Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>, Walbaum 1792) in the Beagle Channel,Tierra del Fuego: the onset of an invasion

In this paper we provide the first report of the presence of exotic Chinook salmon (Oncorhynchus tshawytscha) in two rivers off the Beagle Channel, Lapataia and Ovando, in southern Tierra del Fuego. We also confirm that successful reproduction occurred in the fall of 2007, as we captured yearlings in freshwater. Scale pattern analyses of adult fish caught were all of the “stream” ecotype, with ages ranging between 3 and 5 (average 4.2 year). Stable isotope analysis of Ovando-Lapataia Chinook population indicates general patterns consistent with those of other populations in the region, but characteristically enriched levels of C indicates a distinct ocean feeding location as compared to Atlantic populations in the Santa Cruz River. Two different haplotypes, one identical to the unique haplotype of the Caterina River population, were found in the Ovando-Lapataia rivers, providing partial evidence for some level of contemporary segregation between these two populations. As an exotic species, Chinook salmon have been able to use the ocean as a waterway to rapidly colonize new habitats both in New Zealand and in several Pacific and Atlantic river basins of continental Patagonia. This record expands the known distribution of this species in Patagonia further south and into the Island of Tierra del Fuego. Its presence in the Beagle Channel creates the conditions for its expansion to a significant collection of new rivers, as well as to adjacent marine areas in and around the Southern Fuegian Channels. Our results provide support to the idea that, in practice, no district of Patagonia is sheltered from the colonization by invasive anadromous Salmonids.     

Identification of multiple genetically distinct populations of Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) in a small coastal watershed

Management and restoration planning for Pacific salmon is often characterized by efforts at broad multi-basin scales. However, finer-scale genetic and phenotypic variability may be present within individual basins and can be overlooked in such efforts, even though it may be a critical component for long-term viability. Here, we investigate Chinook salmon (Oncorhynchus tshawytscha) within the Siletz River, a small coastal watershed in Oregon, USA. Adult Chinook salmon were genotyped using neutral microsatellite markers, single nucleotide polymorphisms and “adaptive” loci, associated with temporal variation in migratory behavior in many salmon populations, to investigate genetic diversity based upon both spatial and temporal variation in migratory and reproductive behavior. Results from all three marker types identified two genetically distinct populations in the basin, corresponding to early returning fish that spawn above a waterfall, a spring-run population, and later returning fish spawning below the waterfall, a fall-run population. This finding is an important consideration for management of the species, as spring-run populations generally only have been recognized in large watersheds, and highlights the need to evaluate population structure of salmon within smaller watersheds, and thereby increase the probability of successful conservation of salmon species.     

Genetic signals of artificial and natural dispersal linked to colonization of South America by non‐native Chinook salmon (Oncorhynchus tshawytscha)

Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non‐native populations. Yet, our understanding of how artificial (human‐mediated) and natural dispersal pathways of non‐native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the widespread colonization of Chinook salmon Oncorhynchus tshawytscha in South America, mediated by both dispersal pathways, to address these issues using data from a panel of polymorphic SNPs. First, genetic diversity and the number of effective breeders (N_b) were higher among artificial than natural populations. Contemporary gene flow was common between adjacent artificial and natural and adjacent natural populations, but uncommon between geographically distant populations. Second, genetic structure revealed four distinct clusters throughout the Chinook salmon distributional range with varying levels of genetic connectivity. Isolation by distance resulted from weak differentiation between adjacent artificial and natural and between natural populations, with strong differentiation between distant Pacific Ocean and Atlantic Ocean populations, which experienced strong genetic drift. Third, genetic mixture analyses revealed the presence of at least six donor geographic regions from North America, some of which likely hybridized as a result of multiple introductions. Relative propagule pressure or the proportion of Chinook salmon propagules introduced from various geographic regions according to government records significantly influenced genetic mixtures for two of three artificial populations. Our findings support a model of colonization in which high‐diversity artificial populations established first; some of these populations exhibited significant admixture resulting from propagule pressure. Low‐diversity natural populations were likely subsequently founded from a reduced number of individuals.     

Managed metapopulations: do salmon hatchery 'sources' lead to in-river 'sinks' in conservation?

