Abstract Delimiting species is challenging in recently diverged species, and adaptive radiation is fundamental to understanding the evolutionary processes because it requires multiple ecological opportunities associated with adaptation to biotic and abiotic environments. The young Petunia genus (Solanaceae) is an excellent opportunity to study speciation because of its association with pollinators and unique microenvironments. This study evaluated the phylogenetic relationships among a Petunia clade species with different floral syndromes that inhabit several environments. We based our work on multiple individuals per lineage and employed nuclear and plastid phylogenetic markers and nuclear microsatellites. The phylogenetic tree revealed two main groups regarding the elevation of the distribution range, whereas microsatellites showed high polymorphism-sharing splitting lineages into three clusters. Isolation by distance, migration followed by new environment colonization, and shifts in floral syndrome were the motors for lineage differentiation, including infraspecific structuring, which suggests the need for taxonomic revision in the genus. environments Solanaceae (Solanaceae microenvironments range polymorphismsharing polymorphism sharing clusters distance colonization differentiation structuring

Abstract This study presents the first complete mitogenome of the Brazilian Atlantic bushmaster Lachesis with insights into snake evolution. The total length was 17,177 bp, consisting of 13 PCGs, 22 tRNAs, two rRNAs and a duplicate control region (CRs). Almost all genes were encoded by the heavy-strand, except for the ND6 gene and eight tRNAs (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser[TGA anticodon], Glu, Pro). Only ATG, ATA, and ATC were starting codons for protein-coding sequences. Stop codons mainly were TAA, AGA, AGG, and TAG; whereas ND1, ND3, and CYTB terminated with incomplete stop codons. Phylogeny retrieved Lachesis within the Crotalinae as the sister group of Agkistrodon; and the Lachesis+Agkistrodon clade as the sister group of (Sistrurus+Crotalus)+Bothrops. The tree supports Crotalinae, Viperinae, and Azemiopinae in the Viperidae family, being sister taxa of Colubridae+(Elapidae+Psammophiidae). The mean genetic distance across 15 snake families and 57 nucleotide sequences was 0.37. The overall mean value of genetic distance across the Crotalinae was 0.23, with Lachesis muta exhibiting the shortest distance of 0.2 with Agkistrodon piscivorus, Protobothrops dabieshanensis and P. flavoviridis and the greatest 0.25 with Gloydius blomhoffii, Trimeresurus albolabris, S. miliarius, and Deinagkistrodon acutus. The complete Atlantic L. muta mitogenome presented herein is only the third annotated mitogenome from more than 430 described Brazilian snake species. evolution 17177 17 177 17,17 bp 1 PCGs 2 CRs. CRs . (CRs) heavystrand, heavystrand heavy strand, strand heavy-strand ND tRNAGln, tRNAGln tRNA Gln, Gln (tRNA-Gln Ala Asn Cys Tyr SerTGA Ser TGA anticodon, anticodon , anticodon] Glu Pro. Pro Pro) ATG ATA proteincoding protein coding TAA AGA AGG TAG ND1 ND3 LachesisAgkistrodon Sistrurus+Crotalus+Bothrops. SistrurusCrotalusBothrops Sistrurus+Crotalus +Bothrops. Sistrurus Crotalus Bothrops (Sistrurus+Crotalus)+Bothrops Viperinae family Colubridae+Elapidae+Psammophiidae. ColubridaeElapidaePsammophiidae Colubridae+ Elapidae+Psammophiidae Colubridae Elapidae Psammophiidae Colubridae+(Elapidae+Psammophiidae) 5 037 0 37 0.37 023 23 0.23 02 0. piscivorus P 025 25 blomhoffii albolabris S miliarius acutus L 43 species 1717 17,1 (CRs Sistrurus+Crotalus+Bothrops SistrurusCrotalus +Bothrops Colubridae+Elapidae+Psammophiidae ElapidaePsammophiidae Colubridae+(Elapidae+Psammophiidae 03 3 0.3 4 171 17,

Abstract Genotypes of 10 microsatellite loci of 420 humpback whales from the Southwestern Atlantic Ocean population were used to estimate for the first time its contemporary effective (Ne) and census (Nc) population sizes and to test the genetic effect of commercial whaling. The results are in agreement with our previous studies that found high genetic diversity for this breeding population. Using an approximate Bayesian computation approach, the scenario of constant Ne was significantly supported over scenarios with moderate to strong size changes during the commercial whaling period. The previous generation Nc (Ne multiplied by 3.6), which should corresponds to the years between around 1980 and 1990, was estimated between ~2,600 and 6,800 whales (point estimate ~4,000), and is broadly compatible with the recent abundance surveys extrapolated to the past using a growth rate of 7.4% per annum. The long-term Nc in the constant scenario (point estimate ~15,000) was broadly compatible (considering the confidence interval) with pre-whaling catch records estimates (point estimate ~25,000). Overall, our results shown that the Southwestern Atlantic Ocean humpback whale population is genetically very diverse and resisted well to the strong population reduction during commercial whaling.

