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PubMed1977

Molecular evolution of human and rabbit beta-globin mRNAs.

The primary structures of human and rabbit beta-globin mRNAs are compared. Using as a standard the extent of nucleotide substitutions inferred from the hypervariable amino acid residues of fibrinopeptides A and B, which are thought to change largely by neutral evolution, we show that not all silent mutations in globin mRNA are neutral. The divergence of the sequences is limited in part by the selective usage of synonymous codons. The divergent nucleotides tend to be distributed nonrandomly: in the coding region silent substitutions are most rare in segments that are also deficient in substitutions leading to replacements.

Animals↗
PubMed1979

Molecular evolution of biomembranes: structural equivalents and phylogenetic precursors of sterols.

Derivatives of one triterpene family, the hopane family, are widely distributed in prokaryotes; they may be localized in membranes, playing there the same role as sterols play in eukaryotes, as a result of their similar size, rigidity, and amphiphilic character. Their biosynthesis embodies many primitive features compared to that of sterols and could have evolved toward the latter once aerobic conditions had been established. Membrane reinforcement appears to be achieved in other prokaryotes by other mechanisms, involving either approximately 40-A-long rigid hydrocarbon chains terminated by one polar group acting like a peg through the double-layer or similar chains terminated by two polar groups acting like tie-bars across the membrane. These inserts can be tetraterpenes (e.g., carotenoids). The biophysical function of membrane optimizers appears to have evolved toward sterols by changes limited to only a few enzymatic steps of the same fundamental biosynthetic processes.

Biological Evolution↗
PubMed2026

Gene-level complexity explains genome-wide variation in the distribution of fitness effects.

The distribution of fitness effects (DFE)-describing how harmful, neutral, or beneficial new mutations are-is central to understanding how populations evolve. Although the DFE varies across genomes and species, it remains unclear which aspects of genomic organization drive this variation. Here, we inferred gene-level selective constraints across the genomes of Mus musculus castaneus, Drosophila melanogaster and Saccharomyces cerevisiae using a combination of population genetics and machine learning trained on diverse gene features. Many gene features were predictive of selective constraint, with conservation, gene structure, and expression being the most informative. These selective constraints delineated gene classes with distinct DFEs. Genes with higher connectivity and expression-features reflecting how many traits a gene influences-experienced stronger and less dispersed deleterious effects with increasing selective constraint. Between species, the rate of adaptation decreased with increasing organismal complexity, whereas across the genome it did not decrease monotonically with selective constraint, but tended to be higher at intermediate levels. While between-species comparisons of DFE parameters were less consistent with predictions of Fisher's geometric model (FGM) based on organismal complexity, variation in DFE parameters across the genome aligned more closely with FGM when complexity was considered at the gene level. Our results suggest that gene-level complexity, captured by genomic feature proxies, provides a more informative definition of complexity for DFE variation than organism-level labels, and highlight the value of using gene features collectively to link genomic architecture, fitness landscapes, and patterns of molecular evolution.

Animals↗
PubMed2025

Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates.

Meiotic recombination is an integral cellular process, required for the production of viable gametes. Recombination rate is a fundamental genomic parameter, modulating genomic responses to selection. Our increasingly detailed understanding of its molecular underpinnings raises the prospect that we can gain insight into trait divergence by examining the molecular evolution of recombination genes from a pathway perspective, as in mammals, where protein-coding changes in later stages of the recombination pathway are connected to divergence in intra-clade recombination rate. Here, we leverage increased availability of avian and teleost genomes to reconstruct the evolution of the recombination pathway across two additional vertebrate clades: birds, which have higher and more variable rates of recombination and similar divergence times to mammals, and teleost fish, which have much deeper divergence times. Rates of molecular evolution of recombination genes are highly correlated between vertebrate clades and significantly elevated compared to control panels, suggesting that they experience similar selective pressures. Avian recombination genes are significantly more likely to exhibit signatures of positive selection than other clades, unrestricted to later stages of the pathway. Signatures of positive selection in genes linked to recombination rate variation in mammalian populations and those with signatures of positive selection across the avian phylogeny are highly correlated. In contrast, teleost fish recombination genes have significantly less evidence of positive selection despite high intra-clade recombination rate variability. Gaining clade-specific understanding of patterns of variation in recombination genes can elucidate drivers of recombination rate and thus, factors influencing genetic diversity, selection efficacy, and species divergence.

Animals↗
PubMed2026

Genome evolution and long-term demographic history in true crocodiles.

Reference-quality genomes remain scarce for true crocodiles (Crocodylus), limiting comparative analyses of genome evolution and demographic history. Here, we generated and analyzed 2 long-read genomes, 1 for Crocodylus intermedius and 1 for C. niloticus, to investigate genome architecture, coalescent effective population size (Ne), and patterns of molecular evolution across crocodilians. Comparative analyses revealed broadly similar repeat landscapes in both species and extensive macro-synteny with Alligator sinensis, indicating strong structural conservation across crocodilian genomes. Using phased diploid assemblies and MSMC2, we reconstructed historical Ne trajectories and found marked differences between species. Crocodylus intermedius exhibited persistently low Ne throughout most of the late Quaternary, with a pronounced decline during the Late Pleistocene-early Holocene transition. In contrast, C. niloticus showed substantially larger Ne over comparable time intervals. Genome-wide codon-based analyses identified significant heterogeneity in dN/dS (ω) among crocodilian lineages. Crocodylus niloticus showed the lowest genome-wide ω, whereas elevated values in C. intermedius and other lineages were consistent with reduced long-term efficacy of purifying selection under smaller historical population sizes. Branch-site tests identified candidate genes under positive selection in both focal species, with functional categories related to ion transport, endocrine regulation, and cellular signaling. Together, these results provide genomic resources for Crocodylus and support an association between long-term demographic history and genome-wide patterns of molecular evolution across crocodilians.

Animals↗
PubMed1978

Marmoset evolution: the molecular evidence.

We report here the results of comparative immunological and electrophoretic studies of the serum proteins of the New World monkeys. Specifically, we find that the New World monkeys share a long period of common ancestry with the Catarrhini and that the divergence between these two groups occurred some 35-40 million years ago. The extant New World monkey lineages are then seen as sharing a long period of common ancestry subsequent to that divergence, with their radiation beginning in the early Miocene. We see seven distinct lineages stemming from this radiation: (1) Aotus, (2) Callicebus, (3) Cebus, (4) Saimiri, (5) Ateles-Lagothrix-Alouatta, (6) Pithecia-Cacajao and (7) Callimico-Callimico with Cebuella-Saguinus-Leontideus. Within those Ateles with Lagonthrix, and Callimico with Callithrix-Cebuella form further subgroups. The marmoset radiation appears to have begun some 7-10 million years ago.

Animals↗
PubMed2025

Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of Gastrodia (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera.

The mystery of genomic alternations in heterotrophic plants is among the most intriguing in evolutionary biology. Compared to plastid genomes (plastomes) with parallel size reduction and gene loss, mitochondrial genome (mitogenome) variation in heterotrophic plants remains underexplored in many aspects. To further unravel the evolutionary outcomes of heterotrophy, we present a comparative mitogenomic study with 13 de novo assemblies of Gastrodia (Orchidaceae), one of the largest fully mycoheterotrophic plant genera, and its relatives. Analyzed Gastrodia mitogenomes range from 0.56 to 2.1 Mb, each consisting of numerous, unequally abundant chromosomes or contigs. Size variation might have evolved through chromosome rearrangements followed by stochastic loss of "dispensable" chromosomes, with deletion-biased mutations. The discovery of a hyper-abundant (∼15 times intragenomic average) chromosome in two assemblies represents the hitherto most extreme copy number variation in any mitogenomes, with similar architectures discovered in two metazoan lineages. Transferred sequence contents highlight asymmetric evolutionary consequences of heterotrophy: despite drastically reduced intracellular plastome transfers convergent across heterotrophic plants, their rarity of horizontally acquired sequences sharply contrasts parasitic plants, where massive transfers from their hosts prevail. Rates of sequence evolution are markedly elevated but not explained by copy number variation, extending prior findings of accelerated molecular evolution from parasitic to heterotrophic plants. Putative evolutionary scenarios for these mitogenomic convergence and divergence fit well with the common (e.g. plastome contraction) and specific (e.g. host identity) aspects of the two heterotrophic types. These idiosyncratic mycoheterotrophs expand known architectural variability of plant mitogenomes and provide mechanistic insights into their content and size variation.

Genome, Mitochondrial↗
PubMed1979

The evolution of an immune system.

A model for the molecular evolution of an imune system is presented. It suggests how a system of cell surface-fixed antigen receptors, called FR, to be thought of as "primitive" but still functional antibodies, could evolve into the "modern" labile T cell and antibody system, the receptors for which may be called CER (clonal expansion receptors). Perhaps the most significant insight to be gained from the theory concerns the conclusion that the immune system of an embryo may be primed by the interaction between two types of cells with complementary surface specificities. In the first type of cell the interacting molecule is an FR molecule coded by a gene of the Major Histocompatibility Complex (MHC) which has undergone a somatic mutation; in the second type it is a CER molecule also coded by a gene which has undergone a recent somatic mutation. It is believed that this insight eliminates some of the problems experienced in understanding generation of diversity, and renders unnecessary some of the more complex hypotheses about immune networks. The mechanism of action of immune response genes is easily explained by the theory.

