Evolution of Helix Formation in the Ribosomal Internal Transcribed Spacer 2 (ITS2) and Its Significance for RNA Secondary Structures

Helices are the most common elements of RNA secondary structure. Despite intensive investigations of various types of RNAs, the evolutionary history of the formation of new helices (novel helical structures) remains largely elusive. Here, by studying the nuclear ribosomal Internal Transcribed Spacer 2 (ITS2), a fast-evolving part of the eukaryotic nuclear ribosomal operon, we identify two possible types of helix formation: one type is “dichotomous helix formation”—transition from one large helix to two smaller helices by invagination of the apical part of a helix, which significantly changes the shape of the original secondary structure but does not increase its complexity (i.e., the total length of the RNA). An alternative type is “lateral helix formation”—origin of an extra helical region by the extension of a bulge loop or a spacer in a multi-helix loop of the original helix, which does not disrupt the pre-existing structure but increases RNA size. Moreover, we present examples from the RNA sequence literature indicating that both types of helix formation may have implications for RNA evolution beyond ITS2.     

Endemic diversification in the mountains: genetic,morphological, and geographical differentiation of the <Emphasis Type="Italic">Hemidactylus</Emphasis> geckos in southwestern Arabia

In this study, we provide genetic, morphological, and geographical comparisons for 11 species of the southwestern Arabian radiation of Hemidactylus geckos, nine of which are endemic to the region. By using a coalescence-based species-tree reconstruction in combination with divergence time estimations and speciation probability testing, we show that most of the speciation events occurred in the Pliocene, which is more recent than previously thought based on calibrations of concatenated data sets. The current dating indicates that the changing climate at the beginning of the Pliocene, from hot and dry to cold and wet, is likely responsible for increased speciation in Hemidactylus. Analyses of geographic and altitudinal overlap of the species and their morphological differentiation show that most species do not occur in sympatry. Those that overlap geographically are usually differentiated by their altitudinal preference, head shape, body size, or their combination. Our results indicate that the topographically complex mountains of southwestern Arabia support a significant radiation of Hemidactylus geckos by allowing multiple allopatric speciation events to occur in a relatively small area. Consequently, we describe two new species endemic to the Asir Mountains of Saudi Arabia, H. alfarraji sp. n. and H. asirensis sp. n., and elevate two former subspecies of H. yerburii to a species level, H. montanus and H. pauciporosus.     

An evaluation of semi‐automated methods for collecting ecosystem‐level data in temperate marine systems

Historically, marine ecologists have lacked efficient tools that are capable of capturing detailed species distribution data over large areas. Emerging technologies such as high‐resolution imaging and associated machine‐learning image‐scoring software are providing new tools to map species over large areas in the ocean. Here, we combine a novel diver propulsion vehicle (DPV) imaging system with free‐to‐use machine‐learning software to semi‐automatically generate dense and widespread abundance records of a habitat‐forming algae over ~5,000 m² of temperate reef. We employ replicable spatial techniques to test the effectiveness of traditional diver‐based sampling, and better understand the distribution and spatial arrangement of one key algal species. We found that the effectiveness of a traditional survey depended on the level of spatial structuring, and generally 10–20 transects (50 × 1 m) were required to obtain reliable results. This represents 2–20 times greater replication than have been collected in previous studies. Furthermore, we demonstrate the usefulness of fine‐resolution distribution modeling for understanding patterns in canopy algae cover at multiple spatial scales, and discuss applications to other marine habitats. Our analyses demonstrate that semi‐automated methods of data gathering and processing provide more accurate results than traditional methods for describing habitat structure at seascape scales, and therefore represent vastly improved techniques for understanding and managing marine seascapes.     

Molting phenology of the Pacific harbor seal (Phoca vitulina richardii) on two islands off the Baja California Peninsula,Mexico

We document and compare the annual molt of the Pacific harbor seal (Phoca vitulina richardii) on two islands off the west coast of the Baja California Peninsula that are the northern and southern extremes of its distribution in Mexico. During 2014, observations were made from March to July on Todos Santos Island (northern extreme) and from January to June on San Roque Island (southern extreme). On Todos Santos, the premolt lasted 15 wk (March–June) and the molt 12 wk (April–July). On San Roque, the premolt lasted 22 wk (January–June) and the molt 17 wk (February–June). The proportion of seals undergoing molt peaked on 26 May on Todos Santos and on 7 June on San Roque. Shedding of old hair most commonly initiated on the torso and progressed to the head and flippers (reverse molting pattern). The period when the highest number of harbor seals haul out in Mexico is in late April on the more southerly islands and in early May on the more northerly islands, when a large proportion of seals are in premolt.     

Lifestyle and Ice: The Relationship between Ecological Specialization and Response to Pleistocene Climate Change

Major climatic changes in the Pleistocene had significant effects on marine organisms and the environments in which they lived. The presence of divergent patterns of demographic history even among phylogenetically closely-related species sharing climatic changes raises questions as to the respective influence of species-specific traits on population structure. In this work we tested whether the lifestyle of Antarctic notothenioid benthic and pelagic fish species from the Southern Ocean influenced the concerted population response to Pleistocene climatic fluctuations. This was done by a comparative analysis of sequence variation at the cyt b and S7 loci in nine newly sequenced and four re-analysed species. We found that all species underwent more or less intensive changes in population size but we also found consistent differences between demographic histories of pelagic and benthic species. Contemporary pelagic populations are significantly more genetically diverse and bear traces of older demographic expansions than less diverse benthic species that show evidence of more recent population expansions. Our findings suggest that the lifestyles of different species have strong influences on their responses to the same environmental events. Our data, in conjunction with previous studies showing a constant diversification tempo of these species during the Pleistocene, support the hypothesis that Pleistocene glaciations had a smaller effect on pelagic species than on benthic species whose survival may have relied upon ephemeral refugia in shallow shelf waters. These findings suggest that the interaction between lifestyle and environmental changes should be considered in genetic analyses.     

Seroepidemiological study of human hydatidosis and trichinosis, with the indirect hemagglutination reaction, in San Juan de la Costa County. Osorno, X Region, Chile. 1990-1991]

San Juan de la Costa County (40 degrees 45' South lat., 73 degrees 19' West long.) is located in the Osorno province, South of Chile. Its population is 8,486 inhabitants. The basic economic activities are agriculture, cattle raising, timber production and manufacture of wood and coal. According to official reports, the incidence of human hydatidosis and trichinosis in this locality in 1989 were 24 and 59 per 100,000 respectively. In order to contribute to a better knowledge of the epidemiology of human hydatidosis and trichinosis in San Juan de la Costa County, an indirect hemagglutination test (IHAT) for these parasitoses was performed to 511 randomized people. Nine (1.8%) individuals resulted positive for hydatidosis and twenty four (4.7%) were positive for trichinosis. Some considerations on the corresponding prophylactic measures are proposed.     

The interaction of decorin core protein fragments with type I collagen.

To further define the molecular interaction between decorin and type I collagen we generated a 20 kD fragment containing the N-terminal half of the core protein by Endoproteinase Arg C digestion and a 40 kD fragment including all leucine-rich repeats in the central part of decorin core by cleavage with 2-nitro-5-thiocyanobenzoate. The fragments did not influence collagen fibril formation, even at high concentration, and radioactive fragments showed little binding to collagen fibrils. Our observations suggest that neither the N-terminal half nor the central leucine-rich repeats of the decorin core protein can, by itself, interact fully with fibrillar collagen.     

Induction of adventitious buds on the cotyledons ofAbies concolor x Abies grandis hybrid seedlings

Possibilities of adventitious buds induction on the cotyledons obtained from sterile seedlings ofAbies concolor xAbies grandis hybrid were investigated. The following variables influencing bud induction and their further development were studied: the effect of expiant age, the effect of different growth regulators and their concentrations and duration of their application. The most suitable expiants proved to be the cotyledons of 7 d old seedlings. The most efficient cytokinin was benzylaminopurine (S mg l^?1) in combination with napthaleneacetic acid (0.01 mg l^?1). The most optimal duration of treatment was 17 to 21 d culture of explants on induction medium. Shoot growth was achieved on basal medium to which 14 mg 1^?1 spermidine was added.