Genomic analysis reveals limited hybridization among three giraffe species in Kenya
DOI: 10.1186/s12915-023-01722-yRead our scientific commentaryResearch by
Raphael T. F. Coimbra, Sven Winter, Arthur Muneza, Stephanie Fennessy, Moses Otiende, Domnic Mijele, Symon Masiaine, Jenna Stacy‐Dawes, Julian Fennessy, Axel Janke
Separates population structure, historical allele sharing and recent migration estimates in a genome-scale analysis of three East African giraffe taxa.
Study summary
Some wild giraffes carry ancestry from another species. In Kenya, the ranges of Nubian, reticulated and Masai giraffes meet, and unusual coat patterns had prompted reports of possible hybrids. The unresolved issue was whether those neighbours regularly interbred or mostly retained separate evolutionary histories despite living close enough to meet.
Raphael Coimbra, Sven Winter and colleagues examined 128 genomes representing the three groups, including 113 newly sequenced giraffes from Kenya. They deliberately sampled suspected contact zones and compared DNA inherited from both parents with mitochondrial DNA, which follows the maternal line. Separate analyses searched for older mixing and estimated gene exchange during the most recent two generations.
Thirteen reticulated giraffes from the Laikipia Plateau showed varying amounts of Nubian ancestry, most consistent with historical interbreeding. One individual had particularly substantial Nubian ancestry and Nubian mitochondrial DNA, suggesting a hybrid or a descendant of one. Yet the three groups remained clearly separated across their genomes. Estimated recent gene flow was low and statistically indistinguishable from zero, which does not prove it never occurs. The result shows why occasional mixed ancestry need not erase species boundaries: interbreeding can leave a trace without turning neighbouring giraffes into a single population.
Summary by The Last Giraffe
Publication details
Study facts
- Method
- Whole-genome population structure, phylogenetic, admixture and demographic analyses with relatedness filtering.
- Location
- Primarily Kenya, with existing comparison genomes from Ethiopia, Tanzania and Uganda.
- Species
- Nubian, reticulated and Masai sensu stricto giraffes, under the authors' four-species classification.
- Sample
- 128 focal genomes (113 new, 15 reused); 116 in structure analysis; 97 in recent-migration analysis.
- Period
- Sampling calendar dates not specified in main Methods; supplementary sample table not inspected.
Full citation
Raphael T. F. Coimbra, Sven Winter, Arthur Muneza, Stephanie Fennessy, Moses Otiende, Domnic Mijele, Symon Masiaine, Jenna Stacy‐Dawes, Julian Fennessy, Axel Janke (2023). Genomic analysis reveals limited hybridization among three giraffe species in Kenya. BMC Biology. https://doi.org/10.1186/s12915-023-01722-y
Open the original publicationOriginal abstract
Background In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa.
Results We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe.
Conclusions Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
Abstract by Raphael T. F. Coimbra, Sven Winter, Arthur Muneza, Stephanie Fennessy, Moses Otiende, Domnic Mijele, Symon Masiaine, Jenna Stacy-Dawes, Julian Fennessy and Axel Janke. Genomic analysis reveals limited hybridization among three giraffe species in Kenya. BMC Biology 21, 215 (2023). Reproduced under CC BY 4.0. No author or publisher endorsement is implied.
Source abstract · Creative Commons Attribution 4.0 International (CC BY 4.0). Abstract text reproduced without changes; formatting adapted for this website.