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PubMed2026

Deconstructing empirical fitness seascapes across scales of granularity.

The fitness landscape metaphor remains resonant in evolutionary theory and has facilitated the birth of newer concepts, like the fitness seascape, that consider the role of environmental context in shaping the dynamics of evolution. Since its emergence, the seascape has appeared in numerous studies examining how different and fluctuating environments shape evolutionary outcomes. Despite growing interest, we lack comprehensive examinations of how environmental context shapes features of fitness seascapes. In this study, we address this gap by deconstructing empirical fitness seascapes across scales of granularity: loci, locus interactions (epistasis), alleles, trajectories, and entire seascapes. For each, we examine how environmental context influences qualitative and quantitative aspects of seascapes, and find that they change appreciably, with patterns specific to individual systems of study. We also quantify how much each scale varies across environments, and find that certain scales tend to be more sensitive to context than others. In summary, we reflect on the implications of the seascape metaphor for the incorporation of environmental effects into theoretical population genetics, for understanding how the environment shapes evolution in disease systems, and for contemporary bioengineering efforts.

Genetic Fitness↗
PubMed2002

Adaptive divergence in experimental populations of Pseudomonas fluorescens. I. Genetic and phenotypic bases of wrinkly spreader fitness.

A central feature of all adaptive radiations is morphological divergence, but the phenotypic innovations that are responsible are rarely known. When selected in a spatially structured environment, populations of the bacterium Pseudomonas fluorescens rapidly diverge. Among the divergent morphs is a mutant type termed "wrinkly spreader" (WS) that colonizes a new niche through the formation of self-supporting biofilms. Loci contributing to the primary phenotypic innovation were sought by screening a WS transposon library for niche-defective (WS(-)) mutants. Detailed analysis of one group of mutants revealed an operon of 10 genes encoding enzymes necessary to produce a cellulose-like polymer (CLP). WS genotypes overproduce CLP and overproduction of the polymer is necessary for the distinctive morphology of WS colonies; it is also required for biofilm formation and to maximize fitness in spatially structured microcosms, but overproduction of CLP alone is not sufficient to cause WS. A working model predicts that modification of cell cycle control of CLP production is an important determinant of the phenotypic innovation. Analysis of >30 kb of DNA encoding traits required for expression of the WS phenotype, including a regulatory locus, has not revealed the mutational causes, indicating a complex genotype-phenotype map.

Adaptation, Physiological↗
PubMed2004

Molecular design of the photosystem II light-harvesting antenna: photosynthesis and photoprotection.

The photosystem II (PSII) light-harvesting system carries out two essential functions, the efficient collection of light energy for photosynthesis, and the regulated dissipation of excitation energy in excess of that which can be used. This dual function requires structural and functional flexibility, in which light-harvesting proteins respond to an external signal, the thylakoid DeltapH, to induce feedback control. This process, referred to as non-photochemical quenching (NPQ) depends upon the xanthophyll cycle and the PsbS protein. In nature, NPQ is heterogeneous in terms of kinetics and capacity, and this adapts photosynthetic systems to the specific dynamic features of the light environment. The molecular features of the thylakoid membrane which may enable this flexibility and plasticity are discussed.

Adaptation, Physiological↗
PubMed2004

Male-biased mutation rate and divergence in autosomal, z-linked and w-linked introns of chicken and Turkey.

To investigate mutation-rate variation between autosomes and sex chromosomes in the avian genome, we have analyzed divergence between chicken (Gallus gallus) and turkey (Meleagris galopavo) sequences from 33 autosomal, 28 Z-linked, and 14 W-linked introns with a total ungapped alignment length of approximately 43,000 bp. There are pronounced differences in the mean divergence among autosomes and sex chromosomes (autosomes [A] = 10.08%, Z chromosome = 10.99%, and W chromosome = 5.74%), and we use these data to estimate the male-to-female mutation-rate ratio (alpha(m)) from Z/A, Z/W, and A/W comparisons at 1.71, 2.37, and 2.52, respectively. Because the alpha(m) estimates of the three comparisons do not differ significantly, we find no statistical support for a specific reduction in the Z chromosome mutation rate (Z reduction estimated at 4.89%, P = 0.286). The idea of mutation-rate reduction in the sex chromosome hemizygous in one sex (i.e., X in mammals, Z in birds) has been suggested on the basis of theory on adaptive mutation-rate evolution. If it exists in birds, the effect would, thus, seem to be weak; a preliminary power analysis suggests that it is significantly less than 18%. Because divergence may vary within chromosomal classes as a result of variation in mutation and/or selection, we developed a novel double-bootstrapping method, bootstrapping both by introns and sites from concatenated alignments, to estimate confidence intervals for chromosomal class rates and for alpha(m). The narrowest interval for the alpha(m) estimate is 1.88 to 2.97 from the Z/W comparison. We also estimated alpha(m) using maximum likelihood on data from all three chromosome classes; this method yielded alpha(m) = 2.47 and approximate 95% confidence intervals of 2.27 to 2.68. Our data are broadly consistent with the idea that mutation-rate differences between chromosomal classes can be explained by the male mutation bias alone.

Animals↗
PubMed1999

The future of gastroenterology in the era of managed care.

Specialty practice in general, and gastroenterology in particular, is undergoing significant transformation as we head into the new millennium. Gastroenterologists will need to adapt to the continued evolution and consolidation of managed care. Among other issues, gastroenterologists will need strategies for dealing with pricing pressures, changing technology, increased consumerism, a perceived specialist oversupply, and a rapidly aging population. These and other developments will drive a myriad of physician responses in an effort to confront changing practice realities.

Delivery of Health Care, Integrated↗
PubMed2000

Towards a unified theory of cooperative breeding: the role of ecology and life history re-examined.

We present quantitative models that unify several adaptive hypotheses for the evolution of cooperative breeding in a single framework: the ecological constraints hypothesis, the life-history hypothesis and the benefits-of-philopatry hypothesis. Our goal is to explain interspecific variation in the occurrence of cooperative breeding in terms of interspecific variation in life-history traits and ecological conditions. We analyse two models, according to whether or not helpers can inherit their parents' territory. Major results are (i) territory inheritance always promotes cooperative breeding; (ii) if territories are not inherited, neither ecological constraints nor variation in life-history traits predict interspecific variation in cooperative breeding; and (iii) if territories are inherited, the mechanism of density regulation is crucial in determining which factors promote cooperative breeding. If density dependence acts on the probability to obtain a free territory or on the survival of dispersers, variation in ecological constraints cannot explain variation in cooperative breeding. Lower adult mortality favours helping, not because it reduces the availability of free territories, but because it enhances the direct benefits of helpers. If density dependence acts on fecundity, lower probability of obtaining a free territory and lower survival of dispersers promote cooperative breeding. In this case, lower adult mortality works against the evolution of helping. We suggest that the difference between birds and social insects in the covariance between cooperative breeding and life-history traits is due to different mechanisms of density regulation that operate in these taxa, and we explain how natural selection on habitat choice might have caused these different mechanisms to operate.

Animals↗
PubMed2004

Reduced flocking by birds on islands with relaxed predation.

Adaptive hypotheses for the evolution of flocking in birds have usually focused on predation avoidance or foraging enhancement. It still remains unclear to what extent each factor has contributed to the evolution of flocking. If predation avoidance were the sole factor involved, flocking should not be prevalent when predation is relaxed. I examined flocking tendencies along with mean and maximum flock size in species living on islands where predation risk is either absent or negligible and then compared these results with matched counterparts on the mainland. The dataset consisted of 46 pairs of species from 22 different islands across the world. The tendency to flock was retained on islands in most species, but in pairs with dissimilar flocking tendencies, island species were less likely to flock. Mean and maximum flock size were smaller on islands than on the mainland. Potential confounding factors such as population density, nest predation, habitat type, food type and body mass failed to account for the results. The results suggest that predation is a significant factor in the evolution of flocking in birds. Nevertheless, predation and other factors, such as foraging enhancement, probably act together to maintain the trait in most species.

Animals↗
PubMed2002

Evolutionary transitions in parental care and live bearing in vertebrates.

