Ancient population genomics and the study of evolution

Abstract

Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions

“…Owing to the abundance and relative stability of mitochondrial DNA relative to the nuclear genome, the authors were able to sequence the mitochondrial genome at relatively high coverage, with sequence depths of the largest contigs between 25 and 47× (Hung et al, ). Parks et al () used a similar approach to sequence whole mitochondrial genomes in a study investigating the population history of Adélie Penguins ( Pygoscelis adeliae ). While mitochondrial DNA may be amenable to whole genome sequencing from historical specimens in certain cases, the same approach may not be feasible on a large scale for the nuclear genome given its substantially lower copy number and less stable nature compared to mitochondrial DNA (Parks et al, ).…”

Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene

“…Due to the existence of relatively few samples and limitations on destructive analyses, early aDNA studies focused on evolutionary relationships and bottleneck detection, and utilized PCR to amplify short mitochondrial fragments or a few nuclear markers and Sanger sequencing methods [83]. However, with HTS technology, it is now possible to study ancient population dynamics and landscape genetics [11,19]. There are now many different ways of collecting genomic data from fresh tissues, including RAD, exome, intron and whole-genome sequencing, and SNP capture.…”

“…This, in turn, results in better wildlife management recommendations, including the preservation of genetic diversity, identification of populations with unique evolutionary history and potential, and the mitigation of the effects of small population sizes on viability [14,15]. While there are challenges in undertaking effective conservation genomics projects [15], genomic analysis of archaeological samples (archaeogenomics) can extend patterns deep into the past and, along with complementary paleogenomic data from fossil and subfossil samples [12,16,17], can provide key information on longterm ecosystem responses to disease, human activities, and climate change [10,11,13,[18][19][20]. Here, we focus on the following question: how can genomic analysis of archaeological materials enhance the conservation, management, and restoration of present-day (and future) biodiversity?…”

Biological Anthropology in the Indo-Pacific Region: New Approaches to Age-Old Questions

“…Similarly, analyses of 83 whole genomes of modern Aboriginal Australians (Malaspinas et al, 2016) have found not only evidence of a single major migration event to Sahul, but have also identified variations in gene regions associated with thyroid hormone and elevated serum urate levels, which are suggestive of selective adaptations in Australian aboriginals for living in cold, desert environments and for dealing with dehydration. As these examples show, many of the advances in interpretation of population history in the region are being driven by new techniques in aDNA research, in particular the introduction of Next Generation Sequencing (NGS) technologies (Linderholm, 2016;Parks et al, 2015). These techniques give researchers the ability to sequence small pieces of fragmented DNA, which when pieced together can result in coverage of the complete mitogenome, or in some cases even coverage of the nuclear genome of typically degraded ancient samples including samples that would not have produced any reliable sequence data using traditional, Sanger sequencing methods (Koboldt et al, 2013).…”