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Results for “Evolutionary adaptability”

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PubMed2005

Subfunctionalization of duplicated genes as a transition state to neofunctionalization.

BACKGROUND: Gene duplication has been suggested to be an important process in the generation of evolutionary novelty. Neofunctionalization, as an adaptive process where one copy mutates into a function that was not present in the pre-duplication gene, is one mechanism that can lead to the retention of both copies. More recently, subfunctionalization, as a neutral process where the two copies partition the ancestral function, has been proposed as an alternative mechanism driving duplicate gene retention in organisms with small effective population sizes. The relative importance of these two processes is unclear. RESULTS: A set of lattice model genes that fold and bind to two peptide ligands with overlapping binding pockets, but not a third ligand present in the cell was designed. Each gene was duplicated in a model haploid species with a small constant population size and no recombination. One set of models allowed subfunctionalization of binding events following duplication, while another set did not allow subfunctionalization. Modeling under such conditions suggests that subfunctionalization plays an important role, but as a transition state to neofunctionalization rather than as a terminal fate of duplicated genes. There is no apparent selective pressure to maintain redundancy. CONCLUSION: Subfunctionalization results in an increase in the preservation of duplicated gene copies, including those that are neofunctionalized, but never represents a substantial fraction of duplicate gene copies at any evolutionary time point and ultimately leads to neofunctionalization of those preserved copies. This conclusion also may reflect changes in gene function after duplication with time in real genomes.

Animals↗

PubMed2004

Transmission rates and adaptive evolution of pathogens in sympatric heterogeneous plant populations.

Diversification in agricultural cropping patterns is widely practised to delay the build-up of virulent races that can overcome host resistance in pathogen populations. This can lead to balanced polymorphism, but the long-term consequences of this strategy for the evolution of crop pathogen populations are still unclear. The widespread occurrence of sibling species and reproductively isolated sub-species among fungal and oomycete plant pathogens suggests that evolutionary divergence is common. This paper develops a mathematical model of host-pathogen interactions using a simple framework of two hosts to analyse the influences of sympatric host heterogeneity on the long-term evolutionary behaviour of plant pathogens. Using adaptive dynamics, which assumes that sequential mutations induce small changes in pathogen fitness, we show that evolutionary outcomes strongly depend on the shape of the trade-off curve between pathogen transmission on sympatric hosts. In particular, we determine the conditions under which the evolutionary branching of a monomorphic into a dimorphic population occurs, as well as the conditions that lead to the evolution of specialist (single host range) or generalist (multiple host range) pathogen populations.

Adaptation, Physiological↗

PubMed2006

The pea aphid, Acyrthosiphon pisum: an emerging genomic model system for ecological, developmental and evolutionary studies.

Aphids display an abundance of adaptations that are not easily studied in existing model systems. Here we review the biology of a new genomic model system, the pea aphid, Acyrthosiphon pisum. We then discuss several phenomena that are particularly accessible to study in the pea aphid: the developmental genetic basis of polyphenisms, aphid-bacterial symbioses, the genetics of adaptation and mechanisms of virus transmission. The pea aphid can be maintained in the laboratory and natural populations can be studied in the field. These properties allow controlled experiments to be performed on problems of direct relevance to natural aphid populations. Combined with new genomic approaches, the pea aphid is poised to become an important model system for understanding the molecular and developmental basis of many ecologically and evolutionarily relevant problems.

Adaptation, Biological↗

PubMed2002

Adaptation, punctuation and information: a rate-distortion approach to non-cognitive 'learning plateaus' in evolutionary process.

We extend recent information-theoretic phase transition approaches to evolutionary and cognitive process via the Rate Distortion and Joint Asymptotic Equipartition Theorems, in the circumstance of interaction with a highly structured environment. This suggests that learning plateaus in cognitive systems and punctuated equilibria in evolutionary process are formally analogous, even though evolution is not cognitive. Extending arguments by Adami et al. (2000), we argue that 'adaptation' is the process by which a distorted genetic image of a coherently structured environment is imposed upon a species.

Adaptation, Biological↗

PubMed2026

The MexMAGIC population reveals the genetic architecture of traits exhibiting clinal variation in Mexican native maize.

