cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jm60b
title: Data from: Population structure and persistence of Pacific herring following the Great Tohoku earthquake

description: We evaluated the effect of the Great Tohoku earthquake, which occurred on
 March 11, 2011 in Japan, on the genetic diversity and population structure
 of Pacific herring (Clupea pallasii). Pacific herring (n = 4466) were
 collected between 2003 and 2014 through more than 20 sampling events
 during spawning periods at nine spawning sites throughout the Pacific
 herring distribution range in Japan. We measured them and genotyped 3784
 fish at five microsatellite loci. Following the tsunami, the sea-spawning
 population at the center of the affected area was almost extirpated and
 was replaced by a genetically distinct lagoon-spawning population from an
 adjacent brackish lake. However, the pattern of gene flow was stable for
 populations, with unique admixture proportions in local populations
 despite the high gene flow (FST = 0.0184). Our results indicate that
 Pacific herring in Japan spawn in a range of salinities and exchange genes
 between local populations regardless of the spawning ecotypes. We
 hypothesize that the combination of constant gene flow between local
 populations from straying of spawners and spawning fidelity creates weak
 but significantly differentiated stable population structure. This process
 can allow restoration of the genetic characteristics of damaged
 populations over many generations and can thereby promote the long-term
 viability of marine fishes that have high gene flow.
description: Japan_herring_genepopMicrosatellite genotypes for 20 samples (n=3,784) collected from nine major spawning sites in Japan during the spawnng season before and after the Great Tohoku earthquake
DOI: 10.5061/dryad.fn675
title: Data from: Patterns of gene flow in Encholirium horridum L.B.Sm., a monocarpic species of Bromeliaceae from Brazil

description: Encholirium horridum is a bromeliad that occurs exclusively on inselbergs
 in the Atlantic Forest biome of Brazil. These rock outcrops form natural
 islands that isolate populations from each other. We investigated gene
 flow by pollen through paternity analyses of a bromeliad population in an
 area of approximately 2 ha in Espírito Santo State, Brazil. To that end,
 seed rosettes and seedlings were genotyped using nuclear microsatellite
 loci. A plot was also established from the same population and specimens
 were genotyped to evaluate their fine-scale spatial genetic structure
 (SGS) through analyses of spatial autocorrelation and clonal growth.
 Paternity analysis indicated that 80% of the attributed progenitors of the
 genotyped seedlings were from inside the study area. The pollen dispersal
 distances within the area were restricted (mean distance of 45.5 m,
 varying from 3 to 156 m) and fine-scale SGS was weak (F ij = 0.0122, P
 &lt; 0.001; Sp = 0.009). Clonal growth was found to be a rare event,
 supporting the monocarpy of this species.
description: Genotypes of Encholirium
 horridum samples (SGS and paternity analyses)This file contains
 genotypes of Encholirium horridum samples used for SGS and paternity
 analyses (seed-rosettes + progenies).Genotypes of Encholirium
 horridum samples used for SGS and paternity
 analyses.xlsxFigure1S_Supp
 materialFigure 1 - Supplementary
 material. Geographical distributions of the maternal seed-rosettes in
 relation to the pollen donor seed-rosettes of Encholirium
 horridum.
DOI: 10.5061/dryad.59433
title: Data from: Centennial-long trends of lake browning show major effect of afforestation

description: Observations of increasing water color and organic carbon concentrations
 in lakes are widespread across the Northern Hemisphere. The drivers of
 these trends are debated. Declining atmospheric sulfur deposition has been
 put forward as an important underlying factor, since recovery from
 acidification enhances mobility of organic matter from surrounding soils.
 This would suggest that the current browning represents a return to a more
 natural state. This study explores historical lake data from Sweden—1935
 to 2015—providing a unique opportunity to see how and why water color has
 varied during almost a century. The data shows that sulfur deposition has
 not been the primary driver of water color trends over this period. I
 propose that the observed browning is to a large extent driven by a major
 transition from agriculture to forestry.
description: Sulfur deposition and
 sulfate concentrationEstimated total
 deposition of S for Lake Skärshultsjön, including wet, dry and sea salt,
 and estimated sulfate concentration in the same lake. Data modeled as in
 Moldan, F., B J. Cosby, and R. F. Wright. 2013. Modeling past and future
 acidification of Swedish Lakes. Ambio 42: 577-586.
 doi:10.1007/s13280-012-0360-8 and provided by Swedish Environment
 InstituteWater color between
 yearsWater color for 50 lakes
 in the years 1935, 1982 and 2015 given in mg Pt/L.Long-term water color in
 18 lakesLake names, years and
 water color in mg Pt/L for 18 lakes.Land-use and climate
 variablesSpruce coverage in
 percent, based on sediment pollen records from Lake Fiolen. The modeling
 of vegetation coverage is assumed to be representative for an area with a
 500-kilometer radius from the lake. 10-running means of growing degree
 days, i.e. number of days each year where average temperature was above
 5°C, in Jönköping. 10-year running means of discharge from Lake
 Allgunnen.
DOI: 10.5061/dryad.42sp54f
title: Data from: Males, but not females, perform strategic mate searching movements between host plants in a leaf beetle with scramble competition polygyny

description: 1. Mate searching is assumed to be performed mostly by males, but when
 females benefit from multiple mating or are under risk of failing to mate,
 they may also perform mate searching. This is especially important in
 scramble competition polygynies, in which mate searching is the main
 mechanism of mate competition. Typically, more mobile individuals are
 expected to achieve higher mating success because mobility increases their
 probability of finding mates. 2. If we assume individual movements are
 mainly explained by mate searching in scramble competition polygynies, we
 can investigate searching strategies by asking when individuals should
 leave their location and where they should go. We hypothesize that
 individuals will leave their locations when mating opportunities are
 scarce and will seek spatially close sites with better mating
 opportunities. 3. We tested these hypotheses for males and females of
 Leptinotarsa undecimlineata, a leaf beetle with scramble competition
 polygyny in which both sexes are promiscuous. Individuals mate and feed
 exclusively on Solanum plants, thus individual movements can be described
 as switches between plants. 4. Females were less likely than males to
 leave isolated plants, and both males and females moved preferentially to
 neighbouring plants. Males were more likely to leave when the local number
 of females was low, and the number of males was high. They moved to plants
 with more females, a behaviour consistent with a mate searching strategy.
 Females were more likely to move to plants with fewer males and many
 females, a behaviour consistent with male harassment avoidance. 5.
 Strategic movement is widely considered in foraging context, but seldom in
 a mate searching context. Considering that selection to minimize searching
 costs, maximize mating success, and minimize harassment may be ubiquitous
 in nature, we argue that strategic movements by mate searching individuals
 are likely to occur in many species.
description: All data from the
 manuscriptAll data files used in
 the analyses of the manuscript. See README for details.muniz_et_al_2018_leptinotarsa.zip
DOI: 10.5061/dryad.g2c8c
title: Data from: Label-free in situ imaging of oil body dynamics and chemistry in germination

description: Plant oleosomes are uniquely emulsified lipid reservoirs that serve as the
 primary energy source during seed germination. These oil bodies undergo
 significant changes regarding their size, composition and structure during
 normal seedling development; however, a detailed characterization of these
 oil body dynamics, which critically affect oil body extractability and
 nutritional value, has remained challenging because of a limited ability
 to monitor oil body location and composition during germination in situ.
 Here, we demonstrate via in situ, label-free imaging that oil bodies are
 highly dynamic intracellular organelles that are morphologically and
 biochemically remodelled extensively during germination. Label-free,
 coherent Raman microscopy (CRM) combined with bulk biochemical
 measurements revealed the temporal and spatial regulation of oil bodies in
 native soya bean cotyledons during the first eight days of germination.
 Oil bodies undergo a cycle of growth and shrinkage that is paralleled by
 lipid and protein compositional changes. Specifically, the total protein
 concentration associated with oil bodies increases in the first phase of
 germination and subsequently decreases. Lipids contained within the oil
 bodies change in saturation and chain length during germination. Our
 results show that CRM is a well-suited platform to monitor in situ lipid
 dynamics and local chemistry and that oil bodies are actively remodelled
 during germination. This underscores the dynamic role of lipid reservoirs
 in plant development.
description: FigureDataThis is the numerical data from the all graphs in the paper.
DOI: 10.5061/dryad.652vq
title: Data from: Life-history characteristics and landscape attributes as drivers of genetic variation, gene flow and fine-scale population structure in Northern Dolly Varden (Salvelinus malma malma) in Canada

description: The Northern Dolly Varden (Salvelinus malma malma) displays variable
 life-history types and occupies freshwater habitats with varying levels of
 connectivity. Here, we assayed microsatellite DNA variation in Northern
 Dolly Varden from the western Canadian Arctic to resolve landscape and
 life history variables driving variation in genetic diversity and
 population structure. Overall, genetic variation was highest in anadromous
 populations and lowest in those isolated above waterfalls with
 stream-resident forms intermediate between the two. Anadromous and
 isolated populations were genetically divergent from each other while no
 genetic differentiation was detectable between sympatric anadromous and
 stream-resident forms. Population structure was stable over 25 years,
 hierarchically organized and conformed to an isolation-by-distance
 pattern, but stream-isolated forms often deviated from these patterns.
 Gene flow occurred primarily among Yukon North Slope populations and
 between sympatric anadromous and resident forms. These results were
 sex-dependent to some extent, but were influenced more by reproductive
 status and life history. Our study provides novel insights into the life
 history, population demographic and habitat variables that shape the
 distribution of genetic variation and population structure in Arctic
 fluvial habitats while providing a spatial context for management and
 conservation.
description: Genepop
 FileThis file contains all
 microsatellite data for all samples/individuals. The year the samples were
 collected is included as well as the life history type (either freshwater
 resident (res) or freshwater isolated (iso) forms - note that no code is
 used for anadromous individuals which constitutes the majority of the
 samples).Genepop3D-All
 Samples
DOI: 10.5061/dryad.623
title: Data from: Incongruence of mitochondrial and nuclear gene trees in the carabid beetles Ohomopterus

