1
|
Westbury MV, Lorenzen ED. Iteratively mapping ancient
DNA
to reconstruct highly divergent mitochondrial genomes: An evaluation of software, parameters and bait reference. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
2
|
Hawkins MTR, Flores MFC, McGowen M, Hinckley A. A comparative analysis of extraction protocol performance on degraded mammalian museum specimens. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.984056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The extraction of nucleic acids is one of the most routine procedures used in molecular biology laboratories, yet kit performance may influence the downstream processing of samples, particularly for samples which are degraded, and in low concentrations. Here we tested several commercial kits for specific use on commonly sampled mammalian museum specimens to evaluate the yield, size distribution, and endogenous content. Samples were weighed and had approximately equal input material for each extraction. These sample types are typical of natural history repositories ranged from 53 to 130 years old. The tested protocols spanned spin-column based extractions, magnetic bead purification, phenol/chloroform isolation, and specific modifications for ancient DNA. Diverse types of mammalian specimens were tested including adherent osteological material, bone and teeth, skin, and baleen. The concentration of DNA was quantified via fluorometry, and the size distributions of extracts visualized on an Agilent TapeStation. Overall, when DNA isolation was successful, all methods had quantifiable concentrations, albeit with variation across extracts. The length distributions varied based on the extraction protocol used. Shotgun sequencing was performed to evaluate if the extraction methods influenced the amount of endogenous versus exogenous content. The DNA content was similar across extraction methods indicating no obvious biases for DNA derived from different sources. Qiagen kits and phenol/chloroform isolation outperformed the Zymo magnetic bead isolations in these types of samples. Statistical analyses revealed that extraction method only explained 5% of the observed variation, and that specimen age explained variation (29%) more effectively.
Collapse
|
3
|
Ancient DNA of Metagonimus yokogawai Recovered from Joseon Period Human Remains Newly Discovered at Goryeong County in South Korea. Acta Parasitol 2022; 67:539-545. [PMID: 34731404 DOI: 10.1007/s11686-021-00487-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022]
Abstract
PURPOSE Metagonimiasis, commonly seen in East Asian countries, is a parasitic disorder caused by definitive hosts' ingestion of undercooked freshwater fishes. Recently, genetic analysis has proved 28S rRNA and cytochrome c oxidase subunit I (COI) mtDNA gene to be a successful marker differentiating species of the genus Metagonimus. In the present study, using specimens from the newly discovered Joseon Dynasty human remains of Goryeong, we obtained updated genetic data on genus Metagonimus, which was also prevalent during the Joseon period. METHODS The ancient DNA (aDNA) was retrieved from the coprolite sample of the seventeenth century, half-mummified individual discovered at Goryeong Country, South Korea. Cloning and sequencing were performed on PCR-amplified amplicons for M. yokogawai 28S rRNA and COI mtDNA gene. The consensus sequences were used for species identification and phylogenetic analysis using NCBI/BLAST and MEGA X software. RESULTS Based on the COI mtDNA gene region, the Goryeong sequence was confirmed as belonging to M. yokogawai, as it was shown to form a separate cluster with other M. yokogawai taxa that are distinct also from M. takahashii and M. miyatai. CONCLUSION In a series of our genetic analyses on genus Metagonimus using samples retrieved from Joseon-period cases, aDNA sequences of genus Metagonimus revealed in South Korea thus far are those of M. yokogawai, but not of M. miyatai or M. takahashii yet.
Collapse
|
4
|
Hong JH, Oh CS, Kim S, Kang IU, Shin DH. Genetic analysis of mitochondrial DNA from ancient <i>Equus caballus</i> bones found at archaeological site of Joseon dynasty period capital area. Anim Biosci 2022; 35:1141-1150. [PMID: 35240033 PMCID: PMC9262724 DOI: 10.5713/ab.21.0500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/28/2022] [Indexed: 11/27/2022] Open
Abstract
Objective To understand the domestication and spread of horses in history, genetic information is essential. However, mitogenetic traits of ancient or medieval horses have yet to be comprehensively revealed, especially for East Asia. This study thus set out to reveal the maternal lineage of skeletal horse remains retrieved from a 15th century archaeological site (Gongpyeongdong) at Old Seoul City in South Korea. Methods We extracted DNA from the femur of Equus caballus (SNU-A001) from Joseon period Gongpyeongdong site. Mitochondrial (mt) DNA (HRS 15128-16116) of E. caballus was amplified by polymerase chain reaction. Cloning and sequencing were conducted for the mtDNA amplicons. The sequencing results were analyzed by NCBI/BLAST and phylogenetic tool of MEGA7 software. Results By means of mtDNA cytochrome b and D-loop analysis, we found that the 15th century Korean horse belonged to haplogroup Q representing those horses that have historically been raised widely in East Asia. Conclusion The horse is unique among domesticated animals for the remarkable impact it has on human civilization in terms of transportation and trade. Utilizing the Joseon-period horse remains, we can obtain clues to reveal the genetic traits of Korean horse that existed before the introduction of Western horses.
