cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.w6m905qmf
title: Data from: Overlap of spatial and temporal spawning distributions of spring and summer Chinook Salmon results in hybridization in the upper Columbia River

description: The upper Columbia River in Washington State (main-stem and tributary
 habitat between McNary and Chief Joseph dams) is inhabited by two major
 lineages of Chinook Salmon (Oncorhynchus tshawytscha); endangered spring
 Chinook Salmon and summer Chinook Salmon which are not ESA listed. The
 lineages are highly genetically divergent from one another and
 historically spatial and temporal isolating mechanisms maintained these
 genetic differences. Both lineages occur in the Entiat River, a system
 where anthropogenic activity has changed habitat, flows, species
 composition, and the distribution of the two lineages over the past
 century. We examined the spatial and temporal overlap in spawning
 distributions between Entiat River spring and summer Chinook Salmon and we
 used genetic markers to assess the level of introgression between
 lineages. Redd surveys were conducted from 2003 to 2017 to describe
 spatial and temporal spawning patterns of both lineages. We genotyped
 sub-yearling juvenile Chinook Salmon captured in the Entiat River from
 2009–2014 at 90 SNP loci to determine lineage and hybridization status.
 There was temporal overlap in spawning between lineages in several years
 and considerable spatial overlap in redd locations annually. Genetic
 analysis revealed hybridization between lineages does occur, albeit at
 relatively low rates (2.6% of sub-yearling juveniles genotyped). We
 detected hybrids each year samples were collected and they were
 distributed throughout the Entiat River basin. Hybridization between
 lineages of Chinook Salmon could result in introgression and a loss of
 genetic diversity between the lineages, and/or, a loss of production by
 ESA-listed spring Chinook Salmon. The presence of hybrids warrants concern
 for ESA-listed spring Chinook Salmon in both the Entiat River system and
 throughout the upper Columbia River basin.
description: The 96 SNP makers were processed using TaqMan® SNP Genotyping
 Assays (Life Technologies, Carlsbad, California) on a Fluidigm® EP-1™
 System with 96.96 Dynamic Arrays following the manufacturer’s protocol
 (Fluidigm, San Francisco, California). Multi-locus genotypes of each
 individual fish were visualized and scored using Fluidigm® SNP Genotyping
 Analysis software and were confirmed by two researchers.
description: Genetic marker naming is defined on the "marker key"
 tab.  Definitions of allelic and missing data states are defined in the
 header on each tab.
DOI: 10.5061/dryad.msbcc2fvd
title: The internal region of CtIP functions as a regulator of DNA end resection

description: DNA double-strand breaks are repaired by end-joining or homologous
 recombination. A key-committing step of recombination is DNA end
 resection. In resection, phosphorylated CtIP first promotes the
 endonuclease of the MRE11-RAD50-NBS1 (MRN) complex. Subsequently, CtIP
 also stimulates the BLM-DNA2 helicase-nuclease, coordinating thus both
 short and long-range resection. The structure of CtIP differs from its
 orthologues in yeast, as it contains a large internal region. Here we
 conducted a domain analysis of the internal region of CtIP to define its
 function in DNA end resection. We found that residues 350-600 were
 entirely dispensable for resection in vitro. A mutant lacking these
 residues was unexpectedly more efficient than full-length CtIP in DNA end
 resection and homologous recombination in vivo, and consequently conferred
 resistance to lesions induced by the topoisomerase poison camptothecin,
 which require high MRN-CtIP-dependent resection activity for repair. This
 suggested that the internal region, further mapped to residues 550-600,
 may mediate a negative regulatory function to prevent over resection in
 vivo. Consequently, the CtIP internal deletion mutant exhibited
 sensitivity to other DNA-damaging drugs, showing that upregulated
 resection may be instead toxic under other conditions. These experiments
 together identify a region within the central CtIP domain that negatively
 regulates DNA end resection.
description: This dataset was collected by a variety of methods including
 cell-base flow cytometry reporters, Western blotting, RT-PCR, <em>in
 vitro</em> biochemical assays and clonogenic survival
 assays.
DOI: 10.5061/dryad.02v6wwq0q
title: Data from: A quantitative inventory of yeast P body proteins reveals principles of composition and specificity

description: P bodies are archetypal biomolecular condensates that concentrate proteins
 and RNA without a surrounding membrane. While dozens of P body proteins
 are known, the concentrations of components in the compartment have not
 been measured. We used live cell imaging to generate a quantitative
 inventory of the major proteins in yeast P bodies. Only 7 proteins are
 highly concentrated in P bodies (5.1-15 uM); the 24 others examined are
 appreciably lower (most ≤ 2.6 uM). P body concentration correlates
 inversely with cytoplasmic exchange rate. Sequence elements driving Dcp2
 concentration into P bodies are distributed across the protein and act
 cooperatively. Our data indicate that P bodies, and probably other
 condensates, are biochemically simpler than suggested by proteomic
 analyses, with implications for specificity, reconstitution and evolution.
description: All images were acquired using a Leica SP8 Laser Scanning
 Confocal Microscope using a 100 X 1.4 NA oil immersion objective.
 Unprocessed raw images are in the dataset.
description: <strong>Figure 1__Figure 1_figure supplement 1__Figure 2
 Figure 2_figure supplement 1 2A and 2B__Table 2
 2.zip</strong> This compressed file contains
 unprocessed data of Figure 1, Figure 2, Figure 2 -- figure supplement 1 2A
 and 2B, and Table 2 <strong>Figure 1_figure
 supplement 1B.zip</strong> This compressed file
 contains unprocessed data of Figure 1 -- figure supplement 1B
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 2.zip</strong> This compressed file contains
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 C.zip</strong> This compressed file contains
 unprocessed data of Figure 1 -- figure supplement 3A 3B and 3C
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 4.zip</strong> This compressed file contains
 unprocessed data of Figure 1 -- figure supplement 4
 <strong>Figure 2_figure supplement 2C and
 D.zip</strong> This compressed file contains
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 compressed file contains unprocessed data of Figure 3
 <strong>Figure 4 Figure 1_figure supplement 1A and
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 unprocessed data of Figure 4, Figure 1, Figure 1 -- figure supplement 1A,
 and Figure 1 -- figure supplement 3D
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 <strong>Figure 7.zip</strong> This
 compressed file contains unprocessed data of Figure 7
 <strong>Figure 7_figure supplement
 1.zip</strong> This compressed file contains
 unprocessed data of Figure 7-- figure supplement 1
DOI: 10.25338/b8762g
title: Data from: The role of spatial averaging scale in leaf-to-canopy scaling of non-linear processes in homogeneous canopies

description: Canopy biophysical models require averaging fluxes over some spatial scale
 (sub-leaf, leaf, sub-crown, crown, whole-canopy, etc.). Choice of
 averaging scale can be important when modeling processes like stomatal
 conductance and photosynthesis that have a non-linear response to
 environmental variables such as light interception. The model results
 archived here were used to quantify errors in canopy-level flux
 simulations due to averaging scale choice. A detailed leaf-resolving model
 was used to simulate light interception for a series of homogeneous
 canopies with differing canopy structure. Radiation model parameters and
 non-linearity of the light response were also varied. Averaging over
 individual leaves and over various sub-leaf resolutions were compared with
 averaging approaches used in multi-layer and two-leaf canopy models.
description: Comprehensive usage information is available in README.txt.
DOI: 10.5061/dryad.w6m905qmg
title: Data from: Evolutionary tracking is determined by differential selection on demographic rates and density dependence.

description: Recent ecological forecasts predict that ~25% of species worldwide will go
 extinct by 2050. However, these estimates are primarily based on
 environmental changes alone, and fail to incorporate important biological
 mechanisms such as genetic adaptation via evolution. Thus, environmental
 change can affect population dynamics in ways that classical frameworks
 can neither describe nor predict. Furthermore, often due to a lack of
 data, forecasting models commonly describe changes in population
 demography by summarizing changes in fecundity and survival concurrently
 with the intrinsic growth rate (r). This has been shown to be an
 oversimplification as the environment may impose selective pressure on
 specific demographic rates (birth and death) rather than directly on r
 (the difference between the birth and death rates). This differential
 pressure may alter population response to density, in each demographic
 rate, further diluting the information combined to produce r. Thus, when
 we consider the potential for persistence via adaptive evolution,
 populations with the same r can have different abilities to persist amidst
 environmental change. Therefore we can't adequately forecast
 population response to climate change without accounting for demography,
 and selection on density dependence. Using a continuous-time Markov chain
 model to describe the stochastic dynamics of the logistic model of
 population growth and allow for trait evolution via mutations arising
 during birth events, we find persistence via evolutionary tracking more
 likely when environmental change alters birth rather than the death rate.
 Furthermore, species that evolve responses to changes in the strength of
 density dependence due to environmental change are less vulnerable to
 extinction than species that undergo selection independent of population
 density. By incorporating these key demographic considerations into our
 predictive models we can better understand how species will respond to
 climate change.
DOI: 10.6084/m9.figshare.29650316
title: Kariri-Xocó indigenous resistance in the heart of Brazil

description: This ethnographic video portraits the Kariri-Xocó indigenous resistance in Brasília, capital of Brazil. Since 2018, I have worked with Indigenous communities like the Kariri-Xocó, who, since the 1960s, have resisted environmental injustice and racism and gender and economic inequalities in territorial disputes to real state private corporations, which have pushed these communities out of their homes, with the support of the state, to build luxury condominiums for the wealthy population of the city.
DOI: 10.6084/m9.figshare.29650316.v3
title: Kariri-Xocó indigenous resistance in the heart of Brazil

description: This ethnographic video portraits the Kariri-Xocó indigenous resistance in Brasília, capital of Brazil. Since 2018, I have worked with Indigenous communities like the Kariri-Xocó, who, since the 1960s, have resisted environmental injustice and racism and gender and economic inequalities in territorial disputes to real state private corporations, which have pushed these communities out of their homes, with the support of the state, to build luxury condominiums for the wealthy population of the city.
DOI: 10.6084/m9.figshare.29650316.v2
title: Indigenous resistance in the heart of Brazil

description: This ethnographic video was made with material collected in fieldwork with the Kariri-Xocó Indigenous community, in Brasília, federal district of Brazil, in 2024/25. It is part of research in indigenous resistance to social and environmental injustices and racism and gender and economic inequalities in territorial conflicts against real state private corporations, with the mediation of the state.
DOI: 10.5061/dryad.5dv41ns3d
title: Data from: Factors Influencing Productivity of Eastern Wild Turkeys in Northeastern South Dakota

description: Population growth is highly sensitive to changes in reproductive rates for
 many avian species. Understanding how reproductive rates are related to
 environmental conditions can give managers insight into factors
 contributing to population change. Harvest trends of eastern wild turkey
 (Meleagris gallopavo silvestris) in northeastern South Dakota suggest an
 apparent decline in abundance in recent years.  We therefore
 investigate factors influencing reproductive success of this important
 game bird to identify potential factors contributing to this decline. We
 monitored nesting rate, nest survival, re-nesting rate, clutch size,
 hatchability, and poult survival of 116 eastern wild turkey hens using VHF
 radio-transmitters during the springs and summers of 2017 and 2018.
 Heavier hens were more likely to attempt to nest than lighter hens, and
 adult hens were more likely to re-nest than yearling hens. Nest survival
 probability was lowest in agricultural fields relative to all other cover
 types and positively related to horizontal visual obstruction and distance
 to the nearest road. Daily nest survival probability demonstrated an
 interaction between temperature and precipitation, such that nest survival
 probability was lower on warm, wet days, but lowest on dry days. Egg
 predation was the leading cause of nest failure, followed by haying of the
 nest bowl and death of the incubating hen. Poults reared by adult hens had
 a greater probability of survival than poults reared by yearling hens. Our
 estimate of survival probability of poults raised by yearling hens was low
 relative to other studies, which may be contributing to the apparent
 regional population decline. However, there is little managers can do to
 influence poult survival in yearling hens. Alternatively, we
 found nest survival probability was lowest for nests initiated in
 agricultural fields. Wildlife-friendly harvesting practices in
 the region such as delayed harvesting or installation of flushing bars
 could help increase productivity of eastern wild turkey in northeastern
 South Dakota.
DOI: 10.5061/dryad.cjsxksn34
title: Giant island mice exhibit widespread gene expression changes in key metabolic organs

