Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power

Genetic patterns across an invasion's history: a test of change versus stasis for the Eurasian round goby in North America

Biological invasions comprise accidental evolutionary experiments, whose genetic compositions underlie relative success, spread and persistence in new habitats. However, little is known about whether, or how, their population genetic patterns change temporally and/or spatially across the invasion's history. Theory predicts that most would undergo founder effect, exhibit low genetic divergence across the new range and gain variation over time via new arriving propagules. To test these predictions, we analyse population genetic diversity and divergence patterns of the Eurasian round goby Neogobius melanostomus across the two decades of its North American invasion in the Laurentian Great Lakes, comparing results from 13 nuclear DNA microsatellite loci and mitochondrial DNA cytochrome b sequences. We test whether 'genetic stasis', 'genetic replacement' and/or 'genetic supplement' scenarios have occurred at the invasion's core and expansion sites, in comparison with its primary native source population in the Dnieper River, Black Sea. Results reveal pronounced genetic divergence across the exotic range, with population areas remaining genetically distinct and statistically consistent across two decades, supporting 'genetic stasis' and 'founder takes most'. The original genotypes continue to predominate, whose high population growth likely outpaced the relative success of later arrivals. The original invasion core has stayed the most similar to the native source. Secondary expansion sites indicate slight allelic composition convergence towards the core population over time, attributable to some early 'genetic supplementation'. The geographic and temporal coverage of this investigation offers a rare opportunity to discern population dynamics over time and space in context of invasion genetic theory vs. reality.

Broad-Scale Genetic Diversity of Cannabis for Forensic Applications

Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide.

Surviving in isolation: genetic variation, bottlenecks and reproductive strategies in the Canarian endemic Limonium macrophyllum (Plumbaginaceae)

Oceanic archipelagos are typically rich in endemic taxa, because they offer ideal conditions for diversification and speciation in isolation. One of the most remarkable evolutionary radiations on the Canary Islands comprises the 16 species included in Limonium subsection Nobiles, all of which are subject to diverse threats, and legally protected. Since many of them are single-island endemics limited to one or a few populations, there exists a risk that a loss of genetic variation might limit their long-term survival. In this study, we used eight newly developed microsatellite markers to characterize the levels of genetic variation and inbreeding in L. macrophyllum, a species endemic to the North-east of Tenerife that belongs to Limonium subsection Nobiles. We detected generally low levels of genetic variation over all populations (H _T = 0.363), and substantial differentiation among populations (F _ST = 0.188; R _ST = 0.186) coupled with a negligible degree of inbreeding (F = 0.042). Obligate outcrossing may have maintained L. macrophyllum relatively unaffected by inbreeding despite the species' limited dispersal ability and the genetic bottlenecks likely caused by a prolonged history of grazing. Although several factors still constitute a risk for the conservation of L. macrophyllum, the lack of inbreeding and the recent positive demographic trends observed in the populations of this species are factors that favour its future persistence.

Fine-scale genetic structure analyses reveal dispersal patterns in a critically endangered primate, Trachypithecus leucocephalus

Dispersal is a critically important life history trait of social organisms that has a major impact on the population genetic structure and social relationships within groups. Primates exhibit highly diversified dispersal and philopatry patterns, but knowledge of these patterns is difficult to obtain and usually limited to observations of a small number of focal social groups or individuals. Here, we investigated the dispersal pattern of a critically endangered colobine monkey, the white-headed langur (Trachypithecus leucocephalus), using molecular approaches, and sex-specific population genetic structure analyses at fine geographical scales. We non-invasively collected 403 fecal samples from 41 social groups across 90% of the langur's range in Fusui (FS) and Chongzuo (CZ) in southwestern Guangxi Province, China. We identified 214 unique individuals from the samples by genotyping 15 polymorphic autosomal microsatellite loci, a sex-specific marker, and sequencing the mitochondrial DNA (mtDNA) hypervariable region I (HVRI). We found higher intragroup than intergroup genetic relatedness in males and females in both populations. A significant positive correlation between genetic distance and geographical distance, that is a pattern of isolation-by-distance, was detected in females from the FS population, but not in males. Spatial autocorrelation analyses revealed high within-group relatedness in both sexes and populations, as well as an additional positive correlation at the 0.5-km distance class in females from the FS population. Furthermore, we inferred first-generation migrants using genetic assignment tests. Our results suggest that male T. leucocephalus disperse at random distances within habitat areas, whereas dispersal of females may mainly occur among adjacent groups near their home site. Our study provides the first genetic evidence for sex-biased dispersal in T. leucocephalus, which has important management and conservation implications for the species.

