cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.72ft2
title: Data from: Locomotion during digestion changes current estimates of seed dispersal kernels by fish

description: Dispersal of seeds by animals is an important mechanism regulating plant
 diversity, range expansions and invasions. Many birds, mammals, fish, and
 reptiles regularly ingest, transport and excrete viable seeds (known as
 endozoochory). The effectiveness of endozoochory is modelled in dispersal
 kernels: functions that describe seed shadows in the landscape by
 combining movement of animals with experimentally obtained seed retention
 times and survival. Currently, dispersal kernels use experimental data
 from resting animals, yet only moving animals disperse seeds. Although
 physical activity is known to affect digestive processes, little is known
 on how and to what extent this may influence current estimates of
 endozoochory. Activity may either prolong seed retention in the
 animal's gut (locomotion-priority mode hypothesis) or may not affect
 seed excretion rate (digestion-priority mode hypothesis), and may affect
 seed survival and germination positively or negatively. We tested how
 activity alters dispersal estimates in fish. We compared the seed
 dispersal potential of two riparian plant species (Carex acuta and C.
 riparia) by the common carp (Cyprinus carpio) subjected to three different
 activity levels: low (basal metabolic rate, BMR), medium (2×BMR), or high
 activity (3×BMR). Physical activity of the fish did not affect the number
 of intact retrieved seeds over 15 h of activity, but significantly
 affected seed retrieval patterns over time for both seed species. More
 active fish started seed excretion about 1 h later and kept excreting
 seeds at least 2 h longer. Effects of gut passage on germination could
 only be tested for C. acuta, where it reduced the percentage of
 germinating seeds by 22%, independent of the activity level. Seeds
 ingested by the fish germinated on average 3.5 days later than
 non-ingested control seeds. Seed retention times did not affect the timing
 of germination. Our results support the locomotion-priority mode
 hypothesis, and show that modelling dispersal kernels using parameters
 from inactive fish may underestimate potential dispersal distances.
 Because a trade-off between physical activity and digestive physiology is
 likely common in animals, it should be taken into account in future
 modelling of endozoochorous seed dispersal kernels.
description: Seed retrieval
 dataSeed retrieval
 dataRetrieval
 data.xlsxGermination
 dataSeed germination
 data
DOI: 10.5061/dryad.4r1f0
title: Data from: Using branch-and-bound algorithms to optimize selection of a fixed-size breeding population under a relatedness constraint

description: Tree breeders often face the challenge of conserving genetic diversity,
 while at the same time maximizing response to selection. When selecting
 advanced-generation breeding populations, the best-performing candidates
 will quite often be closely related and selecting them without
 consideration of their relatedness will very quickly erode genetic
 diversity. Optimal selection will not completely avoid kinship, but rather
 maximize gain while imposing a constraint on average relatedness. Genetic
 contributions are most easily optimized if breeders can manage a real,
 continuous distribution of contributions from parents. While generally
 possible when establishing seed orchards, unequal contributions to a
 breeding population may present difficult and time-consuming operational
 constraints. In these situations, a specified number of parents
 contributing equally may be a preferred configuration for the breeding
 population. Here we formulate the selection of a fixed-size breeding
 population while imposing a constraint on relatedness of the population
 members. The problem is expressed as a Mixed Integer Quadratically
 Constrained Optimization (MIQCO) and solved using branch-and-bound
 techniques (BB). An open-source solver, dsOpt, was developed and embedded
 into a user-friendly tool, OPSEL, designed to simplify the process of
 optimizing selection of breeding populations. Case studies optimizing
 selection of breeding populations for Scots pine and loblolly pine
 illustrate the superiority of the BB solution compared with selection from
 ranked lists with restrictions on numbers of genotypes contributed by each
 full-sib family, and with solutions from GENCONT, a publically available
 optimum selection program using an algorithm with Lagrangian multipliers.
 The case studies also illustrate the extreme differences that can occur
 with respect to time required to confirm the optimality of solutions found
 by BB.
description: Tpop_T11_top6perfamPedigree and EBVs for Scots pine case study, for branch-and-bound optimization by OPSELResende_BPPedigree and EBVs for loblolly pine case study for branch-and-bound optimization by OPSEL
DOI: 10.5061/dryad.11d82
title: Data from: Plant community evenness responds to spatial plant-soil feedback heterogeneity primarily through the diversity of soil conditioning

description: 1.Plant-soil feedback (PSF) has been identified as a key driver of local
 plant diversity and evenness in competitive communities. However, while it
 has been shown that spatial PSF heterogeneity can alter plant performance
 and competitive interactions, there is no proof of principle that spatial
 PSF heterogeneity enhances community diversity. 2.Using a grassland model
 system we separated two aspects of spatial heterogeneity: the number of
 species conditioning the soil and spatial distribution of the PSFs. 3.Our
 data show that PSFs promoted a higher plant evenness when the soil was
 conditioned by multiple species (mixed-conditioned), then when the soil
 was conditioned by a single species (mono-conditioned). On
 mono-conditioned soils, heterospecifics typically outperformed the focal
 species. In addition, there was a trend for increasing community evenness
 from uniform, via fine-grained to coarse-grained mixed-conditioned soils,
 but this was not significant. 4.On mixed-conditioned soils, performance of
 all competing species was intermediate to the best and the worst
 mono-conditioned soils, leading to higher community evenness. 5.Our data
 demonstrate that PSFs play a role in promoting plant evenness. Across
 mono-conditioned soils, PSF led to altered competitive hierarchies.
 However, on soils conditioned by multiple species, competitive ability
 among species was more similar and this led to higher plant evenness. The
 spatial distribution of the heterogeneity, on the other hand, did not
 significantly affect plant evenness. Our data therefore show that
 community evenness was more strongly related to the number of plant
 species that conditioned the soil than the spatial distribution of the PSF
 heterogeneity. Future studies need to investigate the importance of PSFs
 in the field across plant life-stages and multiple generations.
description: Phase 2 shoot and root
 biomassThis data file contains
 the raw shoot and root biomass observed in the experiment on gridcell
 level.Phase 1 Soil
 chemistryThis file contains the
 abiotic variables measured at the end of the conditioning
 phase.Phase 1
 T-RFLPThis file contains the
 T-RFLP data for fungal communities in response to soil conditioning by six
 different plant species.
DOI: 10.5061/dryad.cc3rb
title: Data from: Optimal switching between geocentric and egocentric strategies in navigation

description: Animals use a combination of egocentric navigation driven by the internal
 integration of environmental cues, interspersed with geocentric course
 correction and reorientation. These processes are accompanied by
 uncertainty in sensory acquisition of information, planning and execution.
 Inspired by observations of dung beetle navigational strategies that show
 switching between geocentric and egocentric strategies, we consider the
 question of optimal reorientation rates for the navigation of an agent
 moving along a preferred direction in the presence of multiple sources of
 noise. We address this using a model that takes the form of a correlated
 random walk at short time scales that is punctuated by reorientation
 events leading to a biased random walks at long time scales. This allows
 us to identify optimal alternation schemes and characterize their
 robustness in the context of noisy sensory acquisition as well as
 performance errors linked with variations in environmental conditions and
 agent–environment interactions.
description: figure3_AThis data is made available to support the paper “Optimal Geocentric/Egocentric Switching Strategies in Navigation”, by Orit Peleg and L. Mahadevan, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138,USA Data description, corresponding to the manuscript’s figures: % figure3_A.txt N, $theta^*$, reorientation interval $n$, cost $f$figure3_BThis data is made available to support the paper “Optimal Geocentric/Egocentric Switching Strategies in Navigation”, by Orit Peleg and L. Mahadevan, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138,USA Data description, corresponding to the manuscript’s figures: % figure3_B.txt N, $theta^*$, n^{opt}figure4_AThis data is made available to support the paper “Optimal Geocentric/Egocentric Switching Strategies in Navigation”, by Orit Peleg and L. Mahadevan, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138,USA Data description, corresponding to the manuscript’s figures: % figure4_A.txt and figure4_B.txt $N$, $theta^$, penalty $A\theta^$, detection_error, Optimal estimated $n$, optimal attention span $\tau$figure4_B
DOI: 10.5061/dryad.f45q2
title: Data from: How generalist herbivores exploit belowground plant diversity in temperate grasslands

description: Belowground herbivores impact plant performance, thereby inducing changes
 in plant community composition, which potentially leads to cascading
 effects onto higher trophic levels and ecosystem processes and
 productivity. Amongst soil-living insects, external root-chewing
 generalist herbivores have the strongest impact on plants. However, the
 lack of knowledge on their feeding behaviour under field conditions
 considerably hampers achieving a comprehensive understanding of how they
 affect plant communities. Here, we address this gap of knowledge by
 investigating the feeding behaviour of Agriotes click beetle larvae, which
 are common generalist external root-chewers in temperate grassland soils.
 Utilizing diagnostic multiplex PCR to assess the larval diet, we examined
 the seasonal patterns in feeding activity, putative preferences for
 specific plant taxa, and whether species identity and larval instar
 affects food choices of the herbivores. Contrary to our hypothesis, most
 of the larvae were feeding-active throughout the entire vegetation period,
 indicating that the grassland plants are subjected to constant belowground
 feeding pressure. Feeding was selective, with members of Plantaginaceae
 and Asteraceae being preferred; Apiaceae were avoided. Poaceae, although
 assumed to be most preferred, had an intermediate position. The food
 preferences exhibited seasonal changes, indicating a fluctuation in plant
 traits important for wireworm feeding choice. Species- and instar-specific
 differences in dietary choice of the Agriotes larvae were small,
 suggesting that species and larval instars occupy the same trophic niche.
 According to the current findings, the food choice of these larvae is
 primarily driven by plant identity, exhibiting seasonal changes. This
 needs to be considered when analysing soil herbivore-plant interactions.
description: MEC-13-0732 raw
 dataThe file contains
 ingested plant species/Groups detected in wireworms (Agriotes larvae,
 Elateridae, Coleoptera) - seven plants were targeted and the wireworms
 were identified molecularly to species Level. They were collected in
 perennial grasslands in Central Europe, Tyrol, Austria in summer 2008 and
 2009.
DOI: 10.5061/dryad.s24b9
title: Data from: Developmental effects of visual environment on species-assortative mating preferences in Lake Victoria cichlid fish

description: Local adaptation can be a potent force in speciation, with environmental
 heterogeneity leading to niche specialization and population divergence.
 However, local adaption often requires non-random mating in order to
 generate reproductive isolation. Population divergence in sensory
 properties can be particularly consequential in speciation, affecting both
 ecological adaptation and sexual communication. Pundamilia pundamila and
 Pundamilia nyererei are two closely related African cichlid species that
 differ in male coloration, blue vs. red. They co-occur at rocky islands in
 southern Lake Victoria, but inhabit different depth ranges with different
 light environments. The species differ in colour vision properties and
 females exert species-specific preferences for blue vs. red males. Here,
 we investigated the mechanistic link between colour vision and preference,
 which could provide a rapid route to reproductive isolation. We tested the
 behavioural components of this link by experimentally manipulating colour
 perception – we raised both species and their hybrids under light
 conditions mimicking shallow and deep habitats - and tested female
 preference for blue and red males under both conditions. We found that
 rearing light significantly affected female preference: shallow-reared
 females responded more strongly to P. pundamilia males and deep-reared
 females favored P. nyererei males - implying that visual development
 causally affects mate choice. These results are consistent with
 sensory-drive predictions, suggesting that the visual environment is key
 to behavioural isolation of these species. However, the observed
 plasticity could also make the species barrier vulnerable to environmental
 change: species-assortative preferences were weaker in females that were
 reared in the other species’ light condition.
description: F1 mate preference
 datasetCombined data set of F1
 mate preference experiment. Sheet #1 ("Key") details the
 contents of the data found in sheet #2.F1 mate
 preference.xlsx
DOI: 10.5061/dryad.3s36r118
title: Data from: The robustness and restoration of a network of ecological networks

description: Understanding species’ interactions and the robustness of interaction
 networks to species loss is essential to understand the effects of
 species’ declines and extinctions. In most studies, different types of
 networks (such as food webs, parasitoid webs, seed dispersal networks, and
 pollination networks) have been studied separately. We sampled such
 multiple networks simultaneously in an agroecosystem. We show that the
 networks varied in their robustness; networks including pollinators
 appeared to be particularly fragile. We show that, overall, networks did
 not strongly covary in their robustness, which suggests that ecological
 restoration (for example, through agri-environment schemes) benefitting
 one functional group will not inevitably benefit others. Some individual
 plant species were disproportionately well linked to many other species.
 This type of information can be used in restoration management, because it
 identifies the plant taxa that can potentially lead to disproportionate
 gains in biodiversity.
description: norwood
DOI: 10.5061/dryad.3jv54
title: Data from: Biogeographic, climatic and spatial drivers differentially affect α-, β- and γ-diversities on oceanic archipelagos

description: Island biogeographic studies traditionally treat single islands as units
 of analysis. This ignores the fact that most islands are spatially nested
 within archipelagos. Here, we took a fundamentally different approach and
 focused on entire archipelagos using species richness of vascular plants
 on 23 archipelagos worldwide and their 174 constituent islands. We
 assessed differential effects of biogeographic factors (area, isolation,
 age, elevation), current and past climate (temperature, precipitation,
 seasonality, climate change velocity) and intra-archipelagic spatial
 structure (archipelago area, number of islands, area range, connectivity,
 environmental volume, inter-island distance) on plant diversity. Species
 diversity of each archipelago (γ) was additively partitioned into α, β,
 nestedness and replacement β-components to investigate the relative
 importance of environmental and spatial drivers. Multiple regressions
 revealed strong effects of biogeography and climate on α and γ, whereas
 spatial factors, particularly number of islands, inter-island distance and
 area range, were key to explain β. Structural equation models additionally
 suggested that γ is predominantly determined by indirect abiotic effects
 via its components, particularly β. This highlights that β and the spatial
 arrangement of islands are essential to understand insular ecology and
 evolution. Our methodological framework can be applied more widely to
 other taxa and archipelago-like systems, allowing new insights into
 biodiversity origin and maintenance.
description: Island level data for 23
 oceanic archipelagos worldwideVascular plant species
 richness, island area and climatic information at island level for the 23
 archipelagos investigated in Cabral et al. 2014, Proceedings B. The data
 are described in detail in the paper and in the readme
 file.Cabral_etal_2014_PRSB_islanddata.csv
DOI: 10.5061/dryad.rm611
title: Data from: Family-assisted inference of the genetic architecture of MHC variation

description: With their direct link to individual fitness, genes of the major
 histocompatibility complex (MHC) are a popular system to study the
 evolution of adaptive genetic diversity. However, owing to the highly
 dynamic evolution of the MHC region, the isolation, characterization and
 genotyping of MHC genes remain a major challenge. While high-throughput
 sequencing technologies now provide unprecedented resolution of the high
 allelic diversity observed at the MHC, in many species, it remains unclear
 (i) how alleles are distributed among MHC loci, (ii) whether MHC loci are
 linked or segregate independently and (iii) how much copy number variation
 (CNV) can be observed for MHC genes in natural populations. Here, we show
 that the study of allele segregation patterns within families can provide
 significant insights in this context. We sequenced two MHC class I (MHC-I)
 loci in 1267 European barn owls (Tyto alba), including 590 offspring from
 130 families using Illumina MiSeq technology. Coupled with a high
 per-individual sequencing coverage (~3000×), the study of allele
 segregation patterns within families provided information on three aspects
 of the architecture of MHC-I variation in barn owls: (i) extensive sharing
 of alleles among loci, (ii) strong linkage of MHC-I loci indicating tandem
 architecture and (iii) the presence of CNV in the barn owl MHC-I. We
 conclude that the additional information that can be gained from
 high-coverage amplicon sequencing by investigating allele segregation
 patterns in families not only helps improving the accuracy of MHC
 genotyping, but also contributes towards enhanced analyses in the context
 of MHC evolutionary ecology.
description: MHC-I genotypes and
 family informationThe file includes three
 sheets: (i) MHC-I genotypes (columns: individual ID, individual coverage,
 allele name and allele coverage), (ii) family information for 130 families
 (columns: family ID, male name male, female name and juvenile name), (iii)
 family information for 40 families used to estimate genetic architecture
 (columns: family ID, individual ID, status, sex, allele name and the
 relative coverage for each allele).Data_MHC-I.xlsx
DOI: 10.5061/dryad.h360q
title: Data from: Reproductive skew drives patterns of sexual dimorphism in sponge-dwelling snapping shrimps

description: Sexual dimorphism is typically a result of strong sexual selection on male
 traits used in male–male competition and subsequent female choice.
 However, in social species where reproduction is monopolized by one or a
 few individuals in a group, selection on secondary sexual characteristics
 may be strong in both sexes. Indeed, sexual dimorphism is reduced in many
 cooperatively breeding vertebrates and eusocial insects with totipotent
 workers, presumably because of increased selection on female traits. Here,
 we examined the relationship between sexual dimorphism and sociality in
 eight species of Synalpheus snapping shrimps that vary in social structure
 and degree of reproductive skew. In species where reproduction was shared
 more equitably, most members of both sexes were physiologically capable of
 breeding. However, in species where reproduction was monopolized by a
 single individual, a large proportion of females—but not males—were
 reproductively inactive, suggesting stronger reproductive suppression and
 conflict among females. Moreover, as skew increased across species,
 proportional size of the major chela—the primary antagonistic weapon in
 snapping shrimps—increased among females and sexual dimorphism in major
 chela size declined. Thus, as reproductive skew increases among
 Synalpheus, female–female competition over reproduction appears to
 increase, resulting in decreased sexual dimorphism in weapon size.
description: Synalpheus
 dimorphism_all mature individualsSex, gonad maturity and
 size of each mature individualSynalpheus
 dimorphism_statistics by colonysex ratio, percentage
 maturity and eusociality index for each colony.Synalpheus
 dimorphism_statistics by speciesSex ratio, allometry,
 proportion maturity and eusociality index of each
 species
DOI: 10.5061/dryad.gh49142
title: Data from: Looking up: a dozen years of evolution of neurology clerkships in the United States

description: Objective: To report a 2017 survey of all US medical school neurology
 clerkship directors (CDs) and to compare the results to similar surveys
 conducted in 2005 and 2012. Methods: An American Academy of Neurology
 (AAN) Consortium of Neurology Clerkship Directors (CNCD) workgroup
 developed the survey that was sent to all neurology CDs listed in the AAN
 CNCD database. Comparisons were made to similar 2005 and 2012 surveys.
 Results: The response rate was 92 of 146 programs (63%). Among the
 responding institutions, neurology is required in 94% of schools and is 4
 weeks in length in 75%. From 2005 to 2017, clerkships shifted out of a
 fourth-year-only rotation (p = 0.035) to earlier curricular time points.
 CD protected time averages 0.24 full-time equivalent (FTE), with 31% of
 CDs reporting 0.26 to 0.50 FTE support, a &gt;4-fold increase from
 prior surveys (p &lt; 0.001). CD service of &gt;12 years increased
 from 9% in 2005 to 23% in 2017. Twenty-seven percent also serve as
 division chief/director, and 22% direct a preclinical neuroscience course.
 Forty-nine percent of CDs are very satisfied in their role, increased from
 34% in 2012 (p = 0.046). The majority of CDs identify as white and male,
 with none identifying as black/African American. Conclusion: Changes since
 2005 and 2012 include shifting of the neurology clerkship to earlier in
 the medical school curriculum and an increase in CD salary support. CDs
 are more satisfied than reflected in previous surveys and stay in the role
 longer. There is a lack of racial diversity among neurology CDs.
description: AAN CNCD 2017 Survey
 QuestionsSupplementary data to
 the article is the list of questions that were asked in the survey which
 the article analyzes.2017 Clerkship Director
 Survey.pdf