Find research datasets worth reusing

Data from: Genetic pedigree analysis of the pilot breeding program for the rediscovered Galapagos giant tortoise from Floreana island

An aim of many captive breeding programs is to increase population sizes for reintroduction and establishment of self-sustaining wild populations. Genetic analyses play a critical role in these programs: monitoring genetic variation, identifying the origin of individuals, and assigning parentage to track family sizes. Here we use genetic pedigree analyses to examine three seasons of a pilot breeding program for the Floreana island Galapagos giant tortoise, C. niger, that had been declared extinct for ~150 years until individuals with mixed ancestry were recently discovered. We determined that eight of nine founding individuals were assigned parentage to at least one of 130 offspring produced, though there was considerable reproductive skew. In addition, we observed that genetic diversity of the progeny was lower than that of the founders. Despite the observed reproductive skew, we did not see evidence for assortative mating based on relatedness, but there was a trend towards reduced fitness when more related individuals bred. Finally, we found that the majority of progeny had ancestry assigned to the Floreana species (mean±SE = 0.51±0.02), though individual estimates varied. The success of these pilot seasons bodes well for a larger breeding program to help restore the previously extinct tortoise from Floreana island. Future efforts should continue to monitor for reproductive skew and assortative mating in order to maintain allelic diversity. We would also recommend forming smaller breeding groups and rotating individuals among them to prevent long-term reproductive skew among pairs.

opencc-zeroDec 2011View details →

Data from: A new analytical approach to landscape genetic modeling: least-cost transect analysis and linear mixed models

Landscape genetics aims to assess the effect of the landscape on intraspecific genetic structure. To quantify interdeme landscape structure, landscape genetics mostly uses landscape resistance surfaces and least-cost paths or straight-line transects. However, both approaches have drawbacks. Parameterization of resistance surfaces is a subjective process, and least-cost paths represent a single migration route. A transect-based approach might oversimplify migration patterns by assuming rectilinear migration. To overcome these limitations, we combined these two methods in a new landscape genetic approach: least-cost transect analysis (LCTA). Habitat-matrix resistance surfaces were used to create least-cost paths, which were subsequently buffered to form transects in which the abundance of several landscape elements was quantified. To maintain objectivity, this analysis was repeated so that each landscape element was in turn regarded as migration habitat. The relationship between landscape predictor variables and genetic distances was then assessed following a mixed modeling approach to account for the non-independence of values in distance matrices. Subsequently, predictor variables were selected making use of the R_β^2 statistic. We applied LCTA and the mixed model approach to an empirical genetic dataset on the endangered damselfly, Coenagrion mercuriale. We compared the results to those obtained from traditional least-cost, effective and resistance distance analysis and showed that LCTA not only outperforms existing methods in a statistical way, but also provides more information about the migration ecology of the focal species. Although we believe the statistical approach to be an improvement for the analysis of distance matrices in landscape genetics, more stringent testing is needed.

Data from: The analysis and interpretation of critical temperatures

Critical temperatures are widely used to quantify the upper and lower thermal limits of organisms. But measured critical temperatures often vary with methodological details, leading to spirited discussions about the potential consequences of stress and acclimation during the experiments. We review a model based on the simple assumption that failure rate increases with increasing temperature, independent of previous temperature exposure, water loss or metabolism during the experiment. The model predicts that mean critical thermal maximal temperatures (CTmax) increases nonlinearly with starting temperature and ramping rate, a pattern frequently observed in empirical studies. We then develop a statistical model that estimates a failure rate function (the relationship between failure rate and current temperature) using maximum likelihood; the best model accounts for 58% of the variation in CTmax in an exemplary dataset for tsetse flies. We then extend the model to incorporate potential effects of stress and acclimation on the failure rate function; the results show how stress accumulation at low ramping rate may increase the failure rate and reduce observed values of CTmax. We also applied the model to an acclimation experiment with hornworm larvae that used a single starting temperature and ramping rate; the analyses show that increasing acclimation temperature significantly reduced the slope of the failure rate function, increasing the temperature at which failure occurred. The model directly applies to critical thermal minima, and can utilize data from both ramping and constant temperature assays. Our model provides a new approach to analyzing and interpreting critical temperatures.

Data from: A pantropical analysis of the impacts of forest degradation and conversion on local temperature

Temperature is a core component of a species' fundamental niche. At the fine scale over which most organisms experience climate (mm to ha), temperature depends upon the amount of radiation reaching the Earth's surface, which is principally governed by vegetation. Tropical regions have undergone widespread and extreme changes to vegetation, particularly through the degradation and conversion of rainforests. Since most terrestrial biodiversity is in the tropics, and many of these species possess narrow thermal limits, it is important to identify local thermal impacts of rainforest degradation and conversion. We collected pan-tropical, site-level (< 1 ha) temperature data from the literature to quantify impacts of land-use change on local temperatures, and to examine whether this relationship differed above-ground relative to below-ground and between wet and dry seasons. We found that local temperature in our sample sites was higher than primary forest in all human-impacted land-use types (N = 113,894 day-time temperature measurements from 25 studies). Warming was pronounced following conversion of forest to agricultural land (minimum +1.6°C, maximum +13.6°C), but minimal and non-significant when compared to forest degradation (e.g. by selective logging; minimum +1°C, maximum +1.1°C). The effect was buffered below-ground (minimum buffering 0°C, maximum buffering 11.4°C), whereas seasonality had minimal impact (maximum buffering 1.9°C). We conclude that forest-dependent species that persist following conversion of rainforest have experienced substantial local warming. Deforestation pushes these species closer to their thermal limits, making it more likely that compounding effects of future perturbations, such as severe droughts and global warming, will exceed species' tolerances. By contrast, degraded forests and below-ground habitats may provide important refugia for thermally-restricted species in landscapes dominated by agricultural land.

Data from: Resource-Area-Dependence Analysis: inferring animal resource needs from home-range and mapping data

An animal's home-range can be expected to encompass the resources it requires for surviving or reproducing. Thus, animals inhabiting a heterogeneous landscape, where resource patches vary in size, shape and distribution, will naturally have home-ranges of varied sizes, so that each home-range encompasses a minimum required amount of a resource. Home-range size can be estimated from telemetry data, and often key resources, or proxies for them such as the areas of important habitat types, can be mapped. We propose a new method, Resource-Area-Dependence Analysis (RADA), which uses a sample of tracked animals and a categorical map to i) infer in which map categories important resources are accessible, ii) within which home range cores they are found, and iii) estimate the mean minimum areas of these map categories required for such resource provision. We provide three examples of applying RADA to datasets of radio-tracked animals from southern England: 15 red squirrels Sciurus vulgaris, 17 gray squirrels S. carolinensis and 114 common buzzards Buteo buteo. The analyses showed that each red squirrel required a mean (95% CL) of 0.48 ha (0.24-0.97) of pine wood within the outermost home-range, each gray squirrel needed 0.34 ha (0.11-1.12) ha of mature deciduous woodland and 0.035-0.046 ha of wheat, also within the outermost home-range, while each buzzard required 0.54 ha (0.35-0.82) of rough ground close to the home-range center and 14 ha (11-17) of meadow within an intermediate core, with 52% of them also relying on 0.41 ha (0.29-0.59) of suburban land near the home-range center. RADA thus provides a useful tool to infer key animal resource requirements during studies of animal movement and habitat use.

Data from: Belowground community responses to fire: meta-analysis reveals contrasting responses of soil microorganisms and mesofauna

Global fire regimes are shifting due to climate and land use changes. Understanding the responses of belowground communities to fire is key to predicting changes in the ecosystem processes they regulate. We conducted a comprehensive meta-analysis of 1634 observations from 131 empirical studies to investigate the effect of fire on soil microorganisms and mesofauna. Fire had a strong negative effect on soil biota biomass, abundance, richness, evenness, and diversity. Fire reduced microorganism biomass and abundance by up to 96%. Bacteria were more resistant to fire than fungi. Fire reduced nematode abundance by 88% but had no significant effect on soil arthropods. Fire reduced richness, evenness and diversity of soil microorganisms and mesofauna by up to 99%. We found little evidence of temporal trends towards recovery within 10 years post-disturbance suggesting little resilience of the soil community to fire. Interactions between biome, fire type, and depth explained few of these negative trends. Future research at the intersection of fire ecology and soil biology should aim to integrate soil community structure with the ecosystem processes they mediate under changing global fire regimes.

