Oscar Johnson

Acoustic signal complexity varies widely in animals from single notes to highly sophisticated vocal displays. In birds, vocal complexity can evolve
as an honest signal of individual quality driven by sexual selection.
However, this hypothesis is rarely explored in conjunction with alternative drivers, including competition for ecological resources (social selection) and intra-group communication, both of which may favour increased signal complexity. Using Bayesian phylogenetic models, we test whether these alternative mechanisms predict the complexity of innate songs in 1,288 species of suboscine passerine birds, while accounting for ecological constraints on sound production, transmission and detection. We found that overall song complexity was reduced by sexual selection (estimated from mating systems), and declined with body size and vegetation density. Conversely, note count and song length increased in territorial species, particularly those using song to defend year-round territories during the non-breeding season. These findings challenge the common assumption that sexual selection is the main driver of increased signal complexity, and highlight the role of social selection via territorial competition as a factor increasing the temporal complexity of songs. Our results suggest that signal complexity depends on social, cultural and ecological contexts, reflecting a combination of multiple inter-related drivers and constraints.

Understanding the factors that govern variation in genetic structure
across species is key to the study of speciation and population genetics.
Genetic structure has been linked to several aspects of life history, such
as foraging strategy, habitat association, migration distance, and
dispersal ability, all of which might influence dispersal and gene flow.
Comparative studies of population genetic data from species with differing
life histories provide opportunities to tease apart the role of dispersal
in shaping gene flow and population genetic structure. Here, we examine
population genetic data from sets of bird species specialized on a series
of Amazonian habitat types hypothesized to filter for species with
dramatically different dispersal abilities: stable upland forest, dynamic
floodplain forest, and highly dynamic riverine islands. Using genome-wide
markers, we show that habitat type has a significant effect on population
genetic structure, with species in upland forest, floodplain forest, and
riverine islands exhibiting progressively lower levels of structure.
Although morphological traits used as proxies for individual-level
dispersal ability did not explain this pattern, population genetic
measures of gene flow are elevated in species from more dynamic riverine
habitats. Our results suggest that the habitat in which a species occurs
drives the degree of population genetic structuring via its impact on
long-term fluctuations in levels of gene flow, with species in highly
dynamic habitats having particularly elevated gene flow. These differences
in genetic variation across taxa specialized in distinct habitats may lead
to disparate responses to environmental change or habitat-specific
diversification dynamics over evolutionary time scales.

The stipple-throated antwrens of the genus Epinecrophylla (Aves:
Thamnophilidae) are represented by eight species primarily found in the
lowlands of the Amazon Basin and the Guiana Shield. The genus has a long
and convoluted taxonomic history, with many attempts made to address the
taxonomy and systematics of the group. Here we employ massively parallel
sequencing of thousands of ultraconserved elements (UCEs) to provide both
the most comprehensive subspecies-level phylogeny of Epinecrophylla
antwrens and the first population-level genetic analyses for most species
in the genus. Most of our results are robust to a diversity of
phylogenetic and population genetic methods, but we show that even with
thousands of loci we are unable to fully resolve the relationships between
some western Amazonian species in the haematonota group. We uncovered
phylogenetic relationships between taxa and patterns of population
structure that are discordant with both morphology and current taxonomy.
For example, we found deep genetic breaks between taxa in the ornata group
that are currently regarded as species, and in the haematonota and
leucophthalma groups we found paraphyly at the species and subspecies
levels, respectively. As has been found in many Amazonian taxa, our
phylogenetic results show that the major river systems of the Amazon Basin
appear to have an effect on the genetic structure and range limits within
Epinecrophylla. Our population genetics analyses showed extensive
admixture between some taxa despite their deep genetic divergence.
 We present a revised taxonomy for the group and suggest areas
for further study.

How the microbiome interacts with hosts across evolutionary time is poorly understood. To address this question, datasets comprised of many host species are required to conduct comparative analyses. Here, we have analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses and used phylogenetic comparative methods to assess the evolution of the microbiome as a trait of bird species. We find that raw abundances and diversity varied between the datasets but relative patterns were largely consistent across datasets. Host taxonomy, diet and locality were significantly associated with microbiomes, at generally similar levels using three distance metrics. Phylogenetic comparative methods were used to assess the relationship between the microbiome as a trait of a host species and the underlying bird phylogeny. We find that a neutral Brownian motion model does not explain variation in microbiomes. Instead, a White Noise model that indicates the trait contains little to no phylogenetic signal, is most likely across many definitions of "microbiome trait". While there was some support for the Ornstein-Uhlenbeck model (that invokes selection), the level of support was similar to our White Noise simulation, further supporting the White Noise model as the best explanation for the evolution of the microbiome as a trait of avian hosts. Our study highlights the qualitatively minor impact that different analytical choices can have on results and that biological interpretations can be robust to method choice.

Migratory birds often form flocks on their wintering grounds, but important details of social structure such as the patterns of association between individuals are virtually unknown. We analysed networks of co-membership in short-term flocks for wintering golden-crowned sparrows (Zonotrichia atricapilla) across three years and discovered social complexity unsuspected for migratory songbirds. The population was consistently clustered into distinct social communities within a relatively small area (~ 7 ha). Birds returned to the same community across years, with mortality and recruitment leading to some degree of turnover in membership. These spatiotemporal patterns were explained by the combination of space use and social preference – birds that flocked together in one year flocked together again in the subsequent year more often than were expected based on degrees of home range overlap. Our results suggest that a surprising level of social fidelity across years leads to repeatable patterns of social network structure in migratory populations.