description: We studied the molecular phylogeny of the carabid subgenus Ohomopterus
 (genus Carabus) using two mtDNA regions (16SrRNA and ND5) and three
 nuclear DNA regions (wingless, phosphoenolpyruvate carboxykinase, and an
 anonymous locus). We revisited the previously reported incongruence
 between the distribution of mtDNA markers and morphologically defined
 species (Su et al., 1996, J. Mol. Evol., 43:662-671) which they attributed
 to "type switching", a concerted change in many morphological
 characters that results in the repeated evolution of a particular
 morphological type. Our mtDNA gene tree obtained from 44 individuals
 representing all 15 currently recognized species of Ohomopterus revealed
 that haplotypes isolated from individuals of a single "species"
 were frequently separated into distant clades, confirming the previous
 report. The three nuclear markers generally conformed better with the
 morphologically defined species. The phylogenetic signal in mtDNA and
 nuclear DNA data differed strongly and these two partitions were
 significantly incongruent with each other according to Farris et
 al.'s (1994) ILD test, although the three nuclear partitions were not
 homogeneous either. Our results did not support the type switching
 hypothesis which was proposed to fit the morphological data to the
 mitochondrial gene tree: incongruence of the mtDNA tree with other nuclear
 markers indicates that the mtDNA-based tree does not reflect species
 history any better than the morphological data. Incongruence of gene trees
 in Ohomopterus may have been promoted by the complex processes of
 geographic isolation and hybridization in the Japanese Archipelago that
 led to occasional gene flow and recombination between separated entities.
 It is intriguing that reticulate patterns occurred in this group, as
 species of Ohomopterus exhibit extremely divergent genitalic structures
 that represent a highly efficient reproductive isolation mechanism.
description: Sota and Vogler Data
 SetSota_Vogler.nexus
DOI: 10.5061/dryad.2nh8c43
title: Data from: The genetic variance but not the genetic covariance of life-history traits changes towards the north in a time-constrained insect

description: Seasonal time constraints are usually stronger at higher than lower
 latitudes and can exert strong selection on life history traits and the
 correlations among these traits. To predict the response of life history
 traits to environmental change along a latitudinal gradient, information
 must be obtained about genetic variance in traits and also genetic
 correlation between traits, i.e., the genetic variance-covariance matrix,
 G. Here, we estimated G for key life history traits in an obligate
 univoltine damselfly that faces seasonal time constraints. We exposed
 populations to simulated native temperatures and photoperiods and common
 garden environmental conditions in a laboratory setup. Despite differences
 in genetic variance in these traits between populations (lower variance at
 northern latitudes), there was no evidence for latitude-specific
 covariance of the life history traits. At simulated native conditions, all
 populations showed strong genetic and phenotypic correlations between
 traits that shaped growth and development. The variance-covariance matrix
 changed considerably when populations were exposed to common garden
 conditions compared with the simulated natural conditions, showing the
 importance of environmentally induced changes in multivariate genetic
 structure. Our results highlight the importance of estimating
 variance-covariance matrixes in environments that mimic selection
 pressures and not only trait variances or mean trait values in common
 garden conditions for understanding the trait evolution across populations
 and environments.
description: Life history traits
 measurements of Lestes sponsaData on life history
 traits received during experiment with (1) simulated natural temperature
 and photoperiod conditions and (2) common garden
 conditions.Sniegula et
 al._JEB.xlsx
DOI: 10.5061/dryad.8835
title: Data from: Range-wide distribution of genetic diversity in the North American tree Juglans cinerea: a product of range shifts, not ecological marginality or recent population decline

