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At least 19 recordsLinked to original sources
PubMed1991

Evolutionary analysis of the nucleus-encoded subunits of mammalian cytochrome c oxidase.

The cytochrome c oxidase enzyme complex of eukaryotes is made up of three mitochondrial-coded subunits and a variable number of nuclear-coded subunits. Some nuclear-coded subunits are present in multiple forms and probably perform a tissue- or development-specific function. A detailed evolutionary analysis of the cytochrome c oxidase subunits that have been sequenced to date is reported here. We have found that gene duplication events from which the liver and heart isoforms of rat subunits VIa and subunit VIII originated can both be dated at about 240 +/- 90 million years ago, long before the radiation of mammalian lineages. Sequence divergence between the processed-type pseudogenes for the subunits IV, VIc and VIII have been estimated. Our results indicate that they arose fairly recently, thus suggesting that retroposition is a continuing process. We show that the rate of silent substitution in mitochondrial-coded subunits is 5-10 times higher than in nuclear-coded subunits; on the other hand replacement rates, although differing from gene to gene, are roughly of the same order of magnitude in both nuclear and mitochondrial genes. In the case of most of the nuclear-coded proteins we observed a slightly greater similarity between rats and cow, which agrees with the data obtained for mitochondrial-coded subunits.

Amino Acid Sequence↗
PubMed1986

Genomic blot hybridization as a tool of phylogenetic analysis: evolutionary divergence in the genus Drosophila.

Comparative, quantitative Southern analysis of genomic DNA, using single-copy sequence probes, potentially is valuable for phylogenetic analysis. We have examined 27 Drosophila species, belonging to two subgenera, seven species groups, and ten subgroups, using a variety of cloned and characterized probes: twelve cloned sequences from D. melanogaster, two from D. pseudoobscura, and two from D. grimshawi. The data are generally congruent with accepted phylogenetic relationships in Drosophila, and confirm or clarify some previously uncertain relationships. The potential and limitations of the method are discussed.

Animals↗
PubMed2026

Comprehensive genomic and computational insights into Brucella suis: pan-genome analysis, evolutionary perspectives, and in-silico vaccine design.

BACKGROUND: Brucella suis is a zoonotic intracellular pathogen responsible for brucellosis, mainly in swine and humans. Although numerous genome sequences are publicly available, an integrative genomic analysis combining pan-genome architecture, structural organization, evolutionary relationships, and vaccine-associated targets remains limited. RESULTS: In this study, we analyzed 91 publicly available B.suis genomes to characterize their pan-genome composition and genomic structure. The pan-genome exhibited an open configuration, indicating continued genomic diversification. A total of 2,146 core genes were identified, representing conserved functions essential for species maintenance, while the accessory genome reflected strain-level variability. Phylogenetic reconstruction based on single-copy orthologs revealed distinct evolutionary clades among the strains. A complementary phylogenetic analysis of pan-genome gene presence-absence patterns further supported clade differentiation and highlighted variation in accessory gene repertoires. Comparative synteny and genome structural analyses demonstrated largely conserved chromosomal organization with localized rearrangements across strains. Screening of the core proteome identified 64 putative antigenic proteins with predicted surface localization and immunogenic properties. Additionally, resistance-associated determinants related to tetracycline and doxycycline were detected in one genome within the dataset. CONCLUSIONS: This comprehensive genomic analysis defines the pan-genome structure, evolutionary relationships, and genome organization of B.suis. The integration of core and pan-genome-based phylogenies provides complementary insights into strain diversification, while the identified conserved antigenic candidates offer a foundation for future experimental validation and rational vaccine development strategies.

Genome, Bacterial↗
PubMed2026

Genome-wide identification, characterization, evolutionary analysis, and expression profiling of the FCS-like zinc finger (FLZ) gene family in soybean (Glycine max L.) under abiotic stresses.

Drought and salinity limit soybean yield. Despite their role in the SnRK1 energy-sensing complex, a systematic study of FCS-Like Zinc Finger (FLZ) proteins in soybean has not been reported. We performed a genome-wide identification of the GmFLZ gene family, identifying 40 members distributed across 18 of the 20 soybean chromosomes. Phylogenetic analysis of 87 FLZ proteins from Glycine max, Arabidopsis thaliana, and Oryza sativa revealed four major evolutionary clades, suggesting that diversification predates the separation of monocots and dicots. Structural analysis identified ten conserved motifs, with Motifs 1 and 2 present in all family members. Gene duplication analysis identified 304 paralogous pairs, most arising from segmental duplication. Ka/Ks analysis indicated localized positive selection in six gene pairs and purifying selection in 97.9% of pairs. Tissue-specific expression profiling across nine tissues showed that GmFLZ5, GmFLZ15, GmFLZ25, and GmFLZ34 had the highest expression levels detected across the GmFLZ family, with GmFLZ5 the most highly expressed member in leaves, nodules, and stem and showing moderate expression in pod, root, and root hairs, whereas GmFLZ18, GmFLZ23, and GmFLZ37 showed root-preferential expression. RT-qPCR validation under drought (20% PEG-6000) and salt (200 mM NaCl) treatments in the Giza 5 cultivar showed that 36 and 34 of the 40 GmFLZ genes, respectively, exhibited at least a two-fold change in expression, with GmFLZ21 and GmFLZ35 among the most strongly induced under salt stress. These findings provide an evolutionary and functional framework for the GmFLZ family and identify candidate genes for future functional studies in soybean stress tolerance.

Glycine max↗
PubMed2026

Comprehensive identification and evolutionary analysis of the Wnt gene family in bivalves: Insights into the larval development of the noble scallop Chlamys nobilis.

The Wnt gene family regulates fundamental developmental processes in metazoans, but its evolutionary composition and developmental deployment in bivalves remain largely unresolved. Here, we performed a comparative genomic analysis of Wnt genes in 19 bivalve species and examined developmental expression profiles in the noble scallop Chlamys nobilis, with Crassostrea gigas and Chlamys farreri used for cross-species comparison. A total of 235 Wnt genes were identified and assigned to 12 subfamilies. No reliable Wnt3 ortholog was detected in any analyzed bivalve, supporting the view that Wnt3 loss occurred early during lophotrochozoan evolution rather than representing a lineage-specific absence. Most Wnt proteins retained the conserved WNT domain, indicating strong structural conservation, whereas lineage-specific copy-number variation and gene loss were observed among species. C. farreri and C. gigas each retained 12 Wnt genes and lacked Wnt3, whereas C. nobilis lacked Wnt3, Wnt7, and Wnt16. Developmental transcriptome analysis and RT-qPCR revealed clear stage-specific expression patterns. In C. gigas, Wnt2/10/A were highly expressed during earlydevelopment and peaked around the D-shaped larval stage, while Wnt8 and Wnt11 showed distinct stage-specific peaks. By contrast, Wnt1/5/6/9 were more active during later larval development or juvenile formation. These results provide a comparative framework for bivalve Wnt evolution and identify candidate Wnt genes potentially involved in larval development and aquaculture-relevant developmental transitions.

Animals↗
PubMed2026

Genome-wide identification and evolutionary analysis of the ERF-VII gene family in the tea plant (Camellia sinensis) and functional characterization of CsRAP2.2 in response to cold stress.

