Evolutionary history of the Paradoxurus palm civets – a new model for Asian biogeography

Aim Using molecular data and dental features, we investigated the genetic and morphological diversity among species of palm civets in the genus Paradoxurus, with a focus on the common palm civet, Paradoxurus hermaphroditus (Carnivora, Viverridae), in order to address biogeographic scenarios and provide recommendations for a taxonomic revision. Location Asia: Pakistan to the Lesser Sunda Islands. Methods We investigated the genetic diversity within Paradoxurus using two mitochondrial (cytochrome b, control region) and one nuclear (intron 7 of the β‐fibrinogen) markers. We used samples from 85 individuals of P. hermaphroditus (including 20 museum specimens) and one representative of each of the other species in the genus Paradoxurus: Paradoxurus jerdoni and Paradoxurus zeylonensis. DNA sequences were analysed using phylogenetic and haplotype network methods, and divergence dates were estimated for the clades retrieved. Furthermore, we examined dental characters from a large series of specimens and compared the morphological variation with the molecular data. Results Our phylogenetic analyses revealed that P. hermaphroditus is paraphyletic. We identified three major lineages distributed: (1) in the Indian subcontinent, south China, Hainan and in areas above 200 m in Indochina; (2) in Peninsular Malaysia, Java, Sumatra and in areas below 200 m in Indochina; and (3) in Borneo, the Philippines and the Mentawai archipelago. Our morphological observations were congruent with these three molecular lineages. Divergence date estimates inferred a Pliocene origin for Paradoxurus (2.8–5.7 Ma), with the three main clades diversifying from the mid–Early Pliocene to the end of the Pliocene. We suggest that the flooding of the Isthmus of Kra during the Pliocene was a major event shaping the diversification of Paradoxurus palm civets. We also hypothesize that the elevational segregation of the two lineages on the mainland could have resulted from the vegetational changes that were induced by Late Pliocene glacial episodes. Main conclusions The Isthmus of Kra is a major boundary between two major lineages of P. hermaphroditus. There is a need for a taxonomic revision for P. hermaphroditus, and we suggest that this species should be split into at least three species.     

Intrinsic secondary structure propensities of the amino acids,using statistical ϕ–ψ matrices: Comparison with experimental scales

Today there are several different experimental scales for the intrinsic α-helix as well as β-strand, propensities of the 20 amino acids obtained from the thermodynamic analysis of various model systems. These scales do not compare well with those extracted from statistical analysis of three-dimensional structure databases. Possible explanations for this could be the limited size of the databases used, the definitions of intrinsic propensities, or the theoretical approach. Here we report a statistical determination of α-helix and β-strand propensities derived from the analysis of a database of 279 three-dimensional structures. Contrary to what has been generally done, we have considered a particular residue as in α-helix or β-strand conformation by looking only at its dihedral angles (?–ψ matrices). Neither the identity nor the conformation of the surrounding residues in the amino acid sequence has been taken into consideration. Pseudoenergy empirical scales have been calculated from the statistical propensities. These scales agree very well with the experimental ones in relative and absolute terms. Moreover, its correlation with the average of the experimental scales for α-helix or β-strand is as good as the correlations of the individual experimental scales with the average. These results show that by using a large enough database and a proper definition for the secondary structure propensities, it is possible to obtain a scale as good as any of experimental origin. Interestingly the ?–ψ analysis of the Ramachandran plot suggests that the amino acids could have different β-strand propensities in different subregions of the β-strand area. © 1994 Wiley-Liss, Inc.     

Genetic divergences and intraspecific variation in corvids of the genus Corvus (Aves: Passeriformes: Corvidae) – a first survey based on museum specimens

The first comprehensive overview of intra‐ and interspecific variation within the genus Corvus as well as first insights into the phylogenetic relationships of its species is presented. DNA sequences of the mitochondrial control region were obtained from 34 of the 40 described species (including subspecies: 56 taxa). As the study was based mainly on museum material, several specimens did not yield the full length marker sequence. In these cases, only a short section of the control region could be analysed. Nevertheless, even these individuals could be assigned tentatively to clades established on the full length marker sequence. Inclusion of sequences of other corvid genera as available in GenBank clearly confirmed the monophyly of the genus Corvus. Within the Corvus clade several distinct subclades can be distinguished. Some represent lineages of single species or species pairs while other clades are composed of many species. In general, the composition of the clades reflects geographical contiguousness and confirms earlier assumptions of a Palearctic origin of the genus Corvus with several independent colonizations of the Nearctic and the Aethiopis. The Australasian radiation seems to be derived from a single lineage. The distribution of plumage colour in the phylogenetic tree indicates that the pale markings evolved several times independently. The white/grey plumage colour pattern – which is found also in other genera of the family Corvidae, for example, in Pica– occurs already in the species pair representing the first split within the genus Corvus (Corvus monedula, Corvus dauuricus). Thus, reversal to full black colour seems to have occurred as well. The use of colour traits as a phylogenetic marker within Corvus should be considered with severe caution.     