Collapse
|
5
|
Hong JH, Seo M, Oh CS, Chai JY, Shin DH. Metagonimus yokogawai Ancient DNA Recovered from 16th- to 17th-Century Korean Mummy Feces of the Joseon Dynasty. J Parasitol 2021; 106:802-808. [PMID: 33351947 DOI: 10.1645/20-42] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Metagonimiasis is foodborne intestinal parasitism occurring by the definitive hosts' ingestion of raw or undercooked fish, mostly commonly sweetfish. Most Metagonimus infection is caused by Metagonimus yokogawai but also rarely by Metagonimus takahashii as well as Metagonimus miyatai. Despite recent molecular work on Metagonimus spp., there are still insufficient data to reveal the genetic characteristics of ancient M. yokogawai in a wide geo-historical scope. In this study, we were successful in the analysis of M. yokogawai ancient DNA (aDNA) using coprolite samples retrieved from 16th- to 17th-century Korean mummies. In BLAST and phylogenetic analyses, M. yokogawai 28S rDNA of Korean mummies were clustered along with the 28S rDNA taxa of M. takahashii and M. miyatai in GenBank. Conversely, the cytochrome c oxidase subunit I (COI) of M. yokogawai aDNA from Korean mummies was distinctly clustered apart from M. takahashii and M. miyatai sequences. This study is the first report of its kind to identify M. yokogawai aDNA retrieved from the archaeological specimens and confirms the usefulness of COI in molecular diagnosis of M. yokogawai. Considering the rarity of reports on the genetics of genus Metagonimus spp., our study will be fundamental for the future study of M. yokogawai paleogenetics.
Collapse
Affiliation(s)
- Jong Ha Hong
- Institute of Korean Archaeology and Ancient History, Kyung Hee University, Seoul, South Korea.,Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, South Korea
| | - Min Seo
- Department of Parasitology, Dankook University College of Medicine, Cheonan, South Korea
| | - Chang Seok Oh
- Department of Mortuary Science, Eulji University, Seongnam-Si, Gyeonggi-Do, South Korea.,Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Jong-Yil Chai
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul, South Korea.,Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul, South Korea
| | - Dong Hoon Shin
- Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, South Korea.,Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea
| |
Collapse
|
6
|
Abstract
The study of ancient genomes has burgeoned at an incredible rate in the last decade. The result is a shift in archaeological narratives, bringing with it a fierce debate on the place of genetics in anthropological research. Archaeogenomics has challenged and scrutinized fundamental themes of anthropological research, including human origins, movement of ancient and modern populations, the role of social organization in shaping material culture, and the relationship between culture, language, and ancestry. Moreover, the discussion has inevitably invoked new debates on indigenous rights, ownership of ancient materials, inclusion in the scientific process, and even the meaning of what it is to be a human. We argue that the broad and seemingly daunting ethical, methodological, and theoretical challenges posed by archaeogenomics, in fact, represent the very cutting edge of social science research. Here, we provide a general review of the field by introducing the contemporary discussion points and summarizing methodological and ethical concerns, while highlighting the exciting possibilities of ancient genome studies in archaeology from an anthropological perspective.
Collapse
Affiliation(s)
- Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14221, USA
| | - Michael Frachetti
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| |
Collapse
|
7
|
Hong JH, Oh CS, Seo M, Shin DH. Analysis of COI and ITS2 regions of DNA obtained from Paragonimus westermani eggs in ancient coprolites on Joseon dynasty mummies. Mem Inst Oswaldo Cruz 2019; 114:e180595. [PMID: 31116227 PMCID: PMC6524962 DOI: 10.1590/0074-02760180595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/04/2019] [Indexed: 11/22/2022] Open
Abstract
The genetic information of ancient Paragonimus westermani, the oriental lung fluke infecting over 20 million people worldwide, has not been thoroughly investigated thus far. We analysed genetic markers (COI and ITS2) of P. westermani from coprolite specimens (n = 6) obtained from 15th to 18th century Korean mummies. Our results indicated that all P. westermani sequences were generally distinct from the other species of the genus Paragonimus. The sequences were clustered into three groups: Group I for East Asia; Group II for South and Southeast Asia; and Group III for India and Sri Lanka. In this study, we found that ancient P. westermani sequences in Korea belong to Group I, adding invaluable information to the existing knowledge of Paragonimus paleogenetics.
