Geomorphic influence on intraspecific genetic differentiation and diversity along hyporheic corridors

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High‐throughput SNPs for all: genotyping‐in‐thousands

Understanding the genetic structure of species is essential for conservation. It is only with this information that managers, academics, user groups and land‐use planners can understand the spatial scale of migration and local adaptation, source‐sink dynamics and effective population size. Such information is essential for a multitude of applications including delineating management units, balancing management priorities, discovering cryptic species and implementing captive breeding programmes. Species can range from locally adapted by hundreds of metres (Pavey et al. 2010 ) to complete species panmixia (Côté et al. 2013 ). Even more remarkable is that this essential information can be obtained without fully sequenced or annotated genomes, but from mere (putatively) nonfunctional variants. First with allozymes, then microsatellites and now SNPs, this neutral genetic variation carries a wealth of information about migration and drift. For many of us, it may be somewhat difficult to remember our understanding of species conservation before the widespread usage of these useful tools. However most species on earth have yet to give us that ‘peek under the curtain’. With the current diversity on earth estimated to be nearly 9 million species (Mora et al. 2011 ), we have a long way to go for a comprehensive meta‐phylogeographic understanding. A method presented in this issue by Campbell and colleagues (Campbell et al. 2015 ) is a tool that will accelerate the pace in this area. Genotyping‐in‐thousands (GT‐seq) leverages recent advancements in sequencing technology to save many hours and dollars over previous methods to generate this important neutral genetic information.     

Genes,psychological traits and civic engagement

Civic engagement is a classic example of a collective action problem: while civic participation improves life in the community as a whole, it is individually costly and thus there is an incentive to free ride on the actions of others. Yet, we observe significant inter-individual variation in the degree to which people are in fact civically engaged. Early accounts reconciling the theoretical prediction with empirical reality focused either on variation in individuals’ material resources or their attitudes, but recent work has turned to genetic differences between individuals. We show an underlying genetic contribution to an index of civic engagement (0.41), as well as for the individual acts of engagement of volunteering for community or public service activities (0.33), regularly contributing to charitable causes (0.28) and voting in elections (0.27). There are closer genetic relationships between donating and the other two activities; volunteering and voting are not genetically correlated. Further, we show that most of the correlation between civic engagement and both positive emotionality and verbal IQ can be attributed to genes that affect both traits. These results enrich our understanding of the way in which genetic variation may influence the wide range of collective action problems that individuals face in modern community life.     

Mastering health: liberating beauty: Will the cosmetics of tomorrow be genetic?

Systems that have yet to stand the test of time carry imperfections that need to be skillfully addressed with the least amount of authoritarianism as possible. The communication and transmission of knowledge that we hold dear are essential pillars to social progress. As such, it is necessary to analyze with the greatest scientific objectivity the applications arising from the deep revolution rooted in the total sequencing of the human genome which affects all aspects of our societies. This extraordinary advance in human knowledge and the resulting technological achievements should not lend themselves to the fears or fantasies often fueled by those who criticize all scientific progress calling into question the most established dogmas. Certain supposedly scholarly analyses of the health situation with which we are currently confronted worldwide are a perfect illustration of this unfortunate trend. It is undeniable that the progress of molecular genetics has opened up a wide range of applications in many fields, affecting the well-being of humans, their mental and physical health. The apparent universal and individual interest for the most advanced genetic profile analyzing technologies is a testimony to this strong common desire to better understand one’s genetic heritage and to control their usage. Despite this movement, little attention is given to the recent advances in genetics applied to essential aspects of the social life of individuals through their inter-personal interactions. It is particularly distressing that the contributions of molecular biology and genetics to the daily well-being of individuals have not yet allowed open-access non-medical genetic testing to gain the recognition it deserves and are still viewed as recreational applications. Through an analysis of the cross influences that genetic biotechnologies have had since the beginning of the century in the fields of nutrition and cosmetics, we have tried to project ourselves into the near future which should witness major behavioral and social upheavals.     

