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Data from: Evidence for sex-specific selection in brain: a case study of the nine-spined stickleback
Theory predicts that the sex making greater investments into reproductive behaviours demands higher cognitive ability, and as a consequence, larger brains or brain parts. Further, the resulting sexual dimorphism can differ between populations adapted to different environments, or among individuals developing under different environmental conditions. In the nine-spine stickleback (Pungitius pungitius), males perform nest building, courtship, territory defence and parental care, whereas females perform mate choice and produce eggs. Also, predation-adapted marine and competition-adapted pond populations have diverged in a series of ecologically relevant traits, including the level of phenotypic plasticity. Here, we studied sexual dimorphism in brain size and architecture in nine-spined stickleback from marine and pond populations reared in a factorial experiment with predation and food treatments in a common garden experiment. Males had relatively larger brains, larger telencephala, cerebella and hypothalami (6–16% divergence) than females, irrespective of habitat. Females tended to have larger bulbi olfactorii than males (13%) in the high food treatment, whereas no such difference was found in the low food treatment. The strong sexual dimorphism in brain architecture implies that the different reproductive allocation strategies (behaviour vs. egg production) select for different investments into the costly brains between males and females. The lack of habitat dependence in brain sexual dimorphism suggests that the sex-specific selection forces on brains differ only negligibly between habitats. Although significance of the observed sex-specific brain plasticity in the size of bulbus olfactorius remains unclear, it demonstrates the potential for sex-specific neural plasticity.
Data from: Ascertaining gene flow patterns in livestock populations of developing countries: a case study in Burkina Faso goat
BACKGROUND: Introgression of Sahel livestock genes southwards in West Africa may be favoured by human activity and the increase of the duration of the dry seasons since the 1970's. The aim of this study is to assess the gene flow patterns in Burkina Faso goat and to ascertain the most likely factors influencing geographic patterns of genetic variation in the Burkina Faso goat population. RESULTS: A total of 520 goat were sampled in 23 different locations of Burkina Faso and genotyped for a set of 19 microsatellites. Although overall differentiation is poor (FST = 0.067 ± 0.003), the goat population of Burkina Faso is far from being homogeneous. Barrier analysis pointed out the existence of: a) genetic discontinuities in the Central and Southeast Burkina Faso; and b) genetic differences within the goat sampled in the Sahel or the Sudan areas of Burkina Faso. Principal component analysis and admixture proportion scores were computed for each population sampled and used to construct interpolation maps. Furthermore, Population Graph analysis revealed that the Sahel and the Sudan environmental areas of Burkina Faso were connected through a significant number of extended edges, which would be consistent with the hypothesis of long-distance dispersal. Genetic variation of Burkina Faso goat followed a geographic-related pattern. This pattern of variation is likely to be related to the presence of vectors of African animal trypanosomosis. Partial Mantel test identified the present Northern limit of trypanosome vectors as the most significant landscape boundary influencing the genetic variability of Burkina Faso goat (p = 0.008). The contribution of Sahel goat genes to the goat populations in the Northern and Eastern parts of the Sudan-Sahel area of Burkina Faso was substantial. The presence of perennial streams explains the existence of trypanosome vectors. The South half of the Nakambé river (Southern Ouagadougou) and the Mouhoun river loop determined, respectively, the Eastern and Northern limits for the expansion of Sahelian goat genes. Furthermore, results from partial Mantel test suggest that the introgression of Sahelian goat genes into Djallonké goat using human-influenced genetic corridors has a limited influence when compared to the biological boundary defined by the northern limits for the distribution of the tsetse fly. However, the genetic differences found between the goat sampled in Bobo Dioulasso and the other populations located in the Sudan area of Burkina Faso may be explained by the broad goat trade favoured by the main road of the country. CONCLUSIONS: The current analysis clearly suggests that genetic variation in Burkina Faso goat: a) follows a North to South clinal; and b) is affected by the distribution of the tsetse fly that imposes a limit to the Sahelian goat expansion due to their trypanosusceptibility. Here we show how extensive surveys on livestock populations can be useful to indirectly assess the consequences of climate change and human action in developing countries.
