Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression

The exact mechanisms by which HIV overwhelms the immune system remain poorly understood. Among the several explanations of HIV disease progression, most include adaptation of the viral genome to the host environment as a causal factor. Therefore, quantifying the rate and pattern of adaptive evolution within infected patients is critical to understanding the development of AIDS. Using sequence data from infected individuals sampled at multiple time points, I estimate the within-host adaptation rate of the HIV-1 env gene for viral populations from 50 different patients. I find that, averaging across patients, one adaptive substitution occurs every 3.3 months. Also, one adaptive mutation is driven to a high frequency (>50% but <100%) every 2.5 months. Taken together, such adaptive events occur once every 25 viral generations, which is the fastest adaptation rate ever recorded for a single protein-coding gene. Within the entire env gene, I estimate that a majority ( approximately 55%) of both nonsynonymous substitutions and high-frequency polymorphisms are adaptive. Further, in the C2-V5 region of env, I find that patients with longer asymptomatic periods have virus populations with higher adaptation rates, corroborating the notion that a broad, strong immune response against epitopes in the env gene product leads to longer asymptomatic periods. I conclude by discussing the distribution of nonsynonymous changes over the env gene.     

Interpopulation variation in a fish predator drives evolutionary divergence in prey in lakes

Ecological factors are known to cause evolutionary diversification. Recent work has shown that evolution in strongly interacting predator species has reciprocal impacts on ecosystems. These divergent impacts of predators may alter the selective landscape and cause the evolution of prey. Yet, this link between intraspecific variation and evolution is unexplored. We compared the life history of a species of zooplankton (Daphnia ambigua) from lakes in New England in which the dominant planktivorous predator, the alewife (Alosa pseudoharengus), differs in feeding traits and migratory behaviour. Anadromous alewife (seasonal migrants) exhibit larger gapes, gill-raker spacing and target larger prey than landlocked alewife (year-round freshwater resident). In 'anadromous' lakes, Daphnia are abundant in the spring but extirpated by alewife predation in summer. Daphnia are rare year-round in 'landlocked' lakes. We show that Daphnia from lakes with anadromous alewife grew faster, matured earlier but at the same size and produced more offspring than Daphnia from lakes with landlocked or no alewife across multiple temperature and resource treatments. Our results are inconsistent with a response to size-selective predation but are better explained as an adaptation to colder temperatures and shorter periods of development (countergradient variation) mediated by seasonal alewife predation.     

Rapid adaptive divergence between ecotypes of an aquatic isopod inferred from FST–QST analysis

Divergent natural selection is often thought to be the principal factor driving phenotypic differentiation between populations. We studied two ecotypes of the aquatic isopod Asellus aquaticus which have diverged in parallel in several Swedish lakes. In these lakes, isopods from reed belts along the shores colonized new stonewort stands in the centre of the lakes and rapid phenotypic changes in size and pigmentation followed after colonization. We investigated if selection was likely to be responsible for these observed phenotypic changes using indirect inferences of selection (F_ST–Q_ST analysis). Average Q_ST for seven quantitative traits were higher than the average F_ST between ecotypes for putatively neutral markers (AFLPs). This suggests that divergent natural selection has played an important role during this rapid diversification. In contrast, the average Q_ST between the different reed ecotype populations was not significantly different from the mean F_ST. Genetic drift could therefore not be excluded as an explanation for the minor differences between allopatric populations inhabiting the same source habitat. We complemented this traditional F_ST–Q_ST approach by comparing the F_ST distributions across all loci (n = 67–71) with the Q_ST for each of the seven traits. This analysis revealed that pigmentation traits had diverged to a greater extent and at higher evolutionary rates than size‐related morphological traits. In conclusion, this extended and detailed type of F_ST–Q_ST analysis provides a powerful method to infer adaptive phenotypic divergence between populations. However, indirect inferences about the operation of divergent selection should be analyzed on a per‐trait basis and complemented with detailed ecological information.     

