Biology subjects

Braun, M. J.

Publications and source records attributed to Braun, M. J..

9 recordsLinked to original sources

bioRxiv2026

Can the Z:A ratio serve as a genomic index of sexual selection? An assessment across space and time in a genus of lekking birds

Understanding the role of sexual selection in shaping evolutionary trajectories is a key goal of biology, and thus developing a genomic measure of sexual selection strength is desirable. In systems with ZW sex determination, the ratio of nucleotide diversity ({pi}) on the male-biased Z chromosome to that on the autosomes (the Z:A ratio) is expected to decline as male effective population size decreases under strong sexual selection, offering one such measure. However, non-equilibrium processes other than sexual selection (e.g., hybridization, changes in population size) can influence levels of Z-linked diversity relative to the rest of the genome, complicating interpretation of this metric and necessitating a systematic evaluation of how Z:A ratios vary across known demographic and selective circumstances. We leveraged longitudinal sampling over a [~]25-year period in Manacus manakin populations in western Panama, spanning a mainland transect (including M. candei, M. vitellinus, and their hybrid zone) and insular populations of the Bocas del Toro Archipelago. On the mainland, Z:A ratios were temporally stable within populations, but varied across populations: (1) Z:A ratios were lower in M. vitellinus than M. candei, likely due to stronger sexual selection in the former; and (2) Z:A ratios increased at the hybrid zone center, likely due to fast-Z effects in parentals inflating Z:A ratios in recent hybrids. Island populations exhibited significantly lower Z:A ratios than mainland populations, consistent with theoretical expectations of Z:A reductions following population contractions as the islands became isolated. Insular Z:A ratios increased with proximity to other landmasses, suggesting gene flow mitigates these effects in this system. While the Z:A ratio behaved predictably in relation to known non-equilibrium processes, our results demonstrate the potentially strong effects of demographic history and admixture on Z-linked diversity, which should be considered in studies aiming to use the Z:A ratio as a measure of sexual selection.

evolutionary biology↗

bioRxiv2026

Retention of a female-specific growth hormone receptor gene correlates with reverse sexual size dimorphism in birds

In bird species, larger males are the most common, followed by equal-sized sexes; larger females are rarest. Although multiple forces have been proposed to select for larger female body size, the molecular mechanisms determining this trait remain uncharacterized. The avian gene for growth hormone receptor (GHR) on the Z chromosome is a known factor in sex-specific development. Male birds (ZZ) have two copies of this gene, while females (ZW) typically have one. In addition to the Z copy of GHR found in all birds, we identified a second copy of GHR, documenting its presence or absence across the avian phylogeny by searching over a thousand genomes. This copy was solely found in females. When this second copy can be assigned to a chromosome, it is always located on the W. We infer that this second copy is a gametolog that was present in the common ancestor of extant birds, but has been lost from most lineages. GHR-W has notably been retained in hawks, eagles, vultures (Accipitriformes) and owls (Strigiformes). These groups display larger female size, making GHR-W an intriguing potential contributor to reverse sexual dimorphism. In these lineages, GHR-W retains intact gene structure, despite W-chromosome degradation that leads to loss of this gene from most birds. Analysis of published RNA-seq data demonstrates that GHR-W is expressed in accipitriform fibroblasts. Using available sex-specific mass data and correcting for phylogenetic structure, we report a robust correlation between retention of GHR-W and reverse sexual size dimorphism across avian clades.

evolutionary biology↗

bioRxiv2026

Geomorphic evolution of a Caribbean biological hotspot

Continental shelf archipelagos offer rare opportunities to test island biogeography in a time-resolved, non-equilibrium setting because postglacial sea-level rise drives datable changes in both island area and isolation. Yet most near-shore systems still lack reconstructions that integrate spatial changes in island configuration with duration-weighted histories of fragmentation. Such information is essential for interpreting modern genomic and biodiversity patterns and for evaluating responses to fragmentation such as extinction debt, immigration lag and adaptive responses over time. Here we reconstruct the land-sea geomorphic history of the Bocas del Toro Archipelago, Panama, combining high-resolution bathymetry and topography with a sea-level model corrected for sedimentation and tectonic movement. From this, we quantify multi-scale isolation, historical fragmentation dynamics, and composite metrics that integrate space and time. We show that present-day islands became isolated sequentially from 9.5 to 2.9 ka, with post-isolation area contraction rates varying 20-fold among islands. Over the same interval, shallow marine habitat (0-10 m depth) expanded ninefold as shelf flooding created space for reefs, seagrass, and mangroves. Extending the analyses through the Pleistocene reveals the modern archipelago is atypical and for much of the last million years, the region existed as continuous coastal lowland rather than discrete islands. Projections under moderate emissions scenarios predict [~]5% terrestrial habitat loss but [~]50% expansion of shallow marine habitat by 2150, though whether degraded Caribbean reefs can exploit this expansion remains uncertain. Exploratory correlations between species richness of terrestrial vertebrate groups and geomorphometric predictors reveal that island area, maximum elevation, and cumulative habitat availability since isolation are the strongest correlates of diversity, whilst buffer-zone isolation indices are confounded by covariation between island size and surrounding landmass in this continental shelf context. Overall, Bocas del Toro provides a time-calibrated natural experiment for testing how dynamic connectivity and isolation shaped island and coastal biodiversity.

evolutionary biology↗

bioRxiv2025

Reduced offspring viability is associated with long-term stability of a narrow avian hybrid zone

Fitness of hybrid individuals can shape the dynamics of hybrid zones and offer insight into speciation processes. Yet, accounts of hybrid fitness in natural hybrid zones are few, especially from tropical regions where species diversity is high, and speciation processes could contrast with those at higher latitudes. We investigated a hybrid zone between the white-collared manakin (Manacus candei) and the golden-collared manakin (M. vitellinus), two lek-breeding species characteristic of lowland forest habitat in Central America. Despite evidence of asymmetrical introgression and selection on male secondary sexual traits, ongoing sampling indicates that this hybrid zone is spatially stable with narrow clines, thus implying selection against hybrids. To evaluate hybrid viability, we estimated two components of hybrid fitness: survival of adults and egg hatching rates, and a possible selective pressure: prevalence of parasitism by vector-borne haemosporidian parasites. Estimated survival was similar between parental and hybrid populations and the prevalence of infections by Plasmodium spp. or Haemoproteus spp. parasites was uniformly low. Estimated rates of hatching success, however, were lower in nests from our hybrid population (one or two eggs failed to hatch in 70% of nests) compared to nests at the parental species (M. candei 28.6% and M. vitellinus 19.0%). Thus, despite extensive admixture and clear evidence of introgression of male plumage traits under sexual selection, partial infertility or elevated rates of developmental mortality in hybrid offspring may underlie long-term stability in this hybrid zone.

evolutionary biology↗

bioRxiv2025

Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life

The exponential growth of molecular sequence data over the past decade has enabled the construction of numerous clade-specific phylogenies encompassing hundreds or thousands of taxa. These independent studies often include overlapping data, presenting a unique opportunity to build macrophylogenies (phylogenies sampling > 1,000 taxa) for entire classes across the Tree of Life. However, the inference of large trees remains constrained by logistical, computational, and methodological challenges. The Avian Tree of Life provides an ideal model for evaluating strategies to robustly infer macrophylogenies from intersecting datasets derived from smaller studies. In this study, we leveraged a comprehensive resource of sequence capture datasets to evaluate the phylogenetic accuracy and computational costs of four methodological approaches: (1) supermatrix approaches using concatenation, including the "fast" maximum likelihood (ML) methods, (2) filtering datasets to reduce heterogeneity, (3) supertree estimation based on published phylogenomic trees, and (4) a "divide-and-conquer" strategy, wherein smaller ML trees were estimated and subsequently combined using a supertree approach. Additionally, we examined the impact of these methods on divergence time estimation using a dataset that includes newly vetted fossil calibrations for the Avian Tree of Life. Our findings highlight that recently developed fast tree search approaches offer a reasonable compromise between computational efficiency and phylogenetic accuracy, facilitating inference of macrophylogenies.

evolutionary biology↗

bioRxiv2024

Transcripts with high distal heritability mediate genetic effects on complex metabolic traits

Although many genes are subject to local regulation, recent evidence suggests that complex distal regulation may be more important in mediating phenotypic variability. To assess the role of distal gene regulation in complex traits, we combined multi-tissue transcriptomes with physiological outcomes to model diet-induced obesity and metabolic disease in a population of Diversity Outbred mice. Using a novel high-dimensional mediation analysis, we identified a composite transcriptome signature that summarized genetic effects on gene expression and explained 30% of the variation across all metabolic traits. The signature was heritable, interpretable in biological terms, and predicted obesity status from gene expression in an independently derived mouse cohort and multiple human studies. Transcripts contributing most strongly to this composite mediator frequently had complex, distal regulation distributed throughout the genome. These results suggest that trait-relevant variation in transcription is largely distally regulated, but is nonetheless identifiable, interpretable, and translatable across species.

