Nobuyuki Yamaguchi

Zoology

BSc, MSc, DPhil
30.06

Publications

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    ABSTRACT: Biologists focus on thermoregulation of desert mammals in terms of how they minimize heat gain, and put less effort on how they maximize heat gain during the cooler months. Heat gain may contribute to significant energy savings in desert mammals when the ambient temperature is substantially lower than body temperature. We investigated winter thermoregulation in free-ranging Ethiopian hedgehogs, Paraechinus aethiopicus, during winter using radio-telemetry in Qatar. Hedgehog temperatures (Animal Ta) were significantly higher than ambient temperatures (Ta) throughout the day, the difference was more extreme during the mid-day. We observed several hedgehogs basking with their radio-tags exposed to direct sunlight. We suggest that basking is beneficial for the hedgehog's thermoregulation in the desert where plenty of solar radiation is available with few predators. This is the first report of basking in the subfamily Erinaceinae.
    No preview · Article · Feb 2016 · Journal of Arid Environments
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    ABSTRACT: As species become rare and approach extinction, purported sightings can be controversial, especially when scarce management resources are at stake. We consider the probability that each individual sighting of a series is valid. Obtaining these probabilities requires a strict framework to ensure that they are as accurately representative as possible. We used a process, which has proven to provide accurate estimates from a group of experts, to obtain probabilities for the validation of 32 sightings of the Barbary lion. We consider the scenario where experts are simply asked whether a sighting was valid, as well as asking them to score the sighting based on distinguishablity, observer competence, and verifiability. We find that asking experts to provide scores for these three aspects resulted in each sighting being considered more individually, meaning that this new questioning method provides very different estimated probabilities that a sighting is valid, which greatly affects the outcome from an extinction model. We consider linear opinion pooling and logarithm opinion pooling to combine the three scores, and also to combine opinions on each sighting. We find the two methods produce similar outcomes, allowing the user to focus on chosen features of each method, such as satisfying the marginalisation property or being externally Bayesian.
    Full-text · Article · Sep 2015 · PeerJ
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    Full-text · Dataset · Mar 2015
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    ABSTRACT: The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1-2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating litter or no matrilineal gene flow among the islands after they were colonized. The close phylogenetic relationship among Sunda tiger subspecies suggests either recent colonization across the islands, or else a once continuous tiger population that had subsequently isolated into different island subspecies. This supports the hypothesis that the Sumatran tiger is the closest living relative to the extinct Javan and Bali tigers. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
    Full-text · Article · Mar 2015 · Journal of Heredity
  • Mohammad A. Abu Baker · Ivan Mohedano · Nigel Reeve · Nobuyuki Yamaguchi
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    ABSTRACT: The postnatal growth and development of the Ethiopian hedgehog (Paraechinus aethiopicus) were studied in captivity. Seven females produced seven litters that ranged between two and five young (average 3.3, SE±0.42) with an estimated gestation period of 34–46 days. Offspring sex ratio was heavily skewed toward females by 1:6.5. Newborns were altricial and weighed an average of 8.8±1.25 g (n=6) at 2–5 days old. Young were observed rolling-up for the first time at 7–22 days old, and their eyes opened at 22–30 days. They sampled solid food for the first time at 16–27 days, weaned at 30–38 days, and were feeding solely on solid food at 38–40 days old. Body weight increased on average by 3.6±0.28 g/day before weaning, 1.4±0.38 g/day during the weaning period, and 4.7±0.82 g/day after weaning. The slow growth during the weaning period marks the shift to solid food and independence from the mother. Development was generally faster in litters born later in the season. Despite the variation between litters, key postnatal developmental milestones and body length provided better estimates of growth and development than body weight.
    No preview · Article · Jan 2015 · Mammalia
