Towards an assessment of character interdependence in avian RNA phylogenetics: A general secondary structure model for the avian mitochondrial 16S rRNA

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Nutrition in Transition: Dietary Patterns of Rural Amazonian Women During a Period of Economic Change

Objectives: The goal of this study was to understand the relationship between economic change (wage labor, retirement, and the Bolsa Familia program) and dietary patterns in the rural Amazon and to determine the extent to which these changes followed the pattern of the nutrition transition. Methods: The study was longitudinal. The weighed-inventory method and economic interviews were used to collect data on dietary intake and household economics in a sample of 30 and 52 women in 2002 and 2009, respectively. Twenty of the women participated in both years and make-up the longitudinal sub-sample. Comparative statistics were used to identify changes in dietary patterns over time and multiple linear regressions were used to explore the relationship between economics, subsistence strategies, and diet. Results: There was a significant decline in kcal (P < 0.01) and carbohydrate (P < 0.01) but no change in protein intake over time in both the larger and smaller, longitudinal subsample. The percent of energy, carbohydrate, protein, and fat purchased increased in the larger and longitudinal samples (P <= 0.02) and there was an increase in refined carbohydrate and processed, fatty-meat consumption over time. The abandonment of manioc gardens was associated with increased dependence on purchased food (P = 0.03) while receipt of the Bolsa Familia was associated with increased protein intake and adequacy (P = 0.02). Conclusions: The dietary changes observed are only in partial agreement with predictions of the nutrition transition literature. The relationship between the economic and diet changes was shaped by the local context which should be considered when implementing CCT programs, like the Bolsa Familia. Am. J. Hum. Biol. 23:458-469, 2011. (C) 2011 Wiley-Liss, Inc.

SIZE AS A LINE OF LEAST RESISTANCE II: DIRECT SELECTION ON SIZE OR CORRELATED RESPONSE DUE TO CONSTRAINTS?

Evolutionary change in New World Monkey (NWM) skulls occurred primarily along the line of least resistance defined by size (including allometric) variation (g(max)). Although the direction of evolution was aligned with this axis, it was not clear whether this macroevolutionary pattern results from the conservation of within population genetic covariance patterns (long-term constraint) or long-term selection along a size dimension, or whether both, constraints and selection, were inextricably involved. Furthermore, G-matrix stability can also be a consequence of selection, which implies that both, constraints embodied in g(max) and evolutionary changes observed on the trait averages, would be influenced by selection Here, we describe a combination of approaches that allows one to test whether any particular instance of size evolution is a correlated by-product due to constraints (g(max)) or is due to direct selection on size and apply it to NWM lineages as a case study. The approach is based on comparing the direction and amount of evolutionary change produced by two different simulated sets of net-selection gradients (beta), a size (isometric and allometric size) and a nonsize set. Using this approach it is possible to distinguish between the two hypotheses (indirect size evolution due to constraints or direct selection on size), because although both may produce an evolutionary response aligned with g(max), the amount of change produced by random selection operating through the variance/covariance patterns (constraints hypothesis) will be much smaller than that produced by selection on size (selection hypothesis). Furthermore, the alignment of simulated evolutionary changes with g(max) when selection is not on size is not as tight as when selection is actually on size, allowing a statistical test of whether a particular observed case of evolution along the line of least resistance is the result of selection along it or not. Also, with matrix diagonalization (principal components [PC]) it is possible to calculate directly the net-selection gradient on size alone (first PC [PC1]) by dividing the amount of phenotypic difference between any two populations by the amount of variation in PC1, which allows one to benchmark whether selection was on size or not

Ontogenetic Changes in the Bell Morphology and Kinematics and Swimming Behavior of Rowing Medusae: the Special Case of the Limnomedusa Liriope tetraphylla

Swimming animals may experience significant changes in the Reynolds number (Re) of their surrounding fluid flows throughout ontogeny. Many medusae experience Re environments with significant viscous forces as small juveniles but inertially dominated Re environments as adults. These different environments may affect their propulsive strategies. In particular, rowing, a propulsive strategy with ecological advantages for large adults, may be constrained by viscosity for small juvenile medusae. We examined changes in the bell morphology and swimming kinematics of the limnomedusa Liriope tetraphylla at different stages of development. L. tetraphylla maintained an oblate bell (fineness ratio approximate to 0.5-0.6), large velar aperture ratio (R(v) approximate to 0.5-0.8), and rapid bell kinematics throughout development. These traits enabled it to use rowing propulsion at all stages except the very smallest sizes observed (diameter = 0.14 cm). During the juvenile stage, very rapid bell kinematics served to increase Re sufficiently for rowing propulsion. Other taxa that use rowing propulsion as adults, such as leptomedusae and scyphomedusae, typically utilize different propulsive strategies as small juveniles to function in low Re environments. We compared the performance values of the different propulsive modes observed among juvenile medusae.

Naming the Bonaire banded box jelly, Tamoya ohboya, n. sp. (Cnidaria: Cubozoa: Carybdeida: Tamoyidae)

A new species of cubozoan jellyfish has been discovered in shallow waters of Bonaire, Netherlands ( Dutch Caribbean). Thus far, approximately 50 sightings of the species, known commonly as the Bonaire banded box jelly, are recorded, and three specimens have been collected. Three physical encounters between humans and the species have been reported. Available evidence suggests that a serious sting is inflicted by this medusa. To increase awareness of the scientific disciplines of systematics and taxonomy, the public has been involved in naming this new species. The Bonaire banded box jelly, Tamoya ohboya, n. sp., can be distinguished from its close relatives T. haplonema from Brazil and T. sp. from the southeastern United States by differences in tentacle coloration, cnidome, and mitochondrial gene sequences. Tamoya ohboya n. sp. possesses striking dark brown to reddish-orange banded tentacles, nematocyst warts that densely cover the animal, and a deep stomach. We provide a detailed comparison of nematocyst data from Tamoya ohboya n. sp., T. haplonema from Brazil, and T. sp. from the Gulf of Mexico.

A new genus and new species of fan worms (Polychaeta: Sabellidae) from Atlantic and Pacific Oceans-the formal treatment of taxon names as explanatory hypotheses

Members of Parasabella minuta Treadwell, 1941, subsequently moved to Perkinsiana, were collected during a survey of rocky intertidal polychaetes along the state of Sao Paulo, Brazil. Additional specimens, which are referred to two new species, were also found in similar habitats from the Bocas del Toro Archipelago, Caribbean Panama, and Oahu Island, Hawaii. A phylogenetic analysis of Sabellinae, including members of P. minuta and the two new species, provided justification for establishing a new generic hypothesis, Sabellomma gen. nov., for these individuals. Formal definitions are also provided for Sabellomma minuta gen. nov., comb. nov., S. collinae gen. nov., spec. nov., and S. harrisae gen. nov., spec. nov., along with descriptions of individuals to which these hypotheses apply. The generic name Aracia nom. nov., is provided to replace Kirkia Nogueira, Lopez and Rossi, 2004, pre-occupied by a mollusk.

Phylogenetics of Hydroidolina (Hydrozoa: Cnidaria)

Hydroidolina is a group of hydrozoans that includes Anthoathecata, Leptothecata and Siphonophorae. Previous phylogenetic analyses show strong support for Hydroidolina monophyly, but the relationships between and within its subgroups remain uncertain. In an effort to further clarify hydroidolinan relationships, we performed phylogenetic analyses on 97 hydroidolinan taxa, using DNA sequences from partial mitochondrial 16S rDNA, nearly complete nuclear 18S rDNA and nearly complete nuclear 28S rDNA. Our findings are consistent with previous analyses that support monophyly of Siphonophorae and Leptothecata and do not support monophyly of Anthoathecata nor its component subgroups, Filifera and Capitata. Instead, within Anthoathecata, we find support for four separate filiferan clades and two separate capitate clades (Aplanulata and Capitata sensu stricto). Our data however, lack any substantive support for discerning relationships between these eight distinct hydroidolinan clades.

Evolutionary patterns in neotropical Helieae (Gentianaceae): evidence from morphology, chloroplast and nuclear DNA sequences

Parsimony-based phylogenetic analyses of the neotropical tribe Helieae (Gentianaceae) are presented, including 22 of the 23 genera and 60 species. This study is based on data from morphology, palynology, and seed micromorphology (127 structural characters), and DNA sequences (matK, trnL intron, ITS). Phylogenetic reconstructions based on ITS and morphology provided the greatest resolution, morphological data further helping to tentatively place several taxa for which DNA was not available (Celiantha, Lagenanthus, Rogersonanthus, Roraimaea, Senaea, Sipapoantha, Zonanthus). Celiantha, Prepusa and Senaea together appear as the sister clade to the rest of Helieae. The remainder of Helieae is largely divided into two large subclades, the Macrocarpaea subclade and the Symbolanthus subclade. The first subclade includes Macrocarpaea, sister to Chorisepalum, Tochia, and Zonanthus. Irlbachia and Neblinantha are placed as sisters to the Symbolanthus subclade, which includes Aripuana, Calolisianthus, Chelonanthus, Helia, Lagenanthus, Lehmanniella, Purdieanthus, Rogersonanthus, Roraimaea, Sipapoantha, and symbolanthus. Generic-level polyphyly is detected in Chelonanthus and Irlbachia. Evolution of morphological characters is discussed, and new pollen and seed characters are evaluated for the first time in a combined morphological-molecular phylogenetic analysis.

The Cochaperone BAG2 Sweeps Paired Helical Filament-Insoluble Tau from the Microtubule

Tau inclusions are a prominent feature of many neurodegenerative diseases including Alzheimer`s disease. Their accumulation in neurons as ubiquitinated filaments suggests a failure in the degradation limb of the Tau pathway. The components of a Tau protein triage system consisting of CHIP/Hsp70 and other chaperones have begun to emerge. However, the site of triage and the master regulatory elements are unknown. Here, we report an elegant mechanism of Tau degradation involving the cochaperone BAG2. The BAG2/Hsp70 complex is tethered to the microtubule and this complex can capture and deliver Tau to the proteasome for ubiquitin-independent degradation. This complex preferentially degrades Sarkosyl insoluble Tau and phosphorylated Tau. BAG2 levels in cells are under the physiological control of the microRNA miR-128a, which can tune paired helical filament Tau levels in neurons. Thus, we propose that ubiquitinated Tau inclusions arise due to shunting of Tau degradation toward a less efficient ubiquitin-dependent pathway.

Next Generation Sequencing of Pooled Samples Reveals New SNRNP200 Mutations Associated with Retinitis Pigmentosa

The gene SNRNP200 is composed of 45 exons and encodes a protein essential for pre-mRNA splicing, the 200 kDa helicase hBrr2. Two mutations in SNRNP200 have recently been associated with autosomal dominant retinitis pigmentosa (adRP), a retinal degenerative disease, in two families from China. In this work we analyzed the entire 35-Kb SNRNP200 genomic region in a cohort of 96 unrelated North American patients with adRP. To complete this large-scale sequencing project, we performed ultra high-throughput sequencing of pooled, untagged PCR products. We then validated the detected DNA changes by Sanger sequencing of individual samples from this cohort and from an additional one of 95 patients. One of the two previously known mutations (p.S1087L) was identified in 3 patients, while 4 new missense changes (p.R681C, p.R681H, p.V683L, p.Y689C) affecting highly conserved codons were identified in 6 unrelated individuals, indicating that the prevalence of SNRNP200-associated adRP is relatively high. We also took advantage of this research to evaluate the pool-and-sequence method, especially with respect to the generation of false positive and negative results. We conclude that, although this strategy can be adopted for rapid discovery of new disease-associated variants, it still requires extensive validation to be used in routine DNA screenings. (C) 2011 Wiley-Liss, Inc.

Croton campanulatus (Euphorbiaceae s.s.), a new species from the Brazilian Atlantic rain forest

Croton campanulatus, a new species from southeastern Brazil in the states of Minas Gerais and Rio de Janeiro, is here described and illustrated. Morphological data indicate that this species belongs to Croton section Cleodora based on its arborescent habit, pistillate flowers with imbricate sepals, reduced petals, and multifid styles that are fused at the base.

Two new species of Loricariidae (Teleostei: Siluriformes) from main channels of the upper and middle Amazon Basin, with discussion of deep water specialization in loricariids

Hemiancistrus pankimpuju, new species, and Panaque bathyphilus, new species, are described from the main channel of the upper (Maranon) and middle (Solimoes)Amazon River, respectively. Both species are diagnosed by having a nearly white body, long filamentous extensions of both simple caudal-fin rays, small eyes, absence of an iris operculum and unique combinations of morphometrics. The coloration and morphology of these species, unique within Loricariidae, are hypothesized to be apomorphies associated with life in the dark, turbid depths of the Amazon mainstem. Extreme elongation of the caudal filaments in these and a variety of other main channel catfishes is hypothesized to have a mechanosensory function associated with predator detection.

New genera of philopotine spider flies (Diptera, Acroceridae) with a key to living and fossil genera

In this paper we describe two new genera of philopotine Acroceridae: Schlingeriella irwini gen. et sp. n. (New Caledonia) and Quasi fisheri gen. et sp. n. (Mexico). The Baltic amber species Eulonchiella eocenica Meunier, 1912 is rediagnosed and a neotype designated based on a newly discovered specimen. We also provide a dichotomous key to the world genera of Philopotinae, both living and fossil.

A new species of Dendrophryniscus (Amphibia, Anura, Bufonidae) from the Atlantic Rainforest of southern Bahia, Brazil

A new species of the tree toad genus Dendrophryniscus is described from a rainforest habitat at Parque Nacional de Serra das Lontras, municipality of Arataca, southern Bahia, Brazil. Dendrophryniscus oreites sp. nov. is related to the Atlantic forest brevipollicatus group by hand morphology, skin texture, ventral coloration and bromelicolous habits. The new species differs from related species by having a larger size, warty skin, inner finger reduced with presence of a dark nuptial pad in males, and a yellowish coloration with discrete dorsal pattern. This discovery highlights the importance of southern Bahia in terms of conservation, and for our understanding of the evolution of the frog diversity within the Atlantic Rainforest.

Revision of the Asian spider genus Pandava Lehtinen (Araneae: Titanoecidae): description of five new species and first record of Titanoecidae from Africa

The spider genus Pandava Lehtinen previously included two species, P. laminata (Thorell) and P. hunanensis Yin and Bao, known from Asia and the Pacific Islands. The genus is diagnosed by the reduced tegular process on the male palp and the anterior position of the copulatory openings on the female epigynum. In this paper, we present updated descriptions for the known species of Pandava and we describe five new species: Pandava shiva sp. nov. from Pakistan, Pandava sarasvati sp. nov. from Myanmar; Pandava ganesha sp. nov., Pandava kama sp. nov. and Pandava ganga sp. nov., all from India. We also update the generic distribution including the first records of Titanoecidae from Africa.