Community-Wide Genotyping of Batrachochytrium dendrobatidis in Ecuadorian Forests.

The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) is a cosmopolitan pathogen with numerous distinct lineages. The global panzootic lineage (Bd-GPL) is the most widespread and virulent lineage and is responsible for many recorded amphibian declines. Mapping the extent of Bd-GPL and other more established lineages is important for predicting disease dynamics in amphibian communities.

Detection of the Batrachochytrium dendrobatidis global panzootic lineage in Ecuadorian anurans of the Amazonian lowlands.

Considerable attention has been directed to studying the infection dynamics of the fungal pathogen Batrachochytrium dendrobatidis (Bd) affecting amphibians in the high elevations of the Neotropics. However, lowland forests of the same realm remain comparatively understudied in this context. Herein, we attempt to bridge this gap by measuring the prevalence of Bd via quantitative polymerase chain reaction (qPCR) in several anuran taxa inhabiting the Amazonian lowlands in the northeast of Ecuador.

Phylogeographic inference of Sumatran ranids bearing gastromyzophorous tadpoles with regard to the Pleistocene drainage systems of Sundaland.

Rivers are known to act as biogeographic barriers in several strictly terrestrial taxa, while possibly serving as conduits of dispersal for freshwater-tolerant or -dependent species. However, the influence of river systems on genetic diversity depends on taxa-specific life history traits as well as other geographic factors. In amphibians, several studies have demonstrated that river systems have only minor influence on their divergence.

MMDIT: A tool for the deconvolution and interpretation of mitochondrial DNA mixtures.

Short tandem repeats of the nuclear genome have been the preferred markers for analyzing forensic DNA mixtures. However, when nuclear DNA in a sample is degraded or limited, mitochondrial DNA (mtDNA) markers provide a powerful alternative. Though historically considered challenging, the interpretation and analysis of mtDNA mixtures have recently seen renewed interest with the advent of massively parallel sequencing.

International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions.

International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure.

A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures.

Despite the benefits of quantitative data generated by massively parallel sequencing, resolving mitotypes from mixtures occurring in certain ratios remains challenging. In this study, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated. The method was first tested on 270 in silico two-person mixtures varying in mixture proportions.

Numt identification and removal with RtN!

Motivation: Assays in mitochondrial genomics rely on accurate read mapping and variant calling. However, there are known and unknown nuclear paralogs that have fundamentally different genetic properties than that of the mitochondrial genome. Such paralogs complicate the interpretation of mitochondrial genome data and confound variant calling.

Phylogeography of montane dragons could shed light on the history of forests and diversification processes on Sumatra.

Biogeographical evidence, both, for and against the "regional endemism paradigm" hypothesis has been uncovered across the Greater Sunda Region (Sundaland) of Southeast Asia. Additionally, there are competing hypotheses regarding how Pleistocene forests may have impacted biological patterns and processes in Sumatra. Using montane agamid lizards from Sumatra, we derived and analyzed a phylogenetic dataset, genetic divergence estimates, and contemporary distributional patterns among species.

A novel phylogenetic approach for de novo discovery of putative nuclear mitochondrial (pNumt) haplotypes.

Current approaches for parsing true variation (i.e. signal) from noise, broadly involve estimating a baseline value of the latter, below which all sequence data are ignored.

Diversification of bent-toed geckos (Cyrtodactylus) on Sumatra and west Java.

Complex geological processes often drive biotic diversification on islands. The islands of Sumatra and Java have experienced dramatic historical changes, including isolation by marine incursions followed by periodic connectivity with the rest of Sundaland across highland connections. To determine how this geological history influenced island invasions, we investigated the colonization history and diversification of bent-toed geckos (genus Cyrtodactylus) on Sumatra and west Java.

Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes.

Strong spatial sorting of genetic variation in contiguous populations is often explained by local adaptation or secondary contact following allopatric divergence. A third explanation, spatial sorting by stochastic effects of range expansion, has been considered less often though theoretical models suggest it should be widespread, if ephemeral. In a study designed to delimit species within a clade of venomous coralsnakes, we identified an unusual pattern within the Texas coral snake (Micrurus tener): strong spatial sorting of divergent mitochondrial (mtDNA) lineages over a portion of its range, but weak sorting of these lineages elsewhere.