A giraffe can descend from several distinct populations and still have closely related parents. Those two facts describe different parts of its history, and both can be written into the same genome.
That was the central finding of a 2026 study by Mischa Fraser and colleagues. They examined whole-genome data from 13 zoo giraffes, comparing the animals with 71 wild giraffes representing major lineages. Mixed ancestry was common in the zoo sample. Several individuals also carried conspicuous evidence of recent inbreeding.
The results explain why a reassuring average measure of genetic variation can conceal an important feature of recent family history. To understand an individual, the researchers needed to ask where its ancestry came from, how often its two chromosome copies differed, and how those differences were distributed along the genome.
Three questions hidden in the same DNA
Ancestry analysis compares the variants carried by an animal with those in reference populations. In this study, the wild giraffes supplied the reference. The researchers estimated contributions from broad species-level groups and from more detailed population groupings, then used a second statistical test to check a prominent pattern of mixed ancestry.
Heterozygosity asks another question. At a particular position in the genome, are the copies inherited from the mother and father different? Averaging the answer across many positions provides a measure of variation within the individual.
If ancestors came from populations carrying different variants, their descendants may have high heterozygosity. But that average says little about whether particular chromosome stretches were inherited through recent relatives.
For that, the team looked for runs of homozygosity: long regions in which the two copies match. Parents who share an ancestor can pass down copies of the same ancestral chromosome segment. When a descendant receives both copies, that stretch is homozygous by descent.
The length of a matching stretch helps interpret its history. Recombination reshuffles chromosomes over generations, tending to break old inherited segments into smaller pieces. Very long matching stretches therefore point more strongly toward recent shared ancestry than a collection of short ones. The study specifically highlighted runs longer than ten million DNA bases as evidence of recent inbreeding.
A familiar label did not always describe the ancestry
Only three of the 13 zoo giraffes appeared unadmixed relative to the reference populations used. Other animals had contributions assigned to two or more lineages. The animals recorded as reticulated giraffes generally showed an estimated mixture dominated by reticulated ancestry, with a smaller Nubian contribution.
Marius, the Copenhagen Zoo giraffe whose death in 2014 attracted international attention, was among them. His estimated ancestry was approximately 85 percent reticulated and 15 percent Nubian. Similar mixtures in several zoo animals were consistent with their shared pedigree history, rather than representing independent evidence of the same cross occurring repeatedly.
Those proportions are model estimates conditional on the available wild reference panel. They are not measurements of how much of an animal's appearance belongs to each group. A missing or poorly represented source population could change the interpretation.
The study also identified mixed ancestry in the individual used for a widely used giraffe reference genome. That matters for research because a reference assembly is a sequence built from a particular animal, not a guarantee of unmixed ancestry from the name attached to it. Subsequent analyses need to distinguish the utility of that sequence from assumptions about its population identity.
The long stretches change the picture
Marius and another animal, Esta, had large fractions of their genomes in long homozygous runs compared with the wild reticulated reference. Twiga, whose ancestry was assigned to several northern giraffe lineages, also carried extensive long runs. The combination directly demonstrates that mixed ancestry does not prevent recent relatives from breeding with one another.
The researchers then recalculated heterozygosity after excluding the matching runs. This is an informative comparison within each genome: it asks how diverse the remainder is when the regions most affected by shared recent ancestry are set aside.
For the animals with conspicuous long runs, the difference between the two estimates was especially marked. Their remaining genomes contained variation, but the long matching stretches reduced the whole-genome average. In Marius and Esta, this reduction was substantial enough that mixed ancestry did not lift their overall heterozygosity above the corresponding wild comparison.
Pedigree records provided an independent line of support. The family histories included repeated ancestors and matings among relatives. The genomic pattern therefore agreed with evidence from recorded parentage, while showing the particular DNA consequences rather than relying on the pedigree alone.
This does not make a pedigree obsolete. A studbook can record relationships and events that sequence data cannot uniquely reconstruct. Genomes can expose ancestry or inherited matching regions that an incomplete label or family record misses. The two sources answer overlapping but different questions.
A wild population comparison shows why history matters
A 2022 study of northern giraffes likewise separated overall heterozygosity from regions inherited from shared ancestors. West African giraffes had a somewhat lower median heterozygosity than Kordofan giraffes in that study, but the difference in their inferred inbreeding histories was clearer when the researchers examined the matching segments and their lengths.
The studies used different samples, reference genomes and analytical methods, so their raw percentages should not be directly ranked as though they came from one assay. Their shared lesson is methodological: the amount of variation and its arrangement along chromosomes reveal different aspects of population and family history.
In the zoo study, ancestry mixing and subsequent close relationships were both important. A population label alone could not establish the first, and a genome-wide average alone could not fully describe the second.
What the study leaves for larger investigations
The researchers did not measure survival, fertility or disease associated with these genomic patterns. Evidence of inbreeding is not itself a measurement of inbreeding depression, the harmful effects that can occur when relatives breed. Likewise, identifying mixed ancestry does not demonstrate harmful effects from crossing lineages.
The sample also comprised only 13 zoo giraffes. It establishes that both processes occur in those animals and identifies reasons for broader investigation. It cannot give a reliable prevalence for every zoo population or determine the best pairing for animals that were not studied.
The practical scientific advance is a more complete description of genetic background. An animal may retain diverse ancestry across much of its genome while carrying long matching stretches from recent shared ancestors. Keeping both facts visible makes the result understandable—and prevents a single diversity score from being asked to tell a history it cannot contain.
Sources
- Mischa F. Fraser, Rasmus Heller, Laura D. Bertola, Christina Hvilsom, Renzo F. Balboa, Xiaodong Liu and Anna Brüniche-Olsen (2026). “Unfolding admixed ancestry and genomic diversity in zoo giraffes.” Conservation Genetics 27, 21. Full paper.
- Raphael T. F. Coimbra, Sven Winter, Barbara Mitchell, Julian Fennessy and Axel Janke (2022). “Conservation genomics of two threatened subspecies of Northern giraffe: the West African and the Kordofan giraffe.” Genes 13, 221. Related study.
