Herbarium Genomics: Plant Archival DNA Explored

2018 ◽  
pp. 205-224 ◽  
Author(s):  
Freek T. Bakker
Keyword(s):  
Archival Dna

Archival DNA reveals cryptic biodiversity within the Spotted Shag (Phalacrocorax punctatus) from New Zealand

The Condor ◽  
2019 ◽  
Vol 121 (3) ◽  
Author(s):  
Nicolas J Rawlence ◽  
Matt J Rayner ◽  
Tim G Lovegrove ◽  
Debbie Stoddart ◽  
Melanie Vermeulen ◽  
...  
Keyword(s):  
New Zealand ◽  
Conservation Management ◽  
Species Conservation ◽  
Genetic Data ◽  
Mitochondrial Control Region ◽  
Phylogenetic Structure ◽  
Management Guidelines ◽  
Conservation Concern ◽  
Cryptic Biodiversity ◽  
Archival Dna

Abstract Genetic data are increasingly being used to prioritize species conservation in a fiscally constrained age of seemingly boundless conservation crises. Such data can also reveal previously cryptic biodiversity requiring further revision of conservation management guidelines. Using a combination of mitochondrial (control region) and nuclear (beta fibrinogen intron 7) DNA, and morphology, we reveal that the endemic New Zealand Spotted Shag (Phalacrocorax punctatus) complex exhibits phylogenetic structure that is decoupled from previously recorded qualitative morphological variation. Crucially, the most genetically distinct populations within P. punctatus are from northern New Zealand; recent surveys show that these populations, which house important genetic diversity within Spotted Shags, are in danger of being extirpated. In contrast, we find the previously phenotypically differentiated nominate (P. punctatus punctatus) and Blue (P. punctatus oliveri) Shag subspecies show no genetic and morphological separation, and are of least conservation concern.

scholarly journals Decreased NK Cells in Patients with Head and Neck Cancer Determined in Archival DNA

2012 ◽  
Vol 18 (22) ◽  
pp. 6147-6154 ◽  
Author(s):  
William P. Accomando ◽  
John K. Wiencke ◽  
E. Andres Houseman ◽  
Rondi A. Butler ◽  
Shichun Zheng ◽  
...  
Keyword(s):  
Head And Neck Cancer ◽  
Nk Cells ◽  
Head And Neck ◽  
Neck Cancer ◽  
Archival Dna

scholarly journals A century of genetic homogenization in Baltic salmon—evidence from archival DNA

2021 ◽  
Vol 288 (1949) ◽  
Author(s):  
Johan Östergren ◽  
Stefan Palm ◽  
John Gilbey ◽  
Göran Spong ◽  
Johan Dannewitz ◽  
...  
Keyword(s):  
Baltic Sea ◽  
Large Scale ◽  
Isolation By Distance ◽  
Anthropogenic Impacts ◽  
Genetic Change ◽  
Past Century ◽  
The Baltic Sea ◽  
The Baltic ◽  
Archival Dna

Intra-species genetic homogenization arising from anthropogenic impacts is a major threat to biodiversity. However, few taxa have sufficient historical material to systematically quantify long-term genetic changes. Using archival DNA collected over approximately 100 years, we assessed spatio-temporal genetic change in Atlantic salmon populations across the Baltic Sea, an area heavily impacted by hydropower exploitation and associated with large-scale mitigation stocking. Analysis was carried out by screening 82 SNPs in 1680 individuals from 13 Swedish rivers. We found an overall decrease in genetic divergence and diminished isolation by distance among populations, strongly indicating genetic homogenization over the past century. We further observed an increase in genetic diversity within populations consistent with increased gene flow. The temporal genetic change was lower in larger wild populations than in smaller wild and hatchery-reared ones, indicating that larger populations have been able to support a high number of native spawners in relation to immigrants. Our results demonstrate that stocking practices of salmon in the Baltic Sea have led to the homogenization of populations over the last century, potentially compromising their ability to adapt to environmental change. Stocking of reared fish is common worldwide, and our study is a cautionary example of the potentially long-term negative effects of such activities.

Acquired somatic ATRX mutations in myelodysplastic syndrome associated with α thalassemia (ATMDS) convey a more severe hematologic phenotype than germline ATRX mutations

Blood ◽  
2004 ◽  
Vol 103 (6) ◽  
pp. 2019-2026 ◽  
Author(s):  
David P. Steensma ◽  
Douglas R. Higgs ◽  
Chris A. Fisher ◽  
Richard J. Gibbons
Keyword(s):  
Myelodysplastic Syndrome ◽  
High Performance ◽  
Germ Line ◽  
Somatic Mosaicism ◽  
Point Mutations ◽  
Hematologic Malignancies ◽  
Gene Encoding ◽  
Linked Gene ◽  
Molecular Defects ◽  
Archival Dna

Abstract Acquired somatic mutations in ATRX, an X-linked gene encoding a chromatin-associated protein, were recently identified in 4 patients with the rare subtype of myelodysplastic syndrome (MDS) associated with α thalassemia (ATMDS). Here we describe a series of novel point mutations in ATRX detected in archival DNA samples from marrow and/or blood of patients with ATMDS by use of denaturing high-performance liquid chromatography (DHPLC), a technique sensitive to low-level mosaicism. Two of the new mutations result in changes in amino acids altered in previously described pedigrees with germ line ATRX mutations (ATR-X syndrome), but the hematologic abnormalities were much more severe in the patients with ATMDS than in the corresponding constitutional cases. In one ATMDS case where DNA samples from several time points were available, the proportion of ATRX-mutant subclones correlated with changes in the amount of hemoglobin H. This study strengthens the link between acquired, somatic ATRX mutations and ATMDS, illustrates how molecular defects associated with MDS and other hematologic malignancies masked by somatic mosaicism may be detected by DHPLC, and shows that additional factors increase the severity of the hematologic phenotype of ATRX mutations in ATMDS.

scholarly journals Family of Constrained Codes for Archival DNA Data Storage

2018 ◽  
Vol 22 (10) ◽  
pp. 1972-1975 ◽  
Author(s):  
Dixita Limbachiya ◽  
Manish K. Gupta ◽  
Vaneet Aggarwal
Keyword(s):  
Data Storage ◽  
Constrained Codes ◽  
Archival Dna
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