cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d545d55
title: Data from: Combining aggregated and dispersed tree retention harvesting for conservation of vascular plant communities

description: Retention harvesting (also called tree retention or structural retention),
 in which live mature trees are selectively retained within harvested
 stands at different retention levels and in different patterns (aggregated
 to dispersed), is increasingly being used to mitigate the negative impacts
 of forest harvesting on biodiversity. However, the effectiveness of
 combining different patterns of retention harvesting for conservation and
 recovery of understory vascular plants in the long-term is largely
 unknown. To address this gap, we compared understory vascular plant
 diversity, abundance, and composition between aggregated retention and
 five levels of surrounding dispersed retention (0% = clearcut, 10%, 20%,
 50%, 75%) 15 years post-harvest. We also investigated the influence of
 dispersed retention on the ability of embedded retention patches to
 support plant communities characteristic of unharvested forests, and
 whether it varies by patch size of aggregated retention (0.20 ha or 0.46
 ha) and position within patches (edge or interior). Species richness,
 diversity, and cover were higher in the dispersed retention than in the
 patch retention as the harvested areas favored early-seral plant species.
 Graminoid cover was greater at the edges than in the interior of large
 patches. Retention patches as small as 0.2 ha more effectively supported
 shade-tolerant (forest interior) plant communities when they were
 surrounded by higher levels of dispersed retention (as compared to patches
 retained within clearcuts). Overall, the combined use of both aggregated
 and dispersed retention within a given cutblock benefits both late- and
 early-seral plant species and thus could effectively conserve understory
 plant assemblages in harvested landscapes. Sustainable forest management
 should therefore consider using a range of retention patch sizes combined
 with varying levels of surrounding dispersed retention in harvest designs
 to achieve objectives for plant conservation.
description: Data from: Combining
 aggregated and dispersed tree retention harvesting for conservation of
 vascular plant communitiesData collected in the
 field.Data
 for Dryad.xls
DOI: 10.5061/dryad.6sf11
title: Data from: The Azores Bullfinch (Pyrrhula murina) has the same unusual and size-variable sperm morphology as the Eurasian Bullfinch (Pyrrhula pyrrhula)

description: The Azores bullfinch is endemic to the island of São Miguel in the Azores
 archipelago and the sister species to the Eurasian bullfinch. Here we show
 that the spermatozoa of the two species have similar ultrastructure and
 gross morphology. Thus, the unusual and supposedly neotenous sperm
 morphology previously described for the Eurasian bullfinch appears to be
 an ancestral trait that evolved before the two taxa diverged. In addition,
 the coefficients of variation in total sperm length, both within and among
 males, were high in both species and exceed any previously published
 values for free-living passerines. Such high sperm-size variation is
 typically found in species with relaxed sperm competition. However, the
 high variance in mean sperm length among Azores bullfinches is surprising,
 because the trait has high heritability and this small, insular population
 shows clear signs of reduced genetic diversity at neutral loci. A possible
 explanation for this apparent contradiction is that the Azores bullfinch
 has retained more diversity at functional and fitness-related loci than at
 more neutral parts of the genome. Finally, we also present data on
 relative testis size and sperm swimming speed for the Eurasian bullfinch,
 and discuss the hypothesis that the small and putatively neotenous sperm
 in bullfinches has evolved in response to lack of sperm competition.
description: Measurements of
 individual spermatozoa in Azores and Eurasian
 bullfinchesMeasurements of head and
 flagellum length in 10 spermatozoa per male in 11 Azores bullfinches (P.
 murina) and 13 Eurasian bullfinches (P. pyrrhula) with details of sampling
 locality and date. (Raw data file for Table 1 in the
 paper)Pyrrhula sperm
 morphology.xlsPyrrhula pyrrhula sperm
 motilityMotility measures of
 individual sperm tracks analysed by Computer Assisted Sperm Ananlysis
 (CASA). The file lists the sperm tracks from 11 male Eurasian bullfinches
 (P. pyrrhula) with details of sampling locality and date. (Raw data file
 for Table 2 in the paper)
DOI: 10.5281/zenodo.18381976
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Georges M. D. J. Troupin, http://www.wikidata.org/entity/Q5878015. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q5878015
DOI: 10.5281/zenodo.8121716
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Georges M. D. J. Troupin, http://www.wikidata.org/entity/Q5878015. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q5878015
DOI: 10.5061/dryad.gd8jb
title: Data from: A Drosophila laboratory evolution experiment points to low evolutionary potential under increased temperatures likely to be experienced in the future

