Lisa Matisoo-Smith

The Sailing Larder: Using ancient DNA from commensal animals to reconstruct Pacific prehistory and migration pathways

Continental vs Oceanic Perspectives•

Domestication from wild populations

•

Transportation –

need to control animals for days/weeks during voyaging

•

Precariousness and variability of island environments –

may result in introduction followed by extirpation

•

Isolation of island populations –

multiple introductions separated in time

Nielsen et al. 2017

Genomics & Migrations

The Molecular Genetics of Crop Domestication

Doebley, Gaut & Smith 2006

Centres of Animal Domestication

Early Animal Translocations in the Pacific

•

Northern Common Cuscus (Phalanger orientalis) to New Ireland 20,000 BP

FoodFurRitualPets

Sunda and Sahul

From Kirch, P.V. 2000:66

Early Archaeological sites in Sahul

Dated from60,000 BP

HuonPeninsula

Lake Mungo

Kosipe

Madjedbebe(60-65,000 BP)

Note the need for watercraft to reach Sahul from Sunda, the Asian landmass

Near and Remote Oceania

Holocene sea level rise –

10,000 BP

Settlement of Remote Oceania

Lapita Dispersal3350 BP

3100 BP

Spans Near and Remote Oceania and Melanesia and Polynesia

NearRemote Oceania

2900 BP

Lapita pottery

Decorated pots, undecoratedpots, ceramic “faces”

Aotearoa/New Zealand settled in the late 13th

early 14th

century Map by Crid Fraser

Polynesian settlement: nearly 2000 years after Lapita

Origins: Austronesian Languages

“Out of Taiwan” model for Lapita/Polynesian origins

The Lapita Transported Landscapes

“Domesticated”

Dogs, Pigs, and Chickens (and Rats)

“It (Lapita pottery) marks the first appearance of three Pacific domesticates, the pig, dog and chicken, and therefore the beginning of Pacific animal husbandry.”

Spriggs 1997:88

Pacific Commensal Animals

Dog

Rat(Rattus exulans)

Pig

Chicken

The commensal Model

Using animals as a proxy for tracing human migration pathways

Illustration by Mere Roberts

Matisoo-Smith & Robins 2004PNAS 101(24):9167-9172

N=131 R. exulans samples33 from AMNH, 87 archaeological samples11 tissue samples

32 distinct haplotypes, 27 variable sites over 240 –

450 bp of mtDNA

Origins of Remote Oceanic rats

3 distinct haplotypes ofR. exulans

Type III only in RemoteOceania –

and Halmahera

No Type II in RemoteOceania (except Santa Cruz)

R. exulans is not native to Taiwan

Origin for Pacific Pig Clade

Not Taiwan

Not the Philippines

Larson et al. 2007PNAS 104(12):4834-4839

From Mainland SE Asia(Vietnam) along the westernIslands of Island SE AsiaIn to Wallacea and Oceania

Early Lapita pig? Near Oceania?

Yes

Never

?

Directly dated pig bone(2700-3000 BP) lots!

Pigs –

presence/absence

Geoff Clark

(no pig successfully introduced to New Zealand or Easter Is)

No pig

Pig Extirpated

Earliest dogs in the Pacific region

Date of introduction? 3500 BP?

Domesticated?

Dingoes New Guinea Singing dogs

Archaeological remains rare

Lapita DogsLocation Site Dates from Dogs?Mussau ECA, ECB 3550 BP None *Watom SAC 2900 BP None Anir ERA 3380 BP Yes –

early?Apalo FOJ 3500 BP Claimed, no

evidence provided

Nissan DFF 3300 BP NoneReef/SC RF-2 3200 BP NoneTikopia TK-4 2900 BP NISP 1Vanuatu various 3000 BP NoneNew Cal various 3000 BP NoneFiji Yanuka, Lakeba,

Naigani2980 BP ? Yanuka, none,

none

Dog bone at 1000-2000 BP•

Lesu (EAA), New Ireland: 12 teeth, 2 bones•

Hangan (DAI), Buka: dog bones•

Mailu, PNG: mandible & teeth •

Taurama, PNG (AJA): puppy burial•

Sio, Vitiaz Straits: bones and teeth •

Lakeba, Fiji: bones •

Throughout Polynesia –

lots of dog bone & teeth

•

Note: No prehistoric dog bone reported at all for Vanuatu & New Caledonia.

Linguistic Evidence for Dogs in the Pacific•

Proto-Austronesian (*AN) term for dog in the Pacific (*asu).

•

No clear Proto-Oceanic (*OC) term for dog –

in contrast to words for pig and chicken.

•

Interruption in the transport of dogs out of Island Southeast Asia and into Oceania?

•

The Proto-Polynesian (*PN) term for dog (*kuli) and the other domesticates are unique innovations with regular reflexes in most daughter languages but not reflected in higher order subgroups (Osmond and Pawley 2011:242).

•

The introduction of “domesticates”

in the Pacific is complex!

DogsAncient dogmitogenomes

Karen Greig, PhD, Kate McDonald

4 haplogroups in the Pacific

•A2b3 ancient Taiwan, modern Dingoes & NGSD (3500 BP?)•A4’5 Timor (3000 BP)•B ancient Taiwan and ancient New Guinea (2000 BP)•A2b2 mainland SEA, ancient New Guinea, ancient Pacific (after 1500 BP)

Kuri –

selective breeding?

Karen GreigPhD researchon kuri

Pacific Chickens

From Alice Storey PhD

El Arenal 1

pre-Columbian site

South Central Chile

Alice Storey PhD

Radiocarbon Date for El Arenal chicken bone

CHLARA003510+/-30

CHLARA004506+/- 30

CHLARA001622+/-35

Direct dating of the bone to 1307 –

1423 AD

Red arrow = 1492 AD

The El Arenal bone produced an identical sequence to chicken bones from two prehistoric archaeological sites in the Pacific: Mele Havea in Tonga, from upper plainware layers dating to between 2000 and 1550 BP; and Fatu-ma-Futi in American Samoa (1000-500 BP)

PNAS2007

Critiques

•

Only one bone•

Possible problems with dates –

marine diet could make the dates look too old

•

Contamination of the DNA sample with modern chicken DNA

2 Additional Dates

All clearly pre-Columbian at 2 SD

•

Storey et al. 2008 PNAS letter

Radiocarbon dates for all three chicken bones are clearly pre-ColumbianAnd consistent with the TL dates obtained on pottery from the site

Isotope Data: What are the chickens eating? How might this impact the radiocarbon dates?

Two chicken mtDNA lineages in the Pacific

Chile ARA004

Brazilian FC 1

Bolivia TAR001

Chile ARA003

AmericanSamoa FTF001

Chile FEA003

Tonga TD

Chile FEA002

Chile ARA001

Peru LOC001

WhiteLeghorn Reference

Chile FEA001 Full

Brazilian FC 7

Brazilian FC 4

EasterIsland ANA009

Peru TOR001

Brazilian FC 3

Hawaii WAI001

EasterIsland ANA004

Thailand BCH003

4852

44

65

88

43

49

42

42

0.005

AD 1304-1424

AD 950 - 1400

AD 1600s

AD 1580 - 1620

50BC – AD 400

AD 1500 - 1600

AD 1290-1430

AD 1290-1430

AD 1410 - 1530

AD 1331-1447

AD 1330-1445

Group E

Group D

Storey et al 2012 PLoS One

Note: Of the fifteen haplogroup E individuals in the Pacific, twelve were either archaeologically associated with or directly dated to a period before 1000 B.P. Haplogroup D is a post 1000 AD introduction

Ancient Chicken mtDNA

Roullier et al 2012Sweet Potato(Kumara) Evidence in Polynesia from 1000 BP

Pacific commensal animals

•

Dingo and New Guinea Singing dogs by 3500 BP?•

Not sure about “early”

Lapita pig or dog –

need more archaeological investigation and dating –

Teouma pigs from 3000 BP. Probable early Lapita chicken and rat (Mussau)

•

Late Lapita pig and dog? •

Late dog and chicken (around 1000-1500BP) –

in Polynesia but from where?

Slide courtesy of Bill Ayers

Sea level

Slide courtesy of Bill Ayers based on work of Bill Dickinson 2001

Final Sea level change

180 Maori & PacificGeno 2.0750K Ancestry chip

After filtering = 173,252 SNPS

West Polynesians (Tonga & Samoa)

Māori and Cook Island Māori

Wairau Bar

•

One of the oldest archaeological sites in New Zealand

•

Includes the largest sample of burials in NZ and one of the largest in Polynesia

Wairau Bar

•

Dated to 730 BP•

Classic Moa Hunter site

•

Thousands of moa bones and egg shells

•

43 human burials with grave goods

•

Rangitane o Wairau

Repatriation of remains by Rangitane

April 2009

The 1st

New Zealanders: Ancient mitogenomes from Wairau Bar

Burial # of reads % coverage Av. read depth Haplogroup1 9343 100 45.7 B4a1a1c (B4a1a1a3)

2.1 1199 98.4 6.9 B4a1a1n4 434 63.2 8.0 B4a15 3516 99.9 14.1 B4a1a1a

16A 128 29.3 0.8 B4a1a1c18 521 66.3 3.9 B4a1a119 73857 100 232.9 B4a1a1a (+1 unique mutation)

22A 313 89.2 4.8 B4a1a1c25 642 86.4 0.9 B4a1a1a

41A 1853 78.6 1.2 B4a

Burial 1 Burial 25

“Aunty”Burial 1: Young adult female from Wairau

Bar

Image by Susan Hayes

Dr Catherine CollinsDr Michael Knapp

125,454 SNPsAncient DNA samples:-

Wairau Bar (M-S)-

Tonga (Lapita) (S)-

Vanuatu (Lapita) (S)Modern DNA samples:-

NZ Maori (M-S)- Polynesian (M-S, S)- PNG (S)- Asia (S)

South East Asian

Papuan

Maori

Polynesia

WairauBar

Evidence of Tuberculosis in Wairau Bar?

Buckley et al. 2010. Journal of Pacific Archaeology

Bos et al.

Knapp et al.

Examining the origin and evolution of Tuberculosis in New Zealand (Knapp et al.)

Seal bone and human remains

Sequencing the MTB

Technological advances are opening exciting new opportunities, but:•Chronology matters •Archaeological context matters (spatially and temporally)•You need the appropriate samples to test hypotheses•Modern distributions and sequences may not be representative of ancient distributions.•It isn’t simple –

do your homework!

Conclusions for understanding animals in the past

Implications for Livestock Genetics?

•

Human -

Animal interaction histories in the Pacific are unique

•

The relative isolation of Pacific animal populations may provide

the opportunity to investigate some key questions about domestication and animal health

•

The isolation may also preserve some important variation that has been lost elsewhere

http://www.fao.org/news/story/en/item/380

661/icode/

http://www.fao.org/fileadmin/user_upload/newsroom/images/status-worlds-domestic-animal-breeds-fao.jpg

The Lab Team

Dr Michael Knapp

Dr Stefan ProstDr Anna Gosling

Olga Kardailsky

Dr Karen Greig

Dr Ann Horsburgh

Dr Melanie Hingston

Dr Judith Robins

Dr Catherine Collins Dr Andrew Clarke

Dr Alice Storey

Dr Sophia Cameron-Christie

Kate McDonald

Funding and Support

Rangitane o Wairau

Brotherton et al. 2013Nature Communications

4, Article

number:

1764 (2013)doi:10.1038/ncomms2656

Hybridization Capture of ancient DNA (aDNA)

Coverage of dog mitogenome

PhD student: Karen Greig & MSc James Boocock

Average length of DNA fragments

PhD student: Karen Greig

& MSc

James Boocock