cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.55174
title: Data from: The behavioural consequences of sex reversal in dragons

description: Sex differences in morphology, physiology, and behaviour are caused by
 sex-linked genes, as well as by circulating sex-steroid levels. Thus, a
 shift from genotypic to environmental sex determination may create an
 organism that exhibits a mixture of male-like and female-like traits. We
 studied a lizard species (Central Bearded Dragon, Pogona vitticeps), in
 which the high-temperature incubation of eggs transforms genetically male
 individuals into functional females. Although they are reproductively
 female, sex-reversed dragons (individuals with ZZ genotype reversed to
 female phenotype) resemble genetic males rather than females in morphology
 (relative tail length), general behaviour (boldness and activity level),
 and thermoregulatory tactics. Indeed, sex-reversed ‘females’ are more
 male-like in some behavioural traits than are genetic males. This novel
 phenotype may impose strong selection on the frequency of sex reversal
 within natural populations, facilitating rapid shifts in sex-determining
 systems. A single period of high incubation temperatures (generating
 thermally induced sex reversal) can produce functionally female
 individuals with male-like (or novel) traits that enhance individual
 fitness, allowing the new temperature-dependent sex-determining system to
 rapidly replace the previous genetically based one.
description: Behaviour Data
 PogonaBehavioural data on
 Bearded DragonsPogona
 morphologyExcel file
 morphology
DOI: 10.5061/dryad.5j5r0
title: Data from: Glass sponge reefs as a silicon sink

description: Glass sponge reefs concentrate large amounts of biological silicon (Si)
 over relatively small areas of the seafloor. We examined the role of glass
 sponges in biological silicon (Si) cycling by calculating a Si budget for
 3 glass sponge reefs (Howe, Fraser, and Galiano) in the Strait of Georgia
 (SOG), British Columbia, Canada. The main reef-forming glass sponge
 Aphrocallistes vastus is heavily silicified, with 80% of its dry weight
 composed of biogenic silica (bSi). We used a combination of field sampling
 and surveys with a remote-operated vehicle to estimate the volume, mass,
 and bSi content of the reefs. BSi content ranged from 7 to 11 kg m−2 among
 reefs, amounting to a total of 915 t of bSi locked in the exposed portion
 of the 3 reefs. Water column measurements of dissolved Si (dSi) indicated
 that the SOG is a region of high dSi, with average dSi concentrations of
 50 μmol l−1 in waters over the reefs. The skeletons of glass sponges
 showed very little dissolution after 8 mo immersion in seawater, as
 determined by changes in dSi in samples and scanning electron microscopy
 of the spicules. In contrast, diatom frustules, the main source of bSi in
 surface waters of the SOG, were ~200 times more soluble. Our calculations
 of Si flux suggest that glass sponge reefs can equate to 65% of the dSi
 reservoir (3.6 × 109 mol Si) in the SOG and represent a substantial Si
 sink in the continental shelf waters of the northeastern Pacific Ocean.
description: Biomass, bSi, and dSi
 data used to calculate silicon cycling budget in 3 glass sponge
 reefsRaw field data for
 biomass, bSi and dSi sampling of glass sponges in 3 reefs from the Strait
 of Georgia. A Canadian Healthy Oceans Network (CHONe) Marine Biodiversity
 Project, MB-18.CHONe_MB-18_ChuJWF_data.xlsxCalculations used to determine silicon cycling budget in 3 glass sponge reefs.Outline of calculations used to determine silicon cycling budget in 3 glass sponge reefs in the Strait of Georgia. A Canadian Healthy Oceans Network (CHONe) Marine Biodiversity Project, MB-18.CHONe_MB-18_ChuJWF_Calculations.docx
DOI: 10.5061/dryad.869f2
title: Data from: Costs and tradeoffs of resistance and tolerance to belowground herbivory in potato

