Publications by authors named "T W Valk"
Article Synopsis
- - The alignment of sequencing reads is crucial for studying ancient genomes, but challenges like reference bias and spurious mappings can lead to inaccurate results, especially as new lab techniques produce larger datasets.
- - The study introduces AMBER, a new bioinformatics tool designed to evaluate ancient DNA mapping quality, providing insights into reference bias and mismatch rates across various read lengths.
- - AMBER allows researchers to analyze factors affecting mapping accuracy, showing that the choice of mapping algorithms and quality thresholds significantly influences results, which can help improve alignment strategies for ancient DNA.
A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago.
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- Genomic techniques can significantly enhance conservation efforts by identifying threats to various species and populations, as well as assisting in biodiversity restoration.
- The text outlines two main areas of genomic research in conservation: vulnerability genomics, which focuses on assessing risks, and restoration genomics, which is aimed at recovery efforts.
- Current applications of these genomic approaches are examined, along with key questions that remain unanswered and the future possibilities they hold for enhancing conservation strategies.
Genome sequencing is a powerful tool to understand species evolutionary history, uncover genes under selection, which could be informative of local adaptation, and infer measures of genetic diversity, inbreeding and mutational load that could be used to inform conservation efforts. Gorillas, critically endangered primates, have received considerable attention and with the recently sequenced Bwindi mountain gorilla population, genomic data is now available from all gorilla subspecies and both mountain gorilla populations. Here, we reanalysed this rich dataset with a focus on evolutionary history, local adaptation and genomic parameters relevant for conservation.
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- - Genomic studies on endangered species help us understand how they evolve and survive despite population declines and bottlenecks, offering clues on avoiding extinction.
- - The researchers focused on the muskox, which nearly went extinct after the last Ice Age but is now thriving, examining 108 whole genomes from current populations and an ancient specimen.
- - They found that past climate changes influenced muskox demographics, with the white-faced subspecies showing extremely low genetic variation without signs of inbreeding depression, suggesting that gradual population declines might have removed harmful mutations.