Molecular evolution of a primate-specific microRNA family

Lineage-specific microRNA (miRNA) families may contribute to developmental novelties during evolution. However, little is known about the origin and evolution of new miRNA families. We report evidence of an Alu-mediated rapid expansion of miRNA genes in a

Composition and evolution of the V2r vorneronasal receptor gene repertoire in mice and rats

Pheromones are chemicals produced and detected by conspecifics to elicit social/sexual physiological and behavioral responses, and they are perceived primarily by the vomeronasal organ (VNO) in terrestrial vertebrates. Two large superfamilies of G protein-coupled receptors, V1rs and V2rs, have been identified as pheromone receptors in vomeronasal sensory neurons. Based on a computational analysis of the mouse and rat genome sequences, we report the first global draft of the V2r gene repertoire, composed of similar to 200 genes and pseudogenes. Rodent V2rs are subject to rapid gene births/deaths and accelerated amino acid substitutions, likely reflecting the species-specific nature of pheromones. Vertebrate V2rs appear to have originated twice prior to the emergence of the VNO in ancestral tetrapods, explaining seemingly inconsistent observations among different V2rs. The identification of the entire V2r repertoire opens the door to genomic-level studies of the structure, function, and evolution of this diverse group of sensory receptors. (c) 2005 Elsevier Inc. All rights reserved.

A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae

Background: The Galliformes is a well-known and widely distributed Order in Aves. The phylogenetic relationships of galliform birds, especially the turkeys, grouse, chickens, quails, and pheasants, have been studied intensively, likely because of their close association with humans. Despite extensive studies, convergent morphological evolution and rapid radiation have resulted in conflicting hypotheses of phylogenetic relationships. Many internal nodes have remained ambiguous. Results: We analyzed the complete mitochondrial (mt) genomes from 34 galliform species, including 14 new mt genomes and 20 published mt genomes, and obtained a single, robust tree. Most of the internal branches were relatively short and the terminal branches long suggesting an ancient, rapid radiation. The Megapodiidae formed the sister group to all other galliforms, followed in sequence by the Cracidae, Odontophoridae and Numididae. The remaining clade included the Phasianidae, Tetraonidae and Meleagrididae. The genus Arborophila was the sister group of the remaining taxa followed by Polyplectron. This was followed by two major clades: ((((Gallus, Bambusicola) Francolinus) (Coturnix, Alectoris)) Pavo) and (((((((Chrysolophus, Phasianus) Lophura) Syrmaticus) Perdix) Pucrasia) (Meleagris, Bonasa)) ((Lophophorus, Tetraophasis) Tragopan))). Conclusions: The traditional hypothesis of monophyletic lineages of pheasants, partridges, peafowls and tragopans was not supported in this study. Mitogenomic analyses recovered robust phylogenetic relationships and suggested that the Galliformes formed a model group for the study of morphological and behavioral evolution.

A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution

Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale + Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution. (C) 2010 Elsevier Inc. All rights reserved.

Rapid and parallel chromosomal number reductions in muntjac deer inferred from mitochondrial DNA phylogeny

Muntjac deer (Muntiacinae, Cervidae) are of great interest in evolutionary studies because of their dramatic chromosome variations and recent discoveries of several new species. In this paper, we analyze the evolution of karyotypes of muntjac deer in the context of a phylogeny which is based on 1,844-bp mitochondrial DNA sequences of seven generally recognized species in the muntjac subfamily. The phylogenetic results support the hypothesis that karyotypic evolution in muntjac deer has proceeded via reduction in diploid number. However, the reduction in number is not always linear, i.e., not strictly following the order: 46-->14/13-->8/9-->6/7. For example, Muntiacus muntjak (2n = 6/7) shares a common ancestor with Muntiacus feae (2n = 13/14), which indicates that its karyotype was derived in parallel with M. feae's from an ancestral karyotype of 2n greater than or equal to 13/14. The newly discovered giant muntjac (Muntiacus vuquangensis) may represent another pa;allel reduction lineage from the ancestral 2n = 46 karyotype. Our phylogenetic results indicate that the giant muntjac is relatively closer to Muntiacus reevesi than to other muntjacs and may be placed in the genus Muntiacus. Analyses of sequence divergence reveal that the rate of change in chromosome number in muntjac deer is one of the fastest in vertebrates. Within the muntjac subfamily, the fastest evolutionary rate is found in the Fea's lineage, in which two species with different karyotypes diverged in around 0.5 Myr.

KARYOTYPE EVOLUTION OF SHREW MOLES (SORICOMORPHA: TALPIDAE)

The Chinese long-tailed mole (Scaptonyx fusicaudus) closely resembles American (Neurotrichus gibbsii) and Japanese (Dymecodon pilirostris and Urotrichus talpoides) shrew moles in size, appearance, and ecological habits, yet it has traditionally been classified either together with (viz subfamily Urotrichinae) or separately (tribe Scaptonychini) from the latter genera (tribe Urotrichini sensu lato). We explored the merit of these competing hypotheses by comparing the differentially stained karyotypes of S.fusicaudus and N. gibbsii with those previously reported for both Japanese taxa. With few exceptions, diploid chromosome number (2n = 34), fundamental autosomal number (FNa = 64), relative size, and G-banding pattern of S. fusicaudus were indistinguishable from those of D. pilirostris and U. talpoides. In fact, only chromosome 15 differed significantly between these species, being acrocentric in D. pilirostris, subtelocentric in U. talpoides, and metacentric in S. fusicaudus. This striking similarity is difficult to envisage except in light of a shared common ancestry, and is indicative of an exceptionally low rate of chromosomal evolution among these genera. Conversely, the karyotype of N. gibbsii deviates markedly in diploid chromosome and fundamental autosomal number (2n = 38 and FNa = 72, respectively), morphology, and G-banding pattern from those of Scaptonyx and the Japanese shrew moles. These differences cannot be explained by simple chromosomal rearrangements, and Suggest that rapid chromosomal reorganization Occurred ill the karyotype evolution of this species, possibly due to founder or bottleneck events.

Evaluations of the pelagic resources in the Burundi waters of Lake Tanganyika and the evolution of the fisheries

The important pelagic fishery resources of northern Lake Tanganyika were identified after a preliminary scientific evaluation, and in Burundi, with governmental assistance they were rapidly developed and exploited more intensively until overfishing was thought to have occurred. At this point, legal measures were introduced in order to protect the resource by restricting fishing effort and maintaining the total yield near the apparent maximum sustained limit. Complementary biological research on the fish stocks did not accompany the rapid fishery development and now an intensive stock assessment programme has been launched by the Government and UNDP in order to define more precisely the available fish stocks and to consider, with the co-operation of the neighbouring lacustrine states, suitable ways of ensuring optimum levels of fish harvest from year to year.

Thermal evolution of Er silicate thin films grown by rf magnetron sputtering

Stoichiometric Er silicate thin films, monosilicate (Er2SiO 5) and disilicate (Er2Si2O7), have been grown on c-Si substrates by rf magnetron sputtering. The influence of annealing temperature in the range 1000-1200 °C in oxidizing ambient (O 2) on the structural and optical properties has been studied. In spite of the known reactivity of rare earth silicates towards silicon, Rutherford backscattering spectrometry shows that undesired chemical reactions between the film and the substrate can be strongly limited by using rapid thermal treatments. Monosilicate and disilicate films crystallize at 1100 and 1200 °C, respectively, as shown by x-ray diffraction analysis; the crystalline structures have been identified in both cases. Moreover, photoluminescence (PL) measurements have demonstrated that the highest PL intensity is obtained for Er2Si2O7 film annealed at 1200 °C. In fact, this treatment allows us to reduce the defect density in the film, in particular by saturating oxygen vacancies, as also confirmed by the increase of the lifetime of the PL signal. © 2008 IOP Publishing Ltd.

