Plume moths (Lepidoptera, Pterophoridae) reared from the Chilean endemic Steviaphilippiana (Asteraceae).

Taxonomic recommendations for British birds: seventh report

10 - Frequency Domain Techniques in the Analysis of DNA Sequences

Two abundant herbivorous insects, Philaenus spumarius, the meadow spittlebug (Homoptera: Cercopidae), and Platyptilia williamsii, the calendula plume moth (Lepidoptera: Pterophoridae) both spend their immature development on new leaves of Erigeron glaucus. Field experiments were conducted in the natural environment at Bodega Bay, California, to test the persistence and growth of each of these herbivores when they did and when they did not co—occur with the other species. The presence of spittlebugs had no effect on the persistence of plume moths. However, during each of two years, spittlebugs that co—occurred with plume moth caterpillars had lower persistence times than those without caterpillars, and presumably had lower survival. Spittlebug persistence was correlated with production of new leaves by the host plant; plume moth larvae consumed the terminal bud and greatly reduced new leaf production. Spittlebugs on buds that were experimentally made unavailable to spittlebugs for food and refuge had low persistence times, as did spittlebugs on rosettes that had been damaged by moths during the previous winter. This asymmetric interspecific interaction had significant effects on spittlebug populations. Plume moths and spittlebugs come in contact often under natural conditions, and the number of spittlebugs in one year was influenced by persistence of spittlebug nymphs in the previous year. Plume moths and spittlebugs were also found to co—occur on individual rosettes of the host less often than predicted from their abundances. This study and other examples of interspecific competition between plant—feeding insects indicate that more field experiments are needed before any conclusions can be drawn about the significance of competition for insect herbivores.

The Ecuadorian Andes in northwestern South America are well known for being among the hot spots of global vascular plant diversity due to their complex topography (uplift of the mountain chain), varying climatic conditions and different vegetation types. Despite its high biodiversity level, the Ecuadorian Andes represent a most threatened and poorly studied landscape. Especially the páramo and mountain ecosystems are subject to overgrazing, burning, cultivation and deforestation caused by the expansion of human activity during the last decades. The knowledge of palaeoecology and landscape dynamics is important in order to understand past processes that played a major role in the development of the ecosystems and Ecuadorian landscapes of today. Nevertheless only a limited number of palaeoecological studies are available from the Ecuadorian Andes. This thesis presents palynological analyses carried out at three different sites in the central and southern Ecuadorian Andes region to better understand the past vegetation changes, climate and fire dynamics as well as human impact since the late Pleistocene. The analysis of the sediment core El Cristal, located on the eastern slope at the Protective Forest Corazón de Oro in southeastern Ecuador reveals changes in the vegetation distribution, climate, fire regime and human impact since late Pleistocene. During the late Pleistocene mountain forest was the main vegetation type. In particular, there is evidence of a Polylepis forest which does not occur today. Nevertheless there is also evidence of relatively high proportion of páramo, which suggest that an open mountain forest occupied the region. The presence of páramo taxa during the late Pleistocene, points to an upper forest line (UFL) at a markedly lower elevation. The transition from the late Pleistocene to the early mid-Holocene was characterized by mountain forest and a stable proportion of páramo vegetation. However, after ca. 4000 cal yr BP, the Polylepis forest decreased, probably because of an increase in fire frequency. During the mid- to late Holocene the composition of the vegetation changed. The mountain forest was less frequent and the páramo vegetation expanded. Higher proportions of Asteraceae and Muehlenbeckia/Rumex (since ca. 1380 cal yr BP) reflect landscape disturbance probably by human impact. Fires were recorded throughout the late Pleistocene but were more frequent during the wetter late Holocene, which suggests that they were of anthropogenic origin. The pollen record from Cajanuma valley, in the western slope at the Podocarpus National Park, southern Ecuador, reveals environmental changes since the late Glacial. During the late Glacial, herb páramo rich in Poaceae, Cyperaceae and Gentianaceae covered the area. The UFL occurred at a much lower elevation than today. The early to mid-Holocene is characterized by partial replacement of treeless páramo by a mountain forest (Symplocos taxa), which moves into higher elevations where it is today. During the mid- to late Holocene there is evidence of a vegetation change. The páramo re-expanded with the dominance of Poaceae and high presence of Huperzia and Cyatheaceae. During the late Holocene páramo was the main vegetation type that covered the area. Fires became frequent since the late Holocene. The Anteojos valley pollen record, which is located in the western slope at the Llanganates National Park, central Ecuadorian Andes, yields a detailed environmental reconstruction of the past ca. 4100 years. Páramo vegetation had a dominant and stable occurrence in the study area (Poaceae, Cyperaceae and Asteraceae); especially between ca. 4100 to 3100 cal yr BP. Between ca. 3100 to 2100 cal yr BP páramo decreased followed by a slight expansion of mountain forest (Moraceae/Urticaceae, Trema, Celtis and Macrocarpaea). From ca. 2100 cal yr BP to the present páramo once again became more frequent with stable occurrence of mountain forest taxa. Low frequencies of fires were evidenced throughout the record but there is evidence of a slight increase during ca. 4100 to 3100 cal yr BP.

Taxonomic recommendations for British birds: Fourth report

The Great Horned Owl (Bubo virginianus) inhabits myriad habitats throughout the Americas and shows complex patterns of individual and geographic morphological variation. The owl family Strigidae is known to follow ecogeographic rules, such as Gloger's rule. Although untested at the species level, these ecogeographic rules may affect B. virginianus plumage coloration and body size. Previous studies have indicated that, despite this species' morphological variability, little genetic differentiation exists across parts of their range. This study uses reduced representation genome-wide nuclear and complete mitochondrial DNA sequence data to assess range-wide relationships among B. virginianus populations and the disputed species status of B. v. magellanicus (Magellanic or Lesser Horned Owl) of the central and southern Andes. We found shallow phylogenetic relationships generally structured latitudinally to the north of the central Andes, and a deep divergence between a southern and northern clade close to the Marañón Valley in the central Andes, a common biogeographic barrier. We identify evidence of gene flow between B. v. magellanicus and other subspecies based on mitonuclear discordance and F-branch statistics. Overall differences in morphology, plumage coloration, voice, and genomic divergence support species status for B. v. magellanicus.

With 61 species occurring mostly in the Andes and adjacent lowland areas, Stenocercus lizards represent one of the most widespread and well‐represented Andean vertebrate groups. Phylogenetic relationships among species of Stenocercus are inferred using different datasets based on mitochondrial DNA sequence data of 35 species and morphological data of 59 species. Among morphological data, polymorphic and meristic/morphometric characters are coded under the frequency parsimony and gap‐weighting methods, respectively, and the accuracy of these methods is tested. When both types of characters are included, the resulting tree topology is more similar to the topologies obtained from analyses of DNA sequence data than those topologies obtained after exclusion of one or both types of characters. The phylogenetic hypotheses inferred including 59 species of Stenocercus (dataset 1) and excluding those species for which DNA data were not available (dataset 2) are generally congruent with each other, as well as with previously published hypotheses. The most parsimonious tree obtained from analysis of dataset 2 is used in a dispersal‐vicariance analysis to infer ancestral areas and major biogeographical events. Species of Stenocercus are divided into two major clades. Clade A has diversified mostly in the central Andes, with a few species in the northern Andes and one species in the southern Andes. Clade B is more widespread, with species in the northern, central, and southern Andes, as well as in the Atlantic lowlands and Amazon basin. The most recent common ancestor of Stenocercus is inferred to have occurred in the eastern cordillera of the central Andes. Given morphological similarity and altitudinal distribution of some species nested in a northern‐Andes clade, as well as the relatively recent uplift of this Andean region, it is possible that species in this clade have diverged as recently as the mid‐Pliocene.

Computers & graphics best paper award (1989)

With rapid advancement in the field of bioinformatics and computational biology, the collected DNA dataset is growing exponentially, doubling after every 18 months. Due to large-scale and complex structure of the DNA dataset, the analysis of DNA sequence is becoming computationally a challenging issue in bioinformatics field and computational biology. Fast algorithms, capable of analyzing large-scale DNA sequence, are now required in the field of bioinformatics. This paper presents a novel Parallel Vector Space Model (PVSM) approach that supports the analysis of large-scale DNA sequence by taking advantages of multi-core system. The proposed approach is built on top of modified Vector Space Model (VSM). In order to evaluate the performance of PVSM, the proposed technique is extensively evaluated using varied size of DNA sequences in the context of computational efficiency and accuracy. The performance of PVSM is compared with sequential modified VSM. The sequential VSM is implemented on a single processor whereas, the proposed method is initially parallelized on 4 processors and subsequently on 12 processors. The experimental results show that the PVSM performed better than the sequential VSM. The proposed method achieved approximately 2× speedup compared with sequential approach, without affecting the accuracy level. Moreover, the proposed PVSM is highly scalable with an increase in the number of processing cores and support the analysis of large-scale DNA sequences.

