cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s5k85k5
title: Data from: Induced expression of a vestigial sexual signal

description: Vestigial morphological traits are common and well known in a variety of
 taxa. Identification of vestigial genes has illustrated the potential for
 evolutionary reversals and the re-expression of atavistic traits. Here we
 induce expression of a behavioral sexual signal, male calling song, in a
 cricket species, Gryllus ovisopis, which lacks a functional calling song.
 We successfully used acetylcholine (Ach) injections in the frontal space
 of the head of male crickets to activate cerebral command neurons for
 cricket calling, and we recorded calling songs with a temporal chirp
 pattern similar to that of G. ovisopis’ close evolutionary relatives, G.
 firmus and G. pennsylvanicus, implying that the neural pattern generators
 which underlie cricket calling behavior persist in a vestigial state in G.
 ovisopis. To our knowledge, this is the first demonstration of the induced
 expression of a vestigial behavior in any organism. The retention of
 latent neural capacity to express sexual behaviors could have important
 implications for rapid evolution, trait re-emergence, and reproductive
 isolation.
description: Data from Gray et al
 Biology Letters.xls file with data on
 (i) recording times of isolated males, and (ii) song characteristics of
 ACh induced calls.
DOI: 10.5061/dryad.n40m6
title: Data from: Protein and carbohydrate intake influence sperm number and male fertility in male cockroaches but not sperm viability

description: It is commonly assumed that because males produce many, tiny sperm, they
 are cheap to produce. Recent work, however, suggests that sperm production
 is not cost-free. If sperm are costly to produce, sperm number and/or
 viability should be influenced by diet, and this has been documented in
 numerous species. Yet few studies have examined the exact nutrients
 responsible for mediating these effects. Here, we quantify the effects of
 protein (P) and carbohydrate (C) intake on sperm number and viability in
 the cockroach Nauphoeta cinerea, as well as the consequences for male
 fertility. We found the intake of P and C influenced sperm number, being
 maximized at a high intake of diets with a P : C ratio of 1 : 2, but not
 sperm viability. The nutritional landscapes for male fertility and sperm
 number were closely aligned, suggesting that sperm number is the major
 determinant of male fertility in N. cinerea. Under dietary choice, males
 regulate nutrient intake at a P : C ratio of 1 : 4.95, which is midway
 between the ratios needed to maximize sperm production and pre-copulatory
 attractiveness in this species. This raises the possibility that males
 regulate nutrient intake to balance the trade-off between pre- and
 post-copulatory traits in this species.
description: Choice
 dataData on dietary choice
 for nutrientsMale fertility
 dataData examining nutrient
 effects of male fertilitySperm
 dataData examining the
 effects of nutrients on sperm number and sperm
 viability
DOI: 10.5061/dryad.m7m72
title: Data from: Loss of connectivity among island-dwelling Peary caribou following sea ice decline

description: Global warming threatens to reduce population connectivity for terrestrial
 wildlife through significant and rapid changes to sea ice. Using genetic
 fingerprinting, we contrasted extant connectivity in island-dwelling Peary
 caribou in northern Canada with continental-migratory caribou. We next
 examined if sea-ice contractions in the last decades modulated population
 connectivity and explored the possible impact of future climate change on
 long-term connectivity among island caribou. We found a strong correlation
 between genetic and geodesic distances for both continental and Peary
 caribou, even after accounting for the possible effect of sea surface. Sea
 ice has thus been an effective corridor for Peary caribou, promoting
 inter-island connectivity and population mixing. Using a time series of
 remote sensing sea-ice data, we show that landscape resistance in the
 Canadian Arctic Archipelago has increased by approximately 15% since 1979
 and may further increase by 20–77% by 2086 under a high-emission scenario
 (RCP8.5). Under the persistent increase in greenhouse gas concentrations,
 reduced connectivity may isolate island-dwelling caribou with potentially
 significant consequences for population viability.
description: RSBL-2016.Data
 SourceThe file contains
 geographic and genetic information on island and mainland caribou
 populations
DOI: 10.15468/dl.6j4sy9
title: Occurrence Download

description: A dataset containing 3257 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Neptunia plena"
 ]
}

