cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7pvmcvdqt
title: Contrasting influences on bacterial symbiont specificity by co-occurring deep-sea mussels and tubeworms

description: Relationships between deep-sea invertebrates and bacterial symbionts,
 fueled by sulfide and methane, are well known, yet factors influencing
 symbiont specificity remain cryptic. For animals that obtain their
 symbionts from the environment, both host identity and geographic location
 can impact the ultimate symbiont partner. Bacterial symbionts were
 analyzed for 3 co-occurring species each of Bathymodiolus mussels and
 vestimentiferan tubeworms, from three deep methane seeps off the west
 coast of Costa Rica. The bacterial internal transcribed spacer gene was
 analyzed via direct and barcoded amplicon sequencing to reveal fine-scale
 symbiont diversity. Each of the three mussel species (B. earlougheri, B.
 billschneideri and B. nancyschneideri) hosted genetically-distinct
 thiotrophic endosymbionts, despite living nearly side-by-side in their
 habitat, suggesting that host identity is influential in driving symbiont
 specificity. The dominant thiotrophic symbiont of co-occurring tubeworms
 Escarpia spicata and Lamellibrachia (L. barhami and L. donwalshi), on the
 other hand, was identical regardless of host species or sample location,
 suggesting lack of influence by either factor on symbiont selectivity in
 this group of animals. These findings highlight the specific, yet
 distinct, influences on the environmental acquisition of symbionts in two
 foundational invertebrates with similar lifestyles, and provide a rapid
 and precise method of examining symbiont identities.
description: Three co-occurring mussel species (<i>B. earlougheri, B.
 billschneideri </i>and<i> B. nancyschneideri</i>) and
 co-occurring vestimentiferans, <i>Escarpia spicata </i>and two
 species of <i>Lamellibrachia (L. barhami
 </i>and<i> L. donwalshi), </i>were sampled
 from three methane seep sites in 2017 and 2018 ranging from
 990m-1742 m depth off the west coast of Costa Rica
 (Quepos Seep, Mound 12, Jaco Scar). Mound 12 (8° 55.794N / 84° 18.780W),
 Jaco Scar (9° 7.071N / 84° 50.445W), and Quepos Seep (9° 1.904N / 84°
 37.294W).  Total genomic DNA was extracted from
 symbiont-bearing tissues using the Qiagen DNeasy kit (Qiagen, Valencia,
 CA, USA) according to the manufacturer’s instructions. A ~400bp region of
 the ITS gene was amplified using primers with Illumina adapters on the 5′
 end Sym-ITS-1322F
 (5′- TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTTGGAATCGCTAGTAATCG-3′) and Sym-ITS-356R (5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACCAGGCCGACAACGCAGT-3′; according to Won et al. 2003), and an annealing temperature of 54°C for 25 cycles, and further following the details in Goffredi et al. 2020. Data was processed in Quantitative Insights Into Microbial Ecology (v1.8.0) Direct 16S rRNA sequencing was accomplished using the 27F-1492R primer pair. Direct ITS sequencing was accomplished using the Sym-ITS-1322F / Sym-ITS-356R primer pair without the Illumina adapters (underlined above).
DOI: 10.5061/dryad.gqnk98sjz
title: Shell biomass material supported nano-zero valent iron to remove Pb2+ and Cd2+ in water

