Genetic Assignment Tests Research Articles

Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to disease.

Chronic wasting disease (CWD) can spread among cervids by direct and indirect transmission, the former being more likely in emerging areas. Identifying subpopulations allows the delineation of focal areas to target for intervention. We aimed to assess the population structure of white-tailed deer (Odocoileus virginianus) in the northeastern United States at a regional scale to inform managers regarding gene flow throughout the region. We genotyped 10 microsatellites in 5701 wild deer samples from Maryland, New York, Ohio, Pennsylvania, and Virginia. We evaluated the distribution of genetic variability through spatial principal component analysis and inferred genetic structure using non-spatial and spatial Bayesian clustering algorithms (BCAs). We simulated populations representing each inferred wild cluster, wild deer in each state and each physiographic province, total wild population, and a captive population. We conducted genetic assignment tests using these potential sources, calculating the probability of samples being correctly assigned to their origin. Non-spatial BCA identified two clusters across the region, while spatial BCA suggested a maximum of nine clusters. Assignment tests correctly placed deer into captive or wild origin in most cases (94%), as previously reported, but performance varied when assigning wild deer to more specific origins. Assignments to clusters inferred via non-spatial BCA performed well, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. Differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for inferring the geographic origin of deer using 10 microsatellites. However, the genetic distinction between clusters may indicate natural and anthropogenic barriers of interest for management.

Breeding origins of a uniquely regular migrant songbird in the Galápagos Islands.

Little is known about the causes and consequences of alternative pathways flown by long-distance migratory birds. Bobolinks (Dolichonyx oryzivorus) breed in grasslands across northern North America and migrate from their breeding grounds toward the eastern Atlantic Coast and then proceed through the Caribbean to South America. However, a small but regular number of Bobolinks have been recorded on the Galapagos Islands. We collected genetic samples from nine Galapagos Bobolinks and performed double-digest restriction site-associated sequencing. We compared them with samples from seven locations across their breeding distribution to determine their population of origin. Galapagos Bobolinks shared the genetic structure of a cluster in the eastern portion of the breeding range that includes New Brunswick and Ontario, Canada, and Vermont, United States. Genetic assignment tests largely corroborated this finding, although slightly different results were obtained for the two methods. All individuals were assigned to the Ontario breeding population using AssignPop, while Rubias assigned six of the migrants to Ontario and three to a Midwest breeding population. Low average relatedness among Galapagos individuals indicates that they are not more related to one another than to individuals within a breeding population and are therefore likely not from a single, small isolated population. Our results do not support the probability hypothesis-that Galapagos Bobolinks originated from the region that includes the greatest proportion of their breeding range (Great Plains)-or the vagrant hypothesis-that migrants are displaced onto Galapagos due to weather events. Instead, our findings support the proximity hypothesis, where migrants originate from the geographically closest-breeding populations.

Effects of environment and genotype on dispersal differ across departure, transfer and settlement in a butterfly metapopulation.

Active dispersal is driven by extrinsic and intrinsic factors at the three stages of departure, transfer and settlement. Most empirical studies capture only one stage of this complex process, and knowledge of how much can be generalized from one stage to another remains unknown. Here we use genetic assignment tests to reconstruct dispersal across 5 years and 232 habitat patches of a Glanville fritillary butterfly (Melitaea cinxia) metapopulation. We link individual dispersal events to weather, landscape structure, size and quality of habitat patches, and individual genotype to identify the factors that influence the three stages of dispersal and post-settlement survival. We found that nearly all tested factors strongly affected departure probabilities, but that the same factors explained very little variation in realized dispersal distances. Surprisingly, we found no effect of dispersal distance on post-settlement survival. Rather, survival was influenced by weather conditions, quality of the natal habitat patch, and a strong interaction between genotype and occupancy status of the settled habitat patch, with more mobile genotypes having higher survival as colonists rather than as immigrants. Our work highlights the multi-causality of dispersal and that some dispersal costs can only be understood by considering extrinsic and intrinsic factors and their interaction across the entire dispersal process.

Population connectivity in voles (Microtus sp.) as a gauge for tall grass prairie restoration in midwestern North America.

