Comprehensive molecular phylogeny of barn owls and relatives (Family: Tytonidae), and their six major Pleistocene radiations

Characterization of the diversity of barn owl's mitochondrial genome reveals high copy number variations in the control region

Mitochondria are known to play an essential role in the cell. These organelles contain their own DNA, which is divided in a coding and non-coding region (NCR). While much of the NCR's function is unknown, tandem repeats have been observed in several vertebrates, with extreme intra-individual, intraspecific and interspecific variation. Taking advantage of a new complete reference for the mitochondrial genome of the Afro-European Barn Owl (Tyto alba), as well as 172 whole genome-resequencing; we (i) describe the reference mitochondrial genome with a special focus on the repeats in the NCR, (ii) quantify the variation in number of copies between individuals, and (iii) explore the possible factors associated with the variation in the number of repetitions. The reference mitochondrial genome revealed a long (256bp) and a short (80bp) tandem repeat in the NCR region. The re-sequenced genomes showed a great variation in number of copies between individuals, with 4 to 38 copies of the Long and 6 to 135 copies of the short repeat. Among the factors associated with this variation between individuals, the tissue used for extraction was the most significant. The exact mechanisms of the formations of these repeats are still to be discovered and understanding them will help explain the maintenance of the polymorphism in the number of copies, as well as their interactions with the metabolism, the aging and health of the individuals.

Muscle architecture of the hindlimb of Tyto furcata (Aves Strigiformes): Highlights in owl morphology

The American barn owl is a nocturnal bird of prey in which hind limb movements are a key factor in obtaining food; however, the architectural properties of its hind limb muscles have not been studied. This study sought to identify functional trends in the Tyto furcata hindlimb muscles by studying muscular architecture. The architectural parameters of the selected hip, knee, ankle, and digit muscles were studied in three specimens of the Tyto furcata and joint muscular proportions with an additional dataset were calculated. Previously published information on Asio otus was used for comparison. The flexor muscles of the digits had the highest muscle mass. Regarding architectural parameters, the main flexor of the digits (flexor digitorum longus) and the muscles that extend the knee and ankle joints (femorotibialis and gastrocnemius) showed a high physiological cross-sectional area (PCSA) and short fibers, allowing powerful digit flexion and knee and ankle extension. These mentioned features are in accordance with hunting behavior, in which prey capture is not only closely linked to the flexion of the digits but also to the movements of the ankle. During hunting, the distal hind limb is flexed and then fully extended at the moment of contact with the prey, whereas the digits are close to grasping the prey. The hip muscles showed a predominance of extensors over flexors, which were more massive, with parallel fibers and without tendons or short fibers. These features lead to a higher capacity to generate velocity to the detriment of forces, as indicated by the high values of the architectural index, their relatively low PCSA, and short or intermediate fiber length, which enhance the control of the joint positions and muscle length. Compared to Asio otus, Tyto furcata showed longer fibers; however, the relationship between fiber length and PCSA was similar for both species.

Mitochondrial genome analysis, phylogeny and divergence time evaluation of Strixaluco (Aves, Strigiformes, Strigidae)

Background Prior research has shown that the European peninsulas were the main sources of Strixaluco colonisation of Northern Europe during the late glacial period. However, the phylogenetic relationship and the divergence time between S.aluco from Leigong Mountain Nature Reserve, Guizhou Province, China and the Strigiformes from overseas remains unclear. The mitochondrial genome structure of birds is a covalent double-chain loop structure that is highly conserved and, thus, suitable for phylogenetic analysis. This study examined the phylogenetic relationship and divergence time of Strix using the whole mitochondrial genome of S.aluco. New information In this study, the complete mitochondrial genome of Strixaluco, with a total length of 18,632 bp, is reported for the first time. A total of 37 genes were found, including 22 tRNAs, two rRNAs, 13 protein-coding genes and two non-coding control regions. Certain species of Tytoninae were used as out-group and PhyloSuite software was applied to build the ML-tree and BI-tree of Strigiformes. Finally, the divergence time tree was constructed using BEAST 2.6.7 software and the age of Miosurniadiurna fossil-bearing sediments (6.0-9.5 Ma) was set as internal correction point. The common ancestor of Strix was confirmed to have diverged during the Pleistocene (2.58-0.01 Ma). The combined action of the dramatic uplift of the Qinling Mountains in the Middle Pleistocene and the climate oscillation of the Pleistocene caused Strix divergence between the northern and southern parts of mainland China. The isolation of glacial-interglacial rotation and glacier refuge was the main reason for the divergence of Strixuralensis and S.aluco from their common ancestor during this period. This study provides a reference for the evolutionary history of S.aluco.

Systematics of Thraupis (Aves, Passeriformes) reveals an extensive hybrid zone between T. episcopus (Blue-gray Tanager) and T. sayaca (Sayaca Tanager)

The Neotropical avian genus Thraupis (Passeriformes, Thraupidae) currently comprises seven species that are widespread and abundant throughout their ranges. However, no phylogenetic hypothesis with comprehensive intraspecific sampling is available for the group and, therefore, currently accepted species limits remain untested. We obtained sequence data for two mitochondrial (ND2, cyt-b) and three non-coding nuclear (TGFB2, MUSK, and βF5) markers from 118 vouchered museum specimens. We conducted population structure and coalescent-based species-tree analyses using a molecular clock calibration. We integrated these results with morphometric and coloration analyses of 1,003 museum specimens to assess species limits within Thraupis. Our results confirm that Thraupis is a monophyletic group and support its origin in the late Miocene and subsequent diversification during the Pleistocene. However, we found conflicts with previous phylogenies. We recovered Thraupis glaucocolpa to be sister to all other species in the genus, and T. cyanoptera to the remaining five species. Our phylogenetic trees and population structure analyses uncovered phylogeographic structure within Thraupis episcopus that is congruent with geographic patterns of phenotypic variation and distributions of some named taxa. The first genetic and phenotypic cluster in T. episcopus occurs east of the Andes and is diagnosed by the white patch on the lesser and median wing coverts, whereas the second group has a blue patch on the wing and distributes to the west of Colombia's eastern Andes. Finally, we present evidence of hybridization and ongoing gene flow between several taxa at different taxonomic levels and discuss its taxonomic implications.

Genomic basis of insularity and ecological divergence in barn owls (Tyto alba) of the Canary Islands

Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities to study the effect of neutral and adaptive mechanisms in determining genomic and phenotypical divergence. In the Canary Islands, an archipelago rich in endemics, the barn owl (Tyto alba), present in all the islands, is thought to have diverged into a subspecies (T. a. gracilirostris) on the eastern ones, Fuerteventura and Lanzarote. Taking advantage of 40 whole-genomes and modern population genomics tools, we provide the first look at the origin and genetic makeup of barn owls of this archipelago. We show that the Canaries hold diverse, long-standing and monophyletic populations with a neat distinction of gene pools from the different islands. Using a new method, less sensitive to structure than classical F_ST, to detect regions involved in local adaptation to insular environments, we identified a haplotype-like region likely under selection in all Canaries individuals and genes in this region suggest morphological adaptations to insularity. In the eastern islands, where the subspecies is present, genomic traces of selection pinpoint signs of adapted body proportions and blood pressure, consistent with the smaller size of this population living in a hot arid climate. In turn, genomic regions under selection in the western barn owls from Tenerife showed an enrichment in genes linked to hypoxia, a potential response to inhabiting a small island with a marked altitudinal gradient. Our results illustrate the interplay of neutral and adaptive forces in shaping divergence and early onset speciation.

