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opencc-zeroJan 2021View details →

Data associated with: Going round the twist – An empirical analysis of shell coiling in helicospiral gastropods

The logarithmic helicospiral has been the most widely accepted model of regularly coiled mollusc form since it was proposed by Moseley (1838) and popularised by Thompson (1942) and Raup (1966). It is based on an explicit assumption that shells are isometric and grow exponentially, and an implicit assumption that the external form of the shell follows the internal shape, which implies that the parameters of the spiral could, theoretically, be reconstructed from the external whorl profile. In this contribution, we show that these assumptions fail on all 25 gastropod species we examine. Using a dataset of 176 fossil and modern gastropod shells, we construct an empirical morphospace of coiling using the familiar three parameters of whorl expansion rate, translation rate, and rate of increasing distance from coiling axis, plus rate of aperture shape change, from their best-fit models. We present a case study of change in shell form through geological time in the austral family Struthiolariidae to demonstrate the utility of our approach for evolutionary paleobiology. We fit various functions to the four shell-coiling parameters, to demonstrate that the best morphological model is not the same for each parameter. We present a set of R routines that will calculate helicospiral parameters from sagittal sections through coiled shells and allow workers to compare models and choose appropriate sets of parameters for their own datasets. Shell form parameters in the Struthiolariidae highlight a hitherto-neglected hypothesis of relationship between Antarctic Perissodonta and the enigmatic Australian genus Tylospira that fits the biogeographic and stratigraphic distribution of both genera.

Data from: Age-dependent speciation can explain the shape of empirical phylogenies

Tens of thousands of phylogenetic trees, describing the evolutionary relationships between hundreds of thousands of taxa, are readily obtainable from various databases. From such trees inferences can be made about the underlying macroevolutionary processes, yet remarkably these processes are still poorly understood. Simple and widely used evolutionary null models are problematic: empirical trees show very different imbalance between the sizes of the daughter clades of ancestral taxa compared to what models predict. Obtaining a simple evolutionary model that is both biologically plausible and produces the imbalance seen in empirical trees is a challenging problem, to which none of the existing models provide a satisfying answer. Here we propose a simple, biologically-plausible macroevolutionary model in which the rate of speciation decreases with species age, while extinction rates can vary quite generally. We show that this model provides a remarkable fit to the thousands of trees stored in the online database TreeBase. The biological motivation for the identified age-dependent speciation process may be that recently evolved taxa often colonise new regions or niches and may initially experience little competition. These new taxa are thus more likely to give rise to further new taxa than a taxon that has remained largely unchanged and is therefore well-adapted to its niche. We show that age-dependent speciation may also be the result of different within-species populations following the same laws of lineage splitting to produce new species. As the fit of our model to the tree database shows, this simple biological motivation provides an explanation for a long standing problem in macroevolution.

opencc-zeroDec 2017View details →

Data from: The architecture of an empirical genotype-phenotype map

Recent advances in high-throughput technologies are bringing the study of empirical genotype-phenotype (GP) maps to the fore. Here, we use data from protein binding microarrays to study an empirical GP map of transcription factor (TF) binding preferences. In this map, each genotype is a DNA sequence. The phenotype of this DNA sequence is its ability to bind one or more TFs. We study this GP map using genotype networks, in which nodes represent genotypes with the same phenotype, and edges connect nodes if their genotypes differ by a single small mutation. We describe the structure and arrangement of genotype networks within the space of all possible binding sites for 525 TFs from three eukaryotic species encompassing three kingdoms of life (animal, plant, and fungi). We thus provide a high-resolution depiction of the architecture of an empirical GP map. Among a number of findings, we show that these genotype networks are "small-world" and assortative, and that they ubiquitously overlap and interface with one another. We also use polymorphism data from Arabidopsis thaliana to show how genotype network structure influences the evolution of TF binding sites in vivo. We discuss our findings in the context of regulatory evolution.

