cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.59zw3r2c5
title: Hybrid cline or hybrid lineage: A genomic reevaluation of Sibley’s classic species conundrum in Pipilo towhees

description: Hybrid zones are often described as clines of genetic and phenotypic
 traits moving across species barriers through introgression. Yet, hybrid
 zones can also be spatially complex and shift over time, and dispersal and
 vicariance can isolate portions of a cline, potentially leading to hybrid
 lineage formation. We reassessed Sibley’s (1950) gradient between Collared
 Towhee (Pipilo ocai) and Spotted Towhee (P. maculatus) in Central Mexico
 to test whether it conformed to a typical tension-zone cline model. By
 comparing historical and modern data, we found that cline centers for
 genetic and phenotypic traits have not shifted over the course of 70
 years. This equilibrium suggests that secondary contact between these
 species, which originally diverged over 2 million years ago, likely dates
 to the Pleistocene. Given the amount of mtDNA divergence, parental ends of
 the cline have very low autosomal nuclear differentiation (FST = 0.12).
 Dramatic and coincident cline shifts in mtDNA and throat color suggest the
 possibility of sexual selection as a factor in differential introgression,
 while a contrasting cline shift in green back color hints at a role for
 natural selection. Supporting the idea of a continuum between hybrid
 clines and hybrid lineage formation, the towhee gradient can be analyzed
 as one population under isolation-by-distance, as a two-population cline,
 and as three lineages experiencing divergence with gene flow. In the
 middle of the gradient, a hybrid lineage has become partly isolated,
 likely due both to forested habitat shrinking and fragmenting as it moved
 upslope after the last glacial maximum and a stark environmental
 transition. The towhee system offers a window into the potential outcomes
 of hybridization across a dynamic landscape including the creation of
 novel genomic and phenotypic combinations and incipient hybrid lineages.
description: Morphological data: traits measured from specimens with ruler and
 digital calipers Genetic data: SNPs generated from
 sequence capture of ultraconserved elements and Illumina
 sequencing Environmental data: extracted from
 environmental layers from localities associated with photo vouchers on
 iNaturalist
DOI: 10.5061/dryad.1vhhmgqx6
title: Photoelectrochemical performance of BiOI/TiO2 Nanotube Arrays (TNAs) p-n heterojunction synthesized by SILAR-ultrasonication-assisted methods

description: In order to extend the visible region activity of titania nanotube array
 (TNAs) films, the Successive Ionic Layer Adsorption and Reaction
 (SILAR)-ultrasonication-assisted method has been used to prepare
 BiOI-modified TiO2 nanotube arrays (BiOI/TNAs). The band gap of BiOI/TNAs
 for all the variations reveals absorption in the visible absorption. The
 surface morphology of BiOI/TNAs is shown in the nanoplate, nanoflake, and
 nanosheet forms with a vertical orientation perpendicular to TiO2. The
 crystalline structure of BiOI did not change the structure of the anatase
 TNAs, with the band gap energy of the BiOI/TNAs semiconductor in the
 visible region. The photocurrent density of the BiOI/TNAs extends to the
 visible-light range. BiOI/TNAs with 1 mM Bi and 1 mM KI on TNAs 40 V 1 h
 50 V 30 min shows the optimum photocurrent density. A tandem
 dye-sensitized solar cell (DSSC)-photoelectrochemical (PEC) was used for
 hydrogen production in salty water. BiOI/TNAs optimum was used as the
 photoanode of the PEC cell. Solar to hydrogen conversion efficiency (STH)
 of tandem DSSC-PEC reaches 1.34% in salty water.
description: TNAs were synthesized by modifying the second-step potentials of the two-step anodization method. The applied potential used in the first step method was fixed at 40 V for 60 min, and the second step anodization voltage was 50 V with various anodization times, i.e., 15 min, 30 min, and 60 min. BiOI/TNAs were prepared through the SILAR-ultrasonication-assisted method. The cationic precursor was used Bi(NO<sub>3</sub>)<sub>3</sub>.5H<sub>2</sub>O with various concentrations, and a solution of KI with various molar ratios was used as the anionic precursor. Deionized water was used as the solvent to dilute the precursors. TNAs foil was immersed in the cationic precursors with a time variation of 10 s, 45 s, and 90 s., followed by immersion in deionized water. After that, the TNAs foils were immersed in anionic precursors solution and then deionized water immersion to remove the not adsorbed ion. SILAR cycles, the concentration of the precursors, and immersion time were varied to get the optimum condition. BiOI/TNAs dried in open-air conditions. SILAR-Ultrasonication assisted illustration is shown in Figure.1. For comparison, BiOI/TNAs also prepared by SILAR without ultrasonication assisted, that symbolized by S (SILAR without ultrasonication assisted).
DOI: 10.5061/dryad.5x69p8d7f
title: Data and R scripts for: Ant invasions is associated with lower root density and different root distribution of a foundational savanna tree species

description: Some invasive ants have worldwide distributions and impose substantial
 impacts on human society and native biodiversity. Yet we know little about
 how ants impact soil ecosystems in general, much less how soil ecosystems
 shift when invasive ants move in. We excavated the coarse roots of a
 monodominant savanna tree in invaded and uninvaded areas to test the
 hypothesis that the presence of invasive ants would be associated with
 changes in root distribution and biomass across the landscape. We found
 that in the presence of invasive ants, trees had a shifted distribution of
 lateral coarse roots, with proportionally less root biomass near the
 surface and far from tree stems. In addition, the density of lateral
 coarse-root biomass was ~20% lower for trees within invaded landscapes.
 Our results suggest that soil-nesting invasive ants can drive important
 changes in rooting strategy for a tree species that serves a foundational
 role in the biogeochemical cycles of vertisol savannas.
description: Biological samples were collected by John Lemboi and John Mosiany
 at Ol Pejeta Conservancy, and then processed and entered at Mpala Research
 Centre by JL, JM, and Patrick Milligan. These samples were stored and used
 to check outliers in the data, and then analyses were conducted in R using
 scripts included in the zipped files here. PM and Elizabeth Pringle
 conducted analyses at the University of Nevada, Reno. No other processing
 was done beyond transformations and manipulations outlined in the R script
 and associated article.
description: R version 4.0.5 is required to open files and run scripts in this
 zipped folder. All package dependencies are outlined in the main R script.
 A README txt file is included as an introduction to the data organization
 and script functions.
DOI: 10.5061/dryad.0gb5mkm57
title: Divergent foraging strategies between populations of sympatric matrilineal killer whales

description: In gregarious species, collective behavior maximizes individual fitness
 benefits while minimizing costs. Despite the relevance of behavior to
 conservation, the link between the robustness of behavioral patterns
 across populations and population health is poorly understood. We studied
 the collective foraging behavior of two closed, sympatric populations of
 piscivorous killer whales, leveraging two contemporaneously-collected data
 sets from suction cup-attached bio-logging tags, to quantify patterns of
 fine-scale foraging movements and their relationships with demography. We
 reveal striking plasticity in collective foraging behavior between
 populations. Prey capture rate and foraging efficiency were greater for
 males in the endangered Southern Resident (SRKW) population, yet greater
 for females in the Northern Resident (NRKW) population. The presence of a
 calf (≤ 3 y) reduced the number of prey captured by adult females in both
 populations, with the greatest effect in SRKW, in which no mothers with
 calves captured prey while bearing tags. SRKW adult males with a living
 mother tended to capture more prey than those whose mother had died,
 whereas the opposite was true for NRKW adult males. Moreover, males
 generally tended to forage in areas with deeper bathymetry than females,
 and SRKW captured prey deeper than NRKW. These population-level
 differences in sex-specific foraging behavior challenge the existing
 paradigm that mothers are disproportionate foragers in gregarious killer
 whales, underscoring that an endangered population is employing a
 potentially unstable collective foraging strategy mismatched to recovery.
 Thus, our study provides a mechanistic link between fine-scale, collective
 foraging behavior and population health in an apex marine predator.
DOI: 10.5061/dryad.pzgmsbcr7
title: Spatial learning overshadows learning odors and sounds in both predatory and frugivorous bats

description: To forage efficiently, animals should selectively attend to and remember
 the cues of food that best predict future meals. One hypothesis is that
 animals with different foraging strategies should vary in their reliance
 on spatial versus feature cues. Specifically, animals that store food in
 dispersed caches or that feed on spatially stable food, like fruit or
 flowers, should be relatively biased to learning a meal’s location,
 whereas predators that hunt mobile prey should instead be relatively
 biased towards learning feature cues such as odor or sound. Several
 authors have predicted that nectar-feeding and fruit-feeding bats would
 rely relatively more on spatial cues, whereas closely related predatory
 bats would rely more on feature cues, yet no experiment has compared these
 two foraging strategies under the same conditions. To test this
 hypothesis, we compared learning in the frugivorous bat, Artibeus
 jamaicensis, and the predatory bat, Lophostoma silvicolum, which hunts
 katydids using acoustic cues. We trained bats to find food paired with a
 unique and novel odor, sound, and location. To assess which cues each bat
 had learned, we then dissociated these cues to create conflicting
 information. Rather than finding that the frugivore and predator clearly
 differ in their relative reliance on spatial versus feature cues, we found
 that both species used spatial cues over sounds or odors in subsequent
 foraging decisions. We interpret these results alongside past findings on
 how foraging animals use spatial cues versus feature cues and explore why
 spatial cues may be fundamentally more rich, salient, or memorable.
description: Observers that were blind to which cues
 had been rewarded watched videos of the one-hour trials (in VLC media
 player) and recorded which feeder a bat chose first in a trial and the
 total number of choices to each feeder during the trial. Choices were
 counted if the bat hovered within 1 body length (about 7 cm) from the top
 of a feeder for more than 0.1 s (3 video frames) or if they touched down
 atop a feeder.
description: R
DOI: 10.5061/dryad.jdfn2z3fc
title: Data for: Inhibition drives habituation of a larval zebrafish visual response

description: Habituation allows animals to learn to ignore persistent but
 inconsequential stimuli. Despite being the most basic form of learning, a
 consensus model on the underlying mechanisms has yet to emerge. To probe
 relevant mechanisms we took advantage of a visual habituation paradigm in
 larval zebrafish, where larvae reduce their reactions to abrupt global
 dimming (a dark flash). Using Ca2+ imaging during repeated dark flashes,
 we identified 12 functional classes of neurons that differ based on their
 rate of adaptation, stimulus response shape, and anatomical location.
 While most classes of neurons depressed their responses to repeated
 stimuli, we identified populations that did not adapt, or that potentiated
 their response. To identify molecular players, we used a small
 molecule-screening approach to search for compounds that alter habituation
 learning. Among the pathways we identified were Melatonin and Estrogen
 signaling, as well as GABAergic inhibition. By analyzing which functional
 classes of neurons are GABAergic, and the result of pharmacological
 manipulations of the circuit, we propose that GABAergic inhibitory motifs
 drive habituation, perhaps through the potentiation of GABAergic synapses.
 Our results have identified multiple molecular pathways and cell types
 underlying a form of long-term plasticity in a vertebrate brain, and allow
 us to propose the first iteration of a model for how and where this
 learning process occurs.
DOI: 10.5061/dryad.280gb5mt3
title: SNPs genotypes of southern beech Nothofagus dombeyi

