Coalescent analysis of mtDNA indicates Pleistocene divergence among three species of howler monkey (Alouatta spp.) and population subdivision within the Atlantic Coastal Forest species, A. guariba

We have used coalescent analysis of mtDNA cytochrome b (cyt b) sequences to estimate times of divergence of three species of Alouatta-A. caraya, A. belzebul, and A. guariba-which are in close geographic proximity. A. caraya is inferred to have diverged from the A. guariba/A. belzebul clade approximately 3.83 million years ago (MYA), with the later pair diverging approximately 1.55 MYA. These dates are much more recent than previous dates based on molecular-clock methods. In addition, analyses of new sequences from the Atlantic Coastal Forest species A. guariba indicate the presence of two distinct haplogroups corresponding to northern and southern populations with both haplogroups occurring in sympatry within Sao Paulo state. The time of divergence of these two haplogroups is estimated to be 1.2 MYA and so follows quite closely after the divergence of A. guariba and A. belzebul. These more recent dates point to the importance of Pleistocene environmental events as important factors in the diversification of A. belzebul and A. guariba. We discuss the diversification of the three Alouatta species in the context of recent models of climatic change and with regard to recent molecular phylogeographic analyses of other animal groups distributed in Brazil.

Optimal subdivision of land in agrarian reform projects: an analysis using genetic algorithms

J.A. Ferreira Neto, E.C. Santos Junior, U. Fra Paleo, D. Miranda Barros, and M.C.O. Moreira. 2011. Optimal subdivision of land in agrarian reform projects: an analysis using genetic algorithms. Cien. Inv. Agr. 38(2): 169-178. The objective of this manuscript is to develop a new procedure to achieve optimal land subdivision using genetic algorithms (GA). The genetic algorithm was tested in the rural settlement of Veredas, located in Minas Gerais, Brazil. This implementation was based on the land aptitude and its productivity index. The sequence of tests in the study was carried out in two areas with eight different agricultural aptitude classes, including one area of 391.88 ha subdivided into 12 lots and another of 404.1763 ha subdivided into 14 lots. The effectiveness of the method was measured using the shunting line standard value of a parceled area lot`s productivity index. To evaluate each parameter, a sequence of 15 calculations was performed to record the best individual fitness average (MMI) found for each parameter variation. The best parameter combination found in testing and used to generate the new parceling with the GA was the following: 320 as the generation number, a population of 40 individuals, 0.8 mutation tax, and a 0.3 renewal tax. The solution generated rather homogeneous lots in terms of productive capacity.

Relief influence on tree species richness in secondary forest fragments of Atlantic Forest, SE, Brazil

(Relief influence on tree species richness in secondary forest fragments of Atlantic Forest, SE, Brazil). The aim of this work was to explore the relationship between tree species richness and morphological characteristics of relief at the Ibiuna Plateau (SE Brazil). We sampled 61 plots of 0.30 ha, systematically established in 20 fragments of secondary forest (2-274 ha) and in three areas within a continuous secondary forest site, Morro Grande Reserve (9,400 ha). At each plot, 100 trees with diameter at breast height > 5 cm were sampled by the point centered quarter method, and total richness and richness per dispersal and succession class were obtained. The relief was characterized by the mean and variance of slope, elevation, aspect and slope location. There was no significant relationship between relief heterogeneity and tree species richness. Relief parameters generally did not affect tree richness, but elevation was particularly important especially in the continuous forest. Despite the limited range of altitudinal variation (150 m), species richness increases with elevation. The highest areas were also those with the largest forest cover and the lowest disturbance degree, which should contribute to the greater richness of those sites. Our results suggest an indirect influence of relief, due to the fact that deforestation is less intense in higher regions, rather than a direct influence of abiotic factors related to the altitudinal gradient.

Morphology and phylogenetic relationships of a remarkable new genus and two new species of Neotropical freshwater stingrays from the Amazon basin (Chondrichthyes: Potamotrygonidae)

The morphology and phylogenetic relationships of a new genus and two new species of Neotropical freshwater stingrays, family Potamotrygonidae, are investigated and described in detail. The new genus, Heliotrygon, n. gen., and its two new species, Heliotrygon gomesi, n. sp. (type-species) and Heliotrygon rosai, n. sp., are compared to all genera and species of potamotrygonids, based on revisions in progress. Some of the derived features of Heliotrygon include its unique disc proportions (disc highly circular, convex anteriorly at snout region, its width and length very similar), extreme subdivision of suborbital canal (forming a complex honeycomb-like pattern anterolaterally on disc), stout and triangular pelvic girdle, extremely reduced caudal sting, basibranchial copula with very slender and acute anterior extension, and precerebral and frontoparietal fontanellae of about equal width, tapering very little posteriorly. Both new species can be distinguished by their unique color patterns: Heliotrygon gomesi is uniform gray to light tan or brownish dorsally, without distinct patterns, whereas Heliotrygon rosai is characterized by numerous white to creamy-white vermiculate markings over a light brown, tan or gray background color. Additional proportional characters that may further distinguish both species are also discussed. Morphological descriptions are provided for dermal denticles, ventral lateral-line canals, skeleton, and cranial, hyoid and mandibular muscles of Heliotrygon, which clearly corroborate it as the sister group of Paratrygon. Both genera share numerous derived features of the ventral lateral-line canals, neurocranium, scapulocoracoid, pectoral basals, clasper morphology, and specific patterns of the adductor mandibulae and spiracularis medialis muscles. Potamotrygon and Plesiotrygon are demonstrated to share derived characters of their ventral lateral-line canals, in addition to the presence of angular cartilages. Our morphological phylogeny is further corroborated by a molecular phylogenetic analysis of cytochrome b based on four sequences (637 base pairs in length), representing two distinct haplotypes for Heliotrygon gomesi. Parsimony analysis produced a single most parsimonious tree revealing Heliotrygon and Paratrygon as sister taxa (boot-strap proportion of 70%), which together are the sister group to a clade including Plesiotrygon and species of Potamotrygon. These unusual stingrays highlight that potamotrygonid diversity, both in terms of species composition and undetected morphological and molecular patterns, is still poorly known.

The hidden diversity of Coleodactylus amazonicus (Sphaerodactylinae, Gekkota) revealed by molecular data

Coleodactylus amazonicus, a small leaf-litter diurnal gecko widely distributed in Amazon Basin has been, considered a single species with no significant morphological differences between populations along its range. A recent molecular study, however, detected large genetic differences between populations of central Amazonia and those in the easternmost part of the Amazon Basin, suggesting the presence of taxonomically unrecognised diversity. In this study, DNA sequences of three mitochondrial (165, cytb, and ND4) and two nuclear genes (RAG-1, c-mos) were used to investigate whether the species currently identified as C. amazonicus contains morphologically cryptic species lineages. The present phylogenetic analysis reveals further genetic subdivision including at least five potential species lineages, restricted to northeastern (lineage A), southeastern (lineage B), central-northern (lineage E) and central-southern (lineages C and D) parts of Amazon Basin. All clades are characterized by exclusive groups of alleles for both nuclear genes and highly divergent mitochondrial haplotype clades, with corrected pairwise net sequence divergence between sister lineages ranging from 9.1% to 20.7% for the entire mtDNA dataset. Results of this study suggest that the real diversity of ""C. amazonicus"" has been underestimated due to its apparent cryptic diversification. (C) 2009 Elsevier Inc. All rights reserved.

Multiple origins of vagrant Subantarctic fur seals: A long journey to the Brazilian coast detected by molecular markers

In this study, we present the first data about putative source populations of the vagrant Subantarctic fur seal, Arctocephalus tropicalis, found on the Brazilian coast, through the comparison of their mitochondrial DNA control sequences to exclusive haplotypes from the main breeding colonies of the species. The results indicated that, despite the majority of the vagrant individuals are from Gough Island (the closest breeding site to the Brazilian coast), they also come from other reproductive colonies, such as Crozet Island, a distance around 16,500 km from the Brazilian coast. Furthermore, the molecular data identified three possible management units: (1) Gough, (2) Amsterdam, and (3) Marion, Macquarie and Crozet. This significant genetic subdivision must be taken into account in any future management plan for the species conservation, including rehabilitation and even reintroduction of vagrant fur seals.

