The Sailing Larder: Using ancient DNA from commensal ... Lisa Matisoo... · Not the Philippines....
Transcript of The Sailing Larder: Using ancient DNA from commensal ... Lisa Matisoo... · Not the Philippines....
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
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Transportation –
need to control animals for days/weeks during voyaging
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Precariousness and variability of island environments –
may result in introduction followed by extirpation
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Isolation of island populations –
multiple introductions separated in time
Early Animal Translocations in the Pacific
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Northern Common Cuscus (Phalanger orientalis) to New Ireland 20,000 BP
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
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
“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
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).
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No clear Proto-Oceanic (*OC) term for dog –
in contrast to words for pig and chicken.
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Interruption in the transport of dogs out of Island Southeast Asia and into Oceania?
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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)
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)
Critiques
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Only one bone•
Possible problems with dates –
marine diet could make the dates look too old
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Contamination of the DNA sample with modern chicken DNA
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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
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
Pacific commensal animals
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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)
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Late Lapita pig and dog? •
Late dog and chicken (around 1000-1500BP) –
in Polynesia but from where?
180 Maori & PacificGeno 2.0750K Ancestry chip
After filtering = 173,252 SNPS
West Polynesians (Tonga & Samoa)
Māori and Cook Island Māori
Wairau Bar
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One of the oldest archaeological sites in New Zealand
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Includes the largest sample of burials in NZ and one of the largest in Polynesia
Wairau Bar
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Dated to 730 BP•
Classic Moa Hunter site
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Thousands of moa bones and egg shells
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43 human burials with grave goods
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Rangitane o Wairau
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
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?
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Human -
Animal interaction histories in the Pacific are unique
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The relative isolation of Pacific animal populations may provide
the opportunity to investigate some key questions about domestication and animal health
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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
Brotherton et al. 2013Nature Communications
4, Article
number:
1764 (2013)doi:10.1038/ncomms2656
Hybridization Capture of ancient DNA (aDNA)