cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f1vhhmgs8
title: Extraordinary variation in a simple song: No geographical patterns in initial phrase variation of the Yellowhammer, a passerine with pronounced dialects

description: Geographical variation of birdsong is used to study various topics from
 cultural evolution to mechanisms responsible for reproductive
 barriers or song acquisition. In species with pronounced dialects,
 however, patterns of variation in nondialect parts of the song
 are usually overlooked. We focused on the individually variable initial
 phrase of the song of the Yellowhammer (Emberiza citrinella), a
 common Palearctic passerine which became a model species for dialect
 research. We used a quantitative method to compare the similarity
 of initial phrases from the repertoires of 237 males recorded at
 different spatial scales in a central European country covering all main
 dialect types. We hypothesized that patterns of initial phrase
 sharing and/or phrase similarity are affected by dialect boundaries and
 geographical proximity (i.e. that birds from the same dialect
 regions use more similar phrases or share them more often). Contrary to
 our expectations, initial phrase variation seems unrelated to
 dialects, as we did not find higher similarity either among recordings
 from the same dialect areas or among those from the same
 locality. Interestingly, despite the immense variability of
 phrase types detected (only 16% of 368 detected initial phrase
 types were shared between at least 2 males), a relatively
 high proportion of males (45%) was involved in sharing, and males
 using the same initial phrase were located anywhere from tens of
 meters to hundreds of kilometers apart. The patterns of variation suggest
 that precise copying during song learning as well as
 improvisation play important roles in forming individual repertoires in
 the Yellowhammer. Our data also confirm previous indications that
 the repertoires of Yellowhammer males (i.e. the composition of initial
 phrases) are individually unique and temporally stable. This
 makes the species a good candidate for individual acoustic
 monitoring, useful for detailed population or behavioral studies
 without the need for physical capture and marking of males.
DOI: 10.5061/dryad.0k6djh9w3
title: Data from: Ecological consequences of parasite host shifts under changing environments: more than a change of partner

description: (1) Parasitic plants, among many other parasitic organisms, are shifting
 in their geographic distribution in response to global change,
 establishing novel interactions with susceptible but previously unexposed
 host plants. Projections of future species assemblages in increasingly
 changing environments frequently overlook the strong capacity of these
 parasites to transform ecological systems, and host switching is
 considered a mere change of partner with no subsequent impact on ecosystem
 properties. (2) We explore the ecological consequences of parasite host
 shifts analysing the growth and reproductive responses of two host trees
 that share a different interaction-history with the parasitic plant Viscum
 album: recent in the case of Pinus sylvestris subsp. nevadensis and
 longstanding in that of Pinus nigra. We quantified growth by measuring
 primary (bud elongation) and secondary (dendrochronology) tree growth, and
 reproduction by quantifying cone crops, cone size, seed production, seed
 weight, seed germination, and emergence success. (3) Pinus nigra
 registered a minor effect on reproduction but a major reduction in
 biomass, clearly reflected in lower primary and secondary tree growth,
 smaller cones and lighter seeds. On the contrary, P. sylvestris subsp.
 nevadensis underwent a strong decline of its reproductive capacity with no
 effects on growth, manifested in smaller cone crops, less seed production,
 and lower germination and emergence success.
             (4) Synthesis: Mistletoe parasitism unleashes contrasting responses in taxonomically close host species with sharply different consequences for the forest ecosystem. While old hosts tolerate better the effect of parasitism, minimizing the impact on reproduction at the expense of their growth, recent hosts undergo greater effects of parasitism, suffering reproductive collapse with no perceptible loss of growth.  We conclude that the increasing phenomenon of parasite host switching is not just a mere change of partner, but a driver of a new ecosystem organization. These results highlight the importance of considering the specific effects of newly established interactions when predicting future species assemblages, as these can trigger different ecological organizations from those we currently know.
DOI: 10.5061/dryad.f7m0cfxrb
title: Data from: Disturbance regulates the density–body mass relationship of soil fauna

description: Theory on the density-body mass (DBM) relationship predicts that the
 density of animal species decreases by the power of −0.75 per unit
 increase in their body mass, or by the power of −1 when taxa across
 trophic levels are studied. This relationship is, however, largely debated
 as the slope often deviates from the theoretical predictions. Here, we
 tested the ability of the DBM relationship to reflect changes in the
 structure of communities subjected to an anthropogenic disturbance. The
 slope would become less steep if smaller animals were more impacted by the
 disturbance than the larger ones, whereas the slope would become steeper
 if larger animals were more affected than the smaller ones. We tested the
 changes in the DBM relationship by sampling soil fauna, i.e. nematodes,
 Collembola and larger arthropods, from a semi-arid grassland before and
 after spraying diesel fuel as disturbance. We applied three different
 treatments: a control, a light disturbance and an intense disturbance. We
 found that the slopes of the DBM relationships before the disturbance were
 around −1 as predicted by theory. The slope became more positive (i.e.
 less steep) just after the disturbance, especially after the intense
 disturbance as smaller fauna suffered the most and early colonizers had
 larger body mass. Interestingly, we observed that the slopes converged
 back to −1 in two months post-disturbance. Our findings show that the
 response of soil fauna communities to anthropogenic disturbances could
 explain the large variation in observed slopes of the DBM relationships.
 We experimentally demonstrate that an animal community, when disturbed,
 shows a temporal pattern of DBM relationships ranging from deviations from
 the predicted slope to convergence to the predicted slope with time. We
 recommend that deviations in the DBM relationships after disturbances can
 provide insights in the trajectory community recovery, and hence could be
 used for biomonitoring.
DOI: 10.5061/dryad.573n5tb3d
title: Experimental harvest regulations reveal that water availability during spring, not harvest, affects change in a waterfowl population

description: Population change is regulated by vital rates that are influenced by
 environmental conditions, demographic stochasticity and increasingly,
 anthropogenic effects.  Habitat destruction and climate change
 threaten the future of many wildlife populations, and there are additional
 concerns regarding the effects of harvest rates on demographic components
 of harvested organisms. Further, many population managers strictly manage
 harvest of wild organisms to mediate population trends of these
 populations.  The goal of our study was to decouple harvest and
 environmental variability in a closely monitored population of wild ducks
 in North America, where we experimentally regulated harvest independently
 of environmental variation over a period of four years. We used nine years
 of capture-mark-recapture data to estimate breeding population size during
 the spring for a population of wood ducks in Nevada.  We then
 assessed the effect of one environmental variable and harvest pressure on
 annual changes in the breeding population size.  Climatic
 conditions influencing water availability were strongly positively related
 to population growth rates of wood ducks in our study system. In contrast,
 harvest regulations and harvest rates did not affect population growth
 rates.  We suggest efforts to conserve waterfowl should focus on
 the effects of habitat loss in breeding areas and climate change, which
 will likely affect precipitation regimes in the future.  We
 demonstrate the utility of capture-mark-recapture methods to estimate
 abundance of species which are difficult to survey and test the impacts of
 anthropogenic harvest and climate on populations. Finally, our results
 continue to add to the importance of experimentation in applied
 conservation biology, where we believe that continued experiments on
 non-threatened species will be critically important as researchers attempt
 to understand how to quantify and mitigate direct anthropogenic impacts in
 a changing world.
DOI: 10.5061/dryad.fn2z34tpc
title: Population divergence associated with spatial asynchrony in precipitation in neotropical frogs