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    ABSTRACT: The diet of Bubo ascalaphus in Qatar was assessed based on pellets collected from the first known nesting site of the species in the country. The pellets contained a total of 68 prey items, representing 9 different species: 4 mammals, 1 bird, 1 reptile, and at least 3 scorpions. Mammals clearly comprised the major food source (89.7% and 97.7% in frequency and biomass respectively). Our data suggest that Pharaoh Eagle Owls are opportunistic predators that feed on a variety of prey depending on their temporal/spatial availability, which is consistent with previous studies. A literature review clearly suggests that Eagle Owls in arid to semi-arid environments are opportunistic predators with small mammals being their main prey. Predation on migrating Blue-cheeked Bee-eaters Merops persicus supports this hypothesis.
    Full-text · Article · May 2014 · Zoology in the Middle East
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    ABSTRACT: Lion (Panthera leo) populations have dramatically decreased worldwide with a surviving population estimated at 32,000 across the African savannah. Lions have been kept in captivity for centuries and, although they reproduce well, high rates of stillbirths as well as morbidity and mortality of neonate and young lions are reported. Many of these cases are associated with bone malformations, including foramen magnum (FM) stenosis and thickened tentorium cerebelli. The precise causes of these malformations and whether they are unique to captive lions remain unclear. To test whether captivity is associated with FM stenosis, we evaluated 575 lion skulls of wild (N = 512) and captive (N = 63) origin. Tiger skulls (N = 276; 56 captive, 220 wild) were measured for comparison. While no differences were found between males and females or between subadults and adults in FM height (FMH), FMH of captive lions (17.36±3.20 mm) was significantly smaller and with greater variability when compared to that in wild lions (19.77±2.11 mm). There was no difference between wild (18.47±1.26 mm) and captive (18.56±1.64 mm) tigers in FMH. Birth origin (wild vs. captive) as a factor for FMH remained significant in lions even after controlling for age and sex. Whereas only 20/473 wild lions (4.2%) had FMH equal to or smaller than the 5th percentile of the wild population (16.60 mm), this was evident in 40.4% (23/57) of captive lion skulls. Similar comparison for tigers found no differences between the captive and wild populations. Lions with FMH equal to or smaller than the 5th percentile had wider skulls with smaller cranial volume. Cranial volume remained smaller in both male and female captive lions when controlled for skull size. These findings suggest species- and captivity-related predisposition for the pathology in lions.
    Full-text · Article · Apr 2014 · PLoS ONE
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    ABSTRACT: Understanding the demographic history of a population is critical to conservation and to our broader understanding of evolutionary processes. For many tropical large mammals, however, this aim is confounded by the absence of fossil material and by the misleading signal obtained from genetic data of recently fragmented and isolated populations. This is particularly true for the lion which as a consequence of millennia of human persecution, has large gaps in its natural distribution and several recently extinct populations. We sequenced mitochondrial DNA from museum-preserved individuals, including the extinct Barbary lion (Panthera leo leo) and Iranian lion (P. l. persica), as well as lions from West and Central Africa. We added these to a broader sample of lion sequences, resulting in a data set spanning the historical range of lions. Our Bayesian phylogeographical analyses provide evidence for highly supported, reciprocally monophyletic lion clades. Using a molecular clock, we estimated that recent lion lineages began to diverge in the Late Pleistocene. Expanding equatorial rainforest probably separated lions in South and East Africa from other populations. West African lions then expanded into Central Africa during periods of rainforest contraction. Lastly, we found evidence of two separate incursions into Asia from North Africa, first into India and later into the Middle East. We have identified deep, well-supported splits within the mitochondrial phylogeny of African lions, arguing for recognition of some regional populations as worthy of independent conservation. More morphological and nuclear DNA data are now needed to test these subdivisions.
    Full-text · Article · Apr 2014 · BMC Evolutionary Biology
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    Nobuyuki Yamaguchi

