cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qz612jmm9
title: Data from: Convergence in hearing genes between echolocating birds and mammals

description: Echolocation, the detection of objects by means of sound waves, has
 evolved independently in diverse animal lineages. Echolocating lineages
 include not only mammals such as toothed whales, yangochiropteran and
 rhinolophoid bats, but also Rousettus fruit bats, as well as two
 bird lineages, the oilbirds and swiftlets, which use echolocation to
 navigate in caves where they roost. In whales, yangochiropteran and
 rhinolophoid bats, positive selection and molecular convergence has been
 documented in key hearing-related genes, such as prestin (SLC26A5), but
 few studies have examined these loci in other echolocators. Here, we
 examine patterns of selection and convergence in echolocation-related
 genes in echolocating birds and Rousettus bats. Fewer of these loci were
 under selection in Rousettus or birds compared with classically-recognized
 echolocators, and elevated convergence (compared to background lineages)
 was not evident across this gene set. In certain genes, however, we
 detected convergent substitutions with potential functional relevance,
 including convergence between Rousettus and classic echolocators in
 prestin at a site known to affect hair cell electromotility. We also
 detected convergence between Yangochiroptera, Rhinolophidea and oilbirds
 in TMC1, an important mechanosensory transduction channel in vertebrate
 hair cells, and observed an amino acid change at the same site within the
 pore domain. Our results suggest that although most proteins implicated in
 echolocation in specialized mammals may not have been recruited in birds
 or Rousettus fruit bats, certain hearing-related loci may have undergone
 convergent functional changes. Investigating adaptations in diverse
 echolocators such as swiftlets and oilbirds will deepen our understanding
 of this unusual sensory modality.
DOI: 10.6078/d1px3x
title: Data from: Ion correlation and negative lithium transference in polyelectrolyte solutions

description: Polyelectrolyte solutions (PESs) recently have been proposed as high
 conductivity, high lithium transference number (t+) electrolytes where the
 majority of the ionic current is carried by the electrochemically active
 Li-ion. While PESs are intuitively appealing because anchoring the anion
 to a polymer backbone selectively slows down anionic motion and therefore
 increases t+, increasing the anion charge will act as a competing effect,
 decreasing t+. In this work, we directly measure ion mobilities in a model
 non-aqueous polyelectrolyte solution using electrophoretic Nuclear
 Magnetic Resonance Spectroscopy (eNMR) to probe these competing effects.
 While previous studies that rely on ideal assumptions predict that PESs
 will have higher t+ than monomeric solutions, we demonstrate that below
 the entanglement limit, both conductivity and t+ decrease with increasing
 degree of polymerization. For polyanions of 10 or more repeat units, at
 0.5m Li+ we directly observe Li+ move in the “wrong direction” in an
 electric field, evidence of a negative transference number due to
 correlated motion through ion clustering. This is the first experimental
 observation of negative transference in a non-aqueous polyelectrolyte
 solution. We also demonstrate that t+ increases with increasing Li+
 concentration. Using Onsager transport coefficients calculated from
 experimental data, and insights from previously published molecular
 dynamics studies we demonstrate that despite selectively slowing anion
 motion using polyanions, distinct anion-anion correlation through the
 polymer backbone and cation-anion correlation through ion aggregates
 reduce the t+ in non-entangled PESs. This leads us to conclude that
 short-chained polyelectrolyte solutions are not viable high transference
 number electrolytes. These results emphasize the importance of
 understanding the effects of ion-correlations when designing new
 concentrated electrolytes for improved battery performance.
description: Requires Excel, Google Sheets, or other spreadsheet
 programs.
DOI: 10.5061/dryad.pvmcvdnr6
title: Data from: In situ 15N-N2O site preference and O2 concentration dynamics disclose the complexity of N2O production processes in agricultural soil

