Examining Natural History through the Lens of Palaeogenomics.
TL;DR: Palaeogenomics has revealed instances of over and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridization events and hybrid individuals, and highlighted previously unrecognised routes of zoonotic disease transfer.
Abstract: The many high-resolution tools that are uniquely applicable to specimens from the Quaternary period (the past ~2.5 Ma) provide an opportunity to cross-validate data and test hypotheses based on the morphology and distribution of fossils. Among these tools is palaeogenomics – the genome-scale sequencing of genetic material from ancient specimens – that can provide direct insight into ecology and evolution, potentially improving the accuracy of inferences about past ecological communities over longer timescales. Palaeogenomics has revealed instances of over- and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridisation events and hybrid individuals, and has highlighted previously unrecognised routes of zoonotic disease transfer.
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TL;DR: For hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.
Abstract: Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectious diseases. However, the development of best-practices in isolating, processing, and analyzing hDNA remain under-explored, due to the substantial diversity of specimen preparation types, tissue sources, archival ages, and collecting histories. Thus, for hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.
75 citations
TL;DR: It is concluded that the entire temporal Ne continuum can now be inferred using several complementary approaches, bringing together contemporary and long‐term perspectives.
20 citations
TL;DR: A major role in our understanding of the past has been played by ancient DNA (aDNA) as discussed by the authors, and important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understandin...
Abstract: Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understandin...
7 citations
University of Oslo1, Victoria University of Wellington2, McDonald Institute for Archaeological Research3, Norwegian University of Science and Technology4, University of the Highlands and Islands5, University of Oxford6, Bournemouth University7, Marine Scotland8, University of York9, University of Bergen10
TL;DR: In this article, the authors investigated 48 ancient mitogenomes from historical specimens obtained from a range of archaeological excavations in northern Europe dated up to 6500 BCE and compared them to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas.
Abstract: Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archaeological excavations in northern Europe dated up to 6500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium – suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures towards the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
6 citations
TL;DR: This review will approach how biomolecules have been implemented in a broad variety of topics and species, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
Abstract: Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
5 citations
References
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Max Planck Society1, Broad Institute2, University of California, Berkeley3, European Bioinformatics Institute4, National Institutes of Health5, University of Massachusetts Medical School6, Spanish National Research Council7, University of Washington8, University of Montana9, Croatian Academy of Sciences and Arts10, University of Oviedo11, University of Bonn12, Emory University13, University College Cork14, Harvard University15
TL;DR: The genomic data suggest that Neandertals mixed with modern human ancestors some 120,000 years ago, leaving traces of Ne andertal DNA in contemporary humans, suggesting that gene flow from Neand Bertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
Abstract: Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
3,575 citations
TL;DR: At the recent 5th International Ancient DNA Conference in Manchester, U.K., one presentation boldly opened with the claim that the field was now mature and could move ahead with a clear path towards deciphering diet and disease from DNA.
Abstract: At the recent 5th International Ancient DNA Conference in Manchester, U.K., reported by Erik Stokstad in his News Focus article “Divining diet and disease from DNA” (28 Jul., p. [530][1]), one presentation boldly opened with the claim that the field was now mature and could move ahead with
1,150 citations
TL;DR: Re-sequencing the region around EPAS1 in 40 Tibetan and 40 Han individuals finds that this gene has a highly unusual haplotype structure that can only be convincingly explained by introgression of DNA from Denisovan or Denisovan-related individuals into humans.
Abstract: As modern humans migrated out of Africa, they encountered many new environmental conditions, including greater temperature extremes, different pathogens and higher altitudes. These diverse environments are likely to have acted as agents of natural selection and to have led to local adaptations. One of the most celebrated examples in humans is the adaptation of Tibetans to the hypoxic environment of the high-altitude Tibetan plateau. A hypoxia pathway gene, EPAS1, was previously identified as having the most extreme signature of positive selection in Tibetans, and was shown to be associated with differences in haemoglobin concentration at high altitude. Re-sequencing the region around EPAS1 in 40 Tibetan and 40 Han individuals, we find that this gene has a highly unusual haplotype structure that can only be convincingly explained by introgression of DNA from Denisovan or Denisovan-related individuals into humans. Scanning a larger set of worldwide populations, we find that the selected haplotype is only found in Denisovans and in Tibetans, and at very low frequency among Han Chinese. Furthermore, the length of the haplotype, and the fact that it is not found in any other populations, makes it unlikely that the haplotype sharing between Tibetans and Denisovans was caused by incomplete ancestral lineage sorting rather than introgression. Our findings illustrate that admixture with other hominin species has provided genetic variation that helped humans to adapt to new environments.
851 citations
University of Copenhagen1, University of Alberta2, University of California, Santa Cruz3, Technical University of Denmark4, University of Chicago5, University of Bristol6, University of California, Berkeley7, Macau University of Science and Technology8, University of Texas at Austin9, University of Southampton10, Norwegian University of Life Sciences11, Centre national de la recherche scientifique12, Uppsala University13, Cornell University14, Copenhagen Zoo15, King Saud University16, University of York17
TL;DR: Thealyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0–4.5 million years before present, twice the conventionally accepted time to the most recent common ancestor of the genus Equus, and supports the contention that Przewalski's horses represent the last surviving wild horse population.
Abstract: The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.
708 citations
TL;DR: A 38,000-year-old Neanderthal fossil that is exceptionally free of contamination from modern human DNA is identified and it is revealed that modern human and Neanderthal DNA sequences diverged on average about 500,000 years ago.
Abstract: Neanderthals are the extinct hominid group most closely related to contemporary humans, so their genome offers a unique opportunity to identify genetic changes specific to anatomically fully modern humans. We have identified a 38,000-year-old Neanderthal fossil that is exceptionally free of contamination from modern human DNA. Direct high-throughput sequencing of a DNA extract from this fossil has thus far yielded over one million base pairs of hominoid nuclear DNA sequences. Comparison with the human and chimpanzee genomes reveals that modern human and Neanderthal DNA sequences diverged on average about 500,000 years ago. Existing technology and fossil resources are now sufficient to initiate a Neanderthal genome-sequencing effort.
677 citations