The evolutionary potential of Baker's weediness traits in the common morning glory, Ipomoea purpurea (Convolvulaceae)

? Premise of the study: Many reports have cited Baker's list of weediness traits, or those that exemplify the "ideal" weed, yet few have considered the evolutionary potential of such traits as a group. Thus, it is unknown whether constraints on the evolution of increased weediness, such as a lack of genetic variation or genetic correlations between the traits, are present. Ipomoea purpurea, the common morning glory, is a problematic weed that exhibits many of Baker's ideal weed traits. ? Methods: We used progeny from a half/full-sib breeding design in a series of three greenhouse experiments to assess the presence of genetic variation, narrow sense heritabilities, and genetic correlations in Baker's growth, competition, and fitness "weediness" traits in two populations of I. purpurea. ? Key results: We uncovered genetic variation underlying reproductive fitness traits and competitive ability in at least one population, but no evidence of genetic variation underlying growth rate in either population. Genetic correlations between many of the weediness characters differed significantly from zero; however, their direction and/or magnitude differed between populations. ? Conclusions: We found that increased weediness in the common morning glory is more likely to occur through selection on reproductive output and competitive ability rather than through selection on growth rate. Assessing Baker's traits in a quantitative genetics framework can provide a solid perspective on their evolutionary potential and a unique framework within which to determine how weeds will respond to different environmental stresses and/or scenarios of global climate change.     

Tracking down human contamination in ancient human teeth

DNA contamination arising from the manipulation of ancient calcified tissue samples is a poorly understood, yet fundamental, problem that affects the reliability of ancient DNA (aDNA) studies. We have typed the mitochondrial DNA hypervariable region I of the only 6 people involved in the excavation, washing, and subsequent anthropological and genetic study of 23 Neolithic remains excavated from Granollers (Barcelona, Spain) and searched for their presence among the 572 clones generated during the aDNA analyses of teeth from these samples. Of the cloned sequences, 17.13% could be unambiguously identified as contaminants, with those derived from the people involved in the retrieval and washing of the remains present in higher frequencies than those of the anthropologist and genetic researchers. This finding confirms, for the first time, previous hypotheses that teeth samples are most susceptible to contamination at their initial excavation. More worrying, the cloned contaminant sequences exhibit substitutions that can be attributed to DNA damage after the contamination event, and we demonstrate that the level of such damage increases with time: contaminants that are >10 years old have approximately 5 times more damage than those that are recent. Furthermore, we demonstrate that in this data set, the damage rate of the old contaminant sequences is indistinguishable from that of the endogenous DNA sequences. As such, the commonly used argument that miscoding lesions observed among cloned aDNA sequences can be used to support data authenticity is misleading in scenarios where the presence of old contaminant sequences is possible. We argue therefore that the typing of those involved in the manipulation of the ancient human specimens is critical in order to ensure that generated results are accurate.     

Gene flow on ice: the role of sea ice and whaling in shaping Holarctic genetic diversity and population differentiation in bowhead whales (Balaena mysticetus)

Sea ice is believed to be a major factor shaping gene flow for polar marine organisms, but it remains unclear to what extent it represents a true barrier to dispersal for arctic cetaceans. Bowhead whales are highly adapted to polar sea ice and were targeted by commercial whalers throughout Arctic and subarctic seas for at least four centuries, resulting in severe reductions in most areas. Both changing ice conditions and reductions due to whaling may have affected geographic distribution and genetic diversity throughout their range, but little is known about range‐wide genetic structure or whether it differed in the past. This study represents the first examination of genetic diversity and differentiation across all five putative stocks, including Baffin Bay‐Davis Strait, Hudson Bay‐Foxe Basin, Bering‐Beaufort‐Chukchi, Okhotsk, and Spitsbergen. We also utilized ancient specimens from Prince Regent Inlet (PRI) in the Canadian Arctic and compared them with modern stocks. Results from analysis of molecular variance and demographic simulations are consistent with recent and high gene flow between Atlantic and Pacific stocks in the recent past. Significant genetic differences between ancient and modern populations suggest PRI harbored unique maternal lineages in the past that have been recently lost, possibly due to loss of habitat during the Little Ice Age and/or whaling. Unexpectedly, samples from this location show a closer genetic relationship with modern Pacific stocks than Atlantic, supporting high gene flow between the central Canadian Arctic and Beaufort Sea over the past millennium despite extremely heavy ice cover over much of this period.     