description: The spatial distribution of genetic diversity is a product of recent and
 historical ecological processes, as well as anthropogenic activities. A
 current challenge in population and conservation genetics is to
 disentangle the relative effects of these processes, as a first step in
 predicting population response to future environmental change. In this
 investigation we compare the influence of contemporary population decline,
 contemporary ecological marginality, and postglacial range shifts. Using
 classical model comparison procedures and Bayesian methods, we have
 identified postglacial range shift as the clear determinant of genetic
 diversity, differentiation, and bottlenecks in 29 populations of
 butternut, Juglans cinerea L., a North American outcrossing forest tree.
 Although butternut has experienced dramatic 20th century decline due to an
 introduced fungal pathogen, our analysis indicates that recent population
 decline has had less genetic impact than postglacial recolonization
 history. Location within the range edge vs. the range core also failed to
 account for the observed patterns of diversity and differentiation. Our
 results suggest that the genetic impact of large-scale recent population
 losses in forest trees should be considered in the light of
 Pleistocene-era large-scale range shifts that may have had long-term
 genetic consequences. The data also suggest that the population dynamics
 and life history of wind-pollinated forest trees may provide a buffer
 against steep population declines of short duration, a result having
 important implications for habitat management efforts, ex-situ
 conservation sampling, and population viability analysis.
description: Hoban_J_cinerea_Mol_Ecol_2010_Microsat_Data_DryadThis file contains the microsatellite genotypes for 11 loci and 904 individuals, in 29 natural populations (forest) of butternut (J cinerea L) across eastern North America. These are the data referred to in the first sentence of the Results. They are data AFTER removal of hybrid individuals, identical genotypes, or individuals with too much missing data. These data are therefore the data used to calculate all statistics in the paper. The data are in GENEPOP format. The names of individuals are unique identification numbers used in our lab. The names of the loci correspond to those from Robichaud et al, and Hoban et al, as described in the Materials and Methods of the paper.
DOI: 10.5061/dryad.m3913
title: Data from: Population structure in Atlantic cod in the eastern North Sea-Skagerrak-Kattegat: early life stage dispersal and adult migration

description: Background: In marine fish species, where pelagic egg and larvae drift
 with ocean currents, population structure has been suggested to be
 maintained by larval retention due to hydrographic structuring and by
 homing of adult fish to natal areas. Whilst natal homing of adults has
 been demonstrated for anadromous and coral reef fishes, there are few
 documented examples of philopatric migration in temperate marine fish
 species. Results: Here, we demonstrate temporally stable genetic
 differentiation among spawning populations of Atlantic cod (Gadus morhua
 L.), and present genetic and behavioural evidence for larval drift and
 philopatric migration in the eastern North Sea-Skagerrak-Kattegat area. We
 show that juvenile cod collected in the eastern Skagerrak and central
 Kattegat are genetically similar to cod from offshore spawning areas in
 the eastern North Sea. Genetic assignment of individual 2–5 year old fish
 indicates that cod residing at, or migrating towards, spawning areas in
 Kattegat and the North Sea display philopatric behaviours. Conclusions:
 Together these findings suggest a loop between spawning, larval drift and
 adult return-migrations to spawning areas and underlines that both
 oceanographic processes and migratory behaviour in the adult phase may be
 important for stock separation and integrity in marine temperate fishes
 such as Atlantic cod.
description: Atlantic cod
 microsatellite genotype dataGenotype data for 8
 microsatellite loci in 15 Atlantic cod samplesAndre cod msat
 dryad.xlsx
DOI: 10.5061/dryad.d141n
title: Data from: Commonness, rarity and oligarchies of woody plants in the tropical dry forests of Mexico

description: We assessed woody plant communities in two widely separated forests in the
 tropical dry forest (TDF) biome of Mexico for evidence of similar patterns
 of species commonness and rarity. We used belt transects laid out along
 contour lines (i.e., constant elevation) and stratified across elevation
 gradients at sites in Jalisco and Oaxaca to sample woody plant species
 diversity, abundance, relative frequency and basal area. We assembled a
 combined species list and compared species found in both sites (shared) to
 species found in only one site, assessing whether the most and least
 common species at a site tended to be shared or unshared. Of the 8242
 individuals sampled, 370 species or morpho-species were identified, with
 222 species recorded at the Jalisco site and 270 at the Oaxaca site—122
 (33%) species were shared across sites. Abundance, frequency and basal
 area of shared species were greater on average than for unshared species,
 and were positively correlated across sites. A subset of 68 shared species
 (18%) accounted for over half of all individuals encountered at the two
 sites. Species in the most common quartile were more likely to be shared
 than expected by chance, while species in the least common quartile were
 less likely. A genus-level analysis found similar patterns. Our findings
 suggest that the TDF of Pacific coast Mexico shows evidence of widespread
 dominance by a small subset of species. These findings have potentially
 important implications for predicting species composition, understanding
 the role of oligarchic species in ecological processes, and conserving
 rare species.
description: Williams_etal-TDF_Supplementary_InformationMap of study site; species lists by site with importance measure values (density, frequency and basal area information); Kruskal-Wallis test results for significance between shared and unshared species by importance measure.