cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wstqjq2nj
title: ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process

description: Modern phylogenetic methods allow inference of ancestral molecular
 sequences given an alignment and phylogeny relating present day sequences.
 This provides insight into the evolutionary history of molecules, helping
 to understand gene function and to study biological processes such as
 adaptation and convergent evolution across a variety of applications. Here
 we propose a dynamic programming algorithm for fast joint likelihood-based
 reconstruction of ancestral sequences under the Poisson Indel Process
 (PIP). Unlike previous approaches, our method, named ARPIP, enables the
 reconstruction with insertions and deletions based on an explicit indel
 model. Consequently, inferred indel events have an explicit biological
 interpretation. Likelihood computation is achieved in linear time with
 respect to the number of sequences. Our method consists of two steps,
 namely finding the most probable indel points and reconstructing ancestral
 sequences. First, we find the most likely indel points and prune the
 phylogeny to reflect the insertion and deletion events per site. Second,
 we infer the ancestral states on the pruned subtree in a manner similar to
 FastML. We applied ARPIP on simulated datasets and on real data from the
 Betacoronavirus genus. ARPIP reconstructs both the indel events and
 substitutions with a high degree of accuracy. Our method fares well when
 compared to established state-of-the-art methods such as FastML and PAML.
 Moreover, the method can be extended to explore both optimal and
 suboptimal reconstructions, include rate heterogeneity through time and
 more. We believe it will expand the range of novel applications of
 ancestral sequence reconstruction.
DOI: 10.5061/dryad.mkkwh711s
title: Extreme temperatures help in identifying thresholds in phenological responses

description: Aim: To investigate temperature drivers of the spring phenology of 12
 flowering events and 6 leafing events. Boreal phenology has previously
 exhibited only a modest response to temperature but record breaking
 temperatures in March 2020 led to some extreme phenological timing and
 provided the opportunity for a more rigorous look at the nature and
 complexity of the relationship between temperature and phenology.
 Location: Boreal habitat in the Tatarstan Republic of Russia Time
 period: 1989-2020 Major taxa studied: 18 plant species
 Methods: We examined for changes over time in the timing of
 phenological events and the relationship with temperature drivers using a
 range of regression techniques. Extreme temperatures caused some extreme
 phenology and visually suggested temperature thresholds which were
 investigated using segmented regression (broken stick models). The
 performance of these models was subsequently compared to more complex
 alternatives based on accumulated daily temperatures.
 Results: Temperatures in March 2020 were the warmest for this
 month in a record covering 200 years and were 5.9°C above the 1989-2020
 average. Significant advances over time were detected for only seven of
 the events, but all events demonstrated significant relationships with
 temperature variables. Segmented regression identified significant
 temperature thresholds for 13 of the events with substantially stronger
 temperature relationships above these thresholds. Segmented regressions
 outperformed models based on accumulated daily temperatures for 12 of 18
 events. Main conclusions: The threshold models were a significant
 improvement over a linear response to temperature for 13 of the 18 events.
 The presence of thresholds partly explains why the response of boreal
 phenology to temperature previously seemed lower than in, for example,
 Western Europe. Responses to temperature above the identified thresholds
 were closer to those widely published from milder locations.
description: Dates of first observed flowering or leafing on study
 transects.
description: No missing values Data are days of the year,
 e.g. Jan 1 = day 1
DOI: 10.5061/dryad.xsj3tx9gm
title: Salinity Legacy: Foliar microbiome’s history affects mutualist-conferred salinity tolerance

description: The rapid human-driven changes in the environment during the Anthropocene
 have placed extreme stress on many plants and animals. Beneficial
 interactions with microorganisms may be crucial for ameliorating these
 stressors and facilitating the ecosystem services host organisms provide.
 Foliar endophytes, microorganisms that reside within leaves, are found in
 essentially all plants and can provide important benefits (e.g., enhanced
 drought tolerance or resistance to herbivory). However, it remains unclear
 how important the legacy effects of the abiotic stressors that select on
 these microbiomes are for affecting the degree of stress amelioration
 provided to their hosts. To elucidate foliar endophytes’ role in host
 plant salt-tolerance, especially if salinity experienced in the field
 selects for endophytes that are better suited to improve salt-tolerance of
 their hosts, we combined field collections of 90 endophyte communities
 from 30 sites across the coastal Everglades with a manipulative growth
 experiment assessing endophyte inoculation effects on host plant
 performance. Specifically, we grew &gt;350 red mangrove (Rhizophora
 mangle) seedlings in a factorial design that manipulated the salinity
 environment the seedlings experienced (freshwater vs. saltwater), the
 introduction of field-collected endophytes (live vs. sterilized inoculum),
 and the legacy of salinity stress experienced by these introduced
 endophytes [ranging from no salt stress (0 ppt salinity) to high salt
 stress (40 ppt) environments]. We found that inoculation with
 field-collected endophytes significantly increased mangrove performance
 across almost all metrics examined (15-20% increase on average) and these
 beneficial effects typically occurred when grown in saltwater.
 Importantly, our study revealed the novel result that endophyte-conferred
 salinity tolerance depended on microbiome salinity legacy in a key coastal
 foundation species. Salt-stressed mangroves inoculated with endophyte
 microbiomes from high salinity environments performed, on average, as well
 as plants grown in low-stress freshwater, while endophytes from freshwater
 environments did not relieve host salinity stress. Given the increasing
 salinity stress imposed by sea level rise and the importance of foundation
 species like mangroves for ecosystem services, our results indicate that
 consideration of endophytic associations and their salinity legacy may be
 critical for successful restoration and management of coastal habitats.
DOI: 10.5281/zenodo.11356526
title: What's in a name:  The multifaceted function of DNA- and RNA-binding proteins in T cell responses

description: Data and analyses code used in the manuscript "What’s in a name: The multifaceted function of DNA- and RNA-binding proteins in T cell responses." (DOI: 10.1111/febs.17273).

Analyses can also be found here: https://github.com/kasbress/DRBP_Tcell_responses

 

"Data" folder contains all data used for the analysis.

"Output" folder contains all output generated in the analysis.

"Figs" folder contains all figures generated in the analysis.

The R markdown file contains all analysis code used.
DOI: 10.5281/zenodo.11356525
title: What's in a name:  The multifaceted function of DNA- and RNA-binding proteins in T cell responses

description: Data and analyses code used in the manuscript "What’s in a name: The multifaceted function of DNA- and RNA-binding proteins in T cell responses." (DOI: 10.1111/febs.17273).

Analyses can also be found here: https://github.com/kasbress/DRBP_Tcell_responses

 

"Data" folder contains all data used for the analysis.

"Output" folder contains all output generated in the analysis.

"Figs" folder contains all figures generated in the analysis.

The R markdown file contains all analysis code used.
DOI: 10.5061/dryad.6djh9w12c
title: Climate and conspecific density inform phenotypic forecasting of juvenile Pacific salmon body size

description: 1. Predicting effects of climate on fitness-linked phenotypic traits, such
 as body size, is important for the management and conservation of species
 in the face of global change. During sensitive life stages, small changes
 in mean trait values can have large effects on survival and population
 productivity. 2. The transition from freshwater to saltwater by migrating
 anadromous fishes such as Pacific salmon (genus Oncorhynchus) is a
 critical life history transition, where survival is mediated by the size
 of migrating individuals. For salmon that spend extended periods rearing
 in freshwater, the size at ocean entry (i.e., smolt length) may be
 sensitive to changes in freshwater conditions shaped by biotic and abiotic
 factors, yet long-term phenotypic time series for exploring these
 responses are rare. 3. We reconstructed a four-decade time series of smolt
 length from archives of returning adult scales to quantify
 population-specific responses to climate and conspecific density in a
 small watershed. 4. Dynamic linear modeling found that the relationship
 between a proxy for cohort density and smolt length at ocean entry was
 consistently negative, suggestive of competition. In contrast, there was a
 positive, yet dynamic, relationship between a proxy for density of
 emerging fry during the second summer of growth and smolt length. 5. The
 effect of temperature on smolt length was not consistent between two
 populations of sockeye salmon O. nerka that likely use distinct habitats
 within the watershed. A positive relationship between smolt length and
 temperature was only detected for the less abundant, early returning
 population. 6. Predictions of smolt length showed variable responses under
 scenarios of increasing temperature and high and low densities of
 conspecifics. Collectively, these results reveal population-specific
 responses to temperature and density, suggesting that local habitat
 conditions may filter larger-scale climate drivers.
DOI: 10.5061/dryad.crjdfn35g
title: More or less? The effect of symbiont density in protective mutualisms

description: Symbionts can provide hosts with effective protection from natural
 enemies, but it can sometimes come at a cost. It is unclear to what extent
 the density of symbionts modulates the cost and benefits of conferred
 protection. Here we use a meta-analysis of 103 effect sizes from a broad
 taxonomic range of protective symbioses, to show that the degree of both
 protection and cost afforded to hosts is a positive function of symbiont
 density. We found that the effects of symbiont density on protection and
 cost are robust across ecological contexts. Density-function relationships
 did not vary with host type, symbiont localization or transmission mode,
 nor the method of density manipulation. Together, our results suggest
 symbiont density can be a key variable determining the costs and benefits
 of a protective interaction.
DOI: 10.5061/dryad.brv15dvb5
title: VCF datasets and analysis scripts for: The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability

description: Global warming is increasingly exacerbating biodiversity loss. Populations
 locally adapted to spatially heterogeneous environments may respond
 differentially to climate change, but this intraspecific variation has
 only recently been considered when modelling vulnerability under climate
 change. Here, we incorporate intraspecific variation in genomic offset and
 ecological niche modelling to estimate climate change-driven vulnerability
 in two bird species in the Sino-Himalayan Mountains. We found that the
 cold-tolerant populations show higher genomic offset but risk less
 challenge for niche suitability decline under future climate than the
 warm-tolerant populations. Based on a genome-niche index estimated by
 combining genomic offset and niche suitability change, we identified the
 populations with the least genome-niche interruption as potential donors
 for evolutionary rescue, i.e., the populations tolerant to climate change.
 We evaluated potential rescue routes via a landscape genetic analysis.
 Overall, we demonstrate that the integration of genomic offset, niche
 suitability modelling, and landscape connectivity can improve climate
 change-driven vulnerability assessments and facilitate effective
 conservation management.
description: Please refer to README
 file.
DOI: 10.5061/dryad.05qfttf44
title: Data from: A national VS30 model for South Korea to combine nationwide dense borehole measurements with ambient seismic noise analysis

description: The average shear-wave velocity within the top 30 m from the surface,
 VS30, represents site characteristics including the soil classification
 and site amplification that are essential information for building codes
 and seismic design. A novel method to determine a VS30 model based on a
 composite analysis of borehole standard penetration test numbers (SPT N)
 and horizontal-to-vertical (H/V) spectral ambient noise ratios is
 introduced. A national VS30 model for South Korea is determined using the
 method. The shear-wave velocity structures beneath 20 nationwide broadband
 seismic stations are determined using the H/V analysis. The SPT N data are
 collected from 175,619 nationwide densely-distributed boreholes. The
 shear-wave velocity models from SPT N values are calibrated for the local
 reference velocity models from H/V analysis. A representative relationship
 between the SPT N values and shear-wave velocities is introduced. A
 national VS30 model for South Korea is determined using the calibrated SPT
 N models at the nationwide boreholes. The VS30 model is verified by
 comparisons with local field measurements. The proposed model is
 consistent with the USGS model based on a surface slope analysis. The VS30
 structure presents high correlation with geological and topographic
 features. The VS30 values are low in coastal (low topographic) areas, and
 high in mountain (high topographic) areas. Apparent linear relationship is
 observed between VS30 and topography. The western and southeastern coastal
 regions may be vulnerable to strong seismic shaking.
description: This data set is concerned with the paper "A national
 V<sub>S30</sub> model for South Korea to combine nationwide
 dense borehole measurements with ambient seismic noise analysis"
 submitted to Earth and Space Science by Byeongwoo Kim and Tae-Kyung Hong
 in 2021. We provide data files to produce seven figures in the paper:
 Figures 3, 8, 9, 11, 14, 17, and 21. All data files are given in the ASCII
 format. 
 Please see the detailed information in the file
 "README.md" included in the zip file.
DOI: 10.5061/dryad.bzkh189b2
title: Long distance migration is a major factor driving local adaptation at continental scale in a Pacific Salmon

description: Inferring the genomic basis of local adaptation is a long-standing goal of
 evolutionary biology. Beyond its fundamental evolutionary implications,
 such knowledge can guide conservation decisions for populations of
 conservation and management concern. Here, we investigated the genomic
 basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across
 its entirety North American range. We hypothesized that extensive spatial
 variation in environmental conditions and the species’ homing behavior may
 promote the establishment of local adaptation. We genotyped 7,829
 individuals representing 217 sampling locations at more than 100,000
 high-quality RADseq loci to investigate how recombination might affect the
 detection of loci putatively under selection and took advantage of the
 precise description of the demographic history of the species from our
 previous work to draw accurate population genomic inferences about local
 adaptation. Results indicated that genetic differentiation scans and
 genetic-environment association analyses were both significantly affected
 by variation in recombination rate as low recombination regions displayed
 increased rate of outliers. By taking these confounding factors into
 consideration, we revealed that migration distance was the primary
 selective factor driving local adaptation and partial parallel divergence
 among distant populations. Moreover, we identified several candidates SNP
 associated with long distance migration and altitude including gene known
 to be involved in adaptation to altitude in other species. The
 evolutionary implications of our findings are discussed along with
 conservation applications.
DOI: 10.5061/dryad.mw6m905xq
title: EHR screen, test, and refer to HFMH DPP

description: Objective: Determine if certified electronic health record technology
 (CEHRT) can be used to identify and refer patients with prediabetes to
 lifestyle change programs (LCPs) recognized by the National Diabetes
 Prevention Program (DPP). Materials and Methods: This pilot utilized a
 prediabetes registry, patient portal, and clinical decision support to
 increase referrals. Results: Data from 36 primary care providers showed
 4,930 patients were eligible for DPP LCP, 293 referrals were generated,
 compared to 20 referrals in the baseline period, and 116 patients
 enrolled. Referral to enrollment conversion rates were 41% in the study
 period and 69% in the post-study 1-year period. Discussion: CEHRT
 functionalities can support systematic identification and management of
 prediabetes.  The referral rate increased seven-fold compared to
 the baseline period, with high referral to enrollment conversion rates.
 Conclusions: CEHRT coupled with active provider engagement can serve as a
 tool to identify prediabetes patients and facilitate LCP
 referrals and enrollment.
description: Data were extracted from the EHR to obtain de-identified
 aggregated counts of patients attributed to the providers in the pilot
 study.
DOI: 10.5061/dryad.rn8pk0pbw
title: Data for: Size spectrum model reveals importance of considering species interactions in a freshwater fisheries management context

