cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3dv00
title: Data from: Genetic relationships, structure and parentage simulation among the olive tree (Olea europaea L. subsp. europaea) cultivated in Southern Italy revealed by SSR markers

description: In this work, we assess both the morphological and genetic diversity of 68
 important olive cultivars from three Southern Italian regions: Calabria,
 Campania and Sicily. Twenty-five phenotypic traits were evaluated and 12
 simple sequence repeat (SSR) markers were analysed. All SSR primers were
 polymorphic and reliable. The total number of alleles per locus varied
 from 5 to 19 with an average number of 13.1 and a mean polymorphic
 information content (PIC) of 0.81. These results suggested high genetic
 diversity within these three olive germplasm collections. Morphological
 traits also showed significant variability amongst cultivars. Two cases of
 identity were found and ten statistically significant cases of putative
 parent/sibling were discovered by performing a SSR-based parentage
 simulation analysis with CERVUS. The Mantel test indicated low but
 significant correlations between the morphological data and SSR allelic
 frequency, origin and SSR allelic frequency, and origin and morphology.
 Structure software allowed inference of relationships between the three
 olive germplasm collections and allowed us to obtain the most consistent
 grouping and to identify putative admixed or exchanged cultivars. Cluster
 and multivariate analysis, based on morphological traits, revealed
 geographic grouping in agreement with UPGMA dendrogram and structure
 analysis using SSRs. Sicilian cultivars showed a more homogenous genetic
 makeup, probably due to geographical isolation, whilst Calabrian and
 Campanian cultivars seemed to have a less distinct genetic structure, with
 a greater degree of intermixing. A correlation between the presence of
 certain SSR alleles and fruit size was also found.
description: SSR allelic profiles of
 the 68 olive cultivars from southern Italy analyzed at 12 SSR
 lociTab3_SSR_submitted_to_dryad.txtThirty quantitative and qualitative morphological traits analysed in 68 olive cultivars from southern ItalyMorfologici_def04_12_12.txt
DOI: 10.5061/dryad.m85n7
title: Data from: Importance of the coronary circulation for cardiac and metabolic performance in rainbow trout (Oncorhynchus mykiss)

description: Cardiac oxygenation is achieved via both coronary arterial and luminal
 venous oxygen supply routes in many fish species. However, the relative
 importance of these supplies for cardiac and aerobic metabolic performance
 is not fully understood. Here, we investigated how coronary artery
 ligation in rainbow trout (Oncorhynchus mykiss), implanted with heart rate
 loggers, affected cardiorespiratory performance in vivo. While coronary
 ligation significantly elevated resting heart rate, the standard metabolic
 rate was unchanged compared to sham treated controls. However, coronary
 ligation reduced the maximum metabolic rate while heart rate remained
 unchanged following enforced exercise. Thus, coronary ligation reduced
 metabolic and heart rate scopes by 29 and 74%, respectively. Our findings
 highlight the importance of coronary oxygen supply for overall
 cardiorespiratory performance in salmonid fish, and suggest that
 pathological conditions that impair coronary flow (e.g., coronary
 arteriosclerosis) constrain the ability of fish to cope with metabolically
 demanding challenges such as spawning migrations and environmental
 warming.
description: Supporting data, Ekstrom
 et al.File containing the data
 for the submitted manuscript "Importance of the coronary circulation
 on cardiac and metabolic performance in rainbow trout (Oncorhynchus
 mykiss)"
DOI: 10.6084/m9.figshare.31156900
title: Supplementary File

description: Ecosystem modelling is becoming increasingly important, as it reveals how energy flows and species interactions shape ecosystem stability, resilience, and the sustainability of fisheries. However, model-based ecosystem studies are scarce for the Kaptai Lake (KL) of Bangladesh. Therefore, a mass-balanced trophic model was built to illustrate the trophic structure and ecosystem features of KL. The model outputs indicated that the apex predator, Catfish (TL-3.364), occupied the top trophic niches, while the overabundant (B: 3.264 t/km²) Clupeid (TL-2.56) dominated the lower trophic level in the food web. The higher values of ecotrophic efficiency (&gt;0.5) for most of the groups indicate heavy fishing pressure. The ecosystem is Phytoplankton-based, where two core food chains that make up the majority of the food web are the Detritus (35.12%) and primary production (64.88%). The mixed trophic impact plot revealed a substantial positive effect of Detritus and Phytoplankton on majority of the fish groups. Clupeids displayed negative effect on most of the fish groups, indicating a lack of major predators of this group. In the KL ecosystem, Catfish and Phytoplankton were the key predator and producer groups respectively. The network analysis indicates that the KL is a developing ecosystem with moderate system maturity, as evidenced by total primary production and respiration ratio (2.034), total primary production and biomass ratio (71.764), and Finn Cycling Index (5.627%). The low connectance index (0.426) indicates that the food web is still linear rather than a web-like structure and thereby vulnerable to external influences. Besides, the ever-increasing trend of Clupeid and declination of large fish populations indicates that the KL ecosystem may encounter severe consequences in the future. Consequently, ecosystem-based management interventions have been proposed that will help to restore food web integrity, recover vulnerable species and ensure long-term sustainability of fisheries in this lake.
DOI: 10.6084/m9.figshare.31156900.v1
title: Supplementary File

description: Ecosystem modelling is becoming increasingly important, as it reveals how energy flows and species interactions shape ecosystem stability, resilience, and the sustainability of fisheries. However, model-based ecosystem studies are scarce for the Kaptai Lake (KL) of Bangladesh. Therefore, a mass-balanced trophic model was built to illustrate the trophic structure and ecosystem features of KL. The model outputs indicated that the apex predator, Catfish (TL-3.364), occupied the top trophic niches, while the overabundant (B: 3.264 t/km²) Clupeid (TL-2.56) dominated the lower trophic level in the food web. The higher values of ecotrophic efficiency (&gt;0.5) for most of the groups indicate heavy fishing pressure. The ecosystem is Phytoplankton-based, where two core food chains that make up the majority of the food web are the Detritus (35.12%) and primary production (64.88%). The mixed trophic impact plot revealed a substantial positive effect of Detritus and Phytoplankton on majority of the fish groups. Clupeids displayed negative effect on most of the fish groups, indicating a lack of major predators of this group. In the KL ecosystem, Catfish and Phytoplankton were the key predator and producer groups respectively. The network analysis indicates that the KL is a developing ecosystem with moderate system maturity, as evidenced by total primary production and respiration ratio (2.034), total primary production and biomass ratio (71.764), and Finn Cycling Index (5.627%). The low connectance index (0.426) indicates that the food web is still linear rather than a web-like structure and thereby vulnerable to external influences. Besides, the ever-increasing trend of Clupeid and declination of large fish populations indicates that the KL ecosystem may encounter severe consequences in the future. Consequently, ecosystem-based management interventions have been proposed that will help to restore food web integrity, recover vulnerable species and ensure long-term sustainability of fisheries in this lake.
DOI: 10.5061/dryad.mm3kr
title: Data from: Egg discrimination along a gradient of natural variation in eggshell coloration

description: Accurate recognition of salient cues is critical for adaptive responses,
 but the underlying sensory and cognitive processes are often poorly
 understood. For example, hosts of avian brood parasites have long been
 assumed to reject foreign eggs from their nests based on the total degree
 of dissimilarity in colour to their own eggs, regardless of the foreign
 eggs' colours. We tested hosts' responses to gradients of
 natural (blue-green to brown) and artificial (green to purple) egg
 colours, and demonstrate that hosts base rejection decisions on both the
 direction and degree of colour dissimilarity along the natural, but not
 artificial, gradient of egg colours. Hosts rejected brown eggs and
 accepted blue-green eggs along the natural egg colour gradient,
 irrespective of the total perceived dissimilarity from their own
 egg's colour. By contrast, their responses did not vary along the
 artificial colour gradient. Our results demonstrate that egg recognition
 is specifically tuned to the natural gradient of avian eggshell colour and
 suggest a novel decision rule. These results highlight the importance of
 considering sensory reception and decision rules when studying perception,
 and illustrate that our understanding of recognition processes benefits
 from examining natural variation in phenotypes.
description: Associated
 dataThese are the field and
 colour data used in "Egg discrimination along a gradient of natural
 variation in eggshell coloration." Data were processed in R. For
 further details see Materials and Methods.Hanley et al_Egg discrimination
 along a gradient of natural variation in eggshell
 coloration_Data.csv
DOI: 10.5061/dryad.dg41r
title: Data from: Matching habitat choice in nomadic crossbills appears most pronounced when food is most limiting

description: Of the various forms of non-random dispersal, matching habitat choice,
 whereby individuals preferentially reside in habitats where they are best
 adapted, has relatively little empirical support. Here I use
 mark-recapture data to test for matching habitat choice in two nomadic
 ecotypes of North American Red Crossbills (Loxia curvirostra complex) that
 occur in the lodgepole pine (Pinus contorta) forests in the South Hills,
 Idaho every summer. Crossbills are adapted for foraging on seeds in
 conifer cones, and in the South Hills the cones are distinctive, favoring
 a relatively large bill. During a period when seed was most limiting, only
 the largest individuals approximating the average size of the locally
 adapted ecotype remained for a year or more. During a period when seed was
 less limiting, proportionately more individuals remained and the trend for
 larger individuals to remain was weaker. Although matching habitat choice
 is difficult to demonstrate, it likely contributed to the observed
 patterns. Otherwise, nearly unprecedented intensities of natural selection
 would be needed. Given the nomadic behavior of most crossbill ecotypes and
 the heterogeneous nature of conifer seed crops, matching habitat choice
 should be favored and likely contributes to their adaptation to
 alternative conifers and rapid diversification.
description: Capture data for
 ecotypes 2 and 5 in South HillsThese are the capture
 data for the individuals of Red Crossbill (Loxia curvirostra) ecotypes 2
 and 5, including the mean bill depth (mm) of each individual used in the
 analyses. The initial capture date is provided, and birds included in the
 analyses were only birds that were initially captured between 2009 and
 2014. Nearly all captures were made at the site described in the paper -
 at the base of a cabin in the South Hills (Sawtooth National Forest),
 Idaho.
DOI: 10.5061/dryad.kv011
title: Data from: Exogenous kisspeptin enhances seasonal reproductive function in male Siberian hamsters

