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 timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.

Peptide-polyurea hybrids: a platform for tunable, thermally-stable, and injectable hydrogels.

Drawing inspiration from natural systems, such as the highly segmented structures found in silk fibroin, is an important strategy when designing strong, yet dynamic biomaterials. Polymer-peptide hybrids aim to incorporate the benefits of hierarchical polypeptide structures into synthetic platforms that are promising materials for hydrogel systems due to aspects such as their biocompatibility and structural tunability. In this work, we demonstrated the utility of poly(ethylene glycol) (PEG) peptide-polyurea hybrids as self-assembled hydrogels. Specifically, poly(ε-carbobenzyloxy-L-lysine)-b-PEG-b-poly(ε-carbobenzyloxy-L-lysine) and poly(ß-benzyl-L-aspartate)-b-PEG-b-poly(ß-benzyl-L-aspartate) triblock copolymers were used as the soft segments in linear peptide-polyurea (PPU) hybrids. We systematically examined the effect of peptide secondary structure and peptide segment length on hydrogelation, microstructure, and rheological properties of our PPU hydrogels. Polymers containing α-helical secondary structures resulted in rapid gelation upon the addition of water, as driven by hierarchical assembly of the peptide segments. Peptide segment length dictated gel strength and resistance to deformation via complex relationships. Simulated injection experiments demonstrated that PPU hydrogels recover their original gel network within 10 s of cessation of high shear. Finally, we showed that PPU hydrogels remain solid-like within the range of 10 to 80 °C; however, a unique softening transition occurs at temperatures corresponding to slight melting of secondary structures. Overall, this bioinspired PPU hybrid platform provides opportunities to design synthetic, bioinspired polymers for hydrogels with tunable microstructure and mechanics for a wide range of thermal and injection-based applications.

Place of alcohol in the 'wellness toolkits' of midlife women in different social classes: A qualitative study in South Australia.

In this article, we explore how women in different social classes had differential access to resources and services to enhance their 'wellness'-resulting in classed roles in alcohol consumption. We analyse data from a qualitative study on alcohol by midlife women in South Australia and employ the analogy of a 'toolkit' in order to understand the structural patterning of 'wellness tools'. Bourdieu's relational model of class guides our exploration of women's inequitable opportunities for wellness. Higher social class women had 'choices' facilitated by bulging wellness toolkits, such as yoga, exercise and healthy eating regimens-alcohol consumption was not essential to promoting 'wellness' and did not have an important place in their toolkits. Middle-class women had less well-stocked toolkits and consumed alcohol in a 'compensation approach' with other wellness tools. Alcohol consumption received positive recognition and was a legitimised form of enjoyment, fun and socialising, which needed counterbalancing with healthy activities. Working-class women had sparse toolkits-other than alcohol-which was a tool for dealing with life's difficulties. Their focus was less on 'promoting wellness' and more on 'managing challenging circumstances'. Our social class-based analysis is nestled within the sociology of consumption and sociological critiques of the wellness industry.

Exploring the potential of citizen science for public health through an alcohol advertising case study.

Citizen science connects academic researchers with the public through combined efforts in scientific inquiry. The importance of involving impacted populations in health research is well established. However, how to achieve meaningful participation and the methodological impact of citizen science needs further examination. We examined the feasibility of using citizen science to understand the impact of alcohol advertising on Australian women through a breast cancer prevention project. Two hundred and eighty-two ('participants') citizen scientists completed demographic and behavioural questions via an online survey. The research participants moved into the role of citizen scientists by completing the data collection tasks of capturing and classifying images of alcohol advertising they saw online. Interrater reliability tests found high levels of agreement between citizen scientists and academic researchers with the classification of alcohol advertising brand (Kappa = 0.964, p < 0.001) and image type (Kappa = 0.936, p < 0.000). The citizen scientists were women aged 18 and over, with 62% between 35 and 55 years old. The majority were from major cities (78%), had attained a bachelor's degree or higher-level education (62%) and were recruited via email or Facebook (86%). The use of citizen science provided methodological gains through the creation of a unique dataset with higher levels of validity than the existing literature, which employed traditional investigator-driven research methodologies. Citizen science enriched the dataset and provided a powerful methodological vehicle to understand an environmental determinant of health. The study illuminates how public participation benefitted the research process, the challenges and the potential for citizen science to improve public health.

