cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d21d8
title: Data from: Different modes of migration among Late Cretaceous ammonoids in northwestern Hokkaido, Japan: evidence from the analyses of shell whorls

description: The thickness ratios of shell whorls (= whorl breadth / shell diameter) in
 the ammonoids Damesites sugata, Hypophylloceras subramosum, and
 Gaudryceras tenuiliratum from the Late Cretaceous outer shelf deposits in
 the Kotanbetsu area of northwestern Hokkaido, Japan, were examined in
 order to determine their mode of migration. The thickness ratios of D.
 sugata differ significantly with depth on the outer shelf environment, but
 show no significant difference laterally at a similar depth. These results
 suggest that D. sugata did not frequently migrate to different depths on
 the outer shelf environment, but tended to live and migrate laterally at a
 similar depth on the outer shelf. The thickness ratios of H. subramosum
 and G. tenuiliratum show no significant difference between different
 depths on the outer shelf environment nor for lateral direction at a
 similar depth. This suggests that H. subramosum and G. tenuiliratum
 frequently migrated at different depths on the out er shelf environment
 and laterally at a similar depth. There is no difference in hatchling
 diameters in all the examined species at different depths on the outer
 shelf environment, suggesting that the thickness ratios became manifest
 after the post-hatchling stage due to limited migration, which would have
 been in a nektobenthic habitat. The various modes of migration in the
 study area are reconstructed in this study, suggesting a diversified
 paleoecology of Late Cretaceous ammonoids.
description: Appendix1Appendix2Appendix3
DOI: 10.5061/dryad.v1r28
title: Data from:A large eagle (Aves, Accipitridae) from the early Miocene of Panama

description: We report the first Tertiary bird fossil from Central America, an ungual
 phalanx from a large, unknown genus and species of Accipitridae from the
 early Miocene Centenario Fauna, Panama. This specimen provides another
 example of a Neogene bird from North and Central America with its possible
 closest living relatives occurring today in Africa. In contrast, there is
 no evidence of African affinities among the reptile or mammal fossils from
 the Centenario Fauna.
description: Suppl.Doc.J.Paleo.Steadman.MacFaddenSupplemental File. Archival photo of the Gaillard Cut, Panama Canal, with annotations by Dr. John Turner concerning the fossil site (UF VP Locality YPA 002) where UF 281480 was collected. Image provided courtesy of J. Turner.
DOI: 10.5061/dryad.6df73
title: Data from: Evolutionary rescue of sexual and asexual populations in a deteriorating environment

description: The environmental change experienced by many contemporary populations of
 organisms poses a serious risk to their survival. From the theory of
 evolutionary rescue we predict that the combination of sex and genetic
 diversity should increase the probability of survival by increasing
 variation and thereby the probability of generating a type that can
 tolerate the stressful environment. We tested this prediction by comparing
 experimental populations of Chlamydomonas reinhardtii that differ in
 sexuality and in the initial amount of genetic diversity. The lines were
 serially propagated in an environment where the level of stress caused by
 salt increased over time from fresh water to the limits of marine
 conditions. In the long term, the combination of high diversity and
 obligate sexuality was most effective in supporting evolutionary rescue.
 Most of the adaptation to high-salt environments in the obligate
 sexual-high diversity lines had occurred by mid-way through the
 experiment, indicating that positive genetic correlations of adaptation to
 lethal stress with adaptation to sublethal stress greatly increased the
 probability of evolutionary rescue. The evolutionary rescue events
 observed in this study provide evidence that major shifts in ways of life
 can arise within short time frames through the action of natural selection
 in sexual populations.
description: assay_control_linesassay_selection_lines_gradient_trialhistorical_assay_sexual_linesreciprocal_transplantssalt_tolerance_ancestorstime_to_extinctionReadME
DOI: 10.5061/dryad.jk12v
title: Data from: Metapopulation dynamics of the mistletoe and its host in savanna areas with different fire occurrence

