Gene duplications in early metazoan evolution

Major increases in complexity during animal evolution occurred at the transition from a unicellular protozoan to a multicellular metazoan, the evolution of Bilateria from diploblasts (possibly the Cambrian explosion) and during early vertebrate evolution. A role for gene duplication in the third event has been widely discussed. Here I examine the possible role of gene duplications and domain shuffling in the first two events. There is evidence for a wave of gene duplications and shuffling which may have paved the way for multicellularity; there are also examples of gene duplications that may have facilitated the transition from diploblasts to Bilateria.     

The Cambrian explosion triggered by critical turning point in genome size evolution

The Cambrian explosion is a grand challenge to science today and involves multidisciplinary study. This event is generally believed as a result of genetic innovations, environmental factors and ecological interactions, even though there are many conflicts on nature and timing of metazoan origins. The crux of the matter is that an entire roadmap of the evolution is missing to discern the biological complexity transition and to evaluate the critical role of the Cambrian explosion in the overall evolutionary context. Here, we calculate the time of the Cambrian explosion by a “C-value clock”; our result quite fits the fossil records. We clarify that the intrinsic reason of genome evolution determined the Cambrian explosion. A general formula for evaluating genome size of different species has been found, by which the genome size evolution can be illustrated. The Cambrian explosion, as a major transition of biological complexity, essentially corresponds to a critical turning point in genome size evolution.     

Signatures of selection and sex-specific expression variation of a novel duplicate during the evolution of the Drosophila desaturase gene family

The tempo and mode of evolution of loci with a large effect on adaptation and reproductive isolation will influence the rate of evolutionary divergence and speciation. Desaturase loci are involved in key biochemical changes in long-chain fatty acids. In insects, these have been shown to influence adaptation to starvation or desiccation resistance and in some cases act as important pheromones. The desaturase gene family of Drosophila is known to have evolved by gene duplication and diversification, and at least one locus shows rapid evolution of sex-specific expression variation. Here, we examine the evolution of the gene family in species representing the Drosophila phylogeny. We find that the family includes more loci than have been previously described. Most are represented as single-copy loci, but we also find additional examples of duplications in loci which influence pheromone blends. Most loci show patterns of variation associated with purifying selection, but there are strong signatures of diversifying selection in new duplicates. In the case of a new duplicate of desat1 in the obscura group species, we show that strong selection on the coding sequence is associated with the evolution of sex-specific expression variation. It seems likely that both sexual selection and ecological adaptation have influenced the evolution of this gene family in Drosophila.     

The origin of the animals and a ‘Savannah’ hypothesis for early bilaterian evolution

The earliest evolution of the animals remains a taxing biological problem, as all extant clades are highly derived and the fossil record is not usually considered to be helpful. The rise of the bilaterian animals recorded in the fossil record, commonly known as the ‘Cambrian explosion’, is one of the most significant moments in evolutionary history, and was an event that transformed first marine and then terrestrial environments. We review the phylogeny of early animals and other opisthokonts, and the affinities of the earliest large complex fossils, the so‐called ‘Ediacaran’ taxa. We conclude, based on a variety of lines of evidence, that their affinities most likely lie in various stem groups to large metazoan groupings; a new grouping, the Apoikozoa, is erected to encompass Metazoa and Choanoflagellata. The earliest reasonable fossil evidence for total‐group bilaterians comes from undisputed complex trace fossils that are younger than about 560 Ma, and these diversify greatly as the Ediacaran–Cambrian boundary is crossed a few million years later. It is generally considered that as the bilaterians diversified after this time, their burrowing behaviour destroyed the cyanobacterial mat‐dominated substrates that the enigmatic Ediacaran taxa were associated with, the so‐called ‘Cambrian substrate revolution’, leading to the loss of almost all Ediacara‐aspect diversity in the Cambrian. Why, though, did the energetically expensive and functionally complex burrowing mode of life so typical of later bilaterians arise? Here we propose a much more positive relationship between late‐Ediacaran ecologies and the rise of the bilaterians, with the largely static Ediacaran taxa acting as points of concentration of organic matter both above and below the sediment surface. The breaking of the uniformity of organic carbon availability would have signalled a decisive shift away from the essentially static and monotonous earlier Ediacaran world into the dynamic and burrowing world of the Cambrian. The Ediacaran biota thus played an enabling role in bilaterian evolution similar to that proposed for the Savannah environment for human evolution and bipedality. Rather than being obliterated by the rise of the bilaterians, the subtle remnants of Ediacara‐style taxa within the Cambrian suggest that they remained significant components of Phanerozoic communities, even though at some point their enabling role for bilaterian evolution was presumably taken over by bilaterians or other metazoans. Bilaterian evolution was thus an essentially benthic event that only later impacted the planktonic environment and the style of organic export to the sea floor.     