Intron sequences of arginine kinase in an intertidal snail suggest an ecotype-specific selective sweep and a gene duplication

Many species with restricted gene flow repeatedly respond similarly to local selection pressures. To fully understand the genetic mechanisms behind this process, the phylogeographic history of the species (inferred from neutral markers) as well as the loci under selection need to be known. Here we sequenced an intron in the arginine kinase gene (Ark), which shows strong clinal variation between two locally adapted ecotypes of the flat periwinkle, Littorina fabalis. The ‘small-sheltered'' ecotype was almost fixed for one haplotype, H1, in populations on both sides of the North Sea, unlike the ‘large-moderately exposed ecotype'', which segregated for ten different haplotypes. This contrasts with neutral markers, where the two ecotypes are equally variable. H1 could have been driven to high frequency in an ancestral population and then repeatedly spread to sheltered habitats due to local selection pressures with the colonization of both sides of the North Sea, after the last glacial maximum (∼18 000 years ago). An alternative explanation is that a positively selected mutation, in or linked to Ark, arose after the range expansion and secondarily spread through sheltered populations throughout the distribution range, causing this ecotype to evolve in a concerted fashion. Also, we were able to sequence up to four haplotypes consistently from some individuals, suggesting a gene duplication in Ark.     

The role of meiofauna in the marine ecosystem: evolutionary considerations*

The meiobenthos are regarded as the first metazoans to appear on earth This paper considers some aspects of their role in the marine ecosystem over evolutionary time. It is speculatively suggested that they have had a profound influence on many structural and functional attributes of the marine ecosystem as we see it today, both in the benthic and pelagic realms. Certain features such as size spectra, the life-history characteristics of the macrobenthos, and the energetic balance between ecological compartments of the marine ecosystem are considered to result from evolution away from negative interactions with the meiobenthos.     

Dinoflagellate Evolution: Speculation and Evidence*†

SYNOPSIS. Nuclear features of dinoflagellates that were used originally to support the Mesocaryota concept are reviewed. The fibrillar diameter of dinoflagellate chromatin, low level of chromosomal basic proteins, membrane attachment of chromosomes and swirl pattern observed in sectioned chromosomes are features that support a prokaryotic affinity. The presence of repeated and highly complex DNA, a S-phase of DNA synthesis in the cell cycle, presence of basic proteins, and the reinterpretation of extranuclear microtubules as a spindle support the contention that dinoflagellates are eukaryotes. This combination of prokaryotic and eukaryotic features suggests that dinoflagellates are a geologically old group and that perhaps they diverged from the higher eukaryotic lineage before evolution of eukaryotic chromatin but after the evolution of repeated DNA. The 2 patterns of carotenoid composition exemplified by the presence of peridinin or fucoxanthin suggest separate origins of dinoflagellate plastids, perhaps by prokaryotic and eukaryotic capture. It is suggested that the species possessing fucoxanthin obtained their plastids by capture of photosynthetic eukaryotes. A new class and order, Syndiniophyceae and Syndiniales, are proposed for the dinoflagellates with low chromosome numbers, V-shaped chromosomes, chromosomes containing a sufficient quantity of basic proteins detectable histochemically, possession of centrioles associated with mitosis, intracellular parasitism as a mode of nutrition, and lack of a cellular covering containing plates. Ultrastructural and paleontologic evidence indicates that the thecate is more primitive than the nonthecate condition. The Prorocentrales are considered to be primitive and their thecal construction is reinterpreted as having epithecal and hypothecal regions surrounding a flagellar pore region containing 7 plates. Acritarchs resemble cysts of modern dinoflagellates in size, structure, and chemical composition except for the absence of a polygonal excystment aperture and lack of any indication of transverse and longitudinal flagellar grooves on the acritarchs. The suggestion that some acritarchs may have dinoflagellate affinities is supported by the occurrence of modern dinoflagellates (Prorocentrales) which lack a theca of numerous polygonal plates and lack transverse and longitudinal flagellar arrangement. The Prorocentrales, as opposed to the more typical Dinophyceae, perhaps represent the type of organism that produced some acritarchs.     

