Multimodal Foundation Models for Zero-shot Animal Species Recognition in Camera Trap Images

Due to deteriorating environmental conditions and increasing human activity, conservation efforts directed towards wildlife is crucial. Motion-activated camera traps constitute an efficient tool for tracking and monitoring wildlife populations across the globe. Supervised learning techniques have been successfully deployed to analyze such imagery, however training such techniques requires annotations from experts. Reducing the reliance on costly labelled data therefore has immense potential in developing large-scale wildlife tracking solutions with markedly less human labor. In this work we propose WildMatch, a novel zero-shot species classification framework that leverages multimodal foundation models. In particular, we instruction tune vision-language models to generate detailed visual descriptions of camera trap images using similar terminology to experts. Then, we match the generated caption to an external knowledge base of descriptions in order to determine the species in a zero-shot manner. We investigate techniques to build instruction tuning datasets for detailed animal description generation and propose a novel knowledge augmentation technique to enhance caption quality. We demonstrate the performance of WildMatch on a new camera trap dataset collected in the Magdalena Medio region of Colombia.Comment: 18 pages, 9 figure

New insights into the fossil record of the turtle genus Chelus Duméril, 1806 including new specimens with information on cervicals and limb bones

Matamata turtles (Chelus Duméril, 1806) are composed of two extant species, Chelus fimbriata ­Schneider, 1783 and Chelus orinocensis Vargas-Ramírez, Caballero, Morales-Betancourt, Lasso, Amaya, Martínez, Silva-Viana, Vogt, Farias, Hrbek, Campbell & Fritz, 2020, inhabitants of the main freshwater drainages of northern South America. The systematics and palaeobiogeography of Chelus is still unresolved. Here, we describe several new fossil specimens from the Late Miocene of Urumaco (Venezuela) and Tatacoa (Colombia). The fossils are mostly complete, articulated shells that allow reestablishing validity of two extinct taxa, Chelus colombiana Wood, 1976 and Chelus lewisi Wood, 1976. One of the specimens of C. lewisi from Urumaco represents the first record within the genus for which autopodial bones (a left manus) and additional limb bones are preserved together with ashell, demonstrating evolutionary conservatism in limb anatomy for the genus. The specimen comes from the Socorro Formation, representing the earliest so far known record of Chelus for the Urumaco sequence. Additionally, one specimen from Tatacoa is the first fossil for which cervical and pectoral girdle elements are preserved. Phylogenetic analysis supports the existence of two separate clades inside of Chelus, one formed by the extinct species and the other by the extant ones

INSIGHTS INTO THE HABITS OF THE ELUSIVE NOCTURNAL CURASSOW (NOTHOCRAX URUMUTUM)

Nocturnal curassows (Nothocrax urumutum) are one of the most enigmatic birds from South American rainforests. Their elusive habits and their nocturnal vocal behavior have led to the generalized assumption that they differ from other curassows in their presumable nocturnal habits. Here, we compiled camera trap data from long term projects in the Amazon rainforest and the Andes Cordillera piedmont to describe the temporal activity of Nocturnal Curassows. Based on an overall sampling effort of 68838 camera nights we obtained 274 independent records of their activity. The results of this study evidence that Nothocrax has diurnal habits and resembles in activity patterns to all other cracids more than previously expected. This study highlights the use of novel technologies and collaborative research towards the understanding of the natural history, ecology and behavior of animals with cryptic behaviors such as the Nocturnal Curassows

Causes and consequences of recent degradation of the Magdalena River basin, Colombia

The Magdalena River in Colombia is one of the world's largest (discharge = 7100 m3 s−1) tropical rivers, hosting > 170 aquatic vertebrate species. However, concise synthesis of the current ecological and environmental status is lacking. By documenting the anthropogenic stressors impacting the river on time scales ranging from centuries to decades, we found that the river system is subject to the compounding impacts of climate change, river impoundment, invasive alien species (IAS), catchment deforestation, and water pollution. We show that the Magdalena is a woefully understudied ecosystem relative to its critical importance to Colombia's economy, culture, and biodiversity compared with other similarly sized tropical rivers. We emphasize the need for research on (1) IAS population and ecological dynamics, (2) river damming and its links with IAS and climate change, and (3) land-use changes as well as identifying sources of water pollution and strategies for mitigation

Biodiversity of protists and nematodes in the wild nonhuman primate gut

Documenting the natural diversity of eukaryotic organisms in the nonhuman primate (NHP) gut is important for understanding the evolution of the mammalian gut microbiome, its role in digestion, health and disease, and the consequences of anthropogenic change on primate biology and conservation. Despite the ecological significance of gut-associated eukaryotes, little is known about the factors that influence their assembly and diversity in mammals. In this study, we used an 18S rRNA gene fragment metabarcoding approach to assess the eukaryotic assemblage of 62 individuals representing 16 NHP species. We find that cercopithecoids, and especially the cercopithecines, have substantially higher alpha diversity than other NHP groups. Gut-associated protists and nematodes are widespread among NHPs, consistent with their ancient association with NHP hosts. However, we do not find a consistent signal of phylosymbiosis or host-species specificity. Rather, gut eukaryotes are only weakly structured by primate phylogeny with minimal signal from diet, in contrast to previous reports of NHP gut bacteria. The results of this study indicate that gut-associated eukaryotes offer different information than gut-associated bacteria and add to our understanding of the structure of the gut microbiome.Fil: Mann, Allison E.. University of British Columbia; CanadáFil: Mazel, Florent. University of British Columbia; CanadáFil: Lemay, Matthew A.. University of British Columbia; CanadáFil: Morien, Evan. University of British Columbia; CanadáFil: Billy, Vincent. University of British Columbia; CanadáFil: Kowalewski, Miguel Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia". Estación Biológica de Usos Múltiples (Sede Corrientes); ArgentinaFil: Di Fiore, Anthony. University of Texas at Austin; Estados UnidosFil: Link, Andrés. Universidad de los Andes; ColombiaFil: Goldberg, Tony L.. University of Wisconsin; Estados UnidosFil: Tecot, Stacey. University of Arizona; Estados UnidosFil: Baden, Andrea L.. City University Of New York. Hunter College; Estados UnidosFil: Gomez, Andres. University of Minnesota; Estados UnidosFil: Sauther, Michelle L.. State University of Colorado at Boulder; Estados UnidosFil: Cuozzo, Frank P.. Lajuma Research Centre; SudáfricaFil: Rice, Gillian A. O.. Dartmouth College; Estados UnidosFil: Dominy, Nathaniel J.. Dartmouth College; Estados UnidosFil: Stumpf, Rebecca. University of Illinois at Urbana; Estados UnidosFil: Lewis, Rebecca J.. University of Texas at Austin; Estados UnidosFil: Swedell, Larissa. University of Cape Town; Sudáfrica. City University of New York; Estados UnidosFil: Amato, Katherine. Northwestern University; Estados UnidosFil: Wegener Parfrey, Laura. University of British Columbia; Canad

Review of GPS Collar Deployments and Performance on Nonhuman Primates

Over the past twenty years, GPS collars have emerged as powerful tools for the study of nonhuman primate (hereafter, "primate") movement ecology. As the size and cost of GPS collars have decreased and performance has improved, it is timely to review the use and success of GPS collar deployments on primates to date. Here we compile data on deployments and performance of GPS collars by brand and examine how these relate to characteristics of the primate species and field contexts in which they were deployed. The compiled results of 179 GPS collar deployments across 17 species by 16 research teams show these technologies can provide advantages, particularly in adding to the quality, quantity, and temporal span of data collection. However, aspects of this technology still require substantial improvement in order to make deployment on many primate species pragmatic economically. In particular, current limitations regarding battery lifespan relative to collar weight, the efficacy of remote drop-off mechanisms, and the ability to remotely retrieve data need to be addressed before the technology is likely to be widely adopted. Moreover, despite the increasing utility of GPS collars in the field, they remain substantially more expensive than VHF collars and tracking via handheld GPS units, and cost considerations of GPS collars may limit sample sizes and thereby the strength of inferences. Still, the overall high quality and quantity of data obtained, combined with the reduced need for on-the-ground tracking by field personnel, may help defray the high equipment cost. We argue that primatologists armed with the information in this review have much to gain from the recent, substantial improvements in GPS collar technology

The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics

Fruit dispersal syndromes in animal disseminated plants at Tinigua National Park, Colombia Síndromes de dispersión en plantas dispersadas por animales en el Parque Nacional Tinigua, Colombia

