Find research datasets worth reusing

opencc-by-4.0Jan 2022View details →

Data for V1298 Tau TESS Transit Fits

Light curve and Gaussian-process model data for the TESS observations of V1298 Tau. See our GitHub repository (<a href="https://github.com/afeinstein20/v1298tau_tess">https://github.com/afeinstein20/v1298tau_tess</a>) for Jupyter Notebooks on how to interact with these files.

opencc-by-4.0Jan 2022View details →

Navel healing and calf fitness for transport

Dairy male calves are at risk of welfare compromise as they are usually transported at a very young age. The European Union has set a “completely healed navel” requirement for calf transport; moreover, a minimum age is established for longer journeys. However, this requirement has proven to be prone to misinterpretation. This study aimed to clarify what is meant by “navel healing” and to provide strong elements for reaching a consensus. The navels of 299 dairy calves (55 males, 244 females) aged 0–90 days were examined and scored 1 to 5 according to their healing status. Based on our results, a completely dry and shriveled navel (score 3) would imply a 25.5–38.0% risk of transporting too young calves. Alternatively, the presence of a scab covering the umbilical wound (score 4) would entail a 4.3% risk of transporting calves less than 10 days old and could be considered good practice for transporting calves (except for journeys exceeding 8 h). Conversely, complete navel healing (score 5) guarantees that calves that are too young are not transported; therefore, it should be considered best practice for transporting calves in general and the minimum requirement for transporting calves for journeys exceeding 8 h.

opencc-by-4.0Feb 2022View details →

Fit to template of horseback shapes

The  csv file contains the polynomial coefficients of   10th order polynoms for  reconstructing the different horses profiles on templates obtained by a professional horse saddler. All the dimensions in x and y are in cm. Column 1 contains an id for each horse. Columns  2 and 3 contain the bounds of the intervals on the x axis. Columns 4 to  14 give the coefficients of the polynom for the CL curve Columns   15 and 16 contain the bounds of the intervals on the x axis. Columns 17 to  27 give the coefficients of the polynom for the CT1 curve Columns  28 and 29 contain the bounds of the intervals on the x axis. Columns 30 to  40 give the coefficients of the polynom for the CT2 curve Columns  41 and 42 contain the bounds of the intervals on the x axis. Columns 43 to  53 give the coefficients of the polynom for the CT3 curve

opencc-zeroApr 2022View details →

The quantitative genetics of fitness in a wild seabird

Additive genetic variance in fitness is a prerequisite for adaptive evolution, as a trait must be genetically correlated with fitness to evolve. Despite its relevance, additive genetic variance in fitness has not often been estimated in nature. Here, we investigate additive genetic variance in lifetime and annual fitness components in common terns (Sterna hirundo). Using 28 years of data comprising ca. 6000 pedigreed individuals, we find that additive genetic variances in the Zero-inflated and Poisson components of lifetime fitness were effectively zero, but estimated with high uncertainty. Similarly, additive genetic variances in adult annual reproductive success and survival did not differ from zero, but were again associated with high uncertainty. Simulations suggested that we would be able to detect additive genetic variances as low as 0.05 for the Zero-inflated component of fitness, but not for the Poisson component, for which adequate statistical power would require c. two more decades (four tern generations) of data collection. As such, our study suggests heritable variance in common tern fitness to be rather low if not zero, shows how studying the quantitative genetics of fitness in natural populations remains challenging, and highlights the importance of maintaining long-term individual-based studies of natural populations.

opencc-zeroDec 2021View details →

Fitness effects of mutations: An assessment of PROVEAN predictions using mutation accumulation data

