CETACEAN OCCURRENCE PATTERNS IN THE AMUNDSEN AND SOUTHERN BELLINGSHAUSEN SEA SECTOR, SOUTHERN OCEAN

We conducted 239.5 h and 3,494 km of cetacean surveys in the Amundsen and Bellingshausen seas, from 15 February to 31 March 1994; most of the area, the large portion of which was ice covered, had never before nor has it since been surveyed for cetaceans, even to the date when this paper was prepared (2006). Logistic regression and an information-theoretic approach related the occurrence of Antarctic minke whales Balaenoptera bonaerensis (the most abundant species) to whether we were in open- or pack-ice-covered pelagic or neritic waters, in or out of the marginal ice zone (MIZ), and north or south of the Antarctic Circumpolar Current southern boundary. Other variables included date and distance to the MIZ and shelfbreak front. Statistical analysis showed that the probability of sighting a minke, as well as killer whale—but not the case for an index to whale density—was related to the proximity of coastal polynyas in early autumn, switching offshore to the MIZ once waters within the pack began to freeze persistently later in the season. Probability of detection was higher with distance into the MIZ. Supporting these findings, the density index was strongly related to ice concentration in an inverse relationship. The strong relationship to polynyas and the MIZ indicate that sea-ice divergence altered by decadal or longer-term climate change, as described in the recent literature, could well affect any apparent, long-term trends evident in this species' abundance if surveyed only in open or near-to-ice waters. We speculate on how the minke whale's pagophilic nature (1) could have been encouraged by large-scale industrial whaling and by competition with species more characteristic of open waters and the outer MIZ, and (2) may have protected the population somewhat during industrial whaling resulting in the much greater abundance of this species now compared to other targeted species.     

Prediction of protein secondary structure content for the twilight zone sequences

Secondary protein structure carries information about local structural arrangements, which include three major conformations: alpha-helices, beta-strands, and coils. Significant majority of successful methods for prediction of the secondary structure is based on multiple sequence alignment. However, multiple alignment fails to provide accurate results when a sequence comes from the twilight zone, that is, it is characterized by low (<30%) homology. To this end, we propose a novel method for prediction of secondary structure content through comprehensive sequence representation, called PSSC-core. The method uses a multiple linear regression model and introduces a comprehensive feature-based sequence representation to predict amount of helices and strands for sequences from the twilight zone. The PSSC-core method was tested and compared with two other state-of-the-art prediction methods on a set of 2187 twilight zone sequences. The results indicate that our method provides better predictions for both helix and strand content. The PSSC-core is shown to provide statistically significantly better results when compared with the competing methods, reducing the prediction error by 5-7% for helix and 7-9% for strand content predictions. The proposed feature-based sequence representation uses a comprehensive set of physicochemical properties that are custom-designed for each of the helix and strand content predictions. It includes composition and composition moment vectors, frequency of tetra-peptides associated with helical and strand conformations, various property-based groups like exchange groups, chemical groups of the side chains and hydrophobic group, auto-correlations based on hydrophobicity, side-chain masses, hydropathy, and conformational patterns for beta-sheets. The PSSC-core method provides an alternative for predicting the secondary structure content that can be used to validate and constrain results of other structure prediction methods. At the same time, it also provides useful insight into design of successful protein sequence representations that can be used in developing new methods related to prediction of different aspects of the secondary protein structure.     

Phenols removal in musts: Strategy for wine stabilization by laccase

The potential of laccase from Trametes versicolor for phenolic removal in must for wine stabilization was evaluated through a combination of an analytical methodology (capillary zone electrophoresis) and kinetics of phenols removal as the total antioxidant potential variation. Total phenolic content, total antioxidant potential and polyphenols were monitored from 0 to 3 h of must treatment. The results indicated that the treatment of a red must with laccase affect mainly the phenolic compounds responsible for the must antioxidant properties. The treatment of white musts with laccase showed higher reduction in total phenol than in the total antioxidant potential. Phenol degradation by laccase was very fast for catechins, and slowly for stilbenes (cis- and trans-resveratrol) and derivatives of cinnamic (ferulic and caffeic) and benzoic (syringic, vanillic, and gallic) acids. It is possible to conclude in this case that the use of laccase in white wines is perfectly feasible. This would allow softer and ecologically correct treatments, which would diminish the cost of processing and avoid deterioration of wines for long storage times.     