genetics↗

bioRxiv2024

Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny

The evolutionary histories of different genomic regions typically differ from each other and from the underlying species phylogeny. This makes species tree estimation challenging. Here, we examine the performance of phylogenomic methods using a well-resolved phylogeny that nevertheless contains many difficult nodes, the species tree of living birds. We compared trees generated by maximum likelihood (ML) analysis of concatenated data, gene tree summary methods, and SVDquartets. We also conduct the first empirical test of a "new" method called METAL (Metric algorithm for Estimation of Trees based on Aggregation of Loci), which is based on evolutionary distances calculated using concatenated data. We conducted this test using a novel dataset comprising more than 4,000 ultraconserved element (UCE) loci from almost all bird families and two existing UCE and intron datasets sampled from almost all avian orders. We identified "reliable clades" very likely to be present in the true avian species tree and used them to assess method performance. ML analyses of concatenated data recovered almost all reliable clades with less data and greater robustness to missing data than other methods. METAL recovered many reliable clades, but only performed well with the largest datasets. Gene tree summary methods (weighted ASTRAL and weighted ASTRID) performed well; they required less data than METAL but more data than ML concatenation. SVDquartets exhibited the worst performance of the methods tested. In addition to the methodological insights, this study provides a novel estimate of avian phylogeny with almost 99% of the currently recognized avian families. Only one of the 181 reliable clades we examined was consistently resolved differently by ML concatenation versus other methods, suggesting that it may be possible to achieve consensus on the deep phylogeny of extant birds.

evolutionary biology↗

bioRxiv2023

Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone

AO_SCPLOWBSTRACTC_SCPLOWHybrid zones are dynamic systems where natural selection, sexual selection, and other evolutionary forces can act on reshuffled combinations of distinct genomes. The movement of hybrid zones, individual traits, or both are of particular interest for understanding the interplay between selective processes. In a hybrid zone involving two lek-breeding birds, secondary sexual plumage traits of Manacus vitellinus, including bright yellow collar and olive belly color, have introgressed asymmetrically [~]50 km across the genomic center of the zone into populations more genetically similar to Manacus candei. Males with yellow collars are preferred by females and are more aggressive than parental M. candei, suggesting that sexual selection was responsible for the introgression of male traits. We assessed the spatial and temporal dynamics of this hybrid zone using historical (1989 - 1994) and contemporary (2017 - 2020) transect samples to survey both morphological and genetic variation. Genome-wide SNP data and several male phenotypic traits show that the genomic center of the zone has remained spatially stable, whereas the olive belly color of male M. vitellinus has continued to introgress over this time period. Our data suggest that sexual selection can continue to shape phenotypes dynamically, independent of a stable genomic transition between species.

evolutionary biology↗

bioRxiv2022

Evolution of the Growth Hormone Gene Duplication in Passerine Birds

Birds of the order Passeriformes represent the most speciose radiation of land vertebrates, yet the cause or causes of their elevated species richness have not been satisfactorily explained. One potential key adaptation is their sole lineage-specific gene, a duplicate copy of growth hormone (GH), present in all major lineages of passerines, but in no other group of birds. Growth hormone genes plausibly influence extreme life history traits that passerines exhibit, including the shortest embryo-to-fledging developmental period of any avian order. To unravel the implications of this GH duplication, we investigated the molecular evolution of the ancestral avian GH gene (GH or GH1) and the novel passerine GH paralog (GH2), using 497 gene sequences extracted from 342 genomes. Passerine GH1 and GH2 are reciprocally monophyletic, consistent with a single duplication event from a microchromosome onto a macrochromosome in a common ancestor of extant passerines. Additional chromosomal rearrangements have changed the syntenic and potential regulatory context of these genes. Both passerine GH1 and GH2 paralogs display substantially higher rates of nonsynonymous codon change than non-passerine avian GH, suggesting positive selection following duplication. A site involved in signal peptide cleavage is under selection in both paralogs. Other sites under positive selection differ between the two paralogs, but many are clustered in one region of a 3D model of the protein. Both paralogs retain key functional features and are actively but differentially expressed in two major passerine suborders. These phenomena suggest that growth hormone genes may be evolving novel adaptive roles in passerine birds.

molecular biology↗