Design,synthesis, and conformational studies of the hGM‐CSF derived peptide (13–27)–Gly–(75–87)

An analogue of the human granulocyte–macrophage colony‐stimulating factor (hGM‐CSF), hGM‐CSF(13–27)–Gly–(75–87) was synthesized by solid phase methodology. This analogue was designed to comprise helices A and C of the native growth factor, linked by a glycine bridge. Helices A and C form half of a four‐helix bundle motif in the crystal structure of the native factor and are involved in the interaction with α‐ and β‐chains of the heterodimeric receptor. A conformational analysis of the synthetic analogue by CD, two‐dimensional nmr spectroscopy, and molecular dynamics calculations is reported. The analogue is in a random structure in water and assumes a partially α‐helical conformation in a 1 : 1 trifluoroethanol/water mixture. The helix content in this medium is ∼ 70%. By 2D‐nmr spectroscopy, two helical segments were identified in the sequences corresponding to helices A and C. In addition to medium‐ and short‐range NOESY connectivities, a long‐range cross peak was found between the Cβ proton of Val¹⁶ and NH proton of His⁸⁷ (using the numbering of the native protein). Experimentally derived interproton distances were used as restraints in molecular dynamics calculations, utilizing the x‐ray coordinates as the initial structure. The final structure is characterized by two helical segments in close spatial proximity, connected by a loop region. This structure is similar to that of the corresponding domain in the x‐ray structure of the native growth factor in which helices A and C are oriented in an antiparallel fashion. The N‐terminal residues Gly–Pro of helix C are involved in an irregular turn connecting the two helical segments. As a consequence, helix C is appreciably shifted and slightly rotated with respect to helix A compared to the x‐ray structure of the native growth factor. These small differences in the topology of the two helices could explain the lower biological activity of this analogue with respect to that of the native growth factor. © 1999 John Wiley & Sons, Inc. Biopoly 50: 545–554, 1999     

Strategic analysis in evolutionary genetics and the theory of games

This paper is written in memory of John Maynard Smith. In a brief survey it discusses essential aspects of how game theory in biology relates to its counterpart in economics, the major transition in game theory initiated by Maynard Smith, the discrepancies between genetic and phenotypic models in evolutionary biology, and a balanced way of reconciling these models. In addition, the paper discusses modern problems in understanding games at the genetic level using the examples of conflict between endosymbionts and their hosts, and the molecular interactions between parasites and the mammalian immune system.     

“Trace Metabolites”–Effect of High Concentrations on Leishmania tarentolae Promastigotes*

SYNOPSIS. Relatively high concentrations (10–100 μM) of chromate, selenate, and vanadate ions accelerated growth of Leishmania tarentolae in a chemically defined medium containing taurine as the sole sulfur source. These ions also enhanced the incorporation of [³⁵S]taurine label in whole cell, 10% trichloroacetic acid insoluble, and 10% trichloroacetic acid soluble cell fractions.     

Mountain birch under multiple stressors – heavy metal‐resistant populations co‐resistant to biotic stress but maladapted to abiotic stress

Stress adaptations often include a trade‐off of weakened performance in nonlocal conditions, resulting in divergent selection, and potentially, genetic differentiation and evolutionary adaptation. Results of a two‐phase (greenhouse and field) common garden experiment demonstrated adaptation of mountain birch (Betula pubescens subsp. czerepanovii) populations from industrially polluted areas of the Kola Peninsula, north‐western Russia, to heavy metals (HM), whereas no adaptations to wind or drought stress were detected in populations from wind‐exposed sites. HM‐adapted seedlings were maladapted to drought but less palatable (co‐resistant) to insect herbivores, even under background HM concentrations. The absence of adaptations to harsh microclimate and the generally high adaptive potential of mountain birch, a critical forest forming tree in subarctic Europe, need to be accounted for in models predicting consequences of human‐driven environmental changes, including the projected climate change.     