Defect evolution and accompanied change of electrical properties during the GaN growth by metalorganic chemical vapor deposition

The defect evolution and its correlation with electrical properties of GaN films grown by metalorganic chemical vapor deposition are investigated. It is found that the dislocation density decreases gradually during the growth process, and the dislocation reduction rate in the island coalescence process is especially rapid. The changes in electron mobility of GaN with the increase of growth time are mainly dependent on the dislocations acting as scattering centers. Furthermore, the variation of carrier concentration in GaN may be related with the point defects and their clusters. The quality of GaN could be improved by suitably increasing the film thickness. (C) 2009 Elsevier B.V. All rights reserved.

Evolution from point defects to arsenic clusters in low-temperature grown GaAs/AlGaAs multiple quantum wells

Optical transient current spectroscopy (OTCS), photoluminescence (PL) spectroscopy and excitonic electroabsorption spectroscopy have been used to investigate the evolution of defects in the low-temperature grown GaAs/AlGaAs multiple quantum well structures during the postgrowth rapid thermal annealing. The sample was grown at 350 degrees C by molecular beam epitaxy on miscut (3.4 degrees off (001) towards (111)A) (001) GaAs substrate. After growth, the sample was subjected to 30s rapid thermal annealing in the range of 500-800 degrees C. It is found that the integrated PL intensity first decreases with the annealing temperature, then gets a minimum at 600 degrees C and finally recovers at higher temperatures. OTCS measurement shows that besides As,, antisites and arsenic clusters, there are several relatively shallower deep levels with excitation energies less than 0.3 eV in the as-grown and 500 degrees C-annealed samples. Above 600 degrees C, OTCS signals from As,, antisites and shallower deep levels become weaker, indicating the decrease of these defects. It is argued that the excess arsenic atoms group together to form arsenic clusters during annealing. (C) 2000 Elsevier Science B.V. All rights reserved.

Strain-induced morphological evolution and preferential interdiffusion in SiGe epitaxial film on Si(100) during high-temperature annealing

Strain relaxation in initially flat SiGe film on Si(1 0 0) during rapid thermal annealing is studied. The surface roughens after high-temperature annealing, which has been attributed to the intrinsic strain in the epilayers. It is interesting to find that high-temperature annealing also results in roughened interface, indicating the occurrence of preferential interdiffusion. It is suggested that the roughening at the surface makes the intrinsic strain in the epilayer as well as the substrate unequally distributed, causing preferential interdiffusion at the SiGe/Si interface during high-temperature annealing. (C) 1999 Elsevier Science B.V. All rights reserved.

Strain-induced morphological evolution and preferential interdiffusion in SiGe epitaxial film on Si(100) during high-temperature annealing

Strain relaxation in initially flat SiGe film on Si(1 0 0) during rapid thermal annealing is studied. The surface roughens after high-temperature annealing, which has been attributed to the intrinsic strain in the epilayers. It is interesting to find that high-temperature annealing also results in roughened interface, indicating the occurrence of preferential interdiffusion. It is suggested that the roughening at the surface makes the intrinsic strain in the epilayer as well as the substrate unequally distributed, causing preferential interdiffusion at the SiGe/Si interface during high-temperature annealing. (C) 1999 Elsevier Science B.V. All rights reserved.

Surface morphology evolution of a thin polymeric supramolecular film by tuning interactions

A polymeric supramolecule consisting of symmetric polystyrene-block-poly(4-vinylpytidine) (PS-b-P4VP), dodecylbenzenesulfonic acid (DBSA), and 3-pentadecylphenol (PDP) was formed by proton transfer and hydrogen bonding. The surface morphology,of a thin film of the polymeric supramolecule has been investigated. The spherical PS microdomains embedded in a P4VP(DBSA)(1.0)(PDP)(1.0) matrix are observed for the as-cast film because the weight fraction, f(comb), of the P4VP(DBSA) (1.0)(PDP)(1.0) blocks is much higher than that of PS as a result of the non-covalent interactions of P4VP and DBSA and DBSA and PDR Upon annealing the PS-b-P4VP(1:1)(DBSA)(1.0)(PDP)(1.0) film at high temperatures, the hydrogen bonding between the DBSA and PDP diminishes, which leads to a change of overall morphology from an ordered sphere to a pitted structure.

Tectonic Evolution and Dynamics of Deepwater Area of Pearl River Mouth Basin, Northern South China Sea

Quantitative studies on the evolution and dynamics of the deepwater area of Pearl River Mouth basin (PRMB) were carried out based on the latest geological and seismic data. The study area is generally in an extensional state during the Cenozoic. The major extension happened in the earlier syn-rift stages before 23 Ma and the extension after 23 Ma is negligible. Two rapid subsidence periods, 32-23 Ma and 5.3-2.6 Ma, are identified, which are related to the abrupt heat decay during margin breakup and the collision between the Philippine Sea plate and the Eurasian plate, respectively. The strongest crustal thinning in the Baiyun (sic) sag may trigger the syn-rift volcanism along the weak faulted belt around the sag. The Cenozoic tectonic evolution of the study area could be divided into five stages: rifting (similar to 50-40 Ma), rift-drift transition (similar to 40-32 Ma), early post-breakup (similar to 32-23 Ma), thermal subsidence (similar to 23-5.3 Ma) and neotectonic movement (similar to 5.3-0 Ma).

Molecular phylogeny, recent radiation and evolution of gross morphology of the rhubarb genus Rheum (Polygonaceae) inferred from chloroplast DNA trnL-F sequences

Background and Aims Rheum, a highly diversified genus with about 60 species, is mainly confined to the mountainous and desert regions of the Qinghai-Tibetan plateau and adjacent areas. This genus represents a good example of the extensive diversification of the temperate genera in the Qinghai-Tibetan plateau, in which the forces to drive diversification remain unknown. To date, the infrageneric classification of Rheum has been mainly based on morphological characters. However, it may have been subject to convergent evolution under habitat pressure, and the systematic position of some sections are unclear, especially Sect. Globulosa, which has globular inflorescences, and Sect. Nobilia, which has semi-translucent bracts. Recent palynological research has found substantial contradictions between exine patterns and the current classification of Rheum. Two specific objectives of this research were (1) to evaluate possible relationships of some ambiguous sections with a unique morphology, and (2) to examine possible occurrence of the radiative speciation with low genetic divergence across the total genus and the correlation between the extensive diversification time of Rheum and past geographical events, especially the recent large-scale uplifts of the Qinghai-Tibetan Plateau.Methods The chloroplast DNA trnL-F region of 29 individuals representing 26 species of Rheum, belonging to seven out of eight sections, was sequenced and compared. The phylogenetic relationships were further constructed based on the sequences obtained.Key Results Despite the highly diversified morphology, the genetic variation in this DNA fragment is relatively low. The molecular phylogeny is highly inconsistent with gross morphology, pollen exine patterns and traditional classifications, except for identifying all samples of Sect. Palmata, three species of Sect. Spiciformia and a few species of Sect. Rheum as corresponding monophyletic groups. The monotypic Sect. Globulosa showed a tentative position within the clade comprising five species of Sect. Rheum. All of the analyses revealed the paraphyly of R. nobile and R. alexandrae, the only two species of Sect. Nobilia circumscribed by the possession of large bracts. The crude calibration of lineages based on trnL-F sequence differentiation implied an extensive diversification of Rheum within approx. 7 million years.Conclusions Based on these results, it is suggested that the rich geological and ecological diversity caused by the recent large-scale uplifts of the Qinghai-Tibetan Plateau since the late Tertiary, coupled with the oscillating climate of the Quaternary stage, might have promoted rapid speciation in small and isolated populations, as well as allowing the fixation of unique or rare morphological characters in Rheum. Such a rapid radiation, combined with introgressive hybridization and reticulate evolution, may have caused the transfer of cpDNA haplotypes between morphologically dissimilar species, and might account for the inconsistency between morphological classification and molecular phylogeny reported here.