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opencc-by-4.0Jun 2021View details →

Data for: Faster rates of molecular sequence evolution in reproduction-related genes and in species with hypodermic sperm morphologies

This repository contains a record of analysis scripts and sequence alignments used for the analyses presented in the manuscript. Some of the R scripts depend on supplementary tables associated with the manuscript.

opencc-zeroJan 2016View details →

Raw NGS data for the study 'Spouse-to-spouse Transmission and Evolution of Hypervariable Region 1 and 5’ Untraslated Region of Hepatitis C Virus Analyzed by Next-generation Sequencing'

This file contains the original next-generation sequencing data (raw sequences in fastq format) which were analyzed in the study titled: "Spouse-to-spouse Transmission and Evolution of Hypervariable Region 1 and 5’ Untraslated Region of Hepatitis C Virus Analyzed by Next-generation Sequencing".

opencc-zeroFeb 2024View details →

Deep sequencing datasets from: RNA-catalyzed evolution of catalytic RNA

This dataset includes raw and processed sequencing data from evolving RNA populations described in Nikos Papastavrou, David P Horning, Gerald F Joyce. "RNA-Catalyzed Evolution of Catalytic RNA" (submitted). Briefly, directed evolution of a hammerhead ribozyme sequence was carried out over eight rounds of three steps each: 1) templated synthesis of the reverse-complement hammerhead RNA by a polymerase ribozyme; 2) templated synthesis of a new copy of the hammerhead RNA from the reverse-complement by a polymerase ribozyme; 3) selective recovery of hammerhead RNA that cleaved an attached RNA substrate. Cleaved RNA was reverse transcribed, PCR amplified, and archived for sequencing, while a portion was in vitro transcribed with T7 RNA polymerase to initiate the next round of evolution. Two distinct branches of evolution were carried out for 8 rounds, using the '52-2' or '71-89' polymerase ribozymes to replicate RNA, respectively. Sequenced RNA populations were analyzed to determine polymerase ribozyme fidelity and study the evolution of hammerhead sequences replicated by polymerases with low or high RNA copying fidelities. The dataset includes raw sequence files, processed tables of mutations by position along the sequence for each polymerase, processed tables of the sequence frequency distribution from each round in the evolving populations, and spreadsheets containing final processed data used directly in manuscript figures and tables.

opencc-zeroMar 2024View details →

Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes

Variation in gene tree estimates is widely observed in empirical phylogenomic data and is often assumed to be the result of biological processes. However, a recent study using tetrapod mitochondrial genomes to control for biological sources of variation due to their haploid, uniparentally inherited, and non-recombining nature found that levels of discordance among mitochondrial gene trees were comparable to those found in studies that assume only biological sources of variation. Additionally, they found that several of the models of sequence evolution chosen to infer gene trees were doing an inadequate job of fitting the sequence data. These results indicated that significant amounts of gene tree discordance in empirical data may be due to poor fit of sequence evolution models and that more complex and biologically realistic models may be needed. To test how the fit of sequence evolution models relates to gene tree discordance, we analyzed the same mitochondrial datasets as the previous study using two additional, more complex models of sequence evolution that each model a different biologically realistic aspect of the evolutionary process: a covarion model to incorporate heterotachy, and a model partitioned model to incorporate variable evolutionary patterns by codon position. Our results show that both additional models fit the data better than the models used in the previous study, with the covarion being consistently and strongly preferred as tree size increases. However, even these more preferred models still inferred highly discordant mitochondrial gene trees, thus deepening the mystery around what we label the "Mito-Phylo Paradox" and leading us to ask whether the observed variation could be biological after all.

opencc-by-4.0Dec 2021View details →

apomixis_parallel_evolution, and Fortunella hindsii (Citrus hindsii )Genome sequencing and assembly

##The assemble(genome) files Citrus hindsii (Mini citrus)Genome assembly Citrus hindsii (Mini citrus)Genome assembly gene model gff3 file Citrus hindsii (Mini citrus)Genome assembly function annotation Citrus hindsii (Mini citrus)Genome assembly TE gff3 file ##The population dataset LD_pur.vcf.gz  //The LD purning SNP vcfs (1.4 M sites) used in analysis log10_auxin.txt //The expression (log10) related to auxin pathway sjg.temergedref.fasta.gz //The TE insertion modify genome in popTE2 analysis SVs.vcf.gz //The SV vcfs  used in the paper te-hierarchy.txt //The TE classfication in popTE2 analysis TPM_count.txt //All samples expression in TMP count unfiltered.vcf.gz //The unfiltered vcfs file (7.3 M sites, within 0.4 M indels)

opencc-by-4.0Jun 2024View details →

Enhanced Sequence-Activity Mapping and Evolution of Artificial Metalloenzymes by Active Learning

This entry contains data, pretrained models and supplementary files for our enzyme engineering study: Title: Enhanced Sequence-Activity Mapping and Evolution of Artificial Metalloenzymes by Active Learning Journal: ACS Central Science If you use any of the data or code in the <a href="https://github.com/lasgroup/ml-protein-design-sav-gold">repository</a>, please cite the paper. The contents of this entry are: <ol> <li>Sequence embeddings needed for reproducing the code are found in data.zip. Unzip the contents of the folder to <code>/data</code> in the code structure. </li> <li>NGS sequencing analysis and raw data in <code>NGS analysis.zip</code></li> <li>10% subset of structures generated with the Rosetta software in <code>structures.zip</code></li> <li>Pretrained and saved models for plotting, clustering and further prediction are saved in <code>models.zip</code></li> <li>Raw assay data including our designed libraries by active learning are found in <code>assay_and_ML_data.zip</code></li> </ol>

opencc-by-4.0Nov 2021View details →

Fig. 5 – The herein sequenced specimen 10301 in A new hypothesis on the evolution of the hybosorid beetle capacity to conglobate their bodies into a tight ball (Coleoptera: Scarabaeoidea)

Fig. 5 – The herein sequenced specimen 10301 of Ivieolus pseudoscutellatus illustrating all 13 unambiguously optimized morphological apomorphic characters in support of the Ivieolini plus Scarabatermitini clade (character/state numbering follows Ballerio & Grebennikov 2016). Three of these characters (in square brackets and marked with a question mark) need critical re-assessment and perhaps rescoring.

opencc-by-4.0Dec 2019View details →

Fig. 5. Parsimony splits network constructed from a per and ITS2 concatenated sequence data set. Heterozygous specimens are indicated with A and B in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism

Fig. 5. Parsimony splits network constructed from a per and ITS2 concatenated sequence data set. Heterozygous specimens are indicated with A and B. 'bufonivora_EUROPE_A' represents a consistent haplotype present in all 12 samples from Europe (Table 1), of which just two were heterozygous ('bufonivora_frog' and 'bufonivora_NLWi'). 'bufonivora_CAN' and 'elongata_CAN' are represented by two samples each, none of which were heterozygous. Scale bar represents expected changes per site.

Fig. 3 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data

Fig. 3. — Strict consensus of 10,000 most parsimonious trees resulting from the analysis of 58 ITS sequences; tree length = 725 steps; consistency index = 0.518; retention index = 0.734. Clades denoted by brackets are those referred to in text. Values along branches are bootstrap percentages. Placement of Polyscias elegans (discussed in text) is denoted by an asterisk. Labels for the Tieghemopanax group and other clades in "Polyscias sensu lato" follow PLUNKETT et al. (2001).

Fig. 2 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data

Fig. 2. — The single most parsimonious tree resulting from the combined analysis of ITS + trnL-trnF + 5S spacer sequences, based on the identical 24-taxon sampling as used in Fig. 1; tree length = 349 steps; consistency index = 0.663; retention index = 0.770. Values along nodes are bootstrap percentages; nodes with dashed branches have bootstraps below 70%. Identical or near identical clades (labeled A-E) from Fig. 1 are also labeled, as is the placement of Polyscias sambucifolia and P. microbotrys (asterisks), as discussed in text. Outgroups indicated by "OG."