description: 1. The success of sustainable crop production depends on our ability to
 select or create varieties that can allocate resources to both growth and
 defence. However, breeding efforts have emphasized increases in yields but
 have partially neglected defence traits against pests. Estimating the
 costs of multiple defences against tuber herbivores and the tradeoffs
 among them, as well as understanding the relationship between yield and
 multiple defences is still unknown but relevant to both basic and applied
 ecology. 2. Using twenty commercial potato varieties available in Colombia
 and the tuber herbivore Tecia solanivora, we tested whether high yielding
 varieties show a reduction in three types of defence: constitutive and
 induced resistance, as well as tolerance. Specifically, we determined (1)
 the costs in terms of yield of all three defences, (2) the possible
 tradeoffs among them, and (3) if oviposition preference was related to the
 expression of these defences. 3. We detected no costs in terms of yield of
 constitutive and induced resistance to tuber damage. We did, however, find
 evidence of costs of being able to tolerate tuber herbivory. While we
 found no tradeoffs among any of the estimated defences, there was a
 positive correlation between aboveground compensatory growth and tolerance
 in terms of tuber production, suggesting that after damage there are no
 shifts in the allocation of resources from aboveground to belowground
 biomass. Finally, we found that females laid more eggs on those varieties
 with the lowest level of constitutive resistance. 4. Synthesis and
 applications. Our findings suggest that in potatoes, breeding for higher
 yields has not caused any reduction in constitutive or induced resistance
 to tuber damage. This is not the case for tolerance where those varieties
 with higher yields are also less likely to tolerate tuber damage. Given
 the high incidence of tuber pests in Colombia, selecting for higher
 tolerance could allow for high productivity in the presence of herbivores.
 Finding mechanisms to decouple the tolerance response from yield should be
 a new priority in potato breeding in Colombia to guarantee a higher yield
 in both the presence and absence of herbivores.
description: Costs_Tradeoffs_Defence_PotatoThe file contains multiple sheets, each sheet with a different response variable (defence) measured in all the potato varieties studied.
DOI: 10.5061/dryad.46vq7
title: Data from: Evaluating anthropogenic threats to endangered killer whales to inform effective recovery plans

description: Understanding cumulative effects of multiple threats is key to guiding
 effective management to conserve endangered species. The critically
 endangered, Southern Resident killer whale population of the northeastern
 Pacific Ocean provides a data-rich case to explore anthropogenic threats
 on population viability. Primary threats include: limitation of preferred
 prey, Chinook salmon; anthropogenic noise and disturbance, which reduce
 foraging efficiency; and high levels of stored contaminants, including
 PCBs. We constructed a population viability analysis to explore possible
 demographic trajectories and the relative importance of anthropogenic
 stressors. The population is fragile, with no growth projected under
 current conditions, and decline expected if new or increased threats are
 imposed. Improvements in fecundity and calf survival are needed to reach a
 conservation objective of 2.3% annual population growth. Prey limitation
 is the most important factor affecting population growth. However, to meet
 recovery targets through prey management alone, Chinook abundance would
 have to be sustained near the highest levels since the 1970s. The most
 optimistic mitigation of noise and contaminants would make the difference
 between a declining and increasing population, but would be insufficient
 to reach recovery targets. Reducing acoustic disturbance by 50% combined
 with increasing Chinook by 15% would allow the population to reach 2.3%
 growth.
description: Vortex PVA input files
 for threat assessment of Southern Resident Killer WhalesInput files used in
 modeling threats and management options for the Southern Resident Killer
 Whale population – for “Evaluating anthropogenic threats to endangered
 killer whales to inform effective recovery plans” by Lacy et al. Used with
 Vortex PVA software, version 10.2.9. (Available at
 www.vortex10.org/Vortex10.aspx)SRKW.zip
DOI: 10.5061/dryad.hk2v3
title: Data from: Convergent evolution of sexual dimorphism in skull shape using distinct developmental strategies

description: Studies integrating evolutionary and developmental analyses of
 morphological variation are of growing interest to biologists as they
 promise to shed fresh light on the mechanisms of morphological
 diversification. Sexually dimorphic traits tend to be incredibly divergent
 across taxa. Such diversification must arise through evolutionary
 modifications to sex differences during development. Nevertheless, few
 studies of dimorphism have attempted to synthesize evolutionary and
 developmental perspectives. Using geometric morphometric analysis of head
 shape for 50 Anolis species, we show that two clades have converged on
 extreme levels of sexual dimorphism through similar, male-specific changes
 in facial morphology. In both clades, males have evolved highly elongate
 faces whereas females retain faces of more moderate proportion. This
 convergence is accomplished using distinct developmental mechanisms; one
 clade evolved extreme dimorphism through the exaggeration of a widely
 shared, potentially ancestral, developmental strategy whereas the other
 clade evolved a novel developmental strategy not observed elsewhere in the
 genus. Together, our analyses indicate that both shared and derived
 features of development contribute to macroevolutionary patterns of
 morphological diversity among Anolis lizards.
description: Ontogenetic allometry
 dataData used for analysis
 of ontogenetic allometry assessing when in development variation in
 variation in facial morphology arises.Static allometry
 dataData used for analysis
 of static allometry determining that most species develop sexual
 dimorphism prior to sexual maturity.
DOI: 10.5061/dryad.46170
title: Data from: Using multiple markers to elucidate the ancient, historical, and modern relationships among North American Arctic dog breeds

description: Throughout most of the Americas, post-colonial dogs largely erased the
 genetic signatures of pre-historical dogs. However, the North American
 Arctic harbors dogs that are potentially descended from pre-historical
 ancestors, as well as those affected by post-colonial translocations and
 admixtures. In particular, Inuit dogs from Canada and Greenland are
 thought to descend from dogs associated with Thule peoples, who relied on
 them for transportation ca. 1000 years ago. Whether Thule dogs reflected
 an earlier colonization by Paleoeskimo dogs ca. 4500 years ago is unknown.
 During the Alaskan Gold Rush, additional sled dogs, possibly of
 post-colonial derivation, the Alaskan Husky, Malamute and Siberian Husky,
 were used in the Arctic. The genealogical relationships among and origins
 of these breeds are unknown. Here we use autosomal, paternal and maternal
 DNA markers to (1) test the hypothesis that Inuit dogs have retained their
 indigenous ancestry, (2) characterize their relationship to one another
 and to other Arctic breeds, and (3) estimate the age of North American
 indigenous matrilines and patrilines. On the basis of the agreement of all
 three markers we determined that Inuit dogs have maintained their
 indigenous nature, and that they likely derive from Thule dogs. In
 addition, we provide support for previous research that the Inuit dogs
 from Canada and Greenland dog should not be distinguished as two breeds.
 The Alaskan Husky displayed evidence of European introgression, in
 contrast to the Malamute and Siberian Husky, which appear to have
 maintained most of their ancient Siberian ancestry.
description: Brown_et_al_Appendix_1Contains general sample information, mtDNA haplotype data, Y chromosome haplotypes and microsatellite data for Arctic dogs and wolves.
DOI: 10.5061/dryad.gj1mg
title: Data from: Experimental manipulation reveals a trade-off between weapons and testes

description: Theory predicts a trade-off between sexually-selected weapons used to
 secure mates and post-copulatory traits used to maximize fertilization
 success. However, individuals that have a greater capacity to acquire
 resources from the environment may invest more in both pre- and
 post-copulatory traits, and trade-offs may not be readily apparent. Here,
 we manipulate the phenotype of developing individuals to examine
 allocation trade-offs between weapons and testes in Mictis profana
 (Hemiptera: Coreidae), a species where the hind legs are sexually selected
 weapons used in contests over access to females. We experimentally
 prevented males from developing weapons by inducing them to autotomize
 their hind legs before the final molt to adulthood. We compared trait
 expression in this group to males where autotomy was induced in the mid
 legs, which are presumably not under sexual selection to the same extent.
 We found males without weapons invested proportionally more in testes mass
 than those with their mid legs removed. Males that developed to adulthood
 without weapons did not differ from the mid leg removal group in other
 traits potentially under pre-copulatory sexual selection, other
 post-copulatory traits, or naturally selected traits. In addition, a
 sample of adult males from the same population in the wild revealed a
 positive correlation between investment in testes and weapons. Our study
 presents a critical contribution to a growing body of literature
 suggesting the allocation of resources to pre- and post-copulatory sexual
 traits is influenced by a resource allocation trade-off and that this
 trade-off may only be revealed with experimental manipulation.
description: Morphology of Mictis
 profana after experimentally preventing leg developement. Data also from
 wild caught M. profana.This data consists of
 morphological measurements of multiple morphological traits
 (pre-copulatory, post-copulatory and naturally selected), from two
 experimental groups. One group was prevented from developing mid-legs at
 their 5th instar, the other was prevented from developing much larger
 hind-legs. This data also contains morphological measures of wild-caught
 adults.Somjee_MictisData_JEB-2017_DRYAD.xls
DOI: 10.5061/dryad.p2t0t00
title: Data from: Caught in the web: spider web architecture affects prey specialization and spider–prey stoichiometric relationships

