ViPRA-Haplo: De Novo Reconstruction of Viral Populations Using Paired End Sequencing Data.

We present ViPRA-Haplo, a de novo strain-specific assembly workflow for reconstructing viral haplotypes in a viral population from paired-end next generation sequencing (NGS) data. The proposed Viral Path Reconstruction Algorithm (ViPRA) generates a subset of paths from a De Bruijn graph of reads using the pairing information of reads. The paths generated by ViPRA are an over-estimation of the true contigs.

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.

Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting (ILS), introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce an implementation of a multi-tree mixture model that we call mixtures across sites and trees (MAST).

Genetic Variants of and Are Associated With Risk of Non-Small Cell Lung Cancer.

Background: Single nucleotide polymorphisms (SNPs) are often associated with distinct phenotypes in cancer. The present study investigated associations of cancer risk and outcomes with SNPs discovered by whole exome sequencing of normal lung tissue DNA of 15 non-small cell lung cancer (NSCLC) patients, 10 early stage and 5 advanced stage.

Methods: DNA extracted from normal lung tissue of the 15 NSCLC patients was subjected to whole genome amplification and sequencing and analyzed for the occurrence of SNPs.

pgHMA: Application of the heteroduplex mobility assay analysis in phylogenetics and population genetics.

The heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis.

An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes.

A current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns.

Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage.

Following publication of the original article [1], the author reported that there are several errors in the original article.

Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage.

Background: In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence reconstruction from the reads can be difficult because of the occurrence of uncovered gaps. Reference guided assembly can then improve these assemblies.

HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations.

Background: Pooling techniques, where multiple sub-samples are mixed in a single sample, are widely used to take full advantage of high-throughput DNA sequencing. Recently, Ranjard et al. (PLoS ONE 13:0195090, 2018) proposed a pooling strategy without the use of barcodes.

Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation.

Background: Most empirical studies tend to focus on microbiome dynamics within hosts or microbiome compositional differences between hosts over short periods. However, there is still a dearth of formal models that allow us to investigate the observed short-term dynamics of microbiomes under a unified ecological and evolutionary framework. In our previous study, we developed a computational agent-based neutral framework that simulates microbiome dynamics spanning many host generations with the added dimension of a genealogy of hosts.

Reassembling haplotypes in a mixture of pooled amplicons when the relative concentrations are known: A proof-of-concept study on the efficient design of next-generation sequencing strategies.

Next-generation sequencing can be costly and labour intensive. Usually, the sequencing cost per sample is reduced by pooling amplified DNA = amplicons) derived from different individuals on the same sequencing lane. Barcodes unique to each amplicon permit short-read sequences to be assigned appropriately.

Complete mitochondrial genome of the green-lipped mussel, (Mollusca: Mytiloidea), from long nanopore sequencing reads.

We describe here the first complete genome assembly of the New Zealand green-lipped mussel, , mitochondrion. The assembly was performed from a mix of long nanopore sequencing reads and short sequencing reads. The genome is 16,005 bp long.

Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes.

Bamboo specialization is one of the most extreme examples of convergent herbivory, yet it is unclear how this specific high-fiber diet might selectively shape the composition of the gut microbiome compared to host phylogeny. To address these questions, we used deep sequencing to investigate the nature and comparative impact of phylogenetic and dietary selection for specific gut microbial membership in three bamboo specialists-the bamboo lemur (Hapalemur griseus, Primates: Lemuridae), giant panda (Ailuropoda melanoleuca, Carnivora: Ursidae), and red panda (Ailurus fulgens, Carnivora: Musteloideadae), as well as two phylogenetic controls-the ringtail lemur (Lemur catta) and the Asian black bear (Ursus thibetanus). We detected significantly higher Shannon diversity in the bamboo lemur (10.

Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs.

Many studies have demonstrated the effects of host diet on gut microbial membership, metagenomics, and fermentation individually; but few have attempted to interpret the relationship among these biological phenomena with respect to host features (e.g. gut morphology).

Models of microbiome evolution incorporating host and microbial selection.

Background: Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts.

Identifying predictors of time-inhomogeneous viral evolutionary processes.

Various factors determine the rate at which mutations are generated and fixed in viral genomes. Viral evolutionary rates may vary over the course of a single persistent infection and can reflect changes in replication rates and selective dynamics. Dedicated statistical inference approaches are required to understand how the complex interplay of these processes shapes the genetic diversity and divergence in viral populations.

Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution.

Transposable elements (TEs) are DNA sequences that are able to replicate and move within and between host genomes. Their mechanism of replication is also shared with endogenous retroviruses (ERVs), which are also a type of TE that represent an ancient retroviral infection within animal genomes. Two models have been proposed to explain TE proliferation in host genomes: the strict master model (SMM), and the random template (or transposon) model (TM).

Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals.

Background: Over the last decade, next generation sequencing (NGS) has become widely available, and is now the sequencing technology of choice for most researchers. Nonetheless, NGS presents a challenge for the evolutionary biologists who wish to estimate evolutionary genetic parameters from a mixed sample of unlabelled or untagged individuals, especially when the reconstruction of full length haplotypes can be unreliable. We propose two novel approaches, least squares estimation (LS) and Approximate Bayesian Computation Markov chain Monte Carlo estimation (ABC-MCMC), to infer evolutionary genetic parameters from a collection of short-read sequences obtained from a mixed sample of anonymous DNA using the frequencies of nucleotides at each site only without reconstructing the full-length alignment nor the phylogeny.

Neutral Models of Microbiome Evolution.

There has been an explosion of research on host-associated microbial communities (i.e.,microbiomes).

Patterns of gut bacterial colonization in three primate species.

Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood.

Frequency-dependent selection drives HBeAg seroconversion in chronic hepatitis B virus infection.

HBeAg seroconversion is an important stage in the evolution of a chronic hepatitis B virus (HBV) infection that usually leads to control of viral replication and a reduced risk for liver cirrhosis and cancer. Since current therapies for the HBV-associated liver inflammation that is known as chronic hepatitis B (CHB). Rarely induce permanent HBeAg seroconversion, there is a need to understand the mechanisms responsible for the purpose of identifying new therapeutic targets.

HIV-1 transmission during early antiretroviral therapy: evaluation of two HIV-1 transmission events in the HPTN 052 prevention study.

In the HPTN 052 study, transmission between HIV-discordant couples was reduced by 96% when the HIV-infected partner received suppressive antiretroviral therapy (ART). We examined two transmission events where the newly infected partner was diagnosed after the HIV-infected partner (index) initiated therapy. We evaluated the sequence complexity of the viral populations and antibody reactivity in the newly infected partner to estimate the dates of transmission to the newly infected partners.

Transient compartmentalization of simian immunodeficiency virus variants in the breast milk of african green monkeys.

Natural hosts of simian immunodeficiency virus (SIV), African green monkeys (AGMs), rarely transmit SIV via breast-feeding. In order to examine the genetic diversity of breast milk SIV variants in this limited-transmission setting, we performed phylogenetic analysis on envelope sequences of milk and plasma SIV variants of AGMs. Low-diversity milk virus populations were compartmentalized from that in plasma.

Science incubators: synthesis centers and their role in the research ecosystem.

How should funding agencies enable researchers to explore high-risk but potentially high-reward science? One model that appears to work is the NSF-funded synthesis center, an incubator for community-led, innovative science.