Centro de Investigación de la Biodiversidad y Cambio Climático
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Molecular phylogeny of stream treefrogs (Hylidae: Hyloscirtus bogotensis Group), with a new species from the Andes of Ecuador

2015 , Guayasamin J.M. , Rivera-Correa M. , Arteaga A. , Culebras J. , Bustamante L. , Pyron R.A. , Peñafiel N. , Morochz C. , Hutter C.R.

We present a new molecular phylogeny of the stream treefrog genus Hyloscirtus, with an improved taxon sampling in the Hyloscirtus bogotensis group. The tree supports the existence of three clades within the genus (Hyloscirtus armatus group, H. bogotensis group and Hyloscirtus larinopygion group) in congruence with previous studies, and suggests the presence of at least three new species in the H. bogotensis group. Herein, we describe one of these species, Hyloscirtus mashpi n. sp. from the Pacific slope of the Ecuadorian Andes. The validity of the latter is supported by molecular, morphological and acoustic data. We also tested individuals of the new species for the chytrid fungus Batrachochytrium dendrobatidis, finding a prevalence of 17.6% (6 positives and 28 negatives). However, at sampled streams, frog densities were high, suggesting that H. mashpi n. sp. may be tolerant to the infection. © 2015, © 2015 The Author(s). Published by Taylor & Francis.

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Birds of Bosque Protector Jerusalem, Guayllabamba Valley, Ecuador

2015 , Cadena-Ortiz H. , Varela S. , Bahamonde-Vinueza D. , Freile J.F. , Bonaccorso E.

The Ecuadorian inter-Andean dry valleys are highly affected by human intervention. Currently, less than 5% of the original vegetation cover of these valleys remains on creeks and hillsides. Bosque Protector Jerusalem (1,110 ha), in the upper Guayllabamba River valley, protects the largest remnants of inter-Andean dry forest in Ecuador. Here, we present data derived from two recent studies (from 2009 to 2013), as well as information collected by other authors in previous studies, between the years 2002 and 2009. We present a unified list of 75 species of birds, accounts for species of particular interest, new distributional records, and considerations about the conservation of the study area. © 2015 Check List and Authors.

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Associations among MHC genes, latitude, and avian malaria infections in the rufous‐collared sparrow (Zonotrichia capensis)

2024 , Juan Rivero de Aguilar , Omar Barroso , Bonaccorso, Elisa , Hector Cadena , Lucas Hussing , Josefina Jorquera , Javier Martinez , Josué Martínez‐de la Puente , Alfonso Marzal , Fabiola León Miranda , Santiago Merino , Nubia E. Matta , Marilyn Ramenofsky , Ricardo Rozzi , Carlos E. Valeris‐Chacín , Rodrigo A. Vásquez , Juliana A. Vianna , John C. Wingfield

The major histocompatibility complex (MHC) is a genetic region in jawed vertebrates that contains key genes involved in the immune response. Associations between the MHC and avian malaria infections in wild birds have been observed and mainly explored in the Northern Hemisphere, while a general lack of information remains in the Southern Hemisphere. Here, we investigated the associations between the MHC genes and infections with Plasmodium and Haemoproteus blood parasites along a latitudinal gradient in South America. We sampled 93 rufous-collared sparrows (Zonotrichia capensis) individuals from four countries, Colombia, Ecuador, Peru, and Chile, and estimated MHC-I and MHC-II allele diversity. We detected between 1–4 (MHC-I) and 1–6 (MHC-II) amino acidic alleles per individual, with signs of positive selection. We obtained generalized additive mixed models to explore the associations between MHC-I and MHC-II diversity and latitude. We also explored the relationship between infection status and latitude/biome. We found a non-linear association between the MHC-II amino acidic allele diversity and latitude. Individuals from north Chile presented a lower MHC genetic diversity than those from other locations. We also found an association between deserts and xeric shrublands and a lower prevalence of Haemoproteus parasites. Our results support a lower MHC genetic in arid or semi-arid habitats in the region with the lower prevalence of Haemoproteus parasites.

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A Comprehensive Database of Expert‐Curated Occurrences for the Genus Carex L. (Cyperaceae)

2025 , María Sanz‐Arnal , Pablo García‐Moro , Carmen Benítez‐Benítez , Marina Coca‐de‐la‐Iglesia , Angélica Gallego‐Narbón , Consolación Barciela , Fabrizio Bartolucci , Prabin Bhandari , Matthew Bradley , Asunción Cano , Antoine Derouaux , Sabina Donadío , Marcial Escudero , Mariela Fabbroni , Kerry A. Ford , Gabriele Galasso , Sebastian Gebauer , M. Socorro González‐Elizondo , David Hamon , Matthias H. Hoffmann , Xiao‐Feng Jin , Jacob Koopman , Bangze Li , Raúl Lois , Yi‐Fei Lu , Modesto Luceño , José Ignacio Márquez‐Corro , Santiago Martín‐Bravo , Attila Mesterházy , Mónica Míguez , Ana Morales‐Alonso , A. Muthama Muasya , Paulo Muñoz‐Schüler , Robert F. C. Naczi , Oleas Gallo, Nora Helena , Luciana Pereira‐Silva , Radomír Řepka , Anton A. Reznicek , Katie K. Sanbonmatsu , Enmily Sánchez , Daniel Spalink , Arne Strid , Pieter Vanormelingen , Filip Verloove , Karen L. Wilson , Okihito Yano , Shuren Zhang , Pedro Jiménez‐Mejías