Forensic assignment to geographic origin, a useful tool in seafood fraud control

Seafood fraud is an economically motivated and widely spread problem encompassing drastic consequences in both public health and species conservation. In Northern Spain, only the first Atlantic salmon (Salmo salar) catch of the angling season (named Campanu) can be sold. In the year 2011, an angler denounced it on regional Court claiming that the Campanu (which was sold in 6000€) was fraudulent because it had been caught from another river than the fisherman ("the seller") stated. Here, we report the first judicial case of application of geographical genetic assignment in a fish species in Spain. In order to accomplish this, genetic assignments to their rivers of origin of the Campanu and another three following salmon catches of the angling season of the year 2011 were performed. A panel of eight microsatellite loci together with a comprehensive genetic baseline of the rivers of the region were employed. Results showed that the Campanu was the only case in which genetic assignment and fisherman declaration of the river of origin did not match. The methodology here employed showed to be very useful as a reinforcement of other evidences contributing to fight against seafood fraud in Courts.

No signs of inbreeding despite long-term isolation and habitat fragmentation in the critically endangered Montseny brook newt (Calotriton arnoldi)

Endemic species with restricted geographic ranges potentially suffer the highest risk of extinction. If these species are further fragmented into genetically isolated subpopulations, the risk of extinction is elevated. Habitat fragmentation is generally considered to have negative effects on species survival, despite some evidence for neutral or even positive effects. Typically, non-negative effects are ignored by conservation biology. The Montseny brook newt (Calotriton arnoldi) has one of the smallest distribution ranges of any European amphibian (8 km²) and is considered critically endangered by the International Union for Conservation of Nature. Here we apply molecular markers to analyze its population structure and find that habitat fragmentation owing to a natural barrier has resulted in strong genetic division of populations into two sectors, with no detectable migration between sites. Although effective population size estimates suggest low values for all populations, we found low levels of inbreeding and relatedness between individuals within populations. Moreover, C. arnoldi displays similar levels of genetic diversity to its sister species Calotriton asper, from which it separated around 1.5 million years ago and which has a much larger distribution range. Our extensive study shows that natural habitat fragmentation does not result in negative genetic effects, such as the loss of genetic diversity and inbreeding on an evolutionary timescale. We hypothesize that species in such conditions may evolve strategies (for example, special mating preferences) to mitigate the effects of small population sizes. However, it should be stressed that the influence of natural habitat fragmentation on an evolutionary timescale should not be conflated with anthropogenic habitat loss or degradation when considering conservation strategies.

Population genetics of the Manila clam (Ruditapes philippinarum) introduced in North America and Europe

Globally, the Manila clam (Ruditapes philippinarum) stands as the second most important bivalve species in fisheries and aquaculture. Native to the Pacific coast of Asia, it is now well-established in North America and Europe, where its on-going management reflects local economic interests. The historic record of transfers spans the 20th century and suggests sequential movement from Japan to North America, as a hitch-hiker on oysters, and then intentional introduction in Europe, but global genetic data are missing. We have studied mitochondrial DNA and microsatellite markers in nine populations from Asia, North America and Europe. The results from the two types of markers indicated a good concordance of present-day genetic structure with the reported history of clam transfers across continents, and no evidence of relevant concealed introductions from continental Asia in Europe and North America. However, European populations showed a loss of genetic variability and significant genetic differentiation as compared to their American counterparts. Our study shows that in spite of the increasing ease for species to spread out of their native range, in the case of the Manila clam this has not resulted in new invasion waves in the two studied continents.

Migration by seed dispersal of ACCase-inhibitor-resistant Avena fatua in north-western Mexico

BACKGROUND

Biotypes of Avena fatua resistant to ACCase-inhibiting herbicides have been reported in the States of Baja California (BC) and Sonora (SON), Mexico. We hypothesised that resistant biotypes present in SON (Valle de Hermosillo and Valle del Yaqui) are derived from a resistant population from BC (Valle de Mexicali) via gene flow through the transport and exchange of contaminated wheat seed. This study aimed to determine (1) the resistance of A. fatua to ACCase-inhibiting herbicides in populations from BC and SON, (2) the mutation at the site of action and (3) the genetic structure and gene flow among populations.

RESULTS

DNA sequencing showed that all biotypes shared the same mutation (Leu × Ile at codon 1781). Microsatellites showed evidence of a genetic bottleneck in SON, and spatial analysis of molecular variance grouped one biotype from the Valle de Mexicali with two biotypes from the Valle de Hermosillo. Migration analysis suggested gene flow from the Valle de Mexicali to the Valle de Hermosillo, but not to the Valle del Yaqui.

CONCLUSIONS

The presence of resistant biotypes of A. fatua in the Valle de Hermosillo, SON, are likely derived from seeds from BC, possibly through the transport of contaminated wheat seeds. © 2016 Society of Chemical Industry.

Inferring the timing of long-distance dispersal between Rail metapopulations using genetic and isotopic assignments

The stochastic and infrequent nature of long-distance dispersal often makes it difficult to detect. We quantified the frequency, distance, and timing of long-distance dispersal in a nonmigratory, secretive wetland bird, the California Black Rail (Laterallus jamaicensis coturniculus), between an inland and a coastal metapopulation separated by greater than 100 km. Using 15 microsatellites in conjunction with stable carbon, nitrogen, and sulfur isotopes, we classified Rails as residents of their capture population, recent migrants that dispersed to their capture population less than one year before capture, established migrants that dispersed to their capture population more than one year before capture, and seasonal migrants that dispersed away from their capture population to forage, but returned the next season. Most Rails (195 of 204, or 95.6%) were classified as residents, but we detected two established migrants that had moved >100 km more than a year before capture. Seven Rails appeared to be seasonal migrants, but comparisons of feather isotope values with isotope values from wetland soils indicated that the isotope values in the feathers of these Rails likely resulted from natural environmental variation (e.g., source element effects) rather than long-distance dispersal of individuals. Thus, these seven Rails were most likely misassigned by isotopic population assignments due to small-scale variation in the isoscape. Using genetic data in conjunction with isotopic data allowed us to not only infer the timing of long-distance dispersal events, but to successfully track long-distance movements of nonmigratory Rails between metapopulations even when environmental variation of isotopes occurred across small spatial scales.

Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest

INTRODUCTION

Theory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate), indirect gene flow and contemporary pollen dynamics in the understory herb Aphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios.

METHODS

Twelve populations of A. aurantiaca were sampled in large (4), medium (3), and small (5) forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28-30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population.

RESULTS

Despite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (He  = 0.61), weak genetic structure (Rst  = 0.037), and slight inbreeding in small fragments. Effective population sizes (Ne ) were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events were detected. Aphelandra aurantiaca shows a mixed mating system (tm  = 0.81) and the outcrossing rate have not been affected by habitat fragmentation. A strong pollen pool structure was detected due to few effective pollen donors (Nep ) and low distance pollen movement, pointing that most plants received pollen from close neighbors. Past demographic fluctuations may have affected the present population genetic structure as Bayesian coalescent analysis revealed the signature of past population expansion, possibly during warmer conditions after the last glacial maximum.

DISCUSSION

Habitat fragmentation has not increased genetic differentiation or reduced genetic diversity of A. aurantiaca despite dozens of generations since the onset of fragmentation in the region of Los Tuxtlas. Instead, past population expansion is compatible with the lack of observed genetic structure. The predicted negative effects of rainforest fragmentation on genetic diversity and population structure of A. aurantiaca seem to have been buffered owing to its large effective populations and long-distance dispersal events. In particular, its mixed-mating system, mostly of outcrossing, suggests high efficiency of pollinators promoting connectivity and reducing inbreeding. However, some results point that the effects of fragmentation are underway, as two small fragments showed higher membership probabilities to their population of origin, suggesting genetic isolation. Our findings underscore the importance of fragment size to maintain genetic connectivity across the landscape.