The ERF-VII gene family, a critical branch of the AP2/ERF superfamily, is central to plant stress adaptation. However, its evolutionary history and function in tea plant (Camellia sinensis) remain unclear. Here, we performed integrated evolutionary, genomic, and functional analyses of ERF-VII genes across 14 plant lineages and 20 tea plant cultivars. The phylogenetic analysis revealed that ERF-VII proteins originated after vascular plant divergence, coinciding with the emergence of the N-terminal MCGGA/I motif linked to the oxygen-dependent N-degron pathway. Gymnosperms retained few conserved members, whereas angiosperms exhibited lineage-specific expansion-extensive in monocots via whole-genome duplication, moderate in eudicots with functional diversification. Pan-genome analysis across 20 tea plant cultivars further revealed varietal differences in ERF-VII gene distribution. Transcriptome profiling via the Tea Plant Information Archive identified CsRAP2.2 as a cold-inducible ERF-VII member with sustained expression under low-temperature stress. Functional assays demonstrated that silencing CsRAP2.2 reduced cold tolerance, while overexpression in tea leaves and heterologous expression in Arabidopsis thaliana enhanced cold tolerance by maintaining photosystem II efficiency, reducing membrane lipid peroxidation, and improving antioxidant capacity. Weighted gene co-expression network analysis positioned CsRAP2.2 as a regulatory hub integrating cold, hormone, and oxygen-sensing pathways. These results clarify the evolutionary trajectory of ERF-VII genes and establish CsRAP2.2 as a core cold-tolerance regulator in tea plant. These findings may inform future breeding of cold-resilient tea cultivars.

Camellia sinensis↗
PubMed1992

Evolutionary analysis of the plastid-encoded gene for the alpha subunit of the DNA-dependent RNA polymerase of Pyrenomonas salina (Cryptophyceae).

The nucleotide sequence of the gene coding for the plastid-encoded alpha subunit of DNA-dependent RNA polymerase from the cryptomonad alga Pyrenomonas salina was determined. The deduced amino-acid sequence, corresponding to a 35.2 kDa polypeptide, was compared to homologues from other organisms. Evolutionary relationships were analyzed in detail by the parsimony method together with bootstrap analysis. The deduced phylogenetic tree shows that the cryptomonad gene is the most ancient type of known plastid-encoded RNA polymerase.

Amino Acid Sequence↗
PubMed1992

Sequencing errors and molecular evolutionary analysis.

Heuristic approaches were used to quantify the influence that sequencing errors have on estimates of nucleotide diversity, substitution rate, and the construction of genealogies. Error rates of less than 1 nucleotide/kb probably have little affect on conclusions about the evolutionary history of highly polymorphic organisms such as Drosophila and Escherichia coli, but organisms with very low nucleotide diversity, such as humans, require greater sequencing accuracy. A scan of GenBank for corrections of previous errors reveals that sequencing errors are highly nonrandom.

Animals↗
PubMed1989

Population differences in susceptibility to AIDS: an evolutionary analysis.

Previously we have reported population differences in sexual restraint such that, higher socio-economic status greater than lower socio-economic status, and Mongoloids greater than Caucasoids greater than Negroids. This ordering was predicted from a gene-based evolutionary theory of r/K reproductive strategies in which a trade-off occurs between gamete production and social behaviors such as intelligence, law-abidingness, and parental care. Here we consider the implications of these analyses for sexual dysfunction, including susceptibility to AIDS. We conclude that relative to Caucasians, populations of Asian ancestry are inclined to a greater frequency of inhibitory disorders such as low sexual excitement and premature ejaculation and to a lower frequency of sexually transmitted diseases including AIDS, while populations of African ancestry are inclined to a greater frequency of uninhibited disorders such as rape and unintended pregnancy and to more sexually transmitted diseases including AIDS.

Acquired Immunodeficiency Syndrome↗
PubMed1991

An evolutionary analysis of psychological pain following human (Homo sapiens) rape: IV. The effect of the nature of the sexual assault.

Mental pain is hypothesized to manifest an adaptation for analyzing and coping with social problems that would have reduced inclusive fitness in human (Homo sapiens) evolutionary history. We examined this hypothesis in the psychological pain of 790 rape victims. Reproductive-aged and postreproductive-aged victims were more likely than prereproductive-aged victims to have experienced vaginal intercourse and to have had sperm present in the reproductive tract. As predicted, vaginal intercourse constituted the most psychologically devastating form of sexual assault for reproductive-aged women. Nonreproductive-aged victims were not more traumatized by vaginal rapes. When rapes included ejaculation in the victim's reproductive tract, reproductive-aged victims may have been more traumatized. These results suggest that the psychology that regulates mental pain processes information about the nature of the sexual act in the event of a woman's rape.

