Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae)

In order to obtain insights into the evolution of colorless (apochlorotic) diatoms, we investigated newly established apochlorotic strains of Nitzschia spp. using light and electron microscopy and molecular phylogenetic analyses. Fluorescence microscopic observations demonstrated that the apochlorotic diatoms lack chlorophylls. Transmission electron microscopy of two apochlorotic strains also demonstrated that their plastids lacked thylakoids; instead, having four‐membrane‐bound organelles without thylakoids, similar to nonphotosynthetic plastid remnants. From the apochlorotic strains, we also found plastid small subunit rRNA genes that were unusually long branched in phylogenetic analyses, as observed in other nonphotosynthetic plastids. Molecular phylogenetic analysis of the nucleus‐encoded large subunit rRNA genes showed eight distinct lineages for apochlorotic diatoms. The eight apochlorotic lineages were not monophyletic, suggesting that the loss of photosynthesis took place multiple times independently within Nitzschia. Several diatoms, including Nitzschia spp., are mixotrophic, which is an expected mode of nutrition that would help explain the evolutionary switch from a photosynthetic lifestyle to a heterotrophic lifestyle.     

甲藻的异养营养型

综述了甲藻的异养类型。目前已知异养营养型在甲藻中广泛存在,只有很少几种甲藻营严格自养营养方式。有近一半的甲藻物种是没有色素体的,还有很多甲藻即使具有色素体也会有异养营养需求,称为兼养营养类型。这些兼养类群不一定主要以有机物作为其获取碳的来源,而仅仅是补充一些生长必需的有机物如维生素、生物素等。兼养类群以渗透营养和腐食营养方式进行,同时也可以寄生方式和共生方式进行兼养生活。无色素体的甲藻以有机物作为碳的唯一来源,仅仅依靠异养方式生存,属于严格异养营养方式,又称有机营养型。它们是甲藻异养营养型的主体,其主要类型有寄生、渗透营养和吞噬营养。由于吞噬营养是甲藻异养的主要类型,因此论述了3种吞噬营养型:吞噬营养方式、捕食茎营养方式和捕食笼营养方式。吞噬营养方式在无甲类和具甲类甲藻中都有存在,主要通过甲藻细胞的纵沟或底部对猎物进行吞噬,也有研究发现吞噬部位为顶孔或片间带。捕食茎营养方式是通过捕食茎刺穿猎物细胞膜并吸食其细胞质来获取营养,在异养甲藻中也较常见。捕食笼营养方式只在原多甲藻属(Protoperidinium)和翼藻属(Diplopsalis)里发现,是甲藻通过鞭毛孔分泌细胞质到胞外形成捕食笼将猎物包裹并进行消化来摄食的。甲藻摄食对象尺寸范围变化较大,小至几微米,大至几百微米。有些甲藻具有摄食选择性,通过感应猎物释放的化学物质来判断猎物的位置并进行摄食,摄食完成后由于体积的增加经常会发生细胞分裂和蜕鞘。对于甲藻异养的其他形式如拦截摄食营养方式、伪足摄食营养方式、口足摄食营养方式、触手摄食营养方式等只作简单介绍。还就甲藻异养的研究方法、其生态学意义和进化学意义进行简要论述,并对相关研究进行展望。     

Phylogeny and Molecular Evolution of the Green Algae

The green lineage (Viridiplantae) comprises the green algae and their descendants the land plants, and is one of the major groups of oxygenic photosynthetic eukaryotes. Current hypotheses posit the early divergence of two discrete clades from an ancestral green flagellate. One clade, the Chlorophyta, comprises the early diverging prasinophytes, which gave rise to the core chlorophytes. The other clade, the Streptophyta, includes the charophyte green algae from which the land plants evolved. Multi-marker and genome scale phylogenetic studies have greatly improved our understanding of broad-scale relationships of the green lineage, yet many questions persist, including the branching orders of the prasinophyte lineages, the relationships among core chlorophyte clades (Chlorodendrophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae), and the relationships among the streptophytes. Current phylogenetic hypotheses provide an evolutionary framework for molecular evolutionary studies and comparative genomics. This review summarizes our current understanding of organelle genome evolution in the green algae, genomic insights into the ecology of oceanic picoplanktonic prasinophytes, molecular mechanisms underlying the evolution of complexity in volvocine green algae, and the evolution of genetic codes and the translational apparatus in green seaweeds. Finally, we discuss molecular evolution in the streptophyte lineage, emphasizing the genetic facilitation of land plant origins.     

