Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux

Falcons are diverse birds of cultural and economic importance. They have undergone major lineage specific chromosomal rearrangements, resulting in greatly-reduced chromosome counts relative to other birds. Here, we use 10X Genomics linked reads to provide new high-contiguity genomes for two gyrfalcons, a saker falcon, a lanner falcon, three subspecies of peregrine falcons, and the common kestrel. Assisted by a transcriptome sequenced from 22 gyrfalcon tissues, we annotate these genomes for a variety of genomic features, estimate historical demography, and then investigate genomic equilibrium in the context of falcon-specific chromosomal rearrangements. We find that falcon genomes are not in AT-GC equilibrium with a bias in mutations towards higher AT content; this bias is predominantly driven by, but not dependent on, hypermutability of CpG sites. Small indels and large structural variants were also biased towards insertions rather than deletions. Patterns of disequilibrium were linked to chromosomal rearrangements: falcons have lost GC content in regions that have fused to larger chromosomes from microchromosomes and gained GC content in regions of macrochromosomes that have translocated to microchromosomes. Inserted bases have accumulated on regions ancestrally belonging to microchromosomes, consistent with insertion-biased gene conversion. We also find an excess of interspersed repeats on regions of microchromosomes that have fused to macrochromosomes. Our results reveal that falcon genomes are in a state of flux. They further suggest that many of the key differences between microchromosomes and macrochromosomes are driven by differences in chromosome size, and indicate a clear role for recombination and biased gene conversion in determining genomic equilibrium.

Implications of captive breeding for the reintroduction of the Saker falcon (Falco cherrug) in Bulgaria

The Saker falcon (Falco cherrug) is a globally endangered species recovered in 2018 in Bulgaria. The only known active pair currently breeding in the wild in the country is made up of captive-bred and released birds, part of the first reintroduction programme for the species in Bulgaria and globally. As part of the project, sourced Saker falcons of known European origin are bred ex situ, the juveniles are parent-reared and released in the wild by means of the hacking method. The aim of this study was to evaluate the success and effectiveness of the captive breeding and rearing methods. The objective of the study was to investigate, compare and assess the results from fertilization, hatching, survival and hacking of captive bred Saker falcons registered over a 10-year period (2011-2021) at the Wildlife Rehabilitation and Breeding Centre (WRBC) Green Balkans, with a more detailed comparison of the breeding activities carried out in 2020 and 2021 (as the reintroduction programme was restarted in 2020). The results show more than threefold increase in output of laid eggs with the employment of the double clutching method in 2020 and 2021, and an overall 65% release rate of the hatched in the WRBC Saker falcons, for the investigated period.

Use of DNA metabarcoding of bird pellets in understanding raptor diet on the Qinghai-Tibetan Plateau of China

Background Diet analysis is essential to understanding the functional role of large bird species in food webs. Morphological analysis of regurgitated bird pellet contents is time intensive and may underestimate biodiversity. DNA metabarcoding has the ability to circumvent these issues, but has yet to be done. Methods We present a pilot study using DNA metabarcoding of MT-RNR1 and MT-CO1 markers to determine the species of origin and prey of 45 pellets collected in Qinghai and Gansu Provinces, China. Results We detected four raptor species [Eurasian Eagle Owl (Bubo bubo), Saker Falcon (Falco cherrug), Steppe Eagle (Aquila nipalensis), and Upland Buzzard (Buteo hemilasius)] and 11 unique prey species across 10 families and 4 classes. Mammals were the greatest detected prey class with Plateau Pika (Ochotona curzoniae) being the most frequent. Observed Shannon’s and Simpson’s diversity for Upland Buzzard were 1.089 and 0.479, respectively, while expected values were 1.312 ± 0.266 and 0.485 ± 0.086. For Eurasian Eagle Owl, observed values were 1.202 and 0.565, while expected values were 1.502 ± 0.340 and 0.580 ± 0.114. Interspecific dietary niche partitioning between the two species was not detected. Conclusions Our results demonstrate successful use of DNA metabarcoding for understanding diet via a novel noninvasive sample type to identify common and uncommon species. More work is needed to understand how raptor diets vary locally, and the mechanisms that enable exploitation of similar dietary resources. This approach has wide ranging applicability to other birds of prey, and demonstrates the power of using DNA metabarcoding to study species noninvasively.

