The timing of Neotropical speciation dynamics: A reconstruction of Myiopagis flycatcher diversification using phylogenetic and paleogeographic data

Neotropical forests have brought forth a large proportion of the world`s terrestrial biodiversity, but the underlying evolutionary mechanisms and their timing require further elucidation. Despite insights gained from phylogenetic studies, uncertainties about molecular clock rates have hindered efforts to determine the timing of diversification processes. Moreover, most molecular research has been detached from the extensive body of data on Neotropical geology and paleogeography. We here examine phylogenetic relationships and the timing of speciation events in a Neotropical flycatcher genus (Myiopagis) by using calibrations from modern geologic data in conjunction with a number of recently developed DNA sequence dating algorithms and by comparing these estimates with those based on a range of previously proposed molecular clock rates. We present a well-supported hypothesis of systematic relationships within the genus. Our age estimates of Myiopagis speciation events based on paleogeographic data are in close agreement with nodal ages derived from a ""traditional"" avian mitochondrial 2%/My clock, while contradicting other clock rates. Our comparative approach corroborates the consistency of the traditional avian mitochondrial clock rate of 2%/My for tyrant-flycatchers. Nevertheless, our results argue against the indiscriminate use of molecular clock rates in evolutionary research and advocate the verification of the appropriateness of the traditional clock rate by means of independent calibrations in individual studies. (C) 2009 Elsevier Inc. All rights reserved.

Emergence and loss of assortative mating in sympatric speciation

We have studied an agent model which presents the emergence of sexual barriers through the onset of assortative mating, a condition that might lead to sympatric speciation. In the model, individuals are characterized by two traits, each determined by a single locus A or B. Heterozygotes on A are penalized by introducing an adaptive difference from homozygotes. Two niches are available. Each A homozygote is adapted to one of the niches. The second trait, called the marker trait has no bearing on the fitness. The model includes mating preferences, which are inherited from the mother and subject to random variations. A parameter controlling recombination probabilities of the two loci is also introduced. We study the phase diagram by means of simulations, in the space of parameters (adaptive difference, carrying capacity, recombination probability). Three phases are found, characterized by (i) assortative mating, (ii) extinction of one of the A alleles and (iii) Hardy-Weinberg like equilibrium. We also make perturbations of these phases to see how robust they are. Assortative mating can be gained or lost with changes that present hysteresis loops, showing the resulting equilibrium to have partial memory of the initial state and that the process of going from a polymorphic panmictic phase to a phase where assortative mating acts as sexual barrier can be described as a first-order transition. (C) 2009 Published by Elsevier Ltd.

EVOLUTIONARY BIOLOGY IN BIODIVERSITY SCIENCE, CONSERVATION, AND POLICY: A CALL TO ACTION

Evolutionary biologists have long endeavored to document how many species exist on Earth, to understand the processes by which biodiversity waxes and wanes, to document and interpret spatial patterns of biodiversity, and to infer evolutionary relationships. Despite the great potential of this knowledge to improve biodiversity science, conservation, and policy, evolutionary biologists have generally devoted limited attention to these broader implications. Likewise, many workers in biodiversity science have underappreciated the fundamental relevance of evolutionary biology. The aim of this article is to summarize and illustrate some ways in which evolutionary biology is directly relevant We do so in the context of four broad areas: (1) discovering and documenting biodiversity, (2) understanding the causes of diversification, (3) evaluating evolutionary responses to human disturbances, and (4) implications for ecological communities, ecosystems, and humans We also introduce bioGENESIS, a new project within DIVERSITAS launched to explore the potential practical contributions of evolutionary biology In addition to fostering the integration of evolutionary thinking into biodiversity science, bioGENESIS provides practical recommendations to policy makers for incorporating evolutionary perspectives into biodiversity agendas and conservation. We solicit your involvement in developing innovative ways of using evolutionary biology to better comprehend and stem the loss of biodiversity.

Phylogenetic relationships and infrageneric classification of Epidendrum subgenus Amphiglottium (Laeliinae, Orchidaceae)

Epidendrum L. is the largest genus of Orchidaceae in the Neotropical region; it has an impressive morphological diversification, which imposes difficulties in delimitation of both infrageneric and interspecific boundaries. In this study, we review infrageneric boundaries within the subgenus Amphiglottium and try to contribute to the understanding of morphological diversification and taxa delimitation within this group. We tested the monophyly of the subgenus Amphiglottium sect. Amphiglottium, expanding previous phylogenetic investigations and reevaluated previous infrageneric classifications proposed. Sequence data from the trnL-trnF region were analyzed with both parsimony and maximum likelihood criteria. AFLP markers were also obtained and analyzed with phylogenetic and principal coordinate analyses. Additionally, we obtained chromosome numbers for representative species within the group. The results strengthen the monophyly of the subgenus Amphiglottium but do not support the current classification system proposed by previous authors. Only section Tuberculata comprises a well-supported monophyletic group, with sections Carinata and Integra not supported. Instead of morphology, biogeographical and ecological patterns are reflected in the phylogenetic signal in this group. This study also confirms the large variability of chromosome numbers for the subgenus Amphiglottium (numbers ranging from 2n = 24 to 2n = 240), suggesting that polyploidy and hybridization are probably important mechanisms of speciation within the group.

Pollination biology of Syngonanthus elegans (Eriocaulaceae - Poales)

Studies on the pollination biology of Eriocaulaceae are scarce although particularly interesting because of its inclusion in the Poales, a predominantly wind-pollinated order. The pollination biology of Syngonanthus elegans (Bong.) Ruhland was studied during two annual flowering periods to test the hypothesis that insect pollination was its primary pollination system. A field study was carried out, including observations of the morphology and biology of the flowers, insect visits and pollinator behaviour. We also evaluated seed set, seed germination and seedling development for different pollination modes. Although seeds were produced by self-pollination, pollination by small insects contributed most effectively to the reproductive success of S. elegans, resulting in the greatest seed set, with the highest germination percentage and optimum seedling vigour. The. oral resources used by flower visitors were pollen and nectar that was produced by staminate and pistillate flowers. Self-pollination played a minor role and its consequence was inbreeding depression.

Observations on the Breeding Biology of the Collared Crescentchest (Melanopareia torquata)

The Collared Crescentchest (Melanopareia torquata) is an endemic bird of the Cerrado (Family: Melanopareiidae), and is listed in the State of Sao Paulo, Brazil as ""endangered"". We studied the breeding biology of Collared Crescentchest at two nests in the State of sao Paulo, southeast Brazil. Males were identified genetically and equipped with radio-transmitters. The incubation period was 12-16 days and the nestling period was 12-14 days. Nestling body mass was measured every second day for the first 10 days. Males participated in incubation and helped with nesting care. Measurements of eggs and nests are compared to those from the single previously known nest. These data are the first for any member of the Family Melanopareiidae. Received 27 March 2009. Accepted 28 August 2009.

Reproductive biology of six Brazilian Myrtaceae: is there a syndrome associated with buzz-pollination?

The floral phenology and reproductive biology of six sympatric arboreal Myrtaceae species were studied in the coastal plain forest (Ubatuba, Brazil, 44 degrees 48`W 23 degrees 22`S), from September 1999 to April 2002. Flowering started in the transition from the driest to the most humid season (Sep/Oct) and lasted until March. The sequence with which the species flowered each year was consistently the same. However, the timing of flowering onset, peak, end, and overlap differed from one year to another. Myrtaceae species were classified as xenogamic according to the pollen:ovule ratios, but two of them seem to present some degree of self-compatibility. Flowers of all species opened at sunrise and lasted for I day. Bombus morio (Apidae: Bombini) was the most common visitor followed by Melipona rufiventris (Apidae: Meliponini). Buzz pollination in Myrtaceae was common at the study area and seems to be related to bees` behaviour and to some aspects of flowers` morphology.

Independent fusions and recent origins of sex chromosomes in the evolution and diversification of glass knife fishes (Eigenmannia)

The genus Eigenmannia comprises several species groups that display a surprising variety of diploid chromosome numbers and sex-determining systems. In this study, hypotheses regarding phylogenetic relationships and karyotype evolution were investigated using a combination of molecular and cytogenetic methods. Phylogenetic relationships were analyzed for 11 cytotypes based on sequences from five mitochondrial DNA regions. Parsimony-based character mapping of sex chromosomes confirms previous suggestions of multiple origins of sex chromosomes. Molecular cytogenetic analyses involved chromosome painting using probes derived from whole sex chromosomes from two taxa that were hybridized to metaphases of their respective sister cytotypes. These analyses showed that a multiple XY system evolved recently (<7 mya) by fusion. Furthermore, one of the chromosomes that fused to form the neo-Y chromosome is fused independently to another chromosome in the sister cytotype. This may constitute an efficient post-mating barrier and might imply a direct function of sex chromosomes in the speciation processes in Eigenmannia. The other chromosomal sex-determination system investigated is shown to have differentiated by an accumulation of heterochromatin on the X chromosome. This has occurred in the past 0.6 my, and is the most recent chromosomal sex-determining system described to date. These results show that the evolution of sex-determining systems can proceed very rapidly. Heredity (2011) 106, 391-400; doi:10.1038/hdy.2010.82; published online 23 June 2010

Hybridization and introgression across different ploidy levels in the Neotropical orchids Epidendrum fulgens and E-puniceoluteum (Orchidaceae)

The hypothesis of gene flow between species with large differences in chromosome numbers has rarely been tested in the wild, mainly because species of different ploidy are commonly assumed to be reproductively isolated from each other because of instantaneous and strong postzygotic barriers. In this study, a broad-scale survey of molecular variation was carried out between two orchid species with different ploidy levels: Epidendrum fulgens (2n = 2x = 24 chromosomes) and Epidendrum puniceoluteum (2n = 4x = 52 chromosomes). To test the strength of their reproductive barriers, we investigated the distribution of genetic variation in sympatric and allopatric populations of these two species and conducted crossing experiments. Nuclear and plastid microsatellite loci were used to genotype 463 individuals from eight populations across the geographical range of both species along the Brazilian coastal plain. All six sympatric populations analysed presented hybrid zones, indicating that hybridization between E. fulgens and E. puniceoluteum is a common phenomenon. Bayesian assignment analysis detected the presence of F(1) and F(2) individuals and also signs of introgression, demonstrating a high potential for interspecific gene flow. Introgression occurs preferentially from E. fulgens to E. puniceoluteum. Pure parental individuals of both species display strong genotype-habitat associations, indicating that environment-dependent selection could be acting in all hybrid zones. This study suggests that hybridization and introgression are evolutionary processes playing a role in the diversification of Epidendrum and indicates the importance of investigations of hybrid zones in understanding reproductive barriers and speciation processes in Neotropical orchid species.

BREEDING BIOLOGY OF KELP GULLS ON THE BRAZILIAN COAST

We studied clutch size, hatching and fledging success, and time necessary for chick Kelp Gulls (Larus dominicanus) to leave the nest throughout two breeding seasons (2004 and 2005) on Guararitama Island, Sao Paulo, Brazil. We followed 93 nests in 2004 and 97 nests in 2005. The average (+/- SD) clutch size was 2.09 +/- 0.64 in 2004 and 1.93 +/- 0.59 in 2005. Hatching success was 74% in 2004 and 53% in 2005, and fledging success was 54% in 2004 and 58% in 2005. Chicks grew quickly, following the linear equation y(t) = 61g + 17.03g X age (in days), and began to fly at 40 days. Received 11 August 2008. Accepted 28 August 2009.

Checklist and morphometry of benthic cnidarians from the Fernando de Noronha Archipelago, Brazil

The Fernando de Noronha Archipelago (Pernambuco State, Brazil), a national marine park, is formed by 21 islands and islets of volcanic origin. An update of the checklist of the benthic cnidarians from some of the archipelago`s reef environments, as well as a study of their corals and calcified hydroids morphometry, was the major goal of this work. Fieldwork was undertaken in February 2005 and in April 2006 and observations were carried out at 13 stations during snorkeling and/or scuba diving up to 30 m deep. Thirty-four species of cnidarians were recorded, of which 17 are new occurrences for the studied area. When added to the species previously listed in the literature, the total number of benthic cnidarians recorded for the Archipelago increases to 57. Stephanocoenia michelini, a new occurrence of zooxanthellate coral, is worthy of mention, as well as the calcified hydroid Millepora braziliensis. Mussismilia hispida tenuisepta showed several variations among its skeletal characters that surpassed the limits of intraspecific morphological variation when compared to those of Mussismilia hispida.

Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests

The small-sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages. (C) 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102, 527-539.

Population biology and regeneration of forbs and shrubs after fire in Brazilian Campos grasslands

Fire is an important factor in several ecosystems, affecting plant population biology. Campos grasslands are under constant influence of disturbance, mostly grazing and fire. However, few studies evaluated the effect of fire on plant population biology of grassland species. Therefore, we aim to analyze the effect of fire on the population biology of four species, from different functional groups and regeneration strategies: Chaptalia runcinata (forb, resprouter, absence of belowground organ), Vernonia flexuosa (forb, resprouter, presence of rhizophore), Eupatorium ligulaefolium (shrub, resprouter, presence of xylopodium) and Heterothalamus psiadioides (shrub, obligate seeder). Seven plots were established in different sites in southern Brazil: frequently burned (FB) and excluded from fire since 6 years (E). All plots were subjected to controlled burns during summer. Before experiments, populations were sampled. Further observations were carried out after 90 and after 360 days of fire experiments. In addition, we counted the number of seedlings and resprouters recruited after fire. Heat shock experiments were conducted with two species (H. psiadioides and V. flexuosa), as well as the study of the bud bank of the following species: E. ligulaefolium and V. flexuosa. The obligate seeder species had all individuals killed by fire and established only after 1 year. Resprouters, however, showed new stems immediately after fire. E. ligulaefolium and V. flexuosa showed only vegetative regeneration from belowground organs and more individuals in excluded sites 1 year after the fire. The bud bank of E. ligulaefolium tended to be larger in excluded sites, whilst V. flexuosa showed an opposite result. High temperatures did not enhance nor kill seeds from both studied species. Vegetative regeneration was the most important strategy for all studied species, except for H. psiadioides, the obligate seeder species. Fire thus, plays an important role on population structure and demography, being also important for plant recruitment.

Replacement of the arginine biosynthesis operon in Xanthomonadales by ateral gene transfer

The role of lateral gene transfer (LGT) in prokaryotes has been shown to rapidly change the genome content, providing new gene tools for environmental adaptation. Features related to pathogenesis and resistance to strong selective conditions have been widely shown to be products of gene transfer between bacteria. The genomes of the gamma-proteobacteria from the genus Xanthomonas, composed mainly of phytopathogens, have potential genomic islands that may represent imprints of such evolutionary processes. In this work, the evolution of genes involved in the pathway responsible for arginine biosynthesis in Xanthomonadales was investigated, and several lines of evidence point to the foreign origin of the arg genes clustered within a potential operon. Their presence inside a potential genomic island, bordered by a tRNA gene, the unusual ranking of sequence similarity, and the atypical phylogenies indicate that the metabolic pathway for arginine biosynthesis was acquired through LGT in the Xanthomonadales group. Moreover, although homologues were also found in Bacteroidetes (Flavobacteria group), for many of the genes analyzed close homologues are detected in different life domains (Eukarya and Archaea), indicating that the source of these arg genes may have been outside the Bacteria clade. The possibility of replacement of a complete primary metabolic pathway by LGT events supports the selfish operon hypothesis and may occur only under very special environmental conditions. Such rare events reveal part of the history of these interesting mosaic Xanthomonadales genomes, disclosing the importance of gene transfer modifying primary metabolism pathways and extending the scenario for bacterial genome evolution.

Symmetry in biology: from genetic code to stochastic gene regulation

Mathematical models, as instruments for understanding the workings of nature, are a traditional tool of physics, but they also play an ever increasing role in biology - in the description of fundamental processes as well as that of complex systems. In this review, the authors discuss two examples of the application of group theoretical methods, which constitute the mathematical discipline for a quantitative description of the idea of symmetry, to genetics. The first one appears, in the form of a pseudo-orthogonal (Lorentz like) symmetry, in the stochastic modelling of what may be regarded as the simplest possible example of a genetic network and, hopefully, a building block for more complicated ones: a single self-interacting or externally regulated gene with only two possible states: ` on` and ` off`. The second is the algebraic approach to the evolution of the genetic code, according to which the current code results from a dynamical symmetry breaking process, starting out from an initial state of complete symmetry and ending in the presently observed final state of low symmetry. In both cases, symmetry plays a decisive role: in the first, it is a characteristic feature of the dynamics of the gene switch and its decay to equilibrium, whereas in the second, it provides the guidelines for the evolution of the coding rules.