cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6v89fj76
title: Data from: Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae)

description: Recent evidence suggests that survival of arctic-alpine organisms in
 peripheral or interior glacial refugia are not mutually exclusive and may
 both be involved in shaping an organisms’ Pleistocene history, yet
 potentially at different time levels. Here, we test this hypothesis in a
 high-mountain plant (diploid lineage of Senecio carniolicus, Asteraceae)
 from the Eastern European Alps, in which patterns of morphological
 variation and current habitat requirements suggest survival in both types
 of refugia. To this end, we used AFLPs, nuclear and plastid DNA sequences
 and analysed them, amongst others, within a graph theoretic framework and
 using novel Bayesian methods of phylogeographic inference. Based on
 patterns of genetic diversity, occurrence of rare markers, distribution of
 distinct genetic lineages, and patterns of range connectivity both
 interior refugia in the formerly strongly glaciated central Alps and
 peripheral refugia along the southern margin of the Alps were identified.
 The presence of refugia congruently inferred by markers resolving at
 different time levels suggests that these refugia acted as such throughout
 several glacial cycles. The high degree of range persistence together with
 gradual range expansion, which contrasts with the extent of range shifts
 implied for other Alpine species, is likely responsible for incipient
 lineage differentiation evident from the genetic data. Replacing a
 simplistic peripheral versus interior refugia dualism by more complex
 models involving both types of refugia and considering different time
 levels will help identifying common phylogeographic patterns with respect
 to, for instance, location of refugia and colonization routes and
 elucidating their underlying genetic and/or ecological causes.
description: SenecioCarniolicus_2x_13regions_reversible_model_run1BEAST input file using the reversible discrete phylogeographic model with 13 geographic regions using default settings for geographic model. Populations acronyms as in Table S1 (online supplementary material).SenecioCarniolicus_2x_8regions_irreversible_model_run1BEAST input file form irreversible discrete phylogeographic region with 8 geographic regions and default settings for the geographic model. Populations acronyms as in Table S1 (online supplementary material).SenecioCarniolicus_2x_AFLPmatrixAFLP data matrix. Populations acronyms as in Table S1 (online supplementary material)SenecioCarniolicus_2x_plus_outgroups_uncoded_plastidSequencesAlignment of plastid sequences from Senecio carniolicus and related taxa (the alignment with sequences coded for statistical parsimony analysis is available from TreeBase). Populations acronyms of S. carniolicus as in Table S1, out-group taxa information in Table S2 (online supplementary information)
DOI: 10.5061/dryad.mp924433
title: Data from: Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data

description: BACKGROUND: In trying to understand the evolutionary relationships of
 organisms, the current flood of sequence data offers great opportunities,
 but also reveals new challenges with regard to data quality, the selection
 of data for subsequent analysis, and the automation of steps that were
 once done manually for single-gene analyses. Even though genome or
 transcriptome data is available for representatives of most bilaterian
 phyla, some enigmatic taxa still have an uncertain position in the animal
 tree of life. This is especially true for myzostomids, a group of
 symbiotic (or parasitic) protostomes that are either placed with annelids
 or flatworms. METHODOLOGY: Based on similarity criteria, Illumina-based
 transcriptome sequences of one myzostomid were compared to protein
 sequences of one additional myzostomid and 29 reference Metazoa and
 clustered into gene families. These families were then used to investigate
 the phylogenetic position of Myzostomida using different approaches:
 Alignments of 989 sequence families were concatenated, and the resulting
 superalignment was analyzed under a Maximum Likelihood criterion. We also
 used all 1,878 gene trees with at least one myzostomid sequence for a
 supertree approach: the individual gene trees were computed and then
 reconciled into a species tree using gene tree parsimony. CONCLUSIONS:
 Superalignments require strictly orthologous genes, and both the gene
 selection and the widely varying amount of data available for different
 taxa in our dataset may cause anomalous placements and low bootstrap
 support. In contrast, gene tree parsimony is designed to accommodate
 multilocus gene families and therefore allows a much more comprehensive
 data set to be analyzed. Results of this supertree approach showed a
 well-resolved phylogeny, in which myzostomids were part of the annelid
 radiation, and major bilaterian taxa were found to be monophyletic.
description: geneTrees1878 gene trees used in our study
DOI: 10.5281/zenodo.18391434
title: 奈良田方言の昔話

description: この資料は、奈良田方言(山梨県南巨摩郡早川町奈良田)の昔話の語りの音声データとそれを文字化したものである。

収録は2003年と2005年に行った。語り手は次のかたである。

  深沢文江 氏(1924(大正13)年生まれ・女性・故人)

 収録した話は次の3種である。

「琴路(ことじ)のこと」 「よくばりなお上人」 「鳥呑み爺(とりのみじい)」

詳細は narada_fumie_mukasibanasi_v1_readme.pdf を参照してほしい。



Creative Commons Attribution 4.0 International として公開するが、語り手の尊厳を損なうような改変は禁止する。
DOI: 10.5061/dryad.34g16868
title: Data from: Allee effects may slow the spread of parasites in a coastal marine ecosystem

description: Allee effects are thought to mediate the dynamics of population
 colonization, particularly for invasive species. However, Allee effects
 acting on parasites have rarely been considered in the analogous process
 of infectious disease establishment and spread. We studied the
 colonization of uninfected wild juvenile Pacific salmon populations by
 ectoparasitic salmon lice (Lepeophtheirus salmonis) over four years. From
 a dataset of 67,896 fish, we observed 88 occurrences of pre-copular pair
 formation among 1258 pre-adult female and 611 adult male lice. The
 probability of pair formation was dependent on the local abundance of
 lice, but this mate limitation is likely offset somewhat by mate-searching
 dispersal of males among host fish. A mathematical model of macroparasite
 population dynamics that incorporates the empirical results suggests a
 high likelihood of a demographic Allee effect, which can cause the
 colonizing parasite populations to die out. These results may provide the
 first empirical evidence for Allee effects in a macroparasite.
 Furthermore, the data give a rare detailed view of Allee effects in
 colonization dynamics and suggest that Allee effects may dampen the spread
 of parasites in a coastal marine ecosystem.
description: Sea lice mate guarding
 databaseThese data were
 published as: Krkosĕk, M., B. Connors, M. Lewis, and R. Poulin, 2012.
 Allee effects may slow the spread of parasites in a coastal marine
 ecosystem. American Naturalist, In press. The data were gathered as part
 of a long-term monitoring program led by M. Krkosek of sea lice
 (Lepeophtheirus salmonis) on wild juvenile salmon in the Broughton
 Archipelago, British Columbia, Canada. The meta-data sheet gives relevant
 information for each collection of fish: Collection ID; Date; Longitude of
 collection; Latitude of collection; Sea surface temperature (Celsius,
 measuered with a thermometer); Sea surface salinity (parts per thousand,
 measured with a refractometer). The database gives the raw data for each
 collection of fish: Collection ID; Fish number within collection; Fish
 species (p=Pink salmon, Oncorhynchus gorbuscha; c=chum salmon, O. keta);
 Fork length of fish (mm); Number of adult male lice on each fish (Male);
 Number of pre-adult female lice on each fish (Female); Occurance of mate
 guarding (1=yes, 0=no).MG_Dryad_Data_FINAL.xlsx
DOI: 10.5061/dryad.1qr41s56
title: Data from: Determinants and dynamics of banded vegetation pattern migration in arid climates

description: Dense vegetation bands aligned parallel to contour levels and alternating
 at regular intervals with relatively barren interbands have been reported
 at the margins of all tropical deserts. Since their discovery in the
 1950s, it has been suspected that these vegetation bands migrate upslope,
 forming a space-time cyclic pattern. Evidence to date has been relatively
 sparse and indirect, and observations have remained conflicting.
 Unequivocal photographic evidence of upslope migration (a few dm yr-1) is
 provided here for three independent dryland areas exhibiting periodic
 banded pattern the U.S. northeastern Chihuahuan Desert (1), the Somalian
 Haud (2), and the Mediterranean steppes of eastern Morocco (3). Migration
 speeds, averaged through time and space using Fourier cross-spectral
 analysis, are shown to be directly proportional to pattern scale
 (wavelength). An aerial photography sequence of (1) showed that migration
 was not continuous but intermittent in response to fluctuating weather
 regimes. The rates at which bands expanded upslope and contracted
 downslope were better predicted by the change in annual rainfall than by
 its average level. However, migration of banded pattern cannot be
 considered as systematic because observations are reported from three
 other banded systems located in the Somalian Haud, central Australia, and
 western New South Wales in which migration was undetectable at the
 available image resolution. In each of the six sites under study, the
 modal value of band orientation axes was verified to be approximately
 orthogonal to the steepest slope. Our results underscore the importance of
 taking both the spatial structure and the past climate sequence into
 account for understanding vegetation dynamics in arid to semi-arid
 ecosystems. In addition, we show how Fourier spectral analysis applied to
 historical series of optical images can serve to quantify landscape
 dynamics at a decadal time scale.
description: CAData for site CA.
 Projection and datum for X and Y are UTM Zone 53 S, WGS
 1984.MSData for site MS.
 Projection and datum for X and Y are UTM Zone 30 N, WGS
 1984.NCDData for site NCD.
 Projection and datum for X and Y are UTM Zone 13 N, NAD
 1983.NSWData for site NSW.
 Projection and datum for X and Y are UTM Zone 54 S, WGS
 1984.SH1Data for site SH1.
 Projection and datum for X and Y are UTM Zone 38 N, WGS
 1984.SH2Data for site SH2.
 Projection and datum for X and Y are UTM Zone 39 N, WGS
 1984.NCD_time_seriesData for Fig. 5 & Fig. 6. Projection and datum of geotiff files are UTM Zone 13 N, NAD 1983.
DOI: 10.5281/zenodo.18391433
title: 奈良田方言の昔話

