cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1146
title: Data from: A worldwide perspective on the population structure and genetic diversity of bottlenose dolphins (Tursiops truncatus) in New Zealand

description: Bottlenose dolphins (Tursiops truncatus) occupy a wide range of coastal
 and pelagic habitats throughout tropical and temperate waters worldwide.
 In some regions, "inshore" and "offshore" forms or
 ecotypes differ genetically and morphologically, despite no obvious
 boundaries to interchange. Around New Zealand, bottlenose dolphins inhabit
 3 coastal regions: Northland, Marlborough Sounds, and Fiordland. Previous
 demographic studies showed no interchange of individuals among these
 populations. Here, we describe the genetic structure and diversity of
 these populations using skin samples collected with a remote biopsy dart.
 Analysis of the molecular variance from mitochondrial DNA (mtDNA) control
 region sequences (n = 193) showed considerable differentiation among
 populations (Fst = 0.17, Φst = 0.21, P &lt; 0.001) suggesting little
 or no female gene flow or interchange. All 3 populations showed higher
 mtDNA diversity than expected given their small population sizes and
 isolation. To explain the source of this variation, 22 control region
 haplotypes from New Zealand were compared with 108 haplotypes worldwide
 representing 586 individuals from 19 populations and including both
 inshore and offshore ecotypes as described in the Western North Atlantic.
 All haplotypes found in the Pacific, regardless of population habitat use
 (i.e., coastal or pelagic), are more divergent from populations described
 as inshore ecotype in the Western North Atlantic than from populations
 described as offshore ecotype. Analysis of gene flow indicated
 long-distance dispersal among coastal and pelagic populations worldwide
 (except for those haplotypes described as inshore ecotype in the Western
 North Atlantic), suggesting that these populations are interconnected on
 an evolutionary timescale. This finding suggests that habitat
 specialization has occurred independently in different ocean basins,
 perhaps with Tursiops aduncus filling the ecological niche of the inshore
 ecotype in some coastal regions of the Indian and Western Pacific Oceans.
description: esn039_supp.docTable of haplotype sequences (including their frequency by population) obtained from published sequences, biopsy samples,‘‘whale meat’’ products, and GenBank sources
DOI: 10.5061/dryad.rj653
title: Data from: Characterising the ecological trade-offs throughout the early ontogeny of coral recruitment

description: Drivers of recruitment in sessile marine organisms are often poorly
 understood, due to the rapidly changing requirements experienced during
 early ontogeny. The complex suite of physical, biological, and ecological
 interactions beginning at larval settlement involves a series of
 trade-offs that influence recruitment success. For example, while cryptic
 settlement within complex microhabitats is a commonly observed phenomenon
 in sessile marine organisms, it is unclear whether trade-offs between
 competition in cryptic refuges and predation on exposed surfaces leads to
 higher recruitment.To explore the trade-offs during the early ontogeny of
 scleractinian corals, we combined field observations with laboratory and
 field experiments to develop a mechanistic understanding of coral
 recruitment success. Multiple experiments conducted over 15 months in
 Palau (Micronesia) allowed a mechanistic approach to study the individual
 factors involved in recruitment: settlement behavior, growth, competition,
 and predation, as functions of microhabitat and ontogeny. We finally
 developed and tested a predictive recruitment model with the broader aim
 of testing whether our empirical insights explained patterns of coral
 recruitment and quantifying the relative importance of each
 trade-off.Coral settlement was higher in crevices than exposed
 microhabitats, but post-settlement bottlenecks differed markedly in the
 presence (uncaged) and absence (caged) of predators. Incidental predation
 by herbivores on exposed surfaces at early post-settlement (&lt;3 mm)
 stages and targeted predation by corallivores at late post-settlement
 (3–10 mm) stages exceeded competition in crevices as major drivers of
 mortality. In contrast, when fish were excluded, competition with
 macroalgae and heterotrophic invertebrates intensified mortality,
 particularly in crevices. As a result, post-settlement trade-offs were
 reversed, and recruitment was more than twofold higher on exposed surfaces
 than crevices. Once post-settlement bottlenecks were overcome, survival
 was higher on exposed surfaces regardless of fish exclusion. However,
 maximum recruitment occurred in crevices of uncaged treatments, being
 ninefold higher than caged treatments. Overall, we characterize
 recruitment success throughout the earliest life-history stages of corals
 and uncover some intriguing trade-offs between growth, competition and
 predation, highlighting how these change and even reverse during ontogeny
 and under alternate disturbance regimes.
description: Doropoulos_Ecol
 Mono_DryadData
DOI: 10.5061/dryad.rg4dc36s
title: Data from: Evidence for evolutionary change associated with the recent range expansion of the British butterfly, Polyommatus agestis, in response to climate change

