Biology subjects

Campagna, L.

Publications and source records attributed to Campagna, L..

13 recordsLinked to original sources

bioRxiv2026

Gene conversion facilitates rapid evolution of inversions across avian immunoglobulin loci

The genomic architecture of immunoglobulin (IG) loci in birds has received remarkably little attention, despite their relevance to infectious disease susceptibility. One of the few exceptions is the domestic chicken, which has been found to use a completely different mechanism to generate a diverse IG repertoire than most vertebrates; rather than relying on V(D)J recombination, chickens primarily use somatic gene conversion. Whether this is true of all birds has remained unknown and untestable at scale until now. And importantly, it is not known how this alternative mechanism for antibody generation shapes, and is shaped by, genome evolution in birds. Leveraging IG locus annotations from 122 bird species generated through the Vertebrate Genomes Project and 17 species from the California Conservation Genomics Project, we show that avian IGH loci display a striking, previously unreported architecture of recurrent inverted duplications that generate direct and inverted copies of the same repeat unit, found in no other vertebrate lineage. Inversion density varies considerably across species, and population-level analyses reveal that these inversions evolve rapidly. We propose a model in which these inversions are actively maintained because they continuously replenish a pool of highly similar pseudogenes that serve as donors for somatic gene conversion, substituting for the large functional V gene repertoires other vertebrates use to generate IG diversity. This model makes a direct prediction: IGH loci should harbor few functional genes and many pseudogenes, while IGL loci, which typically lack this inversion architecture, should show the opposite pattern. Our cross-species analysis confirms this. To test the model at the level of the expressed repertoire, we generated paired whole-genome and Iso-seq data from a single wild-caught Red-winged Blackbird. Consistent with our predictions, a single terminal IGLV gene is diversified through gene conversion from surrounding pseudogenes, while IGH carries a large donor pool at which we also detect gene conversion. Together, these findings reveal that the molecular evolution of IG in birds is governed by fundamentally different constraints and processes than in the rest of known vertebrates.

evolutionary biology↗

bioRxiv2025

Continental diversification and insular speciation in a widespread passerine (Troglodytes musculus) in southern South America

Understanding how the evolutionary dynamics of geographically widespread species play out in space and time is critical for uncovering the processes shaping biodiversity. We integrated mitochondrial DNA and genome-wide SNPs to investigate the history of diversification of the Southern House Wren (Troglodytes musculus) in southern South America and its insular relative, Cobbs Wren (T. cobbi), from the Malvinas/Falkland Islands (MFI). T. musculus is an abundant and widespread species, and by studying its population structure and demographic history we aim to uncover the processes that may have shaped the evolutionary history of this and other co-distributed taxa in southern South America. All analyses indicate a latitudinal divergence, with an initial split between northern populations (Bolivia, Northern and Central Argentina, Uruguay) and southern populations from Patagonia and the MFI. Shortly after this initial divergence, further diversifications occurred, including the colonization of the MFI from Patagonia, where this newly formed insular population became isolated from the continent, and the split between an Andean lineage and a widespread, lowland lineage occurring in lowland Bolivia, Northern and Central Argentina and Uruguay. Both the timing of these splits and the mitochondrial and genomic patterns of variation uncovered in T. musculus are consistent with a major role of glaciations -and particularly the Great Patagonian Glaciation-in the diversification of this species in the southern Neotropics. The negligible gene flow between the MFI and the continent, which derived in the formation of a new species, Cobbs Wren, contrasts with the notorious gene flow in the secondary, post-glacial contact zones between the northern and southern lineages, although with reduced gene flow between the Andean and lowland populations. We also observed cases of mito-nuclear discordance, highlighting the value of multi-locus approaches in revealing complex evolutionary histories. These results underscore how historical divergence, ecological barriers and corridors, and secondary contact after varying degrees of differentiation in allopatry jointly shape population structure and genetic diversity, with implications for understanding the diversification of widely distributed taxa.

evolutionary biology↗

bioRxiv2025

A multiscale physicochemical characterization of melanin-based feather coloration in the rapid Capuchino Seedeater radiation

