A genomic basis of vocal rhythm in birds.

Vocal rhythm plays a fundamental role in sexual selection and species recognition in birds, but little is known of its genetic basis due to the confounding effect of vocal learning in model systems. Uncovering its genetic basis could facilitate identifying genes potentially important in speciation. Here we investigate the genomic underpinnings of rhythm in vocal non-learning Pogoniulus tinkerbirds using 135 individual whole genomes distributed across a southern African hybrid zone. We find rhythm speed is associated with two genes that are also known to affect human speech, Neurexin-1 and Coenzyme Q8A. Models leveraging ancestry reveal these candidate loci also impact rhythmic stability, a trait linked with motor performance which is an indicator of quality. Character displacement in rhythmic stability suggests possible reinforcement against hybridization, supported by evidence of asymmetric assortative mating in the species producing faster, more stable rhythms. Because rhythm is omnipresent in animal communication, candidate genes identified here may shape vocal rhythm across birds and other vertebrates.

Continent-wide patterns of song variation predicted by classical rules of biogeography.

Physiological constraints related to atmospheric temperature pose a limit to body and appendage size in endothermic animals. This relationship has been summarised by two classical principles of biogeography: Bergmann's and Allen's rules. Body size may also constrain other phenotypic traits important in ecology, evolution and behaviour, and such effects have seldom been investigated at a continental scale. Through a multilevel-modelling approach, we demonstrate that continent-wide morphology of related African barbets follows predictions of Bergmann's rule, and that body size mirrors variation in song pitch, an acoustic trait important in species recognition and sexual selection. Specifically, effects on song frequency in accordance with Bergmann's rule dwarf those of acoustic adaptation at a continental scale. Our findings suggest that macroecological patterns of body size can influence phenotypic traits important in ecology and evolution, and provide a baseline for further studies on the effects of environmental change on bird song.

Entomological risk of African tick-bite fever (Rickettsia africae infection) in Eswatini.

BACKGROUND: Rickettsia africae is a tick-borne bacterium that causes African tick-bite fever (ATBF) in humans. In southern Africa, the tick Amblyomma hebraeum serves as the primary vector and reservoir for R. africae and transmits the bacterium during any life stage. Previous research has shown that even when malaria has been dramatically reduced, unexplained acute febrile illnesses persist and may be explained by the serological evidence of rickettsiae in humans. METHODOLOGY/PRINCIPAL FINDINGS: We collected 12,711 questing Amblyomma larvae across multiple land use types in a savanna landscape in Eswatini. Our results show that host-seeking Amblyomma larvae are abundant across both space and time, with no significant difference in density by land use or season. We investigated the entomological risk (density of infected larvae) of ATBF from A. hebraeum larvae by testing over 1,600 individual larvae for the presence of R. africae using a novel multiplex qPCR assay. We found an infection prevalence of 64.9% (95% CI: 62.1-67.6%) with no land use type significantly impacting prevalence during the dry season of 2018. The mean density of infected larvae was 57.3 individuals per 100m2 (95% CI: 49-65 individuals per 100m2). CONCLUSIONS: Collectively, our results demonstrate R. africae infected A. hebraeum larvae, the most common tick species and life stage to bite humans in southern Africa, are ubiquitous in the savanna landscape of this region. Increased awareness of rickettsial diseases is warranted for policymakers, scientists, clinicians, and patients. Early detection of disease via increased clinician awareness and rapid diagnostics will improve patient outcomes for travelers and residents of this region.

Influence of sugarcane growth stages on bird diversity and community structure in an agricultural-savanna environment.

Agricultural intensification is a threat to terrestrial ecosystems around the world. Agricultural areas, especially monocultures, create homogenous landscapes for wildlife. However, certain crops, such as sugarcane, are harvested in phases, creating a mosaic of fields in different stages of growth. We investigated changes in avian communities across four different sugarcane growth stages: emerging, short, medium and tall sugarcane, as well as control sites that represented native savanna habitat in northeast Eswatini prior to conversion to agriculture. In total, we sampled nine sites in sugarcane fields (at different growth stages) and three in native savanna. We conducted bird counts at 5-week intervals along 200m line transects over both the breeding and non-breeding seasons. We recorded a total of 124 bird species belonging to 58 families. Bird species richness and diversity were higher in savannas compared to any stages of growth in sugarcane. In contrast, functional beta diversity and uniqueness were higher in sugarcane than in savanna. Community composition was also different between the two land-uses. While there was overlap in bird species composition between different sugarcane growth stages, there was high beta diversity and high turnover between sites, indicative of the high temporal and spatial variability in bird communities in sugarcane fields. We demonstrated that the spatial and temporal variability created by the different growth stages of sugarcane promotes the occurrence of species with different traits, which may contribute to ecosystem functioning and promote the conservation of bird species as sugarcane fields can provide resource complementation for species with different needs.

CYP2J19 mediates carotenoid colour introgression across a natural avian hybrid zone.

It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene CYP2J19 identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. However, evidence that CYP2J19 explains variation between red and yellow feather coloration in wild populations of birds is lacking. Hybrid zones provide the opportunity to identify genes associated with specific traits. Here we investigate genomic regions associated with colour in red-fronted and yellow-fronted tinkerbirds across a hybrid zone in southern Africa. We sampled 85 individuals, measuring spectral reflectance of forecrown feathers and scoring colours from photographs, while testing for carotenoid presence with Raman spectroscopy. We performed a genome-wide association study to identify associations with carotenoid-based coloration, using double-digest RAD sequencing aligned to a short-read whole genome of a Pogoniulus tinkerbird. Admixture mapping using 104,933 single nucleotide polymorphisms (SNPs) identified a region of chromosome 8 that includes CYP2J19 as the only locus with more than two SNPs significantly associated with both crown hue and crown score, while Raman spectra provided evidence of ketocarotenoids in red feathers. Asymmetric backcrossing in the hybrid zone suggests that yellow-fronted females mate more often with red-fronted males than vice versa. Female red-fronted tinkerbirds mating assortatively with red-crowned males is consistent with the hypothesis that converted carotenoids are an honest signal of quality.