cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2280gb5q5
title: Centaurea population effects on nematode communities

description: Data set belonging to the study 'Plant population and soil origin
 effects on nematode community composition in the rhizosphere of a
 range-expanding plant species and a native congener'. In this study,
 we experimentally compared the development of nematode communities
 originating from northern and southern European soils in the rhizospheres
 of different populations of the range-expanding plant species
 Centaurea stoebe and the native plant species Centaurea
 jacea. The experiment was carried out in a greenhouse of the Netherlands
 Institute of Ecology (NIOO-KNAW; Wageningen, The Netherlands). 
description: The presented nematode community data was collected from
 micro-cosms containing sterilized background soil inoculated with 10% live
 soil from either Slovenian or Dutch grassland systems. These microcosms
 were grown for 11 weeks with a single individual of <em>Centaurea
 stoebe, </em>a range-expanding plant species that recently has
 established in north-western Europe, or the native plant
 species <em>Centaurea jacea. </em>These plants originated from
 three different populations from both northern Europe (Netherlands) and
 southern Europe (Slovenia). After 11 weeks, aboveground and belowground
 plant parts were harvested, dried and weighed. Nematode communities were
 collected using Oostenbrink elutriators. Nematodes were identified up to
 trophic groups (bacterivores, fungivores, predators + omnivores) or, in
 the case of root-feeding nematodes, up to the level of family or
 genus. 
description: No missing values; a couple of samples (N = 4) were lost during
 the nematode analyses. ReadMe-file is included in the document.
DOI: 10.5061/dryad.t1g1jwt0n
title: Data from: An early Miocene extinction in pelagic sharks

description: Sharks populations have been decimated in recent decades due to
 over-fishing and other anthropogenic stressors, however the long-term
 impacts of such changes in marine predator abundance and diversity are
 poorly constrained. We present evidence for a previously unknown major
 extinction event in sharks that occurred in the Early Miocene,
 approximately 19 million years ago (Ma). During this interval, sharks
 virtually disappeared from open-ocean sediments, declining in abundance by
 &gt;90%, and morphological diversity by &gt;70%, an event from
 which they never recovered. This abrupt extinction occurred independently
 from any known global climate event, and ~2-5 million years prior to
 diversifications in the highly migratory, large-bodied predators that
 dominate today, indicating that the Early Miocene was a formative period
 of rapid, transformative change for open ocean ecosystems.
description: Ichthyoliths (shark dermal scales and fish teeth) were isolated
 from deep-sea sediments, following Sibert et al (2017). Ichthyoliths
 larger than106 µm were picked out of the sediments and placed on cardboard
 microfossil slides. The slides were imaged on the Hull Lab Imaging System
 at Yale University and a VHX-6000 Keyence Digital Microscope at Harvard
 University. Individual ichthyoliths were identified using the AutoMorph
 software developed by Hsiang et al (2017), and each object was made into a
 single image with a unique object number in the filename. Images with
 denticles were isolated (versus images with teeth or images with no
 fossils picked up by the software as 'noise'), and each denticle
 image was classified into a distinct denticle morphotype.
 References: Hsiang, A. Y., K. Nelson, L. E.
 Elder, E. C. Sibert, S. S. Kahanamoku, J. E. Burke, A. Kelly, Y. Liu and
 P. M. Hull (2018). "AutoMorph: Accelerating morphometrics with
 automated 2D and 3D image processing and shape extraction." Methods
 in Ecology and Evolution: 605-612. Sibert, E. C., K. L.
 Cramer, P. A. Hastings and R. D. Norris (2017). "Methods for
 isolation and quantification of microfossil fish teeth and elasmobranch
 dermal denticles (ichthyoliths) from marine sediments."
 Palaeontologia Electronica 20(1): 1-14.
description: Data S1: Images: These are images from DSDP Site 596 and ODP Site
 886. Each directory contains all of the images of denticles from one
 discrete sediment sample, and the labeling is conventional from IODP. Each
 denticle is identified by its IODP identifier, which gives the Site, Hole,
 Core, Section, and Interval, to the precise depth in the core that the
 sample was taken from, and by a unique object number assigned by
 AutoMorph. Data S2: Morphotypes.pdf: PowerPoint
 slideshow showing every morphotype identified in this study, along with
 examples of fossils fitting that morphotype, and, where present, images of
 modern shark skin samples that share the morphotype, and the reference
 that those images were taken from.
DOI: 10.5061/dryad.nvx0k6dqm
title: Data from: Genetic structure in Orkney island mice: isolation promotes morphological diversification

