Richard Allen

Inferring allele frequency trajectories from ancient DNA indicates that selection on a chicken gene coincided with changes in medieval husbandry practices

Abstract Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here, we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both hypothesised to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of preindustrial domesticate trait selection in response to a historically attested cultural shift in food preference. For BCDO2, we find support for selection, but demonstrate that the recent rise in allele frequency could also have been driven by gene flow from imported Asian chickens during more recent breed formations. Our findings highlight that traits found ubiquitously in modern domestic species may not necessarily have originated during the early stages of domestication. In addition, our results demonstrate the importance of precise estimation of allele frequency trajectories through time for understanding the drivers of selection.

Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesis fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesis three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2–3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.

Predicting the viability of archaic human hybrids using a mitochondrial proxy

Ancient DNA evidence has confirmed hybridization between humans and Neanderthals and revealed a complex pattern of admixture between hominin lineages. Many segments of the modern human genome are devoid of Neanderthal ancestry, however, and this non-random distribution has raised questions regarding the frequency and success of hybridisation between ancient human lineages. Here, we examine the hypothesis that hominin hybrid offspring suffered a reduction in fertility by comparing patterns of sequence divergence of mitochondrial and nuclear DNA from numerous hybridising pairs of mammals. Our results reveal a threshold separating species pairs whose divergence values fall within two categories: those whose hybrid offspring can successfully reproduce without backcrossing with their parent species, and those whose hybrid offspring cannot. Using this framework, we predict that the potential hybrid offspring of Neanderthals, Denisovans, the ancient individuals from the Sima de los Huesos and anatomically modern humans would not have suffered a reduction in fertility.

Celebrating Easter, Christmas and their associated alien fauna

ABSTRACT Easter and Christmas are the most important events in the Christian calendar. Despite their global reach and cultural significance, astonishingly little is known about the festivals’ genesis. Equally obscure is our understanding of the animals that have come to be associated with these celebrations – notably the Christmas Turkey and the Easter ‘Bunny’ (brown hare and the European rabbit). Like Christianity, none of these animals are native to Britain and the timing and circumstances of their arrivals are poorly understood, often obfuscated by received wisdom. This paper firstly refines the bio-cultural histories of the species that, in contemporary Britain, form integral parts of Easter and Christmas festivities. Secondly, we celebrate the non-native species which have played such an important role in the creation of Britain’s cultural heritage.

The Reform of the Chapter of Sées (1131) Reconsidered: The Evidence of the Episcopal Acta

This paper reexamines the reform of the cathedral chapter of Sees in 1131. It does so by looking primarily, though not exclusively, at the almost 400 acta – that is, the charters and documents –issued by the bishops of the diocese in the period up to 1220. It shows that this underused material has the potential better to contextualise this key event in the ecclesiastical history of medieval France and radically to improve our understanding of its wider effects. It also looks in detail at the careers of the bishops during this period and shows that these prelates, contrary to popular belief, were often supportive not only of the reform established within their cathedral, but also of the wider Augustinian movement. It concludes by briefly considering what the example of Sees can tell us about the regularisation of cathedral chapters in the Middle Ages.

The earliest known list of excommunicates from ducal Normandy

Of the many additions made by the canons of Rouen cathedral to the Anglo-Saxon manuscript known today as the Benedictional of Archbishop Robert, the shortest is a list of 17 persons who are recorded as having been either ‘summoned’ (vocandi) or ‘excommunicated’ (excommunicandi). Although known to scholars for almost two centuries, the list has never been analysed to any great extent, despite the fact that it not only contains the earliest Norman register of excommunicates in existence, but is also apparently unique within the history of the Anglo-Norman realm. This article examines the list in detail for the first time, and addresses some of the most fundamental questions concerning the rationale behind its creation, its place within the history of excommunication in ducal Normandy, and the identity of the people it names. It will also be argued that the first (and largest) part of the list, the entirety of which is traditionally dated to the reign of Robert Curthose (1087–1106), was most likely compiled during the reign of his father, William the Conqueror (1035–87).

Robert Cénalis et l'histoire épiscopale d'Avranches de 1100 à 1253

En raison de l’effondrement de la cathedrale d’Avranches au crepuscule de l’Ancien Regime et de la destruction des Archives departementales de la Manche en 1944, l’histoire du diocese d’Avranches est tres mal servie par la documentation medievale. Il nous reste cependant quelques collections d’erudits contenant des copies de documents avranchais dont l’une des plus importantes fut compilee par Robert Cenalis, eveque d’Avranches (1532-1560). Conserve actuellement a la Bibliotheque nationale de France, ce manuscrit meconnu, dont le contenu est souvent tire de documents perdus depuis longtemps, nous offre un apercu important sur l’histoire du diocese a partir du debut du xiie siecle jusqu’au milieu du xiiie, ainsi que la possibilite de mieux nous renseigner sur plusieurs faits diplomatiques, archeologiques, prosopographiques et topographiques.