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Fig. 14. Sequenced Lymantini specimen 10067 in Phylogeny, diversity and biogeography of flightless amphi-Pacific lymantine weevils (Coleoptera: Curculionidae: Molytinae)

Fig. 14. Sequenced Lymantini specimen 10067: Lymantina.

Fig. 10. Sequenced Lymantini specimen 9819 in Phylogeny, diversity and biogeography of flightless amphi-Pacific lymantine weevils (Coleoptera: Curculionidae: Molytinae)

Fig. 10. Sequenced Lymantini specimen 9819: Epibaenus pinicola Kuschel, 1959.

Fig. 13. Sequenced Lymantini specimen 10060 in Phylogeny, diversity and biogeography of flightless amphi-Pacific lymantine weevils (Coleoptera: Curculionidae: Molytinae)

Fig. 13. Sequenced Lymantini specimen 10060: Lymantina.

Fig. 12. Sequenced Lymantini specimen 9829 in Phylogeny, diversity and biogeography of flightless amphi-Pacific lymantine weevils (Coleoptera: Curculionidae: Molytinae)

Fig. 12. Sequenced Lymantini specimen 9829: Theognete galvezi Anderson, 2010.

MinION sequencing data of mtDNA from BH10 cells

Mitochondrial DNA (mtDNA) recombination in animals has remained enigmatic because of its uniparental inheritance and subsequent homoplasmic state, which excludes the biological need for genetic recombination, as well as limits tools to study it. However, molecular recombination is an important genome maintenance mechanism for all organisms, most notably being required for double-strand break repair. To demonstrate the existence of mtDNA recombination, we have taken advantage of a cell model with two different types of mitochondrial genomes and impaired ability to turn over broken mtDNA. The resulting excess of linear DNA fragments caused increased formation of cruciform mtDNA, appearance of heterodimeric mtDNA complexes and recombinant mtDNA genomes, detectable by Southern blot. Combining our observations with previously published work, we propose that the mitochondrial replisome can catalyze microhomology-mediated recombination of linear mtDNA ends, thus rendering a specialized mitochondrial recombinase unnecessary. The error-proneness of this system is likely to contribute to the formation of pathological mtDNA rearrangements.

Aligned and curated mtDNA sequences from: Ancient DNA of narrow-headed voles reveals common features of the Late Pleistocene population dynamics in cold-adapted small mammals

Narrow-headed vole, together with collared lemming and common vole, was the most abundant small mammal species across Eurasian Late Pleistocene steppe-tundra environments. Previous ancient DNA studies of the latter two revealed dynamic past population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprising mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from multiple sites across Europe and north-western Asia and covering the last ca. 100 thousand years (ka). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples for calibration of the molecular clock. We found that across the three species, divergence of the main mtDNA lineages occurred during Marine Isotope Stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat to the interglacial environments. In European narrow-headed voles, we identified multiple time-structured mtDNA lineages, implying lineage turnovers. Timing of some of these turnovers was synchronous across all three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

opencc-zeroJan 2023View details →

nRCFV: A sequence, taxon and character state-normalised metric for the pre-reconstruction evaluation of compositional heterogeneity

Motivation Compositional heterogeneity – when the proportions of nucleotides and amino acids are not broadly similar across the dataset – is a cause of a great number of phylogenetic artefacts. Whilst a variety of methods can identify it post-hoc, few metrics exist to quantify compositional heterogeneity prior to the computationally intensive task of phylogenetic tree reconstruction. Here we assess the efficacy of one such existing, widely used, metric: Relative Composition Frequency Variability (RCFV), using both real and simulated data. Results Our results show that RCFV can be biased by sequence length, the number of taxa, and the number of possible character states within the dataset. However, we also find that missing data does not appear to have an appreciable value on RCFV. We discuss the theory behind this and the consequences of this for the future of the usage of the RCFV value and propose a new metric, nRCFV, which accounts for these biases. Alongside this, we present a new software that easily calculates both RCFV and nRCFV, called nRCFV_Reader. Availability and Implementation nRCFV has been implemented in RCFV_Reader, available at: <a href="https://github.com/JFFleming/RCFV_Reader">https://github.com/JFFleming/RCFV_Reader</a>. Both our simulation and real data are available in this dataset.

