• Premise of the study: To study gene expression in plants, high-quality RNA must be extracted in quantities sufficient for subsequent cDNA library construction. Field-based collections are often limited in quantity and quality of tissue and are typically preserved in RNAlater. Obtaining sufficient and high-quality yield from variously preserved samples is essential to studies of comparative biology. We present a protocol for the extraction of high-quality RNA from even the most recalcitrant plant tissues.• Methods and Results: Tissues from mosses, cycads, and angiosperm floral organs and leaves were preserved in RNAlater or frozen fresh at −80°C. Extractions were performed and quality was measured for yield and purity.• Conclusions: This protocol results in the extraction of high-quality RNA from a variety of plant tissues representing vascular and nonvascular plants. RNA was used for cDNA synthesis to generate libraries for next-generation sequencing and for expression studies using quantitative PCR (qPCR) and semiquantitative reverse transcription PCR (RT-PCR).
Rapid radiations are notoriously difficult to resolve, yet understanding phylogenetic patterns in such lineages can be useful for investigating evolutionary processes associated with bursts of speciation and morphological diversification. Here we present an expansive molecular phylogeny of Costus L. (Costaceae Nakai) with a focus on the Neotropical species within the clade, sampling 47 of the known 51 Neotropical species and including five molecular markers for phylogenetic analysis (ITS, ETS, rps16, trnL-F, and CaM). We use the phylogenetic results to investigate shifts in pollination syndrome, with the intention of addressing potential mechanisms leading to the rapid radiation documented for this clade. Our ancestral reconstruction of pollination syndrome presents the first evidence in this genus of an evolutionary toggle in pollination morphologies, demonstrating both the multiple independent evolutions of ornithophily (bird pollination) as well as reversals to melittophily (bee pollination). We show that the ornithophilous morphology has evolved at least eight times independently with four potential reversals to melittophilous morphology, and confirm prior work showing that neither pollination syndrome defines a monophyletic lineage. Based on the current distribution for the Neotropical and African species, we reconstruct the ancestral distribution of the Neotropical clade as the Pacific Coast of Mexico and Central America. Our results indicate an historic dispersal of a bee-pollinated taxon from Africa to the Pacific Coast of Mexico/Central America, with subsequent diversification leading to the evolution of a bird-pollinated floral morphology in multiple derived lineages.
Species can arise via the divisive effects of allopatry as well as due to ecological and/or reproductive character displacement within sympatric populations. Two separate lineages of Costaceae are native to the Neotropics; an early-diverging clade endemic to South America (consisting of ca. 16 species in the genera Monocostus, Dimerocostus and Chamaecostus); and the Neotropical Costus clade (ca. 50 species), a diverse assemblage of understory herbs comprising nearly half of total familial species richness. We use a robust dated molecular phylogeny containing most of currently known species to inform macroevolutionary reconstructions, enabling us to examine the context of speciation in Neotropical lineages. Analyses of speciation rate revealed a significant variation among clades, with a rate shift at the most recent common ancestor of the Neotropical Costus clade. There is an overall predominance of allopatric speciation in the South American clade, as most species display little range overlap. In contrast, sympatry is much higher within the Neotropical Costus clade, independent of node age. Our results show that speciation dynamics during the history of Costaceae is strongly heterogeneous, and we suggest that the Costus radiation in the Neotropics arose at varied geographic contexts.
Comparative studies of streams with altered versus conserved riparian zones are important to evaluate the degree of alterations caused by inappropriate use of these streams' vital buffer zones. The aim of this study was to determine the impact of riparian deforestation on the habitat structure of southern Brazilian Amazonian headwater streams, as well as to provide elements for impact assessment and the monitoring of these water bodies. We selected ten sites and two headwater streams at each site; one stream was located in an area with preserved riparian vegetation (pristine streams) and the other stream in a deforested riparian zone (altered streams). Stretches of these streams were analyzed across hydrological periods (dry period, beginning of the rainy period, and end of the rainy period) for hydromorphological aspects, water physical-chemical variables, and habitat integrity (proportion of forestation in buffer zones and habitat integrity index). Compared to pristine streams in all the hydrological periods analyzed, altered streams presented lower oxygen concentration (~1.0 mg/L), an increase of 1 o C in water temperature, and less organic material availability. We found that riparian deforestation affects habitat structure variability among hydrological periods, making them more homogeneous. Therefore, beyond the necessary broadening of the spatial scale of studies in this region, monitoring these understudied headwater stream environments is also crucial for determining the magnitude of deforestation effects on these vulnerable aquatic ecosystems.Key-words: riparian zone; environmental impact; lotic ecosystems; temporal variation; water physical-chemical conditions ResumoEstudos comparativos entre riachos com zona ripária alterada e conservada são importantes para avaliar o grau de alteração provocado pelo uso indevido desta zona tampão vital aos corpos de água. Logo, o objetivo deste estudo foi determinar o impacto do desmatamento da florestal ripária sobre a estrutura do habitat de riachos de cabeceira no sul da Amazônia, e fornecer elementos para avaliação de impacto e monitoramento desses corpos de água. Nós selecionamos 10 locais e em cada local 2 riachos, sendo um riacho localizado em área com floresta ripária preservada (riachos pristinos) e outro riacho com a floresta ripária desmatada (riachos alterados). Trechos destes riachos foram analisados durante 3 períodos hidrológicos (período de seca, enchente e vazante) para a caracterização de aspectos hidromorfologicos, variáveis físico-químicas e de controle para a integridade do habitat (proporção de floresta em área ripária e índice de integridade do habitat). Em relação aos riachos íntegros, em todos os períodos hidrológicos avaliados, os riachos alterados apresentaram menor concentração de oxigênio (~ 1,0 mg/L), aumento de 1 o C na temperatura da água e menor disponibilidade de material orgânico alóctone. Nós detectamos que o desmatamento da floresta ripária afeta a variabilidade na estrutura do habitat entre os períodos hidrológicos, torn...
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