Data from: How shrub encroachment under climate change could threaten pollination services for alpine wildflowers: a case study using the alpine skypilot, Polemonium viscosum
Under climate change, shrubs encroaching into high altitude plant communities disrupt ecosystem processes. Yet effects of encroachment on pollination mutualisms are poorly understood. Here, we probe potential fitness impacts of interference from encroaching Salix (willows) on pollination quality of the alpine skypilot, Polemonium viscosum. Overlap in flowering time of Salix and Polemonium is a precondition for interference and was surveyed in four extant and 25 historic contact zones. Pollinator sharing was ascertained from observations of willow pollen on bumble bees visiting Polemonium flowers and on Polemonium pistils. We probed fitness effects of pollinator sharing by measuring the correlation between Salix pollen contamination and seed set in naturally pollinated Polemonium. To ascertain whether Salix interference occurred during or after pollination, we compared seed set under natural pollination, conspecific pollen addition, and Salix pollen addition. In current and past contact zones Polemonium and Salix overlapped in flowering time. After accounting for variance in flowering date due to latitude, Salix and Polemonium showed similar advances in flowering under warmer summers. This trend supports the idea that sensitivity to temperature promotes reproductive synchrony in both species. Salix pollen is carried by bumble bees when visiting Polemonium flowers and accounts for up to 25% of the grains on Polemonium pistils. Salix contamination correlates with reduced seed set in nature and when applied experimentally. Postpollination processes likely mediate these deleterious effects as seed set in nature was not limited by pollen delivery. Synthesis: As willows move higher with climate change, we predict that they will drive postpollination interference, reducing the fitness benefits of pollinator visitation for Polemonium and selecting for traits that reduce pollinator sharing.
Data from: Effects of sample size and full sibs on genetic diversity characterization: a case study of three syntopic Iberian pond-breeding amphibians
Accurate characterization of genetic diversity is essential for understanding population demography, predicting future trends and implementing efficient conservation policies. For that purpose, molecular markers are routinely developed for nonmodel species, but key questions regarding sampling design, such as calculation of minimum sample sizes or the effect of relatives in the sample, are often neglected. We used accumulation curves and sibship analyses to explore how these 2 factors affect marker performance in the characterization of genetic diversity. We illustrate this approach with the analysis of an empirical dataset including newly optimized microsatellite sets for 3 Iberian amphibian species: Hyla molleri, Bufo calamita, and Pelophylax perezi. We studied 17–21 populations per species (total n = 547, 652, and 516 individuals, respectively), including a reference locality in which the effect of sample size was explored using larger samples (77–96 individuals). As expected, FIS and tests for Hardy–Weinberg equilibrium and linkage disequilibrium were affected by the presence of full sibs, and most initially inferred disequilibria were no longer statistically significant when full siblings were removed from the sample. We estimated that to obtain reliable estimates, the minimum sample size (potentially including full sibs) was close to 20 for expected heterozygosity, and between 50 and 80 for allelic richness. Our pilot study based on a reference population provided a rigorous assessment of marker properties and the effects of sample size and presence of full sibs in the sample. These examples illustrate the advantages of this approach to produce robust and reliable results for downstream analyses.
Data from: Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates
Recent studies have advocated biomonitoring using DNA techniques. In this study, two high-throughput sequencing (HTS)-based methods were evaluated: amplicon metabarcoding of the cytochrome C oxidase subunit I (COI) mitochondrial gene and gene enrichment using MYbaits (targeting nine different genes including COI). The gene-enrichment method does not require PCR amplification and thus avoids biases associated with universal primers. Macroinvertebrate samples were collected from 12 New Zealand rivers. Macroinvertebrates were morphologically identified and enumerated, and their biomass determined. DNA was extracted from all macroinvertebrate samples and HTS undertaken using the illumina miseq platform. Macroinvertebrate communities were characterized from sequence data using either six genes (three of the original nine were not used) or just the COI gene in isolation. The gene-enrichment method (all genes) detected the highest number of taxa and obtained the strongest Spearman rank correlations between the number of sequence reads, abundance and biomass in 67% of the samples. Median detection rates across rare (<1% of the total abundance or biomass), moderately abundant (1–5%) and highly abundant (>5%) taxa were highest using the gene-enrichment method (all genes). Our data indicated primer biases occurred during amplicon metabarcoding with greater than 80% of sequence reads originating from one taxon in several samples. The accuracy and sensitivity of both HTS methods would be improved with more comprehensive reference sequence databases. The data from this study illustrate the challenges of using PCR amplification-based methods for biomonitoring and highlight the potential benefits of using approaches, such as gene enrichment, which circumvent the need for an initial PCR step.
