Facilitating high throughput collections-based genomics: a comparison of DNA extraction and library building methods.

While DNA barcoding methods are an increasingly important tool in biological conservation, the resource requirements of constructing reference libraries frequently reduce their efficacy. One efficient way of sourcing taxonomically validated DNA for reference libraries is to use museum collections. However, DNA degradation intrinsic to historical museum specimens can, if not addressed in the wet lab, lead to low quality data generation and severely limit scientific output.

The genome sequence of the moss carder bee, (Linnaeus, 1758).

We present a genome assembly from an individual female (the moss carder bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence spans 317.70 megabases.

The genome sequence of the Banded Burying beetle, Zetterstedt, 1824.

We present a genome assembly from a female (Banded Burying beetle; Arthropoda; Insecta; Coleoptera; Silphidae). The genome sequence is 202.3 megabases in span.

A sampling strategy for genome sequencing the British terrestrial arthropod fauna.

The Darwin Tree of Life (DToL) project aims to sequence and assemble high-quality genomes from all eukaryote species in Britain and Ireland, with the first phase of the project concentrating on family-level coverage plus species of particular ecological, biomedical or evolutionary interest. We summarise the processes involved in (1) assessing the UK arthropod fauna and the status of individual species on UK lists; (2) prioritising and collecting species for initial genome sequencing; (3) handling methods to ensure that high-quality genomic DNA is preserved; and (4) compiling standard operating procedures for processing specimens for genome sequencing, identification verification and voucher specimen curation. We briefly explore some lessons learned from the pilot phase of DToL and the impact of the Covid-19 pandemic.

Ancient human DNA recovered from a Palaeolithic pendant.

Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited.

Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data.

Background: The inference of biological relations between individuals is fundamental to understanding past human societies. Caregiving, resource sharing and sexual behaviours are often mediated by biological kinship and yet the identification and interpretation of kin relationships in prehistoric human groups is difficult. In recent years, the advent of archaeogenetic techniques have offered a fresh approach, and when combined with more traditional osteological and interpretive archaeological methods, allows for improved interpretation of the burial practices, cultural behaviours, and societal stratification in ancient societies.

Dual ancestries and ecologies of the Late Glacial Palaeolithic in Britain.

Genetic investigations of Upper Palaeolithic Europe have revealed a complex and transformative history of human population movements and ancestries, with evidence of several instances of genetic change across the European continent in the period following the Last Glacial Maximum (LGM). Concurrent with these genetic shifts, the post-LGM period is characterized by a series of significant climatic changes, population expansions and cultural diversification. Britain lies at the extreme northwest corner of post-LGM expansion and its earliest Late Glacial human occupation remains unclear.

The Anglo-Saxon migration and the formation of the early English gene pool.

The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans-including 278 individuals from England-alongside archaeological data, to infer contemporary population dynamics.

Genomes from a medieval mass burial show Ashkenazi-associated hereditary diseases pre-date the 12th century.

We report genome sequence data from six individuals excavated from the base of a medieval well at a site in Norwich, UK. A revised radiocarbon analysis of the assemblage is consistent with these individuals being part of a historically attested episode of antisemitic violence on 6 February 1190 CE. We find that four of these individuals were closely related and all six have strong genetic affinities with modern Ashkenazi Jews.

Signatures of increasing environmental stress in bumblebee wings over the past century: Insights from museum specimens.

Determining when animal populations have experienced stress in the past is fundamental to understanding how risk factors drive contemporary and future species' responses to environmental change. For insects, quantifying stress and associating it with environmental factors has been challenging due to a paucity of time-series data and because detectable population-level responses can show varying lag effects. One solution is to leverage historic entomological specimens to detect morphological proxies of stress experienced at the time stressors emerged, allowing us to more accurately determine population responses.

FTIR product study of the Cl-initiated oxidation products of CFC replacements: (/)-1,2,3,3,3-pentafluoropropene and hexafluoroisobutylene.