Maintaining viable populations of salmon in the wild is a primary goal for many conservation and recovery programs. The frequency and extent of connectivity among natal sources defines the demographic and genetic boundaries of a population. Yet, the role that immigration of hatchery-produced adults may play in altering population dynamics and fitness of natural populations remains largely unquantified. Quantifying, whether natural populations are self-sustaining, functions as sources (population growth rate in the absence of dispersal, λ>1), or as sinks (λ<1) can be obscured by an inability to identify immigrants. In this study we use a new isotopic approach to demonstrate that a natural spawning population of Chinook salmon, (Oncorhynchus tshawytscha) considered relatively healthy, represents a sink population when the contribution of hatchery immigrants is taken into consideration. We retrieved sulfur isotopes ((34)S/(32)S, referred to as δ(34)S) in adult Chinook salmon otoliths (ear bones) that were deposited during their early life history as juveniles to determine whether individuals were produced in hatcheries or naturally in rivers. Our results show that only 10.3% (CI = 5.5 to 18.1%) of adults spawning in the river had otolith δ(34)S values less than 8.5‰, which is characteristic of naturally produced salmon. When considering the total return to the watershed (total fish in river and hatchery), we estimate that 90.7 to 99.3% (CI) of returning adults were produced in a hatchery (best estimate = 95.9%). When population growth rate of the natural population was modeled to account for the contribution of previously unidentified hatchery immigrants, we found that hatchery-produced fish caused the false appearance of positive population growth. These findings highlight the potential dangers in ignoring source-sink dynamics in recovering natural populations, and question the extent to which declines in natural salmon populations are undetected by monitoring programs.     

Population structure and gene flow reversals in Atlantic salmon (Salmo salar) over contemporary and long-term temporal scales: effects of population size and life history

Metapopulation dynamics are increasingly invoked in management and conservation of endangered species. In this context, asymmetrical gene flow patterns can be density dependent, with migration occurring mainly from larger into smaller populations, which may depend on it for their persistence. Using genetic markers, such patterns have recently been documented for various organisms including salmonids, suggesting this may be a more general pattern. However, metapopulation theory does not restrict gene flow asymmetry to 'source-sink' structures, nor need these patterns be constant over longer evolutionary timescales. In anadromous salmonids, gene flow can be expected to be shaped by various selective pressures underlying homing and dispersal ('straying') behaviours. The relative importance of these selective forces will vary spatially and for populations of different census size. Furthermore, the consequences of life-history variation among populations for dispersal and hence gene flow remain poorly quantified. We examine population structure and connectivity in Atlantic salmon (Salmo salar L.) from Newfoundland and Labrador, a region where populations of this species are relatively pristine. Using genetic variation at 13 microsatellite loci from samples (N=1346) collected from a total of 20 rivers, we examine connectivity at several regional and temporal scales and test the hypothesis that the predominant direction of gene flow is from large into small populations. We reject this hypothesis and find that the directionality of migration is affected by the temporal scale over which gene flow is assessed. Whereas large populations tend to function as sources of dispersal over contemporary timescales, such patterns are often changed and even reversed over evolutionary, coalescent-derived timescales. These patterns of population structure furthermore vary between different regions and are compatible with demographic and life-history attributes. We find no evidence for sex-biased dispersal underlying gene flow asymmetry. Our findings caution against generalizations concerning the directionality of gene flow in Atlantic salmon and emphasize the need for detailed regional study, if such information is to be meaningfully applied in conservation and management of salmonids.     

Chinook salmon invade southern South America

We document the invasion of Chinook salmon (Oncorhynchus tshawytscha) to southern South America providing historical, current and future perspectives. We conducted field sampling, angler surveys, and analyzed all written records, and found evidence of reproductive populations in more than ten Andean (and many more coastal) watersheds draining mainly to the Pacific Ocean in Chile (39°–53° S), but also to the Atlantic Ocean in Argentina (50° S). Invasion begun ∼25 years ago apparently from a few point sources of introduction by ocean ranching operations using spring-run Chinook salmon originated from tributaries of the lower Columbia River, USA. The rapid spread suggests that Chinook salmon were pre-adapted to their novel marine and freshwater environments because of similarities to equivalent North Pacific habitats, and invasion may have been facilitated by low ecological resistance. Preliminary data suggest that populations express a latitudinal gradient in juvenile migration life histories equivalent to that in their native range. Parallels to the only other establishment of anadromous Chinook salmon outside their native range, New Zealand, suggests a predictable invasion rate. In South America, the invasion is ongoing in southern areas, yet we deem unlikely colonization of rivers north of the range reached thus far. This is the first anadromous salmon species to have invaded such a large range in South America, and it raises many evolutionary, ecological, environmental and socioeconomic issues, with several discussed here.

