Quaternary range and demographic expansion of Liolaemus darwinii (Squamata: Liolaemidae) in the Monte Desert of Central Argentina using Bayesian phylogeography and ecological niche modelling

Until recently, most phylogeographic approaches have been unable to distinguís between demographic and range expansion processes, making it difficult to test for the possibility of range expansion without population growth and vice versa. In this study, we applied a Bayesian phylogeographic approach to reconstruct both demographic and range expansion in the lizard Liolaemus darwinii of the Monte Desert in Central Argentina, during the Late Quaternary. Based on analysis of 14 anonymous nuclear loci and the cytochrome b mitochondrial DNA gene, we detected signals of demographic expansion starting at ~55 ka based on Bayesian Skyline and Skyride Plots. In contrast, Bayesian relaxed models of spatial diffusion suggested that range expansion occurred only between ~95 and 55 ka, and more recently, diffusion rates were very low during demographic expansion. The possibility of population growth without substantial range expansion could account for the shared patterns of demographic expansion during the Last Glacial Maxima (OIS 2 and 4) in fish, small mammals and other lizards of the Monte Desert. We found substantial variation in diffusion rates over time, and very high rates during the range expansion phase, consistent with a rapidly advancing expansion front towards the southeast shown by palaeo-distribution models. Furthermore, the estimated diffusion rates are congruent with observed dispersal rates of lizards in field conditions and therefore provide additional confidence to the temporal scale of inferred phylogeographic patterns. Our study highlights how the integration of phylogeography with palaeo-distribution models can shed light on both demographic and range expansion processes and their potential causes.Fil: Camargo Bentaberry, Arley. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Werneck, Fernanda P.. Brigham Young University. Life Science Museum. Department of Biology & Bean; Estados Unidos. Universidade de Brasılia. Departamento de Zoologia; BrasilFil: Morando, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Sites Jr., Jack W.. Brigham Young University. Life Science Museum. Department of Biology & Bean; Estados UnidosFil: Avila, Luciano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentin

Molecular phylogenetic relationships and generic placement of dryaderces inframaculata Boulenger, 1882 (Anura: Hylidae)

Dryaderces inframaculata Boulenger, 1882, is a rare species known only from a few specimens and localities in the southeastern Amazonia rainforest. It was originally described in the genus Hyla, after ~ 130 years transferred to Osteocephalus, and more recently to Dryaderces. These taxonomic changes were based solely on the similarity of morphological characters. Herein, we investigate the phylogenetic relationships and generic placement of D. inframaculata using molecular data from a collected specimen from the middle Tapajós River region, state of Pará, Brazil. Two mitochondrial DNA fragments (16S and COI) were assessed among representative species in the subfamily Lophiohylinae (Anura: Hylidae) to reconstruct phylogenetic trees under Bayesian and Maximum Likelihood criteria. Our results corroborate the monophyly of Dryaderces and the generic placement of D. inframaculata with high support. Dryaderces inframaculata is sister to an undescribed taxon, Dryaderces pearsoni Ca1 Jungfer et al., 2013, and both are sister to Dryaderces pearsoni Gaige, 1929. These findings are relevant for further research on the systematics and biogeography of the genus

Deforestation limits evolutionary rescue under climate change in Amazonian lizards

Aim: The impact of climate change on biodiversity is often analysed under a stable evolutionary perspective focused on whether species can currently tolerate warmer climates. However, species may adapt to changes, and particularly under conditions of low habitat fragmentation, standing adaptive genetic variation can spread across populations tracking changing climates, increasing the potential for evolutionary rescue. Here, our aim is to integrate genomic data, niche modelling and landscape ecology to predict range shifts and the potential for evolutionary rescue. Location: The megadiverse Amazonian rainforest. Methods: We use genome–environment association analyses to search for candidate loci under environmental selection, while accounting for neutral genetic variation in a widespread Amazonian whiptail lizard (Teiidae: Kentropyx calcarata). We then model the distribution of individuals with genotypes adapted to different climate conditions. We predict range shifts for each genotype in distinct future climate change scenarios by integrating this information with dispersal constraints based on predicted scenarios of forest cover across Amazonia. The predicted ranges of each genotype were then overlapped to infer the potential for evolutionary rescue. Results: We find that the potential for evolutionary rescue and, therefore, a smaller degree of range loss buffering extinction risk in the future is considerably high, provided that current forest cover is retained and climate change is not extreme. However, under extreme environmental change scenarios, range loss will be high in central and southern Amazonia, irrespective of the degree of deforestation. Main Conclusions: Our results suggest that protecting the Amazonian rainforest against further deforestation and mitigating climate change to moderate scenarios until 2070 could foster evolutionary rescue of ectothermic organisms. These actions could prevent substantial biodiversity loss in Amazonia, emphasizing the importance of understanding species adaptability in maintaining biodiversity

In the Wake of Invasion: Tracing the Historical Biogeography of the South American Cricetid Radiation (Rodentia, Sigmodontinae)

