Browsing by Autor "Carlos Daniel Cadena"

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A latitudinal gradient of reference genomes
(2024) Ethan Linck; Carlos Daniel Cadena
Abstract Global inequality rooted in legacies of colonialism and uneven development can lead to systematic biases in scientific knowledge. In ecology and evolutionary biology, findings, funding and research effort are disproportionately concentrated at high latitudes while biological diversity is concentrated at low latitudes. This discrepancy may have a particular influence in fields like phylogeography, molecular ecology and conservation genetics, where the rise of genomics has increased the cost and technical expertise required to apply state-of-the-art methods. Here we ask whether a fundamental biogeographic pattern—the latitudinal gradient of species richness in tetrapods—is reflected in available reference genomes, an important data resource for various applications of molecular tools for biodiversity research and conservation. We also ask whether sequencing approaches differ between the Global South and Global North, reviewing the last five years of conservation genetics research in four leading journals. We find that extant reference genomes are scarce relative to species richness at low latitudes, and that reduced-representation and whole-genome sequencing are disproportionately applied to taxa in the Global North. We conclude with recommendations to close this gap and improve international collaborations in biodiversity genomics.
Bird songs on the shelf: assessing vocal activity and output using data hidden in sound archives
(2017) Oscar Laverde-R.; Paula Caycedo‐Rosales; Paulo-C. Pulgarín-R.; Carlos Daniel Cadena
Abstract Understanding how often do animals emit communication signals is of critical importance to address a variety of research questions in behavioral ecology and sexual selection. However, information on vocal output, a central component of investment in signaling, is lacking for most species employing acoustic communication. Because this lack of information is partly due to logistical and methodological difficulties in monitoring animal signaling over time, developing new approaches to quantify vocal output is of special importance. We asked whether the number of recordings of avian vocalizations in sound archives and the times when such recordings were obtained reflect estimates of vocal output and temporal patterns of vocal activity obtained through systematic monitoring of wild bird populations in tropical forest sites. Based on a sample of 43 montane forest species, we found significant relationships between the number of recordings of species detected through continuous monitoring over several months and the number of recordings archived in sound collections, especially when accounting for the area of distribution of each species. In addition, daily activity patterns based on data collected through continuous monitoring over several days did not differ from those based on recordings archived in sound collections in 12 of 15 species of lowland forest birds. Annual patterns in vocal activity of two species estimated based on recordings in collections closely resembled previously published patterns. We conclude that recordings in sound collections contain valuable yet previously unappreciated information about the vocal output and temporal patterns in vocal activity of birds. This opens the possibility of using sound collections to assess vocal output and to consider it as a variable of interest in studies on the ecology and evolution of birds and other animals that use acoustic signals for communication. We encourage field workers to keep the ears wide open, and the recorders wide ready to record.
Caldas meets Janzen: Thermal regimes of montane plants and implications for global patterns of speciation
(2024) Adriana Sánchez; Ignacio Quintero; Sara Pedraza; Diana Bonilla; Lúcia G. Lohmann; Carlos Daniel Cadena; Felipe Zapata
Abstract The seasonality hypothesis posits that limited seasonal temperature variability in tropical mountains leads to greater climatic zonation along elevation gradients compared to temperate regions. This is predicted to result in narrow thermal tolerances and restricted dispersal for organisms, which may reduce gene flow and increase opportunities for climate-associated parapatric or allopatric speciation in tropical mountains relative to temperate-zone mountains. This hypothesis has been tested in various animal groups but not in plants. We examine the elevational and thermal ranges of pairs of sister species of angiosperms from mountains worldwide. Our findings indicate no significant difference in the breadth and overlap of elevational ranges between tropical and temperate species. However, tropical species have narrower thermal ranges and show greater similarity in these ranges between sister species compared to temperate ones. Such narrow thermal specialization in tropical plants facilitates population divergence and allopatric speciation within thermal zones more than in temperate species.
