cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7291/d18t0c
title: Birth timing after the long feeding migration in northern elephant seals

description: A prominent phase of the annual cyle in migratory animals is the
 transition between migration and reproduction. The transition is a small
 part of the annual cycle, but details of its timing deserve attention.
 From a distant location, animals must initiate a long migration so that
 they arrive at the breeding ground on a precise schedule. Here we take
 advantage of a sample of female northern elephant seals that were tracked
 by satellite during their migration prior to parturition. In these
 animals, we could estimate the time interval between arrival and birth,
 allowing tests of the following hypotheses: 1) More experienced mothers
 could time arrival more precisely and thus reduce the pre-parturition
 interval. 2) Mothers in poor body condition were forced to forage longer
 and thus shorten the interval. 3) Late-arriving mothers had a shorter
 interval because they foraged longer. We also calculated the distance
 traveled in the last two weeks of the migration to examine females'
 ability to control arrival time, hypothesizing that animals further from
 the colony traveled back at a higher speed.
description: Seals were identified by numbered plastic tags attached to their
 flippers, allowing individuals to be tracked throughout their 22-year
 lifespans. ARGOS satellite transmitters, GPS, and Time-Depth Recorders
 were deployed on individuals to document movements while at sea. The
 instruments were attached prior to foraging migrations and removed
 immediately thereafter. While the animals were sedated, detailed
 morphometric measurements were collected, allowing percent body fat to be
 calculated; percent fat was assumed to reflect female condition. When
 satellite records showed animals near the colony, daily searches were
 carried out in order to observe them on the breeding beaches and find
 their newborn pups. The table below documents 106 cases in which there was
 no gap between the last day a female was seen without a pup and the first
 with a pup. In all, the time of birth was known with a precision of 24
 hours, while the time of arrival was known within a few minutes from
 satellite and depth tracks, so the delay between arrival and birth could
 be estimated with a precision of one day.
description: The table includes observations from 106 female migrations ending
 at the Año Nuevo colony in California. It is tab-delimited ascii. The
 columns are: animalID: Unique individual
 identifier season: Year of birth (arrival dates were
 in Dec of previous year in several cases) age: Age of
 female in years (85 of the records have age) adate:
 Arrival date, Year-month-day format aday: Arrival day
 (days since 1 December of the year before
 <i>season</i>) firstwith: First day with
 a pup (days since 1 December) dist15: Distance from
 colony (km) 15 days prior to birth (99 of the records have
 distances) dist10: Distance from colony (km) 10 days
 prior to birth dist5: Distance from colony (km) 5
 days prior to birth distmax: Maximum distance from
 colony (km) during entire migration prior to birth
DOI: 10.5061/dryad.pg4f4qrnr
title: Avian color expression and perception: Is there a carotenoid link?

description: Carotenoids color many of the red, orange and yellow ornaments of birds
 and also shape avian vision. The carotenoid-pigmented oil droplets in cone
 photoreceptors filter incoming light and are predicted to aid in color
 discrimination. Carotenoid use in both avian coloration and color vision
 raises an intriguing question: is the evolution of visual signals and
 signal perception linked through these pigments? Here, we explore the
 genetic, physiological and functional connections between these traits.
 Carotenoid color and droplet pigmentation share common mechanisms of
 metabolic conversions and are both affected by diet and immune-system
 challenges. Yet, the timescale and magnitude of these effects differ
 greatly between plumage and the visual system. Recent observations suggest
 a link between retinal carotenoid levels and color discrimination
 performance, but the mechanisms underlying these associations remains
 unclear. Therefore, we performed a modeling exercise to ask whether and
 how changes in droplet carotenoid content could alter the perception of
 carotenoid-based plumage. This exercise revealed that changing oil droplet
 carotenoid concentration does not substantially affect the discrimination
 of carotenoid-based colors, but might change how reliably a receiver can
 predict the carotenoid content of an ornament. These findings suggest
 that, if present, a carotenoid link between signal and perception is
 subtle. Deconstructing this relationship will require a deeper
 understanding of avian visual perception and the mechanisms of color
 production. We highlight several areas where we see opportunities to gain
 new insights, including comparative genomic studies of shared mechanisms
 of carotenoid processing and alternative approaches to investigating color
 vision.
description: This dataset includes house finch plumage spectrum measures and
 feather carotenoid content measures collected following methods
 in: <b>Butler, M., Toomey, M. and McGraw,
 K.</b> (2011). How many color metrics do we need? Evaluating how
 different color-scoring procedures explain carotenoid pigment content in
 avian bare-part and plumage ornaments. <i>Behavioral Ecology and
 Sociobiology</i> <b>65</b>, 401–413; 413.
 House finch cone oil droplet absorbance spectra collected
 following methods in: <b>Toomey, M. B., Collins,
 A. M., Frederiksen, R., Cornwall, M. C., Timlin, J. A. and Corbo, J.
 C.</b> (2015). A complex carotenoid palette tunes avian colour
 vision. <i>J. R. Soc. Interface</i> <b>12</b>,
 20150563. Irradiance spectra, ocular media
 transmittance spectra, and visual system parameters used in the modeling
 of avian visual performance. Also included are example R-scripts and
 R.data files to run the analyses presented in the associated
 publication.
DOI: 10.5061/dryad.bvq83bk80
title: Food resource partitioning between juvenile and mature weatherfish Misgurnus fossilis

description: This study represents a description of the diet composition of one of the
 largest European cobitids, the weatherfish Misgurnus fossilis. Specimens
 were collected in a drainage canal, representing a typical habitat for
 weatherfish, and with gut content analysis conducted with regard to
 individual total length and maturity stage. Overall, the weatherfish diet
 mainly consisted of Copepoda, Cladocera, Oligochaeta, Crustacea (Asellus
 aquaticus), Chironomidae, detritus and insect larvae. To evaluate
 size-related patterns of resource use, fish were assigned to two size
 classes, deﬁned according to size at ﬁrst maturation. ANOSIM analyses
 revealed major ontogenetic shifts in feeding strategy that were related to
 size and maturity, with a significant ontogenetic shift in feeding
 pattern, marked by differences in the proportions of the main taxonomic
 groups of prey consumed. Copepoda and Cladocera dominated in the diet of
 small and immature individuals, while large weatherfish primarily fed on
 detritus. Similarly, cluster analysis of diet classified into these food
 types showed distinct two groups comprising juvenile and mature fish.
 Spatially, weatherfish showed a change in feeding sites from the water
 column to substrate.
DOI: 10.5061/dryad.rxwdbrv7b
title: The Prevalence of 30 HPV genotypes detected by EUROArray HPV in cervical samples among unvaccinated women from Vojvodina province, Serbia

description: This study evaluates the pre-vaccination prevalence of HPV infection in
 women from Vojvodina, Serbia, according to age and cytological status. A
 total of 1,495 women, ranging from 18 to 65 years of age, with different
 cytological results were enrolled. The HPV genotyping assay was performed
 using the EUROArray HPV test in order to detect thirty genitally relevant
 HPV subtypes. In our study, the most prevalent genotypeswere HPV 16, 31,
 51, and 53. Among these, HPV 16 was consistently present in all
 cytological subgroups. Twelve HPV genotypes classified as carcinogenic to
 humans (Group 1) were detected in 77.8% of HSIL/ASCH and 55.0% of NILM
 with abnormal colposcopy findings. Six possible carcinogens - HRs (group
 2B) were often found in women with normal cytology (14.8%) and mild
 abnormalities (ASCUS and LSIL), but with lower frequence in HSIL/ASCH
 lesions (7.1%). HPVs 6 and 11(Group 3) were not found in the cases of
 HSIL/ASCH. Unclassified HPV types were equally distributed in all cytology
 groups: 20.7%, 19.1%, 16.3% and 13% of NILM, ASCUS, LSIL and HSIL/ASCH,
 respectively. Our findings highlight that majority of abnormal Pap test
 results are caused by Group 1 HPVs among women from our region. Low
 frequency HPVs of group 2A/2B, especially HSIL/ASCH, supports the
 conclusion that individual genotypes require consideration of each type as
 an individual agent. We expect a positive impact of HPV vaccine in
 reducing HPV-associated cervical lesions among women from Vojvodina
 province, after establishing vaccination programs in our country.
description: This study was conducted within the ongoing project:
 “Significance of HPV DNA analysis in the prevention of cervical cancer”
 and the results outcome of the analysis conducted from 2016 to 2018. This
 was a cross-sectional study with convenience type of sampling. HPV DNA was
 generated from the laboratory analysis from the specimens provided by
 study participants.
description: Samples for HPV DNA analysis were collected using ThinPrep Pap
 (Hologic Inc.) or eNAT (Copan, Italy) specimen transport
 medium.
DOI: 10.15468/dl.fjmc3g
title: Occurrence Download

