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Data from: RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R

Partially clonal species are common in the Tree of Life. And yet, population genetics models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here we present an R package built upon GenClone software including new functions and several improvements. The RClone package includes functions to handle clonal datasets, allowing (i) checking for dataset reliability to discriminate multi-locus genotypes (MLG), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii) genotypic richness and evenness indices calculation based on MLGs or MLLs, and (iv) describing several spatial components of clonality. RClone allows the one shot analysis of multi-population datasets without size limitation, suitable for datasets now increasingly produced through Next Generation Sequencing. A major improvement compared to existing software is the ability to determine the threshold to cluster similar MLGs into MLLs, based on implemented simulations of sexual events. Several functions allow data importation, conversion and exportation with adegenet, Genetix or Arlequin. RClone is provided with two vignettes to handle analysis on one (RClone_quickmanual) or several populations (RClone_qmsevpops).

Data from: Tuning Geometric Morphometrics: an R tool to reduce information loss caused by surface smoothing

The application of Geometric Morphometrics has remarkably increased since 3D imaging techniques have become widespread, such as high-resolution computerised tomography, laser scanning and photogrammetry. Acquisition, 3D rendering and simplification of virtual objects produce faceting and topological artefacts, which can be counteracted by applying decimation and smoothing algorithms. Nevertheless, smoothing algorithms can have detrimental effects. This work aims at developing a method to assess the amount of information loss or recovery after the application of 3D surface smoothing. The method presented here is conceived to optimise the smoothing procedure for 3D surfaces used in Geometric Morphometrics. We implemented the method in a tool running in the r statistical environment. The tool requires one surface, one landmark set and one surface semilandmark set to estimate the best smoothing settings, including algorithm type, iteration and scale factor value. Additional parameters can be tuned by the user. We describe the method in detail, reporting the tool usage, including its main settable parameters. One example is provided as a further explanation of the method. Our method reduces the chances of losing information in Geometric Morphometrics applications and is a unique attempt of standardising a widespread, potentially damaging procedure. The tool represents an advance in the application of Geometric Morphometrics.

opencc-zeroDec 2012View details →

Data from: pavo: an R package for the analysis, visualization and organization of spectral data

1. Recent technical and methodological advances have led to a dramatic increase in the use of spectrometry to quantify reflectance properties of biological materials, as well as models to determine how these colours are perceived by animals, providing important insights into ecological and evolutionary aspects of animal visual communication. 2. Despite this growing interest, a unified cross-platform framework for analyzing and visualizing spectral data has not been available. We introduce pavo, an R package that facilitates the organization, visualization, and analysis of spectral data in a cohesive framework. pavo is highly flexible, allowing users to (a) organize and manipulate data from a variety of sources, (b) visualize data using R's state-of-the-art graphics capabilities, and (c) analyze data using spectral curve shape properties and visual system modeling for a broad range of taxa. 3. In this paper, we present a summary of the functions implemented in pavo and how they integrate in a workflow to explore and analyze spectral data. We also present an exact solution for the calculation of colour volume overlap in colourspace, thus expanding previously published methodologies. 4. As an example of pavo's capabilities, we compare the colour patterns of three African Glossy Starling species, two of which have diverged very recently. We demonstrate how both colour vision models and direct spectral measurement analysis can be used to describe colour attributes and differences between these species. Different approaches to visual models and several plotting capabilities exemplify the package's versatility and streamlined workflow. 5. pavo provides a cohesive environment for handling spectral data and addressing complex sensory ecology questions, while integrating with R's modular core for a broader and comprehensive analytical framework, automated management of spectral data, and reproducible workflows for colour analysis.

Figure 7 from: Szawaryn K, Nedvěd O, Biranvand A, Czerwiński T, Nattier R (2021) Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae). ZooKeys 1043: 61-85. https://doi.org/10.3897/zookeys.1043.65829

Figure 7 Coccidula rufa (Reitter) SEM illustrations A body, dorsal B pronotum C head and prothorax, ventral D antenna E mesoventrite, metaventrite and ventrite 1 F ventrites 4–6, female. Scale bars: 1 mm (A); 500 µm (B, C, E, F); 400 µm (D).

