cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z08kprrbx
title: Data from: Local prey shortages drive foraging costs and breeding success in a declining seabird, the Atlantic puffin

description: As more and more species face anthropogenic threats, understanding causes
 of population declines in vulnerable taxa is essential. However, long-term
 datasets, ideal to identify lasting or indirect effects on fitness
 measures such as those caused by environmental factors, are not always
 available.  Here we use a single year but multi-population
 approach on populations with contrasting demographic trends to identify
 possible drivers and mechanisms of seabird population changes in the
 north-east Atlantic, using the Atlantic puffin, a declining species, as a
 model system.  We combine miniature GPS trackers with camera
 traps and DNA metabarcoding techniques on four populations across the
 puffins’ main breeding range to provide the most comprehensive study of
 the species’ foraging ecology to date.  We find that puffins use
 a dual foraging tactic combining short and long foraging trips in all four
 populations, but declining populations in southern Iceland and north-west
 Norway have much greater foraging ranges, which require more (costly)
 flight, as well as lower chick-provisioning frequencies, and a more
 diverse but likely less energy-dense diet, than stable populations in
 northern Iceland and Wales.  Together, our findings suggest that
 the poor productivity of declining puffin populations in the north-east
 Atlantic is driven by breeding adults being forced to forage far from the
 colony, presumably because of low prey availability near colonies,
 possibly amplified by intraspecific competition. Our results provide
 valuable information for the conservation of this and other important
 North-Atlantic species and highlight the potential of multi-population
 approaches to answer important questions about the ecological drivers of
 population trends.
description: There are six data files, each corresponding to a different type
 of data, and a ReadMe file which details the content of each
 file. Bird_metadata.csv contains data on
 the colony, id, weight and sex of each tagged bird
 GPS_tracking_data.csv contains the raw GPS tracking
 data.  Camera_traps_feeding_visits.csv contains data
 on feeding visits recorded from the camera traps
 Prey_size_from_video_data.csv contains prey size data measured
 from the camera trap footage Video stills for prey
 size measurements.zip contains one still per video used to measure prey
 size DNA_metabarcoding.csv contains the DNA
 metabarcoding data The tracking data can
 also be visualised on the Birdlife Seabird Tracking Database.
DOI: 10.5061/dryad.dv41ns1x7
title: Distribution and habitat attributes associated with the Himalayan red panda in the westernmost distribution range

description: The Himalayan red panda (Ailurus fulgens), a recently confirmed distinct
 species in the red panda genus, is distributed in Nepal, India, Bhutan and
 south Tibet. Nepal represents the western most distribution of the
 Himalayan red panda. This study aim to determine important habitat
 features influencing the distribution of red panda and recommend possible
 habitat corridors. This manuscript described current potential habitat of
 3,222 km2 with the relative abundance of 3.34 signs/km in Nepal. Aspect,
 canopy cover, bamboo cover and distance to water were the important
 habitat attributes. It suggested five potential corridors in western
 Nepal. Overall, the study has important implications for conservation of
 the Himalayan red panda in western distribution range.
DOI: 10.5061/dryad.3r2280gfb
title: Comparative biogeography and the evolution of population structure for bottlenose and common dolphins in the Indian Ocean