Dynamics of Dissolved Forms of Carbon and Inorganic Nitrogen in Small Watersheds of the Coastal Atlantic Forest in Southeast Brazil

Based on the fact that streamwater quality reflects landscape conditions, the objectives of this study were: to investigate nitrogen (N), carbon (C), and major ion concentrations in six streams crossing minimally disturbed Atlantic Forest areas, with similar geomorphological characteristics; to determine N and C fluxes in one of these pristine streams (Indaia); and assess the impact of human activity on the biogeochemistry of two other streams in the same region, crossing urbanized areas. The distribution pattern of carbon and inorganic nitrogen dissolved forms, as well as the major ion and biogenic gas concentrations in the streamwater, was similar in pristine streams, indicating that the C and N dynamics were determined by influence of some factors, such as climate, atmospheric deposition, geology, soil type, and land covering, which were analogous in the forested watersheds. The urban streams were significantly different from the pristine streams, showing low dissolved oxygen concentrations, high respiration rates, and high concentrations of carbon dioxide, dissolved inorganic nitrogen, dissolved inorganic carbon, and major ion. These differences were attributed to anthropogenic impact on water quality, especially domestic sewage discharge. Additionally, in the Indaia stream, it was possible to observe the importance of rainfall over temporal dynamics of dissolved carbon forms, and also, the obtained specific flux of dissolved inorganic nitrogen was relatively elevated (approximately 11 kg ha(-1) year(-1)). These results reveal the influence of human activity over the biogeochemistry of coastal streams and also indicate the importance N export of Atlantic Forest to the ocean.

Chemical identity and connections of medial preoptic area neurons expressing melanin-concentrating hormone during lactation

Lactation is an energy-demanding process characterized by massive food and water consumption, cessation of the reproductive cycle and induction of maternal behavior. During lactation, melanin-concentrating hormone (MCH) mRNA and peptide expression are increased in the medial preoptic area (MPO) and in the anterior paraventricular nucleus of the hypothalamus. Here we show that MCH neurons in the MPO coexpress the GABA synthesizing enzyme GAD-67 mRNA. We also show that MCH neurons in the MPO of female rats are innervated by neuropeptides that control energy homeostasis including agouti-related protein (AgRP), alpha-melanocyte stimulating hormone (alpha MSH) and cocaine- and amphetamine-regulated transcript (CART). Most of these inputs originate from the arcuate nucleus neurons. Additionally, using injections of retrograde tracers we found that CART neurons in the ventral premammillary nucleus also innervate the MPO. We then assessed the projections of the female MPO using injections of anterograde tracers. The MPO densely innervates hypothalamic nuclei related to reproductive control including the anteroventral periventricular nucleus, the ventrolateral subdivision of the ventromedial nucleus (VMHvl) and the ventral premammillary nucleus (PMV). We found that the density of MCH-ir fibers is increased in the VMHvl and PMV during lactation. Our findings suggest that the expression of MCH in the MPO may be induced by changing levels of neuropeptides involved in metabolic control. These MCH/GABA neurons may, in turn, participate in the suppression of cyclic reproductive function and/or sexual behavior during lactation through projections to reproductive control sites. (C) 2009 Elsevier B.V. All rights reserved.

Architectonic subdivisions of the amygdalar complex of a primitive marsupial (Didelphis aurita)

The architecture of the amygdaloid complex of a marsupial, the opossum Didelphis aurita, was analyzed using classical stains like Nissl staining and myelin (Gallyas) staining, and enzyme histochemistry for acetylcholinesterase and NADPH-diaphorase. Most of the subdivisions of the amygdaloid complex described in eutherian mammals were identified in the opossum brain. NADPH-diaphorase revealed reactivity in the neuropil of nearly all amygdaloid subdivisions with different intensities, allowing the identification of the medial and lateral subdivisions of the cortical posterior nucleus and the lateral subdivision of the lateral nucleus. The lateral, central, basolateral and basomedial nuclei exhibited acetylcholinesterase positivity, which provided a useful chemoarchitectural criterion for the identification of the anterior basolateral nucleus. Myelin stain allowed the identification of the medial subdivision of the lateral nucleus, and resulted in intense staining of the medial subdivisions of the central nucleus. The medial, posterior, and cortical nuclei, as well as the amygdalopiriform area did not exhibit positivity for myelin staining. On the basis of cyto- and chemoarchitectural criteria, the present study highlights that the opossum amygdaloid complex shares similarities with that of other species, thus supporting the idea that the organization of the amygdala is part of a basic plan conserved through mammalian evolution. (C) 2008 Elsevier Inc. All rights reserved.

Evolutionary placement of Xanthomonadales based on conserved protein signature sequences

Xanthomonadales comprises one of the largest phytopathogenic bacterial groups, and is currently classified within the gamma-proteobacteria. However, the phylogenetic placement of this group is not clearly resolved, and the results of different studies contradict one another. In this work, the evolutionary position of Xanthomonadales was determined by analyzing the presence of shared insertions and deletions (INDELs) in highly conserved proteins. Several distinctive insertions found in most of the members of the gamma-proteobacteria are absent in Xanthomonadales and groups such as Legionelalles, Chromatiales, Methylococcales, Thiotrichales and Cardiobacteriales. These INDELs were most likely introduced after the branching of Xanthomonadales from most of the gamma-proteobacteria and provide evidence for the phylogenetic placement of the early gamma-proteobacteria. Moreover, other proteins contain insertions exclusive to the Xanthomonadales order, confirming that this is a monophyletic group and provide important specific genetic markers. Thus, the data presented clearly support the Xanthomonadales group as an independent subdivision, and constitute one of the deepest branching lineage within the gamma-proteobacteria clade. (C) 2009 Elsevier Inc. All rights reserved.

Phylogeography and evolutionary history of dengue virus type 3

In this study, we revisited the phylogeography of the three of major DENV-3 genotypes and estimated its rate of evolution, based on the analysis of the envelope (E) gene of 200 strains isolated from 31 different countries around the world over a time period of 50 years (1956-2006). Our phylogenetic analysis revealed a geographical subdivision of DENV-3 population in several country-specific clades. Migration patterns of the main DENV-3 genotypes showed that genotype I was mainly circumspect to the maritime portion of Southeast-Asia and South Pacific, genotype 11 stayed within continental areas in South-East Asia, while genotype III spread across Asia, East Africa and into the Americas. No evidence for rampant co-circulation of distinct genotypes in a single locality was found, suggesting that some factors, other than geographic proximity, may limit the continual dispersion and reintroduction of new DENV-3 variants. Estimates of the evolutionary rate revealed no significant differences among major DENV-3 genotypes. The mean evolutionary rate of DENV-3 in areas with long-term endemic transmissions (i.e., Indonesia and Thailand) was similar to that observed in the Americas, which have been experiencing a more recent dengue spread. We estimated the origin of DENV-3 virus around 1890, and the emergence of current diversity of main DENV-3 genotypes between the middle 1960s and the middle 1970s, coinciding with human population growth, urbanization, and massive human movement, and with the description of the first cases of DENV-3 hemorrhagic fever in Asia. (C) 2008 Elsevier B.V. All rights reserved.

Twofold adaptive partition of unity implicits

Partition of Unity Implicits (PUI) has been recently introduced for surface reconstruction from point clouds. In this work, we propose a PUI method that employs a set of well-observed solutions in order to produce geometrically pleasant results without requiring time consuming or mathematically overloaded computations. One feature of our technique is the use of multivariate orthogonal polynomials in the least-squares approximation, which allows the recursive refinement of the local fittings in terms of the degree of the polynomial. However, since the use of high-order approximations based only on the number of available points is not reliable, we introduce the concept of coverage domain. In addition, the method relies on the use of an algebraically defined triangulation to handle two important tasks in PUI: the spatial decomposition and an adaptive polygonization. As the spatial subdivision is based on tetrahedra, the generated mesh may present poorly-shaped triangles that are improved in this work by means a specific vertex displacement technique. Furthermore, we also address sharp features and raw data treatment. A further contribution is based on the PUI locality property that leads to an intuitive scheme for improving or repairing the surface by means of editing local functions.

The Cariris Velhos tectonic event in Northeast Brazil

The Borborema Province in northeastern South America is a typical Brasiliano-Pan-African branching system of Neoproterozoic orogens that forms part of the Western Gondwana assembly. The province is positioned between the Sao Luis-West Africa craton to the north and the Sao Francisco (Congo-Kasai) craton to the south. For this province the main characteristics are (a) its subdivision into five major tectonic domains, bounded mostly by long shear zones, as follows: Medio Coreau, Ceara Central, Rio Grande do Norte, Transversal, and Southern; (b) the alternation of supracrustal belts with reworked basement inliers (Archean nuclei + Paleoproterozoic belts); and (c) the diversity of granitic plutonism, from Neoproterozoic to Early Cambrian ages, that affect supracrustal rocks as well as basement inliers. Recently, orogenic rock assemblages of early Tonian (1000-920 Ma) orogenic evolution have been recognized, which are restricted to the Transversal and Southern domains of the Province. Within the Transversal Zone, the Alto Pajeu terrane locally includes some remnants of oceanic crust along with island arc and continental arc rock assemblages, but the dominant supracrustal rocks are mature and immature pelitic metasedimentary and metavolcaniclastic rocks. Contiguous and parallel to the Alto Pajeu terrane, the Riacho Gravata subterrane consists mainly of low-grade metamorphic successions of metarhythmites, some of which are clearly turbiditic in origin, metaconglomerates, and sporadic marbles, along with interbedded metarhyolitic and metadacitic volcanic or metavolcaniclastic rocks. Both terrane and subterrane are cut by syn-contractional intrusive sheets of dominantly peraluminous high-K calc-alkaline, granititic to granodioritic metaplutonic rocks. The geochemical patterns of both supracrustal and intrusive rocks show similarities with associations of mature continental arc volcano-sedimentary sequences, but some subordinate intra-plate characteristics are also found. In both the Alto Pajeu and Riacho Gravata terranes, TIMS and SHRIMP U-Pb isotopic data from zircons from both metavolcanic and metaplutonic rocks yield ages between 1.0 and 0.92 Ga, which define the time span for an event of orogenic character, the Cariris Velhos event. Less extensive occurrences of rocks of Cariris Velhos age are recognized mainly in the southernmost domains of the Province, as for example in the Polo Redondo-Maranco terrane, where arc-affinity migmatite-granitic and meta-volcano-sedimentary rocks show U-Pb ages (SHRIMP data) around 0.98-0.97 Ga. For all these domains, Sm-Nd data exhibit Tom model ages between 1.9 and 1.1 Ga with corresponding slightly negative to slightly positive epsilon(Nd)(t) values. These domains, along with the Borborema Province as a whole, were significantly affected by tectonic and magmatic events of the Brasiliano Cycle (0.7-0.5 Ga), so that it is possible that there are some other early Tonian rock assemblages which were completely masked and hidden by these later Brasiliano events. Cariris Velhos processes are younger than the majority of orogenic systems at the end of Mesoproterozoic Era and beginning of Neoproterozoic throughout the world, e.g. Irumide belt, Kibaride belt and Namaqua-Natal belt, and considerably younger than those of the youngest orogenic process (Ottawan) in the Grenvillian System. Therefore, they were probably not associated with the proposed assembly of Rodinia. We suggest, instead, that Cariris Velhos magmatism and tectonism could have been related to a continental margin magmatic arc, with possible back-arc associations, and that this margin may have been a short-lived (<100 m.y.) leading edge of the newly assembled Rodinia supercontinent. (C) 2009 Elsevier Ltd. All rights reserved.