Sampling in ecology and evolution – bridging the gap between theory and practice

Sampling is a key issue for answering most ecological and evolutionary questions. The importance of developing a rigorous sampling design tailored to specific questions has already been discussed in the ecological and sampling literature and has provided useful tools and recommendations to sample and analyse ecological data. However, sampling issues are often difficult to overcome in ecological studies due to apparent inconsistencies between theory and practice, often leading to the implementation of simplified sampling designs that suffer from unknown biases. Moreover, we believe that classical sampling principles which are based on estimation of means and variances are insufficient to fully address many ecological questions that rely on estimating relationships between a response and a set of predictor variables over time and space. Our objective is thus to highlight the importance of selecting an appropriate sampling space and an appropriate sampling design. We also emphasize the importance of using prior knowledge of the study system to estimate models or complex parameters and thus better understand ecological patterns and processes generating these patterns. Using a semi‐virtual simulation study as an illustration we reveal how the selection of the space (e.g. geographic, climatic), in which the sampling is designed, influences the patterns that can be ultimately detected. We also demonstrate the inefficiency of common sampling designs to reveal response curves between ecological variables and climatic gradients. Further, we show that response‐surface methodology, which has rarely been used in ecology, is much more efficient than more traditional methods. Finally, we discuss the use of prior knowledge, simulation studies and model‐based designs in defining appropriate sampling designs. We conclude by a call for development of methods to unbiasedly estimate nonlinear ecologically relevant parameters, in order to make inferences while fulfilling requirements of both sampling theory and field work logistics.     

Local adaptation,evolutionary potential and host–parasite coevolution: interactions between migration,mutation, population size and generation time

Local adaptation of parasites to their sympatric hosts has been investigated on different biological systems through reciprocal transplant experiments. Most of these studies revealed a local adaptation of the parasite. In several cases, however, parasites were found to be locally maladapted or neither adapted nor maladapted. In the present paper, we try to determine the causes of such variability in these results. We analyse a host–parasite metapopulation model and study the effect of several factors on the emergence of local adaptation: population sizes, mutation rates and migration rates for both the host and the parasite, and parasite generation time. We show that all these factors may act on local adaptation through their effects on the evolutionary potential of each species. In particular, we find that higher numbers of mutants or migrants do, in general, promote local adaptation. Interestingly, shorter parasite generation time does not always favour parasite local adaptation. When genetic variability is limiting, shorter generation time, via an increase of the strength of selection, decreases the capacity of the parasite to adapt to an evolving host.     

Roughness perception in tactile channels: Evidence for an opponent process in the sense of touch

Abstract

Magnitude estimates of the tactile roughness of raised-dot surfaces revealed that perceived overall roughness, defined as the combination of the perceived roughness of the dot pattern and the perceived roughness of the individual dots in the pattern, is an inverted U-shaped function of dot spacing, reaching a maximum at approximately 3.0?mm of dot separation. The hypothesis that Pacinian corpuscles are involved in roughness perception has been supported by the finding that selective adaptation of the Pacinian corpuscle (PC) channel with a 250-Hz stimulus at 20-dB SL results in a decrease in the perceived overall roughness of the raised-dot surface at the fingertip. The effect of PC channel adaptation on perceived overall roughness was attributable entirely to a reduction in the perceived roughness of the individual raised dots; PC adaptation had no effect on the perceived roughness of the raised-dot pattern. Selective adaptation of the slowly adapting type I (SA I) channel with a 5-Hz stimulus at 20-dB SL had the opposite effect of PC channel adaptation and resulted in an increase in the perceived roughness of the individual raised dots, and consequently the perceived overall roughness of the raised-dot surface. As was the case with PC channel adaptation, SA I channel adaptation had no effect on the perceived roughness of the pattern. Adaptation with a compound adapting stimulus containing 5- and 250-Hz components at 20-dB SL had no effect on perceived overall roughness, which suggests that the PC and SA I channels operate antagonistically in an opponent-process fashion in the perception of the microstructure of a textured surface. Neither PC adaptation nor SA I adaptation affected perceived pattern roughness, which suggests that pattern roughness is coded by relative rather than by absolute spatial variation in firing rate.     

The nut-crackers – a new theory of the adaptations of the Ramapithecinae

Molar enamel is thicker among frugivorous extant Old World monkeys and apes than among their folivorous close relatives. Furthermore, species that have the thickest molar enamel reportedly eat fruits, seeds, and nuts that are so hard that they cannot be broken by their sympatric thinner-enameled relatives. Species with relatively thick enamel show no tendency toward a terrestrial feeding pattern. Members of the Ramapithecinae, the stock which probably gave rise to Pliocene-Recent hominids, had very thick molar enamel. This suggests that they ate hard seeds, nuts, and fruits previously available only to arboreal rodents and forest-floor pigs. There is no reason to believe that these anatomical features had to evolve in non-rain-forest environments, as others have argued.