cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2nk5p
title: Data from: The role of immigration and local adaptation on fine-scale genotypic and phenotypic population divergence in a less mobile passerine

description: Dispersal and local patterns of adaptation play a major role on the
 ecological and evolutionary trajectory of natural populations. In this
 study, we employ a combination of genetic (25 microsatellite markers) and
 field-based information (seven study years) to analyse the impact of
 immigration and local patterns of adaptation in two nearby (&lt; 7 km)
 blue tit (Cyanistes caeruleus) populations. We used genetic assignment
 analyses to identify immigrant individuals and found that dispersal rate
 is female-biased (72%). Data on lifetime reproductive success indicated
 that immigrant females produced fewer local recruits than their
 philopatric counterparts whereas immigrant males recruited more offspring
 than those that remained in their natal location. In spite of the
 considerably higher immigration rates of females, our results indicate
 that, in absolute terms, their demographic and genetic impact in the
 receiving populations is lower than that in immigrant males. Immigrants
 often brought novel alleles into the studied populations and a high
 proportion of them were transmitted to their recruits, indicating that the
 genetic impact of immigrants is not ephemeral. Although only a few
 kilometres apart, the two study populations were genetically
 differentiated and showed strong divergence in different phenotypic and
 life-history traits. An almost absent inter-population dispersal, together
 with the fact that both populations receive immigrants from different
 source populations, is probably the main cause of the observed pattern of
 genetic differentiation. However, phenotypic differentiation (PST) for all
 the studied traits greatly exceeded neutral genetic differentiation (FST),
 indicating that divergent natural selection is the prevailing factor
 determining the evolutionary trajectory of these populations. Our study
 highlights the importance of integrating individual- and population-based
 approaches to obtain a comprehensive view about the role of dispersal and
 natural selection on structuring the genotypic and phenotypic
 characteristics of natural populations.
description: Phenotypic and genotypic
 characteristics of immigrant and resident blue titsPhenotypic and genotypic
 characteristics of adult blue tits in relation to sex and origin
 (immigrant/resident)CharacteristicsBlueTits.xlsGenotype dataGenotype information from 25 microsatellite markersGenotypeBlueTits.xls
DOI: 10.5061/dryad.v7c54
title: Data from: Admixture of eastern and western European red deer lineages as a result of postglacial re-colonisation of the Czech Republic (Central Europe)

description: Due to a restriction of the distributional range of European red deer
 (Cervus elaphus L.) during the Quaternary and subsequent recolonization of
 Europe from different refugia, a clear phylogeographical pattern in
 genetic structure has been revealed using mitochondrial DNA markers. In
 Central Europe, 2 distinct, eastern and western, lineages of European red
 deer are present; however, admixture between them has not yet been studied
 in detail. We used mitochondrial DNA (control region and cytochrome b
 gene) sequences and 22 microsatellite loci from 522 individuals to
 investigate the genetic diversity of red deer in what might be expected to
 be an intermediate zone. We discovered a high number of unique mtDNA
 haplotypes belonging to each lineage and high levels of genetic diversity
 (cyt b H = 0.867, D-loop H = 0.914). The same structuring of red deer
 populations was also revealed by microsatellite analysis, with results
 from both analyses thus suggesting a suture zone between the 2 lineages.
 Despite the fact that postglacial recolonization of Central Europe by red
 deer occurred more than 10000 years ago, the degree of admixture between
 the 2 lineages is relatively small, with only 10.8% admixed individuals
 detected. Direct translocations of animals by humans have slightly blurred
 the pattern in this region; however, this blurring was more apparent when
 using maternally inherited markers than nuclear markers.
description: Cytb_alignmentAlignment of cytochrome b gene haplotypes used in phylogenetic analysisDloop_alignmentAlignment of Dloop haplotypes used in the phylogenetic analysisCzech red deer_microsatellitesMicrosatellite data set used in the study
DOI: 10.5061/dryad.q7vk2
title: Data from: Life-history diversity and its importance to population stability and persistence of a migratory fish: steelhead in two large North American watersheds

