Genomic adaptation to acidic environment: evidence from Helicobacter pylori

The origin of new functions is fundamental in understanding evolution, and three processes known as adaptation, preadaptation, and exaptation have been proposed as possible evolutionary pathways leading to the origin of new functions. Here we examine the origin of an acid resistance mechanism in the mammalian gastric pathogen Helicobacter pylori, with reference to these three evolutionary pathways. The mechanism involved is that H. pylori, when exposed to the acidic environment in mammalian stomach, restricts the acute proton entry across its membrane by its increased usage of positively charged amino acids in the inner and outer membrane proteins. The results of our comparative genomic analysis between H. pylori, the two closely related species Helicobacter hepaticus and Campylobacter jejuni, and other relevant proteobacterial species are incompatible with the hypotheses invoking preadaptation or exaptation. The acid resistance mechanism most likely arose by selection favoring an increased usage of positively charged lysine in membrane proteins.     

Hearing in the Asian honeybeesApis dorsata andApis florea

Summary In the dance language of the western honeybee,Apis mellifera, airborne near field sound signals and a sense of hearing are used to communicate the locations of food sources. In the Asian honeybeeApis dorsata similar acoustical signals have been found recently, whereasApis florea does not emit dance sounds to transfer information about the location of food sources. The aim of the present study was to investigate the sense of hearing in these two species. Operant conditioning experiments reveal that both species are able to detect such near field sounds. The results support the hypothesis of acoustical communication inApis dorsata. The auditory sense ofApis florea, which does not use acoustical signals in the dance language, is discussed as a preadaptation for the evolution of an acoustical dance communication in ancestral honeybees.     

THE INFLUENCE OF LIGHT ADAPTATION ON SUBSEQUENT DARK ADAPTATION OF THE EYE

The course of dark adaptation of the human eye varies with the intensity used for the light adaptation which precedes it. Preadaptation to intensities below 200 photons is followed only by rod adaptation, while preadaptation to intensities above 4000 photons is followed first by cone adaptation and then by rod adaptation. With increasing intensities of preadaptation, cone dark adaptation remains essentially the same in form, but covers an increasing range of threshold intensities. At the highest preadaptation the range of the subsequent cone dark adaptation covers more than 3 log units. Rod dark adaptation appears in two types—a rapid and a delayed. The rapid rod dark adaptation is evident after preadaptations to low intensities corresponding to those usually associated with rod function. The delayed rod dark adaptation shows up only after preadaptation to intensities which are hundreds of times higher than those which produce the maximal function of the rods in flicker, intensity discrimination, and visual acuity. The delayed form remains essentially constant in shape following different intensities of preadaptation. However, its time of appearance increases with the preadaptation intensity; after the highest preadaptation, it appears only after 12 or 13 minutes in the dark. These two modes of rod dark adaptation are probably the expression of two methods of formation of visual purple in the rods after its bleaching by the preadaptation lights.     

The role of preadaptation,propagule pressure and competition in the colonization of new habitats

To successfully colonize new habitats, organisms not only need to gain access to it, they also need to cope with the selective pressures imposed by the local biotic and abiotic conditions. The number of immigrants, the preadaptation to the local habitat and the presence of competitors are important factors determining the success of colonization. Here, using two experimental set-ups, we studied the effect of interspecific competition in combination with propagule pressure and preadaptation on the colonization success of new habitats. Our model system consisted of tomato plants (the novel habitat), the two-spotted spider mite Tetranychus urticae as our focal species and the red spider mite Tetranychus evansi as a competitor. Our results show that propagule pressure and preadaptation positively affect colonization success. More successful populations reach larger final population sizes either by having higher per capita growth rates (due to preadaptation effects) or by starting a population with a larger number of individuals. Although populations are more successful colonizing non-competitive environments than competitive ones, propagule pressure and preadaptation counteract the negative effects of competition, promoting colonization success. Our study shows the importance of propagule pressure and preadaptation for successful colonization of new habitats by providing the ability to cope with both the exigencies of new environments and the community context.     