description: Poleward range expansions are a widespread response to recent climate
 change and are crucial for many species’ future persistence. However for
 many species evolutionary change in traits such as colonisation history
 and habitat preference may be necessary to track environmental change
 across a fragmented landscape. Understanding the likelihood and speed of
 such adaptive change has therefore become an important issue in
 determining the effect of ongoing climate change on extinction rates. We
 conducted an AFLP-based genome scan across the recently-expanded UK range
 of the Brown Argus butterfly, Polyommatus (subgenus Aricia) agestis, and
 used both outlier-based (DFDIST and BayeScan) and association-based
 (Isolation-By-Adaptation) statistical approaches to identify signatures of
 evolutionary change associated with range expansion, and shifts in host
 plant use. We present evidence for (a) little effect of range expansion on
 neutral genetic structure and (b) strong signatures of selection at ~5%
 AFLP loci associated with both the poleward range expansion of P.agestis
 and differences in habitat use across the long-established and
 recently-colonised areas. Patterns of allele frequency change at these
 candidate loci suggest that adaptation to new habitats at the range margin
 has involved selection on genes already involved in adaptation to these
 habitats across the long-established part of the range. Our results
 suggest that evolutionary change is likely to affect species’ responses to
 climate change and that genetic variation in ecological traits across
 species’ distributions should be maximised to facilitate range shifts
 across a fragmented landscape, particularly in species that show strong
 associations with particular habitats.
description: A.agestis_2004_AFLPdataAFLP genotypes for individual male Brown Argus butterflies (Aricia agestis). See ReadMe file for detailed description of file contents.
DOI: 10.5061/dryad.q98202jk
title: Data from: Reconstruction of a beech population bottleneck using archival demographic information and Bayesian analysis of genetic data

description: Range expansion and contraction has occurred in the history of most
 species and can seriously impact patterns of genetic diversity. Historical
 data about range change are rare and generally appropriate for studies at
 large scales, whereas the individual pollen and seed dispersal events that
 form the basis of geneflow and colonization generally occur at a local
 scale. In this study we investigated range change in Fagus sylvatica on
 Mont Ventoux, France, using historical data from 1838 to the present and
 Approximate Bayesian Computation (ABC) analyses of genetic data. From the
 historical data we identified a population minimum in 1845 and located
 remnant populations at least 200 years old. The ABC analysis selected a
 demographic scenario with three populations, corresponding to two remnant
 populations and one area of recent expansion. It also identified expansion
 from a smaller ancestral population but did not find that this expansion
 followed a population bottleneck, as suggested by the historical data.
 Despite a strong support to the selected scenario for our dataset, the ABC
 approach showed a low power to discriminate among scenarios on average and
 a low ability to accurately estimate effective population sizes and
 divergence dates, probably due to the temporal scale of the study. This
 study provides an unusual opportunity to test ABC analysis in a system
 with a well documented demographic history and identify discrepancies
 between the results of historical, classical population genetic and ABC
 analyses. The results also provide valuable insights into genetic
 processes at work at a fine spatial and temporal scale in range change and
 colonization.
description: DataMEC-11-0816.R1Individuals genotypes of 1916 European Beech trees at 13 microsatellite markers
DOI: 10.5061/dryad.vg1g6
title: Data from: Phylogeny and circumscription of Cephalocereus (Cactaceae) based on molecular and morphological evidence