description: 1. Quantitative approaches to predator-prey interactions are central to
 understanding the structure of food webs and their dynamics. Different
 predatory strategies may influence the occurrence and strength of trophic
 interactions likely affecting the rates and magnitudes of energy and
 nutrient transfer between trophic levels, and the stoichiometry of
 predator-prey interactions. 2. Here, we used spider-prey interactions as a
 model system to investigate whether different spider web
 architectures—orb, tangle, and sheet-tangle—affect the composition and
 diet breadth of spiders and whether these, in turn, influence
 stoichiometric relationships between spiders and their prey. 3. Our
 results showed that web architecture partially affects the richness and
 composition of the prey captured by spiders. Tangle-web spiders were
 specialists, capturing a restricted subset of the prey community
 (primarily Diptera), whereas orb and sheet-tangle web spiders were
 generalists, capturing a broader range of prey types. 4. We also observed
 elemental imbalances between spiders and their prey. In general, spiders
 had higher requirements for both nitrogen (N) and phosphorus (P) than
 those provided by their prey even after accounting for prey biomass.
 Larger P imbalances for tangle-web spiders than for orb and sheet-tangle
 web spiders suggest that trophic specialization may impose strong
 elemental constraints for these predators unless they display behavioural
 or physiological mechanisms to cope with nutrient limitation.
description: Spider-prey
 interactionsData on spider-prey
 interactions including metadata and brief description of the
 methods.Spider.Prey.xls
DOI: 10.5061/dryad.82
title: Data from: Hunting to extinction: biology and regional economy influence extinction risk and the impact of hunting in artiodactyls

description: Half of all artiodactyls (even-toed hoofed mammals) are threatened with
 extinction, around double the mammalian average. Here, using a complete
 species-level phylogeny, we construct a multivariate model to assess for
 the first time which intrinsic (biological) and extrinsic (anthropogenic
 and environmental) factors influence variation in extinction risk in
 artiodactyls. Globally artiodactyls at greatest risk live in economically
 less developed areas, have older weaning ages and smaller geographical
 ranges. Our findings suggest that identifying predictors of threat is
 complicated by interactions between both biological and anthropogenic
 factors, resulting in differential responses to threatening processes.
 Artiodactyl species that experience unregulated hunting live in
 significantly less economically developed areas than those that are not
 hunted; however, hunted species are more susceptible to extinction if they
 have slower reproductive rates (older weaning ages). In contrast, risk in
 non-hunted artiodactyls is unrelated to reproductive rate and more closely
 associated with the economic development of the region in which they live.
description: Price and Gittleman Data
 SetPriceGittleman_2007_append.xls
DOI: 10.5061/dryad.6rq0c
title: Data from: Experimental feeding regime influences urban bird disease dynamics

