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PubMed2002

Functional genomics and the comparative physiology of hypoxia.

Comparative physiology has proven a powerful approach to our understanding of how animals function under hypoxic conditions and to identifying potential adaptations to environmental oxygen levels. This review considers the potential for using a similar comparative approach with functional genomics to understand the genetic basis of such physiological processes and evolutionary adaptations. Comparative functional genomics is currently limited by genome data, which are available for only a few model organisms. However, comparative studies between model organisms of the same species having slightly different genomes (e.g., in-bred strains of laboratory rodents, transgenic mice, and consomic rats) demonstrate the types of results, as well as the analytical challenges, that are possible if comparative functional genomics is applied to more species. Results from wild and domestic animal studies suggest new models to investigate physiological and evolutionary responses to oxygen levels with functional genomics.

Animals↗

PubMed2001

Genetic and environmental adaptation in high altitude natives. Conceptual, methodological, and statistical concerns.

A great number of physiological and anthropological studies have investigated Andean and Himalayan populations native to high altitude (HA). A non-scientific survey of the extant literature reveals a relatively liberal tradition of inferring genetic (evolutionary) adaptation to HA in these groups, often based on limited evidence and/or based on study designs insufficient to fully address the issue. Rather than review the evidence for or against genetic adaptation, and in order to provide some perspective, this paper will review relevant conceptual, methodological, and statistical issues that are germane to the study of HA native human groups. In particular, focus will be on the limitations of the most common research approach which bases evolutionary inference on the comparison of phenotypic mean differences between highland and lowland native populations. The migrant study approach is discussed, as is a relatively new approach based on genetic admixture in hybrid populations.

Acclimatization↗

PubMed2004

Deconvoluting lung evolution using functional/comparative genomics.

Parathyroid Hormone-related Protein (PTHrP) is a highly evolutionarily conserved, stretch-regulated gene that is necessary for the embryonic transition from branching morphogenesis to alveolization of the lung. It is expressed throughout vertebrate phylogeny, beginning with its expression in the fish swim bladder as an adaptation to gravity; microgravity downregulates the expression of PTHrP by alveolar type II cells, and by bones from rats exposed to 0 x g, suggesting that PTHrP signaling has been exploited for adaptation to 1 x g. PTHrP/PTHrP receptor signaling is upregulated by stretching alveolar type II cells and intersitial lung fibroblasts, whereas overdistension downregulates PTHrP and PTHrP receptor mRNA, further suggesting an evolutionary adaptation. Both surfactant homeostasis and alveolar capillary perfusion are under PTHrP control, indicating that alveolization and ventilation/perfusion matching may have evolved under the influence of PTHrP signaling. Phylogenetic analysis of lung evolution reflects the concomitant increases in alveolar surface area and surfactant production by "amplifying" the PTHrP pathway signal. This mechanism is discussed as a function of increased evolutionary respiratory demand to keep up with the increased metabolic demand for oxygen, and the role of the PTHrP signaling mechanism in leveraging this process.

Animals↗

PubMed2001

Limits on inferring genetic adaptation to high altitude in Himalayan and Andean populations.

Many physiological and anthropological studies have investigated the unique Andean and Himalayan populations that have resided for many hundreds of generations at high altitude (HA). A nonscientific survey of the extant literature reveals a relatively liberal tradition of inferring genetic (evolutionary) adaptation to HA in these groups, often based on limited evidence and/or based on study designs insufficient to fully address the issue. In order to provide some perspective, I review relevant methodological issues that should be considered before evolutionary inference is made. On the whole, this paper takes a conservative stance and cautions against evolutionary inference based on the serious limitations of currently applied research approaches.

Acclimatization↗

PubMed2004

Seasonal affective disorder: a vestigial evolutionary advantage?

The typical symptoms of recurrent winter depression include lowered mood, lethargy, hypersomnia, social withdrawal, decreased libido, increased appetite and weight gain. Mild hypomania often occurs in spring and summer. It is argued that this pattern of attenuated hibernation constituted an adaptive evolutionary mechanism which enhanced the likelihood of reproductive success, most notably for females, among populations living at temperate latitudes. Women were more likely to become pregnant in the summer and thus to give birth at a time of year when their babies had a higher chance of survival. Winter depression symptoms also promoted healthier pregnancies and gave rise to enhanced female-male pair-bonding which improved the survival chances of both mothers and babies. Hypomania in spring and summer also served to increase the likelihood of procreation at the optimal time of year. In the modern era, it is probable that recurrent winter depression is becoming a reproductive disadvantage.

