The Evolution of Sex: Domains and Explanatory Pluralism

The evolution of sexual reproduction is a striking case of explanatory pluralism, meaning that one needs to refer to more than one explanation in order to adequately account for it. I develop the concept a domain of phenomena in order to analysis this pluralism. Pluralism exists when a phenomenon can be included in more that one homogeneous domain or in a heterogeneous domain. I argue that in some cases domain partitioning can be used to decrease pluralism, but that in the case of sex domains are overlapping and interconnecting, or in other words bear an orthogonal relationship to one another, and hence cannot be partitioned in such a way as to eliminate pluralism.     

基因的推理设计与改造—体外分子进化的捷径

体外分子进化是改造基因、获得新的功能蛋白质重要手段之一,已经取得了令人瞩目的成就。推理设计是利用序列和结构的比较信息创造新的基因和蛋白质,是研究改造蛋白质功能的有效方法。文章着重介绍了基因推理设计在基因体外分子进化中的应用,从简单实用的基因密码偏爱设计,结合多个不同性状相关功能基因信息的基因推理设计,关键功能区域的简并引物设计,位点直接蛋白质重组4个方面进行描述,并综述了该方法近年来的应用。     

Beyond the phenotypic gambit: molecular behavioural ecology and the evolution of genetic architecture

Most studies of behaviour examine traits whose proximate causes include sensory input and neural decision-making, but conflict and collaboration in biological systems began long before brains or sensory systems evolved. Many behaviours result from non-neural mechanisms such as direct physical contact between recognition proteins or modifications of development that coincide with altered behaviour. These simple molecular mechanisms form the basis of important biological functions and can enact organismal interactions that are as subtle, strategic and interesting as any. The genetic changes that underlie divergent molecular behaviours are often targets of selection, indicating that their functional variation has important fitness consequences. These behaviours evolve by discrete units of quantifiable phenotypic effect (amino acid and regulatory mutations, often by successive mutations of the same gene), so the role of selection in shaping evolutionary change can be evaluated on the scale at which heritable phenotypic variation originates. We describe experimental strategies for finding genes that underlie biochemical and developmental alterations of behaviour, survey the existing literature highlighting cases where the simplicity of molecular behaviours has allowed insight to the evolutionary process and discuss the utility of a genetic knowledge of the sources and spectrum of phenotypic variation for a deeper understanding of how genetic and phenotypic architectures evolve.     

Beyond simple adaptation: Incorporating other evolutionary processes and concepts into eco-evolutionary dynamics

Studies of eco-evolutionary dynamics have integrated evolution with ecological processes at multiple scales (populations, communities and ecosystems) and with multiple interspecific interactions (antagonistic, mutualistic and competitive). However, evolution has often been conceptualised as a simple process: short-term directional adaptation that increases population growth. Here we argue that diverse other evolutionary processes, well studied in population genetics and evolutionary ecology, should also be considered to explore the full spectrum of feedback between ecological and evolutionary processes. Relevant but underappreciated processes include (1) drift and mutation, (2) disruptive selection causing lineage diversification or speciation reversal and (3) evolution driven by relative fitness differences that may decrease population growth. Because eco-evolutionary dynamics have often been studied by population and community ecologists, it will be important to incorporate a variety of concepts in population genetics and evolutionary ecology to better understand and predict eco-evolutionary dynamics in nature.     

Evolution of brain size and juvenile periods in primates

This paper assesses selective pressures that shaped primate life histories, with particular attention to the evolution of longer juvenile periods and increased brain sizes. We evaluate the effects of social complexity (as indexed by group size) and foraging complexity (as indexed by percent fruit and seeds in the diet) on the length of the juvenile period, brain size, and brain ratios (neocortex and executive brain ratios) while controlling for positive covariance among body size, life span, and home range. Results support strong components of diet, life span, and population density acting on juvenile periods and of home range acting on relative brain sizes. Social-complexity arguments for the evolution of primate intelligence are compelling given strong positive correlations between brain ratios and group size while controlling for potential confounding variables. We conclude that both social and ecological components acting at variable intensities in different primate clades are important for understanding variation in primate life histories.     