Marked phylogeographic structure of Gentoo penguin reveals an ongoing diversification process along the Southern Ocean

Two main hypotheses have been debated about the biogeography of the Southern Ocean: (1) the Antarctic Polar Front (APF), acting as a barrier between Antarctic and sub-Antarctic provinces, and (2) the Antarctic Circumpolar Current (ACC), promoting gene flow among sub-Antarctic areas. The Gentoo penguin is distributed throughout these two provinces, separated by the APF. We analyzed mtDNA (HVR1) and 12 microsatellite loci of 264 Gentoo penguins, Pygoscelis papua, from 12 colonies spanning from the Western Antarctic Peninsula and the South Shetland Islands (WAP) to the sub-Antarctic Islands (SAI). While low genetic structure was detected among WAP colonies (mtDNA Ф_ST=0.037-0.133; microsatellite F_ST=0.009-0.063), high differentiation was found between all SAI and WAP populations (mtDNA Ф_ST=0.678-0.930; microsatellite F_ST=0.110-0.290). These results suggest that contemporary dispersal around the Southern Ocean is very limited or absent. As predicted, the APF appears to be a significant biogeographical boundary for Gentoo penguin populations; however, the ACC does not promote connectivity in this species. Our data suggest demographic expansion in the WAP during the last glacial maximum (LGM, about 20kya), but stability in SAI. Phylogenetic analyses showed a deep divergence between populations from the WAP and those from the SAI. Therefore, taxonomy should be further revised. The Crozet Islands resulted as a basal clade (3.57Mya), followed by the Kerguelen Islands (2.32Mya) as well as a more recent divergence between the Falkland/Malvinas Islands and the WAP (1.27Mya). Historical isolation, local adaptation, and past climate scenarios of those Evolutionarily Significant Units may have led to different potentials to respond to climate changes.

Genetic diversity and population structure in Bactrocera correcta (Diptera: Tephritidae) inferred from mtDNA cox1 and microsatellite markers

Bactrocera correcta is one of the most destructive pests of horticultural crops in tropical and subtropical regions. Despite the economic risk, the population genetics of this pest have remained relatively unexplored. This study explores population genetic structure and contemporary gene flow in B. correcta in Chinese Yunnan Province and attempts to place observed patterns within the broader geographical context of the species’ total range. Based on combined data from mtDNA cox1 sequences and 12 microsatellite loci obtained from 793 individuals located in 7 countries, overall genetic structuring was low. The expansion history of this species, including likely human-mediated dispersal, may have played a role in shaping the observed weak structure. The study suggested a close relationship between Yunnan Province and adjacent countries, with evidence for Western and/or Southern Yunnan as the invasive origin of B. correcta within Yunnan Province. The information gleaned from this analysis of gene flow and population structure has broad implications for quarantine, trade and management of this pest, especially in China where it is expanding northward. Future studies should concentrate effort on sampling South Asian populations, which would enable better inferences of the ancestral location of B. correcta and its invasion history into and throughout Asia.

High Interannual Variability in Connectivity and Genetic Pool of a Temperate Clingfish Matches Oceanographic Transport Predictions

Adults of most marine benthic and demersal fish are site-attached, with the dispersal of their larval stages ensuring connectivity among populations. In this study we aimed to infer spatial and temporal variation in population connectivity and dispersal of a marine fish species, using genetic tools and comparing these with oceanographic transport. We focused on an intertidal rocky reef fish species, the shore clingfish Lepadogaster lepadogaster, along the southwest Iberian Peninsula, in 2011 and 2012. We predicted high levels of self-recruitment and distinct populations, due to short pelagic larval duration and because all its developmental stages have previously been found near adult habitats. Genetic analyses based on microsatellites countered our prediction and a biophysical dispersal model showed that oceanographic transport was a good explanation for the patterns observed. Adult sub-populations separated by up to 300 km of coastline displayed no genetic differentiation, revealing a single connected population with larvae potentially dispersing long distances over hundreds of km. Despite this, parentage analysis performed on recruits from one focal site within the Marine Park of Arrábida (Portugal), revealed self-recruitment levels of 2.5% and 7.7% in 2011 and 2012, respectively, suggesting that both long- and short-distance dispersal play an important role in the replenishment of these populations. Population differentiation and patterns of dispersal, which were highly variable between years, could be linked to the variability inherent in local oceanographic processes. Overall, our measures of connectivity based on genetic and oceanographic data highlight the relevance of long-distance dispersal in determining the degree of connectivity, even in species with short pelagic larval durations.

