cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gk300
title: Data from: Protein synthesis inhibition in the peri-infarct cortex slows motor recovery in rats

description: Neuroplasticity and reorganization of brain motor networks are thought to
 enable recovery of motor function after ischemic stroke. Especially in the
 cortex surrounding the ischemic scar (i.e., peri-infarct cortex), evidence
 for lasting reorganization has been found at the level of neurons and
 networks. This reorganization depends on expression of specific genes and
 subsequent protein synthesis. To test the functional relevance of the
 peri-infarct cortex for recovery we assessed the effect of protein
 synthesis inhibition within this region after experimental stroke.
 Long-Evans rats were trained to perform a skilled-reaching task (SRT)
 until they reached plateau performance. A photothrombotic stroke was
 induced in the forelimb representation of the primary motor cortex (M1)
 contralateral to the trained paw. The SRT was re-trained after stroke
 while the protein synthesis inhibitor anisomycin (ANI) or saline were
 injected into the peri-infarct cortex through implanted cannulas. ANI
 injections reduced protein synthesis within the peri-infarct cortex by 69%
 and significantly impaired recovery of reaching performance through
 re-training. Improvement of motor performance within a single training
 session remained intact, while improvement between training sessions was
 impaired. ANI injections did not affect infarct size. Thus, protein
 synthesis inhibition within the peri-infarct cortex impairs recovery of
 motor deficits after ischemic stroke by interfering with consolidation of
 motor memory between training sessions but not short-term improvements
 within one session.
description: Schubring2016_finSource data
DOI: 10.5061/dryad.8pm7h
title: Data from: Genetic by environmental variation but no local adaptation in oysters (Crassostrea virginica)

description: Functional trait variation within and across populations can strongly
 influence population, community, and ecosystem processes, but the relative
 contributions of genetic vs. environmental factors to this variation are
 often not clear, potentially complicating conservation and restoration
 efforts. For example, local adaptation, a particular type of genetic by
 environmental (G*E) interaction in which the fitness of a population in
 its own habitat is greater than in other habitats, is often invoked in
 management practices, even in the absence of supporting evidence. Despite
 increasing attention to the potential for G*E interactions, few studies
 have tested multiple populations and environments simultaneously, limiting
 our understanding of the spatial consistency in patterns of adaptive
 genetic variation. In addition, few studies explicitly differentiate
 adaptation in response to predation from other biological and
 environmental factors. We conducted a reciprocal transplant experiment of
 first-generation eastern oyster (Crassostrea virginica) juveniles from six
 populations across three field sites spanning 1000 km in the southeastern
 Atlantic Bight in both the presence and absence of predation to test for
 G*E variation in this economically valuable and ecologically important
 species. We documented significant G*E variation in survival and growth,
 yet there was no evidence for local adaptation. Condition varied across
 oyster cohorts: Offspring of northern populations had better condition
 than offspring from the center of our region. Oyster populations in the
 southeastern Atlantic Bight differ in juvenile survival, growth, and
 condition, yet offspring from local broodstock do not have higher survival
 or growth than those from farther away. In the absence of
 population-specific performance information, oyster restoration and
 aquaculture may benefit from incorporating multiple populations into their
 practices.
description: Oyster survival during
 6-week reciprocal transplant experimentOyster survival across
 predation treatments at 3 experimental sites at the end of a 6-week
 reciprocal transplant experiment.oyster
 survival.csvOyster growth during
 6-week reciprocal transplant experimentOyster shell length in
 no predation (cage; C) treatments at the beginning and end of a 6-week
 reciprocal transplant experiment across three sites.oyster
 growth.csvOyster condition during
 6-week reciprocal transplant experimentOyster condition in the
 absence of predation (cage treatment; C) at the end of a 6-week reciprocal
 transplant experiment at 3 sites. Data were analyzed both as tissue mass
 per top shell area and tissue mass per length cubed.oyster
 condition.csv
DOI: 10.5061/dryad.f2mp4
title: Data from: Time-lagged effects of weather on plant demography: drought and Astragalus scaphoides

description: Temperature and precipitation determine the conditions where plant species
 can occur. Despite their significance, to date, surprisingly few
 demographic field studies have considered the effects of abiotic drivers.
 This is problematic because anticipating the effect of global climate
 change on plant population viability requires understanding how weather
 variables affect population dynamics. One possible reason for omitting the
 effect of weather variables in demographic studies is the difficulty in
 detecting tight associations between vital rates and environmental
 drivers. In this paper, we applied Functional Linear Models (FLMs) to
 long-term demographic data of the perennial wildflower, Astragalus
 scaphoides, and explored sensitivity of the results to reduced amounts of
 data. We compared models of the effect of average temperature, total
 precipitation, or an integrated measure of drought intensity (Standardized
 Precipitation Evapotranspiration Index, SPEI), on plant vital rates. We
 found that transitions to flowering and recruitment in year t were highest
 if winter/spring of year t was wet (positive effect of SPEI).
 Counterintuitively, if the preceding spring of year t-1 was wet, flowering
 probabilities were decreased (negative effect of SPEI). Survival of
 vegetative plants from t-1 to t was also negatively affected by wet
 weather in the spring of year t-1, and for large plants, even wet weather
 in the spring of t-2 had a negative effect. We assessed the integrated
 effect of all vital rates on life history performance by fitting FLMs to
 the asymptotic growth rate, log(λt). Log(λt) was highest if dry conditions
 in year t-1 were followed by wet conditions in the year t. Overall, the
 positive effects of wet years exceeded their negative effects, suggesting
 that increasing frequency of drought conditions would reduce population
 viability of A. scaphoides. The drought signal weakened when reducing the
 number of monitoring years. Substituting space for time did not recover
 the weather signal, probably because the weather variables varied little
 between sites. We detected the SPEI signal when the analysis included data
 from two sites monitored over 20 years (2x20 observations), but not when
 analyzing data from four sites monitored over 10 years (4x10
 observations).
description: Code and data for
 Tenhumberg et al.tenhumberg_etal_astragalus_scaphoides.zip
DOI: 10.5061/dryad.35jt8
title: Data from: Contrasting evolutionary histories of MHC class I and class II loci in grouse - effects of selection and gene conversion

description: Genes of the major histocompatibility complex (MHC) encode receptor
 molecules that are responsible for recognition of intra- and
 extra-cellular pathogens (class I and class II genes, respectively) in
 vertebrates. Given the different roles of class I and II MHC genes, one
 might expect the strength of selection to differ between these two
 classes. Different selective pressures may also promote different rates of
 gene conversion at each class. Despite these predictions, surprisingly few
 studies have looked at differences between class I and II genes in terms
 of both selection and gene conversion. Here, we investigated the molecular
 evolution of MHC class I and II genes in five closely related species of
 prairie grouse (Centrocercus and Tympanuchus) that possess one class I and
 two class II loci. We found striking differences in the strength of
 balancing selection acting on MHC class I versus class II genes. More than
 half of the putative antigen-binding sites (ABS) of class II were under
 positive or episodic diversifying selection, compared with only 10% at
 class I. We also found that gene conversion played a stronger role in
 shaping the evolution of MHC class II than class I. Overall, the
 combination of strong positive (balancing) selection and frequent gene
 conversion has maintained higher diversity of MHC class II than class I in
 prairie grouse. This is one of the first studies clearly demonstrating
 that macroevolutionary mechanisms can act differently on genes involved in
 the immune response against intra- and extra-cellular pathogens.
description: Grouse MHC class IA
 sequencesGrouse MHC class IA
 sequences. Aligned fasta file.Grouse MHC class II BLB
 sequences (all)Grouse MHC class II BLB
 sequences (BLB1 and BLB2 locus). Aligned fasta file.Grouse MHC class II BLB
 sequences (BLB1 locus)Grouse MHC class II BLB
 sequences (BLB1 locus). Aligned fasta file.Grouse MHC genotypes by
 individual (454 pyrosequencing)Grouse MHC class I and
 class II genotypes by individual, as identified with 454 pyrosequencing.
 See Grouse MHC class IA sequences.fasta and Grouse MHC class II BLB
 sequences (all).fasta files for aligned sequences.Grouse MHC genotypes by
 individual (BLB1 locus sequencing)Grouse MHC class II BLB1
 genotypes by individual, as identified with nested PCR locus-specifc
 approach. See Grouse MHC class II BLB sequences (BLB1 locus).fasta file
 for aligned sequences.
DOI: 10.5061/dryad.f8p63
title: Data from: Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees

description: Inbreeding (mating between relatives) can dramatically reduce the fitness
 of offspring by causing parts of the genome to be identical by descent.
 Thus, measuring individual inbreeding is crucial for ecology, evolution
 and conservation biology. We used computer simulations to test whether the
 realized proportion of the genome that is identical by descent (IBDG) is
 predicted better by the pedigree inbreeding coefficient (FP) or by genomic
 (marker-based) measures of inbreeding. Genomic estimators of IBDG included
 the increase in individual homozygosity relative to mean Hardy–Weinberg
 expected homozygosity (FH), and two measures (FROH and FE) that use mapped
 genetic markers to estimate IBDG. IBDG was more strongly correlated with
 FH, FE and FROH than with FP across a broad range of simulated scenarios
 when thousands of SNPs were used. For example, IBDG was more strongly
 correlated with FROH, FH and FE (estimated with greater than or equal
 to10 000 SNPs) than with FP (estimated with 20 generations of complete
 pedigree) in populations with a recent reduction in the effective
 populations size (from Ne=500 to Ne=75). FROH, FH and FE generally
 explained &gt;90% of the variance in IBDG (among individuals) when
 35 K or more SNPs were used. FP explained &lt;80% of the variation in
 IBDG on average in all simulated scenarios, even when pedigrees included
 20 generations. Our results demonstrate that IBDG can be more precisely
 estimated with large numbers of genetic markers than with pedigrees. We
 encourage researchers to adopt genomic marker-based measures of IBDG as
 thousands of loci can now be genotyped in any species.
description: individualBasedSimModel_HeredityInbreeding_13Feb2015.rsimulation model (run this in R)concatenateIBDTracts_13Feb2015.rThis script concatenates IBD chromosome segments which are directly adjacent to each other (i.e., IBD segments with exactly zero base pairs between them). See the README file for the simulation model for further information.
DOI: 10.5061/dryad.r6q3d
title: Data from: Cascading effects of host plant inbreeding on the larval growth, muscle molecular composition, and flight capacity of an adult herbivorous insect.

description: A primary function of adult winged insects is dispersal. Limiting larval
 dietary intake (partial starvation) has been shown to affect the flight
 muscle metabolism of adult moths reared on artificial diet, but a more
 ecologically relevant question is whether natural variation in host plant
 quality can lead to differences in the flight capacity of adult insects.
 Recent studies have shown that inbreeding compromises plant anti-herbivore
 defenses. We created inbred and outbred progeny from locally collected
 horsenettle (Solanum carolinense L.) and examined how host plant
 inbreeding affects the growth, development, and flight muscle physiology
 of tobacco hornworm (Manduca sexta L.), a specialist herbivore on
 Solanaceae. We tested the hypothesis that within population genetic
 variation in host plant quality, resulting from inbreeding, can create
 significant changes to the larval development and flight physiology of an
 adult insect. We found that Manduca larvae reared on inbred horsenettle
 plants grew faster and developed into larger pupae compared to larvae
 reared on outbred plants. Adult flight metabolic rate was greater in
 adults reared on inbred plants compared to outbred plants, and this
 elevation was independent of body mass when we excluded one plant family
 that produced small, low metabolic rate moths regardless of breeding
 regime. Differences in mass-specific flight metabolism were associated
 with changes in alternative splicing of Troponin t, a flight muscle
 protein that regulates muscle contraction. These results show that host
 plant inbreeding can create effects that cascade through larval and pupal
 development to affect dispersal-related traits of the adult stage. Hence,
 plant inbreeding may also impact herbivore population dynamics,
 particularly their ability to spread away from, and possibly into,
 isolated patches of inbred plants creating increased herbivore pressure on
 these plant populations. More generally, our findings reveal that changes
 in population biology at one trophic level can affect the metabolic
 physiology and flight capacity of an animal at a higher trophic level.
description: Larval Growth
 DataPupa Size
 DataPupa
 Data.xlsxAdult
 DataFile contains data for
 adult body size, flight metabolic output and Troponin t relative
 abundances (arc sine Transformed)
DOI: 10.5061/dryad.812rc
title: Data from: Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome

description: Deforestation has detrimental consequences on biodiversity, affecting
 species interactions at multiple scales. The associations among
 vertebrates, pathogens and their commensal/symbiotic microbial communities
 (i.e. microbiomes) have important downstream effects for biodiversity
 conservation, yet we know little about how deforestation contributes to
 changes in host microbial diversity and pathogen abundance. Here, we
 tested the effects of landcover, forest connectivity and infection by the
 chytrid fungus Batrachochytrium dendrobatidis (Bd) on amphibian skin
 bacterial diversity along deforestation gradients in Brazilian landscapes.
 If disturbance to natural habitat alters skin microbiomes as it does in
 vertebrate host communities, then we would expect higher host bacterial
 diversity in natural forest habitats. Bd infection loads are also often
 higher in these closed-canopy forests, which may in turn impact
 skin-associated bacterial communities. We found that forest corridors
 shaped composition of host skin microbiomes; high forest connectivity
 predicted greater similarity of skin bacterial communities among host
 populations. In addition, we found that host skin bacterial diversity and
 Bd loads increased towards natural vegetation. Because symbiotic bacteria
 can potentially buffer hosts from Bd infection, we also evaluated the
 bi-directional microbiome-Bd link but failed to find a significant effect
 of skin bacterial diversity reducing Bd infections. Although weak, we
 found support for Bd increasing bacterial diversity and/or for core
 bacteria dominance reducing Bd loads. Our research incorporates a critical
 element in the study of host microbiomes by linking environmental
 heterogeneity of landscapes to the host–pathogen–microbiome triangle.
description: Mapping file
 (OTUs)Mapping file
 (OTUs)GuiBz_map_050617.txtFull_Dataset_CSS_BokuNormalized_FOTU alpha diversity indices, Bd infection load data and abiotic variables for each sample.
DOI: 10.5061/dryad.1j7q2
title: Data from: Geographic distribution of the invasive cattle tick Rhipicephalus microplus, a country-wide survey in Benin

description: The cattle tick Rhipicephalus microplus is currently invading the West
 African region, and little information is available on the spread of this
 exotic tick in this region. We set out a country-wide field survey to
 determine its current distribution in Benin. Ticks were collected on
 cattle from 106 farms selected by random sampling covering all regions of
 the country. Rhipicephalus annulatus was found on 70 % of all farms, R.
 decoloratus on 42 %, R. geigyi on 58 %, and R. microplus on 49 %. There is
 a clear geographic separation between the indigenous Rhipicephalus species
 and R. microplus. Rhipicephalus annulatus occurs mainly in the northern
 departments, but it was also observed in lower numbers in locations in the
 south. The presence of R. decoloratus is limited to the northern region,
 and in most locations, this tick makes up a small proportion of the
 collected ticks. The tick R. geigyi tends to be dominant, but occurs only
 in the four northern departments. The observations concerning R. microplus
 are entirely different, this species occurs in the southern and central
 region. The results of this survey confirm the invasive character and
 displacement properties of R. microplus, since in less than a decade it
 has colonized more than half of the country and has displaced indigenous
 ticks of the same genus in many of the sampled locations.
description: Occurrence of
 Rhipicephalus sp in Benin (2011)This dataset includes
 the occurrence of Rhipicephalus sp in a cross-sectional survey on cattle
 in Benin in 2011. Four Rhipicephalus species were encountered during
 identification. Latitude and longitude is provided in decimal degrees in
 the WGS84 reference system. The date of sampling has the format
 'dd/mm/yyyy'. A value ‘0’ indicates absence, ‘1’ indicates
 presence of a given species in the sample. The data is in a tab-delimited
 text file.TickAbsencePresence.txt
DOI: 10.5061/dryad.1c394
title: Data from: Atmospheric conditions create freeways, detours and tailbacks for migrating birds

