Origin and Diversification of TRIM Ubiquitin Ligases

Most proteins of the TRIM family (also known as RBCC family) are ubiquitin ligases that share a peculiar protein structure, characterized by including an N-terminal RING finger domain closely followed by one or two B-boxes. Additional protein domains found at their C termini have been used to classify TRIM proteins into classes. TRIMs are involved in multiple cellular processes and many of them are essential components of the innate immunity system of animal species. In humans, it has been shown that mutations in several TRIM-encoding genes lead to diverse genetic diseases and contribute to several types of cancer. They had been hitherto detected only in animals. In this work, by comprehensively analyzing the available diversity of TRIM and TRIM-like protein sequences and evaluating their evolutionary patterns, an improved classification of the TRIM family is obtained. Members of one of the TRIM subfamilies defined, called Subfamily A, turn to be present not only in animals, but also in many other eukaryotes, such as fungi, apusozoans, alveolates, excavates and plants. The rest of subfamilies are animal-specific and several of them originated only recently. Subfamily A proteins are characterized by containing a MATH domain, suggesting a potential evolutionary connection between TRIM proteins and a different type of ubiquitin ligases, known as TRAFs, which contain quite similar MATH domains. These results indicate that the TRIM family emerged much earlier than so far thought and contribute to our understanding of its origin and diversification. The structural and evolutionary links with the TRAF family of ubiquitin ligases can be experimentally explored to determine whether functional connections also exist.     

A theoretical investigation of the role of social transmission in evolution

This paper contains an investigation of the interaction between protocultural processes in animals, generated by social learning and the processes of biological evolution. It addresses the question of whether mechanisms of social learning and transmission can play an evolutionary role by allowing learned patterns of behavior to spread through animal populations, in the process changing the selection pressures acting on them. Simple models of social transmission and gene-meme coevolution are developed to investigate three hypotheses related to the role of social transmission in animal evolution. Simulations using the models suggest that social transmission would have to be particularly stable and be associated with estremely strong selection, if it were to result in the fixation of alleles. A more likely hypothesis is that social transmission might allow animals to respond adaptively to novelty in their environment, rendering a genetic response unnecessary, or only partially necessary. Socially transmitted traits appear to spread sufficiently rapidly, relative to changes in gene frequency, that it would be quite feasible for a socially transmitted response to an environmental change to occur, preempting a genetic response. Social transmission is probably more likely to slow down evolutionary rates than to speed them up through changing selection pressures. However, cultural and evolutionary processes are likely to interact in complex ways, and a “behavioral drive” effect cannot be ruled out.     

Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes

Plant disease resistance genes (R genes) encode proteins that function to monitor signals indicating pathogenic infection, thus playing a critical role in the plant's defense system. Although many studies have been performed to explore the functional details of these important genes, their origin and evolutionary history remain unclear. In this study, focusing on the largest group of R genes, the nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes, we conducted an extensive genome-wide survey of 38 representative model organisms and obtained insights into the evolutionary stage and timing of NBS-LRR genes. Our data show that the two major domains, NBS and LRR, existed before the split of prokaryotes and eukaryotes but their fusion was observed only in land plant lineages. The Toll/interleukin-1 receptor (TIR) class of NBS-LRR genes probably had an earlier origin than its nonTIR counterpart. The similarities of the innate immune systems of plants and animals are likely to have been shaped by convergent evolution after their independent origins. Our findings start to unravel the evolutionary history of these important genes from the perspective of comparative genomics and also highlight the important role of reorganizing pre-existing building blocks in generating evolutionary novelties.     

动物对孢子植物的传播模式及进化意义

孢子植物物种多样性丰富, 是自然生态系统的重要组成部分。孢子植物的传播通常被认为主要依靠风、水、弹力等非生物媒介, 而动物的作用往往被忽略。本文主要概述了: (1)孢子植物对动物传播的适应: 一方面孢子植物可为动物提供食物、庇护所、繁殖场所等, 另一方面孢子植物也可产生视觉、嗅觉等方面的线索来吸引动物, 从而促进动物传播其繁殖体。(2)动物对孢子植物的传播模式: 包括体内传播(消化道和组织寄生)和体外传播两种, 这些模式都能对孢子植物繁殖体进行有效传播。由于动物间形态或生活习性的不同, 以致传播距离存在差异, 最短距离为0.1 cm, 最长距离可从北半球至南半球。(3)动物对孢子植物传播的生态与进化意义; 由于某些孢子植物繁殖体的结构特点或萌发的需求, 以致其繁殖体只能通过动物的传播才能得以定殖, 因此动物与孢子植物之间存在密不可分的关系。目前, 动物对孢子植物的传播研究主要是描述性的内容以及研究单方面的传播途径, 建议在今后的研究中考虑动物对孢子植物传播的有效性以及多途径同时传播对孢子植物定殖的影响, 同时应更加关注孢子植物和动物互惠关系的形成、维持机制及将来的进化趋势。     

Partial migration in fishes: causes and consequences

Partial migration, where only some individuals from a population migrate, has been widely reported in a diverse range of animals. In this paper, what is known about the causes and consequences of partial migration in fishes is reviewed. Firstly, the ultimate and proximate drivers of partial migration are reflected upon: what ecological factors can shape the evolution of migratory dimorphism? How is partial migration maintained over evolutionary timescales? What proximate mechanisms determine whether an individual is migratory or remains resident? Following this, the consequences of partial migration are considered, in an ecological and evolutionary context, and also in an applied sense. Here it is argued that understanding the concept of partial migration is crucial for fisheries and ecosystem managers, and can provide information for conservation strategies. The review concludes with a reflection on the future opportunities in this field, and the avenues of research that are likely to be fruitful to shed light on the enduring puzzle of partial migration in fishes.     

Playing for keeps

The hypothesis that play behavior is more prevalent in larger-brained animals has recently been challenged. It may be, for example, that only certain brain structures are related to play. Here, we analyze social play behavior with regards to the cerebellum: a structure strongly implicated in motor-development, and possibly also in cognitive skills. We present an evolutionary analysis of social play and the cerebellum, using a phylogenetic comparative method. Social play frequency and relative cerebellum size are positively correlated. Hence, there appears to be a link between the evolutionary elaboration of social play and the cerebellum. Kerrie Lewis recently received her Ph.D. from the University of Durham, U.K., under the supervision of Robert Barton. She is currently working in a postdoctoral position at Duke University, conducting research into primate numerical cognition. Robert Barton is a Reader in Evolutionary Anthropology at the University of Durham. His interests comprise primate behavior and brain evolution. Both authors are keen advocates for the use of the comparative method in evolutionary studies.     

Physiological ecology meets climate change

In this article, we pointed out that understanding the physiology of differential climate change effects on organisms is one of the many urgent challenges faced in ecology and evolutionary biology. We explore how physiological ecology can contribute to a holistic view of climate change impacts on organisms and ecosystems and their evolutionary responses. We suggest that theoretical and experimental efforts not only need to improve our understanding of thermal limits to organisms, but also to consider multiple stressors both on land and in the oceans. As an example, we discuss recent efforts to understand the effects of various global change drivers on aquatic ectotherms in the field that led to the development of the concept of oxygen and capacity limited thermal tolerance (OCLTT) as a framework integrating various drivers and linking organisational levels from ecosystem to organism, tissue, cell, and molecules. We suggest seven core objectives of a comprehensive research program comprising the interplay among physiological, ecological, and evolutionary approaches for both aquatic and terrestrial organisms. While studies of individual aspects are already underway in many laboratories worldwide, integration of these findings into conceptual frameworks is needed not only within one organism group such as animals but also across organism domains such as Archaea, Bacteria, and Eukarya. Indeed, development of unifying concepts is relevant for interpreting existing and future findings in a coherent way and for projecting the future ecological and evolutionary effects of climate change on functional biodiversity. We also suggest that OCLTT may in the end and from an evolutionary point of view, be able to explain the limited thermal tolerance of metazoans when compared to other organisms.     

Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes

Sequence similarity and profile searching tools were used to analyze the genome sequences of Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and Drosophila melanogaster for genes encoding three families of histone deacetylase (HDAC) proteins and three families of histone acetyltransferase (HAT) proteins. Plants, animals and fungi were found to have a single member of each of three subfamilies of the GNAT family of HATs, suggesting conservation of these functions. However, major differences were found with respect to sizes of gene families and multi-domain protein structures within other families of HATs and HDACs, indicating substantial evolutionary diversification. Phylogenetic analysis identified a new class of HDACs within the RPD3/HDA1 family that is represented only in plants and animals. A similar analysis of the plant-specific HD2 family of HDACs suggests a duplication event early in dicot evolution, followed by further diversification in the lineage leading to Arabidopsis. Of three major classes of SIR2-type HDACs that are found in animals, fungi have representatives only in one class, whereas plants have representatives only in the other two. Plants possess five CREB-binding protein (CBP)-type HATs compared with one to two in animals and none in fungi. Domain and phylogenetic analyses of the CBP family proteins showed that this family has evolved three distinct types of CBPs in plants. The domain architecture of CBP and TAF(II)250 families of HATs show significant differences between plants and animals, most notably with respect to bromodomain occurrence and their number. Bromodomain-containing proteins in Arabidopsis differ strikingly from animal bromodomain proteins with respect to the numbers of bromodomains and the other types of domains that are present. The substantial diversification of HATs and HDACs that has occurred since the divergence of plants, animals and fungi suggests a surprising degree of evolutionary plasticity and functional diversification in these core chromatin components.     

Striking convergence in the mouthpart evolution of stream-living algae grazers

This scanning-electron microscopic study demonstrates the convergent evolution of the mouthparts of various herbivorous stream animals (insects from different orders, an isopod, snails, fish, and a tadpole) feeding on epilithic algal pastures. This food source is rich but is often difficult to harvest. Nevertheless, a large number of species can live on it because they have evolved highly specialized mouthparts. There are four functional problems that an algae grazer has to solve: the algae must be removed from the stone, they have to be collected and crushed, and a current shield is needed to prevent the water flow sweeping away the food. Among the 30 algae grazers examined in this study, a limited number of morphological solutions have been found for each of these adaptational problems. There are multiple evolutionary pathways for mouthpart adaptation and even closely related species have often evolved different types of tools for the same function. This refects the existence of a certain amount of evolutionary scope. Such freedom of evolution is present, however, only at the beginning of the adaptiogenesis of an algae grazer. Once one of the evolutionary pathways is taken, further improvement of the mouthparts is possible only by the refinement of the ‘chosen’ type of tools. The consequence of this is that a large number of astonishing convergences have occurred in algae grazers that have independently trodden the same evolutionary pathway.     

The origins of human ageing.

The origins of human ageing are to be found in the origins and evolution of senescence as a general feature in the life histories of higher animals. Ageing is an intriguing problem in evolutionary biology because a trait that limits the duration of life, including the fertile period, has a negative impact on Darwinian fitness. Current theory suggests that senescence occurs because the force of natural selection declines with age and because longevity is only acquired at some metabolic cost. In effect, organisms may trade late survival for enhanced reproductive investments in earlier life. The comparative study of ageing supports the general evolutionary theory and reveals that human senescence, while broadly similar to senescence in other mammalian species, has distinct features, such as menopause, that may derive from the interplay of biological and social evolution.     

Do miRNAs have a deep evolutionary history?

The recent discovery of microRNAs (miRNAs) in unicellular eukaryotes, including miRNAs known previously only from animals or plants, implies that miRNAs have a deep evolutionary history among eukaryotes. This contrasts with the prevailing view that miRNAs evolved convergently in animals and plants. We re-evaluate the evidence and find that none of the 73 plant and animal miRNAs described from protists meet the required criteria for miRNA annotation and, by implication, animals and plants did not acquire any of their respective miRNA genes from the crown ancestor of eukaryotes. Furthermore, of the 159 novel miRNAs previously identified among the seven species of unicellular protists examined, only 28 from the algae Ectocarpus and Chlamydomonas, meet the criteria for miRNA annotation. Therefore, at present only five groups of eukaryotes are known to possess miRNAs, indicating that miRNAs have evolved independently within eukaryotes through exaptation of their shared inherited RNAi machinery.     

Shared signals and the potential for phylogenetic espionage between plants and animals

Until recently, the study and understanding of plant and animalsignalling and response mechanisms have developed independently.Recent biochemical and molecular work is producing a growinglist of elements involved in responses to biotic and abioticstimuli that are very similar across kingdoms. Some of the moreinteresting examples of these include prostaglandin/octadecanoid-mediatedresponses to wounding, steroid-based signalling systems, andpathogen-recognition mechanisms. Some of these similaritiesprobably represent evolutionary convergence; others may be ancestralto plants and animals. Ecological and evolutionary implicationsof such overlaps include the existence of pathogens that cancause disease in plants and animals, the ability of herbivoresto manipulate plant responses, usurpation of microbial mechanismsand genes by herbivorous animals and plants, evolution of plantdefenses exploiting shared signals in animals, and the medicinaluse of plants by humans. Comparative study of the signallingand response mechanisms used by plants, animals, and microbesprovides novel and useful insights to the ecology and evolutionof interactions across kingdoms.     

The shape of life: how much is written in stone?

Considering the enormous diversity of living organisms, representing mostly untapped resources for studying ecological, ontogenetic and phylogenetic patterns and processes, why should evolutionary biologists concern themselves with the remains of animals and plants that died out tens or even hundreds of millions of years ago? The reason is that important new insights into some of the most vexing evolutionary questions are being revealed at the interfaces of palaeontology, developmental biology and molecular biology. Attempts to synthesise information from these disciplines, however, often encounter their greatest hurdles in considerations of the radiation of the Metazoa. Ongoing challenges relate to the origins of body plans, the relationships of the metazoan phyla and the timing of major evolutionary radiations. Palaeontology not only has its own unique contributions to the study of evolutionary processes, but provides a lynchpin for many of the emerging techniques.     

If animals know their own fighting ability, the evolutionarily stable level of fighting is reduced

We consider a version of the Hawk-Dove game in which an animal knows its own fighting ability but not the ability of its opponent. For this game at evolutionary stability there is a critical level of ability such that animals with ability greater than the critical level play Hawk and animals with ability below the critical level play Dove. We define the level of fighting to be the probability of a Hawk-Hawk fight when two opponents meet. We show that even if an animal does not know the ability of its opponent, knowing its own ability results in a lower level of fighting at evolutionary stability than is found in the standard Hawk-Dove game in which there are no differences in ability or abilities are not known.     

A meta‐analysis of the strength and nature of cytoplasmic genetic effects

Genetic variation in cytoplasmic genomes (i.e. the mitochondrial genome in animals, and the combined mitochondrial and chloroplast genomes in plants) was traditionally assumed to accumulate under a neutral equilibrium model. This view has, however, come under increasing challenge from studies that have experimentally linked cytoplasmic genetic effects to the expression of life history phenotypes. Such results suggest that genetic variance located within the cytoplasm might be of evolutionary importance and potentially involved in shaping population evolutionary trajectories. As a step towards assessing this assertion, here we conduct a formal meta‐analytic review to quantitatively assess the extent to which cytoplasmic genetic effects contribute to phenotypic expression across animal and plant kingdoms. We report that cytoplasmic effect sizes are generally moderate in size and associated with variation across a range of factors. Specifically, cytoplasmic effects on morphological traits are generally larger than those on life history or metabolic traits. Cytoplasmic effect sizes estimated at the between‐species scale (via interspecies mix‐and‐matching of cytoplasmic and nuclear genomes) are larger than those at the within‐species scale. Furthermore, cytoplasmic effects tied to epistatic interactions with the nuclear genome tend to be stronger than additive cytoplasmic effects, at least when restricting the data set to gonochorous animal species. Our results thus confirm that cytoplasmic genetic variation is commonly tied to phenotypic expression across plants and animals, implicate the cytoplasmic–nuclear interaction as a key unit on which natural selection acts and generally suggest that the genetic variation that lies within the cytoplasm is likely to be entwined in adaptive evolutionary processes.     

Natural History of Innate Host Defense Peptides

Host defense peptides act on the forefront of innate immunity, thus playing a central role in the survival of animals and plants. Despite vast morphological changes in species through evolutionary history, all animals examined to date share common features in their innate immune defense strategies, hereunder expression of host defense peptides (HDPs). Most studies on HDPs have focused on humans, domestic and laboratory animals. More than a thousand different sequences have been identified, yet data on HDPs in wild-living animals are sparse. The biological functions of HDPs include broad-spectrum antimicrobial activity and immunomodulation. Natural selection and coevolutionary host-pathogen arms race theory suggest that the extent and specificity of the microbial load influences the spectrum and potency of HDPs in different species. Individuals of extant species—that have lived for an extended period in evolutionary history amid populations with intact processes of natural selection—likely possess the most powerful and well-adapted “natural antibiotics”. Research on the evolutionary history of the innate defense system and the host in context of the consequences of challenges as well as the efficacy of the innate immune system under natural conditions is therefore of immediate interest. This review focuses on evolutionary aspects of immunophysiology, with emphasis on innate effector molecules. Studies on host defense in wild-living animals may significantly enhance our understanding of inborn immune mechanisms, and help identify molecules that may assist us to cope better with the increasing microbial challenges that likely follow from the continuous amplification of biodiversity levels on Earth.     

The unexpected mating system of the androdioecious barnacle Chelonibia testudinaria (Linnaeus 1758)

Androdioecy was first described by Darwin in his seminal work on barnacle diversity; he identified males and hermaphrodites in the same reproductive population. Today, we realize that many androdioecious plants and animals share astonishing similarities, particularly with regard to their evolutionary history and mating system. Notably, these species were ancestrally dioecious, and their mating system has the following characteristics: hermaphrodites self‐fertilize frequently, males are more successful in large mating groups, and males have a mating advantage. A male mating advantage makes androdioecy more likely to persist over evolutionary times. Androdioecious barnacles, however, appear to persist as an outlier with a different evolutionary trajectory: they originate from hermaphroditic species. Although sexual systems of androdioecious barnacles are known, no information on the mating system of androdioecious barnacles is available. This study assessed the mating system of the androdioecious barnacle Chelonibia testudinaria. In contrast to other androdioecious species, C. testudinaria does not self‐fertilize, males do not have a mating advantage over hermaphrodites, and the average mating group is quite small, averaging only three individuals. Mating success is increased by proximity to the mate and penis length. Taken together, the mating system of C. testudinaria is unusual in comparison with other androdioecious plants and animals, and the lack of a male mating advantage suggests that the mating system alone does not provide an explanation for the maintenance of androdioecy in this species. Instead, we propose that sex‐specific life history equalizes male and hermaphroditic overall fitness.     

Similarity of mammalian body size across the taxonomic hierarchy and across space and time

Although it is commonly assumed that closely related animals are similar in body size, the degree of similarity has not been examined across the taxonomic hierarchy. Moreover, little is known about the variation or consistency of body size patterns across geographic space or evolutionary time. Here, we draw from a data set of terrestrial, nonvolant mammals to quantify and compare patterns across the body size spectrum, the taxonomic hierarchy, continental space, and evolutionary time. We employ a variety of statistical techniques including "sib-sib" regression, phylogenetic autocorrelation, and nested ANOVA. We find an extremely high resemblance (heritability) of size among congeneric species for mammals over approximately 18 g; the result is consistent across the size spectrum. However, there is no significant relationship among the body sizes of congeneric species for mammals under approximately 18 g. We suspect that life-history and ecological parameters are so tightly constrained by allometry at diminutive size that animals can only adapt to novel ecological conditions by modifying body size. The overall distributions of size for each continental fauna and for the most diverse orders are quantitatively similar for North America, South America, and Africa, despite virtually no overlap in species composition. Differences in ordinal composition appear to account for quantitative differences between continents. For most mammalian orders, body size is highly conserved, although there is extensive overlap at all levels of the taxonomic hierarchy. The body size distribution for terrestrial mammals apparently was established early in the Tertiary, and it has remained remarkably constant over the past 50 Ma and across the major continents. Lineages have diversified in size to exploit environmental opportunities but only within limits set by allometric, ecological, and evolutionary constraints.     

To boldly go: individual differences in boldness influence migratory tendency

Partial migration, whereby only a fraction of the population migrates, is thought to be the most common type of migration in the animal kingdom, and can have important ecological and evolutionary consequences. Despite this, the factors that influence which individuals migrate and which remain resident are poorly understood. Recent work has shown that consistent individual differences in personality traits in animals can be ecologically important, but field studies integrating personality traits with migratory behaviour are extremely rare. In this study, we investigate the influence of individual boldness, an important personality trait, upon the migratory propensity of roach, a freshwater fish, over two consecutive migration seasons. We assay and individually tag 460 roach and show that boldness influences migratory propensity, with bold individuals being more likely to migrate than shy fish. Our data suggest that an extremely widespread personality trait in animals can have significant ecological consequences via influencing individual-level migratory behaviour.     

On the eve of animal radiation: phylogeny, ecology and evolution of the Ediacara biota

Ediacara fossils document an important evolutionary episode just before the Cambrian explosion and hold critical information about the early evolution of macroscopic and complex multicellular life. They also represent an enduring controversy in paleontology. How are the Ediacara fossils related to living animals? How did they live? Do they share any evolutionary patterns with other life forms? Recent developments indicate that Ediacara fossils epitomize a phylogenetically diverse biosphere, probably including animals, protists, algae, fungi and others. Their simple ecology is dominated by epibenthic osmotrophs, deposit feeders and grazers, but few if any predators. Their evolution started with an early morphospace expansion followed by taxonomic diversification within confined morphospace, and concluded by extinction of many taxa at the Ediacaran-Cambrian boundary.