Abstract Prior to the formation of the North Sea during the mid-Holocene, North-Western Europe was connected through the Doggerland landmass. Whilst it has been known for the past century that forests grew in Doggerland, it has not been clear how this environment compares to the surrounding European areas. Here, we reconstruct the palaeoecology of a river system from the Late Pleistocene to the late Holocene using sedimentary ancient DNA (sedaDNA) from 252 sediment samples from 36 cores spanning the length of the river system and headwater area. We determined that in low kinetic energy environments 95-98% of sedaDNA originates from local deposition and 2-5% is associated with influxed sediments, enabling the identification of secure deposits. High energy environments are insecure with 15-70% of sedaDNA associated with reworked and influxed sediment. Secure sediments reveal the presence of several tree species such as Alnus, Quercus, Ulmus and Corylus over 16000 years ago, and thermal indicator tree species like Tilia several thousand years earlier than has been recorded for surrounding European areas. In this area we also detect the presence of Pterocarya, previously unobserved since the Hoxnian. These observations are consistent with colonization from glacial refugia closer than the classic southern Europe refugia.

Assigning metagenomic reads to taxa presents significant challenges. Existing approaches address some issues, but are mostly limited to metabarcoding or optimized for microbial data. We present PIA (Phylogenetic Intersection Analysis): a taxonomic binner that works from standard BLAST output while mitigating key effects of incomplete databases. Benchmarking against MEGAN using sedaDNA suggests that, while PIA is less sensitive, it can be more accurate. We use known sequences to estimate the accuracy of PIA at up to 96% when the real organism is not represented in the database. For ancient DNA, where taxa of interest are frequently over-represented domesticates or absent, poorly-known organisms, more accurate assignment is critical, even at the expense of sensitivity. PIA offers an approach to objectively filter out false positive hits without the need to manually remove taxa and so make presuppositions about past environments and their palaeoecologies.

AbstractTo meet their demand for food, Eurasian pygmy shrews (Sorex minutus) require large territories, normally in fields, woodlands, and meadows. Their high metabolism and food requirement often leads to high mortality during winter. However, evidence of shrews in the roof voids of residential buildings has recently been observed, contrary to ecological expectations. Here, five faecal samples collected from different locations were studied by metagenomic analysis to gain information about the shrew’s diets and environments. Two of the samples were collected from novel indoor locations, while the other three were from outdoors in ‘traditional’ habitats. Distinct differences were observed between the diets of the two populations, suggesting a commensal niche expansion has occurred inS. minutus.We found thatS. minutusexploit man-made spaces for foraging, potentially at the cost of a greater parasite burden.

Doggerland was a landmass occupying an area currently covered by the North Sea until marine inundation took place during the mid-Holocene, ultimately separating the British landmass from the rest of Europe. The Storegga Event, which triggered a tsunami reflected in sediment deposits in the northern North Sea, northeast coastlines of the British Isles and across the North Atlantic, was a major event during this transgressive phase. The spatial extent of the Storegga tsunami however remains unconfirmed as, to date, no direct evidence for the event has been recovered from the southern North Sea. We present evidence of a tsunami deposit in the southern North Sea at the head of a palaeo-river system that has been identified using seismic survey. The evidence, based on lithostratigraphy, geochemical signatures, macro and microfossils and sedimentary ancient DNA (sedaDNA), supported by optical stimulated luminescence (OSL) and radiocarbon dating, suggests that these deposits were a result of the tsunami. Seismic identification of this stratum and analysis of adjacent cores showed diminished traces of the tsunami which was largely removed by subsequent erosional processes. Our results confirm previous modelling of the impact of the tsunami within this area of the southern North Sea, and also indicate that these effects were temporary, localized, and mitigated by the dense woodland and topography of the area. We conclude that clear physical remnants of the wave in these areas are likely to be restricted to now buried, palaeo-inland basins and incised river valley systems.

Bats are primary consumers of nocturnal insects, disperse nutrients across landscapes, and are excellent bioindicators of an ecosystem’s health, however four of the seventeen Great British species are listed as declining. In this study we aim to investigate the link between bat guano morphology and diet, specifically looking at the ability to predict 1) species, 2) dietary guild, and 3) bat size, using guano morphology alone. Guano from 16 bat species sampled from across Great Britain were analysed to determine various morphological metrics. These data were coupled with diet data obtained by an extensive literature review. It was found that guano morphology overlapped too much to make predictions on the species of bat which deposited the guano, however, in some cases, it could be used to indicate the dietary guild to which the bat belonged. In general, guano morphology seems more correlated to diet than species. This enables the identification of the most important prey taxa within a local environment; a crucial step for informing conservation strategies.

To meet their demand for food, Eurasian pygmy shrews () require large territories, normally in fields, woodlands, and meadows. Their high metabolism and food requirement often leads to high mortality during winter. However, evidence of shrews in the roof voids of residential buildings has recently been observed, contrary to ecological expectations. Here, five faecal samples collected from different locations were studied by metagenomic analysis to gain information about the shrew’s diets and environments. Two of the samples were collected from novel indoor locations, while the other three were from outdoors in ‘traditional’ habitats. Distinct differences were observed between the diets of the two populations, suggesting a commensal niche expansion has occurred in We found that exploit man-made spaces for foraging, potentially at the cost of a greater parasite burden.

Bats are primary consumers of nocturnal insects, disperse nutrients across landscapes, and are excellent bioindicators of an ecosystem’s health, however four of the seventeen Great British species are listed as declining. In this study we aim to investigate the link between bat guano morphology and diet, specifically looking at the ability to predict 1) species, 2) dietary guild and 3) bat size, using guano morphology alone. It was found that guano morphology overlapped too much to make predictions on species however, in some cases, it could be used to predict dietary guild or size.

