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opencc-by-4.0Dec 2020View details →

Convergent geographic patterns between grizzly bear population genetic structure and Indigenous language groups in coastal British Columbia

Microsatellite loci calls, sex, and mean centre detection per individual (GrizzlyMicroLociMeanXY.csv) and code associated with the paper: "Convergent geographic patterns between grizzly bear population genetic structure and Indigenous language groups in coastal British Columbia". All code is from published R packages or GitHub repositories not created by the author. Code used is best described in these alternate resources.

opencc-by-4.0Dec 2016View details →

Disease Spread in Age Structured Populations with Maternal Age Effects

Fundamental ecological processes, such as extrinsic mortality, determine population age structure. This influences disease spread when individuals of different ages differ in susceptibility or when maternal age determines offspring susceptibility. We show that Daphnia magna offspring born to young mothers are more susceptible than those born to older mothers, and consider this alongside previous observations that susceptibility declines with age in this system. We used a susceptible- infected compartmental model to investigate how age-specific susceptibility and maternal age effects on offspring susceptibility interact with demographic factors affecting disease spread. Our results show a scenario where an increase in extrinsic mortality drives an increase in transmission potential. Thus, we identify a realistic context in which age effects and maternal effects produce conditions favouring disease transmission. epi model R script.R This is the script for the SIR model as well as the associated script for life history data. main.body size.csv This is the data for the body size data collected in the main experiment. This was measured using imageJ, was recorded in pixels and converted into millimetres. main.exposed.csv This is the proportion of infected/not infected individuals from an exposed treatment group. This was a subset of individuals from the entire experiment. This was the result of the exposures from the main experiment. main.reproduction.csv This document records reproduction for individuals from old or young mothers. It is a count of the offspring born at each reproductive event, which occurs generally every three days, though variation in interclutch interval increases with age. This was from the main experiment. Only those who were unexposed to the parasite, where used for this portion of the experimental work. sm.body size.csv This records body size similarly to above, and was an independent replication of the main experiment. sm.infection status.csv This is infection outcomes of exposures carried out as above, in an independent replication of the main experiment. sm.total babies.csv This is the reproductive output, carried out similarly to above, but in an independent replication of the main experiment.

opencc-by-4.0Jun 2017View details →

Effect of variable thresholds on calculating linkage disequilibrium and population structure, using Plink 1.9

The figure presented here shows how the number of LD-independent SNPs and the apparent population structure can change drastically, depending on what input thresholds are used for the calculations. The population sample consists of 220 fruit-fly (Drosophila melanogaster). Most of the population structure plots indicate four subpopulations, which on further investigation using Fst indicate that this is caused by defined trans-centromeric regions, without evidence for genotyping error, and probably reflective of historic admixture. In the plots of population structure, the number in each box indicates the number of independent SNPs which were used in the IBD calculatations. Points are coloured by order in which each fly was sequenced, and some error is noticable for the beige points in the top-right plots. The Plink program provides a useful method for selecting single-nucleotide polymorphisms (SNPs) which are independent of linkage disequilibrium (LD), and also of visualising the genetic relatedness between individuals in a population sample, using identity-by-descent analysis (IBD). The selection of LD-independent SNPs requires three user-specfied paramaters, alongside the genotype data: i. Window-size, in kilobases (Kb) within which all pairwise comparisons between SNPs will be made, ii. Step-size, in number of SNPs, iii. r2 threshold between any two SNPs, below which they are considered to be independent (fixed here at 0.5).

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Male song structure predicts offspring recruitment to the breeding population in a migratory bird

Bird song is a classic example of a sexually selected trait, but much of the work relating individual song components to fitness has not accounted for song typically being composed of multiple, often-correlated components, necessitating a multivariate approach. We explored the role of sexual selection in shaping complex male song of house wrens (Troglodytes aedon) by simultaneously relating its multiple components to fitness using multivariate selection analysis, which is widely used in insect and anuran studies but not in birds. The analysis revealed significant variation in the form and strength of selection acting on song across different selection episodes, from nest-site defense to recruitment of offspring to the breeding population. Males that sang more song typically employed in close communication sired more offspring that were subsequently recruited to the breeding population than those that sang far-communication song. However, this relationship was not consistent across earlier selection episodes, as evidenced by non-linear selection acting on these song components in other contexts. Collectively, our results present a complex picture of multivariate selection on male song structure that would not be evident using univariate approaches and suggest possible trade-offs within and among song components at different points of the breeding season.

opencc-zeroNov 2023View details →

opencc-by-4.0Mar 2020View details →

Figure 5 in Population structure of Hepatus pudibundus (Decapoda: Aethridae) off the coast of Sergipe State, northeastern Brazil

Figure 5. Length at first morphological maturity (CWm) for females and males of Hepatus pudibundus off Sergipe (northeastern Brazil) in March/2015–May/2016.