'I have a healthy relationship with alcohol': Australian midlife women, alcohol consumption and social class.

Alcohol consumption by Australian women during midlife has been increasing. Health promotion efforts to reduce alcohol consumption in order to reduce alcohol-related disease risk compete with the social contexts and value of alcohol in women's lives. This paper draws on 50 qualitative interviews with midlife women (45-64 years of age) from different social classes living in South Australia in order to gain an understanding of how and why women might justify their relationships with alcohol. Social class shaped and characterized the different types of relationships with alcohol available to women, structuring their logic for consuming alcohol and their ability to consider reducing (or 'breaking up with') alcohol. We identified more agentic relationships with alcohol in the narratives of affluent women. We identified a tendency for less control over alcohol-related decisions in the narratives of women with less privileged life chances, suggesting greater challenges in changing drinking patterns. If classed differences are not attended to in health promotion efforts, this might mitigate the effectiveness of alcohol risk messaging to women.

Ancient proteins resolve the evolutionary history of Darwin's South American ungulates.

No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as 'South American native ungulates'. To Charles Darwin, who first collected their remains, they included perhaps the 'strangest animal[s] ever discovered'. Today, much like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago, or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies) of superorder Laurasiatheria. Morphology-based analyses have proved unconvincing because convergences are pervasive among unrelated ungulate-like placentals. Approaches using ancient DNA have also been unsuccessful, probably because of rapid DNA degradation in semitropical and temperate deposits. Here we apply proteomic analysis to screen bone samples of the Late Quaternary South American native ungulate taxa Toxodon (Notoungulata) and Macrauchenia (Litopterna) for phylogenetically informative protein sequences. For each ungulate, we obtain approximately 90% direct sequence coverage of type I collagen α1- and α2-chains, representing approximately 900 of 1,140 amino-acid residues for each subunit. A phylogeny is estimated from an alignment of these fossil sequences with collagen (I) gene transcripts from available mammalian genomes or mass spectrometrically derived sequence data obtained for this study. The resulting consensus tree agrees well with recent higher-level mammalian phylogenies. Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed, but instead crown Perissodactyla (horses, tapirs, and rhinoceroses). These results are consistent with the origin of at least some South American native ungulates from 'condylarths', a paraphyletic assembly of archaic placentals. With ongoing improvements in instrumentation and analytical procedures, proteomics may produce a revolution in systematics such as that achieved by genomics, but with the possibility of reaching much further back in time.

Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family.

The mammalian evolutionary tree has lost several major clades through recent human-caused extinctions. This process of historical biodiversity loss has particularly affected tropical island regions such as the Caribbean, an area of great evolutionary diversification but poor molecular preservation. The most enigmatic of the recently extinct endemic Caribbean mammals are the Nesophontidae, a family of morphologically plesiomorphic lipotyphlan insectivores with no consensus on their evolutionary affinities, and which constitute the only major recent mammal clade to lack any molecular information on their phylogenetic placement. Here, we use a palaeogenomic approach to place Nesophontidae within the phylogeny of recent Lipotyphla. We recovered the near-complete mitochondrial genome and sequences for 17 nuclear genes from a ∼750-year-old Hispaniolan Nesophontes specimen, and identify a divergence from their closest living relatives, the Solenodontidae, more than 40 million years ago. Nesophontidae is thus an older distinct lineage than many extant mammalian orders, highlighting not only the role of island systems as "museums" of diversity that preserve ancient lineages, but also the major human-caused loss of evolutionary history.

The future of ancient DNA: Technical advances and conceptual shifts.

Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7× coverage (mammoth) in 2008 to more than 50× coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.

Relaxed phylogenetics and the palaeoptera problem: resolving deep ancestral splits in the insect phylogeny.

