The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences

In a previous study based on 100 whole mitochondrial genome (mitogenome) sequences, we sought to provide a new perspective on the ordinal relationships of higher ray-finned fish (Actinopterygii). The study left unexplored the phylogenetic position of toadfishes (order Batrachoidiformes), as data were unavailable owing to technical difficulties. In the present study, we successfully determined mitogenomic sequences for two toadfish species ( Batrachomoeus trispinosus and Porichthys myriaster ) and found that the difficulties resulted from unusual gene arrangements and associated repetitive non-coding sequences. Unambiguously aligned, concatenated mitogenomic sequences (13 461 bp) from 102 higher actinopterygians (excluding the ND6 gene and control region) were divided into five partitions (1st, 2nd and 3rd codon positions of the protein-coding genes, tRNA genes and rRNA genes) and partitioned Bayesian analyses were conducted. The resultant phylogenies strongly suggest that the toadfishes are not members of relatively primitive higher actinopterygians (Paracanthopterygii), but belong to a crown group of actinopterygians (Percomorpha), as was demonstrated for ophidiiform eels (Ophidiiformes) and anglerfishes (Lophiiformes) in the previous study. We propose revised limits of major unranked categories for higher actinopterygians and a new name (Berycomorpha) for a clade comprising two reciprocally paraphyletic orders (Beryciformes and Stephanoberyciformes) based on the present mitogenomic phylogenies.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 289–306.     

基于Rag1基因序列变异的鲤形目鱼类系统发育重建:采样策略对生命之树的影响

The phylogenetic relationships of species are fundamental to any biological investigation, including all evolutionary studies. Accurate inferences of sister group relationships provide the researcher with an historical framework within which the attributes or geographic origin of species (or supraspecific groups) evolved. Taken out of this phylogenetic context, interpretations of evolutionary processes or origins, geographic distributions, or speciation rates and mechanisms, are subject to nothing less than a biological experiment without controls. Cypriniformes is the most diverse clade of freshwater fishes with estimates of diversity of nearly 3,500 species. These fishes display an amazing array of morphological, ecological, behavioral, and geographic diversity and offer a tremendous opportunity to enhance our understanding of the biotic and abiotic factors associated with diversification and adaptation to environments. Given the nearly global distribution of these fishes, they serve as an important model group for a plethora of biological investigations, including indicator species for future climatic changes. The occurrence of the zebrafish, Danio rerio, in this order makes this clade a critical component in understanding and predicting the relationship between mutagenesis and phenotypic expressions in vertebrates, including humans. With the tremendous diversity in Cypriniformes, our understanding of their phylogenetic relationships has not proceeded at an acceptable rate, despite a plethora of morphological and more recent molecular studies. Most studies are pre-Hennigian in origin or include relatively small numbers of taxa. Given that analyses of small numbers of taxa for molecular characters can be compromised by peculiarities of long-branch attraction and nodal-density effect, it is critical that significant progress in our understanding of the relationships of these important fishes occurs with increasing sampling of species to mitigate these potential problems. The recent Cypriniformes Tree of Life initiative is an effort to achieve this goal with morphological and molecular (mitochondrial and nuclear) data. In this early synthesis of our understanding of the phylogenetic relationships of these fishes, all types of data have contributed historically to improving our understanding, but not all analyses are complementary in taxon sampling, thus precluding direct understanding of the impact of taxon sampling on achieving accurate phylogenetic inferences. However, recent molecular studies do provide some insight and in some instances taxon sampling can be implicated as a variable that can influence sister group relationships. Other instances may also exist but without inclusion of more taxa for both mitochondrial and nuclear genes, one cannot distinguish between inferences being dictated by taxon sampling or the origins of the molecular data.     

Higher and lower‐level relationships of the deep‐sea fish order Alepocephaliformes (Teleostei: Otocephala) inferred from whole mitogenome sequences

