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1. Rapid evolution of mitochondrion-related genes in haplodiploid arthropods

   https://doi.org/10.1186/s12915-024-02027-4  

   Li, Yiyuan; Thomas, Gregg_W C; Richards, Stephen; Waterhouse, Robert M; Zhou, Xin; Pfrender, Michael E (December 2024, BMC Biology)

   Abstract BackgroundMitochondrial genes and nuclear genes cooperate closely to maintain the functions of mitochondria, especially in the oxidative phosphorylation (OXPHOS) pathway. However, mitochondrial genes among arthropod lineages have dramatic evolutionary rate differences. Haplodiploid arthropods often show fast-evolving mitochondrial genes. One hypothesis predicts that the small effective population size of haplodiploid species could enhance the effect of genetic drift leading to higher substitution rates in mitochondrial and nuclear genes. Alternatively, positive selection or compensatory changes in nuclear OXPHOS genes could lead to the fast-evolving mitochondrial genes. However, due to the limited number of arthropod genomes, the rates of evolution for nuclear genes in haplodiploid species, besides hymenopterans, are largely unknown. To test these hypotheses, we used data from 76 arthropod genomes, including 5 independently evolved haplodiploid lineages, to estimate the evolutionary rates and patterns of gene family turnover of mitochondrial and nuclear genes. ResultsWe show that five haplodiploid lineages tested here have fast-evolving mitochondrial genes and fast-evolving nuclear genes related to mitochondrial functions, while nuclear genes not related to mitochondrion showed no significant evolutionary rate differences. Among hymenopterans, bees and ants show faster rates of molecular evolution in mitochondrial genes and mitochondrion-related nuclear genes than sawflies and wasps. With genome data, we also find gene family expansions and contractions in mitochondrion-related genes of bees and ants. ConclusionsOur results reject the small population size hypothesis in haplodiploid species. A combination of positive selection and compensatory changes could lead to the observed patterns in haplodiploid species. The elevated evolutionary rates in OXPHOS complex 2 genes of bees and ants suggest a unique evolutionary history of social hymenopterans. 

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2. Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants

   https://doi.org/10.3389/fpls.2023.1125107  

   Tyszka, Alexa S.; Bretz, Eric C.; Robertson, Holly M.; Woodcock-Girard, Miles D.; Ramanauskas, Karolis; Larson, Drew A.; Stull, Gregory W.; Walker, Joseph F. (March 2023, Frontiers in Plant Science)

   Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles’ evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles’ evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole. 

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3. Patterns of Gene Family Evolution and Selection Across Daphnia

   https://doi.org/10.1002/ece3.71453  

   Murray, Connor S; Bergland, Alan O (May 2025, Ecology and Evolution)

   ABSTRACT Gene family expansion underlies a host of biological innovations across the tree of life. Understanding why specific gene families expand or contract requires comparative genomic investigations clarifying further how species adapt in the wild. This study investigates the gene family change dynamics within several species ofDaphnia, a group of freshwater microcrustaceans that are insightful model systems for evolutionary genetics' research. We employ comparative genomics approaches to understand the forces driving gene evolution and draw upon candidate gene families that change gene numbers acrossDaphnia. Our results suggest that genes related to stress responses and glycoproteins generally expand across taxa, and we investigate evolutionary hypotheses of adaptation that may underpin expansions. Through these analyses, we shed light on the interplay between gene expansions and selection within other ecologically relevant stress response gene families. While we show generalities in gene family turnover in genes related to stress response (i.e., DNA repair mechanisms), most gene family evolution is driven in a species‐specific manner. Additionally, while we show general trends toward positive selection within some expanding gene families, many genes are not under selection, highlighting the complexity of diversification and evolution withinDaphnia. Our research enhances the understanding of individual gene family evolution withinDaphniaand provides a case study of ecologically relevant genes prone to change. 

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4. Predicting evolutionary targets and parameters of gene deletion from expression data

   https://doi.org/10.1093/bioadv/vbae002  

   Campelo dos Santos, Andre Luiz; DeGiorgio, Michael; Assis, Raquel; Forslund, ed., Sofia (January 2024, Bioinformatics Advances)

   Abstract MotivationGene deletion is traditionally thought of as a nonadaptive process that removes functional redundancy from genomes, such that it generally receives less attention than duplication in evolutionary turnover studies. Yet, mounting evidence suggests that deletion may promote adaptation via the “less-is-more” evolutionary hypothesis, as it often targets genes harboring unique sequences, expression profiles, and molecular functions. Hence, predicting the relative prevalence of redundant and unique functions among genes targeted by deletion, as well as the parameters underlying their evolution, can shed light on the role of gene deletion in adaptation. ResultsHere, we present CLOUDe, a suite of machine learning methods for predicting evolutionary targets of gene deletion events from expression data. Specifically, CLOUDe models expression evolution as an Ornstein–Uhlenbeck process, and uses multi-layer neural network, extreme gradient boosting, random forest, and support vector machine architectures to predict whether deleted genes are “redundant” or “unique”, as well as several parameters underlying their evolution. We show that CLOUDe boasts high power and accuracy in differentiating between classes, and high accuracy and precision in estimating evolutionary parameters, with optimal performance achieved by its neural network architecture. Application of CLOUDe to empirical data from Drosophila suggests that deletion primarily targets genes with unique functions, with further analysis showing these functions to be enriched for protein deubiquitination. Thus, CLOUDe represents a key advance in learning about the role of gene deletion in functional evolution and adaptation. Availability and implementationCLOUDe is freely available on GitHub (https://github.com/anddssan/CLOUDe). 

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5. DNA methylation signatures of duplicate gene evolution in angiosperms

   https://doi.org/10.1093/plphys/kiad220  

   Kenchanmane Raju, Sunil K.; Ledford, Marshall; Niederhuth, Chad E. (April 2023, Plant Physiology)

   Abstract Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomic approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole-genome duplicates were typically enriched for CG-only gene body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was a characteristic of more recent single-gene duplicates. Core angiosperm gene families were differentiated into those which preferentially retain paralogs and “duplication-resistant” families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence–absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication. 

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