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PubMed2025

Ancient dog mitogenomes support the dual dispersal of dogs and agriculture into South America.

Archaeological and palaeogenomic data show that dogs were the only domestic animals introduced during the early peopling of the Americas. Hunter-gatherer groups spread quickly towards the south of the continent, but it is unclear when dogs reached Central and South America. To address this issue, we generated and analysed 70 complete mitochondrial genomes from archaeological and modern dogs ranging from Central Mexico to Central Chile and Argentina, revealing the dynamics of dog populations. Our results demonstrate that pre-contact Central and South American dogs are all assigned to a specific clade that diverged after dogs entered North America. Specifically, the divergence time between North, Central and South American dog clades is consistent with the spread of agriculture and the adoption of maize in South America between 7000 and 5000 years ago. An isolation-by-distance best characterizes how dogs expanded into South America. We identify the arrival of new lineages of dogs in post-contact South America, likely of European origin, and their legacy in modern village dogs. Interestingly, the pre-contact Mesoamerican maternal origin of the Chihuahua has persisted in some modern individuals.

Animals↗
PubMed2025

Genetic structure and demographic history of house mice in western Europe inferred using whole-genome sequences.

The western house mouse, Mus musculus domesticus, is a human commensal and an outstanding model organism for studying a wide variety of traits and diseases. However, we have few genomic resources for wild mice and only a rudimentary understanding of the demographic history of house mice in Europe. Here, we sequenced 59 whole genomes of mice collected from England, Scotland, Wales, Guernsey, northern France, Italy, Portugal and Spain. We combined this dataset with 24 previously published sequences from southern France, Germany and Iran and compared patterns of population structure and inferred demographic parameters for house mice in western Europe to patterns seen in humans. Principal component and phylogenetic analyses identified three genetic clusters in western European mice. Admixture and f-branch statistics identified historical gene flow between these genetic clusters. Demographic analyses suggest a shared history of population bottlenecks prior to 20 000 years ago. Estimated divergence times between populations of house mice from western Europe ranged from 1500 to 5500 years ago, in general agreement with the zooarchaeological record. These results correspond well with key aspects of contemporary human population structure and the history of migration in western Europe, highlighting the commensal relationship of this important genetic model.

Animals↗
PubMed2025

Two-Step Loss of GLUTs in the High-Metabolism Passerines.

Glucose transporters (GLUTs) play vital roles in cellular metabolism. Understanding their evolutionary dynamics in birds is essential for elucidating avian physiology and adaptation. However, the choice of gene detection method in gene family analysis may affect the conclusion. Here, we present a comprehensive investigation of methodologies and GLUT gene loss events in avian lineages, focusing on the loss of GLUT4 and GLUT8. To illustrate the effects of these methods, we first employed BUSCO-based homolog identification, calculated pairwise evolutionary distances between different species, and performed separate blastn and blastp searches to identify homologs in two groups of animals. Our analyses revealed a significant decline in blastn accuracy with increasing evolutionary distance, represented by relative divergence times. Through a more robust blastp-based gene detection pipeline, we provide evidence for the loss of GLUT genes in birds based on 58 vertebrate genomes, including 47 bird species. Our results support the reported early loss of GLUT4 in Aves. We also newly emphasize the absence of GLUT8 in passerines, potentially due to adaptation to high-sugar diets in their ancestors. These findings enhance our knowledge of avian metabolism and the evolution of GLUT genes.

Animals↗
PubMed1979

Frequency distribution of histocompatibility-2 antigenic specificities in the Japanese wild mouse genetically remote from the European subspecies.

