cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zw3r2288c
title: Modeled trajectories of the Mediterranean squamates

description: Mediterranean islands have a high diversity of squamates, although they
 are unevenly distributed. This variability in the composition of the
 reptile assemblages across islands may have been influenced by differences
 in the colonization abilities of these species. To evaluate the dispersal
 capacities of squamate species, we modeled their sea routes using cost
 surface models. We estimated the effects of some life-history traits and
 the phylogenetic signal in the characteristics of the modeled dispersal
 paths. We hypothesized that a significant phylogenetic signal should be
 present if the dispersal ability is enhanced by traits shared among
 evolutionarily related species. The results showed that no phylogenetic
 signal was present in the characteristics of the dispersal paths (i.e., in
 the distance traveled/bypassed sea depth). Thus, no superior
 island-colonizer lineages were detected in Mediterranean Squamata.
 However, our analyses also revealed that small-sized lizards were superior
 to other groups of squamates at dispersing over long distances on the
 sea.Mediterranean islands have a high diversity of squamates, although
 they are unevenly distributed. This variability in the composition of the
 reptile assemblages across islands may have been influenced by differences
 in the colonization abilities of these species. To evaluate the dispersal
 capacities of squamate species, we modeled their sea routes using cost
 surface models. We estimated the effects of some life-history traits and
 the phylogenetic signal in the characteristics of the modeled dispersal
 paths. We hypothesized that a significant phylogenetic signal should be
 present if the dispersal ability is enhanced by traits shared among
 evolutionarily related species. The results showed that no phylogenetic
 signal was present in the characteristics of the dispersal paths (i.e., in
 the distance traveled/bypassed sea depth). Thus, no superior
 island-colonizer lineages were detected in Mediterranean Squamata.
 However, our analyses also revealed that small-sized lizards were superior
 to other groups of squamates at dispersing over long distances on the sea.
description: <b>Variables
 </b>definition <b>Total Steiner</b>
 = minimum-cost vector connecting the islands, in km <b>Total travel</b> =
 summation of travel lengths, in km <b>Mean distance</b>
 = total travel/ number of travels, in km <b>Max distance</b> =
 longest travel, in km <b>Average depth</b>
 = mean sea depth along the travel, in m <b>Max depth</b> =
 maximum depth along the travel, in m <b>%above -150m</b> =
 proportion of the travel with sea depth &lt; ‒150 m The attached number 1,2,
 & 3 referred to the resistance models 1 = minimum resistance, M2 =
 mean resistance, M3 = maximum resistance.
DOI: 10.15468/dl.jr2ujr
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Sea lamprey distribution and abundance in the River Spey: phases II and III, 2001/2002"
 ]
}

 The dataset includes 92 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002938-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7h44j0zv4
title: Are Palmer’s elm-leaf goldenrod and the smooth elm-leaf goldenrod real? The Angiosperms353 kit provides within-species signal in Solidago ulmifolia s.l.

description: Abstract — The genus Solidago represents a taxonomically
 challenging group due to its sheer number of species, putative
 hybridization, polyploidy, and shallow genetic divergence among
 species. Here we use a dataset obtained exclusively from
 herbarium specimens to evaluate the status of Solidago ulmifolia var.
 palmeri, a morphologically subtle taxon potentially confined to Alabama,
 Arkansas, Mississippi, and Missouri. A multivariate analysis of
 both discrete and continuous morphological data revealed no clear
 distinction between S. ulmifolia var. palmeri and Solidago ulmifolia var.
 ulmifolia. Solidago ulmifolia var. palmeri’s status was also
 assessed with a phylogenomic and SNP clustering analysis of data generated
 with the “Angiosperms353” probe kit.  Neither analysis supported
 Solidago ulmifolia var. palmeri as a distinct taxon, and we suggest that
 this name should be discarded. The status of Solidago delicatula
 (formerly known as Solidago ulmifolia var. microphylla) was also assessed.
 Both morphological and phylogenetic analyses supported the species status
 of S. delicatula and we suggest maintaining this species at its current
 rank.  These results highlight the utility of the Angiosperms353
 probe kit, both with herbarium tissue and at lower taxonomic
 levels. Indeed, this is the first study to utilize this kit to
 identify genetic groups within a species.
description: These morphological data were collected using an Olympus SZX10
 dissecting microscope fitted with a digital camera.
description: See associated README file.
DOI: 10.7280/d15x1j
title: Indirect measurements of the composition of ultrafine particles in the Arctic late-winter

