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.

Conventional and ultrastructural analyses of the chromosomes of Discocyrtus pectinifemur (Opiliones, Laniatores, Gonyleptidae)

Among the Opiliones, species of the suborders Cyphophthalmi, Eupnoi, Dyspnoi and Laniatores have shown very diverse diploid chromosome numbers. However, only certain Eupnoi species exhibit XY/XX and ZZ/ZW sex chromosome systems. Considering the scarcity of karyotypical information and the absence of structurally identifiable sex chromosomes in the suborder Laniatores, we decided to analyse the chromosomes and bivalents of Discocyrtus pectinifemur (Gonyleptidae) to identify possible sex differences. Testicular cells examined under light microscopy showed it high diploid number, 2n = 88, meta/submetacentric chromosome morphology and a nucleolar organizer region on pair 35. Prophase I microspreading observed in transmission electron microscopy exhibited 44 synaptonemal complexes with similar electron density and thickness. The total and regular synapsis between the chromosomes of the bivalents was also noted in pachytene nuclei. Male mitotic and meiotic chromosomes revealed no distinct characteristic that could be related to the occurrence of heteromorphic sex chromosomes. Evolutionary trends of chromosome differentiation in the four suborders of Opiliones are discussed here.

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.

The genus Coleodactylus (Sphaerodactylinae, Gekkota) revisited: A molecular phylogenetic perspective

Nucleotide sequence data from a mitochondrial gene (16S) and two nuclear genes (c-mos, RAG-1) were used to evaluate the monophyly of the genus Coleodactylus, to provide the first phylogenetic hypothesis of relationships among its species in a cladistic framework, and to estimate the relative timing, of species divergences. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the combined data sets retrieved Coleodactylus as a monophyletic genus, although weakly Supported. Species were recovered as two genetically and morphological distinct clades, with C. amazonicus populations forming the sister taxon to the meridionalis group (C. brachystoma, C. meridionalis, C. natalensis, and C. septentrionalis). Within this group, C. septentrionalis was placed as the sister taxon to a clade comprising the rest of the species, C. meridionalis was recovered as the sister species to C. brachystoma, and C natalensis was found nested within C. meridionalis. Divergence time estimates based on penalized likelihood and Bayesian dating methods do not Support the previous hypothesis based on the Quaternary rain forest fragmentation model proposed to explain the diversification of the genus. The basal cladogenic event between major lineages of Coleodactylus was estimated to have occurred in the late Cretaceous (72.6 +/- 1.77 Mya), approximately at the same point in time than the other genera of Sphaerodactylinae diverged from each other. Within the meridionalis group, the split between C. septentrionalis and C. brachystoma + C. meridionalis was placed in the Eocene (46.4 +/- 4.22 Mya), and the divergence between C. brachystoma and C. meridionalis was estimated to have occurred in the Oligocene (29.3 +/- 4.33 Mya). Most intraspecific cladogenesis occurred through Miocene to Pliocene, and only for two conspecific samples and for C. natalensis could a Quaternary differentiation be assumed (1.9 +/- 1.3 Mya). (C) 2008 Elsevier Inc. All rights reserved.

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.

Stem anatomy of Rhipsalis (Cactaceae) and its relevance for taxonomy

Several species of the genus Rhipsalis (Cactaceae) are extremely important as ornamentals and are endangered in their natural habitat. However, only a few studies have addressed its taxonomy, morphology (including anatomy), phylogeny and evolutionary history. Consequently, the limited knowledge of the genus coupled with the problematic delimitation of species had led to problems in the identification of taxa. In the current work six species of Rhipsalis, R. cereoides, R. elliptica, R. grandiflora, R. paradoxa, R. pentaptera and R. teres were studied to evaluate the relevance of anatomical characters for the taxonomy of the genus. An anatomical characterization of the primary structure of the stem of Rhipsalis is provided highlighting the differences between species. Features of the stem epidermis are found to discriminate best between species and therefore provide clear and useful characters for the separation of species.

Neotypifications of Linnaean names in Hybanthus (Violaceae)

Current studies in South American Violaceae detected the necessity of neotypes for Viola calceolaria L. (equivalent to Hybanthus calceolaria (L.) Oken) and Viola oppositifolia L. (equivalent to Hvbanthus oppositifolius (L.) Taub.), names of species originally described in Loefling`s her Hispanicum, but without validly published names.

The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: diversification of an Atlantic Forest passerine

The increase in biodiversity from high to low latitudes is a widely recognized biogeographical pattern. According to the latitudinal gradient hypothesis (LGH), this pattern was shaped by differential effects of Late Quaternary climatic changes across a latitudinal gradient. Here, we evaluate the effects of climatic changes across a tropical latitudinal gradient and its implications to diversification of an Atlantic Forest (AF) endemic passerine. We studied the intraspecific diversification and historical demography of Sclerurus scansor, based on mitochondrial (ND2, ND3 and cytb) and nuclear (FIB7) gene sequences. Phylogenetic analyses recovered three well-supported clades associated with distinct latitudinal zones. Coalescent-based methods were applied to estimate divergence times and changes in effective population sizes. Estimates of divergence times indicate that intraspecific diversification took place during Middle-Late Pleistocene. Distinct demographic scenarios were identified, with the southern lineage exhibiting a clear signature of demographic expansion, while the central one remained more stable. The northern lineage, contrasting with LGH predictions, exhibited a clear sign of a recent bottleneck. Our results suggest that different AF regions reacted distinctly, even in opposite ways, under the same climatic period, producing simultaneously favourable scenarios for isolation and contact among populations.

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.

Head shape evolution in Tropidurinae lizards: does locomotion constrain diet?

Different components of complex integrated systems may be specialized for different functions, and thus the selective pressures acting on the system as a whole may be conflicting and can ultimately constrain organismal performance and evolution. The vertebrate cranial system is one of the most striking examples of a complex system with several possible functions, being associated to activities as different as locomotion, prey capture, display and defensive behaviours. Therefore, selective pressures on the cranial system as a whole are possibly complex and may be conflicting. The present study focuses on the influence of potentially conflicting selective pressures (diet vs. locomotion) on the evolution of head shape in Tropidurinae lizards. For example, the expected adaptations leading to flat heads and bodies in species living on vertical structures may conflict with the need for improved bite performance associated with the inclusion of hard or tough prey into the diet, a common phenomenon in Tropidurinae lizards. Body size and six variables describing head shape were quantified in preserved specimens of 23 species, and information on diet and substrate usage was obtained from the literature. No phylogenetic signal was observed in the morphological data at any branch length tested, suggesting adaptive evolution of head shape in Tropidurinae. This pattern was confirmed by both factor analysis and independent contrast analysis, which suggested adaptive co-variation between the head shape and the inclusion of hard prey into the diet. In contrast to our expectations, habitat use did not constrain or drive head shape evolution in the group.

Mitochondrial sequence data and Dipsacales phylogeny: Mixed models, partitioned Bayesian analyses, and model selection

Phylogenetic analyses of chloroplast DNA sequences, morphology, and combined data have provided consistent support for many of the major branches within the angiosperm, clade Dipsacales. Here we use sequences from three mitochondrial loci to test the existing broad scale phylogeny and in an attempt to resolve several relationships that have remained uncertain. Parsimony, maximum likelihood, and Bayesian analyses of a combined mitochondrial data set recover trees broadly consistent with previous studies, although resolution and support are lower than in the largest chloroplast analyses. Combining chloroplast and mitochondrial data results in a generally well-resolved and very strongly supported topology but the previously recognized problem areas remain. To investigate why these relationships have been difficult to resolve we conducted a series of experiments using different data partitions and heterogeneous substitution models. Usually more complex modeling schemes are favored regardless of the partitions recognized but model choice had little effect on topology or support values. In contrast there are consistent but weakly supported differences in the topologies recovered from coding and non-coding matrices. These conflicts directly correspond to relationships that were poorly resolved in analyses of the full combined chloroplast-mitochondrial data set. We suggest incongruent signal has contributed to our inability to confidently resolve these problem areas. (c) 2007 Elsevier Inc. All rights reserved.

Toward a resolution of Campanulid phylogeny, with special reference to the placement of Dipsacales

Broad-scale phylogenetic analyses of the angiosperms and of the Asteridae have failed to confidently resolve relationships among the major lineages of the campanulid Asteridae (i.e., the euasterid II of APG II, 2003). To address this problem we assembled presently available sequences for a core set of 50 taxa, representing the diversity of the four largest lineages (Apiales, Aquifoliales, Asterales, Dipsacales) as well as the smaller ""unplaced"" groups (e.g., Bruniaceae, Paracryphiaceae, Columelliaceae). We constructed four data matrices for phylogenetic analysis: a chloroplast coding matrix (atpB, matK, ndhF, rbcL), a chloroplast non-coding matrix (rps16 intron, trnT-F region, trnV-atpE IGS), a combined chloroplast dataset (all seven chloroplast regions), and a combined genome matrix (seven chloroplast regions plus 18S and 26S rDNA). Bayesian analyses of these datasets using mixed substitution models produced often well-resolved and supported trees. Consistent with more weakly supported results from previous studies, our analyses support the monophyly of the four major clades and the relationships among them. Most importantly, Asterales are inferred to be sister to a clade containing Apiales and Dipsacales. Paracryphiaceae is consistently placed sister to the Dipsacales. However, the exact relationships of Bruniaceae, Columelliaceae, and an Escallonia clade depended upon the dataset. Areas of poor resolution in combined analyses may be partly explained by conflict between the coding and non-coding data partitions. We discuss the implications of these results for our understanding of campanulid phylogeny and evolution, paying special attention to how our findings bear on character evolution and biogeography in Dipsacales.

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.

Coding behavioural data for cladistic analysis: using dynamic homology without parsimony

Many of the controversies around the concept of homology rest on the subjectivity inherent to primary homology propositions. Dynamic homology partially solves this problem, but there has been up to now scant application of it outside of the molecular domain. This is probably because morphological and behavioural characters are rich in properties, connections and qualities, so that there is less space for conflicting character delimitations. Here we present a new method for the direct optimization of behavioural data, a method that relies on the richness of this database to delimit the characters, and on dynamic procedures to establish character state identity. We use between-species congruence in the data matrix and topological stability to choose the best cladogram. We test the methodology using sequences of predatory behaviour in a group of spiders that evolved the highly modified predatory technique of spitting glue onto prey. The cladogram recovered is fully compatible with previous analyses in the literature, and thus the method seems consistent. Besides the advantage of enhanced objectivity in character proposition, the new procedure allows the use of complex, context-dependent behavioural characters in an evolutionary framework, an important step towards the practical integration of the evolutionary and ecological perspectives on diversity. (C) The Willi Hennig Society 2010.

Lapanthus (Bromeliaceae, Bromelioideae): A New Genus from the Southern Espinhaco Range, Brazil

In this paper we describe a new genus of Bromehaceae, Lapanthus, restricted to the southern portion of the Espinhaco Range, Minas Germs State, in southeastern Brazil Two new combinations to accommodate species previously described in the genera Orthophytum and cryptanthus and one new synonym are proposed Lapanthus has morphological affinities with both Cryptanthus and Orthophytum but nevertheless differs by the combination of margins of the petals ciliate, presence of lanceolate petal appendages and free stamens, and also by molecular data Cryptanthus and Orthophytum have petals entire along the margins, and the filaments of the most internal whorl are adnate to the petals Lapanthus stands out by having a pair of lanceolate petal appendages, which are almost completely adnate to the petals In Orthophytum, however, appendages are cupuhform or sacciform and they are totally absent in the genus Cryptanthus Lapanthus and Orthophytum present meiotic and mitotic chromosome numbers equal to n=25 and 2n=50, 100 and 150 respectively, while Cryptanthus presents meiotic and mitotic chromosome numbers n=17 and 2n=34, 36, 54 respectively, and this difference is considered to be an autapomorphic feature of Cryptanthus Descriptions of the genus and species, identification keys, illustrations, photographs of living specimens, and taxonomic comments are provided