Papers by Valeria Mattiangeli
Evolutionary human sciences, 2023
A tripartite structure for the genetic origin of Japanese populations states that present-day pop... more A tripartite structure for the genetic origin of Japanese populations states that present-day populations are descended from three main ancestors: (1) the indigenous Jomon hunter-gatherers; (2) a Northeast Asian component that arrived during the agrarian Yayoi period; and (3) a major influx of East Asian ancestry in the imperial Kofun period. However, the genetic heterogeneity observed in different regions of the Japanese archipelago highlights the need to assess the applicability and suitability of this model. Here, we analyse historic genomes from the southern Ryukyu Islands, which have unique cultural and historical backgrounds compared with other parts of Japan. Our analysis supports the tripartite structure as the best fit in this region, with significantly higher estimated proportions of Jomon ancestry than mainland Japanese. Unlike the main islands, where each continental ancestor was directly brought by immigrants from the continent, those who already possessed the tripartite ancestor migrated to the southern Ryukyu Islands and admixed with the prehistoric people around the eleventh century AD, coinciding with the emergence of the Gusuku period. These results reaffirm the tripartite model in the southernmost extremes of the Japanese archipelago and show variability in how the structure emerged in diverse geographic regions.
Fasta consensus sequences for 24 goat mitochondria published in the study
This protocol describes the steps to extraction degraded DNA molecules from ancient or historic b... more This protocol describes the steps to extraction degraded DNA molecules from ancient or historic bone and teeth powder, rst washing the powder with dilute bleach (0.5% sodium hypochlorite) to improve the retrieval of endogenous DNA molecules. It is an implementation of the bleach washes reported in (Boessenkool et al, 2017) and (Dabney et al, 2019), combined with elements of the extraction protocols described by
The protocol described here is a multi-day extraction protocol for the recovery of fragment DNA m... more The protocol described here is a multi-day extraction protocol for the recovery of fragment DNA molecules from bone or teeth powder obtained from ancient or historical remains. The protocol is based on a silica-column method described initially in (Yang et al, 1998). Further modifications were made to this base protocol and reported (MacHugh et al, 2000), (Gamba et al, 2014), (Daly et al, 2018), and (Verdugo et al, 2019). The instructions presented here describe the totality of these modifications and are one of the aDNA extraction methods employed by the Molecular Population Genetics group at Trinity College Dublin.
Proceedings of the National Academy of Sciences, 2021
Significance Goats were among the first domestic animals and today are an important livestock spe... more Significance Goats were among the first domestic animals and today are an important livestock species; archaeozoological evidence from the Zagros Mountains of western Iran indicates that goats were managed by the late ninth/early eighth millennium. We assess goat assemblages from Ganj Dareh and Tepe Abdul Hosein, two Aceramic Neolithic Zagros sites, using complementary archaeozoological and archaeogenomic approaches. Nuclear and mitochondrial genomes indicate that these goats were genetically diverse and ancestral to later domestic goats and already distinct from wild goats. Demographic profiles from bone remains, differential diversity patterns of uniparental markers, and presence of long runs of homozygosity reveal the practicing and consequences of management, thus expanding our understanding of the beginnings of animal husbandry.
Science (New York, N.Y.), Jul 6, 2018
Current genetic data are equivocal as to whether goat domestication occurred multiple times or wa... more Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.
The domestic goat (<i>Capra hircus</i>) plays a key role in global agriculture, being... more The domestic goat (<i>Capra hircus</i>) plays a key role in global agriculture, being especially prized in regions of marginal pasture. However, the advent of industrialized breeding has seen a dramatic reduction in genetic diversity within commercial populations, while high extinction rates among feral herds have further depleted the reservoir of genetic variation available. Here, we present the first survey of whole mitochondrial genomic variation among the modern and historical goat populations of Britain and Ireland using a combination of mtDNA enrichment and high throughput sequencing. Fifteen historical taxidermy samples, representing the indigenous 'Old Goat' populations of the islands, were sequenced alongside five modern Irish dairy goats and four feral samples from endangered populations in western Ireland. Phylogenetic and network analyses of European mitochondrial variation revealed distinct groupings dominated by historical British and Irish samples, which demonstrate a degree of maternal genetic structure between the goats of insular and continental Europe. Several Irish modern feral samples also fall within these clusters, suggesting continuity between these dwindling populations and the ancestral 'Old Goats' of Ireland and Britain.
International Journal of Osteoarchaeology, 2016
Many archaeological bones display a heterogeneous degradation pattern. Highly degraded bones coul... more Many archaeological bones display a heterogeneous degradation pattern. Highly degraded bones could contain pockets of well-preserved bone, harbouring good quality DNA. This dichotomy may explain why the relationships between global bone preservation parameters such as histological integrity, bone mineral crystallinity or collagen yield, and bulk DNA preservation / amplification success rate, have been found to be at best, weak to moderate. In this pilot study, we explore whether or not a more localized approach will highlight a stronger relationship between diagenetic parameters and DNA preservation. This study includes a This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as
Direkli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleoli... more Direkli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra species, find a novel lineage best represented by a ∼14,000 year old 2.59X genome sequenced from specimen Direkli4. This newly discovered Capra lineage is a sister clade to the Caucasian tur species (Capra cylindricornis and Capra caucasica), both now limited to the Caucasus region. We identify genomic regions introgressed in domestic goats with high affinity to Direkli4, and find that West Eurasian domestic goats in the past, but not those today, appear enriched for Direkli4-specific alleles at a genome-wide level. This forgotten “Taurasian tur” likely survived Late Pleistocene climatic change in a Taurus Mountain refugia and its genomic fat...
Description of SourceTracker2 datasets and MIDAS outputs for novel ancient samples
MALDI-TOF data files for York Gospel samples including spreadsheet with sample informatio
Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable docume... more Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object
Damage patterns for novel and previously published ancient livestock genomes
The domestic goat (Capra hircus) plays a key role in global agriculture, being especially prized ... more The domestic goat (Capra hircus) plays a key role in global agriculture, being especially prized in regions of marginal pasture. However, the advent of industrialized breeding has seen a dramatic reduction in genetic diversity within commercial populations, while high extinction rates among feral herds have further depleted the reservoir of genetic variation available. Here, we present the first survey of whole mitochondrial genomic variation among the modern and historical goat populations of Britain and Ireland using a combination of mtDNA enrichment and high throughput sequencing. Fifteen historical taxidermy samples, representing the indigenous ‘Old Goat’ populations of the islands, were sequenced alongside five modern Irish dairy goats and four feral samples from endangered populations in western Ireland. Phylogenetic and network analyses of European mitochondrial variation revealed distinct groupings dominated by historical British and Irish samples, which demonstrate a degree of maternal genetic structure between the goats of insular and continental Europe. Several Irish modern feral samples also fall within these clusters, suggesting continuity between these dwindling populations and the ancestral ‘Old Goats’ of Ireland and Britain
<b>Copyright information:</b>Taken from "A genome-wide approach to identify gene... more <b>Copyright information:</b>Taken from "A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population"Genome Biology 2006;7(8):R74-R74.Published online 11 Aug 2006PMCID:PMC1779589.45); = 334. Data were from Akey and colleagues [12]. The 23 loci circled in the plot have an EU Absolute LSBL value = 0.8 and were considered in this study as outliers. EU, European-Americans; AF, African-Americans; AS, East Asian.
Sample information for published whole mitochondrial genomes used in this study
This file contains supplementary methods, figures and tables relating to the manuscript - The Yor... more This file contains supplementary methods, figures and tables relating to the manuscript - The York Gospels: a one thousand year biological palimpsest.
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Papers by Valeria Mattiangeli