The order in which the 3 groups of winged insects (the Pterygota) diverged from their common ancestor has important implications for understanding the origin of insect flight. But despite this importance, the split between the Odonata (dragonflies and damselflies), Ephemeroptera (mayflies), and Neoptera (the other winged orders) remains very much unresolved. Indeed, previous studies have obtained strong apparent support for each of the 3 possible branching patterns. Here, we present a systematic reinvestigation of the basal pterygote split. Our results suggest that outgroup choice and limited taxon sampling have been major sources of systematic error, even for data sets with a large number of characters (e.g., in phylogenomic data sets). In particular, a data set of 113 taxa provides consistent support for the Palaeoptera hypothesis (the grouping of Odonata with Ephemeroptera), whereas results from data sets with fewer taxa give inconsistent results and are highly sensitive to minor changes in data and methods. We also focus on recent methods that exploit temporal information using fossil calibrations, combined with additional assumptions about the evolutionary process, and so reduce the influence of outgroup choice. These methods are shown to provide more consistent results, for example, supporting Palaeoptera, even for data sets that previously supported other hypotheses. Together, these results have implications for understanding insect origins and for resolving other problematic splits in the tree of life.

Holarctic genetic structure and range dynamics in the woolly mammoth.

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32-34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20-15 kyr BP, when a severe population size decline occurred.

Lifestyle Interventions through Participatory Research: A Mixed-Methods Systematic Review of Alcohol and Other Breast Cancer Behavioural Risk Factors.

Breast cancer is one of the most frequently diagnosed cancers in women globally. Sex and advancing age represent the dominant risk factors, with strong evidence of alcohol as a modifiable risk factor. The carcinogenic nature of alcohol has been known for over twenty years; however, this has failed to translate into significant behavioural, practice, or policy change. As a result, women have not benefitted from this research and, by extension, have been exposed to unnecessary breast cancer risk. Participatory research presents a solution to research translation in public health through the collaboration of impacted populations with academics in research. This systematic review examines peer-reviewed research studies where participants were involved in the research process and the outcomes related to breast cancer prevention (either alcohol or broader lifestyle modification). Seven of the eight studies reported positive effects, and the collaboration between academic researchers and impacted populations may have supported positive outcomes. Women were receptive and responsive to participatory approaches, and their participation is important to address socially entrenched behaviours such as alcohol consumption. Participatory research presents opportunities for future interventions to improve (or address) modifiable risk factors for breast cancer.

Modern and ancient red fox (Vulpes vulpes) in Europe show an unusual lack of geographical and temporal structuring, and differing responses within the carnivores to historical climatic change.

BACKGROUND: Despite phylogeographical patterns being well characterised in a large number of species, and generalised patterns emerging, the carnivores do not all appear to show consistent trends. While some species tend to fit with standard theoretical phylogeographic expectations (e.g. bears), others show little obvious modern phylogeographic structure (e.g. wolves). In this study we briefly review these studies, and present a new phylogeographical study of the red fox (Vulpes vulpes) throughout Europe, using a combination of ancient DNA sequences obtained from museum specimens, and modern sequences collated from GenBank. We used cytochrome b (250 bp) and the mitochondrial control region (268 bp) to elucidate both current and historical phylogeographical patterning. RESULTS: We found evidence for slight isolation by distance in modern populations, as well as differentiation associated with time, both of which can likely be attributed to random genetic drift. Despite high sequence diversity (11.2% cytochrome b, 16.4% control region), no evidence for spatial structure (from Bayesian trees) is found either in modern samples or ancient samples for either gene, and Bayesian skyline plots suggested little change in the effective population size over the past 40,000 years. CONCLUSIONS: It is probable that the high dispersal ability and adaptability of the red fox has contributed to the lack of observable differentiation, which appears to have remained consistent over tens of thousands of years. Generalised patterns of how animals are thought to have responded to historical climatic change are not necessarily valid for all species, and so understanding the differences between species will be critical for predicting how species will be affected by future climatic change.

A generation time effect on the rate of molecular evolution in invertebrates.

The rate of genome evolution varies significantly between species. Evidence is growing that at least some of this variation is associated with species characteristics, such as body size, diversification rate, or population size. One of the strongest correlates of the rate of molecular evolution in vertebrates is generation time (GT): Species with faster generation turnover tend to have higher rates of molecular evolution, presumably because their genomes are copied more frequently and therefore collect more DNA replication errors per unit time. But the GT effect has never been tested for nonvertebrate animals. Here, we present the first general test of the GT effect in invertebrates, using 15 genes from 143 species spread across the major eumetazoan superphyla (including arthropods, nematodes, molluscs, annelids, platyhelminthes, cnidarians, echinoderms, and urochordates). We find significant evidence that rates of molecular evolution are correlated with GT in invertebrates and that this effect applies consistently across genes and taxonomic groups. Furthermore, the GT effect is evident in nonsynonymous substitutions, whereas theory predicts (and most previous evidence has supported) a relationship only in synonymous changes. We discuss both the practical and theoretical implications of these findings.

