Million year old genomes DNA has been isolated and sequenced from inside the teeth of three prehistoric mammoths, smashing the record for the
was the ancestor of the woolly mammoth. Earlier studies of woolly mammoth genomes had identified a set of genetic changes that likely allowed these animals to thrive in the frozen Arctic climate. Not surprisingly, the vast majority of these adaptive changes were already present in the DNA of the Siberian ancestors. The oldest tooth comes from a previously unknown branch of the mammoth family tree. The descendants of these mammoths ultimately migrated into North America. The data also implies the mammoth groups interbred at least a handful of times.
most ancient DNA ever analyzed. The molars were found in the Siberian permafrost, which helped preserve the DNA molecules. The samples are too old for carbon dating, so their ages were estimated using a combination of other approaches, including molecular dating of their mitochondrial DNA. The most recent of the mammoths lived more than 680,000 years ago, while the most ancient was estimated at 1.65 million years. The previous record for ancient DNA extraction was a horse that lived sometime between 560,000 and 780,000 years ago. Analysis of the samples suggests there were two different groups of mammoths living in Siberia during this timeframe. One population
REFERENCE: Van der Valk T. et al. Million- year-old DNA sheds light on the genomic his- tory of mammoths. Nature (2021) 591:265-269. DOI: 10.1038/s41586-021-03224-9.
Environmental DNA from air, land and sea
for thousands of years, meaning eDNA can be used to paint a portrait of ancient ecosystems. Several recent publications have recovered eDNA from the animal and human inhabitants of early communities and cave dwellings. One cave site in Spain contained Neanderthal nuclear and mi- tochondrial DNA frommultiple soil layers deposited 80,000 to 113,000 years ago.
Environmental DNA (eDNA) are trace amounts of DNA gathered indirectly from environmental samples rather than directly from an organism. Genetic material from the sample is amplified by polymerase chain reaction (PCR), followed by DNA sequenc- ing and analysis. Over the past twenty years, as sampling and sequencing technologies have become more sensitive, faster and cheaper, eDNA has been detected in water, ice cores, soil, sediment and even the air. Through a process known as eDNA metabarcoding, a single sample can provide a snapshot of an entire community or organisms. This makes eDNA a powerful tool for biodiversity inventory and monitoring. Because it can be applied to ancient as well as modern sites, it has growing applica- tions in paleobiology, archeology, conservation, wildlife trafficking and public health.
Air: Two recent papers describe vacuuming DNA from the air around zoos. Zoos are a useful location for a proof of concept study like this because they generally contain animals not found in the surrounding countryside. The snippets of captured DNA were amplified, sequenced and compared to those from a reference da- tabase. In each case, DNA was consistently identified from dozens of zoo animals. It’s unclear how much DNA floats off organisms into the air, how long those molecules remain aloft and how far they can travel. Those questions require further study.
Water: In the wild, eDNA’s ability to quanti- fy the number of individuals per identified species hadn’t previously been verified. In part, this was because the process requires catching and counting all the organisms in an ecosystem. Fortunately, a UK program aimed at eradicating an invasive freshwater fish species did exactly that. A set of fish ponds were drained and
all non-invasive fish were collect- ed, counted and placed in temporary holding ponds while the invasive species were killed. After the fish were returned to the original ponds, eDNA analysis was carried out and the
results were compared to the manually-collected data. All the fish species were identified and the total biomass of each species correlated closely with the eDNA findings. Separately, the eBioAtlas program announced plans to collect samples from 30,000 freshwater river systems around the globe over the next three years. The data from this $15M initiative will be used to identify freshwater species most at risk of extinction. Soil: Soil not only contains DNA frommicrobial organisms, but also genetic material that has been shed, excreted or decayed from larger organisms. These fragments of DNA can persist
REFERENCES: Di Muri C. et al. Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds. Metabarcoding
and Metagenomics (2020) 4: e56959. DOI: 10.3897/mbmg.4.56959. eBioAtlas — https://ebioatlas.org/ accessed 29 August 2021
Vernot B. et al. Unearthing Neanderthal population history using nuclear and mi- tochondrial DNA from cave sediments. Science (2021) 372:eabf1667. DOI: 10.1126/ science.abf1667. Lynggaard C. et al. Airborne environmental DNA for terrestrial vertebrate communi- ty monitoring. BioRxiv (2021) www.biorxiv.org/content/10.1101/2021.07.16.452634v1. Accessed 29 August 2021. Preprint. Clare E. et al. Measuring biodiversity from DNA in the air. BioRxiv (2021) www.biorxiv.org/content/10.1101/2021.07.15.452392v1. Accessed 29 August 2021. Preprint.
9
SCIENCE FOR LIFE
Made with FlippingBook - Online magazine maker