Yamashina Institute for Ornithology

Abiko, Japan

Yamashina Institute for Ornithology

Abiko, Japan
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Saitoh T.,Rikkyo University | Saitoh T.,Yamashina Institute for Ornithology | Alstrom P.,Swedish University of Agricultural Sciences | Alstrom P.,Swedish Museum of Natural History | And 5 more authors.
BMC Evolutionary Biology | Year: 2010

Background. Unlike northern Europe and most of northern North America, the Eastern Palearctic and the northwesternmost tip of North America are believed to have been almost unglaciated during the Quarternary glacial periods. This could have facilitated long-term survival of many organisms in that area. To evaluate this, we studied the phylogeography in east Asia and Alaska of a boreal migratory passerine bird, the Arctic Warbler Phylloscopus borealis, and compared our results with published data on especially North American species. Results. In a sample of 113 individuals from 18 populations we identified 42 haplotypes of the mitochondrial cytochrome b gene, which separated into three clades: A - Alaska and mainland Eurasia (except Kamchatka); B - Kamchatka, Sakhalin and Hokkaido; and C - Honshu, Shikoku and Kyushu (i.e. Japan except Hokkaido). The oldest split among these clades, between A/B and C, is estimated to have taken place sometime between the mid Pliocene and early Pleistocene, and the second divergence, between clades A and B, in the early to mid Pleistocene. Within all of the three main clades, there are signs of population expansion. Conclusions. The Arctic Warbler separated into three main clades in close succession around the Pliocene/Pleistocene border, with the two northern clades diverging last. All three clades probably experienced population bottlenecks during the Pleistocene as a result of range shifts and contractions, but nevertheless survived and maintained their integrities. Several other clades of Northeastern Palearctic birds are noted to have diversified during the Pliocene. In contrast, avian species or phylogroups presently occupying formerly glaciated North American ground are generally younger. The differences between these regions could be due to slower speciation rates in the Eastern Palearctic due to less fragmentation of forest habitats during glacial periods, or to longer survival of Eastern Palearctic clades as a result of less severe conditions in that region compared to northern North America. Several other Palearctic organisms show concordant biogeographical patterns to that of the Arctic Warbler, indicating common causes of their diversifications. © 2010 Saitoh et al.


Yoda K.,Nagoya University | Tomita N.,Meijo University | Tomita N.,Yamashina Institute for Ornithology | Mizutani Y.,Nagoya University | And 2 more authors.
Marine Ecology Progress Series | Year: 2012

Urbanization affects animal movements. However, how urban omnivores respond to natural and human-related food sources with different spatio-temporal structures remains poorly understood. Here, we used animal-borne GPS, video data loggers and high-resolution mapping to examine the foraging behaviour of black-tailed gulls Larus crassirostris during their incubation and hatching period. As expected, the gulls fed not only on natural food at sea (e.g. anchovy and cuttlefish), but also on human-related food sources in 3 kinds of feeding grounds on land, i.e. fishery- or meat-processing plants or markets, private houses and paddy fields. Furthermore, the gulls responded to the different temporal and spatial dynamics of the feeding grounds. The gulls were distributed among these feeding grounds in response to the availability and ephemerality of each food source. Natural-food foraging trips (i.e. ocean) and anthropogenic-food trips (i.e. inland) have different spatial properties, showing a Lévy search of μ = 2 with larger foraging range and patterns closer to ballistic movement with smaller foraging range, respectively. Thus, the gulls responded flexibly to the contrasting food resources of natural and human-related food sources with different temporal and spatial heterogeneities. © Inter-Research 2012.


Mizutani Y.,Nagoya University | Tomita N.,Meijo University | Niizuma Y.,Meijo University | Niizuma Y.,Yamashina Institute for Ornithology | Yoda K.,Nagoya University
Biology Letters | Year: 2013

Telomeres are regarded as markers of biological or cellular ageing because they shorten with the degree of stress exposure. Accordingly, telomere lengths should show different rates of change when animals are faced with different intensities of environmental challenges. However, a relationship between telomere length and the environment has not yet been tested within a natural setting. Here, we report longitudinal telomere dynamics in free-living, blacktailed gulls (Larus crassirostris) through the recapture of birds of a known age over 2-5 consecutive years. The rate of change in telomere lengths differed with respect to year but not sex or age. The years when gulls showed stable telomere lengths or increases in telomere lengths (from 2009 to 2010) and decreases in telomere lengths (from 2010 to 2011) were characterized by El Nin o and the Great Japan Earthquake, respectively. Both events are suspected to have had long-lasting effects on food availability and/or weather conditions. Thus, our findings that telomere dynamics in long-lived birds are influenced by dramatic changes in environmental conditions highlight the importance of environmental fluctuations in affecting stress and lifespan. © 2013 The Author(s) Published by the Royal Society. All rights reserved.


Ozaki K.,Yamashina Institute for Ornithology | Yamamoto Y.,Hyogo College of Medicine | Yamagishi S.,Yamashina Institute for Ornithology
Genes and Genetic Systems | Year: 2010

Genetic diversity of the wild population of the endangered Okinawa Rail, Gallirallus okinawae, was revealed by analyzing haplotypes in the mitochondrial control region for 177 individuals. We found 6 haplotypes with nucleotide differences at 6 sites. The four major haplotypes, Type 1 to Type 4, were present in 121 (68.4%), 21 (11.9%), 8 (4.5%) and 25 individuals (14.1%), respectively. Type 5 and Type 6 were each found in one individual. The gene diversity (h) and nucleotide diversity (π) of Okinawa Rail were calculated to be 0.499 ± 0.040 and 0.00146 ± 0.00098, respectively. Gene diversity in Okinawa Rail is higher than that found in other endangered avian species, but the relative nucleotide diversity is lower due to few nucleotide differences among the haplotypes. Our sample of 177 individuals represents 20-25% of the total population, and thus allows a rigorous estimate of the population structure of Okinawa Rail, and makes it unlikely that more haplotypes would be found with additional sampling. The low nucleotide diversity in the control region may indicate that Okinawa Rail has gone through a recent bottleneck. The minimal span network of haplotypes, and the distribution pattern of sampled individuals, indicate that the number of birds with rare haplotypes, Type 5 and 6, decreased during the recent population decline caused by habitat loss and introduced predators. Our results are relevant to the current conservation program for the endangered Okinawa Rail, and perhaps for other species of flightless rails.


Oka N.,Yamashina Institute for Ornithology
Journal of the Yamashina Institute for Ornithology | Year: 2011

In June 2011, an unusually high mortality of the migratory Short-tailed Shearwater Pu$nus tenuirostris occurred in Mutsu Bay in northernmost Honshu, Japan. One hundred and fifty six carcasses were recorded along a 1 km stretch of beach. Prior to this stranding, 40 birds had been observed floating in the nearby area of the bay. All of them were presumably juveniles that had departed from their natal places in the austral autumn in late April or early May and mistakenly entered into the semi-enclosed bay through Tsugaru Strait en route to the northern summering waters of the cooler current. © Yamashina Institute for Ornithology.


Oka N.,Yamashina Institute for Ornithology
Ornithological Science | Year: 2011

Procellariiform seabirds accumulate large amounts of lipid during the nestling period. Chick obesity functions as a buffer against irregular attentiveness by parents delivering meals. Surprisingly the assimilation mechanism necessary to attain obesity remains unclear. This study presents the first measurements of assimilation efficiency in relation to age and diet throughout the long nestling period of a Procellariidae. To determine the assimilation efficiency and diet effects on growth, Shorttailed Shearwater Puffinus tenuirostris chicks were fed in captivity on different diets of marine organisms (krill Euphausia superba, squid Nototodarus sloani and fish Hyperlophus vittatus) from age 10 to 85 days. Assimilation efficiency was highest (mean 93.7%) among young chicks (10-29 days old) then declined, becoming stable (mean 80.9%) among older (70-85 days old) pre-fledging chicks. It was noted that the krill-fed chicks showed consistently higher assimilation efficiencies, not only when young (mean 95.4%) but also when older (mean 84.8%), than the squid-fed or fish-fed chicks (means 92.4-93.3% when young and 78.4-79.5% when older). The krill diet contributed to better growth in body mass (close to that of free-living chicks at the source colony), while the squid- and fish-fed chicks grew slowly. The dietary effects on feather growth and molting did not parallel those on body mass increments. Squid-fed chicks had similar feather growth rates and molt progress to those of krillfed chicks, whereas fish-fed chicks often vomited their food when given sizable quantities of fish and had slower feather development and molting. These findings suggest that chicks may need parental digestive fluids in order to facilitate their digestion of larger amounts of fish, whereas they were competent to digest krill and squid on their own. When the diet of older (over 85 days of age) fish-fed chicks was changed to krill they stopped regurgitating food, gained weight and began rapid molting. Likewise, squid-fed chicks gained mass at a faster rate when they were switched to a diet of krill. The experimental Short-tailed Shearwater chicks were found to have a high absorption capability during the early nestling stage allowing for considerable lipid accumulation and resulting in obesity. This obesity facilitates the fasting necessary while their parents commute to distant nutritive waters. The shearwaters have a highly adaptive potential to assimilate krill, which are abundant organisms with a large biomass in the higher latitudes that shearwaters prefer to inhabit for foraging throughout the year. Even the krill-fed chicks, the best among the three experimental dietary groups, only attained similar body masses to free-living chicks despite being given 1.9 times as heavy meals as shearwater parents provided to their free-living chicks. This evidence indicates that in order for free-living Short-tailed Shearwater chicks to grow to obesity, they depend on a far higher energy intake than that available in their diet alone. The specific oil, accumulated in the shearwater parents' proventriculus, and delivered to the chick, is an important contribution. In other words, digestible prey, such as krill, and parental stomach oil, are both essential to insure obesity for Short-tailed Shearwater chicks. © The Ornithological Society of Japan 2011.