    Full-text · Chapter · Jan 2014
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    Nobuyuki Yamaguchi · Afra Al-Hajri · Hayat Al-Jabiri
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    ABSTRACT: There is little information pertaining to the breeding behaviour and reproductive biology of free-ranging hedgehog populations outside of Europe. We monitored the seasonal changes in courtship behaviour and the presence of new young animals from a free-ranging Ethiopian hedgehog population in Qatar between 2010 and 2012. Based on frequencies of courtship behaviour and deduced frequencies of successful mating, the mating season of the Ethiopian hedgehog is believed to start in January and continue through until July with a clear peak during the February/March period. We propose the existence of two mating peaks, one in February/March and the second in June, suggesting that free-ranging Ethiopian hedgehogs breed more than twice a year in Qatar. Successful mating in late winter/early spring may be more important for the increasing the inclusive fitness of the parents based on the number of young individuals that survive beyond one month of age.
    Full-text · Article · Dec 2013 · Journal of Arid Environments
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    ABSTRACT: Recent advances in multivariate statistics, and in ancient DNA techniques, have greatly increased understanding of tiger phylogeography. However, regardless of advances in analytical methodology, researchers will continue to need access to specimens for morphological measurements and sampling for genetic analysis. The tiger has become increasingly endangered, and out of the nine putative tiger subspecies, three (Javan, Balinese, and Caspian) have become extinct in the last 100 years, leaving the specimens kept in natural history collections as the only materials available for research. Frustratingly little information is widely available concerning the specimens of these extinct tiger subspecies. We conducted an extensive search for specimens of extinct tiger subspecies, and also developed a simple on-site method to assign unprovenanced and probable Indonesian specimens to either Javan/Balinese or Sumatran subspecies. We located a total of 88 Javan, 11 Balinese, and 46 Caspian tigers, including seven new Javan tigers, and three Balinese tigers that were not widely known previously. These specimens are critical for research in order to understand the intraspecific phylogeny and evolutionary history of the tiger.
    Full-text · Article · Sep 2013 · Mammal Study
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    Simon A. Black · Amina Fellous · Nobuyuki Yamaguchi · David L. Roberts
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    ABSTRACT: Estimations of species extinction dates are rarely definitive, yet declarations of extinction or extirpation are important as they define when conservation efforts may cease. Erroneous declarations of extinctions not only destabilize conservation efforts but also corrode local community support. Mismatches in perceptions by the scientific and local communities risk undermining sensitive, but important partnerships. We examine observations relating to the decline and extinction of Barbary lions in North Africa. Whilst the extinction predates the era of the scientific conservation movement, the decline is relatively well documented in historical records. Recently unearthed accounts suggest Barbary lions survived later than previously assumed. We use probabilistic methods to estimate a more recent extinction date for the subspecies. The evidence presented for a much later persistence of lions in North Africa, including generations when sightings were nil, suggests caution when considering felid populations as extinct in the wild. The case raises the possibility that captive animals descended from the Moroccan royal collection are closer contemporaries to wild Barbary lions. Furthermore, our results highlight the vulnerability of very small lion populations and the significance of continued conservation of remnant lion populations in Central and West Africa.
    Full-text · Article · Apr 2013 · PLoS ONE
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    Full-text · Dataset · Oct 2012
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    Full-text · Dataset · Oct 2012
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    Full-text · Article · Jun 2012
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    ABSTRACT: Erinaceidae is a family of small mammals that include the spiny hedgehogs (Erinaceinae) and the silky-furred moonrats and gymnures (Galericinae). These animals are widely distributed across Eurasia and Africa, from the tundra to the tropics and the deserts to damp forests. The importance of these animals lies in the fact that they are the oldest known living placental mammals, which are well represented in the fossil record, a rarity fact given their size and vulnerability to destruction during fossilization. Although the Family has been well studied, their phylogenetic relationships remain controversial. To test previous phylogenetic hypotheses, we combined molecular and morphological data sets, including representatives of all the genera. We included in the analyses 3,218 bp mitochondrial genes, one hundred and thirty-five morphological characters, twenty-two extant erinaceid taxa, and five outgroup taxa. Phylogenetic relationships were reconstructed using both partitioned and combined data sets. As in previous analyses, our results strongly support the monophyly of both subfamilies (Galericinae and Erinaceinae), the Hylomys group (to include Neotetracus and Neohylomys), and a sister-relationship of Atelerix and Erinaceus. As well, we verified that the extremely long branch lengths within the Galericinae are consistent with their fossil records. Not surprisingly, we found significant incongruence between the phylogenetic signals of the genes and the morphological characters, specifically in the case of Hylomys parvus, Mesechinus, and relationships between Hemiechinus and Paraechinus. Although we discovered new clues to understanding the evolutionary relationships within the Erinaceidae, our results nonetheless, strongly suggest that more robust analyses employing more complete taxon sampling (to include fossils) and multiple unlinked genes would greatly enhance our understanding of the Erinaceidae. Until then, we have left the nomenclature of the taxa unchanged; hence it does not yet precisely reflect their phylogenetic relationships or the depth of their genetic diversity.
