A Paleogenomic Reconstruction of the Deep Population History of the Andes.

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

Refining the Maritime Foundations of Andean Civilization: How Plant Fiber Technology Drove Social Complexity During the Preceramic Period.

Moseley's (1975) Maritime Foundations of Andean Civilization hypothesis challenges, in one of humanity's few pristine hearths of civilization, the axiom that agriculture is necessary for the rise of complex societies. We revisit that hypothesis by setting new findings from La Yerba II (7571-6674 Cal bp) and III (6485-5893 Cal bp), Río Ica estuary, alongside the wider archaeological record for the end of the Middle Preceramic Period on the Peruvian coast. The La Yerba record evinces increasing population, sedentism, and "Broad Spectrum Revolution" features, including early horticulture of Phaseolus and Canavalia beans. Yet unlike further north, these changes failed to presage the florescence of monumental civilization during the subsequent Late Preceramic Period. Instead, the south coast saw a profound "archaeological silence." These contrasting trajectories had little to do with any relative differences in marine resources, but rather to restrictions on the terrestrial resources that determined a society's capacity to intensify exploitation of those marine resources. We explain this apparent miscarriage of the Maritime Foundations of Andean Civilization (MFAC) hypothesis on the south coast of Peru by proposing more explicit links than hitherto, between the detailed technological aspects of marine exploitation using plant fibers to make fishing nets and the emergence of social complexity on the coast of Peru. Rather than because of any significant advantages in quality, it was the potential for increased quantities of production, inherent in the shift from gathered wild Asclepias bast fibers to cultivated cotton, that inadvertently precipitated revolutionary social change. Thereby refined, the MFAC hypothesis duly emerges more persuasive than ever.

Archaeogenomic evidence of punctuated genome evolution in Gossypium.

Transposable elements (TEs) are drivers of evolution resulting in episodic surges of genetic innovation and genomic reorganization (Oliver KR, Greene WK. 2009. TEs: powerful facilitators of evolution. Bioessays 31:703-714.), but there is little evidence of the timescale in which this process has occurred (Gingerich PD. 2009. Rates of evolution. Ann Rev Ecol Evol Syst. 40:657-675.). The paleontological and archaeological records provide direct evidence for how evolution has proceeded in the past, which can be accessed through ancient DNA to examine genomes using high-throughput sequencing technologies (Palmer SA, Smith O, Allaby RG. 2011. The blossoming of plant archaeogenetics. Ann Anat. 194:146-156.). In this study, we report shotgun sequencing of four archaeological samples of cotton using the GS 454 FLX platform, which enabled reconstruction of the TE composition of these past genomes and species identification. From this, a picture of lineage specific evolutionary patterns emerged, even over the relatively short timescale of a few thousand years. Genomic stability was observed between South American Gossypium barbadense samples separated by over 2,000 miles and 3,000 years. In contrast, the TE composition of ancient Nubian cotton, identified as G. herbaceum, differed dramatically from that of modern G. herbaceum and resembled closely the A genome of the New World tetraploids. Our analysis has directly shown that considerable genomic reorganization has occurred within the history of a domesticated plant species while genomic stability has occurred in closely related species. A pattern of episodes of rapid change and periods of stability is expected of punctuated evolution. This observation is important to understanding the process of evolution under domestication.