Ancient mtDNA sequences from the First Australians revisited

Abstract

The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537–542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the “Out of Africa” model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains.

Aboriginal Australian mitochondrial genome variation – an increased understanding of population antiquity and diversity

“…The TMRCA for haplogroup S is between 49 and 51 KYA and it may have been one of the first Australian-specific haplogroups to diversify after it evolved from its ancestral N type, which is consistent with the fact that the root of S is only one mutation step from N. The recent mitogenome sequencing of the skeletal remains of WLH4 of Lake Mungo, New South Wales16 has determined that this individual (chronologically dated to the late Holocene by Durband, et al 61…”

How many individuals share a mitochondrial genome?

“…Human mitochondrial DNA (mtDNA) has long been a useful tool to identify war casualties and victims of mass disasters, the sources of biological samples derived from crime scenes or to confirm matrilineal relatedness [1, 2, 3]. The autosomal genome is much larger and has higher discriminatory power, but the mitochondrial genome (mitogenome) has multiple copies per cell, allowing better recovery of sequence information from degraded samples [1, 3], including ancient DNA [4, 5]. In addition, some biological samples such as fingernails, old bones, teeth and hair have mtDNA but little or heavily degraded autosomal DNA.…”

Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing

“…Nowadays Next Generation Sequencing technology (NGS) provides a growing number of high quality aDNA sequence data, but until recently the majority of aDNA studies have been restricted to short fragments from the hypervariable region-1 (HVR-I) of the mitochondrial DNA (mtDNA) genome, using PCR based methods. PCR based methods are very sensitive for contamination, as low amounts of exogenous DNA can easily dominate PCR products resulting in the recovery of irrelevant sequences (Richards et al, 1995) (Malmström et al, 2005) (Pilli et al, 2013) (Heupink et al, 2016). As a result, in spite of the applied authenticity criteria (Knapp et al, 2012), many of the published databases may contain unreliable sequences, which distort statistical analyses.…”