Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America.

The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.

Retailer experiences with tobacco sales bans: lessons from two early adopter jurisdictions.

BACKGROUND: Beverly Hills and Manhattan Beach, California, are the first two US cities to prohibit the sale of tobacco products, passing ordinances that went into effect on 1 January 2021. We sought to learn about retailers' experiences with these laws 22 months after implementation. METHODS: Brief in-person interviews with owners or managers of businesses that formerly sold tobacco (n=22). RESULTS: Participant experiences varied by type of retailer. Managers at large chain stores reported no problems adapting to the law and little effect on overall sales. Many were largely indifferent to the sales bans. By contrast, most managers or owners of small, independent retailers reported losses of both revenue and customers, and expressed dissatisfaction with the laws. Small retailers in Beverly Hills objected particularly to exemptions that city made allowing hotels and cigar lounges to continue their sales, which they saw as undermining the health rationale for the law. The small geographical area covered by the policies was also a source of frustration, and retailers reported that they had lost business to retailers in nearby cities. The most common advice small retailers had for other retailers was to organise to oppose any similar attempts in their cities. A few retailers were pleased with the law or its perceived effects, including a reduction in litter. CONCLUSION: Planning for tobacco sales ban or retailer reduction policies should include considering impacts on small retailers. Adopting such policies in as wide a geographical area as possible, as well as allowing no exemptions, may help reduce opposition.

Racial differences in legal socialization models across adolescence and emerging adulthood.

OBJECTIVE: White and non-White adolescents report different experiences in the legal system. This disparity impacts their evaluations of, and attitudes toward, legal authorities such that non-White and older adolescents tend to perceive the legal system more negatively. Yet, many researchers assume that the process of legal socialization, which involves internalizing norms and information about the law and the legal system, is universal for all ages and races. HYPOTHESES: We hypothesized that legal socialization models would change over the course of adolescent development and would differ by race. METHOD: We used data from two longitudinal studies to examine racial differences in the integrated legal socialization model in early, middle, and late adolescence. Study 1 included 140 young adolescents (59% White, 41% non-White), and Study 2 included 296 midadolescents (82% White, 18% non-White) followed into late adolescence/emerging adulthood. RESULTS: Study 1 identified differences in the integrated legal socialization model for young White and non-White adolescents. Normative status predicted rule-violating behavior for White participants, whereas no predictors or mediators related to rule-violating behavior for non-White participants. In Study 2, legal and moral reasoning during midadolescence became relevant in the model for both groups. Enforcement status predicted rule-violating behavior for non-White youth, whereas normative status continued to predict rule-violating behavior for White youth. In late adolescence/emerging adulthood, differences in the model shifted toward the relation between reasoning and legal attitudes. CONCLUSIONS: Our findings suggest that legal socialization is a developmental process occurring and changing throughout adolescence and that this developmental process differs for White and non-White youth. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

A genomic history of Aboriginal Australia.

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

An argument for phasing out sales of cigarettes.

The successes of tobacco control in some countries and locales have led to discussions of ending the tobacco epidemic, often called the 'endgame'. In this paper, we recommend articulating the endgame goal as phasing out sales of cigarettes, a goal once called 'unthinkable'. We develop a logic and argumentation for ending cigarette sales intended to move the discussion beyond the shadow of 'prohibition', proposing an approach that appeals to consumer protection standards and suggesting that the effort be led by low-prevalence communities. While phasing out cigarettes will not happen everywhere all at once, and may unfold differently along several lines, we argue that the gradual phase-out approach we propose will reduce the likelihood of the negative consequences often predicted to come with such a policy. To continue permitting widespread sales of the single most deadly consumer product in history is a public health failure that must be addressed.

Leadership Perceptions of Endgame Strategies for Tobacco Control in California.