Predicting fitness in natural populations is a major challenge in biology. It may be possible to leverage fast-accumulating genomic datasets to infer the fitness effects of mutant alleles, allowing evolutionary questions to be addressed in any organism. In this paper, we investigate the utility of one such tool, called PROVEAN. This program compares a query sequence with existing data to provide an alignment-based score for any protein variant, with scores categorized as neutral or deleterious based on a preset threshold. PROVEAN has been used widely in evolutionary studies, e.g., to estimate mutation load in natural populations, but has not been formally tested as a predictor of aggregate mutational effects on fitness. Using three large, published datasets on the genome sequences of laboratory mutation accumulation lines, we assessed how well PROVEAN predicted the actual fitness patterns observed, relative to other metrics. In most cases, we find that a simple count of the total number of mutant proteins is a better predictor of fitness than the number of variants scored as deleterious by PROVEAN. We also find that the sum of all mutant protein scores explains variation in fitness better than the number of mutant proteins in one of the datasets. We discuss the implications of these results for studies of populations in the wild.

opencc-zeroApr 2022View details →

Data from: Sustained positive consequences of genetic rescue of fitness and behavioural traits in inbred populations of Drosophila melanogaster

One solution to alleviate the detrimental genetic effects associated with reductions in population size and fragmentation is to introduce immigrants from other populations. While the effects of this genetic rescue on fitness traits are fairly well known, it is less clear to what extent inbreeding depression and subsequent genetic rescue affects behavioural traits. In this study, replicated crosses between inbred lines of Drosophila melanogaster were performed in order to investigate the effects of inbreeding and genetic rescue on egg-to-adult viability and negative geotaxis behaviour - a locomotor response used to measure e.g. the effects of physiological ageing. Transgenerational effects of outcrossing were investigated by examining the fitness consequences in both the F1 and F4 generation. The majority of inbred lines showed evidence for inbreeding depression for both egg-to-adult viability and behavioural performance (95% and 66% of lines, respectively), with inbreeding depression being more pronounced for viability compared to locomotor response. Subsequent outcrossing with immigrants led to an alleviation of the negative effects for both viability and geotaxis response resulting in inbred lines being similar to the outbred controls, with beneficial effects persisting from F1 to F4. Overall, the results clearly show that genetic rescue can provide transgenerational rescue of small, inbred populations by rapidly improving population fitness components. Thus, we show that even the negative effects of inbreeding on behaviour, similar to that of neurodegeneration associated with physiological ageing, can be reversed by genetic rescue.

Maximization of fitness by phenological and phenotypic plasticity in range expanding rabbitfish (Siganidae)

Global warming is modifying the phenology, life-history traits and biogeography of species around the world. Evidence of these effects have increased over recent decades; however, we still have a poor understanding of the possible outcomes of their interplay across global climatic gradients, hindering our ability to accurately predict the consequences of climate change in populations and ecosystems. We examined the effect that changes in biogeography can have on the life-history traits of two of the most successful range-extending fish species in the world: the tropical rabbitfishes Siganus fuscescens and Siganus rivulatus. Both species have established abundant populations at higher latitudes (poleward) in the northern and southern hemispheres and have been identified as important ecological engineers with the potential to alter the community structure of seaweed forests (Laminariales and Fucales) in temperate regions. Life-history trait information from across their global distribution was compiled from the published literature and meta-analyses were conducted to assess changes in (i) the onset and duration of reproductive periods, (ii) fecundity, (iii) size at maturity, (iv) growth rates, (v) maximum body sizes and (vi) longevity in populations at the leading edge of range expansion in relation to sea surface temperature and primary productivity (i.e., a common proxy for nutritional resource levels). Populations at highest latitudes had shortened their reproductive periods and reduced growth rates, taking longer to reach sexual maturity and maximum sizes, but compensated this with higher fecundity per length class and longer lifespans than populations in warmer environments. Low primary productivity and temperature in the Mediterranean Sea resulted in lower growth rates and body sizes for S. rivulatus, but also lower length at maturity, leading to increased life-time reproductive output. The results suggest that plasticity in the phenology and life-history traits of range-expanding species would be important to enhance their fitness in high latitude environments, facilitating their persistence and possible further poleward expansions. Quantifying the magnitude and direction of these responses can improve our understanding and ability to forecast species redistributions and its repercussions in the functioning of temperate ecosystems.