Flight demand and environmental niche are associated with molecular evolutionary rates in a large avian radiation
(2020) David A. Duchêne; Paola Montoya; Santiago Claramunt; Carlos Daniel Cadena
Abstract Among the macroevolutionary drivers of molecular evolutionary rates, metabolic demands and environmental energy have been a central topic of discussion. The large number of studies examining these associations have found mixed results, and have rarely explored the interactions among various factors impacting molecular evolutionary rates. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with proxies of metabolic demands imposed by flight (wing loading and the hand-wing index) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). We found evidence that species that fly less have greater wing loading and this is associated with accelerated rates of mutation. An elongated wing morphology is associated with greater flight activity and with molecular signatures of positive selection or reduced population sizes. Meanwhile, environmental temperature and UV radiation interact to explain molecular rates at sites affected by selection and population size, contrary to the expectation of their impact on mutation rates. Our results suggest that the demands of flight and environmental energy pose multiple evolutionary pressures on the genome either by driving mutation rates or via their association with natural selection or population size.
Henicorhina anachoreta (Troglodytidae), another endemic bird species for the Sierra Nevada de Santa Marta, Colombia
(2021) Carlos Daniel Cadena; Maria Leitner; Paula Caycedo; Andrés M. Cuervo; Rauri C. K. Bowie; Hans Slabbekoorn
En un estudio previo, presentamos evidencia que el cucaracho del género Henichorhina que habita las elevaciones superiores de la Sierra Nevada de Santa Marta, H. anachoreta, amerita el rango de una especie distinta del táxon de elevaciones más bajas, H. bangsi, con base en diferencias genéticas y fenotípicas y de sus cantos. Además, encontramos que, en una zona estrecha de simpatría, ellos mostraron respuestas diferentes a sus propios cantos vs. los del otro taxon. Sin embargo, no presentamos en detalle las diferencias en plumaje y medidas morfométricas y no presentamos una recomendación taxonómica formal. Aquí hacemos tal recomendación y describimos en detalle las diferencias en plumaje y mediciones para apoyar esta recomendación.
Host phylogeny and elevation predict infection by avian haemosporidians in a diverse New Guinean bird community (R script for analyses, figures, and supplemental figures )
(European Organization for Nuclear Research, 2022) Geoffrey Lau; Alexandra Class Freeman; Paulo Pulgarin-R; Robert E. Ricklefs; Carlos Daniel Cadena; Benjamin G. Freeman
This script performs the glmm analysis of the elevation and infection prevalence data as well as the script required to generate the figures in the article.
Host phylogeny and elevation predict infection by avian haemosporidians in a diverse New Guinean bird community (R script for analyses, figures, and supplemental figures )
(European Organization for Nuclear Research, 2022) Geoffrey Lau; Alexandra Class Freeman; Paulo Pulgarin-R; Robert E. Ricklefs; Carlos Daniel Cadena; Benjamin G. Freeman
This script performs the glmm analysis of the elevation and infection prevalence data as well as the script required to generate the figures in the article.
Nest location and architecture as primary drivers of variation in UV reflectance in avian eggs
(Royal Society, 2025) Maria Elisa Mendiwelso; Carlos Daniel Cadena; David Ocampo
Two main hypotheses have been proposed to explain the function of ultraviolet (UV) reflection in avian eggs. The UV resistance hypothesis suggests that high UV reflectance protects embryos against solar exposure in open nests, whereas the egg detectability hypothesis posits that higher UV reflectance helps eggs stand out against the dark background of the nest, making them easier for parents to locate in enclosed nests. Therefore, eggshell reflection in the UV spectrum may serve multiple (possibly even opposing) forces, including UV protection and visual signalling. We tested these two hypotheses using large-scale comparative analyses of eggshell UV reflection for over 500 avian species while considering the influence of various ecological, life history and environmental traits associated with light exposure. We did not find strong support for either of the two hypotheses across all birds. However, in two clades exhibiting notably high levels of UV reflectance (Passeriformes and Charadriiformes), species with higher UV reflectance values predominantly nest in open nests, suggesting a stronger effect of the UV resistance hypothesis. This research contributes to a deeper understanding of the mechanisms driving UV coloration in avian eggs and unravels the interplay between life history traits potentially associated with UV reflectance in specific clades under variable nesting conditions.
New genomic resources and the historical demography of the Tourmaline Sunangel (Trochilidae, <i>Heliangelus exortis</i> ) in the Colombian Andes
(Oxford University Press, 2026) Carlos Daniel Cadena; Laura Pabón; Andrés Felipe Díaz-Salazar; Maria Elisa Mendiwelso; Natalia Ocampo-Peñuela; Nelsy Niño-Rodríguez; Juliana Soto-Patiño; Glenn F. Seeholzer; Suzette G. A. Flantua; Linelle Abueg
Understanding the demographic history of tropical montane species offers insights into how climate-driven habitat dynamics shape genetic diversity and population structure. The Tourmaline Sunangel (Heliangelus exortis), a hummingbird endemic to the Northern Andes of Colombia and Ecuador, inhabits high-elevation ecosystems that were repeatedly impacted by Pleistocene glacial-interglacial cycles. To enable genomic and evolutionary studies in this system, we generated a high-quality, chromosome-level reference genome using PacBio HiFi long reads and Hi-C scaffolding. The resulting 1.05 Gb assembly has contig and scaffold N50s of 8.4 Mb and 73.9 Mb, respectively, with >94 % BUSCO completeness. Using this reference, we analyzed whole-genome resequencing data from ten individuals collected at a single locality in the Eastern Andes of Colombia and reconstructed demographic history with pairwise sequentially Markovian coalescent models. Our results indicate a pronounced population expansion between ~1 Mya and ~300 kya, likely driven by increased habitat connectivity during glacial periods when highland vegetation was displaced downslope, followed by a decline likely associated with interglacial fragmentation. These trends broadly align with paleoecological records, suggesting that populations of forest-associated species such as H. exortis responded to Pleistocene climatic oscillations, though demographic patterns did not strictly mirror known glacial-interglacial dynamics. This work establishes a foundation for future genomic studies in Andean birds, and highlights the potential of combining genomic and paleoecological data to unravel how biodiversity responds to environmental change.
Novel tetranucleotide microsatellite DNA markers for members of the Henicorhina Wood-wren species complex (Aves, Troglodytidae)
(Springer Science+Business Media, 2011) Rauri C. K. Bowie; Kevin A. Feldheim; Lina María; Carlos Daniel Cadena
Phylogeography of the Critically Endangered Brown Spider Monkey (Ateles hybridus): Testing the Riverine Barrier Hypothesis
(Springer Science+Business Media, 2015) Andrés Link; Lina M. Valencia; Laura N. Céspedes; Liz Diana Duque; Carlos Daniel Cadena; Anthony Di Fiore
R script for analyses, figures, and supplemental figures
(European Organization for Nuclear Research, 2022) Geoffrey Lau; Alexandra Class Freeman; Paulo Pulgarin-R; Robert E. Ricklefs; Carlos Daniel Cadena; Benjamin G. Freeman
This script performs the glmm analysis of the elevation and infection prevalence data as well as the script required to generate the figures in the article.
R script for analyses, figures, and supplemental figures
(European Organization for Nuclear Research, 2022) Geoffrey Lau; Alexandra Class Freeman; Paulo Pulgarin-R; Robert E. Ricklefs; Carlos Daniel Cadena; Benjamin G. Freeman
This script performs the glmm analysis of the elevation and infection prevalence data as well as the script required to generate the figures in the article.
R script for glmm analysis
(European Organization for Nuclear Research, 2022) Geoffrey Lau; Alexandra Class Freeman; Paulo Pulgarin-R; Robert E. Ricklefs; Carlos Daniel Cadena; Benjamin G. Freeman
This script performs the glmm analysis of the elevation and infection prevalence data as well as the script required to generate the figures in the article.