Flight of Rhyzopertha dominica (Coleoptera: Bostrichidae)-a Spatio-Temporal Analysis With Pheromone Trapping and Population Genetics

The flight of the lesser grain borer, Rhyzopertha dominica (F.), near grain storages and at distances from them, was investigated to assess the potential of these beetles to infest grain and spread insecticide resistance genes. We caught R. dominica in pheromone-baited flight traps (and blank controls) set at storages, in fields away from storages, and in native vegetation across a 12-mo period. A functional set of highly polymorphic microsatellite markers was developed, enabling population genetic analyses on the trapped beetles. Pheromone-baited traps caught just as many R. dominica adults at least 1 km from grain storages as were caught adjacent to grain storages. Samples of beetles caught were genetically homogeneous across the study area (over 7,000 km²) in South Queensland, Australia. However, a change in genetic structure was detected at one bulk storage site. Subsequent analysis detected a heterozygous excess, which indicated a population bottleneck. Only a few beetles were caught during the winter months of June and July. To assess the mating status and potential fecundity of dispersing R. dominica females, we captured beetles as they left grain storages and quantified offspring production and life span in the laboratory. Nearly all (95%) of these dispersing females had mated and these produced an average of 242 offspring. We demonstrated that R. dominica populations in the study area display a high degree of connectivity and this is a result of the active dispersal of mated individuals of high potential fecundity.

Patterns of Fish Connectivity between a Marine Protected Area and Surrounding Fished Areas

Patterns of connectivity and self-recruitment are recognized as key factors shaping the dynamics of marine populations. Connectivity is also essential for maintaining and restoring natural ecological processes with genetic diversity contributing to the adaptation and persistence of any species in the face of global disturbances. Estimates of connectivity are crucial to inform the design of both marine protected areas (MPAs) and MPA networks. Among several approaches, genetic structure is frequently used as a proxy for patterns of connectivity. Using 8 microsatellite loci, we investigated genetic structure of the two-banded sea bream Diplodus vulgaris, a coastal fish that is both commercially and ecologically important. Adults were sampled in 7 locations (stretches of coastline approximately 8 km long) and juveniles in 14 sites (~100 to 200 m of coastline) along 200 km of the Apulian Adriatic coast (SW Adriatic Sea), within and outside an MPA (Torre Guaceto MPA, Italy). Our study found similar genetic diversity indices for both the MPA and the surrounding fished areas. An overall lack of genetic structure among samples suggests high gene flow (i.e. connectivity) across a scale of at least 200 km. However, some local genetic divergences found in two locations demonstrate some heterogeneity in processes renewing the population along the Apulian Adriatic coast. Furthermore, two sites appeared genetically divergent, reinforcing our observations within the genetic makeup of adults and confirming heterogeneity in early stage genetics that can come from either different supply populations or from chaotic genetic patchiness occurring under temporal variation in recruitment and in the reproductive success. While the specific role of the MPA is not entirely known in this case, these results confirm the presence of regional processes and the key role of connectivity in maintaining the local population supply.

Genetic Diversity and Population Structure of Mesoamerican Jaguars (Panthera onca): Implications for Conservation and Management

Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars (northern Guatemala and central Belize), whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of understanding levels of genetic diversity and connectivity to making informed management and conservation decisions with the goal to maintain functional connectivity across the region.

Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range

Background

Seabirds are important components of marine ecosystems, both as predators and as indicators of ecological change, being conspicuous and sensitive to changes in prey abundance. To determine whether fluctuations in population sizes are localised or indicative of large-scale ecosystem change, we must first understand population structure and dispersal. King penguins are long-lived seabirds that occupy a niche across the sub-Antarctic zone close to the Polar Front. Colonies have very different histories of exploitation, population recovery, and expansion.

Results

We investigated the genetic population structure and patterns of colonisation of king penguins across their current range using a dataset of 5154 unlinked, high-coverage single nucleotide polymorphisms generated via restriction site associated DNA sequencing (RADSeq). Despite breeding at a small number of discrete, geographically separate sites, we find only very slight genetic differentiation among colonies separated by thousands of kilometers of open-ocean, suggesting migration among islands and archipelagos may be common. Our results show that the South Georgia population is slightly differentiated from all other colonies and suggest that the recently founded Falkland Island colony is likely to have been established by migrants from the distant Crozet Islands rather than nearby colonies on South Georgia, possibly as a result of density-dependent processes.