Perianth evolution and implications for generic delimitation in the Eucalypts (Myrtaceae): DNA sequences, morphological data

Eucalyptus was traditionally defined by the operculate perianth—hence the generic name (Latin, meaning "well-covered"). But after previous phylogenetic analysis placed Angophora, which has free sepals and petals, as sister to the bloodwood eucalypts, the latter were segregated into a new genus, Corymbia. We made a targeted capture of 101 low-copy nuclear exons from 392 samples representing 329 species-level taxa. The phylogeny was estimated using maximum likelihood (IQtree and RAxML) and the multi-species coalescent (Astral). We tested alternative relationships between four genera within Eucalypteae (Arillastrum, Angophora, Eucalyptus, Corymbia) at each of two nodes critical to generic delimitation using Shimodaira's Approximately Unbiased (AU) test. Monophyly of Arillastrum + (Corymbia + Angophora) relative to Eucalyptus sensu stricto was supported whereas monophyly of Corymbia relative to Angophora was decisively rejected. These results indicate that either Eucalyptus should be expanded to include all four genera or Corymbia should be split into two. All of the alternative relationships among the four currently recognised genera imply homoplasy in perianth evolution, specifically with respect to origins of the bud cap (operculum or calyptra), which has been traditionally used to define Eucalyptus. Inferred evolutionary transitions in perianth traits are generally congruent with divergences between major clades with a single exception: expression of separate sepals and petals in Angophora, which is nested within the operculate genus Corymbia, appears prima facie to be a reversal to the plesiomorphic perianth structure. Strictly, this is not a reversal because the petals of Angophora and Corymbia have a novel compound keel-and-limb structure that is absent in the outgroups. This structure is evident in early development, irrespective of whether the petals remain free or later become part of an operculum. Many of the currently recognised infrageneric taxa down to sectional level (and below in some cases) are well-supported by the sequence data and definable by morphological traits. Inclusion of Angophora within Eucalyptus was formally proposed two decades ago but did not gain acceptance. Here instead, we formally raise Corymbia subg. Blakella to genus rank and make the relevant new combinations.

Raw sequence data and OTU tables of soil microorganisms obtained across a summit in the Lesotho highlands

Mountain regions represent unique environments characterized by strong topographical diversity which drive climatic and environmental variability within these environments. These regions thus provide an opportunity to explore the relationships between various environmental factors and soil microorganisms. In this study, we investigated the impact of micro-topographical (i.e., north/south-facing slope aspects and flat plateau between them) variations on microbial diversity and community structures across a Lesotho mountain summit. Raw sequenced data were generated using the Illumina MiSeq platform on DNA extracted from soil samples collected across the plateau, north- and south-facing slopes. This data was then used for taxonomic classification of the bacterial and fungal OTUs for the determination of the alpha- and beta-diversity across the slopes. These analyses revealed that a relatively greater bacterial and fungal diversity could be observed for the north-facing slope compared to the south-facing slope and plateau. While there was no difference in group variance of bacterial and fungal community structures across the plateau, north- and south-facing slopes. Multiple comparison analyses were conducted to determine the impact of various abiotic and geographical factors on bacterial and fungal diversity and community structures. These analyses indicated that the slope aspect significantly affects bacterial and fungal community structures at this location. These results provide an original insight into soil microbial diversity in the Lesotho highlands and offer an opportunity to investigate the response of soil microorganisms to changes in environmental and climatic factors in highly variable mountain environments such as the Lesotho highlands.

Aligned DNA sequence matrix for phylogenetic analyses in the article "A new species of spiny-backed tree frog, genus Osteocephalus (Anura: Hylidae), from the Yanachaga Chemillén National Park in central Peru"

Aligned DNA sequence matrix for phylogenetic analyses of the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species" The matrix is in NEXUS format and has 14791 bp and 38 terminals. Partitions are as follows: charset 12S_16S = 1-2442;     charset mtGenome_other_genes = 2443-9180;    charset nonCoding =  3132- 3138 4776- 4857 5203- 5214;     charset codonPos1 =  2443-3130\3 3139-4774\3 4858-5200\3 5215-9178\3;     charset codonPos2 =  2444-3131\3 3140-4775\3 4859-5201\3 5216-9179\3;     charset codonPos3 =  2445-3129\3 3141-4773\3 4860-5202\3 5217-9180\3;     charset 16S_ND1nonCoding =  9181- 9428 10390- 10506 ;     charset 16S_ND1codonPos1 =  9429-10389\3;     charset 16S_ND1codonPos2 =  9430-10387\3;     charset 16S_ND1codonPos3 =  9431-10388\3;     charset POMCcodonPos1 =  10507-11068\3;     charset POMCcodonPos2 =  10508-11066\3;     charset POMCcodonPos3 =  10509-11067\3;     charset CO1codonPos1 =  11069-12608\3;     charset CO1codonPos2 =  11070-12609\3;     charset CO1codonPos3 =  11071-12610\3;     charset CytbcodonPos1 =  12611-13757\3;     charset CytbcodonPos2 =  12612-13758\3;     charset CytbcodonPos3 =  12613-13759\3;     charset ND2codonPos1 =  13760-14789\3;     charset ND2codonPos2 =  13761-14790\3;     charset ND2codonPos3 =  13762-14791\3;