Ecological restoration can promote biodiversity conservation in anthropogenically fragmented habitats, but effectiveness of these management efforts need to be statistically validated to determine ’success.’ One such approach is to gauge the extent of recolonization as a measure of landscape permeability and, in turn, population connectivity. In this context, we estimated dispersal and population connectivity in prairie vole (Microtus ochrogaster; N = 231) and meadow vole (M. pennsylvanicus; N = 83) within five tall-grass prairie restoration sites embedded within the agricultural matrix of midwestern North America. We predicted that vole dispersal would be constrained by the extent of agricultural land surrounding restored habitat patches, spatially isolating vole populations and resulting in significant genetic structure. We first employed genetic assignment tests based on 15 microsatellite DNA loci to validate field-derived species-designations, then tested reclassified samples with multivariate and Bayesian clustering to assay for spatial and temporal genetic structure. Population connectivity was further evaluated by calculating pairwise FST, then potential demographic effects explored by computing migration rates, effective population size (Ne), and average relatedness (r). Genetic species assignments reclassified 25% of initial field identifications (N = 11 M. ochrogaster; N = 67 M. pennsylvanicus). In M. ochrogaster population connectivity was high across the study area, reflected in little to no spatial or temporal genetic structure. In M. pennsylvanicus genetic structure was detected, but relatedness estimates identified it as kin-clustering instead, underscoring social behavior among populations rather than spatial isolation as the cause. Estimates of Ne and r were stable across years, reflecting high dispersal and demographic resilience. Combined, these metrics suggest the agricultural matrix is highly permeable for voles and does not impede dispersal. High connectivity observed confirms that the restored landscape is productive and permeable for specific management targets such as voles and also demonstrates population genetic assays as a tool to statistically evaluate effectiveness of conservation initiatives.

Developing a Standardized Single Nucleotide Polymorphism Panel for Rangewide Genetic Monitoring of Bull Trout

AbstractConservation of threatened and endangered species often involves large‐scale collaboration across jurisdictional boundaries, but such efforts are typically hampered by a lack of consistent monitoring data at local, regional, and species‐distributional scales. Contemporary methods of genetic monitoring that are grounded in sequencing‐based approaches offer a powerful means to achieve the data consistency necessary for conservation of high‐profile species. Here, we describe the collaborative, multiagency development of a genotyping‐in‐thousands by sequencing panel for genetic monitoring of threatened Bull Trout Salvelinus confluentus across its range in North America. The resulting panel consists of 266 single nucleotide polymorphisms, a subset of which differentiate Salvelinus species (Arctic Char S. alpinus, Brook Trout S. fontinalis, Bull Trout, Dolly Varden S. malma, Lake Trout S. namaycush, and Whitespotted Char S. leucomaenis), as well as one sex ID locus. We then used case studies from the Pacific Northwest and northern Rocky Mountains to demonstrate the efficacy of the panel for addressing local conservation needs (e.g., genetic variation, genetic differentiation, genetic assignment tests, and number of effective breeders) and compatibility with legacy data sets. Future genotyping with this panel will provide opportunities for improved conservation prioritization across the species range and collaboration among the numerous agencies charged with conserving this species. This effort provides framework to develop population genetic tools that will contribute to robust and efficient monitoring of biodiversity.

Occasional long-distance dispersal may not prevent inbreeding in a threatened butterfly

BackgroundTo set up successful conservation measures, detailed knowledge on the dispersal and colonization capacities of the focal species and connectivity between populations is of high relevance. We developed species-specific nuclear microsatellite molecular markers for the grayling (Hipparchia semele), a butterfly endemic to Europe and of growing conservation concern in North-West Europe, and report on its population genetics, in a fragmented, anthropogenic landscape in Belgium. Our study included samples from 23 different locations nested in two regions and additional historical samples from two locations. We assessed contemporary, long-distance dispersal based on genetic assignment tests and investigated the effect of habitat loss and fragmentation on the population genetic structure and genetic variation using data of nine microsatellite loci.ResultsDetected dispersal events covered remarkably long distances, which were up to ten times larger than previously reported colonisation distances, with the longest movement recorded in this study even exceeding 100 km. However, observed frequencies of long-distance dispersal were low. Our results point to the consequences of the strong population decline of the last decades, with evidence of inbreeding for several of the recently sampled populations and low estimates of effective population sizes (Ne) (ranging from 20 to 54 individuals).ConclusionsOur study shows low frequencies of long-distance dispersal, which is unable to prevent inbreeding in most of the local populations. We discuss the significance for species conservation including future translocation events and discuss appropriate conservation strategies to maintain viable grayling (meta) populations in highly fragmented, anthropogenic landscapes.

