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opencc-by-4.0Sep 2023View details →

Dataset for: "Parameter identifiability and model selection for partial differential equation models of cell invasion"

This is the dataset accompanying the paper "Parameter identifiability and model selection for partial differential equation models of cell invasion" (https://arxiv.org/abs/2309.01476). It consists of a series of images taken of a barrier assay experiment to study tissue expansion of MDCK cells, along with cell density data in MATLAB format. File structure: the contents of the four zip files should be combined (they were split into four files for practical reasons regarding file size). The data corresponds to eight experiments, four with circular initial conditions, and four with triangular initial conditions, the associated data are located in 04-05-22 exp1/Circle and 04-05-22 exp1/Triangle respectively, each labeled "xy<n>", where <n> from 1 to 8 is an identifier for the experiment. The images under the xy<n>_Phase folders are the raw images taken of the experiment, those under the xy<n>_mask folder are processed images indicating the extend of the spread of the cell population. The DensityCellcyleFraction folder contain data files in MATLAB format. The most relevant is the "density" variable, which is a rank-3 tensor of size 150x150x77 such that density(i,j,k) corresponds to the cell density at location (x_i,y_j) and time t_k. The process for calculating the cell density is described in the paper. Alternatively, the density data is also provided in csv format. In the csv_data folder, xy<n>/t<k>.csv encodes a matrix representing cell density for experiment <n> at time t_k. The code for processing and analysing these data are provided in the "code" folder. It is also available at https://github.com/liuyue002/woundhealing . Abstract of the paper: When employing a mechanistic model to study biological systems, practical parameter identifiability is important for making predictions in a wide range of scenarios, as well as for understanding the mechanisms driving the system behaviour. We argue that parameter identifiability should be considered alongside goodness-of-fit and model complexity as criteria for model selection. To demonstrate, we use a profile likelihood approach to investigate parameter identifiability for four extensions of the Fisher--KPP model, given experimental data from a cell invasion assay. We show that more complicated models tend to be less identifiable, with parameter estimates being more sensitive to subtle differences in experimental procedures, and require more data to be practically identifiable. The results from identifiability analysis can inform model selection, as well as data collection and experimental design.

Fig. 4 in Body size differentiation in selected carabid species inhabiting Puszcza Piska forest stands disturbed by the hurricane

Fig. 4. The differences between the mean body length and the median value of body length for Pterostichus niger individuals inhabiting post-hurricane (Pisz) and control (Maskulińskie) stands in years 2003-2007.

Fig. 6 in Body size differentiation in selected carabid species inhabiting Puszcza Piska forest stands disturbed by the hurricane

Fig. 6. The differences between the mean body length and the median value of body length for Carabus violaceus individuals inhabiting post-hurricane (Pisz) and control (Maskulińskie) stands in years 2003-2007.

Fig. 5 in Body size differentiation in selected carabid species inhabiting Puszcza Piska forest stands disturbed by the hurricane

Fig. 5. The mean body length for Carabus violaceus individuals inhabiting post-hurricane (Pisz) and control (Maskulińskie) stands in years 2003-2007.

Fig. 3 in Body size differentiation in selected carabid species inhabiting Puszcza Piska forest stands disturbed by the hurricane

Fig. 3. The mean body length for Pterostichus niger individuals inhabiting post-hurricane (Pisz) and control (Maskulińskie) stands in years 2003-2007.

Fig. 2 in Body size differentiation in selected carabid species inhabiting Puszcza Piska forest stands disturbed by the hurricane

Fig. 2. The differences between the mean body length and the median value of body length for Carabus arcensis individuals inhabiting post-hurricane (Pisz) and control (Maskulińskie) stands in years 2003-2007.

Fig. 1 in Body size differentiation in selected carabid species inhabiting Puszcza Piska forest stands disturbed by the hurricane

Fig. 1. The mean body length for Carabus arcensis individuals inhabiting post-hurricane (Pisz) and control (Maskulińskie) stands in years 2003-2007.

opencc-by-4.0Sep 2022View details →

EEG Dataset for 'Decoding of selective attention to continuous speech from the human auditory brainstem response' and 'Neural Speech Tracking in the Theta and in the Delta Frequency Band Differentially Encode Clarity and Comprehension of Speech in Noise'.