description: Aim: To test the role of asynchrony in precipitation patterns among
 populations –a proxy for asynchronous breeding– as a driver of
 intraspecific genetic divergence across 38 species of Neotropical frogs.
 In addition, to examine whether regions with more asynchronous
 precipitation regimes across space have higher frog species richness and
 have experienced greater speciation rates than regions with more spatially
 synchronous precipitation regimes. Location: Central and South America
 Taxon: Anurans Methods: For microevolutionary analyses, we assessed the
 relationship between spatial asynchrony in precipitation and mtDNA genetic
 divergence accounting for ecological connectivity using multiple
 regression and phylogenetic meta-analyses. For macroevolutionary analyses,
 we assessed the relationship between species richness, speciation rates
 estimated from a comprehensive molecular phylogeny, and the degree of
 spatial asynchrony in precipitation using generalized linear models.
 Results and Main conclusions: Beyond a generalized effect of
 ecological connectivity on intraspecific genetic divergence, we found that
 spatial asynchrony in precipitation is positively associated with genetic
 differentiation in 39% of the species tested, resulting in a weak
 cross-species effect. However, the effect of asynchrony in precipitation
 on population divergence seems not to scale to macroevolutionary patterns
 because spatial asynchrony in precipitation was not associated with
 geographical patterns of species richness nor present-day speciation
 rates. Our results indicate that asynchronous breeding may promote genetic
 divergence even in the absence of geographic barriers in species where
 breeding is associated with water availability, but such effects may not
 be stable enough through time to influence macroevolutionary patterns.
DOI: 10.5061/dryad.5dv41ns2f
title: Testing urban drivers of riparian woody vegetation composition in a precipitation-limited system

description: In precipitation-limited regions, where water availability is a key driver
 of vegetation patterns, altered hydrology in urban areas may have a
 particularly strong effect on riparian plant communities. Urban water
 inputs can create perennial flows in formerly intermittent streams,
 potentially providing a water subsidy to riparian plants during dry
 seasons. However, during rainy seasons, increased storm flow magnitudes in
 urban areas can cause stream channel incision and associated lowered water
 tables. Channel incision may reduce riparian soil moisture throughout the
 year and limit the effect of dry-season stream flow. We asked whether
 channel incision and dry-season stream flow were related to the
 composition of riparian vegetation communities along small streams in
 Sacramento, California, United States, and whether these two factors
 interacted. Sacramento has a Mediterranean climate with a long summer dry
 season. We sampled the riparian woody plant community along 66 stream
 reaches that created a gradient of channel incision severity across sites
 with and without dry-season flow. The riparian vegetation community was
 more strongly related to channel incision than dry-season flow. The two
 factors did interact in relation to the overall community composition
 based on multivariate analyses, but we did not detect interactions in
 univariate generalized linear mixed models predicting specific components
 of the woody vegetation community, with the exception of large native oak
 trees. We found that wetland-associated species and non-native species
 both became less prevalent with increasing channel incision. Conversely,
 native upland oak trees became more prevalent with increasing incision,
 although large oak trees only showed this pattern along flowing streams.
 Wetland-associated seedlings were almost exclusively found along flowing
 streams. Synthesis Our findings suggest that channel incision is a key
 driver of riparian woody vegetation composition. Although the effects of
 dry-season flow were less pronounced, urban water subsidies may be
 essential for the establishment of wetland-associated trees along
 historically intermittent streams. Varied hydrological conditions in
 precipitation-limited cities are associated with divergent assemblages of
 woody species in riparian zones.
DOI: 10.5061/dryad.x69p8czd9
title: Data from: Human endometrial transcriptome and progesterone receptor cistrome reveal important pathways and epithelial regulators

description: Context. Poor uterine receptivity is one major factor leading to pregnancy
 loss and infertility. Understanding the molecular events governing
 successful implantation is hence critical in combating
 infertility. Objective. To define PGR-regulated molecular
 mechanisms and epithelial roles in receptivity. Design. RNA-seq
 and PGR-ChIP-seq were conducted in parallel to identify PGR-regulated
 pathways during the WOI in endometrium of fertile women. Setting.
 Endometrial biopsies from the proliferative and mid-secretory phases were
 analyzed. Patients or Other Participants. Participants were
 fertile, reproductive aged (18-37) women with normal cycle length, without
 any history of dysmenorrhea, infertility, or irregular cycles. In total,
 42 endometrial biopsies obtained from 42 women were analyzed in this
 study. Interventions. There were no interventions during this
 study. Main Outcome Measures. Here we measured the alterations in
 gene expression and PGR occupancy in the genome during the WOI, based on
 the hypothesis that PGR binds uterine chromatin cycle-dependently to
 regulate genes involved in uterine cell differentiation and
 function. Results. 653 genes were identified with regulated PGR
 binding and differential expression during the WOI. These were involved in
 regulating inflammatory response, xenobiotic metabolism, EMT, cell death,
 interleukin/STAT signaling, estrogen response, and MTORC1 response.
 Transcriptome of the epithelium identified 3,052 DEGs, of which 658 were
 uniquely regulated. Transcription factors IRF8 and MEF2C were found to be
 regulated in the epithelium during the WOI at the protein level,
 suggesting potentially important functions that are previously
 unrecognized. Conclusion. PGR binds the genomic regions of genes
 regulating critical processes in uterine receptivity and function.
DOI: 10.5061/dryad.cc2fqz62j
title: Synthesis and characterization of cyclodextrin-based acrylamide polymer flocculant for adsorbing water-soluble dyes in dye wastewater