    Full-text · Article · Jun 2012 · PLoS ONE
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    ABSTRACT: The wildcat (Felis silvestris ssp.) is a conservation concern largely due to introgressive hybridization with its congener F. s. catus, the common domestic cat. Because of a recent divergence and entirely overlapping ranges, hybridization is common and pervasive between these taxa threatening the genetic integrity of remaining wildcat populations. Identifying pure wildcats for inclusion in conservation programs using current morphological discriminants is difficult because of gross similarity between them and the domestic, critically hampering conservation efforts. Here, we present a vetted panel of microsatellite loci and mitochondrial polymorphisms informative for each of the 5 naturally evolved wildcat subspecies and the derived domestic cat. We also present reference genotypes for each assignment class. Together, these marker sets and corresponding reference genotypes allow for the development of a genetic rational for defining “units of conservation” within a phylogenetically based taxonomy of the entire F. silvestris species complex. We anticipate this marker panel will allow conservators to assess genetic integrity and quantify admixture in managed wildcat populations and to be a starting point for more in-depth analysis of hybridization.
    Full-text · Article · Aug 2011 · The Journal of heredity
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    Andrew C. Kitchener · Nobuyuki Yamaguchi
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    ABSTRACT: The tiger has always had a considerable impact on human cultures, especially where people and tigers have lived together and still do co-exist. It is certainly one of the most easily recognizable cats, with its distinctive and unique striped coat and is also commonly believed to be the biggest cat species alive today, although this claim is questionable. The tiger shows considerable variation in its size, coloration and markings, reflecting the variety of habitats it occupies throughout its wide geographical distribution from the temperate oak forests of the north to the humid tropical forests on the Equator. Understanding this variation is a key to its successful current and future conservation, but people are still uncertain of its significance. Its large size and consequent need for large prey have brought it into conflict with people by preying on them and their livestock, but it has also earned our respect and admiration for its power and prowess as a killer. Research on geographical variation in tigers is suggesting two possible models, which have enormous significance for future tiger conservation. The more conservative model, based both on molecular and morphological research, suggests that eight or more subspecies, some of which may even be distinct phylogenetic species, should be recognized.
    Full-text · Chapter · Dec 2010
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    Simon Black · Nobuyuki Yamaguchi · Adrian Harland · Jim Groombridge
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    ABSTRACT: The last representatives of the Barbary lion (Panthera leo leo), once numerous in North Africa but exterminated from the wild by the 1940s, are believed to be the captive lions descended from the Moroccan Royal Collection, numbering less than 90 animals in zoos worldwide. The genetic fitness of these captive “Royal Lions” may now be under threat since, although most zoos have avoided hybridisation with animals of other origin, no formal breeding programme currently exists and several institutions have halted breeding activities. This situation has arisen since the distinctiveness of Barbary lions and the representative status of Royal Lions remain inconclusive and definitive molecular studies have yet to be completed. Previously, in the 1970s, morphological and phenotypic traits were used to match Royal Lions and the historic Barbary lion and an ex situ breeding programme was initiated involving a number of selected “founder” animals. This paper outlines the status of the descendent population within zoos in Morocco and Europe, including all known pure-bred descendents from the Royal Palace collection. Founder representation is shown to be greater across European collections than the Moroccan collection. Breeding exchanges are recommended between institutions in order to improve genetic diversity and maintain the genetic health of the population and a studbook for European zoo animals has been developed to support this action. This analysis serves as a benchmark for guiding effective maintenance of the captive population, thereby allowing time to clarify the conservation value of Royal Lions and their relevance to North African ecology.
    Full-text · Article · Feb 2010 · European Journal of Wildlife Research
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    A. Kitchener · N. Yamaguchi

    Full-text · Chapter · Jan 2010

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