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Ancient DNA Suggests Dwarf and 'Giant' Emu Are Conspecific

Tim H. Heupink, Leon Huynen, David M. Lambert, Robert C. Fleischer
2011 PLoS ONE  
Citation: Heupink TH, Huynen L, Lambert DM (2011) Ancient DNA Suggests Dwarf and 'Giant' Emu Are Conspecific. PLoS ONE 6(4): e18728.  ...  KI02 H . . . . T . . T T A C . . KI03 G . . . . T . C T T A C . . KI04 G . . . . T . C T T A C . .  ... 
doi:10.1371/journal.pone.0018728 pmid:21494561 pmcid:PMC3073985 fatcat:siyryfdngjhebjm37ujwnz2j2m

Bayesian Estimation of Sequence Damage in Ancient DNA

Simon Y. W. Ho, Tim H. Heupink, Andrew Rambaut, Beth Shapiro
2007 Molecular biology and evolution  
DNA extracted from archaeological and paleontological remains is usually damaged by biochemical processes postmortem. Some of these processes lead to changes in the structure of the DNA molecule, which can result in the incorporation of incorrect nucleotides during polymerase chain reaction. These base misincorporations, or miscoding lesions, can lead to the inclusion of spurious additional mutations in ancient DNA (aDNA) data sets. This has the potential to affect the outcome of phylogenetic
more » ... d population genetic analyses, including estimates of mutation rates and genetic diversity. We present a novel model, termed the delta model, which estimates the amount of damage in DNA data and accounts for its effects in a Bayesian phylogenetic framework. The ability of the delta model to estimate damage is first investigated using a simulation study. The model is then applied to 13 aDNA data sets. The amount of damage in these data sets is shown to be significant but low (about 1 damaged base per 750 nt), suggesting that precautions for limiting the influence of damaged sites, such as cloning and enzymatic treatment, are worthwhile. The results also suggest that relatively high rates of mutation previously estimated from aDNA data are not entirely an artifact of sequence damage and are likely to be due to other factors such as the persistence of transient polymorphisms. The delta model appears to be particularly useful for placing upper credibility limits on the amount of sequence damage in an alignment, and this capacity might be beneficial for future aDNA studies or for the estimation of sequencing errors in modern DNA.
doi:10.1093/molbev/msm062 pmid:17395598 fatcat:czhcigqkfzg25i2x74gqneob6u

The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred

Tim H Heupink, Hein van Grouw, David M Lambert
2014 BMC Evolutionary Biology  
The closely related and extinct Dodo (Raphus cucullatus) and Rodrigues Solitaire (Pezophaps solitaria), both in the subfamily Raphinae, are members of a clade of morphologically very diverse pigeons. Genetic analyses have revealed that the Nicobar Pigeon (Caloenas nicobarica) is the closest living relative of these birds, thereby highlighting their ancestors' remarkable migration and morphological evolution. The Spotted Green Pigeon (Caloenas maculata) was described in 1783 and showed some
more » ... arities to the Nicobar Pigeon. Soon however the taxon fell into obscurity, as it was regarded as simply an abnormal form of the Nicobar Pigeon. The relationship between both taxa has occasionally been questioned, leading some ornithologists to suggest that the two may in fact be different taxa. Today only one of the original two specimens survives and nothing is known about the origin of the taxon. Due to its potential close relationship, the Spotted Green Pigeon may hold clues to the historical migration, isolation and morphological evolution of the Dodo and its kindred. We use ancient DNA methodologies to investigate the phylogeny and authenticity of the Spotted Green Pigeon. A novel extraction method with the ability to retain and purify heavily fragmented DNA is used to investigate two feathers from the sole surviving specimen. Maximum Likelihood phylogenetic analyses reveal that the Spotted Green Pigeon is a unique lineage and together with the Nicobar Pigeon, is basal to the Dodo and Rodrigues Solitaire. The distance observed for the Spotted Green Pigeon and Nicobar Pigeon is larger than that observed within other Pigeon species, indicating that the Spotted Green pigeon is a unique taxon, thereby also indicating it is a genuine addition to the list of extinct species. The phylogenetic placement of the Spotted Green Pigeon indicates that the ancestors of both Caloenas and therefore Raphinae displayed and shared the following traits: ability of flight, semi-terrestrial habits and an affinity towards islands. This set of traits supports the stepping stone hypothesis, which states that the Raphinae got to their respective localities by island hopping from India or Southeast Asia.
doi:10.1186/1471-2148-14-136 pmid:25027719 pmcid:PMC4099497 fatcat:qqi4wojmbrbpri4iaimcpjluoy

Identifying isoniazid resistance markers to guide inclusion of high-dose isoniazid in tuberculosis treatment regimens: a systematic review