Data from: What have been and what can be delimited as species using molecular data under the multi-species coalescent model? A case study using Hercules beetles (Dynastes; Dynastidae)
Molecular species delimitation using the multi-species coalescent model has become common for statistically and objectively determining species limits. Empirical examples of how consistently different molecular data sets delimit the same level of divergence as species using coalescent-based methods are still lacking. I applied the method of molecular species delimitation in the Bayesian Phylogenetics and Phylogeography (BPP) program to study species delimitation in the divergence between populations and between putative species across four species of Hercules beetles. The quantity and variability of the molecular data affected species delimitation. A divergence that represented a late stage along the speciation continuum, e.g. between sympatric biological species, could be delimited by BPP by fewer and less variable loci than a recent divergence, e.g. between geographic populations. My results further indicated that the use of genomic data could even over-split geographically continuously distributed populations into species. I compared my results with those from other empirical studies and argue for the need of a thorough review of the kind of evolutionary entities, e.g. geographic populations versus morphologically distinct taxa, that have been designated as species and whether such designations are consistent among studies.
Data from: Optimising trait and source selection for explaining occurrence and abundance changes: a case study using British Butterflies
Functional traits that define the ecological role of an organism are increasingly being used to determine and predict responses to environmental change. Functional trait analyses of butterflies remain underexplored compared with other taxa, such as plants. Previous works using butterfly functional traits have not comprehensively addressed issues about the quality of trait data sets used and the relative predictive power of different trait types. We compare the consistency of trait descriptions between six widely used trait sources for the British butterfly fauna. We analysed consistency of trait sources using Fleiss's kappa and ICC. PCA was used to produce species ordinations, comparing outputs to examine which trait sets were better at explaining recent species range and abundance changes within the UK. There was a large range in congruence values for specific traits between sources. No single source can be relied upon to produce accurate trait information for British butterflies. Most trait sets are poor predictors of abundance and occurrence changes but are better at predicting current occurrence. An extensive trait set, supplementing biotope-related traits with explicit resource-based information recovers more informative ecological classifications and models than those primarily based on life-history traits or biotope descriptors. Smaller trait sets do, however, recover the specialist-generalist continuum. We conclude that analyses of distribution and abundance changes that rely on traits are highly dependent on trait source and trait type. For butterflies, traits that are based on measures of biotope occupancy should be avoided in explaining changes of abundance and distribution. Including trait information that describes their resource requirements is essential for such analyses.
Data from: An unfavorable body composition is common in early arthritis patients: a case control study
Background. An unfavorable body composition is often present in chronic arthritis patients. This unfavorable composition is a loss of muscle mass, with a stable or increased (abdominal) fat mass. Since it is unknown when this unfavorable composition develops, we compared body composition in disease-modifying antirheumatic drugs (DMARD)-naive early arthritis patients with non-arthritis controls and explored the association, in early arthritis patients, with disease activity and traditional cardiovascular risk factors. Methods. 317 consecutive early arthritis patients (84% rheumatoid arthritis according to 2010 ACR/EULAR criteria) and 1268 age-/gender-/ethnicity-matched non-arthritis controls underwent a Dual-energy X-ray absorptiometry scan to assess fat percentage, fat mass index, fat mass distribution and appendicular lean (muscle) mass index. Additionally, disease activity, health assessment questionnaire (HAQ), acute phase proteins, lipid profile and blood pressure were evaluated. Results. Loss of muscle mass (corrected for age suspected muscle mass) was 4-5 times more common in early arthritis patients, with a significantly lower mean appendicular lean mass index (females 6% and males 7% lower, p<0.01). Patients had more fat distributed to the trunk (females p<0.01, males p=0.07) and females had a 4% higher mean fat mass index (p<0.01). An unfavorable body composition was associated with a higher blood pressure and an atherogenic lipid profile. There was no relationship with disease activity, HAQ or acute phase proteins. Conclusion. Loss of muscle mass is 4-5 times more common in early arthritis patients, and is in early arthritis patients associated with a higher blood pressure and an atherogenic lipid profile. Therefore, cardiovascular risk is already increased at the clinical onset of arthritis making cardiovascular risk management necessary in early arthritis patients.
