Telling the tree: Narrative representation and the study of evolutionary history

Accounts of the evolutionary past have as much in common with works of narrative history as they do with works of science. Awareness of the narrative character of evolutionary writing leads to the discovery of a host of fascinating and hitherto unrecognized problems in the representation of evolutionary history, problems associated with the writing of narrative. These problems include selective attention, narrative perspective, foregrounding and backgrounding, differential resolution, and the establishment of a canon of important events. The narrative aspects of evolutionary writing, however, which promote linearity and cohesiveness in conventional stories, conflict with the underlying chronicle of evolution, which is not linear, but branched, and which does not cohere, but diverges. The impulse to narrate is so great, however, and is so strongly reinforced by traditional schemes of taxonomic attention, that natural historians have more often abandoned the diverging tree than they have abandoned the narrative mode of representation. If we are to understand the true nature of the evolutionary past then we must adopt tree thinking, and develop new and creative ways, both narrative and non-narrative, of telling the history of life.     

Fructose-bisphosphate aldolases: an evolutionary history.

Two mechanistically distinct forms of fructose-bisphosphate aldolase are known to exist. It has been assumed that the Class II (metallo) aldolases are evolutionary more primitive than their Class I (Schiff-base) analogs since the latter had only been found in eukaryotes. With the identification of prokaryotic Class I aldolases, we present here an alternative scheme of aldolase evolution. This scheme proposes that both aldolase classes are evolutionarily ancient and rationalizes the observed highly variable expression of both enzyme types in contemporary file forms.     

The tree of life: introduction to an evolutionary debate

The ‘Tree of Life’ is intended to represent the pattern of evolutionary processes that result in bifurcating species lineages. Often justified in reference to Darwin’s discussions of trees, the Tree of Life has run up against numerous challenges especially in regard to prokaryote evolution. This special issue examines scientific, historical and philosophical aspects of debates about the Tree of Life, with the aim of turning these criticisms towards a reconstruction of prokaryote phylogeny and even some aspects of the standard evolutionary understanding of eukaryotes. These discussions have arisen out of a multidisciplinary collaboration of people with an interest in the Tree of Life, and we suggest that this sort of focused engagement enables a practical understanding of the relationships between biology, philosophy and history.     

Curious chiral cases of caddisfly larvae: handed behavior, asymmetric forms, evolutionary history

Studies of right-left asymmetries have yielded valuable insights into the mechanisms of both development and evolution. Larvae from several groups of caddisflies (Trichoptera) build portable asymmetrical cases within which they live. In nearly all species that build spiral-walled tubular cases, the direction of wall coiling is random (equal numbers of dextral and sinistral cases within species) whereas in all species that build helicospiral, snail-like cases the direction of coiling is exclusively dextral. Asymmetrical tubes result from handed behavior, and ～20% of larvae removed from a spiral-walled, tubular case build a replacement case of opposite chirality. So handed behavior (and hence direction of tube-wall spiraling) is likely learned rather than determined genetically. Asymmetrical larval cases appear to have evolved at least seven times in the Trichoptera, five times as spiral-walled tubes and twice as snail-like helicospiral cases. Helicospiral cases may reduce vulnerability to predation by mimicking snail shells, whereas spiral arrangements of vegetation fragments in tube walls may be more robust mechanically than other arrangements, but experimental evidence is lacking. Within one family (Phryganeidae), one or perhaps two species exhibit an excess of sinistral-walled cases, suggesting that genes that bias handed behavior in a particular direction evolved after handed behaviors already existed (genetic assimilation).     

Species traits and abundance influence the organization of liana–tree antagonistic interaction

The interaction among species can be influenced by neutral processes, in which more abundant species have high effect on the structure of interaction, or can be influenced by trait matching. Despite both variables (abundance and species traits) influencing the interaction of species in mutualistic networks, few studies showed their importance in antagonistic networks. Here, we posed the question: what are the main predictors of the liana–tree interactions: species abundance, biological traits or both? In a savanna woodland fragment in south‐eastern Brazil, we sampled lianas and trees in 1 ha, where we recorded the abundance, maximum height and bark roughness of tree species, as well as abundance, maximum diameter and climbing system of liana species. For each species, we calculated their contribution to nestedness (n_i), which is a measure of network structure, and performed simple linear regressions between n_i and abundance and species traits. Abundant species contribute more to n_i than rare species, indicating that neutral processes affect interactions between lianas and trees, probably because lianas are opportunistic and climb trees in their neighbourhood. The only trait related to n_i was tree height, which can indicate that light availability can have a considerable role on network structure between both growth forms. Therefore, the importance of species abundance and tree height can be related to opportunism of lianas on climbing the most suitable tree in their neighbourhood.     

Antifungal activity of oosporein from an antagonistic fungus against Phytophthora infestans

An antifungal metabolite, oosporein, was isolated from the culture of Verticillium psalliotae that produced the antagonistic effects on Phytophthora infestans. Oosporein exhibited a significant growth-inhibitory effect on P. infestans in comparison with other phytopathogenic fungi.     

Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum.

Actinobacteria constitute one of the largest phyla among bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.     

Multilocus genotypes, a tree of individuals, and human evolutionary history.

Our goal is to infer, from human genetic data, general patterns as well as details of human evolutionary history. Here we present the results of an analysis of genetic data at the level of the individual. A tree relating 144 individuals from 12 human groups of Africa, Asia, Europe, and Oceania, inferred from an average of 75 DNA polymorphisms/individual, is remarkable in that most individuals cluster with other members of their regional group. In order to interpret this tree, we consider the factors that influence the tree pattern, including the number of genetic loci examined, the length of population isolation, the sampling process, and the extent of gene flow among groups. Understanding the impact of these factors enables us to infer details of human evolutionary history that might otherwise remain undetected. Our analyses indicate that some recent ancestor(s) of each of a few of the individuals tested may have immigrated. In general, the populations within regional groups appear to have been isolated from one another for <25,000 years. Regional groups may have been isolated for somewhat longer.     

A smelling trip into the past: the influence of synthetic materials on the history of perfumery

Contemporary perfumery has its roots in the work of the past, and many of the perfumes from this time have long since disappeared. What follows is a short account of some of the most famous perfumes from the past which have been inspired by the novel synthetic materials of the time. These important creations include, ‘Fougère Royale’ by Houbigant (1884) containing coumarin ( 1 ), ‘Jicky’ by Guerlain (1889) containing vanillin ( 2 ) and linalool ( 3 ), ‘Vera Violetta’ by Roger & Gallet (1892) containing α‐ and β‐ionone ( 4 and 5 , resp.), ‘Trèfle Incarnat’ by Piver (1898) containing isoamyl salicylate ( 6 ), ‘La Rose Jacqueminot’ of Coty (1904) containing Rhodinol ( 7 ), ‘Après l'Ondée’ by Guerlain (1906) containing para‐anisaldehyde ( 8 ), ‘Quelques Fleurs’ by Houbigant (1912) containing hydroxycitronellal ( 9 ), ‘N°5’ by Chanel (1921) containing the aldehydes C‐10 ( 10 ), C‐110 ( 11 ), and C‐12 ( 12 ), ‘Nuit De Noël’ by Caron (1922) containing 6‐isobutylquinoline ( 14 ), and ‘Femme’ by Rochas (1944) containing the so‐called ‘aldehyde C‐14’ ( 15 , γ‐undecalactone). The Osmotheque, the International Conservatory of Perfumes, was launched in 1990 and is regarded as a primary source of knowledge for the history of perfumery. Its vocation is to compile an amazing collection of 1700 perfumes (400 of them almost forgotten fragrances) – jewels of perfumery.     

Phylogenetic analysis of carbamoylphosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the tree of life

Carbamoylphosphate synthetase (CPS) catalyzes the first committed step in pyrimidine biosynthesis, arginine biosynthesis, or the urea cycle. Organisms may contain either one generalized or two specific CPS enzymes, and these enzymes may be heterodimeric (encoded by linked or unlinked genes), monomeric, or part of a multifunctional protein. In order to help elucidate the evolution of CPS, we have performed a comprehensive phylogenetic analysis using the 21 available complete CPS sequences, including a sequence from Sulfolobus solfataricus P2 which we report in this paper. This is the first report of a complete CPS gene sequence from an archaeon, and sequence analysis suggests that it encodes an enzyme similar to heterodimeric CPSII. We confirm that internal similarity within the synthetase domain of CPS is the result of an ancient gene duplication that preceded the divergence of the Bacteria, Archaea, and Eukarya, and use this internal duplication in phylogenetic tree construction to root the tree of life. Our analysis indicates with high confidence that this archaeal sequence is more closely related to those of Eukarya than to those of Bacteria. In addition to this ancient duplication which created the synthetase domain, our phylogenetic analysis reveals a complex history of further gene duplications, fusions, and other events which have played an integral part in the evolution of CPS.      

一株具有抗疟活性的金鸡纳树内生真菌的研究

为筛选具抗疟疾活性的的内生真菌,采用平板分离法对海南金鸡那树内生真菌进行分离纯化。利用"4日抑制疟疾"测试内生真菌发酵液的抗疟活性,采用TLC、HPLC等分析技术对内生菌发酵液等成分进行分析。从金鸡那树叶片分离到31种内生真菌,通过筛选找到了1株具有抗疟疾活性的产奎宁或奎宁类似物的内生真菌。从金鸡那树叶片中分离得到1株产奎宁的结实串孢霉属内生真菌,为奎宁的资源开发开辟了新途径。     

Natural history of whitefly in Costa Rica: an evolutionary starting point

Abstract.  1. To understand evolution of foraging behaviour in the whitefly parasitoid Encarsia formosa (Hymenoptera, Aphelinidae), natural densities and distributions of whitefly (Homoptera, Aleyrodidae) were quantified in E. formosa 's presumed area of origin, the Neotropics.
2. Leaves were collected in Costa Rican nature areas along long transects (2–4 km), short transects (100 m), within 3-D plots (50 dm³−2.3 m³) and along suspension bridges within the canopy, and checked for presence of whitefly nymphs.
3. Generalised linear mixed modelling revealed that the number of hosts on the lower side of a leaflet of an average plant within an average spot of an average transect could be described by a Poisson distribution with mean and variance equal to 0.241, in a ratio of I1:I2:I3:I4 = 0.14:0.23:0.26:0.37. The Poisson mean was affected largely by the plant and less by the spot or transect. Variation in leaf area explained little of the variation between plants. Based on the shape of the opening in vacated puparia, the probability that a whitefly became parasitised eventually was 12% on an average leaflet. Whitefly density was much lower in the canopy than at the forest floor in the same area.
4. Semivariance analyses showed that in one of the three short transects, the numbers of whiteflies on leaves were spatially dependent. In four of seven 3-D plots at least one level of spatial dependence could be detected.
5. Results are discussed in the context of understanding evolution of foraging behaviour by E. formosa .     

Evaluating evolutionary history in the face of high gene tree discordance in Australian Gehyra (Reptilia: Gekkonidae)

Species tree methods have provided improvements for estimating species relationships and the timing of diversification in recent radiations by allowing for gene tree discordance. Although gene tree discordance is often observed, most discordance is attributed to incomplete lineage sorting rather than other biological phenomena, and the causes of discordance are rarely investigated. We use species trees from multi-locus data to estimate the species relationships, evolutionary history and timing of diversification among Australian Gehyra—a group renowned for taxonomic uncertainty and showing a large degree of gene tree discordance. We find support for a recent Asian origin and two major clades: a tropically adapted clade and an arid adapted clade, with some exceptions, but no support for allopatric speciation driven by chromosomal rearrangement in the group. Bayesian concordance analysis revealed high gene tree discordance and comparisons of Robinson–Foulds distances showed that discordance between gene trees was significantly higher than that generated by topological uncertainty within each gene. Analysis of gene tree discordance and incomplete taxon sampling revealed that gene tree discordance was high whether terminal taxon or gene sampling was maximized, indicating discordance is due to biological processes, which may be important in contributing to gene tree discordance in many recently diversified organisms.     

ORI-GENE: gene classification based on the evolutionary tree

MOTIVATION: Genome projects have produced large amounts of data on the sequences of new genes whose functions are as yet unknown. The functions of new genes are usually inferred by comparing their sequences with those of known genes, but evaluation of the sequence homology of individual genes does not make the most of the available sequence information. Therefore, new methods and tools for extracting more biological information from homology searches would be advantageous. RESULTS: We have developed a computational tool, ORI-GENE, to analyze the results of sequence homology searches from the perspective of the evolution of selected sets of new genes. ORI-GENE has a graphical interface and accomplishes two important tasks: first, based on the output of homology searches, it identifies species with similar genes and displays their pattern of distribution on the phylogenetic tree. This function enables one to infer the way in which a given gene may have propagated among species over time. Second, from the distribution patterns, it predicts the point at which a given gene may have been first acquired (i.e. its 'origin'), then classifies the gene on that basis. Because it makes use of available evolutionary information to show the way in which genes cluster among species, ORI-GENE should be an effective tool for the screening and classification of new genes revealed by genome analysis. AVAILABILITY: ORI-GENE is retrievable via the Internet at: http://www.rtc.riken.go.jp/jouhou/ORI-GENE.     

Mudwhelks and mangroves: the evolutionary history of an ecological association (Gastropoda: Potamididae)

Most of the 29 living species of Potamididae show a close association with mangroves. The trees provide the snails with shelter, protection from predators, a solid substrate and sometimes food. Using sequences from three genes (nuclear 18S rRNA and 28S rRNA, mitochondrial COI) we derive a molecular phylogeny and recognize six living genera (Terebralia, Telescopium, Tympanotonos, Cerithidea, Cerithideopsis, Cerithideopsilla). The oldest modern genera (Terebralia, Cerithideopsis) appeared in the Tethyan realm in the Middle Eocene, shortly after the origin of mangrove trees. Whereas most potamidid genera are now restricted to either the Indo-West Pacific (IWP) or to the eastern Pacific plus Atlantic (EPA), sister clades of Cerithideopsis survive in both realms. Based on a reinterpretation of the fossil record (particularly of the monotypic Tympanotonos and extinct Potamides), and parsimonious reconstruction of ancestral habitats, we suggest that the living potamidids are an adaptive radiation that has always been closely associated with mangroves. The specialized tree-climbing groups Cerithidea and Cerithideopsis were independently derived from mud-dwelling ancestors. Cerithideopsilla cingulata (a species complex in the IWP) and 'Potamides' conicus (in the Mediterranean and Indian Ocean) form a single clade within the genus Cerithideopsilla. This refutes the hypothesis that 'P.'conicus is the sole relict of the Tethyan Potamides that has occurred in the Mediterranean region since the Palaeocene. Instead, the phylogeny and fossil record suggest that an ancestor of Cerithideopsilla conica with planktotrophic larvae dispersed from the IWP to the Mediterranean in the Middle Miocene, that its direct development evolved in the Mediterranean during the Pliocene, and that it reinvaded the Indian Ocean during the Plio-Pleistocene.     

Cabbage family affairs: the evolutionary history of Brassicaceae

Life without the mustard family (Brassicaceae) would be a world without many crop species and the model organism Arabidopsis (Arabidopsis thaliana) that has revolutionized our knowledge in almost every field of modern plant biology. Despite this importance, research breakthroughs in understanding family-wide evolutionary patterns and processes within this flowering plant family were not achieved until the past few years. In this review, we examine recent outcomes from diverse botanical disciplines (taxonomy, systematics, genomics, paleobotany and other fields) to synthesize for the first time a holistic view on the evolutionary history of the mustard family.