A cost‐effective high‐throughput metabarcoding approach powerful enough to genotype ~44 000 year‐old rodent remains from Northern Africa

We present a cost‐effective metabarcoding approach, aMPlex Torrent, which relies on an improved multiplex PCR adapted to highly degraded DNA, combining barcoding and next‐generation sequencing to simultaneously analyse many heterogeneous samples. We demonstrate the strength of these improvements by generating a phylochronology through the genotyping of ancient rodent remains from a Moroccan cave whose stratigraphy covers the last 120 000 years. Rodents are important for epidemiology, agronomy and ecological investigations and can act as bioindicators for human‐ and/or climate‐induced environmental changes. Efficient and reliable genotyping of ancient rodent remains has the potential to deliver valuable phylogenetic and paleoecological information. The analysis of multiple ancient skeletal remains of very small size with poor DNA preservation, however, requires a sensitive high‐throughput method to generate sufficient data. We show this approach to be particularly adapted at accessing this otherwise difficult taxonomic and genetic resource. As a highly scalable, lower cost and less labour‐intensive alternative to targeted sequence capture approaches, we propose the aMPlex Torrent strategy to be a useful tool for the genetic analysis of multiple degraded samples in studies involving ecology, archaeology, conservation and evolutionary biology.     

After the deluge: mitochondrial DNA indicates Miocene radiation and Pliocene adaptation of tree and giant weta (Orthoptera: Anostostomatidae)

Aim New Zealand broke away from the margins of Gondwana c. 75 Ma. Since then, New Zealand taxa derived from the Gondwanan biota are thought to have been exposed first to a subtropical climate on a low lying terrain, then severe land reduction during the Oligocene marine transgression, followed by much cooler climates of the Pliocene and Pleistocene, at which time mountain ranges emerged. The biological consequence of New Zealand's geological and climatic history is not well understood, in particular the extent to which the Oligocene acted as a biological bottleneck remains unresolved. Methods We used mitochondrial cytochrome oxidase I and 12S DNA sequences to examine the extent of diversity and inferred timing of speciation of New Zealand weta (Anostostomatidae), a group of Orthoptera with a Gondwanan distribution generally thought to be ancient inhabitants of New Zealand. Main conclusions We hypothesize that at least three distinct groups of weta survived the Oligocene marine transgression and radiated subsequently. Speciation followed during the Miocene and radiation into new habitats occurred during the Pliocene when mountain building created novel environments. Patterns of genetic diversity within species reflect, in some instances, geographical subdivision in the Pliocene, and in other cases, Pleistocene range changes resulting from climate change.     

Southward Pleistocene migration of Douglas-fir into Mexico: phylogeography, ecological niche modeling, and conservation of 'rear edge' populations

? Poleward Pleistocene plant migration has been an important process structuring modern temperate and boreal plant communities, but the contribution of equatorward migration remains poorly understood. Paleobotanical evidence suggests Miocene or Pleistocene origin for temperate 'sky island' plant taxa in Mexico. These 'rear edge' populations situated in a biodiversity hotspot may be an important reserve of genetic diversity in changing climates. ? We used mtDNA sequences, cpDNA sequences and chloroplast microsatellites to test hypotheses of Miocene vs Pleistocene colonization of temperate Douglas-fir in Mexico, explore geographic patterns of molecular variation in relation to Pleistocene climate history using ecological niche models, and assess the taxonomic and conservation implications. ? We found strong evidence for Pleistocene divergence of Douglas-fir in Mexico (958 thousand yr before present (ka) with the 90% highest posterior density interval ranging from 1.6 million yr before present (Ma) to 491 ka), consistent with the southward Pleistocene migration hypothesis. Genetic diversity was high and strongly partitioned among populations. Spatial patterns of molecular variation and ecological niche models suggest a complex late Pleistocene history involving periods of isolation and expansion along mountain corridors. ? These results highlight the importance of southward Pleistocene migration in establishing modern high-diversity plant communities and provide critical insights into proposals to conserve the unique biodiversity of Mexican Douglas-fir and associated taxa.     

Keeping pace with fast climate change: can arctic life count on evolution?

