Origin and History of Mitochondrial DNA Lineages in Domestic Horses

Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability

Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse

Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ²=1022.00, p<<0.0005), and CSNB, testing 43 horses (χ2=43, p<<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.Rebecca R. Bellone … David L. Adelson, Sim Lin Lim … et al

Death and the Societies of Late Antiquity

Ce volume bilingue, comprenant un ensemble de 28 contributions disponibles en français et en anglais (dans leur version longue ou abrégée), propose d’établir un état des lieux des réflexions, recherches et études conduites sur le fait funéraire à l’époque tardo-antique au sein des provinces de l’Empire romain et sur leurs régions limitrophes, afin d’ouvrir de nouvelles perspectives sur ses évolutions possibles. Au cours des trois dernières décennies, les transformations considérables des méthodologies déployées sur le terrain et en laboratoire ont permis un renouveau des questionnements sur les populations et les pratiques funéraires de l’Antiquité tardive, période marquée par de multiples changements politiques, sociaux, démographiques et culturels. L’apparition de ce qui a été initialement désigné comme une « Anthropologie de terrain », qui fut le début de la démarche archéothanatologique, puis le récent développement d’approches collaboratives entre des domaines scientifiques divers (archéothanatologie, biochimie et géochimie, génétique, histoire, épigraphie par exemple) ont été décisives pour le renouvellement des problématiques d’étude : révision d’anciens concepts comme apparition d’axes d’analyse inédits. Les recherches rassemblées dans cet ouvrage sont articulées autour de quatre grands thèmes : l’évolution des pratiques funéraires dans le temps, l’identité sociale dans la mort, les ensembles funéraires en transformation (organisation et topographie) et les territoires de l’empire (du cœur aux marges). Ces études proposent un réexamen et une révision des données, tant anthropologiques qu’archéologiques ou historiques sur l’Antiquité tardive, et révèlent, à cet égard, une mosaïque de paysages politiques, sociaux et culturels singulièrement riches et complexes. Elles accroissent nos connaissances sur le traitement des défunts, l’emplacement des aires funéraires ou encore la structure des sépultures, en révélant une diversité de pratiques, et permettent au final de relancer la réflexion sur la manière dont les sociétés tardo-antiques envisagent la mort et sur les éléments permettant d’identifier et de définir la diversité des groupes qui les composent. Elles démontrent ce faisant que nous pouvons véritablement appréhender les structures culturelles et sociales des communautés anciennes et leurs potentielles transformations, à partir de l’étude des pratiques funéraires.This bilingual volume proposes to draw up an assessment of the recent research conducted on funerary behavior during Late Antiquity in the provinces of the Roman Empire and on their borders, in order to open new perspectives on its possible developments. The considerable transformations of the methodologies have raised the need for a renewal of the questions on the funerary practices during Late Antiquity, a period marked by multiple political, social, demographic and cultural changes. The emergence field anthropology, which was the beginning of archaeothanatology, and then the recent development of collaborative approaches between various scientific fields (archaeothanatology, biochemistry and geochemistry, genetics, history, epigraphy, for example), have been decisive. The research collected in this book is structured around four main themes: Evolution of funerary practices over time; Social identity through death; Changing burial grounds (organisation and topography); Territories of the Empire (from the heart to the margins). These studies propose a review and a revision of the data, both anthropological and archaeological or historical on Late Antiquity, and reveal a mosaic of political, social, and cultural landscapes singularly rich and complex. In doing so, they demonstrate that we can truly understand the cultural and social structures of ancient communities and their potential transformations, based on the study of funerary practices

Regards croisés sur une pratique funéraire marginale à Reims aux III^e - IV^e s. de n. è. : études archéo-anthropologique, isotopique et paléogénomique