Population assignment tests uncover rare long-distance marine larval dispersal events.

Long-distance dispersal (LDD) is consequential to metapopulation ecology and evolution. In systems where dispersal is undertaken by small propagules, such as larvae in the ocean, documenting LDD is especially challenging. Genetic parentage analysis has gained traction as a method for measuring larval dispersal, but such studies are generally spatially limited, leaving LDD understudied in marine species. We addressed this knowledge gap by uncovering LDD with population assignment tests in the coral reef fish Elacatinus lori, a species whose short-distance dispersal has been well-characterized by parentage analysis. When adults (n = 931) collected throughout the species' range were categorized into three source populations, assignment accuracy exceeded 99%, demonstrating low rates of gene flow between populations in the adult generation. After establishing high assignment confidence, we assigned settlers (n = 3,828) to source populations. Within the settler cohort, <0.1% of individuals were identified as long-distance dispersers from other populations. These results demonstrate an exceptionally low level of connectivity between E. lori populations, despite the potential for ocean currents to facilitate LDD. More broadly, these findings illustrate the value of combining genetic parentage analysis and population assignment tests to uncover short- and long-distance dispersal, respectively.

Genetic Assignment Tests to Identify the Probable Geographic Origin of a Captive Specimen of Military Macaw (Ara militaris) in Mexico: Implications for Conservation

The Military Macaw (Ara militaris) faces a number of serious conservation threats. The use of genetic markers and assignment tests may help to identify the geographic origin of captive individuals and improve conservation and management programs. The purpose of this study was to identify the possible geographic origin of a captive individual using genetic markers. We used a reference database of genotypes of 86 individuals previously shown to belong to two different genetic groups to determine the genetic assignment of the captive individual of unknown origin (captive specimen) and five individuals of known geographic origin (as positive controls). We evaluated the accuracy of three assignment/exclusion criteria to determine the success of correct assignment of the individual of unknown origin and the five positive control individuals. WICHLOCI estimated that eight loci were required to achieve an assignment success of 83%. The correct geographic origin of positive controls was identified with 83% confidence. All of the analyses assigned the captive individual to the genetic group from the Sierra Madre Oriental. Bayesian assignment tests, tests for genetic distance and allele frequency tests assigned the unknown individual to the locations from the Sierra Madre Oriental with a probability of 71.2–82.4%. We show that the use of genetic markers provides a promising tool for determining the origin of pets and individuals seized from the illegal animal trade to better inform decisions on reintroduction and improve conservation programs.

Use of genetic tools to assess predation on reintroduced howler monkeys (Alouatta caraya) in Northeastern Argentina.

Despite strong support from the media, the reintroduction of animals into natural environments does not always achieve its goal. Alouatta caraya is the primate species facing the greatest hunting pressure due to the illegal pet trade in Argentina. Confiscations of this species are common, as is the voluntary surrender of animals by owners no longer able or willing to care for them. These animals ultimately arrive at rehabilitation centers and, in many cases, are released into natural environments that may differ from the original sites where they were captured. Until recently, the lack of genetic analysis of the individuals involved led to biased relocation decisions. We followed the reintroduction of 12 A. caraya individuals in a protected area (Isla Palacio, Misiones, Argentina). The presence of potential predators such as pumas (Puma concolor) and jaguars (Panthera onca) in this area was confirmed by camera traps, footprints and feces. After the disappearance of four A. caraya at the reintroduction site, we investigated the applicability of genetic assignment tests based on genotypic data to accurately identify predated individuals. Genetic analyses allowed us to determine the predator species (P. onca) and to identify the predated individuals as two of the reintroduced animals. This procedure is promising for identifying the remains of predated individuals, and can contribute to the design of reintroduction policies based on scientific evidence.