description: この資料は、奈良田方言(山梨県南巨摩郡早川町奈良田)の昔話の語りの音声データとそれを文字化したものである。

収録は2003年と2005年に行った。語り手は次のかたである。

  深沢文江 氏(1924(大正13)年生まれ・女性・故人)

 収録した話は次の3種である。

「琴路(ことじ)のこと」 「よくばりなお上人」 「鳥呑み爺(とりのみじい)」

詳細は narada_fumie_mukasibanasi_v1_readme.pdf を参照してほしい。



Creative Commons Attribution 4.0 International として公開するが、語り手の尊厳を損なうような改変は禁止する。
DOI: 10.5281/zenodo.18377716
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - ALMERIA - (June 24 - May 25)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2024, to May 31, 2025, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Almería:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5061/dryad.607ds5q5
title: Data from: Phylogeography of a Tertiary relict plant, Meconopsis cambrica (Papaveraceae), implies the existence of northern refugia for a temperate herb

description: The perennial herb Meconopsis cambrica, a western European endemic, is the
 only European species of the otherwise Himalayan genus Meconopsis and has
 been interpreted as a Tertiary relict species. Using rbcL and ITS sequence
 variation, we date the split between M. cambrica and its sister clade
 Papaver s.str. to the Middle to Upper Miocene (12.8 My, 6.4-19.2 My HPD).
 Within M. cambrica, cpDNA sequence variation reveals the existence of two
 groups of populations with a comparable level of genetic variation: a
 northern group from Great Britain, the Massif Central, the western
 Pyrenees and the Iberian System, and a southern group from the central and
 eastern Pyrenees. Populations from the Cantabrian Mountains were found in
 both groups. Based on ITS sequence variation, the divergence between these
 two groups can be dated to 1.5 My (0.4-2.8 My HPD), and the age of the
 British populations is estimated as 0.37 My (0.0-0.9 My HPD). AFLP results
 confirm the distinctive nature of the populations from Britain, the Massif
 Central and the central and eastern Pyrenees. These patterns of
 latitudinal variation of M. cambrica differ from patterns of longitudinal
 differentiation found in many other temperate species and imply glacial
 survival of the northern populations in northerly refugia. The primary
 differentiation into northern and southern cpDNA groups dates to near the
 onset of the Quaternary and suggests that an ancient phylogeographic
 pattern has survived through several glacial periods. Our data provide
 evidence that the species has persisted for a long period with a highly
 fragmented and probably very localized distribution.
description: M_cambrica_AFLP2
DOI: 10.5281/zenodo.18377715
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - ALMERIA - (June 24 - May 25)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2024, to May 31, 2025, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Almería:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5281/zenodo.18391680
title: Migration Survey Western Province, Zambia, 2022

description: The data were collected in June 2022 through structured interviews with household heads or other relevant household members (N=460). Interviews were conducted in fiveagricultural camps in Mongu district and one in Nalolo district. Ethical clearances were obtained from the institutional research ethics committees of Charles University (2022/15) and the University of Zambia (HSSREC-2022-MAY-014).
DOI: 10.5281/zenodo.18391681
title: Migration Survey Western Province, Zambia, 2022

description: The data were collected in June 2022 through structured interviews with household heads or other relevant household members (N=460). Interviews were conducted in fiveagricultural camps in Mongu district and one in Nalolo district. Ethical clearances were obtained from the institutional research ethics committees of Charles University (2022/15) and the University of Zambia (HSSREC-2022-MAY-014).
DOI: 10.5061/dryad.7pg045t2
title: Data from: Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)

description: PREMISE OF THE STUDY: The stability of the bimodal karyotype found in
 Agave and closely related species has long interested botanists. The
 origin of the bimodal karyotype has been attributed to allopolyploidy, but
 this hypothesis has not been tested. Next Generation transcriptome
 sequence data were used to test whether a paleopolyploid event occurred on
 the same branch of the Agavoideae phylogenetic tree as the origin of the
 Yucca-Agave bimodal karyotype. METHODS: Illumina RNAseq data were
 generated for phylogenetically strategic species in Agavoideae.
 Paleopolyploidy was inferred in analyses of frequency plots for synonymous
 substitutions per synonymous site (Ks) between Hosta, Agave and
 Chlorophytum paralogous and orthologous gene pairs. Phylogenies of gene
 families including paralogous genes for these species and outgroup species
 were estimated in order to place inferred paleopolyploid events on a
 species tree. KEY RESULTS: Ks frequency plots suggested paleopolyploid
 events in the history of the genera Agave, Hosta and Chlorophytum.
 Phylogenetic analyses of gene families estimated from transcriptome data
 revealed two polyploid events: one predating the last common ancestor of
 Agave and Hosta and one within the lineage leading to Chlorophytum.
 CONCLUSIONS: We found that allopolyoidy and the origin of the Yucca-Agave
 bimodal karyotype co-occur on the same lineage consistent with the
 hypothesis that the bimodal karyotype is a consequence of allopolyploidy.
 We discuss this and alternative mechanisms for the formation of the
 Yucca-Agave bimodal karyotype. More generally, we illustrate how the use
 of next generation sequencing technology is a cost-efficient means for
 assessing genome evolution in non-model species.
description: Agavoideae
 PolyploidyAgavoideae_polyploidy.tar.bz2
DOI: 10.5061/dryad.66h5g23t
title: Data from: The W100 pocket on HIV-1 gp120 penetrated by b12 is not a target for other CD4bs monoclonal antibodies

description: BACKGROUND: The conserved CD4 binding site (CD4bs) on HIV-1 gp120 is a
 major target for vaccines. It is a priority to determine sites and
 structures within the CD4bs that are important for inclusion in vaccines.
 We studied a gp120 pocket penetrated by W100 of the potent CD4bs
 monoclonal antibody (mab), b12. We compared HIV-1 envelopes and
 corresponding mutants that carried blocked W100 pockets to evaluate
 whether other CD4bs mabs target this site. FINDINGS: All CD4bs mabs tested
 blocked soluble CD4 binding to gp120 consistent with their designation as
 CD4bs directed antibodies. All CD4bs mabs tested (except for b12)
 neutralized pseudovirions carrying NL4.3 wt envelope. However, only b12
 failed to neutralize pseudoviruses carrying mutant envelopes with a
 blocked W100 pocket. Similarly, for CD4bs mabs that neutralized
 pseudovirions carrying primary envelopes, mutation of the W100 pocket had
 little or no effect on neutralization sensitivity. CONCLUSIONS: Our data
 indicate that the b12 W100 pocket on gp120 is targeted infrequently by
 CD4bs mabs. This site is therefore not a priority for preservation in
 vaccines aiming to elicit antibodies targeting the CD4bs.
description: Duenas-Decamp figure 2
 dataData set for figure
 2Duenas-Decamp figure 3
 dataData set for figure
 3Duenas-Decamp Additional
 figure 1 dataData set for Additional
 figure 1
DOI: 10.5061/dryad.hd301f6n
title: Data from: Generalized movement strategies for constrained consumers: ignoring fitness can be adaptive

description: Movements made by real organisms---such as movements involved in
 dispersal, migration, and habitat selection---are expected to be
 suboptimal occasionally due to realistic constraints imposed by incomplete
 information, perceptual limitations, and stochasticity. Previous theory
 considering such constraints has shown that movements appropriately
 conditioned upon habitat or resource characteristics can balance out
 suboptimal components of movement and thereby lead organisms to ideal free
 distributions and fitness maxima, whereas movements conditioned upon
 fitness differentials cannot. These findings suggest a somewhat
 paradoxical hypothesis: even if organisms have information about their
 fitness, movement strategies that maximize fitness may be conditioned upon
 something other than fitness per se. We test this hypothesis by
 investigating the evolutionary stability of generalized, conditional
 movement strategies that vary in their use of information on fitness
 versus information on habitat characteristics. We show that when costs of
 sensory machinery are included, natural selection should favor movement
 strategies that completely ignore fitness information. Finally, we
 synthesize previous work by showing how several previous important
 theoretical results on adaptive movement strategies are united under our
 one general model.
description: FilesForDryadThis .zip file includes the Matlab computer code and some simulation data used in the article. There is a readme.txt file which lists the function and scripts. The code is well-documented and includes specific information about each function.