Strong selective environments determine evolutionary outcome in time-dependent fitness seascapes

The impact of fitness landscape features on evolutionary outcomes has attracted considerable interest in recent decades. However, evolution often occurs under time-dependent selection in so-called fitness seascapes where the landscape is under flux. Fitness seascapes are an inherent feature of natural environments, where the landscape changes owing both to the intrinsic fitness consequences of previous adaptations and extrinsic changes in selected traits caused by new environments. The complexity of such seascapes may curb the predictability of evolution. However, empirical efforts to test this question utilising a comprehensive set of regimes are lacking. Here we employed an in vitro microbial model system to investigate differences in evolutionary outcomes between time-invariant and -dependent environments, including all possible temporal permutations, with three subinhibitory antimicrobials and a viral parasite (phage) as selective agents. Expectedly, time-invariant environments caused stronger directional selection for resistances compared to time-dependent environments. Intriguingly, however, multidrug resistance outcomes in both cases were largely driven by two strong selective agents (rifampicin and phage) out of four agents in total. These agents either caused cross-resistance or obscured the phenotypic effect of other resistance mutations, modulating the evolutionary outcome overall in time-invariant environments and as a function of exposure epoch in time-dependent environments. This suggests that identifying strong selective agents and their pleiotropic effects is critical for predicting evolution in fitness seascapes, with ramifications for evolutionarily informed strategies to mitigate drug resistance evolution.

Mating and fitness consequences of variation in male allocation in a wind pollinated plant

In hermaphrodites, the allocation of resources to each sex function can influence fitness through mating success. A prediction that arises from sex allocation theory is that in wind-pollinated plants, male fitness should increase linearly with investment of resources into male function but there have been few empirical tests of this prediction. In a field experiment we experimentally manipulated allocation to male function in Ambrosia artemisiifolia (common ragweed) and measured mating success in contrasting phenotypes using genetic markers. We investigated the effects of morphological traits and flowering phenology on male siring success, and on the diversity of mates. Our results provide evidence for a linear relation between allocation to male function, mating and fitness. We find earlier onset of male flowering time increases reproductive success, whereas later flowering increases the probability of mating with diverse individuals. Our study is among the first empirical studies testing the prediction of linear male fitness returns in wind pollinated plants and emphasize the importance of a large investment into male function by wind pollinated plants and mating consequences of temporal variation in sex allocation.

opencc-by-4.0May 2022View details →

Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection - microscopic dataset

Microscopic datasets (TEM, SEM and AFM) supporting the manuscript entitled: Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection.

opencc-by-4.0May 2022View details →

Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection - mutants genomes dataset

Raw genome sequence (genomes of the phage-resistant D. solani Tn5 mutants) dataset supporting the manuscript entitled: Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection.

Data from: Loss-of-heterozygosity facilitates a fitness valley crossing in experimentally evolved multicellular yeast

These data sets are generated to investigate a simple evolutionary landscape that arises from underdominance at a single locus where the fitness valley consists of only one less-fit genotype. We make use of an experimental system previous evolved in the laboratory, the Saccharomyces cerevisiae snowflake system. This system was experimentally selected resulting in a significant evolutionary shift, the transition from uni-to-multicellularity in asexual diploid populations. We carried out the phenotypic and fitness characterization of the strains. Additionally, we observed a rapid loss of heterozygosity (LOH) events in the heterozygote strains. Experimental evolution starting with the heterozygote strains suggests that LOH is common both under selection and without selection. LOH event drive adaptation that may enable rapid evolution in diploid yeast.

