cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2k4vc
title: Data from: Fluctuating temperature leads to evolution of thermal generalism and preadaptation to novel environments

description: Environmental fluctuations can select for generalism, which is also
 hypothesized to increase organisms’ ability to invade novel environments.
 Here, we show that across a range of temperatures, opportunistic bacterial
 pathogen Serratia marcescens that evolved in fluctuating temperature
 (daily variation between 24°C and 38°C, mean 31°C) outperforms the strains
 that evolved in constant temperature (31°C). The growth advantage was also
 evident in novel environments in the presence of parasitic viruses and
 predatory protozoans, but less clear in the presence of stressful
 chemicals. Adaptation to fluctuating temperature also led to reduced
 virulence in Drosophila melanogaster host, which suggests that generalism
 can still be costly in terms of reduced fitness in other ecological
 contexts. While supporting the hypothesis that evolution of generalism is
 coupled with tolerance to several novel environments, our results also
 suggest that thermal fluctuations driven by the climate change could
 affect both species’ invasiveness and virulence.
description: Ketola_etal_MainData_to_Dryadbacterial growth data (maximum growth rate and yield) in various stressors.Ketola_Evolution_virulence_to_DryadVirulence of evolved Serratia marcescens clones in Drosophila melanogaster
DOI: 10.15468/dl.zpmxux
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "GadmGid is MEX.17_1",
 "TaxonKey is Herpailurus yagouaroundi"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000764-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m6v2305
title: Data from: Progression of cognitive decline before and after incident stroke

description: Objective: To determine the trajectory of cognitive decline before and
 after incident stroke. Methods: By using data from the English
 Longitudinal Study of Ageing, we studied 9278 nondemented participants
 with no history of stroke who underwent cognitive assessment at baseline
 (wave 1), and at least one other timepoint (waves 2 to 7). We used linear
 mixed models to analyze repeated measures and longitudinal data. Results:
 Among the 9278 participants (56.8% women, mean age 63.1±10.3 years), 471
 (5.1%) incident stroke events were identified. Compared with stroke-free
 participants, multivariable-adjusted rates of prestroke cognitive decline
 in global cognition, memory, semantic fluency, and temporal orientation of
 participants who later experienced an incident stroke were increased by
 −0.029 standard deviation (SD)/year, −0.016 SD/year, −0.022 SD/year, and
 −0.024 SD/year, respectively. Among the 471 stroke survivors, the
 multivariable-adjusted acute changes in the four cognitive domains were
 −0.257 SD, −0.150 SD, −0.121 SD, and −0.272 SD, respectively. In the years
 following stroke, global cognition declined over time and was steeper than
 its prestroke slope, i.e. by −0.064 SD/year after multivariable
 adjustment. The rates of memory, semantic fluency, and temporal
 orientation decline were −0.046 SD/year, −0.033 SD/year, and −0.037
 SD/year, respectively. Conclusions: Accelerated prestroke and poststroke
 cognitive decline were associated with incident stroke over a follow-up
 period of 12 years. Attention should be paid to the long-term cognitive
 problems of stroke survivors, and intervention and management of major
 vascular risk factors should start from early- or mid-life to reduce the
 risk of cerebrovascular disease and the associated cognitive impairment.
description: Supplementary-2018-10-23Supplementary File
DOI: 10.5061/dryad.dp380n8s
title: Data from: Characterization of new microsatellite loci isolated from Santiria trimera (Burseraceae)

description: PREMISE OF THE STUDY: To study the genetic structure among three
 morphotypes of an African rainforest tree species, Santiria trimera,
 nuclear microsatellite markers were isolated and characterized. METHODS
 AND RESULTS: Seven polymorphic loci were isolated using a
 pyrosequencing-based protocol. The seven loci were successfully amplified
 on three different morphotypes of S. trimera. For six of the seven loci,
 there is at least one private allele for one of the three morphotypes. The
 mean effective number of alleles is about four for each of the three
 morphotypes. CONCLUSIONS: These microsatellite markers are promising to
 explore the genetic delimitation among sympatric morphotypes found in
 Gabonese forests and to study the spatial genetic structure within each
 gene pool.
description: Koffi_AJB-D-12-00041R1_Supplemental Online MaterialThe file is the Supplemental Online Material of the "AJB Primer Notes & Protocols" manuscript published by Guillaum Koffi et al. This manuscript presents a microsatellite primer set to be used in Santiria trimera, an African tropical tree species. The SOM present: the tested sequences that proved amplifiable with polymorphism described in the article; the tested sequences that did not lead to a readable product; the untested sequences containing a microsatellite motif (more than 400 different sequences).
DOI: 10.5061/dryad.f4ts3
title: Data from: Resolution of a global mango and fig pest identity crisis

description: Hypocryphalus Hopkins, 1915 and Cryphalus Erichson, 1836 (Curculionidae:
 Scolytinae: Cryphalini) are significant pests of fig, mango, and other
 economically important fruit trees, yet have received little attention
 from systematists. An integrated approach using molecular and
 morphological evidence resolved the identities of the species feeding on
 mango and fig. The following taxonomic changes are proposed: Hypocryphalus
 mangiferae (Stebbing, 1914), stat. rev.; Hypocryphalus dilutus (Eichhoff,
 1878a), stat. rev. (=Cryphalus dilutusEichhoff, 1878b, syn. n.);
 Hypocryphalus discretus (Eichhoff, 1878a), stat. rev. (=Cryphalus
 discretusEichhoff, 1878b, syn. n.; Cryphalus scabricollisEichhoff, 1878b,
 syn. n.; Cryphalus brevisetosus Schedl, 1943, syn. n.). We identified
 widespread misidentification of specimens of Hypocryphalus from mango. The
 pest of mango trees in Oman, Pakistan, Bangladesh and Mexico, and
 putatively the vector of the pathogen responsible for mango wilt, is H.
 dilutus, a resurrected species. The pest of figs in the Mediterranean is
 also H. dilutus, but a distinct genetic lineage. The globally distributed
 but seemingly harmless mango bark beetle is H. mangiferae: a genetically
 complex species in its region of origin, with a single haplotype on mango
 trees outside the native range. We provide DNA sequences and describe
 novel morphological characters for identification of these species.
description: Hypocryphalus alignment
 and treeMolecular data matrix
 and phylogenetic treeHypocryphalus_final_alignment_and_tree.nexus
DOI: 10.5061/dryad.5nj81nf
title: Data from: Linking pollinator efficiency to patterns of pollen limitation: small bees exploit the plant-pollinator mutualism

description: Seemingly mutualistic relationships can be exploited, in some cases
 reducing fitness of the exploited species. In plants, the insufficient
 receipt of pollen limits reproduction. While infrequent pollination
 commonly underlies pollen limitation (PL), frequent interactions with
 low-efficiency, exploitative pollinators may also cause PL. In the
 widespread protandrous herb, Campanula americana, visitation by three
 pollinators explained 63% of the variation in PL among populations
 spanning the range. Bumblebees and the medium-sized Megachile campanulae
 enhanced reproductive success, but small solitary bees exacerbated PL. To
 dissect mechanisms behind these relationships we scored sex-specific
 floral visitation, and the contributions of each pollinator to plant
 fitness using single-flower visits. Small bees and M. campanulae
 overvisited male-phase flowers but bumblebees frequently visited
 female-phase flowers. Fewer bumblebee visits were required to saturate
 seed set compared to other bees. Scaling pollinator efficiency metrics to
 populations, small bees deplete large amounts of pollen due to highly
 male-biased flower visitation and infrequent pollen deposition. Thus,
 small bees reduce plant reproduction by limiting pollen available for
 transfer by efficient pollinators, and appear to exploit the
 plant-pollinator mutualism, acting as functional parasites to C.
 americana. It is therefore unlikely that small bees will compensate for
 reproductive failure in C. americana when bumblebees are scarce.
description: Koski et al.
 2018_Data_ProcRoySocData are in separate
 tabs. Please refer to the "Metadata" tab for header
 descriptions. 1) Data on pollen limitation, pollinator visitation rates,
 and pollen depletion metrics across 23 populations of Campanula americana.
 2) The relationship between pollen grains deposited on stigmas and seed
 set. 3) Data used to calculate pollen deposition efficiency for
 pollinators, 4) Data used to calculate seed set efficiency for
 pollinators, 5) Data used to calculate pollen removal efficiency for
 pollinators.
DOI: 10.5061/dryad.26mv3f6d
title: Data from: Sex-biased genetic component distribution among populations: additive genetic and maternal contributions to phenotypic differences among populations of Chinook salmon

description: An approach frequently used to demonstrate a genetic basis to
 population-level phenotypic differences is to employ common garden rearing
 designs, where observed differences are assumed to be attributable to
 primarily additive genetic effects. Here, in two common garden
 experiments, we employed factorial breeding designs between wild and
 domestic, and among wild populations of Chinook salmon (Oncorhynchus
 tshawytscha). We measured the contribution of additive (VA) and maternal
 (VM) effects to the observed population differences for 17 life history
 and fitness-related traits. Our results show that, in general, maternal
 effects contribute more to phenotypic differences among populations than
 additive genetic effects. These results suggest that maternal effects are
 important in population phenotypic differentiation, and also signify that
 the inclusion of the maternal source of variation is critical when
 employing models to test population differences in salmon, such as in
 local adaptation studies.
description: Aykanat et
 al_JEBThe zip file contains
 raw data within several text files (trait measurement, family and stock
 information) as well as an r script (.r extension executable in notepad)
 by which the results in the MS can be replicated using raw data files.
 More information can be found within the r script.
DOI: 10.5061/dryad.1576
title: Data from: Parallel polyploid speciation: distinct sympatric gene-pools of recurrently derived allo-octoploid Asplenium ferns

description: Although polyploidy is widespread, its significance to the generation of
 biodiversity remains unclear. Many polyploids have been derived
 recurrently. For a particular polyploid, gene-flow between the products of
 independent origin is typical where they come into contact. Here, we use
 AFLP DNA-fingerprinting and chloroplast DNA sequences to demonstrate
 parallel polyploid speciation within both of the ferns Asplenium
 cimmeriorum and A. gracillimum. Both of these taxa comprise at least two
 allopolyploids, recurrently derived from the same progenitor pair. Each of
 these allopolyploids remain genetically distinguishable even with
 extensive sympatry, and could therefore be considered distinct species. To
 our knowledge, parallel speciation on this scale amongst recurrent
 polyploids has not been previously reported. With their parallel origins,
 these 'evolutionary replicates' provide an unrivalled
 opportunity to investigate how the reproductive barriers and ecological
 differentiation necessary for speciation arise following polyploidy.
description: AFLP data in nexus
 formatMEC-10-0241DataS1.txt
DOI: 10.5061/dryad.5f41fq18
title: Data from: Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers

description: Hybridization has played a central role in the evolutionary history of
 domesticated plants. Notably, several breeding programs relying on gene
 introgression from the wild compartment have been performed in fruit tree
 species within the genus Prunus but few studies investigated spontaneous
 gene flow among wild and domesticated Prunus species. Consequently, a
 comprehensive understanding of genetic relationships and levels of gene
 flow between domesticated and wild Prunus species is needed. Combining
 nuclear and chloroplastic microsatellites, we investigated the gene flow
 and hybridization among two key almond tree species, the cultivated Prunus
 dulcis and one of the most widespread wild relative Prunus orientalis in
 the Fertile Crescent. We detected high genetic diversity levels in both
 species along with substantial and symmetric gene flow between the
 domesticated P. dulcis and the wild P. orientalis. These results were
 discussed in light of the cultivated species diversity, by outlining the
 frequent spontaneous genetic contributions of wild species to the
 domesticated compartment. In addition, crop-to-wild gene flow suggests
 that ad hoc transgene containment strategies would be required if
 genetically modified cultivars were introduced in the northwestern
 Mediterranean.
description: almond INFO
 collectionThis file gives
 information for each sample (tag, species, sampling location, GPS
 coordinates, abreviation)almond
 NuclearDATAthis file gives nuclear
 genotypes for all nuclear markers used in the study. Data are given using
 a two column format for each sample (ligne). alleles are given in size
 length.almond Chloro
 DATAthis files gives
 chloroplastic genotypes. alleles are given in size length, in a one column
 format.
DOI: 10.5061/dryad.430s7
title: Data from: Experimentally increased nest temperature affects body temperature, growth and apparent survival in blue tit nestlings

description: The thermal environment experienced by birds during early postembryonic
 development may be an important factor shaping growth and survival.
 However, few studies have directly manipulated nest temperature (Tn)
 during the nestling phase, and none have measured the consequences of
 experimental heat stress on nestlings’ body temperature (Tb). It is
 therefore not known to what extent any fitness consequences of development
 in a thermally challenging environment arise as a direct, or indirect,
 effect of heat stress. We, therefore, studied how experimentally increased
 Tn affected Tb in 8-12 days old blue tit (Cyanistes caeruleus) nestlings,
 to investigate if increased thermoregulatory demands to maintain
 normothermic Tb influenced nestling growth and apparent long-term
 survival. Nestlings in heated nest-boxes had significantly higher Tb
 compared to unheated nestlings during most of the experimental period.
 Yet, despite facing Tn &gt; 50 °C (as measured in the bottom of the
 nest cup below the nestlings), the highest nestling Tb recorded was 43.8
 °C with nestlings showing evidence of controlled facultative hyperthermia
 without any increased nestling mortality in heated nests. However, body
 mass gain was lower in these nestlings compared to nestlings from control
 nest-boxes. Contrary to our prediction, a larger proportion of nestlings
 from heated nest-boxes were recaptured during their first winter, or
 subsequently recruited into the breeding population as first- or
 second-year breeders. This result should, however, be treated with caution
 because of low recapture rates. This study highlights the importance of
 the thermal environment during nestling development, and its role in
 shaping both growth patterns and possibly also apparent survival.
description: Measurements of body-
 and nest temperatures, nestling biometrics and survival data of blue tit
 nestlingsBody-, ambient- and nest
 temperature together with nestling biometrics, survival data and direction
 of nest-boxes. The last sheet, named Metadata, contains descriptions of
 all variables.Andreassonetal2017.xlsx
DOI: 10.5061/dryad.s171t
title: Data from: The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature

description: Understanding the extent, scale and genetic basis of local adaptation (LA)
 is important for conservation and management. Its relevance in salmonids
 at microgeographic scales, where dispersal (and hence potential gene flow)
 can be substantial, has however been questioned. Here, we compare the
 fitness of communally reared offspring of local and foreign Atlantic
 salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid
 crosses between them, in the wild ‘home’ environment of the local
 population. Experimental groups did not differ in wild smolt output but a
 catastrophic flood event may have limited our ability to detect freshwater
 performance differences, which were evident in a previous study. Foreign
 parr exhibited higher, and hybrids intermediate, emigration rates from the
 natal stream relative to local parr, consistent with genetically based
 behavioural differences. Adult return rates were lower for the foreign
 compared to the local group. Overall lifetime success of foreigners and
 hybrids relative to locals was estimated at 31% and 40% (mean of both
 hybrid groups), respectively. The results imply a genetic basis to fitness
 differences among populations separated by only 50 km, driven largely by
 variation in smolt to adult return rates. Hence even if supplementary
 stocking programs obtain broodstock from neighbouring rivers, the risk of
 extrinsic outbreeding depression may be high.
description: FamiliesData on crosses to make experimental families and associated phenotypic data on broodstockOffspringData on sampled offspring (inlcuding assigments back to parents) caught at various life stages by electrofishing, in traps, or in the hatchery
DOI: 10.5061/dryad.58bm7
title: Data from: Environmental stress correlates with increases in both genetic and residual variances: a meta-analysis of animal studies

