Biology subjects

Cadena, D.

Publications and source records attributed to Cadena, D..

16 recordsLinked to original sources

bioRxiv2025

Foraging behavior and ecology drive the evolution of humeral shape in hummingbirds

Understanding how locomotion-related skeletal elements evolve under biomechanical and ecological constraints is central to animal evolutionary biology. In hummingbirds (Trochilidae), the humerus plays a key role in force transmission during hovering and flapping flight, yet the drivers of its shape evolution have not been examined. We combined geometric morphometrics with phylogenetic comparative analyses to examine humeral shape variation, evolutionary rates, and phenotypic integration in male hummingbirds from 78 species. Our analyses identified humerus allometry as the dominant predictor of shape, revealing a pattern in which larger humeri show broader proximal epiphyses, increased shaft robustness, and reduced curvature. In addition to this scaling pattern, we find that male humerus shape differs subtly among hummingbird species that differ in the use of aggression during nectar foraging. Evolutionary rates of humeral shape were heterogeneous and decoupled from ecological predictors. We also find phenotypic integration between the proximal and distal regions of the humerus, indicating coordinated evolution. Together, these results show that humeral evolution in hummingbirds is governed primarily by biomechanical scaling and internal integration, with foraging ecology introducing secondary, size-dependent modifications. This work highlights the importance of considering scaling and internal integration when interpreting morphological evolution in locomotor systems across vertebrates.

evolutionary biology↗

bioRxiv2025

Replicate avian hybrid zones reveal the progression of genetic and trait introgression through time

Replicate hybrid zones between the same taxa provide a unique opportunity to assess the repeatability 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. Here 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.

evolutionary biology↗

bioRxiv2025

Host-specific bacterial modulation of airway gene expression and alternative splicing

The human microbiome varies extensively between individuals. While there are numerous studies investigating the effects of inter-individual differences on microbiome composition, there are few studies investigating inter-individual effects on microbial modulation of the host, or host-specific effects. To address this knowledge gap, we colonized human bronchial epithelial air-liquid interface tissue cultures generated from six different adults with one of three phylogenetically diverse bacteria and compared how each microbe differentially modulated host gene expression in each of the six donors. Microbial treatment had the strongest effect on transcription, followed by donor-specific effects. Gene pathways differed markedly in their donor- and microbe-specificity; interferon expression was highly donor-dependent while transcription of epithelial barrier and antibacterial innate immunity genes were predominantly microbially driven. Moreover, we evaluated whether microbial regulation of alternative splicing was modulated by donor. Strikingly, we found significant non-redundant, donor-specific regulation of alternative splicing exclusively in the Gram-positive commensal microbes. These findings highlight that microbial effects on the human airway epithelium are not only species-specific but also deeply individualized, scoring the importance of host context in shaping microbe-induced transcriptional and splicing responses.

microbiology↗

bioRxiv2024

A latitudinal gradient of reference genomes

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.

genomics↗

bioRxiv2024

Caldas meets Janzen: Thermal regimes of montane plants and implications for global patterns of speciation

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.

evolutionary biology↗

bioRxiv2024

Changes in bird migration phenology over one century: a perspective from the Neotropical non-breeding grounds

Changes in the migration phenology of birds linked to global change are extensively documented. Longitudinal studies from temperate breeding grounds have mostly shown earlier arrivals in the spring and a variety of patterns during fall migration 1,2, yet no studies have addressed whether and how migration phenology has changed using data from the tropical non-breeding grounds. Understanding whether changes in migratory phenology are also evident in non-breeding sites is essential to determine the underlying causes of patterns documented in breeding areas. Using data from historical scientific collections and modern repositories of community-science records, we assessed changes in migration phenology of 12 Nearctic-Neotropical long-distance migratory birds in Colombia over six decades. We also explored whether shared breeding and non-breeding climatic niches explained variation in phenological patterns observed among species. All species showed shifts in spring (range -37 - 9 days from peak passage date) or fall (range -26 - 36 days) migration, but patterns differed among species in ways partly attributable to shared breeding or wintering climatic niches. Our results, although not yet broadly generalizable, suggest that birds use cues to time their migration at their non-breeding grounds which are most likely different to those they use on their breeding grounds. To better understand the effects of global change on biodiversity, exploring the underlying drivers of phenological changes with further research integrating more long-term datasets available through scientific collections and community science platforms should be a priority.

ecology↗

bioRxiv2023

A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments

Animals living in caves are of broad relevance to evolutionary biologists interested in understanding the mechanisms underpinning convergent evolution. In the Eastern Andes of Colombia, populations from at least two distinct clades of Trichomycterus catfishes (Siluriformes) independently colonized cave environments and converged in phenotype by losing their eyes and pigmentation. We are pursuing several research questions using genomics to understand the evolutionary forces and molecular mechanisms responsible for repeated morphological changes in this system. As a foundation for such studies, here we describe a diploid, chromosome-scale, long-read reference genome for Trichomycterus rosablanca, a blind, depigmented species endemic to the karstic system of the department of Santander. The nuclear genome comprises 1Gb in 27 chromosomes, with a 40.0x HiFi long-read genome coverage having a N50 scaffold of 40.4 Mb and N50 contig of 13.1 Mb, with 96.9% (Eukaryota) and 95.4% (Actinopterygii) universal single-copy orthologs (BUSCO). This assembly provides the first reference genome for the speciose genus Trichomycterus, which will serve as a key resource for research on the genomics of phenotypic evolution.

genomics↗

bioRxiv2023

The role of learning in the evolution of status signalling: a modeling approach

Adaptive behavioural responses often depend on qualities of the interacting partner of an individual. For example, when competing for resources, an individual might be better off escalating fights with individuals of lower quality, while restraining from fighting individuals of higher quality. Communication systems involving signals of quality allow individuals to reduce uncertainty regarding the fighting ability of their partners and make more adaptive behavioral decisions. However, dishonest individuals can destabilize such communications systems. An open question is whether cognitive mechanisms, such as learning, can maintain the honesty of signals, thus favoring their evolutionary stability. We present evolutionary simulations where individuals can produce a signal proportional to their quality and learn along their lifetime the best response to the signals emitted by their peers. Our simulations replicate previous results where the handicap principle mediates the evolution of signals. In our simulations learning on the receiver side can mediate the evolution of signals of quality on the sender side. When the cost of the signal is proportional to the quality of the sender, all individuals in populations are honest signalers. In contrast to traditional models which predict the absence of signals when the cost is not proportional to the quality of the signaler, our model revealed that learning facilitates the evolution of a polymorphism in which populations comprise both honest and dishonest signalers. We argue that learning may have a role in the evolution and dynamics of a wide range of communication systems and more generally in behavioral responses.

evolutionary biology↗

bioRxiv2020

100+ years of bird survey data reveal changes in functional fingerprints indexing ecosystem health of a tropical montane forest through time

Ecologically relevant traits of organisms inhabiting an ecosystem determine its functional fingerprint. Quantifying changes in the shape, volume and shifts in the position of functional fingerprints can provide information about the effects of diversity loss or gain through time, and is a promising means to monitor ecological integrity. This, however, is seldom possible owing to limitations in historical surveys and lack of data on organismal traits, particularly in diverse tropical regions. Using detailed bird surveys from four time periods across more than one century and morphological traits of 233 species, we quantified changes in the avian functional fingerprint of a tropical montane forest site in the Andes of Colombia. We found that 79% of the variation in functional space, regardless of time period, was described by three major axes summarizing body size, dispersal ability, and habitat breadth. Changes in species composition caused significant alterations of the functional fingerprint of the assemblage, with 35 – 60% reductions in functional richness and dispersion. Owing to species extirpations and to novel additions to the assemblage, functional space is currently smaller and at least 11% different to what it was a century ago, with fewer large-sized species, more good dispersers, and fewer habitat specialists. Extirpated species had high values of functional uniqueness and distinctiveness, resulting in large reductions of functional richness and dispersion after their loss, implying potentially important consequences for ecosystem functioning. Conservation efforts aimed at maintaining ecosystem function must move beyond maintaining species numbers to designing strategies for the maintenance of ecological function by identifying and conserving species with traits conferring high vulnerability.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗

bioRxiv2020

Complete mitochondrial genomes do not distinguish phenotypically distinct lineages of Andean Coeligena hummingbirds

