Find research datasets worth reusing

Figure 4 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains

Figure 4. Maximum likelihood-based phylogeny, with 100 bootstrap replicates and using all the 26 mitochondrial genomes generated in this study. The dataset was supplemented with Thyropygus sp. and Abacion magnum as outgroups, with sequences derived from GenBank. GenBank accession numbers are given in parentheses. Colours represent Tropostreptus sample origins. The upper right inset shows the topology of the Tropostreptus hamatus lineage, enlarged to clarify the branching order. Only support values <100 are shown. *Thyropygus sp. (red font) is very likely to be a species misidentification; for more information, see Discussion text.

Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains

Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 mitochondrial genomes generated in this study. The dataset was supplemented with Thyropygus sp. and Abacion magnum as outgroups, derived from GenBank. GenBank accession numbers are provided in parentheses. Blue bars indicate the 95% highest probability density intervals for node ages. Age estimation for lineage divergence was based on a general arthropod mitochondrial DNA substitution rate and should be considered with caution. *Thyropygus sp. (red font) is very likely to be a misidentification; for more information, see the Discussion.

Figure 1 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains

Figure 1. Typical Tropostreptus appearance exemplified by a Tropostreptus hamatus individual from Udzungwa Mountains, Tanzania (photograph credit: Nikolaj Scharff).

Figure 2 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains

Figure 2. Map showing the origin of the millipede specimens used in the study, with the accuracy of location restricted to mountain blocks. Coloured circles all represent Tropostreptus species, whereas grey symbols represent species from other millipede genera. Base map published by permission of the Eastern Arc Mountains Conservation Endowment Fund.

Figure 3 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains

Figure 3. The gene order of mitochondrial coding sequences shared among all analysed millipede species in this study, which include all known species of Tropostreptus (T. droides, T. hamatus, T. kipunji, T. microcephalus, T. severus and T. sigmatospinus), in addition to Archispirostreptus gigas, Chaleponcus netus, Macrolenostreptus orestes, Prionopetalum kraepelini and Pseudotibiozus cerasopus. Colour key: red, ribosomal RNA (rRNA); pink, transfer RNA (tRNA); yellow, protein-coding sequences (CDS). Arrows indicate gene transcription orientation.

opencc-zeroDec 2019View details →

Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta)

The Cyanidiophyceae is an early-diverged red algal class that thrives in extreme conditions around acidic hot springs. Although this lineage has been highlighted as a model for understanding the biology of extremophilic eukaryotes, little is known about the molecular evolution of their mitochondrial genomes (mitogenomes). To fill this knowledge gap, we sequenced five mitogenomes from representative clades of Cyanidiophyceae and identified two major groups, here referred to as Galdieria-type (G-type) and Cyanidium-type (C-type). G-type mitogenomes exhibit the following three features: (i) reduction in genome size and gene inventory, (ii) evolution of unique protein properties including charge, hydropathy, stability, amino acid composition, and protein size, and (iii) distinctive GC-content and skewness of nucleotides. Based on GC-skew-associated characteristics, we postulate that unidirectional DNA replication may have resulted in the rapid evolution of G-type mitogenomes. The high divergence of G-type mitogenomes was likely driven by natural selection in the multiple extreme environments that Galdieria species inhabit combined with their highly flexible heterotrophic metabolism. We speculate that the interplay between mitogenome divergence and adaptation may help explain the dominance of Galdieria species in diverse extreme habitats.

opencc-zeroNov 2023View details →

Data for: The pace of mitochondrial molecular evolution varies with seasonal migration distance

This repository contains data associated with "The pace of mitochondrial molecular evolution varies with seasonal migration distance." This study demonstrates relationships between traits (migration distance, mass, population genetic parameters representing genetic diversity) and molecular evolutionary rates (dS and dN/dS). The main conclusions are based on models from the program Coevol. The files included here are input files necessary to run models with Coevol, as well as selected Coevol output files used for figure generation associated with the manuscript. We also include a copy of a GitHub repository of manuscript code. Other necessary data for replicating analyses in the manuscript are included in the manuscript supplement.

opencc-zeroJul 2024View details →

Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans data

Mitochondrial genomes exist in a nested hierarchy of populations where mitochondrial variants are subject to genetic drift and selection at each level of organization, sometimes engendering conflict between different levels of selection, and between the nuclear and mitochondrial genomes. Deletion mutants in the Caenorhabditis elegans mitochondrial genome can reach high intracellular frequencies despite strongly detrimental effects on fitness. During a mutation accumulation (MA) experiment in C. elegans, a 499 bp deletion in ctb-1 rose to 90% frequency within cells while significantly reducing fitness. During the experiment, the deletion-bearing mtDNA acquired three additional mutations in nd5, namely two single insertion frameshift mutations in a homopolymeric run, and a base substitution. Despite an additional fitness cost of these secondary mutations, all deletion-bearing molecules contained the nd5 mutations at the termination of the MA experiment. The presence of mutant mtDNA was associated with increased mtDNA copy-number. Variation in mtDNA copy-number was greater in the MA lines than in a wildtype nuclear background, including a severe reduction in copy-number at one generational timepoint. Evolutionary replay experiments using different generations of the MA experiment as starting points suggests that two of the secondary mutations contribute to the proliferation of the original ctb-1 deletion by unknown mechanisms.

opencc-zeroApr 2023View details →

Mitochondrial genome evolution in Annelida: A systematic study on conservative and variable gene orders and the factors influencing its evolution

The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene-order variability including, among others, increased substitution rates, base composition differences, structure of non-coding regions, parasitism, living in extreme habitats, short generation times and biomineralization. However, these analyses were neither done systematically, nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, gene order variability does not predict difficulty in placing certain taxa within molecular phylogenetic studies. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why they do not always fit to the observed patterns without nuisance.