Collapse
Affiliation(s)
- Jong Ha Hong
- Seoul National University College of Medicine, Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul, South Korea
| | - Chang Seok Oh
- Seoul National University College of Medicine, Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul, South Korea.,Seoul National University College of Medicine, Institute of Forensic Science, Seoul, South Korea
| | - Min Seo
- Dankook University College of Medicine, Department of Parasitology, Cheonan, South Korea
| | - Dong Hoon Shin
- Seoul National University College of Medicine, Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul, South Korea.,Seoul National University College of Medicine, Institute of Forensic Science, Seoul, South Korea
| |
Collapse
|
8
|
Medieval mummies of Zeleny Yar burial ground in the Arctic Zone of Western Siberia. PLoS One 2019; 14:e0210718. [PMID: 30682121 PMCID: PMC6347368 DOI: 10.1371/journal.pone.0210718] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 01/01/2019] [Indexed: 11/19/2022] Open
Abstract
Notwithstanding the pioneering achievements of studies on arctic mummies in Siberia, there are insufficient data for any comprehensive understanding of the bio-cultural details of medieval people living in the region. In the Western Siberian arctic, permafrost mummies have been found in 12th to 13th century graves located in the Zeleny Yar (Z-Y) burial ground (66°19'4.54"С; 67°21'13.54"В). In 2013-2016, we were fortunate to be able to excavate that cemetery, locating a total of 47 burials, including cases of mummification. Some of these mummies had been wrapped in a multi-layered birch-bark cocoon. After removal of the cocoon, we conducted interdisciplinary studies using various scientific techniques. Gross anatomical examination and CT radiography showed that the internal organs were still well preserved inside the body cavities. Under light and electron microscopy, the histological findings were very similar to those for naturally mummified specimens discovered in other countries. Ancient DNA analysis showed that the Z-Y mummies' mtDNA haplotypes belong to five different haplogroups, namely U5a (#34), H3ao (#53), D (#67-1), U4b1b1 (#67-2), and D4j8 (#68), which distinguish them for their unique combination of Western- and Eastern Siberia-specific mtDNA haplogroups. Our interdisciplinary study obtained fundamental information that will form the foundation of successful future investigations on medieval mummies found in the Western Siberian arctic.
Collapse
|
9
|
Cruz-Dávalos DI, Nieves-Colón MA, Sockell A, Poznik GD, Schroeder H, Stone AC, Bustamante CD, Malaspinas AS, Ávila-Arcos MC. In-solution Y-chromosome capture-enrichment on ancient DNA libraries. BMC Genomics 2018; 19:608. [PMID: 30107783 PMCID: PMC6092841 DOI: 10.1186/s12864-018-4945-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/16/2018] [Indexed: 12/04/2022] Open
Abstract
Background As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach—in-solution capture-enrichment—retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. Results The six samples show different levels of initial endogenous content, with very low (< 0.05%, 4 samples) or low (0.1–1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12–9549 times more targeted unique Y-chromosome sequences after capture, where 0.0–6.2% (WGC + YCC) and 0.0–23.5% (YCC) of the sequence reads were on-target, compared to 0.0–0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC + YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries’ initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins. Conclusions We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC + YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round. Electronic supplementary material The online version of this article (10.1186/s12864-018-4945-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Diana I Cruz-Dávalos
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,International Laboratory for Human Genome Research, National Autonomous University of Mexico, Mexico, Mexico.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - María A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, USA
| | | | | | - Hannes Schroeder
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Faculty of Archaeology, Leiden University, Leiden, Netherlands
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, USA.,Institute of Human Origins, Arizona State University, Tempe, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, Stanford, USA.,Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Anna-Sapfo Malaspinas
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. .,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Mexico, Mexico.
| |
Collapse
|
10
|
Tong KJ, Duchêne DA, Duchêne S, Geoghegan JL, Ho SYW. A comparison of methods for estimating substitution rates from ancient DNA sequence data. BMC Evol Biol 2018; 18:70. [PMID: 29769015 PMCID: PMC5956955 DOI: 10.1186/s12862-018-1192-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 05/04/2018] [Indexed: 12/02/2022] Open
Abstract
Background Phylogenetic analysis of DNA from modern and ancient samples allows the reconstruction of important demographic and evolutionary processes. A critical component of these analyses is the estimation of evolutionary rates, which can be calibrated using information about the ages of the samples. However, the reliability of these rate estimates can be negatively affected by among-lineage rate variation and non-random sampling. Using a simulation study, we compared the performance of three phylogenetic methods for inferring evolutionary rates from time-structured data sets: regression of root-to-tip distances, least-squares dating, and Bayesian inference. We also applied these three methods to time-structured mitogenomic data sets from six vertebrate species. Results Our results from 12 simulation scenarios show that the three methods produce reliable estimates when the substitution rate is high, rate variation is low, and samples of similar ages are not all grouped together in the tree (i.e., low phylo-temporal clustering). The interaction of these factors is particularly important for least-squares dating and Bayesian estimation of evolutionary rates. The three estimation methods produced consistent estimates of rates across most of the six mitogenomic data sets, with sequence data from horses being an exception. Conclusions We recommend that phylogenetic studies of ancient DNA sequences should use multiple methods of inference and test for the presence of temporal signal, among-lineage rate variation, and phylo-temporal clustering in the data. Electronic supplementary material The online version of this article (10.1186/s12862-018-1192-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- K Jun Tong
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
| |
Collapse
|
11
|
Nieves-Colón MA, Ozga AT, Pestle WJ, Cucina A, Tiesler V, Stanton TW, Stone AC. Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 166:824-836. [PMID: 29603124 DOI: 10.1002/ajpa.23472] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 12/15/2017] [Accepted: 03/13/2018] [Indexed: 12/22/2022]
Abstract
OBJECTIVES The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi-tropical sites in Tanzania, Mexico, and Puerto Rico (N = 12). MATERIALS AND METHODS All samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step. RESULTS No significant difference was found in overall ancient DNA yields or post-mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality-filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments. DISCUSSION Both methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.