Pathogen burden,co‐infection and major histocompatibility complex variability in the European badger (Meles meles)

Pathogen‐mediated selection is thought to maintain the extreme diversity in the major histocompatibility complex (MHC) genes, operating through the heterozygote advantage, rare‐allele advantage and fluctuating selection mechanisms. Heterozygote advantage (i.e. recognizing and binding a wider range of antigens than homozygotes) is expected to be more detectable when multiple pathogens are considered simultaneously. Here, we test whether MHC diversity in a wild population of European badgers (Meles meles) is driven by pathogen‐mediated selection. We examined individual prevalence (infected or not), infection intensity and co‐infection of 13 pathogens from a range of taxa and examined their relationships with MHC class I and class II variability. This population has a variable, but relatively low, number of MHC alleles and is infected by a variety of naturally occurring pathogens, making it very suitable for the investigation of MHC–pathogen relationships. We found associations between pathogen infections and specific MHC haplotypes and alleles. Co‐infection status was not correlated with MHC heterozygosity, but there was evidence of heterozygote advantage against individual pathogen infections. This suggests that rare‐allele advantages and/or fluctuating selection, and heterozygote advantage are probably the selective forces shaping MHC diversity in this species. We show stronger evidence for MHC associations with infection intensity than for prevalence and conclude that examining both pathogen prevalence and infection intensity is important. Moreover, examination of a large number and diversity of pathogens, and both MHC class I and II genes (which have different functions), provide an improved understanding of the mechanisms driving MHC diversity.     

Evolution of taxonomic diversity in amphiaspids (Agnatha,Heterostraci: Amphiaspidiformes) and the causes of extinction in ecologically favorable conditions

Changes in the taxonomic composition of Early Devonian amphiaspids represented in Siberia by two assemblages (from the northwestern Siberian Platform and Taimyr) are analyzed. The study is performed at the generic level and represented by diagrams. Changes in the amphiaspid composition are compared with changes in the development of the Taimyr and platform paleobasins. It is shown that shifts in ecological conditions at the stages of extinction of amphiaspids occurred within the limits of changes of abiotic factors (depth, salinity, etc.) that are usual for heterostracans. The disappearance (extinction) of amphiaspids is attributable to the level of their morphological organization, which caused inefficient adaptations to the developing paleoecosystems. The disappearance (extinction) of groups resulting from inadequate vital adaptations to the changing structure of paleoecosystems is considered to be a general law of evolution.     

Animal migrations and parasitism: reciprocal effects within a unified framework

Migrations, i.e. the recurring, roundtrip movement of animals between distant and distinct habitats, occur among diverse metazoan taxa. Although traditionally linked to avoidance of food shortages, predators or harsh abiotic conditions, there is increasing evidence that parasites may have played a role in the evolution of migration. On the one hand, selective pressures from parasites can favour migratory strategies that allow either avoidance of infections or recovery from them. On the other hand, infected animals incur physiological costs that may limit their migratory abilities, affecting their speed, the timing of their departure or arrival, and/or their condition upon reaching their destination. During migration, reduced immunocompetence as well as exposure to different external conditions and parasite infective stages can influence infection dynamics. Here, we first explore whether parasites represent extra costs for their hosts during migration. We then review how infection dynamics and infection risk are affected by host migration, thereby considering parasites as both causes and consequences of migration. We also evaluate the comparative evidence testing the hypothesis that migratory species harbour a richer parasite fauna than their closest free-living relatives, finding general support for the hypothesis. Then we consider the implications of host migratory behaviour for parasite ecology and evolution, which have received much less attention. Parasites of migratory hosts may achieve much greater spatial dispersal than those of non-migratory hosts, expanding their geographical range, and providing more opportunities for host-switching. Exploiting migratory hosts also exerts pressures on the parasite to adapt its phenology and life-cycle duration, including the timing of major developmental, reproduction and transmission events. Natural selection may even favour parasites that manipulate their host's migratory strategy in ways that can enhance parasite transmission. Finally, we propose a simple integrated framework based on eco-evolutionary feedbacks to consider the reciprocal selection pressures acting on migratory hosts and their parasites. Host migratory strategies and parasite traits evolve in tandem, each acting on the other along two-way causal paths and feedback loops. Their likely adjustments to predicted climate change will be understood best from this coevolutionary perspective.     