COVID-19, Alcohol Consumption and Stockpiling Practises in Midlife Women: Repeat Surveys During Lockdown in Australia and the United Kingdom.

Introduction: This project examined the impact of COVID-19 and associated restrictions on alcohol practises (consumption and stockpiling), and perceptions of health risk among women in midlife (those aged 45-64 years). Methods: We collected online survey data from 2,437 midlife women in the United Kingdom (UK) and Australia in May 2020, recruited using a commercial panel, in the early days of mandated COVID-19 related restrictions in both countries. Participants were surveyed again (N = 1,377) in July 2020, at a time when COVID-19 restrictions were beginning to ease. The surveys included the Alcohol Use Disorder Identification Test-Consumption (AUDIT-C) and questions alcohol stockpiling. Analysis involved a range of univariate and multivariate techniques examining the impact of demographic variables and negative affect on consumption and acquisition outcomes. Results: In both surveys (May and July), UK women scored higher than Australian women on the AUDIT-C, and residence in the UK was found to independently predict stockpiling of alcohol (RR: 1.51; 95% CI: 1.20, 1.91). Developing depression between surveys (RR: 1.53; 95% CI: 1.14, 2.04) and reporting pessimism (RR: 1.42; 95% CI: 1.11, 1.81), and fear/anxiety (RR: 1.33; 95% CI: 1.05, 1.70) at the beginning of the study period also predicted stockpiling by the end of the lockdown. Having a tertiary education was protective for alcohol stockpiling at each time point (RR: 0.69; 95% CI: 0.54, 0.87). Conclusions: COVID-19 was associated with increases in risky alcohol practises that were predicted by negative emotional responses to the pandemic. Anxiety, pessimism and depression predicted stockpiling behaviour in UK and Australian women despite the many demographic and contextual differences between the two cohorts. Given our findings and the findings of others that mental health issues developed or were exacerbated during lockdown and may continue long after that time, urgent action is required to address a potential future pandemic of alcohol-related harms.

Social Class and Changes in Australian Women's Affect and Alcohol Consumption During COVID-19.

Introduction: Before the pandemic, mid-life women in Australia were among the "heaviest" female alcohol consumers, giving rise to myriad preventable health risks. This paper uses an innovative model of social class within a sample of Australian women to describe changes in affective states and alcohol consumption patterns across two time points during COVID-19. Methods: Survey data were collected from Australian mid-life women (45-64 years) at two time points during COVID-19-May 2020 (N = 1,218) and July 2020 (N = 799). We used a multi-dimensional model for measuring social class across three domains-economic capital (income, property and assets), social capital (social contacts and occupational prestige of those known socially), and cultural capital (level of participation in various cultural activities). Latent class analysis allowed comparisons across social classes to changes in affective states and alcohol consumption patterns reported at the two time points using alcohol consumption patterns as measured by the Alcohol Use Disorders Identification Test-Consumption (AUDIT-C) and its component items. Results: Seven social classes were constructed, characterized by variations in access to capital. Affective states during COVID-19 differed according to social class. Comparing between the survey time points, feeling fearful/anxious was higher in those with high economic and cultural capital and moderate social capital ("emerging affluent"). Increased depression was most prominent in the class characterized by the highest volumes of all forms of capital ("established affluent"). The social class characterized by the least capital ("working class") reported increased prevalence of uncertainty, but less so for feeling fearful or anxious, or depressed. Women's alcohol consumption patterns changed across time during the pandemic. The "new middle" class-a group characterized by high social capital (but contacts with low prestige) and minimal economic capital-had increased AUDIT-C scores. Conclusion: Our data shows the pandemic impacted women's negative affective states, but not in uniform ways according to class. It may explain increases in alcohol consumption among women in the emerging affluent group who experienced increased feelings or fear and anxiety during the pandemic. This nuanced understanding of the vulnerabilities of sub-groups of women, in respect to negative affect and alcohol consumption can inform future pandemic policy responses designed to improve mental health and reduce the problematic use of alcohol. Designing pandemic responses segmented for specific audiences is also aided by our multi-dimensional analysis of social class, which uncovers intricate differences in affective states amongst sub-groups of mid-life women.