description: Abstract Aim: In the marine environment, where there are few
 physical boundaries to gene flow, there is often nevertheless
 intraspecific diversity with consequences for effective conservation and
 management.  Here we compare two closely
 related dolphin species with a shared distribution in the Indian Ocean
 (IO) to better understand the biogeographic drivers of their population
 structure. Location: Global oceans and seas with a focus on the
 Indian Ocean Taxon: Tursiops sp.
 and Delphinus sp. Methods: Bayesian,
 ordination, assignment, statistical and phylogenetic analyses to assess
 phylogeography, connectivity and population structure using microsatellite
 and mitochondrial DNA genetic markers.
 Results: Both Tursiops sp.
 and Delphinus sp. showed population structure across the
 western IO and, in each case, populations in the Arabian Sea (off India,
 Pakistan and Oman) were most differentiated. Comparisons with other
 populations worldwide revealed independent lineages in this geographic
 region for both genera.  For T.
 aduncus, (for which multiple sites within the IO could be
 compared), Bayesian modelling best supported a scenario of expansion
 southwards following a bottleneck event resulting in differentiation
 between the northern and western IO. For Delphinusthe same
 pattern is even more pronounced.  Populations in the
 Arabian Sea region of the northwestern IO show genetic isolation for each
 of the two genera, consistent with other studies of cetacean species in
 this region.  Main Conclusions: We propose that changes
 in the intensity of the southwest monsoon during the climate cycles of the
 Pleistocene could have affected regional patterns of productivity and
 represent an important biogeographic driver promoting the observed
 patterns of differentiation and population dynamics seen in our focal
 species. Patterns of population genetic structure are consistent with
 phenotypic differences, suggesting an influence from distinct habitats and
 resources, and emphasising the need for effective conservation measures in
 this geographic region.  
description: Microsatellite genotype data for <em>Delphinus</em>
 and <em>Tursiops</em> populations studied as
 'genepop' files.
DOI: 10.5061/dryad.4b8gthtbs
title: Identifying biotic drivers of population dynamics in a benthic–pelagic community

description: Benthic species and communities are linked to pelagic zooplankton through
 life-stages encompassing both benthic and pelagic habitats and through a
 mutual dependency on primary producers as a food source. Many zooplankton
 taxa contribute to the sedimentary system as benthic eggs. Our main aim
 was to investigate the nature of the population level biotic interactions
 between and within these two seemingly independent communities, both
 dependent on the pelagic primary production, while simultaneously
 accounting for environmental drivers (salinity, temperature and oxygen
 conditions). To this end we applied multivariate autoregressive
 state-space models to long (1966–2007) time-series of annual abundance
 data, comparing models with and without interspecific interactions, as
 well as models with and without environmental variables included. We were
 not able to detect any direct coupling between sediment-dwelling benthic
 taxa and pelagic copepods and cladocerans on the annual scale, but the
 most parsimonious model indicated that interactions within the benthic
 community are important. There were also positive residual correlations
 between the copepods and cladocerans potentially reflecting the
 availability of a shared resource or similar seasonal dependence, whereas
 both groups tended to correlate negatively with the zoobenthic taxa. The
 most notable single interaction within the benthic community was a
 tendency for a negative effect of Limecola balthica on the amphipods
 Monoporeia affinis and Pontoporeia femorata, which can help explain the
 observed decrease of amphipods due to increased competitive interference.
description: The data consist of field data on zooplankton abundances gathered
 during 2016, as well as the time-series used for the community model
 described in the paper.
DOI: 10.5061/dryad.r7sqv9sbf
title: Data from: Why time-limited individuals can make populations more vulnerable to disturbance

description: Individual variation in disturbance vulnerability (i.e. the likelihood
 that disturbance negatively affects an individual’s fitness) can affect
 how disturbance impacts animal populations, as even at low disturbance
 levels some individuals could be severely affected and die. Individual
 variation in vulnerability can arise due to different responses to
 disturbance. We propose a new hypothesis that even when individuals
 respond similarly to disturbance, time-limited individuals are more at
 risk that their condition deteriorates since they have limited ability to
 extend their foraging time to compensate for disturbance. We investigate
 this ‘time-limitation hypothesis’ both empirically and mathematically by
 studying how individuals that differ in their average foraging time
 (presumably due to differences in foraging efficiency) are affected by
 disturbance. We used tracking data of 22 wintering Eurasian oystercatchers
 Haematopus ostralegus to compare time budgets between disturbed and
 undisturbed tidal periods. In three tidal periods with severe disturbance
 by transport airplane, more than a third of the variation in additional
 flight time and foraging time loss was explained by individual
 differences. Inefficient individuals that foraged longer in undisturbed
 tidal periods experienced higher costs in disturbed tidal periods, since
 they lost more foraging time. We next used an analytical energy balance
 model to study how time-limited individuals differed in their maximum
 disturbance thresholds. Both our theoretical model and empirical study
 suggest that inefficient individuals in a time-limited environment may be
 unable to increase their foraging time to compensate for the effects of
 disturbance. Consequently, the magnitude of individual variation in time
 budgets strongly determines what proportion of the population is at risk
 that their condition deteriorates due to disturbance. Our hypothesis
 implies that, when assessing disturbance effects on a population, it is
 not only important to consider individual variation in disturbance
 responses, but also variation in time budgets that determine the
 consequences of disturbance.
description: See the article in Oikos for how data was collected.
description: The dataset consists of four files:
 <em>Tidal_Foraging_and_Flight_times.csv</em> includes
 all tidal flight time and tidal foraging time estimates and all
 covariates. <em>Column descriptions.xlsx </em>provides a
 description of each column in the tidal foraging and flight time csv data
 file.  Code for the mathematical model used to
 calculate disturbance thresholds, foraging times and energetic losses is
 provided
 in <em>model_disturbance_costs_foraging_time.R</em>. <em>mean_FT_all_2017_2019.csv </em>is a file containing mean foraging times of all GPS tracked individuals in our study area (see Supplementary Text 2 in main article in Oikos for more information) and needed as input for the R script.
DOI: 10.5061/dryad.3bk3j9kj7
title: Dataset for: Rio de Janeiro and other paleodrainages evidenced by the genetic structure of an Atlantic Forest catfish

description: Aim: The disjunct distributions of freshwater organisms along coastal
 drainages are usually explained by paleodrainages formed during sea-level
 retreats that connected currently isolated basins, or by river capture
 from tectonic adjustments between adjoining watersheds. We evaluate the
 relative importance of these events on the genetic variation of freshwater
 fishes inhabiting the Serra do Mar in eastern Brazil, a region with steep
 mountains and pronounced bays. Location: Coastal river drainages in
 southeastern Brazil. Taxon: Catfishes of the Trichomycterus alternatus
 group. Methods: We tested the effects of paleolandscape connections
 (GIS-reconstructed paleodrainages and putative river captures) on the
 genetic structure (mitochondrial and nuclear markers) of T. alternatus
 from 15 drainages using phylogenetic reconstructions, lineage delimitation
 methods and analyses of molecular variance. Results: Trichomycterus
 alternatus is monophyletic and comprised of three main lineages: two
 restricted to the basin at its northernmost distribution and another
 broadly distributed to the south. In the latter, seven major cytb clades
 were geographically compatible with the eight paleodrainages, with three
 incongruences matching river captures previously described for the
 Guanabara Bay (GB). Shared haplotypes among isolated rivers flowing into
 GB provide the first molecular evidence of the ‘Rio de Janeiro’
 paleoriver. Main conclusions: Dispersal via paleorivers is an important
 process, but it is not enough to recover the most recent dispersive
 events. Therefore, integrating both paleo-riverine configuration
 (GIS-based) and localized river captures (geological studies) is crucial
 to reveal the role of past geological and climatic events on the
 distribution of freshwater organisms. Taken together, these two factors
 significantly explained a high portion T. alternatus genetic structure
 along coastal drainages, revealing a paleolandscape scenario that may have
 been used by other freshwater Atlantic Forest taxa.
description: All methodology used for sampling collection and processing is
 described in the Materials and Methods session of the original
 manuscript.
description: This dataset contain the following files: 1)
 Two '.fas' files with the sequences (one for cytb and another
 for  its1) used for the phylogenetic and phylogeographic reconstructions
 used in this study. 2) One '.trait' file was
 used to for defining lineages for every sequenced used in the phylogenetic
 reconstruction. 3) A '.tree' file  with the
 concatenated species tree generated in the software STARBEAST  as
 described in the 'phylogenetic analyses' section of the
 manuscript. 4) A '.zip' file containing all
 the relevant files, scripts and results from the species delimitation
 methods. 5) A '.md' file containing a README
 file describing the step-by-step protocol for the paleodrainages
 reconstructions.   Please, contact
 smaialimag@gmail.com or waldirmbf@gmail.com should any question arise.
DOI: 10.5061/dryad.kd51c5b4v
title: Supplementary results for: Visit-to-visit blood pressure variability, neuropathology and cognitive function

description: Objective Large systolic blood pressure (SBP) variability has been
 proposed as a novel risk factor for dementia above and beyond SBP levels,
 but the underlying neuropathology is largely unknown. We investigated the
 relationship among visit-to-visit SBP variability, cognitive deterioration
 and underlying neuropathological changes. Methods We used longitudinal
 data (between 2005 and 2019) from the National Alzheimer’s Coordinating
 Center. 13,284 dementia-free participants aged≥50 years were followed over
 a median of 5.0 (interquartile range: 3.1-7.6) years. Neuropathology data
 were available in 1,400 autopsied participants. Visit-to-visit SBP
 variability was quantified from repeated annual SBP measurements.
 Cognitive deterioration was defined as conversion from normal cognition to
 mild cognitive impairment (MCI) or dementia, or from MCI to dementia.
 Results Larger visit-to-visit SBP variability was associated with
 cognitive deterioration (adjusted odds ratio comparing extreme quintiles:
 2.64; 95%CI:2.29-3.04, P &lt;0.001). It was also associated with a
 higher burden of vascular pathology (including microinfarcts, white matter
 lesion, atherosclerosis of the circle of Willis and arteriolosclerosis)
 and with neurofibrillary tangle pathology assessed by Braak staging (All P
 &lt; 0.05). The association with cognitive deterioration and vascular
 pathology appeared stronger among those with normal cognition versus MCI
 at baseline. These findings were observed after adjusting for age, sex,
 mean SBP and other confounding variables. Similar results were observed
 for diastolic BP variability. Conclusion Larger visit-to-visit SBP
 variability was associated with cognitive deterioration. It was also
 associated with cerebrovascular pathology and neurofibrillary tangles.
 These results suggest the intertwined role of vascular and
 Alzheimer's disease pathology in the etiology of dementia.
DOI: 10.5061/dryad.wm37pvmmh
title: Genome-wide supermatrix analyses of maples (Acer, Sapindaceae) reveal recurring inter-continental migration, mass extinction, and rapid lineage divergence

description: Acer (Sapindaceae) is an exceptional study system for understanding the
 evolutionary history, divergence, and assembly of broad-leaved deciduous
 forests at higher latitudes. Maples stand out due to their high diversity,
 disjunct distribution pattern across the northern continents, and rich
 fossil record dating back to the Paleocene. Using a genome-wide
 supermatrix combining plastomes and nuclear sequences (~585 kb) for 110
 Acer taxa, we built a robust time-calibrated hypothesis investigating the
 evolution of maples, inferring ancestral ranges, reconstructing
 diversification rates over time, and exploring the impact of
 mass-extinction on lineage accumulation. Contrary to fossil evidence, our
 results indicate Acer first originated in the (north)eastern Palearctic
 region, which acted as a source for recurring outward migration. Warm
 conditions favored rapid Eocene-onward divergence, but ranges and
 diversity declined extensively as a result of the Plio-Pleistocene glacial
 cycles. These signals in genome-wide sequence data corroborate
 paleobotanical evidence for other major woody north-temperate groups,
 highlighting the significant (disparate) impact of climatic changes on the
 evolution, composition, and distribution of the vegetation in the northern
 hemisphere.
description: This data file includes the DNA sequence alignment used in the
 analyses of the paper cited above.
DOI: 10.34740/kaggle/dsv/14645257
title: ONCO-360 | DATASUS | INCA | CNES | SIOPS
DOI: 10.5061/dryad.931zcrjjj
title: Herbivores reduce seedling recruitment in alpine plant communities

description: Through changes in climate and other environmental factors, alpine tundra
 ecosystems are subject to increased cover of erect shrubs, reduced
 predictability of rodent dynamics, and changes in wild and domesticated
 herbivore densities. To predict the dynamics of these ecosystems, we need
 to understand how these simultaneous changes affect alpine vegetation. In
 the long term, vegetation dynamics may depend critically on seedling
 recruitment. To study drivers of alpine plant seedling recruitment, we set
 up a field experiment where we manipulated the opportunity for plant-plant
 interactions through vegetation removal and introduction of willow
 transplants, the occurrence of herbivory through caging of plots, and then
 sowed 14 species into the plots. We replicated the experiment in three
 common alpine vegetation types (heath, meadow, and willow shrub) and
 recorded seedling emergence and survival over five years. Strong effects
 of vegetation removal and substantial differences in recruitment among
 dominant vegetation types suggested important effects of local vegetation
 on the recruitment success of vascular-plant seedlings. Similarly,
 herbivore exclusion had strong positive effects on recruitment success.
 This effect arose primarily via reduced seedling mortality in plots from
 which herbivores had been experimentally excluded and became noticeably
 stronger over time. In contrast, we detected no consistent effects of
 experimental willow shrub introduction on seedling recruitment. These
 results demonstrate that large and small herbivores can affect alpine
 plant seedling recruitment negatively by trampling and feeding on
 seedlings. Importantly, the effects became stronger over time, suggesting
 that effects of herbivory on seedling recruitment accumulates over time
 and may relate to recruitment phases beyond initial seedling emergence.
description: Data from a seed sowing experiment conducted at Dovrefjell,
 Central Norway. Seeds of 14 alpine plant species were sown in a field
 experiment where we manipulated the opportunity for plant-plant
 interactions through vegetation removal and introduction of willow
 transplants, the occurrence of herbivory through caging of plots. We
 replicated the experiment in three common alpine vegetation types (heath,
 meadow, and willow shrub) and recorded seedling emergence and survival
 over five years. Data include seedling records from 2014 to 2018, as well
 as microenvironmental data for each plot. 
description: Please see 'read me' files for each dataset.
DOI: 10.5061/dryad.5dv41ns5g
title: Web wars: Males of the golden orb-web spider invest more in fights for mated and aggregated females

description: In addition to resource value, the cost of finding mates may affect how
 much males invest in fights for females. The cost of finding females may
 be imposed through natural factors extrinsic to males, such as female
 spatial distribution and predation pressure, which can be challenging to
 simulate in laboratory conditions. Therefore, studies under natural
 conditions may be suitable for understanding how the costs of finding
 mating partners affect male investment in fights. We used the spider
 Trichonephila clavipes to evaluate the hypotheses that males in field
 conditions invest more in contests for access to (1) unmated and (2) more
 fecund females, and (3) when access to females is harder. To test these
 hypotheses, we recorded the occurrence, duration and escalation of induced
 contests between males located in webs of females that differed in
 reproductive status (estimated by female life stage), fecundity (estimated
 by female abdominal area) and spatial distribution (i.e. isolated or
 aggregated with webs of other females). The occurrence and duration of
 contests were unrelated to female value or search costs. However, the
 probability for escalation was higher when males were fighting for adult
 (and probably mated) females. We also found that males tended to start a
 contest more often in aggregated webs. These results indicate that males
 of T. clavipes adjust investment in contests, but contrarily to what we
 expected. We suggest males invest more in contests for adult females
 because they are defending females that they previously fertilized to
 avoid sperm competition.