A product study of the reactions of (/)-1,2,3,3,3-pentafluoropropene ((/)-CFCF[double bond, length as m-dash]CHF) and hexafluoroisobutylene ((CF)C[double bond, length as m-dash]CH) initiated by Cl atoms were developed at 298 ± 2 K and atmospheric pressure. The experiments were carried out in a 1080 L quartz-glass environmental chamber coupled FTIR spectroscopy to monitor the reactants and products. The main products observed and their yields were as follows: CFC(O)F (106 ± 9)% with HC(O)F (100 ± 8)% as a co-product for (/)-CFCF[double bond, length as m-dash]CHF, and CFC(O)CF (94 ± 5)% with HC(O)Cl (90 ± 7)% as a co-product for (CF)C[double bond, length as m-dash]CH.

Degradation mechanism of 2-fluoropropene by Cl atoms: experimental and theoretical products distribution studies.

The gas-phase reaction products of 2-fluoropropene (2FP) with Cl atoms have been determined for the first time at 298 K and atmospheric pressure using a 1080 L quartz-glass photoreactor coupled with FTIR spectroscopy to monitor reactants and products. Acetyl fluoride and formyl chloride were observed as the main products with yields of (106 ± 10)% and (100 ± 11)%, respectively. Electronic structure calculations of reactants, intermediates, products and transition states on a detailed mechanism of the reaction were performed by DFT procedures (BMK, M06, M062X/D3), as well as accurate composite methods on both the addition and abstraction reaction channels.

Ancient and historical DNA in conservation policy.

Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even less appreciated is the role that ancient and historical DNA (aDNA and hDNA, respectively) could play in unlocking the temporal dimension of genetic diversity, allowing key conservation issues to be resolved, including setting baselines for intraspecies genetic diversity, estimating changes in effective population size (N, and identifying the genealogical continuity of populations. Here, we discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations.

Large-scale migration into Britain during the Middle to Late Bronze Age.

Present-day people from England and Wales have more ancestry derived from early European farmers (EEF) than did people of the Early Bronze Age. To understand this, here we generated genome-wide data from 793 individuals, increasing data from the Middle to the Late Bronze Age and Iron Age in Britain by 12-fold, and western and central Europe by 3.5-fold.

Preoperative radiographs to predict component malposition in direct anterior approach total hip arthroplasty.

Introduction: There is conflicting evidence as to whether or not patients undergoing total hip arthroplasty (THA) via the direct anterior approach (DAA) have increased risk of component malposition. The aim of this study was to investigate whether specific preoperative radiographic features were predictive of postoperative component malposition in DAA THA.

Patients And Methods: We examined 204 THA operations performed for osteoarthritis via the DAA at a single institution.

Exploring the phylogeography and population dynamics of the giant deer () using Late Quaternary mitogenomes.

Late Quaternary climatic fluctuations in the Northern Hemisphere had drastic effects on large mammal species, leading to the extinction of a substantial number of them. The giant deer () was one of the species that became extinct in the Holocene, around 7660 calendar years before present. In the Late Pleistocene, the species ranged from western Europe to central Asia.

Experimental and theoretical study of the reactivity of a series of epoxides with chlorine atoms at 298 K.

Evaluating the reactivity of epoxides in the gas phase is very important due to their wide distribution in the atmosphere, potential health implications and atmospheric impact. The kinetic rate constants for the oxidation of epoxides have been very little studied until now. From the experimental data obtained in this work has been observed that there is an increase in reactivity towards chlorine atoms as a CH2 group is added to the hydrocarbon chain.

Million-year-old DNA sheds light on the genomic history of mammoths.

Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago.

Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents.

Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.

Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean "island-shrews".

Background: The Caribbean offers a unique opportunity to study evolutionary dynamics in insular mammals. However, the recent extinction of most Caribbean non-volant mammals has obstructed evolutionary studies, and poor DNA preservation associated with tropical environments means that very few ancient DNA sequences are available for extinct vertebrates known from the region's Holocene subfossil record. The endemic Caribbean eulipotyphlan family Nesophontidae ("island-shrews") became extinct ~ 500 years ago, and the taxonomic validity of many Nesophontes species and their wider evolutionary dynamics remain unclear.

Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion.

The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of C and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene.