cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j0zpc86m3
title: Historical Mark Release Recapture (MRR) studies of selection and plasticity in butterflies

description: Historical data on plasticity, selection and evolution of phenotypic
 traits in the wild provide an important resource for understanding how
 populations are responding to ongoing anthropogenic environmental changes.
 We provide the datasets associated with a series of Mark Release Recapture
 (MRR) studies that quantified seasonal variation in plasticity and
 phenotypic selection in a natural population of Pontia occidentalis
 butterflies in southcentral WA USA between 1989–1996. The studies examined
 both natural and experimentally-generated variation in two types of
 traits: wing melanin pattern on each wing surface; and wing and body size
 and shape. Papers published during the 1990s that summarized the results
 of these studies demonstrated phenotypic plasticity and directional
 selection on some of the traits that varied with seasonal weather
 conditions. Here we present the original, underlying data for each of the
 nine studies.  These data may be valuable for exploring newer
 statistical approaches for modeling MRR studies of selection and
 plasticity, and for evaluating historical changes in selection and
 evolution of traits related to climate adaptation in response to ongoing
 climate and other environmental changes.
description: These datasets provide the
 original data for a series of mark-recapture studies, and associated
 research publications, with <em>Pontia occidentalis</em>
 butterflies near Corfu WA between 1989 and 1996.  Details of the study
 site, methodology, and associated publications for each study are
 described in the Combined ReadMe file and in the associated document file:
 <strong>Kingsolver Historical MRR datasets for Pontia
 occidentalis.doc</strong>, and in the list of related works below.
 The dataset for each study is provided as a separate MS .xls file.
 Most
 datasets consisted of two original files: one that contained initial
 capture data (treatment group, wing condition, mass, etc.), and one that
 contained subsequent recapture data (behavior when recaptured, time of
 day, etc.). For each experiment, we followed the same
 workflow: We
 scanned and transcribed the field notebooks as written into the two
 separate files We checked for errors by checking for duplicate
 IDs, mistyped treatment group labels, etc. 
 We concatenated these two
 datafiles into one long datafile by marking the initial capture as
 recapture # 0. By doing so, we could keep all of the affiliated data
 unique to each sample and be able to analyze the recaptures alongside
 these data.
 <br> Due to the shared workflow, all of the final
 datafiles have the same structure: a set of initial captures as the
 beginning rows of the datafile (marked as recapture #0), and then
 subsequent recaptures (with duplicated identifying data) following in
 later rows. Details are provided in the Combined ReadMe
 file.<br>
description: Standard document reader and spreadsheet are needed.
DOI: 10.5061/dryad.xwdbrv1js
title: Tempo-spatial evolution of seed plant endemism in Taiwan island

description: Aim: In Taiwan island, dispersal through recent land-bridge and
 oversea after the appearance of proto-Taiwan (&lt;6.5 Ma) is
 responsible for its biodiversity assembly. While radiations have also been
 widely reported in mountain systems. So, the tempo-spatial route to the
 floral hotspot was determined through a meta-analysis of
 evolution of endemic plants. Location: Taiwan island and adjacent
 Asian regions. Taxon: Seed plants. Methods: Published
 dated phylogenies were compiled, and the stem ages were considered as
 origin times. Ancestral range shift pattern and/or
 distribution of sister lineage/species were used to determine the
 speciation mode, in situ origin or dispersal. The distributions
 of sister taxa were assigned to ten different biogeographical regions.
 Histograms quantifying the number of different origin mode events within
 0.5 Ma bins were constructed. Possibility of long-distance dispersal
 (LDD) was evaluated. Results: The 125 sampled endemic plants
 originated between the late Eocene and late Pleistocene, with 111 species
 (88.8%) originating after the emergence of proto-Taiwan and 14 species
 (11.2%) before. Spatially, in situ speciation contributed more to the
 formation of endemism than dispersal (56.8% vs 43.2%). The mean
 ages of in situ origin species (1.83 Ma) are significantly
 younger than that of dispersal (6.34 Ma). The main regions from
 which dispersal occurred were south-central (n=29) and southeast China
 (n=28) (referred to as south China), followed by Japan
 (n=14). High ratio (60.8%) of LDD ability is found. Main
 conclusions: Spatially, recent land-bridge and
 oversea dispersal from the adjacent flora of Asia is supported and
 southwest and southeast China are the most important sources. In
 situ speciation that may be correlated with mountain
 uplift, monsoon intensification and Pleistocene climatic fluctuations
 exert greater contributions. Temporally, floral endemism is predominantly
 origin after the emergence of proto-Taiwan. Additional investigations with
 more sophisticated sampling and genetic data are needed in the future.
DOI: 10.7914/fnv9-9r38
title: Kil_Act_HVOnodes

description: Hawaiian Volcano Observatory Smart Solo 5-second nodes deployed across Kīlauea volcano's caldera floor in 2023. This deployment was part of a larger active source experiment across Kīlauea's summit. These data are associated with 6F_2023 and Assembled_ID 23-031.
DOI: 10.5061/dryad.fxpnvx0xq
title: Data from: A global assessment of Bergmann’s rule in mammals and birds

description: Bergmann’s rule states that endotherms have a large body size in high
 latitudes and cold climates. However, previous empirical studies have
 reported mixed evidence on the relationships between body size and
 latitude, raising the question of why some clades of endotherms follow
 Bergmann’s rule whereas others do not. Here, we synthesized the
 interspecific relationships between body size and latitude among 16,187
 endothermic species (5,422 mammals and 10,765 birds) using Bayesian
 phylogenetic generalized linear mixed models to examine the strength and
 magnitude of Bergmann’s rule. We further assessed the effect of biological
 and ecological factors (i.e., body mass categories, dietary guild, winter
 activity, habitat openness, and climate zone) on the variations in the
 body mass–latitude relationships by adding an interaction term in the
 models. Our results revealed a generally weak but significant adherence to
 Bergmann’s rule among all endotherms at the global scale. Despite
 taxonomic variation in the strength of Bergmann’s rule, the body mass of
 species within most animal orders showed an increasing trend toward high
 latitudes. Generally, large-bodied, temperate species, non-hibernating
 mammals, and migratory and open-habitat birds tend to conform to
 Bergmann’s rule more than their relatives do. Our results suggest that
 whether Bergmann’s rule applies to a particular taxon is mediated by not
 only geographical and biological features but also potential alternate
 strategies that species might have for thermoregulation. Future studies
 could explore the potential of integrating comprehensive trait data into
 phylogenetic comparative analysis to re-assess the classic ecogeographical
 rules on a global scale.
DOI: 10.5061/dryad.1g1jwsv29
title: Summer litter decomposition is moderated by scale-dependent microenvironmental variation in tundra ecosystems

description: Tundra soils are one of the world’s largest organic carbon stores, yet
 this carbon is vulnerable to accelerated decomposition as climate warming
 progresses. The landscape-scale controls of litter decomposition are
 poorly understood in tundra ecosystems, which hinders our understanding of
 the global carbon cycle. We examined the extent to which the thermal sum
 of surface air temperature, soil moisture and permafrost thaw depth
 influenced litter mass loss and decomposition rates (k), and at which
 spatial thresholds an environmental variable becomes a reliable predictor
 of decomposition, using the Tea Bag Index protocol across a heterogeneous
 tundra landscape on Qikiqtaruk - Herschel Island, Yukon, Canada. We found
 greater green tea litter mass loss and faster decomposition rates (k) in
 wetter areas within the landscape, and to a lesser extent in areas with
 deeper permafrost active layer thickness and higher surface thermal sums.
 We also found higher decomposition rates (k) on north-facing relative to
 south-facing aspects at microsites that were wetter rather than warmer.
 Spatially heterogeneous belowground conditions (soil moisture and active
 layer depth) explained variation in decomposition metrics at local scales
 (&lt; 50 m2) better than thermal sum. Surprisingly, there was no
 strong control of elevation or slope on litter decomposition. Our results
 reveal that there is considerable scale dependency in the environmental
 controls of tundra litter decomposition, with moisture playing a greater
 role than the thermal sum at &lt; 50 m2 scales. Our findings highlight
 the importance and complexity of microenvironmental controls on litter
 decomposition in estimates of carbon cycling in a rapidly warming tundra
 biome.
description: We used the ‘<em>brms</em>’ package (Bürkner, 2017)
 and weakly informative priors (half Student-t priors with 3 degrees of
 freedom) for all models, with two chains of 8000 iterations each and a
 warmup value of 2000. We conducted all analyses in R version 3.6.3. The
 code and data used for this study can be found at the following
 repository: https://github.com/ShrubHub/MicroTeaHub/    Large data: https://zenodo.org/record/6411321
DOI: 10.5061/dryad.x69p8czpv
title: Data from: Analysing ecological dynamics with relational event models: the case of biological invasions

description: Dynamic species invasions network: sender nodes are species and receiver
 nodes are regions as defined in the FirstRecords database. The dataset
 covers four taxonomic groups (i.e., mammals, birds, plants, insects) and a
 fixed time-frame [1880–2005] over which the invasion process of the
 species occurs into the regional set of the 272 pre-specified regions. The
 dataset includes 16,403 invasion events recorded for 4,835 species (615
 birds, 186 mammals, 3,920 plants, and 114 insect species). The average
 number of invasion events per taxonomic group is ~5 records per insect
 species, ~4 per bird and mammal species, and ~3 recorded events per plant
 species. On average, ~46 invasion events are recorded per region, ranging
 from 1 to 1,685 events. 157 regions had less than 15 observations, with
 33% of these regions located in Africa; 36 regions had more than 100
 records.
DOI: 10.5061/dryad.6q573n63n
title: Ecological correlates of cranial evolution in the megaradiation of dipsadine snakes

description: Background Dipsadine snakes represent one of the most spectacular
 vertebrate radiations that have occurred in any continental setting, with
 over 800 species in South and Central America. Their species richness is
 paralleled by stunning ecological diversity, ranging from arboreal
 snail-eating and aquatic eel-eating specialists to terrestrial
 generalists. Despite the ecological importance of this clade, little is
 known about the extent to which ecological specialization shapes broader
 patterns of phenotypic diversity within the group. Here, we test how
 habitat use and diet have influenced morphological diversification in
 skull shape across 160 dipsadine species using micro-CT and 3-D geometric
 morphometrics, and we use a phylogenetic comparative approach to test the
 contributions of habitat use and diet composition to variation in skull
 shape among species. Results We demonstrate that while both habitat use
 and diet are significant predictors of shape in many regions of the skull,
 habitat use significantly predicts shape in a greater number of skull
 regions when compared to diet. We also find that across ecological
 groupings, fossorial and aquatic behaviors result in the strongest
 deviations in morphospace for several skull regions. We use simulations to
 address the robustness of our results and describe statistical anomalies
 that can arise from the application of phylogenetic generalized least
 squares to complex shape data. Conclusions Both habitat and dietary
 ecology are significantly correlated with skull shape in dipsadines; the
 strongest relationships involved skull shape in snakes with aquatic and
 fossorial lifestyles. This association between skull morphology and
 multiple ecological axes is consistent with a classic model of adaptive
 radiation and suggests that ecological factors were an important component
 in driving morphological diversification in the dipsadine megaradiation.
DOI: 10.5061/dryad.tdz08kq4q
title: Biological links between personality and plasticity: testing some alternative hypotheses

description: When organisms respond behaviorally to a stimulus, they exhibit
 plasticity, but some individuals respond to the same stimulus consistently
 differently than others, thereby also exhibiting personality differences.
 Parent house sparrows express individual differences in how often they
 feed offspring and how that feeding rate changes with nestling age. Mean
 feeding rate and its slope with respect to nestling age were positively
 correlated at median nestling ages but not at hatching, indicating that
 individuality is primarily in plasticity. Individual differences could
 arise due to 1) interactions between environmental variables, 2)
 differences in underlying state or ‘quality’, or 3) differences in the
 ability to update cues of changing nestling demand. Individual slopes were
 modestly repeatable across breeding attempts, hinting at the likely action
 of additional environmental variables, but only brood size was important.
 I also found few correlates suggesting quality differences. I used
 short-term brood size manipulations at two nestling ages to test divergent
 predictions between the three hypotheses. The pattern of correlations
 between response to the manipulation and individual slope did not fit any
 single hypothesis. Patterns of sparrow parental care reveal that
 personality and plasticity are not cleanly separable, and their biology is
 likely intertwined. New thinking may be needed about the factors parents
 use in decisions about care and the relevant fitness consequences.
description: Data were extracted from videos of marked adults at labelled nest
 sites. Videos were taken multiple times during the first 9 days of
 nestling development; most were of unmanipulated nests, but some nests
 were targetted for short-term (2 h) brood size manipulations. From the raw
 score sheets, several metrics, primarily the number of feeding visits and
 the length of the video, were extracted and entered into the data file.
 Additional information on the marked adults or the location and date of
 the video were added. Analysis was conducted in the R computing
 environment. 
description: Saved as Excel.csv file, so openable by many programs.
DOI: 10.5061/dryad.ffbg79d0q
title: Computational IHC-H&E mapping in mouse models of colitis (IHC WSIs from paired H&E-IHC WSIs, Part 1/2)

description: Inflammatory Bowel Disease (IBD) is characterized by chronic, dysregulated
 inflammation in the gastrointestinal tract. The heterogeneity of IBD is
 reflected through two major subtypes, Crohn’s Disease (CD) and Ulcerative
 Colitis (UC). CD and UC differ across symptomatic presentation, histology,
 immune responses, and treatment. While colitis mouse models have been
 influential in deciphering IBD pathogenesis, no single model captures the
 full heterogeneity of clinical disease. The translational capacity of
 mouse models may be augmented by shifting to multi-mouse model studies
 that aggregate analysis across various well-controlled phenotypes. Here,
 we evaluate the value of histology in multi-mouse model characterizations
 by building upon a previous pipeline that detects histological disease
 classes in hematoxylin and eosin (H&E)-stained murine colons.
 Specifically, we map immune marker positivity across serially-sectioned
 slides to H&E histological classes across the dextran sodium
 sulfate (DSS) chemical induction model and the intestinal
 epithelium-specific, inducible Villin-CreERT2;Klf5fl/fl
 (Klf5ΔIND) genetic model. In this study, we construct the beginning
 frameworks to define H&E-patch-based immunophenotypes based on
 IHC-H&E mappings.
description: The slides are multi-resolution and openable utilizing WSI
 viewing software, such as QuPath. Data can also be accessed using standard
 Python libraries like Openslide.
DOI: 10.5061/dryad.wm37pvmt0
title: Computational IHC-H&E mapping in mouse models of colitis (IHC WSIs from paired H&E-IHC WSIs, Part 2/2)

description: Inflammatory Bowel Disease (IBD) is characterized by chronic, dysregulated
 inflammation in the gastrointestinal tract. The heterogeneity of IBD is
 reflected through two major subtypes, Crohn’s Disease (CD) and Ulcerative
 Colitis (UC). CD and UC differ across symptomatic presentation, histology,
 immune responses, and treatment. While colitis mouse models have been
 influential in deciphering IBD pathogenesis, no single model captures the
 full heterogeneity of clinical disease. The translational capacity of
 mouse models may be augmented by shifting to multi-mouse model studies
 that aggregate analysis across various well-controlled phenotypes. Here,
 we evaluate the value of histology in multi-mouse model characterizations
 by building upon a previous pipeline that detects histological disease
 classes in hematoxylin and eosin (H&E)-stained murine colons.
 Specifically, we map immune marker positivity across serially-sectioned
 slides to H&E histological classes across the dextran sodium
 sulfate (DSS) chemical induction model and the intestinal
 epithelium-specific, inducible Villin-CreERT2;Klf5fl/fl
 (Klf5ΔIND) genetic model. In this study, we construct the beginning
 frameworks to define H&E-patch-based immunophenotypes based on
 IHC-H&E mappings.
description: The slides are multi-resolution and openable utilizing WSI
 viewing software, such as QuPath. Data can also be accessed using standard
 Python libraries like Openslide.
DOI: 10.5061/dryad.cvdncjt8d
title: Data for: Number of cards to infer rule for placing cards into piles

description: Nearly sixty years ago, in a publication with a growing rate of citation
 ever since, JR Platt presented “strong inference” (SI) as an accumulative
 method of inductive inference to produce much more rapid progress than
 others. The article offered persuasive testimony for the use of multiple
 working hypotheses combined with disconfirmation. It is often cited as an
 exemplar of scientific practice. However, the article provides no evidence
 of greater efficacy. Over a 34 year period a total 780 matched trials were
 completed in 56 labs in a university course in statistical science. The
 reduction from random (18.9 cards) to selected cards was 7.2 cards,
 compared to a further reduction of 0.3 cards from selected to SI. In 46%
 of the 780 trials, the number of cards to infer a rule was greater for
 strong inference than for a less rigid experimental method. Based on the
 evidence, strong inference added little additional strength beyond that of
 less rigidly structured experiments.
description: Using inductive
 cards as a model (Gardner 1959 Inductive Cards. <em>Scientific
 American</em> 200:160), I devised a lab for a course in statistics
 for  graduate and upper level undergraduate university students. Students
 worked in groups of three or four. One person (Nature) devises a rule for
 placing cards in piles. The other students in the group work together to
 infer a rule for cards placed by Nature according to the unknown rule. On
 the first round cards are drawn from a shuffled deck. This is an
 observational study with an uncontrolled random component. On the second
 round (Selected cards) each rule moves to a different group, where
 students chose cards to present to Nature (an experimental study). On the
 third round a new group applies the strong inference (SI) method to a
 rule. The lab required students to list multiple working hypotheses at
 each step, list one or more “crucial test” cards, present them to Nature
 for placement, and disconfirm one or more hypotheses. The procedure is
 repeated until the rule is discovered. The number of cards to infer the
 rule is tallied by the instructor and distributed to students for their
 lab write-ups.
description: The data were intially stored as ascii (.txt) files (1989 to
 2003). This data was moved to excel files in 2023. Data from 2004 through
 2022 were stored as excel files.
DOI: 10.5061/dryad.9w0vt4bmq
title: Reimagined MPFL Reconstruction: Retinacular fixation of the doubled hamstring graft at the patella and suture anchor-based femoral fixation

description: Background. Lateral patellar dislocation is frequently observed among
 teenagers and young adults. There is no consensus on the best type of
 graft or fixation strategy for the femur and patella, and complications
 such as iatrogenic patella fracture, tunnel malposition, and grafting
 failure are common. The objective of our research is to outline a new
 method of medial patellofemoral ligament (MPFL) reconstruction, which
 involves two key components: (1) Patellar fixation is accomplished by
 suturing the two limbs of the looped doubled hamstring graft in a
 divergent fashion to the retinaculum at the medial border of the upper
 half of patella and, (2) the placement of a suture anchor tied to the
 graft at the isometric point on the medial femur condyle. Methods. This
 study is a retrospective assessment of patients who underwent MPFL
 reconstruction at our hospital during the period between September 2018
 and August 2020. Patients were monitored for at least 2 years after the
 initial procedure until August 2022. Results. A total of 29 patients were
 recruited for the study, with 22 being females and the average age being
 30.38 years. During the postoperative period, none of the participants
 experienced instability, re-dislocation, or patellar/femoral fractures.
 The Tegner-Lysholm Knee Score was good to excellent for 17 (58.6%)
 participants, fair for 10 (34.5%) participants, and poor for 2 (6.9%)
 participants. The Kujala Anterior Knee pain score was more than 80 for 19
 (65.5%) participants. No cases of abnormal growth were reported during a
 follow-up period of 30.6 months. Conclusion. The outcomes observed with
 this technique in terms of function were comparable to those reported with
 alternative surgical methods.
description: This dataset provided here is the raw data of a retrospective
 assessment of patients who underwent MPFL reconstruction at out hospital
 between September 2018 and August 2020. The data collection was done
 during the period between September 2020 and August 2022 and it includes
 the functional assessment of the patients at least 2 years after the index
 procedure. Patients were enquired about any episodes of knee instability
 or re-dislocation or fractures. The data includes patients' age, 
 postoperative clincal evaluation along with functional scores i.e
 Tegner-lysholm knee score, and Kujala anterior knee pain
 scores. 
description: Microsoft Excel