New developments in ancient genomics

Abstract

Ancient DNA research is on the crest of a 'third wave' of progress due to the introduction of a new generation of DNA sequencing technologies. Here we review the advantages and disadvantages of the four new DNA sequencers that are becoming available to researchers. These machines now allow the recovery of orders of magnitude more DNA sequence data, albeit as short sequence reads. Hence, the potential reassembly of complete ancient genomes seems imminent, and when used to screen libraries of ancient sequences, these methods are cost effective. This new wealth of data is also likely to herald investigations into the functional properties of extinct genes and gene complexes and will improve our understanding of the biological basis of extinct phenotypes.

Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

“…Even with NGSTs' growing familiarity and broad range of applications such as ChIPseq, RNA-seq, and genome-wide association studies, NGSTs still have the potential to influence the field of population genetics and phylogenetics with new methods to obtain genomic sequences of rare, difficult to sample, or extinct species (Millar et al 2008). The ability to uncover the phylogenetic history of recently extinct species has rapidly improved due to the reduced cost and increased sequence capacity of NGSTs (Gilbert et al 2007(Gilbert et al , 2008Miller et al 2008Miller et al , 2009); however, obstacles do remain.…”

“…The difficulties with applying NGSTs to phylogenetic problems do not lie with the sequencing technology itself, but with the preparative procedures for isolation and sequencing of large, orthologous DNA regions across multiple divergent species (Summerer 2009). This problem is exacerbated for museum specimens, where DNA quality varies greatly between samples and contamination levels are often high (Millar et al 2008). Generation of whole genome sequences for museum specimens, or even complete mitochondrial DNA (mtDNA) genome sequences, is not cost-effective for most laboratories due to the large amount of sequencing required for adequate genome coverage of a single individual.…”

Museum collections reveal that Buff-breasted Sandpipers (Calidris subruficollis) maintained mtDNA variability despite large population declines during the past 135 years

“…Analyses of contemporary populations with nuclear markers did not find evidence of a genetic signal associated with a population decline nor did they reveal any sex-biased population structure (Lounsberry et al 2013). We chose not to use nuclear markers such as microsatellites due to the age of specimens and quality and quantity of DNA, which can result in high genotyping error rates and underestimates (due to allelic dropout) or, less frequently, overestimates (due to false alleles) of historic allelic variation (Wandeler et al 2007;Millar et al 2008). Previous studies have successfully used mitochondrial markers in hDNA samples to reveal declines in genetic diversity over time in several species of birds (Martinez-Cruz et al 2007;Solovyeva and Pearce 2011;Draheim et al 2012).…”

Moa's Ark or volant ghosts of Gondwana? Insights from nineteen years of ancient DNA research on the extinct moa (Aves: Dinornithiformes) of New Zealand

“…two decades of aDNA research on moa, it seems timely to look back, provide an overview of the 79 achievements, and identify the gaps in our knowledge. This is particularly pertinent because Next 80 Generation Sequencing (NGS) technology (e.g., Marguelis et al, 2005) is presently revolutionising 81 molecular biology, and this 'revolution' has also affected the field of aDNA (Millar et al, 2008), most 82 notably with the sequencing of whole ancient genomes (Green et al, 2010;Rasmussen et al, 2010;83 Reich et al, 2010). By assessing previous genetic research on moa, the future directions of aDNA 84 research on these birds can be discussed in light of the potential offered by NGS.…”