Impacts of climatic factors on evolution of molecular diversity and the natural distribution of wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii)

Natural distributions of most freshwater taxa are restricted geographically, a pattern that reflects dispersal limitation. Macrobrachium rosenbergii is unusual because it occurs naturally in rivers from near Pakistan in the west, across India and Bangladesh to the Malay Peninsula, and across the Sunda Shelf and Indonesian archipelago to western Java. Individuals cannot tolerate full marine conditions, so dispersal between river drainage basins must occur at limited geographical scales when ecological or climatic factors are favorable. We examined molecular diversity in wild populations of M. rosenbergii across its complete natural range to document patterns of diversity and to relate them to factors that have driven evolution of diversity in this species. We found 3 clades in the mitochondrial deoxyribonucleic acid (mtDNA) data set that corresponded geographically with eastern, central, and western sets of haplotypes that last shared a common ancestor 1 × 106 y ago. The eastern clade was closest to the common ancestor of all 3 clades and to the common ancestor with its congener, Macrobrachium spinipes, distributed east of Huxley's Line. Macrobrachium rosenbergii could have evolved in the western Indonesian archipelago and spread westward during the early to mid-Pleistocene to India and Sri Lanka. Additional groups identified in the nuclear DNA data set in the central and western clades probably indicate secondary contact via dispersal between regions and modern introductions that have mixed nuclear and mtDNA genes. Pleistocene sea-level fluctuations can explain dispersal across the Indonesian archipelago and parts of mainland southeastern Asia via changing river drainage connections in shallow seas on wide continental shelves. At the western end of the modern distribution where continental shelves are smaller, intermittent freshwater plumes from large rivers probably permitted larval dispersal across inshore areas of lowered salinity.

Morphological and molecular diversity of Colletotrichum spp. causing pepper spot and anthracnose of lychee (Litchi chinensis) in Australia

Since the 1980s a new disease has been affecting Australian lychee. Pepper spot appears as small, black superficial lesions on fruit, leaves, petioles and pedicels and is caused by Colletotrichum gloeosporioides, the same fungus that causes postharvest anthracnose of lychee fruit. The aim of this study was to determine if a new genotype of C.gloeosporioides is responsible for the pepper spot symptom. Morphological assessments, arbitrarily-primed PCR (ap-PCR) and DNA sequencing studies did not differentiate isolates of C.gloeosporioides from anthracnose and pepper spot lesions. The ap-PCR identified 21 different genotypes of C.gloeosporioides, three of which were predominant. A specific genotype identified using ap-PCR was associated with the production of the teleomorph in culture. Analysis of sequence data of ITS and -tubulin regions of representative isolates did not group the lychee isolates into a monophyletic clade; however, given the majority of the isolates were from one of three genotypes found using ap-PCR, the possibility of a lychee specific group of C.gloeosporioides is discussed.

Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination – a driving force in the emergence of new strains

In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.

Temporal Stability of Molecular Diversity Measures in Natural Populations of Drosophila pseudoobscura and Drosophila persimilis

Many molecular ecological and evolutionary studies sample wild populations at a single point in time, failing to consider that data they collect represents genetic variation from a potentially unrepresentative snapshot in time. Variation across time in genetic parameters may occur quickly in species that produce multiple generations of offspring per year. However, many studies of rapid contemporary microevolution examine phenotypic trait divergence as opposed to molecular evolutionary divergence. Here, we compare genetic diversity in wild caught populations of Drosophila persimilis and D. pseudoobscura collected 16 years apart at the same time of year and same site at four X-linked and two mitochondrial loci to assess genetic stability. We found no major changes in nucleotide diversity in either species, but we observed a drastic shift in Tajima’s D between D. pseudoobscura timepoints at one locus associated with the increased abundance of a set of related haplotypes. Our data also suggests that D. persimilis may have recently accelerated its demographic expansion. While the changes we observed were modest, this study reinforces the importance of considering potential temporal variation in genetic parameters within single populations over short evolutionary timescales.

Molecular diversity of the HLA-C gene identified in a Caucasian population

A DNA typing procedure, based on a two stage polymerase chain reaction-sequence-specific oligonucleotide probe (PCR-SSOP) typing strategy, has been developed and applied to DNA from 1000 healthy individuals from the Northern Ireland region. The two-stage procedure involves human leukocyte antigen (HLA-C) identification through the use of a medium resolution PCR-SSOP system, followed by four secondary group specific PCR-SSOP systems, to enable allele resolution. The PCR-SSOP systems were designed for the identification of HLA-Cw alleles with possible discrimination within exons 2 and 3 of the HLA-C gene, i.e., HLA-Cw*01-Cw*16. PCR-SSP tests were designed for the resolution of HLA-Cw*17 and -Cw*18 alleles. The systems can also be used independently of each other if selective allele resolution is required. HLA-Cw allele frequencies occuring within the Northern Ireland population have been compiled, along with estimations of HLA-B/Cw haplotype frequencies. (C) American Society for Histocompatibility and Immunogenetics, 2002. Published by Elsevier Science Inc.

Molecular diversity and transferability of integrons from wastewaters

Na evolução bacteriana, a capacidade de explorar novos ambientes e de responder a diferentes pressões selectivas deve-se principalmente à aquisição de novos genes por transferência horizontal. Integrões são elementos genéticos bacterianos que constituem sistemas naturais de captura e expressão de cassetes de genes, sendo um dos principais mecanismos bacterianos envolvidos na aquisição de resistências a antibióticos. Estudos recentes suportam a hipótese de que os ambientes naturais constituem importantes reservatórios de integrões e cassetes de genes. Uma vez que as águas residuais são descarregadas em receptores naturais, torna-se fundamental conhecer a presença e dispersão de integrões nestes ambientes, assim como a sua associação a outros elementos genéticos móveis e a genes de resistências a antibióticos. Neste trabalho, pretendeu-se avaliar a prevalência e diversidade de integrões em águas residuais de origem animal e doméstica, bem como a sua associação a plasmídeos conjugativos, usando metodologias dependentes e independentes do cultivo de microrganismos em laboratório. Os resultados obtidos sustentam assim a hipótese de que ambientes particularmente ricos em matéria orgânica, como é o caso das águas residuais, constituem ambientes propícios à presença de integrões e à ocorrência de transferência horizontal de genes de resistência a antibióticos, embora a sua prevalência e diversidade seja influenciada pelo tipo de efluente em questão. A presença de integrões em estações de tratamento de águas residuais, e em especial nos efluentes tratados, constitui assim um factor preocupante, uma vez que tal contribui para a sua disseminação e dispersão por outros ecossistemas aquáticos, nomeadamente rios e mares. Os métodos utilizados permitiram também detectar uma elevada diversidade de cassetes de genes associadas a integrões, sendo possível que algumas dessas sequências codifiquem para proteínas que desempenhem um importante papel na adaptação bacteriana às intensas pressões selectivas características deste tipo de ambientes. Assim, é possível concluir que as comunidades bacterianas presentes em águas residuais reúnem diferentes tipos de elementos geneticamente móveis que desempenham um importante papel não só na adaptação bacteriana, mas também na disseminação de determinantes genéticos de resistência para ambientes naturais. Adicionalmente, a presença de potenciais proteínas com possíveis aplicações biotecnológicas reforça a importância das águas residuais como fontes de diversidade funcional. Este trabalho incluiu também a criação e implementação da base de dados INTEGRALL, desenvolvida com o intuito de congregar informação acerca de integrões e de uniformizar a nomenclatura de cassetes de genes.

Gut Associated Lactic Acid Bacteria Isolated from the Estuarine Fish Mugil cephalus: Molecular Diversity and Antibacterial Activities against Pathogens

In the present study we address the issue on gut associated lactic acid bacteria (LAB) isolated from the intestine of estuarine fish Mugil cephalus using de Man Rogossa and Sharpe (MRS) agar. LAB isolates were identified biochemically and screened for their ability to inhibit in vitro growth of various fish, shrimp and human pathogens. Most of the LAB isolates displayed an improved antagonism against fish pathogens compared to shrimp and human pathogens. Selected representative strains displaying high antibacterial activity were identified using 16S rRNA gene sequence analysis. Of the selected strains Lactobacillus brevis was the most predominant. Four other species of Lactobacillus, Enterobacter hormaechei and Enterobacter ludwigii were also identified. It was also observed that even among same species, considerable diversity with respect to substrate utilization persisted. Considering the euryhaline nature of grey mullet (Mugil cephalus), the LAB isolated from the gut possessed good tolerance to varying salt concentrations. This finding merits further investigation to evaluate whether the isolated LAB could be used as probiotics in various fresh and sea water aquaculture

Nubbe natural products, source of molecular diversity for the design of new anticancer agents

Pós-graduação em Química - IQ

Molecular diversity of fungal and bacterial communities in the marine sponge Dragmacidon reticulatum

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

Molecular diversity of Primula apennina and phylogeny of Primula Subsection Euauricula

Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations representative of the species distribution range. High levels of genetic diversity were revealed both at population (PPB = 75.92%, HS = 0.204, Hpop = 0.319) and at species level (PPB = 96.95%, HT = 0.242, Hsp = 0.381). Nei gene diversity statistics (15.7%), Shannon diversity index (16.3%) and AMOVA (14%) detected a moderate level of interpopulation diversity. Principal coordinate and bayesian analyses clustered the populations in three major groups along a geographic gradient. The correlation between genetic and geographic distances was positive (Mantel test, r = 0.232). All together, these analyses revealed a weak but significant spatial genetic structure in P. apennina, with gene flow acting as a homogenizing force that prevents a stronger differentiation of populations. Conservation measures are suggested based on the observed pattern of genetic variability. P. apennina belongs to Primula subsect. Euauricula which includes 15 species distributed on the whole Alps and Apennines. A phylogenetic analysis was carried out using AFLP markers in order both to clarify the relationships among the species of subsection Euauricula that remained unresolved in previous works and to make some hypoteses on their evolutive dynamics. NJ, PCO and BAPS analyses strongly confirmed the monophyly of P. subsect. Euauricula and all the species form strongly supported clades. NJ tree topology suggested a simultaneous fragmentations of ancestral species in a large number of isolated populations that survived in refugia along the unglaciated margins of the Alps in response to the Pleistocene climatic oscillations.

Antibiotic susceptibility and molecular diversity of Bacillus anthracis strains in Chad: detection of a new phylogenetic subgroup

We genotyped 15 Bacillus anthracis isolates from Chad, Africa, using multiple-locus variable-number tandem repeat analysis and three additional direct-repeat markers. We identified two unique genotypes that represent a novel genetic lineage in the A cluster. Chadian isolates were susceptible to 11 antibiotics and free of 94 antibiotic resistance genes.