cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7h44j0zv3
title: Drivers of genetic differentiation and recent evolutionary history of an Eurasian wild pea

description: Aim: Genetic diversity is a major determinant for the capacity of
 species to persist and adapt to their environments. Unraveling the factors
 affecting genetic differentiation is crucial to understand how genetic
 diversity is shaped and species may react to changing environments. We
 investigated the drivers of genetic differentiation and their interplay
 with the evolutionary history in a wild pea to test how those may have
 affected the distribution of genetic diversity. Location: Mediterranean
 basin, western Asia Taxon: Pisum sativum (Fabaceae) Methods: We
 employed RAD-seqencing to test the influence of environmental
 factors on genetic differentiation in a collection of 81 wild pea
 samples. Demographic history and past expansion patterns were analyzed
 to test their effect on the current distribution of
 genetic diversity. Association of SNPs with
 environmental variables were analyses to find signatures of local
 adaptation. Results: Genetic variation was geographically
 structured into six distinct genetic clusters. The effect of the tested
 factors influencing genetic differentiation was variable among genetic
 clusters. Climate predictors were most important in all clusters.
 Land use was more important in clusters from areas strongly influenced by
 human land use, especially by agriculture. We found statistically
 significant associations of 3,623 SNPs with
 environmental variables. Most of them were correlated with
 latitude followed by temperature. Wild peas went through a genetic
 bottleneck during the last glacial period followed by population recovery.
 The detected range expansion patterns suggested
 an eastward range expansion of the European cluster to
 Turkey and thereof southwards and eastwards. Main
 conclusion: Our results suggest that it is insufficient
 to consider the present distribution of genetic diversity alone but rather
 consider it in conjunction with the evolutionary history of the respective
 species. Moreover, the distribution of genetic variation has to
 be viewed in the context of its hierarchical structure and the environment
 of its genetic entities to understand how this variation was shaped
 and may change in the future.
DOI: 10.5061/dryad.2v6wwpznx
title: Enhancing ecological integrity while preserving ecosystem services: constructing soft-sediment islands in a shallow lake

description: 1. Ecosystems are increasingly managed to provide multiple benefits to
 humans, which often degrades their ecological integrity. This strongly
 applies to aquatic ecosystems, in which engineering can enhance flood
 protection, drinking water supply, fisheries and recreation. Although
 these activities typically increase ecosystem functionality to humans,
 they often impair key aspects of biodiversity and natural functioning. 2.
 Classical restoration of such degrading freshwater ecosystems can lead to
 societal opposition, if returning to a former ecosystem state affects
 previously acquired ecosystem services. Innovative nature-based solutions
 are therefore needed that enhance natural values in ecosystems, without
 affecting existing services. 3. We present a large-scale project aiming to
 increase the ecological integrity of a human-modified freshwater lake,
 while maintaining its services to humans. The freshwater lake Markermeer
 in the Netherlands was formed by closing off an estuary for flood
 protection. The ecological integrity of this lake diminished over time,
 likely because a declining primary productivity impaired biodiversity at
 higher trophic levels. This decline is associated with a lack of gradual
 land-water transitions, strong resuspension of fine sediments, a low
 nutrient availability and lack of dynamics typically to be expected in a
 natural temperate freshwater lake. Restoring the lake to its former marine
 state would conflict with current ecosystem services. 4. A nature-based
 solution was initiated in 2016, consisting of constructing a five-island
 archipelago from the lake’s own soft-sediments called the “Marker Wadden”.
 The project aims to increase the lake’s primary production by creating
 gradual land-water transitions, more heterogeneity in water depths, and
 decreasing turbidity by creating shelter and deep sinks reducing
 fine-sediment resuspension by wind – thus introducing currently missing
 elements that are typical for natural lakes. We present the underlying
 ecological framework and first scientific results of this innovative
 on-going project. 5. Within four years, the Marker Wadden project shows
 how forward-looking sustainable development of lake ecosystems using a
 rewilding approach can enhance natural processes and attract birds and
 fish, without conflicting with existing ecosystem services. This inspires
 new directions for halting and reversing the degradation of other vital
 ecosystems worldwide.
description: Field sampling at six locations on and close to the new Marker
 Wadden archipelago in The Netherlands. Sampling included phytoplankton,
 zooplankton, macrophytes and macrofauna.
DOI: 10.5061/dryad.j9kd51cd4
title: Ediacara growing pains: Modular addition and development in Dickinsonia costata