 The dataset includes 3257 records from 232 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001061-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tp08m60
title: Data from: Assessment of disease progression in dysferlinopathy – a one year cohort study

description: Objective: To assess the ability of functional measures to detect disease
 progression in dysferlinopathy over 6 months and 1 year. Methods: 193
 patients with dysferlinopathy were recruited to the Jain Foundation’s
 International Clinical Outcome Study for Dysferlinopathy. Baseline, 6
 months and 1 year assessments included: adapted North Star Assessment
 (a-NSAA), Motor Function Measure (MFM-20), timed function tests, 6 minute
 walk test (6MWT), Brooke Scale, Jebsen Test, manual muscle testing (MMT)
 and hand-held dynamometry (HHD). Patients also completed the ACTIVLIM
 questionnaire. Change in each measure over 6 months and 1 year was
 calculated and compared between disease severity (ambulant (mild, moderate
 or severe based on a-NSAA score) or non-ambulant (unable to complete a 10m
 walk)) and clinical diagnosis. Results: The functional a-NSAA test was the
 most sensitive to deterioration for ambulant patients overall. The a-NSAA
 score was the most sensitive test in the mild and moderate group while
 6MWT was most sensitive in the severe group. The 10m walk test was the
 only test showing significant change across all ambulant severity groups.
 In non-ambulant patients, the MFM domain 3, wrist flexion strength and
 pinch grip were most sensitive. Progression rates did not differ by
 clinical diagnosis. Power calculations determined that 46 moderately
 affected patients are required to determine clinical effectiveness for a
 hypothetical 1 year clinical trial based on the a-NSAA as a clinical
 endpoint. Conclusion: Certain functional outcome measures can detect
 changes over 6 months and one year in dysferlinopathy and potentially be
 useful in monitoring progression in clinical trials.
description: Supplementary Table
 1Supplementary Table 1 –
 this table lists the change scores for clinical outcome measures and
 strength tests over 1 year in mildly, moderately and severely affected
 ambulant patients and non-ambulant patientssupplementary table
 1.docx
DOI: 10.5061/dryad.qq08m
title: Data from: Invasive plants have scale-dependent effects on diversity by altering species-area relationships

description: Although invasive plant species often reduce diversity, they rarely cause
 plant extinctions. We surveyed paired invaded and uninvaded plant
 communities from three biomes. We reconcile the discrepancy in diversity
 loss from invaders by showing that invaded communities have lower local
 richness but steeper species accumulation with area than that of uninvaded
 communities, leading to proportionately fewer species loss at broader
 spatial scales. We show that invaders drive scale-dependent biodiversity
 loss through strong neutral sampling effects on the number of individuals
 in a community. We also show that nonneutral species extirpations are due
 to a proportionately larger effect of invaders on common species,
 suggesting that rare species are buffered against extinction. Our study
 provides a synthetic perspective on the threat of invasions to
 biodiversity loss across spatial scales.
description: Relationship between
 species richness and areaData for all 10 of our
 study sites. This data matches figure 1 in the manuscript. Columns in this
 excel file are: Plot size (m^2), Log plot size, number of species observed
 in the plot (i.e., richness), log number of species observed in the plot,
 site (corresponds to the figure), site number (corresponds to figure),
 Community (whether or not the community is in invaded or
 uninvaded)summary.data-SAD.SAR.to.upload.xlsx
DOI: 10.5061/dryad.tt78r
title: Data from: Evolutionary patterns and processes: lessons from ancient DNA

description: Ever since its emergence in 1984, the field of ancient DNA has struggled
 to overcome the challenges related to the decay of DNA molecules in the
 fossil record. With the recent development of high-throughput DNA
 sequencing technologies and molecular techniques tailored to ultra-damaged
 templates, it has now come of age, merging together approaches in
 phylogenomics, population genomics, epigenomics, and metagenomics.
 Leveraging on complete temporal sample series, ancient DNA provides direct
 access to the most important dimension in evolution—time, allowing a
 wealth of fundamental evolutionary processes to be addressed at
 unprecedented resolution. This review taps into the most recent findings
 in ancient DNA research to present analyses of ancient genomic and
 metagenomic data.
description: Data from: Evolutionary
 patterns and processes: lessons from ancient DNAWhole mitochondrial
 genomes from present-day and ancient horses used for the reconstruction of
 the Bayesian skyline plot shown in figure 2bTable S1
 database_mtDNA_SYS_BIOL.xlsx
DOI: 10.5061/dryad.f1948
title: Data from: Litter removal in a tropical rain forest reduces fine root biomass and production but litter addition has few effects

description: Many old-growth lowland tropical rain forests are potentially nutrient
 limited, and it has long been thought that many such forests maintain
 growth by recycling nutrients from decomposing litter. We investigated
 this by continuously removing (for ten years) freshly fallen litter from
 five (45 m x 45 m) plots, adding it to five other plots, there were five
 controls. From monthly measures over one year we show that litter removal
 caused lower: fine root (≤2 mm diameter) standing mass, fine root standing
 length, fine root length production and fine root length survivorship.
 Litter addition did not significantly change fine root mass or length or
 production. Nutrient concentrations in fine roots in litter removal plots
 were lower than those in controls for nitrogen (N), calcium (Ca) and
 magnesium (Mg), concentrations in fine roots in litter addition plots were
 higher for N and Ca. Chronic litter removal has resulted in reduced forest
 growth due to lack of nutrients, probably nitrogen. Conversely, long-term
 litter addition has had fewer effects.
description: Root_Ecology_supplementary_materials
DOI: 10.5061/dryad.k2152
title: Data from: Functional groups, species, and light interact with nutrient limitation during tropical rainforest sapling bottleneck

description: 1. Potential variability in nutrient limitation among tree size classes,
 functional groups, and species calls for an integrated community- and
 ecosystem-level perspective of lowland tropical rainforest nutrient
 limitation. In particular, canopy trees determine ecosystem nutrient
 conditions, but competitive success for nutrients and light during the
 sapling bottleneck determines canopy composition. 2. We conducted an in
 situ multi-nutrient sapling fertilization experiment at La Selva
 Biological Station, Costa Rica, to determine how functional group
 identity, species identity, and light availability can impact nutrient
 limitation of stem growth in three functional groups and nine species. 3.
 Despite high soil fertility, we found nutrient-light limitation in two
 functional groups and four species. Unexpectedly, the nitrogen-fixing
 (“N2fixers”) and shade-tolerant functional groups were significantly
 nutrient limited, while the light-demanding functional group was not. 4.
 This was partially explained by species-level variation of nutrient
 limitation within these functional groups, with only some species
 conforming to the prediction of stronger nutrient limitation in light
 demanders compared to shade tolerants. 5. Most surprisingly, we found
 strong nutrient limitation at low light levels in the N2 fixers (which
 were shade-tolerant), but not in the shade-tolerant non-fixers. We
 hypothesize that the N2 fixers were actually nitrogen limited at low light
 levels because of their nitrogen rich leaves and the high carbon cost of
 their symbionts. 6. This finding suggests a highly shade-tolerant N2
 fixation strategy, in addition to the perception that N2 fixation is
 mostly advantageous in high light environments during early and gap
 succession. The shade-tolerant N2 fixation strategy may be part of a
 sapling and canopy tree feedback, where the canopy N2 fixers enrich the
 soil N, enhancing growth of their shade-tolerant saplings relative to
 non-fixing competitors, enabling further canopy domination by
 shade-tolerant N2 fixers, as seen at La Selva. 7. Synthesis. The
 pervasiveness of functional group- and species-specific nutrient and light
 co-limitation in our saplings indicates that these interactions likely
 play an important role in the dynamics of lowland tropical rainforest
 nutrient limitation, potentially via other such sapling and canopy tree
 feedbacks as the one hypothesized.
description: Chou_sapling_fertilizer_light.csvSapling growth and environmental data collected from our functional group, species, light, and fertilization experiment. See README file for complete documentation.Sapling_data_2_5yrs_dryad.csv
DOI: 10.5061/dryad.h26hs
title: Data from: Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani

description: Background: Dickeya solani is an emerging pathogen that causes soft rot
 and blackleg diseases in several crops including Solanum tuberosum, but
 little is known about its genomic diversity and evolution. Results: We
 combined Illumina and PacBio technologies to complete the genome sequence
 of D. solani strain 3337 that was used as a reference to compare with 19
 other genomes (including that of the type strain IPO2222 T ) which were
 generated by Illumina technology. This population genomic analysis
 highlighted an unexpected variability among D. solani isolates since it
 led to the characterization of two distinct sub-groups within the D.
 solani species. This approach also revealed different types of variations
 such as scattered SNP/InDel variations as well as replacing and additive
 horizontal gene transfers (HGT). Infra-species (between the two D. solani
 sub-groups) and inter-species (between D. solani and D. dianthicola)
 replacing HGTs were observed. Finally, this work pointed that genetic and
 functional variation in the motility trait could contribute to
 aggressiveness variability in D. solani. Conclusions: This work revealed
 that D. solani genomic variability may be caused by SNPs/InDels as well as
 replacing and additive HGT events, including plasmid acquisition; hence
 the D. solani genomes are more dynamic than that were previously proposed.
 This work alerts on precautions in molecular diagnosis of this emerging
 pathogen.
description: Figure
 1This
 is the alignment of the sequences used for the MLSA analysis, these
 sequences are generated by concatenating 11 housekeeping genes as
 described in the publication. the and the tree alignment were performed
 using MEGA 6 software.figure1.rarFigure 4This file contains the alignments and trees generated using MEGA6. the trees are presented in the figure 4 in the publication.figure 4.rarFigures 5_6_7these are the alignments of the sequences genes (amN, oppF, oppB, dnaJ, dnaK, mogA, norF, norR and fumA) used to generate trees that are presented in the figures 5, 6 and 7 in the publication. we have used MEGA6 to perform alignments.figures 5_6_7.rar
DOI: 10.5061/dryad.30sq1
title: Data from: Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique

description: Background: Intraspecific genetic variation of African fauna has been
 signific antly affected by pronounced climatic fluctuations in
 Plio-Pleistocene, but, with the exception of large mammals, very limited
 empirical data on diversity of natural populations are available for
 savanna-dwelling animals. Nothobranchius furzeri is an annual fish from
 south-eastern Africa, inhabiting discrete temporary savannah pools outside
 main river alluvia. Their dispersal is limited and population processes
 affecting its genetic structure are likely a combination of those
 affecting terrestrial and aquatic taxa. N. furzeri is a model taxon in
 ageing research and several populations of known geographical origin are
 used in laboratory studies. Here, we analysed the genetic structure,
 diversity, historical demography and temporal patterns of divergence in
 natural populations of N. furzeri across its entire distribution range.
 Results: Genetic structure and historical demography of N. furzeri were
 analysed using a combination of mitochondrial (partial cytochrome b
 sequences, 687 bp) and nuclear (13 microsatellites) markers in 693 fish
 from 36 populations. Genetic markers consistently demonstrated strong
 population structuring and suggested two main genetic groups associated
 with river basins. The split was dated to the Pliocene (&gt;2 Mya).
 The northern group inhabits savannah pools across the basin of the
 intermittent river Chefu in south-western Mozambique and eastern Zimbabwe.
 The southern group (from southernmost Mozambique) is subdivided, with the
 River Limpopo forming a barrier (maximum divergence time 1 Mya). A strong
 habitat fragmentation (isolated temporary pools) is reflected in
 significant genetic structuring even between adjacent pools, with a major
 influence of genetic drift and significant isolation-by-distance. Analysis
 of historical demography revealed that the expansion of both groups is
 ongoing, supported by frequent founder effects in marginal parts of the
 range and evidence of secondary contact between Chefu and Limpopo
 populations. Conclusions: We demonstrated: (1) ancient (pre-Pleistocene)
 divergence between the two main N. furzeri lineages, their recent
 secondary contact and lack of reproductive isolation; (2) important
 genetic structuring attributed to the fragmented nature of their
 environment and isolation-by-distance, suggesting that dispersal is
 limited, occurs over short distances and is not directly associated with
 river routes; (3) an apparent role of the River Limpopo as a barrier to
 dispersal and gene flow.
description: Bartakova et
 almicrosatellite genotypes
 of all individuals, genepop format + list of loci
DOI: 10.5061/dryad.4qn6n
title: Data from: Phenotypic and genomic plasticity of alternative male reproductive tactics in sailfin mollies

description: A major goal of modern evolutionary biology is to understand the causes
 and consequences of phenotypic plasticity, the ability of a single
 genotype to produce multiple phenotypes in response to variable
 environments. While ecological and quantitative genetic studies have
 evaluated models of the evolution of adaptive plasticity, some
 long-standing questions about plasticity require more mechanistic
 approaches. Here, we address two of those questions: does plasticity
 facilitate adaptive evolution? And do physiological costs place limits on
 plasticity? We examine these questions by comparing genetically and
 plastically regulated behavioural variation in sailfin mollies (Poecilia
 latipinna), which exhibit striking variation in plasticity for male mating
 behaviour. In this species, some genotypes respond plastically to a change
 in the social environment by switching between primarily courting and
 primarily sneaking behaviour. In contrast, other genotypes have fixed
 mating strategies (either courting or sneaking) and do not display
 plasticity. We found that genetic and plastic variation in behaviour were
 accompanied by partially, but not completely overlapping changes in brain
 gene expression, in partial support of models that predict that plasticity
 can facilitate adaptive evolution. We also found that behavioural
 plasticity was accompanied by broader and more robust changes in brain
 gene expression, suggesting a substantial physiological cost to
 plasticity. We also observed that sneaking behaviour, but not courting,
 was associated with upregulation of genes involved in learning and memory,
 suggesting that sneaking is more cognitively demanding than courtship.
description: Focal male
 dataThis file contains all
 the data on focal male phenotypes (morphological and behavioral), and data
 on collection dates and behavioral trial conditions.BaldPoint_molly_data.xlsx
DOI: 10.5061/dryad.bb28n
title: Data from: Soil drainage facilitates earthworm invasion and subsequent carbon loss from peatland soil

description: 1. Human activities have been a significant driver of environmental
 changes with tremendous consequences for carbon dynamics. Peatlands are
 critical ecosystems because they store ~30% of the global soil organic
 carbon pool and are particularly vulnerable to anthropogenic changes. The
 Zoige peatland on the eastern Tibet Plateau, as the largest alpine
 peatland in the world, accounts for 1‰ of global peat soil organic carbon
 storage. However, this peatland has experienced dramatic climate change
 including increased temperature and reduced precipitation in the past
 decades, which likely is responsible for a decline of the water table and
 facilitated earthworm invasion, two major factors reducing soil organic
 carbon (SOC) storage of peatlands. 2. Because earthworms are often more
 active in low- than in high- moisture peatlands, we hypothesized that the
 simultaneous occurrence of water table decline and earthworm invasion
 would synergistically accelerate the release of SOC from peatland soil. We
 conducted a field experiment with a paired split-plot design, i.e.
 presence vs. absence of the invasive earthworms (Pheretima aspergillum)
 nested in drained vs. undrained plots, respectively, for three years
 within the homogenous Zoige peatland. 3. Water table decline significantly
 decreased soil water content and bulk density, resulting in a marked
 reduction of SOC storage. Moreover, consistent with our hypothesis,
 earthworm presence dramatically reduced SOC in the drained but not in the
 undrained peatland through the formation of deep burrows and decreasing
 bulk density of the lower soil layer over three years. The variation in
 SOC likely was due to changes in aboveground plant biomass, root growth,
 and earthworm behavior induced by the experimental treatments.4. Synthesis
 and applications. We suggest that incentive measures should be taken to
 prevent further water table decline and earthworm invasion for maintaining
 the soil C pool in Zoige peatland. Artificial filling of drainage canals
 should be implemented to increase the water table level, facilitating the
 recovery of drained peatlands. Moreover, the dispersal of earthworms and
 their cocoons attached to the roots of crop plants and tree saplings from
 low-lying areas to the Zoige region should be prevented.
description: data from: Soil drainage
 facilitates earthworm invasion and subsequent carbon loss from peatland
 soildataset for both the
 earthworm response experiment and the primary
 experimentdataset_JAPE.xlsx