cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p563h62
title: Data from: Viability selection by invertebrate predators in the polyphenic scavenger fly Sepsis thoracica

description: Predation is a major factor influencing the fitness and life history of
 animals. Two key traits affecting prey survival are body size and
 coloration. Sepsis thoracica males display a sigmoid relationship between
 these two traits, defining a size threshold above which investment in
 melanin drastically drops, producing small melanic (black) or large amber
 morphs. In trying to understand the evolution of this rare dimorphism, we
 performed laboratory predation experiments to estimate the intensity of
 adult viability selection exerted by various arthropod predators (bugs,
 flies, spiders) on male body size and coloration. Selection was performed
 against two different backgrounds mimicking the natural habitat (dung and
 grass) in which the camouflage and/or warning effect of the morphs should
 vary. Body size was mainly under positive selection (larger survived
 better), which overpowered selection on coloration and varied somewhat
 among predator species but not backgrounds. No disruptive selection was
 found, nor did selection change the sigmoid relationship between the two
 traits. We conclude that, for this fly, predator evasion and escaping
 skills determined by body size are more effective against invertebrate
 predators than its conspicuousness determined by coloration, contrasting
 what has been found for vertebrate predators, where prey coloration is
 important and negative selection on size dominates. Because arthropod
 predators have strong effects on insect populations, the positive
 directional selection imposed by invertebrate predators is likely an
 important force driving the evolution of body size in S. thoracica and
 insects in general.
description: Predation experiment
 S.thoracica Data BehEcol00463Arthropod predation data
 as a function of size and coloration of the sexually selected forelegs of
 European populations of the dimorphic dung fly Sepsis
 thoracica
DOI: 10.5061/dryad.457fc
title: Data from: Polyamines in the life of Arabidopsis: profiling the expression of S-adenosylmethionine decarboxylase (SAMDC) gene family during its life cycle

description: Arabidopsis has 5 paralogs of the S-adenosylmethionine decarboxylase
 (SAMDC) gene. Neither their specific role in development nor the role of
 positive/purifying selection in genetic divergence of this gene family is
 known. While some data are available on the organ-specific expression of
 AtSAMDC1, AtSAMDC2, AtSAMDC3 and AtSAMDC4 at transcript level, not much is
 known about their promoters including AtSAMDC5 (another paralog), which is
 believed to be non-functional.
description: SAMDC
 3'UTRSAMDC
 3'UTRSAMDC
 3'UTRMegSAMDC 5'UTR
 Orthologues MEGSAMDC 5'UTR
 OrthologuesSAMDC
 5'UTRSAMDC
 5'UTRMegSAMDC3'UTRnwkSAMDC3'UTRorignwkSAMDC5'UTRnwkSAMDC5'UTRorignwkSAMDCpromoters align MEGSAMDCpromoters alignSAMDC1Vs3.rtf - CopySAMDC1Vs4.rtf - CopySAMDC2Vs4.rtf - CopySAMDC3Vs5genes.rtf - CopySAMDCgenes 1Vs2.rtf - CopySAMDC1Vs2GATASAMDC1Vs3SAMDC1Vs4SAMDC3Vs4SAMDCGATASAMDCGATAREF
DOI: 10.5061/dryad.7v67c
title: Data from: Macronutrient intake regulates sexual conflict in decorated crickets

description: Sexual conflict results in a diversity of sex-specific adaptations,
 including chemical additions to ejaculates. Male decorated crickets
 (Gryllodes sigillatus) produce a gelatinous nuptial gift (the
 spermatophylax) that varies in size and free amino acid composition, which
 influences a female's willingness to fully consume this gift.
 Complete consumption of this gift maximizes sperm transfer through
 increased retention of the sperm-containing ampulla, but hinders
 post-copulatory mate choice. Here, we examine the effects of protein (P)
 and carbohydrate (C) intake on the weight and amino acid composition of
 the spermatophylax that describes its gustatory appeal to the female, as
 well as the ability of this gift to regulate sexual conflict via ampulla
 attachment time. Nutrient intake had similar effects on the expression of
 these traits with each maximized at a high intake of nutrients with a P :
 C ratio of 1 : 1.3. Under dietary choice, males actively regulated their
 nutrient intake but this regulation did not coincide with the peak of the
 nutritional landscape for any trait. Our results therefore demonstrate
 that a balanced intake of nutrients is central to regulating sexual
 conflict in G. sigillatus, but males are constrained from reaching the
 optima needed to bias the outcome of this conflict in their favour.
description: Rapkin et
 al_JEB-2015-00624Standardized data from
 the no-choice experiment and raw data from the choice
 experiment
DOI: 10.5061/dryad.g2b10
title: Data from: Genetic structure and demographic history of the endangered tree species Dysoxylum malabaricum (Meliaceae) in Western Ghats, India: implications for conservation in a biodiversity hotspot