description: Cephalocereus, Neobuxbaumia, and Pseudomitrocereus (Cactaceae, Cactoideae,
 Echinocereeae) are related genera of columnar cacti native to Mexico with
 current ambiguous circumscription. We applied maximum parsimony and
 Bayesian inference methods to reconstruct the phylogeny of the
 Cephalocereus group using molecular data from seven chloroplast regions
 (petL-psbE, psbA-trnH, rpl16, rpl32-trnLUAG, trnL-F, trnQrps16, andycf1),
 simple coded indels, and 46 structural characters. The Cephalocereus group
 was recovered as monophyletic with high support values, whereas
 Neobuxbaumia appeared as paraphyletic, due to the polyphyly of
 Cephalocereus and the derived position of Pseudomitrocereus within this
 group. Topology was mostly congruent among the different phylogenetic
 methods explored, and three pervasive clades were observed. Two structural
 characters were confirmed as synapomorphies for the Cephalocereus group:
 prismatic crystals in the dermal system and a perianth woody cap
 persistent in the fruit. The derived position of Pseudomitrocereus
 suggests that new hypotheses must be explored regarding the possible
 hybrid origin of this taxon. We propose the transfer of all species of
 Neobuxbaumia, Cephalocereus, and Pseudomitrocereus to a single genus, in
 which Cephalocereus takes priority over the other names. Based on our
 results, a new circumscription for Cephalocereus is proposed, including a
 taxonomic synthesis, two new combinations (Cephalocereus multiareolatus
 and Cephalocereus sanchezmejoradae), and a key for species.
description: Combined analysis
 dataset (molecular+structural data)Molecular data from
 seven chloroplast loci: rpl16, trnL-F, psbA-trnH, rpl32-trnLUAG,
 trnQ-rps16, petL-psbE, ycf1, and codified indels. The structural dataset
 consist of 46 characters described in the paper.Neob2016_COMB.nexMolecular datasetMolecular data from seven chloroplast loci: rpl16, trnL-F, psbA-trnH, rpl32-trnLUAG, trnQ-rps16, petL-psbE, ycf1, and codified indels for 40 included terminals.Neob2016_MOL.nexBayesian tree for molecular dataBayesian tree for MrBayes analysis using the molecular data matrix.Neob2016_MOL_IB.treParsimony tree for molecular dataMolecular analysis using PAUP and parsimony ratchet. Consensus tree is presented with bootstrap support values.Neob2016_MOL_MP.treCombined analysis treeConsensus tree for PAUP and parsimony Ratchet analysis of combined dataset, with bootstrap support values above branches.Neob2016_COMB.tre
DOI: 10.5061/dryad.bn184
title: Data from: New insights on equid locomotor evolution from the lumbar region of fossil horses

description: The specialization of equid limbs for cursoriality is a classic case of
 adaptive evolution, but the role of the axial skeleton in this famous
 transition is not well understood. Extant horses are extremely fast and
 efficient runners, which use a stiff-backed gallop with reduced bending of
 the lumbar region relative to other mammals. This study tests the
 hypothesis that stiff-backed running in horses evolved in response to
 evolutionary increases in body size by examining lumbar joint shape from a
 broad sample of fossil equids in a phylogenetic context. Lumbar joint
 shape scaling suggests that stability of the lumbar region does correlate
 with size through equid evolution. However, scaling effects were dampened
 in the posterior lumbar region, near the sacrum, which suggests strong
 selection for sagittal mobility in association with locomotor-respiratory
 coupling near the lumbosacral joint. I hypothesize that small-bodied
 fossil horses may have used a speed-dependent running gait, switching
 between stiff-backed and flex-backed galloping as speed increased.
description: FINAL
 DATA_newLandmarks, Procrustes
 coordinates, PC scores, Eigenvalues and species mean scores used in PIC
 analysis.Jones_treePhylogenetic tree used in the comparative analyses. See supplemental Figure 2 for more information.
DOI: 10.5061/dryad.m9j80
title: Data from: Moving on with foraging theory: incorporating movement decisions into the functional response of a gregarious shorebird

