Phylogeographical patterns shed light on evolutionary process in South America.

The South American continent is composed of several biogeographical regions harbouring the highest biodiversity on the globe, encompassing five of the world's biodiversity 'hot spots'. Nonetheless, the patterns and processes responsible for shaping its astonishing species diversity are largely unknown. Here, we present a review of current South American phylogeographical knowledge based on published articles on this topic. An appraisal of the literature reveals emerging phylogeographical patterns in the biota of South America. The striking phylogeographical divergence observed among organism lineages in South American studies is suggestive of high levels of undocumented species diversity. The interplay between Pleistocene climatic oscillations and Pliocene/Miocene orogenic events has contributed to shaping the current diversity and distribution of modern lineages in both the tropical and temperate regions of South America. Although older divergence times were observed for a range of species, most herpetofauna underwent an intraspecific lineage split much earlier than other organisms. The geographical ranges of species associated with forest habitats were reduced mainly during glacial cycles, whereas species associated with open vegetation domains have shown variable responses to climatic oscillations. The results suggest a highly complex mosaic of phylogeographical patterns in South America. We suggest future research directions to promote a better understanding of the origin and maintenance of the South American biota.

Sympatric bromeliad species (Pitcairnia spp.) facilitate tests of mechanisms involved in species cohesion and reproductive isolation in Neotropical inselbergs.

The roles of intra- and interspecific gene flow in speciation and species evolution are topics of great current interest in molecular ecology and evolutionary biology. Recent modelling studies call for new empirical data to test hypotheses arising from the recent shift from a 'whole-genome reproductive isolation' view to a 'genic' view of species and speciation. Particularly scarce (and thus of particular interest) are molecular genetic data on recently radiated, naturally hybridizing species in strongly structured and species-rich environments. Here, we studied four sympatric plant species (Pitcairnia spp.; Bromeliaceae) adapted to Neotropical inselbergs (isolated outcrops resembling habitat 'islands' in tropical rainforests) using nuclear and plastid DNA. Patterns of plastid DNA haplotype sharing and nuclear genomic admixture suggest the presence of both, incomplete lineage sorting and interspecific gene flow over extended periods of time. Integrity and cohesion of inselberg species of Pitcairnia are maintained despite introgression and in the face of extremely low within-species migration rates (N(e)m < 1 migrant per generation). Cross-evaluation of our genetic data against published pollination experiments indicate that species integrity is maintained by the simultaneous action of multiple prezygotic barriers, including flowering phenology, pollinator isolation and divergent mating systems. Postzygotic Bateson-Dobzhansky-Muller incompatibilities appear to contribute to isolation, as suggested by asymmetric introgression rates of single loci. Our results suggest that incomplete lineage sorting, hybridization and introgression form integral aspects of adaptive radiation in Neotropical inselberg 'archipelagos'. Inselbergs with multiple closely related co-occurring species should be of special interest to students of speciation in mountain systems, and to ongoing conservation programmes in the Atlantic Rainforest biodiversity hotspot.

Range-wide patterns of nuclear and chloroplast DNA diversity in Vriesea gigantea (Bromeliaceae), a neotropical forest species.

The processes that have shaped the extraordinary species diversity in neotropical rainforests are poorly understood, and knowledge about the patterns of genetic diversity across species' ranges is scarce, in contrast to other regions of the globe. We have conducted a range-wide study of genetic diversity in a plant endemic to the Brazilian Atlantic Rainforest, Vriesea gigantea (Bromeliaceae), based on a combined data set of nuclear microsatellites and chloroplast (cp) DNA markers typed in 429 plants from 13 populations. The results indicate a strong negative correlation between genetic diversity and population latitude, consistent with historical forest expansion from the northern half of the present distribution range. A deep phylogeographic split exists between the Brazilian states of São Paulo and Rio de Janeiro at ca. 23 degrees S latitude, probably reflecting past population isolation within more than one glacial refuge during the climatic changes of the Pleistocene. A comparison of genetic structures at cpDNA and nuclear markers revealed a pollen/seed flow ratio of more than 3:1, thus indicating an important role of the pollinating animals (that is, bats) in shaping the population genetic structure of this species. Diversity was reduced for cpDNA markers in the island populations off the coast, and reduced diversity and increased differentiation were observed for both nuclear and cpDNA at the edges of the species' range. The link between patterns of genetic and species diversity supports the hypothesis that both were shaped by the same biogeographic processes, triggered by the climatic oscillations of the Pleistocene.

The role of hybridization and introgression in maintaining species integrity and cohesion in naturally isolated inselberg bromeliad populations.

Hybridization is a widespread phenomenon present in numerous lineages across the tree of life. Its evolutionary consequences range from effects on the origin and maintenance, to the loss of biodiversity. We studied genetic diversity and intra- and interspecific gene flow between two sympatric populations of closely-related species, Pitcairnia flammea and P. corcovadensis (Bromeliaceae), which are adapted to naturally fragmented Neotropical inselbergs, based on nuclear and plastidial DNA. Our main results indicate a strong reproductive isolation barrier, although low levels of interspecific gene flow were observed in both sympatric populations. The low rates of intraspecific gene flow observed for both P. corcovadensis and P. flammea populations corroborate the increasing body of evidence that inselberg bromeliad species are maintained as discrete evolutionary units despite the presence of low genetic connectivity. Nuclear patterns of genetic diversity and gene flow revealed that hybridization and introgression might not cause species extinction via genetic assimilation of the rare P. corcovadensis. In the face of reduced intraspecific gene exchange, hybridization and introgression may be important aspects of the Pitcairnia diversification process, with a positive evolutionary impact at the bromeliad community level, and thus contribute to increasing and maintaining genetic diversity in local isolated inselberg populations.

Macroinvertebrate fauna associated with Pistia stratiotes and Nymphoides indica in subtropical lakes (south Brazil).

This study was carried out at the Biguás and Polegar lakes, both small environments but at different successional stages. The main objective was to characterize the macroinvertebrate community associated to the aquatic macrophyte stand in each lake in order for this community, the environmental conditions and their water quality to interact. The samples were taken in 2003. The abiotic variables of N and P totals, the temperature, electrical conductivity, pH and dissolved oxygen, as well as the determined clorophyll a concentration were measured. Macroinvertebrates were sampled with a 500 micro mesh size net, separated under a stereomicroscope and identified at the lowest possible taxonomic level, and their densities were shown as the number of individuals per 100 g of macrophyte dry weight. The Shannon-Wiener Diversity Index (H'), Pielou evenness (J), frequency of occurrence, abundance and taxa richness were calculated for each invertebrate community. The Lago dos Biguás is undergoing a process of eutrophication and during the study presented a large Pistia stratiotes stand. The Lago Polegar is oligotrophic and had only a small Nymphoides indica bankwe. The macrophyte associated invertebrate communities in each lake were considered significantly different (p < 0.05). Sixty seven taxa were found for the Lago dos Biguás and 32 for the Lago Polegar. For both lakes, most of the taxa were considered rare, with a low dominance in a few months. The taxa with highest densities at Lago dos Biguás were Chironomidae, Daphniidae and Cyclopidae, and Oligochaeta, Chironomidae and Coenagrionidae for Lago Polegar.

De novo assembly and characterization of leaf and floral transcriptomes of the hybridizing bromeliad species (Pitcairnia spp.) adapted to Neotropical Inselbergs.

We present the leaf and floral transcriptomes of two hybridizing bromeliad species that differ in their major pollinator systems. Here we identified candidate genes responsible for pollinator attraction and reproductive isolation in these two species. We searched for candidate genes involved in floral traits, such as colour. Approximately 34 Gbp of cDNA sequence data were produced from both tissues and species, resulting in a total of 424 506 914 raw reads. The de novo-assembled transcriptomes consisted of a total of 263 955 contigs, further clustered into 110 977 unigenes. Over 58% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The transcriptomes revealed 144 unique transcripts that encode key enzymes in the flavonoid and anthocyanin biosynthesis pathways. The domain/family annotation and phylogenetic analysis allowed us to infer, by homology, potential functions of the genes encoding MYB, HD-ZIP and bZIP-HY5 transcription factors, as well as WD40 protein, which may be involved in anthocyanin and flavonoid regulation in these species. These candidate genes are associated with natural regulation in flower colour in other plant species and will facilitate future studies aimed at elucidating the molecular basis of adaptive differentiation and the evolution of mechanisms of pollinator-mediated reproductive isolation in these two bromeliads. In addition, we identified a total of 49 439 microsatellite loci. These resources will assist future research into adaptation and speciation events in bromeliad species, thus providing a starting point for investigation of the molecular mechanisms of the traits responsible for their reproductive isolation.

Charophytes as a nutrient and energy reservoir in a tropical coastal Lagoon impacted by humans (RJ, Brazil).

In the Imboassica Lagoon (22 degrees 24'S and 42 degrees 42'W) (Macaé, RJ, Brazil), two species of macroalgae of the genus Chara (C. angolensis and C. fibrosa) registered in large areas were identified. The lagoon is subject to several relevant anthropic impacts, of which untreated sewage is one of the most important. Results of the biomass distribution as analyzed in different areas of the lagoon showed values ranging from 172 to 510 gDW x m(-2). As for the nutrient concentration, the results presented large fluctuations, with carbon values ranging from 325 to 392 mg x g(-1)DW, those of nitrogen, from 14 to 27 mg x g DW, and of phosphorus from 0.45 to 0.85 mg.g(-1) DW. This led to large fluctuations of the C:N:P ratio (from 387:24:1 to 872:47:1). The minimum and maximum energetic values of the biomass were 9.54 e 12.34 kJ x g(-1)DW. Smaller C:N:P ratios tended to occur in more eutrophic areas. The association between biomass and nutrient concentration showed that the highest quantities in the beds are found in oligotrophic areas. The Spearman correlation between nutrient concentration in the water column and biomass was r(s) = 0.45 (p < 0.05) for nitrogen and r(s) = 0.50 (p < 0.01) for phosphorus (n = 30). The large total biomass associated with nutrient concentration and energy content indicates that Charophytes are an important biological compartment in the structure and metabolism of the lagoon.

Seasonal dynamics of methane in the water column of two subtropical lakes differing in trophic status.

Alterations in methane concentration in the water column of aquatic systems is closely linked to the processes of production and consumption of this gas, i.e., methanogenesis and methanotrophy respectively. The aim of this research is to evaluate methane dynamics through diurnal variation in the concentration of this gas in the water column of two lakes differing in trophic status at the campus of Fundação Universidade do Rio Grande (FURG). In two sampling periods (November 2001 and July 2002) methane concentrations in the water column were significantly higher (3.66 and 0.41 micromoles.L-1, respectively) at Lago dos Biguás, with mesoeutrophic features when related to Lago Polegar (1.43 and 0.19 micromoles.L-1, respectively) which has oligotrophic features. The higher methane concentrations were detected in November 2001 when higher temperature was also detected. The results highlighted the importance of trophic status as well as seasonality for the methane dynamics in these ecosystems.

Isolation and characterization of microsatellite loci in Pitcairnia albiflos (Bromeliaceae), an endemic bromeliad from the Atlantic Rainforest, and cross-amplification in other species.

Eight microsatellite markers were isolated from Pitcairnia albiflos, an endangered endemic bromeliad species restricted to 'inselberg' rock outcrops in the state of Rio de Janeiro, Brazil. The number of alleles observed for each locus ranged from two to 12. Average observed and expected heterozygosities were 0.408 and 0.663, respectively. The cross-amplification test in 16 taxa suggests that the markers will be useful in numerous related bromeliad species. The loci will be used to study genetic structure and reproductive biology in fragmented inselberg populations and the origin and maintenance of barriers to gene flow between sympatric Pitcairnia species.

Isolation and characterization of microsatellite loci in Epidendrum puniceoluteum, an endemic orchid from the Atlantic Rainforest.

Epidendrum puniceoluteum is an endemic orchid of Atlantic Rainforest, restricted to few populations only due to the destruction and fragmentation of its native habitat. Here, we report on the development of 10 microsatellite markers isolated from this orchid species. Genetic variability was characterized in two distant populations from Brazil coast. The number of alleles observed for each locus ranged from two to 12 and with an average of 6.4 alleles per locus. These microsatellites should be valuable tools for studying both fine-scale genetic structure of scattered E. puniceoluteum population and patterns will be useful genetic markers for other closely related taxa.

Seasonal dynamics of methane in the water column of two subtropical lakes differing in trophic status / Dinâmica sazonal do metano na coluna d'água de dois lagos subtropicais em diferentes estados tróficos

Alterations in methane concentration in the water column of aquatic systems is closely linked to the processes of production and consumption of this gas, i.e., methanogenesis and methanotrophy respectively. The aim of this research is to evaluate methane dynamics through diurnal variation in the concentration of this gas in the water column of two lakes differing in trophic status at the campus of Fundação Universidade do Rio Grande (FURG). In two sampling periods (November 2001 and July 2002) methane concentrations in the water column were significantly higher (3.66 and 0.41 μmoles.L-1, respectively) at Lago dos Biguás, with mesoeutrophic features when related to Lago Polegar (1.43 and 0.19 μmoles.L-1, respectively) which has oligotrophic features. The higher methane concentrations were detected in November 2001 when higher temperature was also detected. The results highlighted the importance of trophic status as well as seasonality for the methane dynamics in these ecosystems.

As alterações na concentração de metano na coluna d'água nos ecossistemas aquáticos estão intimamente ligadas aos processos de produção e consumo deste gás, ou seja, à metanogênese e metanotrofia, respectivamente. Esta pesquisa tem como objetivo determinar a dinâmica do metano através da variação diurna da concentração deste gás na coluna d'água em dois lagos de diferentes estados tróficos do Campus da Fundação da Universidade do Rio Grande (FURG). Nos dois períodos de coleta (novembro de 2001 e julho de 2002), as concentrações de metano foram significativamente maiores no lago dos Biguás (3,66 e 0,41 μmoles.L-1, respectivamente) de caráter mesoeutrófico em relação ao lago Polegar (1,43 e 0,19 μmoles.L-1, respectivamente), de característica oligotrófica. Os maiores valores da concentração de metano na coluna d'água nos dois lagos foram observados no período de novembro de 2001, quando foram registrados também os maiores valores de temperatura. Estes resultados evidenciam tanto a importância do caráter trófico dos lagos quanto a sazonalidade em relação à dinâmica do metano nestes ecossistemas.

Macroinvertebrate fauna associated with Pistia stratiotes and Nymphoides indica in subtropical lakes (south Brazil)

This study was carried out at the Biguás and Polegar lakes, both small environments but at different successional stages. The main objective was to characterize the macroinvertebrate community associated to the aquatic macrophyte stand in each lake in order for this community, the environmental conditions and their water quality to interact. The samples were taken in 2003. The abiotic variables of N and P totals, the temperature, electrical conductivity, pH and dissolved oxygen, as well as the determined clorophyll a concentration were measured. Macroinvertebrates were sampled with a 500 µ mesh size net, separated under a stereomicroscope and identified at the lowest possible taxonomic level, and their densities were shown as the number of individuals per 100 g of macrophyte dry weight. The Shannon-Wiener Diversity Index (H'), Pielou evenness (J), frequency of occurrence, abundance and taxa richness were calculated for each invertebrate community. The Lago dos Biguás is undergoing a process of eutrophication and during the study presented a large Pistia stratiotes stand. The Lago Polegar is oligotrophic and had only a small Nymphoides indica bankwe. The macrophyte associated invertebrate communities in each lake were considered significantly different (p < 0.05). Sixty seven taxa were found for the Lago dos Biguás and 32 for the Lago Polegar. For both lakes, most of the taxa were considered rare, with a low dominance in a few months. The taxa with highest densities at Lago dos Biguás were Chironomidae, Daphniidae and Cyclopidae, and Oligochaeta, Chironomidae and Coenagrionidae for Lago Polegar.

Este estudo foi realizado nos lagos dos Biguás e Polegar, ambientes de pequenas dimensões que se encontram em diferentes estágios sucessionais. O objetivo principal foi caracterizar a comunidade de macroinvertebrados, que vive associada ao estande de macrófitas aquáticas encontrado em cada um dos lagos, na tentativa de obter relações entre a comunidade, a saúde dos ambientes e a qualidade de água. As coletas foram feitas durante o ano de 2003. Em cada lago, foram avaliadas as concentrações de N e o P totais, o pH, temperatura, oxigênio dissolvido, condutividade elétrica, e determinadas as concentrações de clorofila a na água. A malha utilizada para a separação dos macroinvertebrados foi de 500 µ e os resultados de densidade foram expressos em 100 gramas de peso seco de macrófita. A triagem foi realizada sob estereomicroscópio e os organismos identificados até o menor nível taxonômico possível. Para cada comunidade foram calculados o Índice de Diversidade de Shannon-Wiener (H'), a homogeneidade de Pielou (J), a freqüência de ocorrência, a abundância e a riqueza de taxa. O Lago dos Biguás, em processo de eutrofização, apresentou durante o período estudado um grande estande de Pistia stratiotes. O Lago Polegar, oligotrófico, abrigou apenas pequenos bancos de Nymphoides indica. As comunidades de macroinvertebrados associados às macrófitas em cada lago foram consideradas significativamente diferentes (p < 0,05). Foram encontrados 67 taxa no Lago dos Biguás e 32 no Lago Polegar. Nos dois ambientes, a maior parte dos taxa foi considerada rara, com pouca dominância em poucos meses. As maiores densidades foram de Chironomidae, Daphniidae e Cyclopidae no Lago dos Biguás, e de Oligochaeta, Chironomidae e Coenagrionidae no Lago Polegar.

Charophytes as a nutrient and energy reservoir in a tropical coastal lagoon impacted by humans (RJ, Brazil)

Na Lagoa Imboassica, localizada em Macaé, RJ, Brasil (22º24'S e 42º42'W), foram identificadas duas espécies de macroalgas do gênero Chara (C. angolensis e C. fibrosa), apresentando ampla distribuição. A lagoa recebe vários impactos antrópicos, e o lançamento de esgoto não tratado é um dos mais importantes. A biomassa variou entre 172 e 510 gDW.mû2 em diferentes áreas da lagoa. A concentração de nutrientes apresentou ampla variação, com os valores de carbono entre 325 e 392 mg.gû1DW, nitrogênio entre 14 e 27 mg.gû1DW e fósforo entre 0,45 e 0,85 mg.gû1DW, assim as taxas C:N:P apresentaram variação de 387:24:1 a 872:47:1. Os valores mínimo e máximo de energia na biomassa foram, respectivamente, 9,54 e 12,34 kJ.gû1DW. Há tendência de as menores taxas C:N:P ocorrerem em áreas mais eutrofizadas. Considerando os valores de biomassa e a concentração de nutrientes na biomassa, os maiores estoques de nutrientes estão associados aos bancos de Carófitas em áreas mais oligotróficas. A correlação de Spearman entre a concentração de nutrientes na coluna de água e a biomassa foi rs = 0,45 (p < 0,05) para o nitrogênio e rs = 0,50 (p < 0,01) para o fósforo (n = 30). A grande biomassa associada à concentração de nutrientes e os valores energéticos indicam que as carófitas são um importante compartimento biológico na estrutura e metabolismo da lagoa.

Charophytes as a nutrient and energy reservoir in a tropical coastal lagoon impacted by humans (RJ, Brazil)

In the Imboassica Lagoon (22º24'S and 42º42'W) (Macaé, RJ, Brazil), two species of macroalgae of the genus Chara (C. angolensis and C. fibrosa) registered in large areas were identified. The lagoon is subject to several relevant anthropic impacts, of which untreated sewage is one of the most important. Results of the biomass distribution as analyzed in different areas of the lagoon showed values ranging from 172 to 510 gDW.m-2. As for the nutrient concentration, the results presented large fluctuations, with carbon values ranging from 325 to 392 mg.g-1DW, those of nitrogen, from 14 to 27 mg.g-1DW, and of phosphorus from 0.45 to 0.85 mg.g-1DW. This led to large fluctuations of the C:N:P ratio (from 387:24:1 to 872:47:1). The minimum and maximum energetic values of the biomass were 9.54 e 12.34 kJ.g-1DW. Smaller C:N:P ratios tended to occur in more eutrophic areas. The association between biomass and nutrient concentration showed that the highest quantities in the beds are found in oligotrophic areas. The Spearman correlation between nutrient concentration in the water column and biomass was r s = 0.45 (p 0.05) for nitrogen and r s = 0.50 (p 0.01) for phosphorus (n = 30). The large total biomass associated with nutrient concentration and energy content indicates that Charophytes are an important biological compartment in the structure and metabolism of the lagoon.

Na Lagoa Imboassica, localizada em Macaé, RJ, Brasil (22º24'S e 42º42'W), foram identificadas duas espécies de macroalgas do gênero Chara (C. angolensis e C. fibrosa), apresentando ampla distribuição. A lagoa recebe vários impactos antrópicos, e o lançamento de esgoto não tratado é um dos mais importantes. A biomassa variou entre 172 e 510 gDW.m-2 em diferentes áreas da lagoa. A concentração de nutrientes apresentou ampla variação, com os valores de carbono entre 325 e 392 mg.g-1DW, nitrogênio entre 14 e 27 mg.g-1DW e fósforo entre 0,45 e 0,85 mg.g-1DW, assim as taxas C:N:P apresentaram variação de 387:24:1 a 872:47:1. Os valores mínimo e máximo de energia na biomassa foram, respectivamente, 9,54 e 12,34 kJ.g-1DW. Há tendência de as menores taxas C:N:P ocorrerem em áreas mais eutrofizadas. Considerando os valores de biomassa e a concentração de nutrientes na biomassa, os maiores estoques de nutrientes estão associados aos bancos de Carófitas em áreas mais oligotróficas. A correlação de Spearman entre a concentração de nutrientes na coluna de água e a biomassa foi r s = 0,45 (p 0,05) para o nitrogênio e r s = 0,50 (p 0,01) para o fósforo (n = 30). A grande biomassa associada à concentração de nutrientes e os valores energéticos indicam que as carófitas são um importante compartimento biológico na estrutura e metabolismo da lagoa.