Melanin-based plumage coloration in birds is shaped by pigment composition as well as melanosome morphology and distribution, however, the ways in which these factors together modulate observable color remain poorly understood. We investigate this relationship in the Capuchino Seedeaters (genus Sporophila), whose recent, rapid radiation driven by sexual selection resulted in 12 species with diverse coloration patterns. Using scanning electron microscopy (SEM) and micro-computed tomography ({micro}CT), combined with a novel application of Fontana-Masson stain to image melanosomes at high resolution, we characterize melanosome distribution and morphology in several variably colored plumage patches across Capuchino species. Melanosome morphologies followed patch-specific patterns that did not directly correlate with coloration: crown feather melanosomes were larger, more elongated, and had greater percent eumelanin content than those in belly, throat, or dorsum/rump patches. We also observed that dorsal patches had more total melanin than ventral ones, with pigment and coloration patterns suggesting possible signaling and photoprotective roles. More generally, we show how the patch-specific coloration of male Capuchinos is accompanied by differences in melanosome morphology and melanin composition and abundance. Our work highlights the challenges that remain in understanding how the nanoscale mechanisms of melanin-based pigmentation translate into macroscale plumage coloration.

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↗

bioRxiv2025

A pangenomic approach reveals the sources of genetic variation fueling the rapid radiation of Capuchino Seedeaters

The search for the genetic basis of phenotypes has primarily focused on single nucleotide polymorphisms, often overlooking structural variants (SVs). SVs can significantly affect gene function, but detecting and characterizing them is challenging, even with long-read sequencing. Moreover, traditional single-reference methods can fail to capture many genetic variants. Using long-reads, we generated a Capuchino Seedeater (Sporophila) pangenome, including 16 individuals from seven species, to investigate how SVs contribute to species and coloration differences. Leveraging this pangenome, we mapped short-read data from 127 individuals to perform FST scans and genome-wide association studies. Species divergence primarily arises from SNPs and indels (< 50 bp) in non-coding regions of melanin-related genes, as larger SVs rarely overlap with divergence peaks. One exception was a 55 bp deletion near the OCA2 and HERC2 genes, associated with feather pheomelanin content. These findings support the hypothesis that the reshuffling of small regulatory alleles, rather than larger species-specific mutations, accelerated plumage evolution leading to prezygotic isolation in Capuchinos. TeaserSNPs and indels primarily shape species differences and plumage diversity in Capuchino Seedeaters.

evolutionary biology↗

bioRxiv2023

Genomic islands of speciation harbor genes underlying coloration differences in a pair of Neotropical seedeaters

Incomplete speciation can be leveraged to associate phenotypes with genotypes, thus providing insights into the traits relevant to the reproductive isolation of diverging taxa. We investigate the genetic underpinnings of the phenotypic differences between Sporophila plumbea and S. beltoni. S. beltoni has only recently been described based, most notably, on differences in bill coloration (yellow vs. black in S. plumbea). Both species are indistinguishable through mtDNA or reduced-representation genomic data, and even whole-genome sequencing revealed low genetic differentiation. Demographic reconstructions attribute this genetic homogeneity to gene flow, despite divergence in the order of millions of generations. We found a narrow hybrid zone in southern Brazil where genetically, yet not phenotypically, admixed individuals appear to be prevalent. Despite the overall low genetic differentiation, we identified three narrow peaks along the genome with highly differentiated SNPs. These regions harbor six genes, one of which is involved in pigmentation (EDN3) and is a candidate for controlling bill color. Within the outlier peaks we found signatures of resistance to gene flow, as expected for islands of speciation. Our study shows how genes related to coloration traits are likely involved in generating prezygotic isolation and establishing species boundaries early in speciation.

evolutionary biology↗

bioRxiv2021

SIA: Selection Inference Using the Ancestral Recombination Graph

Detecting signals of selection from genomic data is a central problem in population genetics. Coupling the rich information in the ancestral recombination graph (ARG) with a powerful and scalable deep learning framework, we developed a novel method to detect and quantify positive selection: Selection Inference using the Ancestral recombination graph (SIA). Built on a Long Short-Term Memory (LSTM) architecture, a particular type of a Recurrent Neural Network (RNN), SIA can be trained to explicitly infer a full range of selection coefficients, as well as the allele frequency trajectory and time of selection onset. We benchmarked SIA extensively on simulations under a European human demographic model, and found that it performs as well or better as some of the best available methods, including state-of-the-art machine-learning and ARG-based methods. In addition, we used SIA to estimate selection coefficients at several loci associated with human phenotypes of interest. SIA detected novel signals of selection particular to the European (CEU) population at the MC1R and ABCC11 loci. In addition, it recapitulated signals of selection at the LCT locus and several pigmentation-related genes. Finally, we reanalyzed polymorphism data of a collection of recently radiated southern capuchino seedeater taxa in the genus Sporophila to quantify the strength of selection and improved the power of our previous methods to detect partial soft sweeps. Overall, SIA uses deep learning to leverage the ARG and thereby provides new insight into how selective sweeps shape genomic diversity.