Fig. 3 in Population structure and reproductive biology of Haemulopsis corvinaeformis (Perciformes, Haemulidae) in the south coast of Pernambuco, northeastern Brazil

Fig. 3. Monthly average (±SD) of the total length (TL, cm) of males, females and pooled sexes of Roughneck Grunt, Haemulopsis corvinaeformis (Steindachner, 1868), captured from August 2011 to July 2012, off the coast of state of Pernambuco, northeastern Brazil. Different letters indicate significant size differences between months for pooled sexes (∗, significant sizes differences between males and females; ∗∗, significant differences in sexual ratio).

Fig. 5 in Population structure and reproductive biology of Haemulopsis corvinaeformis (Perciformes, Haemulidae) in the south coast of Pernambuco, northeastern Brazil

Fig. 5. Total length at first sexual maturity (L 50, cm) and confidence interval (IC, 95%) for females, males and pooled sexes of Roughneck Grunt, Haemulopsis corvinaeformis (Steindachner, 1868), captured from August 2011 to June 2012, off the coast of state of Pernambuco, northeastern Brazil.

Fig. 4 in Population structure and reproductive biology of Haemulopsis corvinaeformis (Perciformes, Haemulidae) in the south coast of Pernambuco, northeastern Brazil

Fig. 4. Bimonthly changes in GSI (± standard error) and frequency of the different gonadal stages for Roughneck Grunt, Haemulopsis corvinaeformis (Steindachner, 1868), captured from August 2011 to June 2012, off the coast of state of Pernambuco, northeastern Brazil (A, immature; B, maturing; C, mature; D, spawned or resting). The numbers above the line represent the sample size of GSI analysis in each bimester.

Fig. 2 in Population structure and reproductive biology of Haemulopsis corvinaeformis (Perciformes, Haemulidae) in the south coast of Pernambuco, northeastern Brazil

Fig. 2. Absolute frequency distribution per length classes of males, females and pooled sexes for Roughneck Grunt, Haemulopsis corvinaeformis (Steindachner, 1868) captured from August 2011 to July 2014, off the coast of State of Pernambuco, northeastern Brazil. The vertical line represents the L50.

Fig. 1 in Population structure and reproductive biology of Haemulopsis corvinaeformis (Perciformes, Haemulidae) in the south coast of Pernambuco, northeastern Brazil

Fig. 1. Study area in the coast of state of Pernambuco, northeastern Brazil. Black dots represent fishing sites.

FIG. 5. Correlation between the spatial distribution index and population density. A in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 5. Correlation between the spatial distribution index and population density. A. For Brephulopsis cylindrica and Xeropicta derbentina at 160 plots for three years. B. For Harmozica ravergiensis in nine sites×20 plots for two years. РИС. 5. Корреляция меЖду индексом пространственного распределения и плотностью популяции. А. Для Brephulopsis cylindrica и Xeropicta derbentina на 160 плоЩадках За три года. В. Для Harmozica ravergiensis на девяти участках по 20 плоЩадок За два года.

FIG. 4 in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 4. Boxplots for estimating the density of different age classes in the Xeropicta derbentina population in warm months of 2017, 2019, and 2020 for 160 test plots. Adult snails are represented by red boxes; juvenile snails are represented by blue boxes. РИС. 4. Боксплоты для оценок плотности раЗличных воЗрастных классов в популяции Xeropicta derbentina в раЗные теплые месяцы 2017, 2019 и 2020 гг. для 160 пробных плоЩадок. ВЗрослые особи покаЗаны красным цветом, ювенильные особи покаЗаны голубым цветом.

FIG. 3 in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 3. Boxplots for estimating the density of different age classes in the Brephulopsis cylindrica population in warm months of 2017, 2019, and 2020 for 160 test plots. Adult snails are represented by red boxes; juvenile snails are represented by blue boxes. РИС. 3. Боксплоты для оценок плотности раЗличных воЗрастных классов в популяции Brephulopsis cylindrica в раЗные теплые месяцы 2017, 2019 и 2020 гг. для 160 пробных плоЩадок. ВЗрослые особи покаЗаны красным цветом, ювенильные особи покаЗаны голубым цветом.

