Search USGS⌕ Search

SEARCH · Search USGS

Results for “PLoS”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26Linked to original sources
USGS2019

Facilitating adaptation to climate change while restoring a montane plant community

Montane plant communities throughout the world have responded to changes in temperature regimes by shifting ranges upward in elevation, and made downslope movements to track shifts in climatic water balance. Organisms that cannot disperse or adapt biologically to projected climate scenarios in situ may decrease in distributional range and abundance over time. Restoration strategies will need to incorporate the habitat suitability of future predicted conditions to ensure long-term persistence. We propagated seedlings of three native Hawaiian montane plant species from high- (~2,500 m asl) and low-elevation (~1,900 m asl) sources, planted them in 8 common plots along a 500 m elevation gradient, and monitored microclimate at each plot for 20 weeks. We explored how temperature and precipitation influenced survival and growth differently among high- and low-elevation origin seedlings. Significantly more seedlings of only one species, Dodonaea viscosa , from high-elevation origin (75.2%) survived than seedlings from low-elevation origin (58.7%) across the entire elevation gradient. Origin also influenced survival in generalized linear mixed models that controlled for temperature, precipitation, and elevation in D . viscosa and Chenopodium oahuense . Survival increased with elevation and soil moisture for Sophora chrysophylla , while it decreased for the other two species. Responses to microclimate varied between the three montane plant species; there were no common patterns of growth or survival. Although limited in temporal scope, our experiment represents one of the few attempts to examine local adaptation to prospective climate scenarios and addresses challenges to restoration efforts within species’ current ranges.

Hawaii↗
USGS2019

Loggerhead sea turtle (Caretta caretta) diving changes with productivity, behavioral mode, and sea surface temperature

The relationship between dive behavior and oceanographic conditions is not well understood for marine predators, especially sea turtles. We tagged loggerhead turtles ( Caretta caretta ) with satellite-linked depth loggers in the Gulf of Mexico, where there is a minimal amount of dive data for this species. We tested for associations between four measurements of dive behavior (total daily dive frequency, frequency of dives to the bottom, frequency of long dives and time-at-depth) and both oceanographic conditions (sea surface temperature [SST], net primary productivity [NPP]) and behavioral mode (inter-nesting, migration, or foraging). From 2011–2013 we obtained 26 tracks from 25 adult female loggerheads tagged after nesting in the Gulf of Mexico. All turtles remained in the Gulf of Mexico and spent about 10% of their time at the surface (10% during inter-nesting, 14% during migration, 9% during foraging). Mean total dive frequency was 41.9 times per day. Most dives were ≤ 25 m and between 30–40 min. During inter-nesting and foraging, turtles dived to the bottom 95% of days. SST was an important explanatory variable for all dive patterns; higher SST was associated with more dives per day, more long dives and more dives to the seafloor. Increases in NPP were associated with more long dives and more dives to the bottom, while lower NPP resulted in an increased frequency of overall diving. Longer dives occurred more frequently during migration and a higher proportion of dives reached the seafloor during foraging when SST and NPP were higher. Our study stresses the importance of the interplay between SST and foraging resources for influencing dive behavior.

Alabama, Florida, Louisiana, Mississippi, Texas↗
USGS2019

Temporal changes in avian community composition in lowland conifer habitats at the southern edge of the boreal zone in the Adirondack Park, NY

Climate change represents one of the most significant threats to human and wildlife communities on the planet. Populations at range margins or transitions between biomes can be particularly instructive for observing changes in biological communities that may be driven by climate change. Avian communities in lowland boreal habitats in the Adirondack Park, located at the North American boreal-temperate ecotone, have been the focus of long-term monitoring efforts since 2007. By documenting long-term changes in community structure and composition, such datasets provide an opportunity to understand how boreal species are responding differently to climate change, and which habitat characteristics may be best able to retain boreal avian communities. We examined three specific questions in order to address how well current biological communities in Adirondack boreal wetland habitats are being maintained in a changing climate: (1) how do trends in occupancy vary across species, and what guilds or characteristics are associated with increasing or decreasing occupancy? (2) how is avian community composition changing differently across sites, and (3) what distinguishes sites which are retaining boreal birds to a higher degree than other sites? Our analysis revealed that (1) boreal species appear to exhibit the largest changes in occupancy among our study locations as compared to the larger avian community, (2) dynamics of community change are not uniform across sites and habitat structure may play an important role in driving observed changes, and (3) the particular characteristics of large open peatlands may allow them to serve as refugia for boreal species in the context of climate change.