Emmanuel Rivière, Michael G. Whitfield, Jochem Nelen, Tim H. Heupink, Annelies Van Rie
2020 Clinical Microbiology and Infection  
Effective use of antibiotics is critical to control the global tuberculosis pandemic. High-dose isoniazid (INH) can be effective in the presence of low-level resistance. We performed a systematic literature review to improve our understanding of the differential impact of genomic Mycobacterium tuberculosis (Mtb) variants on the level of INH resistance. Following online databases were searched: PubMed, Web of Science and Embase. Articles reporting on clinical Mtb isolates with linked genotypic
more » ... d phenotypic data and reporting INH resistance levels were eligible for inclusion. All genomic regions reported in the eligible studies were included in the analysis, including: katG, inhA, ahpC, oxyR-ahpC, furA, fabG1, kasA, rv1592c, iniA, iniB, iniC, rv0340, rv2242 and nat. The level of INH resistance was determined by minimum inhibitory concentration (MIC): low-level resistance was defined as 0.1-0.4μg/ml on liquid and 0.2-1.0μg/ml on solid media, high-level resistance as >0.4μg/ml on liquid and >1.0μg/ml on solid media. 1212 records were retrieved of which 46 were included. These 46 studies reported 1697 isolates of which 21% (n=362) were INH susceptible, 17% (n=287) had low-level, and 62% (n=1048) high-level INH resistance. Overall, 24% (n=402) of isolates were reported as wild type and 76% (n=1295) had ≥1 relevant genetic variant. Among 1295 isolates with ≥1 variant, 78% (n=1011) had a mutation in the katG gene. Of the 867 isolates with a katG mutation in codon 315, 93% (n=810) had high-level INH resistance. In contrast, only 50% (n=72) of the 144 isolates with a katG variant not in the 315-position had high-level resistance. Of the 284 isolates with ≥1 relevant genetic variant and wild type katG gene, 40% (n=114) had high-level INH resistance. Presence of a variant in the katG gene is a good marker of high-level INH resistance only if located in codon 315.
doi:10.1016/j.cmi.2020.07.004 pmid:32653663 fatcat:3tzijf6ebzgi3ptqa34ut4vnoq

Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation

André E. R. Soares, Ben J. Novak, James Haile, Tim H. Heupink, Jon Fjeldså, M. Thomas P. Gilbert, Hendrik Poinar, George M. Church, Beth Shapiro
2016 BMC Evolutionary Biology  
tissues in buffer modified from the Qiagen Blood & Tissue Kit that comprised 150 μL Buffer ATL, 30 μL proteinase K solution, and 20 μL of 1 M dithiothreitol (DTT), in a rotation incubator at 56°C for 48 h,  ... 
doi:10.1186/s12862-016-0800-3 pmid:27782796 pmcid:PMC5080718 fatcat:7pogkouffbgslepdhdg4al5z7q

Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries

Emmanuel Rivière, Tim H Heupink, Nabila Ismail, Anzaan Dippenaar, Charlene Clarke, Gemeda Abebe, Peter Heusden, Rob Warren, Conor J Meehan, Annelies Van Rie
2020 Briefings in Bioinformatics  
Background Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. Methods We assessed the global status of Mtb WGS and developed a 3-week training course coupled with long-term mentoring and WGS infrastructure building. Training focused on genome sequencing, bioinformatics and development of a locally relevant WGS research
more » ... ct. The aim of the long-term mentoring was to support trainees in project implementation and funding acquisition. The focus of WGS infrastructure building was on the DNA extraction process and bioinformatics. Findings Compared to their TB burden, Asia and Africa are grossly underrepresented in Mtb WGS research. Challenges faced resulted in adaptations to the training, mentoring and infrastructure building. Out-of-date laptop hardware and operating systems were overcome by using online tools and a Galaxy WGS analysis pipeline. A case studies approach created a safe atmosphere for students to formulate and defend opinions. Because quality DNA extraction is paramount for WGS, a biosafety level 3 and general laboratory skill training session were added, use of commercial DNA extraction kits was introduced and a 2-week training in a highly equipped laboratory was combined with a 1-week training in the local setting. Interpretation By developing and sharing the components of and experiences with a sequencing and bioinformatics training program, we hope to stimulate capacity building programs for Mtb WGS and empower high-burden countries to play an important role in WGS-based TB surveillance and research.
doi:10.1093/bib/bbaa246 pmid:33009560 pmcid:PMC8293823 fatcat:6fxk3l2s3vdwlkw7snyc4rq3bu

Ancient mtDNA sequences from the First Australians revisited

Tim H. Heupink, Sankar Subramanian, Joanne L. Wright, Phillip Endicott, Michael Carrington Westaway, Leon Huynen, Walther Parson, Craig D. Millar, Eske Willerslev, David M. Lambert
2016 Proceedings of the National Academy of Sciences of the United States of America  
| www.pnas.org/cgi/doi/10.1073/pnas.1521066113 Heupink et al. | www.pnas.org/cgi/doi/10.1073/pnas.1521066113 Heupink et al.  ... 
doi:10.1073/pnas.1521066113 pmid:27274055 pmcid:PMC4922152 fatcat:kfakceqr4rh4hkrwi6qy34cpse