Adaptation, Physiological↗

PubMed2005

Resurrecting the ancestral enzymatic role of a modulatory subunit.

In the post-genomic era, functional prediction of genes is largely based on sequence similarity searches, but sometimes the homologues bear different roles because of evolutionary adaptations. For instance, the existence of enzyme and non-enzyme homologues poses a difficult case for function prediction and the extent of this phenomenon is just starting to be surveyed. Different evolutionary paths are theoretically possible for the loss or acquisition of enzyme function. Here we studied the ancestral role of a model non-catalytic modulatory subunit. With a rational approach, we "resurrected" enzymatic activity from that subunit to experimentally prove that it derived from a catalytic ancestor. We show that this protein (L subunit ADP-glucose pyrophosphorylase) evolved to have a regulatory role, losing catalytic residues more than 130 million years ago, but preserving, possibly as a by-product, the substrate site architecture. Inactivation of catalytic subunits could be the consequence of a general evolutionary strategy to explore new regulatory roles in hetero-oligomers.

Adenosine Diphosphate↗

PubMed1994

Evolution. How does increased fitness evolve?

Populations of bacteria exposed to a new environment have undergone adaptive evolutionary change over 10,000 generations. These populations provide a testing ground for alternative models of long-term evolution.

Adaptation, Biological↗

PubMed2005

Conservation and co-option in developmental programmes: the importance of homology relationships.

One of the surprising insights gained from research in evolutionary developmental biology (evo-devo) is that increasing diversity in body plans and morphology in organisms across animal phyla are not reflected in similarly dramatic changes at the level of gene composition of their genomes. For instance, simplicity at the tissue level of organization often contrasts with a high degree of genetic complexity. Also intriguing is the observation that the coding regions of several genes of invertebrates show high sequence similarity to those in humans. This lack of change (conservation) indicates that evolutionary novelties may arise more frequently through combinatorial processes, such as changes in gene regulation and the recruitment of novel genes into existing regulatory gene networks (co-option), and less often through adaptive evolutionary processes in the coding portions of a gene. As a consequence, it is of great interest to examine whether the widespread conservation of the genetic machinery implies the same developmental function in a last common ancestor, or whether homologous genes acquired new developmental roles in structures of independent phylogenetic origin. To distinguish between these two possibilities one must refer to current concepts of phylogeny reconstruction and carefully investigate homology relationships. Particularly problematic in terms of homology decisions is the use of gene expression patterns of a given structure. In the future, research on more organisms other than the typical model systems will be required since these can provide insights that are not easily obtained from comparisons among only a few distantly related model species.

Journal Article↗

PubMed2002

Self-organization and natural selection in the evolution of complex despotic societies.

Differences between related species are usually explained as separate adaptations produced by individual selection. I discuss in this paper how related species, which differ in many respects, may evolve by a combination of individual selection, self-organization, and group-selection, requiring an evolutionary adaptation of only a single trait. In line with the supposed evolution of despotic species of macaques, we take as a starting point an ancestral species that is egalitarian and mildly aggressive. We suppose it to live in an environment with abundant food and we put the case that, if food becomes scarce and more clumped, natural selection at the level of the individual will favor individuals with a more intense aggression (implying, for instance, biting and fierce fighting). Using an individual-centered model, called DomWorld, I show what happens when the intensity of aggression increases. In DomWorld, group life is represented by artificial individuals that live in a homogeneous world. Individuals are extremely simple: all they do is flock together and, upon meeting one another, they may perform dominance interactions in which the effects of winning and losing are self-reinforcing. When the intensity of aggression in the model is increased, a complex feedback between the hierarchy and spatial structure results; via self-organization, this feedback causes the egalitarian society to change into a despotic one. The many differences between the two types of artificial society closely correspond to those between despotic and egalitarian macaques in the real world. Given that, in the model, the organization changes as a side effect of the change of one single trait proper to an egalitarian society, in the real world a despotic society may also have arisen as a side effect of the mutation of a single trait of an egalitarian species. If groups with different intensities of aggression evolve in this way, they will also have different gradients of hierarchy. When food is scarce, groups with the steepest hierarchy may have the best chance to survive, because at least a small number of individuals in such a group may succeed in producing offspring, whereas in egalitarian societies every individual is at risk of being insufficiently fed to reproduce. Therefore, intrademic group selection (selection within an interbreeding group) may have contributed to the evolution of despotic societies.