description: A novel hydrophobic and cationic cyclodextrin-based acrylamide flocculant
 (AM-β-CD-DMDAAC) was prepared by chemical oxidative polymerization to
 adsorb water-soluble dyes in dye wastewater. Fourier transform infrared
 spectroscopy (FT-IR), X-ray diffraction (XRD), scanning electron
 microscope (SEM), and thermogravimetric (TG) measurements results
 demonstrated that the AM-β-CD-DMDAAC was successfully synthesized. The
 effects of pH, contact time, initial dye concentration, temperature and
 adsorbent dose on dye removal efficiency for AM-β-CD-DMDAAC flocculants
 were investigated. The kinetic data were found to follow
 pseudo-second-order kinetic model. The equilibrium adsorption data were
 fitted to Langmuir isotherm model, with the adsorption capacity
 147.1 mg/g. The adsorbent retained about 60 % of the adsorption efficiency
 after three adsorption/desorption cycles, which implied a promising
 application as the dye adsorbent.
DOI: 10.5061/dryad.tb2rbnzw7
title: Changes in dive patterns of leatherback turtles with sea surface temperature and potential foraging habitats

description: Marine mesotherms are able to occupy broader thermal niches than
 ectotherms; however, this means they must exhibit greater tolerance to
 diverse environmental conditions across the ocean. Knowledge remains
 limited about how differences in environmental conditions within occupied
 habitats affect the bioenergetics of mesotherms and associated ecological
 traits. Here, we report that leatherback turtles (Dermochelys coriacea)
 migrating across the North Pacific changed their dive behavior regionally,
 possibly in response to changes in sea surface temperature and prey
 abundance. Our results demonstrate that dives became deeper when the
 surface water was warmer, presumably because leatherbacks dive to deep
 cold waters to avoid overheating. Moreover, the patterns of
 presumed foraging dives indicate that leatherbacks engage in behavioral
 thermoregulation in warmer foraging regions, which perhaps limit the time
 available for foraging activity. In contrast, mesothermy allows
 leatherbacks to spend more time foraging in cool-temperate regions.
 However, it might not produce greater reproductive output due to
 additional migration cost to these areas, which are more distant from
 their nesting beaches. Our results highlight that mesothermy might not
 provide a direct fitness advantage to all individual leatherback turtles;
 rather, it affords a species-level fitness advantage by allowing a greater
 diversity of habitats to be utilized.
description: We obtained this dataset of dive behavior of 16 leatherback
 turtles migrating across the North Pacific by Satellite relay data
 logger.
DOI: 10.5061/dryad.9kd51c5c7
title: An interaction between host and microbe genotypes determines colonization success of a key bumble bee gut microbiota member

