Reconstructing the Deep Population History of Central and South America.

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

The Andes-Amazon-Atlantic pathway: A foundational hydroclimate system for social-ecological system sustainability.

The Amazon River Basin's extraordinary social-ecological system is sustained by various water phases, fluxes, and stores that are interconnected across the tropical Andes mountains, Amazon lowlands, and Atlantic Ocean. This "Andes-Amazon-Atlantic" (AAA) pathway is a complex hydroclimatic system linked by the regional water cycle through atmospheric circulation and continental hydrology. Here, we aim to articulate the AAA hydroclimate pathway as a foundational system for research, management, conservation, and governance of aquatic systems of the Amazon Basin. We identify and describe the AAA pathway as an interdependent, multidirectional, and multiscale hydroclimate system. We then present an assessment of recent (1981 to 2020) changes in the AAA pathway, primarily reflecting an acceleration in the rates of hydrologic fluxes (i.e., water cycle intensification). We discuss how the changing AAA pathway orchestrates and impacts social-ecological systems. We conclude with four recommendations for the sustainability of the AAA pathway in ongoing research, management, conservation, and governance.

Tropical Andean climate variations since the last deglaciation.

Global warming during the Last Glacial Termination was interrupted by millennial-scale cool intervals such as the Younger Dryas and the Antarctic Cold Reversal (ACR). Although these events are well characterized at high latitudes, their impacts at low latitudes are less well known. We present high-resolution temperature and hydroclimate records from the tropical Andes spanning the past ~16,800 y using organic geochemical proxies applied to a sediment core from Laguna Llaviucu, Ecuador. Our hydroclimate record aligns with records from the western Amazon and eastern and central Andes and indicates a dominant long-term influence of changing austral summer insolation on the intensity of the South American Summer Monsoon. Our temperature record indicates a ~4 °C warming during the glacial termination, stable temperatures in the early to mid-Holocene, and slight, gradual warming since ~6,000 y ago. Importantly, we observe a ~1.5 °C cold reversal coincident with the ACR. These data document a temperature change pattern during the deglaciation in the tropical Andes that resembles temperatures at high southern latitudes, which are thought to be controlled by radiative forcing from atmospheric greenhouse gases and changes in ocean heat transport by the Atlantic meridional overturning circulation.

The ephemeral record: The role of opportunistic animal resources in the archaeology of Pampa and Patagonia.

The acquisition of opportunistic animal resources by hunter-gatherers-such as scavenged carcasses-is a well-known subsistence strategy. It is frequently mentioned in the context of the history of early human evolution, but not regularly considered among the strategies utilized by more recent foragers of the Southern Cone of South America. Historical and ethnographic information presented here suggests that the use of opportunistic animal resources was a strategy used under a number of conditions but only partially documented in the archaeological literature. We also present archaeological evidence from four sites-Guardia del Río, Paso Otero 1, Ponsonby, and Myren-in different Pampean and Patagonian settings where relevant guanaco (Lama guanicoe) bone assemblages were recovered. These sites record minimal anthropic involvement, basically cut marks on some guanaco bones accompanied by few stone tools, that we interpret as evidence for access and use of water logged immobilized or recently dead animals. Archaeological evidence for the use of these scavenging strategies is difficult to obtain at large archaeological sites that usually result from multiple occupations, since the distinction between the acquisition of actively pursued versus opportunistic animal resources is not straightforward. One conclusion from our review is that the best places to find and recognize this evidence are archaeological sites resulting from ephemeral occupations. The inclusion of these sites gives us access to crucial and rarely documented evidence for the long-term survival of hunter-gatherers.

Comparative genomics uncovers the evolutionary history, demography, and molecular adaptations of South American canids.

The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary history remain unknown. Here, we analyzed 31 whole genomes encompassing all extant SA canid species to assess phylogenetic relationships, interspecific hybridization, historical demography, current genetic diversity, and the molecular bases of adaptations in the bush dog and maned wolf. We found that SA canids originated from a single ancestor that colonized South America 3.9 to 3.5 Mya, followed by diversification east of the Andes and then a single colonization event and radiation of Lycalopex species west of the Andes. We detected extensive historical gene flow between recently diverged lineages and observed distinct patterns of genomic diversity and demographic history in SA canids, likely induced by past climatic cycles compounded by human-induced population declines. Genome-wide scans of selection showed that disparate limb proportions in the bush dog and maned wolf may derive from mutations in genes regulating chondrocyte proliferation and enlargement. Further, frugivory in the maned wolf may have been enabled by variants in genes associated with energy intake from short-chain fatty acids. In contrast, unique genetic variants detected in the bush dog may underlie interdigital webbing and dental adaptations for hypercarnivory. Our analyses shed light on the evolution of a unique carnivoran radiation and how it was shaped by South American topography and climate change.

Disentangling the last 1,000 years of human-environment interactions along the eastern side of the southern Andes (34-52°S lat.).

Researchers have long debated the degree to which Native American land use altered landscapes in the Americas prior to European colonization. Human-environment interactions in southern South America are inferred from new pollen and charcoal data from Laguna El Sosneado and their comparison with high-resolution paleoenvironmental records and archaeological/ethnohistorical information at other sites along the eastern Andes of southern Argentina and Chile (34-52°S). The records indicate that humans, by altering ignition frequency and the availability of fuels, variously muted or amplified the effects of climate on fire regimes. For example, fire activity at the northern and southern sites was low at times when the climate and vegetation were suitable for burning but lacked an ignition source. Conversely, abundant fires set by humans and infrequent lightning ignitions occurred during periods when warm, dry climate conditions coincided with ample vegetation (i.e., fuel) at midlatitude sites. Prior to European arrival, changes in Native American demography and land use influenced vegetation and fire regimes locally, but human influences were not widely evident until the 16th century, with the introduction of nonnative species (e.g., horses), and then in the late 19th century, as Euro-Americans targeted specific resources to support local and national economies. The complex interactions between past climate variability, human activities, and ecosystem dynamics at the local scale are overlooked by approaches that infer levels of land use simply from population size or that rely on regionally composited data to detect drivers of past environmental change.

Lower Microscopy Sensitivity with Decreasing Malaria Prevalence in the Urban Amazon Region, Brazil, 2018-2021.

Malaria is increasingly diagnosed in urban centers across the Amazon Basin. In this study, we combined repeated prevalence surveys over a 4-year period of a household-based random sample of 2,774 persons with parasite genotyping to investigate the epidemiology of malaria in Mâncio Lima, the main urban transmission hotspot in Amazonian Brazil. We found that most malarial infections were asymptomatic and undetected by point-of-care microscopy. Our findings indicate that as malaria transmission decreases, the detection threshold of microscopy rises, resulting in more missed infections despite similar parasite densities estimated by molecular methods. We identified genetically highly diverse populations of Plasmodium vivax and P. falciparum in the region; occasional shared lineages between urban and rural residents suggest cross-boundary propagation. The prevalence of low-density and asymptomatic infections poses a significant challenge for routine surveillance and the effectiveness of malaria control and elimination strategies in urbanized areas with readily accessible laboratory facilities.

Molecular Epidemiology of Western Equine Encephalitis Virus, South America, 2023-2024.

Western equine encephalitis virus (WEEV) is a mosquitoborne virus that reemerged in December 2023 in Argentina and Uruguay, causing a major outbreak. We investigated the outbreak using epidemiologic, entomological, and genomic analyses, focusing on WEEV circulation near the Argentina‒Uruguay border in Rio Grande do Sul state, Brazil. During November 2023‒April 2024, the outbreak in Argentina and Uruguay resulted in 217 human cases, 12 of which were fatal, and 2,548 equine cases. We determined cases on the basis of laboratory and clinical epidemiologic criteria. We characterized 3 fatal equine cases caused by a novel WEEV lineage identified through a nearly complete coding sequence analysis, which we propose as lineage C. Our findings highlight the importance of continued surveillance and equine vaccination to control future WEEV outbreaks in South America.

Highly Pathogenic Avian Influenza A(H5N1) Viruses from Multispecies Outbreak, Argentina, August 2023.

We report full-genome characterization of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus from an outbreak among sea lions (August 2023) in Argentina and possible spillover to fur seals and terns. Mammalian adaptation mutations in virus isolated from marine mammals and a human in Chile were detected in mammalian and avian hosts.

Integrating perspectives in developing mycorrhizal trait databases: a call for inclusive and collaborative continental efforts.