description: We present indirect measurements of size-resolved ultrafine particle
 composition conducted during the Ocean–Atmosphere–Sea Ice–Snowpack (OASIS)
 Campaign in Utqiagvik, Alaska, during March 2009. This study focuses on
 measurements of size-resolved particle hygroscopicity and volatility
 measured over two periods of the campaign. During a period that represents
 background conditions in this location, particle hygroscopic growth
 factors (HGF) at 90% relative humidity ranged from 1.45-1.51, which
 combined with volatility measurements suggest a mixture of ~30% ammoniated
 sulfates and ~70% oxidized organics. Two separate regional ultrafine
 particle growth events were also observed during this campaign. Event 1
 coincided with elevated levels of H2SO4 and solar radiation. These
 particles were highly hygroscopic (HGF=2.1 for 35 nm particles), but were
 almost fully volatilized at 160 °C. The air masses associated with both
 events originated over the Arctic Ocean. Event 1 was influenced by the
 upper marine boundary layer (200-350 m AGL), while Event 2 spent more time
 closer to the surface (50-150m AGL) and over open leads, suggesting marine
 influence in growth processes. Event 2 particles were slightly less
 hygroscopic (HGF=1.94 for 35nm and 1.67 for 15nm particles), and similarly
 volatile. We hypothesize that particles formed during both events
 contained 60-70% hygroscopic salts by volume, with the balance for Event 1
 being sulfates and oxidized organics for Event 2. These observations
 suggest that primary sea spray may be an important initiator of ultrafine
 particle formation events in the Arctic late-winter, but a variety of
 processes may be responsible for condensational growth.
description: Data was collected from 5 March - 19 April during Ocean -
 Atmosphere - Sea Ice - Snowpack (OASIS) Campaign in Utqiagvik, Alaska at
 the U.S. Naval Arctic Research Laboratory (NARL) and near the Barrow
 Arctic Research Center (BARC). Times are listed in Alaska Daylight Time
 (UTC - 8 hours).
description: Data information is contained within the read me files
 accompanying each set. Please read carefully.
DOI: 10.7291/d1sh5t
title: Proximity and abundance of mother trees affects recruitment patterns in a long-term tropical forest restoration study

description: Remnant trees and forest fragments in agricultural landscapes can be
 important sources of propagules to facilitate forest recovery. However,
 many studies simply quantify forest cover in the surrounding landscape as
 a percentage, with little attention given to species composition, and
 subsequently fail to detect an effect on recruitment patterns. We assessed
 the relative importance of the spatial distribution and life-history
 traits of 77 tree species on recruitment patterns at a landscape scale in
 a well-replicated long-term restoration study in southern Costa Rica. We
 censused and mapped potential mother trees in a 100-m buffer surrounding
 eight replicate restoration plots and quantified respective tree recruits
 within each plot. We assessed how mother tree abundance, species
 life-history characteristics (seed size, dispersal mode), tree size (DBH,
 height) and distance to restoration plot affected recruitment at coarse
 (plot: 50 × 50 m) and fine (quadrat: 3 × 3 m) spatial scales. The presence
 of a mother tree within 100 m of a restoration plot resulted in a 10-fold
 increase in potential mean recruitment. Mother tree abundance was also an
 important driver of recruit density, and particularly so for large-seeded
 (≥5 mm) zoochorous species with a fivefold increase in recruit density
 across the observed mother tree abundance range. An interaction between
 mother tree abundance and proximity demonstrated that the effect of mother
 tree abundance on recruit density was important but waned with increasing
 distance from restoration plots. At the fine spatial scale, proximity was
 uniformly important; height and DBH of the closest potential mother tree
 also affected recruit abundance but responses differed by seed size.
 Results highlight the importance of remnant vegetation composition to the
 recovery of adjacent degraded habitats, underscoring the outsized role
 nearby remnant forest and isolated trees can play for the persistence of
 localized biodiversity.
description: See Manuscript
DOI: 10.5061/dryad.ffbg79cw1
title: cpDNA sequecnes of Themeda triandra and Heteropogon contortus

description: To investigate the historical continuity of grassy biomes in southwest
 China, we examined the biogeographies and evolutionary histories of two
 widespread and dominant C4 grasses, Themeda triandra and Heteropogon
 contortus, in Yunnan and southern Sichuan provinces, using chloroplast DNA
 markers in combination with climate data.
description: By using chloroplast DNA markers, one shared cpDNA region
 (psbI-psbD intergenic spacer, IGS) and another region that was different
 between the species (ndhF-rpl32 IGS region for <i>T.
 triandra</i> and rpoC2 region for <i>H.
 contortus</i>).
DOI: 10.5061/dryad.8cz8w9gr2
title: Species divergence and repeated ancient hybridization in a Sulawesian lake system

description: An increasing volume of empirical studies demonstrated that hybridization
 between distant lineages may have promoted speciation in various taxa.
 However, the timing, extent, and direction of introgressive hybridization
 remain unknown in many cases. Here, we report a possible case in which
 repeated hybridization promoted divergence
 of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an
 island of Wallacea. Four Oryzias species are endemic to
 the Malili Lake system in central Sulawesi, which is composed of five
 tectonic lakes; of these, one lake is inhabited by two species.
 Morphological and population genomic analyses of genome-wide
 single-nucleotide polymorphisms revealed that these two sympatric species
 are phylogenetically sister to but substantially reproductively isolated
 from each other. Analyses of admixture and comparison of demographic
 models revealed that the two sympatric species experienced several
 substantial introgressions from outgroup populations that probably
 occurred soon after they had secondary contact with each other in the
 lake. However, the ratio of migrants from the outgroups was estimated to
 be different between the two species, which is consistent with the
 hypothesis that these introgressions aided their divergence or prevented
 them from forming a hybrid swarm. Repeated lake fragmentations and fusions
 may have promoted diversification of this freshwater fish species complex
 that is endemic to this ancient lake system.
DOI: 10.5061/dryad.xsj3tx9g6
title: Behavioral data for: Effect of experience on mating behaviour in male Heliconius melpomene butterflies

description: This is the data file that corresponds to "Effect of experience on
 mating behavior in male Heliconius melpomene butterflies" by P.A.
 Rather, A.E. Herzog, D.A. Ernst, & E.L. Westerman, published in
 Animal Behaviour. It contains two spreadsheets, one with all the mating
 outcome data, and one with the corresponding behavioral data for the
 training and testing assays. Due to electrical issues with the data
 recording device during some of our assays, we do not have behavioral
 data, other than courtship and time to courtship (which were recorded both
 electronically and by hand) for all our assays, though we do have complete
 behavioral data for most of our assays. In our study, we show that H.
 melpomene males who have been previously exposed to a female but did not
 mate during that prior exposure are less likely to court during a second
 exposure than a naive male of the same age. This effect appears to be
 driven by H. m. malleti males, as H. m. malleti males exhibited a strong
 response to the exposure, while H. m. rosina males did not.
description: These data were collected during observations of training and
 testing no-choice assays of <em>Heliconius melpomene
 malleti</em> and <em>Heliconius melpomene rosina</em>
 butterflies. Here we report the raw data for the no choice assays, with
 one spreadsheet for mating outcome and one spreadsheet for the full
 behavioral data of males and females.
description: Due to the nature of the data analysis program used, cells in the
 "Time to Court", "CourtedBefore", "Time to
 Court-Mins", "Exp/Naive", "Notes", and "Male
 future court" columns that would be NA in R are left blank. Those are
 not missing data. However, butterfly numbers that are blank are missing,
 as are blank cells in the "phenotype", "watch", and
 "female Type" columns in the Behavioral Data from Watches sheet.
 We include these data because they support our claim in the manuscript
 that butterflies were active during the training and testing periods, even
 though these watches correspond to assays that did not end up being
 included in the final data set due to the death of the male between
 training or testing.
DOI: 10.5061/dryad.66t1g1k2x
title: Genetic and ecomorphological divergence between sympatric Astyanax morphs from Central America

description: Intraspecific ecological and morphological polymorphism can promote
 ecological speciation and the build-up of reproductive isolation. Here, we
 evaluate correlations among morphology, trophic ecology, and genetic
 differentiation between two divergent morphs (elongate and deep-body) of
 the fish genus Astyanax in the San Juan River basin in Central America, to
 infer the putative evolutionary mechanism shaping this system. We
 collected the two morphs from three water bodies and analyzed: 1) the
 correlation between body shape and the shape of the premaxilla, a relevant
 trophic morphological structure, 2) the trophic level and niche width of
 each morph, 3) the correspondence between trophic level and body and
 premaxillary shape, and 4) the genetic differentiation between morphs
 using mitochondrial and nuclear markers. We found a strong correlation
 between the body and premaxillary shape of the morphs. The elongate-body
 morph had a streamlined body, a premaxilla with acuter angles and a
 narrower ascending process, and a higher trophic level, characteristic of
 species with predatorial habits. By contrast, the deep-body morph had a
 higher body depth, a premaxilla with less acute angles, and a broader
 trophic niche, suggesting generalist habits. Despite the strong
 correlation between morphological and ecological divergence, the morphs
 showed limited genetic differentiation, supporting the idea that morphs
 may be undergoing incipient ecological speciation, although alternative
 scenarios such as stable polymorphism or plasticity should also be
 considered. This study provides support for the role of ecological factors
 promoting diversification in lake and stream-dwelling freshwater fish.
description: The readme file contains an
 explanation of each of the variables in the datasets. Information on
 sampling number in each dataset can be found in the associated manuscript
 referenced above. 
description: The geometric morphometric
 and stable isotopes datasets were collected from two morphs of
 <i>Astyanax</i> (elongate and deep-body) from ten sampling
 sites across three water bodies in the San Juan River basin: the two
 Nicaraguan lakes, Managua and Nicaragua, and the Sarapiquí River. Fish
 were collected using either gill or cast nets during sampling campaigns
 that took place between November 2011 and January 2017. The subsample of
 fish used in the isotopic analyses were collected during the dry season
 between December 2016 and January 2017.
DOI: 10.5061/dryad.gxd2547n5
title: Large-scale supplemental feeding alters lay date and nest survival in Eastern Bluebirds but not in two species of chickadees

description: Wild bird feeding is a popular and growing activity, with approximately
 half of households participating in nations including the United States,
 Canada, the United Kingdom, New Zealand, and Australia. Supplemental
 feeding can increase survival and reproductive success of birds (which is
 often a goal of supplemental feeding efforts), but it raises concerns
 about phenological mismatch, reduced clutch size, or increased risk of
 nest predation. Our objectives were to test whether access to supplemental
 food during the breeding season was correlated with (1) advanced
 egg-laying phenology, (2) increased clutch size, or (3) improved nest
 survival of 3 cavity-nesting species (Carolina Chickadee, Poecile
 carolinensis; Black-capped Chickadee, P. atricapillus; and Eastern
 Bluebird, Sialia sialis) at a large spatial scale (United States and
 Canada; 22 degrees latitude difference and 55 degrees longitude
 difference). We examined data from 24,528 nest attempts submitted to
 NestWatch from 2014–2019. For Eastern Bluebirds, birds with access to
 supplemental insects initiated clutches 5.83 (± 0.89 SE) days earlier than
 birds without access to food subsidies, while predicted nest survival was
 5% greater for birds with access to supplemental insects (probability of
 nest success = 0.79, 95% CI = 0.77–0.81) when compared to birds without
 (0.74, 95% CI = 0.72–0.75). Clutch size of Eastern Bluebirds did not
 differ between birds with and without access to supplemental insects. For
 chickadees, supplemental feeding (of seeds, suet, insects, or fruit) was
 not correlated with phenology, clutch size, or nest survival. Our results
 suggest that supplemental feeding of insects can be an effective tool for
 increasing nest survival in Eastern Bluebirds and potentially other
 food-limited insectivores. However, the efficacy of supplemental feeding
 for improving reproductive success varies across taxa. Our results can
 help elucidate how wild bird feeding contributes to global phenomena such
 as earlier nesting, nest survival, and population change.
description: Data were collected by NestWatch, a citizen science program
 operated by the Cornell Lab of Ornithology. Details at www.nestwatch.org
 and in the Methods section of the manuscript. 
description: NestWatch data are completely free and open for use. Data
 summaries are available on the project website: www.nestwatch.org. Raw
 data (the entire NestWatch dataset) are freely available upon request. A
 complete data dictionary describing all data fields and values is
 available.
DOI: 10.5061/dryad.nvx0k6dt6
title: Reoxygenation in the East China Sea

