Phylogenomic insights into the polyphyletic nature of Altai falcons within eastern sakers (Falco cherrug) and the origins of gyrfalcons (Falco rusticolus).

The Altai falcon from Central Asia always attracted the attention of humans. Long considered a totemic bird in its native area, modern falconers still much appreciated this large-bodied and mighty bird of prey due to its rarity and unique look. The peculiar body characteristics halfway between the saker falcon (Falco cherrug) and the gyrfalcon (F. rusticolus) triggered debates about its contentious taxonomy. The weak phylogenetic signal associated with traditional genetic methods could not resolve this uncertainty. Here, we address the controversial evolutionary origin of Altai falcons by means of a genome-wide approach, Restriction-site Associated DNA sequencing, using sympatric eastern sakers falcons, allopatric western saker falcons and gyrfalcons as outgroup. This approach provided an unprecedented insight into the phylogenetic relationships of the studied populations by delivering 17,095 unlinked SNPs shedding light on the polyphyletic nature of Altai falcons within eastern sakers. Thus we concluded that the former must correspond to a low taxonomic rank, probably an ecotype or form of the latter. Also, we found that eastern sakers are paraphyletic without gyrfalcons, thus, these latter birds are best regarded as the direct sister lineage of the eastern sakers. This evolutionary relationship, corroborated also by re-analyzing the dataset with the inclusion of outgroup samples (F. biarmicus and F. peregrinus), put eastern sakers into a new light as the potential ancestral genetic source of high latitude and altitude adaptation in descendent populations. Finally, conservation genomic values hint at the stable genetic background of the studied saker populations.

Clinically relevant antibiotic resistance in Escherichia coli from black kites in southwestern Siberia: a genetic and phenotypic investigation.

Wild birds including raptors can act as vectors of clinically relevant bacteria with antibiotic resistance. The aim of this study was to investigate the occurrence of antibiotic-resistant Escherichia coli in black kites (Milvus migrans) inhabiting localities in proximity to human-influenced environments in southwestern Siberia and investigate their virulence and plasmid contents. A total of 51 E. coli isolates mostly with multidrug resistance (MDR) profiles were obtained from cloacal swabs of 35 (64%, n = 55) kites. Genomic analyses of 36 whole genome sequenced E. coli isolates showed: (i) high prevalence and diversity of their antibiotic resistance genes (ARGs) and common association with ESBL/AmpC production (27/36, 75%), (ii) carriage of mcr-1 for colistin resistance on IncI2 plasmids in kites residing in proximity of two large cities, (iii) frequent association with class one integrase (IntI1, 22/36, 61%), and (iv) presence of sequence types (STs) linked to avian-pathogenic (APEC) and extra-intestinal pathogenic E. coli (ExPEC). Notably, numerous isolates had significant virulence content. One E. coli with APEC-associated ST354 carried qnrE1 encoding fluoroquinolone resistance on IncHI2-ST3 plasmid, the first detection of such a gene in E. coli from wildlife. Our results implicate black kites in southwestern Siberia as reservoirs for antibiotic-resistant E. coli. It also highlights the existing link between proximity of wildlife to human activities and their carriage of MDR bacteria including pathogenic STs with significant and clinically relevant antibiotic resistance determinants. IMPORTANCE Migratory birds have the potential to acquire and disperse clinically relevant antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs) through vast geographical regions. The opportunistic feeding behavior associated with some raptors including black kites and the growing anthropogenic influence on their natural habitats increase the transmission risk of multidrug resistance (MDR) and pathogenic bacteria from human and agricultural sources into the environment and wildlife. Thus, monitoring studies investigating antibiotic resistance in raptors may provide essential data that facilitate understanding the fate and evolution of ARB and ARGs in the environment and possible health risks for humans and animals associated with the acquisition of these resistance determinants by wildlife.

Black Kites on a flyway between Western Siberia and the Indian Subcontinent.

The Black Kite (Milvus migrans) is one of the most widespread raptors in the world. The Palaearctic is populated by two migrating subspecies, Milvus migrans migrans and Milvus migrans lineatus, in the western and eastern part of this realm, respectively. There is a large intergradation zone of M. m. migrans/M. m. lineatus in-between. Although the migration routes of M. m. migrans from Europe to Sub-Saharan Africa and the Middle East are well known, detailed information about migration routes of Black Kites from intergradation zone are missing. Using satellite telemetry we are able to fill this gap in our knowledge of these birds. We tagged with GPS/SMS/GPRS telemetry loggers 13 and 6 Black Kite pulli in lowland around Biysk (Altai Krai, Russia) and in mountains around Kosh-Agach (Altai Republic, Russia), respectively. After fledging, Black Kites from both subpopulations stayed in a small, non-overlapping areas and then migrated to southern Asia through narrow corridors. Black Kites originating from Biysk migrated through the Western Circum-Himalayan Corridor. Black Kites originating from Kosh-Agach used the Trans-Himalayan Corridor crossing the Himalayas in altitudes of up to 6256 m asl. The average total distance travelled of Black Kites from both subpopulations was 9166 km without any significant differences between these subpopulations. Timing of both spring and autumn migration did not vary along different age groups. Black Kites from both subpopulations wintered in low elevations of Pakistan and India. Birds wintered on average for 190 days, and the mean area of individual home ranges in winter was 4704 km2. During the breeding period, birds dwelled in south-western Siberia, where they spent on average 125 days with an average home range size 3537 km2. We found that ontogenetic shifts in migratory behaviour of Black Kites from Eastern Russia differ from those in population/subspecies in Europe. Black Kites crossing the Himalayas fly and, moreover, stay for hours resting at night in the environment of mountains at altitudes over 5000 m.

