Evolution and systematic relationships in theTriticeae (Poaceae)

The evolution and taxonomic relationships in theTriticeae are discussed with the view to highlight aspects of this agronomically important group of plants, which may be of interest to molecular biology. Some of these aspects are addressed in more detail in adjoining papers in which specific genomic loci have been examined at the DNA sequence or isozyme level. Aspects discussed include the systematics and geographic distribution of theTriticeae species, isozyme and chromosome pairing studies on some of the species as well as more recent developments in DNA analyses. A survey of the systematics of theTriticeae indicated that the genomic system ofLöve is probably the most useful starting point for interpreting molecular data even though the system has many problems from a taxonomic point of view. The geographical distribution ofTriticeae species, using both published and unpublished data, suggested that information of this type taken together with the theory of continental drift provides a broad time-span for considering data from DNA sequence studies. The significance, and modes of analyses, of isozyme studies were assessed because they often provide valuable characters in determining relationships between species. The main character underlyingLöve's andDewey's analyses of theTriticeae, namely chromosome pairing, is discussed with particular reference to isozyme studies to show that in some cases, such as species ofHordeum sensu lato, consistent relationships are obtained. Finally, new developments in understanding chromosome structure are considered in relation to the above variables in the taxonomy and evolution of theTriticeae.     

Genomic insights into the adaptation and evolution of the nautilus,an ancient but evolving “living fossil”

The nautilus, commonly known as a “living fossil,” is endangered and may be at risk of extinction. The lack of genomic information hinders a thorough understanding of its biology and evolution, which can shed light on the conservation of this endangered species. Here, we report the first high-quality chromosome-level genome assembly of Nautilus pompilius. The assembled genome size comprised 785.15 Mb. Comparative genomic analyses indicated that transposable elements (TEs) and large-scale genome reorganizations may have driven lineage-specific evolution in the cephalopods. Remarkably, evolving conserved genes and recent TE insertion activities were identified in N. pompilius, and we speculate that these findings reflect the strong adaptability and long-term survival of the nautilus. We also identified gene families that are potentially responsible for specific adaptation and evolution events. Our study provides unprecedented insights into the specialized biology and evolution of N. pompilius, and the results serve as an important resource for future conservation genomics of the nautilus and closely related species.     

Kin selection is the key to altruism

Kin selection theory, also known as inclusive fitness theory, has been the subject of much debate and misunderstanding. Nevertheless, the idea that relatedness among individuals can drive the evolution of altruism has emerged as a central paradigm in evolutionary biology. Or has it? In two recent articles, E.O. Wilson argues that kin selection should no longer be considered the main explanation for the evolution of altruism in insect societies. Here, we discuss what these articles say about kin selection and how it relates to the theory. We conclude that kin selection remains the key explanation for the evolution of altruism in eusocial insects.     

Protein–protein interactions of the cytochrome c oxidase DNA barcoding region

Enzymatic amplification of homologous regions of DNA using ‘universal’ polymerase chain reaction primers has provided insight into insect systematics, phylogeography, molecular evolution and species identification. One of the more commonly amplified and sequenced regions is a short region of the cytochrome c oxidase subunit I gene (COI), commonly called the barcoding region. COI is one of three mitochondrial‐encoded subunits of complex IV (Cox) of the electron transport chain. In addition to the mitochondrial subunits there are nine nuclear‐encoded subunits of the complex in Drosophila. Whereas a number of phylogenetic biases associated with this region have been examined and the quaternary structure of Cox has been modelled, the influence of protein–protein interactions on the observed patterns of evolution in this barcoding region of insects has never been examined critically. Using a well‐resolved independently derived phylogeny of 38 Diptera species, we examined the homogeneity of the substitution processes within the barcoding region. We show that, within Diptera, amino acid residues interacting with nuclear‐encoded subunits of Cox are evolving at elevated rates across the phylogeny. Furthermore, we show that codon position two is biased by protein–protein interactions. In contrast, third codon positions provide a less biased estimate of genetic variation in the region. This study highlights the need to examine the potential for systematic bias in DNA barcoding regions as part of the critical assessment of evidence in systematics and in biodiversity assessments.     

Floral structure and evolution of primitive angiosperms: Recent advances

Concepts of primitive angiosperm flowers have changed in recent years due to new studies on relic archaic groups, new paleobotanical finds and the addition of molecular biological techniques to the study of angiosperm systematics and evolution.Magnoliidae are still the hot group, but emphasis is now on small primitive flowers with few organs and also on the great lability of organ number. Of the extant groups, a potential basal position of the paleoherbs has been discussed by some authors. Although some paleoherbs have a simple gynoecium with a single orthotropous ovule, anatropous ovules may still be seen as plesiomorphic in angiosperms. Anatropy is not necessarily a consequence of the advent of closed carpels. It may also exhibit biological advantages under other circumstances as is the case in podocarps among gymnosperms. Valvate anthers have now been found in most larger subgroups of theMagnoliidae (recently also in paleoherbs) and in some Cretaceous fossils. Nevertheless, as seen from its systematic distribution, valvate dehiscence is not necessarily plesiomorphic for the angiosperms, but may be a facultative by-product of the thick connectives and comparatively undifferentiated anther shape inMagnoliidae and lowerHamamelididae. A perianth is relatively simple in extantMagnoliidae or even wanting in some families. In groups with naked flowers the perianth may have been easily lost because integration in the floral architecture was less pronounced than in more advanced angiosperm groups. Problems with the comparison of paleoherb flowers with those ofGnetales are discussed. The rapid growth of information from paleobotany and molecular systematics requires an especially open attitude towards the evaluation of various hypotheses on early flower evolution in the coming years.     

Parallelism,deep homology,and evo‐devo

Parallelism has been the subject of a number of recent studies that have resulted in reassessment of the term and the process. Parallelism has been aligned with homology leaving convergence as the only case of homoplasy, regarded as a transition between homologous and convergent characters, and defined as the independent evolution of genetic traits. Another study advocates abolishing the term parallelism and treating all cases of the independent evolution of characters as convergence. With the sophistication of modern genomics and genetic analysis, parallelism of characters of the phenotype is being discovered to reflect parallel genetic evolution. Approaching parallelism from developmental and genetic perspectives enables us to tease out the degree to which the reuse of pathways represent deep homology and is a major task for evolutionary developmental biology in the coming decades.     

Mitochondrial genomes of parasitic nematodes--progress and perspectives

Mitochondria are subcellular organelles in which oxidative phosphorylation and other important biochemical functions take place within the cell. Within these organelles is a mitochondrial (mt) genome, which is distinct from, but cooperates with, the nuclear genome of the cell. Studying mt genomes has implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. Importantly, the mt genome is a rich source of markers for population genetic and systematic studies. To date, more than 696 mt genomes have been sequenced for a range of metazoan organisms. However, few of these are from parasitic nematodes, despite their socioeconomic importance and the need for fundamental investigations into areas such as nematode genetics, systematics and ecology. In this article, we review knowledge and recent progress in mt genomics of parasitic nematodes, summarize applications of mt gene markers to the study of population genetics, systematics, epidemiology and evolution of key nematodes, and highlight some prospects and opportunities for future research.     

Systematics and evolutionary biology of the fern genusHymenasplenium (Aspleniaceae)

In Aspleniaceae,Hymenasplenium is a well-defined group with dorsiventral creeping rhizomes. Members ofHymenasplenium are widely distributed in the tropic zones of the world and have great variation in morphology and ecolgy, making it a good model group for plant systematics and evolutionary biology. I have worked on this group using techniques such as comparative morphology, ecology, cytology (for examining chromosomes and reproductive modes), phytochemistry and molecular biology. I considered the evolution of various phenetic characters based on a molecular phylogenetic tree which I recently obtained from sequence comparisons ofrbcL. In this paper, I will summarize the results. Recipient of the Botanical Society Award for Young Scientists, 1993.     

毛茛科分子系统发育研究进展

毛茛科(Ranunculaceae)在被子植物的系统演化中占有十分重要的地位,其系统位置和科下演化关系一直备受争议。近20多年的分子系统学研究表明,以往基于形态学的分类系统与分子系统学研究结果存在巨大差异。通过形态学性状界定的绝大多数亚科都没有得到分子系统学支持。此外,通过形态学确定的一些属如升麻属(Cimicifuga)、黄三七属(Souliea)、獐耳细辛属(Hepatica)、白头翁属(Pulsatilla)和水毛茛属(Batrachium)等,根据分子系统学研究均应予以归并。而分子系统学研究也确立了一些类群的属级地位,如露蕊乌头属(Gymnaconitum)等。以中国分布的毛茛科植物为例,通过以往分子系统学研究,共有10个属被归并,2个属新被确立。然而,毛茛科分子系统学研究对于科下许多类群之间的关系目前仍然没有得到很好的解决,如毛茛亚科和翠雀族等类群的系统发育关系仍需要进行深入研究后方能确定。该文对近年来国内外有关毛茛科的分子系统学研究进展进行了综述,并对该科尚存的一些问题和未来的研究方向进行了讨论。     

分子生物学技术在昆虫系统学研究中的应用

分子生物学技术应用于昆虫系统学研究,是８０年代末新兴起来的,近几年来发展相当迅速。为了把握这个研究方向,并促进这个研究领域的发展,作者从研究方法、研究内容、研究对象等方面着手,对近１０年来分子生物学技术应用于昆虫系统学中的研究进展进行了概括和总结。介绍了ＤＮＡ序列测定、ＲＦＬＰ,分子杂交技术、ＲＦＰＬ、分子杂交技术、ＲＡＰＤ、ＳＳＣＰ及ＤＳＣＰ等几种主要方法及其应用情况,并从种及种下阶元的分类鉴定     

Systematics,morphology and biological control

Accurate systematics is the foundation on which all meaningful research in biology is based. The importance of sound systematics to practical biological control is illustrated by results from several projects on biological control of coccid pests. Correct identification of the pest species or their natural enemies, and recognition of cryptic species or infraspecific entities, have been of utmost importance to the success of many projects. Accurate morphology is the basis of reliable systematics. Unfortunately, basic morphology of the parasitic Hymenoptera is still imperfectly understood and that which is known often is inadequately used. The scanning electron microscope is a valuable tool for comparative morphological research that will go far toward solving these problems. The taxonomic validity of morphological characters, and the extent of intraspecific variation, should be determined by a detailed biometrical study of large series of cultured specimens whenever possible. This approach is illustrated with results obtained in our recent revision of the species ofAphytis, important parasites of diaspine scale insects. Comparative morphology of developmental stages of parasitic Hymenoptera is recognized as an important approach to the study of cryptic species needing much more emphasis.     

TZAP‐ing telomeres down to size

The phenomenon of gradual telomere shortening has become a paradigm for how we understand the biology of aging and cancer. Cell proliferation is accompanied by cumulative telomere loss, and the aged cell either senesces, dies or transforms toward cancer. This transformation requires the activation of telomere elongation mechanisms in order to restore telomere length such that cell death or senescence programs are not induced. Most of the time, this occurs through telomerase reactivation. In other rare cases, the Alternative lengthening of telomeres (ALT) pathway hijacks DNA recombination‐associated mechanisms to hyperextend telomeres, often to more than 50 kb. Why telomere length is restricted and what sets their maximal length has been a long‐standing puzzle in cell biology. Two recent studies published in this issue of EMBO Reports [1] and recently in Science [2] sought to address this important question. Both built on omics approaches that identified ZBTB48 as a potential telomere‐associated protein and reveal it to be a critical regulator of telomere length homeostasis by the telomere trimming mechanism. These discoveries provide fundamental insights for our understanding of telomere trimming and how it impacts telomere integrity in stem and cancer cells.     

羊肚菌分子鉴定及功能基因研究进展

羊肚菌作为珍贵的食药用真菌,具有很高的经济价值.就近年来羊肚菌分子生物学研究的进展从分子鉴定、系统学研究、功能基因等方面进行了分析总结.结果显示,目前利用分子标记已实现羊肚菌属快捷的分子鉴定,较全面揭示了属内种群的遗传多样性和亲缘关系;利用组学技术初步探索了羊肚菌菌核形成及子实体发育机制;此外还克隆表达了与羊肚菌抗逆响...     

Sesamoids in tetrapods: the origin of new skeletal morphologies

Along with supernumerary bones, sesamoids, defined as any organized intratendinous/intraligamentous structure, including those composed of fibrocartilage, adjacent to an articulation or joint, have been frequently considered as enigmatic structures associated with the joints of the skeletal system of vertebrates. This review allows us to propose a dynamic model to account for part of skeletal phenotypic diversity: during evolution, sesamoids can become displaced, attaching to and detaching from the long bone epiphyses and diaphysis. Epiphyses, apophyses and detached sesamoids are able to transform into each other, contributing to the phenotypic variability of the tetrapod skeleton. This dynamic model is a new paradigm to delineate the contribution of sesamoids to skeletal diversity. Herein, we first present a historical approach to the study of sesamoids, discussing the genetic versus epigenetic theories of their genesis and growth. Second, we construct a dynamic model. Third, we present a summary of literature on sesamoids of the main groups of tetrapods, including veterinary and human clinical contributions, which are the best‐studied aspects of sesamoids in recent decades. Finally, we discuss the identity of certain structures that have been labelled as sesamoids despite insufficient formal testing of homology. We also propose a new definition to help the identification of sesamoids in general. This review is particularly timely, given the recent increasing interest and research activity into the developmental biology and mechanics of sesamoids. With this updated and integrative discussion, we hope to pave the way to improve the understanding of sesamoid biology and evolution.     

Infraspecific categories in birds

The systematics of birds has probably received more attention than that of any other animal group. However, a reassessment of many species, from the point of view of their evolution, would prove valuable both from the point of view of their systematics, and the part played by various populations in speciation.
The development of evolutionary biology has resulted in a better understanding of such concepts as geographical isolation and clinal variation, a different interpretation of such terms as 'deme' and 'race', and the rejection of such all-embracing terms as 'variety'. The concept of the 'ecotype' plays little part in the systematics of birds, since they are warm-blooded, and independent of direct environmental effects.     

Infraspecific categories in birds

The systematics of birds has probably received more attention than that of any other animal group. However, a reassessment of many species, from the point of view of their evolution, would prove valuable both from the point of view of their systematics, and the part played by various populations in speciation.
The development of evolutionary biology has resulted in a better understanding of such concepts as geographical isolation and clinal variation, a different interpretation of such terms as 'deme' and 'race', and the rejection of such all-embracing terms as 'variety'. The concept of the 'ecotype' plays little part in the systematics of birds, since they are warm-blooded, and independent of direct environmental effects.     

Tracking <Emphasis Type="Italic">Alu</Emphasis> evolution in New World primates

Background  

Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu sequences for loci specific to platyrrhine (New World) primates.     

Gene trees and species trees – mutual influences and interdependences of population genetics and systematics

Both population genetics and systematics are core disciplines of evolutionary biology. While systematics deals with genealogical relationships among taxa, population genetics has mainly been based on allele frequencies and the distribution of genetic variants whose genealogical relations could for a long time, due mainly to methodological constraints, not be inferred. The advent of mitochondrial DNA analyses and modern sequencing techniques in the 1970s revolutionized evolutionary genetic studies and gave rise to molecular phylogenetics. In the wake of this new development systematic approaches and principles were incorporated into intraspecific studies at the population level, e.g. the concept of monophyly which is used to delineate evolutionarily significant units in conservation biology. A new discipline combining phylogenetic analyses of genetic lineages with their geographic distribution ('phylogeography') was introduced as an explicit synthesis of population genetics and systematics. On the other hand, it has increasingly become obvious that discordances between gene trees and species trees not only result from spurious data sets or methodological flaws in phylogenetic analyses, but that they often reflect real population genetic processes such as lineage sorting or hybridization. These processes have to be taken into account when evaluating the reliability of gene trees to avoid wrong phylogenetic conclusions. The present review focuses on the phenomenon of non-phylogenetic sorting of ancestral polymorphisms, its probability and its consequences for molecular systematics.     

Genetic structure of Partamona helleri (Apidae, Meliponini) from Neotropical Atlantic rainforest

Stingless bees of the genus Partamona are distributed from southern Mexico to southern Brazil. This genus has been subject to different approaches to solve questions concerning general biology, taxonomy, systematics and biogeography, but population studies applying molecular techniques are inexistent. We analyzed the genetic structure of P. helleri across its geographic distribution along the coastal Atlantic tropical rainforest in Brazil. Ten mtDNA haplotypes were observed in 47 colonies of P. helleri of which some were exclusive and others shared among geographic sub-groups. Statistical analysis showed high genetic differentiation between geographic areas sampled. Fragmentation of the Atlantic forest during Pleistocene glaciations is discussed as a possible cause of the present haplotype distribution and frequency.