microRNA complements in deuterostomes: origin and evolution of microRNAs

SUMMARY Although numerous studies have emphasized the role of microRNAs (miRNAs) in the control of many different cellular processes, they might also exert a profound effect on the macroevolution of animal body plans. It has been hypothesized that, because miRNAs increase genic precision and are continuously being added to metazoan genomes through geologic time, miRNAs might be instrumental for canalization of development and morphological evolution. Nonetheless, an outstanding question remains: how are new miRNAs constantly evolving? To address this question, we assessed the miRNA complements of four deuterostome species, chosen because of their sequenced genomes and well‐resolved phylogeny. Our comparative analysis shows that each of these four species is characterized by a unique repertoire of miRNAs, with few instances of miRNA loss. Moreover, we find that almost half of the miRNAs identified in this study are located in intronic regions of protein coding genes, suggesting that new miRNAs might arise from intronic regions in a process we term intronic exaptation. We also show that miRNAs often occur within cotranscribed clusters, and describe the biological function of one of these conserved clusters, the miR‐1/miR‐133 cluster. Taken together, our work shows that miRNAs can easily emerge within already transcribed regions of DNA, whether it be introns or preexisting clusters of miRNAs and/or miRNAs and protein coding genes, and because of their regulatory roles, these novel players change the structure of gene regulatory networks, with potential macroevolutionary results.     

The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint

How complex body plans evolved in animals such as fruit flies and vertebrates, as compared to the relatively simple jellyfish and sponges, is not known, given the similarity of developmental genetic repertoires shared by all these taxa. Here, we show that a core set of 18 microRNAs (miRNAs), non-coding RNA molecules that negatively regulate the expression of protein-coding genes, are found only in protostomes and deuterostomes and not in sponges or cnidarians. Because many of these miRNAs are expressed in specific tissues and/or organs, miRNA-mediated regulation could have played a fundamental evolutionary role in the origins of organs such as brain and heart--structures not found in cnidarians or sponges--and thus contributed greatly to the evolution of complex body plans. Furthermore, the continuous acquisition and fixation of miRNAs in various animal groups strongly correlates both with the hierarchy of metazoan relationships and with the non-random origination of metazoan morphological innovations through geologic time.     

Not armour, but biomechanics, ecological opportunity and increased fecundity as keys to the origin and expansion of the mineralized benthic metazoan fauna

This paper offers a new biotic interaction hypothesis for the Cambrian 'explosion' of mineralized, benthic, metazoan diversity. It proposes that organic-mineral composite structures (e.g. shells and muscle lever-arms) originated in Proterozoic lineages of primary larva-like, but reproductively competent, pelagic bilaterians because mineralization was both mechanically and energetically favourable, not because it provided armour against predation. Increased strength and rigidity of composite structures permitted growth to sizes incompatible with a continued pelagic existence, while the increased density resulting from massive mineralization facilitated settlement into, and stability in, a nutrient-rich, Proterozoic benthic zone that offered new ecological opportunities. Because evolutionary success is recognized by the formation of recoverable fossils, which requires large, enduring populations, successful lineages are those that responded to the new opportunities by achieving broad niche occupancy through the evolution of metamorphosis to larger, mineralized 'adult' body forms with more efficient food-collecting apparatus and higher fecundity. Niche modification (e.g. reef and shell-bed formation) by early mineralized benthic settlers may have increased the likelihood of further successful settlement, leading to the appearance of a period of 'explosive' increase in benthic, mineralized, metazoan diversity. Predator-prey arms races may then have followed, causing early faunal turnover and possible selection for improved armour.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 483–490.     