Motivation: Geographic occurrences are essential for biodiversity studies, but publicly available repositories like GBIF often contain errors and biases, especially for taxonomically complex groups like Carex L. (Cyperaceae). This work provides an expert-curated global dataset of occurrences compiled from different sources to enhance data accuracy and usability. The final dataset includes 384,067 occurrences of 1790 Carex species. Main Types of Variables Contained: The dataset includes species occurrence records with geographic coordinates, taxonomic identifications, and curation flags (e.g., introduced, erroneous records). Spatial Location and Grain: The dataset covers a global scale, using the WGS84 projection. Spatial resolution is standardised to a minimum of three decimal degrees (~1 km, if possible). Time Period and Grain: Online records span from 1950 to 2020, but some manually georeferenced records are earlier (1850). There is also fieldwork data after 2020, specifically up to 2023. Major Taxa and Level of Measurement: Cyperaceae: Carex. Most records have species-level identification, and some of them are identified at subspecies or variety levels. Software Format: Data are supplied as comma-separated values files with UTF-8 encoding.

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Hummingbird diversity in a fragmented tropical landscape in the Chocó biogeographic zone

2023 , Huh K.M. , Ellis M. , Castillo F. , Carrasco L. , Rivero de Aguilar J. , Bonaccorso, Elisa , Browne L. , Karubian J.

Forest loss and fragmentation drive widespread declines in biodiversity. However, hummingbirds seem to exhibit relative resilience to disturbance, characterized by increasing abundance alongside declining species richness and evenness. Yet, how widespread this pattern may be, and the mechanisms by which it may occur, remain unclear. To fill in this knowledge gap, we investigated habitat- and site-level patterns of diversity, and community composition of hummingbirds between continuous forest (transects n = 16 in ~3500 ha) and more disturbed surrounding fragments (n = 39, 2.5–48.0 ha) in the Chocó rain forest of northwestern Ecuador. Next, we assessed within-patch and patch-matrix characteristics associated with hummingbird diversity and composition. We found higher hummingbird species richness in forest fragments relative to the continuous forest, driven by increased captures of rare species in fragments. Community composition also differed between continuous forest and fragments, with depressed evenness in fragments. Increased canopy openness and density of medium-sized trees correlated with hummingbird diversity in forest fragments, although this relationship became nonsignificant after applying false discovery rate (p <.01). Higher species richness in fragments and higher evenness in the continuous forest highlight the complex trade-offs involved in the conservation of this ecologically important group of birds in changing Neotropical landscapes. Abstract in Spanish is available with online material. © 2023 The Authors. Biotropica published by Wiley Periodicals LLC on behalf of Association for Tropical Biology and Conservation.

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Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato

2014 , Nadeau N.J. , Ruiz M. , Salazar P. , Counterman B. , Medina J.A. , Ortiz-Zuazaga H. , Morrison A. , McMillan W.O. , Jiggins C.D. , Papa R.

Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on color pattern. The comimetic species, H. erato and H. melpomene, have parallel hybrid zones in which both species undergo a change from one color pattern form to another. We use restriction-associated DNA sequencing to obtain several thousand genome-wide sequence markers and use these to analyze patterns of population divergence across two pairs of parallel hybrid zones in Peru and Ecuador. We compare two approaches for analysis of this type of data - alignment to a reference genome and de novo assembly - and find that alignment gives the best results for species both closely (H. melpomene) and distantly (H. erato, ∼15% divergent) related to the reference sequence. Our results confirm that the color pattern controlling loci account for the majority of divergent regions across the genome, but we also detect other divergent regions apparently unlinked to color pattern differences. We also use association mapping to identify previously unmapped color pattern loci, in particular the Ro locus. Finally, we identify a new cryptic population of H. timareta in Ecuador, which occurs at relatively low altitude and is mimetic with H. melpomene malleti. © 2014 Nadeau et al.

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Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species

2022 , Cheek, R.G. , Forester, B.R. , Salerno, Patricia E. , Trumbo, D.R. , Langin, K.M. , Chen, N. , Scott Sillett, T. , Morrison, S.A. , Ghalambor, C.K. , Chris Funk, W.

