Reconstructing colonization dynamics to establish how human activities transformed island biodiversity.

Drivers and dynamics of initial human migrations across individual islands and archipelagos are poorly understood, hampering assessments of subsequent modification of island biodiversity. We developed and tested a new statistical-simulation approach for reconstructing the pattern and pace of human migration across islands at high spatiotemporal resolutions. Using Polynesian colonisation of New Zealand as an example, we show that process-explicit models, informed by archaeological records and spatiotemporal reconstructions of past climates and environments, can provide new and important insights into the patterns and mechanisms of arrival and establishment of people on islands.

From clean spaces to crime scenes: Exploring trace DNA recovery from titania-coated self-cleaning substrates.

Titanium dioxide (titania, TiO) is frequently used as a coating for a variety of self-cleaning products, such as antifogging vehicle mirrors, ceramic tiles, and glass windows because of its distinct physiochemical features. When exposed to light TiO causes photocatalytic decomposition of organic contaminants, potentially compromising DNA integrity. The impact of TiO-coated commercial glasses, Bioclean® and SaniTise™, on trace DNA persistence, recovery, and profiling was investigated.

Metal-DNA interactions: Exploring the impact of metal ions on key stages of forensic DNA analysis.

Forensic DNA analysis continues to be hampered by the complex interactions between metals and DNA. Metal ions may cause direct DNA damage, inhibit DNA extraction and polymerase chain reaction (PCR) amplification or both. This study evaluated the impact of metal ions on DNA extraction, quantitation, and short tandem repeat profiling using cell-free and cellular (saliva) DNA.

Quantitative PCR overestimation of DNA in samples contaminated with tin.

Metals can pose challenges while conducting forensic DNA analysis. The presence of metal ions in evidence-related DNA extracts can degrade DNA or inhibit PCR as applied to DNA quantification (real-time PCR or qPCR) and/or STR amplification, leading to low success in STR profiling. Different metal ions were spiked into 0.

Environmental DNA as an innovative technique to identify the origins of falsified antimalarial tablets-a pilot study of the pharmabiome.

Falsified medicines are a major threat to global health. Antimalarial drugs have been particularly targeted by criminals. As DNA analysis has revolutionized forensic criminology, we hypothesized that these techniques could also be used to investigate the origins of falsified medicines.

A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage.

Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA).

Ethics reporting in forensic science research publications - A review.

An essential element of compliance with ethical standards in scientific research is the reporting of a verifiable declaration of ethical approval and, when human subjects are involved - informed consent, in published works. The level of reporting of ethical permission for research published in forensic and investigative sciences journals has not been explored to date. Hence, we examined the reporting of ethical approval and informed consent in original research utilising human or animal subjects published in six forensic science journals from 2010 to 2019.

Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel.

Massively parallel sequencing following hybridisation enrichment provides new opportunities to obtain genetic data for various types of forensic testing and has proven successful on modern as well as degraded and ancient DNA. A customisable forensic intelligence panel that targeted 124 SNP markers (67 ancestry informative markers, 23 phenotype markers from the HIrisplex panel, and 35 Y-chromosome SNPs) was used to examine biogeographic ancestry, phenotype and sex and Y-lineage in samples from different ethnic populations of Pakistan including Pothwari, Gilgit, Baloach, Pathan, Kashmiri and Siraiki. Targeted sequencing and computational data analysis pipeline allowed filtering of variants across the targeted loci.

Historical museum samples enable the examination of divergent and parallel evolution during invasion.

During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline and global climate change. Concurrently, greater globalization is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species' ability to persist or perish within a new or changing environment.

Process-explicit models reveal pathway to extinction for woolly mammoth using pattern-oriented validation.

Pathways to extinction start long before the death of the last individual. However, causes of early stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth.

Comparison of Isohelix™ and Rayon swabbing systems for touch DNA recovery from metal surfaces.

A previous study evaluating two swabbing systems found that DNA was best recovered from sterile metal substrates using an Isohelix™ swab wetted with isopropyl alcohol rather than a Rayon swab with water as the wetting agent. We tested the same swabbing systems on metal (aluminum, brass, and stainless steel) and plastic substrates in a regularly touched environment to simulate the non-deliberate transfer of touch evidence likely seen in a casework scenario, to ascertain the performance of these swabs in an uncontrolled situation. Higher amounts of touch DNA were recovered with Isohelix™ swabs (0.

Genomic Approaches for Conservation Management in Australia under Climate Change.

Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change.