Replicate avian hybrid zones reveal the progression of genetic and trait introgression through time
(Oxford University Press, 2026) María Isabel Castaño; Elizabeth Croyle; Carlos Daniel Cadena; J Albert C Uy
Replicate hybrid zones between the same taxa provide a unique opportunity to assess the repeatability of the outcome of interspecific matings by uncovering recurrent genomic and phenotypic introgression patterns. Replicates also facilitate exploration of the causes of temporal shifts in hybrid zone structure. We sampled transects along three geographically separate hybrid zones between two avian taxa -the Lemon-rumped (Ramphocelus flammigerus icteronotus) and Flame-rumped (R. f. flammigerus) Tanagers-which hybridize in low passes across the Western Andes of Colombia. We examined environmental, phenotypic and genetic variation using reflectance spectrophotometry and genotype-by-sequencing data mapped to a high-quality de novo genome assembly, aiming to assess the repeatability and progression of introgression after hybridization. We found that all hybrid zones formed independently, showed parallel phenotypic divergence along ecological gradients, low population structure across parental ranges and similar demographic histories. Replicates also exhibited asymmetric introgression of neutral markers from the yellow icteronotus into the hybrid zone. However, the age of the hybrid zones differed, resulting in differences in the extent of geographic and genomic cline displacement from environmental transitions into the red flammigerus range. Despite heterogeneity in locus-specific introgression, the only shared introgression outliers across all hybrid zones were in a genomic region linked to plumage color. Clines for these loci were consistently narrow, suggesting a role in long-term reproductive isolation. Altogether, we showed that locus-specific introgression is largely stochastic, but the magnitude and directionality of neutral introgression can be predictable when demographic conditions are similar and for traits involved in reproductive isolation.
Songs in the understory and colors in the canopy: habitat structure leads to different avian communication strategies in a tropical montane forest
(2018) Oscar Laverde-R.; Carlos Daniel Cadena
Abstract Birds inhabit a variety of habitats and they communicate using primarily visual and acoustic signals; two central hypotheses have been postulated to study the evolution of such a signals. The sensory drive hypothesis posits that variation in the physical properties of habitats leads to variation in natural selection pressures by affecting the ease with which different types of signals are perceived. Assuming that resources are limited for animals, the transfer hypothesis predicts a negative relationship between the investments in different types of signals. We evaluated these two hypotheses in a tropical montane forest bird assemblage. We also postulate a possible interaction between these two hypotheses: we predicted that the negative relationships between signals should be observed only when jointly considering birds from different environments (e.g. understory and canopy) due to the expected differences in communication strategies between habitats. The sensory drive hypothesis was supported by the differences we found between strata in vocal output, patch contrast to background and color conspicuousness, but not for the variables associated to song elaboration and hue disparity. We found support for the transfer hypothesis: birds with colors contrasting less against the background sing more frequently and birds with lower diversity of colors produce longer songs, understory birds showed also a negative relationship between signals, but only when accounting for phylogeny. We found partial support for the interaction between the sensory drive and the transfer hypotheses: hue disparity and vocal output were negatively related only when analyzing together birds from the canopy and the understory, but not when analyzing them separately. We conclude that the study of the evolution of communication signals needs to consider more than one channel and the functional interactions between them. The results of the interaction of optimal signaling strategies in two communication channels in the local habitats where animals signaling, are the patterns of colors and songs we revealed in a tropical montane forest bird assemblage.
Systematics, biogeography and diversification of <i>Scytalopus</i> tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds
(2019) Carlos Daniel Cadena; Andrés M. Cuervo; Laura N. Céspedes; Gustavo A. Bravo; Niels Krabbe; Thomas S. Schulenberg; Graham E. Derryberry; Luís Fábio Silveira; Elizabeth P. Derryberry; Robb T. Brumfield
Abstract We studied the phylogeny, biogeography and diversification of suboscine birds in the genus Scytalopus (Rhinocryptidae), a widespread, speciose, and taxonomically challenging group of Neotropical birds. We analyzed nuclear (exons, regions flanking ultraconserved elements) and mitochondrial (ND2) DNA sequence data for a taxonomically and geographically comprehensive sample of specimens collected from Costa Rica to Patagonia and eastern Brazil. We found that Scytalopus is a monophyletic group sister to Eugralla , and consists of three main clades roughly distributed in (1) the Southern Andes, (2) eastern Brazil, and (3) the Tropical Andes and Central America. The clades from the Southern Andes and Eastern Brazil are sister to each other. Despite their confusing overall uniformity in plumage coloration, body shape and overall appearance, rates of species accumulation through time in Scytalopus since the origin of the clade in the Late Miocene are unusually high compared to those of other birds, suggesting rapid non-adaptive diversification in the group which we attribute to their limited dispersal abilities making them speciation-prone and their occurrence in a complex landscape with numerous barriers promoting allopatric differentiation. Divergence times among species and downturns in species accumulation rates in recent times suggest that most speciation events in Scytalopus predate climatic oscillations of the Pleistocene. Our analyses identified various cases of strong genetic structure within species and lack of monophyly of taxa, flagging populations which likely merit additional study to establish their taxonomic status. In particular, detailed analyses of species limits are due in S. parvirostris, S. latrans, S. speluncae , the S. atratus complex, and the Southern Andes clade.
When do tropical birds breed? The case of Colombian species assemblages
(2025) Miguel Moreno-Palacios; David Ocampo; María Ángela Echeverry-Gálvis; Camila Gómez; Gustavo A. Londoño; Carlos Daniel Cadena
ABSTRACT Understanding when tropical birds breed is key to life-history theory and to predicting how species will respond to environmental change. While early views emphasized the potential for year-round breeding in the tropics, accumulating evidence suggests that reproductive activity in most tropical birds follows some degree of seasonality, often linked to rainfall and associated food pulses. However, large-scale evaluations across ecological gradients remain scarce. Here, we investigated the breeding seasonality of Colombian resident birds using over 80,000 records compiled from bird banding programs and the Global Biodiversity Information Facility (GBIF). These data included birds in breeding conditions, active nests, nestlings, and adults displaying reproductive behavior. We asked four main questions: (1) Do Colombian birds exhibit seasonal breeding activity? (2) Does the degree of seasonality vary with latitude and elevation? (3) Are there geographic differences in breeding patterns across Colombia’s biogeographic regions? (4) How does breeding activity vary among feeding guilds? We used time-series, circular statistics, and generalized additive models (GAMs) to evaluate breeding patterns at national and regional levels, incorporating geographic variables and trophic guild. We found a clear seasonal pattern in breeding activity, with a main peak in April and low but consistent activity throughout the year, especially in the Andes. Breeding was more synchronized at higher latitudes and more extended near the Equator. Elevation also shaped seasonality: lowland bird assemblages showed broader breeding seasons, while mid- and high-elevation assemblages had narrower seasonal windows, driven by a shift in the breeding peak toward mid-year in highland birds. Regional and trophic guild variation was also marked. Caribbean birds bred sharply in April, Andean birds had prolonged reproductive activity peaking in March and June, and Chocoan birds peaked in March, followed by a decline. Breeding generally coincided with the start of rains and avoided extreme dry or wet months, in line with hygric niche theory. Feeding guilds differed as well: frugivores-nectarivores, omnivores, and invertivores bred mainly early in the year, while granivores peaked mid-year. Together, our findings offer new insights into tropical bird reproduction by showing that breeding activity in Colombia follows clear seasonal patterns shaped by rainfall regimes, elevation, and trophic ecology, contributing to the growing evidence of the complexity of breeding seasonality at tropical and near-equatorial latitudes.