description: A dataset containing 890 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Museo de Ictiología de la Universidad Tecnológica Indoamérica (MZUTI)"
 ]
}

 The dataset includes 890 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002769-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f7m0cfxv9
title: Tail regeneration alters the digestive performance of lizards

description: Tissue regeneration is a fundamental evolutionary adaptation, which is
 well known in lizards that can regenerate their entire tail. However,
 numerous parameters of this process remain poorly understood. Lizard tail
 serves many functions. Thus, tail autotomy comes with many disadvantages
 and the need for quick regeneration is imperative. To provide the required
 energy and materials for caudal tissue building, lizards are expected to
 undergo a number of physiological and biochemical adjustments. Previous
 research showed that tail regeneration induces changes in the digestive
 process. Here, we investigated if and how tail regeneration affects the
 digestive performance in five wall lizard species deriving from mainland
 and island sites and questioned whether the association of tail
 regeneration and digestion is affected by species relationships or
 environmental features, including predation pressure. We expected that
 lizards from high predation environments would regenerate their tail
 faster and modify accordingly their digestive efficiency, prioritizing the
 digestion of proteins; the main building blocks for tissue repair. Second,
 we anticipated that the general food shortage on islands would inhibit the
 process. Our findings showed that all species shifted their digestive
 efficiency, as predicted. Elongation rate was higher in sites with
 stronger predation regime and this was also applied to the rate with which
 protein digestion raised. Gut passage time increases during regeneration
 so as to improve the nutrient absorbance, but among the islanders the pace
 was more intense. The deviations between species should be attributed to
 the different ecological conditions prevailing on islands rather than to
 their phylogenetic relationships.
DOI: 10.5061/dryad.ncjsxkstp
title: Genome-wide shifts in climate-related variation underpin responses to selective breeding in a widespread conifer

description: Locally adapted temperate tree populations exhibit genetic trade-offs
 among climate-related traits that can be exacerbated by selective
 breeding, and are challenging to manage under climate change. To inform
 climatically adaptive forest management, we investigated the genetic
 architecture and impacts of selective breeding on four climate-related
 traits in 105 natural and 20 selectively bred lodgepole pine populations
 from western Canada. Growth, cold injury and growth initiation and growth
 cessation phenotypes were tested for associations with 18,600 SNPs in
 natural populations to identify ‘positive effect alleles’ (PEAs). The
 effects of artificial selection for faster growth on PEA frequencies for
 each trait were quantified in breeding populations from different
 climates. Substantial shifts in PEA proportions and frequencies were
 observed across many loci after two generations of selective breeding for
 height, and responses of phenology-associated PEAs differed strongly among
 climatic regions. Extensive genetic overlap was evident among traits.
 Alleles most strongly associated with greater height were often also
 associated with greater cold injury and delayed phenology, although it is
 unclear whether potential trade-offs arose directly from pleiotropy or
 indirectly via genetic linkage. Modest variation among populations in PEA
 frequencies across many loci was associated with large phenotypic
 differences and strong climatic gradients, providing support for assisted
 gene flow polices. Relationships among genotypes, phenotypes and climate
 in natural populations were maintained or strengthened by selective
 breeding. However, future adaptive phenotypes and assisted gene flow may
 be compromised if selective breeding further increases the PEA frequencies
 of SNPs involved in adaptive trade-offs among climate-related traits.
description: All usage notes are contained within the accompanying README.txt
 file, and comments within the analyses scripts supplied.
DOI: 10.5061/dryad.jsxksn08g
title: Data from: Metabolomic and transcriptomic responses of ticks during recovery from cold shock reveal mechanisms of survival