Failed despots and the equitable distribution of fitness in a subsidized species

Territorial species are often predicted to adhere to an ideal despotic distribution and under-match local food resources, meaning that individuals in high-quality habitat achieve higher fitness than those in low-quality habitat. However, conditions such as high density, territory compression, and frequent territorial disputes in high-quality habitat are expected to cause habitat quality to decline as population density increases and, instead, promote resource matching. We studied a highly human-subsidized and under-matched population of Steller's jays (Cyanocitta stelleri) to determine how under-matching is maintained despite high densities, compressed territories, and frequent agonistic behaviors, which should promote resource matching. We examined the distribution of fitness among individuals in high-quality, subsidized habitat, by categorizing jays into dominance classes and characterizing individual consumption of human food, body condition, fecundity, and core area size and spatial distribution. Individuals of all dominance classes consumed similar amounts of human food and had similar body condition and fecundity. However, the most dominant individuals maintained smaller core areas that had greater overlap with subsidized habitat than those of subordinates. Thus, we found that 1) jays attain high densities in subsidized areas because dominant individuals do not exclude subordinates from human food subsidies and 2) jay densities do not reach the level necessary to facilitate resource matching because dominant individuals monopolize space in subsidized areas. Our results suggest that human-modified landscapes may decouple dominance from fitness and that incomplete exclusion of subordinates may be a common mechanism underpinning high densities and creating source populations of synanthropic species in subsidized environments.

Mating traits and fitness components in two breeding designs in Drosophila serrata

Misalignment between male and female interests over mating creates inter-locus sexual conflict that is known to drive the coevolution of reproductive traits. Males and females also share the majority of their genome, which may cause these traits to genetically covary between the sexes and experience intra-locus sexual conflict where beneficial alleles in one sex are costly when expressed in the other. Traits expressed during mating may uniquely be subject to both intra- and interlocus sexual conflict. Here, we use a biologically repeated quantitative genetic experiment to test whether intra-locus sexual conflict is operating on mating latency, and copulation duration in the polyandrous fruit-fly Drosophila serrata. Mating latency and copulation duration were both heritable in males but not in females, and within sex and across-sex genetic correlations among the traits were all small. We found no significant genetic covariance between any measured mating behaviours and fitness components, nor between male and female fitness, suggesting that these traits are not under strong selection. Our study, therefore, finds little evidence of ongoing intra-locus sexual conflict over these traits. One explanation for our result is that these mating traits have historically been under strong selection, which has exhausted their genetic variation, making it difficult to detect selection in these populations. Keywords: mating latency, copulation duration, quantitative genetics, sexual conflict, Drosophila serrata, multivariate analyses, cuticula.

Religious celibacy brings inclusive fitness benefits

The influence of inclusive fitness interests on the evolution of human institutions remains unclear. Religious celibacy constitutes an especially puzzling institution, often deemed maladaptive. Here, we present sociodemographic data from an agropastoralist Buddhist population in western China, where parents sometimes sent a son to the monastery. We find that men with a monk brother father more children, and grandparents with a monk son have more grandchildren, suggesting that the practice is adaptive. We develop a model of celibacy to elucidate the inclusive fitness costs and benefits associated with this behaviour. We show that a minority of sons can be favoured to be celibate if this increases their brothers' reproductive success, but only if the decision is under parental, rather than individual, control. These conditions apply to monks in our study site. Inclusive fitness considerations appear to play a key role in shaping parental preferences to adopt this cultural practice.

A simple method to describe the COVID-19 trajectory and dynamics in any country based on Johnson cumulative density function fitting

A simple method is utilised to study and compare COVID-19 infection dynamics between countries based on curve fitting to publicly shared data of confirmed COVID-19 infections. The method was tested using data from 80 countries from 6 continents. We found that Johnson cumulative density functions (CDFs) were extremely well fitted to the data (R2 > 0.99) and that Johnson CDFs were much better fitted to the tails of the data than either the commonly used normal or lognormal CDFs. Fitted Johnson CDFs can be used to obtain basic parameters of the infection wave, such as the percentage of the population infected during an infection wave, the days of the start, peak and end of the infection wave, and the duration of the wave's increase and decrease. These parameters can be easily interpreted biologically and used both for describing infection wave dynamics and in further statistical analysis. The usefulness of the parameters obtained was analysed with respect to the relation between the gross domestic product (GDP) per capita, the population density, the percentage of the population infected during an infection wave, the starting day and the duration of the infection wave in the 80 countries. We found that all the above parameters were significantly associated with GDP per capita, but only the percentage of the population infected was significantly associated with population density. If used with caution, this method has a limited ability to predict the future trajectory and parameters of an ongoing infection wave.

