Combining bleach and mild predigestion improves ancient DNA recovery from bones.

The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany.

Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.Leverhulme Trust (MRF-2013-065

Strong Phylogeographic Structure in a Millipede Indicates Pleistocene Vicariance between Populations on Banded Iron Formations in Semi-Arid Australia

<div><p>The Yilgarn Banded Iron Formations of Western Australia are topographical features that behave as terrestrial islands within the otherwise flat, semi-arid landscape. The formations are characterised by a high number of endemic species, some of which are distributed across multiple formations without inhabiting the intervening landscape. These species provide an ideal context for phylogeographic analysis, to investigate patterns of genetic variation at both spatial and temporal scales. We examined genetic variation in the spirostreptid millipede, <i>Atelomastix bamfordi</i>, found on five of these Banded Iron Formations at two mitochondrial loci and 11 microsatellite loci. Strong phylogeographic structuring indicated the five populations became isolated during the Pleistocene, a period of intensifying aridity in this landscape, when it appears populations have been restricted to pockets of moist habitat provided by the formations. The pattern of reciprocal monophyly identified within the mtDNA and strong differentiation within the nuclear microsatellite data highlight the evolutionary significance of these divergent populations and we suggest the degree of differentiation warrants designation of each as a conservation unit.</p></div

Bayesian population assignment of <i>Atelomastix bamfordi</i> individuals generated in TESS for the optimal grouping of K = 4.

<p>Each vertical line represents an individual and the colour displays the probability of belonging to each genetic cluster.</p

Progeny and maternal genotypes

Microsatellite data for seedlings and mothers used in the analyses. Seedlings were produced by germinating seeds collected from maternal plants in nine populations. Columns are as follows: ID of individual seedlings and maternal plants; ID of the mother of each seedling; Population code; Data for 8 microsatellite loci. Missing data are coded by '0'. For each seedling cohort, the rows of seedling data are preceded by a row containing the maternal genotype. Data were collected by Tanya Llorens and Heidi Nistelberger. Queries should be directed to Tanya Llorens

Diversity statistics for the five <i>Atelomastix bamfordi</i> BIF populations for mitochondrial DNA data and nuclear microsatellite data (bold), standard error in parentheses: N, number of individuals; # haps, number of haplotypes; HD, haplotype diversity; Pi, nucleotide diversity; D, Tajima's D; n, average number of individuals genotyped; AR∧, rarefied allelic richness; * P value<0.05.

<p>Diversity statistics for the five <i>Atelomastix bamfordi</i> BIF populations for mitochondrial DNA data and nuclear microsatellite data (bold), standard error in parentheses: N, number of individuals; # haps, number of haplotypes; HD, haplotype diversity; Pi, nucleotide diversity; D, Tajima's D; n, average number of individuals genotyped; AR∧, rarefied allelic richness; * P value<0.05.</p

Data from: Evaluating the influence of different aspects of habitat fragmentation on mating patterns and pollen dispersal in the bird-pollinated Banksia sphaerocarpa var. caesia

Habitat fragmentation can significantly affect mating and pollen dispersal patterns in plant populations, although the differential effects of the various aspects of fragmentation are poorly understood. In this study we used paternity assignment with eight microsatellite loci to investigate the effect of fragmentation on the mating system and pollen dispersal within one large and eight small population remnants of Banksia sphaerocarpa var. caesia, a bird-pollinated shrub in the southern agricultural region of Western Australia. The large population had a much larger neighbourhood size and lower selfing rate, maternal pollen pool differentiation and within-plot mean pollen dispersal distance than the small populations. Outcrossing was consistently high and ranged from 89% ± 0.8 to 98.5% ± 0.3, and mating patterns suggested nearest-neighbour pollination. Pollen immigration into small populations ranged from 6% ± 0.6 to 15% ± 0.6. Using the small populations, we tested for correlations between various fragmentation variables and mating system and pollen dispersal parameters. We found significant positive linear relationships between population size and number of different fathers per seed crop and between population shape and pollen pool differentiation. There were significant negative linear relationships between population isolation and outcrossing rate; population shape and neighbourhood size; and conspecific density and mean pollen dispersal distance. Our results suggest that birds may use a series of fragmented populations as a vegetation corridor while foraging across the landscape and that population connectivity is a critical determinant of pollinator visitation. Our results also suggest that the effect of a linear population shape on the mating system and pollen dispersal is routinely underestimated

Unrooted neighbour-joining tree of Cavalli-Sforza chord distances between the five BIF populations of <i>Atelomastix bamfordi</i>.

<p>Distances are based on 11 microsatellite loci with bootstrap support shown at nodes.</p

Adult genotypes and coordinates

Microsatellite data for adult plants used in the analyses. Adults were sampled from 9 populations. For 87F, all adults within a focus area were sampled. For the remaining 8 populations, all adults present within the population remnant were sampled. Columns are as follows: ID of adult plants; Population code; Data for 8 microsatellite loci; Geographic coordinates for each plant. Missing data are coded by '0'. Geographic coordinates are latitude and longitude recorded in decimal degrees using a differential GPS. Datum: Geocentric Datum of Australia 1994 (GDA94). Data were collected by Tanya Llorens and Heidi Nistelberger. Queries should be directed to Tanya Llorens

Bayesian cladogram of 75 <i>Atelomastix bamfordi</i> individuals based on combined CO1 and 16 S mtDNA data.

<p>Clades are designated separate colours as per <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093038#pone-0093038-g001" target="_blank">Fig. 1</a>. Numbers on terminals indicate haplotype number. The * denotes major nodes with high support (posterior probability>0.85) and the numbered node indicates divergence estimate in millions of years with confidence intervals in brackets. NB the <i>A. nigrescens</i> branch has been truncated (//) for viewing purposes.</p