description: Mistletoes are aerial hemiparasitic plants which occupy patches of
 favorable habitat (host trees) surrounded by unfavorable habitat and may
 be possibly modeled as a metapopulation. A metapopulation is defined as a
 subdivided population that persists due to the balance between
 colonization and extinction in discrete habitat patches. Our aim was to
 evaluate the dynamics of the mistletoe Psittacanthus robustus and its host
 Vochysia thyrsoidea in three Brazilian savanna areas using a
 metapopulation approach. We also evaluated how the differences in terms of
 fire occurrence affected the dynamic of those populations (two areas
 burned during the study and one was fire protected). We monitored the
 populations at six-month intervals. P. robustus population structure and
 dynamics met the expected criteria for a metapopulation: i) the suitable
 habitats for the mistletoe occur in discrete patches; (ii) local
 populations went extinct during the study and (iii) colonization of
 previously non-occupied patches occurred. The ratio of occupied patches
 decreased in all areas with time. Local mistletoe populations went extinct
 due to two different causes: patch extinction in area with no fire and
 fire killing in the burned areas. In a burned area, the largest decrease
 of occupied patch ratios occurred due to a fire event that killed the
 parasites without, however, killing the host trees. The greatest mortality
 of V. thyrsoidea occurred in the area without fire. In this area, all the
 dead trees supported mistletoe individuals and no mortality was observed
 for parasite-free trees. Because P. robustus is a fire sensitive species
 and V. thyrsoidea is fire tolerant, P. robustus seems to increase host
 mortality, but its effect is lessened by periodic burning that reduces the
 parasite loads.
description: Metapopulation data -
 mistletoe abundance per host in three savanna areas with different fire
 occurrenceWe presented the data
 collected in field of mistletoe abundance per host in each survey realized
 for three sites with different fire occurrence.Metapopulation data - mistletoe
 abundance per host.xlsx
DOI: 10.5061/dryad.rr611
title: Data from: A novel landscape genetics approach demonstrates the effects of human disturbance on the Udzungwa red colobus monkey (Procolobus gordonorum)

description: A comprehensive understanding of how human disturbance affects tropical
 forest ecosystems is critical for the mitigation of future losses in
 global biodiversity. Although many genetic studies of tropical forest
 fragmentation have been conducted to provide insight into this issue,
 relatively few have incorporated landscape data to explicitly test the
 effects of human disturbance on genetic differentiation among populations.
 In this study, we use a newly developed landscape genetic approach that
 relies on a genetic algorithm to simultaneously optimize resistance
 surfaces to investigate the effects of human disturbance in the Udzungwa
 Mountains of Tanzania, which is an important part of a universally
 recognized biodiversity hotspot. Our study species is the endangered
 Udzungwa red colobus monkey (Procolobus gordonorum), which is endemic to
 the Udzungwa Mountains and a known indicator species that thrives in large
 and well-protected blocks of old growth forest. Population genetic
 analyses identified significant population structure among Udzungwa red
 colobus inhabiting different forest blocks, and Bayesian cluster analyses
 identified hierarchical structure. Our new method for creating composite
 landscape resistance models found that the combination of fire density on
 the landscape and distance to the nearest village best explains the
 genetic structure observed. These results demonstrate the effects that
 human activities are having in an area of high global conservation
 priority and suggest that this ecosystem is in a precarious state. Our
 study also illustrates the ability of our novel landscape genetic method
 to detect the impacts of relatively recent landscape features on a
 long-lived species.
description: Genotype and spatial
 data for Udzungwa red colobus monkeysThe data set includes
 the genotypes and spatial data for the samples used in the study: "A
 novel landscape genetics approach demonstrates the effects of human
 disturbance on the Udzungwa red colobus monkey (Procolobus
 gordonorum)". The data set includes: i) the genotypes for all the
 unique individuals identified; ii) the subset of genotypes for the
 individuals that were not related in first degree and were used for the
 landscape analyses; iii) the pairwise Rousset matrix for the individuals
 that were not related in first degree and were included in the landscape
 analyses and iv) the spatial coordinates for the individuals that were not
 related in first degree and were included in the landscape
 analyses.RuizLopezetalgenotypesandspatialdata.xlsx
DOI: 10.15468/dl.8pvya7
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Benthamiella patagonica",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 68 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000821-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fg8kf
title: Data from: Rapid polygenic response to secondary contact in a hybrid species

description: Secondary contact between closely related species can have genetic
 consequences. Competition for essential resources may lead to divergence
 in heritable traits that reduces interspecific competition, thus leading
 to increased genetic divergence. Conversely, hybridization and
 backcrossing can lead to genetic convergence. Here we study a population
 of a hybrid species, the Italian sparrow (Passer italiae), before and
 after it came into secondary contact with one of its parent species, the
 Spanish sparrow (P. hispaniolensis), in 2013. We demonstrate clear
 consequences of interspecific competition: Italian sparrows became
 outcompeted from a popular feeding site by its parent species, resulting
 in poorer body condition and a significant drop in population size.
 Although no significant morphological change could be detected, after only
 3 years of sympatry the Italian sparrows had diverged significantly from
 the Spanish sparrows across a set of 81 protein coding genes. These
 temporal genetic changes are mirrored by genetic divergence observed in
 older sympatric Italian sparrow populations within the same area of
 contact. Compared to microallopatric birds, sympatric ones are genetically
 more diverged from Spanish sparrows. Interestingly, all six significant
 outlier genes in the temporal or spatial comparison (i.e. those showing
 the greatest divergence from Spanish sparrows) have been found to be
 associated with learning and neural development in other species.
description: SNP
 genotypes327 individuals from 6
 localities were genotyped for a set of 81 (1 mitochondrial and 80 nuclear)
 genic, species-informative single nucleotide polymorphism (SNP).
 Individuals per line containing information of Locality, Population code,
 Individual identifier (ID), Sampling year, Species, and 81 loci. Genotyped
 loci are as follow: First marker is haploid, mitochondrial locus ND2_2,
 single allele shown in one column. Each following diploid locus presents
 two columns with biallelic information.proc B
 Data.txt
DOI: 10.5061/dryad.vk283
title: Data from: Mistletoe infection in an oak forest is influenced by competition and host size

description: Host size and distance from an infected plant have been previously found
 to affect mistletoe occurrence in woody vegetation but the effect of host
 plant competition on mistletoe infection has not been empirically tested.
 For an individual tree, increasing competition from neighbouring trees
 decreases its resource availability, and resource availability is also
 known to affect the establishment of mistletoes on host trees. Therefore,
 competition is likely to affect mistletoe infection but evidence for such
 a mechanism is lacking. Based on this, we hypothesised that the
 probability of occurrence as well as the abundance of mistletoes on a tree
 would increase not only with increasing host size and decreasing distance
 from an infected tree but also with decreasing competition by neighbouring
 trees. Our hypothesis was tested using generalized linear models (GLMs)
 with data on Loranthus europaeus Jacq., one of the two most common
 mistletoes in Europe, on 1015 potential host stems collected in a large
 fully mapped plot in the Czech Republic. Because many trees were
 multi-stemmed, we ran the analyses for both individual stems and whole
 trees. We found that the probability of mistletoe occurrence on individual
 stems was affected mostly by stem size, whereas competition had the most
 important effects on the probability of mistletoe occurrence on whole
 trees as well as on mistletoe abundance. Therefore, we confirmed our
 hypothesis that competition among trees has a negative effect on mistletoe
 occurrence.
description: Data on tree size,
 competition and mistletoe occurence on individual stemsData used in the article
 to test effects of tree size, neighbourhood competition and distance from
 nearest infected tree on probability of mistletoe infection and number of
 mistletoe plants on individual stems. Tree size is represented by diameter
 at breast height (DBH), competition by Hegyi competition index (CI_stem)
 and by number of trees in 12m radius around a tree. Distance data stand
 for the nearest distance to an infected stem infected by mistletoe of
 given minimum size (diameter in cm). Infection by mistletoe is indicated
 by 1 = infected, 2 = not infected.Data on tree size,
 competition and mistletoe occurence on whole treesData used in the article
 to test effects of tree size, neighbourhood competition and distance from
 nearest infected tree on probability of mistletoe infection on the whole
 trees (many of them multi-stem polycormons). Tree size is represented by
 basal area, mean stem basal area and the ranges of the trees/polycormons
 in given directions. Competition is represented by Hegyi competition index
 (CI_trees) calculated using basal areas of the whole trees and centres of
 trees/polycormons as positions. Infection by mistletoe is indicated by 1 =
 infected, 2 = not infected.
DOI: 10.5061/dryad.d11rv
title: Data from: Coordinated responses of soil communities to elevation in three subarctic vegetation types

description: Global warming has begun to have a major impact on the species composition
 and functioning of plant and soil communities. However, long-term
 community and ecosystem responses to increased temperature are still
 poorly understood. In this study, we used a well-established elevational
 gradient in northern Sweden to elucidate how plant, microbial and nematode
 communities shift with elevation and associated changes in temperature in
 three highly contrasting vegetation types (i.e. heath, meadow and Salix
 vegetation). We found that responses of both the abundance and composition
 of microbial and nematode communities to elevation differed greatly among
 the vegetation types. Within vegetation types, changes with elevation of
 plant, microbial and nematode communities were mostly linked at fine
 levels of taxonomic resolution, but this pattern disappeared when coarser
 functional group levels were considered. Further, nematode communities
 shifted towards more conservative nutrient cycling strategies with
 increasing elevation in heath and meadow vegetation. Conversely, in Salix
 vegetation microbial communities with conservative strategies were most
 pronounced at the mid-elevation. These results provide limited support for
 increasing conservative nutrient cycling strategies at higher elevation
 (i.e. with a harsher climate). Our findings indicate that climate-induced
 changes in plant community composition may greatly modify or counteract
 the impact of climate change on soil communities. Therefore, to better
 understand and predict ecosystem responses to climate change, it will be
 crucial to consider vegetation type and its specific interactions with
 soil communities.
description: Data Veen et
 al_Oikos_10.1111/oik.04158File contains plant,
 microbial and nematode abundance data + environmental variables (e.g. soil
 parameters) and a description of methods, plots and species/taxa (READ
 ME).Data
 soil biota Abisko ms_for Dryad.xlsx
DOI: 10.5061/dryad.13s7s
title: Data from: Links between plant and fungal diversity in habitat fragments of coastal shrubland

description: Habitat fragmentation is widespread across ecosystems, detrimentally
 affecting biodiversity. Although most habitat fragmentation studies have
 been conducted on macroscopic organisms, microbial communities and fungal
 processes may also be threatened by fragmentation. This study investigated
 whether fragmentation, and the effects of fragmentation on plants, altered
 fungal diversity and function within a fragmented shrubland in southern
 California. Using fluorimetric techniques, we assayed enzymes from plant
 litter collected from fragments of varying sizes to investigate enzymatic
 responses to fragmentation. To isolate the effects of plant richness from
 those of fragment size on fungi, we deployed litter bags containing
 different levels of plant litter diversity into the largest fragment and
 incubated in the field for one year. Following field incubation, we
 determined litter mass loss and conducted molecular analyses of fungal
 communities. We found that leaf-litter enzyme activity declined in smaller
 habitat fragments with less diverse vegetation. Moreover, we detected
 greater litter mass loss in litter bags containing more diverse plant
 litter. Additionally, bags with greater plant litter diversity harbored
 greater numbers of fungal taxa. These findings suggest that both plant
 litter resources and fungal function may be affected by habitat
 fragmentation's constraints on plants, possibly because plant species
 differ chemically, and may thus decompose at different rates. Diverse
 plant assemblages may produce a greater variety of litter resources and
 provide more ecological niche space, which may support greater numbers of
 fungal taxa. Thus, reduced plant diversity may constrain both fungal taxa
 richness and decomposition in fragmented coastal shrublands. Altogether,
 our findings provide evidence that even fungi may be affected by
 human-driven habitat fragmentation via direct effects of fragmentation on
 plants. Our findings underscore the importance of restoring diverse
 vegetation communities within larger coastal sage scrub fragments and
 suggest that this may be an effective way to improve the functional
 capacity of degraded sites.
description: decomposition
 manipulation litter bagsMass remaining in litter
 bags containing litter from increasing numbers of plant species, across
 experimental blocks.NBB litter
 bags.csvFungalTaxaFungal taxa from CSS plant litter in experimental plots; Taxonomy: phylum, class, order, family, genus, species; sequences generated via 454 and normalized to 562 sequences per sample.LitterEnzymeActivityLitter enzyme activity of plant litter from fragmented coastal sage scrub habitats; cellobiohydrolase, beta-glucosidase, and N-acetylglucosaminodase
DOI: 10.5061/dryad.157
title: Data from: Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm

description: The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and
 SSRs are a free by-product of the currently expanding EST (Expressed
 Sequence Tag) data bases. The development of high-throughput methods for
 the detection of SNPs (Single Nucleotide Polymorphism) and small indels
 (insertion / deletion) has led to a revolution in their use as molecular
 markers. Available (5452) Oil palm EST sequences were mined from dbEST of
 NCBI. CAP3 program was used to assemble EST sequences into contigs.
 Candidate SNPs and Indel polymorphisms were detected using the perl script
 auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel
 sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency
 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had
 been generated, mesocarp had high frequency of 2.91 SNPs and indels per
 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100
 bp. We also used the Shannon index to analyze the proportion of ten
 possible types of SNP/indels. ESTs from tissues of normal apex showed
 highest values of Shannon index (0.60) whereas abnormal apex had least
 value (0.02). The present report deals the use of Shannon index for
 comparing SNP/ indel frequencies mined from ESTlibraries and also confirm
 that the frequency of SNP occurrence in oil palm to use them as markers
 for genetic studies.
description: Interspecific Analysis
 for SNPs in EST Libraries of Oil Palm- Elaeis Guineensis and E.
 OleiferaOil palm is the second
 largest source of edible oil, which contributes to approximately 20% of
 the world's production of oils and fats. Expressed sequence tag (EST)
 sequencing programs have provided a wealth of information, identifying
 novel genes from a broad range of organisms and providing an indication of
 gene expression level in particular tissues. It also provides the richest
 source of biologically useful SNPs due to the relatively high redundancy
 of gene sequence, the diversity of genotypes represented within databases,
 and the fact that each SNP would be associated with an expressed gene.
 There are cultivated two species of oil palm, Elaeis guineensis Jacq. from
 tropical western Africa and E. oleifera from Americas. Interspecific SNP
 detection carried but by choosing Lambda Zap II libraries of both species.
 Auto_snp perl script was used to cluster the ESTs and detect SNPs. A total
 of 163 EST sequences belong to Lambda zap libraries analysed here,
 interestingly we have found 60 SNP site (35 Transition transversion 25 )
 in this species specific sequences. Labda Zap tissue also shows the
 similar pattern of SNPs, such as transition type mutation is higher than
 trasnversion type in Oil palm (Riju et al, 2007).Oil palm
 SNPs.pdf