Cryptic Contamination and Phylogenetic Nonsense

Ancient human DNA has been treated cautiously ever since the problems related to this type of material were exposed in the early 1990s, but as sequential genetic data from ancient specimens have been key components in several evolutionary and ecological studies, interest in ancient human DNA is on the increase again. It is especially tempting to approach archaeological and anthropological questions through this type of material, but DNA from ancient human tissue is notoriously complicated to work with due to the risk of contamination with modern human DNA. Various ways of authenticating results based on ancient human DNA have been developed to circumvent the problems. One commonly used method is to predict what the contamination is expected to look like and then test whether the ancient human DNA fulfils this prediction. If it does, the results are rejected as contamination, while if it does not, they are often considered authentic. We show here that human contamination in ancient material may well deviate from local allele frequencies or the distributions to be found among the laboratory workers and archaeologists. We conclude that it is not reliable to authenticate ancient human DNA solely by showing that it is different from what would be expected from people who have handled the material

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process

Southern Italian wild boar population, hotspot of genetic diversity

The wild boar, Sus scrofa, is an important game species widely distributed in Eurasia. Whereas the genetic variability of most European wild boar populations is well known, the status of wild boar living in Southern Italy is not as clear. We evaluated the present and past genetic diversity (D-loop, mtDNA) of the South Italian population, comparing it with that observed in other Mediterranean glacial refugia. Italian population showed highest genetic variability, if compared to other two European refugia (Iberian and Balkan). Most of samples from Italy carried sequences belonging to the European E1 haplogroup (80.9%) with a small proportion of the private Italian E2 (10.2%) and of the Asian (8.9%) ones. Italian samples carrying an Asian haplotype were genotyped by MC1R nuclear gene, failing to disclose a recent introgression from domestic pigs. Mismatch distribution analysis of the Italian population was affected by secondary contacts between these different lin- eages. This genetic melting pot was detected since the Mesolithic and the Neolithic age, during which we found samples belonging to the indigenous Italian and European haplogroups. Further, a Near-Eastern haplotype was found in 1,800 AD samples from Southern and Central Italy. Our res- ults can be in agreement with post-glacial recolonization theories, as well as with the long history of human-mediated translocations of Sus scrofa in the Mediterranean basi

A novel MC1R allele for black coat colour reveals the Polynesian ancestry and hybridization patterns of Hawaiian feral pigs

Pigs (Sus scrofa) have played an important cultural role in Hawaii since Polynesians first introduced them in approximately AD 1200. Additional varieties of pigs were introduced following Captain Cook’s arrival in Hawaii in 1778 and it has been suggested that the current pig population may descend primarily, or even exclusively, from European pigs. Although populations of feral pigs today are an important source of recreational hunting on all of the major islands, they also negatively impact native plants and animals. As a result, understanding the origins of these feral pig populations has significant ramifications for discussions concerning conservation management, identity and cultural continuity on the islands. Here, we analysed a neutral mitochondrial marker and a functional nuclear coat colour marker in 57 feral Hawaiian pigs. Through the identification of a new mutation in the MC1R gene that results in black coloration, we demonstrate that Hawaiian feral pigs are mostly the descendants of those originally introduced during Polynesian settlement, though there is evidence for some admixture. As such, extant Hawaiian pigs represent a unique historical lineage that is not exclusively descended from feral pigs of European originPeer reviewe

Grey wolf genomic history reveals a dual ancestry of dogs

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canisfamiliaris) lived(1-8). Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT8840,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.Peer reviewe

Dire wolves were the last of an ancient New World canid lineage

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Archaeological evidence indicates that pig domestication had begun by ~10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ~8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic con-tribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process

Kulturell inverkan pa uppfattning av auktoritet : en jamforelse mellan studenter pa Karlstads och Alicantes universitet

Denna studie ämnar undersöka vilka egenskaper chefer besitter som bäst kommer motiverar nästa generations anställda att följa chefers order och beslut och hur detta påverkas av kulturella faktorer. För att uppnå detta syfte har en enkätundersökning utförts bland studenter på ett universitet i Sverige och ett i Spanien, mer specifikt Karlstads och Alicantes universitet. Enkätundersökningen visar hur studenter rangordnar fem faktorer som enligt French och Raven (1959) definierar makt. Respondenterna till enkätundersökningen ombads rangordna dessa Power Bases (PB:s) efter hur mycket auktoritet varje PB ansågs ge upphov till i en anställds synvinkel. Stickprovsresultatet från Karlstads universitet anses vara representativt för hela studentpopulationen vid Karlstads universitet. Detta antagande grundas på att stickprovet var slumpvist utvalt, samt att stickprovet är tillräckligt stort med tanke på populationens standardavvikelse och storlek. Stickprovet från Alicantes universitet uppfyller inte ovanstående kriterier och kan ej användas i generaliserade syfte. Skillnader och likheter mellan svaren från de båda universiteten har analyserats utifrån en egentillverkad modell som speglar kulturella faktorers inverkan på hur auktoritet upplevs. Resultatet visar att Karlstads universitets studenter anser att faktorer som chefers kunskapsnivå och officiella titlar är de viktigaste källorna till auktoritet. Chefers personlighet var av medelmåttig betydelse och makten som kommer av att kunna belöna anställda och avskeda anställda var mindre effektiva sätt att motivera svenska anställda på. Att chefer har makten att kunna belöna anställda och att chefer anses besitta mycket kunskap var de viktigaste faktorerna som skapar auktoritet bland de spanska respondenterna i undersökningen. Höga titlar var av medelmåttig betydelse och makten som kommer av att kunna avskeda anställda och chefers personliga karisma ansågs vara av låg betydelse bland de spanska studenterna