description: Animals living in temperate climates are faced with the challenge of
 reproducing only when environmental conditions are suitable for offspring
 survival. Environmental cues signalling current and future energy
 availability (e.g., food availability and photoperiod respectively) are
 used to appropriately time reproduction. The precise neuroendocrine
 mechanisms regulating reproduction in response to these cues are unknown.
 The goal of the present study was to investigate a functional role for
 kisspeptin, a neuropeptide that shows promise as a key regulator of
 seasonal reproduction, in integrating multiple environmental cues to
 regulate reproduction in the Siberian hamster (Phodopus sungorus).
 Siberian hamsters undergo robust gonadal regression and terminate
 reproduction in unsuitable environments [short winter-like day lengths
 (photoperiods), low food availability]. Adult male hamsters were housed in
 short-day or intermediate photoperiods, received either ad-libitum access
 to food or mild food restriction, and were treated with either kisspeptin
 or a vehicle for 6 weeks to determine the ability of kisspeptin to
 attenuate gonadal regression. Hamsters exhibited varying degrees of
 gonadal regression in response to inhibitory environments (short-day
 photoperiod, food restriction). Kisspeptin treatment successfully enhanced
 testis mass under these inhibitory conditions, but did not affect normal
 seasonal changes in body mass and food intake. Thus, kisspeptin
 specifically enhanced reproductive function without altering other,
 non-reproductive physiological responses to these environmental
 treatments. The inhibitory environmental conditions used in this study
 caused little if any decline in serum luteinizing hormone (LH) and
 testosterone over the course of the experiment. Kisspeptin treatment
 tended to exacerbate the decline in LH within individuals, but there were
 no significant effects of kisspeptin when comparing changes in the hormone
 levels amongst groups. The interesting outcome that kisspeptin enhanced
 testis mass, apparently independently of hypothalamic endocrine
 mechanisms, suggests the possibility of local kisspeptin action within the
 gonads. Overall, we show a functional role for kisspeptin in integrating
 complex environmental information to specifically support reproduction.
 Future work should focus on direct effects of kisspeptin at the gonadal
 level of the HPG axis as well as its interactions with the metabolic
 functions and other hormones involved in reproduction, e.g.,
 gonadotropin-inhibitory hormone (GnIH).
description: Exogenous kisspeptin
 enhances seasonal reproductive function in male Siberian
 hamstersContains all raw data
 used in the Functional Ecology article "Exogenous kisspeptin enhances
 seasonal reproductive function in male Siberian hamsters (Phodopus
 sungorus)" by Allison Bailey, Sandra Legan, and Gregory Demas,
 including hamster body mass, food intake, estimated testis volume, final
 reproductive mass, and serum hormone concentrations.
DOI: 10.5061/dryad.5h746tt
title: Data from: The mouth morphology of diving beetle Hyphydrus japonicus (Dytiscidae: Hydroporinae) is specialized for predation on seed shrimps

description: Two-shelled organisms, such as bivalves and seed shrimps, protect
 themselves from external stresses by firmly closing both shells. We found
 that the diving beetle Hyphydrus japonicus Sharp, 1873 (Dytiscidae:
 Hydroporinae) larvae frequently prey on seed shrimps. Other predatory
 aquatic insects have difficulty in capturing seed shrimps owing to the
 general form of their mandibles. Larvae of H. japonicus bear a projection
 on the head (the nasale), which is used in conjunction with vertical
 movements of the mandibles to fixate the valves of their prey and gain
 access to the soft body within them. This capture method does not destroy
 shells and is extremely efficient. The present study provides the first
 report on the use of a unique morphological trait for attacking prey
 animals without destroying their shells.
description: rawdata_Hayashi_and_Ohba
DOI: 10.15468/dl.rayqkb
title: Occurrence Download

description: A dataset containing 4638 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Monotropa uniflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 4638 records from 255 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001378-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f3r1kq3
title: Data from: Heterogeneity in local density allows a positive evolutionary relationship between self-fertilisation and dispersal

description: Despite empirical evidence for a positive relationship between dispersal
 and self-fertilisation (selfing), theoretical work predicts that these
 traits should always be negatively correlated, and the Good Coloniser
 Syndrome of high dispersal and selfing (Cf. Baker’s Law) should not
 evolve. Critically, previous work assumes that adult density is
 spatiotemporally homogeneous, so selfing results in identical offspring
 production for all patches, eliminating the benefit of dispersal for
 escaping from local resource competition. We investigate the joint
 evolution of dispersal and selfing in a demographically structured
 metapopulation model where local density is spatiotemporally heterogeneous
 due to extinction-recolonisation dynamics. Selfing alleviates outcrossing
 failure due to low local density (an Allee Effect) while dispersal
 alleviates competition through dispersal of propagules from high- to
 low-density patches. Because local density is spatiotemporally
 heterogenous in our model, selfing does not eliminate heterogeneity in
 competition, so dispersal remains beneficial even under full selfing.
 Hence the Good Coloniser Syndrome is evolutionarily stable under a broad
 range of conditions, and both negative and positive relationships between
 dispersal and selfing are possible, depending on the environment. Our
 model thus accommodates positive empirical relationships between dispersal
 and selfing not predicted by previous theoretical work and provides
 additional explanations for negative relationships.
description: code_publishedThis Matlab file contains code to simulate the model (producing evolutionary trajectories as in Figs. 1, 2, S1) and the 2-parameter sensitivity analysis (as in Figs. 3, S2). As an example panel A of Figure 3 is shown
DOI: 10.5061/dryad.2h914
title: Data from: Active background choice facilitates crypsis in a tropical crab

description: Animals can evade predators in multiple ways, one of the most effective of
 which is to avoid detection in the first place. We know much about the
 evolution of color patterns that match the visual background to avoid
 detection (i.e., crypsis), yet we know surprisingly less about the
 specific behaviors that have co-evolved with these morphological traits to
 enhance or maintain crypsis. We here explore whether the match between
 body color and background in a seemingly well-camouflaged tropical shore
 crab is a result of active background choice. Taking advantage of a
 coastal area in the Solomon Islands with variable sand color and a
 population of the pallid ghost crab Ocypode pallidula with varying
 carapace color, we experimentally tested whether individuals actively
 choose specific substrate that best matches their color patterns. We found
 that individuals taken from extreme sand colors chose substrate that
 maintained crypsis, with relatively darker crabs typically choosing dark
 sand and lighter crabs choosing light sand. Crabs of intermediate color
 pattern, in contrast, showed no clear preference for dark or light sand.
 Our results suggest that potential prey can actively choose specific
 backgrounds to enhance and maintain crypsis, providing insights into how
 behavior interacts with morphological traits to avoid predator detection.
description: Behavioral substrate
 choice experiments in a tropical cryptic crabObservational data on
 substrate choice experiments in the crab Oocypode
 pallidulaBITR-16-240R1_DataSet.xlsx
DOI: 10.5061/dryad.h3h1n
title: Data from: A tale of two studies: detection and attribution of the impacts of invasive plants in observational surveys

description: Short-term experiments cannot characterize how long-lived, invasive shrubs
 influence ecological properties that can be slow to change, including
 native diversity and soil fertility. Observational studies are thus
 necessary but often suffer from methodological issues. To highlight ways
 of improving the design and interpretation of observational studies that
 assess the impacts of invasive plants, we compare two studies of nutrient
 cycling and earthworms along two separate gradients of invasive shrub
 abundance. By considering the divergent sampling strategies and
 statistical analyses of these two studies, and interpreting their
 contradictory results in the context of other studies, we also aim to
 better describe the impacts of the focal invader, Rhamnus cathartica. In a
 new study of a single site in Minnesota, we observed positive correlations
 between buckthorn abundance and soil pH, soil nutrient pools, nutrient
 fluxes through leaf litterfall, earthworm abundance, and root biomass.
 Multiple regression models showed these relationships persisted after
 accounting for variability in soil texture and tree species composition.
 For a separate, more expansive study in Illinois, other authors reported
 little to no correlation between buckthorn abundance and 10 soil
 properties, including earthworm abundance, pH, and nutrient
 concentrations. However, like many other studies, their regression models
 only assessed predictors related to invader abundance. R2 values for
 models of ecosystem properties ranged from 0–0.79 (adjusted-R2) for our
 study in Minnesota and from &lt;0.05–0.16 (unadjusted) for the prior
 study in Illinois. Differences in sampling error and use of predictor
 variables between the two studies likely explain the contrasting results.
 Synthesis and applications. To reduce the uncertainty of conclusions from
 observational studies of invasive plants, future studies must ensure that
 heterogeneity of soils and vegetation is adequately accounted for in the
 sampling strategy and statistical analyses (e.g., analysis of covariance,
 multiple regression). Particular attention should be given to ecosystem
 properties with variability that likely predates the invader (e.g.,
 geophysical features and tree community composition). In our study,
 effects of buckthorn on ecosystem properties were not only robust to the
 inclusion of potentially confounding predictors but also consistent with
 expectations based on ecological stoichiometry and mass balance of element
 flow.
description: Mueller_buckthorn_gradient_JAE_2018_Dryad_data Dependent and independent variables were measured for 24 plots spanning a gradient in abundance of <em>Rhamnus</em> <em>cathartica</em>.