description: Nanoscale zero-valent iron (NZVI) has a high adsorption capacity for heavy
 metals, but easily forms aggregates. Herein, preprocessed undulating venus
 shell (UVS) is used as support material to prevent NZVI from reuniting.
 The SEM and TEM results show that UVS had a porous layered structure and
 NZVI particles were evenly distributed on the UVS surface. A large number
 of adsorption sites on the surface of UVS-NZVI are conﬁrmed by IR and XRD.
 UVS-NZVI is utilized for adsorption of Pb2+ and Cd2+ at pH=6 in aqueous
 solution, and the experimental adsorption capacities are 29.91 mg•g-1 and
 38.99 mg•g-1 at optimal pH, respectively. Thermodynamic studies indicate
 that the adsorption of ions by UVS-NZVI is more in line with the Langmuir
 model when Pb2+ or Cd2+ existed alone. For the mixed solution of Pb2+ and
 Cd2+, only the adsorption of Pb2+ by UVS-NZVI conforms to the Langmuir
 model. In addition, the maximum adsorption capacities of UVS-NZVI for Pb2+
 and Cd2+ are 93.01 mg•g-1 and 46.07 mg•g-1.Kinetic studies demonstrate
 that the determination coefficients (R2) of the pseudo first-order kinetic
 model for UVS-NZVI adsorption of Cd2+ and Pb2+ are higher than those of
 the pseudo second-order kinetic model and Elovich kinetic model. Highly
 efficient performance for metal removal makes UVS-NZVI show potential
 application to heavy metal ion adsorption.
DOI: 10.5061/dryad.kwh70rz1t
title: Evolutionary history and eco-climatic diversification in southern African Sisyphus (Coleoptera: Scarabaeidae: Scarabaeinae)

description: Aim: The high diversity of species in southern Africa has been attributed
 to geological and palaeoclimatic factors. The timing of radiations in some
 groups is held to be linked to these geoclimatic trends. Using the
 Scarabaeinae dung beetle genus, Sisyphus, as a model system, we
 investigate how geological uplift and climatic changes in the late
 Cenozoic affected its diversification patterns in southern Africa.
 Location: southern Africa. Taxon: The dung beetle genus, Sisyphus
 Latreille, 1807 (Coleoptera: Scarabaeidae: Scarabaeinae). Methods: A dated
 molecular phylogeny of southern African Sisyphus was compared with a
 factor analysis of species distribution data that statistically defined
 groups of species according to current climatic distribution. We used
 these climatic clusters to estimate ancestral ranges using the
 ‘BioGeoBEARS’ R package. A lineage through time plot was calculated using
 the R package ‘APE’. We used Bayesian diversification models (compound
 Poisson process on mass extinction times) to test hypotheses on how late
 Cenozoic uplift and climatic changes affected speciation and extinction of
 Sisyphus. Furthermore, we implemented ecological niche modelling in MaxEnt
 to predict the habitat suitability of species under present climatic
 conditions. Results: Four species groups defined from factor analysis of
 current climatic distribution data are primarily restricted to the moist
 summer rainfall region in the northeast. These groups comprise 10 warm,
 eastern lowland species; eight eastern savannah species; five cool,
 eastern highland species; and just two southwestern low rainfall species.
 Chronology of the phylogeny suggests that species diversification occurred
 from the mid-Miocene until the Pleistocene, during which the central
 southern African plateau was uplifted in tandem with the advent of winter
 rainfall and arid climatic zones to the southwest. The estimation of
 ancestral ranges suggests that the ancestor of Sisyphus was centred in
 eastern low to mid-altitude areas. The diversification model shows no
 evidence of an increase in extinction rate during the late Cenozoic uplift
 and climatic changes. The speciation rates were constantly higher in the
 Miocene to Pliocene, followed by a dramatic drop in speciation rates
 during the transition to the Pleistocene. Modelling of habitat suitability
 of current species ranges supports the eastern trends in distribution
 patterns. Main conclusions: The taxonomic and eco-climatic diversification
 of sisyphines is coincident with geological uplift and changes in climate
 in east-central southern Africa. However, phylogenetic relationships of
 southern African Sisyphus species are not homogenously distributed with
 respect to geography and climate.
DOI: 10.5061/dryad.tb2rbnzxv
title: Amplitude modulations of cortical sensory responses in pulsatile evidence accumulation

description: Condensed neural and behavioral data, included secondary results from
 model fits and analyses. This dataset contains all information required to
 recreate figures from the paper.
description: Transgenic mice expressing the calcium-sensitive fluorescent
 indicator GCamp6f were trained in the Accumulating Towers task and
 two-photon calcium imaging was performed of functionally identified
 primary and secondary visual cortical areas, as well as retrosplenial
 cortex. Regions of interest representing putative single neurons were
 extracted using a semi-customized demixing and deconvolution procedure.
 Behavioral data were separately collected by a computer that ran a virtual
 reality control engine, and synchronized with imaging data via a
 synchronization timestamp sent to the imaging computer at every graphics
 refresh cycle.
DOI: 10.5061/dryad.573n5tb52
title: Data from: The effects of competition on fitness depend on the sex of both competitors