Multiscale Analysis of Topographic Surface Roughness in the Midland Valley, Scotland

Surface roughness is an important geomorphological variable which has been used in the Earth and planetary sciences to infer material properties, current/past processes, and the time elapsed since formation. No single definition exists; however, within the context of geomorphometry, we use surface roughness as an expression of the variability of a topographic surface at a given scale, where the scale of analysis is determined by the size of the landforms or geomorphic features of interest. Six techniques for the calculation of surface roughness were selected for an assessment of the parameter`s behavior at different spatial scales and data-set resolutions. Area ratio operated independently of scale, providing consistent results across spatial resolutions. Vector dispersion produced results with increasing roughness and homogenization of terrain at coarser resolutions and larger window sizes. Standard deviation of residual topography highlighted local features and did not detect regional relief. Standard deviation of elevation correctly identified breaks of slope and was good at detecting regional relief. Standard deviation of slope (SD(slope)) also correctly identified smooth sloping areas and breaks of slope, providing the best results for geomorphological analysis. Standard deviation of profile curvature identified the breaks of slope, although not as strongly as SD(slope), and it is sensitive to noise and spurious data. In general, SD(slope) offered good performance at a variety of scales, while the simplicity of calculation is perhaps its single greatest benefit.

Grain size and heavy minerals of the Late Quaternary eolian sediments from the Imbituba-Jaguaruna coast, Southern Brazil: Depositional controls linked to relative sea-level changes

The stratigraphic subdivision and correlation of dune deposits is difficult, especially when age datings are not available. A better understanding of the controls on texture and composition of eolian sands is necessary to interpret ancient eolian sediments. The Imbituba-Jaguaruna coastal zone (Southern Brazil, 28 degrees-29 degrees S) stands out due to its four well-preserved Late Pleistocene (eolian generation 1) to Holocene eolian units (eolian generations 2, 3, and 4). In this study, we evaluate the grain-size and heavy-mineral characteristics of the Imbituba-Jaguartma eolian units through statistical analysis of hundreds of sediment samples. Grain-size parameters and heavy-mineral content allow us to distinguish the Pleistocene from the Holocene units. The grain size displays a pattern of fining and better sorting from generation 1 (older) to 4 (younger), whereas the content of mechanically stable (dense and hard) heavy minerals decreases from eolian generation 1 to 4. The variation in grain size and heavy-mineral content records shifts in the origin and balance (input versus output) of eolian sediment supply attributable mainly to relative sea-level changes. Dunefields submitted to relative sea-level lowstand conditions (eolian generation 1) are characterized by lower accumulation rates and intense post-depositional dissection by fluvial incision. Low accumulation rates favor deflation in the eolian system, which promotes concentration of denser and stable heavy minerals (increase of ZTR index) as well as coarsening of eolian sands. Dissection involves the selective removal of finer sediments and less dense heavy minerals to the coastal source area. Under a high rate of relative sea-level rise and transgression (eolian generation 2), coastal erosion prevents deflation through high input of sediments to the coastal eolian source. This condition favors dunefield growth. Coastal erosion feeds sand from local sources to the eolian system. including sands from previous dunefields (eolian generation 1) and from drowned incised valleys. Therefore, dunefields corresponding to transgressive phases inherit the grain-size and heavy-mineral characteristics of previous dunefields, leading to selective enrichment of finer sands and lighter minerals. Eolian generations 3 and 4 developed during a regressive-progradational phase (Holocene relative sea level highstand). The high rate of sediment supply during the highstand phase prevents deflation. The lack of coastal erosion favors sediment supply from distal sources (fluvial sediments rich in unstable heavy minerals). Thus, dunefields of transgressive and highstand systems tracts may be distinguished from dunefields of the lowstand systems tract through high rates of accumulation (low deflation) in the former. The sediment source of the transgressive dunefields (high input of previously deposited coastal sands) differs from that of the highstand dunefields (high input of fluvial distal sands). Based on this case study, we propose a general framework for the relation between relative sea level, sediment supply and the texture and mineralogy of eolian sediments deposited in siliciclastic wet coastal zones similar to the Imbituba-Jaguaruna coast (C) 2009 Elsevier B.V. All rights reserved.