Fruit dispersal syndromes (groups of plants with similar fruit morphology, presumably adapted to dispersal by a particular set of vectors) have been described in a variety of tropical localities. In some cases the presence of different syndromes in each locality suggests independent evolution of fruit traits in response to selective pressures imposed by the particular animal community in each place. However, it is still unclear how general are fruit syndromes, and this is important to understand the evolution of mutualistic relationships. We compiled morphological information from about 500 fleshy fruited species at a lowland Neotropical forest in Tinigua National Park, Colombia, in an effort to test for the existence of fruit dispersal syndromes. We found that about two thirds of the plant genera analyzed could be classified in two different fruit types (large, protected, dull colored fruits, vers.us small, unprotected, bright colored fruits). These two syndromes correspond to the mammal and bird dispersal syndromes originally described at Cocha Cashu Biological Station, PeruPeruú. Two years of field observations on several fruiting plants revealed close associations between these fruit syndromes and the presumed animal dispersal vector. Our results support the idea that fruit dispersal syndromes are more general in Neotropical forests than previously inferred. However, we caution that similar syndromes found at Cocha Cashu and Tinigua may be a consequence of the floristic resemblance of both regions, and may not necessarily imply an independent case for the evolution of mammal and bird dispersal syndromes. Therefore, additional studies of fruit syndromes and biogeographical analyses would be necessary to assess how general are dispersal syndromes in the Neotropics<br>Los síndromes de dispersión de frutos han sido descritos para diferentes bosques tropicales. En algunos casos la presencia de diferentes síndromes de dispersión sugiere la evolución independiente de características morfológicas de los frutos como respuesta a presiones de selección particulares. Sin embargo, hasta el momento hay evidencias contrastantes sobre qué tan generales son estos síndromes. Este estudio reúne la información morfológica de aproximadamente 500 especies de plantas con frutos carnosos, en el parque Nacional Tinigua, Colombia, en un esfuerzo por encontrar síndromes de dispersión de semillas. Alrededor de dos tercios de los géneros de plantas analizados se pueden agrupar en dos categorías: (frutos grandes, con protección y colores opacos; y frutos pequeños, sin protección y de colores llamativos), que corresponden a los síndromes de dispersión por mamíferos y aves descritos por Janson (1983) en Cocha Cashu, Perú. Nuestros resultados apoyan la idea que los síndromes de dispersión endozoocórica son más generalizados de lo que se había planteado anteriormente. Consideramos que la similitud en los resultados obtenidos en este estudio y en el Perú no necesariamente implica evolución independiente de los síndromes de dispersión, porque las floras de estos lugares son bastante similares. Por lo tanto más estudios de este tipo son necesarios para entender mejor qué tan generales son los síndromes de dispersión en bosques Neotropicale

Do bairro ao complexo: espaço público e sociabilidade em dois projetos de habitação social em Santiago do Chile.

Chilean housing policy has suffered a profound transformation during the last decades. In the sixties and the beginning of the seventies, a model emerged based on community attributes, promoting community organization and the construction of well-provided neighborhoods that, in addition, had abundant public space. In 1973, the focus shifted with the implementation of a subsidiary model that promoted single-family and individual solutions and payed far less attention to the collective development of the residential habitat. Although the continuation of this model until today has significantly reduced the housing shortage, it has been unable to reproduce a residential space of community ties. This article aims to investigate the impacts of both models on the configuration, use and appropriation of the public space and the neighborhood sociability of the residents through a multi-methods analysis of two social housing projects located in Santiago de Chile. The findings reaffirm the relevance of the history and the organization of the neighborhoods, but also confirm the significance of planned public spaces and the arrangement of the built environment as dimensions that can promote or suppress social practices.La política habitacional chilena sufrió una profunda transformación durante las últimas décadas. En los años sesenta e inicios de los setenta emergió un modelo basado en atributos comunitarios, promoviendo la organización vecinal y la construcción de barrios bien equipados que contaban con abundante espacio público. En 1973, el foco cambió con la instalación de un modelo subsidiario que promovió la postulación familiar e individual con menos atención al desarrollo colectivo del hábitat residencial. Aunque la continuidad de este modelo hasta la actualidad ha logrado una significativa reducción del déficit habitacional, no ha podido reconstituir un espacio residencial de vínculos comunitarios. Este artículo indaga en las consecuencias de ambos modelos, tanto en la configuración y uso del espacio público, como en la sociabilidad vecinal de sus habitantes mediante un análisis de dos proyectos de vivienda social en Santiago de Chile. Los resultados reafirman la relevancia de la historia y organización barrial, pero también evidencian la importancia del espacio público planificado y de la configuración del entorno construido como dimensiones que pueden motivar o inhibir prácticas sociales.A política habitacional chilena passou por uma profunda transformação nas últimas décadas. Na década de 1960 e início da década de 1970, surgiu um modelo baseado em atributos comunitários, promovendo a organização do bairro e a construção de bairros bem equipados e com abundante espaço público. Em 1973, o foco mudou com a instalação de um modelo subsidiário que promovia a aplicação familiar e individual e dava muito menos atenção ao desenvolvimento coletivo do habitat residencial. Embora a continuidade desse modelo até os dias atuais tenha alcançado uma redução significativa do déficit habitacional, ele não conseguiu reconstituir um espaço residencial com vínculos comunitários. Este artigo tem como objetivo investigar os impactos de ambos os modelos na configuração, uso e apropriação do espaço público e na sociabilidade do bairro de seus habitantes através de uma análise multimetodológica de dois projetos de habitação social em Santiago do Chile. Os resultados reafirmam a relevância da história e organização do bairro, mas também confirmam a importância do espaço público planejado e da configuração do ambiente construído como dimensões que podem motivar, colocar em risco e inibir as práticas sociais