Genomes of critically endangered saola are shaped by population structure and purging

Genís Garcia-Erill; Shanlin Liu; Minh Duc Le; Martha M. Hurley; Hung Dinh Nguyen; Dzung Quoc Nguyen; Dzung Huy Nguyen; Cindy G. Santander; Fátima Sánchez Barreiro; Nuno Filipe Gomes Martins; Kristian Hanghøj; Faezah Mohd Salleh; Jazmín Ramos-Madrigal; Xi Wang; Mikkel Holger S. Sinding; Hernán E. Morales; Frederik Filip Stæger; Nicholas Wilkinson; Guanliang Meng; Patrícia Pečnerová; Chentao Yang; Malthe Sebro Rasmussen; Mikkel Schubert; Robert R. Dunn; Ida Moltke; Guojie Zhang; Lei Chen; Wen Wang; Trung Tien Cao; Ha Manh Nguyen; Hans R. Siegismund; Anders Albrechtsen; M. Thomas P. Gilbert; Rasmus Heller

doi:10.1016/j.cell.2025.03.040

Genomes of critically endangered saola are shaped by population structure and purging

Genís Garcia-Erill, Shanlin Liu, Minh Duc Le, Martha M. Hurley, Hung Dinh Nguyen, Dzung Quoc Nguyen, Dzung Huy Nguyen, Cindy G. Santander, Fátima Sánchez Barreiro, Nuno Filipe Gomes Martins, Kristian Hanghøj, Faezah Mohd Salleh, Jazmín Ramos-Madrigal, Xi Wang, Mikkel Holger S. Sinding, Hernán E. Morales, Frederik Filip Stæger, Nicholas Wilkinson, Guanliang Meng, Patrícia PečnerováChentao Yang, Malthe Sebro Rasmussen, Mikkel Schubert, Robert R. Dunn, Ida Moltke, Guojie Zhang, Lei Chen, Wen Wang, Trung Tien Cao, Ha Manh Nguyen, Hans R. Siegismund, Anders Albrechtsen^*, M. Thomas P. Gilbert^*, Rasmus Heller^*

^*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Abstract

The saola is one of the most elusive large mammals, standing at the brink of extinction. We constructed a reference genome and resequenced 26 saola individuals, confirming the saola as a basal member of the Bovini. Despite its small geographic range, we found that the saola is partitioned into two populations with high genetic differentiation (F_ST = 0.49). We estimate that these populations diverged and started declining 5,000–20,000 years ago, possibly due to climate changes and exacerbated by increasing human activities. The saola has long tracts without genomic diversity; however, most of these tracts are not shared by the two populations. Saolas carry a high genetic load, yet their gradual decline resulted in the purging of the most deleterious genetic variation. Finally, we find that combining the two populations, e.g., in an eventual captive breeding program, would mitigate the genetic load and increase the odds of species survival.

Originalsprog	Engelsk
Tidsskrift	Cell
ISSN	0092-8674
DOI	https://doi.org/10.1016/j.cell.2025.03.040
Status	E-pub ahead of print - 2025

Bibliografisk note

Publisher Copyright:
© 2025 The Authors

Adgang til dokumentet

10.1016/j.cell.2025.03.040Licens: CC BY-NC-ND

Citationsformater

Garcia-Erill, G., Liu, S., Le, M. D., Hurley, M. M., Nguyen, H. D., Nguyen, D. Q., Nguyen, D. H., Santander, C. G., Sánchez Barreiro, F., Gomes Martins, N. F., Hanghøj, K., Salleh, F. M., Ramos-Madrigal, J., Wang, X., Sinding, M. H. S., Morales, H. E., Stæger, F. F., Wilkinson, N., Meng, G., ... Heller, R. (2025). Genomes of critically endangered saola are shaped by population structure and purging. Cell. Advance online publication. https://doi.org/10.1016/j.cell.2025.03.040

Garcia-Erill, G , Liu, S, Le, MD, Hurley, MM, Nguyen, HD, Nguyen, DQ, Nguyen, DH, Santander, CG, Sánchez Barreiro, F, Gomes Martins, NF , Hanghøj, K, Salleh, FM, Ramos-Madrigal, J, Wang, X, Sinding, MHS , Morales, HE , Stæger, FF, Wilkinson, N, Meng, G, Pečnerová, P, Yang, C, Rasmussen, MS , Schubert, M, Dunn, RR, Moltke, I , Zhang, G, Chen, L, Wang, W, Cao, TT, Nguyen, HM, Siegismund, HR , Albrechtsen, A , Gilbert, MTP & Heller, R 2025, 'Genomes of critically endangered saola are shaped by population structure and purging', Cell. https://doi.org/10.1016/j.cell.2025.03.040

