Genomic and morphometric evidence for Austronesian-mediated pig translocation in the Pacific

David W. G. Stanton; Aurelie Mannin; Allowen Evin; Kristina Tabbada; Anna Linderholm; Rosie Drinkwater; Olaf Thalmann; Said I Ng’Ang’A; Noel Amano; Atholl Anderson; Ross Barnett; Patrick Barrière; Stuart Bedford; Peter Bellwood; Adam Brumm; Trung Cao Tien; Geoffrey Clark; Richard Crooijmans; Thomas Cucchi; Michelle S. Eusebio; Linus G Flink; Peter Galbusera; Martien Groenen; Budianto Hakim; Stuart Hawkins; Holly Heiniger; Kristofer M Helgen; Michael J. Herrera; Terry Hunt; Andrew C Kitchener; Carol Lee; Alastair A Macdonald; Hendrik-Jan Megens; Erik Meijaard; Kieren J. Mitchell; Christopher Moran; Karen Mudar; Karma Nidup; Marc Oxenham; Rinzin Pem; Philip Piper; Kyle Schachtschneider; Lawrence Schook; Pradeepa Silva; Matthew Spriggs; Samuel Turvey; Una Strand Viðarsdóttir; Murray P. Cox; Tim Denham; Jamie Gongorra; Keith Dobney; Greger Larson; Laurent A. F. Frantz

doi:10.1101/2025.07.07.663491

Genomic and morphometric evidence for Austronesian-mediated pig translocation in the Pacific

David W. G. Stanton
, Aurelie Mannin
, Allowen Evin
, Kristina Tabbada
, Anna Linderholm
, Rosie Drinkwater
, Olaf Thalmann
, Said I Ng’Ang’A
, Noel Amano
, Atholl Anderson
, Ross Barnett
, Patrick Barrière
, Stuart Bedford
, Peter Bellwood
, Adam Brumm
, Trung Cao Tien
, Geoffrey Clark
, Richard Crooijmans
, Thomas Cucchi
, Michelle S. Eusebio

Linus G Flink, Peter Galbusera, Martien Groenen, Budianto Hakim, Stuart Hawkins, Holly Heiniger, Kristofer M Helgen, Michael J. Herrera, Terry Hunt, Andrew C Kitchener, Carol Lee, Alastair A Macdonald, Hendrik-Jan Megens, Erik Meijaard, Kieren J. Mitchell, Christopher Moran, Karen Mudar, Karma Nidup, Marc Oxenham, Rinzin Pem, Philip Piper, Kyle Schachtschneider, Lawrence Schook, Pradeepa Silva, Matthew Spriggs, Samuel Turvey, Una Strand Viðarsdóttir, Murray P. Cox, Tim Denham, Jamie Gongorra, Keith Dobney, Greger Larson^* (Corresponding Author), Laurent A. F. Frantz^* (Corresponding Author)

^*Corresponding author for this work

Archaeology

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

Abstract

Several millennia of human-mediated translocation of non-native pig species (genus Sus) to the islands of Wallacea and Oceania have considerably altered local ecosystems. To investigate the timing and trajectory of these introductions, we conducted both genomic analyses of 576 pig nuclear genomes and a geometric morphometric analysis of 708 modern and ancient dental remains. Our analyses demonstrate that free-living and domestic pigs in Wallacea and Oceania have diverse ancestries resulting from the introduction of multiple sequential pig populations followed by gene flow. Despite the variability in their genomic ancestry, these pigs all have a distinct tooth morphology as well as a genetic link to the Chinese domestic pig populations that accompanied the dispersal of Austronesian language speakers ~4000 to 3000 years ago via Taiwan and the Philippines.

Original language	English
Article number	49
Number of pages	8
Journal	Science
Volume	391
Issue number	6780
DOIs	https://doi.org/10.1101/2025.07.07.663491 https://doi.org/10.1126/science.adv4963
Publication status	Published - 1 Jan 2026

Bibliographical note

We are grateful to M. Golitko and J. E. Terrell for support acquiring material used in this study.

Data Availability Statement

All genomics data have been deposited at the European Nucleotide Archive (ENA) under project number PRJEB83975. All morphometric data are available in data S3.

Funding

L.F., G.L., D.W.G.S., A.M., and K.D. were supported by either European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) or Natural Environmental Research Council grants (NE/K005243/1 and NE/K003259/1) or both. High-performance computing was performed on the BioHPC (DFG INST 86/2050-1 FUGG) and Linux-Cluster of the Leibniz Supercomputing Centre (LRZ Munich). L.F. and R.D. were funded by the NERC-Ristekdikti Newton Wallacea joint research program (grant NE/S007067/1; Ristekdikti Grant NKB-1799/UN2.R3.1/HKP.05.00/2019 “Biodiversity, Environmental Change, and Land-use Policy in Sulawesi and Maluku”).

Funders	Funder number
European Research Council	ERC-2013-StG-337574-UNDEA, ERC-2019-StG-853272-PALAEOFARM
Natural Environment Research Council	NE/K005243/1, NE/K003259/1

Access to Document

10.1101/2025.07.07.663491Licence: CC BY-NC
10.1126/science.adv4963Licence: Other

http://biorxiv.org/content/early/2025/07/07/2025.07.07.663491.abstract

Cite this

Stanton, D. W. G., Mannin, A., Evin, A., Tabbada, K., Linderholm, A., Drinkwater, R., Thalmann, O., Ng’Ang’A, S. I., Amano, N., Anderson, A., Barnett, R., Barrière, P., Bedford, S., Bellwood, P., Brumm, A., Tien, T. C., Clark, G., Crooijmans, R., Cucchi, T., ... Frantz, L. A. F. (2026). Genomic and morphometric evidence for Austronesian-mediated pig translocation in the Pacific. Science, 391(6780), Article 49. https://doi.org/10.1101/2025.07.07.663491, https://doi.org/10.1126/science.adv4963

Stanton, DWG, Mannin, A, Evin, A, Tabbada, K, Linderholm, A, Drinkwater, R, Thalmann, O, Ng’Ang’A, SI, Amano, N, Anderson, A, Barnett, R, Barrière, P, Bedford, S, Bellwood, P, Brumm, A, Tien, TC, Clark, G, Crooijmans, R, Cucchi, T, Eusebio, MS, Flink, LG, Galbusera, P, Groenen, M, Hakim, B, Hawkins, S, Heiniger, H, Helgen, KM, Herrera, MJ, Hunt, T, Kitchener, AC, Lee, C, Macdonald, AA, Megens, H-J, Meijaard, E, Mitchell, KJ, Moran, C, Mudar, K, Nidup, K, Oxenham, M, Pem, R, Piper, P, Schachtschneider, K, Schook, L, Silva, P, Spriggs, M, Turvey, S, Viðarsdóttir, US, Cox, MP, Denham, T, Gongorra, J, Dobney, K, Larson, G & Frantz, LAF 2026, 'Genomic and morphometric evidence for Austronesian-mediated pig translocation in the Pacific', Science, vol. 391, no. 6780, 49. https://doi.org/10.1101/2025.07.07.663491, https://doi.org/10.1126/science.adv4963

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title = "Genomic and morphometric evidence for Austronesian-mediated pig translocation in the Pacific",

abstract = "Several millennia of human-mediated translocation of non-native pig species (genus Sus) to the islands of Wallacea and Oceania have considerably altered local ecosystems. To investigate the timing and trajectory of these introductions, we conducted both genomic analyses of 576 pig nuclear genomes and a geometric morphometric analysis of 708 modern and ancient dental remains. Our analyses demonstrate that free-living and domestic pigs in Wallacea and Oceania have diverse ancestries resulting from the introduction of multiple sequential pig populations followed by gene flow. Despite the variability in their genomic ancestry, these pigs all have a distinct tooth morphology as well as a genetic link to the Chinese domestic pig populations that accompanied the dispersal of Austronesian language speakers \textasciitilde{}4000 to 3000 years ago via Taiwan and the Philippines.",

author = "Stanton, \{David W. G.\} and Aurelie Mannin and Allowen Evin and Kristina Tabbada and Anna Linderholm and Rosie Drinkwater and Olaf Thalmann and Ng{\textquoteright}Ang{\textquoteright}A, \{Said I\} and Noel Amano and Atholl Anderson and Ross Barnett and Patrick Barri{\`e}re and Stuart Bedford and Peter Bellwood and Adam Brumm and Tien, \{Trung Cao\} and Geoffrey Clark and Richard Crooijmans and Thomas Cucchi and Eusebio, \{Michelle S.\} and Flink, \{Linus G\} and Peter Galbusera and Martien Groenen and Budianto Hakim and Stuart Hawkins and Holly Heiniger and Helgen, \{Kristofer M\} and Herrera, \{Michael J.\} and Terry Hunt and Kitchener, \{Andrew C\} and Carol Lee and Macdonald, \{Alastair A\} and Hendrik-Jan Megens and Erik Meijaard and Mitchell, \{Kieren J.\} and Christopher Moran and Karen Mudar and Karma Nidup and Marc Oxenham and Rinzin Pem and Philip Piper and Kyle Schachtschneider and Lawrence Schook and Pradeepa Silva and Matthew Spriggs and Samuel Turvey and Vi{\dh}arsd{\'o}ttir, \{Una Strand\} and Cox, \{Murray P.\} and Tim Denham and Jamie Gongorra and Keith Dobney and Greger Larson and Frantz, \{Laurent A. F.\}",