New York↗
USGS2019

Laboratory assessment of alternative stream velocity measurement methods

Understanding streamflow in montane watersheds on regional scales is often incomplete due to a lack of data for small-order streams that link precipitation and snowmelt processes to main stem discharge. This data deficiency is attributed to the prohibitive cost of conventional streamflow measurement methods and the remote location of many small streams. Expedient and low-cost streamflow measurement methods used by resource professionals or citizen scientists can provide scientifically useful solutions to this data deficiency. To this end, four current velocity measurement methods were evaluated in a laboratory flume: the surface float, rising body, velocity head rod, and rising air bubble methods. The methods were tested under a range of stream velocities, cross-sectional depths, and streambed substrates. The resulting measurements provide estimates of precision and bias of each method, as well as method-specific insight and calibration formulas. The velocity head rod and surface float methods were the easiest methods to use, providing greater precision at large (>=0.6 m/s) and small (<0.6 m/s) velocities, respectively. However, the reliance on a velocity ratio for each of these methods can generate inaccuracy in their results. The rising body method is more challenging to execute and of lower precision than the former two methods but provides low bias measurements. The rising air bubble method has a complex instrument assembly that is considered impractical for potential field user groups.

PLoS ONE↗
USGS2019

Mortality, perception, and scale: Understanding how predation shapes space use in a wild prey population

Attempts to assess behavioral responses of prey to predation risk are often confounded by depredation of prey. Moreover, the scale at which the response of prey is assessed has important implications for discovering how predation risk alters prey behavior. Herein, we assessed space use of wild Ring-necked Pheasants ( Phasianus colchicus ) in response to spatial and temporal variation in recreational hunting. We radio-marked pheasants and monitored space use at two spatial scales: short-term seasonal home range, and nightly resting locations. Additionally, we considered temporal variation in predation risk by monitoring space use prior to and during the pheasant hunting season. Although we found no change in nightly resting location, pheasants subjected to predation risk expanded their home range and shifted home range location even when invulnerable to predation. Home range formation was plastic, with home ranges expanding and contracting as risk fluctuated before and during the hunting season. Depredation reduced the measured response within the population, obscuring the potential importance of perceived predation risk in shaping prey communities, particularly when not measured at the appropriate scale. By assessing space use of a wild prey population at multiple scales, considering spatial and temporal variation in predation risk, we show that not only does predation risk affect space use, but that the effects at the population level may be challenging to assess when not measured at the appropriate ecological scale because of the direct effects of differential mortality on the same behaviors.

Nebraska↗
USGS2019

Projected urban growth in the Southeastern USA puts small streams at risk

Future land-use development has the potential to profoundly affect the health of aquatic ecosystems in the coming decades. We developed regression models predicting the loss of sensitive fish (R2=0.39) and macroinvertebrate (R2=0.64) taxa as a function of urban and agricultural land uses and applied them to projected urbanization of the rapidly urbanizing Piedmont ecoregion of the southeastern USA for 2030 and 2060. The regression models are based on a 2014 investigation of water quality and ecology of 75 wadeable streams across the region. Based on these projections, stream kilometers experiencing >50% loss of sensitive fish and invertebrate taxa will nearly quadruple to 19,500 and 38,950 km by 2060 (16 and 32% of small stream kilometers in the region), respectively. Uncertainty was assessed using the 20 and 80% probability of urbanization for the land-use projection model and using the 95% confidence intervals for the regression models. Adverse effects on stream health were linked to elevated concentrations of contaminants and nutrients, low dissolved oxygen, and streamflow alteration, all associated with urbanization. The results of this analysis provide a warning of potential risks from future urbanization and perhaps some guidance on how those risks might be mitigated.