Low microsatellite frequencies in neuron and brain expressed microRNAs

The locations of microsatellites in mammalian genomes are restricted by purifying selection in a number of ways. For example, with the exception of some trinucleotide repeats they are excluded from protein coding regions of genomes because of their tendency to cause frameshift mutations. Here we investigate whether purifying selection might affect the types and frequencies of microsatellites in microRNA (miRNA). We concentrate on miRNAs expressed in neurons and the brain (NB-miRNAs) as microsatellites in these genes might give rise to similar effects as disease-causing repeats in protein coding genes. We show that in human miRNAs in general AG and AT microsatellites are reduced in frequency compared to AC repeats and that NB-miRNA genes contain significantly fewer microsatellites than expected from frequencies of microsatellites in other miRNA genes. NB-miRNAs show lower levels of sequence divergence in comparisons of human-macaque orthologues and more often have detectable orthologues in non-human mammals than non-NB-miRNAs. This suggests that microsatellites in miRNAs may indeed be constrained by purifying selection and that the strength of this selection may differ between NB-miRNAs and non-NB-miRNAs. We identify a number of ways in which the potential disruption of pre-miRNA secondary structure might result in purifying selection. However other, non-selective forces could also play a role in generating the biases observed in miRNA microsatellites.     

The cambrian evolutionary ‘explosion’ recalibrated

The sudden appearance in the fossil record of the major animal phyla apparently records a phase of unparalleled, rapid evolution at the base of the Cambrian period, 545 Myr ago. This has become known as the Cambrian evolutionary ‘explosion’, and has fuelled speculation about unique evolutionary processes operating at that time. The acceptance of the palaeontological evidence as a true reflection of the evolutionary narrative has been criticised in two ways: from a reappraisal of the phylogenetic relationships of the early fossils, and from predicitions of molecular divergence times, based on six appropriate metazoan genes. Phylogenetic analysis of the arthropods implies an earlier, Precambrian history for most clades, and hence an extensive period of cladogenesis unrecorded by fossils. A similar argument can be applied to molluscs, lophophorates and deuterostomes. Molecular evidence implies divergence between clades to at least 1000 Myr ago. The apparent paradox between the sudden appearance of recognisable metazoans and their extended evolutionary history might be explained by a sudden Cambrian increase in body size, which was accompanied by skeletisation. A new paradigm suggests that the ‘explosion’ in the record may have been decoupled from the evolutionary innovation.     

【特约论文】寒武纪大爆发的过去、现在与未来

人类探索认识寒武纪大爆发的过程先后经历了神创论、渐变论和爆发式演化思想的影响, 形成了越来越接近真理的重要科学认识。寒武纪大爆发本质上是动物门类的大爆发, 同时伴随着属种多样性的增长、体型增大、生物矿化以及海洋生态系统的重大变革。寒武纪大爆发是多因素制衡的自然历史过程, 任何单因素的内、外因驱动假说都不足以解释寒武纪大爆发的复杂过程。分子遗传基础和宜居环境分别是寒武纪大爆发的内在和外在必要条件, 但不是必要充分条件。因此, 寒武纪大爆发, 与其他所有生命演化事件一样, 必须通过生态作用实现。寒武纪大爆发是在氧气和其他资源不太受限、环境多变、生态荒芜的外在条件下, 基因发育调控系统预先高配的内在条件下, 发生的动物门类大爆发。在埃迪卡拉纪晚期, 多细胞的文德生物与动物采取了不同的体型发育策略和演化途径, 共享海底两千万年后, 文德生物灭绝。此后, 动物在寒武纪最初的两千万年间快速分异演化, 产生了大量演化结局各不相同的动物门类, 生态适应策略同步分化, 形成了以动物为主导的海洋生态系统, 踏上显生宙的演化征程。目前对寒武纪大爆发的探索和研究存在着偏向性或局限性, 主要关注动物门类演化和生存环境氧化还原条件, 没有将海洋生态系统作为统一整体开展全面系统的研究工作。未来探索有必要在全球范围内开展广泛全面的研究工作, 揭示寒武纪大爆发时期海洋生态系统的时空演变。     