Adaptations to the cold and to short growing seasons characterizearctic life, but climate in the Arctic is warming at an unprecedentedrate. Will plant and animal populations of the Arctic be ableto cope with these drastic changes in environmental conditions?Here we explore the potential contribution of evolution by naturalselection to the current response of populations to climatechange. We focus on the spring phenology of populations becauseit is highly responsive to climate change and easy to documentacross a wide range of species. We show that evolution can befast and can occur at the time scale of a few decades. We presentan example of reproductive phenological change associated withclimate change (North American red squirrels in the Yukon),where a detailed analysis of quantitative genetic parametersdemonstrates contemporary evolution. We answer a series of frequentlyasked questions that should help biologists less familiar withevolutionary theory and quantitative genetic methods to thinkabout the role of evolution in current responses of ecologicalsystems to climate change. Our conclusion is that evolutionby natural selection is a pertinent force to consider even atthe time scale of contemporary climate changes. However, allspecies may not be equal in their capacity to benefit from contemporaryevolution.     

Using ancient DNA and coalescent-based methods to infer extinction

DNA sequences extracted from preserved remains can add considerable resolution to inference of past population dynamics. For example, coalescent-based methods have been used to correlate declines in some arctic megafauna populations with habitat fragmentation during the last ice age. These methods, however, often fail to detect population declines preceding extinction, most likely owing to a combination of sparse sampling, uninformative genetic markers, and models that cannot account for the increasingly structured nature of populations as habitats decline. As ancient DNA research expands to include full-genome analyses, these data will provide greater resolution of the genomic consequences of environmental change and the genetic signatures of extinction.     

New data on the evolutionary history of the European bison (Bison bonasus) based on subfossil remains from Southeastern Europe

The origin and evolutionary history of the European bison Bison bonasus (wisent) have become clearer after several morphological, genomic, and paleogenomic studies in the last few years, but these paleogenomic studies have raised new questions about the evolution of the species. Here, we present additional information about the population diversity of the species based on the analysis of new subfossil Holocene remains from the Balkan Peninsula. Seven ancient samples excavated from caves in Western Stara Planina in Bulgaria were investigated by mitochondrial D‐loop (HVR1) sequence analysis. The samples were dated to 3,800 years BP by radiocarbon analysis. Additionally, a phylogenetic analysis was performed to investigate the genetic relationship among the investigated samples and all mitochondrial DNA sequences from the genus Bison available in GenBank. The results clustered with the sequences from the extinct Holocene South‐Eastern (Balkan) wisent to the fossil Alpine population from France, Austria, and Switzerland, but not with those from the recent Central European (North Sea) one and the now extinct Caucasian population.In conclusion, these data indicate that the Balkan wisent that existed in historical time represented a relict and probably an isolated population of the Late Pleistocene‐Holocene South‐Western mountainous population of the wisent.     

Multiple receptor-like kinase cDNAs from liverwort Marchantia polymorpha and two charophycean green algae, Closterium ehrenbergii and Nitella axillaris: Extensive gene duplications and gene shufflings in the early evolution of streptophytes

Plant receptor-like kinases (RLKs) comprise a large family with more than several hundred members in vascular plants. The RLK family is thought to have diverged specifically in the plant kingdom, and no family member has been identified in other lineages except for animals and Plasmodium, both of which have RLK related families of small size. To know the time of divergence of RLK family members by gene duplications and domain shufflings, comprehensive isolations of RLK cDNAs were performed from a nonvascular plant, liverwort Marchantia polymorpha and two charophycean green algae, Closterium ehrenbergii, and Nitella axillaris, thought to be the closest relatives to land plants. We obtained twenty-nine, fourteen, and thirteen RLK related cDNAs from M. polymorpha, C. ehrenbergii, and N. axillaris, respectively. The amino acid sequences of these RLKs were compared with those of vascular plants, and phylogenetic trees were inferred by GAMT, a genetic algorithm-based maximum likelihood (ML) method that outputs multiple trees, together with best one. The inferred ML trees revealed ancient gene duplications generating subfamilies with different domain organizations, which occurred extensively at least before the divergence of vascular and nonvascular plants. Rather it remains possible that the extensive gene duplications occurred during the early evolution of streptophytes. Multicellular-specific somatic embryogenesis receptor kinase (SERK) involved in somatic embryogenesis was found in a unicellular alga C. ehrenbergii, suggesting the evolution of SERK by gene recruitment of a unicellular gene.     

Genetic turnovers and northern survival during the last glacial maximum in European brown bears

The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid‐Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter‐specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.     

Ancient DNA from pollen: a genetic record of population history in Scots pine

Assessments of plant population dynamics in space and time have depended on dated records of fossil pollen synthesized on a subcontinental scale. Genetic analyses of extant populations have revealed spatial relationships that are indicative of past spatial dynamics, but lack an explicit timescale. Synthesis of these data requires genetic analyses from abundant dated fossil material, and this has hitherto been lacking. Fossil pollen is the most abundant material with which to fill this data gap. Here we report genetic analyses of fossil pollen retrieved from Holtjärnen postglacial lake sediment in Sweden and show that plastid DNA is recoverable from Scots Pine and Norway spruce pollen grains that are 100 and 10 000 years old. By sequencing clones from two short plastid PCR products and by using multiple controls we show that the ancient sequences were endogenous to the fossil grains. Comparison of ancient sequences and those obtained from an extant population of Scots pine establishes the first genetic link between extant and fossil samples in this species, providing genetic continuity through time. The finding of one common haplotype present in modern, 100-year old and 10 000-year old samples suggests that it may have persisted near Holtjärnen throughout the postglacial period. This retrieval of ancient DNA from pollen has major implications for plant palaeoecology in conifer species by allowing direct estimates of population dynamics in space and time.     

Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe

After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human‐induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present‐day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000 years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting‐associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction.     

Determination of genetic relatedness from low‐coverage human genome sequences using pedigree simulations

We develop and evaluate methods for inferring relatedness among individuals from low‐coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present‐day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present‐day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present‐day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available.     

Pre-adaptation of Arctic Plants to Climate Change*

Re-appraisal of high latitude ice cover during the Weichselian and the recent discovery of pre-Holocene plant communities in Novaya Zemlya and Northern Norway suggests that the contemporary Arctic flora may have had a longer time span in its occupation of high latitude sites than has hitherto been recognised. The present-day Arctic flora in some regions may therefore have derived at least some of its genetic inheritance from populations that survived in ice-free refugia in the high Arctic polar deserts during the latter stages of the Weichselian glaciation. Increasing evidence for sudden changes in climate at high latitudes in the past, suggests that Arctic vegetation would have been subjected to rapid climatic warming if it had maintained a presence in these regions during the late Weichselian. A review of what is known about plant survival in the high Arctic since pre-Holocene times, coupled with an examination of some of the physiological properties of modern populations in these regions is presented in an attempt to ascertain if high Arctic plants possess mechanisms which facilitate their capacity to respond either phenotypically or physiologically to climatic change.     

Local adaptation,genetic divergence,and experimental selection in a foundation grass across the US Great Plains’ climate gradient

Many prior studies have uncovered evidence for local adaptation using reciprocal transplant experiments. However, these studies are rarely conducted for a long enough time to observe succession and competitive dynamics in a community context, limiting inferences for long‐lived species. Furthermore, the genetic basis of local adaptation and genetic associations with climate has rarely been identified. Here, we report on a long‐term (6‐year) experiment conducted under natural conditions focused on Andropogon gerardii, the dominant grass of the North American Great Plains tallgrass ecosystem. We focus on this foundation grass that comprises 80% of tallgrass prairie biomass and is widely used in 20,000 km² of restoration. Specifically, we asked the following questions: (a) Whether ecotypes are locally adapted to regional climate in realistic ecological communities. (b) Does adaptive genetic variation underpin divergent phenotypes across the climate gradient? (c) Is there evidence of local adaptation if the plants are exposed to competition among ecotypes in mixed ecotype plots? Finally, (d) are local adaptation and genetic divergence related to climate? Reciprocal gardens were planted with 3 regional ecotypes (originating from dry, mesic, wet climate sources) of Andropogon gerardii across a precipitation gradient (500–1,200 mm/year) in the US Great Plains. We demonstrate local adaptation and differentiation of ecotypes in wet and dry environments. Surprisingly, the apparent generalist mesic ecotype performed comparably under all rainfall conditions. Ecotype performance was underpinned by differences in neutral diversity and candidate genes corroborating strong differences among ecotypes. Ecotype differentiation was related to climate, primarily rainfall. Without long‐term studies, wrong conclusions would have been reached based on the first two years. Further, restoring prairies with climate‐matched ecotypes is critical to future ecology, conservation, and sustainability under climate change.     

陕北横山杨界沙遗址动物遗存研究

杨界沙遗址位于陕西榆林市横山县雷龙湾乡沙峁村张油坊组, 2010年发掘时出土了大量的动物遗存, 时代为仰韶晚期。按照出土单位对所有的动物骨骼进行了科学的收集以及分类、测量和鉴定。通过系统的分类和研究表明至少代表3纲7目10科11个属种, 包括蚌类、鸟类、环颈雉、刺猬、褐家鼠、中华鼢鼠、甘肃鼢鼠、草兔、黄鼬、狗、猪、鹅喉羚、绵羊。根据对出土动物骨骼的分析结果表明: 遗址周围的自然景观以草原为主, 草原上有草兔、绵羊等食草动物, 不远处有一定面积沙漠, 其间有鹅喉羚出没。草原和沙漠间分布着一定面积的水域, 其间有蚌类出现。家养动物猪的肉量比例占到了整个食用动物群的87.9%, 除了饲养家畜, 捕猎野生动物也是当时人们的肉食来源之一。     

Plant Remains from an Archaeological Site as Indicators of Vegetation and Agricultural Practice Between (3320±400) and (2080±80) yr BP in Gangetic West Bengal, India

Diverse plant remains recovered from an archaeological site of Chalcolithic-Early Historic age in the Bhairabdanga area of Pakhanna (latitude 23°25′N, longitude 87°23′E), situated on the west bank of the Damodar river, Bankura district, West Bengal, India, include food grains, wood charcoals, and palynomorphs. Radiocarbon dating of the recovered biological remains reveal the age of the site as (3320±400) to (2080±80) yr BP. The food grains were identified as Oryza sativa L. and Vigna mungo L, and seeds of Brassica cf.campestris L. were also found; these indicate the agricultural practice and food habits of the ancient people living at Pakhanna from the Chalcolithic to the Early Historic period. Sediments including plant remains have been broadly divided into two zones, considering archaeological findings and radiocarbon dating. Analysis of the plant remains (i.e. wood charcoals and palynomorphs) in addition to cultivated food grains has revealed that a rich vegetation cover existed in this area, with a prevailing tropical and humid climate,comprising the timber-yielding plants Shorea sp., Terminalia sp., and Tamarindus sp., with undergrowths of diverse shrubs and herbs during the Chalcolithic period (zone Ⅰ) dated (3320±400) yr BP. Comparatively poorer representation and frequency of plant remains indicate a drier climate during the Early Historic period (zone Ⅱ) dated as (2110±340) to (2080±80) yr BP. Comparisons of the archaeobotanical data recovered from the Chalcolithic and Early Historic period and also a principle components analysis indicate a change in the climate of the area from tropical and humid at (3 320 ± 400) yr BP to tropical and drier conditions at (2110±340) to (2080±80) yr BP. The present-day tropical, dry deciduous vegetation of the area suggests that climate change has occurred in the area since the contemporaneous past. The plant remains database has been utilized to reconstruct the settlement pattern of the community living in the site between (3320±400) and (2080±80) yr BP. The community settled near the riverbank, practicing cultivation.     

Climate oscillations and species interactions: large‐scale congruence but regional differences in the phylogeographic structures of an alpine plant and its monophagous insect

Aim To predict the fate of alpine interactions involving specialized species, using a monophagous beetle and its host plant as a case study. Location The Alps. Methods We investigated genetic structuring of the herbivorous beetle Oreina gloriosa and its specific host‐plant Peucedanum ostruthium. We used genome fingerprinting (in the insect and the plant) and sequence data (in the insect) to compare the distribution of the main gene pools in the two associated species and to estimate divergence time in the insect, a proxy for the temporal origin of the interaction. We quantified the similarity in spatial genetic structures by performing a Procrustes analysis, a tool from shape theory. Finally, we simulated recolonization of an empty space analogous to the deglaciated Alps just after ice retreat by two lineages from two species showing unbalanced dependence, to examine how timing of the recolonization process, as well as dispersal capacities of associated species, could explain the observed pattern. Results Contrasting with expectations based on their asymmetrical dependence, patterns in the beetle and plant were congruent at a large scale. Exceptions occurred at a regional scale in areas of admixture, matching known suture zones in Alpine plants. Simulations using a lattice‐based model suggested these empirical patterns arose during or soon after recolonization, long after the estimated origin of the interaction c. 0.5 million years ago. Main conclusions Species‐specific interactions are scarce in alpine habitats because glacial cycles have limited the opportunities for co‐evolution. Their fate, however, remains uncertain under climate change. Here we show that whereas most dispersal routes are paralleled at a large scale, regional incongruence implies that the destinies of the species might differ under changing climate. This may be a consequence of the host dependence of the beetle, which locally limits the establishment of dispersing insects.     

Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity

The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second–nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth–nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis.