cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9s4mw6mhf
title: Epistatic interactions between sex chromosomes and autosomes can affect the stability of sex determination systems

description: Sex determination (SD) is an essential and ancient developmental process,
 but the genetic systems that regulate this process are surprisingly
 variable. Why SD mechanisms vary so much is a longstanding question in
 evolutionary biology. SD genes are generally located on sex chromosomes
 which also carry genes that interact epistatically with autosomes to
 affect fitness. How this affects the evolutionary stability of SD
 mechanisms is still unknown. Here, we explore how epistatic interactions
 between a sexually antagonistic (SA) non-SD gene, located on either an
 ancestral or novel sex chromosome, and an autosomal gene affect the
 conditions under which an evolutionary transition to a new SD system
 occurs. We find that when the SD gene is linked to an ancestral sex
 chromosomal gene which engages in epistatic interactions, epistasis
 enhances the stability of the sex chromosomes so that they are retained
 under conditions where transitions would otherwise occur. This occurs both
 when weaker fitness effects are associated with the ancestral sex
 chromosome pair or stronger fitness effects associated with a
 newly-evolved SD gene. However, the probability that novel SD genes spread
 is unaffected if they arise near genes involved in epistasis. This
 discrepancy occurs because on autosomes, SA allele frequencies are
 typically lower than on sex chromosomes. In our model, increased
 frequencies of these alleles contribute to a higher frequency of epistasis
 which may therefore more readily occur on sex chromosomes. Because sex
 chromosome-autosome interactions are abundant and can take several forms,
 they may play a large role in maintaining sex chromosomes.
description: Data were generated using an evolutionary genetic model written
 in R (available through
 https://github.com/MartijnSchenkel/EpistasisSexDetermination); processing
 and analysis files, including secondary data and resulting figures, can be
 found there as well.
DOI: 10.5061/dryad.6q573n60c
title: Labeled motor neurons following single and double nerve reinnervation of the long head of the biceps

description: We developed a novel rat model to investigate the neurophysiological
 effects of peripheral double nerve transfers to a single target
 muscle. In 62 male Sprague-Dawley rats the ulnar nerve of the
 antebrachium alone (n=30) or together with the anterior interosseus nerve
 (n=32) was transferred to reinnervate the long head of the biceps brachii.
 To further assess reinnervation, retrograde labeling was performed. Twelve
 weeks following surgery retrograde tracer dyes were injected
 in the long head of the biceps muscle to stain the
 reinnervating motoneurons. In 7 control animals, the number of innervating
 motorneurons was assessed by injecting retrograde tracer in the untreated
 long head of the biceps. The aim of this dataset was to compare the
 effects of single nerve transfer and double nerve transfer on motor neuron
 count.
DOI: 10.5061/dryad.3bk3j9kkk
title: Tragedy of the commons in Melipona bees revisited

description: Melipona stingless bees display a paradoxical overproduction of queens,
 which are later eliminated by nestmate workers. Mechanistically, it was
 suggested that the monoterpenoid geraniol deposited into newly provisioned
 cells by adult bees would cause larvae to develop into queens in Melipona
 beecheii. This system could be evolutionarily stable if many of these new
 queens would leave the nest and parasitize other genetically unrelated
 colonies nearby, as was shown to occur in a congeneric species. Here, we
 use microsatellite markers to test whether queen overproduction could be a
 strategy by which adult workers control the caste fate of the developing
 larvae to export copies of their own genes to the rest of the population
 via queen parasitism in M. beecheii. In addition, we re-examined whether
 artificially increasing the levels of geraniol indeed caused larvae to
 develop as queens rather than workers. Contrary to our prediction, we
 found no evidence for queen parasitism in M. beecheii and observed no
 effect of geraniol on the rearing of new queens. Together, these results
 support the original “tragedy of the commons” hypothesis for queen
 overproduction in Melipona bees, where individual larvae selfishly bias
 their development towards the queen pathway according to their best
 evolutionary interests.
DOI: 10.5061/dryad.nzs7h44sf
title: Experimental evidence for the recovery of mercury-contaminated fish populations

