Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 ...November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2.
The Eurasian grapevine (Vitis vinifera) has long been important for wine production as well as being a food source. Despite being clonally propagated, modern cultivars exhibit great morphological and ...genetic diversity, with thousands of varieties described in historic and contemporaneous records. Through historical accounts, some varieties can be traced to the Middle Ages, but the genetic relationships between ancient and modern vines remain unknown. We present target-enriched genome-wide sequencing data from 28 archaeological grape seeds dating to the Iron Age, Roman era and medieval period. When compared with domesticated and wild accessions, we found that the archaeological samples were closely related to western European cultivars used for winemaking today. We identified seeds with identical genetic signatures present at different Roman sites, as well as seeds sharing parent-offspring relationships with varieties grown today. Furthermore, we discovered that one seed dated to ~1100 CE was a genetic match to 'Savagnin Blanc', providing evidence for 900 years of uninterrupted vegetative propagation.
An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases ...>20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained <3% endogenous DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size < 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method.
Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome‐scale information from historic, ancient, and even extinct samples. While once inconceivable due to the ...challenges of DNA damage, contamination, and the technical limitations of PCR‐based Sanger sequencing, following the dawn of the second‐generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.
A significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from the ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples.
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•We present the first mitochondrial genomes of three African giant sengis.•Our phylogenetic analyses of the mitogenomes and published sequences show introgression.•Introgression is ...localized to three species around the eastern Udzungwa Mountains.•This degree of introgression among species has not previously been recognized.
Giant sengis, or elephant-shrews (Macroscelidea; Macroscelididae; Rhynchocyon), are small-bodied mammals found in central and eastern African forests. Studies have provided contrasting views of the extent and direction of introgression among species. We generated full mitochondrial genomes, and compiled publically available mtDNA 12S and nuclear vWF sequences from Rhynchocyon cirnei, R. petersi and R. udzungwensis that had not previously been analyzed in concert, to elucidate the phylogenetic and population-specific context of potential introgression. Our spatially and phylogenetically broad sampling across species revealed substantial, unidirectional mitochondrial introgression of the R. petersi lineage into R. cirnei reichardi and R. udzungwensis, and from R. udzungwensis into R. c. reichardi. All introgression was highly localized and found only in the eastern Udzungwa Mountains forests in Tanzania. The nuclear data showed another pattern, with R. petersi haplotypes in R. cirnei cirnei and R. c. reichardi. No individuals showed both mitochondrial and nuclear introgression. Our results suggest higher levels of hybridization among giant sengi species than previously recognized, but also highlight the need for further genome-wide analysis and increased spatial sampling to clarify the many aspects of diversification and introgression in this group.
The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears ...are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modeling, we investigate how Holocene environmental changes affected polar bears around Greenland. We uncover reductions in effective population size coinciding with increases in annual mean sea surface temperature, reduction in sea ice cover, declines in suitable habitat, and shifts in suitable habitat northward. Furthermore, we show that west and east Greenlandic polar bears are morphologically, and ecologically distinct, putatively driven by regional biotic and genetic differences. Together, we provide insights into the vulnerability of polar bears to environmental change and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants.
A multivariate investigation reveals the environment’s role in the evolutionary ecology of Greenlandic polar bears.
Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only ...three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.9 Mb, contig N50 = 36.6 kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis) challenges of sanguivory. These findings highlight the value of a holistic study of both the host and its microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.
Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are ...largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions.
In ancient DNA (aDNA) research, evolutionary and archaeological questions are often investigated using the genomic sequences of organelles: mitochondrial and chloroplast DNA. Organellar genomes are ...found in multiple copies per living cell, increasing their chance of recovery from archaeological samples, and are inherited from one parent without genetic recombination, simplifying analyses. While mitochondrial genomes have played a key role in many mammalian aDNA projects, including research focused on prehistoric humans and extinct hominins, it is unclear how useful plant chloroplast genomes (plastomes) may be at elucidating questions related to plant evolution, crop domestication, and the prehistoric movement of botanical products through trade and migration. Such analyses are particularly challenging for plant species whose genomes have highly repetitive sequences and that undergo frequent genomic reorganization, notably species with high retrotransposon activity. To address this question, we explored the research potential of the grape (Vitis vinifera L.) plastome using targeted-enrichment methods and high-throughput DNA sequencing on a collection of archaeological grape pip and vine specimens from sites across Eurasia dating ca. 4000 BCE–1500 CE. We demonstrate that due to unprecedented numbers of sequence insertions into the nuclear and mitochondrial genomes, the grape plastome provides limited intraspecific phylogenetic resolution. Nonetheless, we were able to assign archaeological specimens in the Italian peninsula, Sardinia, UK, and Armenia from pre-Roman to medieval times as belonging to all three major chlorotypes A, C, and D found in modern varieties of Western Europe. Analysis of nuclear genomic DNA from these samples reveals a much greater potential for understanding ancient viticulture, including domestication events, genetic introgression from local wild populations, and the origins and histories of varietal lineages.
•Non-carbonized archaeological grapevines and seeds frequently contain endogenous DNA, but preservation is highly variable.•Targeted capture of the Vitis plastome is feasible but yields limited phylogenetic information at the intraspecific level.•Analysis of the nuclear genome markers demonstrates great promise for elucidating past cultivation practices.
Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and ...protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past.
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