description: The impact of fragmentation by human activities on genetic diversity of
 forest trees is an important concern in forest conservation, especially in
 tropical forests. Dysoxylum malabaricum (white cedar) is an economically
 important tree species, endemic to the Western Ghats, India, one of the
 world's eight most important biodiversity hotspots. As D. malabaricum
 is under pressure of disturbance and fragmentation together with
 overharvesting, conservation efforts are required in this species. In this
 study, range-wide genetic structure of twelve D. malabaricum populations
 was evaluated to assess the impact of human activities on genetic
 diversity and infer the species’ evolutionary history, using both nuclear
 and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic
 diversity and population structure did not differ among seedling, juvenile
 and adult age classes, reproductive success among the old-growth trees and
 long distance seed dispersal by hornbills were suggested to contribute to
 maintain genetic diversity. The fixation index (FIS) was significantly
 correlated with latitude, with a higher level of inbreeding in the
 northern populations, possibly reflecting a more severe ecosystem
 disturbance in those populations. Both nuclear and cpSSRs revealed
 northern and southern genetic groups with some discordance of their
 distributions; however, they did not correlate with any of the two
 geographic gaps known as genetic barriers to animals. Approximate Bayesian
 computation-based inference from nuclear SSRs suggested that population
 divergence occurred before the last glacial maximum. Finally we discussed
 the implications of these results, in particular the presence of a clear
 pattern of historical genetic subdivision, on conservation policies.
description: Genotype
 dataAllele sizes at each
 locus for all sampled individuals. Genepop format.DMgenepopALLrepcr.txtDIYABC input fileDIYABC4pops_nSSR.txt
DOI: 10.5061/dryad.d6q87
title: Data from: Intraspecific genetic structure, divergence and high rates of clonality in an amphi-Atlantic starfish

description: Intraspecific genetic diversity and divergence have a large influence on
 the adaption and evolutionary potential of species. The widely distributed
 starfish, Coscinasterias tenuispina, combines sexual reproduction with
 asexual reproduction via fission. Here we analyse the phylogeography of
 this starfish to reveal historical and contemporary processes driving its
 intraspecific genetic divergence. We further consider whether asexual
 reproduction is the most important method of propagation throughout the
 distribution range of this species. Our study included 326 individuals
 from 16 populations, covering most of the species’ distribution range. A
 total of 12 nuclear microsatellite loci and sequences of the mitochondrial
 cytochrome c oxidase subunit I (COI) gene were analysed. COI and
 microsatellites were clustered in two isolated lineages: one found along
 the south-western Atlantic and the other along the north-eastern Atlantic
 and Mediterranean Sea. This suggests the existence of two different
 evolutionary units. Marine barriers along the European coast would be
 responsible for population clustering: the Almeria-Oran Front that limits
 the entrance of migrants from the Atlantic to the Mediterranean, and the
 Siculo Tunisian strait that divides the two Mediterranean basins. The
 presence of identical genotypes was detected in all populations, although
 two monoclonal populations where found in two sites where annual mean
 temperatures and minimum values were the lowest. Our results based on
 microsatellite loci showed that intra-population genetic diversity was
 significantly affected by clonality whereas it had lower effect for the
 global phylogeography of the species, although still some impact on
 populations’ genetic divergence could be observed between some
 populations.
description: Genotypes and sequences
 of sampled individualsMicrosatellite genotypes
 in an excel sheet and all sequences obtained in fasta
 format.Sequences and genotypes
 coscinasterias tenuispina.zip
DOI: 10.5061/dryad.17889
title: Data from: Loss of color pigmentation is maintained at high frequency in a monkey flower population