Abstract In spite of many genetic studies that contributed for a deep knowledge about the peopling of the Americas, no consensus has emerged about important parameters such as the effective size of the Native Americans founder population. Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population.

Abstract Recently, it has been suggested that internal transcribed spacer (ITS) sequences are under selective constraints to preserve their secondary structure. Here, we investigate the patterns of the ITS nucleotide and secondary structure conservation across the Passiflora L. genus to evaluate the potential use of secondary structure data as a helpful tool for the alignment in taxonomically complex genera. Considering the frequent use of ITS, this study also presents a perspective on future analyses in other plant groups. The ITS1 and ITS2 sequences presented significant differences for mean values of the lowest energy state (LES) and for number of hairpins in different Passiflora subgenera. Statistical analyses for the subgenera separately support significant differences between the LES values and the total number of secondary structures for ITS. In order to evaluate whether the LES values of ITS secondary structures were related to selective constraints, we compared these results among 120 ITS sequences from Passiflora species and 120 randomly generated sequences. These analyses indicated that Passiflora ITS sequences present characteristics of a region under selective constraint to maintain the secondary structure showing to be a promising tool to improve the alignments and identify sites with non-neutral substitutions or those correlated evolutionary steps.

As part of a long-term investigation on the evolution of Passiflora L., we investigated the divergence ages of the genus and diversification of its subgenera, relating them with biogeographical and/or historical events, and other characteristics of this taxon. The main aim of the present work was to evaluate the biogeographic distribution of this genus to better understand its evolutionary history. This is the first time that representatives from South American and Old World Passifloraceae genera have been studied as a group comprising a total of 106 widely distributed species, with representative samples of the four suggested subgenera. Seven DNA regions were studied, comprising 7,431 nucleotides from plastidial, mitochondrial and nuclear genomes. Divergence time estimates were obtained by using a Bayesian Markov Chain Monte Carlo method and a random local clock model for each partition. Three major subgenera have been shown to be monophyletic and here we are proposing to include another subgenus in the Passiflora infrageneric classification. In general, divergence among the four subgenera in Passiflora is very ancient, ranging from ~32 to ~38 Mya, and Passifloraceae seems to follow a biogeographic scenario proposed for several plant groups, originating in Africa, crossing to Europe/Asia and arriving in the New World by way of land bridges. Our results indicated that Passiflora ancestors arrived in Central America and diversified quickly from there, with many long distance dispersion events.

The discovery and characterization of informative intraspecific genetic markers is fundamental for evolutionary and conservation genetics studies. Here, we used nuclear ribosomal ITS sequences to access intraspecific genetic diversity in 23 species of the genus Passiflora L. Some degree of variation was detected in 21 of these. The Passiflora and Decaloba (DC.) Rchb. subgenera showed significant differences in the sizes of the two ITS regions and in GC content, which can be related to reproductive characteristics of species in these subgenera. Furthermore, clear geographical patterns in the spatial distribution of sequence types were identified in six species. The results indicate that ITS may be a useful tool for the evaluation of intraspecific genetic variation in Passiflora.

Este trabalho apresenta uma análise filogenética molecular das serpentes avançadas (Caenophidia), realizada com base na análise de seqüências de dois genes mitocondriais (rRNA 12S e 16S) e de um gene nuclear (c-mos; 1681 pares de bases no total) e com 131 táxons terminais, amostrados a partir das principais linhagens de Caenophidia, com ênfase nos xenodontíneos neotropicais. A análise de parcimônia dos dados mediante otimização direta resultou em uma árvore filogenética bem resolvida que, por um lado, corrobora alguns dos clados identificados em análises anteriores e por outro, estabelece novas hipóteses sobre a composição de outros grupos e do relacionamento entre eles. Os principais resultados obtidos salientam: (1) a alocação de Achrochordus, xenodermatídeos e pareatídeos como grupos externos sucessivos de todos os demais cenofídios (incluindo viperídeos, elapídeos, atractaspidídeos e todos os grupos de "colubrídeos"); (2) que, em relação ao último grupo, viperídeos e homalopsídeos podem ser considerados como clados irmãos dos demais; (3) a existência, dentro do grande grupo dos cenofidia, dos seguintes sub-grupos: psamophiídeos afro-asiáticos (incluindo o gênero Mimophis, de Madagascar), Elapidae (incluindo os hidrophiíneos, mas excluindo Homoroselaps, associado aos atractaspidídeos), Pseudoxyrhophiinae, Colubrinae, Natricinae, Dipsadinae e Xenodontinae. A análise sugere algumas alterações de cunho taxonômico dentro dos xenodontíneos, incluindo realocações genéricas para Alsophis elegans, Liophis amarali e modificações substanciais em relação a Xenodontini e à radiação dos xenodontíneos das Antilhas. Também é a aqui apresentada uma revisão da classificação de Caenophidia, baseada inicialmente nas análises moleculares, mas provendo diagnoses morfológicas para muitos dos clados incluídos, realçando os grupos que ainda merecem atenção especial no futuro. São aqui nomeados originalmente dois grandes clados dentro de Caenophidia, uma nova subfamília dentro de Dipsadidae e, dentro de Xenodontinae, cinco novas tribos e seis novos gêneros, sendo ainda dois gêneros revalidados. Os gêneros Xenoxybelis e Pseudablabes são considerados sinônimos de Philodryas; Erythrolamprus, sinônimo de Liophis; Lystrophis e Waglerophis, sinônimos de Xenodon.

We present a molecular phylogenetic analysis of caenophidian (advanced) snakes using sequences from two mitochondrial genes (12S and 16S rRNA) and one nuclear (c-mos) gene (1681 total base pairs), and with 131 terminal taxa sampled from throughout all major caenophidian lineages but focussing on Neotropical xenodontines. Direct optimization parsimony analysis resulted in a well-resolved phylogenetic tree, which corroborates some clades identified in previous analyses and suggests new hypotheses for the composition and relationships of others. The major salient points of our analysis are: (1) placement of Acrochordus, Xenodermatids, and Pareatids as successive outgroups to all remaining caenophidians (including viperids, elapids, atractaspidids, and all other "colubrid" groups); (2) within the latter group, viperids and homalopsids are sucessive sister clades to all remaining snakes; (3) the following monophyletic clades within crown group caenophidians: Afro-Asian psammophiids (including Mimophis from Madagascar), Elapidae (including hydrophiines but excluding Homoroselaps), Pseudoxyrhophiinae, Colubrinae, Natricinae, Dipsadinae, and Xenodontinae. Homoroselaps is associated with atractaspidids. Our analysis suggests some taxonomic changes within xenodontines, including new taxonomy for Alsophis elegans, Liophis amarali, and further taxonomic changes within Xenodontini and the West Indian radiation of xenodontines. Based on our molecular analysis, we present a revised classification for caenophidians and provide morphological diagnoses for many of the included clades; we also highlight groups where much more work is needed. We name as new two higher taxonomic clades within Caenophidia, one new subfamily within Dipsadidae, and, within Xenodontinae five new tribes, six new genera and two resurrected genera. We synonymize Xenoxybelis and Pseudablabes with Philodryas; Erythrolamprus with Liophis; and Lystrophis and Waglerophis with Xenodon.

O gênero Ixinandria foi descrito em 1979 para incluir I. steinbachi do alto rio Juramento no norte da Argentina e I. montebelloi do alto rio Bermejo no sul da Bolívia. Utilizamos análise morfométrica multivarida (Análise de Componentes Principais) e uma comparação molecular do gene Citocromo Oxidase I para investigar a variação entre populações distintas da área de distribuição de ambas as espécies. Concluímos que as populações não são significativamente distintas e não merecem reconhecimento como espécies separadas, e colocamos Ixinandria montebelloi na sinonímia de I. steinbachi.

The genus Ixinandria was described in 1979 to include I. steinbachi from the upper río Juramento in northern Argentina and I. montebelloi from the upper río Bermejo in southern Bolivia. We used a multivariate morphometric analysis (Principal Components Analysis) and a molecular comparison of the Cytochrome Oxidase I gene to investigate variation among distinct populations from the known distribution range of both species. We conclude that the populations are not significantly distinct and do not deserve separate species recognition, and we place I. montebelloi in the synonymy of I. steinbachi.