Compilation and network analyses of cambrian food webs

A rich body of empirically grounded theory has developed about food webs—the networks of feeding relationships among species within habitats. However, detailed food-web data and analyses are lacking for ancient ecosystems, largely because of the low resolution of taxa coupled with uncertain and incomplete information about feeding interactions. These impediments appear insurmountable for most fossil assemblages; however, a few assemblages with excellent soft-body preservation across trophic levels are candidates for food-web data compilation and topological analysis. Here we present plausible, detailed food webs for the Chengjiang and Burgess Shale assemblages from the Cambrian Period. Analyses of degree distributions and other structural network properties, including sensitivity analyses of the effects of uncertainty associated with Cambrian diet designations, suggest that these early Paleozoic communities share remarkably similar topology with modern food webs. Observed regularities reflect a systematic dependence of structure on the numbers of taxa and links in a web. Most aspects of Cambrian food-web structure are well-characterized by a simple “niche model,” which was developed for modern food webs and takes into account this scale dependence. However, a few aspects of topology differ between the ancient and recent webs: longer path lengths between species and more species in feeding loops in the earlier Chengjiang web, and higher variability in the number of links per species for both Cambrian webs. Our results are relatively insensitive to the exclusion of low-certainty or random links. The many similarities between Cambrian and recent food webs point toward surprisingly strong and enduring constraints on the organization of complex feeding interactions among metazoan species. The few differences could reflect a transition to more strongly integrated and constrained trophic organization within ecosystems following the rapid diversification of species, body plans, and trophic roles during the Cambrian radiation. More research is needed to explore the generality of food-web structure through deep time and across habitats, especially to investigate potential mechanisms that could give rise to similar structure, as well as any differences.     

Colour in Burgess Shale animals and the effect of light on evolution in the Cambrian

Diffraction gratings are reported from external surfaces of the hard, protective parts of Wiwaxia corrugata, Canadia spinosa and Marrella splendens from the Burgess Shale (Middle Cambrian (515 million years), British Columbia). As a consequence, these animals would have displayed iridescence in their natural environment: Cambrian animals have previously been accurately reconstructed in black and white only. A diversity of extant marine animals inhabiting a similar depth to the Burgess Shale fauna possess functional diffraction gratings. The Cambrian is a unique period in the history of animal life where predatory lifestyles and eyes capable of producing visual images were evolving rapidly. The discovery of colour in Cambrian animals prompts a new hypothesis on the initiation of the ''Big Bang'' in animal evolution which occurred during the Cambrian: light was introduced into the behavioural systems of metazoan animals for the first time. This introduction, of what was to become generally the most powerful stimulus in metazoan behavioural systems, would have triggered turbulence in metazoan evolution.     

Molecular clocks, molecular phylogenies and the origin of phyla

Erwin, Douglas H. 1989 07 15: Molecular clocks, molecular phylogenies and the origin of phyla. Lethaia , Vol. 22, pp. 251–257. Oslo. ISSN 0024–1164.
Protein, RNA and DNA sequences have been widely used to construct phylogenies and to calculate divergence times using a molecular clock. Reliance on molecular information is particularly attractive when fossil evidence is missing or equivocal, as in the Cambrian metazoan radiation. I consider the applicability of molecular clocks and phylogenetic analysis of molecular data to the origin of metazoan phyla, and conclude that molecular information is often ambiguous or misleading. Amino acid sequences are of limited use because the redundancy of the genetic code masks patterns of descent, while in a nucleotide sequence only four potential states exist at each site (the four nucleotide bases). In each case, homoplasy may often go undetected. The application of a molecular clock to resolve the timing of the metazoan radiation is unwarranted, while molecular phylogenetic reconstruction should be approached with care. A potentially more useful technique for phylogenetic reconstruction would be the use of patterns of genome structure and organization as characters. * Molecular clock, phylogenetics, metazoan radiation, origin of phyla .     

EDIACARAN AND CAMBRIAN INDEX FOSSILS FROM SONORA, MEXICO

Abstract:  The Cambrian index fossil Treptichnus pedum is reported from the Puerto Blanco Formation near Pitiquito, Sonora, Mexico, and new occurrences of the Neoproterozoic index fossil Cloudina are reported from the underlying La Ciénega Formation. Considered together, these fossils constrain the location of the Ediacaran/Cambrian boundary in Mexico. The suite of fossils in this sequence is important because it provides an independent biostratigraphic datum for constraining the position of Laurentia during the onset of metazoan diversification, for testing proposed lithostratigraphic correlations among western North American Neoproterozoic–Cambrian successions, and for testing regional tectonic paradigms such as the Mojave-Sonora Megashear hypothesis.     

