cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0vt4b8h2w
title: Unfiltered VCF for pink salmon rapid adaptation

description: Introduced and invasive species make excellent natural experiments for
 investigating rapid evolution. Here, we describe the effects of genetic
 drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha)
 that were accidentally introduced to the Great Lakes via a single
 introduction event 31-generations ago. Using whole-genome resequencing for
 134 fish spanning five sample groups across the native and introduced
 range, we estimate that the source population’s effective population size
 was 146,886 at the time of introduction, whereas the founding population’s
 effective population size was just 72—a 2040-fold decrease. As expected
 with a severe founder event, we show reductions in genome-wide measures of
 genetic diversity, specifically a 37.7% reduction in the number of SNPs
 and an 8.2% reduction in observed heterozygosity. Despite this decline in
 genetic diversity, we provide evidence for putative selection at 47 loci
 across multiple chromosomes in the introduced populations, including
 missense variants in genes associated with circadian rhythm, immunological
 response, and maturation, which match expected or known phenotypic changes
 in the Great Lakes. For one of these genes, we use a species-specific
 agent-based model to rule out genetic drift and conclude our results
 support a strong response to selection that occurred in a period gene
 (per2) that plays a predominant role in determining an organism’s daily
 clock, matching large day-length differences experienced by introduced
 salmon during important phenological periods. Together, these results
 inform how populations might evolve rapidly to new environments, even with
 a small pool of standing genetic variation.
description: This VCF file contains whole-genome resequence data with SNPs
 called from GATK best practices. This file has been filtered for GATK
 flagged SNPs but otherwise is unfiltered (to allow users to filter how
 they choose or to follow manuscript methods). Please see manuscript for
 additional details. Computational methods can be viewed at https://github.com/morgan-sparks/Pink-Salmon-Rapid-Evolution and are archived on Zenodo (DOI: 10.5281/zenodo.8239589).
DOI: 10.5061/dryad.7sqv9s4vz
title: Monarch butterfly roost site variables and habitat conservation

description: The criteria that Monarchs use to select specific roost sites, and the
 landscape context where those sites are found, have received little study.
 We developed ecological niche models for the Atlantic Flyway roost sites
 using modeling algorithms, citizen scientist observations, and
 environmental variables that are known to affect Monarchs in the adult
 stage prior to migration. These models can be used to help prioritize
 survey and conservation efforts for Monarchs in areas most suitable for
 their roosting. We conducted a vulnerability assessment of predicted
 suitable roost habitat, assessed the connectivity of the habitat with
 Morphological Spatial Pattern Analysis, used Zonation software to create a
 relative value ranking of the Atlantic flyway region for Monarch roost
 site conservation, and mapped areas of high conservation value in the
 flyway in regards to their current predicted vulnerability.
DOI: 10.5061/dryad.3n5tb2rm8
title: Data from: Responses of invasive and native plants to different forms and availability of phosphorus

description: Premise—Many studies have assessed the various responses of alien plants
 to changes in overall nutrient or different nitrogen (N) availabilities.
 However, in natural soils, nutrients are present as different chemical
 elements (e.g., N and phosphorus [P]) and forms (e.g., inorganic and
 organic). Few studies have explored yet whether invasive and native
 species differ in their responses to varying P availability and forms. Key
 results—We found that invasive species did not show an overall higher
 biomass production than that of native species under varied P conditions.
 However, the biomass response to organic P was, relative to the response
 to inorganic P, stronger for the invasive species than that for the native
 species. This coincided with the pattern that invasive species mainly
 allocated biomass to the root system under organic P conditions.
 Conclusions—Our study indicates that while invasive species were not more
 promiscuous than native species were, they took great advantage of the
 organic-P forms. Therefore, the invasion risk of alien species may
 increase in habitats with more organic P sources.
description: We grew five taxonomical related pairs of common
 herbaceous invasive and native species alone or in competition under six
 different conditions of P availability or forms, and assessed their growth
 performance.
DOI: 10.5061/dryad.kprr4xh7p
title: Meta-analysis of Antarctic phylogeography reveals strong sampling bias and critical knowledge gaps

