cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t2gr862
title: Data from: Predicting contemporary range-wide genomic variation using climatic, phylogeographic and morphological knowledge in an ancient, unglaciated landscape

description: Aim: Understanding the spatial distribution of genetic variation across a
 species’ range is a central tenet in evolutionary biology and the ability
 to predict such patterns is valuable to conservation management. Genetic
 diversity and differentiation may be explained by present-day niche
 centrality, historical processes, or morphological variation across a
 species’ range, yet few studies evaluate these factors concurrently.
 Moreover, there is a particular lack of knowledge of the influence of
 these factors in ancient, unglaciated landscapes of the Southern
 Hemisphere. We investigate these concepts for their influence upon spatial
 patterns of genetic variation in a widespread plant species in a southern
 biodiversity hotspot. Location: South-western Australia. Taxon:
 Calothamnus quadrifidus. Methods: We use genotyping-by-sequencing to
 assess genome-wide diversity and differentiation across the range of
 Calothamnus quadrifidus, a morphologically variable species that occurs
 over a wide geographic range in an ancient, unglaciated landscape. We
 correlated the patterns of genetic diversity and differentiation with
 those predicted under four hypotheses regarding effects of geographic
 centrality, climatic centrality, historical phylogeography and
 morphological subspecies. Results:We found spatial variation in genetic
 diversity and strong population structuring, and while each hypothesis was
 consistent with some of these patterns, no hypothesis predicted the full
 extent of genetic diversity or structure in C. quadrifidus. Main
 Conclusions: Our results are indicative of a complex evolutionary history,
 with multiple factors shaping contemporary genetic variation in C.
 quadrifidus over time, rather than any one major driving factor. This is
 enabled by the greater capacity to build complex evolutionary signals in
 ancient, more stable landscapes like the southwest of Western Australia
 that aren’t as predictable as those within the younger, post-glacial
 landscapes of the Northern Hemisphere. Finally, our study demonstrates the
 importance of using an interdisciplinary approach to understanding the
 spatial patterns of genetic variation across species’ ranges and the
 influence of ecological, geographical and historical factors.
description: SNP genotype data for
 Calothamnus quadrifidus in STRUCTURE format.CQ_structurefile.txt
DOI: 10.5061/dryad.4319rp6
title: Data from: Perinatal exposure to glyphosate and a glyphosate-based herbicide affect spermatogenesis in mice

description: Glyphosate is the most widely used herbicide in the world. Several studies
 have investigated the effects of glyphosate and
 glyphosate-based-herbicides (GBHs) on male reproduction, but there is
 still little and conflicting evidence for its toxicity. In this study, we
 analyzed the effects of glyphosate, alone or in formula, on the male
 reproductive system. Pregnant mice were treated from E10.5 to 20 days
 postpartum (dpp) by adding glyphosate or a GBH (Roundup® 3 Plus) to their
 drinking water at 0.5 (the acceptable daily intake, ADI dose), 5 and 50
 mg/kg/day. Male offspring derived from treated mice were sacrificed at 5,
 20 and 35 days-old (d.o.) and 8 months-old (m.o.) for analysis. Our result
 showed that exposure to glyphosate, but not GBH, affect testis morphology
 in 20 d.o. and decrease serum testosterone concentrations in 35 d.o.
 males. We identified that the spermatozoa number decreased by 87% and 81%
 in 0.5 and 5 mg/kg/day of GBH and glyphosate groups, respectively.
 Moreover, the undifferentiated spermatogonia numbers were decreased by 60%
 in 5 mg/kg/day glyphosate group, which could be due to the alterations in
 the expression of genes involved in germ cell differentiation such as
 Sall4 and Nano3 and apoptosis as Bax and Bcl2. In 8 m.o. animals, a
 decreased testosterone level was observed in GBH groups. Our data
 demonstrate that glyphosate and GBHs could cause endocrine-disrupting
 effects on male reproduction at low doses. As glyphosate has effects at
 the ADI level, our data suggests that the current ADI for glyphosate could
 be overestimated.
description: Suppl Figure
 1Perinatal exposure to
 glyphosate and a GBH does not affect body weight in mice. Body weight of
 (A) 5, (B) 20 d.o. an 35 d.o. mice derived from control (Ctrl in grey),
 glyphosate (G0.5, G5, G50 in blue) and a GBH (R0.5, R5, R50 in
 green)-treated pregnant female mice.Suppl Figure
 2Perinatal exposure to
 glyphosate does not affect the expression of genes involved in
 endocrine-signaling pathway in 5 d.o. prepubertal mice. RT-QPCR analysis
 of RNA expression in control (Ctrl; in grey) and glyphosate groups (G0.5,
 G5, G50; in blue).
DOI: 10.5061/dryad.jt52151
title: Data from: Characterization of advanced glycation end products and their receptor (RAGE) in an animal model of myocardial infarction

description: Circulating advanced glycation end products (AGE) and their receptor,
 RAGE, are increased after a myocardial infarction (MI) episode and seem to
 be associated with worse prognosis in patients. Despite the increasing
 importance of these molecules in the course of cardiac diseases, they have
 never been characterized in an animal model of MI. Thus, the aim of this
 study was to characterize AGE formation and RAGE expression in plasma and
 cardiac tissue during cardiac remodeling after MI in rats. Adult male
 Wistar rats were randomized to receive sham surgery (n = 15) or MI
 induction (n = 14) by left anterior descending coronary artery ligation.
 The MI group was stratified into two subgroups based on postoperative left
 ventricular ejection fraction: low (MIlowEF) and intermediate
 (MIintermEF). Echocardiography findings and plasma levels of AGEs, protein
 carbonyl, and free amines were assessed at baseline and 2, 30, and 120
 days postoperatively. At the end of follow-up, the heart was harvested for
 AGE and RAGE evaluation. No differences were observed in AGE formation in
 plasma, except for a decrease in absorbance in MIlowEF at the end of
 follow-up. A decrease in yellowish-brown AGEs in heart homogenate was
 found, which was confirmed by immunodetection of N-ε-carboxymethyl-lysine.
 No differences could be seen in plasma RAGE levels among the groups,
 despite an increase in MI groups over the time. However, MI animals
 presented an increase of 50% in heart RAGE at the end of the follow-up.
 Despite the inflammatory and oxidative profile of experimental MI in rats,
 there was no increase in plasma AGE or RAGE levels. However, AGE levels in
 cardiac tissue declined. Thus, we suggest that the rat MI model should be
 employed with caution when studying the AGE-RAGE signaling axis or
 anti-AGE drugs for not reflecting previous clinical findings.
description: Western blots from
 plasma samples - RAGERaw
 images.Western
 blots.zipDatabaseIncludes all quantifiable registered data.Fracasso B. database 2018Dec20.csv
DOI: 10.5281/zenodo.15170923
title: Vegetation canopy height from 1970s and 1980s Hexagon spy satellite images for nine US forest types

description: This dataset features canopy height data derived from 1970s very-high (ca. 1-m) resolution KH-9 Hexagon spy satellite imagery using structure-from-motion point cloud analysis for nine sites of the National Ecological Observatory Network (NEON) in the United States. It also contains contemporary canopy height data for the same sites derived from contemporary airborne LiDAR-data as a reference.

Corresponding publication

Mihai D. Niță, Franz Schug*; Volker C. Radeloff. Changes in tree canopy height over half a century based on 1970s and 1980s Hexagon spy satellite images for nine US forest types (submitted).

Temporal extent

The data contains data representative for ca. 1975 and ca. 2020 (see manuscript).

Data format and units

KH-9 Hexagon data (“hex_images”) are provided as geotiff files with a spatial resolution of ~ 0.6 – 1 m. 

Historic (“hist_canopy_height”) and contemporary (“cont_canopy_height”) canopy height data are provided for nine focus areas in the NEON sites, respectively, as geotiff files with a spatial resolution of ~ 0.6 – 1 m (see manuscript).

Canopy height statistics (“canopy_height_statistics”) are provided as tabular (.csv) data and contain the following information:

*.csv: Descriptive statistics of historic and contemporary canopy height in the focus areas (in m). Avg = average, Std = standard deviation, q10 = 10th percentile, Q90 = 90th percentile, range = range. 

*_change.csv: Fraction of focus areas (in sqm) that fall into seven loss/gain categories according to the publication. 

Further information

For further information, please see the publication or contact Franz Schug (fschug@wisc.edu). Visit the website of SILVIS lab, University of Wisconsin-Madison (https://silvis.forest.wisc.edu/).
DOI: 10.5281/zenodo.15170922
title: Vegetation canopy height from 1970s and 1980s Hexagon spy satellite images for nine US forest types

description: This dataset features canopy height data derived from 1970s very-high (ca. 1-m) resolution KH-9 Hexagon spy satellite imagery using structure-from-motion point cloud analysis for nine sites of the National Ecological Observatory Network (NEON) in the United States. It also contains contemporary canopy height data for the same sites derived from contemporary airborne LiDAR-data as a reference.