Re-introduction of the Saker Falcon (Falco cherrug) in Bulgaria - preliminary results from the ongoing establishment phase by 2020

Considered extinct as breeding species in the early 2000s, the Saker Falcon was recovered when the first active nest from the new history of the species in Bulgaria was discovered in 2018, formed of two birds that were re-introduced back in 2015. Currently, there is only one confirmed wild breeding pair in the country - the male from 2015 with a female changed in 2020, released again as a part of the programme, in 2016. This is a report on the preliminary results and analysis of the ongoing establishment phase of the re-introduction of the Saker Falcon (Falco cherrug) in Bulgaria - first ever performed for this species in the country and globally. The period studied is 2015-2020. Following the re-introduction activities started in 2011, the current phase is defined by standardised methodology and a unified approach. Analysed and presented are methods for captive breeding and hacking, the breeding performance of the falcons, the number of released individuals, data from the post-fledging dependence period and a model of population growth.

Summary of raptor and owl ringing in Slovakia in the period from 2012 to 2019

Between 2012 and 2019, 6523 raptors and owls (30 species) were ringed in Slovakia. The most abundant was the common kestrel (2811 individuals), then the western marsh harrier (664) and saker falcon (517). The proportion of nestlings among all the ringed individuals was 84.4%. In the given period, 340 recoveries of raptors and owls (23 species) were recorded in the ringing station database. This number included 160 recoveries of individuals colour-marked and also recovered in our territory. There were 83 recoveries of birds ringed in Slovakia and resighted abroad. The last 97 recoveries were of individuals ringed abroad and recovered in Slovakia. In summary, most of the recoveries (of all types) were of Eastern imperial eagle (62 recoveries), then red-footed falcon (51) and common kestrel (43). Most of the recovery circumstances were ring reading (44% in total), recaptures (15%) and findings of bird cadavers. Regarding raptors or owls, collisions with vehicles (5%) and electrocutions (5%) were frequent causes of their deaths.

Seasonal variation in gonad physiology indicates juvenile breeding in the Saker Falcon (Falco cherrug)

We describe seasonal changes in the physiology of reproductive organs of Saker Falcons electrocuted on an electricity power line in Mongolia. Macroscopic examination of the gonads revealed asymmetry in testes size, with bias to the left body side. This asymmetry declined with seasonal increase in testes size during the main egg-laying period of the breeding season. In females, 91% possessed both left and right ovaries ( N = 161); there was no visible oviduct associated with the right ovary and it was smaller than the functional left ovary. Both ovaries showed seasonal development in size, becoming larger during the peak egg-laying period. Hierarchical preovulatory follicular development was recorded in two females, with ca. 5 mm difference in the diameter of sequential follicles. Both sexes developed brood patches during the main incubation period, with adults more likely to exhibit brood patches than juveniles. Among juveniles, at least 82% of females and 91% of males were non-breeders without brood patches. The high electrocution rate at our studied power line provided a rare opportunity to examine the non-breeding component of the Saker population. Juveniles predominated in the non-breeding population during the main egg-laying period (89%, N = 65), with the proportion of adults electrocuted being significantly lower among females. Only a small proportion of juvenile females exhibited gonadal evidence of breeding, consistent with the low observed frequency of juvenile breeders at nests. The demographic composition of the non-breeding population is consistent with female mortality rates exceeding that of males, and potentially indicates incipient population decline.

Bird Bone Remains from Two Medieval Settlements in Debrecen (Eastern Hungary)

This paper presents results on three medieval avian bone assemblages found at Debrecen-Monostor-erdő and Debrecen-Tócó-part, respectively. Domestic chicken yielded most of the bird remains to evidence the exploitation of adult birds for egg production and flock maintenance in particular. In addition, feather harvesting and fat production could have been the target of goose (and possibly duck) husbandry. Although the goose bone sizes resemble the greylag goose, the keeping of an unimproved form of domestic goose rather than the hunting of the wild ancestor is suggested by the structure of the assemblage and the presence of healed bones. Wild birds seem to have been rarely consumed by the settlers of the two villages, but the feathers or wings or carcasses of diurnal birds of prey and crows may have been used for special purposes. Either killed for their symbolic meaning or only persecuted for protecting the backyard animals, the red kite (Milvus milvus) and the hen harrier (Circus cyaneus) represent new species for the medieval avifauna of Hungary, similarly to the Northern shoveler (Anas clypeata) and the Northern lapwing (Vanellus vanellus) that could have been hunted in the marshy environment provided by the Tócó creek. Moreover, the use of trained saker falcon (Falco cherrug) for hawking cannot be excluded either. In addition to the exploitation of birds for the abovementioned goods and values, two needle cases made from goose bones evidence the utilization of their skeletal parts as raw material for producing artefacts as well.