistical tests for detecting sex-biased dispersal: bootstrap confidence intervals about autocorrelation r values and recently developed heterogeneity tests at the distance class and whole correlogram levels. Even modest sex bias in dispersal resulted in significantly different fine-scale spatial autocorrelation patterns between the sexes. This was particularly evident when dispersal was strongly restricted in the less-dispersing sex (mean distance <200 m), when differences between the sexes were readily detected over short distances. All tests had high power to detect sex-biased dispersal with large sample sizes (n ≥ 250). However, there was variation in type I error rates among the tests, for which we offer specific recommendations. We found congruence between simulation predictions and empirical data from the agile antechinus, a species that exhibits male-biased dispersal, confirming the power of individual-based genetic analysis to provide insights into asymmetries in male and female dispersal. Our key recommendations for using multilocus spatial autocorrelation analyses to test for sex-biased dispersal are: (i) maximize sample size, not locus number; (ii) concentrate sampling within the scale of positive structure; (iii) evaluate several distance class sizes; (iv) use appropriate methods when combining data from multiple populations; (v) compare the appropriate groups of individuals.

The analysis of association between traits when differences between trait States matter

Because of their elementary significance in almost all fields of science, measures of association between two variables or traits are abundant and multiform. One aspect of association that is of considerable interest, especially in population genetics and ecology, seems to be widely ignored. This aspect concerns association between complex traits that show variable and arbitrarily defined state differences. Among such traits are genetic characters controlled by many and potentially polyploid loci, species characteristics, and environmental variables, all of which may be mutually and asymmetrically associated. A concept of directed association of one trait with another is developed here that relies solely on difference measures between the states of a trait. Associations are considered at three levels: between individual states of two variables, between an individual state of one variable and the totality of the other variable, and between two variables. Relations to known concepts of association are identified. In particular, measures at the latter two levels turn out to be interpretable as measures of differentiation. Examples are given for areas of application (search for functional relationships, distribution of variation over populations, genomic associations, spatiogenetic structure).

Spatial correlations at different spatial scales are themselves highly correlated in isolation by distance processes

Although many properties of spatial autocorrelation statistics are well characterized, virtually nothing is known about possible correlations among values at different spatial scales, which ultimately would influence how inferences about spatial genetics are made at multiple spatial scales. This article reports the results of stochastic space-time simulations of isolation by distance processes, having a very wide range of amounts of dispersal for plants or animals, and analyses of the correlations among Moran's I-statistics for different mutually exclusive distance classes. In general, the stochastic correlations are extremely large (>0.90); however, the correlations bear a complex relationship with level of dispersal, spatial scale and spatial lag between distance classes. The correlations are so large that any existing or conceived statistical method that employs more than one distance class (or spatial scale) should not ignore them. This result also suggests that gains in statistical power via increasing sample size are limited, and that increasing numbers of assayed loci generally should be preferred. To the extent that sampling error for real data sets can be treated as white noise, it should be possible to account for stochastic correlations in formulating more precise statistical methods. Further, while the current results are for isolation by distance processes, they provide some guidance for some more complex stochastic space-time processes of landscape genetics. Moreover, the results hold for several popular measures other than Moran's I. In addition, in the results, the signal to noise ratios strongly decreased with distance, which also has several implications for optimal statistical methods using correlations at multiple spatial scales.

Effects of historical demography and ecological context on spatial patterns of genetic diversity within foxtail pine (Pinus balfouriana; Pinaceae) stands located in the Klamath Mountains, California

The density and dispersion of individuals, nonequilibrium demographics, and habitat fragmentation all affect the magnitude and extent of spatial genetic structure within forest tree populations. Here, we investigate the link between historical demography and spatial genetic structure within ecologically contrasting stands of foxtail pine (Pinus balfouriana) in the Klamath Mountains of northern California. We defined two stand types a priori, based largely on differences in foxtail pine density and basal area, and for each type we sampled two stands. Population expansions, likely from Pleistocene bottlenecks, were detected in three of the four stands. The magnitude and extent of spatial autocorrelation among genotypes at five nuclear microsatellites differed dramatically among stands, with those having lower foxtail pine density exhibiting strong patterns of isolation by distance. Moran's I statistics were 7-fold higher for the first distance class (<25 m) in these stands relative to those observed in stands with higher foxtail pine density (I(25) = 0.14 vs. 0.02). We conclude that differences in spatial genetic structure between stand types are due to differences in ecological attributes that affected expansion from inferred bottlenecks.

Fine-scale spatial genetic structure in a predominantly selfing plant: role of seed and pollen dispersal

We present a study of fine-scale spatial genetic structure (SGS) and assess the impact of seed and pollen dispersal on the pattern of genetic diversity in the predominantly selfing Hordeum spontaneum. The study included (1) direct measurement of dispersal in a controlled environment, and (2) analyses of SGS and estimation of the ratio of pollen to seed flow in three natural populations sampled in linear transects at fixed increasing inter-plant distances. Analysis of SGS with 10 nuclear SSRs showed in all three populations a significant autocorrelation for the distance classes of 1 or 2 m and a negative linear relationship between kinship coefficients, calculated for pairs of individuals, and logarithm of geographical distance between members of the pairs. Major seed dispersal (95%) was found to be within 1.2 m from the mother plant. Pollen flow, estimated from the comparison of nuclear and chloroplast variation, was spatially limited as much as was seed dispersal, and tended to be overestimated when measured at spatial scales exceeding that of SGS. We conclude that combined effects of selfing, occasional outcrossing, localized seed dispersal and high plant density create an equilibrium between drift and gene flow in this species resulting in SGS at a very fine spatial scale.

Statistical methods in spatial genetics

The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only the potential of various approaches but also methodological pitfalls.

Ecologically relevant dispersal of corals on isolated reefs: implications for managing resilience

Coral reefs are in decline worldwide, and marine reserve networks have been advocated as a powerful management tool for maximizing the resilience of coral communities to an increasing variety, number, and severity of disturbances. However, the effective design of reserves must account for the spatial scales of larval dispersal that affect the demography of communities over ecological time frames. Ecologically relevant distances of dispersal were inferred from DNA microsatellite data in a broadcast-spawning (Acropora tenuis) and a brooding (Seriatopora hystrix) coral at isolated reef systems off northwest Australia. Congruent with expectations based on life histories, levels of genetic subdivision among populations were markedly higher in the brooder than in the broadcast spawner. Additionally, significant subdivision for both species between systems (>100 km), and between (>10 km) or within reefs (<10 km) within systems, indicated that many reefs or reef patches are demographically independent. There was also a clear distinction in the scale of genetic structure between the different systems; at the more geographically complex of the systems, a much finer scale structure was detected in both species. This suggested that the hydrodynamics associated with these complex reefs restrict distances regularly traveled by larvae. The primary implication is that short-term recovery of these coral communities after severe disturbance requires the input of larvae from viable communities kilometers to a few tens of kilometers away. Therefore, to be self-sustaining, we suggest that coral reef protected areas need to be large enough to encompass these routine dispersal distances. Further, to facilitate recovery from severe disturbances, protected areas need to be replicated over these spatial scales. However, specific designs also need to account for size, complexity, and isolation of reefs, which will either restrict or enhance dispersal within this range.