On the unique function of selenocysteine — Insights from the evolution of selenoproteins

The process of natural selection leaves signatures in our genome that can be used to identify functionally important amino acid changes in proteins. In natural populations, amino acids that are better adapted to local conditions might increase in frequency, whereas moderately to severely deleterious protein mutations tend to be eliminated and do not contribute to protein differences between species. Amino acid mutations with no fitness consequences are, however, lost or fixed without regard to natural selection. Looking for evidence of natural selection is, therefore, an attractive strategy for characterizing the contribution of a residue to protein function. Because the majority of identified selenoproteins have now been found in Cys-form, the extent of exchangeability between Sec and Cys residues can be measured in proteins over long periods of time. The statistical analysis of the pattern of Sec/Cys exchanges in diversity (within species) and divergence (between species) data, provides robust inferences of the strength and mode of natural selection acting on these protein sites. Such inferences inform us not only of the long-term exchangeability between Sec and Cys residues, but also of the nature of the selective factors shaping Sec usage in proteins.     

Phylogeny and evolution of Malagasy plated lizards

The endemic plated lizards (Gerrhosauridae) of Madagascar are one of the most diverse groups of lizards on the island (19 species) and are found in all ecoregions. On an island that presents so many interesting biological questions, plated lizards are an ideal group for examining patterns of diversification due to their high (but tractable) diversity and wide distribution. To resolve the taxonomy and evolutionary relationships of Malagasy plated lizards, and to explore their biogeographic history, we have generated a molecular phylogeny based on >2kb of both mitochondrial (cob, 1142 bp) and nuclear (NT-3, 419 bp; c-mos, 542 bp) DNA sequences. Phylogenetic relationships and divergence-time estimates indicate Zonosaurinae are monophyletic, arising from a single colonization event, likely from Africa to Madagascar in the Paleogene (Paleocene/early Eocene), with subsequent radiation. Furthermore, our results reveal widespread mischaracterization of species delimitation and assignment based on phenotypic characteristics. Paraphyly of a number of zonosaurine species was strongly supported by our dataset, revealing not only instances of likely cryptic species (phenotypic conservatism) but also phenotypic/genotypic discordance in the delimitation of species (phenotypic variability). These results clearly demonstrate the complex history of biotic diversification on Madagascar and provide novel insight into biogeographic patterns on the island.     

Late Early Triassic climate change: Insights from carbonate carbon isotopes,sedimentary evolution and ammonoid paleobiogeography

The late Early Triassic sedimentary–facies evolution and carbonate carbon-isotope marine record (δ¹³C_carb) of ammonoid-rich, outer platform settings show striking similarities between the South China Block (SCB) and the widely distant Northern Indian Margin (NIM). The studied sections are located within the Triassic Tethys Himalayan belt (Losar section, Himachal Pradesh, India) and the Nanpanjiang Basin in the South China Block (Jinya section, Guangxi Province), respectively. Carbon isotopes from the studied sections confirm the previously observed carbon cycle perturbations at a time of major paleoceanographic changes in the wake of the end-Permian biotic crisis. This study documents the coincidence between a sharp increase in the carbon isotope composition and the worldwide ammonoid evolutionary turnover (extinction followed by a radiation) occurring around the Smithian–Spathian boundary.Based on recent modeling studies on ammonoid paleobiogeography and taxonomic diversity, we demonstrate that the late Early Triassic (Smithian and Spathian) was a time of a major climate change. More precisely, the end Smithian climate can be characterized by a warm and equable climate underlined by a flat, pole-to-equator, sea surface temperature (SST) gradient, while the steep Spathian SST gradient suggests latitudinally differentiated climatic conditions. Moreover, sedimentary evidence suggests a transition from a humid and hot climate during the Smithian to a dryer climate from the Spathian onwards. By analogy with comparable carbon isotope perturbations in the Late Devonian, Jurassic and Cretaceous we propose that high atmospheric CO₂ levels could have been responsible for the observed carbon cycle disturbance at the Smithian–Spathian boundary. We suggest that the end Smithian ammonoid extinction has been essentially caused by a warm and equable climate related to an increased CO₂ flux possibly originating from a short eruptive event of the Siberian igneous province. This increase in atmospheric CO₂ concentrations could have additionally reduced the marine calcium carbonate oversaturation and weakened the calcification potential of marine organisms, including ammonoids, in late Smithian oceans.     

Karyological evolution and systematics of Malagasy microhylid frogs

Microhylid frogs are a group of largely unresolved phylogeny, and diverse data sets are needed to improve the evolutionary understanding of these amphibians. We here report karyological data for 22 species of this family, belonging to the Malagasy genera Anodonthyla, Cophyla, Platypelis, Plethodontohyla, Rhombophryne, and Stumpffia (Cophylinae); Scaphiophryne and Paradoxophyla (Scaphiophryninae); and Dyscophus (Dyscophinae); and the Asian genera Calluella and Ramanella (Microhylinae). All species studied have 2n=26 chromosomes, most of which are metacentric or submetacentric. Chromosome morphology, banding pattern, and position of the nucleolar organizer regions (NORs) provide relevant characters for the understanding of the phylogeny and systematics of these frogs. The species of the Cophylinae are characterized by a subtelocentric or telocentric fourth chromosome pair (submetacentric only in Anodonthyla), which can be seen as a synapomorphy for this subfamily. Shifts in NOR position within the Cophylinae are frequent and agree with recent mitochondrial DNA data, corroborating the non-monophyly of the genus Plethodontohyla. Changes of NOR position and chromosome morphology (i.e., occurrence of subtelocentric and telocentric elements) were also common in this subfamily, possibly being related to their faster mitochondrial substitution rate and high species diversity. The ninth chromosome pair of the examined specimens of Dyscophus guineti, all juveniles, is heteromorphic. In this pair, one of the two chromosomes is longer due to the addition of two heterochromatic segments, raising the possibility that one chromosome of this pair may be a sex chromosome.     

Insights from diploblasts; the evolution of mesoderm and muscle

The origin of both mesoderm and muscle are central questions in metazoan evolution. The majority of metazoan phyla are triploblasts, possessing three discrete germ layers. Attention has therefore been focused on two outgroups to triploblasts, Cnidaria and Ctenophora. Modern texts describe these taxa as diploblasts, lacking a mesodermal germ layer. However, some members of Medusozoa, one of two subphyla within Cnidaria, possess tissue independent of either the ectoderm or endoderm referred to as the entocodon. Furthermore, members of both Cnidaria and Ctenophora have been described as possessing striated muscle, a mesodermal derivative. While it is widely accepted that the ancestor of Eumetazoa was diploblastic, homology of the entocodon and mesoderm as well as striated muscle within Eumetazoa has been suggested. This implies a potential triploblastic ancestor of Eumetazoa possessing striated muscle. In the following review, I examine the evidence for homology of both muscle and mesoderm. Current data support a diploblastic ancestor of cnidarians, ctenophores, and triploblasts lacking striated muscle.     

Insights from amphioxus into the evolution of vertebrate cartilage

Central to the story of vertebrate evolution is the origin of the vertebrate head, a problem difficult to approach using paleontology and comparative morphology due to a lack of unambiguous intermediate forms. Embryologically, much of the vertebrate head is derived from two ectodermal tissues, the neural crest and cranial placodes. Recent work in protochordates suggests the first chordates possessed migratory neural tube cells with some features of neural crest cells. However, it is unclear how and when these cells acquired the ability to form cellular cartilage, a cell type unique to vertebrates. It has been variously proposed that the neural crest acquired chondrogenic ability by recruiting proto-chondrogenic gene programs deployed in the neural tube, pharynx, and notochord. To test these hypotheses we examined the expression of 11 amphioxus orthologs of genes involved in neural crest chondrogenesis. Consistent with cellular cartilage as a vertebrate novelty, we find that no single amphioxus tissue co-expresses all or most of these genes. However, most are variously co-expressed in mesodermal derivatives. Our results suggest that neural crest-derived cartilage evolved by serial cooption of genes which functioned primitively in mesoderm.     

Convergent evolution in discomycetes from bark and wood

Dry weathered wood (lignum and arid bark support a discomycete flora which is taxonomically extremely diverse and contains a high percentage of species with characters not found in Discomycetes of more mesic habitats. A large proportion of filiform-spored, and all muriform-spored non-lichenized Discomycetes occur in this habitat. Most lignicolous Discomycetes have either a pigmented epithecium or a dark margin which covers the hymenium when dry and many have reviving, gelaious ascomata. Their asci often have a simplified structure difficult to interpret. Weathered wood is a niche which has long continuity in geologic time but is relatively unfavorable for fungi because of exposure, aridity and low nutrient levels. Strong selective pressure has consequently been exerted on those fungi able to colonize it, resulting in a high incidence of convergent evolution.     

Insights into vertebrate evolution from the chicken genome sequence

The chicken has recently joined the ever-growing list of fully sequenced animal genomes. Its unique features include expanded gene families involved in egg and feather production as well as more surprising large families, such as those for olfactory receptors. Comparisons with other vertebrate genomes move us closer to defining a set of essential vertebrate genes.     

Insights into vertebrate evolution from the chicken genome sequence

The chicken has recently joined the ever-growing list of fully sequenced animal genomes. Its unique features include expanded gene families involved in egg and feather production as well as more surprising large families, such as those for olfactory receptors. Comparisons with other vertebrate genomes move us closer to defining a set of essential vertebrate genes.     

Perspectives in PDK1 evolution: Insights from photosynthetic and non-photosynthetic organisms

Protein kinases belonging to the AGC group modulate many diverse cellular processes in all eukaryotes. One important way to regulate AGC kinases is through phosphorylation by the upstream kinase PDK1. PDK1 localization and activity usually depend on interactions with phospholipids, which are mediated by a conserved lipid-binding pleckstrin homology (PH) domain. We recently analyzed putative PDK1 sequences from 17 photosynthetic organisms, finding that PDK1s from vascular and nonvascular species seem to be distinguished by the presence or absence of a PH domain, respectively. The only other reported PDK1 lacking a PH domain is from yeast (Saccharomyces cerevisiae). These observations raise questions about how plant PDK1s and their lipid-binding capabilities have evolved in relation to other eukaryotes, and what this means for PDK1 function. Here we use 100 PDK1 sequences from diverse organisms to discuss possible evolutionary aspects of plant PDK1 structure and lipid binding.     

At the interface of behaviour,ecology and evolution: Insights from the world of fishes

We are pleased to present this special issue of Current Zoology entitled Behaviour,Ecology and Evolution of Fishes.The goal of this special issue is to showca...     

Insights into fruit function from the proteome of the hypanthium

Apple (Malus×domestica Borkh.) was used as a model to studying essential biological processes occurring in mature fruit hypanthium, commonly referred to as the fruit flesh or pulp, a highly active tissue where numerous metabolic processes such as carbohydrate metabolism and signal transduction occur. To understand the complex biological processes occurring in the hypanthium, a proteomics approach was used to analyze the proteome from freshly harvested ripe apple fruits. A total of 290 well-resolved spots were detected using two-dimensional gel electrophoresis (2-DE). Out of these, 216 proteins were identified representing 116 non-redundant proteins using matrix-assisted laser-desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and either the MASCOT or ProteinProspector engine for peptide mass fingerprinting (PMF) database searching. Identified proteins were classified into 13 major functional categories. Among these, the energy metabolism class was the most represented and included 50% of proteins homologous to Arabidopsis proteins that are involved in the response to biotic and abiotic stresses, suggesting a dual role for these proteins in addition to energy metabolism. We also identified dynein heavy chain in the hypanthium although this protein has been proposed as absent from angiosperms and thus suggest that the lack of dyneins in higher plants studied to date may not be a general characteristic to angiosperm genomic organisation. We therefore conclude that the detection and elucidation of the apple hypanthium proteome is an indispensable step towards the comprehension of fruit metabolism, the integration of genomic, proteomic and metabolomic data to agronomic trait information and thus fruit quality improvements.     

Insights into neural mechanisms and evolution of behaviour from electric fish

Both behaviour and its neural control can be studied at two levels. At the proximate level, we aim to identify the neural circuits that control behaviour and to understand how information is represented and processed in these circuits. Ultimately, however, we are faced with questions of why particular neural solutions have arisen, and what factors govern the ways in which neural circuits are modified during the evolution of new behaviours. Only by integrating these levels of analysis can we fully understand the neural control of behaviour. Recent studies of electrosensory systems show how this synthesis can benefit from the use of tractable systems and comparative studies.     

Mobility as an emergent property of biological organization: Insights from experimental evolution

Anthropologists accept that mobility is a critical dimension of human culture, one that links economy, technology, and social relations. Less often acknowledged is that mobility depends on complex and dynamic interactions between multiple levels of our biological organization, including anatomy, physiology, neurobiology, and genetics. Here, we describe a novel experimental approach to examining the biological foundations of mobility, using mice from a long‐term artificial selection experiment for high levels of voluntary exercise on wheels. In this experiment, mice from selectively bred lines have evolved to run roughly three times as far per day as those from nonselected control lines. We consider three insights gleaned from this experiment as foundational principles for the study of mobility from the perspective of biological evolution. First, an evolutionary change in mobility will necessarily be associated with alterations in biological traits both directly and indirectly connected to mobility. Second, changing mobility will result in trade‐offs and constraints among some of the affected traits. Third, multiple solutions exist to altering mobility, so that various combinations of adjustments to traits linked with mobility can achieve the same overall behavioral outcome. We suggest that anthropological knowledge of variation in human mobility might be improved by greater research attention to its biological dimensions.     

Synapse formation and function: Insights from identified leech neurons in culture

Identified leech neurons in culture are providing novel insights to the signals underlying synapse formation and function. Identified neurons from the central nervous system of the leech can be removed individually and plated in culture, where they retain their characteristic physiological properties, grow neurites, and form specific synapses that are directly accessible by a variety of approaches. Synapses between cultured neurons can be chemical or electrical (either rectifying or not) or may not form, depending on the neuronal identities. Furthermore, the characteristics of these synapses depend on the regions of the cells that come into contact. The formation and physiology of synapses between the Retzius cell and its partners have been well characterized. Retzius cells form purely chemical, inhibitory synapses with pressuresensitive (P) cells where serotonin (5-HT) is the transmitter. Retzius cells synthesize 5-HT, which is stored in vesicles that recycle after 5-HT is secreted on stimulation. The release of 5-HT is quantal, calcium-dependent, and shows activity-dependent facilitation and depression. Anterograde and retrograde signals during synapse formation modify calcium currents, responses to 5-HT, and neurite outgrowth. The nature of these synaptogenic signals is being elucidated. For example, contact specifically with Retzius cells induces a localized selection of transmitter responses in postsynaptic P cells. This effect is signaled by tyrosine phosphorylation prior to synapse formation. © 1995 John Wiley & Sons, Inc.