Researchers in the ancient DNA community have suspected for well over a decade that ancient whole genomes can be found in sediments. Three new studies now provide such evidence and, with it, endless ...possibilities for future studies of sedimentary ancient DNA.
Researchers in the ancient DNA community have suspected for well over a decade that ancient whole genomes can be found in sediments. Three new studies now provide such evidence and, with it, endless possibilities for future studies of sedimentary ancient DNA.
Large-scale changes in global climate at the end of the Pleistocene significantly impacted ecosystems across North America. However, the pace and scale of biotic turnover in response to both the ...Younger Dryas cold period and subsequent Holocene rapid warming have been challenging to assess because of the scarcity of well dated fossil and pollen records that covers this period. Here we present an ancient DNA record from Hall's Cave, Texas, that documents 100 vertebrate and 45 plant taxa from bulk fossils and sediment. We show that local plant and animal diversity dropped markedly during Younger Dryas cooling, but while plant diversity recovered in the early Holocene, animal diversity did not. Instead, five extant and nine extinct large bodied animals disappeared from the region at the end of the Pleistocene. Our findings suggest that climate change affected the local ecosystem in Texas over the Pleistocene-Holocene boundary, but climate change on its own may not explain the disappearance of the megafauna at the end of the Pleistocene.
The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and ...domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely related haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken.
Ancient DNA: the next generation – chapter and verse Linderholm, Anna
Biological Journal of the Linnean Society/Biological journal of the Linnean Society,
January 2016, Letnik:
117, Številka:
1
Journal Article
Recenzirano
Odprti dostop
As the field of ancient DNA (aDNA) enters its third decade, it is perhaps time to reflect on the amazing transformation that it has undergone. During the first two decades, analyses of aDNA were ...mainly focussed on mitochondrial and/or chloroplast DNA as a result of their multicopy abundance in the cell, making retrieval and reproducibility much easier. Study of mitochondrial DNA through time allows evolutionary relationships between species to be resolved, molecular clocks to be calibrated, the geographical origins of samples to be revealed, and the investigation of demographic histories. However, not until the advent of massive parallel sequencing also know as second‐generation sequencing and next‐generation sequencing (NGS) was possible to retrieve and study nuclear DNA on a more routine base. Ancient nuclear DNA can additionally be used to identify extinct phenotypes, assess the degree of admixture, and examine selection pressures. This is a short review of what has been, what may come, and how aDNA has influenced NGS. Although examples from archaeology are used to illustrate the impact of NGS technologies on the field, this approach has also been successfully applied to a range of disciplines, such as medicine and wildlife forensics.
Stable isotopes (δ
13C, δ
15N) have been studied in human burials from the medieval town Sigtuna in Sweden. Dietary patterns of 80 adult individuals were analyzed on three cemeteries representing the ...phases of establishment, prosperity and decline of the town. All analyzed individuals were radiocarbon dated. One of the cemeteries, Church 1, represents a population of higher social status than those at the other two cemeteries.
The δ
13C values are homogenous and showed that the protein intake was mainly of terrestrial origin in the whole population. δ
15N values varies more and they may indicate a higher input of vegetables in the diet at one of the cemeteries, the Nunnan block.
Already in the initial phases of Sigtuna a social hierarchy had been established which is reflected in dietary patterns. Apparently more animal protein was consumed among the high status population of the town. Furthermore, differences in dietary patterns between the sexes were noted. In all phases the females show more clustered values indicating a more homogeneous diet than that of the males.
Genes and culture are believed to interact, but it has been difficult to find direct evidence for the process. One candidate example that has been put forward is lactase persistence in adulthood, ...i.e. the ability to continue digesting the milk sugar lactose after childhood, facilitating the consumption of raw milk. This genetic trait is believed to have evolved within a short time period and to be related with the emergence of sedentary agriculture.
