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Star, B.

Publications and source records attributed to Star, B..

At least 19 recordsLinked to original sources

Of bone and ivory: Eastern Atlantic sources of the medieval European walrus ivory trade discovered by ancient mitochondrial and nuclear DNA

Previous molecular archaeological research has made the surprising discovery that almost all studied European walrus finds dating between the 11th and 14th centuries CE seemed to be traded from the Norse colony of Greenland. But why has almost no walrus ivory from the Barents Sea region been detected in medieval Europe, despite its closer proximity and being mentioned in historical accounts? Here, we show that the full spatial extent of medieval Atlantic walrus hunting has been underestimated in previous analyses that targeted modified walrus skulls (rostra) with which pairs of attached tusks were traded, because destructive sampling of ivory artefacts is not always practicable. By analysing workshop offcuts from medieval Sigtuna, Sweden, we directly compare the geographical sources of walrus ivory with rostra, and show that isolated tusks were traded in different ways. We first resolve the genome-wide trans-Atlantic walrus population structure, discovering significant genome-wide nuclear differentiation between western and eastern Atlantic walrus populations. By employing spatially diagnostic nuclear SNPs (n = 144,986), we then use low-coverage sequence data to classify historical walrus rostrum and tusk specimens to either western or eastern Atlantic origin, and thus overcome previous limitations when provenancing walruses based on mitochondrial DNA alone. We find that all medieval walrus rostra are assigned exclusively towards the western Atlantic. In contrast, half of the medieval ivory specimens from Sigtuna are assigned to eastern Atlantic sources including Iceland and the Barents Sea region. Moreover, the objects of eastern origin precede those from Norse Greenland in time, suggesting sequential exploitation. Our observations resolve a discrepancy between earlier molecular inference and historical evidence and imply a significantly broader extent and impact of medieval ecological globalisation in the Arctic.

evolutionary biology↗

The Once and Future Fish: 1300 years of Atlantic herring population structure and demography revealed through ancient DNA and mixed-stock analysis

Atlantic herring populations have been the target of highly profitable coastal and pelagic fisheries in northern Europe for well over a thousand years. Their complex and intermingled population dynamics have sparked extensive debate over the impacts of historical overfishing and have complicated their sustainable management today. Recently developed tools - including diagnostic SNP panels for mixed-stock analysis - aim to improve population assignment for fisheries management, however, the biological relevance of such tools over long periods of time remains unknown. Here, we demonstrate the millennium-long applicability of diagnostic SNP panels and identify population perturbations associated with increasing exploitation pressure and climate change by analyzing whole genome data from modern and ancient herring specimens. We find that herring demographic cycles were likely within healthy ecosystem boundaries until the dramatic disruption of these cycles in the 20th century. We find only autumn-spawning herring in our archaeological remains spanning 900 years from 8 sites across Europe, supporting observations that the numerical dominance of specific spawning populations can demographically outcompete other herring types. We also obtain pre-archival aDNA evidence for the famous, cyclical "Bohuslan periods," during which mass quantities of North Sea autumn-spawning herring congregated in the Skagerrak. Finally, the long-term applicability of diagnostic SNP panels underscores their highly cost-effective application for the genetic monitoring of herring stocks. Our results highlight the utility of ancient DNA and genomic analysis to obtain historical and natural insights in herring ecology and population dynamics with relevance for sustainable fisheries management.

ecology↗

Forest edges and other semi-natural habitat edges increase wild bee species richness and habitat connectivity in intensively managed temperate landscapes.