Biology and systematics of heterokont and haptophyte algae

In this paper, I review what is currently known of phylogenetic relationships of heterokont and haptophyte algae. Heterokont algae are a monophyletic group that is classified into 17 classes and represents a diverse group of marine, freshwater, and terrestrial algae. Classes are distinguished by morphology, chloroplast pigments, ultrastructural features, and gene sequence data. Electron microscopy and molecular biology have contributed significantly to our understanding of their evolutionary relationships, but even today class relationships are poorly understood. Haptophyte algae are a second monophyletic group that consists of two classes of predominately marine phytoplankton. The closest relatives of the haptophytes are currently unknown, but recent evidence indicates they may be part of a large assemblage (chromalveolates) that includes heterokont algae and other stramenopiles, alveolates, and cryptophytes. Heterokont and haptophyte algae are important primary producers in aquatic habitats, and they are probably the primary carbon source for petroleum products (crude oil, natural gas).     

Charophyte algae and land plant origins

The charophyte algae are six distinct groups of mostly freshwater green algae that are related to modern land plants. Charophyte algae exhibit diverse morphologies and reproductive strategies, from unicells to branching erect forms, and from swimming asexual spores to sex involving eggs and sperm, respectively. The green algae known as stoneworts (Charales) are suggested to be the extant sister group to all land plants, although the phylogeny is not conclusive. Here we review recent molecular phylogenetic work on the charophyte algae and its implications for our understanding of the origins of land plants and of characters in their aquatic ancestors that might have played a role in the explosive diversification of plants on land.     

Evolutionary relationships among squids of the family Gonatidae (Mollusca: Cephalopoda) inferred from three mitochondrial loci

The oceanic squid family Gonatidae (Mollusca: Cephalopoda) is widely distributed in subpolar and temperate waters, exhibiting behavioral and physiological specializations associated with reproduction. Females of several species undergo muscular degeneration upon maturation; origins of this complex morphogenic change are unknown, hindering our understanding of ecological and morpho-physiological adaptations within the family. To provide further information regarding the evolutionary relationships within Gonatidae, three mitochondrial loci (12S rRNA, 16S rRNA, and cytochrome c oxidase subunit I) were analyzed for 39 individuals representing fourteen gonatid and six outgroup cephalopod species. In addition to elucidating relationships among gonatids, molecular data provided more information than morphological data for problematic specimens. Although some data sets are incongruent or have low nodal support values, combined molecular analysis confirms the presence of gonatid groups previously established by morphological characteristics (i.e., possessing radular teeth in seven longitudinal rows and muscular mantle tissue). These characteristics are basal to taxa possessing radular teeth in five longitudinal rows and less muscular mantle tissue, indicating that the derived forms are those species exhibiting physiological adaptation such as tissue degeneration upon maturation and egg brooding.     

基于核及叶绿体基因序列探讨中国绿水螅共生单细胞绿藻系统发生地位

研究对中国绿水螅共生绿藻的核18S rRNA基因全长序列及其叶绿体9个基因(atpA、chlB、chlN、petA、psaB、psbA、psbC、psbD及rbcL)片段序列进行了克隆和测序, 并基于18S rRNA基因序列及叶绿体9个基因序列的整合数据分别通过最大似然法(Maximum-likelihood)和贝叶斯分析(Bayesian inference)对中国绿水螅(Hydra sinensis)共生单细胞绿藻的系统发生地位进行了探讨。系统发生表明: (1)中国绿水螅共生绿藻属于共球藻纲(Trebouxiophyceae)小球藻目(Chlorellales), 但不属于其中的小球藻属(Chlorella); (2)来源于草履虫、水螅、地衣及银杏的共生绿藻均在共球藻纲支系, 而来源于蛙类和蝾螈的共生绿藻属于绿藻纲(Chlorophyceae)支系。无论在共球藻纲支系还是在绿藻纲支系, 不同来源的共生藻并没有排他性地聚为单系群而在系统树中与其他自由生活的绿藻混杂排列, 来自不同宿主的共生绿藻没有共同起源。     

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

Background  

The assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them.     

Phylogenetic evidence for a major reversal of life-history evolution in plethodontid salamanders

The transition from aquatic to terrestrial eggs is a key evolutionary change that has allowed vertebrates to successfully colonize and exploit the land. Although most amphibians retain the primitive biphasic life cycle (eggs deposited in water that hatch into free-living aquatic larvae), direct development of terrestrial eggs has evolved repeatedly and may have been critical to the evolutionary success of several amphibian groups. We provide the first conclusive evidence for evolutionary reversal of direct development in vertebrates. The family Plethodontidae (lungless salamanders) contains the majority of salamander species, including major radiations of direct developers. We reconstruct the higher level phylogenetic relationships of plethodontid salamanders using molecular and morphological data and use this phylogeny to examine the evolution of direct development. We show that the predominantly biphasic desmognathines, previously considered the sister group of other plethodontids, are nested inside a group of direct-developing species (Plethodontini) and have re-evolved the aquatic larval stage. Rather than being an evolutionary dead end, the reversal from direct developing to biphasic life history may have helped communities in eastern North America to achieve the highest local diversity of salamander species in the world.     

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates

Time-scales of viral evolution and emergence have been studied widely, but are often poorly understood. Molecular analyses of viral evolutionary time-scales generally rely on estimates of rates of nucleotide substitution, which vary by several orders of magnitude depending on the timeframe of measurement. We analysed data from all major groups of viruses and found a strong negative relationship between estimates of nucleotide substitution rate and evolutionary timescale. Strikingly, this relationship was upheld both within and among diverse groups of viruses. A detailed case study of primate lentiviruses revealed that the combined effects of sequence saturation and purifying selection can explain this time-dependent pattern of rate variation. Therefore, our analyses show that studies of evolutionary time-scales in viruses require a reconsideration of substitution rates as a dynamic, rather than as a static, feature of molecular evolution. Improved modelling of viral evolutionary rates has the potential to change our understanding of virus origins.     

The origin of modern amphibians: a re‐evaluation

There are currently three competing hypotheses seeking to explain the evolutionary origins of modern amphibians. The lepospondyl hypothesis holds that the lysorophian lepospondyls constitute the sister taxon to all lissamphibians. The temnospondyl hypothesis suggests that modern amphibians are most closely related to the dissorophoid temnospondyls. Finally, the polyphyletic hypothesis posits that the modern amphibian orders have separate evolutionary origins from among different groups of Palaeozoic tetrapods. Here, we review the character matrices used in previous studies. These data sets differ significantly in choice of characters. Therefore, we built a matrix based on data from all three hypotheses and analysed key taxa phylogenetically using both Bayesian inference and parsimony. Uncorrected, the supermatrix yielded inconclusive results, demonstrating the presence of at least two phylogenetic optima. When the data were corrected according to new observations on Doleserpeton, Eocaecilia, and other fossil forms, the phylogeny supported the temnospondyl hypothesis of lissamphibian origins. This conclusion is also supported by a careful study of character changes in the individual lineages. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 457–469.     

