José Alfredo Samaniego Castruita
A5074161740- Genetic diversity and population structure
- Marine animal studies overview
- Genomics and Phylogenetic Studies
- Forensic and Genetic Research
- SARS-CoV-2 and COVID-19 Research
- Wildlife Ecology and Conservation
- Horticultural and Viticultural Research
- Human-Animal Interaction Studies
- Antimicrobial Resistance in Staphylococcus
- Isotope Analysis in Ecology
- Fermentation and Sensory Analysis
- Marine and coastal plant biology
- Plant Pathogens and Resistance
- Environmental DNA in Biodiversity Studies
- Animal Genetics and Reproduction
- Arctic and Antarctic ice dynamics
- Identification and Quantification in Food
- Plant Disease Resistance and Genetics
- Bacterial biofilms and quorum sensing
- Cephalopods and Marine Biology
- Genetic and phenotypic traits in livestock
- Animal Virus Infections Studies
- Indigenous Studies and Ecology
- Yeasts and Rust Fungi Studies
- Bat Biology and Ecology Studies
Hvidovre Hospital
2021-2024
Amager Hospital
2024
Copenhagen University Hospital
2021-2024
University of Copenhagen
2014-2023
Natural History Museum Aarhus
2012-2019
Natural History Museum of Denmark
2015-2019
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis 48 species representing all orders Neoaves using phylogenomic methods created to handle data. We recovered highly resolved tree that confirms previously controversial sister or close relationships. identified first divergence in Neoaves, two groups named Passerea and Columbea, independent lineages diverse convergently evolved land water bird species. Among Passerea, infer common ancestor core...
Claims of extreme survival DNA have emphasized the need for reliable models degradation through time. By analysing mitochondrial (mtDNA) from 158 radiocarbon-dated bones extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average half-life within this geographically constrained fossil assemblage was estimated to be 521 years 242 bp mtDNA sequence, corresponding per nucleotide fragmentation rate (k) 5.50 × 10(-6) year. With an effective...
Abstract In recent years, massive parallel sequencing has revolutionised the study of degraded DNA , thus enabling field ancient to evolve into that paleogenomics. Despite these advances, recovery and remains challenging due limitations in manipulation chemically damaged highly fragmented molecules. particular, enzymatic reactions purification steps during library preparation can result template loss biases, affecting downstream analyses. The development methods circumvent obstacles enable...
Following emergence of the SARS-CoV-2 variant Omicron in November 2021, dominant BA.1 sub-lineage was replaced by BA.2 Denmark. We analysed first 2,623 cases from 29 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission Capital Region clusters expanding after Christmas holidays. Mutational analysis shows distinct and
Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach the common vampire bat (Desmodus rotundus), one of only three obligate blood-feeding (sanguivorous) mammals, study evolution its complex dietary adaptation. Specifically, we assembled high-quality reference genome (scaffold N50 = 26.9 Mb, contig 36.6 kb) gut metagenome, compared them against those insectivorous, frugivorous carnivorous bats. Our analyses...
Responsible for the Irish potato famine of 1845-49, oomycete pathogen Phytophthora infestans caused persistent, devastating outbreaks late blight across Europe in 19th century. Despite continued interest history and spread pathogen, genome famine-era strain remains entirely unknown. Here we characterize temporal genomic changes introduced P. infestans. We shotgun sequence five 19th-century European strains from archival herbarium samples--including oldest known specimen, collected 1845 first...
Significance The transatlantic slave trade resulted in the forced movement of over 12 million Africans to Americas. Although many coastal shipping points are known, they do not necessarily reflect slaves’ actual ethnic or geographic origins. We obtained genome-wide data from 17th-century remains three enslaved individuals who died on Caribbean island Saint Martin and use them identify their genetic origins Africa, with far greater precision than previously thought possible. study...
North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote latrans) taxonomically controversial red, Eastern timber Great Lakes wolves. We explored their population structure regional gene flow using dataset 40 full genome sequences that represent extant diversity American wolves populations. This included 15 new genomes (13 wolves, 1 red timber/Great wolf), ranging from 0.4 15x coverage. In addition providing support for...
New lineages of SARS-CoV-2 are potential concern due to higher transmissibility, risk severe outcomes, and/or escape from neutralizing antibodies. Lineage B.1.1.7 (the Alpha variant) became dominant in early 2021, but the association between transmissibility and factors, such as age primary case viral load remains poorly understood. Here, we used comprehensive administrative data Denmark, comprising full population (January 11 February 7, 2021), estimate household transmissibility. This...
Sled dog arctic adaptations go far back Dogs have been used for sledding in the Arctic as ∼9500 years ago. However, relationships among earliest sled dogs, other populations, and wolves are unknown. Sinding et al. sequenced an ancient dog, 10 modern wolf analyzed their genetic with dogs. This analysis indicates that dogs represent lineage going at least 9500 bred ancestors of precontact American gene flow between likely stopped before Science , this issue p. 1495
In Denmark, vaccination against Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has been with the Pfizer-BioNTech (BTN162b2) or Moderna (mRNA-1273) mRNA vaccines. Patients chronic hepatitis C virus (HCV) infection followed in our clinic received vaccinations according to Danish roll-out plan. To monitor HCV infection, RNA was extracted from patient plasma and sequencing performed on Illumina platform. 10 of 108 samples, full-length traces SARS-CoV-2 spike vaccine sequences were...
An increasing number of studies are addressing the evolutionary genomics dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled genome currently available against which to map such data - that a boxer (Canis lupus familiaris). We generated first lupus) as an additional choice reference, explored what implications may arise when previously published remapped this reference. Reassuringly, we find regardless...
Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves domestic dogs.1Fan Z. Silva P. Gronau I. Wang S. Armero A.S. Schweizer R.M. Ramirez O. Pollinger J. Galaverni M. Ortega Del-Vecchyo D. et al.Worldwide patterns of genomic variation admixture in gray wolves.Genome Res. 2016; 26: 163-173Crossref PubMed Scopus (125) Google Scholar Genetic studies have suggested these groups trace their origins to a wolf population that...
The Arctic is warming at an unprecedented rate, with unknown consequences for endemic fauna. However, Earth has experienced severe climatic oscillations in the past, and understanding how species responded to them might provide insight into their resilience near-future predictions. Little known about responses of marine mammals past shifts, but narwhals (
Abstract Background In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of world. Denmark, comprehensive and real-time test, contact-tracing, sequencing efforts were applied to sustain epidemic control. Here, we use these data investigate transmissibility, introduction, onward transmission in Denmark. Methods We analyzed a set 60,178 genomes generated from high-throughput by Danish COVID-19 Genome Consortium, representing 34% all positive cases...
As severe acute respiratory coronavirus 2 (SARS-CoV-2) variants continue to emerge, it is important characterize immune responses against which can inform on protection efficacies following booster vaccination. In this study, neutralizing breadth and antigen-specific CD8 + T cell were analyzed in both infection-naïve infection-experienced individuals administration of a bivalent Wuhan-Hu-1+BA.4/5 Comirnaty ® mRNA vaccine. Significantly higher titers found after vaccination compared the...
Niche variation owing to individual differences in ecology has been hypothesized be an early stage of sympatric speciation. Yet date, no study tracked niche width over more than a few generations. In this study, we show the presence isotopic millennial timescales and investigate evolutionary outcomes. Isotopic ratios were measured from tissue samples killer whale Orcinus orca lineages North Sea, spanning 10 000 years. spanned range similar difference values two known prey items, herring...
An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient (aDNA) researchers, especially after reports of endogenous content increases >20-fold in some samples. To investigate the behavior this method, we generated ssDNA and conventional double-stranded (dsDNA) libraries from 23 historic plant animal specimens. We found substantially increased when dsDNA contained <3% DNA, but enrichment is less pronounced preparations successfully recover...