Extinction may not be forever

Here we review the phenomenon of ecomorph evolution and the hypothesis of iterative climatic cycles. Although a widely known phenomenon, convergent evolution has been underappreciated in both its scope and commonality. The power of natural selection to override genealogy to create similar morphologies (even among distantly related organisms) supports classical Darwinian evolution. That this occurs repeatedly in stratigraphically closely spaced intervals is one of the most striking features of Earth history. Periodic extinctions followed by re-evolution of adaptive types (ecomorphs) are not isolated occurrences but are embedded within complex ecological systems that evolve, become extinct, and repeat themselves in temporal synchrony. These complexes of radiation and extinction bundle the biostratigraphic record and provide the basis for a global stratigraphy. At this scale, climatic change is the only mechanism adequate to explain the observed record of repeating faunas and floras. Understanding of the underlying causes may lead to predictive theories of global biostratigraphy, evolutionary processes, and climatic change.     

Ultrastructure of spermatozoa of <Emphasis Type="Italic">Onthophagus taurus</Emphasis> (Coleoptera,Scarabaeidae) exhibits heritable variation

Sperm competition is thought to be an important selective pressure shaping sperm form and function. However, few studies have moved beyond gross examinations of sperm morphology. Sperm length is subject to sexual selection via sperm competition in the scarab beetle Onthophagus taurus. Here, the structure and ultrastructure of spermatozoa in this species were investigated using light and electron microscopy. Spermatozoa were found to be filiform, measuring about 1,200 mm in length. The sperm head consists of a three-layered acrosome and a nuclear region bearing the anterior extension of the centriole adjunct. Acrosome and nuclear regions are bilaterally symmetric, with their axes of symmetry being orthogonal to each other. Head and flagellar structures are connected by a well-developed centriole adjunct. The sperm heads are asymmetrically surrounded by accessory material and embedded into the cytoplasm of the spermatocyst cell. The accessory material is produced inside the spermatids and then transferred to the outside due to a new membrane formed around the sperm’s organelles. The old spermatid membrane separates the accessory material from the cyst cell. The flagellum contains a 9+9+2 axoneme, two accessory bodies, and two mitochondrial derivatives of unequal size. The major mitochondrial derivative is significantly larger than the minor one. The axoneme is arranged in a sinusoidal manner parallel along the major mitochondrial derivative. The spermatozoa show no progressive motility when released in buffer solution which is likely to be the result of the flagellar arrangement and the structure of the major mitochondrial derivative. The cross-sectional area of the minor and the major mitochondrial derivatives show different patterns of genetic variation. The data provide the first estimates of genetic variation in sperm ultrastructure for any species, and give evidence for the persistence of genetic variation in ultrastructure required for the rapid and divergent evolution that characterizes spermatozoa generally.     

Ecological selection of bacterial taxa with larger genome sizes in response to polycyclic aromatic hydrocarbons stress

Polycyclic aromatic hydrocarbons(PAHs) are ubiquitous priority pollutants that cause great damage to the natural environment and health. Average genome size in a community is critical for shedding light on microbiome’s functional response to pollution stress within an environment. Here, microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community. We found the distinct communities of significantly larger genome size w...     

The species flocks of East African cichlid fishes: recent advances in molecular phylogenetics and population genetics

With more than 3,000 species, the fish family Cichlidae is one of the most species-rich families of vertebrates. Cichlids occur in southern and central America, Africa, Madagascar, and India. The hotspot of their biodiversity is East Africa, where they form adaptive radiations composed of hundreds of endemic species in several lakes of various sizes and ages. The unparalleled species richness of East African cichlids has been something of a conundrum for evolutionary biologists and ecologists, since it has been in doubt whether these hundreds of species arose by allopatric speciation or whether it is necessary to invoke somewhat less traditional models of speciation, such as micro-allopatric, peripatric, or even sympatric speciation or evolution through sexual selection mediated by female choice. Ernst Mayrs analyses of these evolutionary uniquely diverse species assemblages have contributed to a more direct approach to this problem and have led to a deeper understanding of the patterns and processes that caused the formation of these huge groups of species. We review here recent molecular data on population differentiation and phylogenetics, which have helped to unravel, to some extent, the patterns and processes that led to the formation and ecological maintenance of cichlid species flocks. It is becoming apparent that sexually selected traits do play an important role in speciation in micro-allopatric or even sympatric settings. Species richness seems to be roughly correlated with the surface area, but not the age, of the lakes. We observe that the oldest lineages of a species flock of cichlids are often less species-rich and live in the open water or deepwater habitats. While the species flocks of the Lake Malawai and the Lake Victoria areas were shown to be monophyletic, the cichlid assemblage of Lake Tanganyika seems to consist of several independent species flocks. Cichlids emerge as an evolutionary model system in which many fundamental questions in evolution and ecology can be tested successfully, yet for other fish species flocks the relative importance of alternative mechanisms of speciation is likely to differ from that in cichlid fish.Dedicated to Prof. Ernst Mayr     

The ant genomes have been invaded by several types of mariner transposable elements

To date, only three types of full-length mariner elements have been described in ants, each one in a different genus of the Myrmicinae subfamily: Sinvmar was isolated from various Solenopsis species, Myrmar from Myrmica ruginodis, and Mboumar from Messor bouvieri. In this study, we report the coexistence of three mariner elements (Tnigmar-Si, Tnigmar-Mr, and Tnigmar-Mb) in the genome of a single species, Tapinoma nigerrimum (subfamily Dolichoderinae). Molecular evolutionary analyses of the nucleotide sequence data revealed a general agreement between the evolutionary history of most the elements and the ant species that harbour them, and suggest that they are at the vertical inactivation stage of the so-called Mariner Life Cycle. In contrast, significantly reduced levels of synonymous divergence between Mboumar and Tnigmar-Mb and between Myrmar and Botmar (a mariner element isolated from Bombus terrestris), relative to those observed between their hosts, suggest that these elements arrived to the species that host them by horizontal transfer, long after the species?? split. The horizontal transfer events for the two pairs of elements could be roughly dated within the last 2 million years and about 14 million years, respectively. As would be expected under this scenario, the coding sequences of the youngest elements, Tnigmar-Mb and Mboumar, are intact and, thus, potentially functional. Each mariner element has a different chromosomal distribution pattern according to their stage within the Mariner Life Cycle. Finally, a new defective transposable element (Azteca) has also been found inserted into the Tnigmar-Mr sequences showing that the ant genomes have been invaded by at least four different types of mariner elements.     

应用荧光原位杂交方法检测赤潮异弯藻

根据对赤潮异弯藻(Heterosigma akashiwo)核糖体大亚基(LSU)和核糖体转录单元内间隔区 (ITS) 序列信息的分析,设计了以胞质rRNA和胞核rDNA为靶序列的特异性探针,建立了赤潮异弯藻的全细胞和细胞核荧光原位杂交快速检测方法.结果表明,探针能分别使整个细胞质和细胞核呈现强烈的绿色荧光;探针是特异性的,不与其他受试藻进行交叉反应.同时,用该方法成功的从模拟自然海区混合样品中检测出赤潮异弯藻.该研究方法可以适用于对实验室和自然海区赤潮异弯藻样品的快速、准确、特异和半定量检测.     

环境DNA宏条形码技术在蓝藻群落监测中的应用

全球气候变化下的蓝藻水华大规模暴发成为重要的环境问题,对蓝藻准确、高效和实时的监测是蓝藻水华防控的关键.近年来,环境DNA（environmental DNA,eDNA）宏条形码技术开始应用于蓝藻群落监测,弥补了显微镜镜检法物种鉴定难和受主观经验影响大的缺点.eDNA宏条形码为快速和大规模蓝藻群落监测提供了可能,其应用尚处于初步探索阶段,数据处理方法尚不成熟,因此有必要从引物选择、序列聚类、注释方法和绝对定量4个层面系统综述eDNA宏条形码技术在蓝藻群落监测中的研究进展,以推进eDNA宏条形码在蓝藻群落监测中的应用.引物选择应针对目标蓝藻类群,16S rRNA基因数据库涵盖蓝藻物种范围广,是最常用的eDNA宏条形码,但16S-23S rRNA基因间隔区域（internal transcribed spacer,ITS）和功能基因在属内物种间具有较好的区分效果,为eDNA宏条形码在蓝藻物种水平注释提供可能.序列聚类一般通过设定物种间分类阈值进行OTUs聚类,但可能丢失序列相似度高于分类阈值的不同物种;序列差异低至单核苷酸变异方法的应用进一步区分了隐蔽的物种和生态型,产生的序列具有生物学意义,可以实现跨数据集间的比较分析.在注释方法上,基于数据库参考序列距离相似度的注释方法,注释结果的分辨率和准确度不高;基于系统进化位置的注释方法,提升了注释结果的准确度,反映了物种间的进化关系.加入外源DNA的内标法,以及基于细胞体积和基因拷贝数目关系的细胞体积校正系数法为eDNA宏条形码物种丰度的绝对定量提供了可能.      

An emergy evaluation of complexity,information and technology,towards maximum power and zero emissions

This paper mostly deals with the role of energy, matter and information flows within both environmental and human-dominated systems. Sustainable growth and development of both kinds of systems require optimum use of available resources for maximum power output, as suggested by Lotka's Maximum Power Principle [Lotka AJ. Contribution to the energetics of evolution. In: Proceedings of the national academy of sciences of the United States of America, vol. 8. 1922, p. 147–50; Lotka AJ. Natural selection as a physical principle. In: Proceedings of the national academy of sciences of the United States of America, vol. 8. 1922, p. 151–5.], recently restated by Odum [Odum HT. Maximum power and efficiency: a rebuttal. Ecol Model 1983;20:71–82; Odum HT. Environmental accounting. Emergy and environmental decision making. N.Y.: John Wiley & Sons; 1996.] as Maximum Em-Power Principle within the framework of his Emergy Synthesis approach. In times of declining resources, this principle translates into increased efficiency and optimum use of any kind of waste and co-products. Ecosystems and any self-organizing systems always apply this strategy and their selection–evolution mechanisms are based on their ability of growing on any untapped resource available. In order to do so, they increase the number of components and patterns for resource degradation in order to optimize the resource throughput and power output. Such a strategy also applies to human-dominated, economic systems, where the ability of dealing with co-products and wastes by means of appropriate designs as well as reuse and recycling processes may lead to “zero-emission” patterns (increased complexity, optimal resource throughput, minimization of emissions, resource exchange among system's components) and be the key for successful and sustainable development. In this paper Life Cycle Assessment and Emergy Synthesis approaches are suggested as joint tools for qualitative and quantitative evaluation of progresses towards industrial symbiosis and more sustainable production and consumption patterns within a zero emission framework.     

Multilevel selection and social evolution of insect societies

How sterile, altruistic worker castes have evolved in social insects and how they are maintained have long been central topics in evolutionary biology. With the advance of kin selection theory, insect societies, in particular those of haplodiploid bees, ants, and wasps, have become highly suitable model systems for investigating the details of social evolution and recently also how within-group conflicts are resolved. Because insect societies typically do not consist of clones, conflicts among nestmates arise, for example about the partitioning of reproduction and the allocation of resources towards male and female sexuals. Variation in relatedness among group members therefore appears to have a profound influence on the social structure of groups. However, insect societies appear to be remarkably robust against such variation: division of labor and task allocation are often organized in more or less the same way in societies with high as in those with very low nestmate relatedness. To explain the discrepancy between predictions from kin structure and empirical data, it was suggested that constraints—such as the lack of power or information—prevent individuals from pursuing their own selfish interests. Applying a multilevel selection approach shows that these constraints are in fact group-level adaptation preventing or resolving intracolonial conflict. The mechanisms of conflict resolution in insect societies are similar to those at other levels in the biological hierarchy (e.g., in the genome or multicellular organisms): alignment of interests, fair lottery, and social control. Insect societies can thus be regarded as a level of selection with novelties that provide benefits beyond the scope of a solitary life. Therefore, relatedness is less important for the maintenance of insect societies, although it played a fundamental role in their evolution.Dedicated to Prof. Ernst Mayr     