description: In intraspecific competition, the sex of competing individuals is likely
 to be important in determining the consequences of competition, both for
 the immediate outcome of competitive interactions, and for long-term
 effects of competition during development on adult fitness traits.
 Previous studies have explored differences between males and females in
 their response to intraspecific competition. However, few have tested how
 the sex of the competitors, or any interactions between focal and
 competitor sex, influence the nature and intensity of competition. We set
 up larval seed beetles Callosobruchus maculatus to develop either alone or
 in the presence of a male or female competitor, and measured a suite of
 traits: development time, emergence weight; male ejaculate mass,
 copulation duration and lifespan; and female lifetime fecundity, offspring
 egg-adult survival and lifespan. We found effects of competition and
 competitor sex on the development time and emergence weight of both males
 and females, and also of an interaction between focal and competitor sex:
 females but not males responded differently to competitor sex. There was
 little effect of larval competition on male and female adult fitness
 traits, with the exception of the effect of a female competitor on a focal
 female’s offspring survival rate. Our results highlight the importance of
 directly measuring the effects of competition on fitness traits, rather
 than distant proxies for fitness, and suggest that competition with the
 sex with the greater resource requirements (here females) might have a
 strong effect in driving trait evolution. We also found that male-male
 competition during development resulted in shorter copulation times than
 male-female competition, a result that remained when controlling for the
 weight of competitors. Although it is difficult to definitively tease
 apart the effects of social environment and access to resources, this
 result suggests that something about the sex of competitors other than
 their size is driving this pattern.
description: Details of data collection methods and data analysis can be found
 in the paper associated with this data.
description: A description of column headings can be found in the data
 files.
DOI: 10.5061/dryad.wwpzgmsgw
title: Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle ( Leptinotarsa decemlineata, Say)

description: In order to understand the evolution of pestiferousness, which we define
 as the accumulation of traits that contribute to an insect population’s
 success in an agroecosystem, we tested the importance of known genomic
 properties associated with rapid adaptation. Within the leaf beetle genus
 Leptinotarsa, only the Colorado potato beetle (CPB), Leptinotarsa
 decemlineata Say, and a few populations therein, has risen to pest status
 on cultivated nightshades, Solanum. Using whole genomes from ten closely
 related Leptinotarsa species native to the United States we reconstructed
 a high-quality species tree and used this phylogenetic framework to assess
 evolutionary patterns in four genomic features of rapid adaptation:
 standing genetic variation, gene family expansion and contraction,
 transposable element variation, and positive selection at protein coding
 genes. Throughout approximately 20 million years of history, Leptinotarsa
 species show little evidence of gene family turnover and transposable
 element variation. However, there is a clear pattern of recently derived
 lineages, including CPB, experiencing higher rates of positive selection
 on protein coding genes. We determine these rates are associated with
 greater standing genetic variation due to larger effective population
 size, which support the theory that the demographic history contributes to
 rates of protein evolution. Furthermore, we identify a suite of genes
 under positive selection that are linked to pestiferousness, exclusively,
 in the Colorado potato beetle lineage. They are involved in the biological
 processes of xenobiotic detoxification, chemosensation, and hormone
 function.
description: Alignments of
 these genes were generated using a multi-phase heuristic algorithm
 implemented by the Spaln v2.3.3(space-efficient spliced alignment)
 program, which efficiently maps cDNA sequences onto whole genomes (Gotoh
 2008). Mapped codons were further isolated from the Spaln output and
 aligned to the CPB reference ortholog sequence, for each species, using a
 custom C program. MAFFT (Multiple sequence alignment fast fourier
 transformation, Katoh et al. 2002). We corrected for mis-alignment and
 quality using Guidance v2.02, at high stringency, with 30 bootstraps per
 alignment (Penn et al. 2010).
description: The alignment data are stored in three compressed tgz folders and
 can be accessed upon expansion either using command line arguments tar
 -xzf *tgz or by double clicking each tarball. Once opened the
 three subfolders need to be further decompressed where you will find the
 alignments and a README.txt. These files do not have file extenstions,
 but are all text based readable files and can be accessed using a variety
 of file reading programs.
DOI: 10.5061/dryad.z8w9ghx8v
title: Data from: The effects of ground-irregularity-cancelling prosthesis control on balance over uneven surfaces

description: Over half of individuals with a lower-limb amputation are unable to walk
 on uneven terrain. Using a prosthesis emulator system, we developed an
 irregularity-cancelling controller intended to reduce the effect of
 disturbances resulting from uneven surfaces. This controller functions by
 changing the neutral angles of two forefoot digits in response to local
 terrain heights. To isolate the effects of the controller, we also
 programmed a spring-like controller that maintained fixed neutral angles.
 Five participants with transtibial amputation walked on a treadmill with
 an uneven walking surface. Compared to the spring-like
 controller, the irregularity-cancelling controller reduced ankle torque
 variability by 41% in the sagittal plane and 64% in the frontal plane.
 However, user outcomes associated with balance were mostly unaffected;
 only trunk movement variability was reduced, whereas metabolic rate,
 mediolateral center of mass motion, and variabilities in step width, step
 length, and step time were unchanged. We conclude that reducing ankle
 torque variability of the affected limb is not sufficient for reducing the
 overall effect of disturbances due to uneven terrain. It is possible that
 other factors, such as changes in step height or disturbances to the
 intact limb, play a larger role in difficulty balancing while walking over
 uneven surfaces.
description: Includes metabolic cost from indirect respirometry, motion
 capture data, and sensor readings from the prosthesis. Files are formatted
 for Matlab.
DOI: 10.5061/dryad.qfttdz0f1
title: Data from: Multi-species restoration accelerates recovery of extinguished oyster reefs

description: 1. A multi-species approach to habitat restoration may boost the key
 processes (e.g. recruitment) that enable foundation species to overcome
 barriers to recovery. Natural systems tend to be formed by co-occurring
 foundation species whose synergy drives ecological productivity and
 resilience beyond that of single foundation species. Yet, restoration
 remains primarily a single-species focus enterprise where positive
 interactions are seldom incorporated into planning. A multi-species
 approach that prioritises species combinations to create emergent
 properties for their persistence may accelerate habitat recovery and the
 success of restoration programs. 2. On the largest oyster reef restoration
 project in the Southern Hemisphere, we experimentally established
 canopy-forming kelp to test whether they could accelerate the natural
 recruitment of oysters to substrata monopolised by turf-forming algae. To
 understand whether facilitation of oysters was a function of the kelp
 themselves (biological facilitation) or the physical environment they
 create (physical facilitation), we compared recruitment to the understorey
 of living kelp and synthetic kelp mimics. 3. Despite observing high
 density oyster recruitment to the turf-free underside of reef boulders
 (8,300 oysters/m2), turf algae appeared to inhibit oyster recruitment to
 the exposed surfaces of the reef, limiting their capacity to grow and form
 complex, three-dimensional habitat. 4. Transplanted kelp, whether living
 or synthetic kelp mimics, effectively reduced the biomass of turf and
 enhanced oyster recruitment, creating turf-free substrata on the upper
 reef surfaces with up to 26 times the oyster recruitment than turf-covered
 substrata. 5. Synthesis and applications. Our results provide
 proof-of-concept that incorporating the transplant of canopy-forming kelp
 to reefs constructed to restore oysters is not only achievable, but may be
 imperative to successfully restore oyster reefs in turf-dominated systems.
 Kelp transplants supressed the turf algae that otherwise excluded oysters
 from the reef surface, effectively shifting the competitive advantage
 toward oyster recovery by maintaining bare substrata for oyster
 recruitment. In demonstrating that co-restoring foundation species
 facilitates interactions that overcome barriers to recovery, we emphasise
 the need for restoration programs to incorporate the functional synergy of
 overlapping foundation species into planning, so to establish emergent
 properties that can accelerate the recovery of restored habitat.
DOI: 10.5061/dryad.h9w0vt4g0
title: Inland walleye genotypes