description: Much of Antarctica’s highly endemic terrestrial biodiversity is found in
 small ice-free patches. Substantial genetic differentiation has been
 detected among populations across spatial scales. Sampling is, however,
 often restricted to commonly-accessed sites, and we therefore lack a
 comprehensive understanding of broad-scale biogeographic patterns, which
 could impede forecasts of the nature and impacts of future change. Here,
 we present a synthesis of published genetic studies across terrestrial
 Antarctica and the broader Antarctic region, aiming to identify current
 biogeographic patterns, environmental drivers of diversity, and future
 research priorities. A database of all published genetic research from
 terrestrial fauna and flora (excl. microbes) across the Antarctic region
 was constructed. This database was then filtered to focus on the most
 well-represented taxa and markers (mitochondrial COI for fauna, and
 nuclear ITS for flora). The final dataset comprised 7222 records, spanning
 153 studies of 335 different species. There was strong taxonomic bias
 towards flowering plants (52% of all floral data sets) and springtails
 (54% of all faunal data sets), and geographic bias towards the Antarctic
 Peninsula and Victoria Land. Recent connectivity between the Antarctic
 continent and neighbouring landmasses, such as South America and the
 Southern Ocean Islands (SOIs), was inferred for some groups, but patterns
 observed for most taxa were strongly influenced by sampling biases.
 Above-ground wind speed and habitat heterogeneity were positively
 correlated with genetic diversity indices overall, though environment was
 a generally poor predictor of genetic diversity. The low resolution and
 variable coverage of data may also have reduced the power of our
 comparative inferences. In the future, higher-resolution data, such as
 genomic SNPs and environmental modelling, alongside targeting sampling of
 remote sites and under-sampled taxa, will address current knowledge gaps
 and greatly advance our understanding of evolutionary processes across the
 Antarctic region.
description: All sequence data were downloaded from GenBank, and processed in
 R. Details please refer to manuscript.
description: Data files contain .doc, .xlsx, and .pdf.
DOI: 10.5061/dryad.8kprr4xrj
title: Range contractions and reduced body mass predicted for endemic skinks of the Cameroon volcanic line with future warming

description: Aim The vulnerability of montane species to environmental change has been
 increasingly recognized over the past decade. However, most of these
 species are regionally endemic with restricted ranges, limiting dispersal
 necessary for avoiding extinction. Threats posed for montane lizards could
 be further complicated in species following Bergmann’s rule, where body
 size increases with altitude. In this study, we applied a bioclimatic and
 body mass trait-based species distribution model approach to identify
 areas suitable for montane endemic skink species of the Cameroon Volcanic
 Line (CVL) under current and future climates. Location Cameroon Volcanic
 Line Methods We recorded occurrence records and measured body mass in the
 field for skink species endemic to the CVL. We additionally supplemented
 our occurrence data with records from an online repository. We projected
 habitat suitability in the region by implementing the occurrence data in
 the bioclimatic species distribution models. We further integrated both
 occurrence and body mass information in our trait-based model to project
 potential body mass. Results Projected currently suitable ranges were
 limited to higher elevation regions, which are inhabited by numerous other
 threatened amphibian and reptile species. We found that, for our two skink
 species following Bergmann clines in body mass, trait model predictions
 covered a slightly larger geographic range than bioclimatic estimates.
 Under future warming, both models predict substantial contractions in
 suitable areas, potentially constraining species to mountain tops. Through
 the trait-based approach, we further detected potential warming-induced
 body mass reductions in projected suitable areas. Main conclusions We thus
 demonstrate how combining occurrence records with species trait
 information in predictive modelling can reveal complementary trends for
 more comprehensive climate change impact assessments. Overall, these
 challenges towards the persistence of CVL-endemic skink species should
 prompt urgent responses in national conservation management and local
 community engagement.
description: We recorded location (as GPS coordinates) and morphological
 measurements of skink species found on the mountains of the Cameroon
 Volcanic Line. We additionally downloaded location data from GBIF for
 these species to supplement our own dataset.
DOI: 10.5061/dryad.qbzkh18mf
title: Differential response of Sichuan snub-nosed monkeys to climate change and human activities

description: Aim: Determining the mechanisms by which climate change and human
 activities affect patterns of ecological specialization in different
 genetic units of the same species is crucial for developing local or
 regionally-based conservation solutions. This study uses species
 distribution models and genetic analysis to 1) identify evidence of
 intraspecific differences in the population size and distribution of the
 three extant lineages (Sichuan/Gansu (SG), Qinling (QL), and Shennongjia
 (SNJ)) of Sichuan snub-nosed monkeys; and 2) determine why some lineages
 have lower population numbers, a smaller geographical distribution, and
 are more threatened with extinction. Location: China Methods: We used
 n-dimensional hypervolume modeling and Genotype–Environment Association
 (GEA) models to compare the climatic niches of three snub-nosed monkey
 lineages, SDMs to reconstruct the historical, current, and future
 distributions of each lineage, and SMC++ to calculate their effective
 population sizes. Results: We found evidence of: 1) climatic niche
 differentiation among the SG, QL, and SNJ lineages of Sichuan snub-nosed
 monkeys; 2) geographical isolation combined with a decrease in population
 size during the LGM resulted in ecological specialization among these
 three lineages; and 3) a decline in climatic suitability and
 anthropogenically-driven land conversion, combined with small population
 size and a narrow distributional range, indicate that the SNJ lineage is
 at a greater risk of extinction than the SG and QL lineages. Main
 conclusions: We demonstrate that during the LGM a reduction in habitat
 suitability driven by climate change, in concert with decreasing
 population size resulted in the geographical isolation of the three
 Sichuan snub-nosed monkey subpopulations, leading to lineage differences
 in ecological specialization. GEA models and hypervolume models
 demonstrated that the three lineages occupy different ecological niches.
 Based on lineage-level models, the SNJ and QL lineages should be the
 immediate focus of conservation efforts due to their small effective
 population size and expected future reductions in available suitable
 habitat. The modeling approach used here is robust and can be applied
 effectively to examine the biogeography, recent evolutionary history, and
 effective population size of other endangered animal taxa.
DOI: 10.7291/d1nh46
title: Vegetation complexity and nesting resource availability predict bee diversity and functional traits in community gardens

description: Urban gardens can support diverse bee communities through resource
 provision in resource poor environments. Yet the effects of local habitat
 and landscape factors on wild bee communities in cities is still
 insufficiently understood, nor how this information could be applied to
 urban wildlife conservation. Here we investigate how taxonomic and
 functional diversity of wild bees and their traits in urban community
 gardens are related to garden factors and surrounding landscape factors
 (e.g., plant diversity, amount of bare ground, amount of nesting
 resources, amount of landscape imperviousness). Using active and passive
 methods in 18 community gardens in Berlin, Germany, we documented 26
 genera and 102 species of bees. We found that higher plant species
 richness and plant diversity as well as higher amounts of deadwood in
 gardens leads to higher numbers of wild bee species and bee (functional)
 diversity. Furthermore, higher landscape imperviousness correlates with
 cavity nesting bees whereas a higher amount of bare ground correlates with
 more ground-nesting bees. Pollen specialisation was positively associated
 with plant diversity, but no factors strongly predicted endangered bees.
 Our results suggest that, aside from foraging resources, nesting resources
 should be implemented in management for more pollinator-friendly gardens.
 If designed and managed using such evidence-based strategies, urban
 gardens can create valuable foraging and nesting habitats for
 taxonomically and functionally diverse bee communities in cities.
DOI: 10.5061/dryad.931zcrjpd
title: Data from: Changes in the foliar fungal community between oak leaf flushes along a latitudinal gradient in Europe

description: Aim: To advance our understanding of how foliar fungal communities are
 structured and assembled, we assessed to what extent leaf flush and
 latitude can explain the within- and among-tree variation in the foliar
 fungal community in a foundation tree species, the pedunculate oak Quercus
 robur. Location: A latitudinal gradient spanning c. 20 degrees in latitude
 in Europe. Major taxa studied: The foliar fungal community on Quercus
 robur. Methods: We examined the main and interactive effects of leaf flush
 and latitude on the foliar fungal community by sampling 20 populations of
 the pedunculate oak Quercus robur across the tree’s range, spanning c. 20
 degrees in latitude. Results: Species composition, but not species
 richness, differed between leaf flushes. Across the latitudinal gradient,
 species richness was highest in the central part of the oak’s
 distributional range, and foliar fungal community composition shifted
 along the latitudinal gradient. Among fungal guilds, the relative
 abundance of plant pathogens and mycoparasites was lower on the first leaf
 flush, and the relative abundance of plant pathogens and saprotrophs
 decreased with latitude. Conclusions: Changes in community composition
 between leaf flushes and along the latitudinal gradient were mostly a
 result of species turnover. Overall, our ﬁndings demonstrate that leaf
 flush and latitude explain 5-22% of the small- and large-scale spatial
 variation in the foliar fungal community on a foundation tree within the
 temperate region, with major consequences for plant health, species
 interactions and ecosystem dynamics.
DOI: 10.5061/dryad.xpnvx0kjr
title: Frequency jumps and subharmonic components in calls of female Odorrana tormota differentially affect the vocal behaviors of male frogs

