Molecular clocks and explosive radiations

Molecular data are ideal for exploring evolutionary history because of its universality, stochasticity, and abundance. These features provide a means of exploring the evolutionary history of all organisms (including those that do not tend to leave fossils), potentially within a statistical framework that allows testing of evolutionary hypotheses. However, the discrepancy between molecular and paleontological dates for three key "explosive" radiations inferred from the fossil record--the Cambrian explosion of animal phyla and the post-KT radiations of modern orders of mammals and birds--have led to a reexamination of the assumptions on which molecular dates are based. Could variation in the rate of molecular evolution, perhaps associated with "explosive" radiations, cause overestimation of diversification dates? Here I examine four hypothetical causes of fast molecular rates in explosive radiations--body size, morphological rate, speciation rate, and ecological diversification--using available empirical evidence on patterns of variation in rate of molecular evolution.     

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.     

【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。     

寒武纪大爆发——来自贵州的化石证据*

寒武纪展示了生物演化和生态创新最为关键的一段历史, 在此期间发生了后生动物快速的辐射性演化事件, 被称为“寒武纪大爆发”。近四十年来, 基于寒武纪特异埋藏生物群的大量研究为解密寒武纪大爆发具体过程、主要动物类群起源与生态演化作出了重要贡献。贵州素有古生物王国之称, 在寒武系地层中不仅保存了大量解剖学细节精美的化石资源, 也在多个地区产出时间连续的生物组合演化序列, 在探讨动物起源与演化、全球地层对比及群落古生态学等方面具有极其重要的科研价值。近年来, 以小壳动物群、牛蹄塘生物群、杷榔生物群、剑河生物群、凯里生物群等多个生物群在贵州的发现提供了早期后生生物的新信息, 加密了中国乃至全球早期后生生物特异埋藏化石群的演化链, 为全面揭示寒武纪生物群落面貌、早期多门类后生动物的辐射演化和海洋生物群落演替提供了独特的意义, 最终为深入解读寒武纪大爆发的过程与发生机制提供重要实证。本文简要总结了贵州地区在该领域的主要学术贡献, 结合全球研究进展, 对目前存在的问题和未来研究方向提出展望。     

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.     

Spatiotemporal Evolution of the Global Species Diversity of Rhododendron

Evolutionary radiation is a widely recognized mode of species diversification, but its underlying mechanisms have not been unambiguously resolved for species-rich cosmopolitan plant genera. In particular, it remains largely unknown how biological and environmental factors have jointly driven its occurrence in specific regions. Here, we use Rhododendron, the largest genus of woody plants in the Northern Hemisphere, to investigate how geographic and climatic factors, as well as functional traits, worked together to trigger plant evolutionary radiations and shape the global patterns of species richness based on a solid species phylogeny. Using 3,437 orthologous nuclear genes, we reconstructed the first highly supported and dated backbone phylogeny of Rhododendron comprising 200 species that represent all subgenera, sections, and nearly all multispecies subsections, and found that most extant species originated by evolutionary radiations when the genus migrated southward from circumboreal areas to tropical/subtropical mountains, showing rapid increases of both net diversification rate and evolutionary rate of environmental factors in the Miocene. We also found that the geographically uneven diversification of Rhododendron led to a much higher diversity in Asia than in other continents, which was mainly driven by two environmental variables, that is, elevation range and annual precipitation, and were further strengthened by the adaptation of leaf functional traits. Our study provides a good example of integrating phylogenomic and ecological analyses in deciphering the mechanisms of plant evolutionary radiations, and sheds new light on how the intensification of the Asian monsoon has driven evolutionary radiations in large plant genera of the Himalaya-Hengduan Mountains.     

Phylogeography: spanning the ecology‐evolution continuum

Synthesis of ecological and evolutionary concepts and tools has led to improved understanding of how diversification, dispersal, community assembly, long‐term coexistence and extinction shape patterns of biological diversity. Phylogeography, with its focus on Quaternary interactions within and between populations, can help elucidate the processes acting between the evolutionary time‐scales on which species arise and the ecological time‐scales on which members of an assemblage interact with each other and their environment. Still, it has yet to be widely incorporated in that synthesis. Here, we highlight three areas where integration of phylogeography with ecological and evolutionary approaches can provide new insights into key questions. First, phylogeography can help clarify the roles of isolation, niche conservatism and environmental stability in generating patterns of alpha‐ and beta‐diversity. Second, phylogeography can help isolate the effects of Quaternary dispersal limitation from other factors driving community assembly and spatial turnover. Third, phylogeography can help identify key processes leading to and resulting from extinction events, including the population dynamics of species range reduction and its effects on the strength and temporal flexibility of networks of species interactions. We conclude with an outlook on the data‐gathering protocols necessary for this collaborative, interdisciplinary research agenda.     

陕南早寒武世早期磷酸盐化Punctatus奇异星状口盘的发现及其形态功能分析

早寒武世最早期梅树村期处于“寒武纪大爆发”序幕阶段。在这一时期,生物类群发生了大规模辐射演化及其身体构型的快速革新,形成与前寒武纪生物群明显不同的生物组合面貌。最近在陕南宽川铺地区早寒武世早期灯影组宽川铺段地层中发现了数十枚呈三维立体精美保存的磷酸盐化奇异星状生物化石标本,通过形态功能分析及与其共生的Punctatus的口盘类比表明,该奇异星状生物很可能属于腔肠动物Punctatus的口盘,星状体的中心为该生物的口部。而腔肠动物的出现标志着真后生动物的开始,在生物起源演化历程上占据着极其关键的位置。本文报道的奇异星状生物可能代表了初具原始触手的腔肠动物早期演化类型,为研究真后生动物起源演化、功能进化提供了新的实证材料。     

Key innovations and island colonization as engines of evolutionary diversification: a comparative test with the Australasian diplodactyloid geckos

The acquisition of key innovations and the invasion of new areas constitute two major processes that facilitate ecological opportunity and subsequent evolutionary diversification. Using a major lizard radiation as a model, the Australasian diplodactyloid geckos, we explored the effects of two key innovations (adhesive toepads and a snake‐like phenotype) and the invasion of new environments (island colonization) in promoting the evolution of phenotypic and species diversity. We found no evidence that toepads had significantly increased evolutionary diversification, which challenges the common assumption that the evolution of toepads has been responsible for the extensive radiation of geckos. In contrast, a snakelike phenotype was associated with increased rates of body size evolution and, to a lesser extent, species diversification. However, the clearest impact on evolutionary diversification has been the colonization of New Zealand and New Caledonia, which were associated with increased rates of both body size evolution and species diversification. This highlights that colonizing new environments can drive adaptive diversification in conjunction or independently of the evolution of a key innovation. Studies wishing to confirm the putative link between a key innovation and subsequent evolutionary diversification must therefore show that it has been the acquisition of an innovation specifically, not the colonization of new areas more generally, that has prompted diversification.     

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.     

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.     

Density-dependent diversification in North American wood warblers

Evidence from both molecular phylogenies and the fossil record suggests that rates of species diversification often decline through time during evolutionary radiations. One proposed explanation for this pattern is ecological opportunity, whereby an initial abundance of resources and lack of potential competitors facilitate rapid diversification. This model predicts density-dependent declines in diversification rates, but has not been formally tested in any species-level radiation. Here we develop a new conceptual framework that distinguishes density dependence from alternative processes that also produce temporally declining diversification, and we demonstrate this approach using a new phylogeny of North American Dendroica wood warblers. We show that explosive lineage accumulation early in the history of this avian radiation is best explained by a density-dependent diversification process. Our results suggest that the tempo of wood warbler diversification was mediated by ecological interactions among species and that lineage and ecological diversification in this group are coupled, as predicted under the ecological opportunity model.     

A critical reappraisal of the fossil record of the bilaterian phyla

It has long been assumed that the extant bilaterian phyla generally have their origin in the Cambrian explosion, when they appear in an essentially modern form. Both these assumptions are questionable. A strict application of stem- and crown-group concepts to phyla shows that although the branching points of many clades may have occurred in the Early Cambrian or before, the appearance of the modern body plans was in most cases later: very few bilaterian phyla sensu stricto have demonstrable representatives in the earliest Cambrian. Given that the early branching points of major clades is an inevitable result of the geometry of clade diversification, the alleged phenomenon of phyla appearing early and remaining morphologically static is seen not to require particular explanation. Confusion in the definition of a phylum has thus led to attempts to explain (especially from a developmental perspective) a feature that is partly inevitable, partly illusory. We critically discuss models for Proterozoic diversification based on small body size, limited developmental capacity and poor preservation and cryptic habits, and show that the prospect of lineage diversification occurring early in the Proterozoic can be seen to be unlikely on grounds of both parsimony and functional morphology. Indeed, the combination of the body and trace fossil record demonstrates a progressive diversification through the end of the Proterozoic well into the Cambrian and beyond, a picture consistent with body plans being assembled during this time. Body-plan characters are likely to have been acquired monophyletically in the history of the bilaterians, and a model explaining the diversity in just one of them, the coelom, is presented. This analysis points to the requirement for a careful application of systematic methodology before explanations are sought for alleged patterns of constraint and flexibility.     

Phylogenetic Patterns of Geographical and Ecological Diversification in the Subgenus Drosophila

Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. Members of the subgenus Drosophila are distributed across the globe and show a large diversity of ecological niches. Furthermore, taxonomic classification of Drosophila includes the rank radiation, which refers to closely related species groups. Nevertheless, it has never been tested if these taxonomic radiations correspond to evolutionary radiations. Here we present a study of the patterns of diversification of Drosophila to test for increased diversification rates in relation to the geographic and ecological diversification processes. For this, we have estimated and dated a phylogeny of 218 species belonging to the major species groups of the subgenus. The obtained phylogenies are largely consistent with previous studies and indicate that the major groups appeared during the Oligocene/Miocene transition or early Miocene, characterized by a trend of climate warming with brief periods of glaciation. Ancestral reconstruction of geographic ranges and ecological resource use suggest at least two dispersals to the Neotropics from the ancestral Asiatic tropical disribution, and several transitions to specialized ecological resource use (mycophagous and cactophilic). Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. However, diversification analyses show no significant support for adaptive radiations as a result of geographic dispersal or ecological resource shift. Also, cactophily has not resulted in an increase in the diversification rate of the repleta and related groups. It is thus concluded that the taxonomic radiations do not correspond to adaptive radiations.     

Diet and Diversification in the Evolution of Coral Reef Fishes

The disparity in species richness among evolutionary lineages is one of the oldest and most intriguing issues in evolutionary biology. Although geographical factors have been traditionally thought to promote speciation, recent studies have underscored the importance of ecological interactions as one of the main drivers of diversification. Here, we test if differences in species richness of closely related lineages match predictions based on the concept of density-dependent diversification. As radiation progresses, ecological niche-space would become increasingly saturated, resulting in fewer opportunities for speciation. To assess this hypothesis, we tested whether reef fish niche shifts toward usage of low-quality food resources (i.e. relatively low energy/protein per unit mass), such as algae, detritus, sponges and corals are accompanied by rapid net diversification. Using available molecular information, we reconstructed phylogenies of four major reef fish clades (Acanthuroidei, Chaetodontidae, Labridae and Pomacentridae) to estimate the timing of radiations of their subclades. We found that the evolution of species-rich clades was associated with a switch to low quality food in three of the four clades analyzed, which is consistent with a density-dependent model of diversification. We suggest that ecological opportunity may play an important role in understanding the diversification of reef-fish lineages.     

Antiquity and evolution of the MADS-box gene family controlling flower development in plants

MADS-box genes in plants control various aspects of development and reproductive processes including flower formation. To obtain some insight into the roles of these genes in morphological evolution, we investigated the origin and diversification of floral MADS-box genes by conducting molecular evolutionary genetics analyses. Our results suggest that the most recent common ancestor of today's floral MADS-box genes evolved roughly 650 MYA, much earlier than the Cambrian explosion. They also suggest that the functional classes T (SVP), B (and Bs), C, F (AGL20 or TM3), A, and G (AGL6) of floral MADS-box genes diverged sequentially in this order from the class E gene lineage. The divergence between the class G and E genes apparently occurred around the time of the angiosperm/gymnosperm split. Furthermore, the ancestors of three classes of genes (class T genes, class B/Bs genes, and the common ancestor of the other classes of genes) might have existed at the time of the Cambrian explosion. We also conducted a phylogenetic analysis of MADS-domain sequences from various species of plants and animals and presented a hypothetical scenario of the evolution of MADS-box genes in plants and animals, taking into account paleontological information. Our study supports the idea that there are two main evolutionary lineages (type I and type II) of MADS-box genes in plants and animals.     

Ecological drivers of the Ediacaran-Cambrian diversification of Metazoa

Organismal modifications to their physical and chemical environment play a significant role in structuring many modern ecosystems, and experimental evidence suggests that such behavior can increase diversity. Despite the important role such activities play in connecting ecology and evolution, less is known of the macroevolutionary impact of such influences, especially their role during major evolutionary transitions. The Ediacaran-Cambrian diversification of Metazoa encompassed the appearance and early diversification of virtually all major clades of marine animals and the establishment of metazoan-dominated ecosystems. Here we assess the role of positive ecological feedbacks using a new compilation of the first occurrences of all metazoan phyla, classes; orders and equivalent stem taxa, as well as data from a previously published compendium on fossils from the early to middle Cambrian of China. The results reveal relatively minor feedback during the Ediacaran, but a substantial increase during the Cambrian, principally through bioturbation and the appearance of a number of structural engineers, including sponges. Chemical modification of the environment through filtering and bioturbation seems to have had the largest impact. Data on taxic diversity is a poor proxy for abundance, or for the actual environmental impact of these activities, however. Future assessments of the influence of ecological feedbacks on this event will require standardized assessments of the abundance of taxa with different ecological roles.     

Climate and history explain the species richness peak at mid-elevation for Schizothorax fishes (Cypriniformes: Cyprinidae) distributed in the Tibetan Plateau and its adjacent regions

Aim  We studied elevational species richness patterns of Schizothorax fishes and identified the roles of ecological and evolutionary factors in shaping the patterns of elevational diversity.
Location  The Tibetan Plateau and its adjacent regions.
Methods  We assembled distribution and altitude data for all Schizothorax species using the literature. We merged ecological and evolutionary approaches to test the relationships between species richness and ecological factors (climate, area, the mid-domain effect) or evolutionary factors (diversification rates and time of colonization).
Results  We found that species richness of Schizothorax fishes peaked at mid-elevations. Rainfall, area, the mid-domain effect and diversification rate were weak predictors of the richness pattern. Temperature showed a nonlinear relationship with species richness. Temperature and time of colonization were the most important variables in explaining the elevational diversity pattern.
Main conclusion  Our findings indicate that the time-for-speciation effect and niche conservatism play important roles in variation of species richness.     

Die kambrische Explosion

This article reviews events during the Proterozoic/ Cambrian turnover, termed the “Cambrian explosion”. The first part heralds observed stages of the organismal evolution and discusses their influence and bearing on the latest concept of the Proterozoic/Cambrian boundary. In addition, the number and extent of Cambrian fossil lagerstaetten and their meaning for the interpretation of Metazoan diversification is discussed. A third part gives a synoptic overview of the most important proposed causes and mechanisms for the Cambrian explosion.     

What causes latitudinal gradients in species diversity? Evolutionary processes and ecological constraints on swallowtail biodiversity

The latitudinal diversity gradient (LDG) is one of the most striking ecological patterns on our planet. Determining the evolutionary causes of this pattern remains a challenging task. To address this issue, previous LDG studies have usually relied on correlations between environmental variables and species richness, only considering evolutionary processes indirectly. Instead, we use a phylogenetically integrated approach to investigate the ecological and evolutionary processes responsible for the global LDG observed in swallowtail butterflies (Papilionidae). We find evidence for the 'diversification rate hypothesis' with different diversification rates between two similarly aged tropical and temperate clades. We conclude that the LDG is caused by (1) climatically driven changes in both clades based on evidence of responses to cooling and warming events, and (2) distinct biogeographical histories constrained by tropical niche conservatism and niche evolution. This multidisciplinary approach provides new findings that allow better understanding of the factors that shape LDGs.