Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile

Storey, Alice A.; Ramírez, José Miguel; Quiroz, Daniel; Burley, David V.; Addison, David J.; Walter, Richard; Anderson, Atholl; Hunt, Terry L.; Athens, J. Stephen; Huynen, Leon; Matisoo-Smith, Elizabeth

doi:10.1073/pnas.0703993104

Cited by 421 publications

(346 citation statements)

References 26 publications

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“…To further investigate the potential Polynesian-Chilean genetic links, we generated mtDNA CR sequences from 41 modern Chilean chickens and analyzed their phylogenetic relationships with a large database of Ϸ1,000 sequences, including those described by Liu et al (6) and available in ancient mtDNA CR sequences from Chile and the Pacific islands (4). In addition, we modeled the potential impact of marine carbon contribution on the calibrated age of the pre-Columbian chicken bone from El Arenal-1, an analysis not undertaken by Storey et al (4).…”

mentioning

confidence: 99%

Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA

Gongora

Rawlence

Mobegi

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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European chickens were introduced into the American continents by the Spanish after their arrival in the 15th century. However, there is ongoing debate as to the presence of pre-Columbian chickens among Amerindians in South America, particularly in relation to Chilean breeds such as the Araucana and Passion Fowl. To understand the origin of these populations, we have generated partial mitochondrial DNA control region sequences from 41 native Chilean specimens and compared them with a previously generated database of Ϸ1,000 domestic chicken sequences from across the world as well as published Chilean and Polynesian ancient DNA sequences. The modern Chilean sequences cluster closely with haplotypes predominantly distributed among European, Indian subcontinental, and Southeast Asian chickens, consistent with a European genetic origin. A published, apparently pre-Columbian, Chilean specimen and six pre-European Polynesian specimens also cluster with the same European/Indian subcontinental/Southeast Asian sequences, providing no support for a Polynesian introduction of chickens to South America. In contrast, sequences from two archaeological sites on Easter Island group with an uncommon haplogroup from Indonesia, Japan, and China and may represent a genetic signature of an early Polynesian dispersal. Modeling of the potential marine carbon contribution to the Chilean archaeological specimen casts further doubt on claims for pre-Columbian chickens, and definitive proof will require further analyses of ancient DNA sequences and radiocarbon and stable isotope data from archaeological excavations within both Chile and Polynesia.Araucana chicken ͉ Gallus gallus ͉ pre-Columbian chicken ͉ control region

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mentioning

confidence: 99%

Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA

Gongora

Rawlence

Mobegi

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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100

145

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“…The earliest archaeological evidence of domestic chicken in Africa dates back to between 1300 BC and 1400 AD (Gifford-Gonzales and Hanotte, 2011). The origin of South American village chicken remains unclear with their eventual presence on the continent before the arrival of Europeans still the subject of debate (Storey et al, 2007;Gongora et al, 2008). Village chickens are typically considered as free-range panmictic birds (Dana et al, 2010a).…”

Section: Introductionmentioning

confidence: 99%

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

et al. 2012

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Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide singlenucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r 2 X0.3) in both traditional and village chickens at pairwise marker distances of B10 Kb; while haplotype block analysis indicates a median block size of 11-12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55-38.89 Mb) and rose comb (Gga 7:18.41-22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25-67.28 Mb, Gga 1:67.28-67.32 Mb) totalling B75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions.

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“…There have been several high-profile studies with mitochondrial DNA sequences obtained from the ancient remains of a whole range of organisms including penguins (Lambert et al 2002), bison (Shapiro et al 2004), and chickens (Storey et al 2007), and one study where portions of the genome of the mammoth were obtained using short-read sequencing (Poinar et al 2006). We, and other researchers, have been involved in the development of evolutionary and phylogenetic methods to model the evolution of sequences sampled serially over time (e.g.…”

Section: Introductionmentioning

confidence: 99%

The perils of plenty: what are we going to do with all these genes?

Rodrigo

Bertels

Heled

et al. 2008

Phil. Trans. R. Soc. B

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This new century's biology promises more of everything-more genes, more organisms, more species and, in short, more data. The flood of data challenges us to find better and quicker ways to summarize and analyse. Here, we present preliminary results and proofs of concept from three of our research projects that are motivated by our search for solutions to the perils of plenty. First, we discuss how models of evolution can accommodate change to better reflect the dynamics of sequence diversity, particularly when it is becoming a lot easier to obtain sequences at different times and across intervals where the probability of new mutations contributing to this diversity is high. Second, we describe our work on the use of a single locus for species delimitation; this research targets the new DNA-barcoding approach that aims to catalogue the entirety of life. We have developed a single-locus test based on the coalescent that tests the null hypothesis of panmixis. Finally, we discuss new sequencing technologies, the types of data available and the efficacy of alignment-free methods to estimate pairwise distances for phylogenetic analyses.

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Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile

Cited by 421 publications

References 26 publications

Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA

Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

The perils of plenty: what are we going to do with all these genes?

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