Adaptation, Physiological↗
PubMed2026

The genetic code at the balance point of error and demand.

The origin and organizing principles of the genetic code remain central problems in molecular evolution. The low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure is optimized for robustness to mutations and translational errors. For the construction of effective molecular machines, the repertoire of encoded amino acids must also be diverse enough in physicochemical features. Here, we examine whether the standard genetic code can be understood as a near-optimal solution balancing these two objectives: minimizing error load and aligning codon assignments with the naturally occurring amino acid composition. Using simulated annealing, we explore this trade-off across a broad range of parameters. We find that the standard genetic code resides near an optimum in the fitness landscape of possible genetic codes. The degeneracy of the code plays a dual role, minimizing mistranslation errors while matching codon multiplicity to amino acid usage frequencies. As a result, uniform codon usage alone is sufficient to recover the empirical amino acid composition, without any additional bias. It is a highly effective solution that balances fidelity against resource availability constraints. A comparative analysis of natural variants also reveals a functional decoupling: error robustness acts as a rigid global constraint determined by code topology, whereas compositional alignment serves as a more flexible variable that adapts to lineage-specific demands. These results support a multi-objective optimization framework in which the genetic code reflects a balance between translational fidelity and proteomic demand.

Genetic Code↗
PubMed2025

Compensatory Evolution Following Deleterious Episodes of GC-biased Gene Conversion in Rodents.

GC-biased gene conversion (gBGC) is a widespread evolutionary force associated with meiotic recombination that favors the accumulation of deleterious AT to GC substitutions in proteins, moving them away from their fitness optimum. In many mammals, recombination hotspots have a rapid turnover, leading to episodic gBGC, with the accumulation of deleterious mutations stopping when the recombination hotspot dies. Selection is therefore expected to act to repair the damage caused by gBGC episodes through compensatory evolution. However, this process has never been studied or quantified so far. Here, we analyzed the nucleotide substitution pattern in coding sequences of a highly diversified group of Murinae rodents. Using phylogenetic analyses of about 70,000 coding exons, we identified numerous exon-specific, lineage-specific gBGC episodes, characterized by a clustering of synonymous AT to GC substitutions and by an increasing rate of nonsynonymous AT to GC substitutions, many of which are potentially deleterious. Analyzing the molecular evolution of the affected exons in downstream lineages, we found evidence for pervasive compensatory evolution after deleterious gBGC episodes. Compensation appears to occur rapidly after the end of the episode and to be driven by the standing genetic variation rather than new mutations. Our results demonstrate the impact of gBGC on the evolution of amino-acid sequences and underline the key role of epistasis in protein adaptation. This study contributes to a growing body of literature emphasizing that adaptive mutations, which arise in response to environmental changes, are just 1 subset of beneficial mutations, alongside mutations resulting from oscillations around the fitness optimum.

Gene Conversion↗
PubMed2026

Comparative genomic and proteomic analysis reveals orthogroup structured evolution of tick protease inhibitors.

Protease inhibitors (PIs) play central roles in regulating endogenous proteolysis and host-parasite interactions in ticks. However, the evolutionary architecture underlying their diversification across tick lineages remains insufficiently resolved. Here, we performed a genome-wide comparative analysis of predicted proteomes from 14 tick species to systematically characterize PI repertoires. In total, 4931 putative PIs were identified and grouped into 20 families using the MEROPS classification system. Further, PI families such as Antistasin, WAP-type, and Pacifastin, which have not previously been systematically reported in tick genomes, were classified. Orthogroup inference demonstrated that PI expansion is structured at the level of evolutionary lineages rather than uniformly across families. By stratifying orthogroups according to duplication burden and taxonomic conservation, we identified a broadly conserved single-copy core under strong purifying selection. Motif level analysis of serpin reactive center loops further revealed conservation of inhibitory specificity within single copy orthogroups and diversification of key functional residues in duplication-associated lineages. Integration of secretion prediction and tissue-resolved proteomics from Hyalomma anatolicum and Rhipicephalus microplus demonstrated that evolutionary stratification is reflected at the protein level. Together, these findings provide an orthogroup-resolved evolutionary framework linking duplication dynamics, molecular evolution, and tissue-level protein deployment. This integrative approach offers a systematic basis for prioritizing conserved and diversified PI lineages for future functional and anti-tick intervention studies.

Animals↗