The Great American Biotic Interchange (GABI) was greatly influenced by the completion of the Isthmus of Panama and impacted the composition of modern faunal assemblages in the Americas. However, the contribution of preceding events has been comparatively less explored, even though early immigrants in the fossil records are evidence for waif dispersals. The cricetid rodents of the subfamily Sigmodontinae are a classic example of a species-rich South American radiation resulting from an early episode of North American invasion. Here, we provide a temporal and spatial framework to address key aspects of the historical biogeography and diversification of this diverse mammal group by using mitochondrial and nuclear DNA datasets coupled with methods of divergence time estimation, ancestral area reconstruction and comparative phylogenetics. Relaxed-clock time estimates indicate that divergence of the Sigmodontinae began in the middle-late Miocene (ca. 12-9 Ma). Dispersal-vicariance analyses point to the arrival of a single lineage of northern invaders with a widespread ancestral distribution and imply that the initial differentiation between Central and South America gave rise to the most basal groups within the subfamily. These two major clades diversified in the late Miocene followed by the radiation of main tribes until the early Pliocene. Within the Oryzomyalia, tribes diverged initially in eastern South America whereas multiple dispersals into the Andes promoted further diversification of the majority of modern genera. A comparatively uniform background tempo of diversification explains the species richness of sigmodontines across most nodes, except for two akodontine genera with recent increases in diversification rates. The bridging of the Central American seaway and episodes of low sea levels likely facilitated the invasion of South America long before the onset of the post-Isthmian phase of the GABI.VoRSUNY DownstateEpidemiology and BiostatisticsN/

Exchanging screen for non-screen sitting time or physical activity might attenuate depression and anxiety: A cross-sectional isotemporal analysis during early pandemics in South America

Objectives: To examine the theoretical substitutions of screen exposure, non-screen sitting time, moderate and vigorous physical activity with depressive and anxiety symptoms in South American adults during the COVID-19 pandemic. Design: A cross-sectional study during the first months of the COVID-19 pandemic with data from 1981 adults from Chile, Argentina, and Brazil. Methods: Depressive and anxiety symptoms were assessed using the Beck Depression and Anxiety Inventories. Participants also reported physical activity, sitting time, screen exposure, sociodemographic, and tobacco use data. Isotemporal substitution models were created using multivariable linear regression methods. Results: Vigorous physical activity, moderate physical activity, and screen exposure were independently associated with depression and anxiety symptoms. In adjusted isotemporal substitution models, replacing 10 min/day of either screen exposure or non-screen sitting time with any intensity of physical activity was associated with lower levels of depressive symptoms. Improvements in anxiety symptoms were found when reallocating either screen exposure or non-screen sitting time to moderate physical activity. Furthermore, replacing 10 min/day of screen exposure with non-screen sitting time was beneficially associated with anxiety (B = − 0.033; 95 % CI = − 0.059, − 0.006) and depression (B = − 0.026; 95 % CI = − 0.050, − 0.002). Conclusions: Replacement of screen exposure with any intensity of physical activity or non-screen sitting time could improve mental health symptoms. Strategies aiming to reduce depressive and anxiety symptoms highlight physical activity promotion. However, future interventions should explore specific sedentary behaviors as some will relate positively while others negatively.Fil: Sadarangani, Kabir P.. Universidad Autónoma de Chile; Chile. Universidad Diego Portales; ChileFil: Schuch, Felipe Barreto. Universidade Federal de Santa Maria; Brasil. Universidad Autónoma de Chile; ChileFil: de Roia, Gabriela Fernanda. Universidad de Flores. Laboratorio de Estudios en Actividad Física;Fil: Martínez Gomez, David. Universidad Autónoma de Madrid; España. Consejo Superior de Investigaciones Científicas; España. Consortium for Biomedical Research in Epidemiology and Public Health; EspañaFil: Chávez, Róbinson. Universidad Andrés Bello; ChileFil: Lobo, Pablo Roberto. Universidad de Flores. Laboratorio de Estudios en Actividad Física;Fil: Cristi Montero, Carlos. Pontificia Universidad Católica de Valparaíso; ChileFil: Werneck, André O.. Universidade de Sao Paulo; BrasilFil: Alzahrani, Hosam. Taif University; Arabia SauditaFil: Ferrari, Gerson. Universidad de Santiago de Chile; ChileFil: Ibañez, Agustin Mariano. Universidad de San Andrés; Argentina. University of California; Estados Unidos. Trinity College Dublin; Irlanda. Universidad Adolfo Ibañez; Chile. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Silva, Danilo R.. Universidade Federal de Sergipe; Brasil. Universidad Pablo de Olavide; EspañaFil: Von Oetinger, Astrid. Universidad Diego Portales; Chile. Universidad Mayor; ChileFil: Matias, Thiago S.. Universidade Federal de Santa Catarina; BrasilFil: Grabovac, Igor. Universidad de Viena; AustriaFil: Meyer, Jacob. Iowa State University; Estados Unido

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Conceptual and empirical advances in Neotropical biodiversity research

The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of “trans-disciplinary biogeography,” which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow’s ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.Keywords: Biogeography, Biotic diversification, Landscape evolution, Phylogeny, Scale, Biodiversity, Community ecology, Phylogeography, Phylogenetics, Tropics</div

Predicting smear negative pulmonary tuberculosis with classification trees and logistic regression: a cross-sectional study

BACKGROUND: Smear negative pulmonary tuberculosis (SNPT) accounts for 30% of pulmonary tuberculosis cases reported yearly in Brazil. This study aimed to develop a prediction model for SNPT for outpatients in areas with scarce resources. METHODS: The study enrolled 551 patients with clinical-radiological suspicion of SNPT, in Rio de Janeiro, Brazil. The original data was divided into two equivalent samples for generation and validation of the prediction models. Symptoms, physical signs and chest X-rays were used for constructing logistic regression and classification and regression tree models. From the logistic regression, we generated a clinical and radiological prediction score. The area under the receiver operator characteristic curve, sensitivity, and specificity were used to evaluate the model's performance in both generation and validation samples. RESULTS: It was possible to generate predictive models for SNPT with sensitivity ranging from 64% to 71% and specificity ranging from 58% to 76%. CONCLUSION: The results suggest that those models might be useful as screening tools for estimating the risk of SNPT, optimizing the utilization of more expensive tests, and avoiding costs of unnecessary anti-tuberculosis treatment. Those models might be cost-effective tools in a health care network with hierarchical distribution of scarce resources

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress