cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8m201
title: Data from: Highly conserved Z and molecularly diverged W chromosomes in the fish genus Triportheus (Characiformes, Triportheidae)

description: The main objectives of this study were to test: (1) whether the
 W-chromosome differentiation matches to species’ evolutionary divergence
 (phylogenetic concordance) and (2) whether sex chromosomes share a common
 ancestor within a congeneric group. The monophyletic genus Triportheus
 (Characiformes, Triportheidae) was the model group for this study. All
 species in this genus so far analyzed have ZW sex chromosome system, where
 the Z is always the largest chromosome of the karyotype, whereas the W
 chromosome is highly variable ranging from almost homomorphic to highly
 heteromorphic. We applied conventional and molecular cytogenetic
 approaches including C-banding, ribosomal DNA mapping, comparative genomic
 hybridization (CGH) and cross-species whole chromosome painting (WCP) to
 test our questions. We developed Z- and W-chromosome paints from T.
 auritus for cross-species WCP and performed CGH in a representative
 species (T. signatus) to decipher level of homologies and rates of
 differentiation of W chromosomes. Our study revealed that the ZW sex
 chromosome system had a common origin, showing highly conserved Z
 chromosomes and remarkably divergent W chromosomes. Notably, the W
 chromosomes have evolved to different shapes and sequence contents within
 ~15–25 Myr of divergence time. Such differentiation highlights a dynamic
 process of W-chromosome evolution within congeneric species of
 Triportheus.
description: Sampling sites with
 coordinatesDescription of the
 sampling sites and their correct GPS coordinatesSamplis sites with
 coordinates.doc
DOI: 10.5061/dryad.5bd50
title: Data from: The basis of antagonistic pleiotropy in hfq mutations that have opposite effects on fitness at slow and fast growth rates

description: Mutations beneficial in one environment may cause costs in different
 environments, resulting in antagonistic pleiotropy. Here we describe a
 novel form of antagonistic pleiotropy that operates even within the same
 environment, where benefits and deleterious effects exhibit themselves at
 different growth rates. The fitness of hfq mutations in Escherichia coli
 affecting the RNA chaperone involved in small-RNA regulation is remarkably
 sensitive to growth rate. E. coli populations evolving in chemostats under
 nutrient limitation acquired beneficial mutations in hfq during slow
 growth (0.1 h-1) but not in populations growing 6-fold faster. Four
 identified hfq alleles from parallel populations were beneficial at 0.1
 h-1 and deleterious at 0.6 h-1. The hfq mutations were beneficial,
 deleterious or neutral at an intermediate growth rate (0.5 h-1) and one
 changed from beneficial to deleterious within a 36 min difference in
 doubling time. The benefit of hfq mutations was due t o the greater
 transport of limiting nutrient, which diminished at higher growth rates.
 The deleterious effects of hfq mutations at 0.6 h-1 were less clear, with
 decreased viability a contributing factor. The results demonstrate
 distinct pleiotropy characteristics in the alleles of the same gene,
 probably because the altered residues in Hfq affected the regulation of
 expression of different genes in distinct ways. In addition, these results
 point to a source of variation in experimental measurement of the
 selective advantage of a mutation; estimates of fitness need to consider
 variation in growth rate impacting on the magnitude of the benefit of
 mutations and on their fitness distributions.
description: Ferenci_Heredity_dataThe file includes all primary data for Figures 1-5. The file is an .xls spreadsheet with all the columns/labels as described in the axes/legends to the figures.
DOI: 10.5061/dryad.m2p20
title: Data from: Nitrogen saturation in humid tropical forests after 6 years of nitrogen and phosphorus addition: hypothesis testing

description: Nitrogen (N) saturation hypothesis suggests that when an ecosystem reaches
 N-saturation, continued N input will cause increased N leaching, nitrous
 oxide (N2O) emission, and N mineralization and nitrification rates. It
 also suggests that a different element will become the main limiting
 factor when N saturation has been reached. Although this hypothesis has
 been tested in temperate forests, whether they can be directly applied to
 N-saturated tropical forests remain poorly addressed. To test this
 hypothesis, soil inorganic N, soil N mineralization and nitrification
 rate, soil N2O emission rate and nitrate (inline image) leaching rate were
 measured in an N-saturated old-growth tropical forest in southern China,
 after 6 years of N and P addition. We hypothesized that N addition would
 stimulate further N saturation, but P addition might alleviate N
 saturation. As expected, our results showed that six continuous years of
 experimental N addition did cause further N saturation, which was
 indicated by significant increases in soil inorganic N concentration, N2O
 emission and nitrate (inline image) leaching. However, in contrast to our
 expectations, N addition significantly decreased in situ rates of net N
 mineralization and nitrification, which could be related to associated
 changes in enzyme activity and microbial community composition. On the
 other hand, P addition mitigated N saturation, as expected. Soil inorganic
 N concentration, N2O emission and inline image leaching decreased
 significantly after P addition, but the net rates of N mineralization and
 nitrification were significantly increased. Our results provide a new
 understanding of the N saturation hypothesis, suggesting that the effects
 of long-term N deposition on net N mineralization and nitrification rates
 in N-saturated tropical forests can be negative and that P addition can
 alleviate N saturation in such tropical systems.
description: Data for soil N
 cycleData-N
 cycle.xls
DOI: 10.5061/dryad.p0h0v
title: Data from: Environmental drivers of mast-seeding in Mediterranean oak species: does leaf habit matter?