Adaptation, Psychological↗
PubMed1986

Cloning, sequencing, and evolutionary analysis of the mouse erythropoietin gene.

The gene for mouse erythropoietin was cloned and sequenced. We present here a preliminary analysis of the overall genomic organization of the coding portions and the two flanking regions of the gene. This is the third mammalian erythropoietin for which the sequence is available, but it represents the first from a nonprimate species. We investigated the evolutionary divergence of sequence and structure of the three erythropoietins and identified specific regions of the molecules that are apparently under various degrees, and perhaps different types, of functional constraint.

Amino Acid Sequence↗
PubMed1991

Isolation and molecular evolutionary analysis of a cytochrome c gene from Oryza sativa (rice)

A cytochrome c gene, OsCc-1, from rice (Oryza sativa) has been isolated and analyzed. The OsCc-1 gene encodes a cytochrome c protein that is typical of higher-plant cytochrome c proteins. OsCc-1 consists of three exons separated by two introns that are 817 and 747 bp in length, respectively. From genomic DNA hybridization analysis, OsCc-1 appears to be one of possibly two cytochrome c genes in several Asian, American, and Indian rice species and varieties surveyed. A single, unique cytochrome c gene appears to be present in one African cultivated rice species. We performed comparative molecular evolutionary analyses of OsCc-1 and other cytochrome c genes. We calculated a unit evolutionary period of 19.4 Myr for cytochrome c DNA sequences, which agrees closely with previous estimates based on protein sequence comparisons.

Amino Acid Sequence↗
PubMed1986

Nucleotide sequence of the goat embryonic alpha globin gene (zeta) and linkage and evolutionary analysis of the complete alpha globin cluster.

In previous studies we identified and sequenced clones containing two adult alpha globin genes of the goat. Additional studies have revealed the presence of an embryonic alpha globin gene termed zeta. Sequence analysis of the gene shows that it is the largest mammalian or avian globin gene cloned to date. Its unusual size is mainly due to a 14 base-pair tandem repeat sequence in its first intron. A similar sequence is also found in the first intron of the human zeta gene. The goat zeta coding sequence differs greatly from that of the adult alpha, particularly at amino acid position 38, where it codes for the amino acid replacement of Gln for Thr. This change may confer a higher intrinsic O2 affinity on the zeta globin protein, ensuring a sufficient O2 supply for the developing goat embryo. The cloning and sequencing of this gene completes the alpha globin locus of the goat, composed of three genes in the following order 5'-zeta-I alpha-II alpha-3'. Evolutionary comparisons of the goat alpha locus with other amphibian, avian and mammalian loci reveal several interesting features. Statistical analysis confirms the hypothesis that the embryonic alpha gene is much older (400 million years) than the embryonic beta gene (200 million years), and that it is descended from a primordial gene, whose present-day counterpart is the Xenopus larval alpha globin gene. Our results also suggest that after the divergence of the avian line, the alpha A gene converted the alpha D gene during the evolution of the pre-mammalian line. The alpha D globin gene remains unconverted in the avian line, potentially because of insertion/deletion sequences that may prevent any gene conversion event. The divergence rates of specific globin genes have been analyzed and found to form an essentially straight line, in agreement with the neutralist view of evolution.

Animals↗
PubMed1990

Compassion and altruism in psychoanalytic theory: an evolutionary analysis of self psychology.

