Genetic and phenotypic diversity in <Emphasis Type="Italic">Burkholderia</Emphasis>: contributions by prophage and phage-like elements

Background  

Burkholderia species exhibit enormous phenotypic diversity, ranging from the nonpathogenic, soil- and water-inhabiting Burkholderia thailandensis to the virulent, host-adapted mammalian pathogen B. mallei. Genomic diversity is evident within Burkholderia species as well. Individual isolates of Burkholderia pseudomallei and B. thailandensis, for example, carry a variety of strain-specific genomic islands (GIs), including putative pathogenicity and metabolic islands, prophage-like islands, and prophages. These GIs may provide some strains with a competitive advantage in the environment and/or in the host relative to other strains.     

SIGI: score-based identification of genomic islands

Background  

Genomic islands can be observed in many microbial genomes. These stretches of DNA have a conspicuous composition with regard to sequence or encoded functions. Genomic islands are assumed to be frequently acquired via horizontal gene transfer. For the analysis of genome structure and the study of horizontal gene transfer, it is necessary to reliably identify and characterize these islands.     

CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?

Background  

CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, are often located in the 5' end of genes and considered gene markers. Hackenberg et al. (2006) recently developed a new algorithm, CpGcluster, which uses a completely different mathematical approach from previous traditional algorithms. Their evaluation suggests that CpGcluster provides a much more efficient approach to detecting functional clusters or islands of CpGs.     

A genomic island present along the bacterial chromosome of the <Emphasis Type="Italic">Parachlamydiaceae</Emphasis> UWE25, an obligate amoebal endosymbiont,encodes a potentially functional F-like conjugative DNA transfer system

Background  

The genome of Protochlamydia amoebophila UWE25, a Parachlamydia-related endosymbiont of free-living amoebae, was recently published, providing the opportunity to search for genomic islands (GIs).     

Genetic diversity and colony structure of Tapinoma melanocephalum on the islands and mainland of South China

Aim

Tapinoma melanocephalum is listed as one of the most important invasive pest species in China. Information regarding the patterns of invasion and effects of geographic isolation on the population genetics of this species is largely lacking.

Location

South China.

Methods

To address this problem, we genotyped 39 colonies (two colonies were collapsed due to genetic similarity) using microsatellite markers and mitochondrial DNA sequencing to compare colony genetic structure of T. melanocephalum on the mainland and islands of South China.

Results

An analysis of the colony genotypes showed that the genetic diversity of the mainland population was slightly higher than that of the island populations but not significantly so. However, the observed heterozygosity on Shangchuan Island (SCD) was significantly lower than that of the other colonies. We also found six haplotypes in 111 mitochondrial DNA COI sequences. The relatedness (r) value between colonies of SCD was 0.410, higher than that of the other populations. The genetic clusters among colonies were not related to geographic locations and exhibited admixture likely due to frequent human‐mediated dispersal associated with trade between the mainland population and the islands. Pairwise F_STs between populations showed differentiation among mainland populations, while SCD displayed high levels of divergence (F_ST > 0.15) from most mainland populations. There was no significant isolation by distance among colonies. Most populations showed signs of a bottleneck effect.

Main conclusions

Our study suggests that there was no significant difference in the genetic diversity among the islands and the mainland; however, the lower genetic diversity, the higher degree of genetic divergence from other colonies, and the higher relatedness among nestmates made the SCD population stand out from all the others.     

Complex inter‐island colonization and peripatric founder speciation promote diversification of flightless Pachyrhynchus weevils in the Taiwan–Luzon volcanic belt

Aim

We investigated the spatial and temporal patterns of diversification among colourful and flightless weevils, the Pachyrhynchus orbifer complex, to test the stepping‐stone hypothesis of colonization across the Taiwan–Luzon volcanic belt.

Location

Southeast Asia.