description: The ability to respond evolutionarily to increasing temperatures is
 important for survival of ectotherms in a changing climate. Recent studies
 suggest that upper thermal limits may be evolutionary constrained. We
 address this hypothesis in a laboratory evolution experiment, encompassing
 ecologically relevant thermal regimes. To examine the potential for
 species to respond to climate change, we exposed replicate populations of
 Drosophila melanogaster to increasing temperatures (0.3 °C every
 generation) for 20 generations, whereas corresponding replicate control
 populations were held at benign thermal conditions throughout the
 experiment. We hypothesized that replicate populations exposed to
 increasing temperatures would show increased resistance to warm and dry
 environments compared with replicate control populations. Contrasting
 replicate populations held at the two thermal regimes showed (i) an
 increase in desiccation resistance and a decline in heat knock-down
 resistance in replicate populations exposed to increasing temperatures,
 (ii) similar egg-to-adult viability and fecundity in replicate populations
 from the two thermal regimes, when assessed at high stressful temperatures
 and (iii) no difference in nucleotide diversity between thermal regimes.
 The limited scope for adaptive evolutionary responses shown in this study
 highlights the challenges faced by ectotherms under climate change.
description: All_Data_Phentypic_and_GenomicEgg-to-adult viability, Fecundity, Pi estimates, Heat knockdown and Desiccation data.Dryad_Concatenated.xls
DOI: 10.5061/dryad.p112b
title: Data from: Climatic variation modulates the indirect effects of large herbivores on small-mammal habitat use

description: Large mammalian herbivores (LMH) strongly shape the composition and
 architecture of plant communities. A growing literature shows that
 negative direct effects of LMH on vegetation frequently propagate to
 suppress the abundance of smaller consumers. Indirect effects of LMH on
 the behaviour of these consumers, however, have received comparatively
 little attention despite their potential ecological significance. We
 sought to understand (i) how LMH indirectly shape small-mammal habitat use
 by altering the density and distribution of understorey plants; (ii) how
 these effects vary with climatic context (here, seasonality in rainfall);
 and (iii) the extent to which behavioural responses of small mammals are
 contingent upon small-mammal density. We tested the effects of a diverse
 LMH community on small-mammal habitat use using 4 years of spatially
 explicit small-mammal trapping and vegetation data from the UHURU
 Experiment, a replicated set of LMH exclosures in semi-arid Kenyan
 savanna. Small-mammal habitat use was positively associated with tree
 density and negatively associated with bare (unvegetated) patches in all
 plots and seasons. In the presence of LMH, and especially during the dry
 season, small mammals consistently selected tree cover and avoided bare
 patches. In contrast, when LMH were excluded, small mammals were weakly
 associated with tree cover and did not avoid bare patches as strongly.
 These behavioural responses of small mammals were largely unaffected by
 changes in small-mammal density associated with LMH exclusion. Our results
 show that LMH indirectly affect small-mammal behaviour, and that these
 effects are influenced by climate and can arise via density-independent
 mechanisms. This raises the possibility that anthropogenic LMH declines
 might interact with changing patterns of rainfall to alter small-mammal
 distribution and behaviour, independent of numerical responses by small
 mammals to these perturbations. For example, increased rainfall in East
 Africa (as predicted in many recent climate-model simulations) may relax
 constraints on small-mammal distribution where LMH are rare or absent,
 whereas increased aridity and/or drought frequency may tighten them.
description: LongRawData_JAERaw data used in all analyses described in the manuscript. See ReadMe file for complete documentation.
DOI: 10.5061/dryad.63sj6f0
title: Data from: From salmon to salmonberry: the effects of salmon-derived nutrients on the stomatal density of leaves of the nitriphillic shrub Rubus spectabilis

description: Background and Aims: Nutrients derived from the carcasses of Pacific
 salmon have been shown to have wide-ranging effects on riparian systems.
 These include changes in community species composition and an increase in
 leaf nitrogen concentration, with the latter effect pronounced in the
 nitriphilic shrub Rubus spectabilis (salmonberry). Experimental work with
 other species has shown that leaf stomatal density increases in response
 to nitrogen fertilization. Therefore, we predicted that the stomatal
 density of salmonberry leaves would vary directly with the density of
 spawning salmon in salmonberry leaves collected from 16 streams in the
 vicinity of Bella Bella, on British Columbia’s central coast. We estimated
 the stomatal density along each stream, and quantified stream
 characteristics, including the number of spawning salmon (Oncorhynchus
 spp.), canopy cover, stem density and soil moisture. Key results: We found
 that salmon have both direct and indirect effects on stomatal density, the
 latter mediated by canopy cover and stem density. Salmonberry stomatal
 density increased by 1.12 stomata per mm-2 (~0.5%) for every kg of salmon
 per meter of stream. Over the range of salmon densities observed (1.8 –
 49.0 kg per meter of stream) stomatal density increased by almost 45 mm-2,
 or more than 20%. Conclusion: These data confirm that the stomatal density
 in salmonberry responds positively to the opportunity for greater
 productivity provided by salmon carcasses. The data provide insight into
 the physiological and morphological processes supporting nitrogen uptake,
 which in turn influences plant community composition.
description: FE-2018-00702-DataAccessibilityRaw data for analyses in "From Salmon to Salmonberry: the effect of salmon-derived nutrients on the stomatal density of leaves of the nitriphillic shrub Rubus spectabilis:.
DOI: 10.5061/dryad.2pb08
title: Data from: Spatio-temporal dynamics of a fish predator: density-dependent and hydrographic effects on Baltic Sea cod population

description: Understanding the mechanisms of spatial population dynamics is crucial for
 the successful management of exploited species and ecosystems. However,
 the underlying mechanisms of spatial distribution are generally complex
 due to the concurrent forcing of both density-dependent species
 interactions and density-independent environmental factors. Despite the
 high economic value and central ecological importance of cod in the Baltic
 Sea, the drivers of its spatio-temporal population dynamics have not been
 analytically investigated so far. In this paper, we used an extensive
 trawl survey dataset in combination with environmental data to investigate
 the spatial dynamics of the distribution of the Eastern Baltic cod during
 the past three decades using Generalized Additive Models. The results
 showed that adult cod distribution was mainly affected by cod population
 size, and to a minor degree by small-scale hydrological factors and the
 extent of suitable reproductive areas. As population size decreases, the
 cod population concentrates to the southern part of the Baltic Sea, where
 the preferred more marine environment conditions are encountered. Using
 the fitted models, we predicted the Baltic cod distribution back to the
 1970s and a temporal index of cod spatial occupation was developed. Our
 study will contribute to the management and conservation of this important
 resource and of the ecosystem where it occurs, by showing the forces
 shaping its spatial distribution and therefore the potential response of
 the population to future exploitation and environmental changes.
description: Standardised CPUE of cod
 and hydrographic dataThe dataset contains
 information on all the variables at the aggregation level of individual
 bottom trawl hauls as used in the analyses presented in
 "Spatio-temporal dynamics of a fish predator: density-dependent and
 hydrographic effects on Baltic Sea cod population". Year: year when
 the cod sample was collected; Lon: longitude (decimal-degree) of the
 position where the cod sample was collected; Lat: latitude
 (decimal-degree) of the position where the cod sample was collected;
 Depth: bottom depth (m) where the cod sample was collected; AG3:
 catch-per-unit-effort (kg/h) of cod of age 3+ of the trawl station; Oxy:
 modelled bottom oxygen (ml/L) associated to the trawl station; Sal:
 modelled bottom salinity (psu) associated to the trawl station; Crv: cod
 reproductive volume (km3) estimated for the year and ICES subdivision of
 the trawl station; Stk: stock size (thousands) of the eastern Baltic cod
 in the year of the sample from stock assessment (ICES
 2013).data_deposited.csv
DOI: 10.26183/e6gs-tt37
title: Pilot testing of educational intervention informing delivery of Cardiopulmonary Resuscitation and Basic Life Support to wheelchair users dataset

description: The dataset contains two excel spreadsheets. Pilot study testing the feasibility and effectiveness of an newly developed educational intervention. 23 participants in a random two arm study.
This dataset cannot be published openly due to ethics considerations. Please contact Elisha Deegan <22061159@student.westernsydney.edu.au> to discuss the research.
DOI: 10.5061/dryad.2j125
title: Data from: Territory surveillance and prey management: wolves keep track of space and time

description: Identifying behavioral mechanisms that underlie observed movement patterns
 is difficult when animals employ sophisticated cognitive-based strategies.
 Such strategies may arise when timing of return visits is important, for
 instance to allow for resource renewal or territorial patrolling. We
 fitted spatially explicit random-walk models to GPS movement data of six
 wolves (Canis lupus; Linnaeus, 1758) from Alberta, Canada to investigate
 the importance of the following: (1) territorial surveillance likely
 related to renewal of scent marks along territorial edges, to reduce
 intraspecific risk among packs, and (2) delay in return to recently hunted
 areas, which may be related to anti-predator responses of prey under
 varying prey densities. The movement models incorporated the
 spatiotemporal variable “time since last visit,” which acts as a
 wolf's memory index of its travel history and is integrated into the
 movement decision along with its position in relation to territory
 boundaries and information on local prey densities. We used a model
 selection framework to test hypotheses about the combined importance of
 these variables in wolf movement strategies. Time-dependent movement for
 territory surveillance was supported by all wolf movement tracks. Wolves
 generally avoided territory edges, but this avoidance was reduced as time
 since last visit increased. Time-dependent prey management was weak except
 in one wolf. This wolf selected locations with longer time since last
 visit and lower prey density, which led to a longer delay in revisiting
 high prey density sites. Our study shows that we can use spatially
 explicit random walks to identify behavioral strategies that merge
 environmental information and explicit spatiotemporal information on past
 movements (i.e., “when” and “where”) to make movement decisions. The
 approach allows us to better understand cognition-based movement in
 relation to dynamic environments and resources.
description: Wolf location
 dataGPS location data for
 the 6 wolves analysed in the paper. First column contains wolf IDs. Second
 and third columns contain observed easting and northing coordinates.
 Fourth and fifth column contain date and time associated with each
 location.rawdata.csv
DOI: 10.5061/dryad.j5c00
title: Data from: ICE1 demethylation drives range expansion of a plant invader through cold-tolerance divergence

description: Cold tolerance of alien invasive plants is a crucial determinant for their
 establishment and expansion into new cold environments. A close
 relationship between cold-tolerance level of 34 populations represented by
 147 accessions and latitude, extreme lowest temperature, coldest month
 average temperature and invasion age revealed that cold-tolerance
 divergence is a key factor driving the spreading of Ageratina adenophora,
 a highly invasive plant in China, to subtropical areas northeastward from
 the first-colonized southwestern region. Four epialles of cold response
 regulator ICE1 were found ranging from 66 to 50 methylated cytosines,
 representing a 4.4% to 3.3% methylation rate and significantly
 corresponded to the lowest to highest cold-tolerance levels among those
 different populations. A comparative study of four geographically-distinct
 populations firstly demonstrated that ICE1 demethylation upregulated
 transcription level of CBF transcription pathway is responsible for this
 evolution. Those facts, combined with the variation of colt-tolerance and
 methylation found among three native and two other introduced populations,
 indicate that demethylation of a gene upregulating cold tolerance may be
 the underlying evolutionary mechanism allowing crofton weed to expand
 northwards in China.
description: Data from: ICE1
 demethylation drives range expansion of a plant invader through
 cold-tolerance divergenceDATA.zip
DOI: 10.5061/dryad.663b4
title: Data from: Greenhouse biogeography: the relationship of geographic range to invasion and extinction in the Cretaceous Western Interior Seaway