Archival genetic analysis suggests recent immigration has altered a population of Chinook salmon in an unsupplemented wilderness area

Detecting genetic population shifts (i.e. allele frequency differences) through time is a primary function of effective conservation monitoring, but it is equally vital to understand the underlying causative factors of change which may be revealed through analyses of long-term, temporal trends. We compared archival and contemporary Chinook salmon (Oncorhynchus tshawytscha) collections from the John Day River in Oregon, USA, to evaluate the temporal relationships among four primary spawning areas over a span of 28 years (1978–2006). Although it lies amid many hatchery-supplemented salmon populations of the Columbia River, the John Day River has itself experienced no directed supplementation. Using a combined panel of 13 microsatellite and 92 single nucleotide polymorphism loci, we observed significant temporal heterogeneity across sample sites and tested for two likely evolutionary influences: stochastic processes (i.e. genetic drift) and gene flow via immigration. Based on abundance and effective population size estimates, we found no evidence indicating a recent bottleneck. We observed a sharp temporal decline in probability of self-assignment of John Day River fish, particularly for the North Fork tributary. There was a corresponding increase in assignment to distant Snake River populations, attributed to accumulating introgression from out-of-basin sources over time. Our study demonstrates that low level immigration sustained over multiple generations can alter the genetic composition of natural populations, and while immigration may help maintain genetic population diversity, it risks reducing adaptive advantages in local ecosystems.     

Retention of gene diversity during the spread of a non‐native plant species

Spatial expansion, which is a crucial stage in the process to successful biological invasion, is anticipated to profoundly affect the magnitude and spatial distribution of genetic diversity in novel colonized areas. Here, we show that, contrasting common expectations, Pyrenean rocket (Sisymbrium austriacum), retained SNP diversity as this introduced plant species descended in the Meuse River Basin. Allele frequencies did not mirror between‐population distances along the predominant expansion axis. Reconstruction of invasion history based on the genotypes of historical herbarium specimens indicated no influence of additional introductions or multiple points of entry on this nongradual pattern. Assignment analysis suggested the admixture of distant upstream sources in recently founded downstream populations. River dynamics seem to have facilitated occasional long‐distance dispersal which brought diversity to the expansion front and so maintained evolutionary potential. Our findings highlight the merit of a historical framework in interpreting extant patterns of genetic diversity in introduced species and underscore the need to integrate long‐distance dispersal events in theoretical work on the genetic consequences of range expansion.     

Diversity of juvenile Chinook salmon life history pathways

Life history variability includes phenotypic variation in morphology, age, and size at key stage transitions and arises from genotypic, environmental, and genotype-by-environment effects. Life history variation contributes to population abundance, productivity, and resilience, and management units often reflect life history classes. Recent evidence suggests that past Chinook salmon (Oncorhynchus tshawytscha) classifications (e.g., ‘stream’ and ‘ocean’ types) are not distinct evolutionary lineages, do not capture the phenotypic variation present within or among populations, and are poorly aligned with underlying ecological and developmental processes. Here we review recently reported variation in juvenile Chinook salmon life history traits and provide a refined conceptual framework for understanding the causes and consequences of the observed variability. The review reveals a broad continuum of individual juvenile life history pathways, defined primarily by transitions among developmental stages and habitat types used during freshwater rearing and emigration. Life history types emerge from discontinuities in expressed pathways when viewed at the population scale. We synthesize recent research that examines how genetic, conditional, and environmental mechanisms likely influence Chinook salmon life history pathways. We suggest that threshold models hold promise for understanding how genetic and environmental factors influence juvenile salmon life history transitions. Operational life history classifications will likely differ regionally, but should benefit from an expanded lexicon that captures the temporally variable, multi-stage life history pathways that occur in many Chinook salmon populations. An increased mechanistic awareness of life history diversity, and how it affects population fitness and resilience, should improve management, conservation, and restoration of this iconic species.     

Self-sustaining populations, population sinks or aggregates of strays: chum (Oncorhynchus keta) and Chinook salmon (Oncorhynchus tshawytscha) in the Wood River system, Alaska

Small populations can provide insights into ecological and evolutionary aspects of species distributions over space and time. In the Wood River system in Alaska, USA, small aggregates of Chinook (Oncorhynchus tshawytscha) and chum salmon (O. keta) spawn in an area dominated by sockeye salmon (O. nerka). Our objective was to determine whether these Chinook and chum salmon are reproductively isolated, self-sustaining populations, population sinks that produce returning adults but receive immigration, or strays from other systems that do not produce returning adults. DNA samples collected from adult chum salmon from 16 streams and Chinook salmon from four streams in the Wood River system over 3 years were compared to samples from large populations in the nearby Nushagak River system, a likely source of strays. For both species, microsatellite markers indicated no significant genetic differentiation between the two systems. Simulations of microsatellite data in a large source and a smaller sink population suggested that considerable immigration would be required to counteract the diverging effects of genetic drift and produce genetic distances as small as those observed, considering the small census sizes of the two species in the Wood River system. Thus, the Wood River system likely receives substantial immigration from neighbouring watersheds, such as the Nushagak River system, which supports highly productive runs. Although no data on population productivity in the Wood River system exist, our results suggest source-sink dynamics for the two species, a finding relevant to other systems where salmonid population sizes are limited by habitat factors.     

Signals of large scale climate drivers,hatchery enhancement,and marine factors in Yukon River Chinook salmon survival revealed with a Bayesian life history model

Understanding how species might respond to climate change involves disentangling the influence of co‐occurring environmental factors on population dynamics, and is especially problematic for migratory species like Pacific salmon that move between ecosystems. To date, debate surrounding the causes of recent declines in Yukon River Chinook salmon (Oncorhynchus tshawytscha) abundance has centered on whether factors in freshwater or marine environments control variation in survival, and how these populations at the northern extremity of the species range will respond to climate change. To estimate the effect of factors in marine and freshwater environments on Chinook salmon survival, we constructed a stage‐structured assessment model that incorporates the best available data, estimates incidental marine bycatch mortality in trawl fisheries, and uses Bayesian model selection methods to quantify support for alternative hypotheses. Models fitted to two index populations of Yukon River Chinook salmon indicate that processes in the nearshore and marine environments are the most important determinants of survival. Specifically, survival declines when ice leaves the Yukon River later in the spring, increases with wintertime temperature in the Bering Sea, and declines with the abundance of globally enhanced salmon species consistent with competition at sea. In addition, we found support for density‐dependent survival limitations in freshwater but not marine portions of the life cycle, increasing average survival with ocean age, and age‐specific selectivity of bycatch mortality in the Bering Sea. This study underscores the utility of flexible estimation models capable of fitting multiple data types and evaluating mortality from both natural and anthropogenic sources in multiple habitats. Overall, these analyses suggest that mortality at sea is the primary driver of population dynamics, yet under warming climate Chinook salmon populations at the northern extent of the species’ range may be expected to fare better than southern populations, but are influenced by foreign salmon production.     

Testing the role of genetic factors across multiple independent invasions of the shrub Scotch broom (Cytisus scoparius)

Knowledge of the introduction history of invasive plants informs on theories of invasiveness and assists in the invasives management. For the highly successful invasive shrub Scotch broom, Cytisus scoparius, we analysed a combination of nuclear and chloroplast microsatellites for eight native source regions and eight independent invasion events in four countries across three continents. We found that two exotic Australian populations came from different sources, one of which was derived from multiple native populations, as was an invasive sample from California. An invasive population from New Zealand appeared to be predominantly sourced from a single population, either from the native or exotic ranges. Four invasive populations from Chile were genetically differentiated from the native range samples analysed here and so their source of introduction could not be confirmed, but high levels of differentiation between the Chilean populations suggested a combination of different sources. This extensive global data set of replicated introductions also enabled tests of key theories of invasiveness in relation to genetic diversity. We conclude that invasive populations have similar levels of high genetic diversity to native ranges; levels of admixture may vary across invasive populations so admixture does not appear to have been an essential requirement for invasion; invasive and native populations exhibit similar level of genetic structure indicating similar gene flow dynamics for both types of populations. High levels of diversity and multiple source populations for invasive populations observed here discount founder effects or drift as likely explanations for previously observed seed size differences between ranges. The high levels of genetic diversity, differential and source admixture identified for most exotic populations are likely to limit the ability to source biocontrol agents from the native region of origin of invasive populations.     

Gene Flow and Maintenance of Genetic Diversity in Invasive Mosquitofish (Gambusia holbrooki)

Genetic analyses contribute to studies of biological invasions by mapping the origin and dispersal patterns of invasive species occupying new territories. Using microsatellite loci, we assessed the genetic diversity and spatial population structure of mosquitofish (Gambusia holbrooki) that had invaded Spanish watersheds, along with the American locations close to the suspected potential source populations. Mosquitofish populations from the Spanish streams that were studied had similar levels of genetic diversity to the American samples; therefore, these populations did not appear to have undergone substantial losses of genetic diversity during the invasion process. Population structure analyses indicated that the Spanish populations fell into four main clusters, which were primarily associated with hydrography. Dispersal patterns indicated that local populations were highly connected upstream and downstream through active dispersal, with an average of 21.5% fish from other locations in each population. After initially introducing fish to one location in a given basin, such dispersal potential might contribute to the spread and colonization of suitable habitats throughout the entire river basin. The two-dimension isolation-by-distance pattern here obtained, indicated that the human-mediated translocation of mosquitofish among the three study basins is a regular occurrence. Overall, both phenomena, high natural dispersal and human translocation, favor gene flow among river basins and the retention of high genetic diversity, which might help retain the invasive potential of mosquitofish populations.     

Standing variation boosted by multiple sources of introduction contributes to the success of the introduced species, Lotus corniculatus

Although ecological differences between native and introduced ranges have been considered to drive rapid expansion of invasive species, recent studies suggest that rapid evolutionary responses of invasive species to local environments may also be common. Such expansion across heterogeneous environments by adaptation to local habitats requires genetic variation. In this study, we investigated the source and role of standing variation in successful invasion of heterogeneous abiotic environments in a self-incompatible species, Lotus corniculatus. We compared phenotypic and genetic variation among cultivars, natives, and introduced genotypes, and found substantial genetic variation within both native and introduced populations. Introduced populations possessed genotypes derived from both cultivars and native populations, and had lower population differentiation, indicating multiple sources of introduction and population admixture among the sources in the introduced range. Both cultivars and introduced populations had similarly outperforming phenotypes on average, with increased biomass and earlier flowering compared with native populations, but those phenotypes were within the range of the variation in phenotypes of the native populations. In addition, clinal variation within introduced populations was detected along a climatic gradient. Multiple introductions from different sources, including cultivars, may have contributed to pre-adaptive standing variation in the current introduced populations. We conclude that both introduction of cultivar genotypes and natural selection in local environments contributed to current patterns of genetic and phenotypic variation observed in the introduced populations.     

Genetic differentiation of Alaska Chinook salmon: the missing link for migratory studies

Most information about Chinook salmon genetic diversity and life history originates from studies from the West Coast USA, western Canada and southeast Alaska; less is known about Chinook salmon from western and southcentral Alaska drainages. Populations in this large area are genetically distinct from populations to the south and represent an evolutionary legacy of unique genetic, phenotypic and life history diversity. More genetic information is necessary to advance mixed stock analysis applications for studies involving these populations. We assembled a comprehensive, open-access baseline of 45 single nucleotide polymorphisms (SNPs) from 172 populations ranging from Russia to California. We compare SNP data from representative populations throughout the range with particular emphasis on western and southcentral Alaska. We grouped populations into major lineages based upon genetic and geographic characteristics, evaluated the resolution for identifying the composition of admixtures and performed mixed stock analysis on Chinook salmon caught incidentally in the walleye pollock fishery in the Bering Sea. SNP data reveal complex genetic structure within Alaska and can be used in applications to address not only regional issues, but also migration pathways, bycatch studies on the high seas, and potential changes in the range of the species in response to climate change.     

Nuclear and chloroplast microsatellites show multiple introductions in the worldwide invasion history of common ragweed, Ambrosia artemisiifolia

Background

Ambrosia artemisiifolia is a North American native that has become one of the most problematic invasive plants in Europe and Asia. We studied its worldwide population genetic structure, using both nuclear and chloroplast microsatellite markers and an unprecedented large population sampling. Our goals were (i) to identify the sources of the invasive populations; (ii) to assess whether all invasive populations were founded by multiple introductions, as previously found in France; (iii) to examine how the introductions have affected the amount and structure of genetic variation in Europe; (iv) to document how the colonization of Europe proceeded; (v) to check whether populations exhibit significant heterozygote deficiencies, as previously observed.

Principal Findings

We found evidence for multiple introductions of A. artemisiifolia, within regions but also within populations in most parts of its invasive range, leading to high levels of diversity. In Europe, introductions probably stem from two different regions of the native area: populations established in Central Europe appear to have originated from eastern North America, and Eastern European populations from more western North America. This may result from differential commercial exchanges between these geographic regions. Our results indicate that the expansion in Europe mostly occurred through long-distance dispersal, explaining the absence of isolation by distance and the weak influence of geography on the genetic structure in this area in contrast to the native range. Last, we detected significant heterozygote deficiencies in most populations. This may be explained by partial selfing, biparental inbreeding and/or a Wahlund effect and further investigation is warranted.