description: Constraining patterns of growth using directly observable and quantifiable
 characteristics can reveal a wealth of information regarding the biology
 of the Ediacara Biota – the oldest macroscopic, complex community forming
 organisms in the fossil record. However, these rely on individuals
 captured at an instant in time at various growth stages, and so different
 interpretations can be derived from the same material. Here we leverage
 newly discovered and well-preserved Dickinsonia costata Sprigg 1947 from
 South Australia, combined with hundreds of previously described specimens,
 to test competing hypotheses for the location of module addition. We find
 considerable variation in the relationship between the total number of
 modules and body size that cannot be explained solely by expansion and
 contraction of individuals. Patterns derived assuming new modules
 differentiated at the anterior result in numerous examples where the
 oldest module(s) must decrease in size with overall growth, potentially
 falsifying this hypothesis. Observed polarity as well as the consistent
 posterior location of defects and indentations support module formation at
 this end in D. costata. Regardless, changes in repeated units with growth
 share similarities with those regulated by morphogen gradients in
 metazoans today, suggesting that these genetic pathways were operating in
 Ediacaran animals.
description: The majority of measurements were obtained using
 digital photographs and the freely available Image J software
 (https://imagej.nih.gov/ij/). Additional measurements were collecting
 using digital calipers either directly on fossil specimens or from latex
 molds. Measurements of module length at the midline and outer margin were
 determined using straight line approximations, while module width was
 measured along the sinusoidal path from the midline to outer
 margin. 
description: See ReadMe file for explanation of variables and
 measurements.
DOI: 10.5061/dryad.x0k6djhk5
title: Bud traits and post-fire responses of Cerrado woody species, Southeastern Brazil

description: 1) Species growing in fire-prone savannas usually persist by resprouting
 from their buds. In this study, we evaluated how various persistence
 traits allow bud protection for improved survival in fire-prone
 ecosystems. 2) Using an integrative morphological and macroanatomical
 approach, we analyzed how woody plants protect their buds. We tested bud
 protection at the community level and evaluated: a) how bud protection
 changes along a fire frequency gradient, b) if it differs between shrubs
 and trees and c) whether the level of bud protection is related to
 post-fire responses of 28 woody savanna species. 3) A mix of traits
 involving bud protection may enable woody species persistence in
 fire-prone ecosystems. Savanna species better protected their buds than
 forest species by developing bark and trichomes that allowed resprouting
 after fire. Regarding growth forms, shrub species capable of resprouting
 aboveground had their buds better protected than trees. 4) Bud protection
 is not only linked with their position to the bark, but also with the
 presence of trichomes. Profuse trichomes covering buds were related to
 savanna species. Some species with no bud protection by bark but with
 trichomes covering their buds were able to resprout after fire. The
 presence of accessory buds is also a trait more related to savannas,
 possibly influencing the resprouting after fire as they are better
 protected and increase the bud bank. Finally, different persistence traits
 interact with one another to better protect the buds, requiring a detailed
 screening of the traits to assess species responses to fire. 5) Synthesis.
 During fire, species have their aerial biomass consumed by the flames. To
 be able to resprout new branches and persist in the environment, they must
 have well-protected buds. In this study, we evaluated different ways that
 woody species protect their buds and related them with their resprouting
 strategy after fire. We investigated the protection by the bark, presence
 of trichomes and accessory buds. By studying the woody community in a
 gradient of savannas and forests we found that buds can be protected by
 bark, trichomes, or soil. Species can present a mix of these traits and
 strategies, which enhances their resprouting after fire.
description: This dataset comprises data used in the "Your best buds are
 worth proctecting: variation in bud protection in a fire-prone cerrado
 system" published manuscript in Functional Ecology.
 Information about the dataset can be found on the
 'readme.txt' file and on the 'Metadata'
 sheet.
DOI: 10.5061/dryad.kwh70rz49
title: NEXMIF encephalopathy: DeNovogear output of WES data of the family

description: The developmental and epileptic encephalopathies (DEE) are the most severe
 group of epilepsies. Recently, NEXMIF mutations have been shown to cause a
 DEE in females, characterized by myoclonic–atonic epilepsy and recurrent
 nonconvulsive status. Here we used advanced neuroimaging techniques in a
 patient with a novel NEXMIF de novo mutation presenting with recurrent
 absence status with eyelid myoclonia, to reveal brain structural and
 functional changes that can bring the clinical phenotype to alteration
 within specific brain networks. Indeed, the alterations found in the
 patient involved the visual pericalcarine cortex and the middle frontal
 gyrus, regions that have been demonstrated to be a core feature in
 epilepsy phenotypes with visual sensitivity and eyelid myoclonia with
 absences.
DOI: 10.5061/dryad.f7m0cfxwz
title: Ageing as early-life inertia: disentangling life-history trade-offs along a lifetime of an individual

