【专辑序言】动物起源和寒武纪大爆发——序 言

动物起源和寒武纪大爆发是生命史上重要的演化创新事件。为展示相关领域的最新进展, 特组织主题为“动物起源和寒武纪大爆发”的论文专辑。作为专辑序言, 本文概述了动物起源和寒武纪大爆发领域的科学意义和当前研究趋势, 并简要介绍了本专辑的内容。专辑包含了来自13个研究单位共42位作者的12篇论文, 包括特约综述论文1篇和研究论文11篇。专辑不仅评述了相关领域的现状和未来发展趋势, 也展示了我国学者在该领域取得的部分新进展。这些进展涉及华南和华北数个特异埋藏化石库, 比如埃迪卡拉纪石板滩生物群、寒武纪宽川铺生物群和寒武纪凯里生物群等, 并涵盖了海绵动物、刺细胞动物、腕足动物、三叶虫和双瓣壳类节肢动物以及分类位置尚不明确的疑难动物化石等诸多类群。     

FOSSILS AND STRATA Shards of the Cambrian explosion

The Meishucunian Stage of south China provides a window on the radiation of skeleton-bearing metazoans at the beginning of the Cambrian. The section at Meishucun has been proposed as a candidate for a global stratotype of the Precambrian-Cambrian boundary. Fossils and Strata No. 24, by Qian Yi & Stefan Bengtson, presents a thorough reinvestigation of the bizarre Meishucunian biota on the basis of exquisitely preserved material. This monograph will become a central reference on the earliest Cambrian faunas and the problem of the Precambrian-Cambrian boundary. Qian Yi & Stefan Bengtson: Palaeontology and biostratigraphy of the early Cambrian Meishucunian Stage in Yunnan Province, south China Abstract: The skeletal fossils of the early Cambrian Meishucunian Stage from two key localities (Meishucun, Jinning County, and Xianfeng, Xundian County) in eastern Yunnan Province, China, are described and illustrated in detail to provide a basis for improved palaeobiological and biostratigraphical work. About 1250 new SEM illustrations (including a large number of stereo-pairs) of well preserved material are presented. The taxonomy is extensively revised. When biological and preservational variability are taken into account, the number of genera and species may be reduced through synonymy to about one third of that reported in the literature. Thirty-eight genera (2 of which are new) and 57 species (5 of which are new) are described. The biology and affinities of many of these taxa are also discussed, but excursions into supra-generic taxonomy are generally restrained. The Meishucunian biotas of Yunnan consist of three successive assemblages with very few taxa in common. The first, the Anabarites-Protohertzina-Arthrochites Assemblage, is dominated by Anabarites and other sedentary tube-dwelling organisms, but non-sedentary benthic mollusc-like fossils (Canopoconus) and probable predators (Protohertzina) also occur. The key elements of this fauna have a wide geographical distribution and may be compared with the earliest skeletal faunas on the Siberian Platform, the Canadian Cordillera, and other regions. The second, the Siphogonuchites-Paragloborilus Assemblage, is characterized by a great diversity of vagile mollusc-like and multisclerite-bearing animals, but also sedentary tube-dwellers and some possible predators (Cyrtochites and Yunnan-odus) occur. This fauna is largely endemic. The third. the Lapworthella-Tannuolina-Sinosachites Assemblage, is mainly characterized by widely distributed taxa of multisclerite-bearing animals (chancelloriids, Halkieria, Tannuolina, and Lap worthella). It has elements in common with late Atdabanian faunas in other regions of the world.     

Adaptive walks in a gene network model of morphogenesis: insights into the Cambrian explosion

The emergence of complex patterns of organization close to the Cambrian boundary is known to have happened over a (geologically) short period of time. It involved the rapid diversification of body plans and stands as one of the major transitions in evolution. How it took place is a controversial issue. Here we explore this problem by considering a simple model of pattern formation in multicellular organisms. By modeling gene network-based morphogenesis and its evolution through adaptive walks, we explore the question of how combinatorial explosions might have been actually involved in the Cambrian event. Here we show that a small amount of genetic complexity including both gene regulation and cell-cell signaling allows one to generate an extraordinary repertoire of stable spatial patterns of gene expression compatible with observed anteroposterior patterns in early development of metazoans. The consequences for the understanding of the tempo and mode of the Cambrian event are outlined.     

Molecular clocks do not support the Cambrian explosion

The fossil record has long supported the view that most animal phyla originated during a brief period approximately 520 MYA known as the Cambrian explosion. However, molecular data analyses over the past 3 decades have found deeper divergences among animals (approximately 800 to 1,200 MYA), with and without the assumption of a global molecular clock. Recently, two studies have instead reported time estimates apparently consistent with the fossil record. Here, we demonstrate that methodological problems in these studies cast doubt on the accuracy and interpretations of the results obtained. In the study by Peterson et al., young time estimates were obtained because fossil calibrations were used as maximum limits rather than as minimum limits, and not because invertebrate calibrations were used. In the study by Aris-Brosou and Yang, young time estimates were obtained because of problems with rate models and other methods specific to the study, and not because Bayesian methods were used. This also led to many anomalous findings in their study, including a primate-rodent divergence at 320 MYA. With these results aside, molecular clocks continue to support a long period of animal evolution before the Cambrian explosion of fossils.     

Cambrian explosion and Permian quiescence: Implications of rugged fitness landscapes

Summary The transition from the late Precambrian to Cambrian coincided with a massive increase in diversity of multicellular organisms and the rapid establishment of a large number of phyla. In contrast, the Permian extinction 200 million years ago was followed by as rapid an increase at the family level, but no new phyla or classes emerged. This asymmetry has suggested alternative theories based on greater ecological opportunity in the Cambrian, or special developmental canalization locking in development by the Permian. I suggest instead that the asymmetry reflects generic features of adaptive evolution on rugged fitness landscapes.     

The evolution of associative learning: A factor in the Cambrian explosion

The Cambrian explosion is probably the most spectacular diversification in evolutionary history, and understanding it has been a challenge for biologists since the time of Darwin. We propose that one of the key factors that drove this great diversification was associative learning. Although the evolutionary emergence of associative learning required only small modifications in already existing memory mechanisms and may have occurred in parallel in several groups, once this type of learning appeared on the evolutionary scene, it led to extreme diversifying selection at the ecological level: it enabled animals to exploit new niches, promoted new types of relations and arms races, and led to adaptive responses that became fixed through genetic accommodation processes. This learning-based diversification was accompanied by neurohormonal stress, which led to an ongoing destabilization and re-patterning of the epigenome, which, in turn, enabled further morphological, physiological, and behavioral diversification. Our hypothesis combines several previous ideas about the dynamics of the Cambrian explosion and provides a unifying framework that includes both ecological and genomic factors. We conclude by suggesting research directions that would clarify the timing and manner in which associative learning evolved, and the effects it had on the evolution of nervous systems, genomes, and animal morphology.     

Disparity, decimation and the Cambrian "explosion": comparison of early Cambrian and present faunal communities with emphasis on velvet worms (Onychophora)

The controversy about a Cambrian "explosion" of morphological disparity (followed by decimation), cladogenesis and fossilization is of central importance for the history of life. This paper revisits the controversy (with emphasis in onychophorans, which include emblematic organisms such as Hallucigenia), presents new data about the Chengjiang (Cambrian of China) faunal community and compares it and the Burgess Shale (Cambrian of Canada) with an ecologically similar but modern tropical marine site where onychophorans are absent, and with a modern neotropical terrestrial onychophoran community. Biovolume was estimated from material collected in Costa Rica and morphometric measurements were made on enlarged images of fossils. Cambrian tropical mudflats were characterized by the adaptive radiation of two contrasting groups: the vagile arthropods and the sessile poriferans. Arthropods were later replaced as the dominant benthic taxon by polychaetes. Vagility and the exoskeleton may explain the success of arthropods from the Cambrian to the modern marine and terrestrial communities, both in population and biovolume. Food ecological displacement was apparent in the B. Shale, but not in Chengjiang or the terrestrial community. When only hard parts were preserved, marine and terrestrial fossil deposits of tropical origin are even less representative than deposits produced by temperate taxa, Chengjiang being an exception. Nutrient limitations might explain why deposit feeding is less important in terrestrial onychophoran communities, where carnivory, scavenging and omnivory (associated with high motility and life over the substrate) became more important. Fossil morphometry supports the interpretation of "lobopod animals" as onychophorans, whose abundance in Chengjiang was equal to their abundance in modern communities. The extinction of marine onychophorans may reflect domination of the infaunal habitat by polychaetes. We conclude that (1) a mature ecological community structure was generalized during the Cambrian, and even biodiversity and equitability indices were surprisingly close to modern values; (2) the morphological diversity and geographic distribution of onychophorans indicate a significant pre-Cambrian evolutionary history which does not support the "explosion" hypothesis; (3) disparity among phyla was not as important as the explosion-decimation model predicts, but in the case of onychophorans, disparity within the phylum was greater than it is today and its reduction may have been associated with migration into the sediment when large predators evolved.     

Divergence with gene flow in the rock-dwelling cichlids of Lake Malawi

Within the past two million years, more than 450 species of haplochromine cichlids have diverged from a single common ancestor in Lake Malawi. Several factors have been implicated in the diversification of this monophyletic clade, including changes in lake level and low levels of gene flow across limited geographic scales. The objectives of this study were to determine the effect of recent lake-level fluctuations on patterns of allelic diversity in the genus Metriaclima, to describe the patterns of population structure within this genus, and to identify barriers to migration. This was accomplished through an analysis of allele frequencies at four microsatellite loci. Twelve populations spanning four species within Metriaclima were surveyed. The effect of lake-level fluctuations can be seen in the reduced genetic diversity of the most recently colonized sites; however, genetic diversity is not depressed at the species level. Low levels of population structure exist among populations, yet some gene flow persists across long stretches of inhospitable habitat. No general barrier to migration was identified. The results of this study are interpreted with respect to several speciation models. Divergence via population bottlenecks is unlikely due to the large allelic diversity observed within each species. Genetic drift and microallopatric divergence are also rejected because some gene flow does occur between adjacent populations. However, the reduced levels of gene flow between populations does suggest that minor changes in the selective environment could cause the divergence of populations.     

Genome rearrangement with gene families

MOTIVATION: The theory and practice of genome rearrangement analysis breaks down in the biologically widespread contexts where each gene may be present in a number of copies, not necessarily contiguous. In some of these contexts it is, however, appropriate to ask which members of each gene family in two genomes G and H, lengths lG and lH, are its true exemplars, i.e. which best reflect the original position of the ancestral gene in the common ancestor genome. This entails a search for the two exemplar strings of same length n (= number of gene families, including singletons), having the smallest possible rearrangement distance: the exemplar distance. RESULTS: A branch and bound algorithm calculates these distances efficiently when based on easily calculated traditional rearrangement distances, such as signed reversals distance or breakpoint distance, which also satisfy a property of monotonicity in the number of genes. Simulations show that in two random genomes, the expected exemplar distance/n is sensitive to the number and size of gene families, but approaches 1 as the number of singleton families increases. When the basic rearrangement distance is just the number of breakpoints, the expected cost of computing the exemplar breakpoints distance (EBD), as measured by total calls to the underlying breakpoint distance routine, is highly dependent on both n and the configuration of gene families. On the other hand, basing exemplar distance on exemplar reversals distance (ERD), the expected computing cost depends on the configuration of gene families but is not sensitive to n. AVAILABILITY: Code for EBD and ERD is available from the author or may be accessed at http://www.crm.umontreal.ca/viart/exemplar_di s. html CONTACT: sankoff@ere.umontreal.ca.     

Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families

The evolution of new gene families subsequent to gene duplication may be coupled to the fluctuation of population and environment variables. Based upon that, we presented a systematic analysis of the animal transmembrane gene duplication events on a macroevolutionary scale by integrating the palaeontology repository. The age of duplication events was calculated by maximum likelihood method, and the age distribution was estimated by density histogram and normal kernel density estimation. We showed that the density of the duplicates displays a positive correlation with the estimates of maximum number of cell types of common ancestors, and the oxidation events played a key role in the major transitions of this density trace. Next, we focused on the Phanerozoic phase, during which more macroevolution data are available. The pulse mass extinction timepoints coincide with the local peaks of the age distribution, suggesting that the transmembrane gene duplicates fixed frequently when the environment changed dramatically. Moreover, a 61-million-year cycle is the most possible cycle in this phase by spectral analysis, which is consistent with the cycles recently detected in biodiversity. Our data thus elucidate a strong coupling of duplication events and macroevolution; furthermore, our method also provides a new way to address these questions.     

Drug-sensitivity pattern analysis for study of functional relationship between gene products

We have developed a method that we call 'drug-sensitivity pattern analysis', or DSPA, for analysis of protein function. Cells are transfected with cDNA of the test molecule, followed by analysis of the sensitivity of the transfected cells to multiple growth-inhibitory drugs. If two cDNA products have similar functions, their transfected cells should show similar drug-sensitivity patterns. The cDNAs of some signaling molecules were transfected into NIH3T3 or Ha-ras-transformed NIH3T3 (ras-NIH) cells and stable transfectants, which expressed high amounts of the gene product, were isolated. Chemosensitivity of the transfected clone was compared with the parental cells by the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide method using more than 40 drugs. The chemosensitivity changes caused by the transfected gene were calculated and expressed numerically as 'drug chemosensitivity index' (DCI). When the DCI values were analyzed by regression analysis, a significant positive relationship between IkappaBalpha superrepressor and dominant-negative IKKbeta and an inverse relationship between p53 and Mdm2 were consistent with previous reports. Thus, the DSPA method is useful for identifying functional similarities between gene products.     

Evolution of gene families and relationship with organismal evolution: rapid divergence of tissue-specific genes in the early evolution of chordates

To determine a possible relationship between organismal and molecular evolution, the divergence patterns of gene families were examined by taking special notice of functional difference, tissue distribution, and intracellular localization of the members. A phylogenetic analysis of 25 different gene families revealed interesting patterns of divergence of these families: Most gene duplications giving rise to different functions antedate the vertebrates-arthropods separation. On the other hand, in a group of members carrying virtually identical function to one another but differing in tissue distribution (tissue- specific isoform), most gene duplications have occurred independently in each of vertebrates and arthropods after the separation of the two animal groups. In family members encoding molecules localizing in cell compartments (compartmentalized isoforms), the gene duplications antedate the animals-fungi separation. In the cases of the Ca2+ pump and rab subfamilies, the compartmentalized isoforms were shown to have diverged during the early evolution of eukaryotes. A phylogenetic analysis of the tissue-specific isoforms from 26 different subfamilies revealed extensive gene duplications and rapid rates of amino acid substitutions in the early evolution of chordates before the separation of fishes and tetrapods. On the contrary, the genetic variations are relatively low in the later period. This pattern of evolution observed at the molecular level is correlated well with that of tissue evolution based on fossil evidence and morphological data, and thus evolution at the two levels may be related.      

Divergence with gene flow within the recent chipmunk radiation (Tamias)

Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years on DGF in the chipmunk (Tamias) radiation with new data that quantify very high rates of mitochondrial DNA (mtDNA) introgression among para- and sympatric species in the T. quadrivittatus group in the central and southern Rocky Mountains. These new data (188 cytochrome b sequences) bring the total number of sequences up to 1871; roughly 16% (298) of the chipmunks we have sequenced exhibit introgressed mtDNA. This includes ongoing introgression between subspecies and between both closely related and distantly related taxa. In addition, we have identified several taxa that are apparently fixed for ancient introgressions and in which there is no evidence of ongoing introgression. A recurrent observation is that these introgressions occur between ecologically and morphologically diverged, sometimes non-sister taxa that engage in well-documented niche partitioning. Thus, the chipmunk radiation in western North America represents an excellent mammalian example of speciation in the face of recurrent gene flow among lineages and where biogeography, habitat differentiation and mating systems suggest important roles for both ecological and sexual selection.     

Divergence of the cytochrome b gene in grouse species

A 720-bp cytochrome b gene fragment of the mitochondrial genome was sequenced in ten species and seven potential subspecies of grouse. Of 187 variable sites detected, 140 were parsimony informative. The distribution of nucleotides in three positions of codons had a similar pattern with and did not fundamentally differ from that of the nucleotide composition of this gene in other animals, including birds. The nucleotides found at the first codon position were shown to be uniformly distributed, whereas the third position was characterized by a significant decrease in the amount of guanine and, to a lesser extent, thymine. Based on the data on the nucleotide sequences of the cytochrome b gene fragment, a phylogenetic tree was constructed. This tree fits well the morphological and ecological differentiation of the species studied.