Technical Advances and Challenges in Genome-Scale Analysis of Ancient DNA

Lan, Tianying; Lindqvist, Charlotte

doi:10.1007/13836_2018_54

Cited by 34 publications

(13 citation statements)

References 176 publications

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“…Natural history collections are repositories of an impressive quantity and variety of biological information (Lane 1996;Schilthuizen et al 2015;Wen et al 2015). Ongoing developments with DNA sequencing technologies are enabling researchers to tap into genetic data that were previously inaccessible (Cooper 1994;Lan & Lindqvist 2019). Incorporating genetic data from natural history collections representing rare/threatened species and species that are otherwise hard to access into genetic-based analyses can provide critical insights (Heckeberg et al 2016;Hundsdoerfer et al 2017;McGuire et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Shotgun sequencing decades-old lichen specimens to resolve phylogenomic placement of type material

Leavitt

Keuler

Newberry

et al. 2019

Plant and Fungal Systematics

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Natural history collections, including name-bearing type specimens, are an important source of genetic information. These data can be critical for appropriate taxonomic revisions in cases where the phylogenetic position of name-bearing type specimens needs to be identified, including morphologically cryptic lichen-forming fungal species. Here, we use high-throughput metagenomic shotgun sequencing to generate genome-scale data from decades-old (i.e., more than 30 years old) isotype specimens representing three vagrant taxa in the lichen-forming fungal genus Rhizoplaca, including one species and two subspecies. We also use data from high-throughput metagenomic shotgun sequencing to infer the phylogenetic position of an enigmatic collection, originally identified as R. haydenii, that failed to yield genetic data via Sanger sequencing. We were able to construct a 1.64 Mb alignment from over 1200 single-copy nuclear gene regions for the Rhizoplaca specimens. Phylogenomic reconstructions recovered an isotype representing Rhizoplaca haydenii subsp. arbuscula within a clade comprising other specimens identified as Rhizoplaca haydenii subsp. arbuscula, while an isotype of R. idahoensis was recovered within a clade with substantial phylogenetic substructure comprising Rhizoplaca haydenii subsp. haydenii and other specimens. Based on these data and morphological differences, Rhizoplaca haydenii subsp. arbuscula is elevated to specific rank as Rhizoplaca arbuscula. For the enigmatic collection, we were able to assemble the nearly complete nrDNA cistron and over 50 Mb of the mitochondrial genome. Using these data, we identified this specimen as a morphologically deviant form representing Xanthoparmelia aff. subcumberlandia. This study highlights the power of high-throughput metagenomic shotgun sequencing in generating larger and more comprehensive genetic data from taxonomically important herbarium specimens.

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Section: Introductionmentioning

confidence: 99%

Shotgun sequencing decades-old lichen specimens to resolve phylogenomic placement of type material

Leavitt

Keuler

Newberry

et al. 2019

Plant and Fungal Systematics

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“…The creation of automated pipelines like PALEOMIX [15] and EAGER [16] have facilitated the streamlining and reproducibility of ancient DNA analyses, which has been particularly helpful for emerging research groups around the world. This has undoubtedly contributed to the growth of the field [17]. Yet, the field of palaeoproteomics still lacks a "democratizing" tool that is approachable to researchers of different backgrounds and expertises.…”

Section: Statement Of Needmentioning

confidence: 99%

PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins

Patramanis

Ramos‐Madrigal

Cappellini

et al. 2022

Preprint

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Ancient proteins from fossilized or semi-fossilized remains can yield phylogenetic information at broad temporal horizons, in some cases even millions of years into the past. In recent years, peptides extracted from archaic hominins and long-extinct mega-fauna have enabled unprecedented insights into their evolutionary history. In contrast to the field of ancient DNA - where several computational methods exist to process and analyze sequencing data - few tools exist for handling ancient protein sequence data. Instead, most studies rely on loosely combined custom scripts, which makes it difficult to reproduce results or share methodologies across research groups. Here, we present PaleoProPhyler: a new fully reproducible pipeline for aligning ancient peptide data and subsequently performing phylogenetic analyses. The pipeline can not only process various forms of proteomic data, but also easily harness genetic data in different formats (CRAM, BAM, VCF) and translate it, allowing the user to create reference panels for phyloproteomic analyses. We describe the various steps of the pipeline and its many functionalities, and provide some examples of how to use it. PaleoProPhyler allows researchers with little bioinformatics experience to efficiently analyze palaeoproteomic sequences, so as to derive insights from this valuable source of evolutionary data.

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“…В этих целях используются специально разработанные программные обеспечения PALEOMIX (набор конвейеров и инструментов, предназначенных для быстрой обработки данных высокопроизводительного секвенирования) и EAGER (effective ancient genome reconstructionэффективная реконструкция древнего генома). Эти методы упрощают анализ наборов геномных данных, помогают предварительно обрабатывать, картировать, аутентифицировать, оценивать качество образцов древней ДНК и предоставляют инструменты для обнаружения, фильтрации и анализа вариантов (Peltzer et al 2016;Lan, Lindqvist, 2019;Lan et al 2022).…”

Section: история становления и методыunclassified

“…Почти полные или частичные геномы были получены от вымерших видов млекопитающих, таких как шерстистый мамонт Mammuthus primigenius (Blumenbach, 1799), белый медведь Ursus maritimus Phipps, 1774, дикая лошадь Equus ferus Boddaert, 1785 и др. (Lan, Lindqvist 2019). Эти данные полезны для изучения генетических изменений, связанных с демографией и вымиранием, одомашниванием и межвидовой гибридизацией в прошлом, а также сохранением видов.…”

Section: животныеunclassified

Paleogenomics (short review)

Chelomina¹

2022

Biota and Environment of Natural Areas

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Paleogenomics is known as the whole genome analysis of ancient DNA (aDNA). This paper provides a brief overview of the achievements of paleogenomics, including its history and research methods. In particular, issues of human evolution, hominid (Neanderthal, Denisovans) and modern morphological type humans hybridization, transcontinental migrations of ancient humans from Siberia to America, migrations of peoples of the Yamnaya culture in the vast Eurasian steppes, the origin both of the extinct (Etruscans, Scythians) and of the modern (Qinghai-Tibetan Plateau populations, Avars) peoples are discussed from the perspective of paleogenomic data, domestication of animals and plants, impacts of climate change on biodiversity, conservation biology and taxonomy, and evolution of pathogens. The prospects of evolutionary medicine, aDNA methylation, the use of aDNA from sediments and ephippial eggs, as well as the possibility of restoring extinct species are discussed as directions for the future development of paleogenomics.

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Technical Advances and Challenges in Genome-Scale Analysis of Ancient DNA

Cited by 34 publications

References 176 publications

Shotgun sequencing decades-old lichen specimens to resolve phylogenomic placement of type material

Shotgun sequencing decades-old lichen specimens to resolve phylogenomic placement of type material

PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins

Paleogenomics (short review)

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