The development of a tool to predict temperature-exposure of incinerated teeth using colourimetric and hydroxyapatite crystal size data.

This study presents a novel tool to predict temperature-exposure of incinerated pig teeth as a proxy for understanding impacts of fire on human teeth. Previous studies on the estimation of temperature-exposure of skeletal elements have been limited to that of heat-exposed bone. This predictive tool was developed using a multinomial regression model of colourimetric and hydroxyapatite crystal size variables using data obtained from unheated pig teeth and teeth incinerated at 300 °C, 600 °C, 800 °C and 1000 °C.

Evaluation of the efficiency of Isohelix™ and Rayon swabs for recovery of DNA from metal surfaces.

Purpose: We investigated the recovery and extraction efficiency of DNA from three metal surfaces (brass, copper, steel) relevant to forensic casework, and plastic (control) using two different swabbing systems; Rayon and Isohelix™ swabs, with sterile water and isopropyl alcohol respectively, as the wetting solutions.

Methods: Twenty nanograms of human genomic DNA were applied directly to Isohelix™ and Rayon swabs; and to the metal and plastic substrates. All substrates were left to dry for 24 h, followed by single wet swabbing and extraction with the DNA IQ™ System.

Forensic touch DNA recovery from metal surfaces - A review.

Trace evidence such as touch (also known as contact) DNA has probative value as a vital forensic investigative tool that can lead to the identification and apprehension of a criminal. While the volume of touch DNA evidence items submitted to forensic laboratories has significantly increased, recovery and amplification of DNA from these items, especially from metal surfaces, remains challenging. Currently little is understood with regards to the underlying mechanisms of metal-DNA interactions in the context of forensic science and how this may impact on DNA recovery.

European and Asian contribution to the genetic diversity of mainland South American chickens.

Chickens () from the Americas have long been recognized as descendants of European chickens, transported by early Europeans since the fifteenth century. However, in recent years, a possible pre-Columbian introduction of chickens to South America by Polynesian seafarers has also been suggested. Here, we characterize the mitochondrial control region genetic diversity of modern chicken populations from South America and compare this to a worldwide dataset in order to investigate the potential maternal genetic origin of modern-day chicken populations in South America.

Integrating spectrophotometric and XRD analyses in the investigation of burned dental remains.

Heat alters colour and crystallinity of teeth by destruction of the organic content and inducing hydroxyapatite crystal growth. The colour and crystallite changes can be quantified using spectrophotometric and x-ray diffraction analyses, however these analyses are not commonly used in combination to evaluate burned dental remains. In this study, thirty-nine teeth were incinerated at 300-1000 °C for 15 and 30 min and then measured using a spectrophotometer and an x-ray diffractometer.

Correction: Low-cost cross-taxon enrichment of mitochondrial DNA using in-house synthesised RNA probes.

[This corrects the article DOI: 10.1371/journal.pone.

Low-cost cross-taxon enrichment of mitochondrial DNA using in-house synthesised RNA probes.

Hybridization capture with in-solution oligonucleotide probes has quickly become the preferred method for enriching specific DNA loci from degraded or ancient samples prior to high-throughput sequencing (HTS). Several companies synthesize sets of probes for in-solution hybridization capture, but these commercial reagents are usually expensive. Methods for economical in-house probe synthesis have been described, but they do not directly address one of the major advantages of commercially synthesised probes: that probe sequences matching many species can be synthesised in parallel and pooled.

Genetic diversity and drivers of dwarfism in extinct island emu populations.

Australia's iconic emu () is the only living representative of its genus, but fossil evidence and reports from early European explorers suggest that three island forms (at least two of which were dwarfs) became extinct during the nineteenth century. While one of these-the King Island emu-has been found to be conspecific with Australian mainland emus, little is known about how the other two forms-Kangaroo Island and Tasmanian emus-relate to the others, or even the size of Tasmanian emus. We present a comprehensive genetic and morphological analysis of diversity, including data from one of the few definitively genuine Tasmanian emu specimens known.

A mini-multiplex SNaPshot assay for the triage of degraded human DNA.

Short Tandem Repeat (STR) genotyping is currently the primary DNA-based method for human identification, however it can have limited success when applied to degraded human remains. Massively parallel sequencing (MPS) provides new opportunities to obtain genetic data for hundreds of loci in a single assay with higher success from degraded samples. However, due to the extra requirement for specialised equipment, expertise and resources, routine use of MPS may not be feasible or necessary for many forensic cases.