Global assessments of mycorrhizal symbiosis present large sampling gaps in rich biodiversity regions. Filling these gaps is necessary to build large-scale, unbiased mycorrhizal databases to obtain reliable analyses and prevent misleading generalizations. Underrepresented regions in mycorrhizal research are mainly in Africa, Asia, and South America. Despite the high biodiversity and endemism in these regions, many groups of organisms remain understudied, especially mycorrhizal fungi. In this Viewpoint, we emphasize the importance of inclusive and collaborative continental efforts in integrating perspectives for comprehensive trait database development and propose a conceptual framework that can help build large mycorrhizal databases in underrepresented regions. Based on the four Vs of big data (volume, variety, veracity, and velocity), we identify the main challenges of constructing a large mycorrhizal dataset and propose solutions for each challenge. We share our collaborative methodology, which involves employing open calls and working groups to engage all mycorrhizal researchers in the region to build a South American Mycorrhizal Database. By fostering interdisciplinary collaborations and embracing a continental-scale approach, we can create robust mycorrhizal trait databases that provide valuable insights into the evolution, ecology, and functioning of mycorrhizal associations, reducing the geographical biases that are so common in large-scale ecological studies.

Resource availability and disturbance frequency shape evolution of plant life forms in Neotropical habitats.

Organisms use diverse strategies to thrive in varying habitats. While life history theory partly explains these relationships, the combined impact of resource availability and disturbance frequency on life form strategy evolution has received limited attention. We use Chamaecrista species, a legume plant lineage with a high diversity of plant life forms in the Neotropics, and employ ecological niche modeling and comparative phylogenetic methods to examine the correlated evolution of plant life forms and environmental niches. Chamaephytes and phanerophytes have optima in environments characterized by moderate water and nutrient availability coupled with infrequent fire disturbances. By contrast, annual plants thrive in environments with scarce water and nutrients, alongside frequent fire disturbances. Similarly, geophyte species also show increased resistance to frequent fire disturbances, although they thrive in resource-rich environments. Our findings shed light on the evolution of plant strategies along environmental gradients, highlighting that annuals and geophytes respond differently to high incidences of fire disturbances, with one enduring it as seeds in a resource-limited habitat and the other relying on reserves and root resprouting systems in resource-abundant habitats. Furthermore, it deepens our understanding of how organisms evolve associated with their habitats, emphasizing a constraint posed by low-resource and high-disturbance environments.

Geoclimatic drivers of diversification in the largest arid and semi-arid environment of the Neotropics: Perspectives from phylogeography.

The South American Dry Diagonal, also called the Diagonal of Open Formations, is a large region of seasonally dry vegetation extending from northeastern Brazil to northern Argentina, comprising the Caatinga, Cerrado, and Chaco subregions. A growing body of phylogeography literature has determined that a complex history of climatic changes coupled with more ancient geological events has produced a diverse and endemic-rich Dry Diagonal biota. However, the exact drivers are still under investigation, and their relative strengths and effects are controversial. Pleistocene climatic fluctuations structured lineages via vegetation shifts, refugium formation, and corridors between the Amazon and Atlantic forests. In some taxa, older geological events, such as the reconfiguration of the São Francisco River, uplift of the Central Brazilian Plateau, or the Miocene inundation of the Chaco by marine incursions, were more important. Here, we review the Dry Diagonal phylogeography literature, discussing each hypothesized driver of diversification and assessing degree of support. Few studies statistically test these hypotheses, with most support drawn from associating encountered phylogeographic patterns such as population structure with the timing of ancient geoclimatic events. Across statistical studies, most hypotheses are well supported, with the exception of the Pleistocene Arc Hypothesis. However, taxonomic and regional biases persist, such as a proportional overabundance of herpetofauna studies, and the under-representation of Chaco studies. Overall, both Pleistocene climate change and Neogene geological events shaped the evolution of the Dry Diagonal biota, though the precise effects are regionally and taxonomically varied. We encourage further use of model-based analyses to test evolutionary scenarios, as well as interdisciplinary collaborations to progress the field beyond its current focus on the traditional set of geoclimatic hypotheses.

Diversity and biogeography of South American mud turtles elucidated by multilocus DNA sequencing (Testudines: Kinosternidae).

Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage.

Infection of South American coatis (Nasua nasua) with highly pathogenic avian influenza H5N1 virus displaying mammalian adaptive mutations.

Deadly outbreaks among poultry, wild birds, and carnivorous mammals by the highly pathogenic H5N1 virus of the clade 2.3.4.4b have been reported in South America. The increasing virus incidence in various mammal species poses a severe zoonotic and pandemic threat. In Uruguay, the clade 2.3.4.4b viruses were first detected in February 2023, affecting wild birds and backyard poultry. Three months after the first reported case in Uruguay, the disease affected a population of 23 coatis (Nasua) in an ecological park. Most animals became infected, likely directly or indirectly from wild birds in the park, and experienced sudden death. Five animals from the colony survived, and four of them developed antibodies. The genomes of the H5N1 strains infecting coatis belonged to the B3.2 genotype of the clade 2.3.4.4b. Genomes from coatis were closely associated with those infecting backyard poultry, but transmission likely occurred through wild birds. Notable, two genomes have a 627K substitution in the RNA polymerase PB2 subunit, a hallmark amino acid linked to mammalian adaptation. Our findings support the ability of the avian influenza virus of the 2.3.4.4b clade to infect and transmit among terrestrial mammals with high pathogenicity and undergo rapid adaptive changes. It also highlights the coatis' ability to develop immunity and naturally clear the infection.