Conclusions

The observed subtle differentiation among king penguin colonies must be considered in future conservation planning and monitoring of the species, and demographic models that attempt to forecast extinction risk in response to large-scale climate change must take into account migration. It is possible that migration could buffer king penguins against some of the impacts of climate change where colonies appear panmictic, although it is unlikely to protect them completely given the widespread physical changes projected for their Southern Ocean foraging grounds. Overall, large-scale population genetic studies of marine predators across the Southern Ocean are revealing more interconnection and migration than previously supposed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0784-z) contains supplementary material, which is available to authorized users.

Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers

Understanding the habitat use patterns of migratory fish, such as Atlantic salmon (Salmo salar L.), and the natural and anthropogenic impacts on them, is aided by the ability to identify individuals to their stock of origin. Presented here are the results of an analysis of informative single nucleotide polymorphic (SNP) markers for detecting genetic structuring in Atlantic salmon in Scotland and NE England and their ability to allow accurate genetic stock identification. 3,787 fish from 147 sites covering 27 rivers were screened at 5,568 SNP markers. In order to identify a cost-effective subset of SNPs, they were ranked according to their ability to differentiate between fish from different rivers. A panel of 288 SNPs was used to examine both individual assignments and mixed stock fisheries and eighteen assignment units were defined. The results improved greatly on previously available methods and, for the first time, fish caught in the marine environment can be confidently assigned to geographically coherent units within Scotland and NE England, including individual rivers. As such, this SNP panel has the potential to aid understanding of the various influences acting upon Atlantic salmon on their marine migrations, be they natural environmental variations and/or anthropogenic impacts, such as mixed stock fisheries and interactions with marine power generation installations.

Multiple dispersal vectors drive range expansion in an invasive marine species

The establishment and subsequent spread of invasive species is widely recognized as one of the most threatening processes contributing to global biodiversity loss. This is especially true for marine and estuarine ecosystems, which have experienced significant increases in the number of invasive species with the increase in global maritime trade. Understanding the rate and mechanisms of range expansion is therefore of significant interest to ecologists and conservation managers alike. Using a combination of population genetic surveys, environmental DNA (eDNA) plankton sampling and hydrodynamic modelling, we examined the patterns of introduction of the predatory Northern Pacific seastar (Asterias amurensis) and pathways of secondary spread within southeast Australia. Genetic surveys across the invasive range reveal some genetic divergence between the two main invasive regions and no evidence of ongoing gene flow, a pattern that is consistent with the establishment of the second invasive region via a human-mediated translocation event. In contrast, hydrodynamic modelling combined with eDNA plankton sampling demonstrated that the establishment of range expansion populations within a region is consistent with natural larval dispersal and recruitment. Our results suggest that both anthropogenic and natural dispersal vectors have played an important role in the range expansion of this species in Australia. The multiple modes of spread combined with high levels of fecundity and a long larval duration in A. amurensis suggests it is likely to continue its range expansion and significantly impact Australian marine ecosystems.

Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift

Studying wild pathogen populations in natural ecosystems offers the opportunity to better understand the evolutionary dynamics of biotic diseases in crops and to enhance pest control strategies. We used simulations and genetic markers to investigate the spatial and temporal population genetic structure of wild populations of the beet cyst nematode Heterodera schachtii on a wild host plant species, the sea beet (Beta vulgaris spp. maritima), the wild ancestor of cultivated beets. Our analysis of the variation of eight microsatellite loci across four study sites showed that (i) wild H. schachtii populations displayed fine-scaled genetic structure with no evidence of substantial levels of gene flow beyond the scale of the host plant, and comparisons with simulations indicated that (ii) genetic drift substantially affected the residual signals of isolation-by-distance processes, leading to departures from migration-drift equilibrium. In contrast to what can be suspected for (crop) field populations, this showed that wild cyst nematodes have very low dispersal capabilities and are strongly disconnected from each other. Our results provide some key elements for designing pest control strategies, such as decreasing passive dispersal events to limit the spread of virulence among field nematode populations.