Distribution and biodiversity of rhizobia nodulating Chamaecrista mimosoides in the Shandong peninsula of china

Chamaecrista mimosoides is an annual herb legume widely distributed in tropical and subtropical Asia and Africa. It may have primitive and independently-evolved root nodule types but its rhizobia have not been systematically studied. Therefore, in order to learn the diversity and species affinity of its rhizobia, root nodules were sampled from C. mimosoides plants growing in seven geographical sites along the coast line of Shandong Peninsula, China. A total of 422 rhizobial isolates were obtained from nodules, and they were classified into 28 recA haplotypes. By using multilocus sequence analysis of the concatenated housekeeping genes dnaK, glnII, gyrB, recA and rpoB, the representative strains for these haplotypes were designated as eight defined and five candidate novel genospecies in the genus Bradyrhizobium. Bradyrhizobium elkanii and Bradyrhizobium ferriligni were predominant and universally distributed. The symbiotic genes nodC and nifH of the representative strains showed very similar topology in their phylogenetic trees indicating their co-evolution history. All the representative strains formed effective root nodules in nodulation tests. The correlation between genospecies and soil characteristics analyzed by CANOCO software indicated that available potassium (AK), organic carbon (OC) and available nitrogen (AN) in the soil samples were the main factors affecting the distribution of the symbionts involved in this current study. The study is the first systematic survey of Chamaecrista mimosoides-nodulating rhizobia, and it showed that Chamaecrista spp. were nodulated by bradyrhizobia in natural environments. In addition, the host spectrum of the corresponding rhizobial species was extended, and the study provided novel information on the biodiversity and biogeography of rhizobia.     

Composition and distribution of indigenous trees and shrubs as possible criteria for indicating adapted species in semi‐arid rangelands

This study assessed the composition and natural distribution of indigenous trees and shrubs as possible criteria for selecting suitable species for rehabilitation of degraded sites in semi‐arid rangelands. Study sites were identified at Nthangu, Kathonzweni and Kibwezi forests of Makueni County, Kenya using existing vegetation, agro‐climatic maps and Landsat imageries. The sites had mean annual rainfalls of 974 mm, 700 mm and 616 mm, respectively, and moisture indices of 49%, 35% and 32%. Data were collected by establishing sample plots and assessing species counts and diameters at breast height (DBH). Basal area, relative dominance, relative abundance, relative frequency and important value indices (IVIs) were computed for individual families and species at each site. The number of families, genera and species declined from Nthangu (33, 60, 77) through Kibwezi (30, 48, 70) to Kathonzweni (28, 42, 69). Corresponding mean basal areas were 16.7 m² ha^?1, 76.8 m² ha^?1 and 19.3 m² ha^?1. The families Combretaceae, Burseraceae and Mimosaceae were the most important and widely distributed. Based on ecological importance values, candidate species for rehabilitation of degraded sites at Nthangu, Kathonzweni and Kibwezi were Combretum molle and Acacia hockii; Combretum collinum, Commiphora campestris and Acacia tortilis; and Commiphora africana and A. tortilis, respectively.     

Quantifying uncertainty in the phylogenetics of Australian numeral systems

Researchers have long been interested in the evolution of culture and the ways in which change in cultural systems can be reconstructed and tracked. Within the realm of language, these questions are increasingly investigated with Bayesian phylogenetic methods. However, such work in cultural phylogenetics could be improved by more explicit quantification of reconstruction and transition probabilities. We apply such methods to numerals in the languages of Australia. As a large phylogeny with almost universal ‘low-limit'' systems, Australian languages are ideal for investigating numeral change over time. We reconstruct the most likely extent of the system at the root and use that information to explore the ways numerals evolve. We show that these systems do not increment serially, but most commonly vary their upper limits between 3 and 5. While there is evidence for rapid system elaboration beyond the lower limits, languages lose numerals as well as gain them. We investigate the ways larger numerals build on smaller bases, and show that there is a general tendency to both gain and replace 4 by combining 2 + 2 (rather than inventing a new unanalysable word ‘four''). We develop a series of methods for quantifying and visualizing the results.     