description: Arable soil continues to be the dominant anthropogenic source of nitrous
 oxide (N2O) emissions owing to application of nitrogen (N) fertilizers and
 manures across the world. Using laboratory and in-situ studies to
 elucidate the key factors controlling soil N2O emissions remains
 challenging due to the potential importance of multiple complex processes.
 We examined soil surface N2O fluxes in an arable soil, combined with
 in-situ high-frequency measurements of soil matrix oxygen (O2) and N2O
 concentrations, in situ 15N labeling, and N2O 15N site preference (SP).
 The in situ O2 concentration and further microcosm visualized
 spatiotemporal distribution of O2 both suggested that O2 dynamics were the
 proximal determining factor to matrix N2O concentration and fluxes due to
 quick O2 depletion after N fertilization. Further SP analysis and in situ
 15N labeling experiment revealed that the main source for N2O emissions
 was bacterial denitrification during the hot-wet summer with lower soil O2
 concentration, while nitrification or fungal denitrification contributed
 about 50.0% to total emissions during the cold-dry winter with higher soil
 O2 concentration. The robust positive correlation between O2 concentration
 and SP values underpinned that the O2 dynamics were the key factor to
 differentiate the composite processes of N2O production in in situ
 structured soil. Our findings deciphered the complexity of N2O production
 processes in real field conditions, and suggest that O2 dynamics rather
 than stimulation of functional gene abundances play a key role in
 controlling soil N2O production processes in undisturbed structure soils.
 Our results help to develop targeted N2O mitigation measures and to
 improve process models for constraining global N2O budget.
description: Please see the README document
 and the accompanying published article: Huanhuan Wei, Xiaotong Song, Yan
 Liu, Rui Wang, Xunhua Zheng, Klaus Butterbach-Bahl, Rodney T. Venterea, Di
 Wu, Xiaotang Ju (2023), Data from: In situ 15N-N2O site preference and O2
 concentration dynamics disclose the complexity of N2O production processes
 in agricultural soil. Global Change Biology. Accepted. DOI:
 10.1111/gcb.16753.
DOI: 10.5061/dryad.tqjq2bw4f
title: Increased importance of cool-water fish at high latitudes emerges from individual level responses to warming

description: High-latitude ecosystems are experiencing the most rapid warming on earth,
 expected to trigger a diverse array of ecological responses. Climate
 warming affects the ecophysiology of fish, and fish close to the cold end
 of their thermal distribution are expected to increase somatic growth from
 increased temperatures and a prolonged growth season, which in turn
 affects maturation schedules, reproduction and survival, boosting
 population growth. Accordingly, fish species living in ecosystems close to
 their northern range edge should increase in relative abundance and
 importance, and possibly displace cold-water adapted species.  We
 aim to document if and how population-level effects of warming are
 mediated by individual-level responses to increased temperatures, shifts
 in community structure and composition in high-latitude ecosystems. We
 studied 11 cool-water adapted freshwater fish populations in communities
 dominated by cold-water-adapted species to investigate changes in the
 relative importance of cool-water fish during the last 30 years of rapid
 warming in high-latitude lakes. In addition, we studied the
 individual-level responses to warming to clarify the potential mechanisms
 underlying the population effects. Our long-term series (1991–2020) reveal
 a marked increase in numerical importance of the cool-water fish species,
 perch, in ten out of eleven populations, and in most fish communities the
 cool-water species is now dominant. Moreover, we show that climate warming
 affects population-level processes via direct and indirect temperature
 effects on the individuals. Specifically, the increase in abundance arises
 from increased recruitment, faster juvenile growth and ensuing earlier
 maturation, all boosted by climate warming. The speed and magnitude of the
 response to warming in these high-latitude fish communities strongly
 suggest that cold-water fish will be displaced by fish adapted to warmer
 water. Consequently, management should focus on climate adaptation
 limiting future introductions and invasions of cool-water fish and
 mitigating harvesting pressure on cold-water fish.
description: Please see the README document
 ("README_Dataset_PerchHighLatitudesIncreasedImportance.md")
 describing the data content and see the published article for description
 of methods used for collecting the data: Smalås, A., Primicerio, R.,
 Kahilainen, K., Terentyev, P., Kashulin, N., Zubova, E., &
 Amundsen, P. A. (2023). Increased importance of cool-water fish at high
 latitudes emerges from individual level responses to warming. Submitted to
 Ecology and Evolution.
description: The uploaded file(s) is a formatted as .csv files.
DOI: 10.5061/dryad.cnp5hqc95
title: The past, present, and future of ecogeographic isolation between closely related Aquilegia plants