Evaluation of Genetic Diversity in Goats of Telangana and Andhra Pradesh States of India

Background: The goat population of Andhra Pradesh and Telangana states is about five million, respectively. The goats of these two states lack phenotypic uniformity. But it is not known whether these populations have any genetically uniform group that can be registered as a breed. The study was undertaken to explore possibility of any potential new goat germplasm.Methods: Study was carried out at ICAR-NBAGR during 2017-19. Genetic diversity and differentiation was evaluated by using 22 microsatellite markers in three goat populations: Telangana Black (TB, n=26), Telangana Mixed (TM, n=49) and one Andhra Pradesh goat population (AP, n=45). Their genetic differentiation was compared with that of geographically closely distributed registered breeds viz. Bidri (n=28) and Nandidurga (n=48) of Karnatka and Ganjam (n=48) of Odisha. Result: The mean allele frequency observed was 6.59 (TB), 7.27 (TM) and 8.36 (AP). Expected number of alleles varied from 3.33 in (TB) to 3.69 in AP goats. Observed heterozygosity was lowest in the TM (0.474) followed by TB (0.504) and was highest in the AP goats (0.569). AP goat population had 6.3% heterozygote deficiency, whereas, both TB (15.4%) and TM (17.5%) had very high inbreeding coefficients. A total of 344 alleles were detected across the 22 loci in six goat groups. F-statistics, the pair-wise Nei’s genetic distance, assignment test and Baysian approach suggested that AP goats are distinct from two Telangana goat populations as well as from the other geographically closely related registered goat breeds. Genetic bottleneck analysis indicated the absence of any detectably large, recent genetic bottleneck in AP population. Altogether, the study identified Andhra Pradesh (AP) goats to be a new potential goat germplasm of India.

No Population Genetic Structure of Skipjack Tuna (Katsuwonus pelamis) in the Tropical Western and Central Pacific Assessed Using Single Nucleotide Polymorphisms

Skipjack tuna (Katsuwonus pelamis) has historically been considered panmictic at the ocean basin scale because of the species’ life history and substantial absolute population size. However, recent advances in population genomics have enabled scientists to demonstrate population structure in other species that were likewise traditionally assumed to be panmictic. Accordingly, we used DArTseq, a proprietary platform of reduced-representation genome sequencing developed by Diversity Arrays Technology (DArTech) to genotype 222 skipjack tuna from 9 sample groups collected across 6 exclusive economic zones (EEZs) and over 6 years in the tropical Western and Central Pacific Ocean. This is one of the most fine-scale population genetics assessments of skipjack tuna to date. We found several statistically significant pairwise FST comparisons using purportedly neutral loci, but very little indication of structure based on observed and expected heterozygosity, effective population size, a Mantel test, AMOVA, numerous genetic clustering and population assignment tests, and exploration of correlation with oceanographic features. Significant pairwise FST values were often shallow and resulted in uncertainty about their biological significance. Furthermore, a test of the hypothesis that the geographic and temporal distribution of the potentially adaptive genetic diversity may depict cryptic fine scale structure using two different outlier detection methods, could not reject panmixia based on estimates of fixation indices and two clustering software. Our results support the presence of a single population of skipjack tuna in the tropical Western and Central Pacific Ocean, but highly recommend the expansion of the study area, in latitude, longitude, and seasonality, before drawing any global conclusions.

Can genetic assignment tests provide insight on the influence of captive egression on the epizootiology of chronic wasting disease?