description: Significant warming of Earth's climate in the near term seems
 increasingly likely. If significant enough, this climatic regime could, in
 the long term, come to resemble previous greenhouse intervals in earth
 history. Consequently, analysis of the fossil record during periods of
 extreme warmth may provide important lessons for species biology,
 including biogeography, in a much warmer world. To explore this issue, we
 analyzed the biogeographic response of 63 molluscan species to the
 long-term global warmth in the Late Cretaceous Western Interior Seaway
 (WIS) of North America, using Geographic Information Systems (GIS) to
 quantitatively measure changes in range size and distribution throughout
 this interval. We specifically considered the role that geographic range
 size played in mediating extinction resistance and invasion potential of
 these WIS species. We found no relationship between geographic range size
 and survivorship. However, endemic species with small range sizes were
 more likely to become invasive. Finally, mollusks did not experience a
 poleward shift in range out of the tropics during this warm regime. To the
 extent that these patterns are representative, and the WIS and taxa
 considered constitute a reasonable ancient analogue to a warmer future
 world, these results suggest that some biogeographic “rules” may not
 prevail under greenhouse conditions of long-term, equable warmth. They
 also suggest that other factors beyond geographic range size, including
 distinctive niche characteristics, may play quite important roles in
 species survival and invasion potential. This potentially complicates
 predictions regarding the future responses of extant species to long-term
 warming.
description: Myers_etal_SuppFig1Supplementary Figure 1. Histogram of log(geographic range) for all reconstructed ranges of molluskan taxa during the Late Cretaceous.Myers_etal_SuppTable1Supplementary Table 1. Species range size (reconstructed area and latitudinal extent) and outcrop area during each geologic stage. Coding for survivors and invaders: 1 = survived or invaded in the subsequent stage, 0 = did not survive or invade in the subsequent stage. Abbreviations of geologic stages: CEN = Cenomanian, TUR = Turonian, CON = Coniacian, SAN = Santonian, CAM = Campanian, MAA = Maastrichtian.Myers_etal_SuppTable2Supplementary Table 2. Contingency table analysis comparing biotic sub-provinces to survivorship and invasion potential. Endemic species are those that occur in only a single BSP. BSP = biotic sub-province and EC = endemic center of Kauffman 1984.Myers_etal_SuppTable3Supplementary Table 3. Contingency table analysis comparing survivorship and invasion potential to benthic vs. pelagic adult lifestyle and clade membership. Endemic species are those that occur in only a single BSP.
DOI: 10.5061/dryad.96818
title: Data from: Olfaction contributes to pelagic navigation in a coastal shark

description: How animals navigate the constantly moving and visually uniform pelagic
 realm, often along straight paths between distant sites, is an enduring
 mystery. The mechanisms enabling pelagic navigation in cartilaginous
 fishes are particularly understudied. We used shoreward navigation by
 leopard sharks (Triakis semifasciata) as a model system to test whether
 olfaction contributes to pelagic navigation. Leopard sharks were captured
 alongshore, transported 9 km offshore, released, and acoustically tracked
 for approximately 4 h each until the transmitter released. Eleven sharks
 were rendered anosmic (nares occluded with cotton wool soaked in petroleum
 jelly); fifteen were sham controls. Mean swimming depth was 28.7 m. On
 average, tracks of control sharks ended 62.6% closer to shore, following
 relatively straight paths that were significantly directed over spatial
 scales exceeding 1600 m. In contrast, tracks of anosmic sharks ended 37.2%
 closer to shore, following significantly more tortuous paths that
 approximated correlated random walks. These results held after swimming
 paths were adjusted for current drift. This is the first study to
 demonstrate experimentally that olfaction contributes to pelagic
 navigation in sharks, likely mediated by chemical gradients as has been
 hypothesized for birds. Given the similarities between the fluid
 three-dimensional chemical atmosphere and ocean, further research
 comparing swimming and flying animals may lead to a unifying paradigm
 explaining their extraordinary navigational abilities.
description: supporting data for
 leopard shark navigation - raw shark tracksRaw data (geographic
 position and mean depth between successive geographic positions) for
 leopard sharks that were manually acoustically tracked after being
 experimentally displaced offshore from the capture site off La Jolla,
 CA.supporting data PLOS ONE
 leopard shark navigation.xlsx