Divide to conquer: a complex pattern of biodiversity depicted by vertebrate components in the Brazilian Atlantic Forest

The identification of northern and southern components in different vertebrate species led researchers to accept a two-component hypothesis for the Brazilian Atlantic forest (BAF). Nevertheless, neither a formal proposal nor a meta-analysis to confirm this coincidence was ever made. Our main objective here was therefore to systematically test in how many vertebrate components the BAF could be divided by analysing existing empirical data. We used two approaches: (1) mapping and comparing the proposed areas of vertebrate endemism in the BAF and (2) analysing studies mentioning spatial subdivisions in distinct forest-dependent vertebrates within the biome, by the use of panbiogeography. The four large-scale endemism area components together with the six small-scale panbiogeographical ones allowed the definition of three BAF greater regions, subdivided into nine vertebrate components, latitudinally and longitudinally organized. Empirical time estimates of the diversification events within the BAF were also reviewed. Diversification of these vertebrates occurred not only in the Pleistocene but also throughout the Miocene. Our results confirm the BAF's complex history, both in space and time. We propose that future research should be small-scale and focused in the vertebrate components identified herein. Given the BAF's heterogeneity, studying via sections will be much more useful in identifying the BAF's historical biogeography. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107, 39-55.

Evolution of Body Elongation in Gymnophthalmid Lizards: Relationships with Climate

The evolution of elongated body shapes in vertebrates has intrigued biologists for decades and is particularly recurrent among squamates. Several aspects might explain how the environment influences the evolution of body elongation, but climate needs to be incorporated in this scenario to evaluate how it contributes to morphological evolution. Climatic parameters include temperature and precipitation, two variables that likely influence environmental characteristics, including soil texture and substrate coverage, which may define the selective pressures acting during the evolution of morphology. Due to development of geographic information system (GIS) techniques, these variables can now be included in evolutionary biology studies and were used in the present study to test for associations between variation in body shape and climate in the tropical lizard family Gymnophthalmidae. We first investigated how the morphological traits that define body shape are correlated in these lizards and then tested for associations between a descriptor of body elongation and climate. Our analyses revealed that the evolution of body elongation in Gymnophthalmidae involved concomitant changes in different morphological traits: trunk elongation was coupled with limb shortening and a reduction in body diameter, and the gradual variation along this axis was illustrated by less-elongated morphologies exhibiting shorter trunks and longer limbs. The variation identified in Gymnophthalmidae body shape was associated with climate, with the species from more arid environments usually being more elongated. Aridity is associated with high temperatures and low precipitation, which affect additional environmental features, including the habitat structure. This feature may influence the evolution of body shape because contrasting environments likely impose distinct demands for organismal performance in several activities, such as locomotion and thermoregulation. The present study establishes a connection between morphology and a broader natural component, climate, and introduces new questions about the spatial distribution of morphological variation among squamates.

Dental health in Northern Chile's Atacama oases: Evaluating the Middle Horizon (AD 500-1000) impact on local diet

As one of the few areas apt for horticulture in Northern Chile's arid landscape, the prehistory of the Atacama oases is deeply enmeshed with that of the inter-regional networks that promoted societal development in the south central Andes. During the Middle Horizon (AD 5001000), local populations experienced a cultural apex associated with a substantial increase in inter-regional interaction, population density, and quantity and quality of mortuary assemblages. Here, we test if this cultural peak affected dietary practices equally among the distinct local groups of this period. We examine caries prevalence and the degree of occlusal wear in four series recovered from three cemeteries. Our results show a reduction in the prevalence of caries for males among an elite subsample from Solcor 3 and the later Coyo 3 cemeteries. Dental wear tends to increase over time with the Late Middle Horizon/Late Intermediate Period cemetery of Quitor 6 showing a higher average degree of wear. When considered in concert with archaeological information, we concluded that the Middle Horizon was marked by dietary variability wherein some populations were able to obtain better access to protein sources (e.g., camelid meat). Not all members of Atacameno society benefited from this, as we note that this dietary change only affected men. Our results suggest that the benefits brought to the San Pedro oases during the Middle Horizon were not equally distributed among local groups and that social status, relationship to the Tiwanaku polity, and interment in particular cemeteries affected dietary composition. Am J Phys Anthropol, 2012. (C) 2012 Wiley Periodicals, Inc.

Homology and errors

A recent review of the homology concept in cladistics is critiqued in light of the historical literature. Homology as a notion relevant to the recognition of clades remains equivalent to synapomorphy. Some symplesiomorphies are homologies inasmuch as they represent synapomorphies of more inclusive taxa; others are complementary character states that do not imply any shared evolutionary history among the taxa that exhibit the state. Undirected character-state change (as characters optimized on an unrooted tree) is a necessary but not sufficient test of homology, because the addition of a root may alter parsimonious reconstructions. Primary and secondary homology are defended as realistic representations of discovery procedures in comparative biology, recognizable even in Direct Optimization. The epistemological relationship between homology as evidence and common ancestry as explanation is again emphasized. An alternative definition of homology is proposed. (c) The Willi Hennig Society 2012.

An Extreme Case of Plant-Insect Codiversification: Figs and Fig-Pollinating Wasps

It is thought that speciation in phytophagous insects is often due to colonization of novel host plants, because radiations of plant and insect lineages are typically asynchronous. Recent phylogenetic comparisons have supported this model of diversification for both insect herbivores and specialized pollinators. An exceptional case where contemporaneous plant-insect diversification might be expected is the obligate mutualism between fig trees (Ficus species, Moraceae) and their pollinating wasps (Agaonidae, Hymenoptera). The ubiquity and ecological significance of this mutualism in tropical and subtropical ecosystems has long intrigued biologists, but the systematic challenge posed by >750 interacting species pairs has hindered progress toward understanding its evolutionary history. In particular, taxon sampling and analytical tools have been insufficient for large-scale cophylogenetic analyses. Here, we sampled nearly 200 interacting pairs of fig and wasp species from across the globe. Two supermatrices were assembled: on an average, wasps had sequences from 77% of 6 genes (5.6 kb), figs had sequences from 60% of 5 genes (5.5 kb), and overall 850 new DNA sequences were generated for this study. We also developed a new analytical tool, Jane 2, for event-based phylogenetic reconciliation analysis of very large data sets. Separate Bayesian phylogenetic analyses for figs and fig wasps under relaxed molecular clock assumptions indicate Cretaceous diversification of crown groups and contemporaneous divergence for nearly half of all fig and pollinator lineages. Event-based cophylogenetic analyses further support the codiversification hypothesis. Biogeographic analyses indicate that the present-day distribution of fig and pollinator lineages is consistent with a Eurasian origin and subsequent dispersal, rather than with Gondwanan vicariance. Overall, our findings indicate that the fig-pollinator mutualism represents an extreme case among plant-insect interactions of coordinated dispersal and long-term codiversification.

Rananos expression pattern during oogenesis and early embryonic development in Rhynchosciara americana

The Dipteran a native Brazilian insect that has become a valuable model system for developmental biology research because it provides an interesting opportunity to study a different type of insect oogenesis. Sequences from a cDNA library that was constructed with poly A + RNA from the ovaries of larvae at different ages were analyzed. Molecular characterization confirmed interesting findings, such as the presence of . The gene encodes a conserved RNA-binding protein that is required during early development for the maintenance and division of the primordial germ cells of Diptera. plays an important role in specifying the posterior regions of insect embryos and is important for abdomen formation. In the present work, we showed the spatial and temporal expression profiles of this important gene, which is involved in oogenesis and early development. Data mining techniques were used to obtain the complete sequence of . Bioinformatic tools were used to determine the following: (1) the secondary structure of the 3'-untranslated region of the mRNA, (2) the encoded protein of the isolated gene, (3) the conserved zinc-finger domains of the Nanos protein, and (4) phylogenetic analyses. Furthermore, RNA in situ hybridization and immunolocalization were used to determine mRNA and protein expression in the tissues that were studied and to define as a germ cell molecular marker.

Multiple Quaternary Refugia in the Eastern Guiana Shield Revealed by Comparative Phylogeography of 12 Frog Species