description: Understanding the proximate factors that govern the widespread
 mast-seeding process is a question of considerable interest that remains
 poorly understood. The identity and effect of these factors may vary among
 coexisting species that differ in leaf habit, potentially resulting in
 temporally asynchronous patterns of seed production. In this study we aim
 to identify the proximate causes of mast-seeding using two oak species
 with contrasting leaf habit that coexist in southern Spain, the deciduous
 Quercus canariensis and the evergreen Q. suber. Simultaneously, we review
 the literature on environmental drivers of mast-seeding in Mediterranean
 oaks, distinguishing between evergreen and deciduous species. Our results
 indicate that Mediterranean oaks are primarily sensitive to weather,
 mast-seeding being strongly correlated with water availability and air
 temperature, mainly in the spring and summer. The two study oak species
 were affected by weather in quite different ways, most likely because of
 different abiotic requirements as well as contrasting functional
 strategies of resource use and biomass allocation. Specifically, annual
 seed production in Q. canariensis was more severely limited by drought
 than in Q. suber, but responded positively to warmer spring temperatures.
 Q. canariensis showed a large interannual variability, whereas Q. suber
 exhibited much more constant seed production. These two species also
 exhibited a very low level of synchrony in their temporal patterns of seed
 crop size, most likely due to phenological differences in the processes of
 flowering and seed maturation. Synthesis. Our results indicate that
 weather plays a crucial role as a proximate driver of mast-seeding in
 Mediterranean oaks. We hypothesize that the current abundance of
 co-occurring species that differ in leaf habit could be altered under
 future climate change scenarios. The decline of seed production with drier
 conditions will be potentially greater in deciduous species, particularly
 those inhabiting wetter sites. Alternatively, the expected warmer
 temperatures could negatively affect evergreen species as a consequence of
 their more conservative strategy of biomass allocation. Our findings
 suggest that understanding how species with different functional or
 phenological attributes adjust their reproductive abilities to weather may
 enable us to infer the effects of ongoing environmental changes on
 population recruitment and dynamics.
description: Data set of seed
 production and environmental factors (Perez-Ramos et al.
 2015_JEcol)Annual mean production
 of initial (including abortions) and mature seeds for the two study oak
 species (Quercus canariensis and Quercus suber) over the ten sampling
 years (from 2002 to 2011) and their associated environmental variables
 (temperature, precipitation, water limitation and drought
 index).Dataset_Perez-Ramos et al.
 2015_JEcol.xls
DOI: 10.5061/dryad.dn663c6
title: Data from: Understanding the function of nocturnal song in ovenbirds: males do not countersing at night

description: Many diurnal bird species vocalize at night, however the function of
 nocturnal song is, generally, still poorly understood. Previous research
 has suggested that nocturnal song may serve a social function and is
 influenced by environmental factors. To test whether males attend to the
 nocturnal song of conspecifics, we experimentally exposed ovenbirds
 (Seiurus aurocapilla) to nocturnal flight songs, and recorded their
 response both during the night and during the following dawn chorus. We
 compared latency to song and vocal output before and after playback
 exposure to determine if males altered their vocalizations in response to
 exposure to flight songs from an unknown male. We found no evidence of
 counter singing or change in nocturnal song output, nor a change in vocal
 output during the dawn chorus following playback exposure. Our results
 suggest that, in ovenbirds, nocturnal song does not serve as an
 intraspecific social function. Nocturnal song, through rare, may be
 significant in the mating systems of some diurnal bird species, and
 requires additional study.
description: JAV-01729
 DataData for playback
 responses, dawn chorus properties, and natural
 countersinging
DOI: 10.5061/dryad.01gr671
title: Data from: Biotic interactions in species distribution models enhance model performance and shed light on natural history of rare birds: a case study using the Straight-billed Reedhaunter (Limnoctites rectirostris)

