Correction of a Hyperflexed Hallux in a Saker Falcon (Falco cherrug) by Hemisectioning the Deep Digital Flexor Tendon

A 3-year-old male saker falcon (Falco cherrug) was presented with a history of hyperflexion of the first digit of the left pelvic limb with what appeared to be a hypercontracted distal end of the deep digital flexor tendon (m. flexor hallucis longus). Conservative treatment, bandaging, and splinting techniques failed to resolve the hypercontraction of the deep digital flexor tendon and improve digit function. Intraoperatively, the deep digital flexor tendon was found to have formed adhesions with the tendon sheath as well as the bone and soft tissue structures underneath it, impeding its ability to move freely within the tendon sheath. The adhesions were surgically resolved, and the tendon was lengthened by hemisectioning the deep digital flexor tendon at its distal end. Postsurgically, the digit was maintained in an extended position by bandaging. Mild physiotherapy was provided at 5-day intervals to retain function and prevent adhesions. Digit extensibility and function were restored to nearly normal levels after 4 weeks.

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 (Falcocherrug) 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.

Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population

Accurate individual identification is required to estimate survival rates in avian populations. For endangered species, non-invasive methods of obtaining individual identification, such as using molted feathers as a source of DNA for microsatellite markers, are preferred because of less disturbance, easy sample preparation and high efficiency. With the availability of many avian genomes, a few pipelines isolating genome-wide microsatellites have been published, but it is still a challenge to isolate microsatellites from the reference genome efficiently. Here, we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome. We have identified over 95 000 microsatellite loci and established a system comprising 10 highly polymorphic markers (PIC value: 0.49-0.93, mean: 0.79) for an endangered species, saker falcon (Falco cherrug). These markers (except 1) were successfully amplified in 126 molted feathers, exhibiting high amplification success rates (83.9-99.7%), high quality index (0.90-0.97) and low allelic dropout rates (1-9.5%). To further assess the efficiency of this marker system in a population study, we identified individual sakers using these molted feathers (adult) and 146 plucked feathers (offspring). The use of parent and offspring samples enabled us to infer the genotype of missing samples (N = 28), and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers. Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.

Striking pseudogenization in avian phylogenetics: Numts are large and common in falcons

Nuclear copies of mitochondrial genes (numts) are a well-known feature of eukaryotic genomes and a concern in systematics, as they can mislead phylogenetic inferences when inadvertently used. Studies on avian numts initially based on the chicken genome suggest that numts may be uncommon and relatively short among birds. Here we ask how common numts are in falcons, based on recently sequenced genomes of the Saker falcon (Falco cherrug) and Peregrine falcon (F. peregrinus). We identified numts by BLASTN searches and then extracted CYTB, ND2 and COI sequences from them, which were then used for phylogeny inference along with several sequences from other species in Falconiformes. Our results indicate that avian numts may be much more frequent and longer than previously thought. Phylogenetic inferences revealed multiple independent nuclear insertions throughout the history of the Falconiformes, including cases of sequences available in public databases and wrongly identified as authentic mtDNA. New sequencing technologies and ongoing efforts for whole genome sequencing will provide exciting opportunities for avian numt research in the near future.

Complete mitochondrial genome of the Saker falcon, Falco cherrug (Falco, Falconidae)

The Falco cherrug (Saker falcon) is a large bird of prey. In this article, the complete mitochondrial genome of F. cherrug has been determined for the first time. The mitogenome (18,059 bp) comprised 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. Most protein-coding genes started with an ATG or ATA codon except for COI, which initiated with nontypical start codon of GTG instead, and terminated with the typical stop codon (TAA/TAG/AGA/AGG) or a single T. Two tandem repeats were identified in the control region, which was almost identical to Falco peregrinus, and the length of these two repeats are 204 bp and 291 bp, respectively.