Structural anther mimics improve reproductive success through dishonest signalling that enhances both attraction and the morphological fit of pollinators with flowers

Numerous studies have identified traits associated with anther mimicry, however, the processes underlying floral deception remains poorly documented for these structures. We studied the importance of pollinator attraction and mechanical fit of anther mimics in Tritonia laxifolia (Iridaceae) and their relative contributions to reproductive success. To determine anther mimics role in pollinator attraction, we offered bees' binary choices to flowers painted with UV absorbent and reflecting paint. We also conducted preference experiments between flowers with excised anther mimics and unmanipulated controls, from which mechanical fit was assessed by allowing single visits. Anther mimics effects on female reproductive success was determined using similar treatments, but on rooted plants. Bees preferred UV absorbent over UV reflecting anther mimics. Bees did not discriminate between flowers with and without three-dimensional anther mimics. Single visits resulted in more pollen deposition on unmanipulated controls over flowers with their anther mimics excised, which was directly linked to pollen-collecting behaviour. Controls with unmanipulated anther mimics had higher seed set than those with their anther mimics excised. This study provides insights into pollinator-mediated selection on deceptive floral signals and shows that three-dimensional anther mimics increases reproductive success through both attraction and pollen-collecting behaviours.

opencc-by-4.0Jun 2022View details →

Dispersal, kin aggregation, and the fitness consequences of not spreading sibling larvae