Freud's creation of psychoanalysis was, in part, a reaction to the societal, religious morality that denied the ubiquitous drivenness that repeatedly confronted him, the essential animal nature of homo sapiens as had been recently made clear by the theory of evolution. For example, Freud (1933) wrote an aggression, It is a general principle. . .that conflicts of interest between men are settled by the use of violence. This is true of the whole animal kingdom, from which men have no business to exclude themselves. Though evolutionary theory was in its infancy, incompletely understood even by its creator, Freud's commitment to facing its truths led to an unswerving stance in reaction to attempts to deny the narcissistic injury inherent in his psychoanalytic discoveries. He insisted on trying to reinterpret virtually all social behaviors in the light of his new theory, and he and his followers have stretched his drive/structure model to its limits. Yet, as we have seen, this evolutionary creation--the human psyche--cannot be fully accounted for utilizing the vicissitudes of Freud's two instincts. What we come to appreciate when we bring the perspective of the theory of evolution to the relational/structure versus drive/structure debate, is that the debate is about the two sides of the same coin. Like this metaphor, in the case of the selfish, yet social, human animal, you cannot have a one-sided coin. Both drives and relationships are biologically inherent and have their structuralizing effect upon the supraordinate self. A modern evolutionary biological, psychoanalytic conception of conflicts and drives may actually be closer to the adaptive/functional tone of aspects of the self psychological paradigm than to the traditional perspective. As human animals we are inherently in conflict over our irreducible biologically based driven, asocial needs (i.e., self-enhancing pleasure seeking and avoidance of unpleasure) and our irreducible biologically based needs for a self-selfobject milieu. A dynamic tension between these two motivational pulls is adaptive (has been selected for) due to the great flexibility it provides in enabling this large brained, nonreflexively driven, social organism fully to exploit all aspects of its environment in pursuit of its own best interest. In its clinical application this viewpoint sees our patients caught between their basic self-enhancing instinctual drivenness for sensual pleasure and power, and their irreducible self-enhancing need for a self-selfobject milieu.(ABSTRACT TRUNCATED AT 400 WORDS)

Adaptation, Psychological↗
PubMed1991

Cloning and evolutionary analysis of msh-like homeobox genes from mouse, zebrafish and ascidian.

The homeobox is a relatively conserved 180-nucleotide-long sequence characterizing a large and phylogenetically wide-spread family of putative regulatory genes, many of which have been implicated in the control of embryonic development. The Drosophila melanogaster muscle segment homeobox (msh) gene contains a homeobox which is markedly divergent from that of any other characterized D. melanogaster gene, yet very similar to that of the mouse Hox-7.1 gene [Robert et al., EMBO J. 8 (1989) 91-100; Hill et al., Genes Develop. 3 (1989) 26-37]. To elucidate the evolutionary relationship between these two genes, and hence facilitate comparative analyses, it is necessary to determine the number of msh-like genes in the two species, and to characterize any msh gene duplication events which may have occurred since their divergence. To address these questions, I have employed the polymerase chain reaction to amplify, clone and sequence msh-related homeobox genes from two divergent vertebrate species (mouse and zebrafish), one ascidian (Ciona intestinalis), and D. melanogaster. Sequence determination of 91 recombinant clones resulted in the identification of three msh-like genes from mouse and three from zebrafish, but only one each from C. intestinalis and D. melanogaster. Sequence analyses suggest that multiple msh gene duplications occurred in the lineage leading to vertebrates, after the divergence of the ascidia.

Amino Acid Sequence↗
PubMed2026

Genomic and evolutionary analysis reveals dynamic variations of MKK3 gene, a key regulator for seed dormancy in barley.