description: Color polymorphisms have long been of evolutionary interest for their
 diverse roles, including mate choice, predator avoidance, and pollinator
 attraction. While color variation is often under strong selection, some
 taxa demonstrate unexpectedly high frequencies of presumed deleterious
 color forms. Here we show that a genetic variant underlying complete loss
 of anthocyanin pigmentation has risen to an unexpectedly high frequency of
 &gt;0.2 in a natural population of the plant Mimulus guttatus.
 Decreased expression of MYB5 transcription factor is associated with
 unpigmented morphs. While the allele was found only in heterozygote adults
 in the wild, suggesting negative selection, experiments were unable to
 demonstrate a fitness cost for unpigmented plants, suggesting a cryptic
 selection pressure in the wild. However, life-history differences among
 morphs suggests that unpigmented individuals benefit from later flowering
 and clonal growth. Overall, our study highlights the complex interplay of
 factors maintaining variation in nature, even for genes of major effect.
description: Performance of pigmented
 and anthocyanin-deficient Mimulus guttatus plants in a common
 gardenMeasures of vigour and
 seed set made in an experimental common garden site in
 Syracuse.Twyford et al Dryad1 Field
 measurements.xlsxPerformance of pigmented
 and anthocyanin-deficient Mimulus guttatus plants in a drought
 experimentTwyford et al Dryad2 Drought
 measurements.xlsxPerformance of pigmented
 and anthocyanin-deficient Mimulus guttatus plants in UV-controlled growth
 chambersTwyford et al Dryad3
 UV.xlsx
DOI: 10.5061/dryad.cp942
title: Data from: A high-resolution panorama camera system for monitoring colony-wide seabird nesting behaviour

description: 1. Obtaining accurate and representative demographic metrics for animal
 populations is critical to many aspects of wildlife monitoring and
 management. However, at remote animal colonies, metrics derived from
 sequential counts or other continuous monitoring are often subject to
 logistical, weather and disturbance challenges.The development of remote
 camera technologies has assisted monitoring, but limitations in spatial
 and temporal resolution and sample sizes remain. 2. Here we describe the
 application of a robotic camera system (Gigapan) which takes a tiled
 sequence of photographs that are automatically stitched together to form
 high-resolution panoramas. We demonstrate the application of the Gigapan
 using data collected during field-testing at a shy albatross colony on
 Albatross Island in northwest Tasmania. 3. We took daily panoramas over
 five days to estimate mean incubation shift-duration, an indirect measure
 for foraging trip duration, in an existing study area. Similar numbers of
 occupied nests could be observed at a distance of ~100m in the Gigapan
 panoramas compared to ground-based counts (115 and 117 respectively). Of
 these, birds on 90% of nests visible in the panoramas could be
 unambiguously identified as marked or unmarked with a small daub of paint
 throughout the study period and thus a shift change reliably recorded.
 Gigapan-based shift duration was estimated using a novel instantaneous
 statistical method and were longer than estimates earlier in the egg
 brooding period, potentially revealing a new pattern in shift duration. 4.
 This example field application provides proof-of-concept and demonstration
 that the relatively low cost Gigapan system provides the spatial
 advantages of satellite or aerial photos with the detail and temporal
 replication of land-based camera systems. The Gigapan system can extend or
 enhance traditional data collection methods, particularly for simultaneous
 observations, at distance, of the behaviour of many surface nesting
 colonial seabirds..
description: Lynch et al
 dataAll data used in Lynch
 et al is provided as an excel file. Sheets include metadata for the
 Gigapan images which include links to the images, all data extracted from
 those images for incubation shift change over between pairs and estimates
 of ambiguity of these observations for each day at each nest, ground
 counts and condensed Gigapan data used for Figure 3 in the
 paper.
DOI: 10.5061/dryad.801r9q8
title: Data from: Effects of removing woody cover on long‐term population dynamics of a rare annual plant (Agalinis auriculata): a study comparing remnant prairie and oldfield habitats