Sequences of bacterial and fungal communities by Next-Generation Sequencing (NGS) associated to wall patinas

These data are the DNA sequences obtained from samples of house plaster with chromatic alteration facies. Three areas (VA1, VA3 and VNA6) of the wall were sampled. the DNA was extracted using the Spin Kit For Soil MPBio. The DNA extracts were sequenced by NGS using Illumina MiSeq Two regions were selected V3V5 16S for Bacteria and ITS1 ITS for Fungi.

opencc-by-4.0Feb 2023View details →

Fasta format protein sequences from assembled kyphosid fish gut metagenomes

Predicted proteins sequences from kyposid fish gut metagenomic samples F5, F6, F7, and F8, obtained as described in the following study: Podell S, Oliver A, Kelly LW, Sparagon W, Plominsky, A, Nelson RS, Laurens LML, Augyte, S, Sims NA, Nelson CE, Allen EE. Herbivorous fish microbiome adaptations to sulfated dietary polysaccharides (2023) manuscript submitted.

opencc-by-4.0Feb 2022View details →

Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures

Imaging data related to the "Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures" manuscript

opencc-by-4.0Feb 2023View details →

MinION plasmid deep long read sequencing for sequence verification

We sequenced four plasmid constructs, each with a whole MinION flowcell, for use in developing and testing a sequence verification procedure. The resulting pipeline can sequence verify plasmid constructs, generating a consensus sequence with associated confidence of each base, adhering to strict acceptance criteria . The data contained herein are a subset of the complete data; 30 fast5 files for each plasmid, to be used as example data.   datHL_001519: BCRxV.TF.1 datHL_001521: BCRxV.VSVG.1 datHL_001617: BCRxV.GagPolRev.1 datHL_001620: BCRxV.VSVG.1_mutant

opencc-by-4.0Feb 2023View details →

Sequence diversity in MAX effectors and other genes in 120 isolates of the rice blast fungus Magnaporthe oryzae

- list_of_accessions_and_assembly_statistics.xlsx: list of 120 isolate and genome assembly statistics - assemblies.zip: genome assemblies with repeats were not masked - orthogroups.txt: list of orthogroups in orthogroups.zip -orthogroups.zip: sequences of orthogroups, as identified using Orthofinder. Sequences were aligned using translatorX (https://doi.org/10.1093/nar/gkq291) - single_copy_orthologs.zip: folder which contains aligned sequences of single-copy orthologs (alignment with translatorX https://doi.org/10.1093/nar/gkq291); three types of genes were distinguished: MAX effectors, other secreted proteins, and other genes; note that to produce this dataset, the 11 orthogroups that included paralogous copies of MAX effectors were split into sets of orthologous sequences using genealogies inferred using RAXML v8, yielding a total of 94 single-copy MAX orthologs; for each split orthogroup, sets of orthologous sequences were assigned a number that was added to the orthogroup’s identifier as a suffix (for instance paralogous sequences of orthogroup OG0000244 were split into orthogroups OG0000244_1 and OG0000244_2)

SARS-COV-2 genomic sequences used as references for the NASCarD method

A set of 9 SARS-CoV-2 genome sequences used as reference in the NASCarD process.

Scaled RNA sequencing counts accompaining the publication Singh and Gollapalli 2023

