Monophyletic origin of brood care in damselfishes

The absence of a pelagic larval stage and brood care has evolved very few times in coral reef fishes. Damselfishes, a widely represented group with more than 380 species, includes only three such species, the monotypic Acanthochromis polyacanthus, and the two Altrichthys species, Altrichthys azurelineatus and Altrichthys curatus. In a recent study, Cooper et al. provided a comprehensive phylogenetic hypothesis for the damselfish family, based on mitochondrial and nuclear sequences, with more than 100 species that included all extant genera (Cooper et al., 2009). A. polyacanthus and sequences from formalin-preserved tissue of A. curatus did not cluster together, indicating that brood care may have evolved independently twice in damselfishes. Here, we use mitochondrial and nuclear molecular markers from fresh specimens of both Altrichthys species. We found that Altrichthys and Acanthochromis are closest relatives, which suggests that brood care may have evolved only once in damselfishes. Due to the limited geographic range of Altrichthys (western Philippines) and the abundant presence of Acanthochromis in that region, we also suggest that brood care may have originated in that region.     

舌鳎亚科鱼类单系起源和同种异名的线粒体DNA证据

舌鳎亚科鱼类因形态特征的特殊性, 其分类及系统发育关系一直存在争议。本研究测定了中国沿海14种舌鳎亚科鱼类线粒体DNA的16S rRNA和Cyt b基因的部分片段。两个基因构建的舌鳎亚科系统发育树结果显示, 中国沿海舌鳎亚科鱼类为明显的单系群, 但舌鳎亚科鱼类内部的系统发育关系与形态分类划分的亚属并不完全一致, 日本须鳎(Paraplagusis japonica)与其他舌鳎属(Cynoglossus)种类并未形成不同的分支。虽然舌鳎属内的舌鳎亚属(Cynoglossus)、拟舌鳎亚属(Cynoglossoides)和三线舌鳎亚属(Areliscus)均可以聚为独立分支, 但长吻红舌鳎(C. lighti)与短吻红舌鳎(C. joyneri)、短吻三线舌鳎(C. abbreviatus)与紫斑舌鳎(C. purpureomaculatus)、半滑舌鳎(C. semilaevis)与窄体舌鳎(C. gracilis)及褐斑三线舌鳎(C. trigrammus)这三组物种可能存在同种异名现象。这一结果提示, 基于形态学对舌鳎亚科的种属分类鉴定尚存在不足, 线粒体DNA的系统发育关系可为其分类的修订提供有意义的参考和佐证。     

Magnetite and magnetotaxis in microorganisms

Magnetotactic bacteria from freshwater and marine sediments orient and navigate along geomagnetic field lines. Their magnetotactic response is based on intracellular, single magnetic domains of ferrimagnetic magnetite, which impart a permanent magnetic dipole moment to the cell.     

Monophyletic origin of the dorsally arched lateral line in Teleostei: evidence from nerve innervation patterns

Branching patterns of the horizontal septum lateral line nerves (HSN) were studied in 123 teleostean species (including literature records) assigned to 96 families in 28 orders, primarily to indentify the group characterized by the presence of the dorsal longitudinal collector nerve (DLCN) for innervation of the trunk lateral line. In nonacanthomorphs, DLCN was absent, the trunk lateral line being mostly innervated by branches directly detached from HSN or those derived from the collector nerve running parallel to the former. In acanthomorphs, the dorsally arched trunk lateral line, typical of the group, was uniformly innervated by DLCN, indicating that presence of the latter was a synapomorphy of the group. Within the latter, DLCN was absent in Gasterosteiformes (Fistularia and Macroramphosus), Mugilidae, Atherinomorpha, Champsodontidae, Blenniidae, Callionymidae, Gobioidei, Istiophoridae, Gempylidae, Cynoglossidae, Ostraciidae, and Molidae. Monophyly of the Mugilidae plus Atherinomorpha was discussed based on the specialized innervation pattern.     

Quantifying the magnetic advantage in magnetotaxis

Magnetotactic bacteria are characterized by the production of magnetosomes, nanoscale particles of lipid bilayer encapsulated magnetite, that act to orient the bacteria in magnetic fields. These magnetosomes allow magneto-aerotaxis, which is the motion of the bacteria along a magnetic field and toward preferred concentrations of oxygen. Magneto-aerotaxis has been shown to direct the motion of these bacteria downward toward sediments and microaerobic environments favorable for growth. Herein, we compare the magneto-aerotaxis of wild-type, magnetic Magnetospirillum magneticum AMB-1 with a nonmagnetic mutant we have engineered. Using an applied magnetic field and an advancing oxygen gradient, we have quantified the magnetic advantage in magneto-aerotaxis as a more rapid migration to preferred oxygen levels. Magnetic, wild-type cells swimming in an applied magnetic field more quickly migrate away from the advancing oxygen than either wild-type cells in a zero field or the nonmagnetic cells in any field. We find that the responses of the magnetic and mutant strains are well described by a relatively simple analytical model, an analysis of which indicates that the key benefit of magnetotaxis is an enhancement of a bacterium's ability to detect oxygen, not an increase in its average speed moving away from high oxygen concentrations.     

Monophyletic origin of multiple clonal lineages in an asexual fish (Poecilia formosa)

Despite the advantage of avoiding the costs of sexual reproduction, asexual vertebrates are very rare and often considered evolutionarily disadvantaged when compared to sexual species. Asexual species, however, may have advantages when colonizing (new) habitats or competing with sexual counterparts. They are also evolutionary older than expected, leaving the question whether asexual vertebrates are not only rare because of their 'inferior' mode of reproduction but also because of other reasons. A paradigmatic model system is the unisexual Amazon molly, Poecilia formosa, that arose by hybridization of the Atlantic molly, Poecilia mexicana, as the maternal ancestor, and the sailfin molly, Poecilia latipinna, as the paternal ancestor. Our extensive crossing experiments failed to resynthesize asexually reproducing (gynogenetic) hybrids confirming results of previous studies. However, by producing diploid eggs, female F(1) -hybrids showed apparent preadaptation to gynogenesis. In a range-wide analysis of mitochondrial sequences, we examined the origin of P. formosa. Our analyses point to very few or even a single origin(s) of its lineage, which is estimated to be approximately 120,000 years old. A monophyletic origin was supported from nuclear microsatellite data. Furthermore, a considerable degree of genetic variation, apparent by high levels of clonal microsatellite diversity, was found. Our molecular phylogenetic evidence and the failure to resynthesize the gynogenetic P. formosa together with the old age of the species indicate that some unisexual vertebrates might be rare not because they suffer the long-term consequences of clonal reproduction but because they are only very rarely formed as a result of complex genetic preconditions necessary to produce viable and fertile clonal genomes and phenotypes ('rare formation hypothesis').     

Monophyletic classification and information content

The connection between monophyly and efficient taxonomic diagnoses is elaborated. The inefficiency of nonmonophyletic groups is shown by reconstructing data matrices from hierarchical sets of diagnoses that are derived from apomorphies and read in order from highest to lowest rank. The practice of diagnosing nonmonophyletic groups either results in omitting data, resulting in errors in reconstructed datasets, or repeating character information to make up for the implied losses. Step-by-step demonstrations with hypothetical and real data are used as guidance. Provisions are made for missing, inapplicable and polymorphic data. Slow optimization (delayed transformation) is useful for choosing a state reconstruction in order to report apomorphies completely. The diagnoses of paraphyletic groups can be expressed in different ways, including regrafting derived clades, reanalyzing data with constraints, and reading the original diagnoses in a different order––the last is the least efficient. A cladistic version of the data compression ratio is proposed to quantify the diagnostic efficiency of a cladogram.     

Monophyletic origin of Caryophyllia (Scleractinia,Caryophylliidae), with descriptions of six new species

The genus Caryophyllia Lamarck, 1816 is the most diverse genus within the azooxanthellate Scleractinia comprising 66 Recent species and a purported 195 nominal fossil species. Examination of part of the deep-sea scleractinian collection made by the Paris Museum off New Caledonia and part of the material collected by CSIRO off Australian waters revealed the occurrence of 23 species of Caryophyllia, of which six are new to science. All new records, including the new species, are described, and synonyms, distribution, type locality, type material and illustration are provided for each species. An identification key to all Recent species of Caryophyllia is presented. In addition, the validity of the genus Caryophyllia was investigated by phylogenetic analyses of a dataset consisting of partial mitochondrial 16S rRNA sequences from 12 species assigned to this genus together with seven species representing some of the most morphologically similar caryophylliid genera, and 14 non-caryophyllid species representing 14 scleractinian families. Irrespective of the method of analysis employed, all of the Caryophyllia species formed a well-supported clade together with Dasmosmilia lymani and Crispatotrochus rugosus. Although based on a subset of the Recent Caryophyllia species, these results are consistent with Caryophyllia being a valid genus, but call for a reexamination of Dasmosmilia and Crispatotrochus.     

Teaching the origin of the first living systems

The most fundamental of questions in biology, namely that of the origin of living systems, is being lost to teaching and a new technique to rekindle interest in it must be found. This paper presents a novel idea of teaching a scientific concept using a poem, which describes the major perspectives on the origins of living systems, as the medium of instruction. All of the major schools of thought — chemical evolution, DNA vs. RNA, protocell formation, coacervates, panspermia and special creation — are discussed. The aim of the paper is not to be a definitive review on the origin of living systems, but rather to be a focal point on which to hinge further discussion.     

Monophyletic origin of domestic bactrian camel (Camelus bactrianus) and its evolutionary relationship with the extant wild camel (Camelus bactrianus ferus)

The evolutionary relationship between the domestic bactrian camel and the extant wild two-humped camel and the factual origin of the domestic bactrian camel remain elusive. We determined the sequence of mitochondrial cytb gene from 21 camel samples, including 18 domestic camels (three Camelus bactrianus xinjiang , three Camelus bactrianus sunite , three Camelus bactrianus alashan , three Camelus bactrianus red , three Camelus bactrianus brown and three Camelus bactrianus normal ) and three wild camels ( Camelus bactrianus ferus ). Our phylogenetic analyses revealed that the extant wild two-humped camel may not share a common ancestor with the domestic bactrian camel and they are not the same subspecies at least in their maternal origins. Molecular clock analysis based on complete mitochondrial genome sequences indicated that the sub-speciation of the two lineages had begun in the early Pleistocene, about 0.7 million years ago. According to the archaeological dating of the earliest known two-humped camel domestication (5000–6000 years ago), we could conclude that the extant wild camel is a separate lineage but not the direct progenitor of the domestic bactrian camel. Further phylogenetic analysis suggested that the bactrian camel appeared monophyletic in evolutionary origin and that the domestic bactrian camel could originate from a single wild population. The data presented here show how conservation strategies should be implemented to protect the critically endangered wild camel, as it is the last extant form of the wild tribe Camelina.     

Magnetotactic bacteria,magnetosomes and their application

Magnetotactic bacteria (MTB) are a diverse group of microorganisms with the ability to orient and migrate along geomagnetic field lines. This unique feat is based on specific intracellular organelles, the magnetosomes, which, in most MTB, comprise nanometer-sized, membrane bound crystals of magnetic iron minerals and organized into chains via a dedicated cytoskeleton. Because of the special properties of the magnetosomes, MTB are of great interest for paleomagnetism, environmental magnetism, biomarkers in rocks, magnetic materials and biomineralization in organisms, and bacterial magnetites have been exploited for a variety of applications in modern biological and medical sciences. In this paper, we describe general characteristics of MTB and their magnetic mineral inclusions, but focus mainly on the magnetosome formation and the magnetisms of MTB and bacterial magnetosomes, as well as on the significances and applications of MTB and their intracellular magnetic mineral crystals.     

Formation of magnetosomes in magnetotactic bacteria

The ability of magnetotactic bacteria to orient and migrate along geomagnetic field lines is based on intracellular magnetic structures, the magnetosomes, which comprise nano-sized, membrane bound crystals of magnetic iron minerals. The formation of magnetosomes is achieved by a biological mechanism that controls the accumulation of iron and the biomineralization of magnetic crystals with a characteristic size and morphology within membrane vesicles. This paper focuses on the current knowledge about magnetotactic bacteria and will outline aspects of the physiology and molecular biology of magnetosome formation. The biotechnological potential of the biomineralization process is discussed.     

Monophyletic Origin of Alu Elements in Primates

To get insight into the early evolution of the primate Alu elements, we characterized sequences of these repeats from the Malagasy prosimians, lemurs (Lemuridae) and sifakas (Indriidae), as well as from galagos (Lorisidae). These sequences were compared with the oldest Alu species known from the human genome: dimeric Alu J and S and free Alu monomers. Our analysis indicates that about 60 Myr ago, before the prosimian divergence, free left and right monomers formed an Alu heterodimer connected by a 19-nucleotide-long A-rich linker. The resulting elements successfully propagated in diverging primate lineages until about ∼20 Myr ago, conserving similar sequence features and essentially the same Alu RNA secondary structure. We suggest that until that time the same ``retropositional niche', molecular machinery making possible the proliferation by retroposition, constrained the evolution of Alu elements in extant primate species. These constraints became subsequently relaxed. In the Malagasy prosimians the dimeric Alu continued to amplify after acquiring a 34- to 36-nucleotide extension of their linker segment, whereas in the galago genome the ``retropositional niche' was occupied by novel short elements. Received: 1 December 1997 / Accepted: 30 January 1998     

The stochastic resonance of magnetosomes fixed in the cytoskeleton

The rotation of microscopic magnetic particles, magnetosomes, embedded into the cytoskeleton and subjected to a magnetic field and thermal noise was considered. The dynamics of magnetosome is shown to comply with the conditions of the stochastic resonance under not too tight constraints on the character of particle fastening. The excursion of regular rotations attains the value of the order of radian, which facilitates explaining the biological effects of low-frequency weak magnetic fields and geomagnetic fluctuations.