Lack of divergence in mitochondrial DNA between species with clear phenotypic differences may be the result of low resolution of markers, incomplete lineage sorting, introgression, or the interplay of various evolutionary mechanisms acting on different traits and genomic regions through time. Previous work revealed that the Andean hummingbirds Coeligena bonapartei and C. helianthea lack genetic divergence in the mitochondrial ND2 gene, which shows variation discordant with coloration phenotype but consistent with geography. We sequenced and analyzed complete mitochondrial genomes for C. b. bonapartei, C. b. consita, C. h. helianthea and C. h. tamai to assess whether patterns revealed by ND2 analyses hold when considering the entire mitogenome, and to shed light into the evolutionary history of these hummingbirds. We found very low genetic differentiation in mitogenomes among the four lineages of Coeligena, confirming patterns based on ND2 data. Estimates of genetic differentiation, phylogenies and haplotype network analyses of complete mitogenomes did not separate phenotypically distinct taxa, but were consistent with a previously described pattern of northern vs. southern divergence along the Cordillera Oriental of Colombia. Mitogenomes of C. b. bonapartei and C. h. helianthea are indistinguishable, suggesting incomplete lineage sorting or strong introgression. Mitogenomes of C. b. consita and C. h. tamai are slightly differentiated, but they are more similar to each other than either is to that of its respective nominate subspecies, a result also suggestive of mtDNA introgression despite distinct phenotypic differences. Our results indicate that various evolutionary mechanisms playing out over a complex biogeographic scenario in the Colombian Andes drove divergence in phenotypes and mitochondrial genomes of Coeligena hummingbirds, and lead to alternative hypotheses to be tested with whole-genome analyses.

evolutionary biology↗

bioRxiv2020

Plumage convergence resulting from social mimicry in birds? A tetrachromatic view

Social mimicry may lead to convergent evolution when interactions with conspecific and heterospecific individuals drive evolution towards similar phenotypes in different species. Several hypotheses accounting for convergence in communication signals based on mechanisms of social mimicry exist, but evaluations of how similar species are given the visual system of receptors of such signals have been ostensibly missing from tests of such hypotheses. We used plumage reflectance measurements and models of avian color discrimination to evaluate the efficacy of visual deception and therefore the plausibility of mimicry hypotheses accounting for plumage convergence among six species of passerine birds in the flycatcher family (Tyrannidae) with strikingly similar plumage. We rejected interspecific social mimicry hypotheses as an explanation for the similarity between one putative model species and putative mimics because deception seems unlikely given the visual system of passerines. However, plumage similarity was consistent with a role for selective pressures exerted by predators because dorsal coloration of putative model and mimic species was indistinguishable by visually oriented raptors. Experiments and behavioral observations are necessary to better characterize social interactions and to test predictions of alternative mimicry hypotheses proposed to account for convergence.

evolutionary biology↗

bioRxiv2019

Origin of elevational replacements in a clade of nearly flightless birds - most diversity in tropical mountains accumulates via secondary contact following allopatric speciation

Tropical mountains are biodiversity hotspots. In particular, mountains in the Neotropics exhibit remarkable beta diversity reflecting species turnover along elevational gradients. Elevational replacements of species have been known since early surveys of the tropics, but data on how such replacements arise are scarce, limiting our understanding of mechanisms underlying patterns of diversity. We employed a phylogenetic framework to evaluate hypotheses accounting for the origin of elevational replacements in the genus Scytalopus (Rhinocryptidae), a speciose clade of passerine birds with limited dispersal abilities occurring broadly in the Neotropical montane region. We found that species of Scytalopus have relatively narrow elevational ranges, closely related species resemble each other in elevational distributions, and most species replacing each other along elevational gradients are distantly related to each other. Although we cannot reject the hypothesis that a few elevational replacements may reflect parapatric speciation along mountain slopes, we conclude that speciation in Scytalopus occurs predominantly in allopatry within elevational zones, with most elevational replacements resulting from secondary contact of formerly allopatric lineages. Our study suggests that accumulation of species diversity in montane environments reflects colonization processes as opposed to in situ divergence even in dispersal-limited animals.

evolutionary biology↗

bioRxiv2019

Systematics, biogeography and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds

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.

evolutionary biology↗

bioRxiv2018

Extreme genetic structure and dynamic range evolution in a montane passerine bird: implications for tropical diversification

AimEmploy phylogeographic analyses of a widespread species complex to examine the role of historical and evolutionary processes in the origin and maintenance of high species diversity in the Neotropical montane region.\n\nLocationNeotropical highlands.\n\nTaxonHenicorhina wood-wrens (Aves, Troglodytidae).\n\nMethodsWe collected mtDNA sequence data for 288 individuals thoroughly covering the range of the Henicorhina leucophrys complex from Mexico to Bolivia. Sequences were employed to characterize population structure, infer phylogenetic relationships among populations and their divergence times, examine lineage accumulation through time, and identify presumptive species using coalescent methods. We also explored the origin of elevational and latitudinal replacements involved in spatial changes in species assemblages in the Andes.\n\nResultsWe found remarkable genetic structure within the complex, which consists of numerous lineages reaching >12% sequence divergence; most divergent populations occur in areas separated by topographic barriers but several of them, typically not sister to each other, co-occur with elevational segregation on mountain slopes or replace each other with latitude along the Andes. Some close relatives occur in areas separated by thousands of kilometers, with more distant relatives occupying intervening areas. The complex likely originated in the Mexican highlands and expanded extensively in South America while diverging rapidly at a constant rate into many different lineages which have persisted for millions of years. Coalescent analyses consistently revealed that the complex may comprise more than 30 species; while we do not suggest these presumptive species should be recognized by taxonomists in the absence of additional data, H. leucophrys is a distant outlier among New World birds in terms of high lineage diversity within a single recognized species.\n\nMain ConclusionsOur study captured wood-wren lineages in the act of building up diversity via divergence and persistence in allopatry, achievement of secondary sympatry, and coexistence at the landscape scale mediated by ecological and evolutionary divergence. Although dispersal by wood-wrens is restricted at present and this likely accounts for strong population structure across topographic barriers, their ranges have been dynamic, managing to disperse over much of the montane Neotropics. Phases of expansion and contraction of ranges and localized extinctions of populations likely account for phylogeographic patterns which are precursors to the origin of new species and the accumulation of diversity in tropical mountains.

evolutionary biology↗

bioRxiv2017

Can net diversification rates account for spatial patterns of species richness?

The diversification rate hypothesis (DRH) proposes that spatial patterns of species richness result from spatial variation in net diversification rates. We developed an approach using a time-calibrated phylogeny and distributional data to estimate the maximum explanatory power of the DRH, over a given time period, to current species richness in an area. We used this approach to study species richness patterns of a large family of suboscine birds across South America. The maximum explanatory power of the DRH increased with the duration of the time period considered and grain size; it ranged from 13 - 37 fold local increases in species richness for T = 33 Ma to less than 2-fold increases for T [≤] 10 Ma. For large grain sizes ([≤] 8{degrees} x 8{degrees}) diversification rate over the last 10 Ma could account for all the spatial variance in species richness, but for smaller grain sizes commonly used in biogeographical studies (1{degrees} x 1{degrees}), it could only explain < 16% of this variance. Thus, diversification since the Late Miocene, often thought to be a major determinant of Neotropical diversity, had a limited imprint on spatial richness patterns at small grain sizes. Further application of our approach will help determine the role of the DRH in explaining current spatial patterns of species richness.\n\nNote to readersThis manuscript has been seen by a few researchers, some of whom suggested that before publishing our work in a peer-reviewed journal we should conduct simulations to demonstrate that our methods properly estimate the contribution of variance in diversification rates to spatial variation in species richness. Although we believe that our approach derives logically from theory and statistics and is therefore valid, we understand that it is rather unique and see why some readers would think that an independent validation is necessary. Unable to complete such validation in the near future, however, we decided to make this manuscript available as a preprint to share our ideas and hopefully stimulate discussion on what we believe is a most interesting topic. We also hope to receive feedback that may enable us to improve our work for publication in a journal at a later date.

evolutionary biology↗

bioRxiv2017

Evolution of bird communication signals: transference between signals mediated by sensory drive

Animals communicate using signals perceived via multiple sensory modalities but usually invest more heavily in one of type of signal. This pattern, observed by Darwin1 and many researchers since, led to development of the transfer hypothesis (see also transferal effect2 and tradeoff hypothesis3,4), which predicts a negative relationship between investment in different signaling modalities dictated by the relative costs and benefits of each. One factor that influences costs and benefits, and is central to the sensory drive hypothesis5 posed to account for signal evolution, is the suitability of the environment for different types of signals. Movement into a dark habitat, for example, should favor investment in acoustic over visual signals. We use phylogenetic comparative methods to analyze the joint effect of transfer and sensory drive on plumage and song variation in 52 species of a large radiation of passerine birds, the New World warblers (Parulidae), and to estimate temporal patterns in the accumulation of differences in visual and vocal signals and habitat along the evolutionary history of this lineage. We found evidence for the predicted negative correlations between a variety of song and plumage traits that vary with habitat type. Plumage contrast to background and chromatic diversity were both negatively related to syllable variety when vegetation structure was a covariate: birds with a greater variety of song syllables and less colorful plumages live in closed or darker habitats. Also as predicted, achromatic or brightness diversity was related to vegetation structure. In addition, disparity-through-time analyses showed that when one set of traits (i.e. songs or colors) diversified at a relatively high rate the other did not, as predicted by the transfer hypothesis. Our results show that sensory drive influences the transfer of investment between traits in different sensory modalities. This interaction between mechanisms shaping signals may be a major determinant in the evolution of animal communication.

evolutionary biology↗