Conclusions

This insight into the sources and pathways of common ragweed expansion may help to better understand its invasion success and provides baseline data for future studies on the evolutionary processes involved during range expansion in novel environments.     

Structured populations of the oriental fruit moth in an agricultural ecosystem

Intercontinental trade has led to multiple introductions of invasive pest species at a global scale. Molecular analyses of the structure of populations support the understanding of ecological strategies and evolutionary patterns that promote successful biological invasions. The oriental fruit moth, Grapholita (=Cydia) molesta, is a cosmopolitan and economically destructive pest of stone and pome fruits, expanding its distribution range concomitantly with global climate warming. We used ten newly developed polymorphic microsatellite markers to examine the genetic structure of G. molesta populations in an agricultural ecosystem in the Emilia‐Romagna region of northern Italy. Larvae collected in eight sampling sites were assigned to a mosaic of five populations with significant intra‐regional structure. Inferred measures of gene flow within populations implicated both active dispersal, and passive dispersal associated with accidental anthropogenic displacements. Small effective population sizes, coupled with high inbreeding levels, highlighted the effect of orchard management practices on the observed patterns of genetic variation within the sampling sites. Isolation by distance did not appear to play a major role at the spatial scale considered. Our results provide new insights into the population genetics and dynamics of an invasive pest species at a regional scale.     

Genetic structure and diversity of a newly invasive species, the codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae) in China

Cydia pomonella (L.) was firstly reported in China in the 1950s and considered as one of the most serious invasive pest in fruit orchards of China. It spread rapidly from the original site in Xinjiang to other northwestern regions. The pest has further penetrated northeastern China since 2006. With its rapid invasion rate, most pome fruit production areas of China are being threatened. As yet there has been no research into the genetic diversity and structure of the codling moth population in China. We investigated the genetic variations of 12 C. pomonella populations collected from the main distribution regions (Xinjiang, Gansu and Heilongjiang Provinces) in China and compared them with one German and one Swiss population using eight microsatellites loci to infer the characteristics of genetic diversity and genetic structure. We observed sequential loss of genetic diversity and significant structuring associated with distribution but no significant correlation between genetic distance and geographic distance among northwestern populations. There was no genetic evidence for bottleneck effects in any of the populations. The results suggest that the loss of genetic diversity in C. pomonella populations resulted from the successive colonization of founder populations. Recent invasion history led to the lack of any bottleneck effect. The high level of population genetic structuring is related to the weak flight capacity of the codling moth and the human-aided dispersal rather than to geographic distance. These genetic data not only provide us with an understanding of the micro-evolutionary processes related to successful biological invasions, but also provide guidance for pest management strategies.     

Isolation by resistance across a complex coral reef seascape

A detailed understanding of the genetic structure of populations and an accurate interpretation of processes driving contemporary patterns of gene flow are fundamental to successful spatial conservation management. The field of seascape genetics seeks to incorporate environmental variables and processes into analyses of population genetic data to improve our understanding of forces driving genetic divergence in the marine environment. Information about barriers to gene flow (such as ocean currents) is used to define a resistance surface to predict the spatial genetic structure of populations and explain deviations from the widely applied isolation-by-distance model. The majority of seascape approaches to date have been applied to linear coastal systems or at large spatial scales (more than 250 km), with very few applied to complex systems at regional spatial scales (less than 100 km). Here, we apply a seascape genetics approach to a peripheral population of the broadcast-spawning coral Acropora spicifera across the Houtman Abrolhos Islands, a high-latitude complex coral reef system off the central coast of Western Australia. We coupled population genetic data from a panel of microsatellite DNA markers with a biophysical dispersal model to test whether oceanographic processes could explain patterns of genetic divergence. We identified significant variation in allele frequencies over distances of less than 10 km, with significant differentiation occurring between adjacent sites but not between the most geographically distant ones. Recruitment probabilities between sites based on simulated larval dispersal were projected into a measure of resistance to connectivity that was significantly correlated with patterns of genetic divergence, demonstrating that patterns of spatial genetic structure are a function of restrictions to gene flow imposed by oceanographic currents. This study advances our understanding of the role of larval dispersal on the fine-scale genetic structure of coral populations across a complex island system and applies a methodological framework that can be tailored to suit a variety of marine organisms with a range of life-history characteristics.