Several genomes of mycoplasmas have been sequenced and here we tried to retrieve the evolutionary relationships of nine species using a phylogenomic approach. Several methods were used to build phylogenetic trees based on protein sequence information, gene-order, and gene-content. We also utilized datasets composed of individual and concatenated sets of orthologous proteins, as well as with reduced unreliable alignment regions. Most of our results converge to a single topology, except for the trees built with both the maximum parsimony method and with the gene-order dataset. The gene-content dataset presented trees consistent with most nodes of the convergent tree, but in the gene-order dataset most internal branches were clearly saturated and unreliable. The topological difference between the trees obtained by the diverse methods could not be explained by regions with unreliable alignments or attributed to horizontal gene transfer among the genomes. It is possible that the incongruence between the methods could be associated with their differential sensibility in relation to certain evolutionary factors. Further analysis using other empirical genomic datasets would be necessary in order to better understand the basis of such conflicts.

The phylum Placozoa, represented by its single species Trichoplax adhaerens, has always been considered one of the most basal animal clades due to its low morphological complexity. However, despite its importance, the phylogenetic position of the Placozoa remains uncertain, as does the relationships between the basal metazoans. We sequenced the nearly complete large subunit (LSU) of the T. adhaerens rRNA gene together with the small subunit (SSU) rRNA and used several methods to infer the phylogenetic position of Placozoa and the relationships between the basal animal phyla. The phylogenetic trees obtained from the LSU, SSU and SSU + LSU datasets support monophyly of all basal metazoan phyla, except the Porifera. However, the relationships between all these phyla were not consistently resolved due to a strong conflict between the LSU and SSU phylogenetic signals. The hypotheses that Placozoa is a derived Cnidaria or the most basal metazoan were not supported by our data. Moreover, our analyses suggests that Placozoa is most likely the sister group of Cnidaria and/or Bilateria.

O vírus linfotrópico de células T-humanas do tipo II (HTLV-II) é identificado em muitos grupos de ameríndios. No Brasil, tem sido encontrado em indivíduos da população urbana, bem como em índios oriundos da região Amazônica. Os Índios Guaraní, do Sul do país, foram investigados para infecção por HTLV-I/II. Três indivíduos, oriundos de uma amostra de 52 índios, demonstraram sororeatividade para HTLV-II (ensaio imunoenzimático e Western blot). Este estudo preliminar foi o primeiro a identificar a presença de infecção por HTLV-II em ameríndios do Sul do Brasil.

Human T-cell lymphotropic virus type II (HTLV-II) is found in many New World Indian groups on the American continent. In Brazil, HTLV-II has been found among urban residents and Indians in the Amazon region, in the North. Guaraní Indians in the South of Brazil were studied for HTLV-I/II infection. Among 52 individuals, three (5.76%) showed positive anti-HTLV-II antibodies (enzyme-linked immunosorbent assay and Western blot). This preliminary report is the first seroepidemiological study showing HTLV-II infection among Indians in the South of Brazil.

O vírus linfotrópico de células T-humanas do tipo II (HTLV-II) é identificado em muitos grupos de ameríndios. No Brasil, tem sido encontrado em indivíduos da população urbana, bem como em índios oriundos da região Amazônica. Os Índios Guaraní, do Sul do país, foram investigados para infecção por HTLV-I/II. Três indivíduos, oriundos de uma amostra de 52 índios, demonstraram sororeatividade para HTLV-II (ensaio imunoenzimático e Western blot). Este estudo preliminar foi o primeiro a identificar a presença de infecção por HTLV-II em ameríndios do Sul do Brasil.

Human T-cell lymphotropic virus type II (HTLV-II) is found in many New World Indian groups on the American continent. In Brazil, HTLV-II has been found among urban residents and Indians in the Amazon region, in the North. Guaraní Indians in the South of Brazil were studied for HTLV-I/II infection. Among 52 individuals, three (5.76%) showed positive anti-HTLV-II antibodies (enzyme-linked immunosorbent assay and Western blot). This preliminary report is the first seroepidemiological study showing HTLV-II infection among Indians in the South of Brazil.

The genes encoding 13 classes of pathogenesis-related (PR) proteins were examined for positive selection using maximum-likelihood (ML) models of codon substitution. The study involved 194 sequences from 54 species belonging to 37 genera. Although the sizes of the sequences examined varied from 237 bp for PR12 to 1,110 bp for PR7, most classes (9 out of 13) contained sequences made up of more than 400 nucleotides. Signs of positive selection were obtained for sites in PR proteins 4, 6, 8, 9 and 15 using an ML-based Bayesian method and likelihood ratio tests. These results confirm the importance of positive selection in proteins related to defense mechanisms already observed in a wide array of organisms.