Biology subjects

Cadena, C. D.

Publications and source records attributed to Cadena, C. D..

14 recordsLinked to original sources

bioRxiv2026

Balancing mechanics and metabolism: elevational variation in the microanatomy of hummingbird flight muscle

Factors varying along elevational gradients impose strong aerodynamic and physiological constraints on powered flight, yet the internal microanatomical variation associated with elevational context in animals under such conditions remains poorly understood. In hummingbirds, sustained hovering requires extreme muscular power output, making the pectoralis muscle a key tissue for evaluating anatomical variation associated with elevational context. We tested whether pectoralis microanatomy differed among hummingbirds sampled at three elevationally distinct sites spanning a [~]1500 m gradient in the Colombian Andes. Using tissue morphometry of trichrome-stained transverse sections of the pectoralis, we measured collagen-rich interstitial extracellular matrix fraction as an anatomical proxy and quantified fiber-profile cross-sectional area, packing density, and size heterogeneity. Collagen-rich ECM fraction differed among sites, with the highest values at the mid-elevation site and the lowest values at the high-elevation site. Fiber-profile cross-sectional area tended to be lower and packing density higher at the high-elevation site, although site-level contrasts showed broad uncertainty. Because species identity and site could not be fully disentangled in this limited dataset, these patterns are interpreted as site-associated anatomical variation rather than definitive evidence of elevation-driven adaptation. These results suggest that hummingbird pectoralis microanatomy differs among sampled elevational contexts in a trait-specific manner, with the strongest evidence in fiber geometry. More broadly, our findings highlight that multiple components of muscle microarchitecture, including the extracellular matrix, are consistent with diffusion-related expectations rather than direct evidence of functional performance differences.

evolutionary biology↗

bioRxiv2026

It is about the shape: Recurrent Body Shape Patterns in Cave- and Surface-Dwelling Trichomycterid Cavefishes

The evolution of body shape reflects the interplay between functional constraints and habitat structure. While cave environments are well known to promote regressive traits in fish such as eye and pigment loss, their influence on overall body form remains poorly understood. Here, we examine patterns of body shape variation in cave-dwelling and surface-dwelling trichomycterid catfishes from northeastern Colombia to assess whether consistent associations exist between habitat type and morphology. Using geometric morphometric analyses, we quantified differences in body shape among species inhabiting subterranean and surface environments. Our results reveal significant habitat-associated differentiation in body shape associated with habitat along the main axes of morphological variation, despite some overlap indicating that habitat does not fully predict morphological variation. Cave-dwelling species exhibit more elongated and fusiform body shapes, whereas surface-dwelling species tend to have deeper and more robust morphologies. These patterns are consistent with differences in habitat-associated ecological conditions, although no direct functional or performance data were evaluated. The recurrence of similar body shapes among species from different clades occupying comparable habitats is consistent with repeated morphological responses to shared ecological constraints. Research HighlightsO_LIMultivariate shape analyses reveal significant habitat-associated variation in trichomycterid fishes, with partial overlap indicating that habitat does not fully predict morphological variation. C_LIO_LIBody shape differs consistently between cave-and surface-dwelling trichomycterids: cave species exhibit more elongated, fusiform forms, whereas surface species display deeper body configurations. C_LIO_LIRecurrent body shape patterns across independent lineages are consistent with repeated phenotypic responses to shared ecological constraints, without directly testing functional or performance mechanisms. C_LI

evolutionary biology↗

bioRxiv2025

History of divergence and gene flow shaping geographic variation in Andean warblers (Myioborus)

Studying how genetic variation is structured across space, and how it relates to divergence in phenotypic traits relevant to reproductive isolation, is important for our overall understanding of the speciation process. We used reduced-representation genomic data (ddRAD-seq) to examine patterns of genetic variation across the full distribution of an Andean warbler species complex (Myioborus ornatus-melanocephalus), which includes a known hybrid zone between two strikingly different plumage forms. Genetic structure largely reflects geographic variation in head plumage, some of which corresponds to major topographic barriers in the Andes. We also found evidence of isolation by distance shaping genetic patterns across the groups broad latitudinal range. We found that chrysops and bairdi, two taxa with marked plumage differences that have a known hybrid zone, were characterized by low overall genetic divergence. Based on our cline analyses of both plumage and genomic hybrid indices, this hybrid zone extends for approximately 250 km, where advanced generation hybrids are likely most common. We also identified a slight difference in the centers of the plumage and genomic clines, potentially suggesting the asymmetric introgression of chrysops-like plumage traits. By studying genetic variation in a phenotypically complex group distributed across a topographically complex area, which includes a hybrid zone, we were able to show how both geographic features and potentially sexually selected plumage traits may play a role in species formation in tropical mountains

evolutionary biology↗

bioRxiv2025

Diversification and divergence in Myioborus warblers: insights into evolutionary relationships and plumage genetics

Genomic data can provide valuable insights into the evolutionary history of rapidly diversifying groups and the genetic basis of phenotypic differences among lineages. We used whole-genome sequencing of the warbler genus Myioborus to investigate dynamics of its recent diversification in Neotropical mountains. We found that mitochondrial and UCE phylogenies are mostly, but not fully, concordant, and we found phylogenetic support for a pattern of north-to-south and low-to-high elevation colonization in the genus. Within the ornatus-melanocephalus complex, which showed topological incongruence between our phylogenies, we found that genetic structure generally coincides with geographic variation in plumage, although three subspecies with striking plumage differences exhibit low mitochondrial divergence. The hybridizing taxa M. o. chrysops and M. m. bairdi show very shallow genomic differentiation, with marked peaks of divergence. Most of these are shared with other parulid warbler pairs, pointing to broad genomic features, like recombination rate, as the processes shaping these regions. However, other highly differentiated regions were unique to Myioborus, including one containing the gene CCDC91, which is associated with melanin-based plumage differences in several other birds. Lastly, we found higher levels of differentiation on the Z chromosome relative to autosomes, including two putative chromosomal inversions. Together, these results highlight the interplay of deep ancestral divergence, recent hybridization, and shared genomic architecture in shaping the evolution of phenotypic and genomic diversity within Myioborus.

evolutionary biology↗

bioRxiv2023

Winging it: Unveiling how hummingbirds alter their flying kinematics during molt.

Hummingbirds are well known for their hovering flight, one of the most energetically expensive modes of locomotion among animals. Molt is a costly event in the annual cycle, in which birds replace their feathers, including all their primary feathers which, in hummingbirds, comprise most of the area of the wing. Despite this, the effects of molt on hovering flight are not well known. Here, we examined high-speed videos (14 individuals of three species from the Colombian Andes recorded at 1200 FPS) comparing molting and non-molting hummingbirds wing kinematics and wingtip trajectories. We found that molting hummingbirds extended their wings in sharper angles during both downstroke and upstroke compared to non-molting individuals (10{degrees} vs 20{degrees}, and 15{degrees} vs 29{degrees}, respectively), while other flight parameters remained unchanged. Our findings show that hummingbirds are capable of sustaining hovering flight kinematics even under impressive wing area reductions by adjusting their wing flapping behavior.

biophysics↗

bioRxiv2022

Adaptive variation in avian eggshell structure and gas conductance across elevational gradients?

Many tropical species have restricted elevational distributions, which are potentially bounded by constraints imposed by physical conditions on physiological processes. Although some studies have examined variation in the physiology of adult birds with respect to elevation, little attention has been paid to the structure and function of eggshells, which mediate gas exchange between the embryo and the environment. At high elevations, dry air is expected to increase water loss from the egg; selection to avoid desiccation might therefore be expected to favor reduced gas conductance by means of increased eggshell thickness or reduced pore size. We used gas diffusion experiments and scanning electron microscopy to examine water vapor conductance rates and eggshell structures in 197 bird species distributed along an elevational gradient in the Andes. As predicted, water vapor conductance across the eggshell declined in a narrow range with elevation among all species and among species within families, but not among individuals within species. Variation among species in eggshell conductance was lower at high-elevation sites, potentially indicating greater constraints at such sites. Structural changes in eggshells with respect to elevation varied among taxonomic families of birds, suggesting potentially different adaptive responses to common selective pressures in terms of eggshell thickness and pore density, and size. We suggest that considering functional and structural traits of eggshells, which influence embryo development, may help one to better understand the elevational distributions of species and to forecast their responses to global climate change.

evolutionary biology↗

bioRxiv2020

Allochronic Divergence Driven by Spatial Asynchrony in Precipitation in Neotropical Frogs?

The role of geographic barriers in promoting reproductive isolation across space is well understood. Isolation by the time of breeding, however, may also promote population divergence when populations reproduce asynchronically in space, even in the absence of geographic barriers. Few examples exist of divergence due to breeding allochrony, particularly in vertebrates. We tested whether in Neotropical frogs asynchrony in precipitation patterns promotes intraspecific genetic divergence, speciation, and regional accumulation of diversity. We assessed the relationship between spatial asynchrony in precipitation and genetic divergence controlling for ecological connectivity across 48 Neotropical frog species. In addition, we examined whether regions within which precipitation regimes are more asynchronous across space have higher species richness and have experienced greater speciation rates. Beyond a generalized expected effect of ecological connectivity on intraspecific genetic divergence, we found that asynchrony in precipitation is positively associated with genetic differentiation in 31% of the species tested, resulting in a significantly positive cross-species effect of asynchrony in precipitation on genetic divergence in a meta-analysis. However, the effect of asynchrony in precipitation on population divergence seems not to scale to macroevolutionary patterns because spatial asynchrony in precipitation was not associated with geographical patterns of species richness or speciation rates. Our results indicate that genetic divergence can be promoted by asynchronous breeding lag in the absence of geographic barriers in species where breeding is associated with water availability, but such effects may not be stable enough through time to influence macroevolutionary patterns.

ecology↗

bioRxiv2020

Repeated colonization of caves leads to phenotypic convergence in catfishes (Siluriformes: Trichomycterus) at a small geographical scale

Across various animal groups, adaptation to the extreme conditions of cave environments has resulted in convergent evolution of morphological, physiological, and behavioral traits. We document a Neotropical cave fish system with ample potential to study questions related to convergent adaptation to cave environments at the population level. In the karstic region of the Andes of Santander, Colombia, cave-dwelling catfishes in the genus Trichomycterus exhibit variable levels of reduction of eyes and body pigmentation relative to surface congeners. We tested whether cave-dwelling, eye reduced, depigmented Trichomycterus from separate caves in Santander were the result of a single event of cave colonization and subsequent dispersal, or of multiple colonizations to caves by surface ancestors followed by phenotypic convergence. Using mitochondrial DNA sequences to reconstruct phylogenetic relationships of Trichomycterus from Santander, we found that caves in this region have been colonized independently by two separate clades. Additional events of cave colonization -and possibly recolonization of surface streams- may have occurred in one of the clades, where surface and cave-dwelling populations exhibit shallow mtDNA differentiation, suggesting recent divergence or divergence in the face of gene flow. We also identified various taxonomic challenges including both a considerable number of potentially undescribed species and likely problems with the circumscription of named taxa. The system appears especially promising for studies on a wide range of ecological and evolutionary questions.

evolutionary biology↗

bioRxiv2019

Genome Report: De novo assembly of a high-quality reference genome for the Horned Lark (Eremophila alpestris)

The Horned Lark (Eremophila alpestris) is a species of small songbird that exhibits remarkable geographic variation in appearance and habitat across an expansive distribution. While E. alpestris and related species have been the focus of many ecological and evolutionary studies, we still lack a highly contiguous genome assembly for horned larks and related taxa (Alaudidae). Here, we present CLO_EAlp_1.0, a highly contiguous assembly for horned larks generated from blood samples of a wild, male bird captured in the Altiplano Cundiboyacense of Colombia. By combining short-insert and mate-pair libraries with the ALLPATHS-LG genome assembly pipeline, we generated a 1.04 Gb assembly comprised of 2708 contigs with an N50 of 10.58 Mb and a L50 of 29. After polishing the genome, we were able to identify 94.5% of single-copy gene orthologs from an Aves data set and 97.7% of single-copy gene orthologs from a vertebrata data set, indicating that our de novo assembly is near complete. We anticipate that this genomic resource will be useful to the broader ornithological community and those interested in studying the evolutionary history and ecological interactions of a widespread, yet understudied lineage of songbirds.

genomics↗

bioRxiv2018

Songs in the understory and colors in the canopy: habitat structure leads to different avian communication strategies in a tropical montane forest

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.

evolutionary biology↗

bioRxiv2018

Shallow evolutionary divergence between two Andean hummingbirds: Speciation with gene flow?

Ecological speciation can proceed despite genetic interchange when selection counteracts homogeneizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, two parapatric Andean hummigbirds with marked plumage divergence. We sequenced neutral markers (mtDNA and nuclear ultra conserved elements) to examine genetic structure and gene flow, and a candidate gene (MC1R) to assess its role underlying divergence in coloration. We also tested the prediction of Glogers rule that darker forms occur in more humid environments, and compared ecomorphological variables to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was very low and coalescent estimates of migration were consistent with divergence with gene flow. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in ecomorphology. Although we reject adaptation to variation in humidity as the cause of divergence, we hypothesize that speciation likely occurred in the face of gene flow, driven by other ecological pressures or by sexual selection. Marked phenotypic divergence with no neutral genetic differentiation is remarkable for Neotropical birds, and makes C. helianthea and C. bonapartei an appropriate system in which to search for the genetic basis of species differences employing genomics.

evolutionary biology↗

bioRxiv2017

Bird songs on the shelf: assessing vocal activity and output using data hidden in sound archives

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.

zoology↗

bioRxiv2017

An extinct hummingbird species that never was: a cautionary tale about sampling issues in molecular phylogenetics

The Bogota Sunangel (Heliangelus zusii) was described based on a historical specimen lacking locality data as a striking-and potentially extinct- new species of hummingbird more than two decades ago. However, it was considered a dubious taxon by some researchers until a molecular study with strong species-level taxon sampling revealed its phylogenetic affinities and validated its status as a distinct species. We reanalysed existing mitochondrial DNA data together with a new data set sampling multiple populations of the Long-tailed Sylph (Aglaiocercus kingii), a species broadly distributed in the Andes of South America. In contrast to previous work, we found that H. zusii shares a haplotype with specimens of A. kingii from the Eastern Cordillera of Colombia, which is phylogenetically nested within a clade formed by populations of A. kingii from the Colombian Andes. These results suggest that H. zusii is not a distinct species, but is most likely the result of hybridization between a female A. kingii and a male of another hummingbird species. These findings highlight the importance of thorough taxonomic and geographic sampling when assessing the likelihood of hybrid origin of an organism, particularly in cases potentially involving wide-ranging species in areas where deep phylogeographic structure is likely.

evolutionary biology↗

bioRxiv2017

Atlantean Evolution in Darwin’s Finches—Issues and Perspectives in Species Delimitation using Phenotypic Data

Progress in the development and use of methods for species delimitation employing phenotypic data lags behind conceptual and practical advances in molecular genetic approaches. The basic evolutionary model underlying the use of phenotypic data to delimit species assumes random mating and quantitative polygenic traits, so that phenotypic distributions within a species should be approximately normal for individuals of the same sex and age. Accordingly, two or more distinct normal distributions of phenotypic traits suggest the existence of multiple species. In light of this model, we show that analytical approaches employed in taxonomic studies using phenotypic data are often compromised by three issues: (1) reliance on graphical analyses of phenotypic space that do not consider the frequency of phenotypes; (2)exclusion of characters potentially important for species delimitation following reduction of data dimensionality; and (3) use of measures of central tendencies to evaluate phenotypic distinctiveness. We outline approaches to overcome these issues based on statistical developments related to normal mixture models and illustrate them empirically with a reanalysis of morphological data recently used to claim that there are no morphologically distinct species of Darwins ground-finches (Geospiza). We found negligible support for this claim relative to taxonomic hypotheses recognizing multiple species. Although species limits among ground-finches merit further assessments using additional sources of information, our results bear implications for other areas of inquiry including speciation research: because ground-finches have likely speciated and are not trapped in a process of \"Sisyphean\" evolution as recently argued, they remain useful models to understand the evolutionary forces involved in speciation. Our work underscores the importance of statistical approaches grounded on appropriate evolutionary models for species delimitation. Approaches allowing one to fit normal mixture models without a priori information about species limits offer new perspectives in the kind of inferences available to systematists, with significant repercusions on ideas about the structure of biological biodiversity. [morphology; normal mixture model; phenotype; principal components analysis; species limits; variable selection.]

evolutionary biology↗