opencc-zeroDec 2015View details →

Data from: Genetic analysis of an ephemeral intraspecific hybrid zone in the hypervariable tree, Metrosideros polymorpha, on Hawai'i Island

Intraspecific hybrid zones involving long-lived woody species are rare and can provide insights into the genetic basis of early-diverging traits in speciation. Within the landscape-dominant Hawaiian tree, Metrosideros polymorpha, are morphologically distinct successional varieties, incana and glaberrima, that dominate new and old lava flows, respectively, below 1200 me on volcanically active Hawai'i Island, with var. glaberrima also extending to higher elevations and bogs. Here, we use morphological measurements on 86 adult trees to document the presence of an incana-glaberrima hybrid zone on the 1855 Mauna Loa lava flow on east Hawai'i Island and parent-offspring analysis of 1311 greenhouse seedlings from 71 crosses involving 72 adults to estimate heritabilities and genetic correlations among vegetative traits. Both the variation in adult leaf pubescence at the site and the consistency between adult and offspring phenotypes suggest the presence of two hybrid classes, F1s and var. incana backcrosses, as would be expected on a relatively young lava flow. Nine nuclear microsatellite loci failed to distinguish parental and hybrid genotypes. All four leaf traits examined showed an additive genetic basis with moderate to strong heritabilities, and genetic correlations were stronger for the more range-restricted var. incana. The differences between varieties in trait values, heritabilities and genetic correlations, coupled with high genetic variation within but low genetic variation between varieties, are consistent with a multi-million-year history of alternating periods of disruptive selection in contrasting environments and admixture in ephemeral hybrid zones. Finally, the contrasting genetic architectures suggest different evolutionary trajectories of leaf traits in these forms.

Data from: Community analysis of microbial sharing and specialization in a Costa Rican ant–plant–hemipteran symbiosis

Ants have long been renowned for their intimate mutualisms with trophobionts and plants and more recently appreciated for their widespread and diverse interactions with microbes. An open question in symbiosis research is the extent to which environmental influence, including the exchange of microbes between interacting macroorganisms, affects the composition and function of symbiotic microbial communities. Here we approached this question by investigating symbiosis within symbiosis. Ant–plant–hemipteran symbioses are hallmarks of tropical ecosystems that produce persistent close contact among the macroorganism partners, which then have substantial opportunity to exchange symbiotic microbes. We used metabarcoding and quantitative PCR to examine community structure of both bacteria and fungi in a Neotropical ant–plant–scale-insect symbiosis. Both phloem-feeding scale insects and honeydew-feeding ants make use of microbial symbionts to subsist on phloem-derived diets of suboptimal nutritional quality. Among the insects examined here, Cephalotes ants and pseudococcid scale insects had the most specialized bacterial symbionts, whereas Azteca ants appeared to consume or associate with more fungi than bacteria, and coccid scale insects were associated with unusually diverse bacterial communities. Despite these differences, we also identified apparent sharing of microbes among the macro-partners. How microbial exchanges affect the consumer-resource interactions that shape the evolution of ant–plant–hemipteran symbioses is an exciting question that awaits further research.

opencc-zeroDec 2015View details →

Data from: A global meta-analysis on the ecological drivers of forest restoration success

Two billion ha have been identified globally for forest restoration. Our meta-analysis encompassing 221 study landscapes worldwide reveals forest restoration enhances biodiversity by 15–84% and vegetation structure by 36–77%, compared with degraded ecosystems. For the first time, we identify the main ecological drivers of forest restoration success (defined as a return to a reference condition, that is, old-growth forest) at both the local and landscape scale. These are as follows: the time elapsed since restoration began, disturbance type and landscape context. The time elapsed since restoration began strongly drives restoration success in secondary forests, but not in selectively logged forests (which are more ecologically similar to reference systems). Landscape restoration will be most successful when previous disturbance is less intensive and habitat is less fragmented in the landscape. Restoration does not result in full recovery of biodiversity and vegetation structure, but can complement old-growth forests if there is sufficient time for ecological succession.

Data from: The relationship between blood parasites and ornamentation depends on the level of analysis in the common yellowthroat

The Hamilton–Zuk hypothesis predicts that ornament expression is a signal of the ability of individuals to resist parasite infection. Thus, across a population (i.e. between-individuals) more ornamented individuals should have lower levels of parasitism. Numerous studies have tested this prediction and the results are mixed. One reason for these conflicting results may be that many studies have examined this relationship at the between-individual level, which may be affected by confounding factors such as selective mortality. Using within-subject centering we examined the relationship between male ornamentation and avian blood parasites at both the between- and within-individual levels. These relationships focus on differences in genetically-based resistance to parasites and the trade-off in resource allocation between parasite resistance and ornament expression within an individual, respectively. We studied male common yellowthroats Geothlypis trichas, which have two plumage ornaments, a yellow, carotenoid-based bib (throat and chest) and a black, melanin-based facial mask. Surprisingly, within-individuals, an increase in parasitism between years was associated with an increase in mask size and, potentially, greater concentration of carotenoids in the yellow feathers. This suggests that males may be able to tolerate an increase in parasitism and still increase ornament expression. In contrast, ornamentation was not related to parasitism at the between-individual level. Thus, our study revealed relationships between ornaments and parasitism at the within-individual level that were not present at the between-individual level. Our results highlight the importance of examining both within- and between-individual relationships as correlations between variables, such as ornaments and parasites, may depend on the level of analysis (i.e. within- or between-individuals).

opencc-zeroDec 2011View details →

Data from: DNA-based analysis of regurgitates: a noninvasive approach to examine the diet of invertebrate consumers

DNA-based gut content analysis has become an important tool for unravelling feeding interactions in invertebrate communities under natural conditions. It usually implies killing of the consumer and extracting the DNA from its food, either using the whole animal or its dissected gut. This post-mortem approach, however, is not suitable for investigating the diet of rare or protected species and also prohibits tracking individual dietary preferences as each consumer can provide trophic information only once. Moreover, removing large numbers of consumers from a habitat for analysis might critically change population densities and affect species interactions. Here, we present DNA-based analysis of invertebrate regurgitates, a novel approach to overcome these limitations. Conducting feeding experiments where adult Poecilus cupreus (Coleoptera: Carabidae) were fed with larvae of Amphimallon solstitiale (Coleoptera: Scarabaeidae), we show that detection success in regurgitates compared to samples prepared from whole beetles was similar or significantly enhanced for small/medium and large prey DNA fragments, respectively. Prey DNA detection success remained high in regurgitates stored in ethanol for 21 months at room temperature prior to DNA extraction. We conclude that in those invertebrates where regurgitates can be obtained, examination of food DNA in regurgitates offers many advantages over conventional post-mortem gut content analysis.

opencc-zeroJun 2021View details →

Data from: Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of Primula veris

This dataset contains genetic and landscape data of 19 Primula veris populations in Muhu and Saaremaa islands in Estonia. Genetic samples were collected in 2015 and 2016. Landscape data was extracted from maps dated 2016 and 2017 for current data and 1930s for historical data. Data is divided to node- and link-based data. Node-based data contains genetic diversity data of the P. veris populations and landscape data in circular buffers surrounding the populations. Link-based data contains genetic differentiation between population pairs and landscape data in buffers surrounding a straight line between population pairs.

opencc-zeroDec 2018View details →

Data from: Comparative analysis of adaptive and neutral markers of Drosophila mediopunctata populations dispersed among forest fragments

Comparison of adaptive and neutral genetic markers is a valuable approach to characterize the evolutionary consequences of populations living in environments threatened by anthropogenic disturbances, such as forest fragmentation. Shifts in allele frequencies, low genetic variability, and a small effective population size can be considered clear signs of forest fragmentation effects (due to genetic drift) over natural populations, while adaptive responses correlate with environmental variables. Brazilian Atlantic Forest had its landscape drastically reduced and fragmented. Now, several forest remnants are isolated from each other by urban and crop areas. We sampled Drosophila mediopunctata populations from eight forest remnants dispersed on two adjacent geomorphological regions, which are physiognomic and climatically quite distinct. Microsatellite data of inversion‐free chromosomes (neutral genetic marker) indicate low structuration among populations suggesting that they were panmictic and greatly influenced by gene flow. Moreover, significant differences in chromosomal inversion frequencies (adaptive genetic marker) among populations and their correlations with climatic and geographical variables indicate that genetic divergence among populations could be an adaptive response to their environment. Nonetheless, we observed a significant difference in inversion frequencies of a population in two consecutive years that may be associated with edge and demographic effects. Also, it may be reflecting seasonal changes of inversion frequencies influenced by great temperature variation due to edge effects. Moreover, the forest fragment size does not affect genetic variation of neutral markers. Our data indicate that despite oscillations in chromosomal inversion frequencies, D. mediopunctata populations from Brazilian Atlantic Forest and their divergence may be driven by adaptive factors to local differences, perhaps because it is a small flying insect easily carried by the wind increasing its migration rates.

opencc-zeroDec 2012View details →

Data from: Identification of Swedish mosquitoes based on molecular barcoding of the COI gene and SNP analysis

Mosquito-borne infectious diseases are emerging in many regions of the world. Consequently, surveillance of mosquitoes and concomitant infectious agents is of great importance for prediction and prevention of mosquito-borne infectious diseases. Currently, morphological identification of mosquitoes is the traditional procedure. However, sequencing of specified genes or standard genomic regions, DNA barcoding, has recently been suggested as a global standard for identification and classification of many different species. Our aim was to develop a genetic method to identify mosquitoes and to study their relationship. Mosquitoes were captured at collection sites in northern Sweden and identified morphologically before the cytochrome c oxidase subunit I (COI) gene sequences of 14 of the most common mosquito species were determined. The sequences obtained were then used for phylogenetic placement, for validation and benchmarking of phenetic classifications, and finally to develop a hierarchical PCR-based typing scheme based on single nucleotide polymorphism sites (SNPs) to enable rapid genetic identification, circumventing the need for morphological characterization. The results showed that exact phylogenetic relationships between mosquito taxa were preserved at shorter evolutionary distances, but at deeper levels they could not be inferred with confidence by using COI gene sequence data alone. Fourteen of the most common mosquito species in Sweden were identified by the SNP/PCR-based typing scheme, demonstrating that genetic typing using SNPs of the COI gene is a useful method for identification of mosquitoes with potential for worldwide application.

opencc-zeroDec 2015View details →

Data from: Phylogeographic analysis reveals northerly refugia for the riverine amphibian Triturus dobrogicus (Caudata: Salamandridae)

We investigated the recent evolutionary history of the Danube crested newt, Triturus dobrogicus through reconstructions of: (1) the number and position of refugia at the last glacial maximum, (2) the role of major central European rivers in pattern of post-glacial dispersal, and (3) the present-day distribution pattern. We analysed sequences of mitochondrial DNA (ND2, 1065 bp) and six microsatellite loci in 363 T. dobrogicus individuals from 58 populations covering the range of the species. Our analyses suggested that T. dobrogicus survived the last glacial maximum in two separate refugia positioned in northwestern Pannonia and in Southern Pannonia from where its range expanded along the Danube and Tisza Rivers. Our findings also confirmed that rivers played an important role in shaping the evolutionary history of amphibian species in Central Europe. We compared the T. dobrogicus range with another lowland amphibian, the fire-bellied toad Bombina bombina, using species distribution modelling. In line with these models, the isolated mountains inside Pannonia are occupied not by B. bombina, but by its mountain-dwelling sister-species B. variegata. However, in contrast to the model, crested newts (including T. dobrogicus) are absent from these mountains. We attribute this biogeographical discrepancy to the positioning of the species' refugia at the last glacial maximum.

Data from: Integrating complementary methods to improve diet analysis in fishery-targeted species

Developing efficient, reliable, cost-effective ways to identify diet is required to understand trophic ecology in complex ecosystems and improve food web models. A combination of techniques, each varying in their ability to provide robust, spatially and temporally explicit information can be applied to clarify diet data for ecological research. This study applied an integrative analysis of a fishery-targeted species group - Plectropomus spp.in the central Great Barrier Reef, Australia by comparing three diet-identification approaches. Visual stomach content analysis provided poor identification with ~14% of stomachs sampled resulting in identification to family or lower. A molecular approach was successful with prey from ~80% of stomachs identified to genus or species, often with several unique prey in a stomach. Stable isotope mixing models utilising experimentally-derived assimilation data, identified similar prey as the molecular technique but at broader temporal scales, particularly when prior diet information was incorporated. Overall, Caesionidae and Pomacentridae were the most abundant prey families (>50% prey contribution) for all Plectropomus spp., highlighting the importance of planktivorous prey. Less abundant prey categories differed among species/colour phases indicating possible niche segregation. This study is one of the first to demonstrate the extent of taxonomic resolution provided by molecular techniques, and, like other studies, illustrates that temporal investigations of dietary patterns are more accessible in combination with stable isotopes. The consumption of mainly planktivorous prey within this species group has important implications within coral reef foodwebs and provides cautionary information regarding the effects that changing resources could have in reef ecosystems.

opencc-zeroDec 2011View details →

Data from: Karyotype analysis of four jewel-beetle species (Coleoptera, Buprestidae) detected by standard staining, C-banding, AgNOR-banding and CMA3/DAPI staining

The male karyotypes of Acmaeodera pilosellae persica Mannerheim, 1837 with 2n=20 (18+neoXY), Sphenoptera scovitzii Faldermann, 1835 (2n=38–46), Dicerca aenea validiuscula Semenov, 1895 – 2n=20 (18+Xyp) and Sphaerobothris aghababiani Volkovitsh et Kalashian, 1998 – 2n=16 (14+Xyp) were studied using conventional staining and different chromosome banding techniques: C-banding, AgNOR-banding, as well as fluorochrome Chromomycin A3 (CMA3) and DAPI. It is shown that C-positive segments are weakly visible in all four species which indicates a small amount of constitutive heterochromatin (CH). There were no signals after DAPI staining and some positive signals were discovered using CMA3 staining demonstrating absence of AT-rich DNA and presence of GC-rich clusters of CH. Nucleolus organizing regions (NORs) were revealed using Ag-NOR technique; argentophilic material mostly coincides with positive signals obtained using CMA3 staining.

Data from: The importance of scattered trees for biodiversity conservation: a global meta-analysis

1. Scattered trees are thought to be keystone structures for biodiversity in landscapes worldwide. However, such trees have been largely neglected by researchers and their importance for biodiversity remains unclear. 2. We completed a global meta-analysis to quantify relationships between scattered trees and the species richness, abundance and composition of vertebrates, arthropods and plants. First, we tested whether areas near scattered trees support higher levels of species richness and abundance than nearby open areas. Second, we compared levels of species richness and abundance in matrix areas with scattered trees and areas embedded within nearby habitat patches. We also compared the composition of biological communities inhabiting habitat patches, open areas and areas with scattered trees. 3. A total of 62 studies contained suitable data for our quantitative analyses. The local abundance of arthropods, vertebrates and woody plants was 60-430% greater and overall species richness was 50-100% higher in areas with scattered trees than in open areas. Conversely, for herbaceous plants, there was no consistent relationship between species abundance and the occurrence of scattered trees, although species richness was, on average, 43% lower. 4. The abundance and richness of all taxonomic groups was similar in matrix areas supporting scattered trees and habitat patches, although the species richness of epiphytes was, on average, 50% higher in habitat patches. Communities inhabiting habitat patches were more similar in composition to the communities inhabiting areas with scattered trees, and less similar to the communities of open areas. 5. Synthesis and applications. Areas with scattered trees support greater levels of biodiversity than open areas, as well as communities that are more similar to those inhabiting habitat patches. Scattered trees can be regarded as keystone structures for vertebrates, arthropods and terrestrial plants in landscapes worldwide. The maintenance of scattered trees may be compatible with livestock grazing in some agricultural landscapes. Greater management effort and targeted, long-term policies are needed to retain or re-establish scattered trees in many farming landscapes in both forest and non-forest biomes around the world.04-May-2017

opencc-zeroFeb 2020View details →

Data from: Comparing the performance of microsatellites and RADseq in population genetic studies: analysis of data for pike (Esox lucius) and a synthesis of previous studies

Population genetic studies reveal biodiversity patterns and inform about drivers of evolutionary differentiation and adaptation, including gene flow, drift and selection. This can advance our understanding and aid decision making regarding management and conservation efforts. Microsatellites have long been used in population genetic studies.Thanks to the development of newer techniques, sequencing approaches such as restriction site associated DNA sequencing (RADseq) are on their way to replace microsatellites for some applications. However, the performance of these two marker types in population genetics have rarely been systematically compared. We utilized three neutrally and adaptively differentiated populations of anadromous pike (Esox lucius) to assess the relative performance of microsatellites and RADseq with respect to resolution and conclusiveness of estimates of population differentiation and genetic structure. To this end, the same set of individuals (N = 64) were genotyped with both RADseq and microsatellite markers. To assess effects of sample size, the same subset of 10 randomly chosen individuals from each population (N = 30 in total) were also genotyped with both methods. Comparisons of estimated genetic diversity and structure showed that both markers were able to uncover genetic structuring. The full RADseq dataset provided the clearest detection of the finer scaled genetic structuring, and the other three datasets (full and subset microsatellite, and subset RADseq) provided comparable results. A search for outlier loci performed on the full SNP dataset poninted to signs of selection potentially associated with salinity and temperature, exemplifying the utility of RADseq to inform about the importance of different environmental factors. To evaluate whether performance differences between the markers are general or context specific, the results of previous studies that have investigated population structure using both marker types were synthesized. The synthesis revealed that RADseq performed as well as, or better than microsatellites in detecting genetic structuring in the included studies. The differences in the ability to detect population structure, both in the present and the previous studies, are likely explained by the higher number of loci typically utilized in RADseq compared to microsatellite analysis, as increasing the number of markers will (regardless of the marker type) increase power and allow for clearer detection and higher resolution of genetic structure.

Data from: Comparison of diets for largemouth and smallmouth bass in Eastern Lake Ontario using DNA barcoding and stable isotope analysis

Largemouth (LMB: Micropterus salmoides) and Smallmouth Bass (SMB: Micropterus dolomieu) are important species in the recreational fisheries of the Laurentian Great Lakes. The invasion of the Round Goby (Neogobius melanostomus) into these lakes has changed several facets of black bass biology, but there is still much to learn about the relationship between these species. Previous dietary analyses have shown Round Goby to be important prey for bass, but have been limited by low visual identification rates of dissected stomach items. Within the present study, DNA barcoding and stable isotope analysis improve prey identification and provide a more quantitative dietary analysis of adult black bass in Lake Ontario, comparing the importance of Round Goby as prey between these two species. Eighty-four LMB (406mm fork length ±4mm SEM) and two hundred sixty-four SMB (422mm ±2mm) obtained as tournament mortalities had prey identified using DNA-based methods. Round Goby was the most prevalent prey species for both predators. The diet of LMB was three times more diverse than that of SMB, which almost entirely consists of Round Goby. Our results provide further support that recent increases in the size of Lake Ontario bass are a result of Round Goby consumption, and that the effects of this dietary shift on body condition are greater for SMB. Techniques developed in this study include: reverse-oriented dual priming oligonucleotides used as blocking primers for predator DNA, and an automated design approach of restriction fragment length polymorphism tests for identifying prey DNA barcodes.