Data from: How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards

Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolved) question is whether sampling should be designed to maximize sampling of taxa or genes, or to minimize the inclusion of missing data cells. Here, we explore this question for an ancient, rapid radiation of lizards, the pleurodont iguanians. Pleurodonts include many well-known clades (e.g., anoles, basilisks, iguanas, and spiny lizards) but relationships among families have proven difficult to resolve strongly and consistently using traditional sequencing approaches. We generated up to 4921 ultraconserved elements with sampling strategies including 16, 29, and 44 taxa, from 1179 to approximately 2.4 million characters per matrix and approximately 30% to 60% total missing data. We then compared mean branch support for interfamilial relationships under these 15 different sampling strategies for both concatenated (maximum likelihood) and species tree (NJst) approaches (after showing that mean branch support appears to be related to accuracy). We found that both approaches had the highest support when including loci with up to 50% missing taxa (matrices with ∼40–55% missing data overall). Thus, our results show that simply excluding all missing data may be highly problematic as the primary guiding principle for the inclusion or exclusion of taxa and genes. The optimal strategy was somewhat different for each approach, a pattern that has not been shown previously. For concatenated analyses, branch support was maximized when including many taxa (44) but fewer characters (1.1 million). For species-tree analyses, branch support was maximized with minimal taxon sampling (16) but many loci (4789 of 4921). We also show that the choice of these sampling strategies can be critically important for phylogenomic analyses, since some strategies lead to demonstrably incorrect inferences (using the same method) that have strong statistical support. Our preferred estimate provides strong support for most interfamilial relationships in this important but phylogenetically challenging group.

Data from: Sexual selection has minimal impact on effective population sizes in species with high rates of random offspring mortality: an empirical demonstration using fitness distributions

The effective population size (Ne) is a fundamental parameter in population genetics that influences the rate of loss of genetic diversity. Sexual selection has the potential to reduce Ne by causing the sex-specific distributions of individuals that successfully reproduce to diverge. To empirically estimate the effect of sexual selection on Ne, we obtained fitness distributions for males and females from an outbred, laboratory-adapted population of Drosophila melanogaster. We observed strong sexual selection in this population (the variance in male reproductive success was ∼14 times higher than that for females), but found that sexual selection had only a modest effect on Ne, which was 75% of the census size. This occurs because the substantial random offspring mortality in this population diminishes the effects of sexual selection on Ne, a result that necessarily applies to other high fecundity species. The inclusion of this random offspring mortality creates a scaling effect that reduces the variance/mean ratios for male and female reproductive success and causes them to converge. Our results demonstrate that measuring reproductive success without considering offspring mortality can underestimate Ne and overestimate the genetic consequences of sexual selection. Similarly, comparing genetic diversity among different genomic components may fail to detect strong sexual selection.

Data from: Empirical and theoretical study of Atelostomate (Echinoidea, Echinodermata) plate architecture: using graph analysis to reveal structural constraints

Describing patterns of connectivity among organs is essential for identifying anatomical homologies among taxa. It is also critical for revealing morphogenetic processes and the associated constraints that control the morphological diversification of clades. This is particularly relevant for studies of organisms with skeletons made of discrete elements such as arthropods, vertebrates, and echinoderms. Nonetheless, relatively few studies devoted to morphological disparity have considered connectivity patterns as a level of morphological organization or developed comparative frameworks with proper tools. Here, we analyze connectivity patterns among apical plates in Atelostomata, the most diversified clade among irregular echinoids. The clade comprises approximately 1600 fossil and Recent species (e.g., 25% of post-Paleozoic species of echinoids) and shows high levels of morphological disparity. Plate connectivity patterns were analyzed using tools and statistics of graph theory. To describe and explore the diversity of connectivity patterns among plates, we symbolized each pattern as a graph in which plates are coded as nodes that are connected pairwise by edges. We then generated a comparative framework as a morphospace of connections, in which the disparity of plate patterns observed in nature was mapped and analyzed. Main results show that apical plate patterns are both highly disparate between and within atelostomate groups and limited in number; overall, they also constitute small, compact, and simple structures compared to possible random patterns. Main traits of the evolution of apical plate patterns reveal the existence of strong morphogenetic constraints that are phylogenetically determined. In contrast, evolutionary radiations within atelostomates were accompanied by a clear increase in disparity, suggesting a release of some constraints at the origin of clades.

