Surprisingly high genome-wide diversity in the California Condor

A genetic legacy from a prehistoric abundance.

In 1987, the California Condor (Gymnogyps californianus) was extinct in the wild. All the remaining wild individuals were captured and entered into an extensive captive breeding program. Beginning in 1991, the condors were reintroduced into the wild. At the moment that I write this blog post, the total population is estimated at 557 birds, of which 343 live in the wild (you can follow the status of the population here).

Having been on the brink of extinction, you might expect very low genetic diversity in the California Condor (see for example this blog post). Surprisingly, that is not the case. A recent study in the journal Current Biology reported that “[f]or a species that was briefly extinct in the wild, the California condor has unexpectedly high genome-wide diversity.” How can we explain this counterintuitive pattern?

Demographic Analyses

Jacqueline Robinson and her colleagues generated a high-quality genome of the California Condor. The largely contiguous genome sequence allowed them to explore the genetic make-up of this vulture in great detail. High levels of inbreeding – even before its near extinction – left a clear genetic signature as so-called “runs of homozygosity” (ROHs). These runs are stretches of DNA with no genetic variation. More than 20% of the Californian Condor genome contained these deserts of low genetic diversity (compared to only 5.7% in the Andean Condor and 4.24% in the Turkey Vulture).

Despite the prevalence of these ROHs, the genome-wide diversity was unexpectedly high (as I already mentioned above). This pattern can be explained by the demographic history of the Californian Condor. Reconstructing the past effective population size of this species revealed that it used to be very abundant (see this blog post for more information about the method). The researchers noted that “California Condors were more abundant than either Andean Condors or Turkey Vultures for much of the Pleistocene” (although this statement has been questioned, see here and here).

Historical effective population sizes of Californian Condor (brown), Andean Condor (blue) and Turkey Vulture (green). From: Robinson et al. (2021).

History Matters

The high genome-wide diversity in the California Condor is thus a legacy from its prehistoric abundance. This finding highlights the importance of taking into account the evolutionary history of a species. Present-day patterns can often be explained by past events. As John Michael Crichton (the author of Jurassic Park) nicely put it: “If you don’t know history, you don’t know anything. You are a leaf that doesn’t know it is part of a tree.”

References

Robinson, J. A., Bowie, R. C., Dudchenko, O., Aiden, E. L., Hendrickson, S. L., Steiner, C. C., Ryder, O. A., Mindell, D. P. & Wall, J. D. (2021). Genome-wide diversity in the California condor tracks its prehistoric abundance and decline. Current Biology, 31(13), 2939-2946.

Featured image: California Condor (Gymnogyps californianus) © Scott Frier Nikon | Wikimedia Commons

Ancient DNA reveals low levels of past genetic diversity in the Andean Condor

Low genetic diversity might be the natural state for this vulture.

Since the first release of Andean Condors (Vultur gryphus) in Colombia in 1989, more than 200 individual birds have be re-introduced in the wild across South America. The goal of these introductions was to reinforce existing populations and re-establish extinct ones. One of the main arguments for such extensive management programs is the augmentation of genetic diversity. However, the relationship between genetic diversity and the risk of species extinction is not always straightforward (see for example this blog post). And in many cases, it is not clear how much genetic variation has been lost over time. So, what about the Andean Condor? A recent study in the journal Ecology and Evolution obtained DNA samples from museum collections to assess the historical levels of genetic diversity in this iconic vulture species.

Haplotypes

Julian Padró and his colleagues sequenced several mitochondrial markers for 42 Andean Condors, covering a time period from 1884 to 2013. The historical and modern samples shared several haplotypes, but one haplotype from 1896 seems to have been lost. This genetic variant belonged to a now extinct population on the Patagonian coast. Demographic analyses indicated that this loss of genetic diversity coincided with the timing of European colonization in South America. Probably, the development of livestock production resulted in conflict between humans and Andean Condors.

In contrast to the southern populations, Andean Condors in the north of their range did lose any haplotypes, despite being driven to near-extinction in recent times. The similar genetic diversity in historical and present times, in combination with the relatively modest loss of one mitochondrial haplotype, suggest that the Andean Condor can cope with low levels genetic diversity. Similar patterns have been reported in other raptor species, such as the Spanish Imperial Eagle (Aquila adalberti) and the Cinereous Vulture (Aegypius monachus).

An overview of the sampling locations for the historical and contemporary samples. The haplotype shows the modest loss of genetic diversity over time. From: Padró et al. (2020) Ecology and Evolution.

Genomics

The researchers concluded that “Low levels of genetic diversity found in the Andean condor represent a natural state of mtDNA, and thus are unlikely to be an immediate threat to long-term viability.” However, mtDNA represents only a tiny fraction of the total genetic diversity in a population. A genomic perspective is needed to assess the impact of population bottlenecks on the genetic make-up of the Andean Condor. These raptors might be able to withstand a decline in mitochondrial diversity, but what if other genomic regions have been eroded?

References

Padró, J., Lambertucci, S. A., Perrig, P. L., & Pauli, J. N. (2020). Andean and California condors possess dissimilar genetic composition but exhibit similar demographic histories. Ecology and Evolution, 10(23), 13011-13021.

Featured image: Andean Condor (Vultur gryphus) © Ltshears | Wikimedia Commons