Here we investigate the frequency of an allele (-13910*T) associated with lactase persistence in a Neolithic Scandinavian population. From the 14 individuals originally examined, 10 yielded reliable results. We find that the T allele frequency was very low (5%) in this Middle Neolithic hunter-gatherer population, and that the frequency is dramatically different from the extant Swedish population (74%).
We conclude that this difference in frequency could not have arisen by genetic drift and is either due to selection or, more likely, replacement of hunter-gatherer populations by sedentary agriculturalists.
The Mesolithic–Neolithic transition in north-west Europe has been described as rapid and uniform, entailing a swift shift from the use of marine and other wild resources to domesticated terrestrial ...resources. Here, we approach the when, what and how of this transition on a regional level, using empirical data from Öland, an island in the Baltic Sea off the Swedish east coast, and also monitor changes that occurred after the shift. Radiocarbon dating and stable carbon and nitrogen isotope analyses of bones and teeth from 123 human individuals, along with faunal isotope data from 27 species, applying to nine sites on Öland and covering a time span from the Mesolithic to the Roman Period, demonstrate a great diversity in food practices, mainly governed by culture and independent of climatic changes. There was a marked dietary shift during the second half of the third millennium from a mixed marine diet to the use of exclusively terrestrial resources, interpreted as marking the large-scale introduction of farming. Contrary to previous claims, this took place at the end of the Neolithic and not at the onset. Our data also show that culturally induced dietary transitions occurred continuously throughout prehistory. The availability of high-resolution data on various levels, from intra-individual to inter-population, makes stable isotope analysis a powerful tool for studying the evolution of food practices.
•Coat colour variability unlikely to be a pleiotropic effect of selection for tameness.•Coat colour variation appeared soon after domestication.•Selection for novelty led to proliferation of coat ...colour genetic variability.
Though the process of domestication results in a wide variety of novel phenotypic and behavioural traits, coat colour variation is one of the few characteristics that distinguishes all domestic animals from their wild progenitors. A number of recent reviews have discussed and synthesised the hundreds of genes known to underlie specific coat colour patterns in a wide range of domestic animals. This review expands upon those studies by asking how what is known about the causative mutations associated with variable coat colours, can be used to address three specific questions related to the appearance of non wild-type coat colours in domestic animals. Firstly, is it possible that coat colour variation resulted as a by-product of an initial selection for tameness during the early phases of domestication? Secondly, how soon after the process began did domestic animals display coat colour variation? Lastly, what evidence is there that intentional human selection, rather than drift, is primarily responsible for the wide range of modern coat colours? By considering the presence and absence of coat colour genes within the context of the different pathways animals travelled from wild to captive populations, we conclude that coat colour variability was probably not a pleiotropic effect of the selection for tameness, that coat colours most likely appeared very soon after the domestication process began, and that humans have been actively selecting for colour novelty and thus allowing for the proliferation of new mutations in coat colour genes.
Multiple geographical regions have been proposed for the domestication of Equus caballus. It has been suggested, based on zooarchaeological and genetic analyses that wild horses from the Iberian ...Peninsula were involved in the process, and the overrepresentation of mitochondrial D1 cluster in modern Iberian horses supports this suggestion. To test this hypothesis, we analysed mitochondrial DNA from 22 ancient Iberian horse remains belonging to the Neolithic, the Bronze Age and the Middle Ages, against previously published sequences. Only the medieval Iberian sequence appeared in the D1 group. Neolithic and Bronze Age sequences grouped in other clusters, one of which (Lusitano group C) is exclusively represented by modern horses of Iberian origin. Moreover, Bronze Age Iberian sequences displayed the lowest nucleotide diversity values when compared with modern horses, ancient wild horses and other ancient domesticates using nonparametric bootstrapping analyses. We conclude that the excessive clustering of Bronze Age horses in the Lusitano group C, the observed nucleotide diversity and the local continuity from wild Neolithic Iberian to modern Iberian horses, could be explained by the use of local wild mares during an early Iberian domestication or restocking event, whereas the D1 group probably was introduced into Iberia in later historical times.
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