Low Spatial Genetic Differentiation Associated with Rapid Recolonization in the New Zealand Fur Seal Arctocephalus forsteri

Population declines resulting from anthropogenic activities are of major consequence for the long-term survival of species because the resulting loss of genetic diversity can lead to extinction via the effects of inbreeding depression, fixation of deleterious mutations, and loss of adaptive potential. Otariid pinnipeds have been exploited commercially to near extinction with some species showing higher demographic resilience and recolonization potential than others. The New Zealand fur seal (NZFS) was heavily impacted by commercial sealing between the late 18th and early 19th centuries, but has recolonized its former range in southern Australia. The species has also recolonized its former range in New Zealand, yet little is known about the pattern of recolonization. Here, we first used 11 microsatellite markers (n = 383) to investigate the contemporary population structure and dispersal patterns in the NZFS (Arctocephalus forsteri). Secondly, we model postsealing recolonization with 1 additional mtDNA cytochrome b (n = 261) marker. Our data identified 3 genetic clusters: an Australian, a subantarctic, and a New Zealand one, with a weak and probably transient subdivision within the latter cluster. Demographic history scenarios supported a recolonization of the New Zealand coastline from remote west coast colonies, which is consistent with contemporary gene flow and with the species' high resilience. The present data suggest the management of distinct genetic units in the North and South of New Zealand along a genetic gradient. Assignment of individuals to their colony of origin was limited (32%) with the present data indicating the current microsatellite markers are unlikely sufficient to assign fisheries bycatch of NZFSs to colonies.

A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea

Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a resurrection approach to examine the potential for genotypic and phenotypic evolution in Ipomoea purpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs. 2012), suggesting that populations of this species sampled from agricultural fields have experienced genetic bottleneck events that have led to lower neutral genetic diversity. Heterozygosity excess tests indicate that these bottlenecks may have occurred prior to 2003. A greenhouse assay of individuals sampled from the field as seed found that populations of this species, on average, exhibited modest increases in herbicide resistance over time. However, populations differed significantly between sampling years for resistance: some populations maintained high resistance between the sampling years whereas others exhibited increased or decreased resistance. Our results show that populations of this noxious weed, capable of adapting to strong selection imparted by herbicide application, may lose genetic variation as a result of this or other environmental factors. We probably uncovered only modest increases in resistance on average between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that nonresistant migrants germinate from the seed bank.

Population Structure, Genetic Diversity, Effective Population Size, Demographic History and Regional Connectivity Patterns of the Endangered Dusky Grouper, Epinephelus marginatus (Teleostei: Serranidae), within Malta's Fisheries Management Zone

The objective of this study is to describe the genetic population structure and demographic history of the endangered marine fish, Epinephelus marginatus, within Malta's Fisheries Management Zone for the purpose of localised conservation planning. Epinephelus marginatus is a long-lived, sedentary, reef-associated protogynous hermaphrodite with high commercial and recreational value that is at risk of extinction throughout its global distribution. Based on global trends, population substructuring and gaps in local knowledge this has led to an increased interest in evaluation of local stock. Assessment of Maltese demography was based on historical and contemporary catch landings data whilst genetic population structure and regional connectivity patterns were evaluated by examining 175 individuals collected within the central Mediterranean region between 2002 and 2009 using 14 nuclear microsatellite loci. Demographic stock assessment of Maltese E. marginatus' revealed a 99% decline in catch landings between 1947 and 2009 within the Fisheries Management Zone. A contemporary modest mean size was observed, 3 ± 3 kg, where approximately 17% of the population was juvenile, 68% female/sex-changing and 15% were male with a male-to-female sex ratio of 1:5. Genetic analysis describes the overall population of E. marginatus' within the Fisheries Management Zone as decreasing in size (ƟH = 2.2), which has gone through a significant size reduction in the past (M = 0.41) and consequently shows signs of moderate inbreeding (FIS = 0.10, p < 0.001) with an estimated effective population size of 130 individuals. Results of spatially explicit Bayesian genetic cluster analysis detected two geographically distinct subpopulations within Malta's Fisheries Management Zone and that they are connected to a larger network of E. marginatus' within the Sicily Channel. Results suggest conservation management should be designed to reflect E. marginatus' within Malta's Fisheries Management Zone as two management units.