description: Geogenomics seeks to understand geological processes linked to lineage
 divergence. However, the mechanisms that conserve ancient signals despite
 gene flow are still unclear. In the southern beech, the deep lineage
 divergence produced by vicariant events is associated with ancient marine
 transgressions. We hereby evaluate the hypothesis that this divergence is
 maintained by diversifying selection. The lineage divergence
 using AMOVA, principal coordinate analysis, assignment tests, and multiple
 matrix regression analyses was assessed using chloroplast DNA and neutral
 and outlier SNPs. Several environmental variables were used to
 characterize potential within-species niche structuring and
 genotype-environment associations. Two deep-rooted latitudinally
 structured lineages resulted from cpDNA, the northern cluster being more
 genetically diverse than the southern one. Of the total of 2,943 SNPs, 33
 were identified as outliers and produced two genetic clusters. Neutral
 SNPs yielded no structure by AMOVA, whereas higher
 (&gt;75%) Fst values were obtained for cpDNA and outlier
 SNPs. Precipitation variables were mostly associated with population
 clusters and suggested two climatic niches, consisting of cold and dry in
 the south and more variable precipitation, temperature, and soil
 conditions in the north. Associations of genetic distance with environment
 and geography suggested IBD and IBE effects. Ancient lineage
 divergence in N. dombeyi, originally driven by vicariance, has
 been maintained by diversifying selection under distinct environmental
 conditions that also define distinct within-species niches. Deeply rooted
 phylogeographic breaks can be conserved in continuously distributed
 species in the absence of current geographic barriers. Yet physical
 gradients exert differential selective pressures, which are maintained in
 the face of potential gene flow. As a result, selection can lead to
 geographically localized and differentially adapted groups of populations
 that can be detected by a combination of traditional phylogeographic and
 novel genomic methods.
description: # SNP genotypes of the southern beech *Nothofagus dombeyi* This dataset
 contains genotypes for 2943 SNPs of 113 *N. dombeyi* individuals
 classified a priori as belonging to each of two intraspecific lineages
 (populations 1 and 2) using chloroplast sequences. ## Description of the
 Data and file structure Each individual consists of a homozygous or
 heterozygous genotype through changes in one base as A, C, G, T. Missing
 data codes: none ## Sharing/Access Information Newly generated DNA
 sequences are deposited in GenBank (accession numbers OP473928-OP473939
 and OP491426-OP491431). Data matrices containing genomic information that
 supports the findings of this study are available from Universidad
 Nacional del Comahue Institutional Digital Repository RDI Unco URI (link
 in Related Works section).
DOI: 10.5061/dryad.63xsj3v69
title: Data for: Traits help explain species’ performance away from their climate niche centre

description: Aim: Climate change impacts on biota are variable across sites, among
 species, and throughout individual species' ranges. Niche theory
 predicts that population performance should decline as site climate
 becomes increasingly different from the species’ climate niche centre,
 though studies find significant variation from these predictions. Here, we
 propose that predictions about climate responses can be improved by
 incorporating species' trait information. Location: Europe Methods:
 We used observations of plant species abundance change over time to assess
 variation in climate difference sensitivity (CDS), defined as how species
 performance (colonization, extinction, and abundance change) relates to
 the difference of site climate from the mean temperature and precipitation
 of each species’ range. We then investigated if leaf economics, plant
 size, and seed mass traits were associated with the species’ climate
 difference sensitivity.   Results: Species that performed better
 (e.g., increased in abundance) towards sites progressively cooler than
 their niche centre were shorter and had more resource-acquisitive leaves
 (i.e., lower leaf dry matter content or LDMC) relative to species with
 zero or the opposite pattern of temperature difference sensitivity. This
 result supports the hypothesis that if sites cooler than niche centre are
 more stressful for a species, then shorter stature is advantageous
 compared to taller species. The LDMC result suggests the environment
 selects for more resource-acquisitive leaf strategies towards relatively
 cooler climates with shorter growing seasons, counter to expectations that
 conservative strategies would be favoured in such environments. We found
 few consistent relationships between precipitation difference
 sensitivities and traits. Main conclusions: The results supported key a
 priori foundations on how trait-based plant strategies dictate species
 responses to climate variation away from their niche centre. Further,
 plant height emerged as the most consistent trait that varied with species
 climate difference sensitivity, suggesting height will be key for theory
 development around species response to climate change.
description: See manuscript.
description: See methods and R code for the analyses can found here: https://github.com/jslynn33/macrocontext-and-traits
DOI: 10.5061/dryad.2280gb5ww
title: Data from: Range reexpansion after long stasis: Italian otters (Lutra lutra) at their northern edge

description: Species range shifts and expansion are subjects of primary research
 interest in the context of climate warming and biological invasions. Few
 studies have focused on reexpansion of species that suffered severe
 declines. Here, we focused on population recovery of Eurasian otters
 (Lutra lutra) in Italy, first detected in 2003 after a southward range
 contraction. We modelled the rate of range expansion and occupancy at the
 northern expanding front (central Italy), to gain insights into the
 progress of recovery and mechanisms of reexpansion. We performed a field
 survey in 2021, which redefined the northern limit of distribution further
 north, in close proximity to the Gran Sasso National Park. Then we
 analyzed a time series (1985–2021) of distances of northernmost
 occurrences from the centre of the 1985 range. Using segmented regression,
 we were able to identify a prolonged stasis of the northern range edge and
 a simultaneous increase in occupancy from 0.151 to 0.4. A breakpoint was
 estimated in 2006, after which the range expanded northwards at an average
 rate of 5.48 km/year. From 2006 to 2021, the overall northward shift was
 about 80 km. Occupancy continued to increase until 2019 and abruptly
 declined in 2021. These patterns suggest that the reexpansion of the range
 can be limited by low occupancy at the expanding front. As occupancy
 increases, long-distance dispersal increases and then range expands. The
 low occupancy at the current distribution limit of otters may reflect a
 higher anthropogenic pressure on northern habitats, which could slow down
 the reexpansion process.
description: Field collection (standard occupancy surveys) and GIS and
 statistical analyses.
description: Windows Editor or WordPad, R statistical
 software.<br>
DOI: 10.5061/dryad.k98sf7m9r
title: The associations of gene-gene interactions among the 6 variants in 3 genes related to inflammation and endothelial function with carotid stenosis were performed by the GMDR approach

description: The associations of gene-gene interactions among the 6 variants in 3 genes
 related to inflammation and endothelial function with carotid stenosis
 were performed by the GMDR approach. The best model for carotid stenosis
 including ITGA2 rs4865756 and HABP2 rs7923349 scored 8/10 for
 cross-validation consistency and 10/10 for sign testing. 
description: During May 2015 and September
 2015, eight communities in Sichuan were randomly selected. We only
 screened all residents aged ≥40 years who lived in the community for more
 than 6 months. A structured face-to-face questionnaire was used in the
 initial screening by interviewers. The
 eight conventional stroke risk factors were assessed in the CNSSS
 questionnaire, including hypertension, diabetes, dyslipidemia, AF,
 overweight/obesity, smoking, physical inactivity, and family history of
 stroke. Subjects were classified as the high-risk population for stroke if
 they experienced at least three of the aforementioned eight stroke-related
 risk factors or a history of stroke. Exclusion criteria included: (i)
 severe cardiovascular, liver or renal disease, (ii) blood system disease
 and coagulation dysfunction, (iii) acute and chronic inflammation,
 malignant tumors and immune system diseases, (iv) transient ischemic
 attack only, and (v) individuals declined to participate in the
 study. Finally,
 16,892 valid individual records were enrolled. Among them, 2,893
 participants were the high-risk population. However, DNA and carotid
 ultrasonography information was obtained from 2,377 participants among the
 2,893 high-risk population. A total of 2,377 subjects were classified into
 carotid stenosis and non-carotid stenosis (&lt;15% stenosis) groups on
 the basis of their vascular imaging. The
 associations of gene-gene interactions among the 6 variants with carotid
 stenosis were performed by the GMDR approach.
description: Microsoft Excel, Adobe Acrobat