Collapse
Affiliation(s)
- Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287
| | - Andrew T Ozga
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287.,Institute of Human Origins, Arizona State University, Tempe, Arizona 85287.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona 85287
| | - William J Pestle
- Department of Anthropology, University of Miami, Coral Gables, Florida 33124
| | - Andrea Cucina
- Facultad de Ciencias Antropológicas Universidad Autónoma de Yucatán, Mérida, Yucatán 97305, México
| | - Vera Tiesler
- Facultad de Ciencias Antropológicas Universidad Autónoma de Yucatán, Mérida, Yucatán 97305, México
| | - Travis W Stanton
- Department of Anthropology, University of California Riverside, Riverside, California 92521
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287.,Institute of Human Origins, Arizona State University, Tempe, Arizona 85287.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona 85287.,Center for Bioarchaeological Research, Arizona State University, Tempe, Arizona 85287
| |
Collapse
|
12
|
Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_45] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
13
|
Chaitanya L, Ralf A, van Oven M, Kupiec T, Chang J, Lagacé R, Kayser M. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine. Hum Mutat 2015; 36:1236-47. [PMID: 26387877 PMCID: PMC5057296 DOI: 10.1002/humu.22905] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/01/2015] [Indexed: 11/13/2022]
Abstract
Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long-range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications.
Collapse
Affiliation(s)
- Lakshmi Chaitanya
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Arwin Ralf
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Mannis van Oven
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Tomasz Kupiec
- Institute of Forensic ResearchSection of Forensic GeneticsKrakówPoland
| | - Joseph Chang
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Robert Lagacé
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| |
Collapse
|
14
|
Devall M, Mill J, Lunnon K. The mitochondrial epigenome: a role in Alzheimer's disease? Epigenomics 2015; 6:665-75. [PMID: 25531259 DOI: 10.2217/epi.14.50] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Considerable evidence suggests that mitochondrial dysfunction occurs early in Alzheimer's disease, both in affected brain regions and in leukocytes, potentially precipitating neurodegeneration through increased oxidative stress. Epigenetic processes are emerging as a dynamic mechanism through which environmental signals may contribute to cellular changes, leading to neuropathology and disease. Until recently, little attention was given to the mitochondrial epigenome itself, as preliminary studies indicated an absence of DNA modifications. However, recent research has demonstrated that epigenetic changes to the mitochondrial genome do occur, potentially playing an important role in several disorders characterized by mitochondrial dysfunction. This review explores the potential role of mitochondrial epigenetic dysfunction in Alzheimer's disease etiology and discusses some technical issues pertinent to the study of these processes.
Collapse
Affiliation(s)
- Matthew Devall
- University of Exeter Medical School, RILD Level 4, Barrack Road, Exeter, Devon, UK
| | | | | |
Collapse
|
15
|
Affiliation(s)
- Anna Linderholm
- Research Laboratory for Archaeology; University of Oxford; Dyson Perrins Building South Parks Road Oxford OX1 3Q UK
| |
Collapse
|
16
|
Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene. Trends Ecol Evol 2015; 30:540-9. [PMID: 26169594 DOI: 10.1016/j.tree.2015.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 11/22/2022]
Abstract
There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity.
Collapse
|
17
|
Huang YF, Midha M, Chen TH, Wang YT, Smith DG, Pei KJC, Chiu KP. Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy. PLoS One 2015; 10:e0130673. [PMID: 26125617 PMCID: PMC4488429 DOI: 10.1371/journal.pone.0130673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/24/2015] [Indexed: 11/18/2022] Open
Abstract
The Taiwanese (Formosan) macaque (Macaca cyclopis) is the only nonhuman primate endemic to Taiwan. This primate species is valuable for evolutionary studies and as subjects in medical research. However, only partial fragments of the mitochondrial genome (mitogenome) of this primate species have been sequenced, not mentioning its nuclear genome. We employed next-generation sequencing to generate 2 x 90 bp paired-end reads, followed by reference-assisted de novo assembly with multiple k-mer strategy to characterize the M. cyclopis mitogenome. We compared the assembled mitogenome with that of other macaque species for phylogenetic analysis. Our results show that, the M. cyclopis mitogenome consists of 16,563 nucleotides encoding for 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. Phylogenetic analysis indicates that M. cyclopis is most closely related to M. mulatta lasiota (Chinese rhesus macaque), supporting the notion of Asia-continental origin of M. cyclopis proposed in previous studies based on partial mitochondrial sequences. Our work presents a novel approach for assembling a mitogenome that utilizes the capabilities of de novo genome assembly with assistance of a reference genome. The availability of the complete Taiwanese macaque mitogenome will facilitate the study of primate evolution and the characterization of genetic variations for the potential usage of this species as a non-human primate model for medical research.
Collapse
Affiliation(s)
- Yu-Feng Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail:
| | - Mohit Midha
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Tzu-Han Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Tai Wang
- National Center for High-Performance Computing, Hsinchu, Taiwan
| | - David Glenn Smith
- Department of Anthropology, University of California Davis, Davis, CA, United States of America
| | - Kurtis Jai-Chyi Pei
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Kuo Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
- College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan
| |
Collapse
|
18
|
Peng MS, Fan L, Shi NN, Ning T, Yao YG, Murphy RW, Wang WZ, Zhang YP. DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals. Mol Ecol Resour 2015; 15:1238-42. [PMID: 25655564 DOI: 10.1111/1755-0998.12386] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/01/2015] [Accepted: 02/02/2015] [Indexed: 01/01/2023]
Abstract
Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up-to-date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high-resolution mtDNA haplogroup trees based on 1240 complete or near-complete mtDNA genome sequences are available in open resource DomeTree (http://www.dometree.org). In addition, we offer the software MitoToolPy (http://www.mitotool.org/mp.html) to facilitate the mtDNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy.
Collapse
Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Long Fan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999077, China
| | - Ni-Ni Shi
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Tiao Ning
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Yong-Gang Yao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, M5S 2C6, Canada
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.,Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| |
Collapse
|
19
|
Just RS, Scheible MK, Fast SA, Sturk-Andreaggi K, Röck AW, Bush JM, Higginbotham JL, Peck MA, Ring JD, Huber GE, Xavier C, Strobl C, Lyons EA, Diegoli TM, Bodner M, Fendt L, Kralj P, Nagl S, Niederwieser D, Zimmermann B, Parson W, Irwin JA. Full mtGenome reference data: Development and characterization of 588 forensic-quality haplotypes representing three U.S. populations. Forensic Sci Int Genet 2015; 14:141-55. [DOI: 10.1016/j.fsigen.2014.09.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/08/2014] [Accepted: 09/26/2014] [Indexed: 11/26/2022]
|
20
|
Chan YL, Schanzenbach D, Hickerson MJ. Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation. Mol Biol Evol 2014; 31:2501-15. [PMID: 24925925 PMCID: PMC4137712 DOI: 10.1093/molbev/msu187] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Methods that integrate population-level sampling from multiple taxa into a single community-level analysis are an essential addition to the comparative phylogeographic toolkit. Detecting how species within communities have demographically tracked each other in space and time is important for understanding the effects of future climate and landscape changes and the resulting acceleration of extinctions, biological invasions, and potential surges in adaptive evolution. Here, we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage. Our method combines population genetic data sets from multiple taxa into a single analysis to estimate: 1) the proportion of a community sample that demographically expanded in a temporally clustered pulse and 2) when the pulse occurred. To validate the accuracy and utility of this new approach, we use simulation cross-validation experiments and subsequently analyze an empirical data set of 32 avian populations from Australia that are hypothesized to have expanded from smaller refugia populations in the late Pleistocene. The method can accommodate data set heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and exploits the statistical strength from the simultaneous analysis of multiple species. This hABC framework used in a multitaxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently and can be used with a wide variety of comparative phylogeographic data sets as biota-wide DNA barcoding data sets accumulate.
Collapse
Affiliation(s)
- Yvonne L Chan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa
| | | | - Michael J Hickerson
- Biology Department, City College of New YorkThe Graduate Center, City University of New York
| |
Collapse
|
21
|
Reconstructing the colonization history of lost wolf lineages by the analysis of the mitochondrial genome. Mol Phylogenet Evol 2014; 80:105-12. [PMID: 25132126 DOI: 10.1016/j.ympev.2014.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/29/2014] [Accepted: 08/03/2014] [Indexed: 11/27/2022]
Abstract
The grey wolves (Canis lupus) originally inhabited major parts of the Northern hemisphere, but many local populations became extinct. Two lineages of wolves in Japan, namely, Japanese or Honshu (C. l. hodophilax) and Ezo or Hokkaido (C. l. hattai) wolves, rapidly went extinct between 100 and 120years ago. Here we analyse the complete mitochondrial genome sequences from ancient specimens and reconstruct the colonization history of the two extinct subspecies. We show a unique status of Japanese wolves in wolf phylogeny, suggesting their long time separation from other grey wolf populations. Japanese wolves appeared to have colonized the Japanese archipelago in the Late Pleistocene (ca. 25,000-125,000years ago). By contrast, Ezo wolves, which are clearly separated from Japanese wolves in phylogeny, are likely to have arrived at Japan relatively recently (<14,000years ago). Interestingly, their colonization history to Japan tallies well with the dynamics of wolf populations in Europe and America during the last several millennia. Our analyses suggest that at least several thousands of wolves once inhabited in the Japanese archipelago. Our analyses also show that an enigmatic clade of domestic dogs is likely to have originated from rare admixture events between male dogs and female Japanese wolves.
Collapse
|
22
|
Paijmans JL, Gilbert MTP, Hofreiter M. Mitogenomic analyses from ancient DNA. Mol Phylogenet Evol 2013; 69:404-16. [DOI: 10.1016/j.ympev.2012.06.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 05/27/2012] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
|
23
|
Fortes GG, Speller CF, Hofreiter M, King TE. Phenotypes from ancient DNA: approaches, insights and prospects. Bioessays 2013; 35:690-5. [PMID: 23703035 DOI: 10.1002/bies.201300036] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The great majority of phenotypic characteristics are complex traits, complicating the identification of the genes underlying their expression. However, both methodological and theoretical progress in genome-wide association studies have resulted in a much better understanding of the underlying genetics of many phenotypic traits, including externally visible characteristics (EVCs) such as eye and hair color. Consequently, it has become possible to predict EVCs from human samples lacking phenotypic information. Predicting EVCs from genetic evidence is clearly appealing for forensic applications involving the personal identification of human remains. Now, a recent paper has reported the genetic determination of eye and hair color in samples up to 800 years old. The ability to predict EVCs from ancient human remains opens up promising perspectives for ancient DNA research, as this could allow studies to directly address archaeological and evolutionary questions related to the temporal and geographical origins of the genetic variants underlying phenotypes.
Collapse
|
24
|
Hung CM, Lin RC, Chu JH, Yeh CF, Yao CJ, Li SH. The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing. PLoS One 2013; 8:e56301. [PMID: 23437111 PMCID: PMC3577829 DOI: 10.1371/journal.pone.0056301] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 01/11/2013] [Indexed: 11/18/2022] Open
Abstract
The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (Ectopistes migratorius) using de novo assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species.
Collapse
Affiliation(s)
- Chih-Ming Hung
- Bell Museum and Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Rong-Chien Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jui-Hua Chu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chia-Fen Yeh
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chiou-Ju Yao
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
25
|
Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D. Ancient DNA studies: new perspectives on old samples. Genet Sel Evol 2012; 44:21. [PMID: 22697611 PMCID: PMC3390907 DOI: 10.1186/1297-9686-44-21] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 06/14/2012] [Indexed: 11/24/2022] Open
Abstract
In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.
Collapse
Affiliation(s)
- Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Via F.lli Cervi 93, Segrate, Milan 20090, Italy
| | | | | | | | | |
Collapse
|
26
|
Ho SYW. Phylogenetic analysis of ancient DNA using BEAST. Methods Mol Biol 2012; 840:229-41. [PMID: 22237538 DOI: 10.1007/978-1-61779-516-9_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Under exceptional circumstances, it is possible to obtain DNA sequences from samples that are up to hundreds of thousands of years old. These data provide an opportunity to look directly at past genetic diversity, to trace the evolutionary process through time, and to infer demographic and phylogeographic trends. Ancient DNA (aDNA) data sets have some degree of intrinsic temporal structure because the sequences have been obtained from samples of different ages. When analyzing these data sets, it is usually necessary to take the sampling times into account. A number of phylogenetic methods have been designed with this purpose in mind. Here I describe the steps involved in Bayesian phylogenetic analysis of aDNA data. I outline a procedure that can be used to co-estimate the genealogical relationships, mutation rate, evolutionary timescale, and demographic history of the study species in a single analytical framework. A number of modifications to the methodology can be made in order to deal with complicating factors such as postmortem damage, sequences from undated samples, and data sets with low information content.
Collapse
Affiliation(s)
- Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, 2006, NSW, Australia.
| |
Collapse
|
27
|
Mourier T, Ho SYW, Gilbert MTP, Willerslev E, Orlando L. Statistical guidelines for detecting past population shifts using ancient DNA. Mol Biol Evol 2012; 29:2241-51. [PMID: 22427706 DOI: 10.1093/molbev/mss094] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Populations carry a genetic signal of their demographic past, providing an opportunity for investigating the processes that shaped their evolution. Our ability to infer population histories can be enhanced by including ancient DNA data. Using serial-coalescent simulations and a range of both quantitative and temporal sampling schemes, we test the power of ancient mitochondrial sequences and nuclear single-nucleotide polymorphisms (SNPs) to detect past population bottlenecks. Within our simulated framework, mitochondrial sequences have only limited power to detect subtle bottlenecks and/or fast post-bottleneck recoveries. In contrast, nuclear SNPs can detect bottlenecks followed by rapid recovery, although bottlenecks involving reduction of less than half the population are generally detected with low power unless extensive genetic information from ancient individuals is available. Our results provide useful guidelines for scaling sampling schemes and for optimizing our ability to infer past population dynamics. In addition, our results suggest that many ancient DNA studies may face power issues in detecting moderate demographic collapses and/or highly dynamic demographic shifts when based solely on mitochondrial information.
Collapse
Affiliation(s)
- Tobias Mourier
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.
| | | | | | | | | |
Collapse
|
28
|
Abstract
Nucleotide sequences sampled at different times (serially-sampled sequences) allow researchers to study the rate of evolutionary change and the demographic history of populations. Some phylogenies inferred from serially-sampled sequences are described as having strong 'temporal clustering', such that sequences from the same sampling time tend to to cluster together and to be the direct ancestors of sequences from the following sampling time. The degree to which phylogenies exhibit these properties is thought to reflect interesting biological processes, such as positive selection or deviation from the molecular clock hypothesis.Here we introduce the Temporal Clustering (TC) statistic, which is the first quantitative measure of the degree of topological 'temporal clustering' in a serially-sampled phylogeny. The TC statistic represents the expected deviation of an observed phylogeny from the null hypothesis of no temporal clustering, as a proportion of the range of possible values, and can therefore be compared among phylogeny of different sizes.We apply the TC statistic to a range of serially-sampled sequence datasets, which represent both rapidly-evolving viruses and ancient mitochondrial DNA. In addition, the TC statistic was calculated for phylogenies simulated under a neutral coalescent process.Our results indicate significant temporal clustering in many empirical datasets. However, we also find that such clustering is exhibited by trees simulated under a neutral coalescent process; hence the observation of significant 'temporal clustering' cannot unambiguously indicate that presence of strong positive selection in a population.Quantifying topological structure in this manner will provide new insights into the evolution of measurably evolving populations.
Collapse
Affiliation(s)
- R R Gray
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | | |
Collapse
|
29
|
Thèves C, Senescau A, Vanin S, Keyser C, Ricaut FX, Alekseev AN, Dabernat H, Ludes B, Fabre R, Crubézy E. Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. PLoS One 2011; 6:e21733. [PMID: 21765907 PMCID: PMC3135582 DOI: 10.1371/journal.pone.0021733] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 06/09/2011] [Indexed: 12/25/2022] Open
Abstract
Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17(th) to the 19(th) century, we propose a methodology that includes the: 1) amplification of all 16S rDNA gene sequences present in each sample; 2) identification of all bacterial DNA sequences with a degree of identity ≥ 95%, according to quality criteria; 3) identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4) establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1) the correct identification of bacterial molecular sequence signatures by quality criteria; 2) the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3) the distribution of bacterial species for each subject and for each burial; and 4) the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17(th) century to the early 18(th) century.
Collapse
Affiliation(s)
- Catherine Thèves
- Laboratoire AMIS, UMR 5288, Université Toulouse IIII/CNRS/Université de Strasbourg, Toulouse, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Ho SYW, Lanfear R, Phillips MJ, Barnes I, Thomas JA, Kolokotronis SO, Shapiro B. Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Syst Biol 2011; 60:366-75. [PMID: 21296909 DOI: 10.1093/sysbio/syq099] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Simon Y W Ho
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia.
| | | | | | | | | | | | | |
Collapse
|
31
|
Albertini E, Raggi L, Vagnini M, Sassolini A, Achilli A, Marconi G, Cartechini L, Veronesi F, Falcinelli M, Brunetti BG, Miliani C. Tracing the biological origin of animal glues used in paintings through mitochondrial DNA analysis. Anal Bioanal Chem 2010; 399:2987-95. [PMID: 20953766 DOI: 10.1007/s00216-010-4287-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 09/21/2010] [Accepted: 10/03/2010] [Indexed: 11/28/2022]
Abstract
We report the development of a suitable protocol for the identification of the biological origin of binding media on tiny samples from ancient paintings, by exploitation of the high specificity and high sensitivity offered by the state-of-the art DNA analysis. In particular, our aim was to molecularly characterize mitochondrial regions of the animal species traditionally employed for obtaining glues. The model has been developed using aged painting models and then tested to analyze the organic components in samples from the polychrome terracotta Madonna of Citerna by Donatello (1415-1420), where, by GC-MS and FTIR spectroscopy, animal glues and siccative oils were identified. The results obtained are good in terms of both sensibility and specificity of the method. First of all, it was possible to confirm that Donatello used animal glue for the preparation of the painted layers of the Madonna of Citerna and, specifically, glue derived from Bos taurus. Data obtained from sequencing confirm that each sample contains animal glue, revealing that it was mostly prepared from two common European taurine lineages called T2 and T3. There is one remarkable exception represented by one sample which falls into a surviving lineage of the now extinct European aurochs.
Collapse
Affiliation(s)
- Emidio Albertini
- Dipartimento di Biologia Applicata, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Knapp M, Hofreiter M. Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives. Genes (Basel) 2010; 1:227-43. [PMID: 24710043 PMCID: PMC3954087 DOI: 10.3390/genes1020227] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 07/20/2010] [Accepted: 07/23/2010] [Indexed: 11/24/2022] Open
Abstract
The invention of next-generation-sequencing has revolutionized almost all fields of genetics, but few have profited from it as much as the field of ancient DNA research. From its beginnings as an interesting but rather marginal discipline, ancient DNA research is now on its way into the centre of evolutionary biology. In less than a year from its invention next-generation-sequencing had increased the amount of DNA sequence data available from extinct organisms by several orders of magnitude. Ancient DNA research is now not only adding a temporal aspect to evolutionary studies and allowing for the observation of evolution in real time, it also provides important data to help understand the origins of our own species. Here we review progress that has been made in next-generation-sequencing of ancient DNA over the past five years and evaluate sequencing strategies and future directions.
Collapse
Affiliation(s)
- Michael Knapp
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy and Structural Biology, University of Otago, 270 Great King Street, 9016 Dunedin, New Zealand.
| | - Michael Hofreiter
- Department of Biology, The University of York, Wentworth Way, Heslington, YO10 5DD, York, UK.
| |
Collapse
|
33
|
Endicott P, Ho SY, Stringer C. Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and modern human origins. J Hum Evol 2010; 59:87-95. [DOI: 10.1016/j.jhevol.2010.04.005] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 03/14/2010] [Accepted: 04/07/2010] [Indexed: 12/20/2022]
|
34
|
Lanfear R, Ho SYW. Mito-communications. MITOCHONDRIAL DNA 2010; 21:57-58. [PMID: 20658959 DOI: 10.3109/19401736.2010.482586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Robert Lanfear
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, Australia
| | | |
Collapse
|
35
|
Morin PA, Archer FI, Foote AD, Vilstrup J, Allen EE, Wade P, Durban J, Parsons K, Pitman R, Li L, Bouffard P, Abel Nielsen SC, Rasmussen M, Willerslev E, Gilbert MTP, Harkins T. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res 2010; 20:908-16. [PMID: 20413674 DOI: 10.1101/gr.102954.109] [Citation(s) in RCA: 292] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Killer whales (Orcinus orca) currently comprise a single, cosmopolitan species with a diverse diet. However, studies over the last 30 yr have revealed populations of sympatric "ecotypes" with discrete prey preferences, morphology, and behaviors. Although these ecotypes avoid social interactions and are not known to interbreed, genetic studies to date have found extremely low levels of diversity in the mitochondrial control region, and few clear phylogeographic patterns worldwide. This low level of diversity is likely due to low mitochondrial mutation rates that are common to cetaceans. Using killer whales as a case study, we have developed a method to readily sequence, assemble, and analyze complete mitochondrial genomes from large numbers of samples to more accurately assess phylogeography and estimate divergence times. This represents an important tool for wildlife management, not only for killer whales but for many marine taxa. We used high-throughput sequencing to survey whole mitochondrial genome variation of 139 samples from the North Pacific, North Atlantic, and southern oceans. Phylogenetic analysis indicated that each of the known ecotypes represents a strongly supported clade with divergence times ranging from approximately 150,000 to 700,000 yr ago. We recommend that three named ecotypes be elevated to full species, and that the remaining types be recognized as subspecies pending additional data. Establishing appropriate taxonomic designations will greatly aid in understanding the ecological impacts and conservation needs of these important marine predators. We predict that phylogeographic mitogenomics will become an important tool for improved statistical phylogeography and more precise estimates of divergence times.
Collapse
Affiliation(s)
- Phillip A Morin
- National Marine Fisheries Service, Southwest Fisheries Science Center, La Jolla, California 92037, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc Natl Acad Sci U S A 2010; 107:5053-7. [PMID: 20194737 DOI: 10.1073/pnas.0914266107] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.
Collapse
|