We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250-km2 island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine–oak ecotones on Santa Cruz Island, California (USA), similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3000 single nucleotide polymorphisms in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing. Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow. © 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

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A First Look at the Inhibitory Potential of Urospatha sagittifolia (Araceae) Ethanolic Extract for Bothrops atrox Snakebite Envenomation

2022 , Vera-Palacios, A.L. , Sacoto-Torres, J.D. , Hernández-Altamirano, J.A. , Moreno, A. , Peñuela-Mora, M.C. , Salazar Valenzuela, David , Mogollón, N.G.S. , Almeida, J.R.

Bothrops atrox snakebites are a relevant problem in the Amazon basin. In this biodiverse region, the ethnomedicinal approach plays an important role as an alternative to antivenom therapy. Urospatha sagittifolia (Araceae) is a plant used for this purpose; however, its neutralizing properties have not been scientifically accessed. To fill this gap, we investigated the ability of U. sagittifolia to modulate the catalytic activity of Bothrops atrox venom, and their toxic consequences, such as local damage and lethality. The venom profile of B. atrox was assessed by chromatography and electrophoresis. Inhibition of the three main enzymatic and medically important toxins from the venom was evaluated using synthetic substrates and quantified by chromogenic activity assays. Additionally, the neutralization of lethality, hemorrhage and edema were investigated by in vivo assays. The possible interactions between venom proteins and plant molecules were visualized by polyacrylamide gel electrophoresis. Finally, the phytochemical constituents present in the ethanolic extract were determined by qualitative and quantitative analyses. The ethanolic extract reduced the activity of the three main enzymes of venom target, achieving ranges from 19% to 81% of inhibition. Our in vivo venom neuralizations assays showed a significant inhibition of edema (38.72%) and hemorrhage (42.90%). Additionally, lethality was remarkably counteracted. The highest extract ratio evaluated had a 75% survival rate. Our data support the biomedical value of U. sagittifolia as a source of natural enzyme inhibitors able to neutralize catalytically active B. atrox venom toxins and their toxic effects. © 2022 by the authors.

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Validating anthropogenic threat maps as a tool for assessing river ecological integrity in Andean-Amazon basins

2019 , Lessmann J. , Troya M.J. , Flecker A.S. , ChrisFunk W.W. , Guayasamin, Juan M. , Ochoa-Herrera V. , LeRoyPoff N.N. , Suárez E. , Encalada A.C.

Anthropogenic threat maps are commonly used as a surrogate for the ecological integrity of rivers in freshwater conservation, but a clearer understanding of their relationships is required to develop proper management plans at large scales. Here, we developed and validated empirical models that link the ecological integrity of rivers to threat maps in a large, heterogeneous and biodiverse Andean-Amazon watershed. Through fieldwork, we recorded data on aquatic invertebrate community composition, habitat quality, and physical-chemical parameters to calculate the ecological integrity of 140 streams/rivers across the basin. Simultaneously, we generated maps that describe the location, extent, and magnitude of impact of nine anthropogenic threats to freshwater systems in the basin. Through seven-fold cross-validation procedure, we found that regression models based on anthropogenic threats alone have limited power for predicting the ecological integrity of rivers. However, the prediction accuracy improved when environmental predictors (slope and elevation) were included, and more so when the predictions were carried out at a coarser scale, such as microbasins. Moreover, anthropogenic threats that amplify the incidence of other pressures (roads, human settlements and oil activities) are the most relevant predictors of ecological integrity. We concluded that threat maps can offer an overall picture of the ecological integrity pattern of the basin, becoming a useful tool for broad-scale conservation planning for freshwater ecosystems. While it is always advisable to have finer scale in situ measurements of ecological integrity, our study shows that threat maps provide fast and cost-effective results, which so often are needed for pressing management and conservation actions. © 2019 Lessmann et al.

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A new species of harlequin toad (Bufonidae: Atelopus) from Amazonian Ecuador

2024 , Plewnia, Amadeus , Terán-Valdez, Andrea , Culebras, Jaime , Boistel, Renaud , Paluh, Daniel , Quezada Riera, Amanda B. , Heine, Christopher H , Reyes-Puig, Juan , Salazar Valenzuela, David , Guayasamin, Juan Manuel

For nearly four decades, harlequin toads, genus Atelopus, have suffered unparalleled population declines. While this also results in limited understanding of alphataxonomic relationships, these toads face an urgent need for advances in systematics to inform conservation efforts. However, high intraspecific variation and cryptic diversity have hindered a comprehensive understanding of Atelopus diversity. This is particularly exemplified among Amazonian populations related to A. spumarius, where decades of taxonomic work have not been able yet to unravel relationships between the many forms, while the names coined so far have led to taxonomic confusion leaving numer-ous lineages unnamed. A recent comprehensive phylogenetic study has revealed new insights into the systematics of harlequin toads with an emphasis on Amazonian forms, identifying several unnamed lineages. We here describe one of these evolutionary lineages as a new species, restricted to the Ecuadorian Amazon basin, in an integrative taxonomic approach using molecular, morphological, bioacoustic and larval information. With this, we contribute to a better understanding of Atelopus diversity as the baseline of conservation action.

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