A Comparison of Aerodynamic Parameters in Two Subspecies of the American Barn Owl (Tyto furcata)

Simple Summary

Morphology and function depend on the ecological niche in which an animal lives. Barn owls, occurring on all continents, occupy a nocturnal niche. These birds prey mainly on small rodents but include other small vertebrates and invertebrates in the diet. The size of the barn-owl species and subspecies varies considerably. The American continent harbors the species Tyto furcata. The body mass of the subspecies in North America (T.f.pratincola) is about a factor of two higher than that of the subspecies living on the Galapagos archipelago (T.f.puncatissima). We asked how this difference translates into aerodynamic parameters. The key question was whether there is so-called similarity scaling or not. In other words, whether important aerodynamic parameters scale according to body mass. This is called isometric scaling. Deviation from isometric scaling is called allometric scaling. If we use the subspecies from the continent as a reference, we find that the Galapagos barn owl has relatively larger wings than expected from isometric scaling. This translates into a lower wing loading in punctatissima than in pratincola. A lower wing loading means higher maneuverability. We speculate that the higher maneuverability allows the Galapagos owl to catch smaller prey, especially insects.

Abstract

Aerodynamic parameters, such as wing loading, are important indicators of flight maneuverability. We studied two subspecies of the American Barn owl (Tyto furcata), the North American subspecies, T.f.pratincola, and the Galapagos subspecies, T.f.punctatissima, with respect to aerodynamic parameters and compared our findings with those in other owl and bird species. The body mass of T.f.pratincola is about two times higher than that of T.f.punctatissima. Wing loading between the two subspecies scales allometrically. Wing loading in T.f.pratincola is about 50% higher than in T.f.punctatissima. The scaling of wing length is not statistically different from the prediction for isometric scaling. By contrast, the wing chord in T.f.punctatissima is larger than predicted by isometric scaling, as is the wing area. The scaling of wing loading observed here for T.f.punctatissima differs considerably from the scaling in other owl and bird species as available in the literature. We speculate that the allometric scaling helps T.f.punctatissima to catch smaller prey such, as insects that are found in many pellets of T.f.punctatissima, despite the fact that in both subspecies, small rodents make up most of the diet.

Early evolution of diurnal habits in owls (Aves, Strigiformes) documented by a new and exquisitely preserved Miocene owl fossil from China

SignificanceOwls, with their largely nocturnal habits, contrast strikingly with the vast majority of diurnal birds. A new spectacular late Miocene owl skeleton from China unexpectedly preserves the oldest evidence for daytime behavior in owls. The extinct owl is a member of the clade Surniini, which contains most living diurnal owl species. Analysis of the preserved eye bones documents them as consistent with diurnal birds, and phylogenetically constrained character mapping coincides with a reconstruction of an early evolutionary reversal away from nocturnal habits in this owl group. These results support a potential Miocene origin of nonnocturnal habits in a globally distributed owl group, which may be linked to steppe habitat expansion and climatic cooling in the late Miocene.

Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean

The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. As a result, apparently identical islands may harbour populations with contrasting histories. Here, we use whole genome sequences of 65 barn owls to investigate the patterns of inbreeding and genetic diversity of insular populations in the eastern Mediterranean Sea. We focus on Crete and Cyprus, islands with similar size, climate and distance to mainland, that provide natural replicates for a comparative analysis of the impacts of microevolutionary processes on isolated populations. We show that barn owl populations from each island have a separate origin, Crete being genetically more similar to other Greek islands and mainland Greece, and Cyprus more similar to the Levant. Further, our data show that their respective demographic histories following colonisation were also distinct. On the one hand, Crete harbours a small population and maintains very low levels of gene flow with neighbouring populations. This has resulted in low genetic diversity, strong genetic drift, increased relatedness in the population and remote inbreeding. Cyprus, on the other hand, appears to maintain enough gene flow with the mainland to avoid such an outcome. Our study provides a comparative population genomic analysis of the effects of neutral processes on a classical island‐mainland model system. It provides empirical evidence for the role of stochastic processes in determining the fate of diverging isolated populations.

Landscape and climatic variations shaped secondary contacts amid barn owls of the Western Palearctic

The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls recolonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.