Identifying the sources of ongoing and novel disease outbreaks is critical for understanding the diffusion of epizootic diseases. Identifying infection sources is difficult when few physical differences separate individuals with different origins. Genetic assignment procedures show great promise for assessing transmission dynamics in such situations. Here, we use genetic assignment tests to determine the source of chronic wasting disease infections in free‐ranging white‐tailed deer (Odocoileus virginianus) populations. Natural dispersal is thought to facilitate the geographic diffusion of chronic wasting disease, but egression from captive cervid populations represents an alternative source of infection that is difficult to detect due to physical similarities with wild deer. Simulated reference populations were created based on allele frequencies from 1,912 empirical microsatellite genotypes collected in four sampling subregions and five captive facilities. These reference populations were used to assess the likelihood of ancestry and assignment of 1,861 free‐ranging deer (1,834 noninfected and 27 infected) and 51 captive individuals to captive or wild populations. The ancestry (Q) and assignment scores (A) for free‐ranging deer to wild populations were high (average Q wild = 0.913 and average A wild = 0.951, respectively), but varied among subregions (Q wild = 0.800–0.947, A wild = 0.857–0.976). These findings suggest that captive egression and admixture are rare, but risk may not be spatially uniform. Ancestry and assignment scores for two free‐ranging deer with chronic wasting disease sampled in an area where chronic wasting disease was previously unobserved in free‐ranging herds indicated a higher likelihood of assignment and proportion of ancestry attributable to captive populations. While we cannot directly assign these individuals to infected facilities, these findings suggest that rare egression events may influence the epizootiology of chronic wasting disease in free‐ranging populations. Continued disease surveillance and genetic analyses may further elucidate the relative disease risk attributable to captive and wild sources.

Seeds in motion: Genetic assignment and hydrodynamic models demonstrate concordant patterns of seagrass dispersal.

Movement is fundamental to the ecology and evolutionary dynamics within species. Understanding movement through seed dispersal in the marine environment can be difficult due to the high spatial and temporal variability of ocean currents. We employed a mutually enriching approach of population genetic assignment procedures and dispersal predictions from a hydrodynamic model to overcome this difficulty and quantify the movement of dispersing floating fruit of the temperate seagrass Posidonia australis Hook.f. across coastal waters in south-western Australia. Dispersing fruit cohorts were collected from the water surface over two consecutive years, and seeds were genotyped using microsatellite DNA markers. Likelihood-based genetic assignment tests were used to infer the meadow of origin for seed cohorts and individuals. A three-dimensional hydrodynamic model was coupled with a particle transport model to simulate the movement of fruit at the water surface. Floating fruit cohorts were mainly assigned genetically to the nearest meadow, but significant genetic differentiation between cohort and most likely meadow of origin suggested a mixed origin. This was confirmed by genetic assignment of individual seeds from the same cohort to multiple meadows. The hydrodynamic model predicted 60% of fruit dispersed within 20km, but that fruit was physically capable of dispersing beyond the study region. Concordance between these two independent measures of dispersal provides insight into the role of physical transport for long distance dispersal of fruit and the consequences for spatial genetic structuring of seagrass meadows.

Limited hatchery introgression into wild brook trout (Salvelinus fontinalis) populations despite reoccurring stocking.

Due to increased anthropogenic pressures on many fish populations, supplementing wild populations with captive‐raised individuals has become an increasingly common management practice. Stocking programs can be controversial due to uncertainty about the long‐term fitness effects of genetic introgression on wild populations. In particular, introgression between hatchery and wild individuals can cause declines in wild population fitness, resiliency, and adaptive potential and contribute to local population extirpation. However, low survival and fitness of captive‐raised individuals can minimize the long‐term genetic consequences of stocking in wild populations, and to date the prevalence of introgression in actively stocked ecosystems has not been rigorously evaluated. We quantified the extent of introgression in 30 populations of wild brook trout (Salvelinus fontinalis) in a Pennsylvania watershed and examined the correlation between introgression and 11 environmental covariates. Genetic assignment tests were used to determine the origin (wild vs. captive‐raised) for 1,742 wild‐caught and 300 hatchery brook trout. To avoid assignment biases, individuals were assigned to two simulated populations that represented the average allele frequencies in wild and hatchery groups. Fish with intermediate probabilities of wild ancestry were classified as introgressed, with threshold values determined through simulation. Even with reoccurring stocking at most sites, over 93% of wild‐caught individuals probabilistically assigned to wild origin, and only 5.6% of wild‐caught fish assigned to introgressed. Models examining environmental drivers of introgression explained <3% of the among‐population variability, and all estimated effects were highly uncertain. This was not surprising given overall low introgression observed in this study. Our results suggest that introgression of hatchery‐derived genotypes can occur at low rates, even in actively stocked ecosystems and across a range of habitats. However, a cautious approach to stocking may still be warranted, as the potential effects of stocking on wild population fitness and the mechanisms limiting introgression are not known.

