TY - JOUR

T1 - Giraffe lineages are shaped by major ancient admixture events

AU - Bertola, Laura D.

AU - Quinn, Liam

AU - Hanghøj, Kristian

AU - Garcia-Erill, Genís

AU - Rasmussen, Malthe Sebro

AU - Balboa, Renzo F.

AU - Meisner, Jonas

AU - Bøggild, Thomas

AU - Wang, Xi

AU - Lin, Long

AU - Nursyifa, Casia

AU - Liu, Xiaodong

AU - Li, Zilong

AU - Chege, Mumbi

AU - Moodley, Yoshan

AU - Brüniche-Olsen, Anna

AU - Kuja, Josiah

AU - Schubert, Mikkel

AU - Agaba, Morris

AU - Santander, Cindy G.

AU - Sinding, Mikkel Holger S.

AU - Muwanika, Vincent

AU - Masembe, Charles

AU - Siegismund, Hans R.

AU - Moltke, Ida

AU - Albrechtsen, Anders

AU - Heller, Rasmus

N1 - Publisher Copyright: © 2024 The Author(s)

PY - 2024

Y1 - 2024

N2 - Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.

AB - Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.

KW - Africa

KW - biodiversity

KW - conservation

KW - evolution

KW - evolutionary history

KW - gene flow

KW - genomic diversity

KW - introgression

KW - population structure

KW - speciation

U2 - 10.1016/j.cub.2024.02.051

DO - 10.1016/j.cub.2024.02.051

M3 - Journal article

C2 - 38479386

AN - SCOPUS:85189016736

VL - 34

SP - 1576-1586.e5

JO - Current Biology

JF - Current Biology

SN - 0960-9822

IS - 7

ER -