description: Inland fisheries have significant cultural and economic value around the
 globe, providing dietary protein, income, and recreation. Consequently,
 methods for monitoring and managing these important fisheries are
 continually being refined. In marine systems, multi-species size spectrum
 models have been increasingly used to explore management scenarios of
 important fish stocks within an ecosystem-based fisheries management
 framework; however, these models have not been applied in freshwater
 systems. In this study, we developed a multi-species size spectrum model
 for the fish community of Lake Nipissing, a large, productive lake in
 Ontario, Canada. To the best of our knowledge, this is the first fully
 calibrated multi-species size spectrum model for an inland fishery. Using
 this model, we explored the impacts of different management scenarios on
 fish community dynamics while taking species interactions into account.
 Specifically, we examined how changes in fishing mortality affect: (1)
 species biomass; (2) community size structure; and (3) stock recovery
 times. We found that community dynamics following changes in fishing
 mortality were driven by complex interactions among species, including
 competition and predation. The greatest changes in biomass and community
 size structure were observed following changes in fishing mortality to top
 predators, with community size structure most strongly influenced by
 changes in mortality to the largest species in the community. Counter to
 predictions based on generation time, the smallest species in our model
 exhibited the longest time to recovery due to strong competition and
 predation. Our results demonstrate the importance of taking an
 ecosystem-based approach and considering species interactions in the
 management of inland fisheries and highlight the potential of size
 spectrum model use in freshwater systems.
description: Parameters relating to growth (asymptotic weight, weight at
 maturity, and the von Bertalanffy growth coefficient) were estimated for
 all species, excluding forage fish, from Fall Walleye Index Netting (FWIN)
 data provided by the Ontario Ministry of Northern Development, Mines,
 Natural Resources and Forestry (OMNDMNRF). As growth rates may vary from
 year to year, we estimated average growth parameters from FWIN data
 spanning two decades (1998 to 2016). To represent the forage fish, we used
 growth parameters for the most abundant forage species, Common Shiner. The
 interaction matrix, which is used to scale feeding interactions between
 all species pairs, was based on spatial overlap across depth strata in the
 lake. Average fishing mortality across time was calculated for each
 species from annual fishing mortality estimates provided by the OMNDMNRF
 spanning 1972 to 2020.
DOI: 10.5061/dryad.vt4b8gtt2
title: Data to: Opportunities for the conservation of migratory birds to benefit threatened resident vertebrates in the Neotropics

description: Neotropical countries receive financing and effort from temperate nations
 to aid the conservation of migratory species that move between temperate
 and tropical regions. If allocated strategically, these resources could
 simultaneously contribute to other conservation initiatives. In this
 study, we use novel distribution maps to show how those resources could
 aid planning for the recovery of threatened resident vertebrates. Using
 eBird-based relative abundance estimates, we first identified areas with
 high richness of Neotropical migrant landbirds of conservation concern (23
 species) during the stationary nonbreeding period. Within these areas, we
 then identified threatened species richness, projected forest loss, and
 conducted a prioritization for 1,261 red-listed vertebrates using
 Terrestrial Area-of-Habitat maps. Richness for migrants was greatest along
 a corridor from the Yucatan peninsula south to the northern Andes but also
 included southwest Mexico and Hispaniola. Protected areas account for
 22.3% of this region while 20.7% is at risk of forest loss. Within this
 focal region for migrants, all four vertebrate groups showed hotspots of
 threatened species richness along the west and east Andean slopes.
 Taxa-specific hotspots included montane areas of southern Mexico and
 central Guatemala (amphibians/reptiles) and the entire east slope of the
 Colombian East Andes (mammals). Our prioritization highlighted several
 areas of importance for conservation due to high threatened species
 richness and projected forest loss including 1) the Pacific dry forests of
 southwest Mexico, 2) montane regions of northern Central America, and 3)
 the west Andean slope of Colombia and Ecuador. At a landscape scale in
 southern Colombia, we show how conservation efforts for 6 Neotropical
 migrants could benefit 56 threatened residents that share a similar
 elevational range. Synthesis and applications. Funding and effort for
 migratory bird conservation also has potential to benefit threatened
 resident vertebrates in the Neotropics. Our study highlights how novel,
 high resolution information on species distributions and risk of forest
 loss can be integrated to identify priority areas for the two groups at
 regional and landscape scales.The approach and data can be further
 modified for more specific goals, such as within-country initiatives.
description: These data are based on publicly available distribution maps
description: see attached readme file