description: Hypoxia and upwelling co-occurred in the summer, and the well-mixed water
 often reaches the subsurface in the East China Sea (ECS), especially off
 the Changjiang River estuary. The impact of upwelling on the hypoxia and,
 therefore, on the ECS ecosystem is not well evaluated. This study
 demonstrates several positive and negative effects of upwelling on hypoxia
 and its impact on the ecosystem. This dataset contains data collected from
 four cruises in the summer of 2003 (June 18–26 and August 13–23) and 2014
 (July 16–29 and August 20–31) on the R/V Ocean Researcher I and V in the
 East China Sea described in the paper: “Chung-Chi Chen, Dong S. Ko,
 Gwo-Ching Gong, Chun-Chi Lien, Wen-Chen Chou, Hung-Jen Lee, Fuh-Kwo Shiah,
 Yu-Sin Wita Huang (2022). Reoxygenation of the hypoxia in the
 East China Sea: A ventilation opening for marine life. Frontiers in Marine
 Science “. The presented variables include: temperature, salinity,
 dissolved oxygen, dissolved inorganic nutrients (nitrate and phosphate),
 and Chl a in this study. Main results of this study included nine
 figures and two tables as described in the paper, and please refer it for
 further details.
description: The designed sampling stations were located throughout the East
 China Sea, but the sampling stations in different sampling periods varied.
 Conductivity, temperature, and depth (CTD) were recorded throughout the
 water column with a CTD instrument (SBE9/11 Plus; Sea-Bird Electronic
 Inc., Bellevue, WA, USA). The water samples were collected in
 Teflon-coated Go-Flo bottles (20 L; General Oceanics Inc., Miami, GL, USA)
 mounted on a Rosette assembly (Model 1015; General Oceanics Inc.). At each
 station, 5–10 samples were taken at depths of 2–50 m, depending on the
 water depth. Subsamples were taken for immediate analyses (DO, dissolved
 inorganic nutrients, and Chl <i>a</i>). The analyzed methods
 for each variable can be found from the paper. The data has been processed
 by a linear regression analysis using “SigmaStat” to produce a ms accepted
 for publication in Frontiers in Marine Science.
description: The “Readme_Reoxygenation” file contains an explanation of each
 of the variables in the dataset, its measurement units. Information on how
 the measurements were done or data were retrieve can be found in the
 associated manuscript referenced above.
DOI: 10.5061/dryad.6q573n609
title: Calcareous and siliceous species on calcareous and siliceous soils over four years of reciprocal transplant experiments

description: This dataset is a collection of data from 4-year experiments conducted in
 the Gironde department in southwestern France. It contains “Block, Year,
 Soil type, neighboring, Species and Origin” as explanatory categorical
 variables and “Target survival” as binomial response variable. These data
 were analyzed in order to characterize and assess how the effect of
 species stress tolerance and community competitive effects lead to
 differences in species composition between calcareous and siliceous plant
 communities. The year, rock and origin variables and their interactions as
 fixed factors, were used to assess the effect of abiotic conditions of the
 soil type and year quality, on the survival of target species from
 calcareous and siliceous soils growing without neighbors, using a general
 linear mixed-effects model with a logit link function for binomial
 distribution. The survival with and without neighbours was also used to
 calculate two indices to characterize the intensity (RII) and the
 importance (Iimp) of plant-plant interactions. RII and Iimp were then
 analyzed separately using linear mixed-effects models with “Year quality”,
 “Soil type”, “Origin” and their interactions as fixed factors and “Year
 nested within Blocks” as a random factor. All data were stored using
 Microsoft Excel and all the statistical analyses were done using R
 software (R Core Team 2016).