Data from: Using citizen-collected wildlife sightings to predict traffic strike hotspots for threatened species: a case study on the southern cassowary
Assessing the causal factors underpinning the distribution and abundance of wildlife road-induced mortality can be challenging. This is particularly ubiquitous for rare or elusive species, because traffic strikes occur infrequently for these populations and information about localized abundance, distribution, and movements are generally lacking. Here we assessed if citizen-collected sightings data may serve as a low cost and efficient means of gathering long-term animal road-side presence and road crossing information, which could then be used to assess the causative factors and direct mitigation actions aimed at reducing wildlife traffic strike frequency. We explored this principle using two decades of traffic strike records and citizen-collected sightings of the southern cassowary Casuarius casuarius johnsonii. Roads have bisected the cassowaries' rainforest habitat and despite considerable investment into mitigation strategies for this species, road-induced mortality is considered one of the primary threatening processes affecting the population. Using a Bayesian approach and controlling for spatial autocorrelation with conditional autoregressive (CAR) models, we demonstrate that traffic strikes are primarily a density-dependent process in the southern cassowary. That is, traffic strike clusters occurred along stretches of road where cassowaries were most frequently sighted. There were, however, road stretches where traffic strike frequency was greater than predicted by the number of road-side sightings, illustrating when and where density-independent processes increased the mortality potential for a road-crossing cassowary. Synthesis and applications. This is the first time that citizen-collected sightings data have been used to systematically inform upon the abundance and distribution of wildlife traffic strike. The technique not only predicts where incidents are likely to occur but also helps us to understand the factors responsible for strike clustering. While not a replacement for systematic surveys, we highlight citizen-collected sightings data as a low-cost option when assessing contributing factors to vehicle-induced mortality. Accounting for density-dependent and independent processes will ensure the most effective allocation of resources when implementing wildlife traffic strike mitigation.
Data from: Case-oriented selection of investigation methods in direct access: A comparison between physiotherapy trainees at professional colleges and in bachelor's study courses
Objective: Direct access to physiotherapy services is currently discussed in Germany. Its introduction would mean that initial diagnoses must be made in physiotherapy practices as well. However, it was not yet investigated whether the current training in physiotherapy is sufficient for this, and whether there are differences between the training systems. This study aims to answer the question of whether trainees at the end of Bachelor's studies (BS) are more reliably able to assess the case-related suitability of examination methods than professional college students (FS). Methodology: Questionnaires were developed to assess the suitability of examination methods for diagnostic inquiries. All professional colleges and bachelor's study courses listed with the German Physiotherapy Association were asked to present the questionnaires to their final classes. Results: In 216 addressed professional colleges and 24 bachelor's study courses, the return rate was 9.26% for professional colleges and 33.33% for study courses. One hundred thirty-eight questionnaires from students in 8 study courses and 368 questionnaires from students at 20 professional colleges were evaluated. The mean of correct decisions in total (of max. 54) was 19.01 (BS) or 15.73 (FS); in structure-related and function-related examination methods (of max. 42), it was 17.22 (BS) and 14.8 (FS); in activity-related methods (of max. 12), it was 1.97 (BS) and 0.89 (FS). Out of a max. of 49 examination methods, 23.45 (BS) and 26.72 (FS) were stated as unknown. Conclusion: The university students made correct decisions on the suitability of examination methods significantly more frequently than the professional college students. However, the determined group difference is low. Overall, the results do not appear sufficient for direct access. Training would have to be adapted for this purpose.