description: Targeted amplicon sequencing methods, such as genotyping-in-thousands by
 sequencing (GT-seq), facilitate rapid, accurate, and cost-effective
 analysis of hundreds of genetic loci in thousands of individuals.
 Development of GT-seq panels is non-trivial, but studies describing
 trade-offs associated with different steps of GT-seq panel development are
 rare. Here, we construct a dual-purpose GT-seq panel for walleye (Sander
 vitreus), discuss trade-offs associated with different development and
 genotyping approaches, and provide suggestions for researchers
 constructing their own GT-seq panels. Our GT-seq panel was developed using
 an ascertainment set consisting of restriction site-associated DNA data
 from 954 individuals sampled from 23 populations in Minnesota and
 Wisconsin. We then conducted simulations to test the utility of all loci
 for parentage analysis and genetic stock identification and designed 600
 primer pairs to maximize joint accuracy for these analyses. We conducted
 three rounds of primer optimization to remove loci that overamplified and
 our final panel consisted of 436 loci. We also explored different
 approaches for DNA extraction, multiplexed polymerase chain reaction (PCR)
 amplification, and cleanup steps during the GT-seq process and discovered
 the following: (1) inexpensive Chelex extractions performed well for
 genotyping, (2) the exonuclease I and shrimp alkaline phosphatase (ExoSAP)
 procedure included in some current protocols did not improve results
 substantially and was likely unnecessary, and (3) it was possible to PCR
 amplify panels separately and combine them prior to adapter ligation.
 Well-optimized GT-seq panels are valuable resources for conservation
 genetics and our findings and suggestions should aid in their construction
 in myriad taxa.
DOI: 10.5061/dryad.bg79cnp8h
title: Data from: Visualizing connectivity of ecological and evolutionary concepts – an exploration of research on plant species rarity

description: Understanding the ecological and evolutionary factors that influence
 species rarity has important theoretical and applied implications, yet the
 reasons why some species are rare while others are common remain
 unresolved. As a novel exploration of scientific knowledge, we used
 network analysis conceptually to visualize the foci of a comprehensive
 base of &gt;800 studies on plant species rarity within the context of
 ecology and evolution. In doing so, we highlight existing research
 strengths that could substantiate novel syntheses and gaps that could
 inspire new research. Our results reveal strong integrated foci on
 population dynamics with other ecological concepts. In contrast, despite
 the potential for ecological and evolutionary processes to interact, few
 studies explored the interplay of environmental factors and
 microevolutionary patterns. The cellular and molecular biology,
 physiology, and plasticity of rare plant species within both ecological
 and evolutionary contexts similarly provide avenues for impactful future
 investigations.
description: Visualizing connectivity of ecological and evolutionary concepts
 –  literature base, keywords & concepts, matrices
 We used <i>ISI</i> <i>Web of Science</i>
 (Thompson Reuters, New York, NY) to screen the primary literature for
 studies of plant species in which their rarity or characterization as rare
 was a focus of the research. We curated 813 relevant articles and
 extracted their keywords. To capture the research foci of this literature
 base, we developed a network of broad 'parent' nodes and more
 specific 'child' nodes that represented ecology and evolution
 comprehensively as broad fields. We assigned each keyword to a parent node
 and child node (if applicable) based on general agreement among the
 authors. Titles, keywords, and abstracts from our curated base of 813
 articles were searched with a Perl script to identify the number of
 articles that focused on each pairwise combination of concepts. Diagonal
 matrices were used to organize results according to the total number of
 studies that were identified for each pairwise concept combination.
 Connectivity values were calculated  as the ratio of the number of studies
 that focused on a given pair of concepts to the total keywords relevant to
 those two concepts. The median of all connectivity values was calculated
 and the importance of each pairwise connection was considered relative to
 the median.