Environmental sensing by chromatin: an epigenetic contribution to evolutionary change

Chromatin structure and function are regulated by families of protein-modifying enzymes that are sensitive to a variety of metabolic and environmental agents. These enzymes, and proteins that read the modifications they maintain, constitute a system by which environmental agents, such as chemical toxins and dietary components, can directly regulate patterns of gene expression. This review describes this environmental sensing system from an evolutionary perspective. It is proposed that persistent environmentally-induced changes in gene expression patterns can cause changes in phenotype that are acted upon by natural selection, and that epigenetic processes can potentially play central roles in evolution.     

Backyard evolutionary biology: Investigating local flowers brings learning to life

Inquiry‐based learning allows students to actively engage in and appreciate the process of science. As college courses transition to online instruction in response to COVID‐19, incorporating inquiry‐based learning is all the more essential for student engagement. However, with the cancelation of in‐person laboratory courses, implementing inquiry can prove challenging for instructors. Here, I describe a case that exemplifies a strategy for inquiry‐based learning and can be adapted for use in various course modalities, from traditional face‐to‐face laboratory courses to asynchronous and synchronous online courses. I detail an assignment where students explore the developmental basis of morphological evolution. Flowers offer an excellent example to address this concept and are easy for students to access and describe. Students research local flowering plants, collect and dissect flower specimens to determine their whorl patterns, and generate hypotheses to explain the developmental genetic basis of the patterns identified. This task allows students to apply their scientific thinking skills, conduct guided exploration in nature, and connect their understanding of the developmental basis of evolutionary change to everyday life. Incorporating inquiry using readily available, tangible, tractable real‐world examples represents a pragmatic and effective model that can be applied in a variety of disciplines during and beyond COVID‐19.     

Gene bionetworks involved in the epigenetic transgenerational inheritance of altered mate preference: environmental epigenetics and evolutionary biology

Background

Mate preference behavior is an essential first step in sexual selection and is a critical determinant in evolutionary biology. Previously an environmental compound (the fungicide vinclozolin) was found to promote the epigenetic transgenerational inheritance of an altered sperm epigenome and modified mate preference characteristics for three generations after exposure of a gestating female.

Results

The current study investigated gene networks involved in various regions of the brain that correlated with the altered mate preference behavior in the male and female. Statistically significant correlations of gene clusters and modules were identified to associate with specific mate preference behaviors. This novel systems biology approach identified gene networks (bionetworks) involved in sex-specific mate preference behavior. Observations demonstrate the ability of environmental factors to promote the epigenetic transgenerational inheritance of this altered evolutionary biology determinant.

Conclusions

Combined observations elucidate the potential molecular control of mate preference behavior and suggests environmental epigenetics can have a role in evolutionary biology.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-377) contains supplementary material, which is available to authorized users.     

The evolutionary consequences of niche construction: a theoretical investigation using two-locus theory

This paper addresses the joint evolution of environment-altering (niche constructing) traits, and traits whose fitness depends on alterable sources of natural selection in environments. We explore the evolutionary consequences of this niche construction using a two-locus population genetic model. The novel conclusions are that niche construction can (1) cause evolutionary inertia and momentum, (2) lead to the fixation of otherwise deleterious alleles, (3) support stable polymorphisms where none are expected, (4) eliminate what would otherwise be stable polymorphisms, and (5) influence disequilibrium. The results suggest that the changes that organisms bring about in their niche can themselves be an important source of natural selection pressures, and imply that evolution may proceed in cycles of selection and niche construction.     

The causal pie model: an epidemiological method applied to evolutionary biology and ecology

A general concept for thinking about causality facilitates swift comprehension of results, and the vocabulary that belongs to the concept is instrumental in cross‐disciplinary communication. The causal pie model has fulfilled this role in epidemiology and could be of similar value in evolutionary biology and ecology. In the causal pie model, outcomes result from sufficient causes. Each sufficient cause is made up of a “causal pie” of “component causes”. Several different causal pies may exist for the same outcome. If and only if all component causes of a sufficient cause are present, that is, a causal pie is complete, does the outcome occur. The effect of a component cause hence depends on the presence of the other component causes that constitute some causal pie. Because all component causes are equally and fully causative for the outcome, the sum of causes for some outcome exceeds 100%. The causal pie model provides a way of thinking that maps into a number of recurrent themes in evolutionary biology and ecology: It charts when component causes have an effect and are subject to natural selection, and how component causes affect selection on other component causes; which partitions of outcomes with respect to causes are feasible and useful; and how to view the composition of a(n apparently homogeneous) population. The diversity of specific results that is directly understood from the causal pie model is a test for both the validity and the applicability of the model. The causal pie model provides a common language in which results across disciplines can be communicated and serves as a template along which future causal analyses can be made.     

Ramularia collo-cygni: the biology of an emerging pathogen of barley.

Ramularia collo-cygni is now recognized as an important pathogen of barley in Northern Europe and New Zealand. It induces necrotic spotting and premature leaf senescence, leading to loss of green leaf area in crops, and can result in substantial yield losses. The fungus produces a number of anthraquinone toxins called rubellins, which act as host nonspecific toxins with photodynamic activity. These toxins induce lipid peroxidation and are possibly the cause of the chlorosis and necrosis observed in leaves infected with R. collo-cygni. The fact that the fungus can remain latent in barley plants until flowering, coupled with its very slow growth in vitro, makes it difficult to detect in crops. As a result, the epidemiology of this pathogen remains poorly understood. However, the recent development of rapid and reliable PCR methods for specific detection of R. collo-cygni offers the prospect of increased understanding of its epidemiology and improved disease control.     

From information to understanding: the role of model organism databases in comparative and functional genomics

Data integration is key to functional and comparative genomics because integration allows diverse data types to be evaluated in new contexts. To achieve data integration in a scalable and sensible way, semantic standards are needed, both for naming things (standardized nomenclatures, use of key words) and also for knowledge representation. The Mouse Genome Informatics database and other model organism databases help to close the gap between information and understanding of biological processes because these resources enforce well-defined nomenclature and knowledge representation standards. Model organism databases have a critical role to play in ensuring that diverse kinds of data, especially genome-scale data sets and information, remain useful to the biological community in the long-term. The efforts of model organism database groups ensure not only that organism-specific data are integrated, curated and accessible but also that the information is structured in such a way that comparison of biological knowledge across model organisms is facilitated.     

呼吸内科重症监护室一起多重耐药鲍曼不动杆菌感染暴发的调查

目的及时发现医院感染暴发苗头,查找感染源,切断传播途径,最大限度减少医院感染发生。方法对2009年4月26～28日期间RICU发生的4例鲍曼不动杆菌感染病例进行聚集感染危险因素调查,采集标本进行目标菌检测,应用ERIC—PCR技术对聚集病例和散发病例菌株进行基因同源性分析,采取综合性防控措施进行医院感染具体干预。结果4例患者确定为医院感染病例,4例患者均有气管插管操作经历,3例患者环境卫生学检测存在耐药谱相同的鲍曼不动杆菌,ERIC—PCR分析4例患者检出的鲍曼不动杆菌具有基因同源性,确定为医院感染暴发。严格执行隔离防护措施和后续加强上呼吸机患者管理,未再出现聚集病例。结论医院感染暴发危及患者医疗安全,应用分子生物学分析手段可以促进医院感染防控措施的效果;加强上呼吸机患者的管理,加强手卫生的管理可以有效防控医院感染聚集暴发。     

The evolutionary effect of endemic infectious disease: Continuous models for an invariant pathogen

Continuous deterministic models are used to investigate the relationship between the epidemiology of endemic infectious disease and the genetics of natural selection in the host population when a specific genetic locus controls susceptibility to disease under a variety of circumstances. One locus, two allele genes are considered in the contexts of haploid and diploid host populations while the agent of infection is assumed to be invariant. It is found that polymorphic equilibria exist and are stable for certain parameter combinations in each of the cases studied. The equilibrium levels of gene frequencies and disease prevalence depend on both genetic and epidemic factors.     

Whole-organism studies of adhesion in pad-bearing lizards: creative evolutionary solutions to functional problems

Understanding the evolution of complex functional traits is a challenge for evolutionary physiology. Here we investigate the evolution of subdigital toepads in lizards, which have arisen independently at least three times, although with subtle anatomical differences. Some designs (anole, gecko) appear functionally equivalent, whereas other designs (skink) are inferior. The functional equivalence of geckos and anoles highlights the creative aspect of the evolutionary process in that these two groups have arrived at the same functional endpoint along very different trajectories. However, this functional equivalence does not result in equivalence for performance at whole-organism tasks (e.g., running uphill), as the evolution of behavior (e.g., toe-furling) has enabled geckos to be superior climbers than anoles. We also show that adaptive increases in the toepad size within a closely related lizard genus (Anolis) has resulted in concomitant evolution of enhanced clinging ability and increased perch heights. A third insight is that pad-bearing geckos are capable of carrying tremendous loads (up to 250% of body weight) up smooth surfaces, and that the toepad itself does not appear limiting. This comparative and whole-organism approach to lizard toepads underscores how organisms can evolve multiple solutions to evolutionary problems.     

The road to the Janiroidea: Comparative morphology and evolution of the asellote isopod crustaceans

This paper presents a new phylogenetic estimate of isopod crustaceans of the suborder Asellota with the aim of clarifying the evolution of the superfamily Janiroidea, a large and diverse group inhabiting all aqueous habitats. The phylogenetic analysis is based on a morphological evaluation of characters used in past classifications, as well as several new characters. The evolutionary polarity of the characters was determined by outgroup analysis. The characters employed were from the pleopods, the copulatory organs, the first walking legs, and the cephalon. The resulting character data set was analyzed with numerical phylogenetic computer programs to find one most parsimonious clado-gram, which is translated into a classification using the sequencing convention. The new phylogenetic estimate is significantly more parsimonious than previous trees from the literature, and several of its monophyletic groups have robust confidence limits. The superfamily Stenetrioidea belongs to the clade including the Janiroidea, not with the Aselloidea as previously suggested. The sister group of the Janiroidea is the family Pseudojaniridae, which is elevated to superfamily rank. The clade including the families Gnathostenetroididae and Protojaniridae is not the sister group of the Janiroidea, and is derived earlier in janiroidean evolution than the Stenetrioidea. Within the Janiroidea, the family Janiridae is not the most primitive taxon as previously believed. The clade including the families Munnidae and Pleurocopidae contains the earliest derived janiroideans. The data also indicate that the unusual sexual morphology of the Janiroidea did not appear suddenly but developed as a series of independent steps within the Asellota.     

Structure and biology of house mouse populations that plague irregularly: an evolutionary perspective

In Australia, populations of mice occasionally irrupt into plagues, mainly in the southern and eastern grain-growing regions. Mus domesticus was the only member of the subgenus Mus identified from a genetic survey of animals collected from four states. Little is known of the origin of these mice but they probably came from Europe where plagues do not occur. We examined whether mice have evolved the ability to plague since their colonization by comparing some population parameters of Australian, European and North American mice. Their helminth fauna were contrasted to gauge the importance of founder effects on the evolution of mice in Australia.
Australian mice share 52% (12 of 23) of the helminths found in mice in Europe and North America. Those not shared mainly had indirect life cycles. The absence of species could be explained by a strong founder effect or the lack of suitable intermediate hosts near Australian ports. There was no evidence that population structure or diet had evolved differently. Population abundance was different in field populations especially during the build-up and irruption of plagues. These differences were related to better breeding by mice in Australia in field environments; average number of embryos per litter was substantially higher and breeding seasons longer. Genetic change is not the only explanation for this increased productivity–a combination of lack of interspecific competition from other granivores and more favourable climatic conditions may be responsible.
All things considered, there was no compelling evidence that Australian mice have evolved the ability to plague. Their ability to respond to good conditions by increasing litter size beyond that recorded elsewhere supports the notion that control of mouse productivity is an appropriate management option for plague prevention.     

Understanding the effect of competition during evolutionary radiations: an integrated model of phenotypic and species diversification

Competition can drive macroevolutionary change, for example during adaptive radiations. However, we still lack a clear understanding of how it shapes diversification processes and patterns. To better understand the macroevolutionary consequences of competition, as well as the signal left on phylogenetic data, we developed a model linking trait evolution and species diversification in an ecological context. We find four main results: first, competition spurs trait diversity but not necessarily species richness; second, competition produces slowdowns in species diversification even in the absence of explicit ecological limits, but not in phenotypic diversification even in the presence of such limits; third, early burst patterns do not provide a reliable way of testing for adaptive radiations; and fourth, looking for phylogenetic signal in trait data and support for phenotypic models incorporating competition is a better alternative. Our results clarify the macroevolutionary consequences of competition and could help design more powerful tests of adaptive radiations in nature.     

Tooth scaling and evolutionary dwarfism: an investigation of allometry in human pygmies

Gould has predicted that in rapidly dwarfed lineages the postcanine teeth exhibit a different scaling pattern than is the normal interspecific trend. His prediction of strong negative allometry has not been frequently tested in quantitative detail. Here we present results of scaling analyses of the molar teeth in African pygmies compared with other Africans of larger size and in Philippine pygmies compared with Filipinos of larger size. We find a pattern of strong negative allometry of tooth size to skull and body size in both these comparisons. This scaling pattern is explained by recourse to the developmental bases (known or inferred) of dwarfing in these populations. Body size decrease is related to low levels of the growth control substance insulin-like growth factor I (IGF-I), which does not appear to affect the size of the dentition. The implications of such developmental information for our understanding of allometric patterns in general, and dwarfing events in particular, are discussed.     

Evolution of regulatory genes and patterns: Relationships to evolutionary rates and to metabolic functions

In an effort to understand the forces shaping evolution of regulatory genes and patterns, we have compared data on interspecific differences in enzyme expression patterns among the rapidly evolving Hawaiian picture-winged Drosophila to similar data on the more conservative virilis species group. Divergence of regulatory patterns is significantly more common in the former group, but cause and effect are difficult to discern. Random fixation of regulatory variants in small populations and/or during speciation may be somewhat more likely than divergence driven by selection. Within the picture-winged group, we also have compared enzymes that fulfill different metabolic roles. There are highly significant differences between individual enzymes, but no obvious correlations to functional categories. Correspondence to: W.J. Dickinson