description: Following human occupation, the house mouse has colonized numerous
 islands, exposing the species to a wide variety of environments. Such a
 colonization process, involving successive founder events and bottlenecks,
 may either promote random evolution or facilitate adaptation, making the
 relative importance of adaptive and stochastic processes in insular
 evolution difficult to assess. Here, we jointly analyse genetic and
 morphometric variation in the house mice (Mus musculus domesticus) from
 the Orkney archipelago. Genetic analyses, based on mitochondrial DNA and
 microsatellites, revealed considerable genetic structure within the
 archipelago, suggestive of a high degree of isolation and long-lasting
 stability of the insular populations. Morphometric analyses, based on a
 quantification of the shape of the first upper molar, revealed
 considerable differentiation compared to Western European populations, and
 significant geographic structure in Orkney, largely congruent with the
 pattern of genetic divergence. Morphological diversification in Orkney
 followed a Brownian motion model of evolution, suggesting a primary role
 for random drift over adaptation to local environments. Substantial
 structuring of human populations in Orkney has recently been demonstrated,
 mirroring the situation found here in house mice. This synanthropic
 species may thus constitute a bio-proxy of human structure and practices
 even at a very local scale.
description: <b>2D morphometric dataset</b>
 (GMM_ContOrk.txt): Individual identifier and locality
 of trapping of the 593 specimens included in the total data set (Orkney +
 continent), with UM1 size and aligned semi-landmarks along the first upper
 molar outline. The dataset includes data for 593 mice
 (Orkney + continent). The fine includes: - specimen
 identifier and locality of trapping, - first upper
 molar length (extracted using Momocs): UM1_Length -
 first upper molar Centroid Size (obtained using a General Procrustes
 Superimposition performed using Geomorph): UM1_Csize -
 aligned coordinates of the 64 points along the outline: variables V1 to
 V128. <b>Microsatellite Dataset</b>
 (279mice_19msat.str): This dataset includes the
 microsatellite data in structure format for 279 mice and 19
 microsatellites. Specimen identifiers and localities are indicated.
 Missing data are indicated by ”-9”.
DOI: 10.5061/dryad.dbrv15dzq
title: A minimal yet flexible likelihood framework to assess correlated evolution

description: An evolutionary process is reflected in the sequence of changes through
 time of any trait (e.g. morphological, molecular). Yet, a better
 understanding of evolution would be procured by characterizing correlated
 evolution, or when two or more evolutionary processes interact. A wide
 range of parametric methods have previously been proposed to detect
 correlated evolution but they often require significant computing time as
 they rely on the estimation of many parameters. Here we propose a minimal
 likelihood framework modelling the joint evolution of two traits on a
 known phylogenetic tree. The type and strength of correlated evolution is
 characterized by few parameters tuning mutation rates of each trait and
 interdependencies between these rates. The framework can be applied to
 study any discrete trait or character ranging from nucleotide substitution
 to gain or loss of a biological function. More specifically, it can be
 used to 1) test for independence between two evolutionary processes, 2)
 identify the type of interaction between them and 3) estimate parameter
 values of the most likely model of interaction. In its current
 implementation, the method takes as input a phylogenetic tree together
 with mapped discrete evolutionary events on it and then maximizes the
 likelihood for one or several chosen scenarios. The strengths and limits
 of the method, as well as its relative power when compared to a few other
 methods, are assessed using both simulations and data from 16S rRNA
 sequences in a sample of 54 γ-enterobacteria. We show that even with
 datasets of less than 100 species, the method performs well in parameter
 estimation and in the selection of evolutionary scenario.
DOI: 10.7272/q6348hmp
title: Heat stress induced nitric oxide (DAF-FM-DA) response in respiratory growing Wild-type, atg32∆ and spe1∆ mutant yeast with and without spermidine addition

description: In Saccharomyces cerevisiae, the selective autophagic degradation of
 mitochondria, termed mitophagy, is critically regulated by the adapter
 protein, Atg32. Despite our knowledge about the molecular mechanisms by
 which Atg32 controls mitophagy, its physiological roles on yeast survival
 and fitness remains less clear. Here, we demonstrate a requirement for
 Atg32 in promoting spermidine production during respiratory growth and
 heat-induced mitochondrial stress. During respiratory growth,
 mitophagy-deficient yeast exhibit profound heat-stress induced defects in
 growth and viability due to impaired biosynthesis of spermidine and its
 biosynthetic precursor S-Adenosyl-Methionine (SAM). Moreover, spermidine
 production is crucial for the induction of cytoprotective nitric oxide
 (NO) during heat stress. Hence, the re-addition of spermidine to Atg32
 mutant yeast is sufficient to both enhance NO production and restore
 respiratory growth during heat stress. Our findings uncover a previously
 unrecognized physiological role for yeast mitophagy in spermidine
 metabolism and illuminate new interconnections between mitophagy,
 polyamine biosynthesis and NO signaling.
description: Yeast cells were cultivated in liquid SD media at 30˚C and grown to A<sub>600</sub> of 0.8-1.2 followed by passage into SGE with/without 0.5mM spermidine starting A<sub>600</sub> of 0.2 and grown at 30˚C until an OD A<sub>600</sub> of 0.5, then fresh SGE media with/without spermidine was replenished and yeast were allowed to continue growing until and OD of 1 at 30˚C. Subsequently, 15 μM DAF-FM-DA (Cayman Chemical Cat No. 18767) (diluted in DMSO) was added and cells were incubated in SGE with/without spermidine for an additional two and a half hours at 37˚C. Cells were next rinsed with respective media lacking DAF-FM-DA and were imaged by fluorescence microscopy using the Delta Vision Elite microscope (Applied Precision GE Healthcare Life Sciences) fitted with a 1.4 -NA 100X objective, PCO Edge cMOS camera, and run by softWoRx Resolve3D software. Capture and post-capture image processing were done using softWoRx software (Applied Precision GE Healthcare Life Sciences) and Fiji [39]. The average fluorescence across each cell was quantified using the line tool and Analyze-Measure functions in Fiji. For each experiment, calculated intensities were normalized by dividing all values by the average intensity calculated from WT 30˚C samples. For each experiment 200 cells per condition were quantified and three biological replicates (n=600 cells/condition) are represented as a violin plot with S.E.M generated in RStudio.
DOI: 10.5061/dryad.2jm63xsmr
title: A re-evaluation of management units based on gene flow of a rare waterbird in the Americas

description: The maintenance of gene flow in species that have experienced population
 contractions and are geographically fragmented is important to the
 maintenance of genetic variation and evolutionary potential; thus, gene
 flow is also important to conservation and management of these species.
 For example, the Reddish Egret (Egretta rufescens) has recovered after
 severe population reductions during the 19th and 20th centuries, but
 population numbers remain below historic levels. In this study, we
 characterized gene flow among management units of the Reddish Egret by
 using ten nuclear microsatellite markers and part of the mitochondrial
 (mtDNA) control region from 176 nestlings captured at eight localities in
 Mexico (Baja California, Chiapas, Tamaulipas, and Yucatan), the U.S.A.
 (Texas, Louisiana, and Florida), and the Bahamas. We found evidence of
 population structure and that males disperse more often and across longer
 distances compared to females, which is congruent with previous banding
 and telemetry data. The maternally inherited mtDNA and biparentally
 inherited microsatellite data supported slightly different MU models;
 however, when interpreted together, a four MU model that considered
 population structure and geographic proximity was most optimal. Namely, MU
 1 (Baja California); MU 2 (Chiapas); MU 3 (Yucatan, Tamaulipas, Texas, and
 Louisiana); and MU 4 (Florida and the Bahamas). Regions outside our
 sampled localities (e.g., the Greater Antilles and South America) require
 additional sampling to fully understand gene flow and movement of
 individuals across the species’ entire range. However, the four MUs we
 have defined group nesting localities into genetically similar
 subpopulations, which can guide future management plans.
description: Blood samples were collected from nestling Reddish Egrets (one
 nestling per nest) at eight breeding sites in Mexico (Baja California,
 Chiapas, Yucatan, and Tamaulipas), the U.S.A. (Texas, Louisiana, and
 Florida), and the Bahamas. DNA from whole blood samples was extracted by
 using the Gentra Puregene kit (Qiagen) following the manufacturer’s
 protocol. To genotype individuals, microsatellite primers designed by Hill
 & Green (2011) were used. Samples were amplified via a semi-nested
 PCR. Primers designed by Bates et al. (2009) were used to amplify the
 mtDNA control region (d-loop). PCRs were carried out in using the same
 reaction concentrations as above but also using the thermal profile
 suggested by Bates et al. (2009).
description: From 176 total birds, 123 individuals from Yucatan, Louisiana,
 Florida, Chiapas, and Texas had not been previously analyzed genetically.
 The remaining 53 samples were chosen randomly from a previous study to
 serve as a reference data set (Hill et al., 2012).
DOI: 10.5281/zenodo.18395337
title: SuperDARN data in netCDF format (2006-Mar)

description: 2006-Mar SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5281/zenodo.6632581
title: SuperDARN data in netCDF format (2006-Mar)

description: 2006-Mar SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5061/dryad.ht76hdrcv
title: Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species - Data supporting published version

description: Invasive freshwater fish systems are known to readily hybridize with
 indigenous congeneric species, driving loss of unique and irreplaceable
 genetic resources. Here we reveal that newly discovered (2013-2016)
 evolutionarily significant populations of Korogwe tilapia (Oreochromis
 korogwe) from southern Tanzania are threatened by hybridization with the
 larger invasive Nile tilapia (Oreochromis niloticus). We use a combination
 of morphology, microsatellite allele frequencies and whole genome
 sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba
 and Mitupa) are distinct from geographically-disjunct populations in
 northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic
 evidence of O. korogwe x niloticus hybrids in three southern lakes and
 demonstrate heterogeneity in the extent of admixture across the genome.
 Finally, using the least admixed genomic regions we estimate that the
 northern and southern O. korogwe populations most plausibly diverged
 approximately 140,000 years ago, suggesting that the geographical
 separation of the northern and southern groups is not a result of a recent
 translocation, and instead these populations represent independent
 evolutionarily significant units. We conclude that these newly-discovered
 and phenotypically unique cichlid populations are already threatened by
 hybridization with an invasive species, and propose that these
 irreplaceable genetic resources would benefit from conservation
 interventions.
description: Full methods are contained within the methods section and
 supporting text of: Blackwell et al. Newly discovered
 cichlid fish biodiversity threatened by hybridization with non-native
 species.
description: The data support the Blackwell et al. Newly discovered cichlid
 fish biodiversity threatened by hybridization with non-native
 species. A README file contains details of the file
 content.
DOI: 10.5061/dryad.z08kprr9r
title: Data from: A mummified Pleistocene gray wolf pup

description: Here we describe the oldest, most complete wolf pup mummy discovered to
 date: “Zhùr”, as she was named by the local indigenous Tr’ondëk Hwëch’in
 community was discovered in 2016 in Yukon, Canada, and is complete with
 skin, fur, and other soft tissues. We infer that Zhùr died ~57,000 years
 ago and was ~7 weeks old at death. Her mitochondrial genome falls within a
 clade comprising ancient Beringian and Russian wolf mitochondrial genomes,
 and isotopic analyses show her diet was composed of mostly aquatic
 resources. Although mummies like Zhùr will, unfortunately, become more
 common as the permafrost thaws, their analysis can provide unprecedented
 insights into extinct ecosystems.
description: This dataset was collected from a wolf pup mummy that was found
 in Yukon, Canada. Morphological data, ancient DNA, radiometric dating, and
 stable isotope analysis were performed on this specimen. The specimen is
 reposited at the Yukon Beringian Interpretive Center.
description: The ReadMe file has all of the data needed to understand and use
 these data files.
DOI: 10.5061/dryad.d2547d81h
title: Parental investment does not directly affect reproductive success in the Saffron Finch

description: In tropical species, the study of parental care and the description of the
 intraspecific variation of parental care remain relatively understudied,
 especially when compared to the vast works dedicated to species from the
 northern hemisphere. In Colombia, the Saffron Finch (Sicalis flaveola), is
 a species with a wide geographical distribution, and despite its abundance
 in open habitats and urban environments, little is known about its
 reproductive ecology. As a small‐bodied, short‐lived passerine, we
 postulated that the Saffron Finch should behave according to the
 “reproductive value hypothesis,’’ investing in the current brood
 at the expense of future survival. Consequently, we predicted: (1) that
 parental investment would be associated with brood size and (2) parental
 investment would be positively associated with nestling growth rate and
 reproductive success (defined as the number of nestlings which reached
 fledging age). In 2018, two reproductive peaks of S. flaveola
 flaveola were documented in the Meléndez campus of Universidad
 del Valle, Cali. Direct observations and video cameras (&gt; 1700
 hours of recording) were used to monitor the nests from 38 different
 breeding pairs. We found that feeding visits and the number of
 regurgitation events were positively related to brood size. In an
 experiment of simulated nest predation, 85% of breeding pairs responded to
 the stimulus and parents who exhibited highly responsive behaviours (50%)
 raised nestlings with a higher growth rate. We also found that egg surface
 area positively affected the number of incubation bouts per hour. Whilst
 no relationship was found between overall parental investment and
 reproductive success, our results appear to show that the intensity of
 parental investment during reproduction was modulated by brood size. Our
 findings suggest that there are multiple ecological factors that influence
 reproductive success in the Saffron Finch, and reinforce the need for
 longer term studies of tropical passerines.