Wolves Recolonizing Islands: Genetic Consequences and Implications for Conservation and Management

After a long and deliberate persecution, the grey wolf (Canis lupus) is slowly recolonizing its former areas in Europe, and the genetic consequences of this process are of particular interest. Wolves, though present in mainland Estonia for a long time, have only recently started to recolonize the country’s two largest islands, Saaremaa and Hiiumaa. The main objective of this study was to analyse wolf population structure and processes in Estonia, with particular attention to the recolonization of islands. Fifteen microsatellite loci were genotyped for 185 individuals across Estonia. As a methodological novelty, all putative wolf-dog hybrids were identified and removed (n = 17) from the dataset beforehand to avoid interference of dog alleles in wolf population analysis. After the preliminary filtering, our final dataset comprised of 168 “pure” wolves. We recommend using hybrid-removal step as a standard precautionary procedure not only for wolf population studies, but also for other taxa prone to hybridization. STRUCTURE indicated four genetic groups in Estonia. Spatially explicit DResD analysis identified two areas, one of them on Saaremaa island and the other in southwestern Estonia, where neighbouring individuals were genetically more similar than expected from an isolation-by-distance null model. Three blending areas and two contrasting transition zones were identified in central Estonia, where the sampled individuals exhibited strong local differentiation over relatively short distance. Wolves on the largest Estonian islands are part of human-wildlife conflict due to livestock depredation. Negative public attitude, especially on Saaremaa where sheep herding is widespread, poses a significant threat for island wolves. To maintain the long-term viability of the wolf population on Estonian islands, not only wolf hunting quota should be targeted with extreme care, but effective measures should be applied to avoid inbreeding and minimize conflicts with local communities and stakeholders.

Insights into the Introduction History and Population Genetic Dynamics of the Nile Monitor (Varanus niloticus) in Florida

Invasive species are widely recognized as important drivers of the ongoing biodiversity crisis. The US state of Florida is especially susceptible to the proliferation of invasive reptiles, and nonnative lizards currently outnumber native lizard species. At present, there are 3 documented breeding populations of the Nile monitor (Varanus niloticus) in different regions of Southern Florida, and these populations are considered potential dangers to threatened, fossorial endemics, such as burrowing owls, American crocodiles, and gopher tortoises. Nevertheless, at present, both the introduction histories of these populations and the degree to which they are connected by gene flow are not known. To address these issues, we genotyped V. niloticus from Cape Coral, Homestead Air Reserve Base, and West Palm Beach at 17 microsatellite loci and conducted a variety of analyses to assess both intrapopulation genetic diversity, the degree of gene flow between populations, and the most likely introduction scenario. The results of our analyses demonstrate that all 3 populations have limited genetic diversity (mean number of effective alleles across loci in all 3 populations ~ 2.00) and are highly differentiated from one another (G ST = 0.268; G″ST = 0.628). Our results also suggest that these populations resulted from independent introduction events that occurred within the past few decades. Consequently, we advise that wildlife managers focus management efforts on containment of existing populations and intensification of monitoring efforts on potential migration corridors.

Patterns and mechanisms of dispersal in a keystone seagrass species

Mechanisms and vectors of long-distance dispersal remain unknown for many coastal benthic species, including plants. Indications for the possibility for long-distance dispersal come from dispersal modelling and from genetic assessments, but have rarely been assessed with both methods. To this end, we assessed dispersal of the seagrass Zostera noltei, an important foundation species of the coastal zone. We investigate whether small scale seed dispersal and long-distance propagule dispersal do play a role for meta-population dynamics, using both genetic assessments based on eight microsatellite markers and physical modelling of ocean currents. Such assessments enhance our understanding of the biology and population dynamics of an important coastal foundation species. They are relevant for large scale conservation strategies as they give insights in the maintenance of genetic diversity and connectivity that may enhance resilience and resistance to stresses associated with seagrass loss.

Phylogenetics and population genetics of Plotosus canius (Siluriformes: Plotosidae) from Malaysian coastal waters

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics of P. canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P. canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395–0.771 and 0.033–0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (H_o) value of 0.2168, which was lower than the standard heterozygosity in marine populations (H_o = 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940, which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in an equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P. canius, and should be necessary highlighted for appropriate management and conservation of species. Further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.