Pollinator conservation schemes are typically focused on conserving existing-, restoring degraded- or establishing new wild bee habitats. The effectiveness of such conservation schemes depends on the presence of dispersal corridors that allow habitat colonization by bees. Nonetheless, we lack an understanding of the role of semi-natural habitats edges on the connectivity of pollinator communities across intensively managed landscapes. Here, we use data from wild bee communities comprising 953 occurrences from 79 species of non-parasitic bees, sampled at 68 locations distributed across a Norwegian and a Danish landscape to show that the proportion of semi-natural habitat edges is positively correlated to bee species richness and habitat connectivity. Specifically, we found that wild bee species richness sampled along roadsides increased with the proportion of semi-natural habitat edges within1.5 km of the study sites and with local plant species richness. We combined maps showing the proportion of seminatural habitat edges with least cost path analysis to find the most likely dispersal route between our bee communities. We find that these least cost path lengths provide better models of bee species compositional similarity than geographic distance (|{Delta}AICc| > 2), suggesting that seminatural habitat edges act as dispersal corridors in intensively managed landscapes. However, we also find that compositional similarity between communities depend on site-specific plant species richness stressing the importance of improving the habitat quality of edge habitats if they are to function as dispersal corridors. We discuss potential management options for improving wild bee habitat conditions along seminatural habitat edges and illustrate how maps of least cost paths can be used to identify dispersal corridors between pollinator habitats of conservation priority. Maps of dispersal corridors can be used to direct wild bee habitat management actions along seminatural habitat edges to facilitate the dispersal of bees between larger grassland habitats.

ecology↗

Distinct genome architecture underlies fine-scale population differentiation in two common European bumblebees (Bombus pascuorum and Bombus lapidarius)

Bumblebees are keystone pollinators which facilitate the reproduction of a wide range of wild and agricultural plants. Their abundance and diversity have been severely reduced by anthropogenic stressors such as land-use change and widespread habitat fragmentation. However, we lack a comprehensive understanding of bumblebee population structure and local adaptation in response to human-altered landscapes. We here discover surprisingly fine-scaled population structure (e.g. [~]300km) within two widely occurring bumblebee species, Bombus lapidarius and Bombus pascuorum, by analysing whole genome data of 106 specimens from 7 sites in Northern Europe. Our sample range encompasses a mosaic of land-use types with varying levels of habitat fragmentation and natural oceanic barriers. While the observed population structure is largely associated with reduced gene flow across natural barriers, we also detect significant divergence between populations sampled from more fragmented, agricultural landscapes. Furthermore, we identify species-specific patterns of population structure which are underpinned by distinct genomic architecture. Whereas genetic divergence in B. lapidarius is spread relatively evenly across the genome, divergence in B. pascuorum is concentrated within several megabase-sized genomic regions with significantly elevated differentiation - including a putative chromosomal inversion - which may underlie well-known colour polymorphisms across its range. Our observations reveal unexpectedly high levels of inter- and intraspecific genomic diversity within the bumblebee genus, and highlight the necessity of increasing our understanding of bumblebee population structure and connectivity to design optimal bumblebee conservation strategies. Significance statementAnthropogenic stressors such as habitat fragmentation have severe impacts on bumblebee abundance and diversity, yet little is known about how bumblebee populations are structured in human-altered landscapes. We analyse whole-genome data from two common bumblebee species (Bombus lapidarius and Bombus pascuorum) across Northern Europe to uncover species-specific patterns of spatial population differentiation and local adaptation, including a chromosomal rearrangement in B. pascuorum. Importantly, our results imply that many of the fragmented bumblebee habitats in Europe comprise locally distinct populations with limited gene flow in between. These findings are therefore of major importance for our overall understanding of bumblebee genomic variation, connectivity and adaptation, offering fundamental insights that are required to effectively mitigate the effects of human activities on wild bee biodiversity.

genomics↗

Five millennia of mitochondrial introgression in Atlantic bluefin tuna identified using ancient DNA

Mitogenomic (MT) introgression between species is readily documented in marine fishes. Such introgression events may either be long-term natural phenomena or the result of human-driven shifts in spatial distributions of previously separated species. Determining the drivers behind MT introgression is stymied by the difficulty of directly observing patterns of interbreeding over long timescales. Using ancient DNA spanning five millennia, we here investigate the long-term presence of MT introgression from Pacific bluefin tuna (Thunnus orientalis) and albacore (Thunnus alalunga) into Atlantic bluefin tuna (Thunnus thynnus), a species with extensive exploitation history and observed shifts in abundance, and demographic distribution. Comparing ancient (n=130) and modern (n=78) mitogenomes of specimens covering most of the range of Atlantic bluefin tuna we detect no significant spatial or temporal population structure. This lack of spatiotemporal genomic differentiation is indicative of ongoing gene flow between populations and large effective population sizes over millennia. Moreover, we identify introgressed MT genomes in ancient specimens up to 5000 years old and find that this rate of introgression has remained similar through time. We therefore conclude that MT introgression in the Atlantic bluefin tuna is to date unaffected by anthropogenic impacts. By providing the oldest example of directly observed MT introgression in the marine environment, our results highlight the utility of ancient DNA to obtain temporal insights in the long-term persistence of such phenomena.