Aggression↗

PubMed1990

Rapid evolution in response to high-temperature selection.

Temperature is an important environmental factor affecting all organisms, and there is ample evidence from comparative physiology that species and even conspecific populations can adapt genetically to different temperature regimes. But the effect of these adaptations on fitness and the rapidity of their evolution is unknown, as is the extent to which they depend on pre-existing genetic variation rather than new mutations. We have begun a study of the evolutionary adaptation of Escherichia coli to different temperature regimes, taking advantage of the large population sizes and short generation times in experiments on this bacterial species. We report significant improvement in temperature-specific fitness of lines maintained at 42 degrees C for 200 generations (about one month). These changes in fitness are due to selection on de novo mutations and show that some biological systems can evolve rapidly in response to changes in environmental factors such as temperature.

Biological Evolution↗

PubMed2005

The phylogenetic and evolutionary history of a novel alpha-globin-type gene in orangutans (Pongo pygmaeus).

The alpha-globin genes are implicated in human resistance to malaria, a disease caused by Plasmodium parasites. This study is the first to analyze DNA sequences from a novel alpha-globin-type gene in orangutans, a species affected by Plasmodium. Phylogenetic methods show that the gene is a duplication of an alpha-globin gene and is located 5' of alpha-2 globin. The alpha-globin-type gene is notable for having four amino acid replacements relative to the orangutan's alpha-1 and alpha-2 globin genes, with no synonymous differences. Pairwise K(a)/K(s) methods and likelihood ratio tests (LRTs) revealed that the evolutionary history of the alpha-globin-type gene has been marked by either neutral or positive evolution, but not purifying selection. A comparative analysis of the amino acid replacements of the alpha-globin-type gene with human hemoglobinopathies and hemoglobin structure showed that two of the four replaced sites are members of the same molecular bond, one that is crucial to the proper functioning of the hemoglobin molecule. This suggested an adaptive evolutionary change. Functionally, this locus may result in a thalassemia-like phenotype in orangutans, possibly as an adaptation to combat Plasmodium.

Amino Acid Sequence↗

PubMed2004

Use of artificial environments to reproduce and exploit genotype x location interaction for lucerne in northern Italy.

Genotype x environment interaction effects can be exploited by breeding for specific adaptation to well-defined subregions within a target region. Previous work showed that genotype x location interaction for dry matter (DM) yield of lucerne (Medicago sativa L. subsp. sativa) cultivars in northern Italy is large and associated with soil type and level of summer drought stress of locations, suggesting the presence of two contrasting subregions. Thirteen farm landraces collected across the region and four control varieties were evaluated for DM yield in four artificial environments created at one site by the factorial combination of soil type (sandy loam or silty clay) and drought stress level (almost nil or high) for: (1) exploring the possibility to reproduce in artificial environments the adaptation patterns occurring across the region; (2) investigating the adaptation pattern of landraces and its relationship with environmental factors at collecting sites; and (3) providing a preliminary comparison of wide- versus specific-adaptation strategies based on yield gains predicted from selection of populations. Different soils filled large (24.0x1.6x0.8-m deep), bottomless containers in concrete. Water amounts were controlled by irrigation under a moving rain shelter. Cultivars varied largely for adaptation pattern across the artificial environments, mainly due to cultivar x stress interaction. Better response to stress conditions of landraces was closely associated with the level of summer drought at collecting sites (r=0.82), highlighting the importance of evolutionary adaptation. The additive main effects and multiplicative interaction-modelled responses of control cultivars successfully reproduced those observed across locations, candidating the artificial environments as a cheaper alternative to more selection locations when breeding for wide or specific adaptation. The latter implied about 40-50% greater estimated gains relative to breeding for wide adaptation.

Adaptation, Physiological↗

PubMed2004

Menstrual variation of autonomic balance may be a factor in exacerbations of certain diseases during the menstrual cycle.

