Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

Schubert, Mikkel; Ermini, Luca; Sarkissian, Clio Der; Jónsson, Hákon; Ginolhac, Aurélien; Schaefer, Robert J.; Martin, Michael D.; Fernández, R.; Kircher, Martin; McCue, Molly E.; Willerslev, Eske; Orlando, Ludovic

doi:10.1038/nprot.2014.063

Cited by 411 publications

(379 citation statements)

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“…To assess DNA damage in the thylacine sample, Illumina reads were processed and mapped to the thylacine reference-based contigs (see next section) using the PALEOMIX pipeline 75 . Briefly, residual adaptor sequences were trimmed and reads shorter than 25 nucleotides were removed, and overlapping paired reads were collapsed using AdapterRemoval v.2.0 76 .…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

et al. 2017

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The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic diversity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis-regulatory evolution.

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Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

et al. 2017

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“…Одним из наиболее популярных программных конвейеров является пакет PALEOMIX [15]. Но его использование сопряжено с некоторыми неудобствами:…”

Section: Introductionunclassified

Integration of Heterogeneous Computing Infrastructures for Genome Sequencing Data Analysis

Aulov¹

2016

Math.Biol.Bioinf.

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Аннотация. Недавние достижения технологий в области геномного секвенирования нового поколения (NGS -Next Generation Genome Sequencing) привели к значительному увеличению объема данных, которые должны быть обработаны, проанализированы и доступны заинтересованным исследователям. Это, в свою очередь, привело к повышению требований к вычислительным платформам обработки данных: потребовалось больше оперативной памяти и более мощные процессоры. Для эффективной обработки данных необходимы принципиально новые подходы в организации вычислений. Авторами статьи было проведено исследование возможности применения методов и подходов, используемых в физике высоких энергий, для объединения гетерогенных вычислительных ресурсов в единую вычислительную платформу. Была разработана полномасштабная система управления данными и заданиями на базе вычислительных мощностей Национального исследовательского центра «Курчатовский институт». В разработанную систему был интегрирован рабочий поток для обработки данных геномного секвенирования с использованием пакета PALEOMIX. Результаты апробации разработанной системы на задаче анализа древней ДНК мамонта показали существенное уменьшение общего времени выполнения задачи.Ключевые слова: распределенные вычисления, суперкомпьютеры, геномное секвенирование.

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“…Applying Zonkey to 18 archaeological specimens spanning the last ∼6000-8000 years, we identify seven mules from Roman and Byzantine assemblages where morphological analyses were inconclusive. Zonkey works on Linux and is freely available online at https://github.com/MikkelSchubert/ paleomix as part of the PALEOMIX pipeline (Schubert et al, 2014).…”

Section: U N C O R R E C T E D P R O O Fmentioning

confidence: 99%

“…The reference panel consists of nine equine genomes, using alignments published in , (Jónsson et al, 2014) and (Der Sarkissian et al, 2015). These include the complete genomes of two caballine individuals (a Przewalski's horse, Equus przewalski, and a Franches-Montagnes horse, Equus caballus) as well as seven non-caballine individuals: a domestic donkey (Equus africanus asinus), an African wild ass (Equus africanus somaliensis), a Grant's zebra (Equus quagga boehmi), a Grevyi's zebra (Equus grevyi), a Hartmann's mountain zebra (Equus zebra hartmannae), an onager (Equus hemionus onager), and a Tibetan kiang (Equus kiang).…”

Section: Reference Panelmentioning

confidence: 99%

“…These include the complete genomes of two caballine individuals (a Przewalski's horse, Equus przewalski, and a Franches-Montagnes horse, Equus caballus) as well as seven non-caballine individuals: a domestic donkey (Equus africanus asinus), an African wild ass (Equus africanus somaliensis), a Grant's zebra (Equus quagga boehmi), a Grevyi's zebra (Equus grevyi), a Hartmann's mountain zebra (Equus zebra hartmannae), an onager (Equus hemionus onager), and a Tibetan kiang (Equus kiang). Samples were genotyped using PALEOMIX (Schubert et al, 2014) as described in (Jónsson et al (2014)), and bi-allelic sites called in all samples were collected, for a total of ∼36.5 million autosomal sites, representing ∼15,000 sites per Mb. We further constructed a multiple mtDNA alignment of all species included in the reference panel, using a selection of complete mitochondrial sequences made available for the same species by , and (Der Sarkissian et al, 2015) (GenBank Accession Numbers: JX312719, JX312722, JX312730, JX312732, KM881680, KM881681, KT368746.1, KX669267, and KX669268).…”

Section: Reference Panelmentioning

confidence: 99%

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Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages

Schubert

Mashkour

Gaunitz

et al. 2017

Journal of Archaeological Science

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Horses, asses and zebras, can produce first-generation F1-hybrids, despite their striking karyotypic and phenotypic differences. Such F1-hybrids are mostly infertile, but often present characters of considerable interest to breeders. They were extremely valued in antiquity, and commonly represented in art and on coinage. However, hybrids appear relatively rarely in archaeological faunal assemblages, mostly because identification based on morphometric data alone is extremely difficult. Here, we developed a methodological framework that exploits high-throughput sequencing data retrieved from archaeological material to identify F1-equine hybrids. Our computational methodology is distributed in the open-source Zonkey pipeline, now part of PALEOMIX (https://github.com/MikkelSchubert/paleomix), together with full documentation and examples. Using both synthetic and real sequence datasets, from living and ancient F1-hybrids, we find that Zonkey shows high sensitivity and specificity, even with limited sequencing efforts. Zonkey is thus well suited to the identification of equine F1-hybrids in the archaeological record, even in cases where DNA preservation is limited. Zonkey can also help determine the sex of ancient animals, and allows species identification, which advantageously complements morphological data in cases where material is fragmentary and/or multiple candidate equine species coexisted in sympatry.

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Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

Cited by 411 publications

References 76 publications

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

Integration of Heterogeneous Computing Infrastructures for Genome Sequencing Data Analysis

Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages

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