Find research datasets worth reusing

opencc-by-4.0Sep 2020View details →

Secondary Vertex Finding in Jets Dataset

This is a dataset for developing secondary vertex finding algorithms. The dataset consists of jets sampled from \( pp\rightarrow t\bar{t}\) events at \(\sqrt{s}=14\) TeV. The events are generated with Pythia8 and a basic detector simulation is performed with Delphes emulating a detector similar to ATLAS. Each jet has a set of associated reconstructed tracks. the task of secondary vertex finding is to partition this set according to the point of origin of the particle that created that track. The dataset includes a label for each track that indicates which vertex it originated from. This label is an arbitrary integer - within one jet a pair of tracks originated from the same point if their labels are equal, and from different points otherwise. charged particle tracks are represented by 6 perigee parameters and their covariance matrix. Noise is added to the track perigee parameters with gaussian smearing. The track parameters resolution depends on the transverse momentum and pseudo-rapidity of the track. The covariance matrix is diagonal in this simplified track smearing model.

opencc-zeroSep 2020View details →

Parasite turnover zone at secondary contact: a new pattern in host-parasite population genetics

We introduce a new pattern of population genetic structure in a host-parasite system that can arise after secondary contact of previously isolated populations. Due to different generation time and therefore different tempo of molecular evolution the host and parasite populations reach different degrees of genetic differentiation during their separation (e.g. in refugia). Consequently, during the secondary contact the host populations are able to re-establish a single panmictic population across the area of contact, while the parasite populations stop their dispersal at the secondary contact zone and create a narrow hybrid zone. From the host's perspective, the parasite's hybrid zone functions on a microevolutionary scale as a "parasite turnover zone": while the hosts are passing from area A to area B, their parasites turn genetically from the area A genotypes to the area B genotypes. We demonstrate this novel pattern on a model composed of Apodemus mice and Polyplax lice by comparing maternally inherited markers (complete mitochondrial genomes, and complete genomes of vertically transmitted symbiont Legionella polyplacis) with SNPs derived from the louse genomic data. We discuss circumstances that may lead to this pattern and possible reasons why it has been overlooked in the studies on host parasite population genetics.

opencc-by-4.0Nov 2020View details →

Infographic: Secondary Immunodeficiency

Infographic about secondary immunodeficiencies.

opennotspecifiedNov 2020View details →

FIGURES 66–71. Pseudosympycnus Robinson. Male secondary sexual characters. 66. P in Review of the Neotropical genus Pseudosympycnus (Diptera: Dolichopodidae) with description of six new species from Brazil and Peru

FIGURES 66–71. Pseudosympycnus Robinson. Male secondary sexual characters. 66. P. araza sp. nov., paratype Ƌ, femur and tibia I; 67. P. latipes (Parent, 1930), syntype Ƌ, femur III (photo: Günther Wöss); 68. P. bickeli sp. nov., holotype Ƌ, femur I; 69. P. perornatus Robinson, 1967, paratype Ƌ, tibia II; 70. P. latitibia sp. nov., paratype Ƌ, tibia I; 71. P. robinsoni sp. nov., holotype Ƌ, femur III. Scale bars = 0.2 mm.

opencc-by-4.0Jan 2021View details →

Secondary formation of aerosols under typical high-humidity conditions in wintertime Sichuan Basin, China: A contrast to the North China Plain