Ocean circulation model predicts high genetic structure observed in a long‐lived pelagic developer

Understanding the movement of genes and individuals across marine seascapes is a long‐standing challenge in marine ecology and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species' dispersive life histories. However, genetic structure is the result of time‐integrated processes and may not capture present‐day connectivity between populations. Here, we use a high‐resolution oceanographic circulation model to predict larval dispersal along the complex coastline of western Canada that includes the transition between two well‐studied zoogeographic provinces. We simulate dispersal in a benthic sea star with a 6–10 week pelagic larval phase and test predictions of this model against previously observed genetic structure including a strong phylogeographic break within the zoogeographical transition zone. We also test predictions with new genetic sampling in a site within the phylogeographic break. We find that the coupled genetic and circulation model predicts the high degree of genetic structure observed in this species, despite its long pelagic duration. High genetic structure on this complex coastline can thus be explained through ocean circulation patterns, which tend to retain passive larvae within 20–50 km of their parents, suggesting a necessity for close‐knit design of Marine Protected Area networks.     

Steady-state analysis of structured population models

Our systematic formulation of nonlinear population models is based on the notion of the environmental condition. The defining property of the environmental condition is that individuals are independent of one another (and hence equations are linear) when this condition is prescribed (in principle as an arbitrary function of time, but when focussing on steady states we shall restrict to constant functions). The steady-state problem has two components: (i). the environmental condition should be such that the existing populations do neither grow nor decline; (ii). a feedback consistency condition relating the environmental condition to the community/population size and composition should hold. In this paper we develop, justify and analyse basic formalism under the assumption that individuals can be born in only finitely many possible states and that the environmental condition is fully characterized by finitely many numbers. The theory is illustrated by many examples. In addition to various simple toy models introduced for explanation purposes, these include a detailed elaboration of a cannibalism model and a general treatment of how genetic and physiological structure should be combined in a single model.     

Individual variation in movement throughout the life cycle of a stream-dwelling salmonid fish

Stream-dwelling fish populations have long served as important models of animal movement. Populations of adult stream-dwelling fishes are generally composed of a mix of relatively sedentary and mobile individuals. However, we do not know whether this pattern that we typically observe among adults is indicative of patterns of movement that occur throughout the life cycle. Therefore, we do not know whether we can apply these patterns to understanding or predicting processes such as migration and thus the potential for the evolution of genetic differences among populations. We test the general hypothesis that patterns of movement throughout the life cycle are consistent with patterns of movement inferred by indirect genetic methods and, more specifically, that the characteristics of the mobile fraction of the population are consistent with patterns of genetic differentiation. We used parentage analyses to infer the movements of alevin brook charr (Salvelinus fontinalis) in Freshwater River, Newfoundland, Canada, and a capture-recapture study of one cohort in this population to infer movement throughout the rest of the life cycle. We found that alevins move large distances shortly after emergence, primarily in the downstream direction, and that the population is composed of a mix of relatively sedentary and mobile individuals throughout all other intervals of the life cycle. In contrast, when we considered movements of individuals first captured as juveniles and eventually recovered as reproductively mature adults, we found relatively large and uniform distributions of net movement distance. Thus, heterogeneity in individual movement of adults is not representative of patterns of movement throughout the life cycle and therefore may provide only limited inference of population-level processes such as gene flow.     

Using isolation‐by‐distance‐based approaches to assess the barrier effect of linear landscape elements on badger (Meles meles) dispersal

As the European badger (Meles meles) can be of conservation or management concern, it is important to have a good understanding of the species’ dispersal ability. In particular, knowledge of landscape elements that affect dispersal can contribute to devising effective management strategies. However, the standard approach of using Bayesian clustering methods to correlate genetic discontinuities with landscape elements cannot easily be applied to this problem, as badger populations are often characterized by a strong confounding isolation‐by‐distance (IBD) pattern. We therefore developed a two‐step method that compares the location of pairs of related badgers relative to a putative barrier and utilizes the expected spatial genetic structure characterized by IBD as a null model to test for the presence of a barrier. If a linear feature disrupts dispersal, the IBD pattern characterising pairs of individuals located on different sides of a putative barrier should differ significantly from the pattern obtained with pairs of individuals located on the same side. We used our new approach to assess the impact of rivers and roads of different sizes on badger dispersal in western England. We show that a large, wide river represented a barrier to badger dispersal and found evidence that a motorway may also restrict badger movement. Conversely, we did not find any evidence for small rivers and roads interfering with badger movement. One of the advantages of our approach is that potentially it can detect features that disrupt gene flow locally, without necessarily creating distinct identifiable genetic units.     

