Universal primer cocktails for fish DNA barcoding

Reliable recovery of the 5′ region of the cytochrome c oxidase 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all fish species. In this study, we develop and test primer cocktails with a view towards increasing the efficiency of barcode recovery. Specifically, we evaluate the success of polymerase chain reaction amplification and the quality of resultant sequences using three primer cocktails on DNA extracts from representatives of 94 fish families. Our results show that M13‐tailed primer cocktails are more effective than conventional degenerate primers, allowing barcode work on taxonomically diverse samples to be carried out in a high‐throughput fashion.     

Behaviour, home-range size and habitat use by male Great Bittern Botaurus stellaris in Britain

This paper describes the first use of radiotracking to follow closely the secretive Great Bittern Botaurus stellaris , and to quantify its reedbed habitat preferences at a fine scale. Eight males were tracked at two sites in Britain, at which they were mainly resident through the winter. Their median home-range sizes were 14.6, 19.3 and 33.1 ha during the booming, moult and winter periods, respectively, and home-ranges were, on average, composed of 30% open pools and 48% reedbed edge (of 30 m width). Great Bitterns were most often active in reed with 20 cm water depth within the 30-m reed edge next to water, whereas areas of reedbed near scrub or further from the water's edge were avoided. Reed edge adjacent to open pools was preferred over that adjacent to channels and ditches. These results provide a basis for conservation recommendations on the quantity and composition of reedbed habitat and provide the scientific basis for a national programme of reedbed rehabilitation and restoration.     

角质形成细胞生长因子(KGF)在喉粘膜良性、癌前及恶性病变中的mRNA水平分析

利用原位杂交的方法检测KGFmRNA在正常喉粘膜上皮（N）、慢性非特异性炎症（IF）、不典型增生（DYS）及鳞癌（SCC）中的转录水平,探讨KGF在喉粘膜良性及恶性病变中的分布和可能的作用。结果表明,KGFmRNA不仅在间质中的成纤维细胞中表达,少量的炎细胞及血管内皮细胞中亦表达,而且从N、IF、DYS到SCC、KGFmRNA转录水平逐渐增强;上皮细胞及肿瘤性上皮细胞不表达KGFmRNA,KGFmRNA在分化差的SCC周围间质中表达较分化好的SCC周围间质增多。结论：KGF在上皮与间充质细胞的交互作用中发挥着重要的作用,对维持喉粘膜正常结构、代谢及喉癌的发生发展具有重要意义。     

Fat frogs,mobile genes: unexpected phylogeographic patterns for the ornate chorus frog (Pseudacris ornata)

The southeastern coastal plain of the United States is a region marked by extraordinary phylogeographic congruence that is frequently attributed to the changing sea levels that occurred during the glacial‐interglacial cycles of the Pleistocene epoch. A phylogeographic break corresponding to the Apalachicola River has been suggested for many species studied to date that are endemic to this region. Here, we used this pattern of phylogeographic congruence to develop and test explicit hypotheses about the genetic structure in the ornate chorus frog (Pseudacris ornata). Using 1299 bp of mtDNA sequence and seven nuclear microsatellite markers in 13 natural populations of P. ornata, we found three clades corresponding to geographically distinct regions; one spans the Apalachicola River (Southern Clade), one encompasses Georgia and South Carolina (Central Clade) and a third comprises more northerly individuals (Northern Clade). However, it does not appear that typical phylogeographic barriers demarcate these clades. Instead, isolation by distance across the range of the entire species explained the pattern of genetic variation that we observed. We propose that P. ornata was historically widespread in the southeastern United States, and that a balance between genetic drift and migration was the root of the genetic divergence among populations. Additionally, we investigated fine‐scale patterns of genetic structure and found the spatial scale at which there was significant genetic structure varied among the regions studied. Furthermore, we discuss our results in light of other phylogeographic studies of southeastern coastal plain organisms and in relation to amphibian conservation and management.     

A phylogeny of the families of fossil and extant tetraodontiform fishes (Acanthomorpha, Tetraodontiformes), Upper Cretaceous to Recent

A data matrix is presented of 210 morphological characters (mostly osteological, some external) for 20 extant taxa of the ten Recent families of tetraodontiform fishes and 36 fossil tetraodontiforms. The oldest of these are from the Upper Cretaceous (95 Mya); most are from the Lower to Middle Eocene (50–58 Mya). There are two outgroup taxa (a zeiform and a caproid). A cladistic analysis of this matrix for only the extant taxa produced two equally parsimonious trees that call into question the monophyly of some of the previously accepted major higher-level tetraodontiform clades. Inclusion in the analysis of the large number of available fossil taxa helps to resolve relationships between family level clades. The new phylogenetic hypothesis, together with stratigraphic and biogeographical data, is used to discuss scenarios of the origin and evolution of the major clades of the order.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 565−617.     

The distribution of breeding dippers (Cinclus cinclus (L.); Aves) in relation to stream acidity in upland Wales

SUMMARY. 1. The distribution of breeding dippers was assessed in 1984 over seventy-four sites on soft-water streams throughout mid and north Wales.
2. Sites without breeding dippers had significantly higher mean concentrations of filterable aluminium, lower mean pH, fewer trichopteran larvae and ephemeropteran nymphs, and were on rivers with more conifer afforestation on their catchments, than sites where dippers were present.
3. We speculate that influences which increase the acidity of soft-water streams could be detrimental to their populations of dippers, although further data are required on causative mechanisms.     

Phylogenetic reconstruction of vertebrate Hox cluster duplications

In vertebrates and the cephalochordate, amphioxus, the closest vertebrate relative, Hox genes are linked in a single cluster. Accompanying the emergence of higher vertebrates, the Hox gene cluster duplicated in either a single step or multiple steps, resulting in the four-cluster state present in teleosts and tetrapods. Mammalian Hox clusters (designated A, B, C, and D) extend over 100 kb and are located on four different chromosomes. Reconstructing the history of the duplications and its relation to vertebrate evolution has been problematic due to the lack of alignable sequence information. In this study, the problem was approached by conducting a statistical analysis of sequences from the fibrillar-type collagens (I, II, III, and IV), genes closely linked to each Hox cluster which likely share the same duplication history as the Hox genes. We find statistical support for the hypothesis that the cluster duplication occurred as multiple distinct events and that the four-cluster situation arose by a three- step sequential process.      

The spectral absorption and scattering properties of dissolved and particulate components in relation to the underwater light field of some tropical Australian fresh waters

SUMMARY. 1. The inherent optical properties (scattering coefficients and absorption coefficients across the photosynthetic waveband) are presented from diverse tropical water bodies (billabongs) in the Alligator Rivers Region of northern Australia.
2. The data are used to interpret observed characteristics of the underwater light field as exemplified by the spectral distribution, and overall rate of attenuation, of photosynthetically available radiation (PAR).
3. Attenuation of PAR, especially in the blue waveband, is caused primarily by intense light absorption by the yellow-brown humic pigments, both soluble and particulate, in the water.
4. It was estimated that in six moderately turbid billabongs, light scattering increased attenuation by an average of 58% above that attributable to absorption alone, whereas in a highly turbid billabong the increase was 111%.
5. A distinguishing feature of the optical character of these billabongs, compared with previously studied water bodies in southern Australia, is the great contribution to light absorption made by the particulate humic material.