Methods

The phylogeny of the P. orbifer complex was reconstructed from a multi‐locus data set of mitochondrial and nuclear genes using maximum likelihood in RAxML and Bayesian inference in MRBAYES. Likelihood‐based tests in CONSEL were used to evaluate alternative tree topologies. Divergence times were estimated in beast based on a range of mutation rates. Ancestral range and biogeographical history were reconstructed using Bayesian binary MCMC (BBM) methods in RASP and in BioGeoBEARS. Demographic histories were inferred using the extended Bayesian skyline plot (EBSP). Species boundaries were tested using BPP.

Results

The phylogeny of the P. orbifer complex indicated strong support for seven reciprocally monophyletic lineages grouped by current island boundaries (Camiguin, Fuga, Dalupiri, Calayan, Babuyan, Orchid and Yaeyama Islands), except for a sister Green + Itbayat lineage. Complex and stochastic colonization of P. orbifer was inferred to have involved both northward and southward directions with short‐ and long‐distance dispersal events, which are strongly inconsistent with the strict stepping‐stone hypothesis. Divergence time estimates for all extant island lineages (<1 Myr of Middle Pleistocene) are much more recent than the geological ages (22.4–1.7 Myr) and subaerial existence (c. 3 Myr) of the islands. The statistically delimited seven cryptic species imply that the diversity of Pachyrhynchus from small peripheral islands continues to be largely under‐estimated.

Main conclusions

The non‐linear, more complex spatial and temporal settings of the archipelago and stochastic dispersal were probable key factors shaping the colonization history of the P. orbifer complex. Speciation of the P. orbifer complex may have occurred only between islands, indicating that peripatric speciation through the founders of stochastic dispersals was the major evolutionary driver.     

Characterization of the dsDNA prophage sequences in the genome of <Emphasis Type="Italic">Neisseria gonorrhoeae</Emphasis> and visualization of productive bacteriophage

Background  

Bioinformatic analysis of the genome sequence of Neisseria gonorrhoeae revealed the presence of nine probable prophage islands. The distribution, conservation and function of many of these sequences, and their ability to produce bacteriophage particles are unknown.     

Molecular dating of caprines using ancient DNA sequences of <Emphasis Type="Italic">Myotragus balearicus</Emphasis>, an extinct endemic Balearic mammal

Background  

Myotragus balearicus was an endemic bovid from the Balearic Islands (Western Mediterranean) that became extinct around 6,000-4,000 years ago. The Myotragus evolutionary lineage became isolated in the islands most probably at the end of the Messinian crisis, when the desiccation of the Mediterranean ended, in a geological date established at 5.35 Mya. Thus, the sequences of Myotragus could be very valuable for calibrating the mammalian mitochondrial DNA clock and, in particular, the tree of the Caprinae subfamily, to which Myotragus belongs.     

Genomic island excisions in Bordetella petrii

Background  

Among the members of the genus Bordetella B. petrii is unique, since it is the only species isolated from the environment, while the pathogenic Bordetellae are obligately associated with host organisms. Another feature distinguishing B. petrii from the other sequenced Bordetellae is the presence of a large number of mobile genetic elements including several large genomic regions with typical characteristics of genomic islands collectively known as integrative and conjugative elements (ICEs). These elements mainly encode accessory metabolic factors enabling this bacterium to grow on a large repertoire of aromatic compounds.     

Virulence potential of five major pathogeniCity islands (SPI-1 to SPI-5) of Salmonella enterica serovar Enteritidis for chickens

Background  

Salmonella is a highly successful parasite of reptiles, birds and mammals. Its ability to infect and colonise such a broad range of hosts coincided with the introduction of new genetic determinants, among them 5 major pathogeniCity islands (SPI1-5), into the Salmonella genome. However, only limited information is available on how each of these pathogeniCity islands influences the ability of Salmonella to infect chickens. In this study, we therefore constructed Salmonella Enteritidis mutants with each SPI deleted separately, with single individual SPIs (i.e. with the remaining four deleted) and a mutant with all 5 SPIs deleted, and assessed their virulence in one-day-old chickens, together with the innate immune response of this host.     

Of mice and mammoths: generality and antiquity of the island rule

Aim

We assessed the generality of the island rule in a database comprising 1593 populations of insular mammals (439 species, including 63 species of fossil mammals), and tested whether observed patterns differed among taxonomic and functional groups.

Location

Islands world‐wide.

Methods

We measured museum specimens (fossil mammals) and reviewed the literature to compile a database of insular animal body size (S_i = mean mass of individuals from an insular population divided by that of individuals from an ancestral or mainland population, M). We used linear regressions to investigate the relationship between S_i and M, and ANCOVA to compare trends among taxonomic and functional groups.

Results

S_i was significantly and negatively related to the mass of the ancestral or mainland population across all mammals and within all orders of extant mammals analysed, and across palaeo‐insular (considered separately) mammals as well. Insular body size was significantly smaller for bats and insectivores than for the other orders studied here, but significantly larger for mammals that utilized aquatic prey than for those restricted to terrestrial prey.

Main conclusions

The island rule appears to be a pervasive pattern, exhibited by mammals from a broad range of orders, functional groups and time periods. There remains, however, much scatter about the general trend; this residual variation may be highly informative as it appears consistent with differences among species, islands and environmental characteristics hypothesized to influence body size evolution in general. The more pronounced gigantism and dwarfism of palaeo‐insular mammals, in particular, is consistent with a hypothesis that emphasizes the importance of ecological interactions (time in isolation from mammalian predators and competitors was 0.1 to > 1.0 Myr for palaeo‐insular mammals, but < 0.01 Myr for extant populations of insular mammals). While ecological displacement may be a major force driving diversification in body size in high‐diversity biotas, ecological release in species‐poor biotas often results in the convergence of insular mammals on the size of intermediate but absent species.     

Escape to Alcatraz: evolutionary history of slender salamanders (Batrachoseps) on the islands of San Francisco Bay

Background  

Island populations are excellent model systems for studies of phenotypic, ecological and molecular evolution. In this study, molecular markers of mitochondrial and nuclear derivation were used to investigate the evolution, structure and origin of populations of the California slender salamander (Batrachoseps attenuatus) inhabiting the six major islands of San Francisco Bay, formed following the rising of sea level around 9,000 years ago.     

The geographic scale of diversification on islands: genetic and morphological divergence at a very small spatial scale in the Mascarene grey white-eye (Aves: <Emphasis Type="Italic">Zosterops borbonicus</Emphasis>)

Background  

Oceanic islands provide unique scenarios for studying the roles of geography and ecology in driving population divergence and speciation. Assessing the relative importance of selective and neutral factors in driving population divergence is central to understanding how such divergence may lead to speciation in small oceanic islands, where opportunities for gene flow and population mixing are potentially high. Here we report a case of genetic and morphological structure in the Mascarene grey white-eye (Zosterops borbonicus) a species that shows a striking, geographically structured plumage polymorphism on the topographically and ecologically complex island of Réunion, yet is monotypic on the relatively uniform neighbouring island of Mauritius.     

A curious coincidence: mosquito biodiversity and the limits of the Japanese encephalitis virus in Australasia

Background  

The mosquito Culex annulirostris Skuse (Diptera: Culicidae) is the major vector of endemic arboviruses in Australia and is also responsible for the establishment of the Japanese encephalitis virus (JEV) in southern Papua New Guinea (PNG) as well as its incursions into northern Australia. Papua New Guinea and mainland Australia are separated by a small stretch of water, the Torres Strait, and its islands. While there has been regular JEV activity on these islands, JEV has not established on mainland Australia despite an abundance of Cx. annulirostris and porcine amplifying hosts. Despite the public health significance of this mosquito and the fact that its adults show overlapping morphology with close relative Cx. palpalis Taylor, its evolution and genetic structure remain undetermined. We address a hypothesis that there is significant genetic diversity in Cx. annulirostris and that the identification of this diversity will shed light on the paradox that JEV can cycle on an island 70 km from mainland Australia while not establishing in Australia itself.     