The Sichuan Basin is one of the regions suffering from severe haze pollution in southwest China. However, the secondary aerosol formation in this region is poorly understood. In this study, the chemical compositions of PM2.5 and molecular compositions of water-soluble organics in wintertime Sichuan were measured to investigate the aerosol sources and formation under typical high relative humidity (RH) conditions. Strong correlations between PM2.5, carbonaceous aerosols and K+ suggested obvious influence of biomass burning. The impacts of biomass burning were also supported by the dominance of primarily emitted reduced/less oxidized nitrogen-containing organics as well as the high peak intensities of secondarily formed nitrocatechols and methyl-nitrocatechols. High humidity (average RH=80%) and aerosol liquid water (ALW) in Sichuan obviously facilitated the secondary formation of sulfate, nitrate and secondary organic aerosols (SOA). The average sulfate oxidation ratio and nitrogen oxidation ratio in Sichuan were 2.5 and 3.1 times of those in winter Beijing (average RH= 27%). This suggested higher potentials of SO2 and NOx to form sulfate and nitrate under high-RH conditions. The abundant aqueous-SOA formation in Sichuan was supported by the dominance of organosulfates (OSs) and nitrooxy-OSs in mass spectra of water-soluble organics, while the OSs in winter Beijing were quite limited. The more abundant OS formation in Sichuan was attributed to the much higher RH, ALW, aerosol acidity and sulfate, which favored the acidic sulfate-catalyzed aqueous-phase reactions for OS formation. Higher concentrations of biogenic volatile organic compounds were additional reasons for the more abundant OSs in Sichuan than in Beijing.

opencc-by-4.0Jan 2021View details →

The datasets used in "RNA secondary structure prediction using deep learning with thermodynamic integration"

The datasets used in "RNA secondary structure prediction using deep learning with thermodynamic integration"

opencc-zeroDec 2012View details →

Data from: Secondary contact and changes in coastal hydrology influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)

Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ~13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years.

opencc-zeroDec 2017View details →

Data from: Male-limited secondary sexual trait interacts with environment in determining female fitness

Selection for secondary sexual traits (SSTs) elaboration may increase intralocus sexual conflict over the optimal values of traits expressed from shared genomes. This conflict can reduce female fitness, and the resulting gender load can be exacerbated by environmental stress, with consequences for a population's ability to adapt to novel environments. However, how the evolution of SSTs interacts with environment in determining female fitness is not well understood. Here, we investigated this question using replicate lines of bulb mites selected for increased or decreased prevalence of a male SST—thickened legs used as weapons. The fitness of females from these lines was measured at a temperature to which the mites were adapted (24°C), as well as at two novel temperatures: 18°C and 28°C. We found the prevalence of the SST interacted with temperature in determining female fecundity. At 28°C, females from populations with high SST prevalence were less fecund than females from populations in which the SST was rare, but the reverse was true at 18°C. Thus, a novel environment does not universally depress female fitness more in populations with a high degree of sexually selected dimorphism. We discuss possible consequences of the interaction we detected for adaptation to novel environments.

Data from: Modeling seasonal surface temperature variations in secondary tropical dry forests

Secondary tropical dry forests (TDFs) provide important ecosystem services such as carbon sequestration, biodiversity conservation, and nutrient cycle regulation. However, their biogeophysical processes at the canopy-atmosphere interface remain unknown, limiting our understanding of how this endangered ecosystem influences, and responds to the ongoing global warming. To facilitate future development of conservation policies, this study characterized the seasonal land surface temperature (LST) behavior of three successional stages (early, intermediate, and late) of a TDF, at the Santa Rosa National Park (SRNP), Costa Rica. A total of 38 Landsat-8 Thermal Infrared Sensor (TIRS) data and the Surface Reflectance (SR) product were utilized to model LST time series from July 2013 to July 2016 using a radiative transfer equation (RTE) algorithm. We further related the LST time series to seven vegetation indices which reflect different properties of TDFs, and soil moisture data obtained from a Wireless Sensor Network (WSN). Results showed that the LST in the dry season was 15–20 K higher than in the wet season at SRNP. We found that the early successional stages were about 6–8 K warmer than the intermediate successional stages and were 9–10 K warmer than the late successional stages in the middle of the dry season; meanwhile, a minimum LST difference (0–1 K) was observed at the end of the wet season. Leaf phenology and canopy architecture explained most LST variations in both dry and wet seasons. However, our analysis revealed that it is precipitation that ultimately determines the LST variations through both biogeochemical (leaf phenology) and biogeophysical processes (evapotranspiration) of the plants. Results of this study could help physiological modeling studies in secondary TDFs.

opencc-zeroNov 2016View details →

Data from: Nutrient limitation in tropical secondary forests following different management practices

Secondary forests now make up more than half of all tropical forests, and constraints on their biomass accumulation will influence the strength of the terrestrial carbon (C) sink in the coming decades. However the variance in secondary tropical forest biomass for a given stand age and climate is high and our understanding of why is limited. We constructed a model of terrestrial C, nitrogen (N), and phosphorus (P) cycling to examine the influence of disturbance and management practices on nutrient limitation and biomass recovery in secondary tropical forests. The model predicted that N limited the rate of forest recovery in the first few decades following harvest, but that this limitation switched to P approximately 30-40 years after abandonment, consistent with field data on N and P cycling from secondary tropical forest chronosequences. Simulated biomass recovery agreed well with field data of biomass accumulation following harvest (R2=0.80). Model results showed that if all biomass remained on site following a severe disturbance such as blowdown, regrowth approached pre-disturbance biomass in 80-90 years, and recovery was faster following smaller disturbances such as selective logging. Field data from regrowth on abandoned pastures were consistent with simulated losses of nutrients in soil organic matter, particularly P. Following any forest disturbance that involved the removal of nutrients (i.e., except blowdown), forest regrowth produced reduced biomass relative to the initial state as a result of nutrient loss through harvest, leaching and/or sequestration by secondary minerals. Differences in nutrient availability accounted for 49-94% of the variance in secondary forest biomass C at a given stand age. Management lessons from this study are the importance of strategies that help retain nutrients on site, recognizing the role of coarse woody debris in immobilization and subsequent release of nutrients, and the potential for nutrient additions to enhance biomass growth and recovery in secondary tropical forests.

Data from: Assessing the conservation value of secondary savanna for large mammals in the Brazilian Cerrado

Debate about the conservation value of secondary habitats has tended to focus on tropical forests, increasingly recognizing the role of secondary forests for biodiversity conservation. However, there remains a lack of information about the conservation value of secondary savannas. Here, we conducted a camera trap survey to assess the effect of secondary vegetation on large mammals in a Brazilian Cerrado protected area, using a single-season occupancy framework to investigate the response of individual species (species-level models) and of all species combined (community-level models). In addition, we investigated the cost effectiveness of different sampling designs to monitor globally threatened species in the study area. At the community level, savanna that regenerated from eucalyptus plantation had similar occupancy estimate as old growth areas. At the species level, none of the ten species individually assessed seemed to respond to succession stage, with greater support for the effect of other covariates on occupancy, such as distance from water and vegetation physiognomy. These results demonstrate that secondary vegetation does not appear to negatively impact large mammals in the study area and suggest that, given a favorable context, Cerrado mammals can recolonize and use secondary savannas that regenerated from clearcut. However, our study area should be considered a best-case scenario, as it retained key ecological attributes of high-value secondary habitats. Our simulations showed that a sampling design with 60 camera trap sites surveyed during nine occasions is appropriate to monitor most globally threatened species in the study area, and could be a useful starting point for new monitoring initiatives in other Cerrado areas.

opencc-zeroDec 2010View details →

Data from: An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

BACKGROUND: Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea. RESULTS: Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea. CONCLUSION: An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution.

opencc-zeroDec 2017View details →

Data from: Soil nutrients and dispersal limitation shape compositional variation in secondary tropical forests across multiple scales