FIG. 2 in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 2. Scheme of plots in a regular grid. A. Study site. B. Brephulopsis cylindrica and Xeropicta derbentina in the field. C. Scheme of plots in a regular grid. РИС. 2. Регулярная сетка плоЩадок. A. РасполоЖение исследуемого участка. B. Brephulopsis cylindrica и Xeropicta derbentina в месте обитания. C. Схема регулярной сетки плоЩадок.

opencc-by-4.0Nov 2024View details →

Assessing size at sexual maturity and fine-scale population structure in a direct developing whelk (Buccinum undatum) in Southern Newfoundland, Canada

R script file used to filter genotype data, estimate L50, and analyze patterns of population structure of Buccinum undatum in Southern Newfoundland, Canada. Also included are the following files required to run the script: populationsNWA.snps.vcf - Northwest Atlantic group output at the conclusion of the Stacks de novo pipeline pop_map_NWA.txt - Population map for the Northwest Atlantic group genlightNWAFullFilt.rds - Filtered genotype data for the Northwest Atlantic group populations3Ps.snps.vcf - 3Ps group output at the conclusion of the Stacks de novo pipeline  pop_map_3Ps.txt - Population map for the 3Ps group genlight3PsFullFilt.rds - Filtered genotype data for the 3Ps group maturity_data.csv - Data set containing, shell length, sex, and maturity status for samples. sample_site_coordinates_3Ps.csv - Data set containing coordinates of 3Ps sample sites

opencc-by-4.0Dec 2021View details →

Supplementary material for: "Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations"

Supplementary material for the publication "Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations" The realated preprint can be found at Research Square (<a href="https://doi.org/10.21203/rs.3.rs-861830/v1">https://doi.org/10.21203/rs.3.rs-861830/v1</a>) Supplementary file 1: Supplementary results, tables and figures. Supplementary file 2: MultiQC report. Supplementary file 3: Observer concordance of the visual filtering step. Supplementary file 4: Snakemake workflow and scripts.

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Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe

Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations. Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters. Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations. Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation. Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation per se. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.

opencc-zeroDec 2021View details →

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Group composition of individual personalities alters social network structure in experimental populations of forked fungus beetles

Social network structure is a critical group character that mediates the flow of information, pathogens, and resources among individuals in a population, yet little is known about what shapes social structures. In this study, we experimentally tested whether social network structure depends on the personalities of group members. Replicate groups of forked fungus beetles (Bolitotherus cornutus) were engineered to include only members previously assessed as either more social or less social. We found that individuals behaved consistently across social contexts, exhibiting repeatable numbers of interactions and numbers of partners. At the group level, networks composed of more social individuals had higher interaction rates, higher tie density, higher global clustering, and shorter average shortest paths than those composed of less social individuals. We highlight group composition of personalities as a source of variance in group traits and a potential mechanism by which networks could evolve.

opencc-zeroDec 2021View details →

opencc-by-4.0Jan 2021View details →

Data from: Chrysolaena obovata, A SPECIES NATIVE OF BRAZILIAN CERRADO: GENETIC DIVERSITY AND STRUCTURE OF NATURAL POPULATIONS AND POTENTIAL FOR INULIN PRODUCTION

Chrysolaena obovata (Less.) M. Dematteis, an herbaceous Asteraceae species widely distributed across different Brazilian Cerrado physiognomies, has underground organs, named rhizophores, that accumulate high concentrations of inulin-type fructans. These carbohydrates are recognized as beneficial soluble fibers for human health and are currently used in the food and pharmaceutical industries. Considering that fructans, in addition to their economic potential, provide plants with greater tolerance to drought, heat and cold, it is important to understand whether their metabolism is conserved in natural populations. In this work, we aimed to investigate if the levels of genetic diversity in the populations studied allow the selection of localities with a high genetic base and higher fructan content for future programs of in situ conservation and genetic improvement for inulin production. Therefore, we characterized the diversity, structure, and gene flow of seven natural populations from Brazilian Cerrado, using nine microsatellite loci (SSR). In addition, we compared whether the fructan composition varied between populations of different Cerrado phytophysiognomies. Overall, we found that C. obovata populations exhibited moderate levels of genetic diversity, low genetic differentiation, and high gene flow. This study identified two populations with less genetic diversity and therefore, greater attention should be given to conservation programs including these populations. Fructan metabolism is conserved in all populations, indicating that C. obovata is an important genetic resource with high potential for inulin production. File descriptions Population_code.txt - Contains a matrix that indicates the population_code, Population_name, Brazilian-state, Phytophysiognomy, Collection coordinates and Altitudes (m). Date_ Diaz et al.xlsx – Contains Genotypes crude of the individuals analyzed. Primer used for nine microsatellite loci (Camacho et al 2017).  Carbohydrates_Diaz et al  - Contains data for carbohydrates in C. obovata plant rhizophores in each population (BRA, UB, SD, SP). Location: Brazilian Cerrado