PLoS ONE↗
USGS2019

Measuring sustainability of seed-funded Earth science informatics projects

Short term funding is a common funding model for informatics projects. Funders are interested in maximizing the sustainability and accessibility of the outputs, but there are no commonly accepted practices to do so in the Earth sciences informatics field. We constructed and applied a framework for sustainability drawing from other disciplines that have more published work in sustainability of projects. This framework had seven sustainability influences (outputs modified, code repository used, champion present, workforce stability, support from other organizations, collaboration/partnership, and integration with policy), and three ways of defining sustainability (at the individual-, organization-, and community-level). Using this framework, we evaluated outputs of projects funded by the U.S. Geological Survey’s Community for Data Integration (CDI). We found that the various outputs are widely accessible, but not necessarily sustained or maintained. Projects with most of the sustainability influences often became institutionalized, and met a required need of the community. Even if proposed outputs were not delivered or sustained, knowledge of lessons learned could be spread to build community capacity in a topic, which is another type of sustainability. We conclude by summarizing lessons for individuals applying for short-term funding, and for organizations running programs that provide such funding, in terms of maximizing sustainability of their projects.

PLoS ONE↗
USGS2019

Growth response of the ichthyotoxic haptophyte, Prymnesium parvum Carter, to changes in sulfate and fluoride concentrations

Golden alga Prymnesium parvum Carter is a euryhaline, ichthyotoxic haptophyte (Chromista). Because of its presumed coastal/marine origin where SO42- levels are high, the relatively high SO 4 2- concentration of its brackish inland habitats, and the sensitivity of marine chromists to sulfur deficiency, this study examined whether golden alga growth is sensitive to SO 4 2- concentration. Fluoride is a ubiquitous ion that has been reported at higher levels in golden alga habitat; thus, the influence of F- on growth also was examined. In low-salinity (5 psu) artificial seawater medium, overall growth was SO 4 2— dependent up to 1000 mg l-1 using MgSO 4 or Na 2 SO 4 as source; the influence on growth rate, however, was more evident with MgSO 4 . Transfer from 5 to 30 psu inhibited growth when salinity was raised with NaCl but in the presence of seawater levels of SO 4 2- , these effects were fully reversed with MgSO 4 as source and only partially reversed with Na 2 SO 4 . Growth inhibition was not observed after acute transfer to 30 psu in a commercial sea salt mixture. In 5-psu medium, F- inhibited growth at all concentrations tested. These observations support the hypothesis that spatial differences in SO 4 2- –but not F-–concentration help drive the inland distribution and growth of golden alga and also provide physiological relevance to reports of relatively high Mg 2+ concentrations in golden alga habitat. At high salinity, however, the ability of sulfate to maintain growth under osmotic stress was weak and overshadowed by the importance of Mg 2+ . A mechanistic understanding of growth responses of golden alga to SO 4 2- , Mg 2+ and other ions at environmentally relevant levels and under different salinity scenarios will be necessary to clarify their ecophysiological and evolutionary relevance.

PLoS ONE↗
USGS2019

Age and growth of stocked juvenile Shoal Bass in a tailwater: Environmental variation and accuracy of daily age estimates

Otolith microanalysis is often used to assess population age structure and growth of fishes during their early stages. Shoal Bass Micropterus cataractae is a recently described species of conservation concern and little is known regarding factors affecting their recruitment. In 2004, Georgia Department of Natural Resources (GADNR) and the US National Park Service (NPS) stocked Shoal Bass marked with oxytetracycline (OTC) in the Chattahoochee River near Atlanta, Georgia in an effort to restore this population, creating known-age fish to examine the effect of environment on daily age accuracy. We obtained samples of stocked juvenile (<150 mm) Shoal Bass from standard monitoring that occurred approximately 30–60 days after stocking in the Chattahoochee River to 1) validate daily rings for estimating age, hatch dates, and growth rates for stocked age-0 Shoal Bass, and 2) evaluate the effect of habitat (location) on age bias. Shoal Bass otoliths were examined for OTC marks and daily rings were counted in reference to OTC marks to assess age estimation accuracy. Age estimation accuracy ranged from -2 to -25 days and was influenced by the environment where Shoal Bass were captured, with greater inaccuracy in colder water temperatures. Fish collected from locations with colder temperatures displayed closer spacing of daily rings, potentially leading to greater underestimation of age. Growth rates of stocked Shoal Bass, corrected for age estimation error, ranged from 0.5 mm/day to 0.8 mm/day. This study demonstrates the effect of environmental variability on age inaccuracy and subsequent interpretation of results. Incorporating methods to assess age estimation accuracy is needed to understand interspecific differences in recruitment among black bass species in the variety of natural and human-modified environments they inhabit.

Georgia↗
USGS2019

13C and 15N NMR identification of product compound classes from aqueous and solid phase photodegradation of 2,4,6-trinitrotoluene

Abstract Photolysis is one of the main transformation pathways for 2,4,6-trinitrotoluene (TNT) released into the environment. Upon exposure to sunlight, TNT is known to undergo both oxidation and reduction reactions with release of nitrite, nitrate, and ammonium ions, followed by condensation reactions of the oxidation and reduction products. In this study, compound classes of transformation products from the aqueous and solid phase photodegradation of 2,4,6-trinitrotoluene (TNT) have been identified by liquid and solid state 13C and 15N NMR. Aqueous phase experiments were performed on saturated solutions of T15NT in deionized water, natural pond water (pH = 8.3, DOC = 3.0 mg/L), pH 8.0 buffer solution, and in the presence of Suwannee River Natural Organic Matter (SRNOM; pH = 3.7), using a Pyrex-filtered medium pressure mercury lamp. Natural sunlight irradiations were performed on TNT in the solid phase and dissolved in the pond water. In deionized water, carboxylic acid, aldehyde, aromatic amine, primary amide, azoxy, nitrosophenol, and azo compounds were formed. 15N NMR spectra exhibited major peaks centered at 128 to 138 ppm, which are in the range of phenylhydroxylamine and secondary amide nitrogens. The secondary amides are proposed to represent benzanilides, which would arise from photochemical rearrangement of nitrones formed from the condensation of benzaldehyde and phenylhydroxylamine derivatives of TNT. The same compound classes were formed from sunlight irradiation of TNT in the solid phase. Whereas carboxylic acids, aldehydes, aromatic amines, phenylhydroxylamines, and amides were also formed from irradiation of TNT in pond water and in pH 8 buffer solution, azoxy and azo compound formation was inhibited. Solid state 15N NMR spectra of photolysates from the lamp irradiation of unlabeled 2,6-dinitrotoluene in deionized water also demonstrated the formation of aromatic amine, phenylhydroxylamine/ 2° amide, azoxy, and azo nitrogens.

PLoS ONE↗
USGS2019

Fossil tabulate corals reveal outcrops of Paleozoic sandstones in the Atlantic Coastal Plain Province, Southeastern USA

The geologic history of the Southeastern United States of America is missing nearly 350-million-years of rocks, sediments, and fossils. This gap defines the Fall Line nonconformity where Upper Ordovician consolidated rocks are directly overlain by Upper Cretaceous unconsolidated sediments of the Atlantic Coastal Plain Province. Here we begin to fill in the missing geologic record by reporting the discovery of fossils of lower-to-middle Paleozoic tabulate corals (Syringophyllidae) in angular, quartz-rich, ferruginous sandstones that crop out in the Carolina Sandhills Physiographic Province that forms the updip margin of the Atlantic Coastal Plain Province near the Fall Line. These fossils of extinct tabulate corals are the first evidence that Paleozoic (Upper Ordovician–Lower Silurian) sandstones crop out amidst the mostly Mesozoic-to-Cenozoic deposits of the Atlantic Coastal Plain Province of the United States of America. This discovery of Paleozoic fossils and strata in a region in which they were previously entirely unknown offers a more complete insight into the geologic history of the Southern Appalachian Mountains Region, Carolina Sandhills and updip margin of the Atlantic Coastal Plain Province and extends the previously identified range of Syringophyllidae in North America.

South Carolina↗
USGS2019

Relative contribution of climate and non-climate drivers in determining dynamic rates ofboreal birds at the edge of their range

The Adirondack Park in New York State contains a unique and limited distribution of boreal ecosystem types, providing habitat for a number of birds at the southern edge of their range. Species are projected to shift poleward in a warming climate, and the limited boreal forest of the Adirondacks is expected to undergo significant change in response to rising temperatures and changing precipitation patterns. Here we expand upon a previous analysis to examine changes in occupancy patterns for eight species of boreal birds over a decade (2007–2016), and we assess the relative contribution of climate and non-climate drivers in determining colonization and extinction rates. Our analysis identifies patterns of declining occupancy for six of eight species, including some declines which appear to have become more pronounced since a prior analysis. Although non-climate drivers such as wetland area, connectivity, and human footprint continue to influence colonization and extinction rates, we find that for most species, occupancy patterns are best described by climate drivers. We modeled both average and annual temperature and precipitation characteristics and find stronger support for species’ responses to average climate conditions, rather than interannual climate variability. In general, boreal birds appear most likely to colonize sites that have lower levels of precipitation and a high degree of connectivity, and they tend to persist in sites that are warmer in the breeding season and have low and less variable precipitation in the winter. It is likely that these responses reflect interactions between broader habitat conditions and temperature and precipitation variables. Indirect climate influences as mediated through altered species interactions may also be important in this context. Given climate change predictions for both temperature and precipitation, it is likely that habitat structural changes over the long term may alter these relationships in the future.

New York↗
USGS2019

Estimating the degree to which distance and temperature differences drive changes in fish community composition over time in the upper Mississippi River

Similarity in community composition declines as distance between locations increases, a phenomenon that has been observed in a wide variety of freshwater, marine and terrestrial ecosystems. One driver of the distance-similarity relationship is the presence of environmental gradients that alter the suitability of sites for particular species. Although some environmental gradients, such as geology, do not change on a year-to-year basis, others, such as temperature, vary annually and over longer time periods. Here, we used a 21-year dataset of fish communities in the upper Mississippi River to identify the effect of distance on variation in community composition and to assess whether the effect of distance is primarily due to its effect on thermal regime. Because the Mississippi River is aligned mostly north-to-south, larger distances along the river roughly correspond to larger differences in latitude and therefore temperature. As expected, there was a moderate distance-similarity relationship, suggesting greater distance leads to less similarity. The effect of distance appeared to increase slightly over time. Using a subset of data for which air temperature was available, we found that difference among sites in degree days (a surrogate for thermal regime) was more strongly associated with similarity in community composition than physical distance (river km). Although physical distance presumably incorporates more environmental gradients than just temperature (and other potential mechanisms), temperature alone appears to be more strongly associated with differences in the Mississippi River fish community.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗
USGS2019

Identifying and characterizing extrapolation in multivariate response data

Faced with limitations in data availability, funding, and time constraints, ecologists are often tasked with making predictions beyond the range of their data. In ecological studies, it is not always obvious when and where extrapolation occurs because of the multivariate nature of the data. Previous work on identifying extrapolation has focused on univariate response data, but these methods are not directly applicable to multivariate response data, which are common in ecological investigations. In this paper, we extend previous work that identified extrapolation by applying the predictive variance from the univariate setting to the multivariate case. We propose using the trace or determinant of the predictive variance matrix to obtain a scalar value measure that, when paired with a selected cutoff value, allows for delineation between prediction and extrapolation. We illustrate our approach through an analysis of jointly modeled lake nutrients and indicators of algal biomass and water clarity in over 7000 inland lakes from across the Northeast and Mid-west US. In addition, we outline novel exploratory approaches for identifying regions of covariate space where extrapolation is more likely to occur using classification and regression trees. The use of our Multivariate Predictive Variance (MVPV) measures and multiple cutoff values when exploring the validity of predictions made from multivariate statistical models can help guide ecological inferences.

PLoS ONE↗
USGS2020

Extreme mortality and reproductive failure of common murres resulting from the northeast Pacific marine heatwave of 2014-2016

About 62,000 dead or dying common murres ( Uria aalge ), the trophically dominant fish-eating seabird of the North Pacific, washed ashore between summer 2015 and spring 2016 on beaches from California to Alaska. Most birds were severely emaciated and, so far, no evidence for anything other than starvation was found to explain this mass mortality. Three-quarters of murres were found in the Gulf of Alaska and the remainder along the West Coast. Studies show that only a fraction of birds that die at sea typically wash ashore, and we estimate that total mortality approached 1 million birds. About two-thirds of murres killed were adults, a substantial blow to breeding populations. Additionally, 22 complete reproductive failures were observed at multiple colonies region-wide during (2015) and after (2016–2017) the mass mortality event. Die-offs and breeding failures occur sporadically in murres, but the magnitude, duration and spatial extent of this die-off, associated with multi-colony and multi-year reproductive failures, is unprecedented and astonishing. These events co-occurred with the most powerful marine heatwave on record that persisted through 2014–2016 and created an enormous volume of ocean water (the “Blob”) from California to Alaska with temperatures that exceeded average by 2–3 standard deviations. Other studies indicate that this prolonged heatwave reduced phytoplankton biomass and restructured zooplankton communities in favor of lower-calorie species, while it simultaneously increased metabolically driven food demands of ectothermic forage fish. In response, forage fish quality and quantity diminished. Similarly, large ectothermic groundfish were thought to have increased their demand for forage fish, resulting in greater top-predator demands for diminished forage fish resources. We hypothesize that these bottom-up and top-down forces created an “ectothermic vise” on forage species leading to their system-wide scarcity and resulting in mass mortality of murres and many other fish, bird and mammal species in the region during 2014–2017.

PLoS ONE↗
USGS2020

An open-sourced, web-based application to improve our ability to understand hunter and angler purchasing behavior from license data

State fish and wildlife agencies rely on hunters and anglers (i.e., sportspersons) to fund management actions through revenue generated from license sales and excise taxes on hunting and fishing equipment. There is a need to develop new techniques that bridge the information gap on participation and provide agencies with an understanding of sportspersons at a resolution that can more directly inform efforts to engage sportspersons. Monitoring sportsperson participation using information about their license-purchasing behavior has the potential to reveal important patterns in recruitment (first-time purchase of a hunting or fishing license), retention (continued purchase of licenses across multiple years), and reactivation (purchase a license after several years with no purchases). Providing up-to-date information on what licenses are purchased, when and by whom may prove invaluable to managers and policy makers. We present a customizable, open-source, web-based application—huntfishapp—that allows the user to query and interact with a structured query language (SQL) hunting and fishing license database. The huntfishapp serves as an informational resource and tool that provides a framework to share information on license sales across an agency, with intent of increasing understanding of (a) sportspersons and (b) how management decisions affect sportspersons. Data dashboards, like the huntfishapp, allow agencies and non-governmental organizations to become more knowledgeable of their customer base and provide a greater understanding of management-decision effects on hunting and fishing participation.

PLoS ONE↗
USGS2019

Applying circuit theory and landscape linkage maps to reintroduction planning for California condors

Conservation practitioners are increasingly looking to species translocations as a tool to recover imperiled taxa. Quantitative predictions of where animals are likely to move when released into new areas would allow managers to better address the social, institutional, and ecological dimensions of conservation translocations. Using >5 million California condor ( Gymnogyps californianus ) occurrence locations from 75 individuals, we developed and tested circuit-based models to predict condor movement away from release sites. We found that circuit-based models of electrical current were well calibrated to the distribution of condor movement data in southern and central California (continuous Boyce Index = 0.86 and 0.98, respectively). Model calibration was improved in southern California when additional nodes were added to the circuit to account for nesting and feeding areas, where condor movement densities were higher (continuous Boyce Index = 0.95). Circuit-based projections of electrical current around a proposed release site in northern California comported with the condor’s historical distribution and revealed that, initially, condor movements would likely be most concentrated in northwestern California and southwest Oregon. Landscape linkage maps, which incorporate information on landscape resistance, complement circuit-based models and aid in the identification of specific avenues for population connectivity or areas where movement between populations may be constrained. We found landscape linkages in the Coast Range and the Sierra Nevada provided the most connectivity to a proposed reintroduction site in northern California. Our methods are applicable to conservation translocations for other species and are flexible, allowing researchers to develop multiple competing hypotheses when there are uncertainties about landscape or social attractants, or uncertainties in the landscape conductance surface.

Central California↗
USGS2020

How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: A case study using the lake whitefish

Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth, as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these “simple” methodological decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) a larger number of loci at low sequencing depth based on a 9mer (library A); and (2) fewer loci at higher sequencing depth based on a 10mer (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters, largely due to retention of more loci in analyses. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. When detecting fine population differentiation, the population map influenced the number of loci and missing data, which generated artefacts in all downstream analyses tested. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay,showing slight differentiation. Overall, we show that apparently simple decisions about library construction and bioinformatics parameters can have important impacts on the interpretation of population subdivision. Although potentially more costly on a per-locus basis, early investment in striking a balance between the number of loci and sequencing effort is well worth the reduced genomic coverage for population genetics studies. More conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation. Overall, we recommend that researchers approach “simple” methodological decisions with caution, especially when working on non-model species for the first time.

Michigan, Ontario, Saskatchewan↗