Juvenile morphology in baleen whale phylogeny

Phylogenetic reconstructions are sensitive to the influence of ontogeny on morphology. Here, we use foetal/neonatal specimens of known species of living baleen whales (Cetacea: Mysticeti) to show how juvenile morphology of extant species affects phylogenetic placement of the species. In one clade (sei whale, Balaenopteridae), the juvenile is distant from the usual phylogenetic position of adults, but in the other clade (pygmy right whale, Cetotheriidae), the juvenile is close to the adult. Different heterochronic processes at work in the studied species have different influences on juvenile morphology and on phylogenetic placement. This study helps to understand the relationship between evolutionary processes and phylogenetic patterns in baleen whale evolution and, more in general, between phylogeny and ontogeny; likewise, this study provides a proxy how to interpret the phylogeny when fossils that are immature individuals are included. Juvenile individuals in the peramorphic acceleration clades would produce misleading phylogenies, whereas juvenile individuals in the paedomorphic neoteny clades should still provide reliable phylogenetic signals.     

Dental microwear in relation to changes in the direction of mastication during the evolution of Myodonta (Rodentia,Mammalia)

Observations of dental microwear are used to analyse the correlation between changes in molar tooth crown morphology and the direction of masticatory movement during the evolution of Myodonta (Rodentia, Mammalia). The studied sample includes 36 specimens representing both superfamilies of Myodonta (Muroidea and Dipodoidea) spanning 16 dipodoid and 9 muroid species. Microscopic scratches on occlusal surfaces resulting from contact between opposite teeth during mastication are analysed. Using these features, we determine the direction of masticatory movements. Microwear patterns display diverse orientations among Dipodoidea: oblique in Sicistinae, Euchoreutinae and Zapodinae, propalinal in Dipodinae and intermediary in Allactaginae. Similarly, Muroidea exhibit the following orientations: oblique in Cricetinae and propalinal in Arvicolinae, Cricetomyinae, Gerbillinae and Murinae. These various chewing types illustrate different evolutionary grades within the superfamilies. Acquisition of the antero-posterior masticatory movement in Dipodoidea is related to flattening of the molar occlusal surface. However, in some muroid subfamilies, this direction of mastication is associated with low-crowned and cuspidate molars (Cricetomyinae, Murinae).     

Inter-comparisons of VOC oxidation mechanisms based on box model: A focus on OH reactivity

Volatile organic compounds (VOCs) oxidation processes play a very important role in atmospheric chemistry, and the chemical reactions are expressed in various manners in chemical mechanisms. To gain an improved understanding of VOCs evolution during oxidation processes and evaluate the discrepancies of VOCs oxidation schemes among different mechanisms, we used the total VOC reactivity as a diagnostic and evaluated tool to explore the differences for six widely used chemical mechanisms. We compared the total VOC reactivity evolution under high-NO_x conditions for several sets of precursors, including n-pentane, toluene, ethene, isoprene and a mixture of 57 Photochemical Assessment Monitoring Stations (PAMS) species in a 0-D photochemical box model. Inter-comparison of total VOC reactivity of individual precursor simulations showed discrepancies to different extent of the oxidation schemes among the studied mechanisms, which are mainly attributed to the different lumping approaches for organic species. The PAMS simulation showed smaller discrepancy than individual precursor cases in terms of total VOC reactivity. SAPRC07 and RACM2 performances are found to better match the MCM for simulation of total VOC reactivity. Evidences suggest that the performance in simulating secondary organic products, OH concentrations and NO_x concentrations are related to the OH reactivity discrepancies among various chemical mechanisms. Information in this study can be used in selection of chemical mechanisms to better model OH reactivity in different environments. The results in this study also provide directions to further improve the ability in modelling total VOC reactivity with the chemical mechanisms.     

噬菌体编码的抗生素抗性基因研究进展

噬菌体作为地球上丰度最高的生物体,对于全球生态系统的微生物群落组成与动态,生物地球化学循环和细菌进化等都具有重要作用,但噬菌体对抗生素抗性的贡献还所知甚少.通过宏基因组测序和定量PCR等技术,发现了海洋,河流,土壤,动物肠道等环境的噬菌体基因组中存在多种耐药基因(antibiotic resistance genes,ARGs).因此,噬菌体及其介导的转导作用可能对ARGs的富集扩散发挥着重要作用.本文综述了不同环境介质的噬菌体基因组中ARGs的分布特征以及噬菌体介导的ARGs水平转移的研究进展,同时展望了为阐明噬菌体对抗生素抗性贡献需要解决的科学问题.本文将为了解噬菌体在ARGs传播扩散中的作用以及扩展对可移动抗性组的认知奠定基础.     

Diversity trends in Neogene European ungulates and rodents: large-scale comparisons and perspectives

The ungulate and rodent fossil records are often used independently to understand mammalian evolutionary history. Few studies have directly compared both records over long time periods and large geographic areas. Here, we compiled two datasets of European fossil localities containing rodents and/or ungulates over 20 My (Early Miocene–Early Pliocene) and processed the data with the same methodology. We counted the raw diversity and calculated a measure of evenness (Pielou’s index). After controlling for potential biases on diversity estimators, we identify the evenness index as a more reliable estimator bringing interesting insights into the way both mammal groups are structured by biotic or abiotic factors. In this study, we consider that an uneven distribution of the species richness among families, when only some families successfully diversify within the “continental-scale community”, represents a lower adaptability of this community to the environmental context. Pielou’s index is used to estimate this adaptability through time. The responses of ungulates and rodents to environmental changes are very divergent, especially facing the climatic changes known since the Middle Miocene. The general patterns suggest that rodent broad-scale assemblages are affected by all kinds of perturbations, even short biotic and abiotic events, but show a better adaptability when facing long-term abiotic changes. Unlike rodents, the ungulate assemblages show more stability in periods of relative environmental stability but show less adaptability to long-term climatic changes. Life-history traits of mammals can help explain patterns of diversity and biogeography at different spatial scales and may probably partly explain the opposite patterns evidenced here.     

Is the ‘Lost World’ really lost? Palaeoecological insights into the origin of the peculiar flora of the Guayana Highlands

The peculiar biogeography of the so-called Lost World, i.e. the summits of sandstone tableaux (tepuis) in the Neotropical Guyana region of Venezuela, has generated a debate regarding the factors that are thought to account for modern vegetation patterns in the region. Some argue that plant communities on these high-elevation summits reflect a long history of evolution in isolation, while others surmise that there has been substantial biotic interchange with the surrounding lowlands during glacial times. Until now, these apparently competing hypotheses have not been tested using palaeoecological methods. I used pollen analysis of Quaternary sediments and documented past vertical migrations of vegetation in response to climate changes, which supports the second hypothesis. Physiographical analysis, however, shows that about half the tableaux summits are too high for their flora to have reached the lowlands during the last glaciation, suggesting that a portion of the tableaux vegetation has always experienced some degree of biotic isolation. Thus, a component of the summit vegetation evolved in isolation, whereas other taxa experienced interchange, as reflected in endemism patterns among the tableaux summits. Biogeographical patterns on the summits are the result of complex evolutionary processes. The two hypotheses invoked to explain the vegetation patterns are not mutually exclusive, but instead complement one another.     

Exome sequencing for gene discovery in lethal fetal disorders – harnessing the value of extreme phenotypes

Massively parallel sequencing has revolutionized our understanding of Mendelian disorders, and many novel genes have been discovered to cause disease phenotypes when mutant. At the same time, next-generation sequencing approaches have enabled non-invasive prenatal testing of free fetal DNA in maternal blood. However, little attention has been paid to using whole exome and genome sequencing strategies for gene identification in fetal disorders that are lethal in utero, because they can appear to be sporadic and Mendelian inheritance may be missed. We present challenges and advantages of applying next-generation sequencing approaches to gene discovery in fetal malformation phenotypes and review recent successful discovery approaches. We discuss the implication and significance of recessive inheritance and cross-species phenotyping in fetal lethal conditions. Whole exome sequencing can be used in individual families with undiagnosed lethal congenital anomaly syndromes to discover causal mutations, provided that prior to data analysis, the fetal phenotype can be correlated to a particular developmental pathway in embryogenesis. Cross-species phenotyping allows providing further evidence for causality of discovered variants in genes involved in those extremely rare phenotypes and will increase our knowledge about normal and abnormal human developmental processes. Ultimately, families will benefit from the option of early prenatal diagnosis. © 2014 John Wiley & Sons, Ltd.     

The modern theory of biological evolution: an expanded synthesis

In 1858, two naturalists, Charles Darwin and Alfred Russel Wallace, independently proposed natural selection as the basic mechanism responsible for the origin of new phenotypic variants and, ultimately, new species. A large body of evidence for this hypothesis was published in Darwins Origin of Species one year later, the appearance of which provoked other leading scientists like August Weismann to adopt and amplify Darwins perspective. Weismanns neo-Darwinian theory of evolution was further elaborated, most notably in a series of books by Theodosius Dobzhansky, Ernst Mayr, Julian Huxley and others. In this article we first summarize the history of life on Earth and provide recent evidence demonstrating that Darwins dilemma (the apparent missing Precambrian record of life) has been resolved. Next, the historical development and structure of the modern synthesis is described within the context of the following topics: paleobiology and rates of evolution, mass extinctions and species selection, macroevolution and punctuated equilibrium, sexual reproduction and recombination, sexual selection and altruism, endosymbiosis and eukaryotic cell evolution, evolutionary developmental biology, phenotypic plasticity, epigenetic inheritance and molecular evolution, experimental bacterial evolution, and computer simulations (in silico evolution of digital organisms). In addition, we discuss the expansion of the modern synthesis, embracing all branches of scientific disciplines. It is concluded that the basic tenets of the synthetic theory have survived, but in modified form. These sub-theories require continued elaboration, particularly in light of molecular biology, to answer open-ended questions concerning the mechanisms of evolution in all five kingdoms of life.Dedicated to Prof. Dr. Dr. hc mult. Ernst Mayr on the occasion of his 100th birthdayThis revised version was published online in March 2004, with corrections to the caption of Figure 6.     

Mandible shape in hybrid mice

Hybridisation between closely related species is frequently seen as retarding evolutionary divergence and can also promote it by creating novel phenotypes due to new genetic combinations and developmental interactions. We therefore investigated how hybridisation affects the shape of the mouse mandible, a well-known feature in evo–devo studies. Parental groups corresponded to two strains of the European mouse sub-species Mus musculus domesticus and Mus musculus musculus. Parents and hybrids were bred in controlled conditions. The mandibles of F₁ hybrids are mostly intermediate between parental phenotypes as expected for a complex multigenic character. Nevertheless, a transgressive effect as well as an increased phenotypic variance characterise the hybrids. This suggests that hybridisation between the two subspecies could lead to a higher phenotypic variance due to complex interactions among the parental genomes including non-additive genetic effects. The major direction of variance is conserved, however, among hybrids and parent groups. Hybridisation may thus play a role in the production of original transgressive phenotypes occurring following pre-existing patterns of variance.