Differential survival throughout the full annual cycle of a migratory bird presents a life-history trade-off.

Long-distance migrations are among the most physically demanding feats animals perform. Understanding the potential costs and benefits of such behaviour is a fundamental question in ecology and evolution. A hypothetical cost of migration should be outweighed by higher productivity and/or higher annual survival, but few studies on migratory species have been able to directly quantify patterns of survival throughout the full annual cycle and across the majority of a species' range. Here, we use telemetry data from 220 migratory Egyptian vultures Neophron percnopterus, tracked for 3,186 bird months and across approximately 70% of the species' global distribution, to test for differences in survival throughout the annual cycle. We estimated monthly survival probability relative to migration and latitude using a multi-event capture-recapture model in a Bayesian framework that accounted for age, origin, subpopulation and the uncertainty of classifying fates from tracking data. We found lower survival during migration compared to stationary periods (ß = -0.816; 95% credible interval: -1.290 to -0.318) and higher survival on non-breeding grounds at southern latitudes (<25°N; ß = 0.664; 0.076-1.319) compared to on breeding grounds. Survival was also higher for individuals originating from Western Europe (ß = 0.664; 0.110-1.330) as compared to further east in Europe and Asia, and improved with age (ß = 0.030; 0.020-0.042). Anthropogenic mortalities accounted for half of the mortalities with a known cause and occurred mainly in northern latitudes. Many juveniles drowned in the Mediterranean Sea on their first autumn migration while there were few confirmed mortalities in the Sahara Desert, indicating that migration barriers are likely species-specific. Our study advances the understanding of important fitness trade-offs associated with long-distance migration. We conclude that there is lower survival associated with migration, but that this may be offset by higher non-breeding survival at lower latitudes. We found more human-caused mortality farther north, and suggest that increasing anthropogenic mortality could disrupt the delicate migration trade-off balance. Research to investigate further potential benefits of migration (e.g. differential productivity across latitudes) could clarify how migration evolved and how migrants may persist in a rapidly changing world.

Plasmid-Mediated mcr-1 Colistin Resistance in Escherichia coli from a Black Kite in Russia.

The gene mcr-1 conferring resistance to last-line antibiotic colistin has been reported globally. Here, we describe the first detection of plasmid-mediated colistin resistance in Russian wildlife, an isolate of Escherichia coli sequence type 2280 from a black kite (Milvus migrans) scavenging raptor. Whole-genome sequencing and plasmid transferability experiments revealed that mcr-1.1 was located on conjugative IncI2 plasmid pDR164 (59891 bp). Migratory black kites may contribute to the global spread of mobile colistin resistance.

Unravelling population processes over the Late Pleistocene driving contemporary genetic divergence in Palearctic buzzards.

Population range expansions and contractions as a response to climate and habitat change throughout the Quaternary are known to have contributed to complex phylogenetic and population genetic events. Speciation patterns and processes in Palearctic buzzards (genus Buteo) are a long-standing example of morphological and genetic data incongruence, attributed to panmixia, habitat range shifts, contact zones, and climate change. Here we assess the systematics, phylogeography and population genetic structure of three nominal species of Palearctic buzzards, Buteo buteo (including B. b. vulpinus), B. rufinus (including B. r. cirtensis) and B. hemilasius. Phylogenetic analyses inferred from mitochondrial data recover B. hemilasius as sister to the sister clades B. r. rufinus and B. buteo complex (B. b. buteo, B. b. vulpinus, but also including B. r. cirtensis). In contrast, we find an unresolved genetic delimitation inferred from four nuclear loci, suggesting an ancestral genetic pool for all species. Time-trees suggest population contractions and expansions throughout the Pleistocene, which likely reflect habitat change and contrasting ecological niche requirements between species. Microsatellite-based extended Bayesian skyline plots reveal relatively constant population sizes for B. hemilasius, B. r. rufinus, and B. b. vulpinus, in contrast to a dramatic population expansion in B. r. cirtensis within the last 3 kya. Overall, our study illustrates how complex population processes over the Late Pleistocene have shaped the patterns of genetic divergence in Palearctic buzzards, due to the joint effects of shared ancestral polymorphisms, population expansions and contractions, with hybridization at contact zones leading to admixture and introgression.