description: Ticks are blood-feeding ectoparasites but spend most of their life
 off-host where they may have to tolerate low winter temperatures. Rapid
 cold-hardening (RCH) is a process commonly used by arthropods, including
 ticks, to improve survival of acute low temperature exposure. However,
 little is known about the underlying mechanisms in ticks associated with
 RCH, cold shock, and recovery from these stresses. In the present study,
 we investigated the extent to which RCH influences gene expression and
 metabolism during recovery from cold stress in Dermacentor variabilis, the
 American dog tick, using a combined transcriptomics and metabolomics
 approach. Following recovery from RCH, 1,860 genes were differentially
 expressed in ticks, whereas only 99 genes responded during recovery to
 direct cold shock. Recovery from RCH resulted in an upregulation of
 various pathways associated with ion binding, transport, metabolism, and
 cellular structures seen in the response of other arthropods to cold. The
 accumulation of various metabolites, including several amino acids and
 betaine, corresponded to transcriptional shifts in the pathways associated
 with these molecules, suggesting congruent metabolome and transcriptome
 changes. Ticks receiving exogenous betaine and valine demonstrated
 enhanced cold tolerance, suggesting cryoprotective effects of these
 metabolites. Overall, many of the responses during recovery from cold
 shock in ticks were similar to those observed in other arthropods, but
 several adjustments may be distinct from other currently examined taxa.
DOI: 10.5061/dryad.cnp5hqc43
title: Photoperiod throughout the maternal life cycle influences seed germination in Arabidopsis thaliana, but seed photoperiod does not

description: Premise of the study: Plants adjust their phenology in response
 to seasonal cues experienced both by their parents and by themselves, and
 coordinating responses to these cues is necessary for expressing adaptive
 phenology. We investigated how cues are integrated across time to
 influence an important progeny phenotype, i.e., seed germination.
 Methods: We used Arabidopsis thaliana to
 investigate how the photoperiod experienced by maternal parents and by
 progeny influences seed germination. We examined when maternal photoperiod
 effects on germination are imposed and how long they persist in progeny.
 Key results: The photoperiod experienced by maternal plants more
 strongly influenced germination than the photoperiod experienced during
 seed imbibition. In addition, the photoperiod experienced at the
 prereproductive stage frequently influenced germination as strongly as
 that experienced during reproduction. In general, seeds from plants grown
 under short days had higher seed germination percentages than seeds from
 plants grown in longer days. These maternal effects diminished with
 after-ripening, but reappeared in seeds induced into secondary dormancy.
 Conclusions: We found no evidence that the effect of photoperiod
 systematically attenuates in proportion to the time that elapsed between
 the cue and the timing of seed germination. Moreover, more recently
 experienced cues did not override the effects of cues experienced
 previously. Instead, specific sequences of photoperiods experienced at the
 prereproductive and reproductive stages appear to influence germination
 behavior.
description: Repeated census of seed germination of individual agar
 plates. Plates were incubated under different conditions, and the number
 of seeds that germinated at each census was recorded.
DOI: 10.5061/dryad.931zcrjjk
title: A shift in ontogenetic timing produced the unique sauropod skull