Hominid brain evolution: two conceptions of science.

This paper re-examines the repeatedly-offered hypothesis (Fialkowski 1978, 1986, 1987, 1988) that hominid brain expansion was largely a side effect of evolutionary response to increased heat stress under conditions of primitive hunting, and resulted in a preadaptation to enhanced cognitive abilities. Fialkowski's hypothesis, previously shown to be based on data that are seriously inaccurate, continues to be presented in a manner that precludes testing. Consequently, however interesting these ideas may be, they are beyond the conventional domain of anthropology as a legitimate subdiscipline of modern science.     

Does It Make Sense to Restore Wildland Fire in Changing Climate?

Forest restoration guided by historical reference conditions of fire regime, forest structure, and composition has been increasingly and successfully applied in fire‐adapted forests of western North America. But because climate change is expected to alter vegetation distributions and foster severe disturbances, does it make sense to restore the ecological role of wildland fire through management burning and related activities such as tree thinning? I suggest that some site‐ and date‐specific historical conditions may be less relevant, but reference conditions in the broad sense are still useful. Reference conditions encompass not only the recent past but also evolutionary history, reflecting the role of fire as a selective force over millennia. Taking a long‐term functional view of historical reference conditions as the result of evolutionary processes can provide insights into past forest adaptations and migrations under various climates. As future climates change, historical reference data from lower, southerly, and drier sites may be useful in places that are higher, northerly, and currently wetter. Almost all models suggest that the future will have substantial increases in wildfire occurrence, but prior to recent human‐caused fire exclusion, fire‐adapted pine forests of western North America were among the most frequently burned in the world. Restoration of patterns of burning and fuels/forest structure that reasonably emulate historical conditions prior to fire exclusion is consistent with reducing the susceptibility of these ecosystems to catastrophic loss. Priorities may include fire and thinning treatments of upper elevation ecotones to facilitate forest migration, whereas vulnerable low‐elevation forests may merit less management investment.     

In What Sense Does ‘Nothing Make Sense Except in the Light of Evolution’?

Dobzhansky argued that biology only makes sense if life on earth has a shared history. But his dictum is often reinterpreted to mean that biology only makes sense in the light of adaptation. Some philosophers of science have argued in this spirit that all work in 'proximal' biosciences such as anatomy, physiology and molecular biology must be framed, at least implicitly, by the selection histories of the organisms under study. Others have denied this and have proposed non-evolutionary ways in which biologists can frame these investigations. This paper argues that an evolutionary perspective is indeed necessary, but that it must be a forward-looking perspective informed by a general understanding of the evolutionary process, not a backward-looking perspective informed by the specific evolutionary history of the species being studied. Interestingly, it turns out that there are aspects of proximal biology that even a creationist cannot study except in the light of a theory of their effect on future evolution.     

Rules of engagement: defining bacterial communication

Microbiologists often describe communication as occurring within and between bacterial species and even across the prokaryote-eukaryote divide. In a strictly evolutionary sense, however, communication should occur only rarely between unrelated organisms. Clearly, the microbiological and evolutionary definitions and standards for what qualifies as communication widely differ. In microbiology, the term "communication" is often used to denote any interaction between two organisms. Advancement in knowledge hinges on precise language and conceptual distinctions when introducing new scientific ideas. While terminology exists for describing interactions which are not true communication, excessive preoccupation with semantics may impede progress. Umbrella terms such as 'communication' are useful, but additional insight can be gained by understanding the fitness consequences and adaptive significance of behaviors observed in multispecies communities.     

Ecological niche modelling as an exploratory tool for identifying species limits: an example based on Mexican muroid rodents

Niche conservatism theory suggests that recently diverged sister species share the same ecological niche. However, if the ecological niche evolves as part of the speciation process, the ecological pattern could be useful for recognizing cryptic species. In a broad sense systematists agree that the niche characters could be used for species differentiation. However, to date such characters have been ignored. We used the genetic algorithm for rule‐set production for modelling the ecological niche as a means of inferring ecological divergence in allopatric populations of muroid rodents for which taxonomic identity is uncertain. Our results show that niche differentiation is significant in most of the identified phylogroups. The differentiation is likely associated with natural evolutionary units, which can be identified by applying species concepts based on phylogenetic and ecological patterns (e.g. phylogenetic, cohesive, evolutionary). Even so, the role of the niche partition within phylogenetic reconstruction may be a limited one.     

The theory of increasing autonomy in evolution: a proposal for understanding macroevolutionary innovations

Attempts to explain the origin of macroevolutionary innovations have been only partially successful. Here it is proposed that the patterns of major evolutionary transitions have to be understood first, before it is possible to further analyse the forces behind the process. The hypothesis is that major evolutionary innovations are characterized by an increase in organismal autonomy, in the sense of emancipation from the environment. After a brief overview of the literature on this subject, increasing autonomy is defined as the evolutionary shift in the individual system–environment relationship, such that the direct influences of the environment are gradually reduced and a stabilization of self-referential, intrinsic functions within the system is generated. This is described as relative autonomy because numerous interconnections with the environment and dependencies upon it are retained. Features of increasing autonomy are spatial separations, an increase in homeostatic functions and in body size, internalizations and an increase in physiological and behavioral flexibility. It is described how these features are present in different combinations in the major evolutionary transitions of metazoans and, consequently, how they should be taken into consideration when evolutionary innovations are studied. The hypothesis contributes to a reconsideration of the relationship between organisms and their environment.     

Evolutionary psychiatry: foundations,progress and challenges

Evolutionary biology provides a crucial foundation for medicine and behavioral science that has been missing from psychiatry. Its absence helps to explain slow progress; its advent promises major advances. Instead of offering a new kind of treatment, evolutionary psychiatry provides a scientific foundation useful for all kinds of treatment. It expands the search for causes from mechanistic explanations for disease in some individuals to evolutionary explanations for traits that make all members of a species vulnerable to disease. For instance, capacities for symptoms such as pain, cough, anxiety and low mood are universal because they are useful in certain situations. Failing to recognize the utility of anxiety and low mood is at the root of many problems in psychiatry. Determining if an emotion is normal and if it is useful requires understanding an individual's life situation. Conducting a review of social systems, parallel to the review of systems in the rest of medicine, can help achieve that understanding. Coping with substance abuse is advanced by acknowledging how substances available in modern environments hijack chemically mediated learning mechanisms. Understanding why eating spirals out of control in modern environments is aided by recognizing the motivations for caloric restriction and how it arouses famine protection mechanisms that induce binge eating. Finally, explaining the persistence of alleles that cause serious mental disorders requires evolutionary explanations of why some systems are intrinsically vulnerable to failure. The thrill of finding functions for apparent diseases is evolutionary psychiatry's greatest strength and weakness. Recognizing bad feelings as evolved adaptations corrects psychiatry's pervasive mistake of viewing all symptoms as if they were disease manifestations. However, viewing diseases such as panic disorder, melancholia and schizophrenia as if they are adaptations is an equally serious mistake in evolutionary psychiatry. Progress will come from framing and testing specific hypotheses about why natural selection left us vulnerable to mental disorders. The efforts of many people over many years will be needed before we will know if evolutionary biology can provide a new paradigm for understanding and treating mental disorders.     

Convergent evolution of insect hearing organs from a preadaptive structure

Flies of the taxon Emblemasomatini (Sarcophagidae: Diptera) independently evolved an ear with the same anatomy and location as the Ormiini (Tachinidae: Diptera). Both ears represent a first case of convergent evolution of homologous insect ears, which raises the question for a preadaptation. Physiological and anatomical data indicate a preadaptive-sound-insensitive, but vibration-sensitive scolopidial chordotonal organ in non-hearing flies. As selective pressure for the evolutionary transformation from a vibration receiver into a sound receiver, fast and precise cues for the localization and detection of the sound producing hosts can be presumed.     