description: 1. Worldwide, grasslands are becoming shrublands/forests. In North
 America, eastern red cedar (Juniperus virginiana) often colonizes
 prairies. Habitat management can focus on woody removal, but we often lack
 long-term data on whether removal leads to population recovery of
 herbaceous plants without seeding. 2. We undertook a long-term study (17
 years) of numbers of the rare annual plant Agalinis auriculata in a
 gridwork of 100 m2 plots in adjacent prairie and oldfield sites in Kansas,
 USA. We collected data before and after removal of Juniperus virginiana at
 the prairie. 3. Plant population sizes were highly variable at both sites
 and over time. High numbers of plants in a plot one year were often
 followed by low numbers the following year, suggesting negative
 density-dependence. Plant numbers were lowest with extensive woody cover
 and with low precipitation. After woody plant removal, A. auriculata
 increased dramatically in abundance and occupancy in most years; increases
 were also seen at the oldfield, suggesting later survey years were overall
 more favorable. 4. Synthesis and applications: Removal of woody plants led
 to increased numbers of a rare annual prairie plant, without seeding.
 Multiple years of data were essential for interpretation given extreme
 temporal variability in numbers. The largest prairie population was seven
 years following tree removal, showing that positive effects of management
 can last this long. This species also fared well in oldfield habitat,
 suggesting restoration opportunities. Given that land managers are busy,
 time-efficient field methods and data analysis approaches such as ours
 offer advantages. In addition to general linear models, we suggest Rank
 Occupancy Abundance Profiles (ROAPs), a simple-to-use data visualization
 and analysis method. Creation of ROAPs for sites before and after habitat
 management helps reveal the degree to which plant populations are
 responding to management with changes in local density, changes in
 occupancy, or both.
description: Average_plant_data_setAverage number of plants in 10 m x 10 m cells in prairie and oldfield habitat over time (see README for details).Prairie_local_data_setData on individual 10 m x 10 m plots in prairie (see README for details)Oldfield_local_data_setData on individual 10 m x 10 m plots in the oldfield (see README for details)ROAPSData organized for Rank occupancy-abundance profiles (see README for details).
DOI: 10.5061/dryad.hf068m7
title: Data from: Seascape genetics of the spiny lobster Panulirus homarus in the Western Indian Ocean: understanding how oceanographic features shape the genetic structure of species with high larval dispersal potential

description: This study examines the fine-scale population genetic structure and
 phylogeography of the spiny lobster Panulirus homarus in the Western
 Indian Ocean. A seascape genetics approach was used to relate the observed
 genetic structure based on 21 microsatellite loci to ocean circulation
 patterns, and to determine the influence of latitude, sea surface
 temperature (SST) and ocean turbidity (KD490) on population-level
 processes. At a geospatial level, the genetic clusters recovered
 corresponded to three putative subspecies, P. h. rubellus from the SW
 Indian Ocean, P. h. megasculptus from the NW Indian Ocean, and P. h.
 homarus from the tropical region in-between. Virtual passive Lagrangian
 particles advected using satellite-derived ocean surface currents were
 used to simulate larval dispersal. In the SW Indian Ocean, the dispersion
 of particles tracked over a 4-month period provided insight into a steep
 genetic gradient observed at the Delagoa Bight, which separates P. h.
 rubellus and P. h. homarus. South of the contact zone, particles were
 advected south-westwards by prevailing boundary currents, or were retained
 in nearshore eddies close to release locations. Some particles released in
 southeast Madagascar dispersed across the Mozambique Channel, and reached
 the African shelf. Dispersal was characterized by high seasonal and
 inter-annual variability, and a large proportion of particles were
 dispersed far offshore and presumably lost. In the NW Indian Ocean,
 particles were retained within the Arabian Sea. Larval retention and
 self-recruitment in the Arabian Sea could explain the recent genetic
 divergence between P. h. megasculptus and P. h. homarus. Geography and
 minimum SST were significantly associated with genetic differentiation in
 multivariate analysis, suggesting that larval tolerance to SST plays a
 role in shaping the population structure of P. homarus.
description: Panulirus_homarus_genotypesThis excel file contains genotypic data and geographic information for Panulirus homarus. It is in GenALex format.Panulirus_homarus.xlsxGeneland_codeThis file contains an R script for running Geneland analysis.
DOI: 10.5061/dryad.vk820
title: Data from: An interspecific comparison between morphology and swimming performance in cyprinids