description: Anthropogenic releases of mercury (Hg) are a human health
 issue because the potent toxicant methylmercury (MeHg), formed
 primarily by microbial methylation of inorganic Hg in aquatic ecosystems,
 bioaccumulates to high concentrations in fish consumed by humans.
 Predicting the efficacy of Hg pollution controls on fish MeHg
 concentrations is complex because many factors influence the production
 and bioaccumulation of MeHg. Here we conducted a 15-year whole-ecosystem,
 single-factor experiment to determine the magnitude and timing of
 reductions in fish MeHg concentrations following reductions in Hg
 additions to a boreal lake and its watershed. During the seven-year
 addition phase, we applied enriched Hg isotopes to increase local Hg wet
 deposition rates fivefold. The Hg isotopes became increasingly
 incorporated into the food web as MeHg, predominantly from additions to
 the lake because most of those added to the watershed remained there.
 Thereafter, isotopic additions were stopped, resulting in an approximately
 100% reduction in Hg loading to the lake. The concentration of labelled
 MeHg quickly decreased by more than 85% in lower trophic level organisms,
 initiating rapid decreases of 38–76% of MeHg concentration in large-bodied
 fish populations in eight years. Although Hg loading from watersheds may
 not decline in step with lowering deposition rates, this experiment
 clearly demonstrates that any reduction in Hg loadings to lakes, whether
 from direct deposition or runoff, will have immediate benefits to fish
 consumers.
description: See manuscript
DOI: 10.5061/dryad.280gb5mqt
title: Competition dynamics in long-term propagations of Schizosaccharomyces pombe strain communities

description: Experimental evolution studies with microorganisms such as bacteria and
 yeast have been an increasingly important and powerful tool to draw
 long-term inferences of how microbes interact. However, while several
 strains of the same species often exist in natural environments, many
 ecology and evolution studies in microbes are typically performed with
 isogenic populations of bacteria or yeast. In the present study, we
 firstly perform a genotypic and phenotypic characterization of two lab and
 eight natural strains of the yeast Schizosaccharomyces pombe. We then
 propagated, in a rich resource environment, yeast communities of 2-, 3-,
 4- and 5-strains for hundreds of generations and asked which fitness
 related phenotypes – maximum growth rate or relative competitive fitness –
 would better predict the outcome of a focal strain during the
 propagations. While the strain’s growth rates would wrongly predict
 long-term co-existence, pairwise competitive fitness with a focal strain
 qualitatively predicted the success or extinction of the focal strain by a
 simple multi-genotype population genetics model, given the initial
 community composition. Interestingly, we have also measured the
 competitive fitness of the ancestral and evolved communities by the end of
 the experiment (≈370 generations) and observed frequent maladaptation to
 the abiotic environment in communities with more than three members.
 Overall, our results aid establishing pairwise competitive fitness as good
 qualitative measurement of long-term community composition but also reveal
 a complex adaptive scenario when trying to predict the evolutionary
 outcome of those communities.
DOI: 10.5061/dryad.34tmpg4m4
title: Oxylipin Data set

description: The soluble epoxide hydrolase (sEH) enzyme is a major regulator of
 bioactive lipids. The enzyme is highly expressed in liver and kidney and
 modulates levels of endogenous epoxy-fatty acids which have pleiotropic
 biological effects including limiting inflammation, neuroinflammation and
 hypertension. It has been hypothesized that inhibiting sEH has beneficial
 effects on limiting obesity and metabolic disease as well. There is a body
 of literature published on these effects, but typically only male subjects
 have been included. Here we investigate the role of sEH in both male and
 female mice and use a global sEH knockout mouse model to compare the
 effects of diet and diet induced obesity. The results demonstrate sEH
 activity in the liver is modulated by high fat diets in male compared to
 female mice. In addition, we characterized the sEH activity in high fat
 content tissues and demonstrated the influence of diet on levels of
 bioactive epoxy-fatty acids. The sEH KO animals had generally increased
 epoxy-fatty acids compared to wildtype mice but gained less body weight on
 higher fat diets. Proinflammatory prostaglandins and triglycerides were
 also lower in livers of sEH KO mice fed HFD. Thus, sEH activity,
 prostaglandins and triglycerides increase in male mice on high fat diet
 but are all limited by sEH ablation. Additionally, these changes also
 occur in female mice though at a different magnitude and are also improved
 by knockout of the sEH enzyme.
description: LC MS/MS quantification and analysis of oxylipin metabolites from
 murine tissue samples.
DOI: 10.5061/dryad.zgmsbccck
title: The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical datasets

description: The software program STRUCTURE is one of the most cited tools for
 determining population structure. To infer the optimal number of clusters
 from STRUCTURE output, the ΔK method is often applied. However, a recent
 study relying on simulated microsatellite data suggested that this method
 has a downward bias in its estimation of K and is sensitive to uneven
 sampling. If this finding holds for empirical datasets, conclusions about
 the scale of gene flow may have to be revised for a large number of
 studies. To determine the impact of method choice, we applied recently
 described estimators of K to re-estimate genetic structure in 41 empirical
 microsatellite datasets; 15 from a broad range of taxa and 26 focused on a
 diverse phylogenetic group, coral. We compared alternative estimates of K
 (Puechmaille statistics) with traditional (ΔK and posterior probability)
 estimates and found widespread disagreement of estimators across datasets.
 Thus, one estimator alone is insufficient for determining the optimal
 number of clusters regardless of study organism or evenness of sampling
 scheme. Subsequent analysis of molecular variance (AMOVA) between
 clustering solutions did not necessarily clarify which solution was best.
 To better infer population structure, we suggest a combination of visual
 inspection of STRUCTURE plots and calculation of the alternative
 estimators at various thresholds in addition to ΔK. Differences between
 estimators could reveal patterns with important biological implications,
 such as the potential for more population structure than previously
 estimated, as was the case for many studies reanalyzed here.
description: These are microsatellite data from 41 empirical datasets. Each
 microsatellite dataset was re-run through the software program STRUCTURE
 (via the R packages ParallelStructure) using the same settings as were
 used in the original publication. They were then processed in R to
 estimate optimal K values according to the Delta K method, the posterior
 probability method, and the Puechmaille statistics. Further, they were
 processed via CLUMPAK.
DOI: 10.5061/dryad.9kd51c5j1
title: Passive acoustic records of Lake Sturgeon calling activity in Detroit River

description: Lake sturgeon (Acipenser fulvescens) are endangered in the Laurentian
 Great Lakes with increasing binational efforts to establish spawning
 grounds to aid restoration. While SCUBA surveys can document spawning
 activity, these are labour-intensive and may disrupt spawning. We used
 passive acoustic monitoring to quantify spawning sounds of lake sturgeon
 as a first step to developing remote sensing of sturgeon spawning grounds.
 Acipenser sp. are known to make a variety of sounds including, “thunders”
 (aka drums), which have been documented in A. fulvescens during spawning.
 We quantified drums from a known spawning bed. We recorded 5 different
 potential sturgeon sounds but only quantified drums as a marker for
 spawning activity. Drums were low frequency with average frequency peaks
 at 40 and 92 Hz and a rapid drop-off thereafter. There was no relationship
 between calling activity and water temperature but calling activity
 increased as the summer progressed. Call production was most active from
 0600-1500h with little calling activity during nighttime recordings. The
 presence of low frequency boat sounds did correlate with a reduction in
 maximum calling rate so it is possible that commercial shipping may
 disrupt sturgeon communication, but more research is necessary to separate
 correlational from causative effects. These recordings represent a
 promising approach to map sturgeon spawning activity and show the
 potential effect of human activity on communication in this threatened
 species.
description: All sounds were collected from passive acoustic hydrophones as
 long-term recorders off a known spawning bed.
DOI: 10.21979/n9/zhz9bh
title: Replication Data for: Dicke superradiance requires interactions beyond nearest-neighbors

description: Photon-mediated interactions within an excited ensemble of emitters can result in Dicke superradiance, where the emission rate is greatly enhanced, manifesting as a high-intensity burst at short times. The superradiant burst is most commonly observed in systems with long-range interactions between the emitters, although the minimal interaction range remains unknown. Here, we put forward a new theoretical method to bound the maximum emission rate by upper bounding the spectral radius of an auxiliary Hamiltonian. We harness this tool to prove that for an arbitrary ordered array with only nearest-neighbor interactions in all dimensions, a superradiant burst is not physically observable. We show that Dicke superradiance requires minimally the inclusion of next-nearest-neighbor interactions. For exponentially decaying interactions, the critical coupling is found to be asymptotically independent of the number of emitters in all dimensions, thereby defining the threshold interaction range where the collective enhancement balances out the decoherence effects. Our findings provide key physical insights to the understanding of collective decay in many-body quantum systems, and the designing of superradiant emission in physical systems for applications such as energy harvesting and quantum sensing.
DOI: 10.5061/dryad.3bk3j9kkm
title: Data from: Multispecies site occupancy modeling and study design for spatially replicated environmental DNA metabarcoding

description: Although environmental DNA (eDNA) metabarcoding has become widely applied
 to gauge ecosystems in a noninvasive and cost-efficient manner, false
 negatives can occur due to various factors in its inherent multistage
 workflow. It is therefore essential to deal with this kind of species
 detection errors in eDNA metabarcoding to achieve accurate assessment of
 species distribution and diversity. To address this issue, we proposed a
 variant of the multispecies site occupancy model for eDNA metabarcoding
 studies and applied it to an eDNA metabarcoding dataset of freshwater fish
 communities collected in the Kasumigaura watershed in Japan.
description: This is an archive of the dataset used for the analysis and
 script files needed to reproduce the results. There are the following five
 files: 
 <strong>1_model_fitting.R</strong>: R script for fitting the
 multispecies site occupancy model proposed in the paper to an eDNA
 metabarcoding dataset of fish communities. The second half of the file
 also contains scripts for assessing and plotting the model-fit
 results. 
 <strong>2_decision_analysis.R</strong>: R script for
 estimating the effectiveness of species detection under various study
 designs based on the model-fit results. The second half of the file
 contains scripts for drawing profiles of the estimated effectiveness of
 the species detection. 
 <strong>data.Rdata</strong>: This file contains sequence read
 count data for 50 fish species groups obtained via environmental DNA
 metabarcoding at 50 sites in the Kasumigaura watershed, Japan. The file is
 in binary format written out using the save() function in R. In addition
 to a three-dimensional array of sequence reads with species, site, and
 replicate dimensions, there are two vectors of covariates (riverbank and
 mismatch) used to explain the variation in the sequence read
 counts. <strong>functions.R</strong>:
 This file defines auxiliary functions for the analyses performed using the
 two R scripts (1_model_fitting.R and 2_decision_analysis.R).
 <strong>model.jags</strong>: JAGS model file that
 defines the multispecies site occupancy model to be fitted in the R script
 1_model_fitting.R.
DOI: 10.5061/dryad.k3j9kd581
title: Butterfly functional diversity in north west Japan

description: Anthropogenic activities can negatively impact the major shifts in
 butterfly functional diversity in semi-natural ecosystems. However, little
 is known about their functional trait diversity, rather than total species
 richness, driven by forest fragmentation and urbanization. In the present
 study, we evaluated whether forest fragmentation and urbanization affects
 the functional diversity and stability of butterfly assemblages. Regarding
 the anthropogenic impacts on butterfly biodiversity loss, we predicted
 that the functional diversity and temporal stability of butterfly species
 would increase with increasing area of fragmented forests, and that they
 would be higher in the rural areas than in the urban areas. The present
 study demonstrated that butterfly functional diversity and stability of
 species composition were maintained in the presence of larger forest
 remnant and less urbanized areas. In particular, the uni-voltine species
 and species overwintering during the egg-pupa stage were significantly
 negatively affected by forest fragmentation. We emphasized that future
 studies should use multi-functional traits of insect species to evaluate
 the impact of human activities on insect declines, as past studies may
 have overlooked this significant key for assessing species vulnerability
 and ecological adaptations under human activities.
description: The dataset was collected during 1999-2005 at Kanazawa City,
 located in the temperate region of Japan. This study has been reviewed in
 Biology letters.
description: The readme file contains an explanation of each of the variables
 in the dataset (species richness, environmental variables), and its
 measurement units (line and site). How to measure these data can be found
 in the manuscript.
DOI: 10.5061/dryad.qnk98sfhj
title: Data from: 2D, 2Layer, interfacial waves due to one vortex pair

description: This data set contains the results of the downstream wave heights of the
 interfacial waves in the 2D, 2Layer fluids flows considered in the
 article Interference of Internal waves due to two point vortices:
 linear analytical solution and nonlinear interaction". This work
 considered the interaction/interference between two vortices int the
 background of the 2D, 2-Layer fluids flows to simulate the ocean internal
 waves. More details about the research can be seen in the draft. Besides,
 MATLAB files that were used to calculate numerical fully nonlinear
 solutions and linearized solutions, to evalutate the downstream
 wave heights/lengths, and to generates figures located in the article are
 contained. The Folder jfnk contains the functions that evaluate
 the nonlinear solutions via JFNK method. The
 Folder linear contains the functions that can be used to evaluate
 the linearized solutions. And the
 folder reusltsAnalysis consists of the tools that
 evaluate the wave height/length of the nonlinear solutions. The results in
 the data provide the nonlinear downstream wave heights which vary
 with the distance between two vortices. Four cases based on different
 signs of these two vortices are considered: both positive (denoted as PP),
 both negative (denoted as NN), one positive one negative (denoted as PN),
 and one negative one positive (denoted as NP). More analysis and
 results are presented in the article.
description: The results data are evaluated from the nonlinear solutions,
 which are obtained by the following functions. The
 functions in the folder<em> jfnk</em> implement the
 calculations of the interfacial waves via JFNK method with a
 preconditioner. The functions in the folder
 <em>linear</em> implements the evaluations of the linearized
 solutions in the form of the Cauchy integral. The
 functions in the folder <em>reusltsAnalysis </em>return
 the<em> </em>wave height/ wave length/ amplitude of the steady
 downstream waves via searching the local minimum/maximum of the nonlinear
 wave profiles.
description: The function <em>mytest_JFNK</em> in the folder
 <em>jfnk</em> is the main function.
 Meanwhile, the function <em>interfaceEta_vp</em>
 and <em>linearizedHeight_vp </em>can be used
 directly.