The repository contains the unprocessed EEG data recorded for the publications [1, 2]. For convenience, the onsets of the EEG data provided here are time-aligned with the onsets of the audio books in the 'audiobooks' folder, and the EEG data are provided in HDF5 format. Please refer to the original version of this dataset for more details. More details, as well as the original data files, are available at the original repository <a href="https://doi.org/10.5281/zenodo.7086209">here</a>. Examples of using these data (preprocessing, fitting linear models) can be found <a href="https://github.com/Mike-boop/trf-examples">here</a>. The English conditions (clean, lb, mb, hb, fM, fW) comprised a single recording session. The Dutch conditions (cleanDutch, lbDutch, mbDutch, hbDutch) comprised a separate recording session. You see which participants took part in each session in session_info.json. Please note some details about the stimulus presentation for the various listening conditions: <ul> <li>English speech-in-babble-noise (lb, mb, hb): babble noise was played by itself for one second before the audiobook track began. The babble noise was also played for one second after the audiobook track ended. Therefore, you should discard the first second and the last second from these trial during your analysis.</li> <li>Dutch speech-in-babble-noise (lbDutch, mbDutch, hbDutch): the story (narrated in Dutch) was played by itself for one second before the babble noise track began. Then, the babble noise was increased linearly in amplitude for one second. Therefore, you should discard the first two seconds from these trials during your analysis.</li> <li>Dutch in quiet, and Dutch-in-babble-noise (cleanDutch, lbDutch, mbDutch, hbDutch): some English sentences were embedded in the Dutch narratives in order to encourage attention. You should crop these from your analysis. The onsets and offsets of the English sentences (in samples, at 44100Hz) are provided in the audiobooks/*Dutch/english_onsets_info.json files.</li> <li>Competing-speakers conditions (fM, fW): sometimes the attended track is longer than the unattended track, or vice-versa. The onsets of both tracks are aligned. You should crop the trial to the length of the shortest track for your analysis.</li> </ul> If you use this data, please cite the original publications, as well as this repository [1,2,3]. [1] Etard O, Kegler M, Braiman C, Forte A E and Reichenbach T. “Decoding of selective attention to continuous speech from the human auditory brainstem response” 2019. NeuroImage 200 1–11 [2] Etard O and Reichenbach T. “Neural speech tracking in the theta and in the delta frequency band differentially encode clarity and comprehension of speech in noise” 2019. J. Neurosci. 39 5750–9 [3] Etard O and Reichenbach T. "EEG Dataset for 'Decoding of selective attention to continuous speech from the human auditory brainstem response' and 'Neural Speech Tracking in the Theta and in the Delta Frequency Band Differentially Encode Clarity and Comprehension of Speech in Noise". Doi: 10.5281/zenodo.7086208

dryad40/100

Differential selection for survival and for growth in adaptive laboratory evolution experiments with benzalkonium chloride

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publicNov 2024View details →

opencc-zeroMay 2020View details →

Forest cover and fruit crop size differentially influence frugivory of select rainforest tree species in Western Ghats, India (Part II)

Forest fragmentation and habitat loss are major disruptors of plant–frugivore interactions, affecting seed dispersal and altering recruitment patterns of tree species dependent on vertebrate dispersers. In a heterogeneous production landscape (primarily tea and coffee plantations) in the southern Western Ghats, India, we examined effects of surrounding forest cover and fruit crop size on frugivory of four rainforest bird-dispersed tree species (N = 131 trees, ≥ 30 trees per species, observed for 623 h). Frugivore composition differed among the four tree species with the large-seeded Canarium strictum and Myristica dactyloides exclusively dependent on large-bodied avian frugivores, whereas, medium-seeded Persea macrantha and Heynea trijuga were predominantlyvisited by small-bodied and large-bodied avian frugivores, respectively. Using the seed-dispersal-effectiveness framework, we identified effective frugivores and examined their response to forest cover and fruit crop size. Results were idiosyncratic and governed by plant and frugivore traits. Visitations to medium-seeded Persea had a positive relationship with forest cover but the relationship was negative for the large-seeded Myristica. In addition, two of the three effective frugivores for Persea responded to the interactive effect of forest cover and fruit crop size. Frugivore visitations to Hyenea were not related to forest cover or fruit crop and there were too few visitations to Canarium to discern any trends. These results highlight the context-specific response of plant-frugivore interactions to forest cover and fruit crop size influenced by the plant and frugivore traits.

opencc-zeroMay 2020View details →

Data from: Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar)

As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 SNPs and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and processes shaping them. We found evidence of high (mean FST=0.26) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans-Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1-3Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16, and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium despite no local reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near fixed and potentially adaptive trans-Atlantic differences concurrent with a background of high genome-wide differentiation supports subspecies designation in Atlantic salmon.

opencc-zeroJun 2020View details →

Forest cover and fruit crop size differentially influence frugivory of select rainforest tree species in Western Ghats, India (Part I)

Forest fragmentation and habitat loss are major disruptors of plant–frugivore interactions, affecting seed dispersal and altering recruitment patterns of tree species dependent on vertebrate dispersers. In a heterogeneous production landscape (primarily tea and coffee plantations) in the southern Western Ghats, India, we examined effects of surrounding forest cover and fruit crop size on frugivory of four rainforest bird-dispersed tree species (N = 131 trees, ≥ 30 trees per species, observed for 623 h). Frugivore composition differed among the four tree species with the large-seeded Canarium strictum and Myristica dactyloides exclusively dependent on large-bodied avian frugivores, whereas, medium-seeded Persea macrantha and Heynea trijuga were predominantly visited by small-bodied and large-bodied avian frugivores, respectively. Using the seed-dispersal-effectiveness framework, we identified effective frugivores and examined their response to forest cover and fruit crop size. Results were idiosyncratic and governed by plant and frugivore traits. Visitations to medium-seeded Persea had a positive relationship with forest cover but the relationship was negativefor the large-seeded Myristica. In addition, two of the three effective frugivores for Persea responded to the interactive effect of forest cover and fruit crop size. Frugivore visitations to Hyenea were not related to forest cover or fruit crop and there were too few visitations to Canarium to discern any trends. These results highlight the context-specific response of plant-frugivore interactions to forest cover and fruit crop size influenced by the plant and frugivore traits.

opencc-zeroAug 2020View details →

The roles of climate, geography and natural selection as drivers of genetic and phenotypic differentiation in a widespread amphibian Hyla annectans (Anura: Hylidae)

The role of geological events and Pleistocene climatic fluctuations as drivers of current patterns of genetic variation in extant species has been a topic of continued interest among evolutionary biologists. Nevertheless, comprehensive studies of widely distributed species are still rare, especially from Asia. Using geographically extensive sampling of many individuals and a large number of nuclear single nucleotide polymorphisms (SNPs), we studied the phylogeography and historical demography of Hyla annectans populations in southern China. Thirty-five sampled populations were grouped into seven clearly defined genetic clusters that closely match phenotype-based subspecies classification. These lineages diverged 2.32–5.23 million years ago, a timing that closely aligns with the rapid and drastic uplifting of the Qinghai-Tibet Plateau and adjacent southwest China. Demographic analyses and species distribution models indicate that different populations of this species have responded differently to past climatic changes. In the Hengduan Mountains, most populations experienced a bottleneck, whereas the populations located outside of the Hengduan Mountains have gradually declined in size since the end of the last glaciation. In addition, the levels of phenotypic and genetic divergence were strongly correlated across major clades. These results highlight the combined effects of geological events and past climatic fluctuations, as well as natural selection, as drivers of contemporary patterns of genetic and phenotypic variation in a widely distributed anuran in Asia.

opencc-zeroDec 2016View details →

Data from: Complex selection on a regulator of social cognition: evidence of balancing selection, regulatory interactions and population differentiation in the prairie vole Avpr1a locus

Adaptive variation in social behavior depends upon standing genetic variation, but we know little about how evolutionary forces shape genetic diversity relevant to brain and behavior. In prairie voles (Microtus ochrogaster), variants at the Avpr1a locus predict expression of the vasopressin 1a receptor in the retrosplenial cortex (RSC), a brain region that mediates spatial and contextual memory; cortical V1aR abundance in turn predicts diversity in space-use and sexual fidelity in the field. To examine the potential contributions of adaptive and neutral forces to variation at the Avpr1a locus, we explore sequence diversity at the Avpr1a locus and throughout the genome in two populations of wild prairie voles. First, we refine results demonstrating balancing selection at the locus by comparing the frequency spectrum of variants at the locus to a random sample of the genome. Next, we find that the four SNPs that predict high V1aR expression in the RSC are in stronger linkage disequilibrium than expected by chance despite high recombination among intervening variants, suggesting that epistatic selection maintains their association despite recombination. Analysis of population structure and a haplotype network for two populations revealed that this excessive LD was unlikely to be due to admixture alone. Furthermore, the two populations differed considerably in the region shown to be a regulator of V1aR expression despite the extremely low levels of genome-wide genetic differentiation. Together, our data suggest that complex selection on Avpr1a locus favors specific combinations of regulatory polymorphisms, maintains the resulting alleles at populations-specific frequencies, and may contribute to unique patterns of spatial cognition and sexual fidelity among populations.

opencc-zeroFeb 2022View details →

Artificial selection for predatory behavior results in dietary niche differentiation in an omnivorous mammal

The diet of an individual is a result of the availability of dietary items and the individual's foraging skills and preferences. Behavioral differences may thus influence diet variation, but the evolvability of diet choice through behavioral evolution has not been studied. We used experimental evolution combined with a field enclosure experiment to test whether behavioral selection leads to dietary divergence. We analysed the individual dietary niche via stable isotope ratios of nitrogen (δ15N) and carbon (δ13C) in the hair of an omnivorous mammal, bank vole, from 4 lines selected for predatory behavior and 4 unselected control lines. Predatory voles had higher hair δ15N values than control voles, supporting our hypothesis that predatory voles would consume a higher trophic level diet (more animal vs. plant foods). This difference was significant in the early but not the late summer season. The δ13C values also indicated a seasonal change in the consumed plant matter and a difference in food sources among selection lines in the early summer. These results imply that environmental factors interact with evolved behavioral tendencies to determine dietary niche heterogeneity. Behavioral selection thus has potential to contribute to the evolution of diet choice and ultimately the species' ecological niche breadth.

