Indigenous peoples in eastern Brazil: insights from 19^th century genomes and metagenomes

Abstract

Although Brazil was inhabited by more than 3,000 Indigenous populations prior to European colonization, today's Indigenous peoples represent less than 1% of Brazil's census population. Some of the decimated communities belonged to the so-called "Botocudos" from central-eastern Brazil. These peoples are thought to represent a case of long-standing genetic continuity bearing a strong craniometric resemblance to that of the oldest Indigenous Americans ("Paleoamericans"). Yet, little is known about their origins and genetic relationship to other Native Americans, as only two "Botocudo" genomes have been sequenced so far and those were surprisingly of Polynesian ancestry. To deepen our knowledge on the genomic history of pre-contact Indigenous Americans and the pathogens they were exposed to, we carbon-dated and sequenced 24 ancient Brazilians (including 22 "Botocudos") whose remains were hosted at the National Museum of Rio de Janeiro and recovered prior to the tragic 2018 fire. The resulting genomes' depth of coverage ranged from 0.001x to 24x. Their genetic ancestry was found to be Indigenous American without gene flow from external populations such as Europeans, Africans or Polynesians. Unlike Mesoamericans, the "Botocudos" and Amazonians do not seem to have experienced a population expansion once in the Americas. Moreover, remarkably, their genomes exhibit amongst the lowest levels of heterozygosity worldwide and long runs of homozygosity, which could be explained by unique social practices or a very small effective size. Finally, whole genomes of likely ancient pathogens were recovered, including lineages of human parvovirus B19 that were possibly introduced after the European contact.

Demographic history and genetic structure in pre-Hispanic Central Mexico

“…S19 and table S12) (17). These results agree with previous studies that report lower genetic diversity and longer ROH in hunter-gatherer populations from South America than those observed in other regions of the Americas (42).…”

A Glimpse into the Past: What Ancient Viral Genomes Reveal About Human History

“…In addition, NGS allowed the quantification of environmental and laboratory contamination as well as the evaluation of fragmentation and deamination patterns expected in aDNA relative to modern contamination (28). To date, the genomes of ∼200 ancient human viruses have been sequenced (Table 1), the majority of which are hepatitis B virus (HBV) (29)(30)(31)(32)(33)(34)(35)(36) but also include human parvovirus B19 (B19V) (29,37,38), measles morbillivirus (MeV) (39), VARV (27,40,41), vaccinia virus (VACV) (42,43), herpes simplex virus 1 (HSV-1) (44), IAV (19,45,46), and HIV-1 (47,48).…”

“…Most ancient viral genomes have been recovered with standard aDNA protocols aimed at retrieving double-stranded DNA (dsDNA) (Figure 2), which may account for the overrepresentation of studies targeting dsDNA viruses such as VARV (27,40,41,55), HBV (29)(30)(31)(32)(33)(34)(35)(36), B19V (29,37,38), and HSV-1 (44). Once the DNA and/or RNA has been isolated from selected human remains in strict aDNA conditions and the aRNA has been retrotranscribed into complementary DNA, adapters are added to the DNA fragments to construct an NGS library.…”

“…Furthermore, compared to multicellular organisms and bacterial pathogens, whose genomes are composed of dsDNA, viral genomes vary widely (i.e., single-or double-stranded, linear or circular, DNA or RNA) and may not be conserved or isolated efficiently enough using standard aDNA protocols aimed at recovering dsDNA (130,131). Indeed, dsDNA regions on B19V and HBV genomes are consistently better covered than single-stranded regions (29,33,35,38). Viruses also have complex replication cycles that alter the availability and abundance of their genomes.…”