OBJECTIVE: To explore the perspectives of key stakeholders regarding advancement of the tobacco endgame in California. DESIGN: Interviews and focus groups exploring participants' knowledge of the tobacco endgame concept, their reactions to 4 endgame policy proposals (banning tobacco sales, registering smokers, retailer reduction, and permanently prohibiting tobacco sales to all those born after a certain year ["tobacco-free generation"]), and policy priorities and obstacles. PARTICIPANTS: Interviews with 11 California legislators/legislative staff members, 6 leaders of national tobacco control organizations, and 5 leaders of California-based organizations or California subsidiaries of national organizations. Focus groups (7) with professional and volunteer tobacco control advocates in Northern, Southern, and Central California. RESULTS: Advocates were more familiar with the endgame concept than legislators or legislative staff. All proposed endgame policies received both support and opposition, but smoker registration and banning tobacco sales were the least popular, regarded as too stigmatizing or too extreme. The tobacco-free generation and retailer-reduction policies received the most support. Both were regarded as politically feasible, given their focus on protecting youth or regulating retailers and their gradual approach. Concerns raised about all the proposals included the creation of black markets and the potential for disparate impacts on disadvantaged communities. CONCLUSION: Participants' willingness to support novel tobacco control proposals suggests that they understand the magnitude of the tobacco problem and have some appetite for innovation despite concerns about specific endgame policies. A preference for more gradual approaches suggests that taking incremental steps toward an endgame policy goal may be the most effective strategy.

Visualizing red blood cell sickling and the effects of inhibition of sphingosine kinase 1 using soft X-ray tomography.

Sickle cell disease is a destructive genetic disorder characterized by the formation of fibrils of deoxygenated hemoglobin, leading to the red blood cell (RBC) morphology changes that underlie the clinical manifestations of this disease. Using cryogenic soft X-ray tomography (SXT), we characterized the morphology of sickled RBCs in terms of volume and the number of protrusions per cell. We were able to identify statistically a relationship between the number of protrusions and the volume of the cell, which is known to correlate to the severity of sickling. This structural polymorphism allows for the classification of the stages of the sickling process. Recent studies have shown that elevated sphingosine kinase 1 (Sphk1)-mediated sphingosine 1-phosphate production contributes to sickling. Here, we further demonstrate that compound 5C, an inhibitor of Sphk1, has anti-sickling properties. Additionally, the variation in cellular morphology upon treatment suggests that this drug acts to delay the sickling process. SXT is an effective tool that can be used to identify the morphology of the sickling process and assess the effectiveness of potential therapeutics.

Mitochondrial genetic variation and gout in Maori and Pacific people living in Aotearoa New Zealand.

OBJECTIVE: Mitochondria have an important role in the induction of the NLRP3 inflammasome response central in gout. The objective was to test whether mitochondrial genetic variation and copy number in New Zealand Maori and Pacific (Polynesian) people in Aotearoa New Zealand associate with susceptibility to gout. METHODS: 437 whole mitochondrial genomes from Maori and Pacific people (predominantly men) from Aotearoa New Zealand (327 people with gout, 110 without gout) were sequenced. Mitochondrial DNA copy number variation was determined by assessing relative read depth using data produced from whole genome sequencing (32 cases, 43 controls) and targeted resequencing of urate loci (151 cases, 222 controls). Quantitative PCR was undertaken for replication of copy number findings in an extended sample set of 1159 Maori and Pacific men and women (612 cases, 547 controls). RESULTS: There was relatively little mitochondrial genetic diversity, with around 96% of those sequenced in this study belonging to the B4a1a and derived sublineages. A B haplogroup heteroplasmy in hypervariable region I was found to associate with a higher risk of gout among the mitochondrial sequenced sample set (position 16181: OR=1.57, P=0.001). Increased copies of mitochondrial DNA were found to protect against gout risk with the effect being consistent when using hyperuricaemic controls across each of the three independent sample sets (OR=0.89, P=0.007; OR=0.90, P=0.002; OR=0.76, P=0.03). Paradoxically, an increase of mitochondrial DNA also associated with an increase in gout flare frequency in people with gout in the two larger sample sets used for the copy number analysis (ß=0.003, P=7.1×10-7; ß=0.08, P=1.2×10-4). CONCLUSION: Association of reduced copy number with gout in hyperuricaemia was replicated over three Polynesian sample sets. Our data are consistent with emerging research showing that mitochondria are important for the colocalisation of the NLRP3 and ASC inflammasome subunits, a process essential for the generation of interleukin-1ß in gout.

Analysis of ER-mitochondria contacts using correlative fluorescence microscopy and soft X-ray tomography of mammalian cells.