description: There has been a proliferation of studies demonstrating an organism’s
 health is influenced by its microbiota. However, factors influencing
 beneficial microbe colonization and the evolution of these relationships
 remain understudied relative to host-pathogen interactions. Vertically
 transmitted beneficial microbes are predicted to show high levels of
 specificity in colonization, including genotype matching, which may
 transpire through coevolution. We investigate how host and bacterial
 genotypes influence colonization of a core coevolved microbiota member in
 bumble bees. The hindgut colonizing Snodgrassella alvi confers direct
 benefits, but, as an early colonizer, also facilitates the further
 development of a healthy microbiota. Due to predominantly vertical
 transmission promoting tight evolution between colonization factors of
 bacteria and host lineages, we predict that genotype-by-genotype
 interactions will determine successful colonization. Germ-free adult bees
 from seven bumble bee colonies (host genotypic units) were inoculated with
 one of six genetically distinct strains of S. alvi. Subsequent
 colonization within host-genotype and microbe-genotype combinations ranged
 from zero to one hundred percent, and an interaction between host and
 microbe genotypes determined colonization success. This novel finding of a
 genotype-by-genotype interaction determining colonization in an animal
 host-beneficial microbe system has implications for the ecological and
 evolutionary dynamics of host and microbe, including associated
 host-fitness benefits.
DOI: 10.5061/dryad.612jm63zm
title: Data from: Environment predicts repeated body size shifts in a recent radiation of Australian mammals

description: Closely related species that occur across steep environmental gradients
 often display clear body size differences, and examining this pattern is
 crucial to understanding how environmental variation shapes diversity.
 Australian endemic rodents in the Pseudomys Division (Muridae: Murinae)
 have repeatedly colonized the arid, monsoon, and mesic biomes over the
 last 5 million years. Using occurrence records, body mass data, and
 Bayesian phylogenetic models we test whether body mass of 31 species in
 the Pseudomys Division can be predicted by their biome association. We
 also model the effect of eight environmental variables on body mass.
 Despite high phylogenetic signal in body mass evolution across the
 phylogeny, we find that mass predictably increases in the mesic biome, and
 decreases in arid and monsoon biomes. As per Bergmann’s rule, temperature
 is strongly correlated with body mass, as well as several other variables.
 Our results highlight two important findings. First, body size in
 Australian rodents has tracked with climate through the Pleistocene,
 likely due to several environmental variables rather than a single factor.
 Second, support for both Brownian motion and predictable change at
 different taxonomic levels in the Pseudomys Division phylogeny
 demonstrates how the level at which we test hypotheses can alter
 interpretation of evolutionary processes.
description: Occurrence data and environmental variables for 31 species of
 murine rodents in the Pseudomys Division was obtained from the Atlas of
 Living Australia (ALA, https://www.ala.org.au/). Body
 size data was obtained from Breed B., Ford F. 2007. Native Mice and Rats.
 CSIRO Publishing, Collingwood, VIC. To account for
 phylogenetic uncertainty in the Pseudomys Division topology, we used 100
 randomly sampled trees from the posterior distribution of trees generated
 by Smissen and Rowe (2018).
DOI: 10.5061/dryad.z612jm67g
title: Global areas of low human impact (‘Low Impact Areas’) and fragmentation of the natural world

description: Habitat loss and fragmentation due to human activities is the leading
 cause of the loss of biodiversity and ecosystem services. protected areas
 are the primary response to this challenge and are
 the cornerstone of biodiversity conservation efforts. Roughly 15%
 of land is currently protected although there is momentum to dramatically
 raise protected area targets towards 50%. But, how much land remains in a
 natural state? We answer this critical question by using open-access,
 frequently updated data sets on terrestrial human impacts to create a new
 categorical map of global human influence (‘Low Impact Areas’) at a 1
 km2 resolution. We found that 56% of the terrestrial surface,
 minus permanent ice and snow, currently has low human impact.
 This suggests that increased protected area targets could be met in areas
 minimally impacted by people, although there is substantial variation
 across ecoregions and biomes. While habitat loss is well documented,
 habitat fragmentation and differences infragmentation rates between biomes
 has received little attention. Low impact Areas uniquely
 enabled us to calculate global fragmentation rates across biomes,
 and we compared these to an idealized globe with no human-caused
 fragmentation. The land in Low Impact Areas is heavily fragmented,
 compromised by reduced patch size and core area, and exposed to edge
 effects. Tropical dry forests and temperate grasslands are the
 world’s most impacted biomes. We demonstrate that when
 habitatfragmentation is considered in addition to habitat loss, the
 world’s species, ecosystems and associated services are in worse
 condition than previously reported.
description: See Methods in manuscript
description: See ReadMe file