evolutionary biology↗

Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA

Marine resources have been important for the survival and economic development of coastal human communities across northern Europe for centuries. Knowledge of the origin of such historic resources can provide key insights into fishing practices and the spatial extent of trade networks. Here, we combine ancient DNA and stable isotopes ({delta}13C, {delta}15N, non-exchangeable {delta}2H and {delta}34S) to investigate the geographical origin of archaeological cod remains in Oslo from the eleventh to seventeenth centuries CE. Our findings provide genetic evidence that Atlantic cod was obtained from different sources, including a variety of distant-water populations like northern Norway and possibly Iceland. Evidence for such long-distance cod trade is already observed from the eleventh century, contrasting with archaeological and historical evidence from Britain and other areas of Continental Europe around the North and Baltic Seas, where such trade developed in a later period. Diverse biological origins are further supported by significant differences of a range of isotopes, indicating that multiple populations living in different environments were exploited. This research highlights the utility of combining ancient DNA methods and stable isotope analysis to describe the development of marine fisheries during the medieval and post-medieval period.

ecology↗

A fast and inexpensive plate-based NGS library preparation method for insect genomics

Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we investigate a fast and economical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs stored under different conditions. Using a standardised input of 6ng DNA, library preparation costs were significantly reduced through the 6-fold dilution of a commercially available tagmentation enzyme. Costs were further suppressed by direct post-amplification pooling, skipping quality assessment of individual libraries. We find that reduced DNA yields associated with ethanol-based storage do not impede overall sequencing success. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By lowering data generation costs, broadening the scope of whole genome studies to include low yield DNA extracts and increasing throughput, we expect this protocol to be of significant value for a range of applications in the field of insect genomics.

genomics↗

Ancient DNA evidence for the ecological globalisation of cod fishing in medieval and post-medieval Europe

Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca. 1050 to 1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens derived from distant sources. Our results further suggest that Icelandic cod was exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole genome sequencing and ancient DNA approaches to describe the globalisation of marine fisheries and increase our understanding regarding the extent of the North-Atlantic fish trade and long-range fisheries in medieval and early modern times.

ecology↗

Serial depletion of Baltic herring since the Viking Age revealed by ancient DNA and population genomics

Marine resource consumption has been a key component in European diet and culture since the Middle Ages, when fish consumption increased dramatically. Yet, the early origins of marine industries and the long-term ecological consequences of historical and contemporary fisheries remain debated. The Baltic Sea was home to the first "industrial" fishery [~]800 years ago targeting the Baltic herring, a species that is still economically and culturally important today. We combine modern whole genome data with ancient DNA (aDNA) to identify the first known long-distance herring trade in the region, illustrating that large-scale fish trade began during the Viking Age. We resolve population structure within the Baltic and observe demographic independence for four local herring stocks over at least 200 generations. It has been suggested that overfishing at Oresund in the 16th century resulted in a demographic shift from autumn-spawning to spring-spawning herring dominance in the Baltic. We show that while the Oresund fishery had a negative impact on the western Baltic herring stock, the existence of autumn-spawning refugia in other regions of the Baltic delayed the demographic shift to spring spawning dominance until the 20th century. Importantly, modelling demographic trajectories over time, we identify a consistent pattern of serial depletion within the Baltic that is associated with changes in fishing pressure and climate, and conclude that herring exploitation at both historical and recent intensities is not sustainable. Our results highlight the complex and enduring impacts humans have had on the marine environment well before the industrial era.

ecology↗

An accurate assignment test for extremely low-coverage whole-genome sequence data

Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. In ancient DNA research, such characters can provide further information on population continuity, evolution, climate change, species migration, or trade, depending on archaeological context. Yet, assignment tests often rely on moderate- to high-coverage sequence data, which can be difficult to obtain for many ancient specimens and in ecological studies, which often use sequencing techniques such as ddRAD to bypass the need for costly whole-genome sequencing. We have developed a novel approach that efficiently assigns biologically relevant information (such as population identity or structural variants) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic Single Nucleotide Polymorphisms (SNPs) associated with a biological characteristic. Low coverage alignment files from ancient specimens are subsequently compared to these databases to ascertain allelic state yielding a joint probability for each association. To assess the efficacy of this approach, we assigned inversion haplotypes and population identity in several species including Heliconius butterflies, Atlantic herring, and Atlantic cod. We used both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage (e.g. 0.0001x fold) based on genome-wide SNPs. This approach will therefore increase the number of ancient samples in ecological and bioarchaeological research for which relevant biological information can be obtained.

bioinformatics↗

Origin and fate of supergenes in Atlantic cod

Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here, we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate that chromosomal inversions underlie all four supergenes, and show that they originated at different times between 0.40 and 1.66 million years ago. While we found no evidence for a role of introgression in the origin of the four supergenes, we reveal gene flux between supergene haplotypes with derived and ancestral arrangements, occurring both through gene conversion and double crossover. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the purging of introduced genetic variation.

evolutionary biology↗

Complex population structure of the Atlantic puffin revealed by whole genome analyses

The factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.

genomics↗

The preservation of ancient DNA in archaeological fish bone

The field of ancient DNA is taxonomically dominated by studies focusing on mammals. This taxonomic bias limits our understanding of endogenous DNA preservation for vertebrate taxa with different bone physiology, such as teleost fish. In contrast to most mammalian bone, teleost bone is typically brittle, porous, lightweight and is characterized by a lack of bone remodeling during growth. Using high-throughput shotgun sequencing, we here investigate the preservation of DNA in a range of different bone elements from over 200 archaeological Atlantic cod (Gadus morhua) specimens from 38 sites in northern Europe, dating up to 8000 years before present. We observe that the majority of archaeological sites (79%) yield endogenous DNA, with 40% of sites providing samples that contain high levels (> 20%). Library preparation success and levels of endogenous DNA depend mainly on excavation site and pre-extraction laboratory treatment. The use of pre-extraction treatments lowers the rate of library success, although -- if successful -- the fraction of endogenous DNA can be improved by several orders of magnitude. This trade-off between library preparation success and levels of endogenous DNA allows for alternative extraction strategies depending on the requirements of down-stream analyses and research questions. Finally, we find that -- in contrast to mammalian bones -- different fish bone elements yield similar levels of endogenous DNA. Our results highlight the overall suitability of archaeological fish bone as a source for ancient DNA and provide novel evidence for a possible role of bone remodeling in the preservation of endogenous DNA across different classes of vertebrates.

evolutionary biology↗

Metagenomic shotgun analyses reveal complex patterns of intra- and interspecific variation in the intestinal microbiomes of codfishes

The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we use metagenomic shotgun sequencing of individual specimens to compare the intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) - that have distinct behavior and habitats- and three Gadidae species that occupy a range of ecological niches. Interestingly, we find significantly diverged microbiomes amongst the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet or a combination there-off comprise major drivers of the intestinal community composition of codfishes. ImportanceThe composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g. diet, temperature or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observe distinct microbiomes amongst two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation are more variable. For instance, we do not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii) whose lineages have evolutionary separated over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.

microbiology↗

Ancient genomes reveal early Andean farmers selected common beans while preserving diversity

All crops are the product of a domestication process that started less than 12,000 years ago from one or more wild populations [1, 2]. Farmers selected desirable phenotypic traits, such as improved energy accumulation, palatability of seeds or reduced natural shattering [3], while leading domesticated populations through several more or less gradual demographic contractions [2, 4]. As a consequence, erosion of wild genetic variation [5] is typical of modern cultivars making them highly susceptible to pathogens, pests and environmental change [6,7]. The loss of genetic diversity hampers further crop improvement programs to increase food production in a changing world, posing serious threats to food security [8,9]. Using both ancient and modern seeds, we analyzed the temporal dynamic of genetic variation and selection during the domestication process of the common bean (Phaseolus vulgaris) that occurred in the Southern Andes. Here we show that most domestic traits were selected for prior to 2,500 years ago, with no or only minor loss of whole-genome variation. In fact, i) all ancient domestic genomes dated between 600 and 2,500 years ago are highly variable - at least as variable as a modern genome from the wild; the genetic erosion that we observe in modern cultivars is therefore a recent process that occurred in the last centuries; ii) the majority of changes at coding genes that differentiate wild and domestic genomes are already present in the ancient genomes analyzed here. Considering that most desirable phenotypic traits are likely controlled by multiple polymorphic genes [10], a likely explanation of this decoupling of selection and genomic erosion is that early farmers applied a relatively weak selection pressure [2] by using many phenotypically similar but genomically diverse individuals as breeders. Selection strategies during the last few centuries were probably less sustainable and produced further improvements focusing on few plants carrying the traits of interest, at the cost of marked genetic erosion.

genomics↗

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

The biological roles of the intestinal microbiome and how it is impacted by environmental factors are yet to be determined in wild marine fish species. Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean. 16S rRNA-based amplicon analyses found no geographical differentiation between the intestinal microbiome of Atlantic cod from different locations. Nevertheless, it is unclear if this lack of differentiation results from an insufficient resolution of this method to resolve fine-scaled biological complexity. Here, we take advantage of the increased resolution provided by metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway - located 470 km apart. Our results show that the intestinal microbiome is dominated by the Vibrionales order, consisting of varying abundances of Photobacterium, Aliivibrio and Vibrio species. Moreover, resolving the species community to unprecedented resolution, we identify two abundant species, P. iliopiscarium and P. kishitanii, which comprise over 50% of the classified reads. Interestingly, genomic data shows that the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution that are well suited to thrive in this host-associated environment.

microbiology↗

Ancient DNA reveals the chronology of walrus ivory trade from Norse Greenland

The search for walruses as a source of ivory -a popular material for making luxury art objects in medieval Europe- played a key role in the historic Scandinavian expansion throughout the Arctic region. Most notably, the colonization, peak and collapse of the medieval Norse colony of Greenland have all been attributed to the proto-globalization of ivory trade. Nevertheless, no studies have directly traced European ivory back to distinct populations of walrus in the Arctic. This limits our understanding of how ivory trade impacted the sustainability of northern societies and the ecology of the species they relied on. Here, we compare the mitogenomes of 27 archaeological walrus specimens from Europe and Greenland (most dated between 900 and 1400 CE) and 10 specimens from Svalbard (dated to the 18th and 19th centuries CE) to partial mitochondrial (MT) data of over 300 modern walruses. We discover two monophyletic mitochondrial clades, one of which is exclusively found in walrus populations of western Greenland and the Canadian Arctic. Investigating the chronology of these clades in our European archaeological remains, we identify a significant shift in resource use from predominantly eastern sources towards a near exclusive representation of walruses from western Greenland. These results provide empirical evidence for the economic importance of walrus for the Norse Greenland settlements and the integration of this remote, western Arctic resource into a medieval pan-European trade network.

genomics↗

A stainless-steel mortar, pestle and sleeve design for the efficient fragmentation of ancient bone

Ancient DNA (aDNA) bone extraction protocols routinely require the fragmentation of larger bone pieces into smaller pieces or powder prior to DNA extraction. To achieve this goal, different types of equipment such as oscillating ball mills, freezer mills, mortar and pestle, or drills can be used. Although all these approaches are suitable, practical drawbacks are associated with each method. Here, we present the design for a stainless-steel mortar and pestle, with a removable sleeve to contain bone material. The tool readily comes apart for ease of cleaning and its simplicity allows university workshops equipped with a lathe, boring tools and milling machine to make these components at local expense. We find that this design allows for the controlled fragmentation of ancient bone and that it significantly improves our sample throughput. We recommend this design as a useful, economical addition to existing laboratory equipment for the efficient handling of ancient bone.

genomics↗