The Andean Mountain range has been recognized as one of the biodiversity hotspots of the world. The proposed mechanisms for such species diversification, among others, are due to the elevation processes occurring during the Miocene and the intensive glacial action during the Pleistocene. In this study we investigated the diversification history of the grasshopper Trimerotropis pallidipennis species complex which shows a particularly wide latitudinal and altitudinal distribution range across the northern, central and southern Andes in South America. Many genetic lineages of this complex have been so far discovered, making it an excellent model to investigate the role of the central Andes Mountains together with climatic fluctuations as drivers of speciation. Phylogenetics, biogeographic and molecular clock analyses using a multi-locus dataset revealed that in Peru there are at least two, and possibly four genetic lineages. Two different stocks originated from a common ancestor from North/Central America—would have dispersed toward southern latitudes favored by the closure of the Panama Isthmus giving rise to two lineages, the coastal and mountain lineages, which still coexist in Peru (i.e., T. pallidipennis and T. andeana). Subsequent vicariant and dispersal events continued the differentiation process, giving rise to three to six genetic lineages (i.e., clades) detected in this study, which were geographically restricted to locations dispersed over the central Andes Mountains in South America. Our results provide another interesting example of “island diversification” motored by the topography plus unstable climatic conditions during the Pleistocene, pointing out the presence of a hotspot of diversification in the Andean region of Peru.

Genetic structure and diversity of the Diachasmimorpha longicaudata species complex in Thailand: SSCP analysis of mitochondrial 16S rDNA and COI DNA sequences

Genomics and Proteomics engineering is an emerging field and involves with the biology, medicine, computer science and engineering. It is an interdisciplinary field and focus on the understanding of the structural and functional relationship among gene sequences. The related computational technologies can be classified as the DNA sequence and DNA mircoarray analysis methods. The DNA sequence analysis methods have been used to extract the useful information related to the sequence structure including the detection of the coding and non-coding regions in DNA sequence and the detection of the similarity among DNA sequences. But, the DNA microarray technology based on the parallel processing has been used to monitor the large scale gene expressions simultaneously. These two technologies have revolutionized the computational biology and biomedical informatics. In this paper, we will discuss the traditional and advanced signal and image processing methods to analyze, model and interpret the DNA, RNA and protein sequences to gain insights into the dynamics of genomic functions for the early diagnosis of diseases and the development of more targeted drugs. We will mainly review the widely used statistical and nonstationary and stationary signal and image processing methods for the DNA structure prediction, detection, feature extraction, and classification of differentially expressed genes. We will mainly discuss the wavelet transform applications in DNA sequence analysis, and on cellular neural network in microarray image analysis, which can have a potentially large impact on the real-time realization of DNA analysis.

A survey of the endophytic fungi in fronds of Livistona chinensis was carried out in Hong Kong. The endophyte assemblages identified using morphological characters consisted of 16 named species and 19 'morphospecies', the latter grouped based on cultural morphology and growth rates. Arrangement of taxa into morphospecies does not reflect species phylogeny, and therefore selected morphospecies were further identified based on ribosomal DNA (rDNA) sequence analysis. The 5.8S gene and flanking internal transcribed spacers (ITS1 and ITS2) regions of rDNA from 19 representative morphospecies were amplified by the polymerase chain reaction and sequenced. Phylogenetic analysis based on 5.8S gene sequences showed that these morphospecies were filamentous Ascomycota, belonging in the Loculoascomycetes and Pyrenomycetes. Further identification was conducted by means of sequence comparison and phylogenetic analysis of both the ITS and 5.8S regions. Results showed that MS704 belonged to the genus Diaporthe and its anamorph Phomopsis of the Valsaceae. MS594 was inferred to be Mycosphaerella and its anamorph Cladosporium of the Mycosphaerellaceae. MS339, MS366, MS370, MS395, MS1033, MS1083 and MS1092 were placed in the genus Xylaria of the Xylariaceae. MS194, MS375 and MS1028 were close to the Clypeosphaeriaceae. MS191 and MS316 were closely related to the Pleosporaceae within the Dothideales. The other 5 morphospecies, MS786, MS1043, MS1065, MS1076 and MS1095, probably belong in the Xylariales. The value of using DNA sequence analysis in the identification of endophytes is discussed.

Molecular analysis of a 444bp fragment of the bovine leukaemia virus gp51 env gene reveals a high frequency of non-silent point mutations and suggests the presence of two subgroups of BLV in Chile

PCR (conventional and real-time) and DNA sequence analysis were used to identify species and genotypes of potato cyst nematodes from sites in Victoria, Australia. Only Globodera rostochiensis was detected. Sequence analyses of these isolates of PCN have confirmed the PCR-based results and have revealed the presence of genetically diverse populations in infested fields. However, the sequence variation was not in the diagnostic primer binding sites. The melting peaks, from multiplex real-time PCR analysis, for Globodera pallida and G. rostochiensis were 83.3 and 88.7, respectively. The importance of DNA extraction, PCR and sequence analysis for the molecular identification of PCN is discussed. This study has significant implications for detecting species of PCN in order to monitor/develop control strategies for the PCN of quarantine importance.