The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated episodes of introgression. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bicolor) from a single locality in Egyptian Nubia. These data indicate no evidence for the effects of a domestication bottleneck, but instead reveal a steady decline in genetic diversity over time coupled with an accumulating mutation load. Dynamic selection pressures acted sequentially to shape architectural and nutritional domestication traits and to facilitate adaptation to the local environment. Later introgression between sorghum races allowed the exchange of adaptive traits and achieved mutual genomic rescue through an ameliorated mutation load. These results reveal a model of domestication in which genomic adaptation and deterioration were not focused on the initial stages of domestication but occurred throughout the history of cultivation.

After domestication in the Near East around 10,000 years ago several founder crops, flax included, spread to European latitudes. On reaching northerly latitudes the architecture of domesticated flax became more suitable to fiber production over oil, with longer stems, smaller seeds and fewer axillary branches. Latitudinal adaptations in crops typically result in changes in flowering time, often involving the PEBP family of genes that also have the potential to influence plant architecture. Two PEBP family genes in the flax genome, LuTFL1 and LuTFL2 , vary in wild and cultivated flax over latitudinal range with cultivated flax receiving LuTFL1 alleles from northerly wild flax populations. Compared to a background of population structure of flaxes over latitude, the LuTFL1 alleles display a level of differentiation that is consistent with selection for an allele III in the north. We demonstrate through heterologous expression in Arabidopsis thaliana that LuTFL1 is a functional homolog of TFL1 in A . thaliana capable of changing both flowering time and plant architecture. We conclude that specialized fiber flax types could have formed as a consequence of a natural adaptation of cultivated flax to higher latitudes.

Domesticated crops show a reduced level of diversity that is commonly attributed to the "domestication bottleneck"; a drastic reduction in the population size associated with subsampling the wild progenitor species and the imposition of selection pressures associated with the domestication syndrome. A prediction of the domestication bottleneck is a sharp decline in genetic diversity early in the domestication process. Surprisingly, archaeological genomes of three major annual crops do not indicate that such a drop in diversity occurred early in the domestication process. In light of this observation, we revisit the general assumption of the domestication bottleneck concept in our current understanding of the evolutionary process of domestication.

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics.

Bats are vital to Great British biodiversity; they are the primary consumers of nocturnal insects, disperse nutrients across landscapes, and are excellent bioindicators of an ecosystem’s health. The diversity of bat species in the UK is thought to be as a result of extensive resource partitioning. There are numerous methods used for studying bat diets, each with benefits and drawbacks. Past research has compared small numbers of species at a time, making inter-species comparisons difficult. Our large repository of bat guano samples, collected from around the UK, has allowed us to study the bat species under one methodological ‘umbrella’. This thesis is divided into 7 chapters. This first chapter gives a broad overview of the project, framing this research and provides an overview of the technologies available, and how their development has enabled environmental research on a scale, which, until recently, would have been unimaginable. The second chapter is a meta-analysis of the literature that pertains to bat diets. These data will be used to inform the design of primers in the barcoding stages of the project. Next is a shotgun metagenomic analysis of a selection of guano samples from across the range of the UK species. This method provides information, not only about diet species, but also about the bat, viral, and bacterial DNA. Analyses of this data show that there are several dietary forms seen between the species. The fourth chapter is a targeted amplicons metagenome study of the mitochondrial COI barcode region from the arthropod species identified in the literature review, and from metagenomic data-set. This provides a greater resolution picture of the diet species present. Analyses of these data use phylogenetic intersection analysis to ensure the robustness of the taxonomic assignments in the face of the patchy databases available. In the fifth chapter, I draw together the data gathered using the different approaches and presented in the previous chapters. I discuss the efficacy of the methods, and assess the role of resource partitioning in bat species co-existence. The sixth section will look at the appropriateness of using guano morphology as a diagnostic of species presence. Finally, in chapter seven, I summarise these data in the wider context of bat ecology, comment on the implications of the research for conservation, and discuss potential directions for the field in the light of this research.

Recently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challenged on the basis of a lack of signal of cytosine deamination relative to three other data sets generated from young samples of herbarium and museum specimens, and a 7,000 year old human skeleton preserved in a cave environment (2). The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 palaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (α,β,γ,ε) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA would be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5’ region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5’ cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3’ end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level.

Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.

The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant–human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively small selective value, punctuated by periods in which changes in one-half of the plant–hominin relationship cause rapid, low-complexity adaptation in the other. A corollary of a single plant–hominin co-evolutionary process is that clues about the initiation of the domestication process may well lie deep within the hominin lineage.

After domestication in the Near East around 10,000 years ago several founder crops spread and adapted to European latitudes. On reaching northerly latitudes the architecture of domesticated flax changed becoming more suitable to fiber production over oil, with longer stems, smaller seeds and fewer axillary branches. Latitudinal adaptations in crops typically result in changes in flowering time, often involving the PEBP family of genes that also have the potential to influence plant architecture. We identify PEBP family genes in the flax genome, describe molecular diversity of two loci, LuTFL1 and LuTFL2 in wild and cultivated flax that vary over latitudinal range, and show that cultivated flax received LuTFL1 alleles from more northerly wild flax populations. Compared to a genomic background of population structure of flaxes over latitude determined using restriction site-associated loci, the LuTFL1 alleles display a level of differentiation that is consistent with selection both for a northern associated allele (III) and against a southern associated allele (I) in the north. We also demonstrate that LuTFL1 alleles are associated with differing flowering time, and through heterologous expression in Arabidopsis thaliana that LuTFL1 is a functional homolog of TFL1 in Arabidopsis thaliana and is capable of changing both flowering time and plant architecture. We conclude that specialized fiber flax types formed as a consequence of a natural adaptation of cultivated flax to higher latitudes.