cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qf4sj
title: Data from: Paleoenvironmental and paleobiogeographical implications of a Middle Pleistocene mollusc assemblage from the marine terraces of Baía das Pipas, southwest Angola

description: Quaternary raised marine terraces containing the remains of diverse,
 shallow water marine invertebrate faunas are widespread across coastal
 Angola. These deposits and faunas have not been studied in the same detail
 as contemporaneous features in northwest and southernmost Africa. We
 analyzed the fossil assemblages and sedimentology of two closely spaced
 Middle Pleistocene marine terrace deposits in Baía das Pipas, southwest
 Angola. This revealed 46 gastropod and 29 bivalve species, along with
 scleractinian corals, encrusting bryozoans, polychaete tubes, barnacles,
 and echinoids. The fauna is characteristic of intertidal and nearshore
 rocky substrates and sandy soft-bottom habitats. Sedimentological analysis
 is consistent with faunal data and indicates an upper shoreface
 paleoenvironment along a gravel coast. This diverse fauna stands out as a
 rare example of a marine Pleistocene assemblage from over 6,000 km of the
 West African coast. The assemblage is dominated by tropical West African
 molluscs, including species from the "Senegalese fauna" that
 colonized northern Africa and beyond during Pleistocene interstadials.
 Additionally, as along the modern Namibe Desert coast, the influence of
 the cool-water Benguela Current is apparent in the paleofauna by the
 occurrence of a few temperate species. The distribution and thermal
 tolerances of extant species identified in the Pipas fauna indicate that
 this region experienced similar climatic and oceanographic conditions as
 that of the present during this interstadial. Seasonal temperature varied
 between ~20 and 28 ºC and resulted from upwelling in this tropical
 setting.
description: SUPPLEMENTAL DATA
 1SUPPLEMENTAL DATA
 2Excel file containing
 supplementary materials.
DOI: 10.5061/dryad.q412q
title: Data from: Heritability of lifespan is largely sex-limited in Drosophila

description: Males and females differ with respect to lifespan and rate of aging in
 most animal species. Such sexual dimorphism can be associated with a
 complex genetic architecture, where only part of the genetic variation is
 shared between the sexes. To the extent this is true for lifespan and
 aging is not known, since studies of lifespan have given contradictory
 results and because aging has not been studied from this perspective. Here
 we investigate the additive genetic architecture of lifespan and aging in
 Drosophila melanogaster. We find substantial amounts of additive genetic
 variation for both traits, and that more than three quarters of this
 variation is available for sex-specific evolutionary change. This result
 shows that the sexes have a profoundly different additive genetic basis
 for these traits, which has several implications. First it translated into
 an, on average, three times higher heritability of lifespan within
 compared to between the sexes. Second, it implies that the sexes are
 relatively free to evolve with respect to these traits. And third, as
 lifespan and aging are traits that integrate over all genetic factors that
 contribute to mortal disease, it also implies that the genetics of
 heritable disease differs vastly between the sexes.
description: Lifespan
 dataLifespan was analyzed
 for 50 hemiclones expressed in males and females and in two different
 social environments. Each sex and environment was replicated in four vials
 with 50 focal flies in each - summing to 800 vials and ~40 000 flies. This
 file presents this data in three different ways. 1) Mean lifespan per
 vial. 2) the lifespan of each individual fly and 3) the number of flies
 that died at a specific age (in days) for each vial.
DOI: 10.5061/dryad.6pd36
title: Data from: Ontogenetic variation in epibiont community structure in the deep-sea yeti crab, Kiwa puravida: convergence among crustaceans

