Dark Morph of the Oriental Honey-Buzzard (Pernis ptilorhynchus orientalis) is Attributable to Specific MC1R Haplotypes.

A thorough understanding of the development of complex plumages in birds necessitates the acquisition of genetic data pertaining to the mechanism underlying this phenomenon from various avian species. The oriental honey-buzzard (Pernis ptilorhynchus orientalis), a tropical summer migrant to Northeast Asia, including Japan, exemplifies this aspect owing to the diversity of its ventral coloration and intra-feather barring patterns. However, genetic polymorphism responsible for this diversity has not been identified yet. This study aimed to investigate the link between dark-plumed phenotypes of this subspecies and haplotypes of the melanocortin-1-receptor (MC1R) gene. A draft sequence of MC1R was constructed using next generation sequencing and subsequently amplified using designed polymerase chain reaction (PCR) primers. The genome sequences of 32 honey-buzzard individuals were determined using PCR, and 12 MC1R haplotype sequences were obtained. Among these haplotypes, we found that unique haplotypes with nine non-synonymous substitutions and four or five synonymous substitutions in the coding region had a perfect correlation with the dark-plumed phenotype. The lack of correlation between the genotype of ASIP coding region and plumage phenotype reiterated that the dark morph is attributable to specific MC1R haplotypes. The absence of a correlation between genetic polymorphisms of MC1R and the intra-feather barring patterns, as well as the diversity observed within lighter ground color classes (pale and intermediate), implies the involvement of alternative molecular mechanisms in the manifestation of the aforementioned phenotypes.

Satellite Tracking of Migration Routes of the Eastern Buzzard (Buteo japonicus) in Japan through Sakhalin.

We satellite-tracked the eastern buzzard (Buteo japonicus) wintering in Japan to delineate both northward and southward migration routes, destinations, and stopover behavior. Twenty-two buzzards were captured and fitted with functional platform transmitter terminals. For these buzzards that departed from the capture sites, we observed a total of 65 northward migrations during 2008-2016 and a total of 55 southward migrations during 2008-2015. In spring, the eastern buzzards migrated eastward along the Seto Inland Sea in the Chugoku region or further inland. In eastern Honshu, they followed two different routes. One was to Hokkaido via the Tsugaru Peninsula from central or northern central Honshu northward along the side of the Sea of Japan in northern Honshu. The other was to Hokkaido via the Shimokita Peninsula, mainly from the Pacific Ocean side of northern Honshu, moving eastward through central Honshu. Of the 17 birds tracked, 10 summered in Sakhalin, three in Hokkaido, three in northern Honshu, and one unknown. In autumn, the buzzards retraced their northward migration routes. Of the 14 birds that were tracked the entire southward migration, 13 (92%) returned to their respective capture sites. One juvenile wintered in an area different from the capture site. Our study contributes to a deeper understanding of the distribution of breeding and wintering grounds and the migration routes of B. japonicus. In addition, the information on migration obtained in this study can contribute toward appropriate environmental impact assessment for wind power facilities in Japan.

The interplay of wind and uplift facilitates over-water flight in facultative soaring birds.

Flying over the open sea is energetically costly for terrestrial birds. Despite this, over-water journeys of many birds, sometimes hundreds of kilometres long, are uncovered by bio-logging technology. To understand how these birds afford their flights over the open sea, we investigated the role of atmospheric conditions, specifically wind and uplift, in subsidizing over-water flight at a global scale. We first established that ΔT, the temperature difference between sea surface and air, is a meaningful proxy for uplift over water. Using this proxy, we showed that the spatio-temporal patterns of sea-crossing in terrestrial migratory birds are associated with favourable uplift conditions. We then analysed route selection over the open sea for five facultative soaring species, representative of all major migratory flyways. The birds maximized wind support when selecting their sea-crossing routes and selected greater uplift when suitable wind support was available. They also preferred routes with low long-term uncertainty in wind conditions. Our findings suggest that, in addition to wind, uplift may play a key role in the energy seascape for bird migration that in turn determines strategies and associated costs for birds crossing ecological barriers such as the open sea.

Genetic Structure in Japanese and Thai Populations of the Japanese Sparrowhawk Accipiter gularis.