Defining the genetic basis of local adaptation is a key goal of evolutionary biology and crop improvement. Theory predicts that when selective pressures follow differences in the environment, a cline will be established. Clines can be exploited to uncover adaptive variation by association of alleles with the environment. However, monotonic phenotypic change over a cline is not necessarily mirrored in the behavior of genetic variants and population structure can further complicate analysis. To study genetic and phenotypic variation across the environment, we developed a multi-parent advanced generation inter-cross (MAGIC) population using eight Mexican native maize (Zea mays L. ssp. mays) varieties sourced from distinct agroecological zones. We evaluated the population in a common garden in Mexico and mapped tassel branching and flowering time, two traits that exhibit clinal variation. Variation in tassel branching was dominated by a single QTL with allele effects aligning to a negative elevational cline. By contrast, allele effects associated with 11 identified flowering time QTL were not consistently correlated with any one source environmental factor. Our observations support the prediction that genotype-environment association will be strongest under simple genetic architecture, although, even then, analysis in native populations may be confounded by population structure.

MAGIC↗

PubMed2005

Evolvability suppression to stabilize far-sighted adaptations.

The opportunistic character of adaptation through natural selection can lead to evolutionary pathologies--situations in which traits evolve that promote the extinction of the population. Such pathologies include imprudent predation and other forms of habitat overexploitation, or the tragedy of the commons, adaptation to temporally unreliable resources, cheating and other antisocial behavior, infectious pathogen carrier states, parthenogenesis, and cancer, an intraorganismal evolutionary pathology. It is known that hierarchical population dynamics can protect a population from invasion by pathological genes. Can it also alter the genotype so as to prevent the generation of such genes in the first place, that is, suppress the evolvability of evolutionary pathologies? A model is constructed in which one locus controls the expression of the pathological trait, and a series of modifier loci exist that can prevent the expression of this trait. It is found that multiple evolvability checkpoint genes can evolve to prevent the generation of variants that cause evolutionary pathologies. The consequences of this finding are discussed.

Adaptation, Physiological↗

PubMed2003

Evolutionary genetics of the melanocortin-1 receptor in vertebrates.

The molecular genetic basis of adaptive change in phenotype is a major outstanding issue in evolutionary biology. Evolutionary change in coat and plumage color is a promising system for making progress in this field. Most notably, recent work on the molecular genetic basis of hair and feather color has identified several genes which are candidates for involvement in evolutionary color change in mammals and birds. We have investigated the evolution of one of these candidate genes, the melanocortin-1 receptor (MC1R) gene, in relation to changes in melanin distribution among a wide variety of primate species, and in bananaquits (Coereba flaveola), which are a classic case of melanic plumage polymorphism in birds. In primates, a role of the MC1R coding region in coat color evolution can be ruled out in several cases in which closely related species have drastically different distributions of eumelanin and/or pheomelanin. However, reconstruction of MC1R sequences over primate evolution shows the presence of mutations at important functional sites in several lineages. Most notably, the lion tamarins (Leontopithecus) show a striking pattern of MC1R evolution, including deletions and several nonconservative amino acid changes. In the bananaquit, an E92K substitution in the MC1R is strongly associated with melanism, and this is likely to be the causative mutation. Reconstruction of the evolution of bananaquit MC1R alleles shows that melanism is a derived trait in this species. These results confirm the utility of a candidate gene approach to color evolution in vertebrates and open the way for extensive future research.

Animals↗

PubMed2005

MIC and other NKG2D ligands: from none to too many.

NKG2D, a prime activatory receptor on human NK, CD8(+) alphabeta and gammadelta cells, has a variety of ligands, which, despite sharing membership of the MHC class I structural club, display an array of unique features. Chronologically, human MIC molecules were the first NKG2D ligands to be identified. Then came RAET1 (ULBP) molecules, which were identified in both man and mouse, as well as H60 and MULT1, which have no counterparts in man to date. The question remains as to why, more than how, the evolutionary conserved, apparently monomorphic, single copy, NKG2D, can/should adapt to this variety of ligands, and when it does, what is the evolutionary advantage of this profusion of ligands for a single receptor?

Animals↗

PubMed2006

Thermal evolution of pre-adult life history traits, geometric size and shape, and developmental stability in Drosophila subobscura.

Replicated lines of Drosophila subobscura originating from a large outbred stock collected at the estimated Chilean epicentre (Puerto Montt) of the original New World invasion were allowed to evolve under controlled conditions of larval crowding for 3.5 years at three temperature levels (13, 18 and 22 degrees C). Several pre-adult life history traits (development time, survival and competitive ability), adult life history related traits (wing size, wing shape and wing-aspect ratio), and wing size and shape asymmetries were measured at the three temperatures. Cold-adapted (13 degrees C) populations evolved longer development times and showed lower survival at the highest developmental temperature. No divergence for wing size was detected following adaptation to temperature extremes (13 and 22 degrees C), in agreement with earlier observations, but wing shape changes were obvious as a result of both thermal adaptation and development at different temperatures. However, the evolutionary trends observed for the wing-aspect ratio were inconsistent with an adaptive hypothesis. There was some indication that wing shape asymmetry has evolutionarily increased in warm-adapted populations, which suggests that there is additive genetic variation for fluctuating asymmetry and that it can evolve under rapid environmental changes caused by thermal stress. Overall, our results cast strong doubts on the hypothesis that body size itself is the target of selection, and suggest that pre-adult life history traits are more closely related to thermal adaptation.

Animals↗

PubMed2005

Parallel genotypic adaptation: when evolution repeats itself.

Until recently, parallel genotypic adaptation was considered unlikely because phenotypic differences were thought to be controlled by many genes. There is increasing evidence, however, that phenotypic variation sometimes has a simple genetic basis and that parallel adaptation at the genotypic level may be more frequent than previously believed. Here, we review evidence for parallel genotypic adaptation derived from a survey of the experimental evolution, phylogenetic, and quantitative genetic literature. The most convincing evidence of parallel genotypic adaptation comes from artificial selection experiments involving microbial populations. In some experiments, up to half of the nucleotide substitutions found in independent lineages under uniform selection are the same. Phylogenetic studies provide a means for studying parallel genotypic adaptation in non-experimental systems, but conclusive evidence may be difficult to obtain because homoplasy can arise for other reasons. Nonetheless, phylogenetic approaches have provided evidence of parallel genotypic adaptation across all taxonomic levels, not just microbes. Quantitative genetic approaches also suggest parallel genotypic evolution across both closely and distantly related taxa, but it is important to note that this approach cannot distinguish between parallel changes at homologous loci versus convergent changes at closely linked non-homologous loci. The finding that parallel genotypic adaptation appears to be frequent and occurs at all taxonomic levels has important implications for phylogenetic and evolutionary studies. With respect to phylogenetic analyses, parallel genotypic changes, if common, may result in faulty estimates of phylogenetic relationships. From an evolutionary perspective, the occurrence of parallel genotypic adaptation provides increasing support for determinism in evolution and may provide a partial explanation for how species with low levels of gene flow are held together.

Adaptation, Biological↗

PubMed1998

An evolutionary link between sporulation and prophage induction in the structure of a repressor:anti-repressor complex.

Spore formation is an extreme response of some bacteria to adversity. In Bacillus subtilis the proteins of the sin, sporulation inhibition, region form a component of an elaborate molecular circuitry that regulates the commitment to sporulation. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer. The interactions governing this curious quaternary transition are revealed in the crystal structure of the SinI-SinR complex. The most striking, and unexpected, finding is that the tertiary structure of the DNA-binding domain of SinR is identical with that of the corresponding domains of the repressor proteins, CI and Cro, of bacteriophage 434 that regulate lysis/lysogeny. This structural similarity greatly exceeds that between SinR and any bacterial protein or between the 434 repressor proteins and their homologues in the closely related bacteriophage lambda. The close evolutionary relationship implied by the structures of SinR and the 434 repressors provokes both comparison of their functions and a speculative consideration of the intriguing possibility of an evolutionary link between the two adaptive responses, sporulation and prophage induction.

Amino Acid Sequence↗

PubMed1993

Structural models of captivity trauma, resilience, and trauma response among former prisoners of war 20 to 40 years after release.

Long-term responses to captivity trauma were measured in a national sample of American former prisoners of war. Their responses included negative affect, positive affect, and somatic symptoms as assessed by the Cornell Medical Index in 1967 and the Center for Epidemiological Study Depression Scale in 1985. These responses were strongly associated with captivity trauma (as indexed by captivity weight loss, torture, and disease) and resilience (as indexed by age and education at capture). Symptoms reported in 1967 were related to symptoms reported in 1985, suggesting symptom stability. These results are consistent with a model of trauma response that incorporates both trauma exposure and individual resilience. The findings are interpreted within a theoretical view of trauma response as adaptive when viewed from an evolutionary perspective.

Aged↗

PubMed2000

Dietary lean red meat and human evolution.

Scientific evidence is accumulating that meat itself is not a risk factor for Western lifestyle diseases such as cardiovascular disease, but rather the risk stems from the excessive fat and particularly saturated fat associated with the meat of modern domesticated animals. In our own studies, we have shown evidence that diets high in lean red meat can actually lower plasma cholesterol, contribute significantly to tissue omega-3 fatty acid and provide a good source of iron, zinc and vitamin B12. A study of human and pre-human diet history shows that for a period of at least 2 million years the human ancestral line had been consuming increasing quantities of meat. During that time, evolutionary selection was in action, adapting our genetic make up and hence our physiological features to a diet high in lean meat. This meat was wild game meat, low in total and saturated fat and relatively rich in polyunsaturated fatty acids (PUFA). The evidence presented in this review looks at various lines of study which indicate the reliance on meat intake as a major energy source by pre-agricultural humans. The distinct fields briefly reviewed include: fossil isotope studies, human gut morphology, human encephalisation and energy requirements, optimal foraging theory, insulin resistance and studies on hunter-gatherer societies. In conclusion, lean meat is a healthy and beneficial component of any well-balanced diet as long as it is fat trimmed and consumed as part of a varied diet.

Adaptation, Biological↗

PubMed1989

Patterns of divergence in homologous proteins as indicators of tertiary and quaternary structure.

A new approach for extracting conformational information from an alignment of homologous proteins is presented. This approach extracts information from the pattern of sequence divergence in proteins, and considers evolutionary issues, such as functional adaptation and neutral drift, in assigning roles in tertiary structure to residues at specific positions in the alignment. A reliable algorithm is developed for identifying surface residues in a protein. An algorithm is also developed for identifying active site residues; this algorithm can be applied in cases where functional divergence occurs in one subgroup of homologous proteins but not in others. Finally, these algorithms are used to make predictions regarding the quaternary structure of alcohol dehydrogenase from yeast.

Alcohol Dehydrogenase↗

PubMed2006

How do obligate parasites evolve? A multi-gene phylogenetic analysis of downy mildews.

Plant parasitism has independently evolved as a nutrition strategy in both true fungi and Oomycetes (stramenopiles). A large number of species within phytopathogenic Oomycetes, the so-called downy mildews, are defined as obligate biotrophs since they have not, to date, been cultured on any artificial medium. Other genera like Phytophthora and Pythium can in general be cultured on standard or non-standard agar media. Within all three groups there are many important plant pathogens responsible for severe economic losses as well as damage to natural ecosystems. Although they are important model systems to elucidate the evolution of obligate parasites, the phylogenetic relationships between these genera have not been clearly resolved. Based on the most comprehensive sampling of downy mildew genera to date and a representative sample of Phytophthora subgroups, we inferred the phylogenetic relationships from a multi-gene dataset containing both coding and non-coding nuclear and mitochondrial loci. Phylogenetic analyses were conducted under several optimality criteria and the results were largely consistent between all the methods applied. Strong support is achieved for monophyly of a clade comprising both the genus Phytophthora and the obligate biotrophic species. The facultatively parasitic genus Phytophthora is shown to be at least partly paraphyletic. Monophyly of a cluster nested within Phytophthora containing all obligate parasites is strongly supported. Within the obligate biotrophic downy mildews, four morphologically or ecologically well-defined subgroups receive statistical support: (1) A cluster containing all species with brownish-violet conidiosporangia, i.e., the genera Peronospora and Pseudoperonospora; (2) a clade comprising the genera with vesicular to pyriform haustoria (Basidiophora, Benua, Bremia, Paraperonospora, Plasmopara, Plasmoverna, Protobremia); (3) a group containing species included in Hyaloperonospora and Perofascia which almost exclusively infect Brassicaceae; (4) a clade including the grass parasites Viennotia oplismeni and Graminivora graminicola. Phylogenetic relationships between these four clades are not clearly resolved, and neither is the position of Sclerospora graminicola within the downy mildews. Character analysis indicates an evolutionary scenario of gradually increasing adaptation to plant parasitism in Peronosporales and that at least the most important of these adaptive steps occurred only once, including major host shifts within downy mildews.

Animals↗

PubMed2025

A One Health perspective: Genomic insights into temporal trends of antimicrobial resistance and zoonotic transmission risks in Escherichia coli from human and swine.

Antimicrobial resistance (AMR) poses a significant challenge within the One Health framework. By integrating genomic data from 824 E. coli isolates obtained from 22 swine farms in southwestern China with 8432 publicly available genomes from human and swine sources, this study provides comprehensive insights into the temporal trends and divergence of AMR in human and swine E. coli populations, the risk of AMR transmission from swine to human, and the evolutionary mechanisms underlying the human adaptation of ST2 strains. The results revealed an overall increase in AMR until approximately 2016, followed by a subsequent decline. However, resistance to tetracyclines, quinolones, and phenicols continues to exhibit an upward trend, highlighting the urgency of enhancing regulatory measures targeting these drugs. Horizontal gene transfer play pivotal roles in shaping distinct AMR profiles in human and swine strains. ST2 E. coli was identified as a major carrier of AMR in both human and swine, and also served as the primary reservoir of blaNDM-5 within the human-associated lineage. During evolution, ST2 E. coli underwent significant genetic changes, including the enrichment of blaNDM-5 and remodeling of virulence factors, facilitating its transition from a generalist lineage colonizing both human and swine to a human-adapted lineage.

Humans↗

PubMed2005

Expressed sequence tag (EST) survey of the highly adapted green algal parasite, Helicosporidium.

Helicosporidia are obligate invertebrate pathogens with a unique and highly adapted mode of infection. The evolutionary history of Helicosporidia has been uncertain, but several recent molecular phylogenetic studies have shown an unexpectedly close relationship to green algae, and specifically to the opportunistic pathogen Prototheca. To date, molecular sequences from Helicosporidia are restricted to those genes used for phylogenetic reconstruction and genes related to the existence and function of its cryptic plastid. We have therefore conducted a small expressed sequence tag (EST) project on Helicosporidium sp., yielding about 700 unique sequences. We have examined the functional distribution of known genes, the distribution of EST abundance, and the prevalence of previously unknown gene sequences. To demonstrate the potential utility of large amounts of data, we have used ribosomal proteins to test whether the phylogenetic position of Helicosporidium inferred from a small number of genes is broadly supported by a large number of genes. We conducted phylogenetic analyses on 69 ribosomal proteins and found that 98% supported the green algal origin of Helicosporidia and 80% support a specific relationship with Prototheca. Overall, these data multiply the available molecular information from Helicosporidium 100-fold, which should provide the basis for new insights into these unusual but interesting parasites.

Chlorophyta↗

PubMed1985

The evolutionary role of recombinational repair and sex.

We have argued that sexual reproduction arose very early in the evolution of life as a way of overcoming informational damage or loss through recombinational repair. As organisms became more complex and genome information content expanded, diploidy, at first transient, became the predominant way of coping with increased vulnerability to mutation. This allowed further genome expansion. Once such expansion had occurred, however, diploidy became essentially irreversible, since reversion to haploidy would lead to expression of accumulated deleterious recessive alleles. This expression of recessive alleles also imposes a stiff penalty on organisms that experiment with close inbreeding forms of recombinational repair. A consequence of sex is that fitness (defined as per capita rate of increase) is density dependent. At low population density, fitness declines due to increased costs of finding a mate. This fundamental constraint on population increase can inhibit evolutionary success of the best adapted species if it is small in numbers. Sexual reproduction also tends to eliminate new coadapted genotypes within a species by breaking up their coadapted gene complexes; this also contributes to the cohesion of species. In general, we think the existence of species and their characteristic cohesion and stability over time are direct consequences of sex; and sex in turn is a consequence of the need to overcome gene damage through recombinational repair while at the same time masking the deleterious effects of mutation.

Animals↗