Barley (Hordeum vulgare L.) is an important crop in the world, and its seed dormancy is primarily controlled by a mitogen-activated protein kinase kinase 3 (MKK3) gene. Although kinase activity of MKK3 and its roles in barley post-domestication have been widely studied, the pre-domestication evolution of MKK3 and the spread of nondormant alleles among global barley varieties remain largely unexplored. In this study, we analyzed MKK3 sequences in barley and its wild progenitor (Hordeum spontaneum K. Koch) and identified two polymorphic miniature inverted-repeat transposable elements (MITEs). Comparative analyses indicated that the insertions/excision of the MITEs predated the current estimates of barley domestication. Examination of the barley pangenomes coupled with droplet digital polymerase chain reaction revealed extensive copy number variation of MKK3 and suggested that transposons likely contributed to tandem amplification of the MKK3 gene on chromosome 5H. Additionally, approximately 1-Kb MKK3 sequences were found on chromosomes 1H and 6H. Further analysis indicated that these short MKK3 sequences were captured by a CACTA transposon that also contained fragments from four other expressed genes. The acquisition of MKK3 was estimated to be between 1.9 and 2.5 million years ago. Together, these findings illuminate the dynamic pre-domestication evolution of the MKK3 gene and identify three divergent MKK3 haplotype groups including a unique lineage predominant in Ethiopian germplasm. This study highlights the contribution of transposons to structural diversification and evolutionary differentiation of the MKK3 locus and provides helpful information for understanding the complex history of MKK3 gene in barley and also for improving preharvest sprouting tolerant varieties under distinct natural conditions.

Hordeum↗
PubMed1991

Evolutionary analysis of the influenza A virus M gene with comparison of the M1 and M2 proteins.

Phylogenetic analysis of 42 membrane protein (M) genes of influenza A viruses from a variety of hosts and geographic locations showed that these genes have evolved into at least four major host-related lineages: (i) A/Equine/prague/56, which has the most divergent M gene; (ii) a lineage containing only H13 gull viruses; (iii) a lineage containing both human and classical swine viruses; and (iv) an avian lineage subdivided into North American avian viruses (including recent equine viruses) and Old World avian viruses (including avianlike swine strains). The M gene evolutionary tree differs from those published for other influenza virus genes (e.g., PB1, PB2, PA, and NP) but shows the most similarity to the NP gene phylogeny. Separate analyses of the M1 and M2 genes and their products revealed very different patterns of evolution. Compared with other influenza virus genes (e.g., PB2 and NP), the M1 and M2 genes are evolving relatively slowly, especially the M1 gene. The M1 and M2 gene products, which are encoded in different but partially overlapping reading frames, revealed that the M1 protein is evolving very slowly in all lineages, whereas the M2 protein shows significant evolution in human and swine lineages but virtually none in avian lineages. The evolutionary rates of the M1 proteins were much lower than those of M2 proteins and other internal proteins of influenza viruses (e.g., PB2 and NP), while M2 proteins showed less rapid evolution compared with other surface proteins (e.g., H3HA). Our results also indicate that for influenza A viruses, the evolution of one protein of a bicistronic gene can affect the evolution of the other protein.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1987

Polymorphism of the vitamin D binding protein (DBP) among primates: an evolutionary analysis.

The distribution of the DBP (vitamin D binding protein) polymorphism is now well characterized among human populations but for primates only limited results are known. The aim of this paper is to describe the electrophoretic polymorphism of this protein among various species. Using three different electrophoretic methods, we are able to detect an unknown polymorphism and to classify the different alleles observed. These results may be used to set an international nomenclature for further comparisons. The different electrophoretic mobilities between Old and New World Monkeys show that: 1) the Cercopithecoïdea are presenting the largest genetic heterogeneity; 2) the DBP among the Galago corresponds to the lowest isoelectric points observed among Primates; 3) during the evolution from nonhuman Primates to Man, the DBP is able to keep its affinity for vitamin D derivatives despite the occurrence of significant molecular modifications; 4) among Anthropoïdea, the electrophoretic patterns of DBP are very close to the human Gc1 proteins. These results show that evolution at the DBP level can be considered as a continuous mechanism of structural modifications. A significant transition occurs during the differentiation between Cercopithecoïdea and Anthropoïdea. It is not too speculative to consider that some electrophoretic forms detected among Gorilla, Pongo, or Pan may be identical to rare variants observed among humans.

Animals↗