description: Sauropod dinosaurs include the largest terrestrial vertebrates that have
 ever lived. Virtually every part of the sauropod body is heavily modified
 in association with gigantic size and associated physiological
 alterations. Sauropod skulls are no exception: they feature elongated,
 telescoped facial regions connected to tilted neurocrania and reoriented
 jaw adductor muscles. Several of these cranial features have been
 suggested to be adaptations for feeding on the one hand and the result of
 paedomorphic transformation near the base of Sauropoda on the other.
 However, the scarcity of sauropodomorph ontogenetic series has impeded
 further investigation of these hypotheses. We re-evaluated the cranial
 material attributed to the early sauropodomorph Anchisaurus, which our
 phylogenetic analyses confirm to be closely related to sauropods. Digital
 assembly of μCT scanned skulls of the two known specimens, a juvenile and
 an adult, permitted us to examine the detailed ontogeny of cranial
 elements. The skull anatomy of Anchisaurus is distinguished by a mosaic of
 ancestral saurischian and sauropod-like characters. Sauropod-like
 characters of the braincase and adductor chamber appear late in ontogeny,
 suggesting that these features first evolved by the developmental
 mechanism of terminal addition. Shape analyses and investigation of
 allometric evolution demonstrate that cranial characters that appear late
 in the ontogeny of sauropodomorphs closely related to sauropods are
 already present in the embryos and juveniles of sauropods, suggesting a
 predisplacement-type shift in developmental timing from the ancestral
 anchisaurian condition. We propose that this developmental shift relaxed
 prior constraints on skull morphology, allowing sauropods to explore a
 novel range of phenotypes and enabling specializations of the feeding
 apparatus. The shift in timing occurred in concert with the evolution of
 gigantism and physiological and locomotory innovations.
DOI: 10.15468/dl.ebqb8x
title: Occurrence Download

description: A dataset containing 4299 records in GBIF matching the query:
SELECT
 '452' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= 95.90519603780048
 AND decimalLongitude &lt;= 107.00476756053553
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 4299 records were derived from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002758-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1jwstqjtp
title: Triennial migration and philopatry in the critically endangered soupfin shark (Galeorhinus galeus)

description: Globally, one-quarter of shark and ray species is threatened with
 extinction due to overfishing. Effective conservation and management can
 facilitate population recoveries; however, these efforts depend on robust
 data on movement patterns and stock structure, which are lacking for many
 threatened species, including the Critically Endangered soupfin shark
 (Galeorhinus galeus), a circumglobal coastal-pelagic species. Using
 passive acoustic telemetry, we continuously tracked 34 mature female
 soupfin sharks, surgically implanted with coded acoustic transmitters, for
 seven years via 337 underwater acoustic receivers stationed along the west
 coast of North America. These sharks and an additional six were also
 externally fitted with spaghetti identification tags. Our tagging site was
 a shallow rocky reef off La Jolla (San Diego County), California, USA,
 where adult females were observed to aggregate every summer. Tagged
 soupfin sharks were highly migratory along the west coast of North
 America, between Washington, USA and Baja California Sur, Mexico. However,
 every three years, they returned to waters off La Jolla, California, where
 they underwent gestation. This is the first conclusive evidence of
 triennial migration and philopatry (‘home-loving’) in any animal, which is
 apparently driven by this species’ unusual triennial reproductive cycle.
 Females of other shark and ray species with triennial reproductive cycles
 are also likely to exhibit triennial cycles of migration and philopatry.
 At least six (15%) of our tagged soupfin sharks were killed in commercial
 gillnets in Mexico. Policy implications. Identifying multiennial migratory
 cycles of mature females can reveal hidden stock structure in the form of
 discrete breeding cohorts, which are spatially and temporally segregated
 as they cycle through different reproductive phases. Accounting for this
 complexity may improve the performance of spatially structured stock
 assessment models, particularly when fishery removals are spatially
 heterogeneous, as well as inform the spatiotemporal design of
 fishery-independent surveys. In the US, the soupfin shark is neither
 actively managed nor recognized as a Highly Migratory Species; however,
 given the highly migratory behavior we report, this designation should be
 revisited by the US Pacific Fishery Management Council. Finally, given the
 extensive fishery removals in Mexico, any future management must be
 internationally cooperative.