We provide the first review of phylogenetic transitions in parental care and live bearing for a wide variety of vertebrates. This includes new analyses of both numbers of transitions and transition probabilities. These reveal numerous transitions by shorebirds and anurans toward uniparental care by either sex. Whereas most or all of the shorebird transitions were from biparental care, nearly all of the anuran transitions have been from no care, reflecting the prevalence of each form of care in basal lineages in each group. Teleost (bony) fishes are similar to anurans in displaying numerous transitions toward uniparental contributions by each sex. Whereas cichlid fishes have often evolved from biparental care to female care, other teleosts have usually switched from no care to male care. Taxa that have evolved exclusive male care without courtship-role reversal are characterized by male territoriality and low costs of care per brood. Males may therefore benefit from care through female preference of parental ability in these species. Primates show a high frequency of transitions from female care to biparental care, reflecting the prevalence of female care in basal lineages. In the numerous taxa that display live bearing by females, including teleosts, elasmobranchs, squamate reptiles and invertebrates, we find that live bearing has always evolved from a lack of care. Although the transition counts and probabilities will undoubtedly be refined as phylogenetic information and methodologies improve, the overall biases in these taxa should help to place adaptive hypotheses for the evolution of care into a stronger setting for understanding directions of change.

Amphibians↗
PubMed2025

Genomic signatures of innovation and selection in the extremotolerant yeast Kluyveromyces marxianus.

Extremophiles can be the product of millions of years of evolutionary engineering and refinement. The underlying mechanisms can be quite distinct from the ones operating at earlier stages of trait innovation. In this work, we have developed the compost yeast Kluyveromyces marxianus, which diverged from its closest relative >20 million years ago, as a model for interspecies comparative biology and genomics. We applied a battery of growth assays to species of the Kluyveromyces genus and found that K. marxianus outperformed its relatives in a battery of heat and chemical stress conditions. We then generated and analyzed genomes from across the genus, to find derived genetic features associated with, and potentially causal for, K. marxianus traits. We found robust expansions in gene families in the K. marxianus genome, most notably among genes annotated as transmembrane transporters and in metabolism. In molecular-evolution tests, we identified adaptive protein variants at hundreds of genes, among which plasma membrane transporters were over-represented. Together, these signals enable a model for the molecular mechanisms and evolutionary pressures underlying K. marxianus traits, including gains in transporter function mediating stress resistance, and metabolic variants contributing to its capacity for rapid growth in challenging conditions. Such oligogenic architectures may be the rule rather than the exception in phenotypes that have evolved over long timescales.

Journal Article↗
PubMed1980

Effects of Chromatic Adaptation on the Photochemical Apparatus of Photosynthesis in Porphyridium cruentum.

Cells of Porphyridium cruentum were grown in different colors of light which would be absorbed primarily by chlorophyll (Chl) (red and blue light) or by the phycobilisomes (green or two intensities of cool-white fluorescent light), and samples of these cells were frozen to -196 C for measurements of absorption and fluorescence emission spectra. Cells grown in the high intensity white light had least of all of the photosynthetic pigments, a higher ratio of carotenoid/Chl, but essentially the same ratio of phycobilin to Chl as cells grown in the low intensity white light. The ratio of photosystem II (PSII) to photosystem I (PSI) pigments was affected by light quality; the ratios of phycobilin to Chl and of short wavelength (PSII) Chl to long wavelength (PSI) Chl were both greater in the cells grown in red or blue light.Light quality also exerted a strong influence on the structural and functional organization of the photochemical apparatus. Data on the relative optical cross-sections of PSI and PSII as a function of excitation wavelength indicate that cells grown in light absorbed primarily by the phycobilisomes package a large fraction of their Chl into PSI (PSI Chl/PSII Chl approximately 20), whereas cells grown in light absorbed by Chl distribute their Chl much more equitably (PSI Chl/PSII Chl approximately 1.5). In both types of cells the phycobilisomes transfer their excitation energy predominantly to PSII Chl with little or no direct energy transfer to PSI, but the yield of energy transfer from PSII to PSI is approximately twice as large for cells grown in the phycobilin wavelengths of light. These differences in functional organization and energy distribution account for the physiological expressions of chromatic adaptation. The effects of chromatic adaptation on O(2) evolution can be predicted from our calculations of energy distribution between PSI and PSII for cells grown in the different colors of light.

Journal Article↗
PubMed2005

Using genome scans of DNA polymorphism to infer adaptive population divergence.