Fifty-eight Japanese wild mice, Mus musculus molossinus, collected from twenty-eight localities were surveyed for twelve H-2 antigens using the haemagglutination method. Significantly higher frequencies of H-2.3 and H-2.5 specifities and relatively lower frequencies of the other public specificities were observed. This was confirmed by examining four specificities, H-2.3, 5, 13 and 23, in 370 mice. Quantitative absorption of the alloantisera by erythrocytes and spleen lymphocytes of molossinus mouse revealed definite absorption of H-2.3, 5 and 8 antigens, though their antigenic strength was apparently weaker than the controls, B10 congenic mice. Comparative assay of the strength of H-2.5 antigen in either homozygous and heterozygous conditions distinctly eliminated the possibility of gene-dose effect for the reduced strength of the public antigens in molossinus mouse. To explain this, divergence time between molossinus and domesticus was computed based on the allelic frequency data already reported on ten loci in both subspecies. It is roughly 1.5 x 10(6) years, which could allow for the occurrence of considerable genetic changes in many public antigens, except those conserved through selection.

Animals↗
PubMed2026

Introgression among maternal lineages inferred from complete mitogenomes and molecular dating helps resolve phylogeography of European roe deer.

BACKGROUND: The European roe deer (Capreolus capreolus) is one of the most widespread ungulates in Europe, with a phylogeographic structure mainly shaped by Pleistocene glacial cycles and secondary contacts with the Siberian roe deer (C. pygargus). METHODS: We sequenced 52 complete mitogenomes of C. capreolus from Slovenia, Poland and France, and combined them with 24 publicly available sequences of C. capreolus and C. pygargus, yielding an alignment of 76 genomes representing 59 haplotypes (42 from C. capreolus and 17 from C. pygargus). Phylogeographic structure was assessed using a median-joining network, and divergence times were estimated using a time-calibrated Bayesian phylogeny based on mitochondrial coding regions, incorporating published ancient C. pygargus mitogenomes. We additionally screened mitochondrial protein-coding genes for selection. RESULTS: The haplotype network recovered the three major European roe deer clades (Eastern, Central, and Western) and detected Central-clade haplotypes in France. Two Polish haplotypes (Cp9 and Cp10), detected in C. capreolus, clustered within the C. pygargus mitochondrial lineage, supporting mitochondrial introgression. Time-calibrated phylogenies placed introgressed haplotypes within established C. pygargus lineages. Selection analyses provided limited evidence for episodic positive selection restricted to a small number of codons. CONCLUSIONS: Whole mitogenomes improve resolution of roe deer phylogeography and reveal introgressed maternal lineages, while time-calibrated phylogenies and selection tests add evolutionary context for interpreting mtDNA diversity in genus Capreolus.

Animals↗
PubMed2026

Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.

Long runtimes, high memory demands, and reliance on high-performance computing impede phylogenomic analyses. We review a scalable phylogenomic subsampling with upsampling (PSU) framework, in which small subsamples of sites from a concatenated alignment are expanded by upsampling before inference, and the resulting analyses are then aggregated to obtain evolutionary estimates. PSU harnesses the fact that the computational cost of maximum likelihood analysis is strongly influenced by the number of distinct site patterns in the concatenated alignment, whereas statistical power depends primarily on the amount of evolutionary information represented by the total number of sites and substitutions. By reducing the former while restoring the latter through upsampling, PSU can approximate many full-data analyses at substantially lower computational cost. Analysis of simulated and empirical datasets shows that PSU can accurately estimate bootstrap support values, select the optimal substitution model, test evolutionary hypotheses, and infer branch lengths, divergence times, and associated uncertainty measures, while reducing runtime and memory requirements by orders of magnitude. PSU also provides distributions of inferred clade support across independent subsamples, enabling detection of conflicting phylogenetic signals that may remain hidden in conventional bootstrap analysis. Automated tuning of subsample size, the number of subsamples, and the number of upsampling replicates make PSU practical across diverse datasets. We suggest that PSU is a general strategy for scalable phylogenomic inference using a broad range of statistical methods. By enabling analyses of genome-scale alignments on commodity hardware, PSU broadens research access and reduces environmental and infrastructural costs of big-data phylogenomics.

confidence limits↗
PubMed1979

Rapid evolution of animal mitochondrial DNA.

Mitochondrial DNA was purified from four species of higher primates (Guinea baboon, rhesus macaque, guenon, and human) and digested with 11 restriction endonucleases. A cleavage map was constructed for the mitochondrial DNA of each species. Comparison of the maps, aligned with respect to the origin and direction of DNA replication, revealed that the species differ from one another at most of the cleavage sites. The degree of divergence in nucleotide sequence at these sites was calculated from the fraction of cleavage sites shared by each pair of species. By plotting the degree of divergence in mitochondrial DNA against time of divergence, the rate of base substitution could be calculated from the initial slope of the curve. The value obtained, 0.02 substitutions per base pair per million years, was compared with the value for single-copy nuclear DNA. The rate of evolution of the mitochondrial genome appears to exceed that of the single-copy fraction of the nuclear genome by a factor of about 10. This high rate may be due, in part, to an elevated rate of mutation in mitochondrial DNA. Because of the high rate of evolution, mitochondrial DNA is likely to be an extremely useful molecule to employ for high-resolution analysis of the evolutionary process.

Animals↗
PubMed1976

Genetic divergence of insular populations of deer mice.

Electrophoretic variants at 28 genetic loci were analyzed in subspecies of Peromyscus maniculatus endemic to the Channel Islands of the California coast. The genetic variability within insular populations was calculated. These deer mice have relatively high levels of polymorphism for insular populations. The mean heterozygosity per individual varies in the populations, being much higher on one of the islands than the others. Nei's measure of genetic distance between groups compared on the basis of electrophoretic variants was used. His estimate of time of divergence of these groups, based on genetic distance, is applicable particularly to closely related groups. The length of time each island population has been isolated from the others was calculated and found to be consistent with the periods of isolation estimated on the basis of geological data.

Alleles↗
PubMed1977

Primary structure of rat lysozyme.

For evolutionary reasons, we determined the primary structure of rat lysozyme. The chymotryptic peptides from the reduced and carboxymethylated protein were sequenced and aligned by homology with the sequence of human lysozyme. Overlaps were confirmed by partial structures of tryptic peptides and an automatic sequencer run on the whole protein. By comparing this lysozyme sequence with those of human and baboon and taking into account paleontological estimates of the times of divergence of these species from one another, an approximate estimate of the average rate of lysozyme evolution was made. This rate is not significantly different from the average rate of lactalbumin evolution in mammals--a finding which is at variance with Dickerson's [Dickerson, R.E. (1971), J. Mol. Evol. 1, 26] and Dayhoff's [Dayhoff, m.o., ed. (1972), Atlas of Protein Structure and Sequence, Vol. 5, Silver Spring, Md., The National Biomedical Research Foundation] conclusion that lactalbumin evolution has been faster than lysozyme evolution. Our finding raises the possibility that the gene duplication event responsible for the origin of lactalbumin from lysozyme was more ancient than is generally supposed. Furthermore, from comparison of the rates of lysozyme evolution in rodents and primates, it is suggested that generation time is not a key factor in lysozyme evolution.

Amino Acid Sequence↗
PubMed1976

Molecular evolution of 5S RNA.

Based on the comparative analyses of the primary structure of 5S RNAs from 19 organisms, a secondary structure model of 5S RNA is proposed. 5S RNA has essentially the same structure among all prokaryotic species. The same is true for eukaryotic 5S RNAs. Prokaryotic and eukaryotic 5S RNAs are also quite similar to each other, except for a difference in a specific region. By comparing the nucleotide alignment from the juxtaposed 5S RNA secondary structures, a phylogenic tree of nineteen organisms was constructed. The time of divergence between prokaryotes and eukaryotes was estimated to be 2.5 X 10(9) years ago (minimum estimate: 2.1 X 10(9).

Base Sequence↗
PubMed1975

Evolution of 5sRNA.

The evolution of 5sRNA of 17 organisms ranging from human to bacteria has been studied using a sequence homology analysis. The evolutionary rate of 5sRNA genes has been estimated to be 2.2x10(-10) replacement per one nucleotide site per year. This value is about the same as that of cytochrome C or tRNA's (congruent to 2x10(-10)). A phylogenic tree of these organisms including both eukaryotes and prokaryotes has been constructed from the evolutionary distances (the rate of nucleotide substitution per site) data. The time of divergence of prokaryotes and eukaryotes was estimated to be greater than or congruent to 1.75x10(9) years ago and the branching order in eukaryotic kingdoms is consistent with the traditional order. Blue-green algae separated from the bacterial stem greater than or congruent to 1.3x10(9) years ago after eukaryotes had branched.

Animals↗
PubMed1977

Haemoglobins of the shark, Heterodontus portusjacksoni. III. Amino acid sequence of the beta-chain.

The amino acid sequence of the beta-chain of the principal haemoglobin from the shark H. portusjacksoni has been determined. The chain has 141 residues, the same as that of mammalian alpha-chains and less than the 146 residues of mammalian beta-chains or the 148 residues of the alpha-chain from the tetrameric shark haemoglobin. The sequence was deduced from the sequences of peptides obtained by digestion of the globin or its cyanogen bromide fragments with trypsin, chymotrypsin, pepsin and papain. The difference in length of the beta-chain is most readily accounted for by the absence of the D helix. This small helical section is normally present in myoglobins and beta-globins but absent in alpha-chains. The deduction that it is absent from shark beta-chain is based on consideration of homology. The beta-chain shows the insertion of histidine beta2 and the deletions corresponding to residues A17 and AB1 relative to alpha-and myoglobin chains. The reactive thiol group in shark haemoglobin was shown by radioactive labelling to be residue 51 in the beta-chain, immediately preceding the E helix. The amino acid sequence of shark beta-chain shows 92 differences from human beta-chain, significantly more differences than shown by chicken or frog beta-chains, in line with its earlier time of divergence. If the tertiary structure of the shark beta-chain is the same as that of the horse then there are two changes in the alpha1beta2 contact site in oxyhaemoglobin and an additional one in deoxyhaemoglobin. When both alpha- and beta-chain contacts are considered there is a total of nine changes in residues involved in the alpha1beta2 contacts. There is no Bohr effect in shark haemoglobin, and of the residues normally involved in this effect the C-terminal histidine residue of the beta-chain is present, but the aspartyl (FG1) residue to which it is salt-linked is not, being replaced by a glutamyl residue.

Amino Acid Sequence↗
PubMed2003

Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes.

In many eukaryotic species, gene order is not random. In humans, flies, and yeast, there is clustering of coexpressed genes that cannot be explained as a trivial consequence of tandem duplication. In the worm genome this is taken a step further with many genes being organized into operons. Here we analyze the relationship between gene location and expression in Caenorhabditis elegans and find evidence for at least three different processes resulting in local expression similarity. Not surprisingly, the strongest effect comes from genes organized in operons. However, coexpression within operons is not perfect, and is influenced by some distance-dependent regulation. Beyond operons, there is a relationship between physical distance, expression similarity, and sequence similarity, acting over several megabases. This is consistent with a model of tandem duplicate genes diverging over time in sequence and expression pattern, while moving apart owing to chromosomal rearrangements. However, at a very local level, nonduplicate genes on opposite strands (hence not in operons) show similar expression patterns. This suggests that such genes may share regulatory elements or be regulated at the level of chromatin structure. The central importance of tandem duplicate genes in these patterns renders the worm genome different from both yeast and human.

Animals↗
PubMed2025

There and back again: historical biogeography of neotropical magnolias based on high-throughput sequencing.

BACKGROUND: The Neotropics are considered one of the most biodiverse areas in the world, housing at least one third of all vascular plant species. One of the genera that has diversified in the Neotropics is Magnolia, with about 174 species of three sections (Macrophylla, Magnolia and Talauma) endemic to the Americas. In this work, we study the biogeographic history of the Neotropical Magnolia species using high-throughput sequencing data. Sequences from 39 species (38 from Magnolia and one from the sister genus Liriodendron) were assembled. The dataset contained sequences from 239 nuclear targets and complete chloroplast genomes. Phylogenomic hypotheses and the ancestral distribution range of Magnolia were reconstructed. RESULTS: The results of the calibrated phylogenetic hypotheses and ancestral range construction suggest that the earliest arrival in the Neotropics were the ancestors of section Talauma (38 million years ago), which colonized the Pacific region. This early presence in South America suggests long-distance, overwater dispersal from North America, the presumed origin of the genus Magnolia. The analysis and the extant Talauma distribution indicate a south to north recolonization. The ancestors of the other two Neotropical sections, Magnolia and Macrophylla, migrated around 19 mya from Asia to North America, radiating southward to the Neotropics afterwards, around 11 mya. CONCLUSIONS: Our results suggest that Neotropical magnolias originated from a North American ancestor. The current sections arrived at the region independently influenced by climatic processes such as temperature drops or the Miocene Climatic Optimum. Additionally, geological processes, such as the movement of the South and North American land masses and the emergence of the Panama isthmus, facilitated the migration between continents.

