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15 Sep 2019 at 01:43
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Bibliography on: Paleontology Meets Genomics — Sequencing Ancient DNA


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RJR: Recommended Bibliography 15 Sep 2019 at 01:43 Created: 

Paleontology Meets Genomics — Sequencing Ancient DNA

The ideas behind Jurassic Park have become real, kinda sorta. It is now possible to retrieve and sequence DNA from ancient specimens. Although these sequences are based on poor quality DNA and thus have many inferential steps (i,e, the resulting sequence is not likely to be a perfect replica of the living DNA), the insights to be gained from paleosequentcing are nonetheless great. For example, paleo-sequencing has shown that Neanderthal DNA is sufficiently different from human DNA as to be reasonably considered as coming from a different species.

Created with PubMed® Query: "ancient DNA" OR "ancient genome" OR paleogenetic OR paleogenetics NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-09-13

Bennett EA, Crevecoeur I, Viola B, et al (2019)

Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals.

Science advances, 5(9):eaaw3950 pii:aaw3950.

A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans.

RevDate: 2019-09-12

Menardo F, Duchêne S, Brites D, et al (2019)

The molecular clock of Mycobacterium tuberculosis.

PLoS pathogens, 15(9):e1008067 pii:PPATHOGENS-D-19-00781 [Epub ahead of print].

The molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the etiologic agent of tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to infer when a particular outbreak begun, when a drug-resistant clone appeared and expanded, or when a strain was introduced into a specific region. Despite the growing importance of the molecular clock in tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and about its rate of evolution. Here we performed a systematic study of the molecular clock of MTB on a large genomic data set (6,285 strains), covering different epidemiological settings and most of the known global diversity. We found that sampling times below 15-20 years were often insufficient to calibrate the clock of MTB. For data sets where such calibration was possible, we obtained a clock rate between 1x10-8 and 5x10-7 nucleotide changes per-site-per-year (0.04-2.2 SNPs per-genome-per-year), with substantial differences between clades. These estimates were not strongly dependent on the time of the calibration points as they changed only marginally when we used epidemiological isolates (sampled in the last 40 years) or three ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and the discrepancies in the results of different methods were sometimes large, highlighting the importance of using different methods, and of considering carefully their assumptions and limitations.

RevDate: 2019-09-12

Cappellini E, Welker F, Pandolfi L, et al (2019)

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.

Nature pii:10.1038/s41586-019-1555-y [Epub ahead of print].

The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5-although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7-9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.

RevDate: 2019-09-10

Moreno-Mayar JV, Korneliussen TS, Dalal J, et al (2019)

A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data.

Bioinformatics (Oxford, England) pii:5554699 [Epub ahead of print].

MOTIVATION: The presence of present-day human contaminating DNA fragments is one of the challenges defining ancient DNA (aDNA) research. This is especially relevant to the ancient human DNA field where it is difficult to distinguish endogenous molecules from human contaminants due to their genetic similarity. Recently, with the advent of high-throughput sequencing and new aDNA protocols, hundreds of ancient human genomes have become available. Contamination in those genomes has been measured with computational methods often developed specifically for these empirical studies. Consequently, some of these methods have not been implemented and tested for general use while few are aimed at low-depth nuclear data, a common feature in aDNA datasets.

RESULTS: We develop a new X-chromosome-based maximum likelihood method for estimating present-day human contamination in low-depth sequencing data from male individuals. We implement our method for general use, assess its performance under conditions typical of ancient human DNA research, and compare it to previous nuclear data-based methods through extensive simulations. For low-depth data, we show that existing methods can produce unusable estimates or substantially underestimate contamination. In contrast, our method provides accurate estimates for a depth of coverage as low as 0.5× on the X-chromosome when contamination is below 25%. Moreover, our method still yields meaningful estimates in very challenging situations, i.e., when the contaminant and the target come from closely related populations or with increased error rates. With a running time below five minutes, our method is applicable to large scale aDNA genomic studies.

AVAILABILITY: The method is implemented in C++ and R and is available in github.com/sapfo/contaminationX and popgen.dk/angsd.

RevDate: 2019-09-10

Bos KI, Kühnert D, Herbig A, et al (2019)

Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens.

Annual review of microbiology, 73:639-666.

The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.

RevDate: 2019-09-09

Shinde V, Narasimhan VM, Rohland N, et al (2019)

An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers.

Cell pii:S0092-8674(19)30967-5 [Epub ahead of print].

We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.

RevDate: 2019-09-08

Littleford-Colquhoun BL, Weyrich LS, Kent N, et al (2019)

City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii).

Molecular ecology [Epub ahead of print].

Urbanisation is one of the most significant threats to biodiversity, due to the rapid and large-scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild non-model species remains sparse. Using an empirical replicated study system, we show that city life alters the gut microbiome and stable isotope profiling of a wild native non-model species - the eastern water dragon (Intellagama lesueurii) in Queensland, Australia. City dragons exhibit a more diverse gut microbiome than their native habitat counterparts and show gut microbial signatures of a high fat and plant rich diet. Additionally, we also show that city dragons have elevated levels of the Nitrogen-15 isotope in their blood suggesting that a city diet, which incorporates novel anthropogenic food sources, may also be richer in protein. These results highlight the role that gut microbial plasticity plays in an animals' response to human-altered landscapes. This article is protected by copyright. All rights reserved.

RevDate: 2019-09-05

Balázs J, Rózsa Z, Bereczki Z, et al (2019)

Osteoarcheological and biomolecular evidence of leprosy from an 11-13th century CE Muslim cemetery in Europe (Orosháza, Southeast Hungary).

Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen [Epub ahead of print].

Orosháza site no. 10 (Southeast Hungary) contains the partially excavated archaeological remains of an 11-13th century CE Muslim merchant village and its cemetery located in close proximity to Christian villages of the same era. The skeleton of a young woman (grave no. 16) from the last phase of the cemetery use was identified with rhinomaxillary lesions associated with lepromatous leprosy. The right parietal bone also exhibited signs of cranial trauma, possibly caused by symbolic trepanation, a well-known ritual practice in the 9-11th century CE Carpathian Basin. The retrospective diagnosis of the disease was supported by ancient DNA analysis, as the samples were positive for Mycobacterium leprae aDNA, shown to be of genotype 3. Contrary to the general practice of the era, the body of the young female with severe signs of leprosy was interred among the regular graves of the Muslim cemetery in Orosháza, which may reflect the unique cultural background of the community.

RevDate: 2019-09-04

Gilbert E, O'Reilly S, Merrigan M, et al (2019)

The genetic landscape of Scotland and the Isles.

Proceedings of the National Academy of Sciences of the United States of America pii:1904761116 [Epub ahead of print].

Britain and Ireland are known to show population genetic structure; however, large swathes of Scotland, in particular, have yet to be described. Delineating the structure and ancestry of these populations will allow variant discovery efforts to focus efficiently on areas not represented in existing cohorts. Thus, we assembled genotype data for 2,554 individuals from across the entire archipelago with geographically restricted ancestry, and performed population structure analyses and comparisons to ancient DNA. Extensive geographic structuring is revealed, from broad scales such as a NE to SW divide in mainland Scotland, through to the finest scale observed to date: across 3 km in the Northern Isles. Many genetic boundaries are consistent with Dark Age kingdoms of Gaels, Picts, Britons, and Norse. Populations in the Hebrides, the Highlands, Argyll, Donegal, and the Isle of Man show characteristics of isolation. We document a pole of Norwegian ancestry in the north of the archipelago (reaching 23 to 28% in Shetland) which complements previously described poles of Germanic ancestry in the east, and "Celtic" to the west. This modern genetic structure suggests a northwestern British or Irish source population for the ancient Gaels that contributed to the founding of Iceland. As rarer variants, often with larger effect sizes, become the focus of complex trait genetics, more diverse rural cohorts may be required to optimize discoveries in British and Irish populations and their considerable global diaspora.

RevDate: 2019-09-04

Gower G, Fenderson LE, Salis AT, et al (2019)

Widespread male sex bias in mammal fossil and museum collections.

Proceedings of the National Academy of Sciences of the United States of America pii:1903275116 [Epub ahead of print].

A recent study of mammoth subfossil remains has demonstrated the potential of using relatively low-coverage high-throughput DNA sequencing to genetically sex specimens, revealing a strong male-biased sex ratio [P. Pečnerová et al., Curr. Biol. 27, 3505-3510.e3 (2017)]. Similar patterns were predicted for steppe bison, based on their analogous female herd-based structure. We genetically sexed subfossil remains of 186 Holarctic bison (Bison spp.), and also 91 brown bears (Ursus arctos), which are not female herd-based, and found that ∼75% of both groups were male, very close to the ratio observed in mammoths (72%). This large deviation from a 1:1 ratio was unexpected, but we found no evidence for sex differences with respect to DNA preservation, sample age, material type, or overall spatial distribution. We further examined ratios of male and female specimens from 4 large museum mammal collections and found a strong male bias, observable in almost all mammalian orders. We suggest that, in mammals at least, 1) wider male geographic ranges can lead to considerably increased chances of detection in fossil studies, and 2) sexual dimorphic behavior or appearance can facilitate a considerable sex bias in fossil and modern collections, on a previously unacknowledged scale. This finding has major implications for a wide range of studies of fossil and museum material.

RevDate: 2019-09-04

Hermes TR, Frachetti MD, Doumani Dupuy PN, et al (2019)

Early integration of pastoralism and millet cultivation in Bronze Age Eurasia.

Proceedings. Biological sciences, 286(1910):20191273.

Mobile pastoralists are thought to have facilitated the first trans-Eurasian dispersals of domesticated plants during the Early Bronze Age (ca 2500-2300 BC). Problematically, the earliest seeds of wheat, barley and millet in Inner Asia were recovered from human mortuary contexts and do not inform on local cultivation or subsistence use, while contemporaneous evidence for the use and management of domesticated livestock in the region remains ambiguous. We analysed mitochondrial DNA and multi-stable isotopic ratios (δ13C, δ15N and δ18O) of faunal remains from key pastoralist sites in the Dzhungar Mountains of southeastern Kazakhstan. At ca 2700 BC, Near Eastern domesticated sheep and goat were present at the settlement of Dali, which were also winter foddered with the region's earliest cultivated millet spreading from its centre of domestication in northern China. In the following centuries, millet cultivation and caprine management became increasingly intertwined at the nearby site of Begash. Cattle, on the other hand, received low levels of millet fodder at the sites for millennia. By primarily examining livestock dietary intake, this study reveals that the initial transmission of millet across the mountains of Inner Asia coincided with a substantial connection between pastoralism and plant cultivation, suggesting that pastoralist livestock herding was integral for the westward dispersal of millet from farming societies in China.

RevDate: 2019-09-01

Oosting T, Star B, Barrett JH, et al (2019)

Unlocking the potential of ancient fish DNA in the genomic era.

Evolutionary applications, 12(8):1513-1522 pii:EVA12811.

Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.

RevDate: 2019-08-28

Lewis D (2019)

'Paralysed by anxiety': researchers speak about life in troubled ancient-DNA lab.

Nature, 572(7771):571-572.

RevDate: 2019-09-01

Leles D, Frías L, Araújo A, et al (2019)

Are immunoenzymatic tests for intestinal protozoans reliable when used on archaeological material?.

Experimental parasitology, 205:107739 pii:S0014-4894(19)30159-6 [Epub ahead of print].