description: Recent investigations have demonstrated that unusually ‘hairy’ yeti crabs
 within the family Kiwaidae associate with two predominant filamentous
 bacterial families, the Epsilon and Gammaproteobacteria. These analyses,
 however, were based on samples collected from a single body region, the
 setae of pereopods. To more thoroughly investigate the microbiome
 associated with Kiwa puravida, a yeti crab species from Costa Rica, we
 utilized barcoded 16S rRNA amplicon pyrosequencing, as well as microscopy
 and terminal restriction fragment length polymorphism analysis. Results
 indicate that, indeed, the bacterial community on the pereopods is far
 less diverse than on the rest of the body (Shannon indices ranged from
 1.30–2.02 and 2.22–2.66, respectively). Similarly, the bacterial
 communities associated with juveniles and adults were more complex than
 previously recognized, with as many as 46 bacterial families represented.
 Ontogenetic differences in the microbial community, from egg to juvenile
 to adult, included a dramatic under-representation of the
 Helicobacteraceae and higher abundances of both Thiotrichaceae and
 Methylococcaceae for the eggs, which paralleled patterns observed in
 another bacteria–crustacean symbiosis. The degree to which abiotic and
 biotic feedbacks influence the bacterial community on the crabs is still
 not known, but predictions suggest that both the local environment and
 host-derived factors influence the establishment and maintenance of
 microbes associated with the surfaces of aquatic animals.
description: A4501_A25_MPyrotag reads acquired for sample A4501_A25_M, in fasta formatA4501_A25_PdPyrotag reads acquired for sample A4501_A25_Pd, in fasta formatA4501_A25_PmA4501_A35_PPyrotag reads acquired for sample A4501_A35_P, in fasta formatA4501_J2.5Pyrotag reads acquired for sample A4501_J2.5, in fasta formatA4511_J2.5Pyrotag reads acquired for sample A4511_J2.5, in fasta formatA4511_J2Pyrotag reads acquired for sample A4511_J2, in fasta formatA4511_J3.5A4511_J3Pyrotag reads acquired for sample A4511_J3, in fasta formatA4511_J6Pyrotag reads acquired for sample A4511_J6, in fasta formatA4586_A22Pyrotag reads acquired for sample A4586_A22, in fasta formatA4586_J5Pyrotag reads for sample A4586_J5, in fasta formatA4586_J9Pyrotag reads for sample A4586_J9, in fasta formatA4587_EggsPyrotag reads for sample A4587_eggs, in fasta format
DOI: 10.5281/zenodo.18268826
title: Project results Teaching competencies and active learning methods. An evaluative research study with pre-service social science teachers

description: The questionnaire for gathering opinions on history teaching methodology among in-service teachers in Spain, along with the resulting data, has been submitted. These results are drawn from the research project "Teaching Competencies and Active Learning Methods: An Evaluative Study with Pre-service Social Science Teachers". Funding entity: Ministry of Science, Innovation and Universities. Duration: January 1, 2019 to December 31, 2020. Grant amount: EUR 13,310. Principal investigators: Pedro Miralles Martínez and Cosme Jesús Gómez Carrasco. Number of participating researchers: 12.
DOI: 10.5281/zenodo.18390507
title: Project results Teaching competencies and active learning methods. An evaluative research study with pre-service social science teachers

description: The questionnaire for gathering opinions on history teaching methodology among in-service teachers in Spain, along with the resulting data, has been submitted. These results are drawn from the research project "Teaching Competencies and Active Learning Methods: An Evaluative Study with Pre-service Social Science Teachers". Funding entity: Ministry of Science, Innovation and Universities. Duration: January 1, 2019 to December 31, 2020. Grant amount: EUR 13,310. Principal investigators: Pedro Miralles Martínez and Cosme Jesús Gómez Carrasco. Number of participating researchers: 12.
DOI: 10.5061/dryad.kd2n4
title: Data from: Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies

description: Gobioidei is one of the largest suborders of teleost fishes, with nearly
 2000 extant species currently recognized. They have a worldwide
 distribution and show a spectacular variety in morphology, ecology, and
 behavior. Despite their importance, phylogenetic relationships among many
 groups of gobioids (including some of the major lineages) still remain
 poorly understood. In this study, we analyze sequence data of five
 molecular markers (two mitochondrial and three nuclear) averaging 6000 bp
 for 222 species of gobioids. Our study is the first to include both
 multiple nuclear and mitochondrial genes to reconstruct a comprehensive
 multilocus phylogeny of gobioids encompassing most major lineages
 representing the overall diversity of one of the most speciose vertebrate
 lineages. Two separate datasets are produced and used to specifically
 address the phylogenetic placement of Rhyacichthyidae and Odontobutidae,
 and the phylogenetic relationships among the lineages of Gobioidei. Our
 results strongly support that the initial split in the gobioid tree
 separated a clade containing Rhyacichthyidae + Odontobutidae as the sister
 group of all other lineages. The family Eleotrididae branches off the
 gobioid tree after the Rhyacichthyidae + Odontobutidae clade, followed by
 the Butidae as sister to the Gobiidae. Additionally, several major
 monophyletic groups are confidently identified within the two major
 Gobiidae subclades, the gobiine-like gobiids and the gobionelline-like
 gobiids. Robustness of the phylogenetic trees inferred here is
 significantly higher than that of previous studies, hence our results
 provide the most compelling molecular phylogenetic hypothesis of Gobioidei
 thus far. For the first time, we provide a comprehensive sampling of
 European gobies that traditionally have been divided into “transverse” and
 “sand gobies”. We show that the European gobies cluster in three distinct
 lineages, the Pomatoschistus-, Aphia-, and Gobius-lineages. The former
 resolved within the gobionelline-like gobiids and the latter two within
 the gobiine-like gobiids. These findings have significant implications for
 our understanding of the phylogeographic origin of European gobies in the
 light of the closure of the Paratethys. A rogue taxon analysis identified
 Kraemeria as an unstable taxon decreasing support at the base of the
 gobiine-like gobiids. Removal of this rogue taxon significantly increased
 phylogenetic resolution in that part of the tree and revealed additional
 insights into early bursts of cladogenesis of the gobiine-like gobiids.
description: Master alignment of the
 main datasetThis dataset includes
 concatenated sequence data of mitochondrial rRNA and cytb, and nuclear
 rag1, sreb2, and zic1 for 222 gobioid specimensMain_dataset.phyMaster alignment of the root datasetThis dataset includes concatenated sequence data of mitochondrial rRNA and cytb, and nuclear rag1, sreb2, and zic1 for 29 gobioid specimens and 2 outgroupsRoot_dataset.phy
DOI: 10.5061/dryad.d83g1
title: Data from: Strike mechanics of an ambush predator: the spearing mantis shrimp

description: Ambush predation is characterized by an animal scanning the environment
 from a concealed position and then rapidly executing a surprise attack.
 Mantis shrimp (Stomatopoda) consist of both ambush predators (ʻspearersʼ)
 and foragers (ʻsmashersʼ). Spearers hide in sandy burrows and capture
 evasive prey, whereas smashers search for prey away from their burrows and
 typically hammer hard-shelled, sedentary prey. Here, we examined the
 kinematics, morphology and field behavior of spearing mantis shrimp and
 compared them with previously studied smashers. Using two species with
 dramatically different adult sizes, we found that strikes produced by the
 diminutive species, Alachosquilla vicina, were faster (mean peak speed
 5.72±0.91 m s^−1; mean duration 3.26±0.41 ms) than the strikes produced by
 the large species, Lysiosquillina maculata (mean peak speed 2.30±0.85 m
 s^−1; mean duration 24.98±9.68 ms). Micro-computed tomography and
 dissections showed that both species have the spring and latch structures
 that are used in other species for producing a spring-loaded strike;
 however, kinematic analyses indicated that only A. vicina consistently
 engages the elastic mechanism. In the field, L. maculata ambushed evasive
 prey primarily at night while hidden in burrows, striking with both long
 and short durations compared with laboratory videos. We expected ambush
 predators to strike with very high speeds, yet instead we found that these
 spearing mantis shrimp struck more slowly and with longer durations than
 smashers. Nonetheless, the strikes of spearers occurred at similar speeds
 and durations to those of other aquatic predators of evasive prey.
 Although counterintuitive, these findings suggest that ambush predators do
 not actually need to produce extremely high speeds, and that the very
 fastest predators are using speed to achieve other mechanical feats, such
 as producing large impact forces.
description: data.filesDescription of 3 data files and associated MatLab files. The data files are named "Field.behavior.data.txt", "Strike.data.txt", and "Lmaculata.raw.digitizing.data.xls". The 2 text files tab delimitated. A detailed description of "Field.behavior.data.txt" can be found in "Field.behavior.Description.txt" in the ReadMe file. A detailed description of the data files "Strike.data.txt" and "Lmaculata.raw.digitizing.data.xls" can be found in "Strike.data.Description" in the ReadMe file. The associated MatLab files are also described in the "Strike.data.Description" text file.
DOI: 10.5061/dryad.j1917
title: Data from: Ecological determinants of mating system within and between three Fagus sylvatica populations along an elevational gradient

description: Studies addressing the variation of mating system between plant
 populations rarely account for the variability of these parameters between
 individuals within populations, although this variability is often
 non-negligible. Here, we propose a new direct method based on paternity
 analyses (Mixed Effect Mating Model) to estimate individual migration (mi)
 and selfing rates (si) together with the pollen dispersal kernel. Using
 this method and the KINDIST approach, we investigated the variation of
 mating system parameters within and between three populations of Fagus
 sylvatica along an elevational gradient. Among the mother trees, si varied
 from 0% to 48%, mi varied from 12% to 86% and the effective number of
 pollen donors (Nepi) varied from 2 to 364. The mating patterns differed
 along the gradient, the top population showing higher m and lower s, and a
 trend to higher Nep than the bottom populations. The phenological lag
 shaped long-distance pollen flow both within population (by increasing mi
 at mother-tree level) and between populations (by increasing m at high
 elevation). Rather than the mate density, the canopy density was detected
 as a major mating system determinant within population; it acted as a
 barrier to pollen flow, decreasing the proportion of long-distance pollen
 flow and increasing si. Overall, the effects of ecological factors on
 mating system were not the same within vs. between populations across the
 gradient, and these factors also differed from those traditionally found
 to shape variation at range-wide scale, highlighting the interest of
 multiscale approaches.
description: Genotype of Fagus
 sylvatica adult and seedlings at Mont VentouxGeneticData.txtEcological variables measured in Fagus sylvatica plots in Mont VentouxEcologicalData.txt
DOI: 10.5061/dryad.jt683
title: Data from: Meta-analysis reveals lower genetic diversity in overfished populations

description: While population declines can drive the loss of genetic diversity under
 some circumstances, it has been unclear whether this loss is a general
 consequence of overharvest in highly abundant marine fishes. Here, we use
 a phylogenetic approach across 160 species and 11,658 loci to show that
 allelic richness was on average 11% lower (p &lt; 0.0001) in
 overharvested populations, even after accounting for the effects of body
 size, latitude, and other factors. Heterozygosity was 2% lower (p =
 0.030). Simulations confirmed that these patterns are consistent with a
 recent bottleneck in abundant species and also showed that our analysis
 likely underestimates the loss of rare alleles by a factor of two or
 three. This evidence suggests that overharvest drives the decay of genetic
 diversity across a wide range of marine fishes. Such reductions of genetic
 diversity in some of the world’s most abundant species may lead to a
 long-term impact of fishing on their evolutionary potential, particularly
 if abundance remains low and diversity continues to decay.
description: Modified BOTTLESIM
 source codeSource code from
 BOTTLESIM program, modified slightly to report A50 (allelic richness from
 50 individuals), to work for population sizes &gt;1000, and to compile
 under Mac OS X 10.8.4 with XCode. The code only allows use of the
 "Diploid singlelocus, constant population size" simulation
 module. For original source code, see Kuo, C.-H. & Janzen, F.J.
 (2003). BOTTLESIM: a Bottleneck Simulation Program for Long-Lived Species
 With Overlapping Generations. Molecular Ecology Notes, 3, 669–673,
 available from
 http://chkuo.name/software/BottleSim.html.BottleSimA50.cppR code for bottlenecks in stepping-stone populationsScript written for R to simulate a bottleneck in a set of populations connected by stepping-stone migration. Assumes diploid individuals and calculates the number of immigrants from each population as a Poisson random number with mean m*Ne2 (for a total of 2*m*Ne2 alleles). We use Ne2 from the focal population (the one receiving the immigrants). Returns a list with two vectors: 1) meanA (allelic richness for each generation, where the first entry is the pre-bottleneck value); and 2) meanHe (expected heterozygosity for each generation, where the first entry is the pre-bottleneck value).bottle_step 2013-04-14.rGenetic diversity databaseThis CSV (comma-separated) file contains microsatellite diversity data from marine fishes that was compiled from published papers, theses, and white papers. See our published paper for the criteria we used to select data. The readme file explains the columns.divloci_2013-07-06.csv
DOI: 10.15159/phytop.158
title: Hurmi