description: Quantifying the strength of the ecogeographic barrier is an important
 aspect of studies of plant speciation and a practical step to
 understanding the evolutionary trajectory of plants under climate change.
 Here, we quantified the extent of ecogeographical isolation of four
 closely related Aquilegia species, which radiated in the Mountains of SW
 China and adjacent regions and often lacked intrinsic barriers. We
 predicted past, present and future species potential distributions using
 environmental niche models, then compared them to determine the degree of
 overlap and ecogeographic isolation. Investigated ecogeographical
 isolation between species pairs, we found significant ecological
 differentiation in all studied species pairs except A. kansuensis and A.
 ecalacarata. The current strengths of ecogeographic isolation are above
 0.5 in most cases. Compared with current climates, most species had an
 expanding range in the Last Glacial Maximum, the Mid Holocene and under
 four future climate scenarios. Our results suggested that ecogeographic
 isolation contributes to the diversification and maintenance of Aquilegia
 species in the Mountains of northern and SW China and would act as an
 essential reproductive barrier in the future.
description: Species occurrence data of
 each species were collected species occurrence
 from field investigations,
 references, the Chinese Virtual Herbarium (CVH; http://www.cvh.ac.cn/;),
 and the Global Biodiversity Information Facility (GBIF;
 https://www.gbif.org/). The occurrence records from the field
 investigation were collected from 2018 to 2020 under the joint efforts of
 our research team members. All
 occurrence records with
 incomplete data, duplicate records, ambiguous identification
 and irrational (on rivers, oceans, or out of range based on our knowledge) were
 removed from our datasets.
DOI: 10.5061/dryad.j6q573nk8
title: Data from: Human atlastin-3 is a constitutive ER fusion catalyst (lipid mixing data)

description: Homotypic membrane fusion catalyzed by the atlastin (ATL) GTPase sustains
 the branched endoplasmic reticulum (ER) network in metazoans. Our recent
 discovery that two of three human ATL paralogs (ATL1/2) are C-terminally
 autoinhibited implied that relief of autoinhibition would be integral to
 the ATL fusion mechanism. An alternative hypothesis is that the third
 paralog ATL3 promotes constitutive ER fusion with relief of ATL1/2
 autoinhibition used conditionally. However, published studies suggest ATL3
 is a weak fusogen at best. Contrary to expectations, we demonstrate here
 that purified human ATL3 catalyzes efficient membrane fusion in vitro and
 is sufficient to sustain the ER network in triple knockout cells.
 Strikingly, ATL3 lacks any detectable C-terminal autoinhibition, like the
 invertebrate Drosophila ATL orthologue. Phylogenetic analysis of
 ATL C-termini indicates that C-terminal autoinhibition is a recent
 evolutionary innovation. We suggest that ATL3 is a constitutive ER fusion
 catalyst and that ATL1/2 autoinhibition likely evolved in vertebrates as a
 means of upregulating ER fusion activity on demand.
description: For all assays, proteoliposomes were mixed with A100 buffer
 containing 5 mM MgCl<sub>2</sub> and then pre-incubated at
 37°C for 5 minutes in a 96-well plate. Following pre-incubation, the plate
 was placed in a Spark plate reader (Tecan), two baseline readings were
 taken, and then 2 mM GTP or A100 buffer of equal volume was added with a
 multichannel pipette. For 60 minutes NBD dequenching was monitored at
 10-second intervals (excitation at 460 nm, dequenching at 538 nm). Maximum
 possible dequenching was determined after 60 minutes via the addition of
 0.5% Anapoe X-100, with two more cycles read on the plate reader after
 Anapoe addition. F<sub>max</sub> was calculated by taking the
 average of these two post-Anapoe cycles. Fusion calculations were
 performed using the function: Fusion=((Fluorescence observed-Initial
 fluoresence observed)/Maximum fluorescence) x 100.
description: Microsoft Excel.
DOI: 10.5061/dryad.7pvmcvdzq
title: Data from: Complex cross incompatibility in morning glories is consistent with a role for mating system in plant speciation

