Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

A systematic revision of Goniosomatinae (Arachnida : Opiliones : Gonyleptidae), with a cladistic analysis and biogeographical notes

Goniosomatine harvestmen have strongly armed pedipalps, generally large bodies and, commonly, very long legs (sometimes more than 20 cm), and are distributed in the Brazilian Atlantic forest, from southern Bahia to Santa Catarina. Since they are conspicuous animals and individuals of some species tend to concentrate in caves (and also under rock boulders), they have been (and still are) the target of several studies, especially those focusing on reproductive and defensive behavior, population ecology, physiology, chromosomes, etc. In spite of their importance for biological studies (some species constitute important and frequently used models for these studies), the taxonomy of Goniosomatinae has faced some problems, including misidentification, a large number of undescribed species and the lack of a phylogenetic hypothesis for the relationships among its species (which would allow evolutionary studies to be made). The last taxonomic changes in the subfamily were made 60 years ago. Considering a taxonomic revision and cladistic analysis of the subfamily to be of paramount importance, the main scope of the present paper is to provide a cladistic analysis and taxonomic revision of the species of Goniosomatinae and a new arrangement of genera (and species). The main taxonomic changes are given as follows. Six genera are recognised within the subfamily: Goniosoma; the newly described genus Pyatan; the reestablished genera Serracutisoma, Heteromitobates and Mitogoniella; and Acutisoma. New generic synonyms include: Glyptogoniosoma = Goniosomella = Lyogoniosoma = Metalyogoniosoma = Xulapona = Goniosoma, Acutisomelloides = Pygosomoides = Spelaeosoma = Serracutisoma; and Acutisomella = Heteromitobates. Newly described species include: Goniosoma capixaba; G. apoain; Pyatan insperatum DaSilva, Stefanini-Jim & Gnaspini; Serracutisoma pseudovarium; S. fritzmuelleri; S. guaricana; Heteromitobates anarchus; H. harlequin; H. alienus; Mitogoniella taquara; M. unicornis; and Acutisoma coriaceum. New combinations include: Goniosoma macracanthum (Mello-Leitao, 1922); G. unicolor (Mello-Leitao, 1932); G. carum (Mello-Leitao, 1936); Serracutisoma proximum (Mello-Leitao, 1922); S. banhadoae (Soares & Soares, 1947); S. molle (Mello-Leitao, 1933); S. thalassinum (Simon, 1879); S. catarina (Machado, Pinto-da-Rocha & Ramires, 2002); S. inerme (Mello-Leitao, 1927); S. spelaeum (MelloLeitao, 1933); Heteromitobates inscriptus (Mello-Leitao, 1922); H. albiscriptus (Mello-Leitao, 1932); Mitogoniella modesta (Perty, 1833); and M. badia (Koch, 1839). Reestablished combinations include: Mitogoniella indistincta MelloLeitao, 1936 and Acutisoma longipes Roewer, 1913. New speci. c synonyms include: Acutisomella cryptoleuca = Acutisomella intermedia = Goniosoma junceum = Goniosoma patruele = Goniosoma xanthophthalmum = Metalyogoniosoma unum = Goniosoma varium, Goniosoma geniculatum = Goniosoma venustum; Goniosomella perlata = Progoniosoma minense = Goniosoma vatrax, Glyptogoniosoma perditum = Progoniosoma cruciferum = Progoniosoma tijuca = Goniosoma dentipes; Leitaoius iguapensis = Leitaoius viridifrons = Serracutisoma proximum; Acutisoma marumbicola = Acutisoma patens = Serracutisoma thalassinum; Progoniosoma tetrasetae = Serracutisoma inerme; and Acutisoma monticola = Leitaoius nitidissimus = Leitaoius xanthomus = Mitogoniella mutila = Acutisoma longipes. The following species are considered species inquirenda: Goniosoma lepidum Gervais, 1844; G. monacanthum Gervais, 1844; G. obscurum Perty, 1833; G. versicolor Perty, 1833; and Mitogoniella badia (Koch, 1839). The monotpic genus Goniosomoides Mello-Leitao, 1932 (and its species, G. viridans Mello-Leitao, 1932) is removed from Goniosomatinae and considered incertae sedis.

Flavonoids and the taxonomy of Camarea (Malpighiaceae)

Camarea is a South-American endemic genus comprising eight species. In the present work leaf flavonoids of seven species of Camarea were identified, aiming to evaluate the usefulness of their distribution as a taxonomic aid. A total of 12 flavonoids were isolated and identified. Free aglycones, such as apigenin, chrysoeriol, kaempferol and quercetin, as well as 7-O-glycosides of apigenin and luteolin, 3-O-glycosides of kaempferol and quercetin were identified. Flavonoid distribution in Camarea species, taking into account aglycones and aglycone moieties of glycosides, was used to obtain a phenogram of chemical affinities. Apigenin, chrysoeriol and kaempferol were the main discriminating characters for links establishment. The resultant tree suggests the links: 1) Camarea hirsuta, Camarea affinis and C. affinis x C. hirsuta; 2) Camarea elongata and Camarea axillaris; 3) Camarea sericea and Camarea humifusa. The results are in agreement with morphological similarities and disagree with several points of n-alkane evidence. The results support the recognition of Camarea triphylla as synonymy of C axillaris. (C) 2009 Elsevier Ltd. All rights reserved.

Evolutionary patterns in neotropical Helieae (Gentianaceae): evidence from morphology, chloroplast and nuclear DNA sequences

Parsimony-based phylogenetic analyses of the neotropical tribe Helieae (Gentianaceae) are presented, including 22 of the 23 genera and 60 species. This study is based on data from morphology, palynology, and seed micromorphology (127 structural characters), and DNA sequences (matK, trnL intron, ITS). Phylogenetic reconstructions based on ITS and morphology provided the greatest resolution, morphological data further helping to tentatively place several taxa for which DNA was not available (Celiantha, Lagenanthus, Rogersonanthus, Roraimaea, Senaea, Sipapoantha, Zonanthus). Celiantha, Prepusa and Senaea together appear as the sister clade to the rest of Helieae. The remainder of Helieae is largely divided into two large subclades, the Macrocarpaea subclade and the Symbolanthus subclade. The first subclade includes Macrocarpaea, sister to Chorisepalum, Tochia, and Zonanthus. Irlbachia and Neblinantha are placed as sisters to the Symbolanthus subclade, which includes Aripuana, Calolisianthus, Chelonanthus, Helia, Lagenanthus, Lehmanniella, Purdieanthus, Rogersonanthus, Roraimaea, Sipapoantha, and symbolanthus. Generic-level polyphyly is detected in Chelonanthus and Irlbachia. Evolution of morphological characters is discussed, and new pollen and seed characters are evaluated for the first time in a combined morphological-molecular phylogenetic analysis.

Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher

Most Neotropical lowland forest taxa occur exclusively on one side of the Andes despite the availability of appropriate habitat on both sides. Almost all molecular phylogenies and phylogenetic analyses of species assemblages (i.e. area cladograms) have supported the hypothesis that Andean uplift during the Late Pliocene created a vicariant barrier affecting lowland lineages in the region. However, a few widespread plant and animal species occurring in lowland forests on both sides of the Andes challenge the generality of this hypothesis. To understand the role of the Andes in the history of such organisms, we reconstructed the phylogeographic history of a widespread Neotropical flycatcher (Mionectes oleagineus) in the context of the other four species in the genus. A molecular phylogeny based on nuclear and mitochondrial sequences unambiguously showed an early basal split between montane and lowland Mionectes. The phylogeographic reconstruction of lowland taxa revealed a complex history, with multiple cases in which geographically proximate populations do not represent sister lineages. Specifically, three populations of M. oleagineus west of the Andes do not comprise a monophyletic clade; instead, each represents an independent lineage with origins east of the Andes. Divergence time estimates suggest that at least two cross-Andean dispersal events post-date Andean uplift.

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.

Do individuals in better condition survive for longer? Field survival estimates according to male alternative reproductive tactics and sex

There is a gap in terms of the supposed survival differences recorded in the field according to individual condition. This is partly due to our inability to assess survival in the wild. Here we applied modern statistical techniques to field-gathered data in two damselfly species whose males practice alternative reproductive tactics (ARTs) and whose indicators of condition in both sexes are known. In Paraphlebia zoe, there are two ART: a larger black-winged (BW) male which defends mating territories and a smaller hyaline-winged (HW) male that usually acts as a satellite. In this species, condition in both morphs is correlated with body size. In Calopteryx haemorrhoidalis, males follow tactics according to their condition with males in better condition practicing a territorial ART. In addition, in this species, condition correlates positively with wing pigmentation in both sexes. Our prediction for both species was that males practicing the territorial tactic will survive less longer than males using a nonterritorial tactic, and larger or more pigmented animals will survive for longer. In P. zoe, BW males survived less than females but did not differ from HW males, and not necessarily larger individuals survived for longer. In fact, size affected survival but only when group identity was analysed, showing a positive relationship in females and a slightly negative relationship in both male morphs. For C. haemorrhoidalis, survival was larger for more pigmented males and females, but size was not a good survival predictor. Our results partially confirm assumptions based on the maintenance of ARTs. Our results also indicate that female pigmentation, correlates with a fitness component - survival - as proposed by recent sexual selection ideas applied to females.

Evolutionary history of Ramphastos toucans: Molecular phylogenetics, temporal diversification, and biogeography

The toucan genus Ramphastos (Piciformes: Ramphastidae) has been a model in the formulation of Neotropical paleobiogeographic hypotheses. Weckstein (2005) reported on the phylogenetic history of this genus based on three mitochondrial genes, but some relationships were weakly supported and one of the subspecies of R. vitellinus (citreolaemus) was unsampled. This study expands on Weckstein (2005) by adding more DNA sequence data (including a nuclear marker) and more samples, including R v. citreolaemus. Maximum parsimony, maximum likelihood, and Bayesian methods recovered similar trees, with nodes showing high support. A monophyletic R. vitellinus complex was strongly supported as the sister-group to R. brevis. The results also confirmed that the southeastern and northern populations of R. vitellinus ariel are paraphyletic. X v. citreolaemus is sister to the Amazonian subspecies of the vitellinus complex. Using three protein-coding genes (COI, cytochrome-b and ND2) and interval-calibrated nodes under a Bayesian relaxed-clock framework, we infer that ramphastid genera originated in the middle Miocene to early Pliocene, Ramphastos species originated between late Miocene and early Pleistocene, and intra-specific divergences took place throughout the Pleistocene. Parsimony-based reconstruction of ancestral areas indicated that evolution of the four trans-Andean Ramphastos taxa (R. v. citreolaemus, R. a. swainsonii, R. brevis and R. sulfuratus) was associated with four independent dispersals from the cis-Andean region. The last pulse of Andean uplift may have been important for the evolution of R. sulfuratus, whereas the origin of the other trans-Andean Ramphastos taxa is consistent with vicariance due to drying events in the lowland forests north of the Andes. Estimated rates of molecular evolution were higher than the ""standard"" bird rate of 2% substitutions/site/million years for two of the three genes analyzed (cytochrome-b and ND2). (C) 2009 Elsevier Inc. All rights reserved.

A set of polymorphic microsatellite loci for Vriesea gigantea and Alcantarea imperialis (Bromeliaceae) and cross-amplification in other bromeliad species

Fifteen polymorphic microsatellite markers were isolated and characterized in two species of Bromeliaceae: Vriesea gigantea and Alcantarea imperialis. The number of alleles observed for each locus ranged from three to 16. The loci will be used for studies of the genetic structure of natural populations, reproductive biology, and evolutionary relationships among and within these genera. A cross-amplification test in 22 taxa suggests that the markers will be useful for similar applications in numerous other bromeliad species.

Evolutionary and biogeographic history of the subfamily Neoplecostominae (Siluriformes: Loricariidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Characterization of invasive fish species in a river transposition region: evolutionary chromosome studies in the genus Hoplias (Characiformes, Erythrinidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The shared influence of phylogeny and ecology on the reproductive patterns of Myrteae (Myrtaceae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evaluation of the floral vasculature of the Janusia, Mascagnia and Tetrapterys species as a tool to explain the decrease of floral organs in Malpighiaceae

The family Malpighiaceae is considered monophyletic, but the intra-family classification is conflicting. Analyses of floral vasculature allow the identification of reductions, connations and adnations and can even reveal evolutionary steps prior to current floral morphology. The present work analysed the floral vasculature of Janusia mediterranea, Mascagnia cordifolia and Tetrapterys chamaecerasifolia using material processed by traditional methods for light microscopy. A general pattern was observed of three bundle traces supplying each sepal and one trace per petal and stamen; Mascagnia is an exception, as its eglandular sepal has only a median trace but shares lateral traces with adjacent sepals. No dorsal traces are emitted to the carpels; however, three intercarpellary complexes are emitted that divide into six ventral bundles, supplying the ovule. Mascagnia demonstrates connation between the anterior and adjacent sepal glands; reductions of the anterior sepal glands were registered in Tetrapterys and Janusia. This work reveals two distinct processes for gland loss in non-related groups of the family that resulted in similar present appearances. Our evaluation of the number of calyx glands and the processes of glandular loss in species with less than ten glands improves our understanding of the evolution of calyx glands in Malpighiaceae. © 2013 Elsevier GmbH.

Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes

Background: Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes. Results: Physical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6. Conclusion: Our data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins. © 2013 Schneider et al.; licensee BioMed Central Ltd.

Population biology of Excirolana armata (Dana, 1853) (Isopoda, Cirolanidae) on an exposed sandy beach in Southeastern Brazil

The reproductive biology and population dynamics of the cirolanid isopod Excirolana armata (Dana, 1853) were analysed through monthly samples from December 2003 to November 2005 on Una beach, Sao Paulo state (24 degrees S), in Southeastern Brazil. Sampling was performed along three transects established from the base of foredunes to the waterline. On Una beach, E. armata showed continuous reproduction with higher abundances of ovigerous females in winter and spring (July-November) with a higher peak of juveniles in spring (November 2004). The fecundity ranged from 2 to 18 eggs/embryos per female, depending on the female length. The incubation period was estimated as 2 months. The life span of males and females was nearly 1 year. The short life span and the high energetic expenditure inherent to reproduction with maternal care, probably kept females from producing more than one brood in their lifetime. When comparing the population of E. armata on Una beach (24 degrees S) with populations in Southern Brazil (32 degrees S), Uruguay (34 degrees S) and Argentina (36 degrees S), it was verified that several biological population traits (length of the smallest juvenile, length of the largest individual, length of the smallest and largest ovigerous females, range of fecundity and life span) tended to increase at higher latitudes, whereas other traits (instantaneous rate of mortality and the curvature parameter of von Bertalanffy growth function) tended to decrease. However, comparing E. armata on Una beach (24 degrees S) with a population situated at a close latitude (25 degrees S), unexpected differences in relation to population structure and to growth demonstrated and reinforced the importance of density-dependent factors over life history traits of E. armata on dissipative beaches.