Figure 3 from: Szawaryn K, Nedvěd O, Biranvand A, Czerwiński T, Nattier R (2021) Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae). ZooKeys 1043: 61-85. https://doi.org/10.3897/zookeys.1043.65829

Figure 3 Coccidula litophiloides Reitter SEM illustrations, paratype HNHMA body, dorsal B pronotum C head and prothorax, ventral D meso and metaventrite E head ventral. Scale bars: 1 mm (A); 500 µm (B–D); 400 µm (E).

Figure 6 from: Szawaryn K, Nedvěd O, Biranvand A, Czerwiński T, Nattier R (2021) Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae). ZooKeys 1043: 61-85. https://doi.org/10.3897/zookeys.1043.65829

Figure 6 Coccidula reitteri Dodge A original drawings of male and female genitalia by Bielawski 1984B tegmen, inner C tegmen, lateral. Scale bar: 500 µm (B, C).

Figure 11 from: Szawaryn K, Nedvěd O, Biranvand A, Czerwiński T, Nattier R (2021) Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae). ZooKeys 1043: 61-85. https://doi.org/10.3897/zookeys.1043.65829

Figure 11 Lithophilus naviauxi Duverger A paratype MNHN, dorsal B paratype labels and abdomen CCoccidula litophiloides Reitter, holotype labels DCoccidula suturalis Reitter, holotype labels.

Figure 10 from: Szawaryn K, Nedvěd O, Biranvand A, Czerwiński T, Nattier R (2021) Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae). ZooKeys 1043: 61-85. https://doi.org/10.3897/zookeys.1043.65829

Figure 10 Coccidula scutellata (Reitter) A tegmen, inner B tegmen, lateral C penis, lateral D male genital segment, dorsal E spermatheca F female genitalia G left and right mandibles H maxilla I metendosternite. Scale bars: 500 µm (A–F); 200 µm (G–I).

Figure 2 from: Szawaryn K, Nedvěd O, Biranvand A, Czerwiński T, Nattier R (2021) Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae). ZooKeys 1043: 61-85. https://doi.org/10.3897/zookeys.1043.65829

Figure 2 Coccidula lepida LeConte SEM illustrations A pronotum B head and prothorax, ventral C meso and metaventrite D elytra dorsal E ventrite 1. Scale bars: 500 µm (A–C); 1 mm (E, D).

Figure 1 from: Szawaryn K, Nedvěd O, Biranvand A, Czerwiński T, Nattier R (2021) Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae). ZooKeys 1043: 61-85. https://doi.org/10.3897/zookeys.1043.65829

Figure 1 Immature stages and habitus of adult species of Coccidula Kugelann AC. rufa larva BC. rufa pupa CC. lepida, dorsal DC. lepida, ventral EC. litophiloidesFC. reitteriGC. rufaHC. scutellataA, B Gilles San Martin, Wikimedia Commons C, D Danny Haelewaters G, H Udo Schmidt. Scale bars: 1 mm (C–H).

Figure 5 from: Szawaryn K, Nedvěd O, Biranvand A, Czerwiński T, Nattier R (2021) Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae). ZooKeys 1043: 61-85. https://doi.org/10.3897/zookeys.1043.65829

Figure 5 Coccidula reitteri Dodge SEM illustrations, HNHMA body, dorsal B pronotum C head and prothorax, ventral D meso and metaventrite E antenna. Scale bars: 1 mm (A); 500 µm (B–D); 300 µm (E).

Figure 8 from: Szawaryn K, Nedvěd O, Biranvand A, Czerwiński T, Nattier R (2021) Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae). ZooKeys 1043: 61-85. https://doi.org/10.3897/zookeys.1043.65829

Figure 8 Coccidula rufa (Reitter) A tegmen, inner B tegmen, lateral C penis, lateral D male genital segment, dorsal E spermatheca. Scale bar: 500 µm (A–E).

Figure 9 from: Szawaryn K, Nedvěd O, Biranvand A, Czerwiński T, Nattier R (2021) Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae). ZooKeys 1043: 61-85. https://doi.org/10.3897/zookeys.1043.65829

Figure 9 Coccidula scutellata (Reitter) SEM illustrations A body, dorsal B pronotum C head, ventral D mesoventrite, metaventrite and ventrite 1 E prosternum F ventrites 4–6, male G pro-tarsal claw. Scale bars: 1 mm (A); 500 µm (B, D, E); 400 µm (C, F); 100 µm (G).

Figure 4 from: Szawaryn K, Nedvěd O, Biranvand A, Czerwiński T, Nattier R (2021) Revision of the genus Coccidula Kugelann (Coleoptera, Coccinellidae). ZooKeys 1043: 61-85. https://doi.org/10.3897/zookeys.1043.65829

Figure 4 Coccidula litophiloides Reitter A tegmen, lateral B tegmen, inner C penis, lateral D spermatheca. Scale bar: 500 µm (A–D).

Data from: ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree. The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion. A two-dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images. The package ggtree is released under the artistic-2.0 license. The source code and documents are freely available through bioconductor (http://www.bioconductor.org/packages/ggtree).

Data from: PrimerMiner: an R package for development and in silico validation of DNA metabarcoding primers

1. DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing a standardized gene marker region. Its success is often limited due to variable binding sites that introduce amplification biases. Thus the development of optimized primers for communities or taxa under study in a certain geographic region and/or ecosystems is of critical importance. However, no tool for obtaining and processing of reference sequence data in bulk that can serve as a backbone for primer design is currently available. 2. We developed the R package PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units (OTUs) to reduce biases introduced by the different number of available sequences per species. Additionally, PrimerMiner offers functionalities to evaluate primers in silico, which are in our opinion more realistic then the strategy employed in another available software for that purpose, ecoPCR. 3. We used PrimerMiner to download cytochrome c oxidase subunit I (COI) sequences for 15 important freshwater invertebrate groups, relevant for ecosystem assessment. By processing COI markers from both databases, we were able to increase the amount of reference data 249-fold on average, compared to using complete mitochondrial genomes alone. Furthermore, we visualized the generated OTU sequence alignments and describe how to evaluate primers in silico using PrimerMiner. 4. With PrimerMiner we provide a useful tool to obtain relevant sequence data for targeted primer development and evaluation. The OTU based reference alignments generated with PrimerMiner can be used for manual primer design, or processed with bioinformatic tools for primer development.

Data from: pcadapt: an R package to perform genome scans for selection based on principal component analysis

The R package pcadapt performs genome scans to detect genes under selection based on population genomic data. It assumes that candidate markers are outliers with respect to how they are related to population structure. Because population structure is ascertained with principal component analysis, the package is fast and works with large-scale data. It can handle missing data and pooled sequencing data. By contrast to population-based approaches, the package handle admixed individuals and does not require grouping individuals into populations. Since its first release, pcadapt has evolved in terms of both statistical approach and software implementation. We present results obtained with robust Mahalanobis distance, which is a new statistic for genome scans available in the 2.0 and later versions of the package. When hierarchical population structure occurs, Mahalanobis distance is more powerful than the communality statistic that was implemented in the first version of the package. Using simulated data, we compare pcadapt to other computer programs for genome scans (BayeScan, hapflk, OutFLANK, sNMF). We find that the proportion of false discoveries is around a nominal false discovery rate set at 10% with the exception of BayeScan that generates 40% of false discoveries. We also find that the power of BayeScan is severely impacted by the presence of admixed individuals whereas pcadapt is not impacted. Last, we find that pcadapt and hapflk are the most powerful in scenarios of population divergence and range expansion. Because pcadapt handles next-generation sequencing data, it is a valuable tool for data analysis in molecular ecology.

opencc-zeroDec 2016View details →

Data from: paco: implementing Procrustean Approach to Cophylogeny in R

1. The concordance of evolutionary histories and extant species interactions provides a useful metric for addressing questions of how the structure of ecological communities is influenced by macro-evolutionary processes. 2. We introduce paco (v.0.3.1), an R package to perform Procrustean Approach to Cophylogeny. This method assesses the phylogenetic congruence, or evolutionary dependence, of two groups of interacting species using both ecological interaction networks and their phylogenetic history. 3. We demonstrate the functionality of paco through its application to empirical host-parasite and plant-pollinator communities 4. Although the package is intended to assess phylogenetic congruence between groups of interacting species, the method is also directly applicable to other scenarios that may show phylogenetic congruence including historical biogeography, molecular systematics, and cultural evolution.

R code to perform distribution models of Plain Tyrannulet

<p>Archiving to Zenodo for peer-review</p>