Corresponding publication

Mihai D. Niță, Franz Schug*; Volker C. Radeloff. Changes in tree canopy height over half a century based on 1970s and 1980s Hexagon spy satellite images for nine US forest types (submitted).

Temporal extent

The data contains data representative for ca. 1975 and ca. 2020 (see manuscript).

Data format and units

KH-9 Hexagon data (“hex_images”) are provided as geotiff files with a spatial resolution of ~ 0.6 – 1 m. 

Historic (“hist_canopy_height”) and contemporary (“cont_canopy_height”) canopy height data are provided for nine focus areas in the NEON sites, respectively, as geotiff files with a spatial resolution of ~ 0.6 – 1 m (see manuscript).

Canopy height statistics (“canopy_height_statistics”) are provided as tabular (.csv) data and contain the following information:

*.csv: Descriptive statistics of historic and contemporary canopy height in the focus areas (in m). Avg = average, Std = standard deviation, q10 = 10th percentile, Q90 = 90th percentile, range = range. 

*_change.csv: Fraction of focus areas (in sqm) that fall into seven loss/gain categories according to the publication. 

Further information

For further information, please see the publication or contact Franz Schug (fschug@wisc.edu). Visit the website of SILVIS lab, University of Wisconsin-Madison (https://silvis.forest.wisc.edu/).
DOI: 10.5061/dryad.15d8dq8
title: Data from: Genome-wide markers untangle the green-lizard radiation in the Aegean Sea and support a rare biogeographical pattern

description: Aim: The Aegean Sea constitutes a major biogeographic barrier between the
 European and Asian continents and several models of diversification in the
 Aegean have been documented. Here we test three of those models for the
 Aegean green-lizards (Lacerta trilineata–pamphylica group): Vicariance vs.
 Overland Dispersal vs. Island Stepping-stone Dispersal. We investigate
 these hypotheses and complement our knowledge on the impact of the Aegean
 Barrier on east Mediterranean taxa. Location: Aegean Sea, east
 Mediterranean Taxon: Lacerta lizards Methods: We analysed ddRAD loci
 (double-digest restriction-site-associated DNA) to estimate species-trees
 under coalescent models and maximum likelihood trees using concatenation.
 We performed hierarchical population structure analyses and inferred
 ancestral distribution-areas. We also sequenced the complete cytochrome b
 gene and produced a time-calibrated mtDNA gene-tree tree to conduct a
 critical comparison with previous studies. Results: Aegean green-lizards
 diverged into four main groups in parallel during the Late Pliocene with
 distributions to the East and West of the Aegean. The Eastern group
 includes Lacerta pamphylica and East Aegean L. trilineata, while the
 Western group contains the Central Cyclades populations and the remaining
 populations of the Balkan Peninsula. The Aegean green-lizards’ ancestor
 occurred in Anatolia, while the West lineage ancestor occurred in the
 Central Cyclades islands, revealing a dispersal between the two regions.
 The radiations of all major green-lizard groups, including
 trilineata+pamphylica, occurred in parallel in the Late Pliocene. Main
 Conclusions: In contrast to previously suggested biogeographical
 hypotheses for the group, based on mtDNA, the Island Stepping-stone
 Dispersal scenario is strongly supported. Green lizards offer a rare
 paradigm of diversification in the Aegean, where populations largely
 expanded their geographical distribution and crossed the Aegean Barrier by
 using the central Aegean islands as stepping stones.
description: Biallelic uSNPs input
 file for SNAPPBiallelic uSNPs input
 file for SNAPPLacerta_biallelic_uSNPs_SNAPP.xmlConcatenated ddRAD loci input file for maximum likelihoodConcatenated ddRAD loci input file for maximum likelihoodLacerta_Concat_ML.phyuSNPs input file for STRUCTUREuSNPs input file for STRUCTURELacerta_uSNPs_STRUCTURE.ustruSNPs input file for SVDquartetsuSNPs input file for SVDquartetsLacerta_uSNPs_SVD.phy
DOI: 10.5061/dryad.83765sm
title: Data from: Genetic analyses reveal complex dynamics within a marine fish management area

description: Genetic data have great potential for improving fisheries management by
 identifying the fundamental management units – i.e. the biological
 populations - and their mixing. However, so far the number of practical
 cases of marine fisheries management using genetics has been limited.
 Here, we used Atlantic cod in the Baltic Sea to demonstrate the
 applicability of genetics to a complex management scenario involving
 mixing of two genetically divergent populations. Specifically, we
 addressed several assumptions used in the current assessment of the two
 populations. Through analysis of 483 single nucleotide polymorphisms
 (SNPs) distributed across the Atlantic cod genome we confirmed that a
 model of mechanical mixing, rather than hybridization and introgression,
 best explained the pattern of genetic differentiation. Thus, the fishery
 is best monitored as a mixed-stock fishery. Next, we developed a targeted
 panel of 39 SNPs with high statistical power for identifying population of
 origin and analysed more than 2000 tissue samples collected between 2011
 and 2015 as well as 260 otoliths collected in 2003/2004. These data
 provided high spatial resolution and allowed us to investigate
 geographical trends in mixing, to compare patterns for different life
 stages and to investigate temporal trends in mixing. We found similar
 geographical trends for the two time points represented by tissue and
 otolith samples and that a recently implemented geographical management
 separation of the two populations provided a relatively close match to
 their distributions. In contrast to the current assumption, we found that
 patterns of mixing differed between juveniles and adults, a signal likely
 linked to the different reproductive dynamics of the two populations.
 Collectively, our data confirm that genetics is an operational tool for
 complex fisheries management applications. We recommend focussing on
 developing population assessment models and fisheries management
 frameworks to capitalize fully on the additional information offered by
 genetically assisted fisheries monitoring.
description: Genotypes and biological
 dataGenotypes and biological
 data. Genotypes are coded with three digit alleles.Dryad_data.xlsx
DOI: 10.5061/dryad.v7q827k
title: Data from: Trilobite evolutionary rates constrain the duration of the Cambrian explosion

description: Trilobites are often considered exemplary for understanding the Cambrian
 explosion of animal life, due to their unsurpassed diversity and
 abundance. These biomineralized arthropods appear abruptly in the fossil
 record with an established diversity, phylogenetic disparity, and
 provincialism at the beginning of Cambrian Series 2 (~521 Ma), suggesting
 a protracted but cryptic earlier history that possibly extends into the
 Precambrian. However, recent analyses indicate elevated rates of
 phenotypic and genomic evolution for arthropods during the early Cambrian,
 thereby shortening the phylogenetic fuse. Furthermore, comparatively
 little research has been devoted to understanding the duration of the
 Cambrian explosion, after which normal Phanerozoic evolutionary rates were
 established. We test these hypotheses by applying Bayesian tip-dating
 methods to a comprehensive new dataset of Cambrian trilobites. We show
 that trilobites have a Cambrian origin, as supported by the trace fossil
 record and molecular clocks. Surprisingly, they exhibit constant
 evolutionary rates across the entire Cambrian, for all aspects of the
 preserved phenotype: discrete, meristic and continuous morphological
 traits. Our data therefore provide robust, quantitative evidence that by
 the time the ‘typical’ Cambrian fossil record begins (~521 Ma), the
 Cambrian explosion had already largely concluded. This suggests that a
 modern-style marine biosphere had rapidly emerged during the latest
 Ediacaran and earliest Cambrian (~20 million years), followed by
 broad-scale evolutionary stasis throughout the remainder of the Cambrian.
description: Dataset_1_Taxa,Dates,CodingRefsExcel file containing the taxon list, associated stratigraphic/age data, and references for character codings.Dataset_2_Discrete_charactersNexus file containing the discrete data matrix; characters and states are described in annotations (see detailed list in SI on journal website).Dataset_3_Meristic_Continuous_charactersExcel file containing the meristic and continuous data matrices; characters and states are described more fully in SI on journal website. The measurements underlying continuous character 111 are also presented.Dataset_4_BEAST_and_BEAST2Zipped file containing the executable xml files for the BEAST and BEAST2 analyses of the combined discrete, meristic and continuous data, as well as the consensus trees in Nexus (FigTree) and pdf format. The Nexus trees contain extensive node and branch annotations, only some of which are shown in the pdf.Dataset_5_TNTZipped file containing the executable plain-text file for the TNT analysis of the combined discrete, meristic and continuous data, as well as the output log and tree files in Nexus and pdf format.
DOI: 10.5061/dryad.85g65v8
title: Data from: Microbiome acquisition during larval settlement of the barnacle Semibalanus balanoides