description: 1. Life-history strategies can buffer individuals and populations from
 environmental variability. For instance, it is possible that asynchronous
 dynamics among different life-histories can stabilize populations through
 portfolio effects. 2. Here we examine life-history diversity and its
 importance to stability for an iconic migratory fish species. In
 particular, we examined steelhead (Oncorhynchus mykiss), an anadromous and
 iteroparous salmonid, in two large, relatively pristine, watersheds, the
 Skeena and Nass, in northwestern British Columbia, Canada. We synthesized
 life-history information derived from scales collected from adult
 steelhead (N = 7227) in these watersheds across a decade. 3. These
 migratory fishes expressed 36 different manifestations of the anadromous
 life-history strategy, with 16 different combinations of freshwater and
 marine ages, 7.6% of fish performing multiple spawning migrations, and up
 to 4 spawning migrations. Furthermore, in the Nass watershed, different
 life-histories were differently prevalent through time—three different
 life-histories were the most prevalent in a given year and no life-history
 ever represented more than 45% of the population. These asynchronous
 dynamics among life-histories decreased the variability of numerical
 abundance and biomass of the aggregated population so that it was more
 than 20% more stable than the stability of the weighted average of
 specific life-histories, evidence of a substantial portfolio effect. Year
 of ocean entry was a key driver of dynamics; the median correlation
 coefficient of abundance of life-histories that entered the ocean the same
 year was 2.5 times higher than the median pairwise coefficient of
 life-histories that entered the ocean at different times. Simulations
 illustrated how different elements of life-history diversity contribute to
 stability and persistence of populations. 4. This study provides evidence
 that life-history diversity can dampen fluctuations in population
 abundances and biomass via portfolio effects. Conserving genetic integrity
 and habitat diversity in this and other large watersheds can enable a
 diversity of life-histories that increases stability to environmental
 variability.
description: Steelhead_Composite_DataAge data for Steelhead in the Nass and Skeena watersheds
DOI: 10.5061/dryad.s7d2d
title: Data from: Robustness of habitat-based surrogates of animal diversity: a multi-taxa comparison over time

description: Many animal taxa respond strongly to spatial and temporal variation in
 vegetation structure and floristic composition, suggesting that changes in
 vegetation could be a cheap and readily observable surrogate for changes
 in animal assemblages. Yet there is considerable uncertainty about how
 different taxa respond to vegetation over time, potentially limiting the
 application of habitat-based surrogates to many areas of applied ecology.
 We examined the strength and temporal consistency of habitat-based
 surrogates of three different vertebrate taxa in a landscape with multiple
 vegetation types. We used regression models to quantify the relationships
 between six vegetation attributes (species richness and percentage cover
 of overstorey, midstorey and understorey) and three measures of bird,
 mammal and reptile assemblages (abundance, species richness and
 composition). We found that overstorey richness and cover had both
 consistent and strong positive effects on bird assemblages. Vegetation
 effects were generally weaker and more variable for mammals and reptiles
 compared with birds. Each taxon displayed different temporal dynamics
 following fire, with negative effects on birds and mammals, but positive
 short-term effects on reptiles. Surprisingly, fire increased vegetation
 effects on birds, but did not consistently alter vegetation effects on
 mammals or reptiles, indicating a lack of concordant responses among taxa.
 Synthesis and applications. Empirical testing of habitat-based surrogates
 of multiple animal taxa is needed to identify reliable and consistent
 management proxies. Our study suggests that habitat-based surrogates could
 be useful metrics for quantifying changes in bird assemblages through time
 and after fire, but that the same metrics could not be applied to mammal
 and reptile assemblages. The absence of both strong and consistent effects
 of vegetation attributes across the three groups of vertebrates suggests
 that taxon-specific habitat surrogates may be required to detect changes
 over time and after disturbance within heterogeneous landscapes.
description: Data for Dryad version
 1Excel Spreadsheet,four
 sheets of data
DOI: 10.5061/dryad.41pj936
title: Data from: A unified model for optimizing riverscape conservation

description: 1.Spatial prioritization tools provide a means of finding efficient
 trade-offs between biodiversity protection and the delivery of ecosystem
 services. Although a large number of prioritization approaches have been
 proposed in the literature, most are specifically designed for terrestrial
 systems. When applied to river ecosystems, they often fail to adequately
 account for the essential role that landscape connectivity plays in
 maintaining both biodiversity and ecosystem services. This is particularly
 true of longitudinal connectivity, which in many river catchments is
 highly altered by the presence of dams, stream-road crossings, and other
 artificial structures. 2.We propose a novel framework for coordinating
 river conservation and connectivity restoration. As part of this, we
 formulate an optimization model for deciding which subcatchments to
 designate for ecosystem services and which to include in a river protected
 area (RPA) network, while also deciding which existing river barriers to
 remove in order to maximize longitudinal connectivity within the RPA
 network. In addition to constraints on the size and makeup of the RPA
 network, the model also considers the suitability of sites for
 conservation, based on a biological integrity index, and connectivity to
 multiple habitat types. We demonstrate the usefulness of our approach
 using a case study involving four managed river catchments located in
 Hungary. 3.Results show that large increases in connectivity-weighted
 habitat can be achieved through targeted selection of barrier removals and
 that the benefits of barrier removal are strongly depend on RPA network
 size. We find that (i) highly suboptimal solutions are produced if habitat
 conservation planning and connectivity restoration are done separately and
 (ii) RPA acquisition provides substantially greater marginal benefits than
 barrier removal given limited resources. 4.Synthesis and applications.
 Finding a balance between conservation and ecosystem services provision
 should give more consideration to connectivity restoration planning,
 especially in multi-use riverscapes. We present the first modelling
 framework to directly integrate and optimize river conservation and
 connectivity restoration planning. This framework can help conservation
 managers to account better for connectivity, resulting in more effective
 catchment scale maintenance of biological integrity and ecosystem services
 delivery.
description: HU data
 v5
DOI: 10.5061/dryad.f727j
title: Data from: Fine-scale population epigenetic structure in relation to gastro-intestinal parasite load in red grouse (Lagopus lagopus scotica)

description: Epigenetic modification of cytosine methylation states can be elicited by
 environmental stresses and may be a key process affecting phenotypic
 plasticity and adaptation. Parasites are potent stressors with profound
 physiological and ecological effects on their host, but there is little
 understanding in how parasites may influence host methylation states.
 Here, we estimate epigenetic diversity and differentiation among 21
 populations of red grouse (Lagopus lagopus scotica) in north-east
 Scotland, and test for association of gastro-intestinal parasite load
 (caecal nematode Trichostrongylus tenuis) with hepatic genome-wide and
 locus-specific methylation states. Following methylation-sensitive AFLP
 (MSAP), 129 bands, representing 73 methylation-susceptible and 56
 non-methylated epiloci, were scored across 234 individuals. The
 populations differed significantly in genome-wide methylation levels and
 were also significantly epigenetically (FST = 0.0227; p &lt; 0.001)
 and genetically (FST = 0.0058; p &lt; 0.001) differentiated. Parasite
 load was not associated with either genome-wide methylation levels or
 epigenetic differentiation. Instead, we found eight disproportionately
 differentiated epilocus-specific methylation states (FST -outliers) using
 bayescan software and significant positive and negative association of 35
 methylation states with parasite load from bespoke generalised estimating
 equations (GEE), simple logistic regression (sam) and Bayesian
 environmental analysis (bayenv). Following Sanger sequencing, genome
 mapping and geneontology (go) annotation, some of these epiloci were
 linked to genes involved in regulation of cell cycle, signalling,
 metabolism, immune system and notably rRNA methylation, histone
 acetylation and small RNAs. These findings demonstrate an epigenetic
 signature of parasite load in populations of a wild bird and suggest
 intriguing physiological effects of parasite-associated cytosine
 methylation.
description: Raw presence/absence
 scores of MSAP bandsThis file contains the
 raw scores of 129 MSAP bands scored across 234 red grouse individuals. Use
 this file as input for the R package "msap" to do basic
 methylation analyses.msap_raw_scores.csvTransformed MSAP scores and morphological dataThis file contains 303 epiloci that were generated by transforming 129 MSAP bands into binary loci. The file also provides morphological data in order to do regression analyses.msap_transformed_scores.txtNomenclature for MSAP bands and corresponding epilociContains identifiers for each MSAP band and each corresponding epilocus alongside represented methylation state (unmethylated, hemimethylated, fully methylated)locus_ids.txtPairwise geographic distancesContains a matrix with pairwise geographic distances among the 21 study populations.geo_distances.txtComplete R analysis scriptContains R code for analysing the input files using "msap" and custom logistic regressions.R_analysis.rReadmeDetails file contents
DOI: 10.5061/dryad.m6n75
title: Data from: The influence of parental effects on transcriptomic landscape during early development in brook charr (Salvelinus fontinalis, Mitchill)

description: Parental effects represent an important source of variation in offspring
 phenotypes. Depending on the specific mechanisms involved, parental
 effects may be caused to different degrees by either the maternal or the
 paternal parent, and these effects may in turn act at different stages of
 development. To detect parental effects acting on gene transcription
 regulation and length phenotype during ontogeny, the transcriptomic
 profiles of two reciprocal hybrids from Laval × Rupert and Laval ×
 Domestic populations of brook charr were compared at hatching, yolk sac
 resorption and 15 weeks after exogenous feeding. Using a salmonid cDNA
 microarray, our results show that parental effects modulated gene
 expression among reciprocal hybrids only at the yolk sac resorption stage.
 In addition, Laval × Domestic and Laval × Rupert reciprocal hybrids
 differed in the magnitude of theses parental effects, with 199 and 630
 differentially expressed transcripts, respectively. This corresponds to a
 maximum of 18.5% of the analyzed transcripts. These transcripts are
 functionally related to cell cycle, nucleic acid metabolism and
 intracellular protein traffic, which is consistent with observed
 differences associated with embryonic development and growth differences
 in other fish species. Our results thus illustrate how parental effects on
 patterns of gene transcription seem dependent on the genetic architecture
 of the parents. In addition, in absence of transcriptional differences,
 non-transcript deposits in the yolk sac could contribute to the observed
 length differences among the reciprocal hybrids before yolk sac
 resorption.
description: Fork length Salvelinus
 fontinalis / File S1Data includes the fork
 length measurement for L♀D♂, D♀L♂, L♀R♂ and R♀L♂ offspring and
 parentsFork
 length Salvelinus fontinalis.xls
DOI: 10.5061/dryad.m7j72
title: Data from: The biogeography of marine invertebrate life histories

description: Biologists have long sought to identify and explain patterns in the
 diverse array of marine life histories. The most famous speculation about
 such patterns is Gunnar Thorson’s suggestion that species producing
 planktonic larvae are rarer at higher latitudes (Thorson’s rule). Although
 some elements of Thorson’s rule have proven incorrect, other elements
 remain untested. With a wealth of new life-history data, statistical
 approaches, and remote-sensing technology, new insights into marine
 reproduction can be generated. We gathered life-history data for more than
 1,000 marine invertebrates and examined patterns in the prevalence of
 different life histories. Systematic patterns in marine life histories
 exist at a range of scales, some of which support Thorson, whereas others
 suggest previously unrecognized relationships between the marine
 environment and the life histories of marine invertebrates. Overall,
 marine life histories covary strongly with temperature and local ocean
 productivity, and different regions should be managed accordingly.
description: Database
 tableDatabase of global
 marine invertebrate life-history patterns. This table contains all of the
 data used in the analyses in Marshall et al. 2012, Annual reviews. Some
 additional data are included, as well as multiple values for some species.
 For those where not all data were present, they are included in the hope
 that additional data can be added later. We would appreciate it if you
 would bring to our attention any errors or ambiguities that you find in
 the database (no doubt there are some). We will periodically update the
 database as needed. In addition, we are very interested in new insights
 you may have about marine invertebrate life-histories from your own
 analyses of this database and relate sources. We’d appreciate it if you
 would tell us what you are finding, or papers that have resulted from it.
 Any questions or comments may be directed to: Dustin marshall, School of
 Biological Sciences, Monash University email:
 dustin.marshall@monash.eduDatabase Reference
 ListHere is the database
 reference list from which most of the species information was sourced.
 Inevitably, some information was taken from multiple sources, not all of
 which may appear here but we did our best to include the primary pieces of
 information.
DOI: 10.5061/dryad.p9743
title: Data from: Novel evidence suggests that a "Rickettsia felis-like" organism is an endosymbiont of the desert flea, Xenopsylla ramesis

description: Fleas are acknowledged vectors and reservoirs of various bacteria that
 present a wide range of pathogenicity. In this study, fleas collected from
 wild rodents from the Negev desert in southern Israel were tested for
 RickettsiaDNA by targeting the 16S rRNA (rrs) gene. Thirty-eight
 Xenopsylla ramesis, 91 Synosternus cleopatrae and 15 Leptopsylla flea
 pools (a total of 568 fleas) were screened. RickettsiaDNA was detected in
 100% of the X. ramesis and in one S. cleopatrae flea pools. None of L.
 algira flea pools was found positive. All positive flea pools were further
 characterized by sequencing of five additional genetic loci (gltA, ompB,
 ompA, htrA and fusA). The molecular identification of the positive samples
 showed all sequences to be closely related to the ‘Rickettsia felis-like’
 organisms (99–100% similarities in the six loci). To further investigate
 the association between ‘R. felis-like’ and X. ramesis fleas, ten
 additional single X. ramesis adult fleas collected from the wild and five
 laboratory-maintained X. ramesis imago, five larva pools (2–18 larvae per
 pool) and two egg pools (18 eggs per pool) were tested for the presence of
 ‘R. felis-like’ DNA. All samples were found positive by a specific ompAPCR
 assay, confirming the close association of this Rickettsia species with X.
 ramesis in all its life stages. These results suggest a symbiotic
 association between ‘Rickettsia felis-like’ and X. ramesis fleas.
description: Table S1. Description of
 rodents collected for the studyTable S2. Composition of
 flea poolsTable S3. Results of PCR
 assays for the Rickettsia-DNA screening in flea poolsAligned sequences from
 positive samplesAligned loci
 sequences.zipTree files
 MEGA
DOI: 10.15493/obsdb.0000.032c
title: Inorganic Carbon - pH, Actual, Potential of Hydrogen for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 14 between 2.83m and 0.00m below sea level from 2021-02-05 to 2026-01-13

description: Inorganic Carbon - pH, Actual, Potential of Hydrogen for Estuaries, Multiparameter Meters, Kariega Estuary, Kariega Salinity 14 between 2.83m and 0.00m below sea level from 2021-02-05T11:35:02+02:00 to 2026-01-13T11:10:36+02:00 at -33.629870,26.637990 (+N-S,-W+E)
DOI: 10.5061/dryad.dd490
title: Data from: Exotic invasive plants increase productivity, abundance of ammonia-oxidizing bacteria, and nitrogen availability in intermountain grasslands

description: 1. Exotic plant invasion is often associated with dramatic increases in
 above-ground net primary productivity and soil nitrogen. However, most
 evidence for these increases comes from correlative studies of single
 species, leaving open the question of whether invasive plants drive these
 processes and if they are consistent among invaders. 2. We combined field
 surveys and measurements within experimental plantings to examine how
 plant productivity, soil nitrogen, and the abundance of ammonia-oxidizing
 bacteria (AOB) change in response to invasions by four exotic species. 3.
 The relationship between plant productivity and soil nitrate differed
 among native and invasive species, suggesting a fundamental disparity in
 the effects of natives and invaders on ecosystem processes. In field
 surveys, dense patches of all invasive species had higher abundances of
 AOB than native-dominated sites. Three of the four invasive species had
 higher productivity, soil nitrate concentrations, and rates of potential
 nitrification as compared to nearby native-dominated communities. In our
 experimental plantings we found that two invasive species drove increases
 in soil nitrate and one invader caused increased productivity after a
 single season. 4. Synthesis:Our results highlight the importance of the
 N-cycling soil microbial community in how exotic invasive plants alter
 ecosystem function and show that shifts in function can occur rapidly.
description: Field, Experimental
 plot, and AOB data for JEcol-2015-0504.R1Microsoft Excel file,
 multiple tabs. Includes all all field collected, experimental plot, and
 AOB data for JEcol-2015-0504.R1.McLeodM JEcol 2016 Dryad
 Data.xlsx