Integrity of and damage to wings, feather vanes and serrations in barn owls

The silent flight of owls is well known. It has served as role model for the designs of new airplane wings and ventilators. One of the structural features that underlies silent flight is the serrated leading edge of the wing that is mainly formed by the tenth primary flight feather (P10). We examined here how much the wings, the P10 feather and the serrations in different populations of barn owls reflect the intact situation. First, when the P10 feather molts, no or fewer serrations are present. Furthermore, damage to feathers and serrations may occur. Damage may be due to several factors like broken feather tips, lost rami, barbules, or broken tips of serrations. The latter may cause a narrowing of the outer vane of the P10 feather. We quantitatively assessed damage by counting the number of wings with missing or broken primary feathers, the number of wings with a narrowed outer vane of the P10 feather, and the number of serrations with reduced length. Considerable damage occurred on wings and feathers on both the macroscopic and microscopic levels. The observed damage most likely influences flight performance. More damage occurred in Galapagos barn owls than in North American and European barn owls. The Galapagos population may be more vulnerable than the other populations because it may at least temporarily be in a bad nutritional state and, thus, postpone molt.

The Galápagos Islands: biogeographic patterns and geology

In the traditional biogeographic model, the Galápagos Islands appeared a few million years ago in a sea where no other islands existed and were colonized from areas outside the region. However, recent work has shown that the Galápagos hotspot is 139 million years old (Early Cretaceous), and so groups are likely to have survived at the hotspot by dispersal of populations onto new islands from older ones. This process of metapopulation dynamics means that species can persist indefinitely in an oceanic region, as long as new islands are being produced. Metapopulations can also undergo vicariance into two metapopulations, for example at active island arcs that are rifted by transform faults. We reviewed the geographic relationships of Galápagos groups and found 10 biogeographic patterns that are shared by at least two groups. Each of the patterns coincides spatially with a major tectonic structure; these structures include: the East Pacific Rise; west Pacific and American subduction zones; large igneous plateaus in the Pacific; Alisitos terrane (Baja California), Guerrero terrane (western Mexico); rifting of North and South America; formation of the Caribbean Plateau by the Galápagos hotspot, and its eastward movement; accretion of Galápagos hotspot tracks; Andean uplift; and displacement on the Romeral fault system. All these geological features were active in the Cretaceous, suggesting that geological change at that time caused vicariance in widespread ancestors. The present distributions are explicable if ancestors survived as metapopulations occupying both the Galápagos hotspot and other regions before differentiating, more or less in situ.

Molecular evolution of the proopiomelanocortin system in Barn owl species

Examination of genetic polymorphisms in outbred wild-living species provides insights into the evolution of complex systems. In higher vertebrates, the proopiomelanocortin (POMC) precursor gives rise to α-, β-, and γ-melanocyte-stimulating hormones (MSH), which are involved in numerous physiological aspects. Genetic defects in POMC are linked to metabolic disorders in humans and animals. In the present study, we undertook an evolutionary genetic approach complemented with biochemistry to investigate the functional consequences of genetic polymorphisms in the POMC system of free-living outbred barn owl species (family Tytonidae) at the molecular level. Our phylogenetic studies revealed a striking correlation between a loss-of-function H9P mutation in the β-MSH receptor-binding motif and an extension of a poly-serine stretch in γ3-MSH to ≥7 residues that arose in the barn owl group 6–8 MYA ago. We found that extension of the poly-serine stretches in the γ-MSH locus affects POMC precursor processing, increasing γ3-MSH production at the expense of γ2-MSH and resulting in an overall reduction of γ-MSH signaling, which may be part of a negative feedback mechanism. Extension of the γ3-MSH poly-serine stretches ≥7 further markedly increases peptide hormone stability in plasma, which is conserved in humans, and is likely relevant to its endocrine function. In sum, our phylogenetic analysis of POMC in wild living owls uncovered a H9P β-MSH mutation subsequent to serine extension in γ3-MSH to 7 residues, which was then followed by further serine extension. The linked MSH mutations highlight the genetic plasticity enabled by the modular design of the POMC gene.

New genome assembly of the barn owl (Tyto alba alba)

New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal raptor, a very fragmented draft genome was assembled for the American species (Tyto furcata pratincola) (Jarvis et al. 2014). To improve the genome, we assembled de novo Illumina and Pacific Biosciences (PacBio) long reads sequences of its European counterpart (Tyto alba alba). This genome assembly of 1.219 Gbp comprises 21,509 scaffolds and results in a N50 of 4,615,526 bp. BUSCO (Universal Single-Copy Orthologs) analysis revealed an assembly completeness of 94.8% with only 1.8% of the genes missing out of 4,915 avian orthologs searched, a proportion similar to that found in the genomes of the zebra finch (Taeniopygia guttata) or the collared flycatcher (Ficedula albicollis). By mapping the reads of the female American barn owl to the male European barn owl reads, we detected several structural variants and identified 70 Mbp of the Z chromosome. The barn owl scaffolds were further mapped to the chromosomes of the zebra finch. In addition, the completeness of the European barn owl genome is demonstrated with 94 of 128 proteins missing in the chicken genome retrieved in the European barn owl transcripts. This improved genome will help future barn owl population genomic investigations.

Wing and tail myology of Tyto furcata (Aves, Tytonidae)

Barn Owls (Tytonidae) are nocturnal raptors with the largest geographical distribution among Strigiformes. Several osteological, morphometrical, and biomechanical studies of this species were performed by previous authors. Nevertheless, the myology of forelimb and tail of the Barn Owls is virtually unknown. This study is the first detailed myological study performed on the wing and tail of the American Barn Owl (Tyto furcata). A total of 11 specimens were dissected and their morphology and muscle masses were described. Although T. furcata has the wing and tail myological pattern present in other species of Strigiformes, some peculiarities were observed including a difference in the attachment of m. pectoralis propatagialis due to the lack of the os prominence, and the presence of an osseous arch in the radius that seems to widen the anchorage area of the mm. pronator profundus, extensor longus alulae, and extensor longus digiti majoris. Furthermore, the m. biceps brachii has an unusual extra belly that flexes the forearm. The interosseous muscles have a small size and lacks ossified tendons. This feature may be indicative of a lower specialization in the elevation and flexion of the digiti majoris. Forelimb and tail muscle mass account for 10.66 and 0.24% of the total body mass, respectively. Forelimb muscle mass value is similar to the nocturnal (Strigiformes) and diurnal (Falconidae and Accipitridae) raptors, while the tail value is lower than in the diurnal raptors (Falconidae and Accipitridae). The myological differences with other birds of prey are here interpreted in association with their "parachuting" hunting style. This work complements our knowledge of the axial musculature of the American Barn owls, and provides important information for future studies related to functional morphology and ecomorphology.

Evolution and Ecology of Silent Flight in Owls and Other Flying Vertebrates

We raise and explore possible answers to three questions about the evolution and ecology of silent flight of owls: (1) do owls fly silently for stealth, or is it to reduce self-masking? Current evidence slightly favors the self-masking hypothesis, but this question remains unsettled. (2) Two of the derived wing features that apparently evolved to suppress flight sound are the vane fringes and dorsal velvet of owl wing feathers. Do these two features suppress aerodynamic noise (sounds generated by airflow), or do they instead reduce structural noise, such as frictional sounds of feathers rubbing during flight? The aerodynamic noise hypothesis lacks empirical support. Several lines of evidence instead support the hypothesis that the velvet and fringe reduce frictional sound, including: the anatomical location of the fringe and velvet, which is best developed in wing and tail regions prone to rubbing, rather than in areas exposed to airflow; the acoustic signature of rubbing, which is broadband and includes ultrasound, is present in the flight of other birds but not owls; and the apparent relationship between the velvet and friction barbules found on the remiges of other birds. (3) Have other animals also evolved silent flight? Wing features in nightbirds (nocturnal members of Caprimulgiformes) suggest that they may have independently evolved to fly in relative silence, as have more than one diurnal hawk (Accipitriformes). We hypothesize that bird flight is noisy because wing feathers are intrinsically predisposed to rub and make frictional noise. This hypothesis suggests a new perspective: rather than regarding owls as silent, perhaps it is bird flight that is loud. This implies that bats may be an overlooked model for silent flight. Owl flight may not be the best (and certainly, not the only) model for "bio-inspiration" of silent flight.