Pediatric neurosurgical medulloblastoma outcomes in La Paz, Bolivia: How a Lower Middle-Income Country (LMIC) institution in South America compares to the United States.

BACKGROUND: How pediatric medulloblastoma patients fare in Lower Middle-Income Country (LMICs) in South America is not well understood. Correspondingly, the aim of this study was to summarize the pediatric neurosurgical experience of an institution in La Paz, and compare outcomes to that of a generalized High Income Country (HIC) United States (US) experience. METHODS: A retrospective review of all pediatric neurosurgical medulloblastoma patients at the Children's Hospital of La Paz, Bolivia (Hospital del Niño "Dr. Ovidio Aliaga Uria") between 2014 and 2023 was conducted and compared to a generalized US experience abstracted from the US National Cancer Database (NCDB) and National Inpatient Sample (NIS) databases. Categorical, continuous and survival data were statistically summarized and compared. RESULTS: A total of 24 pediatric medulloblastoma patients underwent neurosurgical treatment at the Hospital del Niño. In this La Paz cohort, there were 15 (63%) males and 9 (38%) females, with a mean age of 5.6 years old at diagnosis. The majority of patients underwent subtotal resection (STR, 79%), while the remaining patients underwent biopsy only. Ten (42%) patients expired during their hospitalization, and mean length of stay overall was 39 days. Only 8 (33%) patients received adjuvant treatment after surgery. Median overall survival from diagnosis in the La Paz cohort was 1.9 months. Compared to the US databases, the La Paz cohort experienced significantly more emergency room admissions for surgery, less gross total resection, more STR, more return to operating room for ventriculoperitoneal shunting, more bacteremia, more tracheostomy procedures, more percutaneous gastrostomy placements, longer lengths of stay, less adjuvant chemotherapy, less radiation therapy, shorter follow-up, and ultimately, significantly shorter overall survival (all P < 0.050). CONCLUSIONS: Pediatric neurosurgical medulloblastoma outcomes at the Children's Hospital of La Paz, Bolivia are significantly inferior to that of a generalized US experience. Future research is required to identify institution- and country-specific initiatives to improve discrepancies between institutions in LMICs in South America compared to HICs.

Early Eocene infructescences from Argentine Patagonia expand the biogeography of Malvoideae.

PREMISE: Fossil infructescences and isolated fruits with characters of Malvoideae, a subfamily of Malvaceae (mallow family), were collected from early Eocene sediments in Chubut, Argentina. The main goals of this research are to describe and place these fossils systematically, and to explore their biogeographical implications. METHODS: Fossils were collected at the Laguna del Hunco site, Huitrera Formation, Chubut, Patagonia, Argentina. They were prepared, photographed, and compared with extant and fossil infructescences and fruits of various families using herbarium material and literature. RESULTS: The infructescences are panicles with alternate arrangement of fruits. They bear the fruits on short pedicels that are subtended by a bract; the fruits display an infracarpelar disk and split to the base into five ovate sections interpreted as mericarps. Each mericarp is characterized by an acute apex and the presence of a longitudinal ridge. The isolated fruits show the same features as those on the infructescences. The fossils share unique features with members of the cosmopolitan family Malvaceae, subfamily Malvoideae. CONCLUSIONS: The fossils have a unique combination of characters that does not conform to any previously described genus, justifying the erection of a new genus and species, Uiher karuen. This new taxon constitutes the first known Malvoideae reproductive fossils of the Southern Hemisphere, expanding the distribution of Malvoideae during the early Eocene.

Orthohantavirus infections in South America: a systematic review and meta-analysis.

