scholarly journals Population genetics of wild Macaca fascicularis with low‐coverage shotgun sequencing of museum specimens

2020 ◽  
Vol 173 (1) ◽  
pp. 21-33 ◽  
Author(s):  
Lu Yao ◽  
Kelsey Witt ◽  
Hongjie Li ◽  
Jonathan Rice ◽  
Nelson R. Salinas ◽  
...  
Keyword(s):  
Population Genetics ◽  
Macaca Fascicularis ◽  
Shotgun Sequencing ◽  
Museum Specimens ◽  
Low Coverage

Isolation and characterisation via 454 sequencing of microsatellites from the tawny frogmouth, Podargus strigoides (Class Aves, Family Podargidae)

2012 ◽  
Vol 60 (2) ◽  
pp. 133
Author(s):  
Fiona E. Hogan ◽  
Marian Weaving ◽  
Gregory R. Johnston
Keyword(s):  
Population Genetics ◽  
Gene Flow ◽  
Microsatellite Markers ◽  
Reproductive Ecology ◽  
454 Sequencing ◽  
Urban Environments ◽  
Shotgun Sequencing ◽  
Target Species ◽  
Single Population ◽  
Polymorphic Microsatellite

We isolated 24 novel polymorphic microsatellite markers from the tawny frogmouth, a nocturnal bird endemic to Australia, which has successfully adapted to urban environments. Initially, 454 shotgun sequencing was used to identify 733 loci with primers designed. Of these, we trialled 30 in the target species of which all amplified a product of expected size. Subsequently, all 30 of these loci were screened for variation in 25 individuals, from a single population in Melbourne, Victoria, Australia. Twenty-eight loci were polymorphic with observed heterozygosity ranging from 0.03 to 0.96 (mean 0.58) and the number of alleles per locus ranged from 2 to 18 (average of 6.5); we confirmed that 24 loci conformed to Hardy–Weinberg expectations. The 24 loci identified here will be sufficient to unequivocally identify individuals and will be useful in understanding the reproductive ecology, population genetics and the gene flow amongst localities in urban environments where this bird thrives.

scholarly journals Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

PLoS ONE ◽  
2014 ◽  
Vol 9 (5) ◽  
pp. e96793 ◽  
Author(s):  
Mandy Man-Ying Tin ◽  
Evan Philip Economo ◽  
Alexander Sergeyevich Mikheyev
Keyword(s):  
Degraded Dna ◽  
Museum Specimens ◽  
Low Coverage

scholarly journals Squeezing water from a stone: High-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards

2018 ◽  
Author(s):  
Jimmy A McGuire ◽  
Darko D Cotoras ◽  
Brendan O'Connell ◽  
Shobi Z S Lawalata ◽  
Cynthia Y Wang-Claypool ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Extraction Procedure ◽  
Genetic Data ◽  
Museum Specimens ◽  
Base Pairs ◽  
Holotype Specimen ◽  
The Status ◽  
Taxonomic Problem ◽  
Low Coverage

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (547 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.

scholarly journals Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4470 ◽  
Author(s):  
Jimmy A. McGuire ◽  
Darko D. Cotoras ◽  
Brendan O’Connell ◽  
Shobi Z.S. Lawalata ◽  
Cynthia Y. Wang-Claypool ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Extraction Procedure ◽  
Genetic Data ◽  
Museum Specimens ◽  
Base Pairs ◽  
Holotype Specimen ◽  
The Status ◽  
Taxonomic Problem ◽  
Low Coverage

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (721 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.

scholarly journals In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Jonathan Louis Golob ◽  
Samuel Schwartz Minot
Keyword(s):  
Microbial Community ◽  
Computational Efficiency ◽  
High Throughput Sequencing ◽  
Shotgun Sequencing ◽  
Relative Performance ◽  
Protein Coding ◽  
Sequence Detection ◽  
Metagenome Analysis ◽  
Trade Offs ◽  
Low Coverage

Abstract Background High-throughput sequencing can establish the functional capacity of a microbial community by cataloging the protein-coding sequences (CDS) present in the metagenome of the community. The relative performance of different computational methods for identifying CDS from whole-genome shotgun sequencing is not fully established. Results Here we present an automated benchmarking workflow, using synthetic shotgun sequencing reads for which we know the true CDS content of the underlying communities, to determine the relative performance (sensitivity, positive predictive value or PPV, and computational efficiency) of different metagenome analysis tools for extracting the CDS content of a microbial community. Assembly-based methods are limited by coverage depth, with poor sensitivity for CDS at < 5X depth of sequencing, but have excellent PPV. Mapping-based techniques are more sensitive at low coverage depths, but can struggle with PPV. We additionally describe an expectation maximization based iterative algorithmic approach which we show to successfully improve the PPV of a mapping based technique while retaining improved sensitivity and computational efficiency. Conclusion Our benchmarking approach reveals the trade-offs of assembly versus alignment-based approaches and the relative performance of specific implementations when one wishes to extract the protein coding capacity of microbial communities.

scholarly journals Uneven Missing Data Skew Phylogenomic Relationships within the Lories and Lorikeets

2020 ◽  
Vol 12 (7) ◽  
pp. 1131-1147
Author(s):  
Brian Tilston Smith ◽  
William M Mauck ◽  
Brett W Benz ◽  
Michael J Andersen
Keyword(s):  
Missing Data ◽  
Museum Specimens ◽  
Outlier Analysis ◽  
Sequencing Technology ◽  
Data Completeness ◽  
Data Skew ◽  
Outlier Test ◽  
The Stability ◽  
Low Coverage ◽  
Historical Samples

Abstract The resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense taxon sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally degraded, which presents various challenges. In this study, we evaluated how the coverage at variant sites and missing data among historical and modern samples impacts phylogenomic inference. We explored these patterns in the brush-tongued parrots (lories and lorikeets) of Australasia by sampling ultraconserved elements in 105 taxa. Trees estimated with low coverage characters had several clades where relationships appeared to be influenced by whether the sample came from historical or modern specimens, which were not observed when more stringent filtering was applied. To assess if the topologies were affected by missing data, we performed an outlier analysis of sites and loci, and a data reduction approach where we excluded sites based on data completeness. Depending on the outlier test, 0.15% of total sites or 38% of loci were driving the topological differences among trees, and at these sites, historical samples had 10.9× more missing data than modern ones. In contrast, 70% data completeness was necessary to avoid spurious relationships. Predictive modeling found that outlier analysis scores were correlated with parsimony informative sites in the clades whose topologies changed the most by filtering. After accounting for biased loci and understanding the stability of relationships, we inferred a more robust phylogenetic hypothesis for lories and lorikeets.

Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences

2013 ◽  
Vol 26 (3) ◽  
pp. 384-388 ◽  
Author(s):  
F. Keith Barker ◽  
Sara Oyler-McCance ◽  
Diana F. Tomback
Keyword(s):  
Shotgun Sequencing ◽  
Low Coverage ◽  
Tissue Origin

scholarly journals Population genetics of the fish Brycon henni (Characiformes: Bryconidae) using species-specific polymorphic microsatellite loci

2020 ◽  
Vol 68 (3) ◽  
Author(s):  
Ricardo M. Landínez-García ◽  
Edna J. Márquez
Keyword(s):  
Population Genetics ◽  
Microsatellite Loci ◽  
Genomic Library ◽  
International Union ◽  
Genetic Population ◽  
Genetic Diversity And Structure ◽  
Polymorphic Microsatellite ◽  
Species Specific ◽  
Low Coverage ◽  
Risk Categorization

Introduction: The freshwater fish Brycon henni (Characiformes: Bryconidae) is endemic to Colombia and currently considered as “least concern” according to the International Union for Conservation of Nature (IUCN). Objective: To develop microsatellite markers to examine population genetics in Brycon henni. Methods: Using a low-coverage sequenced genomic library, this study developed the first set of microsatellite loci to study the population genetics of this Neotropical species. These loci were used to evaluate the genetic diversity and structure of B. henni from three sites of the Magdalena-Cauca Basin (Colombia). Results: A set of twenty-one polymorphic microsatellite loci was highly informative and revealed that B. henni is evenly genetically structured between two tributaries of the Cauca River separated by only 30 km, a finding that indicates it conforms to reproductively isolated groups. Conclusions: We reported a set of twenty-one polymorphic microsatellite loci that was highly informative and allowed the detection of genetic structure at local and regional scales. This genetic population structure, concordant with that found in eight congeners, is relevant to estimate the B. henni risk categorization as well as for management, conservation, and restocking programs.

scholarly journals Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe

2021 ◽  
Author(s):  
Adam B. Rohrlach ◽  
Luka Papac ◽  
Ainash Childebayeva ◽  
Maïté Rivollat ◽  
Vanessa Villalba-Mouco ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Western Europe ◽  
Shotgun Sequencing ◽  
Sequence Length ◽  
Critical Event ◽  
Capture Assay ◽  
History Of ◽  
Early Farmers ◽  
Low Coverage ◽  
New Evidence

AbstractUniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective.Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture arrays such as the 1240K, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield.Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the “mappable” regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240K capture, YMCA significantly improves the coverage and number of sites hit on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants.To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

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