The Japanese sparrowhawk Accipiter gularis is a small raptor that breeds in Northeast Asia. The species consists of the widespread and mostly migratory subspecies A. g. gularis that is common in East Asia, including Japan, and the resident and endangered subspecies A. g. iwasakii which inhabits the Ryukyu and Yaeyama Islands in Okinawa, southern Japan. Given the minimal knowledge about the migration of the species, in this study we sought to compare the genetic variation of the populations breeding in Japan with those migrating through Southeast Asia. We sequenced 761 bp of mitochondrial DNA Control Region from each of 21 A. gularis collected during the breeding season in Japan and from 20 individuals intercepted on migration in Thailand. We detected 26 haplotypes among the 41 individuals which differed significantly between Japan and Thailand. Migrants in Thailand were presumed to have originated from a wide area in Eastern Eurasia. The phylogenetic and network analyses demonstrated that the haplotypes of all A. g. gularis detected in Japan were genetically close. Moreover, the Okinawa haplotypes of A. g. iwasakii were clustered with moderate genetic variation. The information presented here can be used towards implementing future conservation actions.

Seasonal contrasts in individual consistency of oriental honey buzzards' migration.

Individual consistency in migration can shine light on the mechanisms of migration. Most studies have reported that birds are more consistent in the timing than in the routes or stopover sites during migration, but some specialist species showed the opposite patterns, being more consistent in spatial than temporal aspects of migration. One possible explanation for this contrast is that specialists rely on particular food or habitat resources, which restrict the migratory routes they can take, leading to high spatial consistency. If this is the case, the effect of specialist foraging should become apparent only when birds forage, instead of fasting and flying continuously. To test this effect, we analysed individual consistency in migration of the oriental honey buzzard ( Pernis ptilorhynchus), a specialist raptor that feeds on honeybees and wasps, using a long-term tracking dataset. As honey buzzards make extended stopovers during which they forage in spring but not in autumn, the spatial consistency should be higher in spring than in autumn. Honey buzzards were highly consistent in both their migratory routes and stopover sites in Southeast Asia, but only during spring migration. Our results highlight an important link between species' migratory consistency and foraging ecology.

Hindgut Bacterial Flora Analysis in Oriental Honey Buzzard (Pernis ptilorhynchus).

The intestinal microbiome is known to affect host health through various effects on nutrition and immunity. The oriental honey buzzard (OHB) is a raptor that feeds on bees and wasps. Due to its restricted diet, we reasoned that the OHB may have a unique microbiome. The aim of this study was to characterize the structure of the intestinal flora of oriental honey buzzards and to investigate the difference of intestinal bacterial flora between individuals in the wild and those reared in captivity. We investigated the intestinal microbiome of seven wild buzzards (Wild), one zoo-reared (Zoo), and one individual reared in captivity for one month (Rearing). Average operational taxonomic units in Wild and Rearing were 69.4 and 113, respectively. Diversity indices such as ACE, Chao 1, Shannon, and Alpha were significantly lower in the Wild than in the Rearing samples. These results suggest that the variety of Wild microbiome is remarkably low. At the phylum level, the composition of the microbiome was similar in all three groups, with firmicutes and bacteroidetes predominating. The third most abundant bacterium in Wild was Proteobacteria, whereas it was Actinobacteria in Rearing and unclassified bacteria in Zoo. Thus, microbiome composition is affected even with just one month of human rearing.

Migration Patterns and Characteristics of Eurasian Wigeons (Mareca penelope) Wintering in Southwestern Japan Based on Satellite Tracking.

Understanding migration ecology of Eurasian wigeons (Mareca penelope) is crucial for effective population management, mitigating conflicts with human, and habitat conservation. The objectives of the present study were 1) to determine their migration patterns of Eurasian wigeons in the East Asian flyway, and 2) to identify the key breeding and stopover sites. From 2007 to 2016, a total of the 64 wigeons, which wintered in Japan, were equipped with satellite transmitters. Most Eurasian wigeons migrated to breeding sites in Russia either (a) via a continental route through China, (b) via the Kamchatka Peninsula, or (c) via Sakhalin Island. In spring, many of the Eurasian wigeons (60.98%) migrated via the continental route. In autumn, most Eurasian wigeons (57.14%) migrated through Kamchatka. These differences may be attributable to the influence of Okhotsk Sea air mass on migration decisions due to loop migration. Similarly to the migration of Mallards, Eurasian wigeons employed a "long-stay and short-travel" migration strategy. Eurasian wigeons mainly nested between latitude between 43° to 75°N. From the present findings and the published literature, Eurasian wigeons that winter in Japan are considered to migrate to Russia, China, and the United States during the breeding season, although the main breeding area is in northeastern Russia. A total of 296 important sites to Eurasian wigeons were mapped, and 118 location names with geographic coordinates, and the top five most frequently used sites were identified in each season.

Climate change alters the optimal wind-dependent flight routes of an avian migrant.

Migratory birds can be adversely affected by climate change as they encounter its geographically uneven impacts in various stages of their life cycle. While a wealth of research is devoted to the impacts of climate change on distribution range and phenology of migratory birds, the indirect effects of climate change on optimal migratory routes and flyways, through changes in air movements, are poorly understood. Here, we predict the influence of climate change on the migratory route of a long-distant migrant using an ensemble of correlative modelling approaches, and present and future atmospheric data obtained from a regional climate model. We show that changes in wind conditions by mid-century will result in a slight shift and reduction in the suitable areas for migration of the study species, the Oriental honey-buzzard, over a critical section of its autumn journey, followed by a complete loss of this section of the traditional route by late century. Our results highlight the need for investigating the consequences of climate change-induced disturbance in wind support for long-distance migratory birds, particularly species that depend on the wind to cross ecological barriers, and those that will be exposed to longer journeys due to future range shifts.

The Feather Structure of Oriental Honey Buzzards (Pernis ptilorhynchus) and Other Hawk Species in Relation to Their Foraging Behavior.

The basic structure of a bird feather may be adapted to suit a variety of functions on different parts of the body and in different species. In Oriental honey buzzards (Pernis ptilorhynchus), a species which often preys on the larvae of bees and wasps, it is thought that the bird's integument may provide protection against the stings of these insects. We investigated the structure of Oriental honey buzzard feathers from the face, head, and neck using light and scanning electron microscopy. The structure and appearance of the feathers were compared with those of two other hawk species which live in similar habitats but have different diets: the grey-faced buzzard (Butastur indicus) and the black kite (Milvus migrans). All feathers of Oriental honey buzzards that were examined were smaller than feathers from the same regions of the body of other species and had a reduced number of plumulaceous barbs; barbs were also closer together at the feather tip and had a high barbule density. The small 'scale feathers' on the face had deep barbules with a curved, armor-like appearance, which may help prevent stings from reaching the skin. A unique filamentous substance was observed on all the honey buzzard feathers, particularly those from around the eye of a male bird. It is possible that this may be related to a chemical defense mechanism to deter bees and wasps.

Migration of Tundra Swans (Cygnus columbianus) Wintering in Japan Using Satellite Tracking: Identification of the Eastern Palearctic Flyway.

Migration through the Eastern Palearctic (EP) flyway by tundra swans (Cygnus columbianus) has not been thoroughly documented. We satellite-tracked the migration of 16 tundra swans that winter in Japan. The objectives of this study were 1) to show the migration pattern of the EP flyway of tundra swans; 2) to compare this pattern with the migration pattern of whooper swans; and 3) to identify stopover sites that are important for these swans' conservation. Tundra swans were captured at Kutcharo Lake, Hokkaido, in 2009-2012 and satellite-tracked. A new method called the "MATCHED (Migratory Analytical Time Change Easy Detection) method" was developed. Based on median, the spring migration began on 18 April and ended on 27 May. Autumn migration began on 9 September and ended on 2 November. The median duration of the spring and autumn migrations were 48 and 50 days, respectively. The mean duration at one stopover site was 5.5 days and 6.8 days for the spring and autumn migrations, respectively. The number of stopover sites was 3.0 and 2.5 for the spring and autumn migrations, respectively. The mean travel distances for the spring and autumn migrations were 6471 and 6331 km, respectively. Seven migration routes passing Sakhalin, the Amur River, and/or Kamchatka were identified. There were 15, 32, and eight wintering, stopover, and breeding sites, respectively. The migration routes and staging areas of tundra swans partially overlap with those of whooper swans, whose migration patterns have been previously documented. The migration patterns of these two swan species that winter in Japan confirm the importance of the Amur River, Udyl' Lake, Shchastya Bay, Aniva Bay, zaliv Chayvo Lake, zal Piltun Lake, zaliv Baykal Lake, Kolyma River, Buyunda River, Sen-kyuyel' Lake, and northern coastal areas of the Sea of Okhotsk.

Incorporating color into integrative taxonomy: analysis of the varied tit (Sittiparus varius) complex in East Asia.

Species designations are critically important scientific hypotheses that serve as the foundational units in a wide range of biological subdisciplines. A growing realization that some classes of data fail to delimit species under certain conditions has led to increasingly more integrative taxonomies, whereby species discovery and hypothesis testing are based on multiple kinds of data (e.g., morphological, molecular, behavioral, ecological, etc.). However, although most taxonomic descriptions have been based on morphology, some key morphological features, such as color, are rarely quantified and incorporated into integrative taxonomic studies. In this article, we applied a new method of ultraviolet digital photography to measure plumage variation in a color-variable avian species complex, the varied tit (Sittiparus varius). Plumage measurements corroborated species limits defined by morphometric, mitochondrial DNA, and nuclear DNA disjunctions and provided the only evidence for distinguishing two recently evolved species. Importantly, color quantification also provided a justification for lumping putative taxa with no evidence of evolutionary independence. Our revised taxonomy thus refines conservation units for listing and management and clarifies the primary units for evolutionary studies. Species tree analyses, which applied the newly delimited species as operational taxonomic units, revealed a robust phylogenetic hypothesis for the group that establishes a foundation for future biogeographic analyses. This study demonstrates how digital photography can be used to incorporate color character variation into integrative taxonomies, which should lead to more informed, more rigorous, and more accurate assessments of biodiversity. [Color, digital photography, integrative taxonomy, Sittiparus varius, species delimitation, varied tit.].

Modeling daily flowering probabilities: expected impact of climate change on Japanese cherry phenology.

Understanding the drivers of phenological events is vital for forecasting species' responses to climate change. We developed flexible Bayesian survival regression models to assess a 29-year, individual-level time series of flowering phenology from four taxa of Japanese cherry trees (Prunus spachiana, Prunus × yedoensis, Prunus jamasakura, and Prunus lannesiana), from the Tama Forest Cherry Preservation Garden in Hachioji, Japan. Our modeling framework used time-varying (chill and heat units) and time-invariant (slope, aspect, and elevation) factors. We found limited differences among taxa in sensitivity to chill, but earlier flowering taxa, such as P. spachiana, were more sensitive to heat than later flowering taxa, such as P. lannesiana. Using an ensemble of three downscaled regional climate models under the A1B emissions scenario, we projected shifts in flowering timing by 2100. Projections suggest that each taxa will flower about 30 days earlier on average by 2100 with 2-6 days greater uncertainty around the species mean flowering date. Dramatic shifts in the flowering times of cherry trees may have implications for economically important cultural festivals in Japan and East Asia. The survival models used here provide a mechanistic modeling approach and are broadly applicable to any time-to-event phenological data, such as plant leafing, bird arrival time, and insect emergence. The ability to explicitly quantify uncertainty, examine phenological responses on a fine time scale, and incorporate conditions leading up to an event may provide future insight into phenologically driven changes in carbon balance and ecological mismatches of plants and pollinators in natural populations and horticultural crops.

Beyond seasonal climate: statistical estimation of phenological responses to weather.

Phenological events, such as the timing of flowering or insect emergence, are influenced by a complex combination of climatic and non-climatic factors. Although temperature is generally considered most important, other weather events such as frosts and precipitation events can also influence many species' phenology. Non-climatic variables such as photoperiod and site-specific habitat characteristics can also have important effects on phenology. Forecasting phenological shifts due to climate change requires understanding and quantifying how these multiple factors combine to affect phenology. However, current approaches to analyzing phenological data have a limited ability for quantifying multiple drivers simultaneously. Here, we use a novel statistical approach to estimate the combined effects of multiple variables, including local weather events, on the phenology of several taxa (a tree, an insect, and a fungus). We found that thermal forcing had a significant positive effect on each species, frost events delayed the phenology of the tree and butterfly, and precipitation had a positive effect on fungal fruiting. Using data from sites across latitudinal gradients, we found that these effects are remarkably consistent across sites once latitude and other site effects are accounted for. This consistency suggests an underlying biological response to these variables that is not commonly estimated using data from field observations. This approach's flexibility will be useful for forecasting ongoing phenological responses to changes in climate variability in addition to seasonal trends.

Function of head-bobbing behavior in diving little grebes.

Most birds show a characteristic head movement that consists of head stabilization and quick displacement. In this movement, which is analogous to saccadic eye movement in mammals, head stabilization plays an important role in stabilizing the retinal image. This head movement, called "head bobbing", is particularly pronounced during walking. Previous studies focusing on anatomical and behavioral features have pointed out that visual information is also important for diving birds, indicating its significance in the head movements of diving birds. In the present study, the kinematic and behavioral features of head bobbing in diving little grebes were described by motion analysis to identify the head movement in diving birds. The results showed that head-bobbing stroke (HBS) consisted of a thrust phase and a hold phase as is typical for head bobbing during walking birds. This suggests that HBS is related to visual stabilization under water. In HBS, grebes tended to dive with longer stroke length and smaller stroke frequency than in non-bobbing stroke. This suggests that the behavior, which is related to vision, affects the kinematic stroke parameters. This clarification of underwater head movement will help in our understanding not only of vision, but also of the kinematic strategy of diving birds.

Disentangling the paradox of insect phenology: are temporal trends reflecting the response to warming?

The strength and direction of phenological responses to changes in climate have been shown to vary significantly both among species and among populations of a species, with the overall patterns not fully resolved. Here, we studied the temporal and spatial variability associated with the response of several insect species to recent global warming. We use hierarchical models within a model comparison framework to analyze phenological data gathered over 40 years by the Japan Meteorological Agency on the emergence dates of 14 insect species at sites across Japan. Contrary to what has been predicted with global warming, temporal trends of annual emergence showed a later emergence day for some species and sites over time, even though temperatures are warming. However, when emergence data were analyzed as a function of temperature and precipitation, the overall response pointed out an earlier emergence day with warmer conditions. The apparent contradiction between the response to temperature and trends over time indicates that other factors, such as declining populations, may be affecting the date phenological events are being recorded. Overall, the responses by insects were weaker than those found for plants in previous work over the same time period in these ecosystems, suggesting the potential for ecological mismatches with deleterious effects for both suites of species. And although temperature may be the major driver of species phenology, we should be cautious when analyzing phenological datasets as many other factors may also be contributing to the variability in phenology.

Mosaic gene conversion after a tandem duplication of mtDNA sequence in Diomedeidae (albatrosses).

Although the tandem duplication of mitochondrial (mt) sequences, especially those of the control region (CR), has been detected in metazoan species, few studies have focused on the features of the duplicated sequence itself, such as the gene conversion rate, distribution patterns of the variation, and relative rates of evolution between the copies. To investigate the features of duplicated mt sequences, we partially sequenced the mt genome of 16 Phoebastria albatrosses belonging to three species (P. albatrus, P. nigripes, and P. immutabilis). More than 2,300 base pairs of tandemly-duplicated sequence were shared by all three species. The observed gene arrangement was shared in the three Phoebastria albatrosses and suggests that the duplication event occurred in the common ancestor of the three species. Most of the copies in each individual were identical or nearly identical, and were maintained through frequent gene conversions. By contrast, portions of CR domains I and III had different phylogenetic signals, suggesting that gene conversion had not occurred in those sections after the speciation of the three species. Several lines of data, including the heterogeneity of the rate of molecular evolution, nucleotide differences, and putative secondary structures, suggests that the two sequences in CR domain I are maintained through selection; however, additional studies into the mechanisms of gene conversion and mtDNA synthesis are required to confirm this hypothesis.

Genetic and morphological differences among populations of the Bonin Islands White-eye in Japan.