description: Reproductive isolation between selfing and outcrossing species can arise
 through diverse mechanisms, some of which are directly associated with
 differences in mating system. We dissected cross incompatibility between
 the highly selfing morning glory Ipomoea lacunosa and its mixed-mating
 sister species I. cordatotriloba. We found that cross incompatibility is
 complex, with contributions acting both before and after fertilization. We
 then investigated whether the transition in mating system may have
 facilitated the evolution of these reproductive barrier components through
 mismatched floral morphology, differences in reproductive context, or
 both. We found evidence that morphological mismatch likely contributes to
 reproductive isolation in at least one cross direction and that other
 pollen-pistil interactions are present. We also identified hybrid seed
 inviability consistent with the predictions of the weak-inbreeder,
 strong-outbreeder hypotheses, suggesting endosperm misregulation plays an
 important role in cross incompatibility. In contrast, we did not find
 evidence consistent with the pre-zygotic weak-inbreeder, strong-outbreeder
 hypothesis. Our study highlights the complexity of reproductive isolation
 between outcrossing and selfing species and the extent to which
 evolutionary consequences of mating system transitions can facilitate
 speciation.
description: Please see the methods of our manuscript and the README files
 associated with each dataset for these details. 
description: The data files are a combination of .csvs and .txt files. Data
 analyses done using R version 4.0.3, and you can see the renv.lock file
 for all the R programs we used.
DOI: 10.5061/dryad.83bk3j9x1
title: Sensitivity of different grass functional groups to honey mesquite

description: Quantifying the relationship of different grass functional groups to
 increasing woody plant cover is necessary to better understand the effects
 of woody plant encroachment on grasslands. This study explored biomass
 production responses of three perennial grass groups based on
 photosynthetic pathway and potential canopy height (C4 short-grasses, C3
 mid-grasses and C4 mid-grasses) to different percent canopy covers of the
 surrounding deciduous woody legume, honey mesquite (Prosopis glandulosa).
 Two methods were used to determine mesquite canopy cover, line-intercept
 and geospatial analysis of aerial images, and both were used to predict
 production of the 3 grass groups. Five years of grass production data were
 included in the mesquite cover/grass production regressions. Two years had
 extreme grass production responses, one due to drought and the other to
 high rainfall. Of the 3 remaining years, best-fit curves were negative
 linear for C4 short-grasses and C3 mid-grasses, and negative sigmoidal for
 C4 mid-grasses using both cover determination methods, although slopes of
 the curves differed between cover determination methods. C4 mid-grasses
 were more sensitive than the other grass groups to increasing mesquite
 cover. Loss of production potential when mesquite cover increased from
 0–35% was 75.5, 28.7 and 23.2% for C4 mid-grasses, C3 mid-grasses and C4
 short-grasses, respectively. Moreover, production potential of C4
 mid-grasses under no mesquite cover was 3 and 6 times greater than C3
 mid-grasses or C4 short-grasses, respectively. Spatial settings of the
 different grass groups in relation to mesquite tree size and size of
 intercanopy areas provided indirect evidence that the process of mesquite
 encroachment in the last 50 to 100 years may have negatively impacted C4
 mid-grasses more than the other grass groups. Results suggest that gains
 in grass production following mesquite treatment would be limited if the
 system has degraded to where only C3 mid-grasses and C4 short-grasses
 dominate.
description: Combination of data collected in the fiedl as well as analysis of
 aerial images of the research site.
description: These are all Excel spreadsheets.
DOI: 10.5061/dryad.dr7sqvb3k
title: Anthropogenic disturbance driving population decline of a dominant tree in East Asia evergreen broadleaved forests over the last 11,000 years

description: Current biodiversity loss was generally considered to be caused by
 anthropogenic disturbance, but when anthropogenic activities began to
 impact biodiversity loss is still controversial. One hypothesis suggested
 it was from the industrial era, while others proposed that the
 anthropogenic disturbance had already resulted in biodiversity decline
 since the Early Holocene. To test these hypotheses, we focus on
 subtropical East Asia, which has witnessed a land use and anthropogenic
 history since the Early Holocene. We selected the unique vegetation of
 evergreen broadleaved forests (EBLFs), using a genomic approach to infer
 the demographic history of a dominant plant (Litsea elongata) of EBLFs,
 and to further detangle the impact of climate change and/or anthropogenic
 disturbance on effective population size fluctuation. Nine well-defined
 geographical clades were identified within extant populations of L.
 elongata. The estimated historical population sizes of these clades all
 contracted, indicating persistent population decline over the last 11,000
 years. Significant correlation was detected between demographic history
 and three anthropogenic disturbance factors, rather than the climate
 change in the Holocene. Therefore, we provided the dataset used for
 phylogenomic analysis,  demographic history inference, and
 correlation analysis in this study.
DOI: 10.5061/dryad.stqjq2c7k
title: Supporting data for: Physical controls and ecological implications of the timing of the spring phytoplankton bloom on the Newfoundland and Labrador shelf

description: The Newfoundland and Labrador (NL) shelf and the Grand Banks of
 Newfoundland have been known as iconic fishing areas for centuries. In
 such areas with seasonal sea ice coverage, the timing of the spring bloom
 has been linked to sea ice melting, which stratifies the water column and
 promotes favorable conditions for phytoplankton to grow and accumulate.
 With sea ice gradually disappearing, we revisited the physical drivers
 controlling the initiation of the spring bloom in the region. We found
 that the timing of the phytoplankton bloom on the Grand Banks corresponds
 to the timing of ocean re-stratification following winter mixing. We also
 found that large-scale climate indicators are good proxies for the timing
 of the bloom and the abundance of Calanus finmarchicus, a key zooplankton
 species for the ecosystem. By revealing links between physical and
 biological processes, this work paves the way for an improved ecosystem
 approach to fisheries management.
DOI: 10.5061/dryad.3ffbg79pj
title: Spot test and spore count assay data for combinations of dictyostelid hosts infected by Paraburkholderia spp.

description: The social amoeba Dictyostelium discoideum engages in a complex
 relationship with bacterial endosymbionts in the genus Paraburkholderia,
 which can benefit their host by imbuing it with the ability to carry prey
 bacteria throughout its life cycle.  The relationship between D.
 discoideum and Paraburkholderia has been shown to take place across many
 strains and a large geographical area, but little is known about
 Paraburkholderia’s potential interaction with other dictyostelid
 species.  We explore the ability of three Paraburkholderia
 species to stably infect and induce bacterial carriage in other
 dictyostelid hosts. We found that all three Paraburkholderia species
 successfully infected and induced carriage in seven species of
 Dictyostelium hosts.  While the overall behavior was
 qualitatively similar to that previously observed in infections of D.
 discoideum, differences in the outcomes of different host/symbiont
 combinations suggest a degree of specialization between
 partners.  Paraburkholderia was unable to maintain a stable
 association with the more distantly related host Polysphondylium
 violaceum.  Our results suggest that the mechanisms and
 evolutionary history of Paraburkholderia’s symbiotic relationships may be
 general within Dictyostelium hosts, but not so general that it can
 associate with hosts of other genera.  Our work further develops
 a emerging model system for the study of symbiosis in microbes.
description: Excel or similar.
DOI: 10.5061/dryad.sn02v6x8j
title: Limiting scaring activities reduces economic costs associated with foraging barnacle geese: results from an individual-based model

description: With increasing numbers of large grazing birds on agricultural grassland,
 conflict with farmers is rising. One management approach to alleviate
 conflict allows foraging on dedicated agricultural land (accommodation
 areas) and nature reserves, combined with scaring on remaining
 agricultural land. Here, we examine the cost-effectiveness of these
 measures by studying the influence on barnacle goose distribution and
 associated economic damage. We present an individual/agent-based model of
 barnacle geese (Branta leucopsis) foraging on grasslands in Fryslân, the
 Netherlands. The model is parameterized using field observations and
 GPS-tracks and allows simulation of management scenarios, differing in
 scaring probability and accommodation area size, with different potential
 management costs.  Our model shows that, while yield loss
 decreases with higher scaring probabilities, costs of damage appraisal
 increase because geese graze on more fields. With small accommodation
 areas, achieving high scaring probabilities takes more effort and could
 result in goose population decline. Total management costs are lowest
 without scaring activity.  Synthesis and applications:
 Considering costs of active scaring and the need to maintain the barnacle
 goose population in a favourable conservation status, our model suggests
 that the most cost-effective scenario is to prevent disturbance of geese.
 A high scaring probability could be beneficial if applied in small areas,
 for example around sensitive crops or airfields. Scaring in large areas
 could result in costs outweighing benefits and a declining barnacle goose
 population.
description: This dataset was generated using an individual-based model. The
 model is also included in this Dryad data collection. 
description: The dataset is in Excel format, in order to have a tab with
 metadata on top of the actual dataset. The C++ model was created in Visual
 Studio. Data can be analysed using R, as we have done as well.