Fishes of the order Alepocephaliformes, slickheads and tubeshoulders, constitute a group of deep‐sea fishes poorly known in respect to most areas of their biology and systematics. Morphological studies have found alepocephaliform fishes to display a mosaic of synapomorphic and symplesiomorphic characters, resulting in great difficulties when attempting to resolve intra‐ and interrelationships. Molecular data recently added to the confusion by removing Alepocephaliformes from the Euteleostei and placed them as incertae sedis within the Otocephala. In the present study we attempt to further clarify relationships of Alepocephaliformes by adding newly determined whole mitogenome sequences from 19 alepocephaliforms in order to address 1) phylogenetic position of Alepocephaliformes within the Otocephala; and 2) intrarelationships of Alepocephaliformes. The present study includes 96 taxa of which 30 are alepocephaliforms and unambiguously aligned sequences were subjected to partitioned maximum likelihood and Bayesian analyses. Results from the present study support Alepocephaliformes as a genetically distinct otocephalan order as sister clade to Ostariophysi (mostly freshwater fishes comprising Gonorynchiformes, Cypriniformes, Characiformes, Siluriformes and Gymnotiformes). The disputed family Bathylaconidae was found to be an artificial assemblage of the two genera Bathylaco and Herwigia, with the former as the sister group of the family Alepocephalidae and the latter nested within Alepocephalidae. Platytroctidae was found to be monophyletic as sister clade to the rest of Alepocephaliformes. Previously unrecognized clades within the family Alepocephalidae are presented and a clade comprising Alepocephalus, Conocara and Leptoderma was recovered as the most derived. As long as the current classification is being followed, the genera Alepocephalus, Bathytroctes, Conocara and Narcetes were all found non‐monophyletic. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 923–936.     

Genetic differentiation and distribution routes of the bronze featherback Notopterus notopterus (Osteoglossiformes: Notopteridae) in Indochina

Mitochondrial DNA analysis was used to investigate genetic variation in the bronze featherback fish Notopterus notopterus in Indochina. Five hundred and five fish samples collected from 11 localities were separated into three genetically differentiated intraspecific groups. Chao Phraya River samples formed a distinct group. Mekong River samples were clearly separated into two different groups, namely, middle and lower Mekong groups. The lower Mekong group was closely related to Malay Peninsula group, even though the two groups are separated by a tract of ocean. F‐values (0.82–0.95) also confirmed genetic differentiation of the middle and lower Mekong groups. Although the two Mekong groups inhabit the same river basin, molecular clock calculations indicate they separated approximately 1.2 Mya, suggesting (1) evolutionary divergence before invasion of the Mekong River; (2) differences in migration routes to the river; and/or (3) differences in the timings of invasion. The complexities of historical events cannot be ignored in determinations of factors responsible for the exceptional biodiversity in the Mekong basin. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 575–582.     

Histopathological Analysis of Acinetobacter baumannii Lung Infection in a Mouse Model

Acinetobacter baumannii is the main causative pathogen of nosocomial infections that causes severe infections in the lungs. In this study, we analyzed the histopathological characteristics of lung infection with two strains of A. baumannii (ATCC 19606 and the clinical isolate TK1090) and Pseudomonas aeruginosa PAO-1 in C3H/HeN mice to evaluate the virulence of A. baumannii. Survival was evaluated over 14 days. At 1, 2, 5, or 14 days postinfection, mice of C3H/HeN were sacrificed, and histopathological analysis of lung specimens was also performed. Histopathological changes and accumulation of neutrophils and macrophages in the lungs after infection with A. baumannii and P. aeruginosa were analyzed. Following intratracheal inoculation, the lethality of ATCC 19606- and TK1090-infected mice was lower than that of PAO-1-infected mice. However, when mice were inoculated with a sub-lethal dose of A. baumannii, the lung bacterial burden remained in the mice until 14 days post-infection. Additionally, histopathological analysis revealed that macrophages infiltrated the lung foci of ATCC 19606-, TK1090-, and PAO-1-infected mice. Although neutrophils infiltrated the lung foci of ATCC 19606- and TK1090-infected mice, they poorly infiltrated the lung foci of PAO-1-infected mice. Accumulation of these cells in the lung foci of ATCC 19606- and TK1090-infected mice, but not PAO-1-infected mice, was observed for 14 days post-infection. These results suggest that A. baumannii is not completely eliminated despite the infiltration of immune cells in the lungs and that inflammation lasts for prolonged periods in the lungs. Further studies are required to understand the mechanism of A. baumannii infection, and novel drugs and vaccines should be developed to prevent A. baumannii infection.     

粳稻品种幼苗耐冷性比较研究

利用人工模拟低温胁迫的方法,研究了３个日本粳稻品种日本晴、金南风和福光以及２个台湾粳稻品种台竹１５７、加南２０的苗期耐冷性,并以当地推广高产籼稻品种特三矮２号作对照。从对株高、主茎叶片数、地上部干物重、死苗率等形态性状的调查和叶绿素含量、电解质外渗率等生理性状测定的结果显示,日本晴、金南风、福光和台竹１５７苗期的耐冷性较强,加南２０的耐冷性较弱,但比特三矮２号的耐冷性略强。这为防止早稻烂秧死苗而开     

Life‐history traits related to diapause in univoltine and bivoltine populations of Ypthima multistriata (Lepidoptera: Satyridae) inhabiting similar latitudes

In most temperate insects, diapause strategies and voltinism generally exhibit latitudinal clines, supporting the concept that they represent adaptations to climate. In contrast, in the satyrine butterfly Ypthima multistriata Butler, local populations with different voltinism patterns are geographically intermingled, suggesting that life‐history traits related to diapause may differ even between geographically and phylogenetically close populations. In this study, we experimentally examined the critical photoperiod for diapause induction and the larval developmental period in two univoltine and two bivoltine populations of Y. multistriata, all of which inhabit virtually the same latitude (34.652–34.750°N). We found that the critical photoperiod for diapause induction was longer in the univoltine populations than in the bivoltine populations. Moreover, the larval period under the long day length treatment was different among populations in both sexes, although significant differences were also detected between populations with the same voltinism. These results indicate that in Y. multistriata, life‐history traits related to diapause can not be attributed merely to climatic conditions such as temperature or day length, which depend largely on latitude. Therefore, we suggest that biotic elements, such as leaf toughness, as well as abiotic elements should be taken into account in attempts to explain the enigmatic pattern of geographic variation in the diapause strategies of Y. multistriata.     

Accurate measurement of optical properties of narrow leaves and conifer needles with a typical integrating sphere and spectroradiometer

Accurate information on the optical properties (reflectance and transmittance spectra) of single leaves is important for an ecophysiological understanding of light use by leaves, radiative transfer models and remote sensing of terrestrial ecosystems. In general, leaf optical properties are measured with an integrating sphere and a spectroradiometer. However, this method is usually difficult to use with grass leaves and conifer needles because they are too narrow to cover the sample port of a typical integrating sphere. Although ways to measure the optical properties of narrow leaves have been suggested, they have problems. We propose a new measurement protocol and calculation algorithms. The protocol does not damage sample leaves and is valid for various types of leaves, including green and senescent. We tested our technique with leaves of Aucuba japonica, an evergreen broadleaved shrub, and compared the spectral data of whole leaves and narrow strips of the leaves. The reflectance and transmittance of the strips matched those of the whole leaves, indicating that our technique can accurately estimate the optical properties of narrow leaves. Tests of conifer needles confirmed the applicability.     

The evolution of social behaviour in sentinel crabs (Macrophthalmus): implications from molecular phylogeny

Crabs of the genus Macrophthalmus are known to exhibit highly developed and diverse social behaviour, such as allocleaning, fighting and waving display behaviour, the first being observed widely throughout the genus. Fighting behaviour between males has been classified previously into grasping fighting and claw‐extending fighting, and male waving display into four patterns, the vertical non‐forward‐pointing type, vertical forward‐pointing type, lateral non‐forward‐pointing type and lateral forward‐pointing type, on the basis of interspecific behaviour comparisons. To understand the evolutionary pathways of these social behavioural activities, 978‐bp nucleotide sequences from mitochondrial 16S rRNA genes of 21 species, including two outgroup taxa, were analysed and a molecular phylogeny was reconstructed. The resultant tree demonstrated striking inconsistencies with the relationships inferred from morphological features. Species with similar habitat conditions showed similar morphological features, although they were not phylogenetically close relatives. Phylogenetic analysis of allocleaning behaviour suggested that it evolved once in the early history of the lineage. The analysis of fighting behaviour demonstrated that species with claw‐extending fighting, being a more complex behaviour than grasping fighting, are found in the most ancestral part of the phylogeny. The analysis also revealed that claw‐extending fighting has evolved secondarily on two occasions, suggesting that fighting behaviour is not characterized by sufficient phylogenetic components. The superimposition of a waving pattern on to the phylogeny indicated that the lateral non‐forward‐pointing type has evolved from the vertical non‐forward‐pointing type, the lateral forward‐pointing type having evolved from the vertical forward‐pointing type. This scenario also appeared reasonable with respect to the behavioural trends of cheliped movements in waving. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 88 , 45–59.