GENERAL INFORMATION 1. Title of Dataset: Dispersal, kin aggregation, and the fitness consequences of not spreading sibling larvae 2. Author Information     A. Principal Investigator Contact Information         Name: Scott Burgess         Institution: Florida State University         Address: 319 Stadium Drive, Tallahassee, FL, USA 32306         Email: sburgess@bio.fsu.edu 3. Date of data collection (single date, range, approximate date): 2016-2017 4. Geographic location of data collection: Turkey Point, Florida, USA 5. Information about funding sources that supported the collection of the data: National Science Foundation (NSF; OCE-1948788) and the Florida State University Council on Research and Creativity   DATA & FILE OVERVIEW 1. File List: Figure 2.R Figure 3.R Figure 4.R Figure 5.R Observed sibship.R Clark Evans Corrected function.R Figure 2 data.csv Figure 3 data.csv Figure 4 data.csv Figure 5 data.csv sampleIDfile_msats.csv Sibships.csv 2. Relationship between files: Figure 2.R uses Figure 2 data.csv Figure 3.R uses Figure 3 data.csv and Clark Evans Corrected function.R Figure 4.R uses Figure 4 data.csv and Clark Evans Corrected function.R Figure 5.R uses Figure 5 data.csv Observed sibship.R uses sampleIDfile_msats.csv and Sibships.csv   3. Metadata Figure 2 data.csv deployment: Sequential number for each deployment date deployment.date: The date on which settlement plates were attached to poles in the field treatment: Control = No colony in the center of the array; Treatment = Seven colonies placed in the center of the array. sheet: Unique identifier for each settlement plate (=sheet) distance.m: Distance, in meters, of the settlement plate to the center of the array settlers: The number of settlers recorded in each settlement plate after retrieval days: The number of days between the deployment and retrieval of settlement plates settlers.day: settlers / days = the number of settlers per day   Figure 3 data.csv D.Date: Date on which settlement plates were Deployed R.Date: Date on which settlement plates were Retrieved D.Group: Sequential number for each deployment group Plate.ID: Unique identifier for each settlement plate Deployment: 1 = settlement plates deployed for 3 days; 2 = settlement plates placed back into the water after 3 days, and collected again after another 3 days (capturing larvae that settled on between day 4 and 6). Point: Unique identifier for each settler Raw.X: The distance, in millimeters, from the left side of the image Raw.Y: The distance, in millimeters, from the bottom side of the image True.X: The distance, in millimeters, from the left side of the focal settlement area True.Y: The distance, in millimeters, from the bottom side of the focal settlement area   Figure 4 data.csv Sheet ID: Unique identifier for each settlement plate (=sheet) Relatedness: Sib = each settler came from the same mother (half-sib or full-sib); NonSibs = each settler came from a different (unrelated) mother. Point: Unique identifier for each settler Raw.X: The distance, in millimeters, from the left side of the image Raw.Y: The distance, in millimeters, from the bottom side of the image True.X: The distance, in millimeters, from the left side of the focal settlement area True.Y: The distance, in millimeters, from the bottom side of the focal settlement area   Figure 5 data.csv mother.ID: Unique identifier for each maternal colony sib.total: A code representing the concatenation of sib.group.size and total.group.size sib.group.size: The total number of focal siblings in the group total.group.size: The total number of all settlers in the group age.d: Days since settlement Ind: F = focal individual (an offspring from the corresponding mother.id); NF = Non-focal individual (comes from another maternal colony, NOT from the corresponding mother.id) sheet: Unique identifier for each settlement plate (=sheet) survival: 1 = alive; 0 = dead. bifurcations: The number of bifurcations on the colony. sampleIDfile_msats.csv Ind: Individual ID for each colony that also indicates site ("ML_"). ML=Marine Lab. Sample: Individual ID for each colony. Group: A unique code indicating a seagrass blade. I.e., samples from Group 1 were from the  seagrass blade #1, and so on. Sibships.csv OffspringID1: Individual ID for each colony that matches 'Sample' in sampleIDfile_msats.csv. OffspringID2: Individual ID for each colony that matches 'Sample' in sampleIDfile_msats.csv. Probability: Probability (estimated from COLONY) that OffspringID1 and OffspringID2 are sibship type listed under SibshipType Run: Run number from COLONY Sibship Type: Whether COLONY estimated OffspringID1 and OffspringID2 to have a Full of Half sib relationship.

Variation in reproduction and gene flow between cytotypes in a polyploid complex: one size does not fit all

Whole-genome duplication is considered an important speciation mechanism in plants. However, its effect on reproductive isolation between higher cytotypes is not well understood. We used backcrosses between different ploidy levels and surveys of mixed-ploidy contact zones to determine how reproductive barriers differed with cytotype across a polyploid complex. We backcrossed F1 hybrids derived from 2X-4X and 4X-6X crosses in the Campanula rotundifolia autopolyploid complex, measured backcross fitness, and estimated backcross DNA cytotype. We then sampled four natural mixed-ploidy contact zones (two 2X-4X and two 4X-6X), estimated ploidy, and genotyped individuals across each contact zone. Reproductive success and capacity for gene flow was markedly lower for 2X-4X than 4X-6X hybrids. In fact, 3X hybrids could not backcross; all 2X-4X backcross progeny resulted from neotetraploid F1 hybrids. Further, no 3X individuals were found in 2X-4X contact zones, and 2X and 4X individuals were genetically distinct. By contrast, backcrosses of 5X hybrids were relatively successful, particularly when crossed to 6X individuals. In 4X-6X contact zones, 5X individuals and aneuploids were common and all cytotypes were largely genetically similar and spatially intermixed. Taken together, these results provide strong evidence that reproduction is low between 2X and 4X cytotypes, primarily occurring via unreduced gamete production, but that reproduction and gene flow are ongoing between 4X and 6X cytotypes. Further, it suggests whole genome duplication can result in speciation between diploids and polyploids, but is less likely to create reproductive barriers between different polyploid cytotypes, resulting in two fundamentally different potentials for speciation across polyploid complexes.