Magnolia↗
PubMed2026

Integrative analysis of transcriptome and chromatin accessibility reveals promoter-proximal regulation and identifies candidate ABC transporters associated with cold stress responses in maize.

BACKGROUND: Low-temperature stress is a formidable environmental constraint that severely limits the growth and productivity of maize (Zea mays L.), particularly during the highly vulnerable early seedling stage. While cold tolerance is a critical agronomic objective, the integrated transcriptional and epigenetic regulatory mechanisms that govern this trait remain largely elusive. Characterizing these coordinated molecular networks is fundamental to the genetic enhancement of cold resilience in maize. METHODS: Using two maize inbred lines contrasting in chilling response (ZHB12 tolerant, B73 sensitive), we performed integrative time‑course RNA‑seq and ATAC‑seq to thoroughly and systematically characterize the precise dynamic interplay between gene expression and chromatin accessibility under cold stress conditions at the seedling stage. RESULTS: Physiological assessments confirmed that ZHB12 possesses superior cold tolerance, manifested by significantly attenuated electrolyte leakage and reduced foliar damage compared to B73. Transcriptomic profiling revealed a massive, time-dependent divergence in gene expression between the two genotypes, with a major regulatory transition identified at 24 h of cold exposure. Functional enrichment analysis demonstrated that ZHB12 preferentially activates a robust defense repertoire, including Photosystem II electron transport, diterpenoid biosynthesis, and ATP biosynthetic pathways. Notably, multiple ATP-binding cassette (ABC) transporter genes were coordinately upregulated under chilling, suggesting their potential involvement in cellular homeostasis. ATAC-seq analysis indicated that cold stress is associated with chromatin remodeling in ZHB12, with increased accessibility observed in proximal promoter regions. Integrative analysis identified a core set of dual-responsive genes, in which increased promoter accessibility coincided with transcriptional upregulation. These genes were predominantly enriched in transporter activity and transcriptional regulation, suggesting potential epigenetic link to the superior stress response of ZHB12. CONCLUSION: Our findings reveal extensive transcriptional and chromatin accessibility changes in ZHB12 under cold stress. The observed associations between promoter accessibility and gene activation, particularly in genes involved in transport processes, highlight candidate regulators potentially contributing to cold tolerance. This study provides a molecular framework and identifies high-value candidate genes that may inform future efforts in breeding cold-tolerant maize, pending functional validation.

Zea mays↗
PubMed1976

[Study of mouse liver cell phosphorescence at deep cooling].

The spectrum and decay curves of phosphorescence of mouse liver cells at --180 degrees C was studied using the phosphorescence microscope. The phosphorescence studied was shown to involve two components with different life spans. Part of either component in the total spectrum is estimated. A conclusion is made that at least two different centers (or groups of centers) exist in cells with the same spectral region of phosphorescence with highly diverging life times of triplet states.

Animals↗
PubMed1977

[Artistic production in epilepsy].

In the epileptic's relation to the world, there is--as a particular way of being--an opposition between two constitutive moments: the world of the dark mass and the world of the light tone of colour as moments of an entirety. This can be seen symbolically in pictures as a contrast between light with an upward trend towards heaven and darkness as an earthy mass with a downward tendency. The two worlds are one at the same time, with diverging trends coexisting in a dynamically flowing organic interrelationship. This is combined with a specific religious atmosphere. From this point of view the attempt is made to gain an understanding of the condition of being ill with epilepsy.

Adult↗