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PubMed2025

Primulina pan-genome reveals differential gene retention following whole-genome duplications and provides insights into edaphic specialization.

Primulina, a genus of >200 species specialized to extreme soils, provides a model for edaphic adaptation. We assemble seven genomes and construct a pan-genome spanning nine species from karst, Danxia, and acidic soils. Comparative analyses reveal that karst-adapted species have smaller genomes. Two lineage-specific whole-genome duplications (WGDs) exhibit biased duplicate loss in large gene families but preferential retention of transcription factors, indicating combined adaptive and nonadaptive forces. Pan-genome analyses identify ion channel and transporter genes enriched in variant hotspots and under positive selection in karst lineages. Candidate genes for drought and salt stress tolerance include ABC transporters and ion channels. Notably, an ABC transporter shows positive selection in karst species and unique structural variation in non-karst species. Together, our findings show that genome downsizing, biased post-WGD retention, and evolution of ion-transport pathways shape adaptation to extreme soils. The Primulina pan-genome provides a resource for dissecting mechanisms underlying edaphic specialization.

Gene Duplication↗
PubMed2006

Adaptive divergence in experimental populations of Pseudomonas fluorescens. II. Role of the GGDEF regulator WspR in evolution and development of the wrinkly spreader phenotype.

Wrinkly spreader (WS) genotypes evolve repeatedly in model Pseudomonas populations undergoing adaptive radiation. Previous work identified genes contributing to the evolutionary success of WS. Here we scrutinize the GGDEF response regulator protein WspR and show that it is both necessary and sufficient for WS. Activation of WspR occurs by phosphorylation and different levels of activation generate phenotypic differences among WS genotypes. Five alleles of wspR, each encoding a protein with a single amino acid substitution, were generated by mutagenesis. Two alleles are constitutively active and cause the ancestral genotype to develop a WS phenotype; the phenotypic effects are allele specific and independent of phosphorylation. Three alleles contain changes in the GGDEF domain and when overexpressed in WS cause reversion to the ancestral phenotype. Ability to mimic this effect by overexpression of a liberated N-terminal domain shows that in WS, regulatory components upstream of WspR are overactive. To connect changes at the nucleotide level with fitness, the effects of variant alleles were examined in both structured and unstructured environments: alleles had adaptive and deleterious effects with trade-offs evident across environments. Despite the proclivity of mutations within wspR to generate WS, sequence analysis of wspR from 53 independently obtained WS showed no evidence of sequence change in this gene.

Alleles↗
PubMed2006

Conservation of CD4+ T cell-dependent developmental mechanisms in the blood fluke pathogens of humans.

Schistosoma blood flukes are trematode parasites with a cosmopolitan distribution that infect over 200 million people globally. We previously showed that Schistosoma mansoni growth and development in the mammalian host is dependent on signals from host CD4+ T cells. To gain insight into the mechanisms that underlie this dependence, we sought to determine the evolutionary origins and limits of this aspect of the host-pathogen relationship. By infecting RAG-1-/- mice with a range of different schistosome species and strains, we tested several hypotheses concerning the time during Schistosoma evolution at which this dependence arose, and whether this dependence is specific to Schistosoma or is also found in other blood flukes. Our data indicate that the developmental dependence on CD4+ T cells previously described for S. mansoni is conserved in the evolutionarily basal species Schistosoma japonicum, suggesting this developmental adaptation arose early in Schistosoma evolution. We also demonstrate that the development of the more evolutionarily derived species Schistosoma haematobium and Schistosoma intercalatum are dependent on adaptive immune signals. Together, these data suggest that the blood fluke parasites of humans utilise common mechanisms to infect their hosts and to co-opt immune signals in the coordination of parasite development. Thus, exploitation of host-schistosome interactions to impair or prevent parasite development may represent a novel approach to combating all of the schistosome pathogens of humans.

Animals↗
PubMed1998

On the evolution within the family Gyrodactylidae (Monogenea).

On the basis of six main types of protonephridial systems in the genus Gyrodactylus and results from further studies of the protonephridial systems in other gyrodactylid genera and other monogenean families, evolutionary lines within the Gyrodactylidae and the origin of the genera Ooegyrodactylus, Swingleus, Gyrdicotylus and Polyclithrum are discussed. An excretory bladder (on both sides of the body) with separate openings for the main canals of the anterior and the posterior systems, a median junction between the two anterior systems and likewise a junction between the two posterior systems, many flame bulbs and an absence of lateral flames in the main canals were found to be primitive monogenean characters. A system similar to that in the acanthocotylid larva but with secondarily evolved lateral flames in the posterior systems may have given rise to a first protogyrodactylid system, in turn giving rise to the system of Macrogyrodactylus. In a second protogyrodactylid line, the main canal of the anterior system (on both sides of the body) was connected to that of the posterior system and lateral flames were developed also in the anterior system. From this system all other described gyrodactylid systems may arise: one main line gave rise to the system of the G. (Gyrodactylus) and another to a system of G. (Mesonephrothus) type. The systems of Swingleus and Gyrdicotylus are of the latter type. Through loss of all lateral flames, the system of G. (Metanephrotus) may have evolved. Isancistrum has a system of the G. (Metanephrotus) type. From this type of system, those of Polyclithrum, G. (Neonephrotus), G. (Paranephrotus) and G. (Limnonephrotus) can be derived. The fact that the system of Ooegyrodactylus is more closely related to that of G. (Gyrodactylus) than to that of Macrogyrodactylus prompts discussion regarding the evolution of the viviparity of the family Gyrodactylidae. According to the evolutionary system presented, primitive gyrodactylids parasitise primitive fish species and the most advanced gyrodactylids parasitise the most advanced fish species. However, Anguillidae and Clupeidae may have been secondarily infected by members of G. (Metanephrotus) and G. (Neonephrotus) respectively, and Cyprinidae, Salmonidae and Esocidae may similarly have been secondarily infected by members of G. (Limnonephrotus). Isancistrum may have infected squids (Loligidae) at a medium level in the evolution within the Gyrodactylidae, while progenitors of Gyrdicotylus may have been adapted to clawed toads (Xenopidae) earlier in evolution.

Animals↗
PubMed1996

Exploring phenotype space through neutral evolution.

RNA secondary-structure folding algorithms predict the existence of connected networks of RNA sequences with identical secondary structures. Fitness landscapes that are based on the mapping between RNA sequence and RNA secondary structure hence have many neutral paths. A neutral walk on these fitness landscapes gives access to a virtually unlimited number of secondary structures that are a single point mutation from the neutral path. This shows that neutral evolution explores phenotype space and can play a role in adaptation.

Algorithms↗
PubMed1985

Thermodynamics and the conceptual structure of evolutionary theory.

Thermodynamics and evolutionary theory have spent most of their shared history in adversarial relationship to one another. The point of this paper is to consider some qualitative ways in which thermodynamics can enrich both the theory and epistemology of evolution. The "autonomy of biology" posture in evolutionary theory hangs on the supposed uniqueness of why-questions in biology. With this posture, and with the general obstruction of constructive dialogue between evolution and the physical sciences it fosters, come the perennial accusations that Darwinism deals in adaptational teleology but not mechanisms. Thermodynamics provides for a two-tiered hierarchy of causation in nature in which the why-question is rendered not only legitimate materialistically, but essential to understanding the evolutionary process in its totality--from the emergence of life to the branching of lineages in speciation.

Adaptation, Biological↗
PubMed2006

Has an aquatic diet been necessary for hominin brain evolution and functional development?

A number of authors have argued that only an aquatic-based diet can provide the necessary quantity of DHA to support the human brain, and that a switch to such a diet early in hominin evolution was critical to human brain evolution. This paper identifies the premises behind this hypothesis and critiques them on the basis of clinical literature. Both tissue levels and certain functions of the developing infant brain are sensitive to extreme variations in the supply of DHA in artificial feeding, and it can be shown that levels in human milk reflect maternal diet. However, both the maternal and infant bodies have mechanisms to store and buffer the supply of DHA, so that functional deficits are generally resolved without compensatory diets. There is no evidence that human diets based on terrestrial food chains with traditional nursing practices fail to provide adequate levels of DHA or other n-3 fatty acids. Consequently, the hypothesis that DHA has been a limiting resource in human brain evolution must be considered to be unsupported.

Adaptation, Physiological↗
PubMed1992

Evolutionary aspects of human cancer.

Evolutionary aspects of human cancer can be dealt with at two levels--on the one hand long-term evolution involving hereditary effects between generations; and on the other hand evolutionary processes operating within the organisms between tissues, cells and cell constituents, which also comprise genetic alterations, selection and adaptation. These two levels of evolution can be designated as phylogenetic and ontogenetic evolution, respectively. Concerning phylogenetic evolution there must have been a strong selection against neoplastic diseases occurring at reproductive age and a variety of protective mechanisms against carcinogenic agents have been developed. Cancer is therefore primarily a disease of old age, which does not constitute a significant risk in natural populations for the simple reason that the life length is too short. The development of an individual comprises selection forces between cells and tissues, which are particularly striking for the multistage development of tumours. The accumulation of several genetic alterations in the same cells, as illustrated by the analysis of colorectal tumours, must require a pronounced clonal expansion between each event. Such selective growth effect has recently been demonstrated for the tumour suppressor gene p53 in brain tumours. Cancer often implies a break down of between balanced systems antagonistic forces, such as oncogenes and suppressors of oncogenes. Examples of this are provided by the genetic regulation of metastasis, involving metalloproteinase as well as the inhibitor of metalloproteinase. The immortalization of cells by transformation points to the fact that programmed cell death and the balance between suicide genes and suppressors of such suicide genes is affected.

Apoptosis↗
PubMed2026

Integrative single-cell and genomic analysis reveals NMB as a driver of metastatic adaptation in esophageal squamous cell carcinoma via metabolic rewiring and immune evasion.

BACKGROUND: Esophageal squamous cell carcinoma (ESCC) has high mortality, and metastasis is the leading cause of patient death. Neuromedin B (NMB) promotes tumor development in various cancers, yet its role in ESCC metastasis remains unclear. METHODS: We integrated single-cell transcriptomic data from matched primary and metastatic ESCC lesions (GSE309392) with bulk transcriptomic cohorts from TCGA and GSE53624. In silico gene perturbation, ligand-receptor communication analysis, and single-cell prognostic model construction were performed, followed by functional validation through siRNA-mediated NMB knockdown in TE-1 and KYSE30 cell lines. RESULTS: NMB was identified as a key gene enriched in metastatic ESCC lesions, and its high expression was associated with coordinated upregulation of oxidative phosphorylation pathway genes and aldo-keto reductase family antioxidant enzymes (AKR1C1, AKR1C2, AKR1B10). Genomic analysis revealed that NMB-high tumors carried a higher clonal mutation burden and a markedly increased frequency of NFE2L2 activating mutations (23% vs. 8%, P = 0.04). In silico knockout and correlation analysis identified AKR1C1 as a downstream effector of NMB. NMB expression was negatively correlated with CD8+ T cell and activated NK cell infiltration. CellChat analysis revealed communication between NMB-positive cells and monocytes via the TGM2-ADGRG1 axis, and specifically detected IFNG signaling. In the single-cell prognostic model, NMB-positive cells accounted for 50% of the high-risk group but only 20% of the low-risk group. TCGA-based survival analysis demonstrated that high NMB expression was associated with shorter overall survival (HR = 2.98, P = 0.03). In vitro NMB-targeted RNA interference markedly inhibited proliferation, colony formation, and migration in TE-1 and KYSE30 cells. CMap screening identified the endothelin-PDE5-cGMP axis as a potential therapeutic target. CONCLUSION: NMB serves as a key driver of metastatic adaptation in ESCC, conferring a survival advantage to tumor cells during metastatic colonization through genomic evolution and immune remodeling, with metabolic adaptation as a downstream consequence of genomic alterations.

NMB↗
PubMed2006

The population genetics of adaptation on correlated fitness landscapes: the block model.

Several recent theoretical studies of the genetics of adaptation have focused on the mutational landscape model, which considers evolution on rugged fitness landscapes (i.e., ones having many local optima). Adaptation in this model is characterized by several simple results. Here I ask whether these results also hold on correlated fitness landscapes, which are smoother than those considered in the mutational landscape model. In particular, I study the genetics of adaptation in the block model, a tunably rugged model of fitness landscapes. Considering the scenario in which adaptation begins from a high fitness wild-type DNA sequence, I use extreme value theory and computer simulations to study both single adaptive steps and entire adaptive walks. I show that all previous results characterizing single steps in adaptation in the mutational landscape model hold at least approximately on correlated landscapes in the block model; many entire-walk results, however, do not.

Adaptation, Physiological↗
PubMed1990

Concerted evolution of ruminant stomach lysozymes. Characterization of lysozyme cDNA clones from sheep and deer.

Contradictory evolutionary histories of ruminant lysozymes have been predicted by analysis of genomic blots (Irwin, D.M., Sidow, A., White, R., and Wilson, A.C. (1989) in The Immune Response to Structurally Defined Proteins: The Lysozyme Model (Smith-Gill, S.J., and Sercarz, E.E., eds) pp. 73-85, Adenine Press, Guilderland, NY) and sequences of cow stomach lysozyme cDNAs (Irwin, D.M., and Wilson, A.C. (1989) J. Biol. Chem. 264, 11387-11393). Genomic blots indicate that the amplification of the lysozyme gene family occurred 40-50 million years ago, while the cDNA sequences imply that the stomach genes began diverging from one another after the splitting of the deer and cow lineages, 25 million years ago. To resolve this contradiction, we characterized 111 stomach lysozyme cDNAs from two additional ruminant species: domestic sheep and axis deer. The cDNA sequences of the coding region of mature lysozyme together with the 3'-untranslated region were obtained from abomasum (true stomach) mRNA with the use of the polymerase chain reaction. The two primers for amplifying the cDNA were a lysozyme-specific primer, encoding a conserved sequence at the amino terminus of mature stomach lysozyme, and oligo(dT) as a general mRNA primer. Comparison of the cDNA sequences from these species to one another and to those of the cow revealed that different parts of the ruminant stomach lysozyme genes have had different evolutionary histories. The 3'-untranslated region has evolved in a divergent fashion since the original duplications 40-50 million years ago, supporting the genomic blot interpretation; by contrast, the coding region has evolved in a concerted fashion, that is, the multiple sequences within a species have evolved in unison. The 3'-untranslated portion of the lysozyme genes appears to have escaped from concerted evolution due to inability to initiate concerted evolution, rather than due to reduced sequence similarity. The process of concerted evolution in stomach lysozymes may have had roles both in adapting lysozyme to the stomach environment in early ruminants as well as in retarding amino acid sequence evolution in the well adapted lysozyme of modern ruminants.

Animals↗
PubMed2004

Neurobiology of seizures and behavioral abnormalities.

Seizures are both caused by and induce a complex set of neurobiological alterations and adaptations. The animal model of amygdala kindling provides insight into the spatiotemporal evolution of these changes as a function of seizure development and progression. Intracellular, synaptic, and microstructural changes are revealed as related to both the primary pathophysiology of kindled seizure evolution and compensatory secondary, or endogenous anticonvulsant adaptations. At the level of gene expression, the balance of these pathological and adaptive processes (as augmented by exogenous medications) probably determines whether seizures will be manifest or suppressed and could account for aspects of their intermittency. As anxiety and emotion modulation are subserved by many of the same neuroanatomic substrates involved in the evolution of complex partial seizures, particularly those of the medial temporal lobe, it is readily conceptualized how vulnerability to a range of psychiatric disorders could be related to the primary or secondary neurochemical alterations associated with seizure disorders. The discrete and methodologically controlled elucidation of the cascades and spatiotemporal distributions of neurobiological alterations that accompany seizure evolution in the kindling model may help resolve some of the difficulty and complexity of elucidating these biobehavioral relationships in the clinic.

Amygdala↗
PubMed2000

The Raymond Pearl memorial lecture, 1997: The quest for medical normalcy-who needs it?

Darwinian natural selection is the only factor in evolution that maintains and improves adaptation. It does so by favoring genes that enhance the genetic success of their bearers under historically prevalent conditions, and need not favor health or happiness or conformity to some universally normal state. It may favor unpleasant departures from medical normalcy if they contribute to long-term genetic success, either directly or as unavoidable costs of features that make such contributions. It is also blind to future consequences of current evolution, so that every evolving lineage accumulates historical legacies that may seriously constrain future adaptation. Examples of adaptive but unpleasant abnormality are found in infectious diseases and other instances of conflict (between the sexes, between parent and offspring, between competitors for limited resources). Examples of unfortunate historical legacies are found in limitations on numbers of parts (limbs, sense organs) and in the tight human birth passage. Adaptation is a more useful medical concept than normalcy, but the purpose of medicine is not to facilitate natural selection or uncritically encourage biological adaptations. Medical intervention may legitimately promote human values by frustrating adaptations (e.g., by anesthesia) or by seeking the grossly abnormal (e.g., birth through the abdomen rather than the vagina). Am. J. Hum. Biol. 12:10-16, 2000. Copyright 2000 Wiley-Liss, Inc.

Journal Article↗
PubMed2003

[The pathogenesis and the adaptive value of fever].

Fever is a part of the acute phase response to infection and inflammation. We now understand that fever is a complex physiological response that is aimed at facilitating survival of the host. The fever is induced by endogenous inflammatory mediators, such as prostaglandins and pyrogenic cytokines, that are released by immune cells activated by exogenous pyrogens. Although the pathways (humoral and/or neuronal) responsible for transfer of the pyretic signals from the blood to the brain are still under discussion, it is generally accepted that they act on the level of the anterior hypothalamus to raise the thermoregulatory set-point. Results of studies of the adaptive value of fever demonstrate an association between a rise in body temperature and a decrease in mortality and morbidity during infection. These data along with data from evolutionary studies provide a strong support for the concept that fever is a beneficial during infection in endotherms and ectotherms, vertebrates as well as in invertebrates. There are also evidence showing that fever may be used as a therapeutic tool, especially in cancer therapy. Based on the data reviewed in this article, it can be concluded that fever has evolved as a host defense mechanism which was preserved within the animal kingdom through hundreds of millions of years of evolution.

Adaptation, Physiological↗
PubMed1981

Evolution of cytochrome C investigated by the maximum parsimony method.

Rates of evolution for cytochrome c over the past one billion years were calculated from a maximum parsimony dendrogram which approximates the phylogeny of 87 lineages. Two periods of evolutionary acceleration and deceleration apparently occurred for the cytochrome c molecule. The tempo of evolutionary change indicated by this analysis was compared to the patterns of acceleration and deceleration in the ancestry of several other proteins. The synchrony of these tempos of molecular change supports the notion that rapid genetic evolution accompanied periods of major adaptive radiations. Rates of change at different time in several structural-functional areas of cytochrome c were also investigated in order to test the Darwinian hypothesis that during periods of rapid evolution, functional sites accumulate proportionately more substitutions than areas with no known functions. Rates of change in four proposed functional groupings of sites were therefore compared to rates in areas of unknown function for several different time periods. This analysis revealed a significant increase in the rate of evolution for sites associated with the regions of cytochrome c oxidase and reductase interaction during the period between the emergence of the eutherian ancestor to the emergence of the anthropoid ancestor.

Animals↗
PubMed1976

[Micturitional disorders in multiple sclerosis (author's transl)].

Micturitional disorders in multiple sclerosis have often an insidious onset; they aggravate during acute attacks of the nervous disease and are strongly influenced by the general condition of the patient, the evolution of his muscular spasms and the therapeutical measures. This changing behaviour of the bladder makes it necessary to perform repeated cystometries, uroflowmetries and electromyographies of the striated sphincter in order to adapt vesical therapy to the evolutive stadia of the disease. Although good results are frequently obtained by drugs (sympathicomimetics, sympathicolytics, muscle relaxants, parasympathicomimetics, parasympathicolytics), by transurethral resections of internal and/or external sphincters and by phenolisation, we feel that urinary derivations remain indicated for some patients, especially in order to facilitate social integration.

Aged↗
PubMed1988

Molecular characterization and evolution of sequences encoding light-harvesting components in the chromatically adapting cyanobacterium Fremyella diplosiphon.

The major light-harvesting complex in eukaryotic red algae and prokaryotic cyanobacteria is the phycobilisome, a water-soluble complex located on the outer surface of the photosynthetic membranes and composed of both pigmented phycobiliproteins (85%) and non-pigmented linker (15%) polypeptides. The phycobiliproteins are encoded by a gene family and exhibit varying degrees of sequence homology (25 to 55%). Some cyanobacteria can maximize the absorption of prevalent wavelengths of light by adjusting the phycobiliprotein composition of the phycobilisome, a process called complementary chromatic adaptation. In the chromatically adapting species Fremyella displosiphon, there are at least two sets of phycocyanin genes; one is transcribed as two red light-induced transcripts and the other is encoded on a single transcript present in both red and green light. We have determined the complete nucleotide sequences of both sets of phycocyanin subunit genes and their associated 5' and 3' regulatory regions. Based on S1 nuclease protection experiments, the transcripts (1600 and 3800 bases) encoding the inducible phycocyanin subunits have the same 5' end, and possible mechanisms for their synthesis are presented. The 5' end of the 1500-base transcript encoding the constitutive phycocyanin subunits was determined and revealed an Escherichia coli-like "-10" and "-35" region, and sequences near the transcription initiation site homologous to the analogous region of the phycocyanin gene set of Anabaena sp. 7120. Determination of the 3' ends of the transcripts encoding both F. diplosiphon phycocyanin gene sets revealed regions of potential secondary structure that may be important for transcription termination and/or transcript stability. In addition, the sequence of an open reading frame (encoding a 30 kDa polypeptide), located 3' to the constitutive phycocyanin gene set in F. diplosiphon and highly conserved in at least three cyanobacterial species, is presented. The same high degree of sequence homology between the two F. diplosiphon PC alpha and PC beta sequences (85 and 77%, respectively) was found at both the nucleotide and amino acid levels, and similar results were obtained for interspecies comparisons. Implications of these homologies with regard to the evolution of phycobiliprotein subunits are discussed.

Amino Acid Sequence↗