Elucidating the genetic basis of adaptive population divergence is a goal of central importance in evolutionary biology. In principle, it should be possible to identify chromosomal regions involved in adaptive divergence by screening genome-wide patterns of DNA polymorphism to detect the locus-specific signature of positive directional selection. In the case of spatially separated populations that inhabit different environments or sympatric populations that exploit different ecological niches, it is possible to identify loci that underlie divergently selected traits by comparing relative levels of differentiation among large numbers of unlinked markers. In this review I first address the question of whether diversifying selection on polygenic traits can be expected to produce predictable patterns of allelic variation at the underlying quantitative trait loci (QTL), and whether the locus-specific effects of selection can be reliably detected against the genome-wide backdrop of stochastic variability. I then review different approaches that have been developed to identify loci involved in adaptive population divergence and I discuss the relative merits of model-based approaches that rely on assumptions about population structure vs. model-free approaches that are based on empirical distributions of summary statistics. Finally, I consider the evolutionary and functional insights that might be gained by conducting genome scans for loci involved in adaptive population divergence.

Adaptation, Biological↗
PubMed2005

The biological limitations of transcriptomics in elucidating stress and stress responses.

Global analysis of mRNA abundance via genomic arrays (i.e. transcriptomics or transcriptional profiling) is one approach to finding the genes that matter to organisms undergoing environmental stress. In evolutionary analyses of stress, mRNA abundance is often invoked as a proxy for the protein activity that may underlie variation in fitness. To provoke discussion of the utility and sensible application of this valuable approach, this manuscript examines the adequacy of mRNA abundance as a proxy for protein activity, fitness and stress. Published work to date suggests that mRNA abundance typically provides little information on protein activity and fitness and cannot substitute for detailed functional and ecological analyses of candidate genes. While the transcriptional profile can be an exquisitely sensitive indicator of stress, simpler indicators will often suffice. In view of this outcome, transcriptomics should undergo careful cost-benefit analysis before investigators deploy it in studies of stress responses and their evolution.

Adaptation, Biological↗
PubMed1997

Role of immunity in maternal-infant HIV-1 transmission.

Factors influencing human immunodeficiency virus type 1 (HIV-1) mother-to-child transmission include both immunological and virological parameters: higher viral loads have been associated with clinical stage of HIV-1-infected individuals as well as higher risk of mother-to-child transmission. Furthermore, we have shown that transmitting mothers more frequently harbour HIV-1 isolates with rapid/high syncytium-inducing (SI) biological phenotype than non-transmitting mothers do. Genetically homogeneous virus populations have been found in HIV-1-infected children at birth, in contrast to the heterogeneous virus populations often found in their infected mothers. This observation suggests that a few virus variants are transmitted or initially are replicating in the child. By comparing the HIV-1 gp120 V3 region of sequentially obtained samples from infected children with samples obtained from their mothers at delivery we found, however, that multiple variants of HIV-1 with different outgrowth kinetics can be transmitted. In addition, we have obtained results indicating an impaired ability of the immune response to adapt to the sequence evolution of HIV-1 in transmitting mothers, as assessed by measuring serum reactivities to peptides representing selected yet closely related V3 sequences. By analysing the presence of antibodies in maternal serum at delivery, which neutralize autologous isolates as well as other primary virus isolates, we have indications that a protective immunity in HIV-1 mother-to-child transmission might exist. Immunotherapy has been assessed in infected adult individuals by passive immunization with a variety of HIV-1-specific antibody products. Data from these studies indicated a differential response to therapy according to the stage of the disease. Active vaccine strategies, including envelope glycoproteins, pursued so far in seronegative adult subjects have shown limitations because broadly neutralizing antibodies, such as can be found in infected individuals, have not been evoked. Further investigations are therefore needed to give support for the potential use of either passive and/or active immunization for the prevention of HIV-1 mother-to-child transmission.

Female↗
PubMed2025

Large Haplotypes Linked to Climate and Life History Variation in Divergent Lineages of Atlantic Salmon (Salmo salar).

Advances in sequencing are revealing that linked genomic architectures, enabling the evolution of co-adapted alleles at multiple loci, often shape complex phenotypes. Several recent studies have identified such architectures (e.g., chromosomal rearrangements and supergenes) contributing to adaptation or divergence across diverse species, from plants to mammals. Specifically, within Atlantic salmon (Salmo salar ), genomic studies are revealing large haplotypes and structural variants that may underpin local adaptation in the species. Using data from > 4000 individuals from 134 locations spanning the North Atlantic Ocean, we identify a large (~3 Mbp) genomic region on Ssa18 showing patterns of differentiation and linkage disequilibrium (LD) indicative of a large haplotype block containing three divergent haplotypes (herein A, B and C haplotypes). In Europe, haplotypes A and B were common, whereas A and C were more common within North America, suggesting a shared 'ancestral' A haplotype, with different continent-specific alternative haplotypes. Data support independent origins of divergent haplotypes in each continent, as well as signals of trans-oceanic introgression of haplotypes. Haplotype frequency is strongly associated with latitude, climate and life history (smolt age); however, the strength and direction of these relationships vary across continents. Overall, our analyses were consistent with other studies that identify chromosomal rearrangements; however, long-read sequence data did not find evidence of a structural variant, and instead an ancestral fusion may explain the formation and maintenance of the observed haplotypes. Our study contributes to ongoing efforts to understand the evolutionary role of linked genomic architecture in Atlantic salmon and its significance in salmonid diversification.