Deep-level diagnostic value of the rDNA-ITS region

The similarity of certain reported angiosperm rDNA internal transcribed spacer (ITS) region sequences to those of green algae prompted our analysis of the deep-level phylogenetic signal in the highly conserved but short 5.8S and hypervariable ITS2 sequences. We found that 5.8S sequences yield phylogenetic trees similar to but less well supported than those generated by a ca. 10-fold longer alignment from rDNA-18S sequences, as well as independent evidence. We attribute this result to our finding that, compared to 18S, the 5.8S has a higher proportion of sites subject to vary and greater among-site substitution rate homogeneity. We also determined that our phylogenetic results are not likely affected by intramolecular compensatory mutation to maintain RNA secondary structure nor by evident systematic biases in base composition. Despite historical homology, there appears to be no ITS2 primary sequence similarity shared sufficient similarity to cluster correctly on the basis of alignability. Our results indicate that groups, however, share sufficient similarity to cluster correctly on the basis of alignability. Our results indicate that ITS region sequences can diagnose organismal origins and phylogenetic relationships at many phylogenetic levels and provide a useful paradigm for molecular evolutionary study.      

Phylogenetics and the evolution of major structural characters in the giant genus Euphorbia L. (Euphorbiaceae)

Euphorbia is among the largest genera of angiosperms, with about 2000 species that are renowned for their remarkably diverse growth forms. To clarify phylogenetic relationships in the genus, we used maximum likelihood, bayesian, and parsimony analyses of DNA sequence data from 10 markers representing all three plant genomes, averaging more than 16kbp for each accession. Taxon sampling included 176 representatives from Euphorbioideae (including 161 of Euphorbia). Analyses of these data robustly resolve a backbone topology of four major, subgeneric clades--Esula, Rhizanthium, Euphorbia, and Chamaesyce--that are successively sister lineages. Ancestral state reconstructions of six reproductive and growth form characters indicate that the earliest Euphorbia species were likely woody, non-succulent plants with helically arranged leaves and 5-glanded cyathia in terminal inflorescences. The highly modified growth forms and reproductive features in Euphorbia have independent origins within the subgeneric clades. Examples of extreme parallelism in trait evolution include at least 14 origins of xeromorphic growth forms and at least 13 origins of seed caruncles. The evolution of growth form and inflorescence position are significantly correlated, and a pathway of evolutionary transitions is supported that has implications for the evolution of Euphorbia xerophytes of large stature. Such xerophytes total more than 400 species and are dominants of vegetation types throughout much of arid Africa and Madagascar.     

Spreading and locomotion of tissue cells: factors controlling the distribution of pseudopodia

The spreading and locomotion of cells on substrata can be regarded as a result of the interaction of two groups of processes: pseudopodial attachment and stabilization. Stabilization processes integrate the results of previous pseudopodial reactions and determine the sites of further extensions. Stabilization mechanisms are probably based on the changes in the distribution of cytoskeletal elements. Usually the direction of pseudopodial extensions is approximately parallel to the predominant orientation of actin microfilaments in the nearby cortex. Two variants of stabilization can be distinguished: microtubule-independent and microtubule-dependent processes. Contact paralysis of the upper surfaces of epithelial sheets is possibly a special case of microtubule-independent stabilization. In the course of spreading, the cell may acquire a polarized or discoid shape depending on the efficiency of attachment.     

Estimation of the efficiency of ERIC-PCR typing of Mycobacterium tuberculosis for evaluation of the prevalence of antibiotic-resistant strains

Twenty-four antibiotic-resistant and sensitive strains of M. tuberculosis isolated from different territories of the Irkutsk region (East Siberia) were studied using PCR genotyping by enterobacterial repetitive intergeneric consensus (ERIC). Evolution relationships are illustrated by phylogenetic trees as a result of analysis by UPGMA and ML approaches. It was found that the studied samples belonged to two genetically different groups, both of which included sensitive and resistant strains. The sensitivity of the method was calculated by the Hunter-Gaston index. Based on these data, a probable pattern of emergence and propagation of antibiotic-resistant forms of tuberculosis in the studied region is discussed.     

An Evolutionary Analysis of the Secoviridae Family of Viruses

The plant-infecting Secoviridae family of viruses forms part of the Picornavirales order, an important group of non-enveloped viruses that infect vertebrates, arthropods, plants and algae. The impact of the secovirids on cultivated crops is significant, infecting a wide range of plants from grapevine to rice. The overwhelming majority are transmitted by ecdysozoan vectors such as nematodes, beetles and aphids. In this study, we have applied a variety of computational methods to examine the evolutionary traits of these viruses. Strong purifying selection pressures were calculated for the coat protein (CP) sequences of nine species, although for two species evidence of both codon specific and episodic diversifying selection were found. By using Bayesian phylogenetic reconstruction methods CP nucleotide substitution rates for four species were estimated to range from between 9.29×10⁻³ to 2.74×10⁻³ (subs/site/year), values which are comparable with the short-term estimates of other related plant- and animal-infecting virus species. From these data, we were able to construct a time-measured phylogeny of the subfamily Comovirinae that estimated divergence of ninety-four extant sequences occurred less than 1,000 years ago with present virus species diversifying between 50 and 250 years ago; a period coinciding with the intensification of agricultural practices in industrial societies. Although recombination (modularity) was limited to closely related taxa, significant and often unique similarities in the protein domains between secovirid and animal infecting picorna-like viruses, especially for the protease and coat protein, suggested a shared ancestry. We discuss our results in a wider context and find tentative evidence to indicate that some members of the Secoviridae might have their origins in insects, possibly colonizing plants in a number of founding events that have led to speciation. Such a scenario; virus infection between species of different taxonomic kingdoms, has significant implications for virus emergence.     

Molecular phylogenetics of emydine turtles: taxonomic revision and the evolution of shell kinesis

The 10 extant species of emydine turtles represent an array of morphological and ecological forms recognizable and popular among scientists and hobbyists. Nevertheless, the phylogenetic affinities of most emydines remain contentious. Here, we examine the evolutionary relationships of emydine turtles using 2092 bp of DNA encoding the mitochondrial genes cyt b, ND4, and adjacent tRNAs. These data contain 339 parsimony informative characters that we use to erect hypotheses of relationships for the Emydinae. Both maximum parsimony and maximum likelihood methods yield a monophyletic Emydinae in which all but three nodes are well resolved. Emys orbicularis, Emydoidea blandingii, and Clemmys marmorata form a monophyletic clade, as do the species of Terrapene. Clemmys muhlenbergii and Clemmys insculpta form a third monophyletic group that may be sister to all other emydines. Clemmys guttata is problematic and probably related to Terrapene. Based on this phylogeny, and previous molecular work on the group, we suggest the following taxonomic revisions: (1) Clemmys should be restricted to a single species, C. guttata. (2) Calemys should be resurrected for C. muhlenbergii and C. insculpta. (3) Emys should be expanded to include three species: E. orbicularis, E. blandingii, and E. marmorata. Furthermore, our analyses show that neither kinetic-shelled nor akinetic-shelled emydines form monophyletic groups. Therefore, shell kinesis was either independently gained in Emys and Terrapene or secondarily lost in E. marmorata and C. guttata. Parsimony, paleontological evidence, and the multiple origins of shell kinesis in related turtle lineages (especially geoemydines) support the independent origin of plastral kinesis.     

The evolution of myiasis in blowflies (Calliphoridae)

Blowflies (Calliphoridae) are characterised by the ability of their larvae to develop in animal flesh. Where the host is a living vertebrate, such parasitism by dipterous larvae is known as myiasis. However, the evolutionary origins of the myiasis habit in the Calliphoridae, a family which includes the blowflies and screwworm flies, remain unclear. Species associated with an ectoparasitic lifestyle can be divided generally into three groups based on their larval feeding habits: saprophagy, facultative ectoparasitism, and obligate parasitism, and it has been proposed that this functional division may reflect the progressive evolution of parasitism in the Calliphoridae. In order to evaluate this hypothesis, phylogenetic analysis of 32 blowfly species displaying a range of forms of ectoparasitism from key subfamilies, i.e. Calliphorinae, Luciliinae, Chrysomyinae, Auchmeromyiinae and Polleniinae, was undertaken using likelihood and parsimony methods. Phylogenies were constructed from the nuclear 28S large subunit ribosomal RNA gene (28S rRNA), sequenced from each of the 32 calliphorid species, together with suitable outgroup taxa, and mitochondrial cytochrome oxidase subunit I and II (COI+II) sequences, derived primarily from published data. Phylogenies derived from each of the two markers (28S rRNA, COI+II) were largely (though not completely) congruent, as determined by incongruence-length difference and Kishino-Hasegawa tests. However, the phylogenetic relationships of blowfly subfamilies based on molecular data did not concur with the pattern of relationships defined by previous morphological analysis; significantly, molecular analysis supported the monophyly of blowflies (Calliphoridae), distinct from the bot and warble flies (Oestridae). Comparative analysis of the myiasis habit based primarily on the 28S rRNA phylogeny indicated that obligate parasitism, and the ability to initiate myiasis in higher vertebrates, has multiple independent origins across myiasis-causing flies (Calliphoridae and Oestridae) and in at least three subfamilies of blowfly (Calliphoridae). Finally, the general association of various blowfly genera and subfamily clades with particular continental and geographical regions suggests that these groups probably came into existence in the Late Cretaceous period, following the break-up of Gondwana.     

Developmental mechanism and evolutionary origin of vertebrate left/right asymmetries

The systematically 'handed', or directionally asymmetrical way in which the major viscera are packed within the vertebrate body is known as situs. Other less obvious vertebrate lateralisations concern cognitive neural function, and include the human phenomena of hand-use preference and language-associated cognitive partitioning. An overview, rather than an exhaustive scholarly review, is given of recent advances in molecular understanding of the mechanism that ensures normal development of 'correct' situs. While the asymmetry itself and its left/right direction are clearly vertebrate-conserved characters, data available from various embryo types are compared in order to assess the likelihood that the developmental mechanism is evolutionarily conserved in its entirety. A conserved post-gastrular 'phylotypic' stage, with left- and right-specific cascades of key, orthologous gene expressions, clearly exists. It now seems probable that earlier steps, in which symmetry-breaking information is reliably transduced to trigger these cascades on the correct sides, are also conserved at depth although it remains unclear exactly how these steps operate. Earlier data indicated that the initiation of symmetry-breaking had been transformed, among the different vertebrate classes, as drastically as has the anatomy of pre-gastrular development itself, but it now seems more likely that this apparent diversity is deceptive. Ideas concerning the functional advantages to the vertebrate lifestyle of a systematically asymmetrical visceral packing arrangement, while untestable, are accepted because they form a plausible adaptationist 'just-so' story. Nevertheless, two contrasting beliefs are possible about the evolutionary origins of situs. Major recent advances in analysis of its developmental mechanism are largely due not to zoologists, comparative anatomists or evolutionary systematists, but to molecular geneticists, and these workers have generally assumed that the asymmetry is an evolutionary novelty imposed on a true bilateral symmetry, at or close to the origin of the vertebrate clade. A major purpose of this review is to advocate an alternative view, on the grounds of comparative anatomy and molecular systematics together with the comparative study of expressions of orthologous genes in different forms. This view is that situs represents a co-optation of a pre-existing, evolutionarily ancient non-bilaterality of the adult form in a vertebrate ancestor. Viewed this way, vertebrate or chordate origins are best understood as the novel imposition of an adaptively bilateral locomotory-skeletal-neural system, around a retained non-symmetrical 'visceral' animal. One component of neuro-anatomical asymmetry, the habenular/parapineal one that originates in the diencephalon, has recently been found (in teleosts) to be initiated from the same 'phylotypic' gene cascade that controls situs development. But the function of this particular diencephalic asymmetry is currently unclear. Other left-right partitionings of brain function, including the much more recently evolved, cerebral cortically located one associated with human language and hand-use, may be controlled entirely separately from situs even though their directionality has a particular relation to it in a majority of individuals. Finally, possible relationships are discussed between the vertebrate directional asymmetries and those that occur sporadically among protostome bilaterian forms. These may have very different evolutionary and molecular bases, such that there may have been constraints, in protostome evolution, upon any exploitation of left and right for complex organismic, and particularly cognitive neural function.