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

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

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

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

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

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

Extensive Genetic Connectivity and Historical Persistence Are Features of Two Widespread Tree Species in the Ancient Pilbara Region of Western Australia

Phylogeographic studies can be used as a tool to understand the evolutionary history of a landscape, including the major drivers of species distributions and diversity. Extensive research has been conducted on phylogeographic patterns of species found in northern hemisphere landscapes that were affected by glaciations, yet the body of literature for older, unaffected landscapes is still underrepresented. The Pilbara region of north-western Australia is an ancient and vast landscape that is topographically complex, consisting of plateaus, gorges, valleys, and ranges, and experiences extreme meteorological phenomena including seasonal cyclonic activity. These features are expected to influence patterns of genetic structuring throughout the landscape either by promoting or restricting the movement of pollen and seed. Whilst a growing body of literature exists for the fauna endemic to this region, less is known about the forces shaping the evolution of plant taxa. In this study we investigate the phylogeography of two iconic Pilbara tree species, the Hamersley Bloodwood (Corymbia hamersleyana) and Western Gidgee (Acacia pruinocarpa), by assessing patterns of variation and structure in several chloroplast DNA regions and nuclear microsatellite loci developed for each species. Gene flow was found to be extensive in both taxa and there was evidence of long-distance seed dispersal across the region (pollen to seed ratios of 6.67 and 2.96 for C. hamersleyana and A. pruinocarpa, respectively), which may result from flooding and strong wind gusts associated with extreme cyclonic activity. Both species possessed high levels of cpDNA genetic diversity in comparison to those from formerly glaciated landscapes (C. hamersleyana = 14 haplotypes, A. pruinocarpa = 37 haplotypes) and showed evidence of deep lineage diversification occurring from the late Miocene, a time of intensifying aridity in this landscape that appears to be a critical driver of evolution in Pilbara taxa. In contrast to another study, we did not find evidence for topographic features acting as refugia for the widely sampled C. hamersleyana