Fig. 4 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data

Fig. 4. — Strict consensus of 156 most parsimonious trees resulting from the analysis of 40 trnL-trnF sequences; tree length = 122 steps; consistency index = 0.938; retention index = 0.972. Values along branches are bootstrap percentages. Placement of Polyscias elegans (discussed in text) is denoted by an asterisk. Labels for the Tieghemopanax group and other clades in "Polyscias sensu lato" follow PLUNKETT et al. (2001).

Fig. 5 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data

Fig. 5. — Strict consensus of 156 most parsimonious trees resulting from the analysis of 26 5S spacer sequences; tree length = 147 steps; consistency index = 0.744; retention index = 0.849. Values along branches are bootstrap percentages.

Fig. 5 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 5. The same consensus as shown in figure 4, with stems and taxa identified for ready comparison with evolutionary changes presented in appendix 4 (change list). Stems 5, 6, 16, 20, 23, 24 represent alternative relationships not rejected by the data.

Fig. 3. Sensitivity analysis graphic. Y in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 3. Sensitivity analysis graphic. Yaxis represents the logarithm of the ratio of transversion: transition weights. The xaxis represents the logarithm of the ratio of the indel cost versus the maximal cost of a molecular change. The colors represent the zaxis, which is congruence between the molecular and morphological data partitions. Red is good, blue is bad.

Fig. 2 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 2. Strict consensus of 192 equally parsimonious trees based on morphology alone (length = 276; CI = 0.443; RI = 0.74). Numbers on branches are Bremer values.

Fig. 6 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 6. Phylogenetic hypotheses for the Polychrotidae of Etheridge and de Queiroz (1988), and Frost and Etheridge (1989). Circles represent hypothesized rooting points.

Fig. 1 in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)

Fig. 1. Single tree obtained on molecularonly data (length = 2332; CI = 0.23; RI = 0.68). Numbers on branches are Bremer values.

opencc-zeroJun 2023View details →

Data from: Coding-sequence evolution does not explain divergence in petal anthocyanin pigmentation between Mimulus luteus var. luteus and M. l. variegatus

Biologists have long been interested in understanding genetic constraints on the evolution of development. For example, noncoding changes in a gene might be favored relative to coding changes due to being less constrained by pleiotropic effects. Here we evaluate the importance of coding-sequence changes to the recent evolution of a novel anthocyanin pigmentation trait in the monkeyflower genus Mimulus. The magenta-flowered Mimulus luteus var. variegatus recently gained petal lobe anthocyanin pigmentation via a single-locus Mendelian difference from its sister taxon, the yellow-flowered M. l. luteus. Previous work showed that the differentially expressed transcription factor gene MYB5a/NEGAN is the single causal gene. However, it was not clear whether MYB5a coding-sequence evolution (in addition to the observed patterns of differential expression) might also have contributed to increased anthocyanin production in M. l. variegatus. Quantitative image analysis of tobacco leaves, transfected with MYB5a coding sequence from each taxon, revealed robust anthocyanin production driven by both alleles. Counter to expectations, significantly higher anthocyanin production was driven by the allele from the low-anthocyanin M. l. luteus. Together with previously-published expression studies, this supports the hypothesis that petal pigment in M. l. variegatus was not gained by protein-coding changes, but instead solely via non-coding cis-regulatory evolution. Finally, while constructing the transgenes needed for this experiment, we unexpectedly discovered two sites in MYB5a that appear to be post-transcriptionally edited – a phenomenon that has been rarely reported, and even less often explored, for nuclear-encoded plant mRNAs.

publicAug 2024View details →

Data from: Coding-sequence evolution does not explain divergence in petal anthocyanin pigmentation between Mimulus luteus var. luteus and M. l. variegatus

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