Intestinal protozoans found in ancient human samples have been studied primarily by microscopy and immunodiagnostic assays. However, such methods are not suitable for the detection of zoonotic genotypes. The objectives of the present study were to utilize immunoenzimatic assays for coproantigen detection of Cryptosporidium sp., Giardia duodenalis, and Entamoeba histolytica/Entamoeba dispar in sixty ancient human and animal samples collected from 14 archaeological sites in South America, and to carry out a critical analysis of G. duodenalis according to results obtained from three diagnostic methodologies: microscopy, immunodiagnostic tests (immunoenzymatic and immunofluorescence), and molecular biology (PCR and sequencing). More than half (31/60) of the samples analyzed using immunoenzymatic tests were positive for at least one of the intestinal protozoans, with 46.6% (28/60) corresponding to G. duodenalis, 26.6% (16/60) to Cryptosporidium sp., and 5% (3/60) to E. histolytica/E. dispar. Cryptosporidium sp. and G. duodenalis coinfection was observed in 15% (9/60) of the samples, whereas all three protozoans were found in 5% (3/60) of samples. In the Northeast Region of Brazil, by immunoenzymatic tests there is evidence that G. duodenlais and Cryptosporidium sp. have infected humans and rodents for at least 7150 years. However, for G. duodenalis, the results from the three diagnostic tests were discordant. Specifically, despite the efficiency of the molecular biology assay in the experimental models, G. duodenalis DNA could not be amplified from the ancient samples. These results raise the following question: Are all ancient samples positive for coproantigen of G. duodenalis by immunoenzymatic tests truly positive? This scenario highlights the importance of further studies to evaluate the sensitivity and specificity of the immunoenzymatic method in the archaeological context.

RevDate: 2019-09-05

Fernandes D, Sirak K, Cheronet O, et al (2019)

Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia.

PloS one, 14(8):e0216366 pii:PONE-D-19-00982.

Three individuals dating to the Great Migration Period (5th century CE) were discovered in a pit at the Hermanov vinograd site in Osijek, Croatia. We were inspired to study these individuals based on their unusual burial context as well as the identification of two different types of artificial cranial deformation in two of the individuals. We combine bioarchaeological analysis with radiographic imaging, stable isotopes analysis, and ancient DNA to analyze their dietary patterns, molecular sex, and genetic affinities in the context of the archaeological data and their bioarchaeological attributes. While all three individuals were adolescent males with skeletal evidence of severe malnutrition and similar diets, the most striking observation is that they had major differences in their genetic ancestry. Results of the genetic analyses of the nuclear ancient DNA data for these individuals indicate that the individual without artificial cranial deformation shows broadly West Eurasian associated-ancestry, the individual with tabular oblique-type has East Asian ancestry and the third individual with circular erect-type has Near Eastern associated-ancestry. Based on these results, we speculate that artificial cranial deformation type may have been a visual indicator membership in a specific cultural group, and that these groups were interacting intimately on the Pannonian Plain during the Migration Period.

RevDate: 2019-08-21

Lewis D (2019)

Head of prestigious ancient-DNA lab suspended amid bullying allegations.

Nature, 572(7770):424-425.

RevDate: 2019-08-24

Harney É, Nayak A, Patterson N, et al (2019)

Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India.

Nature communications, 10(1):3670 pii:10.1038/s41467-019-11357-9.

Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups.

RevDate: 2019-08-19

Aris-Brosou S (2019)

Direct Evidence of an Increasing Mutational Load in Humans.

Molecular biology and evolution pii:5551346 [Epub ahead of print].

The extent to which selection has shaped present-day human populations has attracted intense scrutiny, and examples of local adaptations abound. However, the evolutionary trajectory of alleles that, today, are deleterious has received much less attention. To address this question, the genomes of 2,062 individuals, including 1,179 ancient humans, were reanalyzed to assess how frequencies of risk alleles and their homozygosity changed through space and time in Europe over the past 45,000 years. While the overall deleterious homozygosity has consistently decreased, risk alleles have steadily increased in frequency over that period of time. Those that increased most are associated with diseases such as asthma, Crohn disease, diabetes and obesity, which are highly prevalent in present-day populations. These findings may not run against the existence of local adaptations, but highlight the limitations imposed by drift and population dynamics on the strength of selection in purging deleterious mutations from human populations.

RevDate: 2019-08-15

Legrand B, Miras Y, Beauger A, et al (2019)

Akinetes and ancient DNA reveal toxic cyanobacterial recurrences and their potential for resurrection in a 6700-year-old core from a eutrophic lake.

The Science of the total environment, 687:1369-1380.

In order to evaluate the recurrence of toxic cyanobacterial blooms and to determine the survival capabilities of the resistance cells through time, a sedimentary core spanning 6700 years was drilled in the eutrophic Lake Aydat. A multiproxy approach (density, magnetic susceptibility, XRF, pollen and non-pollen palynomorph analyses), was used initially to determine the sedimentation model and the land uses around the lake. Comparison with the akinete count revealed that Nostocales cyanobacteria have been present in Lake Aydat over a six thousand year period. This long-term cyanobacterial recurrence also highlights the past presence of both the anaC and mcyB genes, involved in anatoxin-a and microcystin biosynthesis, respectively, throughout the core. The first appearance of cyanobacteria seems to be linked to the natural damming of the river, while the large increase in akinete density around 1800 cal.yr BP can be correlated with the intensification of human activities (woodland clearance, crop planting, grazing, etc.) in the catchment area of the lake, and marks the beginning of a long period of eutrophication. This first investigation into the viability and germination potential of cyanobacteria over thousands of years reveals the ability of intact akinetes to undergo cell divisions even after 1800 years of sedimentation, which is 10 times longer than previously observed. This exceptional cellular resistance, coupled with the long-term eutrophic conditions of this lake, could partly explain the past and current recurrences of cyanobacterial proliferations.

RevDate: 2019-08-09

Kornienko IV, Faleeva TG, Oreshkova NV, et al (2019)

[Structural and Functional Organization of the Mitochondrial DNA Control Region in the Woolly Mammoth (Mammuthus primigenius)].

Molekuliarnaia biologiia, 53(4):627-637.

The woolly mammoth mitochondrial genome (including the Malolyakhovsky mammoth) has been previously sequenced, followed by the annotation of all its genes (MF770243). In this study, based on the Malolyakhovsky mammoth, we describe for the first time the sites of functional significance in the control region of the woolly mammoth mitogenome.

RevDate: 2019-08-08

DAS R (2019)

OnPeopling of India: Ancient DNA perspectives By K Thangaraj and Niraj Rai.

Journal of biosciences, 44(3):.

RevDate: 2019-08-08

Thangaraj K, N Rai (2019)

Peopling of India: Ancient DNA perspectives.

Journal of biosciences, 44(3):.

To reconstruct and explain patterns of genetic diversity of modern humans, understanding their past and present genetic profile is crucial. While genomes of contemporary people can provide information about present day population structure, analysis of ancient genomes may provide unprecedented insights about the past demographic events that have shaped the contemporary gene pool. Population genetics has recently witnessed an explosion in studies on ancient human population histories, primarily from Europe and America. South Asia has no representation in the ancient genomics literature, despite the wealth of archaeological richness in the form of human skeletal remains that exist in collections all over the country. Representing one-fifth of present day humanity calls for understanding the demographic history of south Asia not merely as a prerequisite but as an urgent need to understand its genetic variations on a global scale. Although the overall picture is taking form, new archaeological and genetic information from the region has started to reveal a more complex scenario of ancient human migrations and admixtures than was ever known before. In this article, we discuss a meaningful insight on the current status of ancient DNA (aDNA) research in India. We have also summarized a few but important aDNA studies, which have been successfully carried out in India. Furthermore, we have highlighted the potential opportunity of aDNA research in the Indian subcontinent.

RevDate: 2019-08-06

Valente L, Etienne RS, JC Garcia-R (2019)

Deep Macroevolutionary Impact of Humans on New Zealand's Unique Avifauna.

Current biology : CB, 29(15):2563-2569.e4.

Islands are at the frontline of the anthropogenic extinction crisis [1]. A vast number of island birds have gone extinct since human colonization [2], and an important proportion is currently threatened with extinction [3]. While the number of lost or threatened avian species has often been quantified [4], the macroevolutionary consequences of human impact on island biodiversity have rarely been measured [5]. Here, we estimate the amount of evolutionary time that has been lost or is under threat due to anthropogenic activity in a classic example, New Zealand. Half of its bird taxa have gone extinct since humans arrived [6, 7] and many are threatened [8], including lineages forming highly distinct branches in the avian tree of life [9-11]. Using paleontological and ancient DNA information, we compiled a dated phylogenetic dataset for New Zealand's terrestrial avifauna. We extend the method DAISIE developed for island biogeography [12] to allow for the fact that many of New Zealand's birds are evolutionarily isolated and use it to estimate natural rates of speciation, extinction, and colonization. Simulating under a range of human-induced extinction scenarios, we find that it would take approximately 50 million years (Ma) to recover the number of species lost since human colonization of New Zealand and up to 10 Ma to return to today's species numbers if currently threatened species go extinct. This study puts into macroevolutionary perspective the impact of humans in an isolated fauna and reveals how conservation decisions we take today will have repercussions for millions of years.

RevDate: 2019-09-03

Oswald JA, Allen JM, Witt KE, et al (2019)

Ancient DNA from a 2,500-year-old Caribbean fossil places an extinct bird (Caracara creightoni) in a phylogenetic context.

Molecular phylogenetics and evolution, 140:106576 pii:S1055-7903(19)30141-1 [Epub ahead of print].

Since the late Pleistocene humans have caused the extinction of species across our planet. Placing these extinct species in the tree of life with genetic data is essential to understanding the ecological and evolutionary implications of these losses. While ancient DNA (aDNA) techniques have advanced rapidly in recent decades, aDNA from tropical species, especially birds, has been historically difficult to obtain, leaving a gap in our knowledge of the extinction processes that have influenced current distributions and biodiversity. Here we report the recovery of a nearly complete mitochondrial genome from a 2,500 year old (late Holocene) bone of an extinct species of bird, Caracara creightoni, recovered from the anoxic saltwater environment of a blue hole in the Bahamas. Our results suggest that this extinct species is sister (1.6% sequence divergence) to a clade containing the extant C. cheriway and C. plancus. Caracara creightoni shared a common ancestor with these extant species during the Pleistocene (1.2-0.4 MYA) and presumably survived on Cuba when the Bahamas was mostly underwater during Quaternary interglacial intervals (periods of high sea levels). Tropical blue holes have been collecting animals for thousands of years and will continue to improve our understanding of faunal extinctions and distributions. In particular, new aDNA techniques combined with radiocarbon dating from Holocene Bahamian fossils will allow us to place other extinct (species-level loss) and extirpated (population-level loss) vertebrate taxa in improved phylogenetic, evolutionary, biogeographic, and temporal contexts.

RevDate: 2019-08-08

Smith O, Dunshea G, Sinding MS, et al (2019)

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival.

PLoS biology, 17(7):e3000166 pii:PBIOLOGY-D-19-00243.

While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data's authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology.

RevDate: 2019-08-06

Ning C, Wang CC, Gao S, et al (2019)

Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan.

Current biology : CB, 29(15):2526-2532.e4.

Recent studies of early Bronze Age human genomes revealed a massive population expansion by individuals-related to the Yamnaya culture, from the Pontic Caspian steppe into Western and Eastern Eurasia, likely accompanied by the spread of Indo-European languages [1-5]. The south eastern extent of this migration is currently not known. Modern-day human populations from the Xinjiang region in northwestern China show a complex population history, with genetic links to both Eastern and Western Eurasia [6-10]. However, due to the lack of ancient genomic data, it remains unclear which source populations contributed to the Xinjiang population and what was the timing and the number of admixture events. Here, we report the first genome-wide data of 10 ancient individuals from northeastern Xinjiang. They are dated to around 2,200 years ago and were found at the Iron Age Shirenzigou site. We find them to be already genetically admixed between Eastern and Western Eurasians. We also find that the majority of the East Eurasian ancestry in the Shirenzigou individuals is-related to northeastern Asian populations, while the West Eurasian ancestry is best presented by ∼20% to 80% Yamnaya-like ancestry. Our data thus suggest a Western Eurasian steppe origin for at least part of the ancient Xinjiang population. Our findings furthermore support a Yamnaya-related origin for the now extinct Tocharian languages in the Tarim Basin, in southern Xinjiang.