RNA-Seq analysis of WT and taurine-deficient osteoblasts. RNA was extracted from the mouse primary calvarial osteoblasts prepared from day 3–5 neonates of WT or Slc6a6-/- genotypes using the RNeasy extraction kit (Qiagen). RNA sequencing libraries were prepared with Illumina-compatible NEBNext UltraTM II Directional RNA library kit at Genotypic Technology, Inc. The raw data were trimmed for adapter sequences and low-quality bases (<q30) using Cutadapt with default parameters [DOI:10.14806/ej.17.1.200] and checked for quality using FastQC [Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data]. Mouse raw reads were aligned to the mouse reference genome (mm9) using Hisat2(24) with default parameters. HTSeq [G Putri, S Anders, PT Pyl, JE Pimanda, F Zanini Analyzing high-throughput sequencing data with HTSeq 2.0 arXiv:2112.00939 (2021)] was used to estimate gene abundance. Downstream analyses were done using the analysis framework tidybulk (25, 26). The filterByExpr functionality of edgeR (27) was used to identify the abundant gene-transcripts included in downstream analyses using default parameters and the knock-out phenotype as the factor of interest. The algorithm trimmed mean of M valued (TMM) values identified sample-wise scaling to compensate for differences in sequencing depth across samples (28). For aiding data exploration, we reduced the data dimensionality using principal component analysis (PCA). Differential expression analyses were performed using the robust likelihood ratio implementation of edgeR, testing for differences in gene transcript abundance greater than 1 log-fold (29, 30). The ppcseq method was used to investigate the presence of outlier observation among the significant results to avoid biases in the statistics (31). The ggplot2 software produced most of the data visualizations, whereas tidyHeatmap was used for heatmap visualization (32-34). We performed gene-set enrichment analyses using the MSigDB C2 experimentally derived gene set, the clusterProfiler algorithm, and the visualization tool enrichplot (cran.r-project.org/) (https://rdrr.io/cran/msigdbr/) (35). An aging signature was composed of a union of gene sets from MSigDB and a set of genes derived from aging datasets identified in this study through gene set enrichment analysis and published literature (36). The p-values of gene set analyses were corrected for multiple testing using the Benjamini Hochberg correction (37).

Antelope Valley Earthquake Sequence Relocated Catalog

Relocated earthquake catalog for the Antelope Valley Earthquake sequence in GrowClust output format. This is a space-delimited file with the following columns: <ul> <li>yr mon day hr min sec: relocated origin time (columns 1-6)</li> <li>evid: event ID (column 7)</li> <li>latR lonR depR: relocated latitude, longitude and depth (decimal degrees and km; columns 8-10)</li> <li>mag: event magnitude (column 11)</li> <li>qID cID nbranch: event serial ID number, cluster serial ID number, total number of events in this cluster (columns 12-14)</li> <li>qnpair qndiffP qndiffS: number of event pairs, P-phase differential times, and S-phase differential times used to relocate this event (columns 15--17)</li> <li>rmsP rmsS: RMS residual differential times for this event for P-phases and S-phases (s; columns 18-19)</li> <li>eh ez et: estimated location errors in horizontal (km), vertical (km), and origin time (s; columns 20-22)</li> <li>latC lonC depC: initial (catalog) latitude, longitude and depth (decimal degrees and km; columns 23-25)</li> </ul> Note that events that are not waveform relocated with have nbranch = 1. This includes the mainshock and several other large events, which typically have waveforms that are too complex to be confidently relocated with waveform cross-correlation.

opencc-zeroMar 2023View details →

Collection and ddRadSeq sequencing data for Sitophilus zeamais from Oaxaca and Chiapas, Mexico

The maize weevil, Sitophilus zeamais, is a ubiquitous pest of maize and other cereal crops worldwide and remains a threat to food security in subsistence communities. Few population genetic studies have been conducted on the maize weevil, but those that exist have shown that there is very little genetic differentiation between geographically dispersed populations and that it is likely the species has experienced a recent range expansion within the last few hundred years. While the previous studies found little genetic structure, they relied primarily on mitochondrial and nuclear microsatellite markers for their analyses. It is possible that more fine-scaled population genetic structure exists due to local adaptation, the biological limits of natural species dispersal, and the isolated nature of subsistence farming communities. In contrast to previous studies, here, we utilized genome-wide single nucleotide polymorphism data to evaluate the genetic population structure of the maize weevil from the southern and coastal Mexican states of Oaxaca and Chiapas. We employed strict SNP filtering to manage large next generation sequencing lane effects and this study is the first to find fine-scale genetic population structure in the maize weevil. Here, we show that although there continues to be gene flow between populations of maize weevil, that fine-scale genetic structure exists. It is possible that this structure is shaped by local adaptation of the insects, the movement and trade of maize by humans in the region, geographic barriers to gene flow, or a combination of these factors.

Supplemental Materials for "Convective boundary mixing in main-sequence stars: theory and empirical constraints"

MESA inlists and data products used for generating the figures of the review paper: "Convective boundary mixing in main-sequence stars: theory and empirical constraints".