Data from: Genetic load, inbreeding depression and hybrid vigor covary with population size: an empirical evaluation of theoretical predictions

Reduced population size is thought to have strong consequences for evolutionary processes as it enhances the strength of genetic drift. In its interaction with selection, this is predicted to increase the genetic load, reduce inbreeding depression, and increase hybrid vigour, and in turn affect phenotypic evolution. Several of these predictions have been tested, but comprehensive studies controlling for confounding factors are scarce. Here we show that populations of Daphnia magna, which vary strongly in genetic diversity, also differ in genetic load, inbreeding depression, and hybrid vigor in a way that strongly supports theoretical predictions: Inbreeding depression is positively correlated with genetic diversity (a proxy for Ne), and genetic load and hybrid vigour are negatively correlated with genetic diversity. These patterns remain significant after accounting for potential confounding factors and indicate that, in small populations, a large proportion of the segregation load is converted into fixed load. Overall, the results suggest that the nature of genetic variation for fitness-related traits differs strongly between large and small populations. This has large consequences for evolutionary processes in natural populations, such as selection on dispersal, breeding systems, ageing, and local adaptation.

opencc-zeroDec 2016View details →

Data from: Empirical and theoretical investigation into the potential impacts of insecticide resistance on the effectiveness of insecticide-treated bed nets

In spite of widespread insecticide resistance in vector mosquitoes throughout Africa, there is limited evidence that long lasting insecticidal bed nets (LLINs) are failing to protect against malaria. Here, we showed that LLIN contact in the course of host-seeking resulted in higher mortality of resistant Anopheles spp. mosquitoes than predicted from standard laboratory exposures with the same net. We also found that sub-lethal contact with an LLIN caused a reduction in blood feeding and subsequent host-seeking success in multiple lines of resistant mosquitoes from the lab and the field. Using a transmission model, we showed that when these LLIN-related lethal and sub-lethal effects were accrued over mosquito lifetimes, they greatly reduced the impact of resistance on malaria transmission potential under conditions of high net coverage. If coverage falls, the epidemiological impact is far more pronounced. Similarly, if the intensity of resistance intensifies, the loss of malaria control increases non-linearly. Our findings help explain why insecticide resistance has not yet led to wide scale failure of LLINs, but reinforce the call for alternative control tools and informed resistance management strategies.

zenodo28/100

Replication Package for "On the Practice of Semantic Versioning for Ansible Galaxy Roles: An Empirical Study and a Change Classification Model"

Replication package for our analysis of Semantic Versioning in Ansible Galaxy role repositories. This replication package consists of three parts: <ul> <li> Classification Model: Contains Jupyter notebooks used to train and evaluate a Random Forest classification model based on structural features. Training and evaluation data is included. </li> <li> Quantitative Notebooks: Contains Jupyter notebooks used to perform quantitative analyses of versions and changes. </li> <li> data: CSV files of the data used in the Quantitative Notebooks, and the source data for the classification model. Should be downloaded separately fromthe classification model. Should be downloaded separately from <a href="https://doi.org/10.5281/zenodo.4991955">https://doi.org/10.5281/zenodo.4991955</a>. </li> </ul> The data is under the Creative Commons Attribution Share-Alike 4.0 license. The source code is under the GNU General Public License.

openother-openJun 2021View details →

opencc-zeroDec 2016View details →

Data from: Detecting environment-dependent diversification from phylogenies: a simulation study and some empirical illustrations

Understanding the relative influence of various abiotic and biotic variables on diversification dynamics is a major goal of macroevolutionary studies. Recently, phylogenetic approaches have been developed that make it possible to estimate the role of various environmental variables on diversification using time-calibrated species trees, paleoenvironmental data, and maximum-likelihood techniques. These approaches have been effectively employed to estimate how speciation and extinction rates vary with key abiotic variables, such as temperature and sea level, and we can anticipate that they will be increasingly used in the future. Here we compile a series of biotic and abiotic paleodatasets that can be used as explanatory variables in these models and use simulations to assess the statistical properties of the approach when applied to these paleodatasets. We demonstrate that environment-dependent models perform well in recovering environment-dependent speciation and extinction parameters, as well as in correctly identifying the simulated environmental model when speciation is environment-dependent. We explore how the strength of the environment-dependency, tree size, missing taxa, and characteristics of the paleoenvironmental curves influence the performance of the models. Finally, using these models, we infer environment-dependent diversification in two empirical phylogenies: temperature-dependence in Cetacea and δ 13C-dependence in Ruminantia. We illustrate how to evaluate the relative importance of abiotic and biotic variables in these two clades and interpret these results in light of macroevolutionary hypotheses. Given the important role paleoenvironments are presumed to have played in species evolution, our statistical assessment of how environment-dependent models behave is crucial for their utility in macroevolutionary analysis.

opencc-zeroDec 2018View details →

Data from: Empirical determination of severe trauma in seals from collisions with tidal turbine blades

1. Tidal energy converters (turbines) are being developed in many countries as part of attempts to reduce reliance on hydrocarbon fuels. However, the moving blades of tidal turbines pose potential collision risks for marine animals. Accurate assessment of mortality risk as a result of collisions is essential for risk management during planning and consenting processes for marine energy developments. In the absence of information on the physical consequences of such collisions, predicting likely risks relies on theoretical collision risk models. The application of these at a population level usually assumes that all collisions result in mortality. This is unlikely and the approach therefore produces upwardly biased estimates of population consequences. 2. In this study, we estimate the pathological consequences of direct collisions with tidal turbines using seal carcasses and physical models of tidal turbine blades. We quantify severe trauma at a range of impact speeds and to different areas of seal carcasses. A dose-response model was developed with associated uncertainty to determine an impact speed threshold of severe trauma to use in future collision risk models. 3. Results showed that severe trauma was: a. restricted to the thoracic region, with no evidence of injury to the lumbar or cervical spine. b. only observed in collision speeds in excess of 5.6 m.s-1 (95% c.i. 4.4 to 6.6). c. affected by body condition; increasing blubber depth reduced the likelihood of severe trauma 4. Synthesis and applications: This study provides important information for policy makers and regulators looking to predict the potential impacts of tidal turbines on marine mammals. We demonstrate that the probability of severe trauma in seals due to collisions with turbine blades is highly dependent upon collision speed, and that the majority of predicted collisions are unlikely to cause fatal skeletal trauma. We recommend that collision risk models incorporate appropriate mortality assumptions to ensure accurate estimates of the population consequences are produced in risk assessments for tidal turbine deployments.

opencc-zeroDec 2017View details →

Data from: Crop-to-wild hybridization in cherries – empirical evidence from Prunus fruticosa

Crop cultivation can lead to genetic swamping of indigenous species and thus pose a serious threat for biodiversity. The rare Eurasian tetraploid shrub Prunus fruticosa (ground cherry) is suspected of hybridizing with cultivated allochthonous tetraploid P. cerasus and autochthonous diploid P. avium. Three Prunus taxa (447 individuals of P. fruticosa, 43 of P. cerasus and 73 of P. avium) and their hybrids (198 individuals) were evaluated using analysis of absolute genome size/ploidy level and multivariate morphometrics. Flow cytometry revealed considerable differentiation in absolute genome size at the tetraploid level (average 2C of P. fruticosa = 1.30 pg, average 2C of P. cerasus = 1.42 pg, i.e. a 9.2% difference). The combination of methods used allowed us to ascertain the frequency of hybrids occurring under natural conditions in Central Europe. The morphological evaluation of leaves was based upon distance-based morphometrics supplemented by elliptic Fourier analysis. The results provided substantial evidence for ongoing hybridization (hybrids occurred in 39.5% of P. fruticosa populations). We detected homoploid introgressive hybridization with alien P. cerasus at the tetraploid level. We also found previously overlooked but frequent triploid hybrids resulting from heteroploid hybridization with indigenous P. avium, which, however, probably represent only the F1 generation. Although both hybrids differ in ploidy, they cannot be distinguished using morphometrics. Hybrids are frequent and may endanger wild populations of genuine P. fruticosa via direct niche competition or, alternatively or in addition, via introgression at the homoploid level (i.e. genetic swamping). The cultivation of cherries thus substantially threatens the existence of genuine P. fruticosa.

Data from: Understanding human queuing behaviour at exits: an empirical study

The choice of the exit to egress from a facility plays a fundamental role in pedestrian modelling and simulation. Yet, empirical evidence for backing up simulation is scarce. In this contribution, we present three new groups of experiments that we conducted in different geometries. We varied parameters such as the width of the doors, the initial location and number of pedestrians which in turn affected their perception of the environment. We extracted and analysed relevant indicators such as distance to the exits and density levels. The results put in evidence the fact that pedestrians use time-dependent information to optimize their exit choice, and that, in congested states, a load balancing over the exits occurs. We propose a minimal modelling approach that covers those situations, especially the cases where the geometry does not show a symmetrical configuration. Most of the models try to achieve the load balancing by simulating the system and solving optimization problems. We show statistically and by simulation that a linear model based on the distance to the exits and the density levels around the exit can be an efficient dynamical alternative.

Data from: Does gene tree discordance explain the mismatch between macroevolutionary models and empirical patterns of tree shape and branching times?

Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because phylogenetic reconstruction methods often infer gene trees rather than species trees, producing an incongruity between models that predict species tree patterns and empirical analyses that consider gene trees. We investigate the extent to which the difference between gene trees and species trees under a combined birth–death and multispecies coalescent model can explain the difference in empirical trees and birth–death species trees. We simulate gene trees embedded in simulated species trees and investigate their difference with respect to tree balance and branching times. We observe that the gene trees are less balanced and typically have branching times closer to the root than the species trees. Empirical trees from TreeBase are also less balanced than our simulated species trees, and model gene trees can explain an imbalance increase of up to 8% compared to species trees. However, we see a much larger imbalance increase in empirical trees, about 100%, meaning that additional features must also be causing imbalance in empirical trees. This simulation study highlights the necessity of revisiting the assumptions made in phylogenetic analyses, as these assumptions, such as equating the gene tree with the species tree, might lead to a biased conclusion.

Data from: Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta-analysis of COI data from previous phylogeographical studies

The use of genetic distances to identify species within the framework of DNA barcoding has to some extent improved the development of biodiversity studies. However, using a fixed empirical threshold to delimit species may lead to overestimating species diversity. In this study, we use a new data set of COI sequences for 366 specimens within the genus of Cletus as well as conduct an analysis on the same genetic data for collected morphologically defined species from previous phylogeographical studies, to test whether high intraspecific genetic divergences are common with the premises of comprehensive sampling. The results indicate C. graminis Hsiao & Cheng 1964, is the same species with C. punctiger (Dallas, 1852) and should be synonymized and that the distributional record of C. pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic differentiations (0%–4.35%) were found in C. punctiger. Furthermore, as to the mined data, the maximum intraspecific K2P distances of 186 species (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into two or more clusters with a threshold of 3% in cluster analysis. If genetic distance is used to delimit species boundaries, the minimum interspecific K2P distance of the congeneric species should be considered rather than only using the fixed empirical value; otherwise, the species richness may be overestimated in some cases.

opencc-zeroDec 2013View details →

Data from: Theoretical and empirical perspectives in ecology and evolution: a survey

Scientific research is often conceptually divided into empirical and theoretical approaches, and researchers often specialize as empiricists or theorists. Both approaches are essential to scientific progress, but interactions between the two groups have at times seemed problematic. I present results from a recent survey of 614 scientists (predominantly ecologists and evolutionary biologists) regarding interactions between theoretical and empirical work. Some overall themes emerged from these results. One theme is a widespread and mutual lack of trust, understanding, and interaction between empiricists and theorists. Another is a general desire, among almost all of the respondents, for greater understanding, more collaboration, and closer interactions between empirical and theoretical work. The final theme is that institutions, such as journals, funding agencies, and universities, are often seen as hindering such interactions. These results provide a clear mandate for institutional changes to improve interactions between theorists and empiricists in ecology and evolutionary biology.

Data from: Synergism and antagonism of proximate mechanisms enable and constrain the response to simultaneous selection on body size and development time: an empirical test using experimental evolution

Natural selection acts on multiple traits simultaneously. How mechanisms underlying such traits enable or constrain their response to simultaneous selection is poorly understood. We show how antagonism and synergism among three traits at the developmental level enable or constrain evolutionary change in response to simultaneous selection on two focal traits at the phenotypic level. After 10 generations of 25% simultaneous directional selection on all four combinations of body size and development time in Manduca sexta (Sphingidae), the changes in the three developmental traits predict 93% of the response of development time and 100% of the response of body size. When the two focal traits were under synergistic selection, the response to simultaneous selection was enabled by juvenile hormone and ecdysteroids and constrained by growth rate. When the two focal traits were under antagonistic selection, the response to selection was due primarily to change in growth rate and constrained by the two hormonal traits. The approach used here reduces the complexity of the developmental and endocrine mechanisms to three proxy traits. This generates explicit predictions for the evolutionary response to selection that are based on biologically informed mechanisms. This approach has broad applicability to a diverse range of taxa, including algae, plants, amphibians, mammals, and insects.

opencc-zeroDec 2007View details →

Data from: Inferring complex phylogenies using parsimony: an empirical approach using three large DNA data sets for angiosperms

To explore the feasibility of parsimony analysis for large data sets, we conducted heuristic parsimony searches and bootstrap analyses on separate and combined DNA data sets for 190 angiosperms and three outgroups. Separate data sets of 18S rDNA (1,855 bp), rbc L (1,428 bp), and atp B (1,450 bp) sequences were combined into a single matrix 4,733 bp in length. Analyses of the combined data set show great improvements in computer run times compared to those of the separate data sets and of the data sets combined in pairs. Six searches of the 18S rDNA rbc L atp B data set were conducted; in all cases TBR branch swapping was completed, generally within a few days. In contrast, TBR branch swapping was not completed for any of the three separate data sets, or for the pairwise combined data sets. These results illustrate that it is possible to conduct a thorough search of tree space with large data sets, given sufficient signal. In this case, and probably most others, sufficient signal for a large number of taxa can only be obtained by combining data sets. The combined data sets also have higher internal support for clades than the separate data sets, and more clades receive bootstrap support of 50% in the combined analysis than in analyses of the separate data sets. These data suggest that one solution to the computational and analytical dilemmas posed by large data sets is the addition of nucleotides, as well as taxa.

Data from: Are extra-pair males different from cuckolded males? An empirical and meta-analytic examination

Traditional models for female extra-pair matings assume that females benefit indirectly from extra-pair mating behaviour. Under these so-called adaptive models, extra-pair males are hypothesized to have more compatible genotypes, larger body size, exaggerated ornaments or to be older than cuckolded males. Alternatively, ('nonadaptive') models that consider female extra-pair matings to be a by-product posit that female extra-pair mating can be maintained even if there is no benefit to females. This could happen if, for example, males gained fitness benefits from extra-pair mating, while female and male extra-pair mating behaviours were genetically correlated. Extra-pair males are also expected to be older and larger if this improves their ability to convince or coerce females to mate. We investigated whether a female's extra-pair mates differed from her cuckolded mate in both genetic and phenotypic traits by analysing data from an insular house sparrow population. We found that extra-pair males were older than cuckolded males, consistent with both models. However, in contrast to the expectations from from adaptive models, extra-pair and cuckolded males were of similar genetic relatedness, and hence expected compatibility, with the female, and had comparable body size and secondary sexual traits. We also updated previous meta-analyses examining differences between extra-pair and cuckolded males. The meta-analytic results matched results from our house sparrow case study. Although we cannot completely exclude indirect benefits for females, nonadaptive models may better explain female extra-pair matings. These neglected alternative models deserve more research attention, and this should improve our understanding of the evolution of mating systems.