Tomita N.,Yamashina Institute for Ornithology | Iwami Y.,Yamashina Institute for Ornithology
Ornithological Science | Year: 2016

We observed three Sand Martin Riparia riparia repeatedly attempting to copulate with a dead bird lying face down on the ground, with its wings spread and lowered. One of the three remained on the ground close to the dead bird and guarded it against copulation from the other two birds. Then, the guarding bird itself attempted to copulate with the dead bird. Based on subsequent dissection the dead Sand Martin was identified as an adult male. Based on our observations, we propose that the observed homosexual necrophilia may be partly explained by the absence of sexual dimorphism in this species and the posture of the dead martin. We suggest that posture is an important trigger arousing male sex drive in a sexually monomorphic species. © The Ornithological Society of Japan 2016.


Saitoh T.,Yamashina Institute for Ornithology | Sugita N.,National Museum of Nature and Science | Someya S.,National Museum of Nature and Science | Iwami Y.,Yamashina Institute for Ornithology | And 6 more authors.
Molecular Ecology Resources | Year: 2015

DNA barcoding using a partial region (648 bp) of the cytochrome c oxidase I (COI) gene is a powerful tool for species identification and has revealed many cryptic species in various animal taxa. In birds, cryptic species are likely to occur in insular regions like the Japanese Archipelago due to the prevention of gene flow by sea barriers. Using COI sequences of 234 of the 251 Japanese-breeding bird species, we established a DNA barcoding library for species identification and estimated the number of cryptic species candidates. A total of 226 species (96.6%) had unique COI sequences with large genetic divergence among the closest species based on neighbour-joining clusters, genetic distance criterion and diagnostic substitutions. Eleven cryptic species candidates were detected, with distinct intraspecific deep genetic divergences, nine lineages of which were geographically separated by islands and straits within the Japanese Archipelago. To identify Japan-specific cryptic species from trans-Paleartic birds, we investigated the genetic structure of 142 shared species over an extended region covering Japan and Eurasia; 19 of these species formed two or more clades with high bootstrap values. Excluding six duplicated species from the total of 11 species within the Japanese Archipelago and 19 trans-Paleartic species, we identified 24 species that were cryptic species candidates within and surrounding the Japanese Archipelago. Repeated sea level changes during the glacial and interglacial periods may be responsible for the deep genetic divergences of Japanese birds in this insular region, which has led to inconsistencies in traditional taxonomies based on morphology. © 2014 John Wiley & Sons Ltd.


Ochi D.,Hokkaido University | Oka N.,Yamashina Institute for Ornithology | Watanuki Y.,Hokkaido University
Journal of Ethology | Year: 2010

Parents of albatross and shearwater species employ a dual foraging strategy, feeding their chicks quickly in repeated short trips and then restoring their own fuel reserves during longer trips. A decline in parental body condition is believed to trigger longer trips, but chick body condition and age may also play a role. To investigate these factors in the little-studied streaked shearwater Calonectris leucomelas, we monitored the nest attendance of 17 pairs on Mikura Island in 2005 using an automated identification system. We also monitored body mass changes and meal masses of 5 of the 17 pairs using an automated weighing system. Although the birds did not show a clear dual foraging pattern, trip duration varied widely from 1 to 15 days. On average, the birds fed chicks 67.6 g during nighttime meals at 2.74-day intervals. Since meal mass did not depend on trip duration, feeding efficiency (meal mass delivered per unit trip duration) decreased as trip duration increased. Parents accumulated more energy reserves when they took longer trips. Parents appeared likely to initiate longer trips when their body condition declined or chick body condition recovered. © Japan Ethological Society and Springer 2009.


Dierickx E.G.,Harvard University | Dierickx E.G.,University of Cambridge | Shultz A.J.,Harvard University | Sato F.,Yamashina Institute for Ornithology | And 2 more authors.
Evolutionary Applications | Year: 2015

Evaluating the genetic and demographic independence of populations of threatened species is important for determining appropriate conservation measures, but different technologies can yield different conclusions. Despite multiple studies, the taxonomic status and extent of gene flow between the main breeding populations of Black-footed Albatross (Phoebastria nigripes), a Near-Threatened philopatric seabird, are still controversial. Here, we employ double digest RADseq to quantify the extent of genomewide divergence and gene flow in this species. Our genomewide data set of 9760 loci containing 3455 single nucleotide polymorphisms yielded estimates of genetic diversity and gene flow that were generally robust across seven different filtering and sampling protocols and suggest a low level of genomic variation (θ per site = ~0.00002-0.00028), with estimates of effective population size (Ne = ~500-15 881) falling far below current census size. Genetic differentiation was small but detectable between Japan and Hawaii (FST ≈ 0.038-0.049), with no FST outliers. Additionally, using museum specimens, we found that effect sizes of morphological differences by sex or population rarely exceeded 4%. These patterns suggest that the Hawaiian and Japanese populations exhibit small but significant differences and should be considered separate management units, although the evolutionary and adaptive consequences of this differentiation remain to be identified. © 2015 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.

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