Positive selection at the ASPM gene coincides with brain size enlargements in cetaceans

The enlargement of cetacean brain size represents an enigmatic event in mammalian evolution, yet its genetic basis remains poorly explored. One candidate gene associated with brain size evolution is the abnormal spindle-like microcephaly associated (ASPM), as mutations in this gene cause severe reductions in the cortical size of humans. Here, we investigated the ASPM gene in representative cetacean lineages and previously published sequences from other mammals to test whether the expansion of the cetacean brain matched adaptive ASPM evolution patterns. Our analyses yielded significant evidence of positive selection on the ASPM gene during cetacean evolution, especially for the Odontoceti and Delphinoidea lineages. These molecular patterns were associated with two major events of relative brain size enlargement in odontocetes and delphinoids. It is of particular interest to find that positive selection was restricted to cetaceans and primates, two distant lineages both characterized by a massive expansion of brain size. This result is suggestive of convergent molecular evolution, although no site-specific convergence at the amino acid level was found.     

Duplication, Selection and Gene Conversion in a Drosophila mojavensis Female Reproductive Protein Family

Protein components of the Drosophila male ejaculate, several of which evolve rapidly, are critical modulators of reproductive success. Recent studies of female reproductive tract proteins indicate they also are extremely divergent between species, suggesting that reproductive molecules may coevolve between the sexes. Our current understanding of intersexual coevolution, however, is severely limited by the paucity of genetic and evolutionary studies on the female molecules involved. Physiological evidence of ejaculate–female coadaptation, paired with a promiscuous mating system, makes Drosophila mojavensis an exciting model system in which to study the evolution of reproductive proteins. Here we explore the evolutionary dynamics of a five-paralog gene family of female reproductive proteases within populations of D. mojavensis and throughout the repleta species group. We show that the proteins have experienced ongoing gene duplication and adaptive evolution and further exhibit dynamic patterns of pseudogenation, copy number variation, gene conversion, and selection within geographically isolated populations of D. mojavensis. The integration of these patterns in a single gene family has never before been documented in a reproductive protein.     

Divergence pattern of animal gene families and relationship with the Cambrian explosion

There are many gene families that are specific to multicellular animals. These have either diverged from ancestral genes that are shared with fungi and/or plants or evolved from an ancestral gene unique to animals. The evolution of gene families involved in cell–cell communication and developmental control has been studied to establish whether the number of member genes increased dramatically immediately prior to or in concert with the Cambrian explosion. A molecular phylogeny‐based analysis of several animal‐specific gene families has revealed that gene diversification by duplication occurred during two active periods interrupted by a long intervening quiescent period. Intriguingly, the Cambrian explosion is situated in the silent period, indicating that there is no direct link between the first burst of gene diversification and the Cambrian explosion itself. The importance of gene recruitment as a possible molecular mechanism for morphological diversity, and its possible role for the Cambrian explosion, are discussed. BioEssays 23:1018–1027, 2001. © 2001 John Wiley & Sons, Inc.     

Precambrian trace fossils and the rise of bilaterian animals

In this attempt to synthesize present knowledge into a coherent story, the Cambrian explosion is interpreted to represent a true adaptive radiation, an event similar to Phanerozoic radiation events in principle but unique in its possibilities. A model of bilaterian evolution helps explain how this particular event involved the sudden initiation of major coelomate phyla. In many of these groups, preservable skeletons are part of the basic body plan. Biochemical‐sequence analyses indicate that acoelomates and pseudocoelomates branched off long before the coelomate radiation. The great differences between Vendian and Cambrian ichnofaunas, therefore, may be the result of a major shift in composition from Vendian acoelomate‐pseudocoelomate‐procoelomate faunas to Phanerozoic faunas dominated by new coelomate groups.     

