Temporal Genomics: Reading Extinction In the Genome
Quick Summary
- As of 2024 the World Wildlife Fund has measured an astonishing 73% decline in the average size of wildlife populations across the planet in the last 50 years.
- An emerging study of temporal genomics have allowed scientists to observe evolutionary, adaptive, and population trends throughout our planets past.
- Nature has demonstrated its ability to adapt but the pace we are transforming the landscape and the climate is pushing species further down the extinction vortex faster than their ancestors before them.
The global biosphere has seen rapid and dramatic shifts due to anthropogenetic climate change and habitat loss. In our contemporary world biodiversity has been plummeting at rapid rates, with the IUCN classifying 48,600 species across the planet as threatened or endangered accounting for roughly 28% of all assessed species. As of 2024 the World Wildlife Fund has measured an astonishing 73% decline in the average size of wildlife populations across the planet in the last 50 years. Understanding the scope of this crisis, the systems in peril, and the potential outcomes have never been more important. As biotechnology sees rapid advancements in recent years contemporary sequencing technology allow scientists to use DNA like historical archive of the history of our planets species. An emerging study of temporal genomics have allowed scientists to observe evolutionary, adaptive, and population trends throughout our planets past. By comparing contemporary population changes with those of the past enables us the ability to read the code of life to discover the precursors of extinction.
The Pleistocene Epoch is the most recent period of geologic time that predates the current Holocene. The Pleistocene also known as the Ice Age, was defined by intermittent patterns of cyclical glacial expansion and retreat. These conditions created a unique natural experiment that showed how populations shift and adapt to climatic changes. By consulting the fossil record and using new advances in genomic biotechnology creates an experimental case study into natural population fluctuations in response to climate change, and importantly both with and without homo sapiens.
Particularly, advances in genomic sequencing technology and the sequencing ancient DNA of the organisms that populated this ancient world have allowed for glimpses into these bygone ecosystems. Genomic data and fossil evidence have revealed shifting population trends aligned with the cyclical glacial periods of the era. Fossil evidence shows during colder periods, cold adapted species such as woolly mammoth, steppe bison, and wild horses were relatively abundant. Yet during interglacial periods they would become much less abundant. DNA analysis of fossils from these interglacial periods correlate with increased levels of genetic bottlenecks, indicating these populations saw declining numbers, lowering of genetic diversity, and inbreeding. Yet extinction levels remained relatively low. Reconstructing these ecosystems with genomic data creates a picture where the regular warming of the planet during interglacial periods restricted the habitats of these cold adapted megafauna, promoting habitat fragmentation and population isolation. As the planet re-cooled during glacial periods, cold adapted species would again expand out from their refugia and the cycle would continue.
These conditions created a natural experiment that demonstrates the biospheres adaptability and plasticity to change. Yet the conditions of the Pleistocene importantly show that planetary warming alone was not enough to lead to the extinction of these species but facilitated the growth of the genetic precursors of extinction. At the end of the last glacial period and the start of the Holocene temperatures warmed and megafauna of both cold adapted species and warm adapted species suddenly plummeted to extinction levels unlike the rest of the Pleistocene. This decline is correlated with the arrival of humans to these regions, indicating that the stress of climate change that facilitated the extinction vortex, a process where declining genetic diversity weakens their ability to adapt. The vortex promoted their initial decline and then when combined with the arrival of a new kind of alien stress was enough to push these species to their absolute breaking point.
These conditions create parallels to our contemporary world. Human expansion across the planet has led to widespread habitat fragmentation and population isolation, artificially promoting population decline that we don't need the fossil record to observe. Using the same genomic technologies used to uncover ancient population oscillations now reveal identical bottleneck patterns in contemporary populations. The mounting anthropogenic stress of habitat loss and climate change has populations on the brink. And as populations are corralled into ever smaller refugia genetic diversity alongside population sizes will continue plummeting.
Today, populations are approaching the same extinction precursors of genetic erosion and population decline that occurred in the Pleistocene. Yet species face these same climatic challenges coupled with the highest level of anthropogenic disturbance ever, accelerating a snowballing extinction event. In the Andes, alpine forests have increasingly shifted upslope to avoid warming, while in the Arctic fauna migrate south as habitats disappear. Genomic monitoring of these regions and others reveal that the same thresholds that triggered ancient extinction vortices are emerging in contemporary species all over the world. And as they shift they become more vulnerable to losses in genetic diversity that facilitate this vortex promoted by these compounding stressors.
By using genomic data to reconstruct the Pleistocene we are provided a window into the trajectory of our planet if nothing is done. Nature has demonstrated its ability to adapt but the pace we are transforming the landscape and the climate is pushing species further down the extinction vortex faster than their ancestors before them. Genomic data from both deep time and the contemporary show that the combination of these stressors simply outpace the adaptability of most species. Temporal genomics is a powerful reconstructive tool that reveals the trajectories of how species respond to accelerating human induced change. Revealing how these responses feed directly into the extinction vortex. Genomic biotechnologies make it clear the Pleistocene experiment is a precedent that reveals the genomic signatures that predate extinction. Yet today the stakes are higher and the outcome will be more intense without the increasing adoption of prudent and informed conservation management.
Sources:
Beth Alison Shapiro. (2016). How to clone a mammoth : the science of de-extinction. Princeton University Press.
Kolbert, E. (2024). The Sixth Extinction (10th Anniversary Edition). Holt Paperbacks.
IUCN Red List of Threatened Species
WWF LPR: Wildlife Populations Down 73% Since 1970 | World Wildlife Fund
Deep-time paleogenomics and the limits of DNA survival - PMC