description: Abstract Island populations repeatedly evolve extreme body sizes, but the
 genomic basis of this pattern remains largely unknown. To understand how
 organisms on islands evolve gigantism, we compared genome-wide patterns of
 gene expression in Gough Island mice, the largest wild house mice in the
 world, and mainland mice from the WSB/EiJ wild-derived inbred strain. We
 used RNASeq to quantify differential gene expression in three key
 metabolic organs: gonadal adipose depot, hypothalamus and liver. Between
 4,000 and 8,800 genes were significantly differentially expressed across
 the evaluated organs, representing between 20 and 50% of detected
 transcripts, with 20% or more of differentially expressed transcripts in
 each organ exhibiting expression fold changes of at least 2X. A minimum of
 73 candidate genes for extreme size evolution, including Irs1 and Lrp1,
 were identified by considering differential expression jointly with other
 data sets: (i) genomic positions of published quantitative trait loci for
 body weight and growth rate; (ii) whole genome sequencing of 16
 wild-caught Gough Island mice that revealed fixed single nucleotide
 differences between the strains; (iii) publicly available tissue-specific
 regulatory elements. Additionally, patterns of differential expression
 across three time points in the liver revealed that Arid5b potentially
 regulates hundreds of genes. Functional enrichment analyses pointed to
 cell cycling, mitochondrial function, signaling pathways, inflammatory
 response, and nutrient metabolism as potential causes of weight
 accumulation in Gough Island mice. Collectively, our results indicate that
 extensive gene regulatory evolution in metabolic organs accompanied the
 rapid evolution of gigantism during the short time house mice have
 inhabited Gough Island.
description: See Material and Methods section in Nolte, M.J., et al. Giant
 Island Mice Exhibit Widespread Gene Expression Changes in Key Metabolic
 Organs.
DOI: 10.7291/d18w9g
title: Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge

description: The Bering Land Bridge (BLB) last connected Eurasia and North America
 during the Pleistocene. Although the BLB would have enabled transfers of
 terrestrial biota in both directions, it also acted as an ecological
 filter whose permeability varied considerably over time. Here we explore
 the possible impacts of this ecological corridor on genetic diversity
 within, and connectivity among, populations of a once wide-ranging group,
 the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and
 eight nuclear genomes recovered from present-day and extinct caballine
 horses sampled across the Holarctic, we found that Eurasian horse
 populations initially diverged from those in North America, their
 ancestral continent, around 1.0-0.8 million years ago. Subsequent to this
 split our mitochondrial DNA analysis identified two bi-directional
 long-range dispersals across the BLB ~875-625 and ~200-50 thousand years
 ago, during the Middle and Late Pleistocene. Whole genome analysis
 indicated low levels of gene flow between North American and Eurasian
 horse populations, which likely occurred as a result of these inferred
 dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine
 horse populations retained strong phylogeographic structuring. Our results
 suggest that barriers to gene flow, currently unidentified but possibly
 related to habitat distribution across Beringia or ongoing evolutionary
 divergence, played an important role in shaping the early genetic history
 of caballine horses, including the ancestors of living horses within Equus
 ferus.
description: BEAST XML files for phylogenetic and phylogeographic
 analysis. Filter regions for G-PhoCS coalescent
 simulation analysis (.bed on EquCab2.0 reference).
description: Beast files are ready to run. For the G-PhoCS
 analysis, one would need scripts from this repo:
 https://github.com/avershinina/BLB_horses
DOI: 10.5061/dryad.h44j0zpgh
title: Behavioural and neurophysiological data from experiments on the impact of spatial frequency information to action comprehension

