Integrins during evolution: Evolutionary trees and model organisms

The integrins form a large family of cell adhesion receptors. All multicellular animals express integrins, indicating that the family evolved relatively early in the history of metazoans, and homologous sequences of the component domains of integrin α and β subunits are seen in prokaryotes. Some integrins, however, seem to be much younger. For example, the αI domain containing integrins, including collagen receptors and leukocyte integrins, have been found in chordates only. Here, we will discuss what conclusions can be drawn about integrin function by studying the evolutionary conservation of integrins. We will also look at how studying integrins in organisms such as the fruit fly and mouse has helped our understanding of integrin evolution-function relationships. As an illustration of this, we will summarize the current understanding of integrin involvement in skeletal muscle formation.     

The origin and evolution of segmentation

Arthropods, annelids and chordates all possess segments. It remains unclear, however, whether the segments of these animals evolved independently or instead were derived from a common ancestor. Considering this question involves examining not only the similarities and differences in the process of segmentation between these phyla, but also how this process varies within phyla, where the homology of segments is generally accepted. This article reviews what is known about the segmentation process and considers various proposals to explain its evolution.     

The origin and evolution of segmentation

Arthropods, annelids and chordates all possess segments. It remains unclear, however, whether the segments of these animals evolved independently or instead were derived from a common ancestor. Considering this question involves examining not only the similarities and differences in the process of segmentation between these phyla, but also how this process varies within phyla, where the homology of segments is generally accepted. This article reviews what is known about the segmentation process and considers various proposals to explain its evolution.     

The origin and evolution of appendages

Current awareness of gene expression patterns and developmental mechanisms involved in the outgrowth and patterning of animal appendages contributes to our understanding of the origin and evolution of these body parts. Nevertheless, this vision needs to be complemented by a new adequate comparative framework, in the context of a factorial notion of homology. It may even be profitable to categorize as appendages also gut diverticula, body ingrowths and 'virtual appendages' such as the eye spots on butterfly wings. Another unwarranted framework is the Cartesian co-ordinate system onto which the appendages are currently described and where it is supposed that one patterning system exists for each separate Cartesian axis. It may be justified, instead, to look for correspondences between the appendages and the main body axis of the same animal, as the latter might be the source of the growth and patterning mechanisms which gave rise to the former. This hypothesis of axis paramorphisms is contrasted with the current hypothesis of gene co-option. Recapitulationism is a common fault in current Evo-Devo perspectives concerning the origin of the appendages, in that the evolutionary origin of appendages is often expected to be the same as one of the key mechanisms involved in the ontogenetic inception of appendage formation. This unwarranted perspective is also evident in the current debate on the nature of the default arthropod appendage. Most likely, a default arthropod appendage never did exist, as the first appendages probably developed along the trunk of an animal already patterned extensively along the antero-posterior body axis.     

The origin and evolution of segmentation

Arthropods, annelids and chordates all possess segments. It remains unclear, however, whether the segments of these animals evolved independently or instead were derived from a common ancestor. Considering this question involves examining not only the similarities and differences in the process of segmentation between these phyla, but also how this process varies within phyla, where the homology of segments is generally accepted. This article reviews what is known about the segmentation process and considers various proposals to explain its evolution.     

鲸的起源与演化

近年发现的一些有腿鲸的化石表明,鲸的大致演化路线是：由主要陆生的巴基鲸;经过水陆两栖的陆行鲸,到基本水生但仍有发达肢体的罗德侯鲸,再到完全水生。后肢大为退化的矛齿鲸和古蜥鲸,最后大概由矛齿鲸演化出现代的齿鲸和须鲸,其间共经历了约5000万年的历史,基于牙齿的相似,原以为鲸的祖先是原始的有蹄动物中兽类。但DNA的序列分析显示,鲸与偶蹄类河马的亲缘关系最为相近,最近发现,古鲸普遍具有偶蹄类那样的双滑车关节面的距骨,因而认为鲸的祖先可能是古偶蹄类。     

Shared forces of sex chromosome evolution in haploid-mating and diploid-mating organisms: Microbotryum violaceum and other model organisms

It is usually posited that the most important factors contributing to sex chromosome evolution in diploids are the suppression of meiotic recombination and the asymmetry that results from one chromosome (the Y) being permanently heterozygous and the other (the X) being homozygous in half of the individuals involved in mating. To distinguish between the roles of these two factors, it would be valuable to compare sex chromosomes in diploid-mating organisms and organisms where mating compatibility is determined in the haploid stage. In this latter group, no such asymmetry occurs because the sex chromosomes are equally heterozygous. Here we show in the fungus Microbotryum violaceum that the chromosomes carrying the mating-type locus, and thus determining haploid-mating compatibility, are rich in transposable elements, dimorphic in size, and carry unequal densities of functional genes. Through analysis of available complete genomes, we also show that M. violaceum is, remarkably, more similar to humans and mice than to yeast, nematodes, or fruit flies with regard to the differential accumulation of transposable elements in the chromosomes determining mating compatibility vs. the autosomes. We conclude that restricted recombination, rather than asymmetrical sheltering, hemizygosity, or dosage compensation, is sufficient to account for the common sex chromosome characteristics.     