Mitochondrial fission is important for organelle transport, quality control and apoptosis. Changes to the fission process can result in a wide variety of neurological diseases. In mammals, mitochondrial fission is executed by the GTPase dynamin-related protein 1 (Drp1; encoded by DNM1L), which oligomerizes around mitochondria and constricts the organelle. The mitochondrial outer membrane proteins Mff, MiD49 (encoded by MIEF2) and MiD51 (encoded by MIEF1) are involved in mitochondrial fission by recruiting Drp1 from the cytosol to the organelle surface. In addition, endoplasmic reticulum (ER) tubules have been shown to wrap around and constrict mitochondria before a fission event. Up to now, the presence of MiD49 and MiD51 at ER-mitochondrial division foci has not been established. Here, we combine confocal live-cell imaging with correlative cryogenic fluorescence microscopy and soft x-ray tomography to link MiD49 and MiD51 to the involvement of the ER in mitochondrial fission. We gain further insight into this complex process and characterize the 3D structure of ER-mitochondria contact sites.

Is it time for a tobacco-free military?

Achieving a tobacco-free military requires rethinking current perceptions of service members' tobacco use and unmasking the forces perpetuating those perceptions. Prohibiting tobacco use would be entirely consistent with other military requirements regarding health.

Perspectives of US military commanders on tobacco use and tobacco control policy.

BACKGROUND: Tobacco use among members of the US military service is unacceptably high, resulting in substantial healthcare and personnel costs. Support of military command is critical to the success of tobacco control policies because line commanders are responsible for implementation and enforcement. This study is the first to examine US military line commanders' perspectives about current tobacco control policies and the impact of tobacco on readiness. METHODS: We conducted key-informant interviews with 20 officers at the US Army's Command and General Staff College about military tobacco use and tobacco control policy. RESULTS: Participants identified the long-term impact of tobacco use on military members, but were unaware of proximal effects on health and readiness other than lost productivity due to smoke breaks. Officers also discussed nicotine addiction and the logistics of ensuring that an addicted population had access to tobacco. Regarding policy, most knew about regulations governing smoke-free areas and were open to stronger restrictions, but were unaware of current policies governing prevention, intervention and product sales. CONCLUSIONS: Findings suggest that strong policy that takes advantage of the hierarchical and disciplined nature of the military, supported by senior line and civilian leadership up to and including the secretaries of the services and the Secretary of Defense, will be critical to substantially diminishing tobacco use by military personnel.

"The Policy Dystopia Model": Implications for Health Advocates and Democratic Governance.

In this Perspective on the research article by Ulucanlar and colleagues, Elizabeth Smith and Patricia McDaniel discuss how industry opposition to regulation can undermine the public's overall confidence in government and science.

Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations.

While terrestrial megafaunal extinctions have been well characterized worldwide, our understanding of declines in marine megafauna remains limited. Here, we use ancient DNA analyses of prehistoric (<1450-1650 AD) sea lion specimens from New Zealand's isolated Chatham Islands to assess the demographic impacts of human settlement. These data suggest there was a large population of sea lions, unique to the Chatham Islands, at the time of Polynesian settlement. This distinct mitochondrial lineage became rapidly extinct within 200 years due to overhunting, paralleling the extirpation of a similarly large endemic mainland population. Whole mitogenomic analyses confirm substantial intraspecific diversity among prehistoric lineages. Demographic models suggest that even low harvest rates would likely have driven rapid extinction of these lineages. This study indicates that surviving Phocarctos populations are remnants of a once diverse and widespread sea lion assemblage, highlighting dramatic human impacts on endemic marine biodiversity. Our findings also suggest that Phocarctos bycatch in commercial fisheries may contribute to the ongoing population decline.

Tobacco Pricing in Military Stores: Views of Military Policy Leaders.

INTRODUCTION: Higher tobacco taxes reduce tobacco use. On military installations, cigarettes and other tobacco products are sold tax-free, keeping prices artificially low. Pricing regulations in the military specify that tobacco should be within 5% of the local most competitive price, but prices still average almost 13% lower than those at local Walmarts. METHODS: To gain insight into policy leaders' ideas and positions on military tobacco pricing, we interviewed members of the Department of Defense (DoD) Addictive Substances Misuse Advisory Committee and the Advisory Committee on Tobacco about tobacco pricing policies (n = 12). RESULTS: Participants frequently lacked specific knowledge of details of military pricing policy, and the impact higher prices might have on military tobacco use. Most participants thought tobacco should not be sold at military stores, but many also felt that this policy change was unlikely due to tobacco industry pressure, and DoD reliance on tobacco profits to support Morale, Welfare, and Recreation funds. CONCLUSIONS: Achieving a tobacco-free military will require changing pricing policy, but this study suggests that for effective implementation, military leadership must also understand and articulate more clearly the rationale for doing so. IMPLICATIONS: Previous work has found that adherence to military tobacco pricing policy is inconsistent at best. This study suggests that lack of knowledge about the policy and conflicting pressures resulting from the funding stream tobacco sales represent extend to high level military policy leaders. Without clearer information and direction, these leaders are unlikely to be able to establish and implement better tobacco pricing policy.