@article{b66f2d7c084c46ee8821c95af480fd76,

title = "Genomes of critically endangered saola are shaped by population structure and purging",

abstract = "The saola is one of the most elusive large mammals, standing at the brink of extinction. We constructed a reference genome and resequenced 26 saola individuals, confirming the saola as a basal member of the Bovini. Despite its small geographic range, we found that the saola is partitioned into two populations with high genetic differentiation (FST = 0.49). We estimate that these populations diverged and started declining 5,000–20,000 years ago, possibly due to climate changes and exacerbated by increasing human activities. The saola has long tracts without genomic diversity; however, most of these tracts are not shared by the two populations. Saolas carry a high genetic load, yet their gradual decline resulted in the purging of the most deleterious genetic variation. Finally, we find that combining the two populations, e.g., in an eventual captive breeding program, would mitigate the genetic load and increase the odds of species survival.",

keywords = "conservation genomics, degraded DNA, evolutionary genomics, genetic rescue, phylogenomics, saola, zoology",

author = "Gen{\'i}s Garcia-Erill and Shanlin Liu and Le, {Minh Duc} and Hurley, {Martha M.} and Nguyen, {Hung Dinh} and Nguyen, {Dzung Quoc} and Nguyen, {Dzung Huy} and Santander, {Cindy G.} and {S{\'a}nchez Barreiro}, F{\'a}tima and {Gomes Martins}, {Nuno Filipe} and Kristian Hangh{\o}j and Salleh, {Faezah Mohd} and Jazm{\'i}n Ramos-Madrigal and Xi Wang and Sinding, {Mikkel Holger S.} and Morales, {Hern{\'a}n E.} and St{\ae}ger, {Frederik Filip} and Nicholas Wilkinson and Guanliang Meng and Patr{\'i}cia Pe{\v c}nerov{\'a} and Chentao Yang and Rasmussen, {Malthe Sebro} and Mikkel Schubert and Dunn, {Robert R.} and Ida Moltke and Guojie Zhang and Lei Chen and Wen Wang and Cao, {Trung Tien} and Nguyen, {Ha Manh} and Siegismund, {Hans R.} and Anders Albrechtsen and Gilbert, {M. Thomas P.} and Rasmus Heller",

note = "Publisher Copyright: {\textcopyright} 2025 The Authors",

year = "2025",

doi = "10.1016/j.cell.2025.03.040",

language = "English",

journal = "Cell",

issn = "0092-8674",

publisher = "Cell Press",

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TY - JOUR

T1 - Genomes of critically endangered saola are shaped by population structure and purging

AU - Garcia-Erill, Genís

AU - Liu, Shanlin

AU - Le, Minh Duc

AU - Hurley, Martha M.

AU - Nguyen, Hung Dinh

AU - Nguyen, Dzung Quoc

AU - Nguyen, Dzung Huy

AU - Santander, Cindy G.

AU - Sánchez Barreiro, Fátima

AU - Gomes Martins, Nuno Filipe

AU - Hanghøj, Kristian

AU - Salleh, Faezah Mohd

AU - Ramos-Madrigal, Jazmín

AU - Wang, Xi

AU - Sinding, Mikkel Holger S.

AU - Morales, Hernán E.

AU - Stæger, Frederik Filip

AU - Wilkinson, Nicholas

AU - Meng, Guanliang

AU - Pečnerová, Patrícia

AU - Yang, Chentao

AU - Rasmussen, Malthe Sebro

AU - Schubert, Mikkel

AU - Dunn, Robert R.

AU - Moltke, Ida

AU - Zhang, Guojie

AU - Chen, Lei

AU - Wang, Wen

AU - Cao, Trung Tien

AU - Nguyen, Ha Manh

AU - Siegismund, Hans R.

AU - Albrechtsen, Anders

AU - Gilbert, M. Thomas P.

AU - Heller, Rasmus

PY - 2025

Y1 - 2025

N2 - The saola is one of the most elusive large mammals, standing at the brink of extinction. We constructed a reference genome and resequenced 26 saola individuals, confirming the saola as a basal member of the Bovini. Despite its small geographic range, we found that the saola is partitioned into two populations with high genetic differentiation (FST = 0.49). We estimate that these populations diverged and started declining 5,000–20,000 years ago, possibly due to climate changes and exacerbated by increasing human activities. The saola has long tracts without genomic diversity; however, most of these tracts are not shared by the two populations. Saolas carry a high genetic load, yet their gradual decline resulted in the purging of the most deleterious genetic variation. Finally, we find that combining the two populations, e.g., in an eventual captive breeding program, would mitigate the genetic load and increase the odds of species survival.

AB - The saola is one of the most elusive large mammals, standing at the brink of extinction. We constructed a reference genome and resequenced 26 saola individuals, confirming the saola as a basal member of the Bovini. Despite its small geographic range, we found that the saola is partitioned into two populations with high genetic differentiation (FST = 0.49). We estimate that these populations diverged and started declining 5,000–20,000 years ago, possibly due to climate changes and exacerbated by increasing human activities. The saola has long tracts without genomic diversity; however, most of these tracts are not shared by the two populations. Saolas carry a high genetic load, yet their gradual decline resulted in the purging of the most deleterious genetic variation. Finally, we find that combining the two populations, e.g., in an eventual captive breeding program, would mitigate the genetic load and increase the odds of species survival.

KW - conservation genomics

KW - degraded DNA

KW - evolutionary genomics

KW - genetic rescue

KW - phylogenomics

KW - saola

KW - zoology

U2 - 10.1016/j.cell.2025.03.040

DO - 10.1016/j.cell.2025.03.040

M3 - Journal article

C2 - 40328258

AN - SCOPUS:105004399666

SN - 0092-8674

JO - Cell

JF - Cell

ER -