cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r4xgxd2cw
title: The locus tags and annotation in Serratia plymuthica UBCF_13 genome

description: Background: The Serratia plymuthica UBCF_13 is a phylloplane associated
 plant bacterium showing antifungal activity. Whole genome sequence
 provides information to get more insight about evolutionary study, unique
 traits in the genome and possibility to explore potential of this
 microorganism for future study. Here, we report the genome sequence of S.
 plymuthica UBCF_13 and the comparison with other seventeen strain.
 Methods: Continuous short reads were attained from Illumina sequencing
 runs and reads of 150 bp were merged into a single dataset. A pan-genome
 based method was used to identify the core-genome of S. plymuthica species
 and the unique gene in UBCF-13. Results: Assembled Illumina reads of S.
 plymuthica strain UBCF_13 genome was produced a 5.46 Mb circular genome
 sequence. 3315 genes were found to belong to the core-genome sheared by
 the 18 strains evaluated. The UBCF_13 genome harbors 488 unique genes,
 where 300 of which only can be found in this strain. The raw and assembled
 data is available via NCBI Short Read Archive (accession Number:
 SRR15012717) and genome database (accession number: CP068771)
DOI: 10.5061/dryad.m63xsj42h
title: Data from: Pyrophilic plants respond to post-fire soil conditions in a frequently burned longleaf pine savanna

description: Fire-plant feedbacks engineer recurrent fires in pyrophilic ecosystems
 like savannas. The mechanisms sustaining these feedbacks may be related to
 plant adaptations that trigger rapid responses to fire’s effects on soil.
 Plants adapted for high fire frequencies should quickly regrow, flower,
 and produce seeds that mature rapidly and disperse post-fire. We
 hypothesized that offspring of such plants would germinate and grow
 rapidly, responding to fire-generated changes in soil nutrients and biota.
 We conducted an experiment using longleaf pine savanna plants that were
 paired based on differences in reproduction and survival under annual
 (“more” pyrophilic) vs. less frequent (“less” pyrophilic) fire regimes.
 Seeds were planted in different soil inoculations from experimental fires
 of varying severity. The “more” pyrophilic species displayed high
 germination rates followed by species specific, rapid growth responses to
 soil location and fire severity effects on soils. In contrast, the “less”
 pyrophilic species had lower germination rates that were not responsive to
 soil treatments. This suggests that rapid germination and growth
 constitute adaptations to frequent fires, and that plants respond
 differently to fire severity effects on soil abiotic factors and microbes.
 Further, variable plant responses to post-fire soils may influence plant
 community diversity and fire-fuel feedbacks in pyrophilic ecosystems.
DOI: 10.5061/dryad.34tmpg4kt
title: Pontocaspian habitat polygon shapefiles from: Decline of unique Pontocaspian biodiversity in the Black Sea Basin: a review

description: The unique aquatic Pontocaspian (PC) biota of the Black Sea Basin (BSB) is
 in decline. The lack of detailed knowledge on the status and trends of
 species, populations and communities hampers a thorough risk assessment
 and precludes effective conservation. This paper  reviews PC
 biodiversity trends in the BSB ( Bulgaria, Romania, Moldova, Ukraine and
 Russia) using endemic molluscs as a model group. We aim to assess changes
 in PC habitats, community structure and species distribution over the past
 century and to identify direct anthropogenic
 threats. Presence/absence data of target mollusc species was
 assembled from literature, reports and personal observations. Pontocaspian
 biodiversity trends in the north-western BSB coastal regions were
 established by comparing 20th and 21st century occurrences. Direct drivers
 of habitat and biodiversity change were identified and documented. A
 pronounced decline of PC species and communities is driven by a) damming
 of rivers, b) habitat modifications that disturbed previous natural
 salinity gradients and settings in the studied area c) pollution and
 eutrophication, d) invasive alien species and e) climate change. Four out
 of the 10 studied regions, namely, the Danube Delta – Razim Lake system,
 Dniester Liman, Dnieper-Bug Estuary and Taganrog Bay-Don Delta contain the
 entire spectrum of ecological conditions to support PC communities and
 still host threatened endemic PC mollusc species. Distribution data is
 incomplete, but the scale of deterioration of PC species and communities
 is evident from the assembled data, as are major direct threats.
 Pontocaspian biodiversity in the BSB is profoundly affected by human
 activities. Standardised observation and collection data as well as
 precise definition of PC biota and habitats are necessary for targeted
 conservation actions. This study will help to set the research and policy
 agenda required to improve data collection to accommodate effective
 conservation of the unique PC biota.
description: Freshwater habitat polygons were retreived from the HydroLAKES
 dataset (https://www.hydrosheds.org/pages/hydrolakes) to map the
 Pontovaspian (PC) habitats in the Black Sea Basin (BSB) using QGIS 3.10 “A
 Coruña”. Those polygons that did not cover the PC habitats, such as swamps
 and marshes, were manually edited based on published literature and expert
 knowledge. Lagoons and bays of Pontocaspian habitats, which are not part
 of the HydroLAKES dataset were also manually drawn based on published
 accounts and expert knowledge. Given the densely aggregated small lakes in
 the Danube Delta with surface areas lesser than 0.2
 km<sup>2</sup> we merged the Chilia branch of the Danube River
 and outer delta lakes both upstream and downstream of Vilkovo.
description: The dataset can be opened and used via Geographic Information
 Systems, such as ArcGIS or Qgis.
DOI: 10.57841/casdc.0007106
title: 铁基多芯长线制备分析
DOI: 10.15468/dl.3zdexz
title: Occurrence Download

description: A dataset containing 19895 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lupinus texensis",
 "Year 1000-2026"
 ]
}

 The dataset includes 19895 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002899-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.15dv41nxt
title: Molecular signatures of resource competition: Clonal interference favors ecological diversification and can lead to incipient speciation

description: Microbial ecosystems harbor an astonishing diversity that can persist for
 long times. To understand how such diversity is structured and maintained,
 ecological and evolutionary processes need to be integrated at similar
 timescales. Here, we study a model of resource competition that allows for
 evolution via de novo mutation, and focus on rapidly adapting asexual
 populations with large mutational inputs, as typical of many bacteria
 species. We characterize the adaptation and diversification of an
 initially maladapted population and show how the eco-evolutionary dynamics
 are shaped by the interaction between simultaneously emerging lineages –
 clonal interference. We find that in large populations, more intense
 clonal interference can foster diversification under sympatry, increasing
 the probability that phenotypically and genetically distinct clusters
 coexist. In smaller populations, the accumulation of deleterious and
 compensatory mutations can push further the diversification process and
 kick-start speciation. Our findings have implications beyond microbial
 populations, providing novel insights about the interplay between ecology
 and evolution in clonal populations.
description: The dataset has been produced via numerical simulations. These
 were performed on R with the script in "Amicone_EcoEvo_Code.R"
 following the model and assumptions described in the paper (Amicone
 & Gordo 2021).
description: The code parameters can be customized. Change the corresponding
 values in lines 9-30. The simulation will then produce
 data files that can be further analysed with the script in
 "Amicone_EcoEvo_Analysis.R". See the
 corresponding README.txt file for more info about the code and the
 dataset.
DOI: 10.5061/dryad.w3r2280rb
title: Strolling through a century: replicating historical bird surveys to explore 100 years of change in an urban bird community

description: In 1898, Herbert and Alice Walter started a 5-year survey of birds in
 Lincoln Park, – the largest park in Chicago, IL – and summarized their
 data in an urban birding field guide, ‘Wild Birds in City Parks’.
 Twenty-nine years later, William Dreuth compared the relative frequency of
 species between the Walter’s study to their own 5-year Lincoln Park
 survey. Between 2012 and 2015, we replicated these surveys to investigate
 a century of bird diversity and community composition change in urban
 Chicago. While species richness did not change, community composition did.
 We found that 1) species with a greater diet breadth and 2) species that
 increased in statewide occupancy were more likely to increase in frequency
 over time. We conclude that factors at multiple scales brought temporal
 changes to Chicago’s bird community. Overall, this survey highlights the
 slow and subtle ways in which species may respond to a century of urban
 intensification.
description: Instructions on how the dataset was collected can be found
 in: Fidino, M., Bender, J., Limbrick, K., Gallo, T.,
 and Magle, S. B. Strolling through a century: recreating historical bird
 surveys to explore 100 years of change in an urban bird community.
 T<em>he American Naturalist.</em> Data was
 cleaned and analyzed in R and is stored on Zenodo. Both data and code can
 be found in Fidino (2021). Fidino, M. (2021).
 mfidino/historic_birds: zenodo_retry (v1.1) [Computer software].
 Zenodo. https://doi.org/10.5281/ZENODO.4916872. If you would like to see the readMe file for the zenodo repository rendered, you can see the same code on GitHub at: https://github.com/mfidino/historic_birds
description: See dryad_readme.pdf for details.
DOI: 10.5061/dryad.qbzkh18hh
title: Data from: Crop health is predicted by soil microbial diversity across phylogenetic scales

description: Soils contain diverse living communities that provide key ecosystem
 functions in agroecosystems. In many systems, ecosystems functions are
 positively related to the taxonomic, phylogenetic, and functional
 diversity of the community. Despite calls to incorporate microbial
 diversity in measures of soil health, whether increased microbial
 diversity per se can predict increased crop health and productivity has
 rarely been documented. Here we used microbial communities from commercial
 potato fields varying in diversity and composition, and experimentally
 assessed their ability to promote crop yield under low or high nutrient
 conditions and to suppress a soil-borne pathogen. Across two independent
 sets of communities, we found that yields under low nutrient conditions
 were predicted by high initial microbial diversity measured at broad
 phylogenetic levels, consistent with greater niche complementarity among
 unrelated taxa leading to greater total resource use. However, disease
 suppression was inconsistently linked to diversity and explained as well
 or better by microbial composition rather than diversity per se. Ecosystem
 multifunctionality was predicted by high diversity at broad to
 intermediate phylogenetic scales. These results indicate that the
 diversity of microbial taxa may influence multiple soil functions;
 however, the mechanisms underlying the diversity-function relationships
 may vary.
DOI: 10.5061/dryad.s7h44j174
title: Expert-based assessment of rewilding indicates progress at site-level, yet challenges for upscaling

description: Rewilding is gaining importance across Europe, as agricultural abandonment
 trajectories provide opportunities for large-scale ecosystem restoration.
 However, its effective implementation is hitherto limited, in part due to
 a lack of monitoring of rewilding interventions and their interactions.
 Here, we provide a first assessment of rewilding progress across seven
 European sites. Using an iterative and participatory Delphi technique to
 standardize and analyze expert-based knowledge of these sites, we 1) map
 rewilding interventions onto the three central components of the rewilding
 framework (i.e., stochastic disturbances, trophic complexity and
 dispersal), 2) assess rewilding progress by quantifying 19 indicators
 spanning human forcing and ecological integrity, and 3) compile key
 success and threat factors for rewilding progress. We find that the most
 common interventions were keystone species reintroductions, whereas the
 least common targeted stochastic disturbances. We find that rewilding
 scores have improved in five sites, but declined in two, partly due to
 competing socio-economic trends. Major threats for rewilding progress are
 related to land-use intensification policies and persecution of keystone
 species. Major determinants of rewilding success are its societal appeal
 and socio-economic benefits to local people. We provide an assessment of
 rewilding that is crucial in improving its restoration outcomes and
 informed implementation at scale across Europe in this decade of ecosystem
 restoration.
DOI: 10.5061/dryad.bg79cnpbg
title: Reservoir dynamics of rabies in Southeast Tanzania and the roles of cross-species transmission and domestic dog vaccination

description: Understanding the role of different species in the transmission of
 multi-host pathogens, such as rabies virus, is vital for effective control
 strategies. Across most of sub-Saharan Africa domestic dogs (Canis
 familiaris) are considered the reservoir for rabies, but the role of
 wildlife has been long debated. Here we explore the multi-host
 transmission dynamics of rabies across southeast Tanzania. Between January
 2011 and July 2019 data on probable rabies cases were collected in the
 regions of Lindi and Mtwara. Hospital records of animal-bite patients
 presenting to healthcare facilities were used as sentinels for animal
 contact tracing. The timing, location and species of probable rabid
 animals was used to reconstruct transmission trees to infer who infected
 whom and the relative frequencies of within- and between-species
 transmission. During the study, 688 probable human rabies exposures were
 identified, resulting in 47 deaths. Of these exposures, 389 were from
 domestic dogs (56.5%) and 262 from jackals (38.1%). Over the same period
 549 probable animal rabies cases were traced: 303 in domestic dogs (55.2%)
 and 221 in jackals (40.3%). Although dog-to-dog transmission was most
 commonly inferred (40.5% of transmission events), a third of inferred
 events involved wildlife-to-wildlife transmission (32.6%) and evidence
 suggested some sustained transmission chains within jackal populations. A
 steady decline in probable rabies cases in both humans and animals
 coincided with the implementation of widespread domestic dog vaccination
 during the first six years of the study. Following the lapse of this
 programme dog rabies cases began to increase in one of the northernmost
 districts. Synthesis and applications: In southeast Tanzania, despite a
 relatively high incidence of rabies in wildlife and evidence of
 wildlife-to-wildlife transmission, domestic dogs remain essential to the
 reservoir of infection. Continued dog vaccination alongside improved
 surveillance would allow a fuller understanding of the role of wildlife in
 maintaining transmission in this area. Nonetheless, dog vaccination
 clearly suppressed rabies in both domestic dog and wildlife populations,
 reducing both public health and conservation risks and, if sustained, has
 potential to eliminate rabies from this region.
description: This dataset contains code and data to reproduce the analyses in
 the paper, however sensitive data (GPS locations and other identifiers)
 have been removed. Full methods are detailed in the paper.
description: All data files are in CSV format and analysis files are provided
 as R scripts. Identifying features such as names and GPS coordinates have
 been removed. See README for more information.
DOI: 10.5061/dryad.f1vhhmgxh
title: Dendritic prioritization through spatial stream network modeling informs targeted management of Himalayan riverscapes under brown trout invasion

description: With the concept of ‘riverscapes’ long pending to be acknowledged in the
 ‘landscape-centric’ legislative framework of Himalayan nations,
 conservation of native riverine species stays practically unheeded. This
 necessitates urgent prioritization of stream networks to conserve the
 lotic taxa under invasion pressures. Himalayan riverscapes are pervaded
 with the invasive-exotic brown trout Salmo trutta, posing serious threats
 to the co-occurring native, the snow trout Schizothorax richardsonii.
 Using intensive surveys (218.7km) and geostatistical stream network models
 (n=537), we contrasted snow trout in two stream networks with and without
 invasives, for assessing differences in their spatial distribution. Our
 models indicate invasion-induced relegations of natives from the river
 mainstem into headwaters, with large sections of mainstem occupied by
 invasives. Furthermore, a concerningly small percentage of potential
 habitat left for natives to occupy in the mainstem is threatened, where a
 100% overlap of native and invasive trout distributions is predicted. With
 a higher presence probability for the natives in headwaters of invaded
 watershed as compared to the non-invaded watershed, we highlight the
 headwater streams as potential refugia for the natives under invasion.
 Synthesis and Applications: Our approach of basin-scale dendritic
 prioritization provides immediate management solutions to tackle brown
 trout invasion threats in Himalaya. We inform decisions on delineation of
 headwaters as invasion refugia for native fish, with assisted recovery of
 their fragmented populations in the river mainstems through targeted
 management of invasives
description: The dataset is collected through field surveys and yearly
 samplings across two watersheds. The data has been processed using ArcGIS
 and R. All the data has been made available in spatial format for easy
 reproducibility.
description: The data is provided as Landscape Network (lsn.ssn) objects,
 which contain the spatial files for the predictions as well as the
 occurrences.
DOI: 10.5061/dryad.q83bk3jj7
title: Pervasive admixture and the spread of a large-lipped form in a cichlid fish radiation

description: Adaptive radiations have proven important for understanding the mechanisms
 and processes underlying biological diversity. The convergence of form and
 function, as well as admixture and adaptive introgression, are common in
 adaptive radiations. However, distinguishing between these two scenarios
 remains a challenge for evolutionary research. The Midas cichlid species
 complex (Amphilophus spp.) is a prime example of adaptive radiation, with
 phenotypic diversification occurring at various stages of genetic
 differentiation. One species, A. labiatus, has large fleshy lips, is
 associated with rocky lake substrates, and occurs patchily within Lakes
 Nicaragua and Managua. By contrast, the similar, but thin-lipped,
 congener, A. citrinellus, is more common and widespread. We investigated
 the evolutionary history of the large-lipped form, specifically regarding
 whether the trait has evolved independently in both lakes from ancestral
 thin-lipped populations, or via dispersal and/or admixture events. We
 collected samples from distinct locations in both lakes, and assessed
 differences in morphology and ecology. Using RAD-seq, we genotyped
 thousands of SNPs to measure population structure and divergence,
 demographic history, and admixture. We found significant between-species
 differences in ecology and morphology, local intraspecific differences in
 body shape and trophic traits, but only limited intraspecific variation in
 lip shape. Despite clear ecological differences, our genomic approach
 uncovered pervasive admixture between species and low genomic
 differentiation, with species within lakes being genetically more similar
 than species between lakes. Taken together, our results suggest a single
 origin of large-lips, followed by pervasive admixture and adaptive
 introgression, with morphology being driven by local ecological
 opportunities, despite on-going gene-flow.
DOI: 10.5061/dryad.qrfj6q5gg
title: Larger guts and faster growth in mice selected for high basal metabolic rate

description: Postnatal growth in birds and mammals is the time of highest vulnerability
 and relatively high energy demands and therefore shapes the organisms
 future outcomes. Several different factors might impose limitations on
 growth in juveniles, one of them being the efficiency of the digestive
 process and size of the gastrointestinal tract. We tested the gut
 size-growth rate relationship using a unique experimental model - mice
 from a selection experiment designed to produce two lines with divergent
 levels of basal metabolic rate (BMR): the high BMR (H-BMR) and low BMR
 line type (L-BMR). These lines differ not only with respect to BMR, but
 also correlated traits—internal organ size and food intake. Applying a
 cross-fostering design and a thermoregulatory burden imposed by shaving
 the mothers, demonstrated that the mass of intestine strongly affected the
 growth rate, with the H-BMR pups having larger intestines and growing
 fastest, and reduced growth rate of pups of both lines nursed by shaved
 L-BMR mothers. Our study also provides a functional link between high
 growth rate of neonates and high BMR of adults, partly reflecting
 metabolic costs of maintenance of their guts.
DOI: 10.5061/dryad.b5mkkwhdn
title: Linking micro and macroevolution of head shape in an island radiation

description: Phenotypic traits have been shown to evolve in response to variation in
 the environment. However, the evolutionary processes underlying the
 emergence of phenotypic diversity can typically only be understood at the
 population level. Consequently, how subtle phenotypic differences at the
 intraspecific level can give rise to larger-scale changes in performance
 and ecology remains poorly understood. We here tested for the covariation
 between ecology, bite force, jaw muscle architecture, and the
 three-dimensional shape of the cranium and mandible in 16 insular
 populations of the lizards Podarcis melisellensis and P. sicula. We then
 compared the patterns observed at the among-population level with those
 observed at the interspecific level. We found that three-dimensional head
 shape as well as jaw musculature evolve similarly under similar ecological
 circumstances. Depending on the type of food consumed or on the level of
 sexual competition, different muscle groups were more developed and
 appeared to underlie changes in cranium and mandible shape. Our findings
 show that the local selective regimes are primary drivers of phenotypic
 variation resulting in predictable patterns of form and function.
 Moreover, intraspecific patterns of variation were generally consistent
 with those at the interspecific level, suggesting that microevolutionary
 variation may translate into macroevolutionary patterns of
 ecomorphological diversity.
description: In-vivo bite force, diet and intrapopulation competition levels
 were investigated throughout 16 insular and mainland populations of
 <em>Podarcis</em> lizards. Data was acquired on the field and
 animals released, although 5 females and 5 males of each population were
 sacrificed, fixed in formalin and CT scanned. Their jaw musculature was
 then dissected to quantify variation in muscle architecture. The scans
 were used to reconstruct cranial and mandible 3D surface which were
 subsequently analysed with geometric morphometrics approach.