An Early Cambrian stem polychaete with pygidial cirri

The oldest annelid fossils are polychaetes from the Cambrian Period. They are representatives of the annelid stem group and thus vital in any discussion of how we polarize the evolution of the crown group. Here, we describe a fossil polychaete from the Early Cambrian Sirius Passet fauna, Pygocirrus butyricampum gen. et sp. nov., with structures identified as pygidial cirri, which are recorded for the first time from Cambrian annelids. The body is slender and has biramous parapodia with chaetae organized in laterally oriented bundles. The presence of pygidial cirri is one of the characters that hitherto has defined the annelid crown group, which diversified during the Cambrian-Ordovician transition. The newly described fossil shows that this character had already developed within the total group by the Early Cambrian.     

Evolution of the vertebrate glucose-dependent insulinotropic polypeptide (GIP) gene

The glucose-dependent insulinotropic polypeptide (GIP) gene is believed to have originated from a gene duplication event very early in vertebrate evolution that also produced the proglucagon gene, yet so far GIP has only been described within mammals. Here we report the identification of GIP genes in chicken, frogs, and zebrafish. The chicken and frog genes are organized in a similar fashion to mammalian GIP genes and contain 6 exons and 5 introns in homologous locations. These genes can also potentially be proteolytically processed in identical patterns as observed in the mammalian sequences that would yield a GIP hormone that is only one amino shorter than the mammalian sequences due to the removal of an extra basic residue by carboxypeptidase E. The zebrafish GIP gene and precursor protein is shorter than other vertebrate GIP genes and is missing exon 5. The predicted zebrafish GIP hormone is also shorter, being only 31 amino acids in length. The zebrafish GIP hormone is similar in length to the proglucagon-derived peptide hormones, peptides encoded from the gene most closely related to GIP. We suggest that the structure of zebrafish GIP is more similar to the ancestral gene, and that tetrapod GIP has been extended. The mammalian GIP hormone has also undergone a period of rapid sequence evolution early in mammalian evolution. The discovery of a conserved GIP in diverse vertebrate suggests that it has an essential role in physiology in diverse vertebrates, although it may have only recently evolved a role as an incretin hormone.     

Hierarchical evolution of animal body plans

An open question in animal evolution is why the phylum- and superphylum-level body plans have changed so little, while the class- and family-level body plans have changed so greatly since the early Cambrian. Davidson and Erwin (Davidson and Erwin, 2006; Erwin and Davidson, 2009) proposed that the hierarchical structure of gene regulatory networks leads to different observed evolutionary rates for terminal properties of the body plan versus major aspects of body plan morphology. Here, we calculated the speed of evolution of genes in these gene regulatory networks. We found that the genes which determine the phylum and superphylum characters evolve slowly, while those genes which determine the classes, families, and speciation evolve more rapidly. This result furnishes genetic support to the hypothesis that the hierarchical structure of developmental regulatory networks provides an organizing structure which guides the evolution of aspects of the body plan.     

Evolution of the differential regulation of duplicate genes after polyploidization

Summary In the 50 million years since the polyploidization event that gave rise to the catostomid family of fishes the duplicate genes encoding isozymes have undergone different fates. Ample opportunity has been available for regulatory evolution of these duplicate genes. Approximately half the duplicate genes have lost their expressions during this time. Of the duplicate genes remaining, the majority have diverged to different extents in their expression within and among adult tissues. The pattern of divergence of duplicate gene expression is consistent with the accumulation of mutations at regulatory genes. The absence of a correlation of extent of divergence of gene expression with the level of genetic variability for isozymes at these loci is consistent with the view that the rates of regulatory gene and structural gene evolution are uncoupled. The magnitude of divergence of duplicate gene expressions varies among tissues, enzymes, and species. Little correlation was found with the extent of divergence of duplicate gene expression within a species and its degree of morphological conservatism, although species pairs which are increasingly taxonomically distant are less likely to share specific patterns of differential gene expression. Probable phylogenetic times of origin of several patterns of differential gene expression have been proposed. Some patterns of differential gene expression have evolved in recent evolutionary times and are specific to one or a few species, whereas at least one pattern of differential gene expression is present in nearly all species and probably arose soon after the polyploidization event. Multilocus isozymes, formed by polyploidization, provide a useful model system for studying the forces responsible for the maintenance of duplicate genes and the evolution of these once identical genes to new spatially and temporally specific patterns of regulation.     

Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement

During evolution, organisms have gained functional complexity mainly by modifying and improving existing functioning systems rather than creating new ones ab initio. Here we explore the interplay between two processes which during evolution have had major roles in the acquisition of new functions: gene duplication and protein domain rearrangements. We consider four possible evolutionary scenarios: gene families that have undergone none of these event types; only gene duplication; only domain rearrangement, or both events. We characterize each of the four evolutionary scenarios by functional attributes. Our analysis of ten fungal genomes indicates that at least for the fungi clade, species significantly appear to gain complexity by gene duplication accompanied by the expansion of existing domain architectures via rearrangements. We show that paralogs gaining new domain architectures via duplication tend to adopt new functions compared to paralogs that preserve their domain architectures. We conclude that evolution of protein families through gene duplication and domain rearrangement is correlated with their functional properties. We suggest that in general, new functions are acquired via the integration of gene duplication and domain rearrangements rather than each process acting independently.     

Distinct cell-specific expression of homospermidine synthase involved in pyrrolizidine alkaloid biosynthesis in three species of the boraginales

Homospermidine synthase (HSS) is the first specific enzyme in pyrrolizidine alkaloid (PA) biosynthesis, a pathway involved in the plant's chemical defense. HSS has been shown to be recruited repeatedly by duplication of a gene involved in primary metabolism. Within the lineage of the Boraginales, only one gene duplication event gave rise to HSS. Here, we demonstrate that the tissue-specific expression of HSS in three boraginaceous species, Heliotropium indicum, Symphytum officinale, and Cynoglossum officinale, is unique with respect to plant organ, tissue, and cell type. Within H. indicum, HSS is expressed exclusively in nonspecialized cells of the lower epidermis of young leaves and shoots. In S. officinale, HSS expression has been detected in the cells of the root endodermis and in leaves directly underneath developing inflorescences. In young roots of C. officinale, HSS is detected only in cells of the endodermis, but in a later developmental stage, additionally in the pericycle. The individual expression patterns are compared with those within the Senecioneae lineage (Asteraceae), where HSS expression is reproducibly found in specific cells of the endodermis and the adjacent cortex parenchyma of the roots. The individual expression patterns within the Boraginales species are discussed as being a requirement for the successful recruitment of HSS after gene duplication. The diversity of HSS expression within this lineage adds a further facet to the already diverse patterns of expression that have been observed for HSS in other PA-producing plant lineages, making this PA-specific enzyme one of the most diverse expressed proteins described in the literature.     

陕南寒武纪西乡生物群中Anabarites对称性演化研究

阿纳巴管(Anabarites)是寒武纪早期一类形态独特的管栖生物,其横切面的轮廓多样,但所有形态都是"3"的倍数。陕南梅树村期西乡生物群产出大量磷质Anabarites,根据管体上纵槽出现的数目和级别,确认Anabarites可分辨出三种对称类型:A型为仅具有三条一级纵槽的三辐射对称类型、B型具有三条一级纵槽和一条二级纵槽类型、C型具有三条一级纵槽和两条二级纵槽。其中B型、C型是从三辐射到六辐射对称之间的过渡类型,为新发现的对称形式。本文以上述三种类型Anabarites为研究材料,对Anabarites对称性演化途径进行了探索性研究,对寒武纪大爆发之初动物的对称性起源演化研究提供了重要证据。     

Anbmp2/4 is a new member of the transforming growth factor-beta superfamily isolated from a crinoid and involved in regeneration

Invertebrates have frequently been used to help understand the complexities of regulatory gene function and evolution. The bone morphogenetic proteins (BMPs) are a highly conserved group of secreted regulatory factors that play an important part in early embryonic patterning. In the present study we have used the remarkable regenerative potential of crinoid echinoderms to explore the BMPs' site of expression in an adult developmental programme. Our results suggest that a crinoid BMP2/4 homologue is actively involved during the early stages of blastemal regeneration at a time when fundamental patterns are being established. This supports the idea of an evolutionary developmental programme where essential gene families are conserved throughout phylogeny in terms of both expression and function.