opencc-zeroAug 2022View details →

BETA values from DNA methylation (selected differential regions)

Studies of DNA methylation have revealed the biological mechanisms by which life adversity confers risk for later physical and mental health problems. What remains unknown is the "biologically embedding" of maternal adverse experiences resulting in maladaptive parenting and whether these epigenetic effects are transmitted to the next generation. This study focuses on neglectful mothering indexed by a severe disregard for the basic and psychological needs of the child. Using the Illumina Human Methylation 850K BeadChip in saliva samples, we identified genes with differentially methylated regions (DMRs) in those mothers with, versus those without, neglectful behavior (n = 51 vs 87) that present similar DMRs patterns in their children being neglected versus non-neglected (n = 40 vs 75). Mothers reported the emotional intensity of adverse life events. After covariate adjustment and multiple testing corrections, we identified 69 DMRs in the mother epigenome and 42 DMRs in the child epigenome that were simultaneously above the α = 0.01 threshold. The common set of nine DMRs contained genes related to childhood adversity, neonatal and infant diabetes, child neurobehavioral development, and other health problems such as obesity, hypertension, cancer, posttraumatic stress, and Alzheimer's disease; four of the genes were associated with maternal life adversity. Identifying a shared epigenetic signature of neglect linked to maternal life adversity is an essential step in breaking the intergenerational transmission of one of the most common forms of childhood maltreatment.

opencc-zeroSep 2022View details →

Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers

Understanding the mechanisms underlying heterogeneous genomic divergence is of particular interest in evolutionary biology. Highly differentiated genomic regions, known as genomic islands, often evolve between diverging lineages. These genomic islands may be related to selection promoting adaptation or reproductive isolation. Based on whole genome assembly and genome-wide RAD sequencing in a pair of yellow croakers (genus: Larimichthys), we investigated the evolutionary processes shaping genomic landscapes of divergence. Demographic modelling indicated that the two species diverged following a secondary contact scenario, where differential introgression and linked selection were suggested to be involved in heterogeneous genomic divergence. We identified reduced recombination rate in genomic islands and a relatively good conservation of both genetic diversity and recombination landscapes between species, which highlight the roles of linked selection and recombination rate variation in promoting heterogeneous divergence in the common ancestral lineage of the two species. In addition, we found a positive correlation between differentiation (FST) and absolute sequence divergence (Dxy), and elevated Dxy in genomic islands, which were different from the patterns under linked selection. Restricted gene flow in highly differentiated regions has likely remodeled the landscape of heterogeneous genomic divergence. Moreover, genomic islands showed little evidence of overlapping within and between species, implying that high gene flow and divergent selection when colonizing new habitats have reshaped the patterns of intraspecific divergence. This study highlights that highly differentiated genomic regions can also be from linked selection and variation of recombination rate, and thus are not necessarily related to speciation islands or local adaptation.

opencc-zeroMar 2023View details →

Differential selection of roosts by Eastern Small-footed Myotis relative to rock structure and microclimate

Roost selection by insectivorous bats in temperate regions is presumably influenced by roost microclimates in relation to thermoregulatory strategies, but few studies have included temperature measurements in habitat selection models. Rocky landscape features are an important source of roosts that provide both shelter from predators and beneficial microclimates for bats. Most information about rock-roosting bats is derived from western North America. We studied microhabitat selection by Eastern Small-footed Bats (Myotis leibii) on natural talus slopes and human-made stone structures in the Appalachian Mountains of Virginia and New Hampshire, relative to thermal and structural characteristics of rock crevices. Roosts were located with a combination of radio-telemetry and randomized visual surveys. Roost switching behavior and structural characteristics of roosts did not appear to be influenced by the methods we used to locate roosts. Compared to random crevices, both sexes selected crevices with narrow openings, likely to provide protection from predators. Reproductive females also selected larger rocks and more stable microclimates; whereas males selected crevices that were structurally similar to but warmed more during the day than random crevices. Rock size and other structural characteristics influenced temperatures of roosts and random crevices alike by inhibiting excessive daytime heating and nighttime cooling. Because large rocks were associated with roost selection by reproductive females, and talus slopes with large rocks could be limited, we recommend including rock size as a variable in landscape scale habitat assessments for Eastern Small-footed Bats. Protecting or managing for habitat features with large rocks that receive high solar exposure could benefit Eastern Small-footed Bats and perhaps other rock-roosting species.