International audienceReims, as the capital of the province Gallia Belgica, is bounded by a wide moat around which several necropolises are mentioned in ancient finds. These necropolises were frequented even when the city's outlines shrank behind a smaller enclosure at the end of the 3rd or at the beginning of the 4th century CE. At the same time, the discovery of about sixty tombs scattered between these two enclosures, in Late Antiquity contexts where dismantling and recovery of materials were intense, raises questions about the appearance of this marginal practice. Is it related to the status of the deceased, workers who came to participate in the construction of the Late Antiquity enclosure?In order to address our problem, the purely anthropological results were crossed with those of biomolecular analyses (isotopic and genomic). The isotopic approach revealed overall differences in dietary behaviour between the two funerary groups, with a greater dietary diversity for the deceased buried in scattered tombs, which could be linked to their geographical origin as attested by the genetic analysis. The autochthonous origin of certain subjects and the antiquity of this original funerary practice highlighted by chronological modelling demonstrate that the exogenous origin of the subjects might not be the only explanatory factor.Reims, capitale de la province de Gaule Belgique, est délimitée par un large fossé aux abords duquel, des découvertes anciennes mentionnent plusieurs nécropoles. Ces nécropoles sont fréquentées même lorsque les contours de la ville se rétractent derrière une enceinte plus réduite à la fin du iiie – début du ive s. de n. è. Parallèlement, la découverte d’une soixantaine de tombes dispersées entre ces deux enceintes, dans des contextes du Bas-Empire où le démantèlement et la récupération de matériaux sont intenses questionne l’apparition de cette pratique marginale. Est-elle en lien avec le statut des défunts, des travailleurs venus participer à l’édification de l’enceinte tardo-antique ?Afin de nourrir notre problématique, les résultats purement anthropologiques ont été croisés avec ceux des analyses biomoléculaires (isotopiques et génomiques). L’approche isotopique a révélé globalement des différences de comportements alimentaires entre les deux groupes funéraires, avec une diversité alimentaire plus importante pour les défunts inhumés en tombes dispersées, qui pourrait être liée à leur origine géographique attestée par l’analyse génétique. L’origine autochtone de certains sujets et l’ancienneté de cette pratique funéraire originale mise en évidence par une modélisation chronologique démontrent que l’origine exogène des sujets ne serait peut-être pas le seul facteur explicatif

Analysis of Ancient DNA in Microbial Ecology.

International audienceThe development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota

Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses.

International audienceLeopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times

Evidence for early dispersal of domestic sheep into Central Asia

Archaeological and biomolecular investigations of ancient sheep remains from the site of Obishir V in southern Kyrgyzstan reveal that domestic livestock and Neolithic lifeways reached the heart of Central Asia by ca. 6,000 BCE, thousands of years earlier than previously recognized. The development and dispersal of agropastoralism transformed the cultural and ecological landscapes of the Old World, but little is known about when or how this process first impacted Central Asia. Here, we present archaeological and biomolecular evidence from Obishir V in southern Kyrgyzstan, establishing the presence of domesticated sheep by ca. 6,000 BCE. Zooarchaeological and collagen peptide mass fingerprinting show exploitation of Ovis and Capra, while cementum analysis of intact teeth implicates possible pastoral slaughter during the fall season. Most significantly, ancient DNA reveals these directly dated specimens as the domestic O. aries, within the genetic diversity of domesticated sheep lineages. Together, these results provide the earliest evidence for the use of livestock in the mountains of the Ferghana Valley, predating previous evidence by 3,000 years and suggesting that domestic animal economies reached the mountains of interior Central Asia far earlier than previously recognized.N

RNA sequencing reads mapped to <i>TRPM1</i>.

<p>RNA-Seq reads from <i>LP/LP</i> CSNB affected and <i>lp/lp</i> CSNB unaffected retina RNA, as well as, from <i>LP/LP, LP/lp</i> and <i>lp/lp</i> skin RNA. ECA1 Mb<i>, TRPM1</i> exon position, location of the insertion, and the number of reads for each sample are presented. (A) exon 0-27 illustrating that in <i>LP/LP</i> samples transcripts were not detected in exons 3’ of the insertion in intron 1. (B) exon 0, 1, 1’, 2 and 3 of TRPM1 illustrating that transcripts from exon 0 (yellow highlight) were detected in retinal samples but not skin while transcripts from exon 1’ (green highlight) were not detected in any of the horse samples, and finally transcripts were detected that mapped to intron 1 of <i>LP/LP</i> and <i>LP/lp</i> samples allowing for the identification of the insertion (denoted by red line). </p

Congenital stationary night blindness is associated with homozygosity for leopard complex spotting in horses.

<p>(A) <i>lp/lp</i> horses do not display a leopard complex spotting pattern and are not night blind as evidenced by normal ERGs. (B) <i>LP/lp</i> horses display one of several characteristic spotting patterns that vary in the amount of un-pigmented hairs in the coat and have pigmented spots (“leopard spots”) in the un-pigmented area. These horses are not night blind as evidenced by normal ERGs. (C) <i>LP/LP</i> horses displaying the characteristic homozygous patterns with varying amounts of white on the coat with few to no “leopard spots”. These horses all have CSNB as evidenced by the “negative” ERG in which the b wave is absent. </p