The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of α + β fold

The structure of AF2331, a 11‐kDa orphan protein of unknown function from Archaeoglobus fulgidus, was solved by Se‐Met MAD to 2.4 Å resolution. The structure consists of an α + β fold formed by an unusual homodimer, where the two core β‐sheets are interdigitated, containing strands alternating from both subunits. The decrease in solvent‐accessible surface area upon dimerization is unusually large (3960 Ų) for a protein of its size. The percentage of the total surface area buried in the interface (41.1%) is one of the largest observed in a nonredundant set of homodimers in the PDB and is above the mean for nearly all other types of homo‐oligomers. AF2331 has no sequence homologs, and no structure similar to AF2331 could be found in the PDB using the CE, TM‐align, DALI, or SSM packages. The protein has been identified in Pfam 23.0 as the archetype of a new superfamily and is topologically dissimilar to all other proteins with the “3‐Layer (BBA) Sandwich” fold in CATH. Therefore, we propose that AF2331 forms a novel α + β fold. AF2331 contains multiple negatively charged surface clusters and is located on the same operon as the basic protein AF2330. We hypothesize that AF2331 and AF2330 may form a charge‐stabilized complex in vivo, though the role of the negatively charged surface clusters is not clear.     

An underground burst of diversity – a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes

Using both nuclear and mitochondrial sequences, we demonstrate high genetic differentiation in the genus Talpa and confirm the existence of cryptic species in the Caucasus and Anatolia, namely, T. talyschensis Vereschagin, 1945, T. ognevi Stroganov, 1948, and Talpa ex gr. levantis. Our data support four clades in the genus Talpa that showed strong geographical associations. The ‘europaea’ group includes six species from the western portion of the genus' range (T. europaea, T. occidentalis, T. romana, T. caeca, T. stankovici, and T. levantis s.l.); another three groups are distributed further east: the ‘caucasica’ group (Caucasus), the ‘davidiana’ group (eastern Anatolia and Elburz) and T. altaica (Siberia). The phylogenetic position of T. davidiana was highlighted for the first time. The order of basal branching remains controversial, which can be attributed to rapid diversification events. The molecular time estimates based on nuclear concatenation estimated the basal divergence of the crown Talpa during the latest Miocene. A putative scenario of Talpa radiation and issues of species delimitation are discussed. © 2015 The Linnean Society of London     

Wright KL,Birnbaum MJ,van Wijnen AJ,Stein GS,Stein JL (1995): Bipartite structure of the proximal promoter of a human H4 histone gene. J Cell Biochem 58:372–379.

The proximal promoter of the human H4 histone gene FO108 contains two regions of in vivo protein-DNA interaction, Sites I and II. electrophoretic, mobility shift assays using a radiolabeled DNA probe revealed that several proteins present in HeLa cell nuclear extracts bound specifically to Site 1 (nt-125 to nt-86). The most prominent complex, designated HiNF-C, and a complex of greater mobility, HiNF-C′, using were specifically competed by an Sp1 consensus oligonucleotide. Fractionation of HiNF-C using wheat germ agglutinin affinity chromatography suggested that, like Sp1, HiNF-C contains N-acetylglucosamine moieties. Two minor complexes of even greater mobility, designated HiNF-E and F, were competed by ATF consensus oligonucleotides. A DNA probe carrying a site-specific mutation in the distal portion of Site I failed to bind HiNF-E, indicating that this protein associated specifically to this region. UV cross-linking analysis showed that several proteins of different molecular wieghts interact specifically with Site I. These data indicate that Site I possesses as bipartite structure and that multiple proteins present in HeLa cell nuclear extracts interact specifically with Site I sequences. © 1995 Wiley-Liss, Inc.