description: The theory that ageing evolves because of competitive resource allocation
 between the soma and the germline has been challenged by studies showing
 that somatic maintenance can be improved without impairing reproduction.
 However, it has been suggested that cost-free improvement in somatic
 maintenance is possible only under a narrow range of benign conditions.
 Here we show that experimental downregulation of insulin/IGF-1 signalling
 (IIS) in C. elegans nematodes, a robustly reproducible lifespan and
 healthspan-extending treatment, reduces fitness in a complex variable
 environment when initiated during development but does not reduce fitness
 when initiated in adulthood. Thus, our results show that the costs and
 benefits of reduced IIS can be uncoupled when organisms inhabit variable
 environments, and, therefore, do not provide support for the resource
 allocation theory. Our findings support the theory that the force of
 natural selection on gene expression in evolutionarily conserved
 signalling pathways that shape life-history traits declines after the
 onset of reproduction resulting in organismal senescence.
description: There are four types of file: qPCR gene
 expression data Reporduction (long and wide
 form) Healthspan Lifespan
description: The readme file decribes all of the relevant columns.
DOI: 10.5061/dryad.v6wwpzgwp
title: Data from: Telomere length declines with age, but relates to immune function independent of age in a wild passerine

description: Telomere length (TL) shortens with age but telomere dynamics can relate to
 fitness components independent of age. Immune function often relates to
 such fitness components and can also interact with telomeres. Studying the
 link between TL and immune function may therefore help us understand
 telomere-fitness associations. We assessed the relationships between
 erythrocyte TL and four immune indices (haptoglobin, natural antibodies,
 complement activity, heterophil-lymphocyte ratio; n=477-589), from
 known-aged individuals of a wild passerine (Malurus coronatus). As
 expected, we find that TL significantly declined with age. To verify
 whether associations between TL and immune function were independent of
 parallel age-related changes (e.g. immunosenescence), we statistically
 controlled for sampling age, and used within-subject centring of TL to
 separate relationships within or between individuals. We found that TL
 positively predicted complement activity at the between-individual level
 (individuals with longer average TL had higher complement activity), but
 no other immune indices. In contrast, age predicted levels of natural
 antibodies and heterophil-lymphocyte ratio, allowing inference that
 respective associations between TL and age with immune indices are
 independent. Any links existing between TL and fitness are therefore
 unlikely to be strongly mediated by innate immune function, while TL and
 immune indices appear independent expressions of individual heterogeneity.
description: These data were collected as part of the long-term purple-crowned
 fairy-wren research project established in 2005 by Anne Peters.
 The data and code in the accompanying R script file were used to
 produce the results presented in the main manuscript and supplementary
 information. The statistical models coded in the R
 script are those described in the stastical methods of the main
 manuscript. Model summaries were extracted to produce the results and
 tables presented in the manuscript. Code for the figures in the main
 manuscript is also included.
description: Individual Band-ID numbers registered with the Australian Bird
 and Bat Banding Scheme (ABBBS) have been de-identified for online
 publication. These Band-ID numbers have been replaced with a 6-character
 alphanumeric string, unique to each individual within each data file.
 Identities of individual Band-ID numbers are kept on record with Michael
 J. Roast and Anne Peters and can be re-identified if necessary.
DOI: 10.5061/dryad.qnk98sfhb
title: Assessing changes in clusters of wildlife road mortalities after the construction wildlife mitigation structures

description: Collisions with vehicles can be a major threat to wildlife populations, so
 wildlife mitigation structures, including exclusionary fencing and
 wildlife crossings, are often constructed. To assess mitigation structure
 effectiveness, it is useful to compare wildlife road mortalities (WRMs)
 before, during, and after mitigation structure construction; however,
 differences in survey methodologies may make comparisons of counts
 impractical. Location-based cluster analyses provide a means to assess how
 WRM spatial patterns have changed over time. We collected WRM data between
 2015 and 2019 on State Highway 100 in Texas, USA. Five wildlife crossings
 and exclusionary fencing, were installed in this area between Sep 2016 and
 May 2018 for the endangered ocelot (Leopardus pardalis) and other
 similarly sized mammals. Roads intersecting State Highway 100 were
 mitigated by gates, wildlife guards, and wing walls. However, these
 structures may have provided wildlife access to the highway. We combined
 local hot spot analysis and time series analysis to assess how WRM cluster
 intensity changed after mitigation structure construction at fine spatial
 and temporal scales and generalized linear regression to assess how gaps
 in fencing and landcover were related to WRM cluster intensity in the
 before, during, and after construction periods. Overall, WRMs/survey day
 decreased after mitigation structure construction and most hot spots
 occurred where there were more fence gaps, and, while cluster intensity
 increased in a few locations, these were not at fence gaps. Cluster
 intensity of WRMs increased when nearer to fence gaps in naturally
 vegetated areas, especially forested areas, and decreased nearer to fence
 gaps in areas with less natural vegetation. We recommend that if fence
 gaps are necessary in forested areas, less permeable mitigation
 structures, such as gates should be used. Local hot spot analysis, coupled
 with time series and regression techniques, can effectively assess how WRM
 clustering changes over time.
description: Regular wildlife road mortality surveys of mammals grouped into
 100-m segments to examine how clustering changed with construction of
 wildlife mtigation structures. Local hot spot analysis was run on 13 time
 blocks using ArcMap 10.6.
description: This dataset includes counts of mortalities, hot spot z-scores
 and p-values for each of the time blocks used in the study.
DOI: 10.5061/dryad.5mkkwh76k
title: Perineuronal nets in HVC and plasticity in male canary song

description: Songbirds learn their vocalizations during developmental sensitive periods
 of song memorization and sensorimotor learning. Some seasonal songbirds,
 called open-ended learners, recapitulate transitions from sensorimotor
 learning and song crystallization on a seasonal basis during adulthood. In
 adult male canaries, sensorimotor learning occurs each year in autumn and
 leads to modifications of the syllable repertoire during successive
 breeding seasons. We previously showed that perineuronal nets (PNN)
 expression in song control nuclei decreases during this sensorimotor
 learning period. Here we explored the causal link between PNN expression
 in adult canaries and song modification by enzymatically degrading PNN in
 HVC, a key song control system nucleus. Three independent experiments
 identified limited effects of the PNN degradation in HVC on the song
 structure of male canaries. They clearly establish that presence of PNN in
 HVC is not required to maintain general features of crystallized song.
 Some suggestion was collected that PNN are implicated in the stability of
 song repertoires but this evidence is too preliminary to draw firm
 conclusions and additional investigations should consider producing PNN
 degradations at specified time points of the seasonal cycle. It also
 remains possible that once song has been crystallized at the beginning of
 the first breeding season, PNN no longer play a key role in determining
 song structure; this could be tested by treatments with chondroitinase ABC
 at key steps in ontogeny. It would in this context be important to develop
 multiple stereotaxic procedures allowing the simultaneous bilateral
 degradation of PNN in several song control nuclei for extended periods.
description: Songs were recorded in sound proof boxes and analyzed with a
 specially designed matlab routine. Brain were processed
 by standard histological techniques and stained for parvalbumin and
 perineuronall nets. All data were analyzed with the
 Graphpad Prism software version 8.2.1 and all files containing the raw
 data that were analyzed in this way are provided.
description: ALL data are provided and can be re-analyzed with the Graphpad
 Prism software version 8.2.1 or more recent
DOI: 10.5061/dryad.5tb2rbp4k
title: Loss of branches due to winter storms could favor deciduousness in oaks

description: Premise of the study. Ecologists have an incomplete understanding of the
 factors that select for deciduous, evergreen, and marcescent leaf habits.
 Evergreens have more opportunities for photosynthesis but may experience
 costs when abiotic conditions are unfavorable such as during ice and
 windstorms. Methods. We documented branch loss for species of oaks
 (Quercus spp) in a common garden in California during an unusual
 windstorm. Key Results. Branches of marcescent trees were more likely to
 break during the storm and this pattern had a negligible phylogenetic
 signature. Branches of evergreen and marcescent species were mostly alive
 prior to breaking, which likely accrued a fitness cost, while those of
 deciduous species were mostly already dead. One explanation for the
 overrepresentation of broken branches from marcescent species is that
 their petioles are inflexible and have greater wind loading compared to
 the flexible petioles of evergreen leaves and the leafless condition of
 deciduous branches. Conclusions. These results suggest that branch loss
 during unusual winter storms may be an important cost of a marcescent leaf
 habit.
description: We recorded the number of branches that had fallen during a
 windstorm in a common garden of oak species. We characterized trees as
 being either evergreen, marcescent, or deciduous and compared the
 likelihood that downed branches were associated with these leaf retension
 habits. We also recorded whether downed branches had leaves and whether
 they were still green and alive when they broke. We evaluated whether
 observed patterns had a phylogenetic signature by mapping the likelihood
 of branch loss on a published oak phylogeny. We evaluated one possible
 mechanism for the high rate of branch loss among marcescent oaks by
 experimentally subjecting green and brown leaves of <em>Quercus
 lobata</em> to a standardized gust of wind and observed how far the
 wind moved the leaves.
description: This file shows the number of branches of each oak species that
 were lost during the windstorm. Species names are shown in column E and
 hybrids are indicated by a diamond symbol. Leaf habit is shown in column F
 where e is evergreen, m is marcescent, and d is deciduous. The number of
 individual trees of each species (or hybrid cross) is shown in column G.
 Columns H and I show the number of branches that were shed and the number
 of individual trees of each species that lost any branches. The number of
 branches that had leaves when it was lost is shown in column J and the
 number of branches that were still living when they were lost is shown in
 column K. Cells that lack values in columns J and K had no lost branches.
 These data are summarized in columns A-D.