description: Wild bird feeding often results in high densities of birds, potentially
 facilitating transmission of disease. Wild birds are major reservoirs of
 many zoonotic diseases, and although a number of avian disease outbreaks
 have been linked to bird feeders, urban bird-feeding and its role in
 disease systems remains poorly studied. We examined the impacts of typical
 supplementary feeding practices on the health status of feeder-visiting
 birds at experimental feeding stations in an urban area of New Zealand.
 Over an 18-month period, we screened birds captured at feeding and
 non-feeding properties for three pathogens and four groups of parasites to
 determine whether feeding altered disease dynamics. We also assessed body
 condition. All pathogens and parasites were detected in at least one
 garden bird species. Feeding stations tested positive for Salmonella
 enterica Typhimurium on ∼7% of occasions, confirming that structures used
 in feeding are a potential transmission pathway. Feeding influenced some
 parasite infection parameters; these effects varied among host species. In
 silvereyes Zosterops lateralis, helminth prevalence and abundance were
 lower at feeding properties compared to non-feeding properties. In
 contrast, Eurasian blackbirds Turdus merula at feeding properties had a
 higher abundance of helminths. House sparrows Passer domesticus at feeding
 properties had a higher abundance of feather lice. Furthermore, our
 feeding regime significantly affected body condition in house sparrow and
 silvereye, though no associations between parasite parameters and body
 condition indices were found. Our results demonstrate that feeding
 practices can have varied effects on avian health, including no observable
 effects for some disease agents in some host species. Disease risks are
 present, however, thus understanding and reducing these risks should be a
 key goal for all stakeholders to protect birds that use feeders and other
 wildlife.
description: Morphometrics and
 disease parameters of common garden birds during a supplementary feeding
 experiment in Auckland, New ZealandMorphometrics and
 disease parameters of house sparrows, silvereyes, and Eurasian blackbirds
 captured (via misnetting) at residential properties in Auckland, New
 Zealand, over the course of a 2-year supplementary feeding
 experiment.Galbraith et al 2016
 JAB.csv
DOI: 10.5061/dryad.h6h7c
title: Data from: Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes

description: Understanding the history that underlies patterns of species richness
 across the Tree of Life requires an investigation of the mechanisms that
 not only generate young species-rich clades, but also those that maintain
 species-poor lineages over long stretches of evolutionary time. However,
 diversification dynamics that underlie ancient species-poor lineages are
 often hidden due to a lack of fossil evidence. Using information from the
 fossil record and time calibrated molecular phylogenies, we investigate
 the history of lineage diversification in Polypteridae, which is the
 sister lineage of all other ray-finned fishes (Actinopterygii). Despite
 originating at least 390 million years (Myr) ago, molecular timetrees
 support a Neogene origin for the living polypterid species. Our analyses
 demonstrate polypterids are exceptionally species depauperate with a stem
 lineage duration that exceeds 380 million years (Ma) and is significantly
 longer than the stem lineage durations observed in other ray-finned fish
 lineages. Analyses of the fossil record show an early Late Cretaceous
 (100.5–83.6 Ma) peak in polypterid genus richness, followed by 60 Ma of
 low richness. The Neogene species radiation and evidence for
 high-diversity intervals in the geological past suggest a “boom and bust”
 pattern of diversification that contrasts with common perceptions of
 relative evolutionary stasis in so-called “living fossils.”
description: polypterid_dataPhylogenetic and paleontological datasets used for analyses of lineage diversification.
DOI: 10.5061/dryad.d2v35
title: Data from: Including community composition in biodiversity-productivity models

description: 1. Studies on biodiversity and ecosystem functioning (BEF) have elicited
 debate over the interpretation of the positive relationship between
 species richness and plant productivity. Manipulating richness cannot be
 achieved without affecting composition; it is thus essential to consider
 the latter in statistical models. 2. We firstly review existing approaches
 that use species richness as an explanatory variable and propose
 modifications to improve their performance. We use an original dataset to
 illustrate the analyses. The classical method where composition is coded
 as a factor with a level for each different species mixture can be
 improved by defining the levels using clustering. Methods based on
 ordinations reduce the dimensionality of plant composition and use the new
 coordinates as fixed effects; they provide a much better fit to our
 observations. 3. Secondly, we develop a new method where composition is
 included as a similarity matrix affecting the residual
 variance-covariance. Similarity in composition between plots is treated in
 the same way as shared evolutionary history between species in
 phylogenetic regression. We find that it outperforms the other models. 4.
 We discuss the different approaches and suggest that our method is
 particularly suited for observational studies or for manipulative studies
 where plant diversity is not kept constant by weeding. By treating species
 composition in an intuitive and sensible way, it offers a valuable and
 powerful complement to existing models.
description: MEE-13-11-651R2_data.xlsxField data used in "Including community composition in biodiversity-productivity models" by Sandau et al.