note = "We are grateful to M. Golitko and J. E. Terrell for support acquiring material used in this study.",

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AU - Mannin, Aurelie

AU - Evin, Allowen

AU - Tabbada, Kristina

AU - Linderholm, Anna

AU - Drinkwater, Rosie

AU - Thalmann, Olaf

AU - Ng’Ang’A, Said I

AU - Amano, Noel

AU - Anderson, Atholl

AU - Barnett, Ross

AU - Barrière, Patrick

AU - Bedford, Stuart

AU - Bellwood, Peter

AU - Brumm, Adam

AU - Tien, Trung Cao

AU - Clark, Geoffrey

AU - Crooijmans, Richard

AU - Cucchi, Thomas

AU - Eusebio, Michelle S.

AU - Flink, Linus G

AU - Galbusera, Peter

AU - Groenen, Martien

AU - Hakim, Budianto

AU - Hawkins, Stuart

AU - Heiniger, Holly

AU - Helgen, Kristofer M

AU - Herrera, Michael J.

AU - Hunt, Terry

AU - Kitchener, Andrew C

AU - Lee, Carol

AU - Macdonald, Alastair A

AU - Megens, Hendrik-Jan

AU - Meijaard, Erik

AU - Mitchell, Kieren J.

AU - Moran, Christopher

AU - Mudar, Karen

AU - Nidup, Karma

AU - Oxenham, Marc

AU - Pem, Rinzin

AU - Piper, Philip

AU - Schachtschneider, Kyle

AU - Schook, Lawrence

AU - Silva, Pradeepa

AU - Spriggs, Matthew

AU - Turvey, Samuel

AU - Viðarsdóttir, Una Strand

AU - Cox, Murray P.

AU - Denham, Tim

AU - Gongorra, Jamie

AU - Dobney, Keith

AU - Larson, Greger

AU - Frantz, Laurent A. F.

N1 - We are grateful to M. Golitko and J. E. Terrell for support acquiring material used in this study.

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N2 - Several millennia of human-mediated translocation of non-native pig species (genus Sus) to the islands of Wallacea and Oceania have considerably altered local ecosystems. To investigate the timing and trajectory of these introductions, we conducted both genomic analyses of 576 pig nuclear genomes and a geometric morphometric analysis of 708 modern and ancient dental remains. Our analyses demonstrate that free-living and domestic pigs in Wallacea and Oceania have diverse ancestries resulting from the introduction of multiple sequential pig populations followed by gene flow. Despite the variability in their genomic ancestry, these pigs all have a distinct tooth morphology as well as a genetic link to the Chinese domestic pig populations that accompanied the dispersal of Austronesian language speakers ~4000 to 3000 years ago via Taiwan and the Philippines.

AB - Several millennia of human-mediated translocation of non-native pig species (genus Sus) to the islands of Wallacea and Oceania have considerably altered local ecosystems. To investigate the timing and trajectory of these introductions, we conducted both genomic analyses of 576 pig nuclear genomes and a geometric morphometric analysis of 708 modern and ancient dental remains. Our analyses demonstrate that free-living and domestic pigs in Wallacea and Oceania have diverse ancestries resulting from the introduction of multiple sequential pig populations followed by gene flow. Despite the variability in their genomic ancestry, these pigs all have a distinct tooth morphology as well as a genetic link to the Chinese domestic pig populations that accompanied the dispersal of Austronesian language speakers ~4000 to 3000 years ago via Taiwan and the Philippines.

U2 - 10.1101/2025.07.07.663491

DO - 10.1101/2025.07.07.663491

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JO - Science

JF - Science

IS - 6780

M1 - 49

ER -

Genomic and morphometric evidence for Austronesian-mediated pig translocation in the Pacific

Abstract

Bibliographical note

Data Availability Statement

Funding

Access to Document

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Cite this