Evenness and diversity in Upper Cambrian – Lower Ordovician trilobite communities from the Central Andean Basin (Cordillera Oriental,Argentina)

Community evenness has recently received much attention, either because it is related to ecosystem functioning or because it may affect estimation of diversity. Temporal and environmental trends in diversity and evenness of trilobite communities during the Late Cambrian – Early Ordovician of the Cordillera Oriental (north‐western Argentina) are here analysed. Richness and evenness increase through time in both deep subtidal (between fair‐weather and storm wave base) and offshore (below storm wave base) communities. Two significant patterns are superimposed on this general trend: (1) the magnitude of the increase in evenness is much more pronounced in deep than in shallower settings, and (2) richness and evenness trajectories are decoupled (while a significant rise in evenness is recorded in the middle Tremadocian (Tr2), an increase in richness is delayed until the late Tremadocian (Tr3)). In contrast to expectations, a single family (Olenidae) is dominant in samples associated with this earlier rise in evenness relative to richness. Hence, this trend is explained neither by the number of families present in the communities nor by the familial identity of the most abundant taxon. Large‐scale comparisons of the timing and geographical components of these trends are restricted to the patterns recognized in Laurentian North American studies. Results from the Cordillera Oriental mirror those of Laurentia regarding the rise in both metrics in deep marine settings. Nevertheless, the timing of this increase in richness and evenness is delayed in the Cordillera Oriental, supporting the idea that palaeogeographical regions differed in the nature and timing of ecological changes. Finally, the rise in trilobite alpha‐diversity through the Late Cambrian – Early Ordovician of the Cordillera Oriental supports the idea that trilobite alpha‐diversity did not decline worldwide, suggesting that the relative decline in trilobite alpha‐diversity is most probably caused by the dilution effect.     

寒武系小碳化石(SCFs)的研究进展及意义

所谓SCFs(Small Carbonaceous Fossils),可译为"小碳化石",其大小跨越了传统的微观与宏观界线(以肉眼可见与否为标准),是一个特定化石群体的统称。它的实质含义,是指通过氢氟酸(HF)等无机酸浸泡泥岩/页岩样品后经过滤、浓缩而获得的一类体积微小的有机碳质薄膜化石,包括后生动物残片、丝状藻/菌类碎片、疑源类等类型。在小碳化石概念被正式提出之前,国外学者曾先后用有机质壁微体化石(Organic-walled microfossils)、碳质微体化石(Carbonaceous microfossils)与布尔吉斯页岩型微体化石(Burgess Shale-type microfossils)来表述此类化石。目前在国际上,与布尔吉斯页岩型(BST)化石库和奥斯坦(Orsten)型化石库一样,小碳化石已经成为寒武纪古生物学及生物埋藏学等领域研究的一个重要的新窗口;同时,通过三类特异埋藏化石的对比研究,实现优势互补,从而能够更好地阐述早期生物的演化与多样性。     

Considerations for Reconstructing Metazoan History: Signal, Resolution, and Hypothesis Testing

SYNOPSIS. Certain issues of metazoan phytogeny remain difficultto resolve even with advances in phylogenetic theory and moleculartools. This lack of resolution might be due to limited phylogeneticsignal in regions of the metazoan tree. For example, 18S rDNAdata are consistent with a rapid radiation early in the historyof bilaterian animals. Despite this lack of resolution, ourunderstanding of metazoan evolutionary history can be furtheredby extracting phylogenetic signal from data with more appropriateevolutionary models and by explicitly testing alternative hypotheses.I examined 18S rDNA data across a diverse number of phyla toidentify potential problems with using genetic data to reconstructmetazoan history. Although the 18S performs well at the mostgeneral level of metazoan phytogeny, it has shortcomings particularlyamong the non-arthropod protostomes. Examples of parametricbootstrap simulation are given to illustrate how we may beginto address methodological issues when there is limited phylogeneticsignal. These simulations suggest that we are more likely tounderstand the bilaterian radiation event by increasing thelength of nucleotide sequences collected than by employing fastergenes.     

新元古代奇异叠层石和凝块石中可疑的动物活动证据

在湖北保康马桥地区,新元古代神农架群石家冲组产出一套奇异的叠层石,凝块石和叠层石－凝块石联合体。其中叠层石具类似于食草和钻孔动物破坏的疤痕,通过对上述构造形态和特征分析,这些构造可能与后生动物的活动有关,但也不排除它们是非生物成因的可能。这些后生动物似乎已显示高度发育的行为。当前的资料表明,在凝块石构造与食草和钻孔动物生态效应之间似乎存在着一种紧密的联系,在生物进化史上,寒武纪生命大爆发似乎仅是一     

Terminal addition, the Cambrian radiation and the Phanerozoic evolution of bilaterian form

We examine terminal addition, the process of addition of serial elements in a posterior subterminal growth zone during animal development, across modern taxa and fossil material. We argue that terminal addition was the basal condition in Bilateria, and that modification of terminal addition was an important component of the rapid Cambrian evolution of novel bilaterian morphology. We categorize the often-convergent modifications of terminal addition from the presumed ancestral condition. Our focus on terminal addition and its modification highlights trends in the history of animal evolution evident in the fossil record. These trends appear to be the product of departure from the initial terminal addition state, as is evident in evolutionary patterns within-fossil groups such as trilobites, but is also more generally related to shifts in types of morphologic change through the early Phanerozoic. Our argument is contingent on dates of metazoan divergence that are roughly convergent with the first appearance of metazoan fossils in the latest Proterozoic and Cambrian, as well as on an inference of homology of terminal addition across bilaterian Metazoa.     

Classification and evolution of metazoan traces at a topological level

Topological fidelity of metazoan traces formed by metazoan behaviour is little influenced by compaction, diagenesis, continuous soft-sediment deformation and biostratinomy, substrate consistency, etc., whereas all of these can greatly alter the Euclidean geometric attributes of metazoan traces. Morphological characteristics of trace fossils can be distinguished and described objectively by both topological and Euclidean geometric parameters. The former constitute the basis of ichnoorder and ichnofamily. On the basis of topological criteria, metazoan traces can be classified as 4 ichnoorders and 22 ichnofamilies, consisting of 9 basic and 3 combined topological configurations. At a topological level, the behavioural diversity and complexity indicated by metazoan topoichnotaxa remain fairly stable in the Phanerozoic. All ichnoorders, 75% of ichnofamilies and all 9 basic topological configurations of metazoan traces are formed in the late Neoproterozoic, and all ichnofamilies, a combination of topological configurations and the most complex and highest level of topological configurations of metazoan traces, occurred in the early Cambrian. The evolution of metazoan traces can be expressed in three ranks. Changes at ichnoorder level constitute the first evolution, which is associated with the advent of kingdoms (animalia and plantae, etc.) and phyla (Ediacara and bilaterian, etc.), and the first level of palaeoecological and palaeoenvironmental changes, such as the appearance or disappearance of an ecosystem (Precambrian biomat). The first evolution terminated in the late Neoproterozoic. Changes at the ichnofamily level constitute the second evolution, which is associated with the advent of important phyla such as coelomate animal explosion and the second level of palaeoecological and palaeoenvironmental changes, such as structural changes within an ecosystem. The second evolution terminated in the early Cambrian. Changes at the ichnogeneric and ichnospecific levels constitute the third evolution, which is associated with the appearance or disappearance of the organic taxa lower than phylum, such as dinosaurs and birds, etc., and the third and fourth levels of palaeoecological and palaeoenvironmental changes, such as community-type level changes, within an established ecological structure and community level. The third evolution has been taking place since the Proterozoic.