description: Species distribution models (SDMs) have become a workhorse to explain,
 understand and predict distributions of birds. However, SDMs at broad
 scales are typically built using climatic variables, while ignoring the
 effects of biotic interactions. Although its role still remains
 controversial, the inclusion of biotic interactions into SDMs could
 confirm and/or provide new ecological insights of poorly known species. We
 modeled the distribution of the rare South American straight-billed
 reedhaunter (Limnoctites rectirostris, Furnariidae), a specialist of
 marshy areas linked to the spiny herb eryngo (Eryngium spp., Apiaceae),
 which provides the main food and nest resources. To do this, we first
 modeled the distribution of three eryngo species considered as the main
 biotic interactors (E. eburneum, E. horridum and E. pandanifolium) and
 included them into the straight-billed reedhaunter SDM. Second, we
 analyzed niche overlap between the straight-billed reedhaunter and eryngos
 in terms of environmental variables using dynamic range boxes, a novel
 approach to quantify size of n-dimensional hypervolumes. The inclusion of
 biotic interactions improved model performance relative to a model with
 climatic variables only. Climatic suitability of E. eburneum and mean
 temperature of wettest quarter were the most important predictors. By
 contrast, E horridum and E. pandanifolium resulted in poor predictors,
 suggesting that the straight-billed reedhaunter’s relative dependence on
 each eryngo species is different. The three eryngo environmental spaces
 largely covered the environmental space of the straight-billed
 reedhaunter, but the opposite was not true. Our findings suggest that
 biotic interactions play an important role in explaining and predicting
 the distribution of a rare bird at macro-scales, and that the assessment
 of niche overlap between interactors may confirm or improve the
 autoecological understanding of rare and cryptic birds. We advocate the
 use of an integrative modeling approach including climate and biotic
 interactions into SDMs to enhance ecological knowledge of poorly known
 bird species.
description: occurrences_Limnoctites_Eryngium_SDMsThis file contains the occurrence data of Limnoctites rectirostris, Eryngium eburneum, E. horridum and E. pandanifolium used to build the species distribution models. This is the source of the dots in Figure 2. The data includes species names (species), coordinates (longitude and latitude), the locality, department and country, the type of record (basisOfRecord) and the source. Citations can be found in the Reference section of the paper.
DOI: 10.5061/dryad.b5rg5cs
title: Data from: Niche and fitness differences determine invasion success and impact in laboratory bacterial communities

description: There is increasing awareness of invasion in microbial communities
 worldwide, but the mechanisms behind microbial invasions remain poorly
 understood. Specifically, we know little about how the evolutionary and
 ecological differences between invaders and natives regulate invasion
 success and impact. Darwin’s naturalization hypothesis suggests that the
 phylogenetic distance between invaders and natives could be a useful
 predictor of invasion, and modern coexistence theory proposes that
 invader-native niche and fitness differences combine to determine invasion
 outcome. However, the relative importance of phylogenetic distance, niche
 and fitness differences for microbial invasions has rarely been examined.
 By using laboratory bacterial microcosms as model systems, we
 experimentally assessed the roles of these differences for the success of
 bacterial invaders and their impact on native bacterial community
 structure. We found that the phylogenetic distance between invaders and
 natives failed to explain invasion success and impact for two of three
 invaders at the phylogenetic scale considered. Further, we found that
 invasion success was better explained by invader-native niche differences
 than relative fitness differences for all three invaders, whereas invasion
 impact was better explained by invader-native relative fitness differences
 than niche differences. These findings highlight the utility of
 considering modern coexistence theory to gain a more mechanistic
 understanding of microbial invasions.
description: Community
 dataThe original data used
 to make the figures in our paper, which include: (1) the phylogenetic
 distances (PD), niche differences (ND), and relative fitness differences
 (RFD) of the 24 pairwise invader-native combinations, (2) the mean PD,
 mean ND, mean RFD, invasion establishment, success, and impact for the 324
 microcosms.community
 data.xlsxBayesian
 phylogenyBayesian phylogeny of
 the bacterial species used in this study. The phylogeny shows eight native
 bacterial species, three invaders, and three out-group species. The tree
 was constructed based on the 16s rRNA genes.phylo.tre
DOI: 10.5061/dryad.dn53j
title: Data from: Evolution in situ: hybrid origin and establishment of willows (Salix L.) on alpine glacier forefields

description: Little attention has been paid to the evolutionary consequences of the
 colonizing dynamics and succession processes following glacier retreat.
 Here we studied hybrid populations that have recently formed and
 established on glacier forefields of the European Alps owing to secondary
 contact of a lowland colonizer with a subalpine species. We analyzed the
 composition of two hybrid populations between Salix purpurea and Salix
 helvetica with nine microsatellite markers by using Bayesian methods
 (structure and NewHybrids), and simulations. We also studied niche
 differentiation between the hybrids and the parental species based on
 indicator values, soil pH and water retention potential measurements.
 Allelic structure of hybrids confirms the assumed parentage and in situ
 origin of the crosses on two independent sites within the last decades.
 Both hybrid populations comprised F1 and later generation hybrids (F2 and
 backcrosses), confirming hybrid fertility. The parental species showed
 significant differences in niche characteristics for temperature, soil pH,
 nutrients and moisture. Remarkably, the hybrids exhibited a higher
 tolerance to cold temperatures, nutrient-poor and acidic soils than either
 parent. Our results show that willow hybrids originated after glacier
 retreat and have established persistent populations within a few decades.
 One factor contributing to hybrid establishment in sympatry with their
 parents is their ability to occupy more extreme niches than either
 parental species within a mosaic-like pattern of microhabitats on the
 forefield. Introgression and/or transgressive segregation may have
 resulted in novel genotypes that are able to expand the ecological
 spectrum of either parent.
description: Microsatellite data
 SalixThis file contains the
 microsatellite data of the Salix populations which were sampled at four
 locations. Please note that each location is on a separate sheet. The
 genotypes are arranged in GenAlEx format.
DOI: 10.5061/dryad.2kt43
title: Data from: Evaluating modularity in morphometric data: challenges with the RV coefficient and a new test measure

description: Modularity describes the case where patterns of trait covariation are
 unevenly dispersed across traits. Specifically, trait correlations are
 high and concentrated within subsets of variables (modules), but the
 correlations between traits across modules are relatively weaker. For
 morphometric data sets, hypotheses of modularity are commonly evaluated
 using the RV coefficient, an association statistic used in a wide variety
 of fields. In this article, I explore the properties of the RV coefficient
 using simulated data sets. Using data drawn from a normal distribution
 where the data were neither modular nor integrated in structure, I show
 that the RV coefficient is adversely affected by attributes of the data
 (sample size and the number of variables) that do not characterize the
 covariance structure between sets of variables. Thus, with the RV
 coefficient, patterns of modularity or integration in data are confounded
 with trends generated by sample size and the number of variables, which
 limits biological interpretations and renders comparisons of RV
 coefficients across data sets uninformative. As an alternative, I propose
 the covariance ratio (CR) for quantifying modular structure and show that
 it is unaffected by sample size or the number of variables. Further,
 statistical tests based on the CR exhibit appropriate type I error rates
 and display higher statistical power relative to the RV coefficient when
 evaluating modular data. Overall, these findings demonstrate that the RV
 coefficient does not display statistical characteristics suitable for
 reliable assessment of hypotheses of modular or integrated structure and
 therefore should not be used to evaluate these patterns in morphological
 data sets. By contrast, the covariance ratio meets these criteria and
 provides a useful alternative method for assessing the degree of modular
 structure in morphological data.
description: Plethodon
 DataTPS file containing
 landmark coordinates on the heads of 289 adult Plethodon jordani
 salamanders. Original data from Adams 2004. EcologyPlethodonData.tps
DOI: 10.5061/dryad.5rn52
title: Data from: On the effect specificity of accessory gland products transferred by the love-dart of land snails

description: Background: Sexual selection favours the evolution of male bioactive
 substances transferred during mating to enhance male reproductive success
 by affecting female physiology. These effects are mainly well documented
 for separate-sexed species. In simultaneous hermaphrodites, one of the
 most peculiar examples of transfer of such substances is via stabbing a
 so-called love-dart in land snails. This calcareous stylet delivers mucous
 products produced by accessory glands into the mate's haemolymph. In
 Cornu aspersum, this mucus temporarily causes two changes in the
 recipient. First, the spermatophore uptake into the
 spermatophore-receiving organ, called diverticulum, is probably favoured
 by contractions of this organ. Second, the amount of stored sperm
 increases by contractions of the copulatory canal, which close off the
 tract leading to the sperm digesting organ. However, it has yet to be
 determined whether these effects are similar across species, which would
 imply a common strategy of the dart in increasing male reproductive
 success. Results: We performed a cross-reactivity test to compare the in
 vitro response of the diverticulum and copulatory canal of C. aspersum
 (Helicidae) to its own and other species' mucus (seven helicids and
 one bradybaenid). We found that the contractions in the diverticulum were
 only induced by dart mucus of certain species, while the copulatory canal
 responded equally to all but one species' mucus tested. In addition,
 we report a newly-discovered effect causing the shortening of the
 diverticulum, which is also only caused by dart mucus of certain species.
 The advantage seems to be a distance reduction to the sperm storage organ.
 Conclusions: All these findings are the first to shed light on the
 evolution of the different functions of accessory gland products in
 dart-bearing species. These functions may be achieved via common
 physiological changes caused by the substances contained in the dart
 mucus, since the responses evoked were similar across species' mucus.
 Moreover, while these substances can act similarly in separate-sexed
 species as in simultaneous hermaphrodites, differences may occur in their
 evolution between the two sexual systems.
description: Cross-reactivity
 testShortening
 effect
DOI: 10.17036/researchdata.aston.ac.uk.00000667
title: Effect of GenAI on Academic Performance - a Scoping Review of Pre-Post Tests