description: Understanding object-directed actions performed by others is central to
 everyday life. This ability is thought to rely on the interaction between
 the dorsal action observation network (AON) and a ventral object
 recognition pathway. On this view, the AON would encode action kinematics,
 and the ventral pathway, the most likely intention afforded by the
 objects. However, experimental evidence supporting this model is still
 scarce. Here, we aimed to disentangle the contribution of dorsal vs.
 ventral pathways to action comprehension by exploiting their differential
 tuning to lowspatial frequencies (LSFs) and high-spatial frequencies
 (HSFs). We filtered naturalistic action images to contain only LSF or HSF
 and measured behavioral performance and corticospinal excitability (CSE)
 using transcranial magnetic stimulation (TMS). Actions were embedded in
 congruent or incongruent scenarios as defined by the compatibility between
 grips and intentions afforded by the contextual objects. Behaviorally,
 participants were better at discriminating congruent actions in intact
 than LSF images. This effect was reversed for incongruent actions, with
 better performance for LSF than intact and HSF. These modulations were
 mirrored at the neurophysiological level, with greater CSE facilitation
 for congruent than incongruent actions for HSF and the opposite pattern
 for LSF images. Finally, only for LSF did we observe CSE modulations
 according to grip kinematics. While results point to differential dorsal
 (LSF) and ventral (HSF) contributions to action comprehension for grip and
 context encoding, respectively, the negative congruency effect for LSF
 images suggests that object processing may influence action perception not
 only through ventral-to-dorsal connections, but also through a
 dorsal-to-dorsal route involved in predictive processing.
DOI: 10.5061/dryad.x0k6djhg5
title: Data from: Bioacoustic monitoring reveals details of tricolored blackbird breeding phenology

description: Bioacoustic monitoring has been used to study behaviors of organisms from
 insects to whales. Studies using multiple vocalizations of a single
 species have the potential to determine detailed phenology, but to date
 are rare. We tested whether bioacoustic monitoring of multiple gender- and
 age-specific vocalizations of the imperiled tricolored blackbird Agelaius
 tricolor could provide detailed information on reproductive phenology and
 breeding success. Using inexpensive cell phones and free software
 applications, we collected audio recordings of tricolored blackbird
 colonies during their breeding season. Adding solar panels enabled the
 stations to run autonomously, and use of cellular data enabled remote
 uploading of recordings. Analysis of the presence or absence of three
 vocalizations (male song, female song, and nestling call) provided a rich
 and detailed description of the breeding phenology, including the dates
 for courtship, onset of nest building, incubation, nestling hatching, and
 fledgling departure from nesting colonies. The resulting detail was more
 granular and accurate than comparable data from field monitoring, although
 field monitoring provides data such as abundance counts that bioacoustic
 monitoring does not. This information has a wide range of applications to
 research and conservation, from enabling more accurate abundance
 estimates, to assessing colony success or failure with fewer visits, to
 providing stronger guidance for when a colony must be protected from
 disruption.
description: We made audio recordings of the colony using a
 custom-designed bioacoustic monitoring station. Our initial
 station included an audio recorder (an LGMS323 cellphone, LG Electronics,
 Seoul, South Korea) that ran the Automated Remote Biodiversity Monitoring
 Network (ARBIMON) Touch audio recording software application (Sieve
 Analytics, San Juan, Puerto Rico), enclosed in a waterproof case
 (Otterbox, Fort Collins, Colorado), with an external microphone
 (Monoprice, Rancho Cucamonga, California; Aide et al. 2013). We attached
 the recorder to a metal t-post with an elastic cord and installed it near
 the edge of the Rush Ranch colony (Figure 5A–B). The recorder collected
 data from 2 March–25 July, recording one minute of audio every 20 minutes,
 collecting 72 minutes of audio daily and more than 8,000 minutes over the
 16-week breeding season.
description: Audio recordings of 5 Tricolored Blackbird colonies during 2017
 and 2018 breeding season