Ancient nuclear genomes enable repatriation of Indigenous human remains

Joanne L. Wright, Sally Wasef, Tim H. Heupink, Michael C. Westaway, Simon Rasmussen, Colin Pardoe, Gudju Gudju Fourmile, Michael Young, Trish Johnson, Joan Slade, Roy Kennedy, Patsy Winch (+16 others)
2018 Science Advances  
After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes
more » ... d 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the present) of known provenance and compared them to 100 high-coverage contemporary Aboriginal Australian genomes, also of known provenance. We report substantial ancient population structure showing strong genetic affinities between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Our findings demonstrate the feasibility of successfully identifying the origins of unprovenanced ancestral remains using genomic methods.
doi:10.1126/sciadv.aau5064 pmid:30585290 pmcid:PMC6300400 fatcat:5v7p2bmjn5djvom6i4ghlrjuwm

A genomic history of Aboriginal Australia

Anna-Sapfo Malaspinas, Michael C. Westaway, Craig Muller, Vitor C. Sousa, Oscar Lao, Isabel Alves, Anders Bergström, Georgios Athanasiadis, Jade Y. Cheng, Jacob E. Crawford, Tim H. Heupink, Enrico Macholdt (+63 others)
2016 Nature  
However, statistical analyses indicate that 32 Australian crania show no evidence of H. erectus admixture 13 .  ... 
doi:10.1038/nature18299 pmid:27654914 fatcat:zush6rpjsvg5zgj7xjfgiriowu

Transparency, trust, and community welfare: towards a precision public health ethics framework for the genomics era

Eric T. Juengst, Annelies Van Rie
2020 Genome Medicine  
Acknowledgements The authors would like to thank the following colleagues for helpful discussions of the ideas presented here: Dario García de Viedma, Conor Meehan, Inaki Comas, Tim H.  ...  Heupink, Elise De Vos, Wouter Arrazola de Oñate, Vanessa Mathys, Pieter-Jan Ceyssens, Guido Groenen, Fernando González-Candelas, Annemie Forier.  ... 
doi:10.1186/s13073-020-00800-y pmid:33218363 pmcid:PMC7677909 fatcat:bkeumg6bp5hg3asggwodmttck4

High mitogenomic evolutionary rates and time dependency

Sankar Subramanian, Dee R. Denver, Craig D. Millar, Tim Heupink, Angelique Aschrafi, Steven D. Emslie, Carlo Baroni, David M. Lambert
2009 Trends in Genetics  
the mutation rate (m H ) of the latter, as m S = m H (d S /d H ) where m H = 0.55 (0.32-0.92) substitutions/site/million years as reported from a previous study [20] (blue column).  ...  The rate for synonymous positions (m S ) was estimated as m S = m H . (d S /d H ), where m H is the neutral mutation rate at the HVR-I region, which was previously estimated as 0.55 s/s/My [20] .  ... 
doi:10.1016/j.tig.2009.09.005 pmid:19836098 fatcat:mudn5atir5e6lhhgchrb2lshm4

Comprehensive and accurate genetic variant identification from contaminated and low coverage Mycobacterium tuberculosis whole genome sequencing data [article]

Tim Heupink, Lennert Verboven, Robin Warren, Annelies Van Rie
2021 bioRxiv   pre-print
The contamination type was either P. aeruginosa, S. epidermidis, H. sapiens, a mixture of P. aeruginosa, S. epidermidis and H. sapiens or a NTM mixture (M. intracellulare, M. abcessus or M. avium up to  ...  20% of the Mtb fraction with the remaining contamination consisting of P. aeruginosa, S. epidermidis or H. sapiens).  ... 
doi:10.1101/2021.09.16.460612 fatcat:jpmokxmxpncsnpamf5lxc2d73e

Avian Mitochondrial DNA and Microevolution across Biological Organisation

Tim Hermanus Heupink, University, My, David Lambert
2018
Creating figures 1 and 2, table 1  Initial drafts of the paper, its angle and the final version  Submission of the paper Tim H.  ...  The bibliographic details for these papers are: HEUPINK, T. H., HUYNEN, L. & LAMBERT, D. M. 2011. Ancient DNA suggests dwarf and 'giant' emu are conspecific. PLoS One, 6, e18728. HEUPINK, T.  ... 
doi:10.25904/1912/3619 fatcat:2qfvidccdja5zis6gg3jlm2y7e

Return to Country: genomics and the repatriation of ancient Aboriginal Australians

Joanne Louise Wright, University, My, David Lambert
2018
To my aDNA lab supervisor Dr Tim Heupink, thanks for helping transform me from a modern DNA girl to an aDNA girl!  ...  For my analyses, some of the sequences included were the result of lab work and sequencing completed by Dr Tim Heupink and Dr Sally Wasef.  ... 
doi:10.25904/1912/795 fatcat:sixr7s34krbc3nab4cxq6fccs4