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.     

The role of context in elucidating drivers of animal movement

Despite its consequences for ecological processes and population dynamics, intra‐specific variability is frequently overlooked in animal movement studies. Consequently, the necessary resolution to reveal drivers of individual movement decisions is often lost as animal movement data are aggregated to infer average or population patterns. Thus, an empirical understanding of why a given movement pattern occurs remains patchy for many taxa, especially in marine systems. Nonetheless, movement is often rationalized as being driven by basic life history requirements, such as acquiring energy (feeding), reproduction, predator‐avoidance, and remaining in suitable environmental conditions. However, these life history requirements are central to every individual within a species and thus do not sufficiently account for the high intra‐specific variability in movement behavior and hence fail to fully explain the occurrence of multiple movement strategies within a species. Animal movement appears highly context dependent as, for example, within the same location, the behavior of both resident and migratory individuals is driven by life history requirements, such as feeding or reproduction, however different movement strategies are utilized to fulfill them. A systematic taxa‐wide approach that, instead of averaging population patterns, incorporates and utilizes intra‐specific variability to enable predictions as to which movement patterns can be expected under a certain context, is needed. Here, we use intra‐specific variability in elasmobranchs as a case study to introduce a stepwise approach for studying animal movement drivers that is based on a context‐dependence framework. We examine relevant literature to illustrate how this context‐focused approach can aid in reliably identifying drivers of a specific movement pattern. Ultimately, incorporating behavioral variability in the study of movement drivers can assist in making predictions about behavioral responses to environmental change, overcoming tagging biases, and establishing more efficient conservation measures.     

Gene flow simulations demonstrate resistance of long-lived species to genetic erosion from habitat fragmentation

Habitat fragmentation restricts the movement of individuals across a landscape. In terrestrial and aquatic systems, barriers to movement can modify population and community dynamics at local or regional scales. This study contrasted life history traits related to lifespan with habitat fragmentation to determine impacts on species population genetic structure in the Neuse River Basin, USA. For this, we simulated gene flow among evenly-spaced populations in a river network and tracked individual and population genetics for 200 years. The modeled scenarios represent a full cross between five life history strategies and four riverscapes representing varying degrees of fragmentation. The five life history strategies include species (based on freshwater mussels) with average lifespans ranging from 10 to 50 years and age at maturity from 2 to 6 years. The movement landscapes included a (1) panmictic, (2) stepping-stone landscape allowing movement to only neighboring populations during each dispersal event, (3) partially-fragmented landscape divided by dams currently in the network, and (4) fully-fragmented landscape. Results suggest species with shorter lifespans have higher population genetic structure in fragmented landscapes than species with longer lifespans. Furthermore, species with shorter lifespans in highly fragmented landscapes may be harboring genetic degradation or decline as allele fixation and loss. Although anthropogenic fragmentation of many river systems is only 100–200 years old, the simulation indicates that species can respond genetically in that period of time. Additionally, the time frame of the simulation suggests that genetic impacts of habitat fragmentation in some species present in the Neuse River Basin may not yet be manifesting and restoration activities could be successful.     

Long‐distance geneflow and habitat specificity of the rock‐dwelling coppertail skink,Ctenotus taeniolatus

Rock boulders or ‘bush‐rocks’ provide essential habitat for many organisms and there has been interest in rehabilitating areas denuded of rock with artificial substitutes. We examine whether the density and size of bush rock influences the density of the coppertail skink (Ctenotus taeniolatus). The success of habitat rehabilitation is contingent on dispersal of rock‐dwelling organisms into areas that have been remediated. To gauge the likelihood of this we characterize geneflow of coppertail skinks among discrete patches of rocky habitat associated with ridge tops. We genotyped 154 individuals from seven localities at six microsatellite DNA loci and from a subset of these individuals we obtained sequence data from the mitochondrial ND4 region. Our field survey established that lizard density was positively associated with the availability of suitably sized bush‐rock (P < 0.001), highlighting the importance of maintaining this habitat element, or replacing it where it has been lost. Despite the presence of habitat features that might be presumed as barriers to dispersal for coppertail skinks, such as intervening gullies and dense vegetation, our genetic data demonstrated high levels of geneflow among rocky ridge tops. Levels of partitioning estimated by global F_ST were significant but low for both microsatellite (F_ST = 0.020) and mitochondrial data (F_ST = 0.113). Spatial autocorrelation of genotypic similarity supports our conclusion of regular longer‐distance geneflow, and we infer lower levels of dispersal in juveniles than in adults. This study suggests that dispersal of coppertail skinks can be sufficient to naturally colonize areas of restored habitat.     

Evaluating methods to visualize patterns of genetic differentiation on a landscape

With advances in sequencing technology, research in the field of landscape genetics can now be conducted at unprecedented spatial and genomic scales. This has been especially evident when using sequence data to visualize patterns of genetic differentiation across a landscape due to demographic history, including changes in migration. Two recent model‐based visualization methods that can highlight unusual patterns of genetic differentiation across a landscape, SpaceMix and EEMS, are increasingly used. While SpaceMix's model can infer long‐distance migration, EEMS’ model is more sensitive to short‐distance changes in genetic differentiation, and it is unclear how these differences may affect their results in various situations. Here, we compare SpaceMix and EEMS side by side using landscape genetics simulations representing different migration scenarios. While both methods excel when patterns of simulated migration closely match their underlying models, they can produce either un‐intuitive or misleading results when the simulated migration patterns match their models less well, and this may be difficult to assess in empirical data sets. We also introduce unbundled principal components (un‐PC), a fast, model‐free method to visualize patterns of genetic differentiation by combining principal components analysis (PCA), which is already used in many landscape genetics studies, with the locations of sampled individuals. Un‐PC has characteristics of both SpaceMix and EEMS and works well with simulated and empirical data. Finally, we introduce msLandscape, a collection of tools that streamline the creation of customizable landscape‐scale simulations using the popular coalescent simulator ms and conversion of the simulated data for use with un‐PC, SpaceMix and EEMS.     

Population structure and migration pattern of a conifer pathogen, Grosmannia clavigera, as influenced by its symbiont, the mountain pine beetle

We investigated the population structure of Grosmannia clavigera (Gc), a fungal symbiont of the mountain pine beetle (MPB) that plays a crucial role in the establishment and reproductive success of this pathogen. This insect-fungal complex has destroyed over 16 million ha of lodgepole pine forests in Canada, the largest MPB epidemic in recorded history. During this current epidemic, MPB has expanded its range beyond historically recorded boundaries, both northward and eastward, and has now reached the jack pine of Alberta, potentially threatening the Canadian boreal forest. To better understand the dynamics between the beetle and its fungal symbiont, we sampled 19 populations in western North America and genotyped individuals from these populations with eight microsatellite markers. The fungus displayed high haplotype diversity, with over 250 unique haplotypes observed in 335 single spore isolates. Linkage equilibria in 13 of the 19 populations suggested that the fungus reproduces sexually. Bayesian clustering and distance analyses identified four genetic clusters that corresponded to four major geographical regions, which suggested that the epidemic arose from multiple geographical sources. A genetic cluster north of the Rocky Mountains, where the MPB has recently become established, experienced a population bottleneck, probably as a result of the recent range expansion. The two genetic clusters located north and west of the Rocky Mountains contained many fungal isolates admixed from all populations, possibly due to the massive movement of MPB during the epidemic. The general agreement in north-south differentiation of MPB and G. clavigera populations points to the fungal pathogen's dependence on the movement of its insect vector. In addition, the patterns of diversity and the individual assignment tests of the fungal associate suggest that migration across the Rocky Mountains occurred via a northeastern corridor, in accordance with meteorological patterns and observation of MPB movement data. Our results highlight the potential of this pathogen for both expansion and sexual reproduction, and also identify some possible barriers to gene flow. Understanding the ecological and evolutionary dynamics of this fungus-beetle association is important for the modelling and prediction of MPB epidemics.     

Genetic Effects of a Persistent Bottleneck on a Natural Population of Ornate Box Turtles (Terrapene ornata)

Human activities in the past few hundred years have caused enormous impacts on many ecosystems, greatly accelerating the rate of population decline and extinction. In addition to habitat alteration and destruction, the loss of genetic diversity due to reduced population size has become a major conservation issue for many imperiled species. However, the genetic effects of persistent population bottlenecks can be very different for long-lived and short-lived species when considering the time scale of centuries. To investigate the genetic effects of persistent population bottlenecks on long-lived species, we use microsatellite markers to assess the level of genetic diversity of a small ornate box turtle population that has experienced a persistent bottleneck in the past century, and compare it to a large relatively undisturbed population. The genetic signature of a recent bottleneck is detected by examining the deviation from mutation-drift equilibrium in the small population, but the bottleneck had little effect on its level of genetic diversity. Computer simulations combined with information on population structure suggest that an effective population size of 300, which results in a census population size of 700, would be required for the small population to maintain 90% of the average number of alleles per locus in the next 200 years. The life history of long-lived species could mask the accelerated rate of genetic drift, making population recovery a relatively slow process. Statistical analysis of genetic data and empirical-based computer simulations can be important tools to facilitate conservation planning.     

Sex ratios observed in 80 species of parrots

A number of potential evolutionary and physiological factors may be involved in avian sex ratio bias so that under certain conditions a sex ratio bias may favour males or females within a population. In addition different factors may be important in manipulating sex ratio bias through the different life stages. In this study sex ratio bias was examined in a total of 16 570 captive parrots, representing 80 species, many of which are endangered in the wild, using database records originating form commercial laboratories that offer genetic sexing. Within the species examined 72% showed a male bias this was significant in three species, when adjusted for multiple comparisons. This preliminary study is limited due to lack of data on the age of the individuals sampled. However, the large dataset do suggest that this phenomenon should be further considered by investigators working at a species level where such data can be collected.     

ESTIMATING GENETIC CORRELATIONS FROM MEASUREMENTS OF FIELD-CAUGHT WATERSTRIDERS

Abstract Lynch (1999) proposed a method for estimation of genetic correlations from phenotypic measurements of individuals for which no pedigree information is available. This method assumes that shared environmental effects do not contribute to the similarity of relatives, and it is expected to perform best when sample sizes are large, many individuals in the sample are paired with close relatives, and heritability of the traits is high. We tested the practicality of this method for field biologists by using it to estimate genetic correlations from measurements of field‐caught waterstriders {Aquarius remigis). Results for sample sizes of less than 100 pairs were often unstable or undefined, and even with more than 500 pairs only half of those correlations that had been found to be significant in standard laboratory experiments were statistically significant in this study. Statistically removing the influence of environmental effects (shared between relatives) weakened the estimates, possibly by removing some of the genetic similarity between relatives. However, the method did generate statistically significant estimates for some genetic correlations. Lynch (1999) anticipated the problems found, and proposed another method that uses estimates of relatedness between members of pairs (from molecular marker data) to improve the estimates of genetic correlations, but that approach has yet to be tested in the field.     

More than meets the eye: detecting cryptic microgeographic population structure in a parasite with a complex life cycle

Nonrandom recruitment of parasites among hosts can lead to genetic differentiation among hosts and mating dynamics that promote inbreeding. It has been hypothesized that strictly aquatic parasites with intermediate hosts will behave as panmictic populations among hosts because ample opportunity exists for random mixing of unrelated individuals during transmission to the definitive host. A previous allozyme study on the marine trematode Lecithochirium fusiforme did not support this hypothesis; in that, there was genetic differentiation among, and significant heterozygote deficiencies within, definitive hosts. We revisit this system and use microsatellites to obtain multilocus genotypes. Our goal was to determine whether cryptic subgroups and/or the presence of clones could account for the apparent deviation from 'panmixia'. We find strong evidence for cryptic subdivision (three genetic clusters) that causes the Wahlund effect and differentiation among definitive hosts. After accounting for these cryptic groups, we see panmictic genetic structure among definitive hosts that is consistent with the 'high mixing in aquatic habitats' hypothesis. We see evidence for cotransmission of clones in all three clusters, but this level of clonal structure did not have a major impact in causing deviations from Hardy-Weinberg equilibrium, and only affected genetic differentiation among hosts in one cluster. A cursory examination of the data may have led to incorrect conclusions about nonrandom transmission. However, it is obvious in this system that there is more than meets the eye in relation to the actual make-up of parasite populations. In general, the methods we employ will be useful for elucidating hidden patterns in other organisms where cryptic structure may be common (e.g. those with limited morphology or complex life histories).