Climate Change↗
PubMed2025

Eco-Evolutionary Genomics Reveal Mountain Range-Specific Adaptation and Intraspecific Variation in Vulnerability to Climate Change of Alpine Endemics.

Alpine plants restricted to rocky habitats exhibit intraspecific diversification due to range fragmentation during Holocene warming, complicating predictions of their climate vulnerability. A lack of understanding of eco-evolutionary mechanisms driving their response to climate change results in ineffective conservation efforts. To uncover the genomic basis of their diversification and explain spatial patterns of their vulnerability, we combine landscape genomics and species distribution modelling. Our model, the Campanula lehmanniana complex, occurs in three distinct central Asian mountain ranges, considered both a biodiversity hotspot and a vascular plant diversity darkspot. Genome-environment association confirmed the adaptive basis of intraspecific diversification, driven by numerous loci of small effect. Genomic and ecological data indicate mountain range-specific climate sensitivity driven by altitude, temperature and precipitation. The cold-dry adapted group from Zeravshan-Hissar Mts will face niche decline but show a higher degree of preadaptation to future climate, while the temperate-humid group from Tian Shan shows an opposite response, with a higher risk of maladaptation despite predicted niche expansion. Maladapted populations at northern margins may require an influx of adaptive variation to cope with predicted changes. However, limited landscape connectivity between island-like habitats, combined with long migration distances required to minimise genotype-environment disruption, highlights the role of human-assisted migration in enabling evolutionary rescue. These results underscore the need to facilitate gene flow from pre- to maladapted populations and the importance of population-specific approaches to inform effective conservation strategies in heterogeneous mountain ecosystems. The results may be relevant to numerous Central Asian mountain species that show similar phylogeographic patterns.

Climate Change↗
PubMed2001

Individual contributions of mutant protease and reverse transcriptase to viral infectivity, replication, and protein maturation of antiretroviral drug-resistant human immunodeficiency virus type 1.

Human immunodeficiency virus type 1 (HIV-1) variants resistant to protease (PR) and reverse transcriptase (RT) inhibitors may display impaired infectivity and replication capacity. The individual contributions of mutated HIV-1 PR and RT to infectivity, replication, RT activity, and protein maturation (herein referred to as "fitness") in recombinant viruses were investigated by separately cloning PR, RT, and PR-RT cassettes from drug-resistant mutant viral isolates into the wild-type NL4-3 background. Both mutant PR and RT contributed to measurable deficits in fitness of viral constructs. In peripheral blood mononuclear cells, replication rates (means +/- standard deviations) of RT recombinants were 72.5% +/- 27.3% and replication rates of PR recombinants were 60.5% +/- 33.6% of the rates of NL4-3. PR mutant deficits were enhanced in CEM T cells, with relative replication rates of PR recombinants decreasing to 15.8% +/- 23.5% of NL4-3 replication rates. Cloning of the cognate RT improved fitness of some PR mutant clones. For a multidrug-resistant virus transmitted through sexual contact, RT constructs displayed a marked infectivity and replication deficit and diminished packaging of Pol proteins (RT content in virions diminished by 56.3% +/- 10.7%, and integrase content diminished by 23.3% +/- 18.4%), a novel mechanism for a decreased-fitness phenotype. Despite the identified impairment of recombinant clones, fitness of two of the three drug-resistant isolates was comparable to that of wild-type, susceptible viruses, suggestive of extensive compensation by genomic regions away from PR and RT. Only limited reversion of mutated positions to wild-type amino acids was observed for the native isolates over 100 viral replication cycles in the absence of drug selective pressure. These data underscore the complex relationship between PR and RT adaptive changes and viral evolution in antiretroviral drug-resistant HIV-1.

Animals↗