Genomic study finds low genetic diversity and high levels of inbreeding in this vulnerable species.
Small populations are often at risk. They can get sucked in a negative feedback loop of genetic and demographic decline that culminates in their extinction (the so-called extinction vortex, which I covered in this blog post). In general, small populations are more vulnerable to genetic drift and inbreeding, leading to a loss of genetic diversity. This lower level of genetic diversity might prevent small populations from adapting to changing environments. However, it is not all misery and mayhem for small populations. One potential benefit of a small population size is genetic purging, the process in which deleterious variants appear more often due to inbreeding and get purged from the population because individuals carrying these variants fail to survive or reproduce. The result is a genetically healthier population, despite low levels of genetic diversity.
A recent study in the journal Molecular Biology and Evolution examined the situation of the brown eared pheasant (Crossoptilon mantchuricum), a vulnerable bird species that is declining across its range in China due to human activities, such as deforestation and hunting. Is this species heading for extinction or does it reap the benefits of genetic purging?
Based on the genomes of 40 individuals, the researchers identified three distinct populations corresponding to locations in Shaanxi (Western), Shanxi (Central), and Hebei & Beijing (Eastern). The genetic diversity across these three populations was extremely low. In fact, it was the lowest genome-wide estimate for any bird species to date. But, as explained above, this low level of genetic diversity might result in genetic purging when deleterious alleles are filtered out by purifying selection.
The action of genetic purging can be tested with the population genetic statistic Tajima’s D. I have explained the rationale behind the statistic in another blog post, but for this story you only need to understand the main interpretation. In general, a negative Tajima’s D points to a selective sweep (and thus genetic purging), while a positive Tajima’s D suggests balancing selection. In the three brown eared pheasant populations, Tajima’s D was highly positive. There is thus no evidence for genetic purging. And that is bad news…
Low genetic diversity is often the outcome of inbreeding. When related individuals mate, their offspring will mostly receive the same genetic variants from both parents. This results in large genomic regions with little genetic variation, also known as runs of homozygosity (ROHs). The brown eared pheasant did indeed show more ROHs compared to its sister species, the blue eared pheasant (C. auritum), that is of little conservation concern.
A closer look at these genomic regions revealed that some brown eared pheasant populations have accumulated missense and loss-of-function mutations. Missense mutations occur when a change in the DNA results in the wrong amino acid being incorporated into a protein. And loss-of-function mutations lead to functional problems in the activity of a protein. Clearly, the brown eared pheasant is suffering from inbreeding depression. Moreover, because natural selection seems unable to eliminate deleterious mutations, this species is accumulating a high genetic load. Unless conservation actions are implemented – such as a genetic rescue program – the brown eared pheasant might be heading for extinction.
Wang et al. (2021). Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant. Molecular Biology and Evolution, 38(1), 263-273.
Featured image: Brown eared pheasant (Crossoptilon mantchuricum) © Josh More | Flickr