Organic Selection: Proximate Environmental Effects on the Evolution of Morphology and Behaviour

Organic selection (the Baldwin Effect) by which an environmentally elicitedphenotypic adaptation comes under genotypic control following selectionwas proposed independently in 1896 by the psychologists James Baldwinand Conwy Lloyd Morgan and by the paleontologist Henry Fairfield Osborn.Modified forms of organic selection were proposed as autonomization bySchmalhausen in 1938, as genetic assimilation by Waddington in 1942, andas an explanation for evolution in changing environments or for speciationby Matsuda and West-Eberhard in the 1980s. Organic selection as amechanism mediating proximate environmental effects on the evolution ofmorphology and behaviour is the topic of this essay. Discussion includesthe context in which organic selection was proposed, Lamarckian or neo-Lamarckian implications of organic selection, Waddingtons experimentalstudies demonstrating the existence and efficacy of genetic assimilation,stabilizing selection and norms of reaction favoured by Schmalhausen, andMatsudas search for a mechanism of organic selection in endocrine changesand in heterochrony.     

Environmental Oxygen is a Key Modulator of Development and Evolution: From Molecules to Ecology

Oxygen is a key regulator of both development and homeostasis and a promising candidate to bridge the influence of the environment and the evolution of new traits. To clarify the various ways in which oxygen may modulate embryogenesis, its effects are reviewed at distinct organizational levels. First, the role of pathways that sense dioxygen levels and reactive oxygen species are reviewed. Then, the effects of microenvironmental oxygen on metabolism, stemness, and differentiation throughout embryogenesis are discussed. Last, the interplay between ecology and development are reexamined with a focus on the evolution of tetrapods, including during the emergence of a novel mechanism that shapes amniote limbs—interdigital cell death. Both genetic and environmental components work together during the formation of organisms, highlighting the importance of a multidisciplinary approach for understanding the evolution of new traits.     

Evolution of gall morphology and host-plant relationships in willow-feeding sawflies (Hymenoptera: Tenthredinidae)

Abstract.— There are over 200 species of nematine sawflies that induce galls on willows (Salix spp.). Most of the species are monoor oligophagous, and they can be separated into seven or eight different groups based on the type of gall that they induce. We studied the evolution of different gall types and host plant associations by reconstructing the phylogeny of five outgroup and 31 ingroup species using DNA sequence data from the mitochondrial cytochrome b gene. Maximum-parsimony and maximum-likelihood analyses resulted in essentially the same phylogeny with high support for important branches. The results show that: (1) the galling species probably form a monophyletic group; (2) true closed galls evolved only once, via leaf folders; (3) with the possible exception of leaf rollers, all gall type groups are mono- or paraphyletic; (4) similar gall types are closer on the phylogeny than would be expected by a random process; (5) there is an apparent evolutionary trend in galling site from the leaf edge towards the more central parts of the host plant; and (6) many willow species have been colonized several times, which excludes the possiblity of parallel cladogenesis between willows and the gallers; however, there are signs of restrictions in the evolution of host use. Many of the patterns in the evolutionary history of nematine gallers have also been observed in earlier studies on other insect gallers, indicating convergent evolution between the independent radiations.     

Environmental stress and the evolution of dioecy: Wurmbea dioica (Colchicaceae) in Western Australia

Stressful ecological conditions have been implicated in the evolution of separate sexes in plants. Gender dimorphic species are often found in drier habitats than their sexually monomorphic relatives, and gynodioecious populations appear closer to a dioecious state as resources, particularly water, become limiting. This pattern could result if dry conditions decrease the relative seed fitness of cosexual plants, allowing female plants to become established in monomorphic populations. We studied geographical variation in gender expression and biomass allocation among 12 monomorphic and dimorphic populations of Wurmbea dioica along a latitudinal precipitation gradient in southwestern Australia to provide insight into mechanisms by which aridity might favor transitions between sexual systems. Plants in monomorphic and dimorphic populations exhibited contrasting gender expression and patterns of biomass allocation in areas with different levels of precipitation. Among dimorphic populations, lower precipitation was associated with a higher frequency of female plants, and reduced allocation to female function by hermaphrodites during flowering. In contrast, stress conditions had no effect on female allocation at flowering in monomorphic populations. Across latitudes, unisexuals and cosexuals exhibited consistent differences in above ground traits, with cosexuals having larger leaves, taller stems and larger flowers. Although all plants were smaller under drier conditions, cosexuals decreased above ground allocation to vegetative and reproductive structures with decreasing latitude. In contrast, unisexuals increased allocation to reproduction in drier areas at the expense of below ground size. Aridity was associated with reduced flower size among all gender classes, but not with changes in flower number. These data do not support the hypothesis that resource limitation of female allocation in cosexual populations favors the establishment of gender dimorphism in W. dioica. Alternative hypotheses, involving higher selfing rates and enhanced survival of unisexuals relative to cosexuals under resource-limited conditions, are discussed as possible explanations for the origin of dioecy in W. dioica. This revised version was published online in August 2006 with corrections to the Cover Date.     

Evolution and medicine in undergraduate education: a prescription for all biology students

The interface between evolutionary biology and the biomedical sciences promises to advance understanding of the origins of genetic and infectious diseases in humans, potentially leading to improved medical diagnostics, therapies, and public health practices. The biomedical sciences also provide unparalleled examples for evolutionary biologists to explore. However, gaps persist between evolution and medicine, for historical reasons and because they are often perceived as having disparate goals. Evolutionary biologists have a role in building a bridge between the disciplines by presenting evolutionary biology in the context of human health and medical practice to undergraduates, including premedical and preprofessional students. We suggest that students will find medical examples of evolution engaging. By making the connections between evolution and medicine clear at the undergraduate level, the stage is set for future health providers and biomedical scientists to work productively in this synthetic area. Here, we frame key evolutionary concepts in terms of human health, so that biomedical examples may be more easily incorporated into evolution courses or more specialized courses on evolutionary medicine. Our goal is to aid in building the scientific foundation in evolutionary biology for all students, and to encourage evolutionary biologists to join in the integration of evolution and medicine.     

On the varied pattern of evolution of 2 fungal genomes: a critique of Hughes and Friedman

A number of statistical tests have been proposed to detect positive Darwinian selection affecting a few amino acid sites in a protein, exemplified by an excess of nonsynonymous nucleotide substitutions. These tests are often more powerful than pairwise sequence comparison, which averages synonymous (d(S)) and nonsynonymous (d(N)) rates over the whole gene. In a recent study, however, Hughes AL and Friedman R (2005. Variation in the pattern of synonymous and nonsynonymous difference between two fungal genomes. Mol Bio Evol. 22: 1320-1324) argue that d(S) and d(N) are expected to fluctuate along the sequence by chance and that an excess of nonsynonymous differences in individual codons is no evidence for positive selection. The authors compared codons in protein-coding genes from the genomes of 2 yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus. They calculated the proportions of synonymous and nonsynonymous differences per site (p(S) and p(N)) in every codon and discovered that p(N) is often greater than p(S) and that among some codons p(S) and p(N) are negatively correlated. The authors argued that these results invalidate previous tests of codons under positive selection. Here I discuss several errors of statistics in the analysis of Hughes and Friedman, including confusion of statistics with parameters, arbitrary data filtering, and derivation of hypotheses from data. I also apply likelihood ratio tests of positive selection to the yeast data and illustrate empirically that Hughes and Friedman's criticisms on such tests are not valid.     

Local adaptation and effect of host genotype on the rate of pathogen evolution: an experimental test in a plant pathosystem

Abstract Virulence is thought to be a driving force in host–pathogen coevolution. Theoretical models suggest that virulence is an unavoidable consequence of pathogens evolving towards a high rate of intrahost reproduction. These models predict a positive correlation between the reproductive fitness of a pathogen and its level of virulence. Theoretical models also suggest that the demography and genetic structure of a host population can influence the evolution of virulence. If evolution occurs faster in pathogen populations than in host populations, the predicted result is local adaptation of the pathogen population. In our studies, we used a combination of molecular and physiological markers to test these hypotheses in an agricultural system. We isolated five strains of the fungal pathogen Mycosphaerella graminicola from each of two wheat cultivars that differed in their level of resistance to this pathogen. Each of the 10 fungal strains had distinct genotypes as indicated by different DNA fingerprints. These fungal strains were re‐inoculated onto the same two host cultivars in a field experiment and their genotype frequencies were monitored over several generations of asexual reproduction. We also measured the virulence of these 10 fungal strains and correlated it to the reproductive fitness of each fungal strain. We found that host genotypes had a strong impact on the dynamics of the pathogen populations. The pathogen population collected from the moderately resistant cultivar Madsen showed greater stability, higher genotype diversity, and smaller selection coefficients than the pathogen populations collected from the susceptible cultivar Stephens or a mixture of the two host cultivars. The pathogen collection from the mixed host population was midway between the two pure lines for most parameters measured. Our results also revealed that the measures of reproductive fitness and virulence of a pathogen strain were not always correlated. The pathogen strains varied in their patterns of local adaptation, ranging from locally adapted to locally maladapted.