The Guiana Shield (GS) is one of the most pristine regions of Amazonia and biologically one of the richest areas on Earth. How and when this massive diversity arose remains the subject of considerable debate. The prevailing hypothesis of Quaternary glacial refugia suggests that a part of the eastern GS, among other areas in Amazonia, served as stable forested refugia during periods of aridity. However, the recently proposed disturbance-vicariance hypothesis proposes that fluctuations in temperature on orbital timescales, with some associated aridity, have driven Neotropical diversification. The expectations of the temporal and spatial organization of biodiversity differ between these two hypotheses. Here, we compare the genetic structure of 12 leaf-litter inhabiting frog species from the GS lowlands using a combination of mitochondrial and nuclear sequences in an integrative analytical approach that includes phylogenetic reconstructions, molecular dating, and Geographic Information System methods. This comparative and integrated approach overcomes the well-known limitations of phylogeographic inference based on single species and single loci. All of the focal species exhibit distinct phylogeographic patterns highlighting taxon-specific historical distributions, ecological tolerances to climatic disturbance, and dispersal abilities. Nevertheless, all but one species exhibit a history of fragmentation/isolation within the eastern GS during the Quaternary with spatial and temporal concordance among species. The signature of isolation in northern French Guiana (FG) during the early Pleistocene is particularly clear. Approximate Bayesian Computation supports the synchrony of the divergence between northern FG and other GS lineages. Substructure observed throughout the GS suggests further Quaternary fragmentation and a role for rivers. Our findings support fragmentation of moist tropical forest in the eastern GS during this period when the refuge hypothesis would have the region serving as a contiguous wet-forest refuge.

A New Subgeneric Classification of Rhipsalis (Cactoideae, Cactaceae)

Most Cactaceae have succulent stems and inhabit dry or arid areas, but some are epiphytes of humid regions. Rhipsalis is the largest genus of epiphytic cacti. Species of Rhipsalis are notoriously difficult to identify, and the subgeneric classification of the genus has remained controversial. Between 1837 and 1995, eight different subgeneric classifications have been proposed for Rhipsalis. The most comprehensive taxonomic treatment of the genus recognized five subgenera, Phyllarthrorhipsalis, Rhipsalis, Epallagogonium, Calamorhipsalis, and Erythrorhipsalis, characterized mainly by stem morphology. Here, molecular phylogenetic information combined with morphological data is used to re-evaluate the former subgeneric classifications proposed for the genus. Three monophyletic subgenera are recognized, Rhipsalis, Calamorhipsalis and Erythrorhipsalis, which are mainly characterized by floral traits. The changes proposed include expanding the circumscription of Rhipsalis by the inclusion of species previously included in Phyllarthrorhipsalis and Epallagogoniwn and recognizing a broader Calamorhipsalis, also including species from subgenus Epallagogonium. The circumscription of Erythrorhipsalis remains unchanged. For each subgenus a list of synonyms, a brief description and a list of species included are presented. A key for the identification of subgenera is also provided.

Avian coronavirus Spike Glycoprotein Ectodomain Shows a Low Codon Adaptation to Gallus gallus with Virus-Exclusive Codons in Strategic Amino Acids Positions

This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1-507) from strains detected worldwide and chicken tissue-specific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC x GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.

Phylogeography of an Atlantic forest passerine reveals demographic stability through the last glacial maximum

In this study we analyzed the phylogeographic pattern and historical demography of an endemic Atlantic forest (AF) bird, Basileuterus leucoblepharus, and test the influence of the last glacial maximum (LGM) on its population effective size using coalescent simulations. We address two main questions: (i) Does B. leucoblepharus present population genetic structure congruent with the patterns observed for other AF organisms? (ii) How did the LGM affect the effective population size of B. leucoblepharus? We sequenced 914 bp of the mitochondrial gene cytochrome b and 512 bp of the nuclear intron 5 of beta-fibrinogen of 62 individuals from 15 localities along the AF. Both molecular markers revealed no genetic structure in B. leucoblepharus. Neutrality tests based on both loci showed significant demographic expansion. The extended Bayesian skyline plot showed that the species seems to have experienced demographic expansion starting around 300,000 years ago, during the late Pleistocene. This date does not coincide with the LGM and the dynamics of population size showed stability during the LGM. To further test the effect of the LGM on this species, we simulated seven demographic scenarios to explore whether populations suffered specific bottlenecks. The scenarios most congruent with our data were population stability during the LGM with bottlenecks older than this period. This is the first example of an AF organism that does not show phylogeographic breaks caused by vicariant events associated to climate change and geotectonic activities in the Quaternary. Differential ecological, environmental tolerances and habitat requirements are possibly influencing the different evolutionary histories of these organisms. Our results show that the history of organism diversification in this megadiverse Neotropical forest is complex. Crown Copyright (c) 2012 Published by Elsevier Inc. All rights reserved.