description: Many studies have demonstrated that sounds containing nonlinear phenomena
 (NLP) can influence the behavior of receivers. However, the specific
 functions of different NLP components have received less attention. In
 most frog species, females produce few or no vocalizations; in contrast,
 female Odorrana tormota exhibit a diverse range of calls that are
 rich in NLP components. Previous field playbacks have shown that female
 calls can elicit responses from male frogs. Therefore, we conducted a
 phonotaxis experiment to investigate the differential effects of different
 NLP calls by female O. tormota on the vocal behavior of male
 frogs. The results of our study revealed that calls with subharmonics
 elicited a greater number of short calls and answering calls from male
 frogs than calls with frequency jumps. Conversely, calls with frequency
 jumps triggered more staccato calls from males than calls with
 subharmonics. Additionally, during the phonotaxis experiments, we recorded
 the initial vocalizations of males in response to playbacks of female
 calls. The majority of males first produced short calls. Under calls with
 frequency jumps, most of the male frogs approaching within 10 cm of the
 loudspeaker produced staccato calls instead of "meow" calls or
 short calls. While under calls with subharmonics, most male frogs
 preferred to produce short calls. Our findings demonstrate that frequency
 jumps and subharmonic components in the calls of female O. tormota have
 different effects on male vocal behaviors.
description: # Title of Dataset: Data for "Frequency Jumps and Subharmonic
 Components in Calls of Female O. tormota Differentially Affect the Vocal
 Behaviors of Male Frogs" --- Two data files of playback experiments
 in male Odorrana tormota frogs ## Description of the Data and file
 structure Fj_Sh.csv contains 5 parameters for the phonotaxis experiment:
 1) the number of short calls produced (C-Sc), 2) the number of “meow” call
 produced (C-Mw), 3) the number of staccato calls produced (C-St), and 4)
 the number of answering calls produced (C-Ac, Figure 2), 5) time taken
 within a proximity of 10 cm to the loudspeaker (T-Sp). First-last.csv
 contains the number of male frogs that choose to emit a short call, meow
 call, or staccato call for the first time, as well as the number of male
 frogs that choose to emit a short call, meow call, or staccato call when
 approaching the speaker within 10 centimeters.
DOI: 10.5061/dryad.rxwdbrvcj
title: Data from: The fate of nitrogen during agricultural intensification in East Africa: nitrogen budgets in contrasting agroecosystems

description: The intensification of agricultural systems in sub-Saharan Africa (SSA) is
 necessary to reduce poverty and improve food security but requires
 increased nutrient applications to smallholder systems. To avoid the
 negative consequences of intensification that result from many large-scale
 agricultural systems (e.g., eutrophication), we must better understand how
 diverse soil systems in SSA will respond to increased fertilizer
 applications. We tracked nitrogen (N) inputs and outputs in fertilizer
 trials at two maize (Zea mays)-agroecological regions of contrasting soil
 type. We measured maize biomass, grain yields, N leaching, and N gaseous
 losses from a clayey soil in Yala, Kenya, and a sandy soil in Tumbi,
 Tanzania, with application rates of 0, 50, 75, 100, 150, and 200 kg N ha-1
 yr‑1 over multiple years. Using measurements of NO, N2O, NO3-,
 biomass N, and an 15N enrichment experiment, we show that N budgets in
 Yala were nearly always negative, meaning more N was exported in yields or
 lost from the system than was added in fertilizer. In Tumbi, however, N
 budgets were negative at lower fertilizer levels (0 and 50 kg N ha-1), but
 positive at higher fertilizer levels (75 and 200 kg N ha-1). At both
 sites, most of the N was lost through maize biomass/grain removal and N
 leaching (over 96% of total losses). Gas losses were a minor component of
 N budgets. These results highlight the importance of tailoring fertilizer
 recommendations to a farm’s specific soil and climatic conditions.
 However, on these two contrasting sites, fertilizer additions at or below
 50 kg N ha-1 do not lead to major losses of N (via gaseous or leaching)
 and may be recommended at a range of sites across SSA soils in maize
 agroecosystems.
DOI: 10.5061/dryad.6djh9w149
title: Data for: Link between glucose metabolism and EMT drives triple negative breast cancer migratory heterogeneity

description: Intracellular and environmental cues result in heterogeneous cancer cell
 populations with different metabolic and migratory behaviors. While
 glucose metabolism and EMT have previously been linked, we aim to
 understand how this relationship fuels cancer cell migration. We show that
 while glycolysis drives single-cell migration in confining microtracks,
 fast and slow cells display different migratory sensitivities to
 glycolysis and oxidative phosphorylation inhibition. Phenotypic sorting of
 highly and weakly migratory subpopulations (MDA+, MDA-) reveals that more
 mesenchymal, highly migratory MDA+ preferentially use glycolysis while
 more epithelial, weakly migratory MDA- utilize mitochondrial respiration.
 These phenotypes are plastic and MDA+ can be made less glycolytic,
 mesenchymal, and migratory and MDA- can be made more glycolytic,
 mesenchymal, and migratory via modulation of glucose metabolism or EMT.
 These findings reveal an intrinsic link between EMT and glucose metabolism
 that controls migration. Identifying mechanisms fueling phenotypic
 heterogeneity is essential to develop targeted metastatic therapeutics.
description: Data was collected using equipment and materials in the
 Reinhart-King lab. Studies were conducted as described in STAR Methods
 section of publication. Data were processed using Fiji/ImageJ and recorded
 in Excel.
description: Microsoft excel is required.