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.

Diet specialization in an insular population of coastal Peregrine Falcons

Individual diet specialization is known to occur in populations of generalist predators, where specific individuals develop specialist feeding strategies. Diet specialization has been reported in many raptor species, and it may be an important driver of intraspecific population structure. Here, we quantify the diet of five breeding pairs of Peregrine Falcons Falco peregrinus from an offshore island determined from prey remains collected over four breeding seasons. Three prey species accounted for 69.8 % of total prey frequency, with Manx Shearwater Puffinus puffinus the primary prey accounting for 47.3 % by frequency and 40.8 % by biomass. Herring Gull Larus argentatus was the second most important prey species by frequency (13.8 %) and biomass (29.8 %) followed by Domestic Pigeon Columba livia (frequency = 8.7 %, biomass = 7.0 %). Predation frequency on specific prey groups varied substantially between breeding pairs and months. Two pairs specialized on Manx Shearwater, one pair specialized on Herring Gull and Manx Shearwater, with the remaining two pairs having a relatively generalist diet of Manx Shearwaters, Domestic Pigeon and small passerines. Predation on Manx Shearwaters increased throughout the breeding season with a peak in total diet frequency of 63.8 % in July, with a concurrent decrease in Herring Gull predation frequency. Higher percentage of Manx Shearwater in the diet was able to explain 87 % of the variation in a narrower dietary breadth for the Peregrine pairs. Our results suggest individual diet specialization may be important for understanding population density in insular raptor populations.

Morphological Characteristics of the Sperm of the Peregrine Falcon (Falco peregrinus) during the Reproductive Season

The morphological characteristics of different sperm cells (normal, abnormal, and immature) in the peregrine falcon during the reproductive season were analysed. We also classified the main sperm defects found in semen. Semen samples were collected from mature peregrine falcons via cloacal massage and stained with Diff-Quik stain. The percentages of normal, abnormal, and immature sperm cells were determined by bright-field optical microscopy. The number of normal spermatozoa were greater at the initial stage and subsequently decreased during the middle and later stages of the reproductive season (p < 0.01). In contrast, the percentage of abnormal spermatozoa increased significantly in the middle and end stages of the reproductive season (p < 0.05), whereas the proportion of immature spermatozoa remained stable during the study. Head defects represented the greatest proportion of morphological abnormalities, followed by the defects in the tail and midpiece regions. A small percentage of multiple defects and cytoplasmic droplets were also observed in the falcon spermatozoa. The findings of this study might be important for the development of future conservation protocols for falcon sperm.

Malar stripe size and prominence in peregrine falcons vary positively with solar radiation: support for the solar glare hypothesis

Many falcons ( Falco spp.) exhibit a distinct dark plumage patch below the eye, termed the malar stripe. This stripe is hypothesized to reduce the amount of solar glare reflected into the eyes while foraging, thereby increasing hunting efficiency in bright conditions. Here, we use a novel, global-scale correlative approach to test this ‘solar glare hypothesis' in peregrine falcons ( Falco peregrinus ), the most widespread falcon species, using web-sourced photographs from across the species' global range. We found that the size and prominence of the malar stripe were positively associated with average annual solar radiation, but not with other environmental variables, such as temperature and rainfall. Our results provide the first published evidence for the hypothesis that this plumage feature functions to reduce the amount of solar glare reflected into the falcon's eyes, thereby improving the ability to pinpoint and target agile prey in bright conditions.

Hopera de citraria de falcone pellegrine et gentile d’Alfonso Caracciolo

Resum: Editem un tractat de falconeria escrit en italià de Calàbria amb alguns trets catalans i amb vincles amb el grup d’obres de la biblioteca napolitana dels reis d’Aragó. El còdex factici de la Reial Biblioteca del Monasterio de San Lorenzo de El Escorial, amb signatura C-IV-6, conté set documents, un dels quals és l’Hopera de citraria de falcone pellegrine et gentile escrita per Alfonso Caracciolo, que ocupa una extensió de més de 40 fulls. Aquest text segueix la tradició dels tractat medievals i segurament està escrit a finals del segle XV. L’objectiu de l’autor és ensenyar bàsicament a ensinistrar falcons pelegrins i gentils, encara que presenta altres continguts de caràcter cinegètic i es basa, segons l’autor, en l’experiència pròpia. Paraules clau: tractat de falconeria, Caracciolo, falcons pelegrins, falcons gentils Abstract: We offer the critical edition of a treatise of falconry written in Italian from Calabria. It also has some Catalan features, and it is linked to a number of texts from the library of Naples belonging to the kings of Aragon. This codex from the Royal Library of the Monastery of San Lorenzo de El Escorial, being its identification C-IV-6, contains seven documents. One of these documents is Hopera de citraria de falcone pellegrine et gentile (Treatise of falconry of peregrine falcon and gentle hawk) written by Alfonso Caracciolo, having more than 40 pages. This text follows the tradition of medieval treatise, and it was probably written at the end of the 15th century. The aim of the author is to teach to train peregrine falcons and gentle hawks, even though it has other content related to hunting, and it is based on the author’s experience. Key words: treatise on falconry, Caracciolo, peregrine falcon, gentle hawk

Influence of introduced peregrine falcons on the distribution of red knots within a spring staging site

Predator recovery driven by single-species management approaches may lead to conservation conflicts between recovered predators and prey species of conservation concern. As part of an aggressive recovery plan, the Eastern Peregrine Falcon Recovery Team released (1975–1985) 307 captive-reared peregrine falcons (Falco peregrinus) and successfully established a breeding population within the mid-Atlantic Coastal Plain, a physiographic region with no historic breeding population and a critical spring staging area for migratory shorebirds. We examined the influence of resident falcons on the distribution of foraging red knots during spring migration. We conducted weekly aerial surveys (2006–2009) along the Virginia barrier islands during the spring staging period (25 April– 6 June) to map foraging red knots (Calidris canutus) and evaluated the influence of proximity (0–3, 3–6, >6 km) of beaches to active peregrine falcon nests on knot density (birds/km). Accumulated use of beaches throughout the season by red knots was significantly influenced by proximity of beaches to active falcon nests such that mean density was more than 6 fold higher on beaches that were >6 km compared to beaches that were only 0–3 km from active eyries. Whether or not an eyrie was used in a given year had a significant influence on the use of associated close (0–3 km) beaches. From 6.5 to 64 fold more knots used beaches when associated eyries were not active compared to when they were active depending on the specific site. Historically, red knots and other migratory shorebirds would have enjoyed a peregrine-free zone within this critical staging site. The establishment of a dense breeding population of falcons within the area represents a new hazard for the knot population.