Evolutionary history of an island endemic, the Azorean common quail.

Oceanic islands are characterized by conditions that favour diversification into endemic lineages that can be very different from their mainland counterparts. This can be the result of fast phenotypic divergence due to drift or the result of slower adaptation to local conditions. This uniqueness can obscure their evolutionary history. Here we used morphological, stable isotope, genetic and genomic data to characterize common quails (Coturnix coturnix) in the Azores archipelago and assess the divergence from neighbouring common quail populations. Historical documents suggested that these quails could have a recent origin associated with the arrival of humans in the last centuries. Our results show that Azorean quails constitute a well-differentiated lineage with small size and dark throat pigmentation that has lost the migratory ability and that diverged from mainland quail lineages more than 0.8 mya, contrary to the notion of a recent human-mediated arrival. Even though some Azorean quails carry an inversion that affects 115 Mbp of chromosome 1 and that has been associated with the loss of the migratory behaviour in other common quail populations, half of the analysed individuals do not have that inversion and still do not migrate. The long coexistence and evolution in isolation in the Azores of two chromosomal variants (with and without the inversion) is best explained by balancing selection. Thus, a unique and long evolutionary history led to the island endemic that we know today, C. c. conturbans.

Full genome sequences are key to disclose RHDV2 emergence in the Macaronesian islands.

A recent publication by Carvalho et al. in "Virus Genes" (June 2017) reported the presence of the new variant of rabbit hemorrhagic disease virus (RHDV2) in the two larger islands of the archipelago of Madeira. Based on the capsid protein sequence, the authors suggested that the high sequence identity, along with the short time spanning between outbreaks, points to dissemination from Porto Santo to Madeira. By including information of the full RHDV2 genome of strains from Azores, Madeira, and the Canary Islands, we confirm the results obtained by Carvalho et al., but further show that several subtypes of RHDV2 circulate in these islands: non-recombinant RHDV2 in the Canary Islands, G1/RHDV2 in Azores, Porto Santo and Madeira, and NP/RHDV2 also in Madeira. Here we conclude that RHDV2 has been independently introduced in these archipelagos, and that in Madeira at least two independent introductions must have occurred. We provide additional information on the dynamics of RHDV2 in the Macaronesian archipelagos of Azores, Madeira, and the Canary Islands and highlight the importance of analyzing RHDV2 complete genome.

Staphylococci among Wild European Rabbits from the Azores: A Potential Zoonotic Issue?

ABSTRACT: The prevalence and diversity of Staphylococcus species from wild European rabbits (Oryctolagus cuniculus) in the Azores were investigated, and the antibiotic resistance phenotype and genotype of the isolates were determined. Nasal samples from 77 wild European rabbits from São Jorge and São Miguel islands in Azores were examined. Antibiotic susceptibility of the isolates was determined using the Kirby-Bauer disk diffusion method, and the presence of antimicrobial resistance genes and virulence factors was determined by PCR. The genetic lineages of S. aureus isolates were characterized by spa typing and multilocus sequence typing. A total of 49 staphylococci were obtained from 35 of the 77 wild rabbits. Both coagulase-positive (8.2%) and coagulase-negative (91.8%) staphylococci were detected: 4 S. aureus, 17 S. fleurettii, 13 S. sciuri, 7 S. xylosus, 4 S. epidermidis, and 1 each of S. simulans, S. saprophyticus, S. succinus, and S. equorum. The four S. aureus isolates showed methicillin susceptibility and were characterized as spa type t272/CC121, Panton-Valentine leukocidin negative, and hlB positive. Most of the coagulase-negative staphylococci showed resistance to fusidic acid and beta-lactams, and multidrug resistance was identified especially among S. epidermidis isolates. The mecA gene was detected in 20 isolates of the species S. fleurettii and S. epidermidis, associated with the blaZ gene in one S. epidermidis isolate. Five antimicrobial resistance genes were detected in one S. epidermidis isolate (mecA,dfrA,dfrG,aac6'-aph2'', and ant4). Our results highlight that wild rabbits are reservoirs or "temporary hosts" of Staphylococcus species with zoonotic potential, some of them carrying relevant antimicrobial resistances.

Tracking the evolution of the G1/RHDVb recombinant strains introduced from the Iberian Peninsula to the Azores islands, Portugal.

Previous genetic characterization of rabbit haemorrhagic disease virus (RHDV) from Azores, Portugal, revealed the presence of genogroup 3-5 (G3-G5) like strains. These strains differed from the genogroup 1 (G1) strains circulating in mainland Portugal, suggesting an independent evolution of RHDV in Azores. More recently, the new variant RHDV (RHDVb) was detected in Azores. In mainland Portugal, current circulating strains resulted from recombination events between RHDVb and non-pathogenic or pathogenic G1 strains. To characterize the RHDVb strains from Azores, a ∼2.5 kb fragment of the RHDV genome (nucleotide positions 4873-7323), including the complete sequence of the capsid gene VP60 (nucleotide positions 5305-7044), was amplified and sequenced. Samples were obtained from rabbits found dead in the field between December 2014 and March 2015 in the Azorean islands Flores, Graciosa, São Jorge, Terceira, Faial, Pico, São Miguel and Santa Maria. For VP60, the highest homology was found with Iberian RHDVb strains, while the upstream fragment revealed high similarity (∼95%) with Iberian G1 strains. Phylogenetic reconstruction based either on VP60 or VP10 grouped the Azorean strains with Iberian RHDVb strains. For the fragment upstream of VP60, the Azorean strains grouped with G1. Our results show that the RHDVb strains circulating in Azores are G1/RHDVb recombinants and we hypothesize that such strains had their origin in Iberian strains. The geographic isolation of Azores suggests that arrival of RHDVb was man-mediated. A network analysis further allowed us to trace virus dispersion in Azores: from an initial outbreak in Graciosa, RHDVb spread to São Jorge and Faial, to Terceira, Flores and Santa Maria, and finally to Pico; dispersion to São Miguel occurred later from Terceira. As the consequences of the presence of G1/RHDVb strains in Azores are unpredictable, we suggest a continued monitoring and characterization of RHD outbreaks.