Chinstrap penguin population genetic structure: one or more populations along the Southern Ocean?

BackgroundHistorical factors, demography, reproduction and dispersal are crucial in determining the genetic structure of seabirds. In the Antarctic marine environment, penguins are a major component of the avian biomass, dominant predators and important bioindicators of ecological change. Populations of chinstrap penguins have decreased in nearly all their breeding sites, and their range is expanding throughout the Antarctic Peninsula. Population genetic structure of this species has been studied in some colonies, but not between breeding colonies in the Antarctic Peninsula or at the species’ easternmost breeding colony (Bouvetøya).ResultsConnectivity, sex-biased dispersal, diversity, genetic structure and demographic history were studied using 12 microsatellite loci and a mitochondrial DNA region (HVRI) in 12 breeding colonies in the South Shetland Islands (SSI) and the Western Antarctic Peninsula (WAP), and one previously unstudied sub-Antarctic island, 3600 km away from the WAP (Bouvetøya). High genetic diversity, evidence of female bias-dispersal and a sign of population expansion after the last glacial maximum around 10,000 mya were detected. Limited population genetic structure and lack of isolation by distance throughout the region were found, along with no differentiation between the WAP and Bouvetøya (overall microsatellite FST = 0.002, p = 0.273; mtDNA FST = − 0.004, p = 0.766), indicating long distance dispersal. Therefore, genetic assignment tests could not assign individuals to their population(s) of origin. The most differentiated location was Georges Point, one of the southernmost breeding colonies of this species in the WAP.ConclusionsThe subtle differentiation found may be explained by some combination of low natal philopatric behavior, high rates of dispersal and/or generally high mobility among colonies of chinstrap penguins compared to other Pygoscelis species.

Survival and Reproductive Success of Hatchery YY Male Brook Trout Stocked in Idaho Streams

AbstractNonnative Brook Trout Salvelinus fontinalis were introduced throughout western North America in the early and mid 1900s, resulting in populations that are difficult to eradicate and that often threaten native salmonids. Male YY Brook Trout (MYY), created in the hatchery by feminizing XY males and then crossing them with normal XY males, comprise a novel approach to eradicating undesirable Brook Trout populations. If stocked MYY Brook Trout survive and reproduce with wild females, it could eventually drive the wild population sex ratio to 100% males, at which point the population would be unable to reproduce and would be eradicated after stocking ceased. In this study, we stocked the limited number of catchable‐size (mean TL = 229 mm) MYY hatchery Brook Trout available from an established MYY broodstock into four streams. In two streams, the wild Brook Trout population was suppressed via electrofishing prior to stocking to determine whether diminished competition with wild fish would increase the survival of hatchery MYY fish. We used genetic assignment testing to identify the successful reproduction of stocked MYY fish. Apparent survival of MYY Brook Trout averaged 18% in streams with wild population suppression (mean suppression, 17%) and 9% in streams without suppression, suggesting that suppression of the wild population before stocking increased MYY survival poststocking. Hatchery MYY Brook Trout comprised an estimated 3.1% of all adult Brook Trout during spawning. Genetic assignment tests identified successful reproduction of MYY fish in all streams in which they were stocked, with an average of 3.7% of fry being the progeny of MYY fish. Our results confirm that hatchery MYY fish stocked in streams can survive and spawn successfully with wild fish and produce all‐male progeny. Despite the slightly reduced fitness of MYY Brook Trout, this technology may be a viable method for eradicating undesirable nonnative Brook Trout populations.

The first detected airline introductions of yellow fever mosquitoes (Aedes aegypti) to Europe, at Schiphol International airport, the Netherlands

BackgroundAir-borne introduction of exotic mosquitoes to Schiphol airport in the Netherlands has been considered plausible based upon findings of mosquitoes in aircraft cabins during 2008, 2010 and 2011. Beginning in 2013, surveillance efforts at Schiphol had focused on promptly detecting accidental introductions at the airport facilities in order to quickly react and avoid temporary proliferation or establishment of mosquito populations, identify the origin of the introductions, and avoid potential transmission of vector-borne diseases.MethodsBG-Mosquitaire mosquito traps were set at the most likely locations for arrival of the invasive Aedes mosquitoes as part of the mosquito monitoring program at Schiphol airport. Samples were collected bi-weekly. Upon detection of exotic specimens, information about the origin of the flights arriving to the particular location at the airport where specimens were captured was requested from airport authorities. The GIS tool Intersect was then used to identify airports of origin common to positive trapping locations during the specific trapping period. Captured Aedes aegypti mosquitoes were subsequently genotyped at 12 highly polymorphic microsatellite markers and compared to a reference database of 79 populations around the world to further narrow down their location of origin.ResultsIn 2016, six adult yellow fever mosquitoes were captured indoors and outdoors at the airport of Schiphol in the Netherlands confirming, for the first time, air-borne transport of this mosquito vector species into Europe. Mosquitoes were captured during three time periods: June, September and October. Containers carried by aircrafts are considered the most likely pathway for this introduction. GIS analysis and genetic assignment tests on these mosquitoes point to North America or the Middle East as possible origins, but the small sample size prevents us from reliably identifying the geographic origin of this introduction.ConclusionsThe arrival of Ae. aegypti mosquitoes to Schiphol airport from flights arriving from overseas, demonstrates the potential risk of international flights to public health as carriers of arthropod vectors of disease. The results strongly suggest that disinsection of containers and their storage compartments inside the aircrafts could contribute to preventing future introductions of mosquito vectors. Invasive mosquito species introduced by aircrafts from overseas could become seasonally established during the warmer months in Europe, or permanently in certain climatically suitable areas for the species, with major consequences for human health.

Applications of random forest feature selection for fine‐scale genetic population assignment

Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine‐learning algorithms (random forest, regularized random forest and guided regularized random forest) compared with F ST ranking for selection of single nucleotide polymorphisms (SNP) for fine‐scale population assignment. We applied these methods to an unpublished SNP data set for Atlantic salmon (Salmo salar) and a published SNP data set for Alaskan Chinook salmon (Oncorhynchus tshawytscha). In each species, we identified the minimum panel size required to obtain a self‐assignment accuracy of at least 90% using each method to create panels of 50–700 markers Panels of SNPs identified using random forest‐based methods performed up to 7.8 and 11.2 percentage points better than F ST‐selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self‐assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each data set, respectively, a level of accuracy never reached for these species using F ST‐selected panels. Our results demonstrate a role for machine‐learning approaches in marker selection across large genomic data sets to improve assignment for management and conservation of exploited populations.

Genetic fingerprinting reveals natal origins of male leatherback turtles encountered in the Atlantic Ocean and Mediterranean Sea

Understanding population dynamics in broadly distributed marine species with cryptic life history stages is challenging. Information on the population dynamics of sea turtles tends to be biased toward females, due to their accessibility for study on nesting beaches. Males are encountered only at sea; there is little information about their migratory routes, residence areas, foraging zones, and population boundaries. In particular, male leatherbacks (Dermochelys coriacea) are quite elusive; little is known about adult and juvenile male distribution or behavior. The at-sea distribution of male turtles from different breeding populations is not known. Here, 122 captured or stranded male leatherback turtles from the USA, Turkey, France, and Canada (collected 1997–2012) were assigned to one of nine Atlantic basin populations using genetic analysis with microsatellite DNA markers. We found that all turtles originated from western Atlantic nesting beaches (Trinidad 55%, French Guiana 31%, and Costa Rica 14%). Although genetic data for other Atlantic nesting populations were represented in the assignment analysis (St. Croix, Brazil, Florida, and Africa (west and south), none of the male leatherbacks included in this study were shown to originate from these populations. This was an unexpected result based on estimated source population sizes. One stranded turtle from Turkey was assigned to French Guiana, while others that were stranded in France were from Trinidad or French Guiana breeding populations. For 12 male leatherbacks in our dataset, natal origins determined from the genetic assignment tests were compared to published satellite and flipper tag information to provide evidence of natal homing for male leatherbacks, which corroborated our genetic findings. Our focused study on male leatherback natal origins provides information not previously known for this cryptic, but essential component of the breeding population. This method should provide a guideline for future studies, with the ultimate goal of improving management and conservation strategies for threatened and endangered species by taking the male component of the breeding population into account.

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.