The tobacco endgame: a qualitative review and synthesis.

The tobacco endgame concept reorients discussion away from the persistent control of tobacco toward plans for ending the tobacco epidemic, and envisions a tobacco-free future. A variety of policy approaches have been proposed, with many offered prior to the introduction of the unifying term 'endgame'. We conducted a qualitative synthesis of the literature on tobacco control endgames, and drew on media accounts and discussion of analogous ideas for illustrative purposes. We identified proposals focused on the product, user, market/supply or larger institutional structures. Research on public support for these proposals was limited, but suggestive of some public appetite for endgame ideas. Advocates should be encouraged to explore new policy options and consider the goal of a tobacco-free future.

Geographically contrasting biodiversity reductions in a widespread New Zealand seabird.

Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the impacts of human arrival on this taxon. Our analyses show that the southeast South Island (Otago) lineage was formerly widespread across coastal South Island, but experienced dramatic population extinctions, range retraction and lineage loss soon after human arrival. By comparison, the southernmost (Foveaux Strait) lineage has experienced a relatively stable demographic and biogeographic history since human arrival, retaining much of its mitochondrial diversity. Archaeological data suggest that these contrasting demographic histories (retraction vs. stability) reflect differential human impacts in mainland South Island vs. Foveaux Strait, highlighting the importance of testing for temporal and spatial variation in human-driven faunal declines.

"It's not a priority when we're in combat": public health professionals and military tobacco control policy.

Tobacco use is prevalent among service members, but civilian public health groups have not effectively addressed military tobacco control policy issues. We conducted focus groups in 2010 and 2012 with participants from public health and tobacco control organizations regarding their understanding of the military and of tobacco use in that context. Misperceptions were common. Military personnel were believed to be young, from marginalized populations, and motivated to join by lack of other options. Tobacco use was considered integral to military life; participants were sometimes reluctant to endorse stronger tobacco control policies than those applied to civilians, although some believed the military could be a social policy leader. Engaging public health professionals as effective partners in tobacco-free military efforts may require education about and reframing of military service and tobacco control policy.

Complete mitochondrial DNA genome sequences from the first New Zealanders.

The dispersal of modern humans across the globe began ~65,000 y ago when people first left Africa and culminated with the settlement of East Polynesia, which occurred in the last 1,000 y. With the arrival of Polynesian canoes only 750 y ago, Aotearoa/New Zealand became the last major landmass to be permanently settled by humans. We present here complete mitochondrial genome sequences of the likely founding population of Aotearoa/New Zealand recovered from the archaeological site of Wairau Bar. These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia.

Quantitatively imaging chromosomes by correlated cryo-fluorescence and soft x-ray tomographies.

Soft x-ray tomography (SXT) is increasingly being recognized as a valuable method for visualizing and quantifying the ultrastructure of cryopreserved cells. Here, we describe the combination of SXT with cryogenic confocal fluorescence tomography (CFT). This correlative approach allows the incorporation of molecular localization data, with isotropic precision, into high-resolution three-dimensional (3-D) SXT reconstructions of the cell. CFT data are acquired first using a cryogenically adapted confocal light microscope in which the specimen is coupled to a high numerical aperture objective lens by an immersion fluid. The specimen is then cryo-transferred to a soft x-ray microscope (SXM) for SXT data acquisition. Fiducial markers visible in both types of data act as common landmarks, enabling accurate coalignment of the two complementary tomographic reconstructions. We used this method to identify the inactive X chromosome (Xi) in female v-abl transformed thymic lymphoma cells by localizing enhanced green fluorescent protein-labeled macroH2A with CFT. The molecular localization data were used to guide segmentation of Xi in the SXT reconstructions, allowing characterization of the Xi topological arrangement in near-native state cells. Xi was seen to adopt a number of different topologies with no particular arrangement being dominant.

From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes.

BACKGROUND: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users. RESULTS: Here we present an 'A to Z' protocol for obtaining complete human mitochondrial (mtDNA) genomes - from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). CONCLUSIONS: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual 'modules' can be swapped out to suit available resources.