Phylogeographical patterns of a generalist acorn weevil: insight into the biogeographical history of broadleaved deciduous and evergreen forests

Background  

Climatic changes during glacial periods have had a major influence on the recent evolutionary history of living organisms, even in temperate forests on islands, where the land was not covered with ice sheets. We investigated the phylogeographical patterns of the weevil Curculio sikkimensis (Curculionidae), a generalist seed predator of Fagaceae plants living in both deciduous oak and evergreen forests of Japan. Its genetic structure was compared to that of another host-specific seed predator, C. hilgendorfi, inhabiting only evergreen forests.     

A computational approach for identifying pathogenicity islands in prokaryotic genomes

Background  

Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs.     

Towards a more general species–area relationship: diversity on all islands, great and small

Aim

To demonstrate a new and more general model of the species–area relationship that builds on traditional models, but includes the provision that richness may vary independently of island area on relatively small islands (the small island effect).

Location

We analysed species–area patterns for a broad diversity of insular biotas from aquatic and terrestrial archipelagoes.

Methods

We used breakpoint or piecewise regression methods by adding an additional term (the breakpoint transformation) to traditional species–area models. The resultant, more general, species–area model has three readily interpretable, biologically relevant parameters: (1) the upper limit of the small island effect (SIE), (2) an estimate of richness for relatively small islands and (3) the slope of the species–area relationship (in semi‐log or log–log space) for relatively large islands.

Results

The SIE, albeit of varying magnitude depending on the biotas in question, appeared to be a relatively common feature of the data sets we studied. The upper limit of the SIE tended to be highest for species groups with relatively high resource requirements and low dispersal abilities, and for biotas of more isolated archipelagoes.

Main conclusions

The breakpoint species–area model can be used to test for the significance, and to explore patterns of variation in small island effects, and to estimate slopes of the species–area (semi‐log or log–log) relationship after adjusting for SIE. Moreover, the breakpoint species–area model can be expanded to investigate three fundamentally different realms of the species–area relationship: (1) small islands where species richness varies independent of area, but with idiosyncratic differences among islands and with catastrophic events such as hurricanes, (2) islands beyond the upper limit of SIE where richness varies in a more deterministic and predictable manner with island area and associated, ecological factors and (3) islands large enough to provide the internal geographical isolation (large rivers, mountains and other barriers within islands) necessary for in situ speciation.

     

Genetic islands of <Emphasis Type="Italic">Streptococcus agalactiae</Emphasis> strains NEM316 and 2603VR and their presence in other Group B Streptococcal strains

Background  

Streptococcus agalactiae (Group B Streptococcus; GBS) is a major contributor to obstetric and neonatal bacterial sepsis. Serotype III strains cause the majority of late-onset sepsis and meningitis in babies, and thus appear to have an enhanced invasive capacity compared with the other serotypes that cause disease predominantly in immunocompromised pregnant women. We compared the serotype III and V whole genome sequences, strains NEM316 and 2603VR respectively, in an attempt to identify genetic attributes of strain NEM316 that might explain the propensity of strain NEM316 to cause late-onset disease in babies. Fourteen putative pathogenicity islands were described in the strain NEM316 whole genome sequence. Using PCR- and targeted microarray- strategies, the presence of these islands were assessed in a diverse strain collection including 18 colonizing isolates from healthy pregnant women, and 13 and 8 invasive isolates from infants with early- and late-onset sepsis, respectively.     

The Salmonella PathogeniCity Island (SPI) 1 contributes more than SPI2 to the colonization of the chicken by Salmonella enterica serovar Typhimurium

Background  

Salmonella enterica serovar Typhimurium (Typhimurium) is an important pathogen that infects a broad range of hosts. In humans, Typhimurium causes a gastroenteritis characterized by vomiting, diarrhea, and abdominal pains. Typhimurium infection occurs mainly through the ingestion of contaminated food including poultry, pork, eggs, and milk. Chickens that are asymptomatic carriers of Typhimurium constitute a potential reservoir for infection. The type three secretion systems encoded by Salmonella pathogeniCity islands (SPI) 1 and 2 are major virulence factors of Salmonella. However, only a few studies have investigated their role during the infection of chickens.