RevDate: 2019-08-22

Molto JE, Kirkpatrick CL, J Keron (2019)

The paleoepidemiology of Sacral Spina Bifida Occulta in population samples from the Dakhleh Oasis, Egypt.

International journal of paleopathology, 26:93-103.

OBJECTIVE: To document sacral spina bifida occulta (SSB0) prevalence in a population sample from the Dakhleh Oasis, Egypt, and address methodological issues in recording and quantifying SSBO variations.

MATERIALS: 442 adult sacra from two temporally disjunct samples from the same deme traversing the 3rd intermediate (TIP) and the Roman Periods.

METHODS: Sacra were scored for SSBO, excluding the sacral hiatus. Risk of SSBO was calculated with the common odds ratio and statistical significance by X2. Data were compared to other archaeological SSBO data.

RESULTS: SSBO was present in 15.6% of the sample with a slight, but not significant, temporal increase (TIP to Roman Period) in males, and a significant age-correlated increase in both sexes. Most open sacra occurred in young adults.

CONCLUSIONS: Data support that SSBO can be considered as a morphogenetic variant. Dakhleh data fall within the prevalence range for most populations, however inter-population comparisons are complicated by methodological inconsistencies.

SIGNIFICANCE: SSBO can be used in paleogenetic research.

LIMITATIONS: Methodological differences in scoring SSBO prevent effective comparative study.

SUGGESTED FUTURE RESEARCH: Future studies require more rigorous and standardized scoring methods. aDNA may be used to corroborate the morphogenetic value of SSBO and determine its clinical significance.

RevDate: 2019-08-16

Günther T, C Nettelblad (2019)

The presence and impact of reference bias on population genomic studies of prehistoric human populations.

PLoS genetics, 15(7):e1008302 pii:PGENETICS-D-19-00061.

Haploid high quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudo-haploid data, i.e. they randomly sample only one sequencing read per site. We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Most genomic regions we investigated show little to no mapping bias but even a small proportion of sites with bias can impact analyses of those particular loci or slightly skew genome-wide estimates. Therefore, reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.

RevDate: 2019-07-22

Mas-Sandoval A, Arauna LR, Gouveia MH, et al (2019)

Reconstructed lost Native American populations from Eastern Brazil are shaped by differential Jê/Tupi ancestry.

Genome biology and evolution pii:5536765 [Epub ahead of print].

After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African and the Native American. The study of the Native American genetic history is challenged by the availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies and the low proportions of the Native American component in the admixed Brazilian populations (in average 7%). We analysed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North East), Bambui (South East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui and 197 in Pelotas). We compared the reconstructed populations with non-admixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê- speaking ancestry related groups. We also show evidence of a decrease of the diversity of non-admixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.

RevDate: 2019-07-26

Prufer KM, Alsgaard AV, Robinson M, et al (2019)

Linking late Paleoindian stone tool technologies and populations in North, Central and South America.

PloS one, 14(7):e0219812 pii:PONE-D-19-13363.

From the perspective of Central and South America, the peopling of the New World was a complex process lasting thousands of years and involving multiple waves of Pleistocene and early Holocene period immigrants entering into the neotropics. These Paleoindian colonists initially brought with them technologies developed for adaptation to environments and resources found in North America. As the ice age ended across the New World people adapted more generalized stone tools to exploit changing environments and resources. In the neotropics these changes would have been pronounced as patchy forests and grasslands gave way to broadleaf tropical forests. We document a late Pleistocene/early Holocene stone tool tradition from Belize, located in southern Mesoamerica. This represents the first endogenous Paleoindian stone tool technocomplex recovered from well dated stratigraphic contexts for Mesoamerica. Previously designated Lowe, these artifacts share multiple features with contemporary North and South American Paleoindian tool types. Once hafted, these bifaces appear to have served multiple functions for cutting, hooking, thrusting, or throwing. The tools were developed at a time of technological regionalization reflecting the diverse demands of a period of pronounced environmental change and population movement. Combined stratigraphic, technological, and population paleogenetic data suggests that there were strong ties between lowland neotropic regions at the onset of the Holocene.

RevDate: 2019-07-16

Hong JH, Seo M, Oh CS, et al (2019)

Genetic Analysis of Small-Subunit Ribosomal RNA, Internal Transcribed Spacer 2, and ATP Synthase Subunit 8 of Trichuris trichiura Ancient DNA Retrieved from the 15th to 18th Century Joseon Dynasty Mummies' Coprolites from Korea.

The Journal of parasitology, 105(4):539-545.

Although parasitic infection by Trichuris trichiura is a very common intestinal helminthic disease worldwide, there is still insufficient information on the genetic characteristics of ancient T. trichiura in different spatiotemporal perspectives. Utilizing coprolite specimens obtained from 15th-18th century mummies dating to the Joseon Dynasty, we analyzed small-subunit ribosomal RNA, internal transcribed spacer 2, and ATP synthase subunit 8 of T. trichiura ancient DNA (aDNA). In BLAST and phylogenetic analyses, the T. trichiura aDNA sequences of this study belong to a separate cluster that is evidently distinct from the other genus Trichuris spp. reported in GenBank. This report characterizes T. trichiura aDNA of pre-20th century East Asia, and in so doing, it also proves the potential of aDNA analysis for differential diagnosis of T. trichiura in cases where ancient parasite eggs are morphologically indeterminate for species identification.

RevDate: 2019-08-09

Bokelmann L, Hajdinjak M, Peyrégne S, et al (2019)

A genetic analysis of the Gibraltar Neanderthals.

Proceedings of the National Academy of Sciences of the United States of America, 116(31):15610-15615.

The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.

RevDate: 2019-07-23

Järve M, Saag L, Scheib CL, et al (2019)

Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance.

Current biology : CB, 29(14):2430-2441.e10.

The Early Iron Age nomadic Scythians have been described as a confederation of tribes of different origins, based on ancient DNA evidence [1-3]. It is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome sequences of 31 ancient Western and Eastern Steppe individuals, including Scythians as well as samples pre- and postdating them, allowing us to set the Scythians in a temporal context (in the Western, i.e., Ponto-Caspian Steppe). We detect an increase of eastern (Altaian) affinity along with a decrease in eastern hunter-gatherer (EHG) ancestry in the Early Iron Age Ponto-Caspian gene pool at the start of the Scythian dominance. On the other hand, samples of the Chernyakhiv culture postdating the Scythians in Ukraine have a significantly higher proportion of Near Eastern ancestry than other samples of this study. Our results agree with the Gothic source of the Chernyakhiv culture and support the hypothesis that the Scythian dominance did involve a demic component.

RevDate: 2019-07-15

Houldcroft CJ, Rifkin RF, SJ Underdown (2019)

Human biology and ancient DNA: exploring disease, domestication and movement.

Annals of human biology, 46(2):95-98.

RevDate: 2019-08-08

Teixeira JC, A Cooper (2019)

Using hominin introgression to trace modern human dispersals.

Proceedings of the National Academy of Sciences of the United States of America, 116(31):15327-15332.

The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace's Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.

RevDate: 2019-07-12

Koch E, Schweizer RM, Schweizer TM, et al (2019)

De novo mutation rate estimation in wolves of known pedigree.

Molecular biology and evolution pii:5531468 [Epub ahead of print].

Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in a pedigree of seven wolves. Putative de novo mutations were discovered by whole-genome sequencing and were verified by Sanger sequencing of parents and offspring. Using stringent filters and an estimate of the false negative rate in the remaining observable genome, we obtain an estimate of ∼4.5 x 10-9 per base pair per generation and provide conservative bounds from 2.6 x 10-9 and 7.1 x 10-9. Although our estimate is consistent with recent mutation rate estimates from ancient DNA (4.0 x 10-9 and 3.0-4.5 x 10-9), it implies a wider possible range. We also examined the consequences of our rate and the accompanying interval for dating several critical events in canid demographic history. For example, applying our full range of rates to coalescent models of dog and wolf demographic history implies a wide set of possible divergence times between the ancestral populations of dogs and extant Eurasian wolves (16,000 - 64,000 years ago) although our point estimate indicates a date between 25,000 and 33,000 years ago. Aside from one study in mice, ours provides the only direct mammalian mutation rate outside of primates, and is likely to be vital to future investigations of mutation rate evolution.

RevDate: 2019-07-23

Cornille A, Antolín F, Garcia E, et al (2019)

A Multifaceted Overview of Apple Tree Domestication.

Trends in plant science, 24(8):770-782.

The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.

RevDate: 2019-07-26

Zimmermann HH, Harms L, Epp LS, et al (2019)

Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly.

PloS one, 14(7):e0216966 pii:PONE-D-19-08275.

Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.

RevDate: 2019-08-20

Lan TM, Lin Y, Njaramba-Ngatia J, et al (2019)

Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data.

Genes, 10(7): pii:genes10070509.

The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.

RevDate: 2019-07-11

Feldman M, Master DM, Bianco RA, et al (2019)

Ancient DNA sheds light on the genetic origins of early Iron Age Philistines.

Science advances, 5(7):eaax0061 pii:aax0061.

The ancient Mediterranean port city of Ashkelon, identified as "Philistine" during the Iron Age, underwent a marked cultural change between the Late Bronze and the early Iron Age. It has been long debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called "Sea Peoples." Here, we report genome-wide data of 10 Bronze and Iron Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European-related admixture. This genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze to Iron Age transition in Ashkelon but did not leave a long-lasting genetic signature.

RevDate: 2019-07-25

Fleskes RE, Bruwelheide KS, West FL, et al (2019)

Ancient DNA and bioarchaeological perspectives on European and African diversity and relationships on the colonial Delaware frontier.

American journal of physical anthropology [Epub ahead of print].

OBJECTIVES: Ancient DNA (aDNA) and standard osteological analyses applied to 11 skeletons at a late 17th to early 18th century farmstead site in Delaware to investigate the biological and social factors of settlement and slavery in colonial America.

MATERIALS AND METHODS: Osteological analysis and mitochondrial DNA (mtDNA) sequencing were conducted for all individuals and the resulting data contextualized with archaeological and documentary evidence.

RESULTS: Individuals of European and African descent were spatially separated in this colonial cemetery. The skeletal remains exhibited differences in osteological features and maternal genetic ancestry. A specific mtDNA haplotype appeared in a subset of the European-descended individuals suggesting they were maternally related. Individuals of African descent were not maternally related, and instead showed a diversity of haplotypes affiliated with present-day Western, Central, and Eastern regions of Africa.

DISCUSSION: Along with the bioarchaeological and documentary evidence, the aDNA findings contribute to our understanding of life on the colonial Delaware frontier. Evidence of maternal relatedness among European-descended individuals at the site demonstrates kin-based settlements in 17th century Delaware and provides preliminary identifications of individuals. The maternal genetic diversity of the individuals with African descent aligns with the routes of the trans-Atlantic slave trade but broadens our understanding of the ancestries of persons involved in it. Burial positioning, osteological pathology, and lack of maternal kinship among individuals of African descent provide tangible evidence for the emergence of racialized labor and society in Delaware during the late 17th century.

RevDate: 2019-08-24

Joseph TA, I Pe'er (2019)

Inference of Population Structure from Time-Series Genotype Data.

American journal of human genetics, 105(2):317-333.

Sequencing ancient DNA can offer direct probing of population history. Yet, such data are commonly analyzed with standard tools that assume DNA samples are all contemporary. We present DyStruct, a model and inference algorithm for inferring shared ancestry from temporally sampled genotype data. DyStruct explicitly incorporates temporal dynamics by modeling individuals as mixtures of unobserved populations whose allele frequencies drift over time. We develop an efficient inference algorithm for our model using stochastic variational inference. On simulated data, we show that DyStruct outperforms the current state of the art when individuals are sampled over time. Using a dataset of 296 modern and 80 ancient samples, we demonstrate DyStruct is able to capture a well-supported admixture event of steppe ancestry into modern Europe. We further apply DyStruct to a genome-wide dataset of 2,067 modern and 262 ancient samples used to study the origin of farming in the Near East. We show that DyStruct provides new insight into population history when compared with alternate approaches, within feasible run time.

RevDate: 2019-08-20
CmpDate: 2019-08-02

Angelici FM, Ciucani MM, Angelini S, et al (2019)

The Sicilian Wolf: Genetic Identity of a Recently Extinct Insular Population.

Zoological science, 36(3):189-197.

Historically, many local grey wolf (Canis lupus) populations have undergone substantial reductions in size or become extinct. Among these, the wolf population once living in Sicily, the largest island in the Mediterranean Sea, was completely eradicated by human activity in the early decades of the 20th century. To gain a better understanding of the genetic identity of the Sicilian wolf, we used techniques for the study of ancient DNA to analyze the mitochondrial (mt) variability of six specimens stored in Italian museums. We were able to amplify a diagnostic mtDNA fragment of the control region (CR) in four of the samples. Two of the samples shared the same haplotype, differing by two substitutions from the currently most diffused Italian wolf haplotype (W14) and one substitution from the only other Italian haplotype (W16). The third sample showed a previously unreported wolf-like haplotype, and the fourth a haplotype commonly found in dogs. All of the wolf haplotypes analyzed in this study belonged to the mitochondrial haplogroup that includes haplotypes detected in all the known European Pleistocene wolves and in several modern southern European populations. Unfortunately, this endemic island population, which exhibited unique mtDNA variability, was definitively lost before it was possible to understand its taxonomic uniqueness and conservational value.

RevDate: 2019-07-31

Silva PC, Malabarba MC, Vari In Memoriam R, et al (2019)

Comparison and optimization for DNA extraction of archived fish specimens.

MethodsX, 6:1433-1442 pii:S2215-0161(19)30158-X.

The DNA extracted from museum alcohol-fixed specimens can be a valuable source of information for solving taxonomic, phylogenetic, ecological and conservational questions. However, this type of DNA, also called ancient DNA, is routinely obtained in small portions and highly fragmented. We have tested two different extraction kits in museum type-specimens of the fish family Characidae. Aiming to increase the DNA yield, we made modifications on a Qiagen manufacturer protocol, in the elution step. Also, to overcome the issue of DNA fragmentation, we applied our efforts in Sanger sequencing, to find a highly variable and, in result, informative COI fragment. Based on our results, there is no correlation between amount of the DNA extracted and the age of the sample. The Sanger sequencing generated sequences which are useful in solving taxonomic puzzles. Here are presented the customization and guidelines that allowed us to recover DNA from the archived fish specimens. •DNA extraction from archived fish specimens is more effective when using silica columns.•Change of the elution times from minutes in room temperature to 24 h in freezer greatly improved the DNA yielded.•Short but highly variable sequences replace the need to sequence the entire gene to identify a species.

RevDate: 2019-06-27

Botbayev D, Ravegnini G, Sammarini G, et al (2019)

Absence of mutations in the human interferon alpha-2b gene in workers chronically exposed to ionising radiation.

Arhiv za higijenu rada i toksikologiju, 70(2):104-108.

Individuals chronically exposed to low-level ionising radiation (IR) run the risk of harmful and long-term adverse health effects, including gene mutations and cancer development. The search for reliable biomarkers of IR exposure in human population is still of great interest, as they may have a great implementation potential for the surveillance of occupationally exposed individuals. In this context, and considering previous literature, this study aimed to identify mutations in the human interferon alpha-2b (hIFNα-2b) as a potential biomarker of occupational chronic low-dose IR exposure linking low-IR exposure to the effects on haematopoiesis and reduced immunity. The analysis was performed in the genomic DNA of 51 uranium miners and 38 controls from Kazakhstan, and in 21 medical radiology workers and 21 controls from Italy. hIFNα-2b gene mutations were analysed with the real-time polymerase chain reaction (PCR) or Sanger sequencing. However, none of the investigated workers had the hIFNα-2b mutation. This finding highlights the need for further research to identify biomarkers for early detection of health effects associated with chronic low-dose IR exposure.

RevDate: 2019-06-25

De Schepper S, Ray JL, Skaar KS, et al (2019)

The potential of sedimentary ancient DNA for reconstructing past sea ice evolution.

The ISME journal pii:10.1038/s41396-019-0457-1 [Epub ahead of print].

Sea ice is a crucial component of the Arctic climate system, yet the tools to document the evolution of sea ice conditions on historical and geological time scales are few and have limitations. Such records are essential for documenting and understanding the natural variations in Arctic sea ice extent. Here we explore sedimentary ancient DNA (aDNA), as a novel tool that unlocks and exploits the genetic (eukaryote) biodiversity preserved in marine sediments specifically for past sea ice reconstructions. Although use of sedimentary aDNA in paleoceanographic and paleoclimatic studies is still in its infancy, we use here metabarcoding and single-species quantitative DNA detection methods to document the sea ice conditions in a Greenland Sea marine sediment core. Metabarcoding has allowed identifying biodiversity changes in the geological record back to almost ~100,000 years ago that were related to changing sea ice conditions. Detailed bioinformatic analyses on the metabarcoding data revealed several sea-ice-associated taxa, most of which previously unknown from the fossil record. Finally, we quantitatively traced one known sea ice dinoflagellate in the sediment core. We show that aDNA can be recovered from deep-ocean sediments with generally oxic bottom waters and that past sea ice conditions can be documented beyond instrumental time scales. Our results corroborate sea ice reconstructions made by traditional tools, and thus demonstrate the potential of sedimentary aDNA, focusing primarily on microbial eukaryotes, as a new tool to better understand sea ice evolution in the climate system.

RevDate: 2019-06-25

Eisenhofer R, A Cooper (2019)

A new home for microbes.

eLife, 8: pii:48493.

Modern microorganisms growing in fossils provide major challenges for researchers trying to detect ancient molecules in the same fossils.

RevDate: 2019-08-21

Borówka P, Pułaski Ł, Marciniak B, et al (2019)

Screening methods for detection of ancient Mycobacterium tuberculosis complex fingerprints in next-generation sequencing data derived from skeletal samples.

GigaScience, 8(6):.

BACKGROUND: Recent advances in ancient DNA studies, especially in increasing isolated DNA yields and quality, have opened the possibility of analysis of ancient host microbiome. However, such pitfalls as spurious identification of pathogens based on fragmentary data or environmental contamination could lead to incorrect epidaemiological conclusions. Within the Mycobacterium genus, Mycobacterium tuberculosis complex members responsible for tuberculosis share up to ∼99% genomic sequence identity, while other more distantly related Mycobacteria other than M. tuberculosis can be causative agents for pulmonary diseases or soil dwellers. Therefore, reliable determination of species complex is crucial for interpretation of sequencing results.

RESULTS: Here we present a novel bioinformatical approach, used for screening of ancient tuberculosis in sequencing data, derived from 28 individuals (dated 4400-4000 and 3100-2900 BC) from central Poland. We demonstrate that cost-effective next-generation screening sequencing data (∼20M reads per sample) could yield enough information to provide statistically supported identification of probable ancient disease cases.

CONCLUSIONS: Application of appropriate bioinformatic tools, including an unbiased selection of genomic alignment targets for species specificity, makes it possible to extract valid data from full-sample sequencing results (without subjective targeted enrichment procedures). This approach broadens the potential scope of palaeoepidaemiology both to older, suboptimally preserved samples and to pathogens with difficult intrageneric taxonomy.

RevDate: 2019-09-02

Xavier C, Eduardoff M, Strobl C, et al (2019)

SD quants-Sensitive detection tetraplex-system for nuclear and mitochondrial DNA quantification and degradation inference.

Forensic science international. Genetics, 42:39-44.

Measuring the quantity of DNA present in a forensic sample is relevant in a number of ways. First, it informs the analyst about the general DNA content to adjust the volume of DNA extract used for the genotyping assay to the optimal conditions (when possible). Second, quantification values can serve as plausibility checks for the performance of the DNA extraction method used as extraction positive and negative controls demand expected values. Third and relevant to highly compromised specimens, DNA quantification can inform about the degradation state of the DNA extracted from the unknown biological sample and aid the choice of downstream genotyping assays. While there are different, commercial products for the quantification of nuclear DNA available, commercial mitochondrial DNA (mtDNA) quantification systems are rare. Even more so, the simultaneous quantification of nuclear and mtDNA that is of relevance in highly degraded forensic specimens has rarely been described. We present here a novel real-time qPCR based tetraplex system termed SD quants that targets two different-sized mtDNA and a nuclear DNA region and includes an internal positive control to monitor potential inhibition. SD quants was compared to other existing quantification systems and subjected to analysis of severely degraded DNA present in ancient DNA and aged forensic specimens. This study complies with the MIQE (Bustin et al., 2009) guidelines (when applicable).

RevDate: 2019-06-30

Wren CD, A Burke (2019)

Habitat suitability and the genetic structure of human populations during the Last Glacial Maximum (LGM) in Western Europe.

PloS one, 14(6):e0217996 pii:PONE-D-19-02959.

Human populations in Western Europe during the Last Glacial Maximum were geographically constrained to glacial refugia by the severity of the climate and ecological risk factors. In this research we use an agent-based model of human mobility and interaction, based on ethnographic and archaeological data, to explore the impact of ecological risk on human population structure via a reconstructed landscape of habitat suitability. The agent-based model allows us to evaluate the size and location of glacial refugia, the size of the populations occupying them and the degree of genetic relatedness between people occupying these areas. To do this, we model the probability of an agent foraging groups' survival as a function of habitat suitability. The model's simulated "genomes" (composed of regionally specific genetic markers) allow us to track long-term trends of inter-regional interaction and mobility. The results agree with previous archaeological studies situating a large glacial refugium spanning southern France and northeastern Spain, but we expand on those studies by demonstrating that higher rates of population growth in this central refugium led to continuous out-migration and therefore genetic homogeneity across Western Europe, with the possible exception of the Italian peninsula. These results concur with material culture data from known archaeological sites dating to the Last Glacial Maximum and make predictions for future ancient DNA studies.

RevDate: 2019-06-19

Epp LS (2019)

A global perspective for biodiversity history with ancient environmental DNA.

Molecular ecology, 28(10):2456-2458.

The past centuries have seen tremendous turnovers in species distributions and biodiversity due to anthropogenic impacts on a global scale. The processes are ongoing and mostly not well documented. Long-term records of biotic change can be recovered from sedimentary deposits, but traditional analyses were restricted to organisms that leave behind visible traces and molecular genetic tools were mostly employed on samples that promised good DNA preservation. In this issue of Molecular Ecology, Shaw, Weyrich, Hallegraeff and Cooper (2019) and Gomez Cabrera et al. (2019) present two studies on marine sedimentary records from warm environments, in which they successfully analyze ancient environmental DNA (aeDNA) on a decadal and centennial scale. Notably, the studies were conducted on novel samples with nonoptimal preservation conditions for ancient DNA - historical collections of ship ballast tank sediments from Australia and two coral reef cores spanning up to 750 years (Figure 1) - but yielded a high diversity of taxa. This highlights that aeDNA is a promising tool to globally study biodiversity history on scales of decades to centuries - the timeframe most relevant to human society in the context of both current climate change and direct anthropogenic modifications of the environment.

RevDate: 2019-06-29

Bradshaw CJA, Ulm S, Williams AN, et al (2019)

Minimum founding populations for the first peopling of Sahul.

Nature ecology & evolution, 3(7):1057-1063.

The timing, context and nature of the first people to enter Sahul is still poorly understood owing to a fragmented archaeological record. However, quantifying the plausible demographic context of this founding population is essential to determine how and why the initial peopling of Sahul occurred. We developed a stochastic, age-structured model using demographic rates from hunter-gatherer societies, and relative carrying capacity hindcasted with LOVECLIM's net primary productivity for northern Sahul. We projected these populations to determine the resilience and minimum sizes required to avoid extinction. A census founding population of between 1,300 and 1,550 individuals was necessary to maintain a quasi-extinction threshold of ≲0.1. This minimum founding population could have arrived at a single point in time, or through multiple voyages of ≥130 people over ~700-900 years. This result shows that substantial population amalgamation in Sunda and Wallacea in Marine Isotope Stages 3-4 provided the conditions for the successful, large-scale and probably planned peopling of Sahul.

RevDate: 2019-08-19

Petrigh RS, Martínez JG, Mondini M, et al (2019)

Ancient parasitic DNA reveals Toxascaris leonina presence in Final Pleistocene of South America.

Parasitology, 146(10):1284-1288.

Parasitological analysis of coprolites has allowed exploring ecological relationships in ancient times. Ancient DNA analysis contributes to the identification of coprolites and their parasites. Pleistocene mammalian carnivore coprolites were recovered from paleontological and archaeological site Peñas de las Trampas 1.1 in the southern Puna of Argentina. With the aim of exploring ancient ecological relationships, parasitological analysis was performed to one of them, dated to 16 573-17 002 calibrated years BP, with 95.4% probability. Parasite eggs attributed to Toxascaris sp. by morphological characters were isolated. DNA of coprolite and eggs was extracted to molecular identification. Ancient mitochondrial DNA analysis confirmed the zoological origin of the coprolite as Puma concolor and that of parasite eggs as Toxascaris leonina. This is the oldest molecular parasite record worldwide, and it supports the presence of this parasite since the Pleistocene in America. These findings have implications for the biogeographic history of parasites and for the natural history of the region.

RevDate: 2019-07-15

Scheib CL, Hui R, D'Atanasio E, et al (2019)

East Anglian early Neolithic monument burial linked to contemporary Megaliths.

Annals of human biology, 46(2):145-149.

In the fourth millennium BCE a cultural phenomenon of monumental burial structures spread along the Atlantic façade. Megalithic burials have been targeted for aDNA analyses, but a gap remains in East Anglia, where Neolithic structures were generally earthen or timber. An early Neolithic (3762-3648 cal. BCE) burial monument at the site of Trumpington Meadows, Cambridgeshire, UK, contained the partially articulated remains of at least three individuals. To determine whether this monument fits a pattern present in megalithic burials regarding sex bias, kinship, diet and relationship to modern populations, teeth and ribs were analysed for DNA and carbon and nitrogen isotopic values, respectively. Whole ancient genomes were sequenced from two individuals to a mean genomic coverage of 1.6 and 1.2X and genotypes imputed. Results show that they were brothers from a small population genetically and isotopically similar to previously published British Neolithic individuals, with a level of genome-wide homozygosity consistent with a small island population sourced from continental Europe, but bearing no signs of recent inbreeding. The first Neolithic whole genomes from a monumental burial in East Anglia confirm that this region was connected with the larger pattern of Neolithic megaliths in the British Isles and the Atlantic façade.

RevDate: 2019-06-18

Delsuc F, Kuch M, Gibb GC, et al (2019)

Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths.

Current biology : CB, 29(12):2031-2042.e6.

Living sloths represent two distinct lineages of small-sized mammals that independently evolved arboreality from terrestrial ancestors. The six extant species are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms at the end of the Quaternary. Until now, sloth evolutionary history has mainly been reconstructed from phylogenetic analyses of morphological characters. Here, we used ancient DNA methods to successfully sequence 10 extinct sloth mitogenomes encompassing all major lineages. This includes the iconic continental ground sloths Megatherium, Megalonyx, Mylodon, and Nothrotheriops and the smaller endemic Caribbean sloths Parocnus and Acratocnus. Phylogenetic analyses identify eight distinct lineages grouped in three well-supported clades, whose interrelationships are markedly incongruent with the currently accepted morphological topology. We show that recently extinct Caribbean sloths have a single origin but comprise two highly divergent lineages that are not directly related to living two-fingered sloths, which instead group with Mylodon. Moreover, living three-fingered sloths do not represent the sister group to all other sloths but are nested within a clade of extinct ground sloths including Megatherium, Megalonyx, and Nothrotheriops. Molecular dating also reveals that the eight newly recognized sloth families all originated between 36 and 28 million years ago (mya). The early divergence of recently extinct Caribbean sloths around 35 mya is consistent with the debated GAARlandia hypothesis postulating the existence at that time of a biogeographic connection between northern South America and the Greater Antilles. This new molecular phylogeny has major implications for reinterpreting sloth morphological evolution, biogeography, and diversification history.

RevDate: 2019-06-29

Presslee S, Slater GJ, Pujos F, et al (2019)

Palaeoproteomics resolves sloth relationships.

Nature ecology & evolution, 3(7):1121-1130.

The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in combination with published mitochondrial DNA evidence, to assess the relationships of tree sloths and their extinct relatives. Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts: Choloepus groups with Mylodontidae, not Megalonychidae; Bradypus and Megalonyx pair together as megatherioids, while monophyletic Antillean sloths may be sister to all other folivorans. Divergence estimates are consistent with fossil evidence for mid-Cenozoic presence of sloths in the West Indies and an early Miocene radiation in South America.

RevDate: 2019-06-29

Keller M, Spyrou MA, Scheib CL, et al (2019)

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750).

Proceedings of the National Academy of Sciences of the United States of America, 116(25):12363-12372.

The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.

RevDate: 2019-07-15

Santander C, Montinaro F, C Capelli (2019)

Searching for archaic contribution in Africa.

Annals of human biology, 46(2):129-139.

Context: Africa's role in the narrative of human evolution is indisputably emphasised in the emergence of Homo sapiens. However, once humans dispersed beyond Africa, the history of those who stayed remains vastly under-studied, lacking the proper attention the birthplace of both modern and archaic humans deserves. The sequencing of Neanderthal and Denisovan genomes has elucidated evidence of admixture between archaic and modern humans outside of Africa, but has not aided efforts in answering whether archaic admixture happened within Africa. Objectives: This article reviews the state of research for archaic introgression in African populations and discusses recent insights into this topic. Methods: Gathering published sources and recently released preprints, this review reports on the different methods developed for detecting archaic introgression. Particularly it discusses how relevant these are when implemented on African populations and what findings these studies have shown so far. Results: Methods for detecting archaic introgression have been predominantly developed and implemented on non-African populations. Recent preprints present new methods considering African populations. While a number of studies using these methods suggest archaic introgression in Africa, without an African archaic genome to validate these results, such findings remain as putative archaic introgression. Conclusion: In light of the caveats with implementing current archaic introgression detection methods in Africa, we recommend future studies to concentrate on unravelling the complicated demographic history of Africa through means of ancient DNA where possible and through more focused efforts to sequence modern DNA from more representative populations across the African continent.

RevDate: 2019-06-10

Ersmark E, Baryshnikov G, Higham T, et al (2019)

Genetic turnovers and northern survival during the last glacial maximum in European brown bears.

Ecology and evolution, 9(10):5891-5905 pii:ECE35172.

The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid-Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter-specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.

RevDate: 2019-07-09

Prendergast ME, Lipson M, Sawchuk EA, et al (2019)

Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.

Science (New York, N.Y.), 365(6448):.

How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.

RevDate: 2019-07-15

Donoghue HD (2019)

Tuberculosis and leprosy associated with historical human population movements in Europe and beyond - an overview based on mycobacterial ancient DNA.

Annals of human biology, 46(2):120-128.

Context: Tuberculosis and leprosy are readily recognised in human remains due to their typical palaeopathology. Both Mycobacterium tuberculosis (MTB) and Mycobacterium leprae (ML) are obligate pathogens and have been detected in ancient human populations. Objective: To demonstrate historical tuberculosis and leprosy cases in Europe and beyond using molecular methods, as human populations are associated with different mycobacterial genotypes. Methods: MTB and ML ancient DNA (aDNA) has been detected by DNA amplification using PCR, or by whole genome sequencing. Mycobacterial cell wall lipids also provide specific markers for identification. Results: In 18th century Hungary, the European indigenous MTB genotype 4 strains have been found. However, many individuals were co-infected with up to three MTB sub-genotypes. In 8th-14th century Europe significant differences in ML genotypes were found between northwest Europe compared with central, southern, or eastern Europe. In addition, several co-infections of MTB and ML were detected in historical samples. Conclusion: Both MTB and ML strain types differ between geographically separate populations. This is associated with ancient human migration after an evolutionary bottleneck and clonal expansion. The absence of indigenous leprosy in Europe today may be due to the greater mortality of tuberculosis in individuals who are co-infected with both organisms.

RevDate: 2019-07-16

Wu X, Ding B, Zhang B, et al (2019)

Phylogenetic and population structural inference from genomic ancestry maintained in present-day common wheat Chinese landraces.

The Plant journal : for cell and molecular biology, 99(2):201-215.

Hexaploid common wheat is one of the most important food crops worldwide. Common wheat domestication began in the Fertile Crescent of the Near East approximately 10 000 years ago and then spread west into Europe and eastward into East Asia and China. However, the possible spreading route into and within China is still unclear. In this study, we successfully extracted DNA from single ancient wheat seeds and sequenced the whole genome of seven ancient samples from Xiaohe and Gumugou cemeteries in Xinjiang, China. Genomic inference and morphological observation confirmed their identity as hexaploid common wheat grown in prehistoric China at least 3200 years before present (BP). Phylogenetic and admixture analyses with RNA-seq data of modern hexaploid wheat cultivars from both China and Western countries demonstrated a close kinship of the ancient wheat to extant common wheat landraces in southwestern China. The highly similar allelic frequencies in modern landraces of the Qinghai-Tibetan plateau with the ancient wheat support the previously suggested southwestern spreading route into highland China. A subsequent dispersal route from the Qinghai-Tibetan plateau margins to the Yangtze valley was proposed in this study. Furthermore, the common wheat populations grown in the Middle and Lower Yangtze valley wheat zones were also proposed to be established by population admixture with the wheat grown in the Upper Yangtze valley. Our study reports ancient common wheat sequences at a genome-wide scale, providing important information on the origin, dispersal, and genetic improvement under cultivation of present-day wheat landraces grown in China.

RevDate: 2019-06-10

Hong JH, Oh CS, Chai JY, et al (2019)

Cytochrome C Oxidase Subunit 1, Internal Transcribed Spacer 1, Nicotinamide Adenine Dinucleotide Hydrogen Dehydrogenase Subunits 2 and 5 of Clonorchis sinensis Ancient DNA Retrieved from Joseon Dynasty Mummy Specimens.

Journal of Korean medical science, 34(20):e149 pii:34.e149.

We analyzed Clonorchis sinensis ancient DNA (aDNA) acquired from the specimens of the Joseon mummies. The target regions were cytochrome C oxidase subunit 1 (CO1), internal transcribed spacer 1 (ITS1), nicotinamide adenine dinucleotide hydrogen (NADH) dehydrogenase subunits 2 (NAD2) and 5 (NAD5). The sequences of C. sinensis aDNA was completely or almost identical to modern C. sinensis sequences in GenBank. We also found that ITS1, NAD2 and NAD5 could be good markers for molecular diagnosis between C. sinensis and the other trematode parasite species. The current result could improve our knowledge about genetic history of C. sinensis.

RevDate: 2019-06-10

Kashuba N, Kırdök E, Damlien H, et al (2019)

Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.

Communications biology, 2:185 pii:399.

Human demography research in grounded on the information derived from ancient DNA and archaeology. For example, the study on the early postglacial dual-route colonisation of the Scandinavian Peninsula is largely based on associating genomic data with the early dispersal of lithic technology from the East European Plain. However, a clear connection between material culture and genetics has been lacking. Here, we demonstrate that direct connection by analysing human DNA from chewed birch bark pitch mastics. These samples were discovered at Huseby Klev in western Sweden, a Mesolithic site with eastern lithic technology. We generated genome-wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers. Our samples date to 9880-9540 calBP, expanding the temporal range and distribution of the early Scandinavian genetic group. We propose that DNA from ancient mastics can be used to study environment and ecology of prehistoric populations.

RevDate: 2019-07-08
CmpDate: 2019-07-08

Hong JH, Oh CS, Seo M, et al (2019)

Analysis of COI and ITS2 regions of DNA obtained from Paragonimus westermani eggs in ancient coprolites on Joseon dynasty mummies.

Memorias do Instituto Oswaldo Cruz, 114:e180595.

The genetic information of ancient Paragonimus westermani, the oriental lung fluke infecting over 20 million people worldwide, has not been thoroughly investigated thus far. We analysed genetic markers (COI and ITS2) of P. westermani from coprolite specimens (n = 6) obtained from 15th to 18th century Korean mummies. Our results indicated that all P. westermani sequences were generally distinct from the other species of the genus Paragonimus. The sequences were clustered into three groups: Group I for East Asia; Group II for South and Southeast Asia; and Group III for India and Sri Lanka. In this study, we found that ancient P. westermani sequences in Korea belong to Group I, adding invaluable information to the existing knowledge of Paragonimus paleogenetics.

RevDate: 2019-07-15

Ham E, Underdown SJ, CJ Houldcroft (2019)

The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans.

Annals of human biology, 46(2):99-108.

Background: Simonti et al. reported variation in the frequency of Neanderthal alleles found in modern humans and argued that they may have provided an evolutionary advantage. One such allele is SNP rs3917862, associated with hypercoagulability. rs3917862 can be deleterious, but can also help prevent blood loss. Aim: To investigate two possible selective pressure hypotheses for rs3917862 surviving to higher frequencies: deaths from interpersonal violent trauma and childbirth. Subjects and methods: Mortality data from modern hunter-gatherers models the living conditions and causes of death of humans and Neanderthals at the point of admixture. Results: National census data indicates a positive correlation between the presence of rs3917862 and decreased maternal mortality ratios. When the maternal mortality ratio is modelled using GDP, births attended by skilled assistants and the presence of rs3917862, women are 0.1% more likely to die in childbirth in populations lacking rs3917862. Deaths due to violence show no correlation with rs3917862. Conclusion: These findings challenge the idea that Neanderthal admixture has negatively impacted the overall health of modern humans. Maternal survival may have acted as a selective pressure for the persistence of hypercoagulability alleles in modern Europeans. Understanding the role of hypercoagulability in childbirth, and the role of rs3917862, could help to reduce maternal mortality ratios.

RevDate: 2019-06-15

Perry GH, CA Makarewicz (2019)

Horse Paleogenomes and Human-Animal Interactions in Prehistory.

Trends in genetics : TIG, 35(7):473-475.

A new analysis of paleogenomic data from 278 ancient horses (Fages et al. Cellhttp://doi.org/10.1016/j.cell.2019.03.049) finds that this animal - crucially important to many ancient and contemporary human societies for subsistence, transportation, conflict, and more - was domesticated in at least two different regions, but with the geographic and cultural origins of the modern domestic horse lineage remaining unknown. By tracing ancient horse population movements and inferring the spatiotemporal trajectories of phenotypic adaptations, this study provides fresh perspectives on past human group interactions and activities.

RevDate: 2019-08-10

Bennett RJ, KS Baker (2019)

Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes.

Journal of clinical microbiology, 57(8): pii:JCM.00100-19.

Many pathogens that caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis, and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied resource. This minireview brings together example studies which have utilized ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequencing and analysis of historical bacterial genomes have made to a wide variety of fields. From providing retrospective diagnosis, to uncovering epidemiological pathways and characterizing genetic diversity, there is clear evidence for the utility of historical isolate studies in understanding disease today. Studies utilizing historical isolate collections, such as those from the National Collection of Type Cultures, the American Type Culture Collection, and the Institut Pasteur, offer enhanced insight since they typically span a wide time period encompassing important historical events and are useful for the investigating the phylodynamics of pathogens. Furthermore, historical sequencing studies are particularly useful for looking into the evolution of antimicrobial resistance, a major public health concern. In summary, although there are limitations to working with historical bacterial isolates, especially when utilizing ancient DNA, continued improvement in molecular and sequencing technologies and the resourcefulness of investigators mean this area of study will continue to expand and contribute to the understanding of pathogens.

RevDate: 2019-08-14

Renaud G, Hanghøj K, Korneliussen TS, et al (2019)

Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.

Genetics, 212(3):587-614.

Both the total amount and the distribution of heterozygous sites within individual genomes are informative about the genetic diversity of the population they belong to. Detecting true heterozygous sites in ancient genomes is complicated by the generally limited coverage achieved and the presence of post-mortem damage inflating sequencing errors. Additionally, large runs of homozygosity found in the genomes of particularly inbred individuals and of domestic animals can skew estimates of genome-wide heterozygosity rates. Current computational tools aimed at estimating runs of homozygosity and genome-wide heterozygosity levels are generally sensitive to such limitations. Here, we introduce ROHan, a probabilistic method which substantially improves the estimate of heterozygosity rates both genome-wide and for genomic local windows. It combines a local Bayesian model and a Hidden Markov Model at the genome-wide level and can work both on modern and ancient samples. We show that our algorithm outperforms currently available methods for predicting heterozygosity rates for ancient samples. Specifically, ROHan can delineate large runs of homozygosity (at megabase scales) and produce a reliable confidence interval for the genome-wide rate of heterozygosity outside of such regions from modern genomes with a depth of coverage as low as 5-6× and down to 7-8× for ancient samples showing moderate DNA damage. We apply ROHan to a series of modern and ancient genomes previously published and revise available estimates of heterozygosity for humans, chimpanzees and horses.

RevDate: 2019-05-15

Upadhyay M, Bortoluzzi C, Barbato M, et al (2019)

Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs.

Evolutionary applications, 12(5):951-963 pii:EVA12770.

The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might account for the presence of non-European cattle ancestry in these cattle breeds.

RevDate: 2019-06-10

Saag L, Laneman M, Varul L, et al (2019)

The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East.

Current biology : CB, 29(10):1701-1711.e16.

In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200-400 BC) (EstBA) and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC-50 AD) (EstIA). We also included 5 Pre-Roman to Roman Iron Age Ingrian (500 BC-450 AD) (IngIA) and 7 Middle Age Estonian (1200-1600 AD) (EstMA) individuals to build a dataset for studying the demographic history of the northern parts of the Eastern Baltic from the earliest layer of Mesolithic to modern times. Our findings are consistent with EstBA receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities and EstIA from populations related to modern Siberians. The latter inference is in accordance with Y chromosome (chrY) distributions in present day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers [1-5]. This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e., in the same time window as the diversification of west Uralic (Finnic) languages [6]. Furthermore, phenotypic traits often associated with modern Northern Europeans, like light eyes, hair, and skin, as well as lactose tolerance, can be traced back to the Bronze Age in the Eastern Baltic. VIDEO ABSTRACT.

RevDate: 2019-07-25

Merheb M, Matar R, Hodeify R, et al (2019)

Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases.

Cells, 8(5): pii:cells8050433.

Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases-and profiling, in certain conditions-especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven's grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.

RevDate: 2019-07-16

Maurer-Alcalá XX, M Nowacki (2019)

Evolutionary origins and impacts of genome architecture in ciliates.

Annals of the New York Academy of Sciences, 1447(1):110-118.

Genome architecture is well diversified among eukaryotes in terms of size and content, with many being radically shaped by ancient and ongoing genome conflicts with transposable elements (e.g., the large transposon-rich genomes common among plants). In ciliates, a group of microbial eukaryotes with distinct somatic and germ-line genomes present in a single cell, the consequences of these genome conflicts are most apparent in their developmentally programmed genome rearrangements. This complicated developmental phenomenon has largely overshadowed and outpaced our understanding of how germ-line and somatic genome architectures have influenced the evolutionary dynamism and potential in these taxa. In our review, we highlight three central concepts: how the evolution of atypical ciliate germ-line genome architectures is linked to ancient genome conflicts; how the complex, epigenetically guided transformation of germline to soma during development can generate widespread genetic variation; and how these features, coupled with their unusual life cycle, have increased the rate of molecular evolution linked to genome architecture in these taxa.

RevDate: 2019-06-18

Schroeder H, Margaryan A, Szmyt M, et al (2019)

Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave.

Proceedings of the National Academy of Sciences of the United States of America, 116(22):10705-10710.

The third millennium BCE was a period of major cultural and demographic changes in Europe that signaled the beginning of the Bronze Age. People from the Pontic steppe expanded westward, leading to the formation of the Corded Ware complex and transforming the genetic landscape of Europe. At the time, the Globular Amphora culture (3300-2700 BCE) existed over large parts of Central and Eastern Europe, but little is known about their interaction with neighboring Corded Ware groups and steppe societies. Here we present a detailed study of a Late Neolithic mass grave from southern Poland belonging to the Globular Amphora culture and containing the remains of 15 men, women, and children, all killed by blows to the head. We sequenced their genomes to between 1.1- and 3.9-fold coverage and performed kinship analyses that demonstrate that the individuals belonged to a large extended family. The bodies had been carefully laid out according to kin relationships by someone who evidently knew the deceased. From a population genetic viewpoint, the people from Koszyce are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in competition for resources and violent conflict. Together with the archaeological evidence, these analyses provide an unprecedented level of insight into the kinship structure and social behavior of a Late Neolithic community.

RevDate: 2019-06-10

Fages A, Hanghøj K, Khan N, et al (2019)

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.

Cell, 177(6):1419-1435.e31.

Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.

RevDate: 2019-06-24
CmpDate: 2019-06-24

Aouizerat T, Gutman I, Paz Y, et al (2019)

Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology.

mBio, 10(2): pii:mBio.00388-19.

Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research.IMPORTANCE So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms-yeast in this case-from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio- and experimental archaeology that aim to reconstruct ancient artifacts and products.

RevDate: 2019-05-17

Stahlschmidt MC, Collin TC, Fernandes DM, et al (2019)

Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia.

Scientific reports, 9(1):6628 pii:10.1038/s41598-019-43147-0.

Metagenomic analysis is a highly promising technique in paleogenetic research that allows analysis of the complete genomic make-up of a sample. This technique has successfully been employed to archaeological sediments, but possible leaching of DNA through the sequence limits interpretation. We applied this technique to the analysis of ancient DNA (aDNA) from Late Quaternary stalagmites from two caves in Western Georgia, Melouri Cave and Solkota. Stalagmites form closed systems, limiting the effect of leaching, and can be securely dated with U-series. The analyses of the sequence data from the Melouri Cave stalagmite revealed potential contamination and low preservation of DNA. However, the two Solkota stalagmites preserved ancient DNA molecules of mammals (bear, roe deer, bats) and plants (chestnut, hazelnut, flax). The aDNA bearing layers from one of the two Solkota stalagmites were dated to between ~84 ka and ~56 ka BP by U-series. The second Solkota stalagmite contained excessive detrital clay obstructing U-series dating, but it also contained bear bones with a minimum age of ~50 BP uncalibrated years and ancient DNA molecules. The preservation of authentic ancient DNA molecules in Late Quaternary speleothems opens up a new paleogenetic archive for archaeological, paleontological and paleoenvironmental research.

RevDate: 2019-06-10

Shaw B, Burrell CL, Green D, et al (2019)

Molecular insights into an ancient form of Paget's disease of bone.

Proceedings of the National Academy of Sciences of the United States of America, 116(21):10463-10472.

