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.DATA AVAILABILITY STATEMENT : The Pogoniulus pusillus genome assembly has been deposited at NCBI SRA in BioProject PRJNA630018, with DDRAD sequencing reads under BioProject PRJNA666541. The master VCF file and gemma and R Code have been deposited in the Dryad Digital Repository (https://doi-org.uplib.idm.oclc.org/10.5061/dryad.jm63xsj87).FP7 Marie Curie Reintegration Grant, a University of Cyprus Research Grant, an AG Leventis Foundation grant and by the AP Leventis Ornithological Research Institute, Jos, Nigeria.http://wileyonlinelibrary.com/journal/mec2021-10-15hj2021Mammal Research InstituteZoology and Entomolog

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

BackgroundRickettsia 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 findingsWe 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).ConclusionsCollectively, 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.http://www.cell.com/heliyonam2022Mammal Research InstituteZoology and Entomolog

Using species distribution models to gauge the completeness of the bat checklist of Eswatini

National species checklists are important for a variety of reasons, including biodiversity conservation. However, these national checklists are rarely complete, and it is not easy to gauge how many species have been overlooked or what the taxonomic identities of overlooked species would be. This is particularly the case for small, elusive, or nocturnal species such as bats. Despite their diversity and importance as ecosystem service providers, bat distributions are poorly known throughout much of Africa. We present a national checklist of bats for a small African country, Eswatini, by compiling species from museum specimens and literature records. A total of 32 species of bats have been recorded from the country. Since 1995, new species have continued to be recorded in Eswatini, with five additional species added since the last published checklist in 2016, suggesting that some species may still be overlooked. In order to determine what species these may be, we used species distribution models based on the occurrence records of bats from southern Africa to predict what species would occur in Eswatini, which was then compared with what has been collected and deposited in museums. Our models predicted that a total of 47 species are likely to occur in Eswatini compared with 32 species collected to date. Our data suggest that the national checklist of bats of Eswatini is not yet complete and that further species are expected to be recorded for the country. We suggest that species distribution models can be useful for gauging the completeness of national checklists and predicting which species may have been overlooked.The National Science Foundation Graduate Research Fellowship, a Student Research Grant from Bat Conservation International, a National Geographic Young Explorer’s Grant 9635-14, and The Explorers Club Exploration Fund – Mamont Scholars Program.http://link.springer.com/journal/103442022-01-26hj2021Mammal Research InstituteZoology and Entomolog

Taxonomic revision of the red-fronted Tinkerbird Pogoniulus pusillus (Dumont, 1816) based on molecular and phenotypic analyses

Red-fronted Tinkerbird Pogoniulus pusillus (Dumont, 1816) presently comprises three recognised subspecies, of which two are found in East Africa and one occurs disjunctly in southern Africa. Based on their respective distributions and phenotypic differences, a taxonomic reassessment of the species is warranted. We performed a phylogenetic reconstruction using the mitochondrial genes ATPase 6/8 based on 33 samples from across the distribution of Red-fronted Tinkerbird and four outgroup samples, and then determined correspondence between genetic distances and differences in song and morphology among clades using the Tobias et al. criteria. Our phylogenetic analyses revealed 4.4% sequence divergence in mtDNA between northern and southern populations, with plumage, morphometric and song differences of a similar magnitude to those between P. pusillus and Yellow-fronted Tinkerbird P. chrysoconus, and above species-level thresholds according to the Tobias et al. criteria. Furthermore, the molecular phylogeny supports recognition of a synonymised taxon (P. p. eupterus) as a distinct, but phenotypically cryptic, subspecies in East Africa, with c.1.5% sequence divergence from P. p. affinis and P. p. uropygialis, which in turn differ less (1%) from each other. We propose that northern and southern Red-fronted Tinkerbirds are treated as separate species, and that the subspecies eupterus is resurrected. Our findings suggest that P. chrysoconus as presently constituted may also merit taxonomic revision.https://boc-online.org/bulletinam2022Mammal Research InstituteZoology and Entomolog

A genomic basis of vocal rhythm in birds

In this repository we provide processed data to reproduce the main results of the manuscript entitled "A genomic basis of vocal rhythm in birds"The data should be used in combination with the scripts available at: [https://github.com/MatteoSebastianelli/Tinkerbird_SongGene]We provide the following files:MS_StabilityMaster_Tinkerbirds_SingleRecs_10Mar23.xlsx: dataset to perform the song stability analyses.southern_africa_biallelic_snps_minDP4_MaxMiss20_MAF5.vcf.gz: ddRAD genomic datatinkerbirds_merged_SNPs_biallelic_max-miss0.95_maf0.03_minmaxDP3.5_50.vcf.gz: whole-genome genomic dataMS_SouthernAfrica_ddRADS_95SympF_14Mar23.xlsx: spreadsheet containing parental ancestry of each sympatric female individualMS_Tinkerbird138_Master_06Oct23.xlsx: main dataset containing mean phenotypic data and ancestry values for the 138 individuals sequenced at the whole-genome level.Fst_average500kb_results_16Feb23.txt: Genome-wide Fst calculated in 500Kb windows used for Figure 2LD_average500kb_results_16Feb23.txt: Genome-wide R2 (LD) calculated in 500Kb windows used for Figure 2GC_CONTENT_500k.bed: GC content calculated in 500Kb windows used for Figure 2REPEATS_500k__.bed: repeat content calculated in 500Kb windows used for Figure 2SNPs_500k__.bed: SNP density content calculated in 500Kb windows used for Figure 2gemma_ioi_Symp_17Nov22_max-miss0.95_maf0.03_minmaxDP3.5_50.assoc.txt: GEMMA output used for figures 3a, cAS28702_AllChr_combined_ave_anc_pos.txt: raw data for Fig4bAS39306_AllChr_combined_ave_anc_pos.txt: raw data for Fig4bAS53235_AllChr_combined_ave_anc_pos.txt: raw data for Fig4btinkerbirds135_symp_chr25_thin2500.geno.ld.txt: raw data for FigS8SourceData.xlsx: Raw data of all manuscript figures</p