Revictimization After Adolescent Dating Violence in a Matched, National Sample of Youth.

Purpose: To assess if adolescent dating violence was associated with physical intimate partner violence victimization in adulthood, using a comprehensive propensity score to create a matched group of victims and nonvictims.

Methods: Secondary analysis of waves 1 (1994-1995), 2 (1996), 3 (2001-2002) and 4 (2007-2008) of the National Longitudinal Study of Adolescent to Adult Health, a nationally representative sample of US high schools and middle schools. Individuals aged 12-18 reporting adolescent dating violence between the wave 1 and 2 interviews (n = 732) were matched to nonvictimized participants of the same sex (n = 1,429) using propensity score matching.

Estimating diversity via frequency ratios.

We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of consecutive probabilities, we construct a nonlinear regression model for the ratios of consecutive frequency counts. This allows us to predict the unobserved count and hence estimate the total diversity.

Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys.

High-throughput sequencing platforms are continuing to increase resulting read lengths, which is allowing for a deeper and more accurate depiction of environmental microbial diversity. With the nascent Reagent Kit v3, Illumina MiSeq now has the ability to sequence the eukaryotic hyper-variable V4 region of the SSU-rDNA locus with paired-end reads. Using DNA collected from soils with analyses of strictly- and nearly identical amplicons, here we ask how the new Illumina MiSeq data compares with what we can obtain with Roche/454 GS FLX with regard to quantity and quality, presence and absence, and abundance perspectives.

Estimation of viral richness from shotgun metagenomes using a frequency count approach.

Background: Viruses are important drivers of ecosystem functions, yet little is known about the vast majority of viruses. Viral shotgun metagenomics enables the investigation of broad ecological questions in phage communities. One ecological characteristic is species richness, which is the number of different species in a community.

Estimating population diversity with CatchAll.

Motivation: The massive data produced by next-generation sequencing require advanced statistical tools. We address estimating the total diversity or species richness in a population. To date, only relatively simple methods have been implemented in available software.

Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life.

This article reviews recent advances in 'microbiome studies': molecular, statistical and graphical techniques to explore and quantify how microbial organisms affect our environments and ourselves given recent increases in sequencing technology. Microbiome studies are moving beyond mere inventories of specific ecosystems to quantifications of community diversity and descriptions of their ecological function. We review the last 24 months of progress in this sort of research, and anticipate where the next 2 years will take us.

Comparing the hyper-variable V4 and V9 regions of the small subunit rDNA for assessment of ciliate environmental diversity.

The hyper-variable V4 and V9 regions of the small subunit (SSU) rDNA have been targeted for assessing environmental diversity of microbial eukaryotes using next generation sequencing technologies. Here, we explore how the genetic distances among these short fragments compare with the distances obtained from near full-length SSU-rDNA sequences by comparing all pairwise estimates, as well as within and among species of ciliates. Results show that pairwise distances from V4 more closely match the near full-length SSU-rDNA and are more comparable with previous studies based on much longer SSU-rDNA fragments, then pairwise distances from V9.

Estimating population diversity with unreliable low frequency counts.

We consider the classical population diversity estimation scenario based on frequency count data (the number of classes or taxa represented once, twice, etc. in the sample), but with the proviso that the lowest frequency counts, especially the singletons, may not be reliably observed. This arises especially in data derived from modern high-throughput DNA sequencing, where errors may cause sequences to be incorrectly assigned to new taxa instead of being matched to existing, observed taxa.

Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness.

Microbial diversity and distribution are topics of intensive research. In two companion papers in this issue, we describe the results of the Cariaco Microbial Observatory (Caribbean Sea, Venezuela). The Basin contains the largest body of marine anoxic water, and presents an opportunity to study protistan communities across biogeochemical gradients.

Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization.

This is the second paper in a series of three that investigates eukaryotic microbial diversity and taxon distribution in the Cariaco Basin, Venezuela, the ocean's largest anoxic marine basin. Here, we use phylogenetic information, multivariate community analyses and statistical richness predictions to test whether protists exhibit habitat specialization within defined geochemical layers of the water column. We also analyze spatio-temporal distributions of protists across two seasons and two geographic sites within the basin.

Estimating the number of species with CatchAll.

In many situations we are faced with the need to estimate the number of classes in a population from observed count data: this arises not only in biology, where we are interested in the number of taxa such as species, but also in many other fields such as public health, criminal justice, software engineering, etc. This problem has a rich history in theoretical statistics, dating back at least to 1943, and many approaches have been proposed and studied. However, to date only one approach has been implemented in readily available software, namely a relatively simple nonparametric method which, while straightforward to program, is not flexible and can be prone to information loss.

Sequence diversity and novelty of natural assemblages of picoeukaryotes from the Indian Ocean.

Despite the ecological importance of marine pico-size eukaryotes, the study of their in situ diversity using molecular tools started just a few years ago. These studies have revealed that marine picoeukaryotes are very diverse and include many novel taxa. However, the amount and structure of their phylogenetic diversity and the extent of their sequence novelty still remains poorly known, as a systematic analysis has been seldom attempted.