Orthohantaviruses are zoonotic pathogens that cause acute and severe syndromes in humans. This review was performed to estimate the occurrence of human orthohantaviruses in South America between 2010 and 2022. A careful evaluation of the eligibility and quality of the articles was carried out after a systematic bibliographic search of four databases. The pooled frequency of human orthohantaviruses was calculated using a random effects model meta-analysis. The heterogeneity of estimates (resulting from the chi2 test and I2 statistics) was investigated by subgroup analysis and meta-regression. 1,962 confirmed cases of orthohantavirus infections were diagnosed among 35,548 individuals from seven South American countries. The general occurrence of orthohantaviruses was estimated to be 4.4% (95% confidence interval: 2.9-6.2%) based on general pooling of human cases from 32 studies. In a subgroup analysis considering the study design and method of diagnosis, the percentages of diagnosed orthohantavirus infections differed substantially (I2 = 97.8%, p = 0.00) among South American countries. Four genetic variants of orthohantavirus have been identified circulating in Argentina, Brazil, Bolivia, Chile, Colombia, and Peru. Although laboratory diagnosis of orthohantaviruses is not performed in many countries in South America, there is evidence that four different orthohantaviruses are circulating in the region. The pooled occurrence of viral infection was approximately 4.0% in more than half of the South American countries. Updated information on the occurrence of human infections is essential for monitoring the territorial spread and determining the frequency of this zoonosis.

Early anthropoid primates: New data and new questions.

Although the evolutionary history of anthropoid primates (monkeys, apes, and humans) appears relatively well-documented, there is limited data available regarding their origins and early evolution. We review and discuss here the earliest records of anthropoid primates from Asia, Africa, and South America. New fossils provide strong support for the Asian origin of anthropoid primates. However, the earliest recorded anthropoids from Africa and South America are still subject to debate, and the early evolution and dispersal of platyrhines to South America remain unclear. Because of the rarity and incomplete nature of many stem anthropoid taxa, establishing the phylogenetic relationships among the earliest anthropoids remains challenging. Nonetheless, by examining evidence from anthropoids and other mammalian groups, we demonstrate that several dispersal events occurred between South Asia and Afro-Arabia during the middle Eocene to the early Oligocene. It is possible that a microplate situated in the middle of the Neotethys Ocean significantly reduced the distance of overseas dispersal.

Genomic characterization of infectious bursal disease virus in Argentina provides evidence of the recent transcontinental spread of Chinese genotype A2dB1b.

The infectious bursal disease virus (IBDV) is a significant pathogen affecting the poultry industry worldwide. Its epidemiological history has been marked by the emergence of strains with different antigenic, pathogenic, and genetic features, some of which have shown notable spread potential. The A2dB1b genotype, also known as novel variant, has become widespread and gained increased relevance in IBDV epidemiology. This genotype was described in China in the 2010s and rapidly spread in Asia and Africa. The present study describes the circulation of the A2dB1b genotype in Argentina. Applying a next-generation sequencing approach, we obtained the complete coding sequence of 18 Argentine viruses. The high level of genomic homogeneity observed amongst these viruses, their monophyletic clustering in both partial and complete segments A and B derived phylogenies, and their close relatedness to some Chinese strains suggest that a unique transcontinental spread event from China to Argentina occurred recently. The apparent success of the A2dB1b genotype spreading throughout Asia, Africa, and South America may partially be due to specific amino acid characteristics. Novel residues in the hypervariable region of VP2 may help A2dB1b IBDVs evade the protection elicited by the applied commercial vaccines. Our findings underscore the importance of continuous characterization of field samples and evaluation of the control measures currently applied to fight against this specific IBDV genotype.

Successful control of Echinococcosis in Argentina and Chile through a One Health approach, including vaccination of the sheep intermediate host.

Cystic echinococcosis control in South American countries requires a comprehensive integrative 'One Health' approach. While insular nations have seen successful in their elimination programmes, South American countries face persistent challenges in hostile environments, with Echinococcus granulosus s.l., posing a significant public health concern. Vaccination of intermediate hosts has demonstrated the efficacy of the EG95 vaccine in reducing transmission rates. For example, since 2009, Rio Negro Province in Argentina has added, with marked success, the EG95 vaccine to the control programme, supplementing dog deworming. The Aysen Region of Chile has also reported encouraging preliminary results in reducing cyst prevalence in vaccinated sheep after 3 years of vaccination. The challenges in aligning control strategies with socio-cultural factors, especially in indigenous communities, underlines the need for context-specific strategies. The Rio Negro programme demonstrated commendable compliance, underlining the importance of community engagement in achieving lasting success. The most promising strategies for effective echinococcosis control involved dog deworming and the routine vaccination of sheep and/or goats, underscoring the importance of sustained implementation until all grazing animals have been replaced. For lasting success, these interventions need to be combined with a robust surveillance system.