Insuring Against The Sixth-Wave Of Mass Extinction – Cryopreservation And Sequencing

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Some ecologists believe the Earth has entered a so-called sixth-wave of mass extinction. In 2018 the last male northern white rhinoceros died, for example. Rivers and lakes cover approximately one percent of Earth’s surface, but are home to one third of all vertebrate species worldwide. At the same time, freshwater life is highly threatened.

Scientists from the Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB) and international colleagues have now quantified the global decline of big freshwater animals: From 1970 to 2012, global populations of freshwater megafauna declined by 88 percent – twice the loss of vertebrate populations on land or in the ocean. Large fish species are particularly affected. And yet there remain large gaps in monitoring and conservation actions for freshwater megafauna, particularly in areas with high levels of biodiversity.

Scientists will also conduct sampling and a number of experiments for four projects – DIAPOD, CHASE, Micro-ARC and PETRA – that are part of the £20 million Changing Arctic Ocean scientific research programme. The programme – funded by the Natural Environment Research Council (NERC) and the German Federal Ministry for Education and Research – seeks to understand the impacts of climate change on marine life in the Arctic.

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The underlying causes of current species extinctions are disputed, however there are practical measures that can be taken to preserve the species record. One of these measures is cryopreservation, which is the freezing of viable cells at very low temperatures. This may in the future allow the revival of a species. Natural history museums which could be seen as guardians of the species record have not, until recently, made cryopreservations. A team from the Smithsonian National Museum of Natural History has set about changing this with the first frozen cell collection of fishes of any natural history museum. They intend that this will be a first step in establishing more collections of both fish and animals.

The international Vertebrate Genome Project (VGP) launched in autumn 2018. The vision of VGP is to sequence all 66,000 vertebrate species on Earth, providing high-quality, near error-less, complete genome assemblies to address fundamental questions in biology, disease and conservation.

The VGP is the project of the Genome 10,000 consortium (G10K), which has members at more than 150 institutions around the globe. It has released in the region of 15 high-quality reference genomes for species including mammals, birds, reptiles, amphibians, and fish.

The Genome Ark database is a digital open-access library of genomes generated by G10K, hosted by Amazon. The contents of the Genome Ark will be processed and annotated so that the sequences can be copied to the National Center for Biotechnology Information (NCBI), Ensembl, and University of California, Santa Cruz (UCSC) genome browser.

Highly accurate genomes deposited on secure servers act as a form of insurance against extinction. As long as the deposited sequences faithfully represent the animal in question, in the future it may be possible to revive the species from the sequence data, should it become extinct. This would also require a good depth of sequences, meaning as many animals within the species being sequenced as possible to reveal the variation that is essential to a species’ survival.

The G10K concluded that the highest quality results were obtained using the new long read DNA sequencers, which helped avoid errors in the sequencing of repetitive DNA. The consortium also assembles chromosomes by considering their 3D arrangement and interactions using long-range scaffolding technologies. The G10K found that the current practice of merging maternal and paternal chromosomes into a single genome caused numerous errors, so they assemble maternal and paternal DNA separately in a process called phasing.

The consortium has been working together with Pacific Biosciences, 10X Genomics, Bionano Genomics, Arima Genomics, Dovetail Genomics, and Phase Genomics to assemble the genomes. The projects corporate informatics partners include DNAnexus and Amazon Web Services.

There are many other active conservation projects and programs underway.

Sources

  1. https://www.igb-berlin.de/en/news/88-percent-decline-big-freshwater-animals
  2. https://www.eurekalert.org/pub_releases/2019-08/uos-ast080219.php
  3. https://www.nytimes.com/2018/03/20/science/rhino-sudan-extinct.html?rref=collection%2Ftimestopic%2FEndangered%20and%20Extinct%20Species
  4. https://doi.org/10.1038/s41598-018-24269-3
  5. https://www.sanger.ac.uk/news/view/international-vertebrate-genomes-project-releases-first-15-high-quality-reference-genomes
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David is a consultant/medical writer for a number of ongoing healthcare initiatives including for Athla LLC/ HealthLabs, a discovery automation company for Big Data leveraging Big Compute. He has a number of years experience in academic R&D and healthcare related projects including the fields of oncology and immunotherapy.