Bacterial diversity in a glacier foreland of the high Arctic.

Over the past 100 years, Arctic temperatures have increased at almost twice the global average rate. One consequence is the acceleration of glacier retreat, exposing new habitats that are colonized by microorganisms whose diversity and function are unknown. Here, we characterized bacterial diversity along two approximately parallel chronosequences in an Arctic glacier forefield that span six time points following glacier retreat.

Spatio-temporal variations in protistan communities along an O/HS gradient in the anoxic Framvaren Fjord (Norway).

Despite its relevance for ecology and biodiversity, the stability of spatial microeukaryote diversity patterns in time has received only little attention using gene-based strategies, and there is little knowledge about the relation of spatial vs. temporal variation. We addressed this subject by investigating seasonal fluctuations in protistan communities in three ecologically distinct marine habitats.

Polymerase chain reaction primers miss half of rRNA microbial diversity.

The rRNA approach is the principal tool to study microbial diversity, but it has important biases. These include polymerase chain reaction (PCR) primers bias, and relative inefficiency of DNA extraction techniques. Such sources of potential undersampling of microbial diversity are well known, but the scale of the undersampling has not been quantified.

Microbial community structure in the North Pacific ocean.

We report a ribosomal tag pyrosequencing study of the phylogenetic diversity of Archaea, Bacteria and Eucarya over a depth profile at the Hawaii Ocean Time-Series Station, ALOHA. The V9 region of the SSU rRNA gene was amplified from samples representing the epi- (10 m), meso- (800 m) and bathy- (4400 m) pelagia. The primers used are expected to amplify representatives of approximately 80% of known phylogenetic diversity across all three domains.

A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization.

Background: Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored.

CotQuest: improved algorithm and software for nonlinear regression analysis of DNA reassociation kinetics data.

Cot analysis (DNA reassociation kinetics) has long been used to explore genome structure in individual species, estimate genome similarity among organisms, and evaluate diversity in ecological samples, yet the algorithms and computational tools designed for analyzing Cot data are outdated, difficult to use, and prone to error. We report a new nonlinear regression procedure for analysis of Cot data and describe our algorithms in detail. Our procedure is implemented as CotQuest, a suite of scripts designed for use with the statistics package SAS.

Environmental rRNA inventories miss over half of protistan diversity.

Background: The main tool to discover novel microbial eukaryotes is the rRNA approach. This approach has important biases, including PCR discrimination against certain rRNA gene species, which makes molecular inventories skewed relative to the source communities. The degree of this bias has not been quantified, and it remains unclear whether species missed from clone libraries could be recovered by increasing sequencing efforts, or whether they cannot be detected in principle.

Parametric models for estimating the number of classes.

We consider parametric distributions intended to model heterogeneity in population size estimation, especially parametric stochastic abundance models for species richness estimation. We briefly review (conditional) maximum likelihood estimation of the number of species, and summarize the results of fitting 7 candidate models to frequency-count data, from a database of >40000 such instances, mostly arising from microbial ecology. We consider error estimation, goodness-of-fit assessment, data subsetting, and other practical matters.

Protistan community patterns within the brine and halocline of deep hypersaline anoxic basins in the eastern Mediterranean Sea.

Environmental factors restrict the distribution of microbial eukaryotes but the exact boundaries for eukaryotic life are not known. Here, we examine protistan communities at the extremes of salinity and osmotic pressure, and report rich assemblages inhabiting Bannock and Discovery, two deep-sea superhaline anoxic basins in the Mediterranean. Using a rRNA-based approach, we detected 1,538 protistan rRNA gene sequences from water samples with total salinity ranging from 39 to 280 g/Kg, and obtained evidence that this DNA was endogenous to the extreme habitat sampled.

Bayesian estimation of the number of species using noninformative priors.

Consider a sample of animal abundances collected from one sampling occasion. Our focus is in estimating the number of species in a closed population. In order to conduct a noninformative Bayesian inference when modeling this data, we derive Jeffreys and reference priors from the full likelihood.

Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin.

The frontiers of eukaryote life in nature are still unidentified. In this study, we analysed protistan communities in the hypersaline (up to 365 g l(-1) NaCl) anoxic L'Atalante deep-sea basin located in the eastern Mediterranean Sea. Targeting 18S ribosomal RNA retrieved from the basin's lower halocline (3501 m depth) we detected 279 protistan sequences that grouped into 42 unique phylotypes (99% sequence similarity).

Protistan diversity in the Arctic: a case of paleoclimate shaping modern biodiversity?

Background: The impact of climate on biodiversity is indisputable. Climate changes over geological time must have significantly influenced the evolution of biodiversity, ultimately leading to its present pattern. Here we consider the paleoclimate data record, inferring that present-day hot and cold environments should contain, respectively, the largest and the smallest diversity of ancestral lineages of microbial eukaryotes.