description: Flow regimes are believed to be of major evolutionary significance in
 fish. The flow regimes inhabited by cyprinids vary extensively from still
 flow regimes to riptide flow regimes. To test (1) whether flow-driven
 swimming performance and relevant morphological differentiation are
 present among fish species and (2) whether evolutionary shifts between
 high-flow and low-flow habitats in cyprinids are associated with
 evolutionary tradeoffs in locomotor performance, we obtained data on both
 steady and unsteady swimming performance and external body shape for 19
 species of cyprinids that typically occur different flow regimes (still,
 intermediate and riptide). We also measured the routine energy expenditure
 (RMR) and maximum metabolic rate (MMR) and calculated the optimal swimming
 speed. Our results showed that fish species from riptide groups tend to
 have a higher critical swimming speed (Ucrit), maximum linear velocity
 (Vmax) and fineness ratio (FR) than fish from the other two groups.
 However, there was no correlation between the reconstructed changes in the
 steady and unsteady swimming performance of the 19 species. According to
 the phylogenetically independent contrast (PIC) method, the Ucrit was
 actively correlated with the MMR. These results indicated that selection
 will favour both higher steady and unsteady swimming performance and a
 more streamlined body shape in environments with high water velocities.
 The results suggested that steady swimming performance was more sensitive
 to the flow regime and that for this reason, changes in body shape
 resulted more from selective pressure on steady swimming performance than
 on unsteady swimming performance. No evolutionary tradeoff was observed
 between steady and unsteady swimming performance, although Ucrit and MMR
 were found to have coevolved. However, a further analysis within each
 typically occur habitat group suggested that the tradeoff that may exist
 between steady and unsteady swimming performance may be concealed by the
 effect of habitat.
description: dataData on the unsteady
 swimming performance, The steady swimming performance and metabolic
 parameters, and the morphology of 19 fish species.
DOI: 10.5061/dryad.08pv2
title: Data from: Evaluation of potential overwinter mortality of age-0 walleye and appropriate age-1 sampling gear

description: Potential recruitment of age-0 Walleye Sander vitreus to adults is often
 indexed by the relative abundance of age-0 individuals during their first
 summer or fall. However, relationships between age-0 and adult Walleye
 abundance are often weak or nonsignificant in many waters. Overwinter
 mortality during the first year of life has been hypothesized as an
 important limitation to Walleye recruitment in lakes, but limited evidence
 of such mortality exists, likely due to difficulties in sampling age-1
 Walleye during spring. The objectives of this study were to: 1) compare
 results from nighttime electrofishing to index relative abundance of age-1
 Walleyes with relative abundance indices of minifyke nets in four eastern
 South Dakota lakes; 2) determine whether size-selective mortality was
 occurring in those four lakes; and 3) if size-selective mortality was
 occurring in these lakes, determine whether that mortality was attributed
 to body condition. We sampled four natural lakes in eastern South Dakota 2
 wk after ice-off in 2013 and 2014. Precision of nighttime electrofishing
 (coefficient of variation = 216.6) was greater than that estimated for
 minifyke nets (coefficient of variation = 338.5) across both years. We
 detected no differences in length-frequency distributions of collected
 spring age-1 Walleye between the two gears. Age-0 fall relative abundance
 indices from electrofishing were significantly greater (P &lt; 0.01)
 than spring age-1 nighttime electrofishing indices of relative abundance
 at three of the four study lakes, indicating that overwinter mortality may
 occur at a substantial rate during the first year of life for Walleye in
 these systems. Quantile–quantile regression plots showed evidence of
 size-selective mortality in three of four lakes sampled. However, body
 condition of age-0 Walleye appeared to have little to no influence on
 overwinter mortality. Instead, we suggest that smaller-sized walleye may
 be more vulnerable to overwinter predation. Collectively, these results
 provide evidence of previously hypothesized overwinter mortality within
 the first year for Walleye and indicate possibilities for indexing
 potential adult recruitment of Walleye just after this critical period.
description: Data
 S1Catch data for age-1
 Walleye Sander vitreus sampled by nighttime electrofishing and mini-fyke
 nets in spring 2013 (South Buffalo Lake) and 2014 (Lake Kampeska, Lake
 Madison, and Roy Lake).Grote et al WAE electro and
 fyke catch.xlsxData
 S2Total length (mm) and
 total weight (g) of fall age-0 and corresponding spring age-1 Walleye
 Sander vitreus collected from South Buffalo Lake (2012 and 2013) and Lake
 Kampeska, Lake Madison, and Roy Lake (2013 and 2014).Grote et al Inc Growth
 Data.xlsx