Paget's disease of bone (PDB) is a chronic skeletal disorder that can affect one or several bones in individuals older than 55 y of age. PDB-like changes have been reported in archaeological remains as old as Roman, although accurate diagnosis and natural history of the disease is lacking. Six skeletons from a collection of 130 excavated at Norton Priory in the North West of England, which dates to medieval times, show atypical and extensive pathological changes resembling contemporary PDB affecting as many as 75% of individual skeletons. Disease prevalence in the remaining collection is high, at least 16% of adults, with age at death estimations as low as 35 y. Despite these atypical features, paleoproteomic analysis identified sequestosome 1 (SQSTM1) or p62, a protein central to the pathological milieu of PDB, as one of the few noncollagenous human sequences preserved in skeletal samples. Targeted proteomic analysis detected >60% of the ancient p62 primary sequence, with Western blotting indicating p62 abnormalities, including in dentition. Direct sequencing of ancient DNA excluded contemporary PDB-associated SQSTM1 mutations. Our observations indicate that the ancient p62 protein is likely modified within its C-terminal ubiquitin-associated domain. Ancient miRNAs were remarkably preserved in an osteosarcoma from a skeleton with extensive disease, with miR-16 expression consistent with that reported in contemporary PDB-associated bone tumors. Our work displays the use of proteomics to inform diagnosis of ancient diseases such as atypical PDB, which has unusual features presumably potentiated by yet-unidentified environmental or genetic factors.

RevDate: 2019-07-25

Santiago-Rodriguez TM, Fornaciari A, Fornaciari G, et al (2019)

Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th Centuries.

Genes, 10(4): pii:genes10040299.

The concept of the human oral microbiome was applied to understand health and disease, lifestyles, and dietary habits throughout part of human history. In the present study, we augment the understanding of ancient oral microbiomes by characterizing human dental calculus samples recovered from the ancient Abbey of Badia Pozzeveri (central Italy), with differences in socioeconomic status, time period, burial type, and sex. Samples dating from the Middle Ages (11th century) to the Industrial Revolution era (19th century) were characterized using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. Consistent with previous studies, individuals from Badia Pozzeveri possessed commensal oral bacteria that resembled modern oral microbiomes. These results suggest that members of the oral microbiome are ubiquitous despite differences in geographical regions, time period, sex, and socioeconomic status. The presence of fecal bacteria could be in agreement with poor hygiene practices, consistent with the time period. Respiratory tract, nosocomial, and other rare pathogens detected in the dental calculus samples are intriguing and could suggest subject-specific comorbidities that could be reflected in the oral microbiome.

RevDate: 2019-05-12

Haber M, Doumet-Serhal C, Scheib CL, et al (2019)

A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences.

American journal of human genetics, 104(5):977-984.

During the medieval period, hundreds of thousands of Europeans migrated to the Near East to take part in the Crusades, and many of them settled in the newly established Christian states along the Eastern Mediterranean coast. Here, we present a genetic snapshot of these events and their aftermath by sequencing the whole genomes of 13 individuals who lived in what is today known as Lebanon between the 3rd and 13th centuries CE. These include nine individuals from the "Crusaders' pit" in Sidon, a mass burial in South Lebanon identified from the archaeology as the grave of Crusaders killed during a battle in the 13th century CE. We show that all of the Crusaders' pit individuals were males; some were Western Europeans from diverse origins, some were locals (genetically indistinguishable from present-day Lebanese), and two individuals were a mixture of European and Near Eastern ancestries, providing direct evidence that the Crusaders admixed with the local population. However, these mixtures appear to have had limited genetic consequences since signals of admixture with Europeans are not significant in any Lebanese group today-in particular, Lebanese Christians are today genetically similar to local people who lived during the Roman period which preceded the Crusades by more than four centuries.

RevDate: 2019-08-04

Membrebe JV, Suchard MA, Rambaut A, et al (2019)

Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates.

Molecular biology and evolution, 36(8):1793-1803.

Many factors complicate the estimation of time scales for phylogenetic histories, requiring increasingly complex evolutionary models and inference procedures. The widespread application of molecular clock dating has led to the insight that evolutionary rate estimates may vary with the time frame of measurement. This is particularly well established for rapidly evolving viruses that can accumulate sequence divergence over years or even months. However, this rapid evolution stands at odds with a relatively high degree of conservation of viruses or endogenous virus elements over much longer time scales. Building on recent insights into time-dependent evolutionary rates, we develop a formal and flexible Bayesian statistical inference approach that accommodates rate variation through time. We evaluate the novel molecular clock model on a foamy virus cospeciation history and a lentivirus evolutionary history and compare the performance to other molecular clock models. For both virus examples, we estimate a similarly strong time-dependent effect that implies rates varying over four orders of magnitude. The application of an analogous codon substitution model does not implicate long-term purifying selection as the cause of this effect. However, selection does appear to affect divergence time estimates for the less deep evolutionary history of the Ebolavirus genus. Finally, we explore the application of our approach on woolly mammoth ancient DNA data, which shows a much weaker, but still important, time-dependent rate effect that has a noticeable impact on node age estimates. Future developments aimed at incorporating more complex evolutionary processes will further add to the broad applicability of our approach.

RevDate: 2019-06-26

Hanghøj K, Renaud G, Albrechtsen A, et al (2019)

DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage.

GigaScience, 8(4):.

BACKGROUND: Recent computational advances in ancient DNA research have opened access to the detection of ancient DNA methylation footprints at the genome-wide scale. The most commonly used approach infers the methylation state of a given genomic region on the basis of the amount of nucleotide mis-incorporations observed at CpG dinucleotide sites. However, this approach overlooks a number of confounding factors, including the presence of sequencing errors and true variants. The scale and distribution of the inferred methylation measurements are also variable across samples, precluding direct comparisons.

FINDINGS: Here, we present DamMet, an open-source software program retrieving maximum likelihood estimates of regional CpG methylation levels from ancient DNA sequencing data. It builds on a novel statistical model of post-mortem DNA damage for dinucleotides, accounting for sequencing errors, genotypes, and differential post-mortem cytosine deamination rates at both methylated and unmethylated sites. To validate DamMet, we extended gargammel, a sequence simulator for ancient DNA data, by introducing methylation-dependent features of post-mortem DNA decay. This new simulator provides direct validation of DamMet predictions. Additionally, the methylation levels inferred by DamMet were found to be correlated to those inferred by epiPALEOMIX and both on par and directly comparable to those measured from whole-genome bisulphite sequencing experiments of fresh tissues.

CONCLUSIONS: DamMet provides genuine estimates for local DNA methylation levels in ancient individual genomes. The returned estimates are directly cross-sample comparable, and the software is available as an open-source C++ program hosted at https://gitlab.com/KHanghoj/DamMet along with a manual and tutorial.

RevDate: 2019-05-14
CmpDate: 2019-05-14

Meffray A, Perrin M, Richier A, et al (2019)

Molecular detection of Treponema pallidum subspecies pallidum in 150-year-old foetal remains, southeastern France.

Journal of medical microbiology, 68(5):761-769.

PURPOSE: Syphilis, caused by Treponema pallidum subspecies pallidum , is considered as an old disease affecting humans; traces of such infections, including congenital syphilis, are potentially identifiable in archaeological samples. The aim of this research was to perform macroscopic and molecular investigations of T. pallidum on six infant remains, buried between 1837 and 1867, from the cemetery of 'Les Crottes' in Marseille city (southeastern France).

METHODOLOGY: Pathological analysis of bones from individuals, aged from the twenty-ninth week of amenorrhea to 4-9 months, was performed. Samples served also as a source of ancient DNA (aDNA) for PCR-based molecular investigations targeting T. pallidum DNA; all samples were also tested for Mycobacterium tuberculosis and Plasmodium falciparum DNA. Sequences characterized were cloned and sequenced, and compared to those available in databases.Results/Key findings. All samples tested displayed widespread osteoporotic lesions across the skeleton possibly related to some metabolic or infectious disorders. Subsequent molecular analysis revealed that one individual, SP332 (unborn, 29 amenorrhea weeks, inhumation date 1864-1866), exhibited positive signals for the five T. pallidum amplification systems tested; sequence analysis provided strong evidence for the effective detection of T. pallidum subspecies pallidum DNA.

CONCLUSIONS: Individual SP332 is the first PCR-confirmed palaeopathological case of syphilis identified in France, and the youngest specimen ever to be diagnosed with certainty for congenital syphilis. Future research aimed at better characterizing this 150-year-old treponeme genome and exploring new archaelogical cases of syphilis in the very young should contribute to a better comprehension of the disease's history.

RevDate: 2019-04-17

Phillips N (2019)

Indigenous groups look to ancient DNA to bring their ancestors home.

Nature, 568(7752):294-297.

RevDate: 2019-08-03

Brace S, Diekmann Y, Booth TJ, et al (2019)

Ancient genomes indicate population replacement in Early Neolithic Britain.

Nature ecology & evolution, 3(5):765-771.

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.

RevDate: 2019-06-22

Kutanan W, Kampuansai J, Srikummool M, et al (2019)

Contrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations.

Molecular biology and evolution, 36(7):1490-1506.

The human demographic history of Mainland Southeast Asia (MSEA) has not been well studied; in particular, there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major Mainland Southeast Asia families: Austroasiatic, Tai-Kadai, and Sino-Tibetan. Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* [O-M95*] and O2a* [O-M324*]) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyze complete mitochondrial DNA genome sequences published previously from the same groups and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of postmarital residence pattern on genetic diversity in patrilocal versus matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 ka), with two later major male-specific expansions during the Neolithic period (∼4-5 ka) and the Bronze/Iron Age (∼2.0-2.5 ka). These two later expansions are characteristic of the modern Austroasiatic and Tai-Kadai groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion, and cultural diffusion) of major Thai groups and find different results from mitochondrial DNA simulations, supporting contrasting male and female genetic histories.

RevDate: 2019-04-12

Oliva A, Pulicani S, Lefort V, et al (2019)

Accounting for ambiguity in ancestral sequence reconstruction.

Bioinformatics (Oxford, England) pii:5448860 [Epub ahead of print].

MOTIVATION: The reconstruction of ancestral genetic sequences from the analysis of contemporaneous data is a powerful tool to improve our understanding of molecular evolution. Various statistical criteria defined in a phylogenetic framework can be used to infer nucleotide, amino-acid or codon states at internal nodes of the tree, for every position along the sequence. These criteria generally select the state that maximizes (or minimizes) a given criterion. Although it is perfectly sensible from a statistical perspective, that strategy fails to convey useful information about the level of uncertainty associated to the inference.

RESULTS: The present study introduces a new criterion for ancestral sequence reconstruction, the minimum posterior expected error (MPEE), that selects a single state whenever the signal conveyed by the data is strong, and a combination of multiple states otherwise. We also assess the performance of a criterion based on the Brier scoring scheme which, like MPEE, does not rely on any tuning parameters. The precision and accuracy of several other criteria that involve arbitrarily set tuning parameters are also evaluated. Large scale simulations demonstrate the benefits of using the MPEE and Brier-based criteria with a substantial increase in the accuracy of the inference of past sequences compared to the standard approach and realistic compromises on the precision of the solutions returned.

AVAILABILITY: The software package PhyML (https://github.com/stephaneguindon/phyml) provides an implementation of the Maximum A Posteriori (MAP) and MPEE criteria for reconstructing ancestral nucleotide and amino-acid sequences.

RevDate: 2019-04-14

Mills JG, Brookes JD, Gellie NJC, et al (2019)

Relating Urban Biodiversity to Human Health With the 'Holobiont' Concept.

Frontiers in microbiology, 10:550.

A relatively unaccounted ecosystem service from biodiversity is the benefit to human health via symbiotic microbiota from our environment. This benefit occurs because humans evolved alongside microbes and have been constantly exposed to diverse microbiota. Plants and animals, including humans, are organised as a host with symbiotic microbiota, whose collective genome and life history form a single holobiont. As such, there are interdependencies between biodiversity, holobionts, and public health which lead us to argue that human health outcomes could be improved by increasing contact with biodiversity in an urban context. We propose that humans, like all holobionts, likely require a diverse microbial habitat to appropriate resources for living healthy, long lives. We discuss how industrial urbanisation likely disrupts the symbiosis between microbiota and their hosts, leading to negative health outcomes. The industrialised urban habitat is low in macro and microbial biodiversity and discourages contact with beneficial environmental microbiota. These habitat factors, alongside diet, antibiotics, and others, are associated with the epidemic of non-communicable diseases in these societies. We suggest that restoration of urban microbial biodiversity and micro-ecological processes through microbiome rewilding can benefit holobiont health and aid in treating the urban non-communicable disease epidemic. Further, we identify research gaps and some solutions to economic and strategic hurdles in applying microbiome rewilding into daily urban life.

RevDate: 2019-05-10

Klunk J, Duggan AT, Redfern R, et al (2019)

Genetic resiliency and the Black Death: No apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark.

American journal of physical anthropology, 169(2):240-252.

OBJECTIVES: In the 14th century AD, medieval Europe was severely affected by the Great European Famine as well as repeated bouts of disease, including the Black Death, causing major demographic shifts. This high volatility led to increased mobility and migration due to new labor and economic opportunities, as evidenced by documentary and stable isotope data. This study uses ancient DNA (aDNA) isolated from skeletal remains to examine whether evidence for large-scale population movement can be gleaned from the complete mitochondrial genomes of 264 medieval individuals from England (London) and Denmark.

MATERIALS AND METHODS: Using a novel library-conserving approach to targeted capture, we recovered 264 full mitochondrial genomes from the petrous portion of the temporal bones and teeth and compared genetic diversity across the medieval period within and between English (London) and Danish populations and with contemporary populations through population pairwise ΦST analysis.

RESULTS: We find no evidence of significant differences in genetic diversity spatially or temporally in our dataset, yet there is a high degree of haplotype diversity in our medieval samples with little exact sequence sharing.

DISCUSSION: The mitochondrial genomes of both medieval Londoners and medieval Danes suggest high mitochondrial diversity before, during and after the Black Death. While our mitochondrial genomic data lack geographically correlated signals, these data could be the result of high, continual female migration before and after the Black Death or may simply indicate a large female effective population size unaffected by the upheaval of the medieval period. Either scenario suggests a genetic resiliency in areas of northwestern medieval Europe.

RevDate: 2019-04-11

Nakagome S, Hudson RR, A Di Rienzo (2019)

Inferring the model and onset of natural selection under varying population size from the site frequency spectrum and haplotype structure.

Proceedings. Biological sciences, 286(1896):20182541.

A fundamental question about adaptation in a population is the time of onset of the selective pressure acting on beneficial alleles. Inferring this time, in turn, depends on the selection model. We develop a framework of approximate Bayesian computation (ABC) that enables the use of the full site frequency spectrum and haplotype structure to test the goodness-of-fit of selection models and estimate the timing of selection under varying population size scenarios. We show that our method has sufficient power to distinguish natural selection from neutrality even if relatively old selection increased the frequency of a pre-existing allele from 20% to 50% or from 40% to 80%. Our ABC can accurately estimate the time of onset of selection on a new mutation. However, estimates are prone to bias under the standing variation model, possibly due to the uncertainty in the allele frequency at the onset of selection. We further extend our approach to take advantage of ancient DNA data that provides information on the allele frequency path of the beneficial allele. Applying our ABC, including both modern and ancient human DNA data, to four pigmentation alleles in Europeans, we detected selection on standing variants that occurred after the dispersal from Africa even though models of selection on a new mutation were initially supported for two of these alleles without the ancient data.

RevDate: 2019-06-11

Siripan S, Wonnapinij P, Auetrakulvit P, et al (2019)

Origin of prehistoric cattle excavated from four archaeological sites in central and northeastern Thailand.

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis, 30(4):609-617.

Cattle have been domesticated in Southeast Asia, including Thailand, for thousands of years, but the history of cattle domestication in the region remains unclear. To date, only genetic studies of modern Thai cattle DNA have been reported. To gain some insight into cattle domestication in the country, a total of 56 cattle remains excavated from four archaeological sites (dated to between 3550 and 1700 years before present (YBP)) in northeastern and central Thailand were analysed in this study. Of 56, the 157-bp D-loop fragment was successfully generated from 26 samples, all of which belonged to Bos taurus in haplogroup T/T3. One haplotype contained 19 members from all four archaeological sites and clustered with the ancient B. taurus from Iran, Turkey and China. Other haplotypes have not shared haplotype with B. taurus from other countries but they showed close relationship to those from China. This represents the first genetic evidence that B.taurus was domesticated in Thailand between 3550 and 1700 YBP. In addition, the close relationship among ancient Thai, Iranian and Chinese taurines suggests that cattle from the Near East were introduced into North China, and were subsequently brought into Thailand thousands of years ago.

RevDate: 2019-04-20

Brunson K, D Reich (2019)

The Promise of Paleogenomics Beyond Our Own Species.

Trends in genetics : TIG, 35(5):319-329.

Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.

RevDate: 2019-07-24
CmpDate: 2019-07-24

Spyrou MA, Bos KI, Herbig A, et al (2019)

Ancient pathogen genomics as an emerging tool for infectious disease research.

Nature reviews. Genetics, 20(6):323-340.

Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.

RevDate: 2019-08-04

Yelmen B, Mondal M, Marnetto D, et al (2019)

Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations.

Molecular biology and evolution, 36(8):1628-1642.

Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high-quality modern genomes, these models can be tested for gene and genome level deviations. Using local ancestry deconvolution and masking, we reconstructed population-specific surrogates of the two main ancestral components for more than 500 samples from 25 South Asian populations and showed our approach to be robust via coalescent simulations. Our f3 and f4 statistics-based estimates reveal that the reconstructed haplotypes are good proxies for the source populations that admixed in the area and point to complex interpopulation relationships within the West Eurasian component, compatible with multiple waves of arrival, as opposed to a simpler one wave scenario. Our approach also provides reliable local haplotypes for future downstream analyses. As one such example, the local ancestry deconvolution in South Asians reveals opposite selective pressures on two pigmentation genes (SLC45A2 and SLC24A5) that are common or fixed in West Eurasians, suggesting post-admixture purifying and positive selection signals, respectively.

RevDate: 2019-04-07

Ciucani MM, Palumbo D, Galaverni M, et al (2019)

Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains.

PeerJ, 7:e6424 pii:6424.

Background: The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated.

Methods: In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses.

Results: Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1.

Discussion: In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence in this area. Moreover, the unexpected discovery of a 24,700-year-old sample carrying a haplotype that, from the fragment here obtained, falls within the canine clade A, could represent the oldest evidence in Europe of such dog-rich clade. All these findings suggest complex population dynamics that deserve to be further investigated based on mitochondrial or whole genome sequencing.

RevDate: 2019-08-29
CmpDate: 2019-08-29

Harris DN, Ruczinski I, Yanek LR, et al (2019)

Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World.

Genome biology and evolution, 11(5):1417-1430.

The metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (>20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. The rate-limiting steps of this process are catalyzed by fatty acid desaturase (FADS) 1 and 2. Therefore, understanding the evolutionary history of the FADS genes is essential to our understanding of hominin evolution. The FADS genes have two haplogroups, ancestral and derived, with the derived haplogroup being associated with more efficient LC-PUFA biosynthesis than the ancestral haplogroup. In addition, there is a complex global distribution of these haplogroups that is suggestive of Neanderthal introgression. We confirm that Native American ancestry is nearly fixed for the ancestral haplogroup, and replicate a positive selection signal in Native Americans. This positive selection potentially continued after the founding of the Americas, although simulations suggest that the timing is dependent on the allele frequency of the ancestral Beringian population. We also find that the Neanderthal FADS haplotype is more closely related to the derived haplogroup and the Denisovan clusters closer to the ancestral haplogroup. Furthermore, the derived haplogroup has a time to the most recent common ancestor of 688,474 years before present. These results support an ancient polymorphism, as opposed to Neanderthal introgression, forming in the FADS region during the Pleistocene with possibly differential selection pressures on both haplogroups. The near fixation of the ancestral haplogroup in Native American ancestry calls for future studies to explore the potential health risk of associated low LC-PUFA levels in these populations.

RevDate: 2019-08-05

Traversari M, Serrangeli MC, Catalano G, et al (2019)

Multi-analytic study of a probable case of fibrous dysplasia (FD) from certosa monumental cemetery (Bologna, Italy).

International journal of paleopathology, 25:1-8.

OBJECTIVE: To evaluate, via a multidisciplinary approach, a distinctive paleopathological condition believed to be fibrous dysplasia, found on a 19th/20th century skeleton from Certosa Monumental Cemetery, Bologna, Italy.

MATERIALS: A skeletonized cranium and mandible recovered from an ossuary in 2014.

METHODS: Pathological alterations were analysed by radiological examination, dental macrowear, histopathological and genetic analyses.

RESULT: The skeleton is believed to be an adult male. Differential diagnoses include Paget's disease, McCune-Albright syndrome, osteochondroma and osteosarcoma. The radiographic findings, along with the solitary nature of the lesions, are strong evidence for the diagnosis of fibrous dysplasia (FD). Genetic analysis further revealed a frequency of ˜1% of mutant alleles with the R201C substitution, one of the post-zygotic activating mutation frequently associated with FD.

CONCLUSIONS: The multi-analytical method employed suggests a diagnosis of monostotic form of FD. The diagnostic design incorporates multiple lines of evidence, including macroscopic, histopathological, and genetic analyses.

SIGNIFICANCE: Through the use of a multi-analytic approach, robust diagnoses can be offered. This case serves as one of the oldest examples of FD from an historical context. The genetic mutation detected, associated with FD, has not been previously reported in historical/ancient samples.

RevDate: 2019-04-02

Di Maida G, Mannino MA, Krause-Kyora B, et al (2019)

Radiocarbon dating and isotope analysis on the purported Aurignacian skeletal remains from Fontana Nuova (Ragusa, Italy).

PloS one, 14(3):e0213173 pii:PONE-D-18-23492.

Proving voyaging at sea by Palaeolithic humans is a difficult archaeological task, even for short distances. In the Mediterranean, a commonly accepted sea crossing is that from the Italian Peninsula to Sicily by anatomically modern humans, purportedly of the Aurignacian culture. This claim, however, was only supported by the typological attribution to the Aurignacian of the lithic industries from the insular site of Fontana Nuova. AMS radiocarbon dating undertaken as part of our research shows that the faunal remains, previously considered Aurignacian, actually date to the Holocene. Absolute dating on dentinal collagen also attributes the human teeth from the site to the early Holocene, although we were unable to obtain ancient DNA to evaluate their ancestry. Ten radiocarbon dates on human and other taxa are comprised between 9910-9700 cal. BP and 8600-8480 cal. BP, indicating that Fontana Nuova was occupied by Mesolithic and not Aurignacian hunter-gatherers. Only a new study of the lithic assemblage could establish if the material from Fontana Nuova is a mixed collection that includes both late Upper Palaeolithic (Epigravettian) and Mesolithic artefacts, as can be suggested by taking into account both the results of our study and of the most recent reinterpretation of the lithics. Nevertheless, this research suggests that the notion that Aurignacian groups were present in Sicily should now be revised. Another outcome of our study is that we found that three specimens, attributed on grounds both of morphological and ZooMS identifications to Cervus elaphus, had δ13C values significantly higher than any available for such species in Europe.

RevDate: 2019-04-05
CmpDate: 2019-04-05

Feldman M, Fernández-Domínguez E, Reynolds L, et al (2019)

Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia.

Nature communications, 10(1):1218 pii:10.1038/s41467-019-09209-7.

Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80-90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.

RevDate: 2019-08-23
CmpDate: 2019-08-23

Weyrich LS, Farrer AG, Eisenhofer R, et al (2019)

Laboratory contamination over time during low-biomass sample analysis.

Molecular ecology resources, 19(4):982-996.

Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a home-made silica-based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human-associated taxa in comparison to the home-made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )