Deep History Research Articles

Phylogenomic analysis restructures the ulvophyceae.

Here, we present new transcriptome sequencing data from seven species of Dasycladales (Ulvophyceae) and a phylogenomic analysis of the Chlorophyta with a particular focus on Ulvophyceae. We have focused on a broad selection of green algal groups and carefully selected genes suitable for reconstructing deep eukaryote evolutionary histories. Increasing the taxon sampling of Dasycladales restructures the Ulvophyceae by identifying Dasycladales as closely related to Scotinosphaerales and Oltmannsiellopsidales. Contrary to previous studies, we do not find support for a close relationship between Dasycladales and a group with Cladophorales and Trentepohliales. Instead, the latter group is sister to the remainder of the Ulvophyceae. Furthermore, our analyses show high and consistent statistical support for a sister relationship between Bryopsidales and Chlorophyceae in trees generated with both homogeneous and heterogeneous (heterotachy) evolutionary models. Our study provides a new framework for interpreting the evolutionary history of Ulvophyceae and the evolution of cellular morphologies.

Reframing the History of the Competition Concept: Neoliberalism, Meritocracy, Modernity

AbstractThis paper reframes the concept of competition, arguing that recent tendencies to frame it in the context of neoliberalism are too narrow to grasp its full significance. We need to see how it operates well beyond the capitalist economy, as a social and not just theoretical concept. I contextualise it in a deeper history, going back to the eighteenth century, beginning with an empirical examination of the development of the concept in English language dictionaries and encyclopaedias, using a method of ‘conceptual history’. I show how the concept, its grammatical forms, and characteristic associations have evolved substantially since the eighteenth century. This finding is placed in a broader explanatory context, arguing that it is the combined rise of a set of core institutions of modernity, not just capitalism but also democracy, adversarial law, science, and civil society, that deeply embeds competition in the modern world. The decline of aristocratic and religious authority, and the national subordination of martial power, opened the way for more ‘liberal’ forms of society in which authority is routinely contested through competition, across economy, politics, culture and beliefs. Appreciating this is a necessary step towards truly grappling with the effects of competition on modern life.

Charting the Pacific ca. 1850: Melville, Maury, Marx, and Mormons [Video

Navigating different media such as maps, names, novels, or data charts, media philosophy complicates the question of how oceans become objects or things. And the Pacific’s ontology appears to be particularly slippery: Around 1850, Herman Melville thinks of the Pacific through metaphysical or literary depictions, while Matthew Maury, one of the pioneers of oceanography, conceives of it as a data composite. Karl Marx understands it in terms of space-time compression, and Mormon missionaries reimagine the Pacific theologically as a deep history. Yet, when read alongside each other, one can discover a media theory in oceanography, and an oceanography in literature, and there never seems to be enough time and space to tell the whole story of the Pacific. <br> Video available at: https://vimeo.com/527398349

Prevalence of Venous Thromboembolism Following Acute Spinal Cord Injury in an Urban Inner City Hospital.

Venous thromboembolism (VTE) is known to occur at high rates in patients who suffer spinal cord injury (SCI). Large population studies in the United States have shown a prevalence of approximately 4-5%, with some studies suggesting higher prevalence. While the specific mechanism behind increased VTE incidence in the SCI population is unknown, it is likely tied to immobility and functional decline. Previous studies have also linked social determinants of health to higher VTE prevalence in certain populations. The purpose of this study is to determine the prevalence of VTE after acute SCI in the inner urban city population and to identify factors that place patients at increased VTE risk. Patients who suffered SCI between 2014 and 2019 were identified from one inner city urban hospital. A retrospective chart review was completed to record the development of VTE after SCI. Medical comorbidities, type of thromboprophylaxis used, patient demographics, injury characteristics, and postinjury sequelae were compared between individuals who did and did not develop VTE. A total of 148 patients were included. These patients were from a low socioeconomic demographic when compared with the larger US population. Average household income based on zip code data for included patients was $56 647, $30 315 below the national average. The prevalence of VTE in this patient population was 19.59%. Weight, deep vein thrombosis history, chemoprophylaxis use, mobility impairment postinjury, neurologic level of SCI, malignancy history, and history of smokeless tobacco were associated with VTE (all P < .05). Low molecular weight heparin (LMWH) use was associated with fewer occurrences of VTE (P < .001). Patients from our urban inner city hospital have a higher VTE prevalence after SCI than shown in previous US-based studies. These patients may be at increased risk due to increased numbers of medical comorbidities, social factors, or undiagnosed medical conditions. Thromboprophylaxis with LMWH appears to lower the risk of VTE after SCI. 3. Patients with the previously mentioned risk factors are at increased risk for VTE development during their acute recovery process. These patients should have a much lower screening threshold for VTE evaluation and likely would benefit from more routine screening to prevent complications related to VTE development or progression. Furthermore, these patients should, when medically appropriate, be treated with low molecular weight heparin for VTE prophylaxis as previously recommended by the Consortium for Spinal Cord Medicine.

Temporality, Space, and Networks in Indo-Pacific Environmental Histories

This special issue of Pacific Historical Review, “Crossroads of Indo-Pacific Environmental Histories,” is guest edited by Gregory A. Barton and Brett M. Bennett. The special issue explores how environmental historians can use the concept of the Indo-Pacific to understand both the deep and contemporary histories of regions that are frequently viewed through Indian Ocean world or Pacific Ocean world perspectives. A preface and this introduction provide a theoretical overview, establishing some of the key temporal, spatial, and causal parameters of the Indo-Pacific. The following articles by Timothy P. Barnard, by Ruth Morgan, and by Gregory Barton and Brett Bennett highlight how local and foreign powers have sought to control the Indo-Pacific’s natural resources to shape new economies, ecologies, and polities within the region during the past two centuries. Broadly, the special issue encourages other historians to engage with the Indo-Pacific concept due to its theoretical depth as well as its relevance to contemporary geopolitical affairs.

Open air laboratories: Amazonian home gardens as sites of experimentation, collaboration, and negotiation across time

In this article, we make the case for home gardens to be understood as “open-air” laboratories— sites of experimentation, collaboration, and negotiation both among humans and non-humans. Our examination specifically draws on case studies from Amazonia to highlight the deep history of concentrated human activities in gardens (or garden-like environments) as well as their ongoing importance for contemporary agrobiodiversity management, historical memory, and socio-cultural continuity in the face of modernization and environmental change. We discuss how Amazonian home gardens have evolved over time and how they serve to challenge Euro-American conceptions of gardens. Through an examination of both ethnobotanical and archaeological research, we show that Amazonian home gardens are manifestations of deeply rooted histories of experimentation with the diversity of Amazonian life.

Phylogeny, function and ecology in the deep evolutionary history of the mammalian forelimb.

Mammals are the only living members of the larger clade Synapsida, which has a fossil record spanning 320 Ma. Despite the fact that much of the ecological diversity of mammals has been considered in the light of limb morphology, the ecological comparability of mammals to their fossil forerunners has not been critically assessed. Because of the wide use of limb morphology in testing ecomorphological hypothesis about extinct tetrapods, we sought: (i) to estimate when in synapsid history, modern mammals become analogues for predicting fossil ecologies; (ii) to document examples of ecomorphological convergence; and (iii) to compare the functional solutions of distinct synapsid radiations. We quantitatively compared the forelimb shapes of the multiple fossil synapsid radiations to a broad sample of extant Mammalia representing a variety of divergent locomotor ecologies. Our results indicate that each synapsid radiation explored different areas of morphospace and arrived at functional solutions that reflected their distinctive ancestral morphologies. This work counters the narrative of non-mammalian synapsid forelimb evolution as a linear progression towards more mammalian morphologies. Instead, a disparate array of early-evolving shapes subsequently contracted towards more mammal-like forms.

About Ancestors

ABSTRACT Though regularly studied as different academic domains, Asian and Oceanian studies are deeply intertwined not only through longstanding political, economic, immigrant – and colonial – ties, but by questions about common ancestry. From popular commercial DNA testing to historical studies in linguistics, folklore, archaeology, biological anthropology, and sophisticated genome sequencing, deep histories of Oceanian Islander peoples have long been tied to ‘origin’ traditions and reconstructions of lineages from the Asian mainland, notably through the Austronesian diaspora. From 19th-century linguistic theories and Lapita sites, to 20th-century ABO blood groupings and contemporary mitochondrial and Y-chromosome DNA assays, scholars have proposed at times conflicting interpretations of Oceania’s possible Asian human heritage. These analyses have themselves been consistently challenged by Indigenous genealogical traditions such as Māori whakapapa and Islander assertions of origins based on ancestral and localized narratives decolonized of Western scientific practices.

Genetic diversity of the Sudanese: insights on origin and implications for health.

By virtue of their cultural, linguistic and genetic legacies, many populations from Sudan have deep histories in the region and retain high genetic diversities. Sudan’s location in north east Africa, a unique spot believed to act as a climatic refuge during periods of climate extremes, might have dictated that fate. Among the marked consequences of this diversity is the potential to provide information on the origin and structure of human populations within and outside the continent, as well as migration patterns towards various parts of the African continent, and out of Africa. The diverse Sudanese gene pool further has the potential to inform on genetic adaptations driven by culture and the environment resulting in unique and interesting traits, some of which are yet to be investigated. In addition, these genomes could offer clues to complex issues of causation amidst the challenge of new paradigms in biology underpinned by the genomic revolution.

Polymorphism analysis of candidate risk genes for pressure injuries in older Japanese patients: A cross-sectional study at a long-term care hospital.

Advances in patient care for pressure injuries (PIs) have reduced the prevalence of PIs in Japan, although not in recent years. Several single-nucleotide polymorphisms (SNPs) have been identified in genes potentially associated with PIs. However, individual variance among PI risks require targeted investigations that may lead to the identification of PI susceptibilities or preventive care options that directly influence PI development pathways. This cross-sectional study examined the association between PIs and SNPs in genes related to tissue tolerance in patients in a long-term care hospital in Japan. A total of 178 participants (130 control, 20 with superficial PI history, and 28 with deep PI history) were enrolled in this study of eight SNPs in hypoxia inducible factor 1 subunit alpha (HIF1A), vascular endothelial growth factor C (VEGFC), heat shock protein 90 alpha family class A member 1 (HSP90AA1), myostatin (MSTN), and vitamin D receptor (VDR). The primary outcome was a history of superficial and deep PIs in the last 6 months. SNPs were examined by real-time polymerase chain reaction, followed by multivariate logistic regression analyses of the associations between the SNPs and PI history. The results showed a significant association between VEGFC rs1485766 and the history of superficial PIs (odds ratio=2.95; 95% confidence interval=1.07-8.11; p=0.04). Stratified analysis using the Braden Scale (≤14) indicated a significant association between HIF1A rs11549465 and deep PIs (p=0.04). Our study demonstrated that VEGFC rs1485766 and HIF1A rs11549465 were associated with superficial and deep PI susceptibilities, respectively.

Archaeologies of Austral: Australian Identities from the Pleistocene to the Anthropocene

ABSTRACT Most Australians are unaware of the deep Pleistocene human history of their continent. Coining the phrase “archaeologies of austral” to refer to the deep time histories of a changing southern continent, this article challenges present assumptions about “Australia” and its identity. It considers archaeology’s contribution towards understanding Australian identity, as a form of translation incorporating Indigenous and non-Indigenous knowledges. It starts with the continent’s oldest known rock art painting—fittingly, of a kangaroo—and then broadens its focus to position the familiar shape of Australia as a geofact of the last 6,000 years. Placing the kangaroo painting within its environmental and human contexts shows how rock art functioned as a means to manage social and environmental change by making, maintaining and sometimes changing human–human and human–world relationships. This work reveals ambiguities in archaeological narratives of “deep histories”, such as reifying things, dates and people, which in Indigenous traditions are fluid and omni-temporal. An archaeological perspective may challenge shallower histories of Australia and reveal much longer processes of identity-making that enhance our understanding in the present. It also explores legacies in the present, and how socially engaged archaeological research may continue to be useful in the Anthropocene.

The Deep History of the Scientific Study of Religious Thought and Behaviour

This article provides a brief overview of the literature on transitions in modes of thought in the evolutionary development of our non-human and pre-historic human forebears. I will argue that this evolutionary history can account for the cognitive foundations underlying modern scientific modes of thought-dedicated to achieving 'disinterested' knowledge for its own sake-although not the actual historical emergence of the sciences. Essential to this task is understanding the continuities and discontinuities between human thought and that of our primate ancestors-the transitions in the cognitive capacities required for dealing with the physical environment-and the transformations essential for dealing with the increasing social complexities of our pre-historic human ancestors.

The history of number words in the world's languages—what have we learnt so far?

For over 100 years, researchers from various disciplines have been enthralled and occupied by the study of number words. This article discusses implications for the study of deep history and human evolution that arise from this body of work. Phylogenetic modelling shows that low-limit number words are preserved across thousands of years, a pattern consistently observed in several language families. Cross-linguistic frequencies of use and experimental studies also point to widespread homogeneity in the use of number words. Yet linguistic typology and field documentation reports caution against positing a privileged linguistic category for number words, showing a wealth of variation in how number words are encoded across the world. In contrast with low-limit numbers, the higher numbers are characterized by a rapid and morphologically consistent pattern of expansion, and behave like grammatical phrasal units, following language-internal rules. Taken together, the evidence suggests that numbers are at the cross-roads of language history. For languages that do have productive and consistent number systems, numerals one to five are among the most reliable available linguistic fossils of deep history, defying change yet still bearing the marks of the past, while higher numbers emerge as innovative tools looking to the future, derived using language-internal patterns and created to meet the needs of modern speakers. This article is part of the theme issue 'Reconstructing prehistoric languages'.

Between Glaciers and Fossils: Landscape, Literature and the Anthropocene in Pakistan

Arguing for an expansion of the subject of ecocriticism beyond climate change fiction, this essay examines strategies of representation of vernacular landscapes in contemporary Anglophone South Asian literature from Pakistan and Bangladesh. It suggests that recent writing by Uzma Aslam Khan, Tahmima Anam and Kamila Shamsie recuperates Pakistani landscape from its imbrication within colonial and post 9/11 spatial discourses, enabling a zoecentric re-ordering of regional history, complicating ideas of authenticity, and engaging with deep history in ways that furnish individual affective investments in landscape instead of reiterating the difference-flattening tendency of species-thinking. Finally, it attempts to articulate the geological turn precipitated by the notion of the Anthropocene with frameworks of postcolonial ecocriticism to adapt them to specific contexts in South Asia.

The Ghosts at the Feast: Contested Land, Settlement, and Identity in the Jordanian Bādīya

Abstract This article considers how enactions of hospitality, everyday politics and livelihoods in the largely sedentarised, but still discursively Bedouin villages south-east of Amman continue to be shaped by long, contested and intersecting processes of land settlement, sedentarisation and state encompassment. I combine a specific ethnographic encounter (a village feast and the anxious, tense talk about land that occurred at it) with a reading of history to show how ideas of settlement remain crucial, though contested, for understanding the positionality of former nomadic pastoralists in Jordan. I focus on how Jordan's Bādīya - its arid and sparsely-populated eastern steppe - has been conceived of as a socially, politically and legally different, but encompassed, part of the nation-state. This discourse, I argue, has precedents in deep history and classical Arabic thought, but has taken on a particular form in the postcolonial and developmental state of Jordan.

Why Eurasia? A probe into the origins of global inequalities

The abundance of domesticable mammals in Eurasia facilitated its early transition from hunter–gatherer to agricultural economies, with dramatic consequences for human history. This paper empirically examines the origins of these biogeographical advantages and finds that the extinction of large mammals during the past 100,000 years was a decisive force in the evolution of mammal domestication. In Eurasia’s domestication cradles, humans had sufficient incentives to continually practice herd management as a hunting strategy to prevent the depletion of their vital common resources. These strategies changed some targeted species and made them more receptive to human domination. The absence of these conditions (human incentive and animal receptivity) in other regions resulted in the paucity of domestication. The paper presents the most comprehensive empirical analysis of the origins of animal domestication and the roots of global inequalities to date and unearths a critical channel for the influence of deep history on comparative economic development.

US fathers' reports of bonding, infant temperament and psychosocial stress based on family sleep arrangements.

Background and objectivesEvolutionary-grounded sleep research has been critical to establishing the mutual dependence of breastfeeding and nighttime sleep proximity for mothers and infants. Evolutionary perspectives on cosleeping also often emphasize the emotional motivations for and potential benefits of sleep proximity, including for parent-infant bonding. However, this potential link between infant sleep location and bonding remains understudied for both mothers and fathers. Moreover, in Euro-American contexts bedsharing has been linked to family stress and difficult child temperament, primarily via maternal reports. We know relatively little about whether paternal psychosocial dynamics differ based on family sleep arrangements, despite fathers and other kin often being present in the cosleeping environment across cultures. Here, we aim to help address some of these gaps in knowledge pertaining to fathers and family sleep arrangements.MethodologyDrawing on a sample of Midwestern U.S. fathers (N=195), we collected sociodemographic and survey data to analyze links between infant nighttime sleep location, paternal psychosocial well-being, father-infant bonding, and infant temperament. From fathers’ reports, families were characterized as routinely solitary sleeping, bedsharing, or roomsharing (without bedsharing).ResultsWe found that routinely roomsharing or bedsharing fathers, respectively, reported stronger bonding than solitary sleepers. Bedsharing fathers also reported that their infants had more negative temperaments and also tended to report greater parenting-related stress due to difficulties with their children.ConclusionsThese cross-sectional results help to highlight how a practice with deep phylogenetic and evolutionary history, such as cosleeping, can be variably expressed within communities with the potential for family-dependent benefits or strains.

Genomic insights into the formation of human populations in East Asia.

The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people1,2. We report genome-wide data from 166 East Asians dating to 6000 BCE – 1000 CE and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan plateau are linked by a deeply-splitting lineage likely reflecting a Late Pleistocene coastal migration. We follow Holocene expansions from four regions. First, hunter-gatherers of Mongolia and the Amur River Basin have ancestry shared by Mongolic and Tungusic language speakers but do not carry West Liao River farmer ancestry contradicting theories that their expansion spread these proto-languages. Second, Yellow River Basin farmers at ~3000 BCE likely spread Sino-Tibetan languages as their ancestry dispersed both to Tibet where it forms up ~84% to some groups and to the Central Plain where it contributed ~59–84% to Han Chinese. Third, people from Taiwan ~1300 BCE to 800 CE derived ~75% ancestry from a lineage also common in modern Austronesian, Tai-Kadai and Austroasiatic speakers likely deriving from Yangtze River Valley farmers; ancient Taiwan people also derived ~25% ancestry from a northern lineage related to but different from Yellow River farmers implying an additional north-to-south expansion. Fourth, Yamnaya Steppe pastoralist ancestry arrived in western Mongolia after ~3000 BCE but was displaced by previously established lineages even while it persisted in western China as expected if it spread the ancestor of Tocharian Indo-European languages. Two later gene flows affected western Mongolia: after ~2000 BCE migrants with Yamnaya and European farmer ancestry, and episodic impacts of later groups with ancestry from Turan.

Leaf turgor loss point shapes local and regional distributions of evergreen but not deciduous tropical trees.

Summary The effects of climate change on tropical forests will depend on how diverse tropical tree species respond to drought. Current distributions of evergreen and deciduous tree species across local and regional moisture gradients reflect their ability to tolerate drought stress, and might be explained by functional traits.We measured leaf water potential at turgor loss (i.e. ‘wilting point’; πtlp), wood density (WD) and leaf mass per area (LMA) on 50 of the most abundant tree species in central Panama. We then tested their ability to explain distributions of evergreen and deciduous species within a 50 ha plot on Barro Colorado Island and across a 70 km rainfall gradient spanning the Isthmus of Panama.Among evergreen trees, species with lower πtlp were associated with drier habitats, with πtlp explaining 28% and 32% of habitat association on local and regional scales, respectively, greatly exceeding the predictive power of WD and LMA. In contrast, πtlp did not predict habitat associations among deciduous species.Across spatial scales, πtlp is a useful indicator of habitat preference for tropical tree species that retain their leaves during periods of water stress, and holds the potential to predict vegetation responses to climate change.

Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders.

The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We performed phylogenomic and molecular dating analyses of 2765 ultraconserved element loci from 185 liphistiid taxa. Our analyses show that the crown group of Liphistiidae appeared in the mid-Cretaceous at 102 Ma (95% credibility interval 92-113 Ma), but it was not until the Neogene that much of the diversification within the family occurred in mainland Southeast and East Asia. This diversification was coincident with tectonic events such as the extension of the East Asian continental margin, as well as geological upheavals in Indochina induced by the collision between India and Asia. Our study highlights the important role of major tectonic events in shaping the evolutionary history, present-day diversity, and geographical distribution of mesothele and liphistiid spiders. [biogeography; concatenation; Liphistiidae; molecular dating; summary coalescent; UCEs.].