description: Phytoplankton biomass, diversity and abundance in samples collected from Lake Hurmi during the period 1960-2015.
DOI: 10.5061/dryad.7nv16
title: Data from: Phylogeography of the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of southeastern Mexico

description: We quantify the population divergence processes that shaped population
 genetic structure in the Trans-Volcanic bunchgrass lizard (Sceloporus
 bicanthalis) across the highlands of south-eastern Mexico. Multilocus
 genetic data from nine nuclear loci and mitochondrial (mt)DNA were used to
 estimate the population divergence history for 47 samples of
 S. bicanthalis. Bayesian clustering methods partitioned S. bicanthalis
 into three populations: (1) a southern population in Oaxaca and southern
 Puebla; (2) a population in western Puebla; and (3) a northern population
 with a broad distribution across Hidalgo, Puebla, and Veracruz. The
 multilocus nuclear data and mtDNA both supported a Late Pleistocene
 increase in effective population size, and the nuclear data revealed low
 levels of unidirectional gene flow from the widespread northern population
 into the southern and western populations. Populations of S. bicanthalis
 experienced different demographic histories during the Pleistocene, and
 phylogeographical patterns were similar to those observed in many
 co-distributed highland taxa. Although we recommend continuing to
 recognize S. bicanthalis as a single species, future research on the
 evolution of viviparity could gain novel insights by contrasting
 physiological and genomic patterns among the different populations located
 across the highlands of south-eastern Mexico.
description: BPP data
 fileInput data file for BPP
 species delimitation: Multilocus nuclear data (phased) for Sceloporus
 bicanthalis.bicanth.txtBPP control fileControl file used in BPP for species delimitation.bicanthA.ctlBPP Imap fileBPP input file for mapping sequences to species for species delimitationbicanthalis_mapping.txtSTAR-BEAST XML fileSTAR-BEAST XML file for Sceloporus bicanthalis species tree analysis, contains multilocus nuclear data.bicanthFOSSIL.xmlGPhoCS control fileControl file for running GPhoCS program.bicanthG1.ctlND1 nexus fileNexus file, formatted with MrBayes block for running Bayesian phylogenetic analysis of the ND1 data.ND1goldrun2.nexStructurama input fileMultilocus nuclear data input file for running Structurama.bicanth.in
DOI: 10.5061/dryad.81p60
title: Data from: Environmental and historical imprints on beta diversity: insights from variation in rates of species turnover along gradients

description: A common approach for analysing geographical variation in biodiversity
 involves using linear models to determine the rate at which species
 similarity declines with geographical or environmental distance and
 comparing this rate among regions, taxa or communities. Implicit in this
 approach are weakly justified assumptions that the rate of species
 turnover remains constant along gradients and that this rate can therefore
 serve as a means to compare ecological systems. We use generalized
 dissimilarity modelling, a novel method that accommodates variation in
 rates of species turnover along gradients and between different gradients,
 to compare environmental and spatial controls on the floras of two regions
 with contrasting evolutionary and climatic histories: southwest Australia
 and northern Europe. We find stronger signals of climate history in the
 northern European flora and demonstrate that variation in rates of species
 turnover is persistent across regions, taxa and different gradients. Such
 variation may represent an important but often overlooked component of
 biodiversity that complicates comparisons of distance–decay relationships
 and underscores the importance of using methods that accommodate the
 curvilinear relationships expected when modelling beta diversity.
 Determining how rates of species turnover vary along and between gradients
 is relevant to understanding the sensitivity of ecological systems to
 environmental change.
description: Plant species
 distribution, seed dispersal traits, and environmental data for southwest
 AustraliaPlant distribution data
 from the Western Australia Herbarium. Environmental data from worldclim
 (climate) and the Australian Natural Resources Data Library (soils). See
 publication for details.SWWA.env.spp.dat.csvPlant species distribution, seed dispersal traits, and environmental data for northern EuropePlant distribution data from Atlas Florae Europaeae. Environmental data from worldclim (climate) and, for soils, Batjes, N. H. 1997 A world dataset of derived soil properties by FAO–UNESCO soil unit for global modelling. Soil Use and Management 13, 9–16. See publication for details.NOR_EU.env.spp.dat.csvR scripts used to perform analyses described in journal article.Annotated R scripts required to run GDM on plant distribution data.code4public_allAnalyses.R