description: Adaptive evolutionary responses are determined by the strength of
 selection and the amount of genetic variation within traits, however, both
 are known to vary across environmental conditions. As selection is
 generally expected to be strongest under stressful conditions,
 understanding how the expression of genetic variation changes across
 stressful and benign environmental conditions is crucial for predicting
 the rate of adaptive change. While theory generally predicts increased
 genetic variation under stress, previous syntheses of the field has found
 limited support for this notion. These studies have focused on
 heritability, which is dependent on other environmentally sensitive, but
 non-genetic, sources of variation. Here, we aim to complement these
 studies with a meta-analysis where we examine changes in coefficient of
 variation (CV) in maternal, genetic, and residual variances across
 stressful and benign conditions. Confirming previous analyses, we did not
 find any clear direction in how heritability changes across stressful and
 benign conditions. However, when analyzing CV, we found higher genetic and
 residual variance under highly stressful conditions in life-history traits
 but not in morphological traits. Our findings are of broad significance to
 contemporary evolution suggesting that rapid evolutionary adaptive
 response may be mediated by increased evolutionary potential in stressed
 populations.
description: Raw data from
 Environmental stress correlates with increases in both genetic and
 residual variances: a meta-analysis of animal studiesThe file contains all
 the data for the analysis presented in the manuscript.data.csv
DOI: 10.5061/dryad.5h187
title: Data from: Reorganization of interaction networks modulates the persistence of species in late successional stages

description: 1.Ecological interaction networks constantly reorganize as interspecific
 interactions change across successional stages and environmental
 gradients. This reorganization can also be associated with the extent to
 which species change their preference for types of niches available in
 their local sites. Despite the pervasiveness of these interaction changes,
 previous studies have revealed that network reorganizations have a minimal
 or insignificant effect on global descriptors of network architecture,
 such as: connectance, modularity, and nestedness. However, little is known
 about whether these reorganizations may have an effect on community
 dynamics and composition. 2.To answer the question above, we study the
 multi-year dynamics and reorganization of plant-herbivore interaction
 networks across secondary successional stages of a tropical dry forest. We
 develop new quantitative tools based on a structural stability approach to
 estimate the potential impact of network reorganization on species
 persistence. Then, we investigate whether this impact can explain the
 likelihood of persistence of herbivore species in the observed
 communities. 3.We find that resident (early-arriving) herbivore species
 increase their likelihood of persistence across time and successional
 stages. Importantly, we demonstrate that, in late successional stages, the
 reorganization of interactions among resident species has a strong
 inhibitory effect on the likelihood of persistence of colonizing
 (late-arriving) herbivores. 4.These findings support earlier predictions
 suggesting that, in mature communities, changes of species interactions
 can act as community-control mechanisms (also known as priority effects).
 Furthermore, our results illustrate that the dynamics and composition of
 ecological communities cannot be fully understood without attention to
 their reorganization processes, despite the invariability of global
 network properties.
description: R-code_and_dataThe file contains: - The R-code: (1) to compute the interaction matrix from the plant-herbivore interaction network before and after reorganization, (2) to compute the critical level of interspecific strength, (3) the structural vector (geometric centroid of the feasibility domain), (4) the impact of network reorganization (the displacement of the structural vector before and after reorganization). - All the network data, species list, and their corresponding barcode (which can be identified in http://www.boldsystems.org/). Note that the network data are named as stage_site_year, e.g., initial_A_7n, where it is the initial successional stage, site A, year 2007. In total we have three stages (initial, middle, and late), we have three sites for each stage (A, B, and C), and we have 4 years for each stage and site (7n, 8n, 9n, 10n). The entries of the network data correspond to the observed co-occurrences of plant and herbivore species (note that we only use the binary presence/absence information for our analysis).