Data from: Conservation planning for offsetting the impacts of development: a case study of biodiversity and renewable energy in the Mojave Desert
Balancing society's competing needs of development and conservation requires careful consideration of tradeoffs. Renewable energy development and biodiversity conservation are often considered beneficial environmental goals. However, the direct footprint and disturbance of renewable energy can displace species' habitat and negatively impact populations and communities if sited without ecological consideration. To mitigate residual impacts, offsets have emerged as a potentially useful tool after trying to avoid, minimize, or restore affected sites. Yet where many species or many sites are involved, the problem of efficiently designing a set of offset sites becomes increasingly complex. Spatial conservation prioritization tools are designed to handle this problem, but have seen little application to offset siting and analysis. To address this need we designed an offset siting support tool for the Desert Renewable Energy Conservation Plan (DRECP) of California, and present a case study of hypothetical impacts from solar development in the Western Mojave subsection. We compare two offset scenarios designed to mitigate a hypothetical 15,331 ha derived from proposed utility-scale solar energy development (USSED) projects. The first prioritizes offsets based precisely on impacted features, while the second offsets impacts based on the potential to maximize biodiversity conservation gains in the region. The two methods only agree on 28% of their prioritized sites and differ in meeting species-specific offset goals. Differences between the two scenarios highlight the importance of clearly specifying choices and priorities for offset siting and mitigation in general. Similarly, the effects of background climate and land use change may lessen the durability or effectiveness of offsets if not considered. Our offset siting support tool was designed specifically for the DRECP area, but with minor code modification could work well in other offset analyses, and provide continuing support for a potentially innovative mitigation solution to environmental impacts.
ACS - case study, simulation data
<p>These data refer to the simulations carried out to verify the ability of this plant to provide flexibility as market services </p>
Data from: The evolution of chemical defenses along invasion routes: Harmonia axyridis Pallas (Coccinellidae: Coleoptera) as a case study
The Evolution of Increased Competitive Ability (EICA) hypothesis (Blossey & Nötzold, 1995) postulates that escaping from coevolved enemies increases invaders fitness by energy reallocation from defenses and immunity to growth and reproduction. In this context, we evaluated the evidence of evolutionary change in invasive populations of Harmonia axyridis Pallas (Coccinellidae: Coleoptera). We measured egg defenses – cocktail of hydrocarbons on the egg's surface flagging egg toxicity, and the concentration of the main alkaloid harmonine - in individuals from three populations along the invasion route (Japan: native, USA: introduced more than 30 years ago, South Africa: introduced in the early 2000s) in a common garden experiment. Our results support the EICA hypothesis: we found changes along the invasion route in the profiles of the hydrocarbons coating the eggs' surface, and a decrease in the concentration of harmonine in eggs from the most recent invasive South African population compared to the long established in the USA and the native Japanese ones.
Data from: Searching for diamonds in the apomictic rough: a case study involving Boechera lignifera (Brassicaceae)
The genus Boechera is one of the most difficult species complexes in North America, with about 70 sexual diploids and hundreds of apomictic taxa representing diverse combinations of nearly every known sexual genome. In this study, we set out to clarify the taxonomy of Boechera lignifera, which currently includes a small number of sexual diploid populations in addition to the widespread apomictic diploid upon which the name is based. Using data from cytological studies, microsatellite DNA analyses, geography, and morphology, we demonstrate that the apomictic populations are genetically quite divergent from the sexual diploids. We propose the name Boechera kelseyana to accommodate the sexual diploid taxon, which occurs entirely south of the geographic range of B. lignifera. Boechera kelseyana is consistently separable from B. lignifera based on pollen and seed morphology, the length and proximal orientation of fruiting pedicels, differences in the branching and orientation of trichomes on the lowers stems, and the number of flowers and cauline leaves on unbranched fertile stems.
Data from: Undocumented beetle diversity in the Southeastern United States: a case study of the minute clubbed beetles (Coleoptera: Monotomidae)
Studies of the saproxylic and predatory beetle family Monotomidae (Coleoptera: Cucujoidea) in the southeastern USA increased the known diversity for the family in the state of Georgia by one genus and nine species. Online records of Monotomidae from Georgia increased from 0 to 885. This work highlights the lack of basic diversity information about small beetles that inhabit wood, leaf litter, and other decaying plant matter in this region.
Data from: Toward a mechanistic understanding of human-induced rapid environmental change: a case study linking energy development, nest predation, and predators
1. Demographic consequences of human-induced rapid environmental change (HIREC) have been widely documented for many populations. The mechanisms underlying such patterns, however, are rarely investigated and yet are critical to understand for effective conservation and management. 2. We investigated the mechanisms underlying reduced avian nest survival with intensification of natural gas development, an increasing source of HIREC globally. We tested the hypothesis that energy development increased the local activity of important nest predator species thereby elevating nest predation rates. During 2011–2012, we surveyed predators and monitored 668 nests of Brewer's sparrows Spizella breweri, sagebrush sparrows Artemisiospiza nevadensis and sage thrashers Oreoscoptes montanus breeding at twelve sites spanning a gradient of habitat loss from energy development in western Wyoming, USA. 3. Nine species, representing four mammalian and three avian families, were video-recorded depredating eggs and nestlings. Important nest predator species differed across songbird species, despite similar nesting habitats. Approximately 75% of depredation events were by rodents. 4. Consistent with our predictions, detections of most rodent nest predators increased with surrounding habitat loss due to natural gas development, which was associated with increased probability of nest predation for our three focal bird species. 5. An altered nest predator assemblage was therefore at least partly responsible for elevated avian nest predation risk in areas with more surrounding energy development. 6. Synthesis and applications. We demonstrate one mechanism, i.e. the local augmentation of predators, by which human-induced rapid environmental change (HIREC) can influence the demography of local populations. Given the accelerating trajectory of global energy demands, an important next step will be to understand why the activity and/or abundance of rodent predators increased with surrounding habitat loss from energy development activities.
Data from: Ecological niche modeling for a cultivated plant species: a case study on taro (Colocasia esculenta) in Hawai'i
Under the threat of ongoing and projected climate change, communities in the Pacific Islands face challenges of adapting culture and lifestyle to accommodate a changing landscape. Few models can effectively predict how biocultural livelihoods might be impacted. Here, we examine how environmental and anthropogenic factors influence an ecological niche model (ENM) for the realized niche of cultivated taro (Colocasia esculenta) in Hawai'i. We created and tuned two sets of ENMs: one using only environmental variables, and one using both environmental and cultural characteristics of Hawa'i. These models were projected under two different Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathways (RCPs) for 2070. Models were selected and evaluated using average omission rate and area under the receiver operating characteristic curve (AUC). We compared optimal model predictions by comparing the percentage of taro plots predicted present and measured ENM overlap using Schoener's D-statistic. The model including only environmental variables consisted of 19 Worldclim bioclimatic variables, in addition to slope, altitude, distance to perennial streams, soil evaporation, and soil moisture. The optimal model with environmental variables plus anthropogenic features also included a road density variable (which we assumed as a proxy for urbanization) and a variable indicating agricultural lands of importance to the State of Hawai'i. The model including anthropogenic features performed better than the environment-only model based on omission rate, AUC, and review of spatial projections. The two models also differed in spatial projections for taro under anticipated future climate change. Our results demonstrate how ENMs including anthropogenic features can predict which areas might be best suited to plant cultivated species in the future, and how these areas could change under various climate projections. These predictions might inform biocultural conservation priorities and initiatives. In addition, we discuss the incongruences that arise when traditional ENM theory is applied to species whose distribution has been significantly impacted by human intervention, particularly at a local scale relevant to biocultural conservation initiatives.
Data from: Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity
The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM). We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with insufficient taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters). Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths.