1. Soil resource partitioning and dispersal limitation have been shown to shape the tree community structure of mature tropical forests, but are poorly studied in the context of forest succession. We examined the relative contributions of both ecological processes to the variation in the species composition of young tropical secondary forests at different spatial scales, and if the relative importance of these two ecological processes changed during succession. At the species level, we examined if the association between species abundances and soil fertility differed between early and late successional species and/or changed over the course of succession. 2. We used vegetation and soil data from 47 secondary forest sites with two plots each in a tropical agricultural landscape. A distance-based redundancy analysis and variation partition were employed to examine the relative importance of spatial distance (proxy for dispersal limitation) and heterogeneity in soil nutrients (proxy for soil nutrient partitioning) at the landscape scale, and a linear regression to test their effects at the local scale. We examined interspecific variation in species' responses to successional age and soil nutrients with a joint species distribution model. 3. Dispersal limitation and soil niche partitioning drove considerable variation in the composition of plant communities at local and landscape scales. The relative contribution of these two ecological processes changed with scale (local versus landscape), topography (lower slope versus upper slope plots). At the species level, significant abundance-soil fertility associations were mostly positive. Most species became less responsive to soil nutrients over the first few decades of tropical forest succession, probably because light became the main limiting resource in older forests. 4. Synthesis. Our key finding is that spatial heterogeneity in soil resources and spatial distance jointly drive compositional variation within and across early successional forests. Our results highlight that a network of forest fragments enhances the resilience of ecological processes and the potential of secondary forests to restore and preserve biodiversity in human-modified landscapes. To advance our understanding of ecological succession, we need to move beyond single-factor and local-scale studies and examine the effects of multiple variables on succession at multiple spatial scales.

Data from: The importance of phytoplankton biomolecule availability for secondary production

The growth and reproduction of animals is affected by their access to resources. In aquatic ecosystems, the availability of essential biomolecules for filter-feeding zooplankton depends greatly on phytoplankton. Here, we analyzed the biochemical composition, i.e., the fatty acid, sterol and amino acid profiles and concentrations as well as protein, carbon, nitrogen, and phosphorus content of 17 phytoplankton monocultures representing the seven most abundant phytoplankton classes in boreal and sub-arctic lakes. To examine how the differences in the biochemical composition between phytoplankton classes affect their nutritional quality for consumers, we assessed the performance of Daphnia, on these diets. Furthermore, we defined the most important biomolecules regulating the somatic growth and reproduction of Daphnia, expecting that higher concentrations of certain biomolecules are needed for reproduction than for growth. Finally, we combined these results with phytoplankton field data from over 900 boreal and sub-arctic lakes in order to estimate whether the somatic growth of Daphnia is sterol-limited when the natural phytoplankton communities are cyanobacteria-dominated. Our analysis shows that Daphnia grows best with phytoplankton rich in sterols, ω-3 fatty acids, protein, and amino acids. Their reproduction follows food sterol and ω-3 concentration as well as C:P-ratio being two times higher in Daphnia feeding on cryptophytes than any other diet. Interestingly, we found that a high dietary ω-6 fatty acid concentration decreases both somatic growth and reproduction of Daphnia. When combined with phytoplankton community composition field data, our results indicate that zooplankton is constantly limited by sterols in lakes dominated by cyanobacteria (≥40% of total phytoplankton biomass), and that the absence of cryptophytes can severely hinder zooplankton production in nature.

opencc-zeroDec 2012View details →

Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia

Tropical rainforests in Southeast Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats (EST-SSRs) and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the southwestern part of Borneo genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28 to 0.09 million years before present, and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.

Data from: Variable drivers of primary versus secondary nesting: density-dependence and drought effects on greater sage-grouse

Organisms seek to maximize fitness by balancing reproductive allocations against mortality risk, given selection pressures inherent to the environment. However, environmental conditions are often dynamic and unpredictable, which complicates the ability to achieve such a balance, and may require reproductive adjustments depending on prevailing conditions. We evaluated the effects of density-dependent, density-independent (drought), and individual (age, body condition) factors on nesting decisions of female greater sage-grouse in the American Great Basin. We obtained relocations and recorded reproductive histories from 287 radio-marked females over a period of 10 yr, and applied these data to a multi-state model that estimated probabilities of initiating a first nest (primary nesting rate) or a second nest, given loss of a first (secondary nesting rate). This approach allowed us to evaluate the relative association between nesting rates and covariates while accounting for imperfect detection of nests. Sage-grouse primary and secondary nesting were influenced differently by density dependence and drought. Primary nesting was high and relatively constant among years despite variable drought conditions, but was negatively associated with population size (density dependence). Secondary nesting was lower and more variable compared to primary nesting, was similarly influenced by density-dependence, and was also sensitive to drought conditions. Females known to initiate second nests were in better body condition than females that only initiated first nests, and females of intermediate age had higher primary nesting rates, whereas secondary nesting was unaffected by age. Our results suggest that females were more flexible and responded more readily to changing conditions when allocating resources to second nests. These results are consistent with patterns that have been demonstrated for female allocation to clutch size in this system, and suggest that when conditions are poor second nests reflect a tipping point where reproductive costs (increased mortality) outweigh benefits (offspring reproductive value).

opencc-zeroDec 2015View details →

Data from: Does competitive interaction drive species recognition in a house mouse secondary contact zone?

Miscommunication may induce a high risk of unnecessary escalated fights between competitors (populations to species), resulting in selection favoring signal divergence through agonistic character displacement (ACD). When signals allowing discrimination between competitors are also involved in mate recognition, ACD could explain reproductive character displacement (RCD). We tested interference competition between males as a potential driver of RCD (here, subspecies recognition) in a secondary contact zone between two mouse subspecies (Mus musculus musculus and Mus musculus domesticus) displaying asymmetric dominance. Since such asymmetry could create a conflict between subspecies (compatibility) and quality (dominance) recognition in the contact zone, we tested for geographic variation in female preference for dominant males in the subordinate subspecies, musculus. We assessed competition between males and tested ACD during dyadic encounters comparing behavior displayed during trials between heterosubspecifics originating from populations close to the secondary contact ("contact") and further away ("allopatric"). We also compared behavior of contact versus allopatric males during homosubspecific versus heterosubspecific trials to test whether subspecies discrimination evolved under competitive interference. Although domesticus dominated most heterosubspecific trials regardless of geographic origin, agonistic behavior was more marked (i.e., lower attack latencies) during contact than allopatric encounters, suggesting that ACD occurred. Comparing behavior during homosubspecific and heterosubspecific encounters, only allopatric musculus displayed differences, that is, higher attack latencies toward heterosubspecifics, indicating that discrimination between competitors did not evolve with ACD. Finally, although allopatric musculus females seemed to prefer dominant males, their contact counterparts did not, suggesting that "compatibility" may have outweighed "quality" under a risk of hybridization.

opencc-zeroDec 2013View details →

Data from: Speciation in Western Scrub-Jays, Haldane's rule, and genetic clines in secondary contact

Background: Haldane's Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior lineages of Western Scrub-Jays (Aphelocoma californica) to test for a signature of Haldane's Rule: a narrower cline of introgression in mtDNA compared to nuclear markers. Results: Our initial phylogeographic analysis revealed that there is only one major area of contact between coastal and interior lineages and identified five genetic clusters with strong spatial structuring: Pacific Slope, Interior US, Edwards Plateau (Texas), Northern Mexico, and Southern Mexico. Consistent with predictions from Haldane's Rule, mtDNA showed a narrower cline than nuclear markers across a transect through the hybrid zone. This result is not being driven by female-biased dispersal because neutral diffusion analysis, which included estimates of sex-specific dispersal rates, also showed less diffusion of mtDNA. Lineage-specific plumage traits were associated with nuclear genetic profiles for individuals in the hybrid zone, indicating that these differences are under genetic control. Conclusions: This study adds to a growing list of studies that support predictions of Haldane's Rule using cline analysis of multiple loci of differing inheritance modes, although alternate hypotheses like selection on different mtDNA types cannot be ruled out. That Haldane's Rule appears to be operating in this system suggests a measure of reproductive isolation between the Pacific Slope and interior lineages. Based on a variety of evidence from the phenotype, ecology, and genetics, we recommend elevating three lineages to species level: A. californica (Pacific Slope); A. woodhouseii (Interior US plus Edwards Plateau plus Northern Mexico); A. sumicrasti (Southern Mexico). The distinctive Edwards Plateau population in Texas, which was monophyletic in mtDNA except for one individual, should be studied in greater detail given habitat threat.

opencc-zeroDec 2014View details →

Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure

Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.