By Marta Koblańska, August 22, 2025, 12:20 Poland’s time, photo: DNA’s clash, Placidplace, Pixabay
The risk for a population to become extinct increases along with extended and intensified inbreeding, American scientists claim. Simultaneously, genetic diversity may be taken as an advantage.
In ancient Egypt, inbreeding was seen as a method to preserve the population’s exceptional traits and contribute to a more advanced society. This approach was effective for a time; however, over time, excessive genetic similarity ultimately led to the collapse of this great civilization. Recently, scientists in California, USA, have confirmed that the extension of homozygous stretches (similar sections) in the genetic code (DNA) serves as a reliable genomic marker for inbreeding breakdown.
These long runs of homozygosity are associated with reduced rates of survival as well as reproduction in diverse mammals and bird species,
claim Christopher C. Kyriazis of Conservation Genetics, San Diego Zoo, Escondido, Jacqueline A. Robinson of Institute for Human Genetics, University of California, San Francisco, and Kirk E. Lohmueller of Department of Ecology and Evolutionary Biology, University of California, Los Angeles.
An overall rule applicable to all societies and species, including humans, is that fitness, typically measured with reproduction and survival rates, represents one of the most important markers to assess a population’s stability or potential deterioration. Many studies have been conducted to prove whether a higher genetic variation is linked to better conditions of a population. Those study results were unclear. However, the is clear that shared ancestry may negatively impact fitness.
With the advancement of modern methods for identifying potentially harmful mutations in genomic variation datasets, new research opportunities have emerged. Scientists now widely use these methods to estimate fitness and genetic load in wild populations, often to assess extinction risk status. Given that earlier discoveries highlighted the similarities between mammalian and human genetic codes, why can’t these methods be applied to human populations as well?
What does homozygosity mean?
To answer the above question, first, let’s try to explain what homozygosity means in reality. Simplifying, these are identical haplotypes from related ancestors inherited in a given genome. A haplotype represents a group of genes that originate from just one parent and are located close to each other, potentially constituting a contiguous stretch in the genome. Not to dive into a dump, this is our past and heritage we all have, whether we like it or not. A simple conclusion could be: the longer similar sections within DNA, the closer ancestors we have inherited.
Because the length of an ROH (long runs of homozygosity) is determined by the number of generations of recombination separating related individuals from a common ancestor, the ROH length distribution in a population is in turn reflective of demographic history,
say scientists in the paper titled,,Long runs of homozygosity are reliable genomic markers of inbreeding depression” and published in ,,Trends in Ecology&Evolution”.
They add that the short stretches with a similar group of genes tend to arise due to historical population bottlenecks, whereas long ROH are a product of more recent inbreeding between closely related individuals. Moreover, it is also possible to estimate the inbreeding coefficient as well as uncover complex traits associated with inbreeding.
The victor and the defeated
Long runs of homozygosity (ROH), while not inherently harmful, may be more susceptible to harmful mutations under certain conditions. In contrast, deleterious mutations are less frequent in shorter ROH stretches. This can create a bottleneck effect. Additionally, short ROH segments are often exposed to purifying selection for a longer period, which helps eliminate recessive deleterious variants more effectively, according to scientists.
In general, the longer the similar stretches of DNA, the worse the outcomes for a species or population. This was demonstrated by Zachary Szpiech in a pioneering paper, which suggested that closer inbreeding increases the likelihood of harmful mutations that negatively affect overall health and fitness. Data from American scientists show that a 1% increase in the prevalence of long runs of homozygosity (ROH) is associated with a 12.4% reduction in first-year survival rates, compared to only a 7.7% reduction for medium ROH. However, evolution sometimes compensates for these adverse effects, demonstrating its remarkable principles and capabilities. How? Long runs of homozygosity (ROH) are primarily caused by rare recessive deleterious mutations, which can have a significant negative impact. However, in certain cases, when two recessive genes come together, the overall effect can be better than average in conditions where neither gene is harmful. The theoretical link between long ROH and fitness is expected, as these long runs consist of younger haplotypes that have experienced limited purifying selection to eliminate strongly deleterious recessive alleles, according to scientists.
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