The evolution of recombination under domestication: a test of two hypotheses

The successful domestication of wild plants has been one of the most important human accomplishments of the last 10,000 yr. Though our empirical knowledge of the genetic mechanisms of plant domestication is still relatively limited, there exists a large body of theory that offers a host of hypotheses on the genetics of domestication. Two of these that have not been addressed concern the role of recombination in the process of domestication. The first predicts an increase in recombination rate through domestication, while the second argues that recombination rate should serve as a preadaptation to domestication. This study makes use of data on chiasma frequencies available from almost a century of plant cytogenetical literature to test these two hypotheses. The results support the hypothesis that domestication selects for an increase in recombination, and in rejecting the preadaptation hypothesis, they suggest directions for future research into the possibility of preadaptation to domestication.     

The evolution and functions of laughter and humor: a synthetic approach

A number of recent hypotheses have attempted to explain the ultimate evolutionary origins of laughter and humor. However most of these have lacked breadth in their evolutionary frameworks while neglecting the empirical existence of two distinct types of laughter--Duchenne and non-Duchenne--and the implications of this distinction for the evolution of laughter as a signal. Most of these hypotheses have also been proposed in relative isolation of each other and remain disjointed from the relevant empirical literature. Here we attempt to remedy these shortcomings through a synthesis of previous laughter and humor research followed by (i) a reevaluation of this research in light of theory and data from several relevant disciplines, and (ii) the proposal of a synthetic evolutionary framework that takes into account phylogeny and history as well as proximate mechanisms and adaptive significance. We consider laughter to have been a preadaptation that was gradually elaborated and co-opted through both biological and cultural evolution. We hypothesize that Duchenne laughter became fully ritualized in early hominids between 4 and 2 mya as a medium for playful emotional contagion. This mechanism would have coupled the emotions of small hominid groups and promoted resource-building social play during the fleeting periods of safety and satiation that characterized early bipedal life. We further postulate that a generalized class of nonserious social incongruity would have been a reliable indicator of such safe times and thereby came to be a potent distal elicitor of laughter and playful emotion. This class of stimuli had its origins in primate social play and was the foundation for formal human humor. Within this framework, Duchenne laughter and protohumor were well established in the hominid biobehavioral repertoire when more cognitively sophisticated traits evolved in the hominid line between 2 mya and the present. The prior existence of laughter and humor allowed them to be co-opted for numerous novel functions, and it is from this process that non-Duchenne laughter and the "dark side" of laughter emerged. This perspective organizes the diversified forms and functions that characterize laughter and humor today and clarifies when and how laughter and humor evolved during the course of human evolution.     

A phylogenetic comparative study of preadaptation for invasiveness in the genus <Emphasis Type="Italic">Silene</Emphasis> (Caryophyllaceae)

The role of preadaptation in ecology and evolution is determined by how the traits evolved by a species in one environment allow it to be successful in novel environments. This concept bears directly on modern biological invasions, as species are introduced to new locations beyond their historical borders. In this study, we used a phylogenetically-controlled analysis of the flowering plant genus Silene (Caryophyllaceae) to show that native geographic range size, along with a suite of life history traits affecting plant growth and reproduction, have preadapted some species for the invasion of new ranges. Using a path analytic approach, we further show that some of the covariance between life history traits and invasiveness is indirect, caused by mutual associations with native range size. Specifically, we found that reproductive traits such as the number of flowers per inflorescence and length of the flowering season directly preadapt species for invasion, while plant height is indirectly associated with invasion through a correlation with native range size. Other traits such as ovule number and leaf size are both directly and indirectly associated with invasion success. Our results reveal the importance of accounting for correlations among plant traits and geographic range size when predicting preadaptation for invasiveness. We also highlight that the traits predictive of invasion success among species of Silene are often those found to be rapidly evolving within introduced populations, suggesting common forces of selection operating at these different biological scales of organization during invasion.     

Climate‐driven build‐up of temporal isolation within a recently formed avian hybrid zone

Divergence in the onset of reproduction can act as an important source of reproductive isolation (i.e., allochronic isolation) between co‐occurring young species, but evidence for the evolutionary processes leading to such divergence is often indirect. While advancing spring seasons strongly affect the onset of reproduction in many taxa, it remains largely unexplored whether contemporary spring advancement directly affects allochronic isolation between young species. We examined how increasing spring temperatures affected onset of reproduction and thereby hybridization between pied and collared flycatchers (Ficedula spp.) across habitat types in a young secondary contact zone. We found that both species have advanced their timing of breeding in 14 years. However, selection on pied flycatchers to breed earlier was weaker, resulting in a slower response to advancing springs compared to collared flycatchers and thereby build‐up of allochronic isolation between the species. We argue that a preadaptation to a broader niche use (diet) of pied flycatchers explains the slower response to raising spring temperature, but that reduced risk to hybridize may contribute to further divergence in the onset of breeding in the future. Our results show that minor differences in the response to environmental change of co‐occurring closely related species can quickly cause allochronic isolation.     

The extended evolutionary synthesis and human origins: Archaeological perspectives

Recent developments in evolutionary biology have led to a call for an extension of standard evolutionary theory, with its emphasis on processes such as selection and drift, into a much larger theoretical framework that includes processes such as niche construction, developmental plasticity, inclusive inheritance, and developmental bias. Skeptics argue that these processes are already subsumed within the standard theory and thus an extension is not required. Here, we outline what this evolutionary “rethink” might mean for the study of human origins. Specifically, can paleoanthropologists benefit from an extended theoretical toolkit? The papers in this special issue suggest it can be useful but may not be necessary, depending on the kinds of questions that are being asked.     

Bioaltruism reconsidered

Altruistic behavior is often regarded as sociobiology's most central theoretical problem, but is it? Altruism in biology, bioaltruism, has many meanings, which can be grouped into two categories. The first I will callcommon bioaltruism. It is primarily of ethological relevance. The second,evolutionary bioaltruism, is a special category in evolutionary respects in that it may indeed pose a problem for evolutionary theory. These categories are logically independent. Moreover, both of them are logically different from altruism in its everyday psychological or moral sense. Sociobiological examples of bioaltruistic behavior concern bioaltruism in the first sense only, so the theoretical problem ‘altruism’ is supposed to pose, is indeed nothing but a theoretical problem and the bioaltruism that actually occurs has no evolutionary relevance. Nevertheless, evolutionary theory is relevant to our understanding of the possibility of common bioaltruism, and that possibility — even though bioaltruism is conceptually different from ethical altruism — is relevant for ethicists: it sheds light on what we can ask people to do or not to do.     

There must be a prokaryote somewhere: microbiology''s search for itself.

While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology's relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows.     

The evolution of moral progress and biomedical moral enhancement

In The Evolution of Moral Progress Allen Buchanan and Russell Powell advance an evolutionary explanation of moral progress by morality becoming more ‘inclusivist’. We are prepared to accept this explanation as far as it goes, but argue that it fails to explain how morality can become inclusivist in the fuller sense they intend. In fact, it even rules out inclusivism in their intended sense of moral progress, since they believe that human altruism and prosocial attitudes are essentially parochial. We also respond to their charge that the possibility of moral enhancement by biomedical means that we have defended in numerous publications assumes that moral attitudes are biologically hard‐wired to an extent that implies that they are resilient to the influence of cognitive or cultural factors. Quite the contrary, we think they are more open to such influence than they seem to do.