Neotropical termites: revision of Armitermes Wasmann (Isoptera, Termitidae, Syntermitinae) and phylogeny of the Syntermitinae

We present a comprehensive phylogenetic analysis of Syntermitinae, including representatives of all genera of the subfamily, along with all 12 species assigned formerly to the genus Armitermes Wasmann (Termitidae, Syntermitinae), and 4 new species described herein. Syntermitinae was recovered as a natural group and the hypothesis that the frontal tube indicates convergence between Syntermitinae and Nasutitermitinae was corroborated. Also, several diagnostic characters proposed in the original description of Syntermitinae are discussed. Alongside the phylogenetic study, a taxonomic revision of the Neotropical genus Armitermes was carried out, resulting in division of the genus into four genera. Taxonomic novelties are: Armitermes now includes A. armiger (Motschulsky), A. bidentatus Rocha & Cancello sp.n. and A. spininotus Rocha & Cancello sp.n.; Silvestritermes Rocha & Cancello gen.n. includes S. euamignathus (Silvestri) comb.n., S. lanei (Canter) comb.n., S. gnomus (Constantino) comb.n., S. duende Rocha & Cancello sp.n., S. minutus (Emerson) comb.n., S. almirsateri Rocha & Cancello sp.n. and S. holmgreni (Snyder) comb.n.; Uncitermes Rocha & Cancello gen.n. includes U. teevani (Emerson) comb.n.; Mapinguaritermes Rocha & Cancello gen.n. includes M. peruanus (Holmgren) comb.n. and M. grandidens (Emerson) comb.n. A new synonymy is proposed for A. cerradoensis Mathews under S. euamignathus. All soldiers are described and illustrated, as are the mandibles and digestive tract of the worker and the imago caste, when available. We provide a dichotomous key, based on soldiers, for all genera of Syntermitinae, and distribution maps and dichotomous keys, based on soldiers, for the species of Armitermes and all the new genera described herein.

Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes

Background: Several studies in Drosophila have shown excessive movement of retrogenes from the X chromosome to autosomes, and that these genes are frequently expressed in the testis. This phenomenon has led to several hypotheses invoking natural selection as the process driving male-biased genes to the autosomes. Metta and Schlotterer (BMC Evol Biol 2010, 10:114) analyzed a set of retrogenes where the parental gene has been subsequently lost. They assumed that this class of retrogenes replaced the ancestral functions of the parental gene, and reported that these retrogenes, although mostly originating from movement out of the X chromosome, showed female-biased or unbiased expression. These observations led the authors to suggest that selective forces (such as meiotic sex chromosome inactivation and sexual antagonism) were not responsible for the observed pattern of retrogene movement out of the X chromosome. Results: We reanalyzed the dataset published by Metta and Schlotterer and found several issues that led us to a different conclusion. In particular, Metta and Schlotterer used a dataset combined with expression data in which significant sex-biased expression is not detectable. First, the authors used a segmental dataset where the genes selected for analysis were less testis-biased in expression than those that were excluded from the study. Second, sex-biased expression was defined by comparing male and female whole-body data and not the expression of these genes in gonadal tissues. This approach significantly reduces the probability of detecting sex-biased expressed genes, which explains why the vast majority of the genes analyzed (parental and retrogenes) were equally expressed in both males and females. Third, the female-biased expression observed by Metta and Schltterer is mostly found for parental genes located on the X chromosome, which is known to be enriched with genes with female-biased expression. Fourth, using additional gonad expression data, we found that autosomal genes analyzed by Metta and Schlotterer are less up regulated in ovaries and have higher chance to be expressed in meiotic cells of spermatogenesis when compared to X-linked genes. Conclusions: The criteria used to select retrogenes and the sex-biased expression data based on whole adult flies generated a segmental dataset of female-biased and unbiased expressed genes that was unable to detect the higher propensity of autosomal retrogenes to be expressed in males. Thus, there is no support for the authors' view that the movement of new retrogenes, which originated from X-linked parental genes, was not driven by selection. Therefore, selection-based genetic models remain the most parsimonious explanations for the observed chromosomal distribution of retrogenes.

From Amazonia to the Atlantic forest: Molecular phylogeny of Phyzelaphryninae frogs reveals unexpected diversity and a striking biogeographic pattern emphasizing conservation challenges

Documenting the Neotropical amphibian diversity has become a major challenge facing the threat of global climate change and the pace of environmental alteration. Recent molecular phylogenetic studies have revealed that the actual number of species in South American tropical forests is largely underestimated, but also that many lineages are millions of years old. The genera Phyzelaphryne (1 sp.) and Adelophryne (6 spp.), which compose the subfamily Phyzelaphryninae, include poorly documented, secretive, and minute frogs with an unusual distribution pattern that encompasses the biotic disjunction between Amazonia and the Atlantic forest. We generated >5.8 kb sequence data from six markers for all seven nominal species of the subfamily as well as for newly discovered populations in order to (1) test the monophyly of Phyzelaphryninae, Adelophryne and Phyzelaphryne, (2) estimate species diversity within the subfamily, and (3) investigate their historical biogeography and diversification. Phylogenetic reconstruction confirmed the monophyly of each group and revealed deep subdivisions within Adelophryne and Phyzelaphryne, with three major clades in Adelophryne located in northern Amazonia, northern Atlantic forest and southern Atlantic forest. Our results suggest that the actual number of species in Phyzelaphryninae is, at least, twice the currently recognized species diversity, with almost every geographically isolated population representing an anciently divergent candidate species. Such results highlight the challenges for conservation, especially in the northern Atlantic forest where it is still degraded at a fast pace. Molecular dating revealed that Phyzelaphryninae originated in Amazonia and dispersed during early Miocene to the Atlantic forest. The two Atlantic forest clades of Adelophryne started to diversify some 7 Ma minimum, while the northern Amazonian Adelophryne diversified much earlier, some 13 Ma minimum. This striking biogeographic pattern coincides with major events that have shaped the face of the South American continent, as we know it today. (C) 2012 Elsevier Inc. All rights reserved.

The Panama microplate, island studies and relictual species of Melipona (Melikerria) (Hymenoptera: Apidae: Meliponini)

The endemic stingless honey-making bee Melipona (Melikerria) insularissp.n. on Coiba and Rancheria Islands in Pacific Panama is described, together with the proposed sister species, M. ambigua sp.n. from northeast Colombia. The Coiba Island group and Panama mainland were surveyed, yielding one meliponine endemic (M. insularissp.n.) and six meliponine genera and species. The poor Coiba fauna of amphibians and birds corresponds to the poor social bee fauna and suggests habitat barriers generally precluded recolonization from the mainland during glacial periods. Many animals became extinct, yet some remain as relicts. Melipona insularissp.n. was isolated on accreted terranes of Coiba rainforest in the Panama microplate. Morphology suggests that M. insularissp.n. is not a direct descendant of the San Blas-E. Panama endemic Melikerria, M. triplaridis. A phylogenetic hypothesis corroborates disjunct distributions. Rainforest endemics such as Peltogyne purpurea (Fabaceae) and Ptilotrigona occidentalis (Apidae, Meliponini) also occur as relictual, disjunct populations in Central and South America. These may have been isolated before accelerated biotic exchange began 2.4 Ma. Our work supports the geological findings of both a volcanic arc and the San Blas massif providing a substantial bridge for Melikerria from Colombia and Panama in Eocene to Miocene times. We suggest there have been taxon cycles permitting recolonization during glaciations, whereby colonies of M. insularissp.n. were able to recolonize Rancheria, a 250 ha island, 2 km from Coiba. However, rafting colonies nesting in trees, carried on vegetation mats, may have produced founding populations of Melipona in Central America and on oceanic islands such as Coiba.

Novel organization of the mitochondrial genome in the deep-sea coral, Madrepora oculata (Hexacorallia, Scleractinia, Oculinidae) and its taxonomic implications

Madrepora is one of the most ecologically important genera of reef-building scleractinians in the deep sea, occurring from tropical to high-latitude regions. Despite this, the taxonomic affinities and relationships within the genus Madrepora remain unclear. To clarify these issues, we sequenced the mitochondrial (mt) genome of the most widespread Madrepora species, M. oculata, and compared this with data for other scleractinians. The architecture of the M. oculara mt genome was very similar to that of other scleractinians, except for a novel gene rearrangement affecting only cox2 and cox3. This pattern of gene organization was common to four geographically distinct M. oculata individuals as well as the congeneric species M. minutiseptum, but was not shared by other genera that are closely related on the basis of cox1 sequence analysis nor other oculinids, suggesting that it might be unique to Madrepora. (C) 2012 Elsevier Inc. All rights reserved.