The structure of protein evolution and the evolution of protein structure

The observed distribution of protein structures can give us important clues about the underlying evolutionary process, imposing important constraints on possible models. The availability of results from an increasing number of genome projects has made the development of these models an active area of research. Models explaining the observed distribution of structures have focused on the inherent functional capabilities and structural properties of different folds and on the evolutionary dynamics. Increasingly, these elements are being combined.     

The evolution of syntactic structure

Two new books—Creating Language: Integrating Evolution, Acquisition, and Processing by Morten H. Christiansen and Nick Chater, and Why Only Us: Language and Evolution by Robert C. Berwick and Noam Chomsky—present a good opportunity to assess the state of the debate about whether or not language was made possible by language-specific adaptations for syntax. Berwick and Chomsky argue yes: language was made possible by a single change to the computation Merge. Christiansen and Chater argue no: our syntactic abilities developed on the back of natural selection for general-purpose sequence learning mechanisms. While Christiansen and Chater’s book testifies to impressive developments in constructivist approaches to language development, it’s not obvious that it has the resources to explain the hierarchical nature of syntactic binding. Despite this, the views have much in common.     

The structure and evolution of parvalbumins

1. Parvalbumins were isolated from the white muscle of Cynoscion regalis, Leiostomus xanthurus, and Menticirrhus americanus of the Sciaenidae and Pomatomus saltatrix of the Pomatomidae. 2. Menticirrhus contains three isoparvalbumins. The other species contain two isoparvalbumins which are designated "fast" and "slow" in accord with their electrophoretic mobilities. Measurements of the denatured molecular weights show the "slow" isoparvalbumins have slightly larger apparent molecular weights, but all apparent molecular weights are in the range 10,400-14,000. 3. Amino acid compositional studies indicate that the fast and slow isoparvalbumins in these fish represent two distinct evolutionary lineages which appear to be evolving at different rates.     

The trophic vacuum and the evolution of complex life cycles in trophically transmitted helminths

Parasitic worms (helminths) frequently have complex life cycles in which they are transmitted trophically between two or more successive hosts. Sexual reproduction often takes place in high trophic-level (TL) vertebrates, where parasites can grow to large sizes with high fecundity. Direct infection of high TL hosts, while advantageous, may be unachievable for parasites constrained to transmit trophically, because helminth propagules are unlikely to be ingested by large predators. Lack of niche overlap between propagule and definitive host (the trophic transmission vacuum) may explain the origin and/or maintenance of intermediate hosts, which overcome this transmission barrier. We show that nematodes infecting high TL definitive hosts tend to have more successive hosts in their life cycles. This relationship was modest, though, driven mainly by the minimum TL of hosts, suggesting that the shortest trophic chains leading to a host define the boundaries of the transmission vacuum. We also show that alternative modes of transmission, like host penetration, allow nematodes to reach high TLs without intermediate hosts. We suggest that widespread omnivory as well as parasite adaptations to increase transmission probably reduce, but do not eliminate, the barriers to the transmission of helminths through the food web.     

Application of trophic transfer efficiency and age structure in the trophic analysis of fossil assemblages

We evaluate onshore-offshore trends in age-frequency distributions and trophic transfer efficiencies using 11 modern death assemblages off the Texas coast. Trophic transfer efficiencies within trophic levels offer little insight over that achieved by a size-frequency distribution. Production/biomass ratios will always be 1 in the fossil record. Within trophic-level estimates of paleogrowth efficiency, the ratio of paleoproduction to paleoingestion (Pⁱ_glt/Iⁱ_lt where i indicates the i^th trophic level and lt indicates the time-averaged value) follow the expected ecological trend precisely in that paleogrowth efficiency is consistently higher in primary consumers than in predators in all 11 death assemblages. Paleoutilization efficiency, the ratio of predator paleoingestion to prey paleoproduction, I²_lt^°/P¹_glt^°, may provide information on the degree of bias in the preservation of primary (1 °) and secondary (2 °) consumer trophic groups. I²_lt^°/P¹_glt^° fell below 0.1 in most cold-seep and bay assemblages, indicating a large surplus of primary consumers. In sharp contrast, I²_lt^°/P¹_glt^°     

Using trophic hierarchy to understand food web structure

Link arrangement in food webs is determined by the species' feeding habits. This work investigates whether food web topology is organized in a gradient of trophic positions from producers to consumers. To this end, we analyzed 26 food webs for which the consumption rate of each species was specified. We computed the trophic positions and the link densities of all species in the food webs. Link density measures how much each species contributes to the distribution of energy in the system. It is expressed as the number of links species establish with other nodes, weighted by their magnitude. We computed these two metrics using various formulations developed in the ecological network analysis framework. Results show a positive correlation between trophic position and link density across all the systems, regardless the specific formulas used to measure the two quantities. We performed the same analysis on the corresponding binary matrices (i.e. removing information about rates). In addition, we investigated the relation between trophic position and link density in: a) simulated binary webs with same connectance as the original ones; b) weighted webs with constant topology but randomized link strengths and c) weighted webs with constant connectance where both topology and link strengths are randomized. The correlation between the two indices attenuates, vanishes or becomes negative in the case of binary food webs and simulated data (weighted and unweighted).
According to our analysis, link density in food webs decreases with trophic position so that it is greatly reduced toward the top of the trophic hierarchy. This outcome, that seems to challenge previous conclusions based on null models, strongly depends on link quantification. Including interaction strengths may improve substantially our understanding of food web organization, and possibly contradict results based on the analysis of binary webs.     

The structure and evolution of angiosperm nuclear genomes

Despite several decades of investigation, the organization of angiosperm genomes remained largely unknown until very recently. Data describing the sequence composition of large segments of genomes, covering hundreds of kilobases of contiguous sequence, have only become available in the past two years. Recent results indicate commonalities in the characteristics of many plant genomes, including in the structure of chromosomal components like telomeres and centromeres, and in the order and content of genes. Major differences between angiosperms have been associated mainly with repetitive DNAs, both gene families and mobile elements. Intriguing new studies have begun to characterize the dynamic three-dimensional structures of chromosomes and chromatin, and the relationship between genome structure and co-ordinated gene function.     

The structure and evolution of Ordovician conodont apparatuses

Multielement taxonomy was instituted for Ordovician conodonts over a decade ago, and probably a majority of the multielement genera have been defined or are well understood. The present systems of notation for elements within apparatuses are inadequate and cumbersome. A new notation scheme is proposed which applies a single-letter code to the position in the apparatus occupied by certain element morphotypes. The taxonomic status of all known Ordovician conodont genera is reviewed (appendix) using the new notation, and a new scheme to classify conodont apparatuses is presented. Five main apparatus types (I-V) and seventeen subtypes (IA-IC, etc.) are defined. Within these groups, all known Ordovician conodont genera can be accommodated, and probably few new groups are required to include all other conodont genera. The apparatus types and subtypes are defined on the basis of symmetry, curvature, and number of the element types, with a clear distinction being made between the first and second transition series. Certain homologous relationships, both between and within many apparatus types, are noted. The evolution of the five major types, and the subtypes, is traced through the Ordovician. The pattern of evolution suggests that the types and subtypes recognized are probably natural biologic groupings, largely reflecting phylogenetic change.     

The evolution,structure and functioning of stomata

Summary

The anatomy and ultrastructure of guard cells from a range of species varying from the primitive types, such as mosses, to the advanced grasses and orchids are described. An attempt is made to trace the lines along which stomata developed and to define what might be considered advanced stomata. Additionally, the differentiation of guard cells from guard mother cells is discussed. Of particular note is the preprophase band of microtubules which marks the zone where the future cell wall will form and the movement of the spindle and developing cell plate through 45 degrees. The structure and function of guard cells are intimately linked. Stomata are turgor regulated valves; the osmotica for absorbing water during opening are K⁺, Cl^- and malate anions which accumulate in the guard cell vacuoles. Upon stomatal closure, K⁺ and Cl^- exit from the guard cells while at least some of the carbon from malate is channelled into starch and there is a resultant loss of guard cell turgor. The Calvin cycle may be absent or of low activity in guard cell chloroplasts and under those circumstances a source of carbon and energy to sustain the guard cells is needed. Hence it is believed that sucrose is transported into the guard cells from mesophyll cells. A brief consideration of the mechanism by which the ions are transported across the plasma membrane and tonoplast is made: the driving force for the K⁺, Cl^- and malate movement across the membranes is the proton motive force set up by proton-pumping ATPases.     

The structure and evolution of archaebacterial ribosomal RNAs

A cladistic analysis of 553 5S rRNA sequences has revealed a Ur-5S rRNA, the ancestor of all present-day 5S rRNA molecules. Previously stated characteristic differences between the eubacterial and eukaryotic molecules, namely, the length base-pairing schemes of helices D, can be used as a marker for the various archaebacterial branches. One model comprises Thermococcus, Thermoplasma, methanobacteria, and halobacteria; a second comprises the Sulfolobales; and a third is represented only by the single organism Octopus Spring species 1. A relaxed selection pressure on helix E with subsequent deletions is observed in Methanobacteriales, Methanococcales, and eubacteria. The secondary structures are supported by enzymatic digestion and chemical modification studies of the 5S rRNAs. Reconstitution of eubacterial 50S ribosomal subunits with 5S rRNA from Halobacterium and Thermoplasma has revealed 100% incorporation, while eukaryotic 5S rRNAs yielded a 50% incorporation. Relevant positions of the small-subunit rRNA are selected to answer the question of the monophyly of archaebacteria. Eight positions account for monophyly, eight for an ancestry of eubacteria with halophile methanogens and eukaryotes with eocytes (paraphyly of archaebacteria), and two for an ancestry of eubacteria with eocytes. A refinement of the neighborliness method of S. Sattath and A. Tversky resulted in a monophyly of archaebacteria when all positions are treated equally and in a paraphyly when tranversions are weighted twice over transitions.     

The evolution of chloroplast genome structure in ferns

The plastid genome (plastome) is a rich source of phylogenetic and other comparative data in plants. Most land plants possess a plastome of similar structure. However, in a major group of plants, the ferns, a unique plastome structure has evolved. The gene order in ferns has been explained by a series of genomic inversions relative to the plastome organization of seed plants. Here, we examine for the first time the structure of the plastome across fern phylogeny. We used a PCR-based strategy to map and partially sequence plastomes. We found that a pair of partially overlapping inversions in the region of the inverted repeat occurred in the common ancestor of most ferns. However, the ancestral (seed plant) structure is still found in early diverging branches leading to the osmundoid and filmy fern lineages. We found that a second pair of overlapping inversions occurred on a branch leading to the core leptosporangiates. We also found that the unique placement of the gene matK in ferns (lacking a flanking intron) is not a result of a large-scale inversion, as previously thought. This is because the intron loss maps to an earlier point on the phylogeny than the nearby inversion. We speculate on why inversions may occur in pairs and what this may mean for the dynamics of plastome evolution.     

Estuarine relationships between zooplankton community structure and trophic gradients

Zooplankton and water quality parameters were investigated ateight mesohaline stations in the lower Chesapeake Bay and ElizabethRiver from January through December 1994 to identify the changesof zooplankton community structure with increased eutrophication.The total micro- and mesozooplankton biomass decreased withthe increase of eutrophication. However, the relative proportionof microzooplankton increased with increased eutrophication.Within highly eutrophied waters, the small oligotrichs (<30µm) and rotifers dominated the total zooplankton biomass(as carbon). However, tintinnids, copepod nauplii and mesozooplanktonsignificantly decreased with the increase of eutrophication.These patterns were consistent throughout the seasons and hadsignificant relationships statistically. These results suggestzooplankton community structures characterize an increasingeutrophication of an ecosystem.     

The proteome: structure, function and evolution

This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family.     

Towards the trophic structure of the Bouvet Island marine ecosystem

Although Bouvet Island is of considerable importance for Southern Ocean species conservation, information on the marine community species inventory and trophic functioning is scarce. Our combined study of stable isotopes and feeding relationships shows that (1) the marine system conforms to the trophic pattern described for other Antarctic systems within the Antarctic circumpolar current (ACC); (2) both the benthic and the pelagic subsystem are almost exclusively linked via suspended particulate organic matter (SPOM); and (3) there is no evidence of a subsystem driven by macroalgae. Bouvet Island can therefore be characterized as a benthic “oasis” within a self-sustaining open ocean pelagic system.     

The complex structure and dynamic evolution of human subtelomeres

Subtelomeres are extraordinarily dynamic and variable regions near the ends of chromosomes. They are defined by their unusual structure: patchworks of blocks that are duplicated near the ends of multiple chromosomes. Duplications among subtelomeres have spawned small gene families, making inter-individual variation in subtelomeres a potential source of phenotypic diversity. The ectopic recombination that occurs between subtelomeres might also have a role in reconstituting telomeres in the absence of telomerase. However, the propensity for subtelomeres to interchange is a double-edged sword, as extensive subtelomeric homology can mediate deleterious rearrangements of the ends of chromosomes to cause human disease.     

The evolution of cerebellum structure correlates with nest complexity

Across the brains of different bird species, the cerebellum varies greatly in the amount of surface folding (foliation). The degree of cerebellar foliation is thought to correlate positively with the processing capacity of the cerebellum, supporting complex motor abilities, particularly manipulative skills. Here, we tested this hypothesis by investigating the relationship between cerebellar foliation and species-typical nest structure in birds. Increasing complexity of nest structure is a measure of a bird''s ability to manipulate nesting material into the required shape. Consistent with our hypothesis, avian cerebellar foliation increases as the complexity of the nest built increases, setting the scene for the exploration of nest building at the neural level.     

The evolution of nuclear genome structure in seed plants

Plant nuclear genomes exhibit extensive structural variation in size, chromosome number, number and arrangement of genes, and number of genome copies per nucleus. This variation is the outcome of a set of highly active processes, including gene duplication and deletion, chromosomal duplication followed by gene loss, amplification of retrotransposons separating genes, and genome rearrangement, the latter often following hybridization and/or polyploidy. While these changes occur continuously, it is not surprising that some of them should be fixed evolutionarily and come to mark major clades. Large-scale duplications pre-date the radiation of Brassicaceae and Poaceae and correlate with the origin of many smaller clades as well. Nuclear genomes are largely colinear among closely related species, but more rearrangements are observed with increasing phylogenetic distance; however, the correlation between amount of rearrangement and time since divergence is not perfect. By changing patterns of gene expression and triggering genome rearrangements, novel combinations of genomes (hybrids) may be a driving force in evolution.