The Bonin Islands White-eye, Apalopteron familiare , is the sole endemic avian species surviving on the Bonin Islands. The current distribution of this species is limited to only three islands of the Hahajima Island group: Hahajima, Imotojima, and Mukohjima. Imotojima and Mukohjima, which are small satellite islands of Hahajima, are about 3.6 km and 5.5 km, respectively, from the larger island. To investigate genetic and morphological differences among A. familiare populations on these islands, we assayed 634 bp of mitochondrial control region sequence for 132 birds from five locations among the three islands. We detected five haplotypes: two endemic haplotypes each on Hahajima and Imotojima and one on Mukohjima. Principal component analysis based on eight morphological characters of 162 birds from the three island populations revealed that birds from the small satellite islands had significantly different beak morphological characters. Our findings indicate that over-sea dispersal is rare in A. familiare , even when islands are separated by only a few kilometers, and suggest that little movement occurs on Hahajima. Thus, each population on each island should be conserved as an evolutionarily significant unit. The low dispersal ability of this species suggests that it is vulnerable to habitat fragmentation. Although the populations are currently stable and do not require rapid countermeasures, they should be monitored, especially those on the smaller islands.

Spring migration routes of mallards (Anas platyrhynchos) that winter in Japan, determined from satellite telemetry.

Wild birds, in particular waterfowl, are common reservoirs of low pathogenic avian influenza viruses, and infected individuals could spread the viruses during migrations. We used satellite telemetry to track the spring migration of the mallard ducks ( Anas platyrhynchos ) that winter in Japan. We studied their migration routes, distribution of stopover and breeding sites, and timing of migration movements. We tracked 23 mallards from four different wintering sites. Nine of the 23 mallards reached presumable breeding sites, where migration terminated. The migration routes of the birds greatly differed not only among the wintering sites but also within the same wintering site, although the general feature of the routes was shared among birds within the same wintering site. The mallards used several stopover sites, and they typically stayed for a long period (about one to four weeks) at a site between migration intervals of two to three days. Stopover sites were located in northeast Japan, the eastern coastline of South Korea and North Korea, and the interior of Far Eastern Russia. Mallards from three different wintering sites used a stopover area near the middle part of the Ussuri river in Russia. The terminal sites, which were presumably also breeding sites, were distributed widely over northeast Asia and Far Eastern Russia. These results suggest that mallards that winter in Japan originate from breeding areas widely distributed across eastern Asia. Mallards could potentially transmit avian influenza viruses between Japan and a broad region of northeastern Asia.

Raptor migration in an oceanic flyway: wind and geography shape the migratory route of grey-faced buzzards in East Asia.

Flapping flight is relatively costly for soaring birds such as raptors. To avoid costly flight, migrating raptors generally avoid flying over water. As a result, all but one of the global raptor migration flyways are largely over land. The East Asian oceanic flyway for raptors is the exception. Raptor species using this flyway migrate by island-hopping, flying over open ocean for distances of up to 300 km between islands. We used satellite telemetry data for grey-faced buzzards Butastur indicus, a species that dominates the southern part of the flyway, to investigate the geographical and atmospheric factors responsible for the suitability of this flyway for raptor migration. Using a combination of least-cost path analysis and a step selection function, we found that the occurrence of numerous islands and also suitable wind support along the oceanic flyway are responsible for route selection in grey-faced buzzards. These results confirm the role of islands, but also wind, in shaping the East Asian oceanic flyway of long-distance raptor migration.

Hopping and climbing gait of Japanese Pygmy Woodpeckers (Picoides kizuki).

Single cycles of hopping and climbing were investigated in Japanese Pygmy Woodpeckers Picoides kizuki using motion analyses on video. Body movements on substrate angled from 0-90 degrees were compared for every 10 degrees. The body was inclined forward during stance phase for both small and large substrate angles, and the inclination amplitude increased when the substrate angle increased. The tail was bent ventrally almost simultaneously to this body inclination, and its amplitude was apparently high at large substrate angles. Most of the gait parameters changed when the stride length increased. The minimum body-tail angle and most of the parameters representing body movements during stance phase changed when the substrate angle increased, probably because gravity pulled the birds further backward when they were moving on a steeper slope. These parameters showed a clear difference between the data on substrate steeper than 40 degrees and lower than 30 degrees. The abrupt changes in these parameters most likely mean that the motor pattern changed from hopping to climbing between these angles.