The origin and early evolution of birds

Birds evolved from and are phylogenetically recognized as members of the theropod dinosaurs; their first known member is the Late Jurassic Archaeopteryx, now represented by seven skeletons and a feather, and their closest known non-avian relatives are the dromaeosaurid theropods such as Deinonychus. Bird flight is widely thought to have evolved from the trees down, but Archaeopteryx and its outgroups show no obvious arboreal or tree-climbing characters, and its wing planform and wing loading do not resemble those of gliders. The ancestors of birds were bipedal, terrestrial, agile, cursorial and carnivorous or omnivorous. Apart from a perching foot and some skeletal fusions, a great many characters that are usually considered ‘avian’ (e.g. the furcula, the elongated forearm, the laterally flexing wrist and apparently feathers) evolved in non-avian theropods for reasons unrelated to birds or to flight. Soon after Archaeopteryx, avian features such as the pygostyle, fusion of the carpometacarpus, and elongated curved pedal claws with a reversed, fully descended and opposable hallux, indicate improved flying ability and arboreal habits. In the further evolution of birds, characters related to the flight apparatus phylogenetically preceded those related to the rest of the skeleton and skull. Mesozoic birds are more diverse and numerous than thought previously and the most diverse known group of Cretaceous birds, the Enantiornithes, was not even recognized until 1981. The vast majority of Mesozoic bird groups have no Tertiary records: Enantiornithes, Hesperornithiformes, Ichthyornithiformes and several other lineages disappeared by the end of the Cretaceous. By that time, a few Linnean ‘Orders’ of extant birds had appeared, but none of these taxa belongs to extant ‘families’, and it is not until the Paleocene or (in most cases) the Eocene that the majority of extant bird ‘Orders’ are known in the fossil record. There is no evidence for a major or mass extinction of birds at the end of the Cretaceous, nor for a sudden ‘bottleneck’ in diversity that fostered the early Tertiary origination of living bird ‘Orders’.     

The origin and evolution of modern metabolism

One fundamental goal of current research is to understand how complex biomolecular networks took the form that we observe today. Cellular metabolism is probably one of the most ancient biological networks and constitutes a good model system for the study of network evolution. While many evolutionary models have been proposed, a substantial body of work suggests metabolic pathways evolve fundamentally by recruitment, in which enzymes are drawn from close or distant regions of the network to perform novel chemistries or use different substrates. Here we review how structural and functional genomics has impacted our knowledge of evolution of modern metabolism and describe some approaches that merge evolutionary and structural genomics with advances in bioinformatics. These include mining the data on structure and function of enzymes for salient patterns of enzyme recruitment. Initial studies suggest modern metabolism originated in enzymes of nucleotide metabolism harboring the P-loop hydrolase fold, probably in pathways linked to the purine metabolic subnetwork. This gateway of recruitment gave rise to pathways related to the synthesis of nucleotides and cofactors for an ancient RNA world. Once the TIM beta/alpha-barrel fold architecture was discovered, it appears metabolic activities were recruited explosively giving rise to subnetworks related to carbohydrate and then amino acid metabolism. Remarkably, recruitment occurred in a layered system reminiscent of Morowitz's prebiotic shells, supporting the notion that modern metabolism represents a palimpsest of ancient metabolic chemistries.     

寄生虫的起源与进化

介绍了寄生虫的提前适应机制在寄生虫起源与进化中的重要作用,同时还推测了寄生虫可能的进化过程,并且阐述了寄生虫对寄生生活的适应对策以及对宿主行为的改变。     

The origin and evolution of the ribosome

Background  

The origin and early evolution of the active site of the ribosome can be elucidated through an analysis of the ribosomal proteins' taxonomic block structures and their RNA interactions. Comparison between the two subunits, exploiting the detailed three-dimensional structures of the bacterial and archaeal ribosomes, is especially informative.     

The origin and evolution of human pathogens

What are the genetic origins of human pathogens? An international group of scientists discussed this topic at a workshop that took place in late October 2004 in Baeza (Spain). Focusing primarily on bacterial pathogens, they examined the role that pathogenicity islands and bacteriophages play on determining the virulence properties that distinguish closely related members of a given species, such as host range and tissue specificity. They also discussed an instance in which closely related bacterial species differ in the production of a cell surface modification mediating resistance to an antibiotic as a result of the disparate regulation of homologous genes. In certain pathogens, genes normally carrying out housekeeping functions may adopt new functions, whereas in other organisms, genes that respond to stresses associated with non-host environments are silenced during infection to prevent the expression of products that interfere with the normal colonization process. The adaptive behaviour of certain pathogens relies on gene variation at certain loci that by virtue of containing polymeric repeats in regulatory or coding regions, can generate variants that may or may not express products that modify the cell surface of the organism. The meeting also addressed the properties of ORFan genes, which have no homologues in the sequence databases, as well as the creation of genes de novo by duplication and divergence.     

The origin and early evolution of mitochondria

Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial (specifically α-proteobacterial) ancestor but raise questions about the evolutionary antecedents of the mitochondrial proteome.