genetics↗

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

Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps

Numerous studies of emerging species have identified genomic "islands" of elevated differentiation against a background of relative homogeneity. The causes of these islands remain unclear, however, with some signs pointing toward "speciation genes" that locally restrict gene flow and others suggesting selective sweeps that have occurred within nascent species after speciation. Here, we examine this question through the lens of genome sequence data for five species of southern capuchino seedeaters, finch-like birds from South America that have undergone a species radiation during the last [~]50,000 generations. By applying newly developed statistical methods for ancestral recombination graph inference and machine-learning methods for the prediction of selective sweeps, we show that previously identified islands of differentiation in these birds appear to be generally associated with relatively recent, species-specific selective sweeps, most of which are predicted to be "soft" sweeps acting on standing genetic variation. Many of these sweeps coincide with genes associated with melanin-based variation in plumage, suggesting a prominent role for sexual selection. At the same time, a few loci also exhibit indications of possible selection against gene flow. These observations shed new light on the complex manner in which natural selection shapes genome sequences during speciation. Significance StatementGenome-wide scans can identify differentiated loci between species that may have promoted speciation. So-called "islands of differentiation" have generally been identified and characterized using standard population genetic summary statistics (e.g., FST and dxy), which are limited in distinguishing among possible causes of differentiation, such as selection against gene flow and selective sweeps. We introduce a powerful strategy for analyzing such islands, combining new methods for inferring the full Ancestral Recombination Graph and machine learning methods for identifying selective sweeps. We applied our methods to genomic sequences from closely related southern capuchino seedeaters (Neotropical tanagers) and found signatures of recent selective sweeps around pigmentation genes, including many "soft" sweeps that acted on standing variation.

evolutionary biology↗

bioRxiv2019

Genomic phylogeography of the White Crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

The complex landscape history of the Neotropics has generated opportunities for population isolation and diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow reveals a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last [~]2.5 Ma.

evolutionary biology↗

bioRxiv2017

Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: a proof of concept in a highly promiscuous bird

Information on genetic relationships among individuals is essential to many studies of the behavior and ecology of wild organisms. Parentage and relatedness assays based on large numbers of SNP loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double-digest restriction site-associated DNA sequencing (ddRAD-seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of SNP markers (typically 150-600 after stringent filtering) from large numbers of individuals (up to 240 per run). We explore the tradeoffs inherent in this approach through a set of experiments in a species with a complex social system, the variegated fairy-wren (Malurus lamberti), and further validate it in a phylogenetically broad set of other bird species. Through direct comparisons with a parallel dataset from a robust panel of highly variable microsatellite markers, we show that this ddRAD-seq approach results in substantially improved power to discriminate among potential relatives and considerably more precise estimates of relatedness coefficients. The pipeline is designed to be universally applicable to all bird species (and with minor modifications to many other taxa), to be cost- and time-efficient, and to be replicable across independent runs such that genotype data from different study periods can be combined and analyzed as field samples are accumulated.

animal behavior and cognition↗

bioRxiv2017

Correlated patterns of genetic diversity and differentiation across an avian family

Comparative studies of genomic differentiation among independent lineages can provide insights into aspects of the speciation process, such as the relative importance of selection and drift in shaping genomic landscapes, the role of genomic regions of high differentiation, and the prevalence of convergent molecular evolution. We investigated patterns of genetic diversity and divergence in stonechats (genus Saxicola), a widely distributed avian species complex with phenotypic variation in plumage, morphology, and migratory behavior, to ask whether similar genomic regions are important in the evolution of independent, but closely related, taxa. We used whole-genome pooled sequencing of 262 individuals from 5 taxa and found that patterns of genetic diversity and divergence are highly similar among different stonechat taxa. We then asked if these patterns remain correlated at deeper evolutionary scales and found that homologous genomic regions have become differentiated in stonechats and the closely related Ficedula flycatchers. Such correlation across a range of evolutionary divergence and among phylogenetically independent comparisons suggests that similar processes may be driving the differentiation of these independently evolving lineages, which in turn may be the result of intrinsic properties of particular genomic regions (e.g., areas of low recombination). Consequently, studies employing genome scans to search for areas important in reproductive isolation should account for corresponding regions of differentiation, as these regions may not necessarily represent speciation islands or facilitate local adaptation.

genomics↗