Data from: Assessing reproductive behavior important to fisheries management: a case study with red drum, Sciaenops ocellatus
Spawning site selection and reproductive timing affect stock productivity and structure in marine fishes but are poorly understood. Traditionally, stock assessments measure reproductive potential as spawning stock biomass or egg production and do not include other aspects of reproductive behavior. Red drum make an excellent case study to assess these other aspects, as (1) they are highly fecund, pelagic spawners, like most exploited marine fishes; (2) their life cycle is delineated between nursery (estuarine) and adult (coastal and offshore) habitat; and (3) they are managed at these two spatial scales. This study was conducted from August 2012 to December 2013 and integrates data from multiple methods and spatial scales. Aerial surveys were used for large-scale monitoring of aggregations off two known estuarine nursery areas, Tampa Bay and Charlotte Harbor, Florida, USA. Capture-based sampling in Tampa Bay coastal (n = 2581) and estuarine waters (n = 158) was used to assess reproductive state and to confirm coastal spawning. To assess spatial dynamics, we acoustically tagged two population components in the Tampa Bay system, subadults from the estuary (n = 20) and adults from the coastal spawning site (n = 60). Behavioral plasticity was seen in subadult recruitment to coastal habitat, with some subadults maturing and recruiting before or during the spawning season and others (14 of 20 acoustically tagged fish) recruiting at the end of the 2012 spawning season. Both adults and recruited subadults (n = 29) were consequently detected in the Charlotte Harbor array, 132 km to the south. Spawning-site fidelity to the Tampa Bay spawning site occurred at both the population and individual scales. Aggregations consistently occurred in Tampa Bay coastal waters during the spawning season, and approximately two-thirds of tagged adults returned in the 2013 spawning season. A similar proportion of subadults returned to the Tampa Bay spawning site, exhibiting natal homing. However, these first-time spawners arrived later than repeat spawners and were detected over shorter time periods. This study, and others like it, demonstrates how integrating data from individuals tracked over space and time with more traditional population-based sampling is changing our understanding of ecological processes that affect marine fish productivity and our ability to manage for sustainablity.
Data from: Morphological vs. molecular delineation of taxa across montane regions in Europe: the case study of Gammarus balcanicus Schäferna, 1922 (Crustacea: Amphipoda)
Mountainous areas are characterized by substantial biodiversity and endemicity due to their complex geological history and habitat fragmentation. Hence, it can be assumed that particularly high species richness can be found in organisms with limited dispersal capabilities that inhabit mountain streams. A number of scientific papers focus on molecular phylogeography or traditional taxonomy of species or species groups inhabiting such habitats. However, there is a lack of studies that integrate morphological and molecular data to identify and delineate cryptic species. For practical reasons, uncovering cryptic diversity is crucial in taxa used in biomonitoring. Distinct species, hard to separate based on morphology only, may have different tolerance ranges towards a variety of factors. Thus, our goal is to combine the two approaches to reveal potential patterns of diversification within a species widely distributed across European mountains: the amphipod crustacean Gammarus balcanicus. The data were obtained from 13 populations spread across the range of the species. Individuals were initially ascribed to G. balcanicus based on conventional fauna key morpho-anatomical diagnostic features and were further analysed for 23 additional features to explore any putative diversification. Morphometric data were analysed with use of the multiple correspondence analysis and anova. Molecular distances were calculated for 551-bp-long COI sequences. Test for isolation by distance was performed for both morphological and molecular data. The morphometric studies showed that some of the analysed features differed significantly between populations, although there was only a weak correlation between the morphological divergence and the between-population geographical distances. Moreover, high morphological diversity was present within sites. A set of 42 COI haplotypes was identified among the 135 individuals sequenced. No haplotype was shared among populations. The molecular p-distances within the nine localities presenting more than one haplotype were either almost null (ca. <0.003 for 7 localities) or relatively low (ca. 0.01–0.02 for 2 localities). In opposite, the molecular p-distances between localities were mostly at a high level (94% of pairwise comparisons being >0.14), similar as between other well-defined species of the genus Gammarus. Surprisingly, G. balcanicus appears to be polyphyletic based on topology of the neighbour-joining tree. The level of genetic distance between localities was not correlated with their geographical proximity. Globally, combining spatial patterns of morphological versus molecular divergence indicates a high level of cryptic diversity within a species conventionally defined based upon fauna key morphological features. In this context, the name G. balcanicus should be applied only to the population from locus typicus, while the other populations represent a number of putative distinct species. We may expect that such phenomenon would apply also to other animal taxa with conserved morphology, which are widespread over different mountain ranges in Europe.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.