A study using sequencing data to evaluate the impact of genetic factors on efforts to conserve the highly endangered vaquita porpoise is presented in Science this week, highlighting the value of genomics in predicting the extinction risk of endangered species. The vaquita is one of the world's most endangered species, as excessive mortality from gillnet fishing has pushed the animal's population to about 10 remaining individuals. While efforts are ongoing to increase the number of vaquita porpoises, it remains unknown how much inbreeding depression could affect recovery. To address this question, a team led by scientists from the University of California, San Francisco, and the National Oceanic and Atmospheric Administration analyzed whole-genome sequences from archival tissue samples from 20 vaquitas and integrated genomic and demographic information into stochastic, individual-based simulations to quantify the species' recovery potential. They find that the vaquita's historical rarity has resulted in a low burden of segregating deleterious variation, reducing the risk of inbreeding depression. As such, "there is a high potential for vaquita recovery in the absence of gillnet mortality, refuting the view that the species is doomed to extinction by genetic factors," the investigators write. The analysis also shows the potential for genomics-informed population viability modeling, "which may have widespread applications given the increasing feasibility of genomic sequencing for non-model species amid a worsening extinction crisis," they conclude.
The first genetic physical unclonable functions (PUFs) in human cells are reported in Science Advances this week. A PUF is a physical entity that provides a measurable output that can be used as a unique and irreproducible identifier for item in which it is embedded. The electronics industry widely uses silicon PUFs, which exploit the inherent physical variation of advanced semiconductor manufacturing processes to establish intrinsic security primitives for verifying the genuineness of integrated circuits. Seeking to extend this approach to the biological sciences, researchers from the University of Texas at Dallas leveraged the complexity of barcode libraries and the inherent stochasticity of DNA error-repair induced via genome editing to engineer CRISPR-based genetic PUFs in human cells. They show that these genetic PUFs repeatedly produce the same output, are unique among other identically produced PUFs, and are unclonable. Genetic PUFs, they write, could be embedded in cell lines to attest their provenance. The producer of a valuable cell line, for instance, could insert a PUF in each legitimately produced copy of this cell line. "Upon thawing of a frozen sample and before its initial use, a customer who purchased a copy of the cell line can obtain this signature and communicate it to the producer who compares it against the signature database of legitimately produced copies of this cell line," they write. "Through this protocol, the producer of the cell line can ensure that anyone publicly claiming ownership of a copy of this cell line has acquired it legitimately. At the same time, the customer can be assured of the source and quality of the procured cell line, as the producer explicitly confirms its origin and assumes responsibility for its production."