description: The extraordinary adaptations of birds to contend with atmospheric
 conditions during their migratory flights have captivated ecologists for
 decades. During the 21st century technological advances have sparked a
 revival of research into the influence of weather on migrating birds.
 Using biologging technology, flight behaviour is measured across entire
 flyways, weather radar networks quantify large-scale migratory fluxes,
 citizen scientists gather observations of migrant birds and mechanistic
 models are used to simulate migration in dynamic aerial environments. In
 this review, we first introduce the most relevant microscale, mesoscale
 and synoptic scale atmospheric phenomena from the point of view of a
 migrating bird. We then provide an overview of the individual responses of
 migrant birds (when, where and how to fly) in relation to these phenomena.
 We explore the cumulative impact of individual responses to weather during
 migration, and the consequences thereof for populations and migratory
 systems. In general, individual birds seem to have a much more flexible
 response to weather than previously thought, but we also note similarities
 in migratory behaviour across taxa. We propose various avenues for future
 research through which we expect to derive more fundamental insights into
 the influence of weather on the evolution of migratory behaviour and the
 life-history, population dynamics and species distributions of migrant
 birds.
description: Publications on weather
 and bird migration in the 20th and 21st centuryThis file contains a
 list of all peer-reviewed publications which we used for our review of
 weather and bird migration literature. Publications were selected based on
 criteria described in the Materials and Methdods section of our paper. To
 produce Figure 1 we categorized publications according to the main method
 used for studying birds´ responses to weather on
 migration.ESM_1-v18042017f.xlsx
DOI: 10.5061/dryad.pd7r6
title: Data from: A metagenetics approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual

description: Distinct populations of the potato cyst nematode (PCN) Globodera pallida
 exist in the UK that differ in their ability to overcome various sources
 of resistance. An efficient method for distinguishing between populations
 would enable pathogen-informed cultivar choice in the field. Science and
 Advice for Scottish Agriculture (SASA) annually undertake national DNA
 diagnostic tests to determine the presence of PCN in potato seed and ware
 land by extracting DNA from soil floats. These DNA samples provide a
 unique resource for monitoring the distribution of PCN and further
 interrogation of the diversity within species. We identify a region of
 mitochondrial DNA descriptive of three main groups of G. pallida present
 in the UK, and adopt a metagenetics approach to the sequencing and
 analysis of all SASA samples simultaneously. Using this approach we
 describe the distribution of G. pallida mitotypes across Scotland with
 field-scale resolution. Most fields contain a single mitotype, one fifth
 contain a mix of mitotypes, and less than 3 % contain all three mitotypes.
 Within mixed fields we were able to quantify the relative abundance of
 each mitotype across an order of magnitude. Local areas within mixed
 fields are dominated by certain mitotypes and indicate towards a complex
 underlying "pathoscape". Finally, we assess mitotype
 distribution at the level of the individual cyst, and provide evidence of
 "hybrids". This study provides a method for accurate,
 quantitative and high throughput typing of up to one thousand fields
 simultaneously, while revealing novel insights into the national genetic
 variability of an economically important plant-parasite.
description: top_50_most_common_refine50 most common amplicons aligned and refined.top_50_midrrMid point re-routed bayesian phylogeny of top 50 most common amplicons with 2 million iterationsConsensus_types_alignConsensus of each mito type alignmentConsensus_types_with_4_alignconsensus of each mito type alignment with addition of "type 4"Barcode_and_typetab separated table of location and relative type percentage with barcodes.CYTB_sequences_used_to_identify_groupsCYTB_sequences_used_to_identify_groups