description: Barnacles are conspicuous members of rocky intertidal communities and
 settlement of the final larval stage, the cyprid, is influenced by the
 presence of biofilms. While modulation of cyprid settlement by biofilms
 has been studied extensively, the acquisition of a specific microbiome by
 the settling larva has not. This study investigated settlement in the
 field of Semibalanus balanoides in two consecutive years when the
 composition of the benthic bacterial community differed. In both years,
 settling cyprids adopted a specific sub-set of benthic bacteria that was
 distinct from the planktonic cyprid and the benthos. This microbiome was
 consistent, regardless of annual variability in the benthic community
 structure, and established within hours of settlement. The results imply
 that a natural process of selection occurs during the critical final
 transition of S. balanoides to the sessile form. The apparent consistency
 of this process between years suggests that optimal growth and survival of
 barnacles could depend upon a complex inter-kingdom relationship, as has
 been demonstrated in other animal systems.
description: SUP2A .biom file containing
 the raw sequencing data used in the analysis.
DOI: 10.5061/dryad.84rs783
title: Data from: Plant interactions shape pollination networks via nonadditive effects

description: Plants grow in communities where they interact with other plants and with
 other living organisms such as pollinators. On the one hand, studies of
 plant–plant interactions rarely consider how plants interact with other
 trophic levels such as pollinators. On the other, studies of plant–animal
 interactions rarely deal with interactions within trophic levels such as
 plant–plant competition and facilitation. Thus, to what degree plant
 interactions affect biodiversity and ecological networks across trophic
 levels is poorly understood. We manipulated plant communities driven by
 foundation species facilitation and sampled plant–pollinator networks at
 fine spatial scale in a field experiment in Sierra Nevada, Spain. We found
 that plant–plant facilitation shaped pollinator diversity and structured
 pollination networks. Nonadditive effects of plant interactions on
 pollinator diversity and interaction diversity were synergistic in one
 foundation species networks while they were additive in another foundation
 species. Nonadditive effects of plant interactions were due to rewiring of
 pollination interactions. In addition, plant facilitation had negative
 effects on the structure of pollination networks likely due to increase in
 plant competition for pollination. Our results empirically demonstrate how
 different network types are coupled, revealing pervasive consequences of
 interaction chains in diverse communities.
description: Data of plant-insect
 interactionsSurvey of plant-insect
 interactions in the experiment.losapio_ecology_facilitation_pollination.csvR codelosapio_ecology19_facilitation_pollination.RR databaselosapio_ecology19_facilitation_pollination.RData
DOI: 10.5061/dryad.60q6876
title: Data from: The spatial ecology of sex ratios in a dioecious plant: relations between ramet and genet sex ratios

description: 1. In clonal dioecious plants, the frequency and spatial distribution of
 flowering ramets contains information on the underlying genet sex ratio.
 These measures can also provide insight on potential ecological mechanisms
 causing variation and bias in sex ratios among populations. 2. We used a
 novel likelihood-based approach and spatial clustering model to estimate
 the genet sex ratios from flowering ramet data collected from 32
 populations of dioecious Thalictrum pubescens, a clonal species from
 eastern N. America that occupies moist wetland and forested environments.
 We investigated sex ratios of seed families, clone size, patterns of
 flowering and plant height to determine potential causes of sex ratio
 bias. 3. Flowering ramet sex ratios varied considerably among populations
 but were significantly male-biased. Seed families grown to flowering also
 exhibited the same degree of male bias. Both models predicted close
 correspondence between ramet and genet sex ratios. The likelihood model
 revealed that gender differences in ramet production could not account for
 biased sex ratios. The spatial clustering model indicated that ramets were
 significantly clustered at two spatial scales and estimated similar
 cluster sizes and densities for both sexes. There was no evidence for
 spatial segregation of the sexes. Both sexes were equally likely to flower
 in consecutive years and repeated bouts of flowering had no effect on
 ramet height. 4. Synthesis. Our analyses suggest that the widespread
 occurrence of male-biased sex ratios in T. pubescens is unlikely to result
 from sexual differences in clonal growth or habitat preferences. The bias
 appears to become established early in the life cycle, perhaps at the seed
 stage as consequence of local resource competition.
description: GIS shape files of male
 and female ramet location dataGIS shape files
 containing male and female ramet location data used to analyze mechanisms
 underlying sex ratio variation.ShapeFiles.zipRamet production for male and female genotypesRAMETS PER PLANT.xlsxSurvivorship and sex ratio of seed families in glasshouse experimentSEX RATIO OF SEED FAMILIES.xlsx