Jacob Enk

Jacob Enk
MYcroarray · Research and Development

Ph.D.

About

53
Publications
15,185
Reads
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1,654
Citations

Publications

Publications (53)
Article
Full-text available
Finding, characterizing, and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive, and cost‐effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples....
Article
Integrating ancient fossil DNA with modern genetic samples is aiding in advancing the fields of ecology and biogeography. However, wide gaps in the fossil record still remain throughout the tropics, while genetic and genomic datasets from tiny (<50 mg) ancient tropical fossils recovered from small mass species (<100 g) are particularly scarce. We s...
Preprint
Finding, characterizing, and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive, and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples....
Article
Full-text available
Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum resistance in domesticated crops. We combined association genetics with R gene enrichment sequencing (AgRenSeq) to exploit pan-genome variation in wild diploid wheat and rapidly clone four stem rust resistance genes. AgRenSeq enables R gene cloning in any crop...
Article
Full-text available
Dogs were present in the Americas before the arrival of European colonists, but the origin and fate of these precontact dogs are largely unknown. We sequenced 71 mitochondrial and 7 nuclear genomes from ancient North American and Siberian dogs from time frames spanning ~9000 years. Our analysis indicates that American dogs were not derived from Nor...
Article
Full-text available
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first collected its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12 880-year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that...
Preprint
Genetic resistance is the most economic and environmentally sustainable approach for crop disease protection. Disease resistance (R) genes from wild relatives are a valuable resource for breeding resistant crops. However, introgression of R genes into crops is a lengthy process often associated with co-integration of deleterious linked genes 1, 2 a...
Article
Full-text available
Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species...
Article
Full-text available
The morphology of mammoth upper third permanent molars (M3) is used to address regional-and continental-scale patterns in the structure of mammoth populations. Recent refinements to the understanding of Mammuthus phylogenetic diversity south of the Laurentide ice show extensive overlap between regional populations. We assess the underlying geograph...
Data
Concatenated alignment of core genes in G. vaginalis.DOI: http://dx.doi.org/10.7554/eLife.20983.017
Data
G. vaginalis core genome alignment trimmed with Gblocks.DOI: http://dx.doi.org/10.7554/eLife.20983.018
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Recombinant fragments detected with BratNextGen in S. saprophyticus alignment.DOI: http://dx.doi.org/10.7554/eLife.20983.030
Data
Maximum likelihood phylogenetic analysis of trimmed G. vaginalis alignment with RAxML.DOI: http://dx.doi.org/10.7554/eLife.20983.019
Data
Maximum likelihood phylogenetic analysis of trimmed S. saprophyticus alignment with RAxML.DOI: http://dx.doi.org/10.7554/eLife.20983.028
Data
Recombinant fragments detected with BratNextGen in trimmed G. vaginalis alignment.DOI: http://dx.doi.org/10.7554/eLife.20983.020
Data
S. saprophyticus plasmid alignment trimmed with trimal.DOI: http://dx.doi.org/10.7554/eLife.20983.029
Data
(A) Troy sample details (B) SEM-EDS results from nodule. For each replicate, upper value is weight %, lower value is atomic %. (C) Common chemical constituents of renal and bladder calculi (kidney and bladder stones) and Troy nodules. + - presence, ND- not detected, Unk- unknown, RF- Relative Frequency in modern populations (C.Y.C Pak (ed.) Pak [19...
Article
Full-text available
After evolving in Africa at the close of the Miocene, mammoths (Mammuthus sp.) spread through much of the northern hemisphere, diversifying morphologically as they entered various habitats. Paleontologically, these morphs are conventionally recognized as species. In Pleistocene North America alone, several mammoth species have been recognized, inha...
Article
Full-text available
Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as...
Article
The processes leading up to species extinctions are typically characterized by prolonged declines in population size and geographic distribution, followed by a phase in which populations are very small and may be subject to intrinsic threats, including loss of genetic diversity and inbreeding [1]. However, whether such genetic factors have had an i...
Article
Full-text available
Most genetic studies of Holocene fauna have been performed with ancient samples from dry and cold regions, in which preservation of fossils is facilitated and molecular damage is reduced. Ancient DNA work from tropical regions has been precluded owing to factors that limit DNA preservation (e.g. temperature, hydrolytic damage). We analysed ancient...
Data
On Jan 26, 2015 this sequence version replaced gi:667795611. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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On Jan 26, 2015 this sequence version replaced gi:667795607. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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On Jan 26, 2015 this sequence version replaced gi:667795609. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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On Jan 26, 2015 this sequence version replaced gi:667795613. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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On Jan 26, 2015 this sequence version replaced gi:667795618. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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On Jan 26, 2015 this sequence version replaced gi:667795612. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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On Jan 26, 2015 this sequence version replaced gi:667795614. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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On Jan 26, 2015 this sequence version replaced gi:667795615. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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On Jan 26, 2015 this sequence version replaced gi:667795617. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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On Jan 26, 2015 this sequence version replaced gi:667795608. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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On Jan 26, 2015 this sequence version replaced gi:667795616. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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On Jan 26, 2015 this sequence version replaced gi:667795610. ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Article
Full-text available
Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of microbial diversi...
Article
Full-text available
We report metrics from complete genome capture of nuclear DNA from extinct mammoths using biotinylated RNAs transcribed from an Asian elephant DNA extract. Enrichment of the nuclear genome ranged from 1.06- to 18.65-fold, to an apparent maximum threshold of ∼80% on-target. This projects an order of magnitude less costly complete genome sequencing f...
Article
Yersinia pestis has caused at least three human plague pandemics. The second (Black Death, 14-17th centuries) and third (19-20th centuries) have been genetically characterised, but there is only a limited understanding of the first pandemic, the Plague of Justinian (6-8th centuries). To address this gap, we sequenced and analysed draft genomes of Y...
Article
Full-text available
In the 19th century, there were several major cholera pandemics in the Indian subcontinent, Europe, and North America. The causes of these outbreaks and the genomic strain identities remain a mystery. We used targeted high-throughput sequencing to reconstruct the Vibrio cholerae genome from the preserved intestine of a victim of the 1849 cholera ou...
Article
Targeted DNA enrichment through hybridization capture (EHC) is rapidly replacing PCR as the method of choice for enrichment prior to genomic resequencing. This is especially true in the case of ancient DNA (aDNA) from long-dead organisms, where targets tend to be highly fragmented and outnumbered by contaminant DNA. However, the behavior of EHC usi...
Data
Additional materials and methods. A detailed description of Materials and methods.
Data
Additional tables. A collection of tables referred to in the text as tables S1 through S7.
Data
Additional figures. A collection of figures referred to in the text as Figures S1 to S8.
Article
Full-text available
Late Pleistocene North America hosted at least two divergent and ecologically distinct species of mammoth: the periglacial woolly mammoth (Mammuthus primigenius) and the subglacial Columbian mammoth (Mammuthus columbi). To date, mammoth genetic research has been entirely restricted to woolly mammoths, rendering their genetic evolution difficult to...
Article
Remains of a woolly mammoth (Mammuthus primigenius) were found in Qagnaxˆ Cave, a lava tube cave on St. Paul Island in the Pribilof Islands, 500 km west of the Alaskan mainland in the Bering Sea. Several dates converge on 5725 14C yr BP, making these the youngest mammoth remains discovered in North America, and among the few Holocene mammoths known...

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Project (1)
Project
The morphology of mammoth upper third permanent molars (M3) is used to address regional- and continental-scale patterns in the structure of mammoth populations. Recent refinements to the understanding of phylogenetic diversity in Mammuthus south of the Laurentide ice show extensive overlap between regional populations. We assess the underlying geographic structure in mammoth tooth morphology in light of these new genetic data.