description: 1. Models relating intake rate to food abundance and competitor densities
 (generalized functional response models) can predict forager distributions
 and movements between patches, but we lack understanding of how
 distributions and small-scale movements by the foragers themselves affect
 intake rates. 2. Using a state-of-the-art approach based on
 continuous-time Markov chain dynamics, we add realism to classic
 functional response models by acknowledging that the chances to encounter
 food and competitors are influenced by movement decisions, and, vice
 versa, that movement decisions are influenced by these encounters. 3. We
 used a multi-state modelling framework to construct a stochastic
 functional response model in which foragers alternate between three
 behavioural states: searching, handling and moving. 4. Using behavioural
 observations on a molluscivore migrant shorebird (red knot, Calidris
 canutus canutus), at its main wintering area (Banc d'Arguin,
 Mauritania), we estimated transition rates between foraging states as a
 function of conspecific densities and densities of the two main bivalve
 prey. 5. Intake rate decreased with conspecific density. This interference
 effect was not due to decreased searching efficiency, but resulted from
 time lost to avoidance movements. 6. Red knots showed a strong functional
 response to one prey (Dosinia isocardia), but a weak response to the other
 prey (Loripes lucinalis). This corroborates predictions from a recently
 developed optimal diet model that accounts for the mildly toxic effects
 due to consuming Loripes. 7. Using model-averaging across the most
 plausible multi-state models, the fully parameterized functional response
 model was then used to predict intake rate for an independent dataset on
 habitat choice by red knot. 8. Comparison of the sites selected by red
 knots with random sampling sites showed that the birds fed at sites with
 higher than average Loripes and Dosinia densities, i.e. sites for which we
 predicted higher than average intake rates. 9. We discuss the limitations
 of Holling's classical functional response model that ignores
 movement and the limitations of contemporary movement ecological theory
 ignoring consumer-resource interactions. With the rapid advancement of
 technologies to track movements of individual foragers at fine spatial
 scales, the time seems ripe to integrate descriptive tracking studies with
 stochastic movement-based functional response models.
description: intake.rate.protocols.2008This file contains the raw data of the intake rate protocols carried out in 2008knot.positions.2007This file contains the positions of the individual knots mapped in 2007raw.prey.densities.2007This file contains the available densities of Loripes and Dosinia per station in 2007raw.prey.densities.2008This file contains the available densities of Loripes and Dosinia per station in 2008
DOI: 10.5061/dryad.vn712
title: Data from: Differential persistence favors habitat preferences that determine the distribution of a reef fish

description: A central focus of population ecology is understanding what factors
 explain the distribution and abundance of organisms within their range.
 This is a key issue in marine systems, where many organisms produce
 dispersive larvae that develop offshore before returning to settle on
 benthic habitat. We investigated the distribution of the neon goby,
 Elacatinus lori, on sponge habitat and evaluated whether variation in the
 persistence of recently settled individuals (i.e., settlers) among
 different sponge types can result in habitat preferences and establish
 their observed distribution. We found that E. lori settlers were more
 likely to occur on large yellow tube sponges (Aplysina fistularis) than on
 small yellow sponges or brown tube sponges (Agelas conifera). An
 experiment seeding settlers onto multiple species and sizes of sponge
 habitat revealed that settlers persist longer on large yellow sponges than
 on small yellow sponges or brown sponges. Habitat preference experiments
 also indicated that settlers prefer large yellow sponges over small yellow
 sponges or brown sponges. Settlers achieved these preference behaviors
 using visual, but not chemical, cues. Finally, new settlers arriving from
 the water column were more likely to occur on large yellow sponges than on
 small yellow sponges or brown sponges, indicating that the observed
 habitat preferences existed independent of prior experience. These results
 support the hypothesis that E. lori have evolved behavioral preferences
 for sponge habitats that will maximize their post-settlement persistence,
 and that decisions at settlement will shape the population level pattern
 of settler distribution on coral reefs.
description: Majoris_etal_BEHECO-2017-0404_DistributionDataDistribution of E. lori settlers on brown and yellow spongesMajoris_etal_BEHECO-2017-0404_PersistenceDataPersistence of E. lori settlers on brown and yellow tube spongesMajoris_etal_BEHECO-2017-0404_HabitatPreferencesDataHabitat preferences of E. lori settlers for sponge habitatMajoris_etal_BEHECO-2017-0404_NewSettlerDistributionDataDistribution of new E. lori settlers (individuals &lt;10mm arriving from the water column) on sponge habitat.
DOI: 10.25919/gep4-8587
title: Parkes observations for project P595 semester 2025OCTS_27

description: We propose to continue the PULSE@Parkes project in which high school students from Australia and around the World use the Parkes radio telescope in a remote observing model to observe and analyse pulsar data. The data from some PULSE@Parkes observations are used to support the space missions, other observations supplement the P456 Pulsar Timing Array project and the remainder were chosen in order to make a detailed analysis of pulsar timing irregularities and intermittency.
DOI: 10.5061/dryad.j18q1
title: Data from: β-adrenergic receptor-dependent alterations in murine cardiac transcript expression are differentially regulated by gefitinib in vivo

description: β-adrenergic receptor (βAR)-mediated transactivation of epidermal growth
 factor receptor (EGFR) has been shown to promote cardioprotection in a
 mouse model of heart failure and we recently showed that this mechanism
 leads to enhanced cell survival in part via regulation of apoptotic
 transcript expression in isolated primary rat neonatal cardiomyocytes.
 Thus, we hypothesized that this process could regulate cardiac transcript
 expression in vivo. To comprehensively assess cardiac transcript
 alterations in response to acute βAR-dependent EGFR transactivation, we
 performed whole transcriptome analysis of hearts from C57BL/6 mice given
 i.p. injections of the βAR agonist isoproterenol in the presence or
 absence of the EGFR antagonist gefitinib for 1 hour. Total cardiac RNA
 from each treatment group underwent transcriptome analysis, revealing a
 substantial number of transcripts regulated by each treatment. Gefitinib
 alone significantly altered the expression of 405 transcripts, while
 isoproterenol either alone or in conjunction with gefitinib significantly
 altered 493 and 698 distinct transcripts, respectively. Further
 statistical analysis was performed, confirming 473 transcripts whose
 regulation by isoproterenol were significantly altered by gefitinib
 (isoproterenol-induced up/downregulation antagonized/promoted by
 gefinitib), including several known to be involved in the regulation of
 numerous processes including cell death and survival. Thus, βAR-dependent
 regulation of cardiac transcript expression in vivo can be modulated by
 the EGFR antagonist gefitinib.
description: Talraico et al. 2014
 Cardiac Transcript DataThis transcriptome
 dataset includes the differential analysis of cardiac transcripts
 modulated in vivo within one hour of treatment with either isoproterenol
 (beta adrenergic receptor agonist, 1 mg/kg), gefitinib (epidermal growth
 factor inhibitor, 5 mg/kg) or both. Analyses are gefitinib versus vehicle,
 isoproterenol versus vehicle, gefitinib+isoproterenol versus vehicle and
 gefitinib+isoproterenol versus isoproterenol.Talarico et al. 2014 Cardiac
 Transcript Data.xlsx
DOI: 10.5061/dryad.4s286
title: Data from: Evolutionary change in continuous reaction norms

description: Understanding the evolution of reaction norms remains a major challenge in
 ecology and evolution. Investigating evolutionary divergence in reaction
 norm shapes between populations and closely related species is one
 approach to provide insights. Here we use a meta-analytic approach to
 compare divergence in reaction norms of closely related species or
 populations of animals and plants, across types of traits and
 environments. We quantified mean-standardized differences in overall trait
 means (Offset) and reaction norm shape (including both Slope and
 Curvature). These analyses revealed that differences in shape (Slope and
 Curvature together) were generally greater than differences in Offset.
 Additionally, differences in Curvature were generally greater than
 differences in Slope. The type of taxon contrast (species vs. population),
 trait, organism, and the type and novelty of environments all contributed
 to the best fitting models, especially for Offset, Curvature and the total
 differences (Total) between reaction norms. Congeneric species had greater
 differences in reaction norms than populations, and novel environmental
 conditions increased the differences in reaction norms between populations
 or species. These results show that evolutionary divergence of curvature
 is common and should be considered an important aspect of plasticity
 together with slope. Biological details about traits and environments,
 including cryptic variation expressed in novel environmental conditions,
 may be critical to understanding how reaction norms may evolve in novel
 and rapidly changing environments.
description: Murren_et_al_AS_UPLOADED_DRYADsee readme file