Diversity and Ecosystem Services of Trichoptera.

The holometabolous insect order Trichoptera (caddisflies) includes more known species than all of the other primarily aquatic orders of insects combined. They are distributed unevenly; with the greatest number and density occurring in the Oriental Biogeographic Region and the smallest in the East Palearctic. Ecosystem services provided by Trichoptera are also very diverse and include their essential roles in food webs, in biological monitoring of water quality, as food for fish and other predators (many of which are of human concern), and as engineers that stabilize gravel bed sediment. They are especially important in capturing and using a wide variety of nutrients in many forms, transforming them for use by other organisms in freshwaters and surrounding riparian areas. The general pattern of evolution for trichopteran families is becoming clearer as more genes from more taxa are sequenced and as morphological characters are becoming understood in greater detail. This increasingly credible phylogeny provides a foundation for interpreting and hypothesizing the functional traits of this diverse order of freshwater organisms and for understanding the richness of the ecological services corresponding with those traits. Our research also is gaining insight into the timing of evolutionary diversification in the order. Correlations for the use of angiosperm plant material as food and case construction material by the earliest ancestors of infraorder Plenitentoria-by at least 175 Ma-may provide insight into the timing of the origin of angiosperms.

First-year success in a nursing baccalaureate plan of study: A descriptive research study.

BACKGROUND: Predicting students' aptitude for post-secondary success remains a widely studied topic. This descriptive study explored demographic variables contributing to success in quantitative courses required by the nursing degree plan. Identification of an "at risk" student profile may inform interventions with which to support attainment of an academic degree. OBJECTIVE: The purpose of this study was to examine the associations between demographic characteristics and successful completion of baccalaureate nursing courses thought to enhance quantitative reasoning skills: first-year math, first-year chemistry, and second-year pathopharmacology nursing. METHODS: This retrospective analysis accessed 4521 academic records of students who took these three courses at a United States university sometime between Fall 2008 and Fall 2015. De-identified student data included course grades, gender, full-time study, income, marital status, first generation, secondary school (also known as high school) location, dual credit, and high school and university grade point averages. Descriptive statistical analysis was conducted to describe the important features of the data. RESULTS: Of the 4521 records, 2556 undergraduates (57%) passed the courses in which they were enrolled. Among successful students, females outnumbered males (66%), ages ranged from 20 to 24 years, 86% were classified as low income, 54% fit the designation of first generation, and 12% earned dual credit (university credit during secondary school). Our data demonstrate a positive relationship between dual credit and success, with the strongest correlation (0.62) noted for students in pathopharmacology. CONCLUSION: In the baccalaureate-nursing plan of study, courses thought to enhance students' quantitative reasoning skills remain difficult for some to successfully complete. We conclude that the more successful students tend to be older, have a higher income, and a higher high school grade point average, while those less successful are directly out of high school and have not earned dual credit.

The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla.

BACKGROUND: Molecular clock dates, which place the origin of animal phyla deep in the Precambrian, have been used to reject the hypothesis of a rapid evolutionary radiation of animal phyla supported by the fossil record. One possible explanation of the discrepancy is the potential for fast substitution rates early in the metazoan radiation. However, concerted rate variation, occurring simultaneously in multiple lineages, cannot be detected by "clock tests", and so another way to explore such variation is to look for correlated changes between rates and other biological factors. Here we investigate two possible causes of fast early rates: change in average body size or diversification rate of deep metazoan lineages. RESULTS: For nine genes for phylogenetically independent comparisons between 50 metazoan phyla, orders, and classes, we find a significant correlation between average body size and rate of molecular evolution of mitochondrial genes. The data also indicate that diversification rate may have a positive effect on rates of mitochondrial molecular evolution. CONCLUSION: If average body sizes were significantly smaller in the early history of the Metazoa, and if rates of diversification were much higher, then it is possible that mitochondrial genes have undergone a slow-down in evolutionary rate, which could affect date estimates made from these genes.