Exacerbation of certain medical conditions during specific phases of the menstrual cycle has long been recognized. Mechanisms of the cyclic variations are poorly understood, but are often attributed to fluctuations in reproductive hormones. We hypothesize that normal variations in autonomic balance during the menstrual cycle, which likely evolved as adaptations for reproduction, may contribute to catamenial variations in diseases independent of hormonal variations. Emerging evidence suggests that autonomic balance shifts towards sympathetic bias during the second half of the menstrual cycle. This shift can be seen as an evolutionary adaptation to address the immunologic and physiologic demands for successful implantation and gestation. Through direct modulation of lymphoid system and activation of the cortisol pathway, sympathetic bias promotes a shift to relative T helper (Th)-2-biased immunity which may favor maternal tolerance of the embryo by attenuating Th-1-mediated interference of implantation. Immune variance during the menstrual cycle has been implicated in menstrual fluctuations of many diseases, but until now the immune variance has been attributed to female hormonal changes. We propose that shifts in autonomic balance independently contribute to fluctuations in diseases by modulating the immune system. Still further, we propose that many other diseases fluctuate due to the direct nervous system actions of shifts in autonomic balance. Our hypothesis portends new therapeutic paradigms based on cyclical modulation of autonomic balance to address catamenial variations of medical conditions.

Adaptation, Physiological↗

PubMed2006

Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage.

At the center of the debate on the emergence of modern humans and their spread throughout the globe is the question of whether archaic Homo lineages contributed to the modern human gene pool, and more importantly, whether such contributions impacted the evolutionary adaptation of our species. A major obstacle to answering this question is that low levels of admixture with archaic lineages are not expected to leave extensive traces in the modern human gene pool because of genetic drift. Loci that have undergone strong positive selection, however, offer a unique opportunity to identify low-level admixture with archaic lineages, provided that the introgressed archaic allele has risen to high frequency under positive selection. The gene microcephalin (MCPH1) regulates brain size during development and has experienced positive selection in the lineage leading to Homo sapiens. Within modern humans, a group of closely related haplotypes at this locus, known as haplogroup D, rose from a single copy approximately 37,000 years ago and swept to exceptionally high frequency (approximately 70% worldwide today) because of positive selection. Here, we examine the origin of haplogroup D. By using the interhaplogroup divergence test, we show that haplogroup D likely originated from a lineage separated from modern humans approximately 1.1 million years ago and introgressed into humans by approximately 37,000 years ago. This finding supports the possibility of admixture between modern humans and archaic Homo populations (Neanderthals being one possibility). Furthermore, it buttresses the important notion that, through such adminture, our species has benefited evolutionarily by gaining new advantageous alleles. The interhaplogroup divergence test developed here may be broadly applicable to the detection of introgression at other loci in the human genome or in genomes of other species.

Adaptation, Biological↗

PubMed1999

Mechanisms of dominance: coexistence of picocyanobacterial genotypes in a freshwater ecosystem

The autotrophic picoplankton of the pelagic zone of the mesotrophic Lake Constance is dominated by phycoerythrin-rich unicellular cyanobacteria phylogenetically related to the marine Synechococcus and Prochlorococcus cluster. In Lake Constance, the abundance of picocyanobacteria shows a recurrent pattern of seasonal variations. Evidence of diverse subpopulations was obtained by electron-microscopic examination of natural water samples and isolated strains that unveiled different surface structures of picocyanobacteria. Further evidence was obtained by DNA analysis of 26 clonal isolates representing 12 different genotypes. Variations in light and nutrient supply revealed distinct abilities of the genetically different strains to cope with these stress situations. Furthermore, cultured heterotrophic nanoflagellates exhibited differential feeding preferences for certain Synechococcus strains. The findings imply that growth and loss rates of the natural cyanobacterial community may be influenced by its genetic composition. Phylogenetic analyses of isolated strains indicated that the physiological diversification of pelagic Synechococcus spp. has occurred during a recent adaptive radiation. An example for genetic mechanisms underlying physiological diversification is indicated by mobile DNA elements found in a Synechocystis strain also isolated from the pelagic zone of Lake Constance. The observations suggest that dominance of Synechococcus spp. was achieved by evolutionary adaptation and coexistence of numerous genotypes generating a physiologically highly diversified population.

Journal Article↗

PubMed1994

From sequences to shapes and back: a case study in RNA secondary structures.

RNA folding is viewed here as a map assigning secondary structures to sequences. At fixed chain length the number of sequences far exceeds the number of structures. Frequencies of structures are highly non-uniform and follow a generalized form of Zipf's law: we find relatively few common and many rare ones. By using an algorithm for inverse folding, we show that sequences sharing the same structure are distributed randomly over sequence space. All common structures can be accessed from an arbitrary sequence by a number of mutations much smaller than the chain length. The sequence space is percolated by extensive neutral networks connecting nearest neighbours folding into identical structures. Implications for evolutionary adaptation and for applied molecular evolution are evident: finding a particular structure by mutation and selection is much simpler than expected and, even if catalytic activity should turn out to be sparse of RNA structures, it can hardly be missed by evolutionary processes.

Base Composition↗

PubMedDate not supplied

[The origin of the biological week from data on the rhythm of cardiac contractions in people during the solar activity cycle].

A human biologic week in the heart rate variations was compared with the variations of the sunspot area and geomagnetic activity over the solar cycle. The low ratio of amplitude of circaseptan rhythm to that of circadian rhythm in the heart rate of several clinically healthy men who did around-the-clock self-measurements in a number of years coincides with the period of anomalously low amplitude of circaseptan rhythm of the solar activity. Results herein suggest that physiologic circaseptan rhythms are built into the genome being adapted evolutionary to the original heliogeomagnetic environmental circaseptans.

Adaptation, Physiological↗

PubMed2026

Potential survival strategies of novel comammox and nitrite-oxidizing Nitrospira synthesizing osmoprotectants in a wastewater microbiome treating high-ammonia brackish landfill leachate.

BACKGROUND: In the late stages of landfill operation, leachate becomes brackish and contains high concentrations of ammonia with limited organic carbon. At leachate treatment facilities, it is typically subjected to nitrification followed by denitrification, with methanol supplied as an external electron donor. This unique environment may harbor novel microorganisms, including nitrifiers. Although a variety of microorganisms are involved in nitrification, their substrate specificity and salinity tolerance remain insufficiently understood. In this study, a genome-centric metagenome analysis was conducted on the microbiome from a leachate treatment facility at a closed landfill. RESULTS: A total of 68 metagenome-assembled genomes (MAGs) were reconstructed, including 64 putative novel species. Among these, two Nitrospira MAGs were recovered: a novel complete ammonia-oxidizing bacterium (comammox), Nitrospira LAS72 (88.72% completeness, 2.10% contamination), and canonical nitrite-oxidizing Nitrospira LAS18 (99.98% completeness, 2.29% contamination). Comparative genomic analysis with 260 publicly available Nitrospira genomes revealed that LAS18 represents a new sub-lineage within lineage VII of the Nitrospira genus. Two ammonia-oxidizing archaea (AOA), Candidatus Nitrosocosmicus LAS21 and Nitrosarchaeum LAS73, were also identified, while canonical ammonia-oxidizing bacteria were not detected. Given the brackish conditions (1.23% salinity) and the methanol-fed operation of the treatment facility, the genomic potential for osmotic stress adaptation and methanol metabolism was investigated. Comammox Nitrospira LAS72 harbors biosynthetic pathways for several compatible solutes (osmoprotectants), including glycine betaine, proline, trehalose, and L-glutamate. Moreover, comammox Nitrospira LAS72 possesses genetic potential for oxidizing formaldehyde, suggesting that it may exploit these methanol-derived intermediates as energy sources. These features indicate that LAS72 may withstand osmotic fluctuations through the production of various osmoprotectants and thrive under the unique conditions of a methanol-fed environment. CONCLUSIONS: The discovery of novel comammox Nitrospira and canonical Nitrospira forming a new sub-lineage within lineage VII of the Nitrospira genus in an ammonia-rich brackish environment provides the first genomic evidence for evolutionary adaptation among nitrifiers to saline, methanol-fed environments. These findings enhance our understanding of the ecological and evolutionary dynamics shaping nitrifier communities in complex treatment ecosystems. Video Abstract.

Ammonia↗