A genetic history of the pre-contact Caribbean

Abstract

Humans settled the Caribbean ~6,000 years ago, with ceramic use and intensified agriculture marking a shift from the Archaic to the Ceramic Age ~2,500 years ago 1 – 3 . We report genome-wide data from 174 individuals from The Bahamas, Hispaniola, Puerto Rico, Curaçao, and Venezuela co-analyzed with published data. Archaic Age Caribbean people derive from a deeply divergent population closest to Central and northern South Americans; contrary to previous work 4 , we find no support for ancestry contributed by a population related to North Americans. Archaic lineages were >98% replaced by a genetically homogeneous ceramic-using population related to Arawak-speakers from northeast South America who moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools reflecting small effective population sizes which we estimate to be a minimum of Ne=500–1500 and a maximum of Ne=1530–8150 on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the analyzed individuals lived. Census sizes are unlikely to be more than ten-fold larger than effective population sizes, so previous estimates of hundreds of thousands of people are too large 5 – 6 . Confirming a small, interconnected Ceramic Age population 7 , we detect 19 pairs of cross-island cousins, close relatives ~75 kilometers apart in Hispaniola, and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically-differentiated groups from the mainland but instead reflected interactions within an interconnected Caribbean world 1 , 8 .

Ancient genomics reveals tripartite origins of Japanese populations

“…Our approach makes use of genome-wide patterns of runs of homozygosity (ROHs) to identify the demographic scenario that best fits the ROH spectrum observed in our oldest and highest coverage sample, JpKa6904 (see note S2). The distribution of ROH tracts reflects the effective population size and the time to the most recent common ancestor between two copies of haplotypes within an individual ( 31 , 32 ). The 8.8-ka-old Jomon carries high levels of ROH, in particular with the highest frequency of short ROH (due to population effects rather than recent inbreeding) yet reported ( Fig.…”

TKGWV2: an ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data

“…With DNA sequencing costs decreasing 22 , aDNA data growing exponentially, and research projects increasingly focusing on analysing the social organisation of populations from specific regions and/or local cemeteries 15 , 20 , 21 , 23 – 25 , a method for detecting kinship from whole genome shotgun screening data with ultra low coverage is valuable, and can translate into larger numbers of relationships detected. This is true even for individuals that would not be expected to yield sufficient data for population genetic analysis, or for which the required sequencing power would require substantially more funds.…”

Close-kin methods to estimate census size and effective population size

“…Successful application of CKMR methods to a number of fish species (Rawding et al 2014;Bravington et al 2016a;Hillary et al 2018;Bradford et al 2018;Ruzzante et al 2019;Bravington et al 2019), together with refinements in statistical methodology (Bravington et al 2016b;Skaug 2017;Conn et al 2020), have generated a great deal of interest in using this approach more broadly to study marine, freshwater, and terrestrial taxa (e.g., Stewart et al 2018;Oleksiak and Rajora 2020). The basic principles of CKMR have also been used to place an upper bound on the pre-Columbian human population size in the Caribbean (Fernandes et al 2020).…”

“…Basic principles of CKMR have also been used to place an upper bound on the pre-Columbian human population size in the Caribbean (Fernandes et al 2020).…”