Characterizing a hybrid zone between a cryptic species pair of freshwater snails

Characterizing hybrid zones and their dynamics is a central goal in evolutionary biology, but this is particularly challenging for morphologically cryptic species. The lack of conspicuous divergence between parental types means intermediate hybrid forms often go undetected. We aimed to detect and characterize a suspected hybrid zone between a pair of morphologically cryptic lineages of the freshwater snail, Radix. We sampled Radix from across a contact zone between two mitochondrial lineages (Radix balthica and an undescribed lineage termed ‘MOTU3’) and detected admixture between two nuclear genotype clusters, which were significantly but not categorically associated with the mitochondrial lineages. Using a model selection approach, we show that the admixture cline is best explained by an interaction between precipitation and temperature gradients over the area, rather than geographic distance. We thus hypothesize that the correlation with climatic gradients suggests environmental selection has played a role in maintaining the hybrid zone. In a 2050 climate change scenario, we furthermore predict an expansion of one of the nuclear clusters and a widening of the hybrid zone as the climate warms and dries.     

The geography of divergence with gene flow facilitates multitrait adaptation and the evolution of pollinator isolation in Mimulus aurantiacus

Ecological adaptation is the driving force during divergence with gene flow and generates reproductive isolation early in speciation. Although gene flow opposes divergence, local adaptation can be facilitated by factors that prevent the breakup of favorable allelic combinations. We investigated how selection, genetic architecture, and geography have contributed to the maintenance of floral trait divergence and pollinator isolation between parapatric ecotypes of Mimulus aurantiacus. Combining greenhouse, field, and genomic studies, we show that sharp clines in floral traits are maintained by spatially varying selection. Although adaptation breaks down where the ecotypes co‐occur, leading to the formation of a hybrid zone, the largely non‐overlapping distributions of the ecotypes shield them from immigrant genes, facilitating divergence across most of the range. In contrast to the sharp genetic discontinuities observed across most hybrid zones, we observed a gradual cline in genome‐wide divergence and a pattern of isolation by distance across the landscape. Thus, contrary to a long period of allopatry followed by recent re‐contact, our data suggest that floral trait divergence in M. aurantiacus may have evolved with locally restricted, but ongoing gene flow. Therefore, our study reveals how the geographic distribution of an organism can contribute to the evolution of premating isolation in the early stages of divergence with gene flow.     

The specialization and structure of antagonistic and mutualistic networks of beetles on rainforest canopy trees

Different kinds of species interactions can lead to different structures within ecological networks. Antagonistic interactions (such as between herbivores and host plants) often promote increasing host specificity within a compartmentalized network structure, whereas mutualistic networks (such as pollination networks) are associated with higher levels of generalization and form nested network structures. However, we recently showed that the host specificity of flower‐visiting beetles from three different feeding guilds (herbivores, fungivores, and predators) in an Australian rainforest canopy was equal to that of herbivores on leaves, suggesting that antagonistic herbivores on leaves are no more specialized than flower‐visitors. We therefore set out to test whether similarities in the host specificity of these different assemblages reflect similarities in underlying network structures. As shown before at the species level, mutualistic communities on flowers showed levels of specialization at the network scale similar to those of the antagonistic herbivore community on leaves. However, the network structure differed, with flower‐visiting assemblages displaying a significantly more nested structure than folivores, and folivores displaying a significantly more compartmentalized structure than flower‐visitors. These results, which need further testing in other forest systems, demonstrate that both antagonistic and mutualistic interactions can result in equally high levels of host specialization among beetle assemblages in tropical rainforests. If this is a widespread phenomenon, it may alter our current perceptions of food web dynamics, species diversity patterns, and co‐evolution in tropical rainforests. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 287–295.     

Selection on outlier loci and their association with adaptive phenotypes in Littorina saxatilis contact zones

A fundamental issue in speciation research is to evaluate phenotypic variation and the genomics driving the evolution of reproductive isolation between sister taxa. Above all, hybrid zones are excellent study systems for researchers to examine the association of genetic differentiation, phenotypic variation and the strength of selection. We investigated two contact zones in the marine gastropod Littorina saxatilis and utilized landmark‐based geometric morphometric analysis together with amplified fragment length polymorphism (AFLP) markers to assess phenotypic and genomic divergence between ecotypes under divergent selection. From genetic markers, we calculated the cline width, linkage disequilibrium and the average effective selection on a locus. Additionally, we conducted an association analysis linking the outlier loci and phenotypic variation between ecotypes and show that a proportion of outlier loci are associated with key adaptive phenotypic traits.