Nobuyuki Yamaguchi

Zoology
BSc, MSc, DPhil
29.22

Publications

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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.
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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.
    Zoology in the Middle East 05/2014; 60(2). DOI:10.1080/09397140.2014.914713 · 0.52 Impact Factor
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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.
    PLoS ONE 04/2014; 9(4):e94527. DOI:10.1371/journal.pone.0094527 · 3.53 Impact Factor
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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.
    BMC Evolutionary Biology 04/2014; 14(1):70. DOI:10.1186/1471-2148-14-70 · 3.41 Impact Factor
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    Nobuyuki Yamaguchi
    Sustainable Development: an introduction focusing on the Gulf region, Edited by P. Sillitoe, 01/2014: pages 291-309; Berghahn Books., ISBN: 9781782383710
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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.
    Journal of Arid Environments 12/2013; 99:1–4. DOI:10.1016/j.jaridenv.2013.09.001 · 1.82 Impact Factor
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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.
    Mammal Study 09/2013; 38:187-198. DOI:10.3106/041.038.0307 · 0.43 Impact Factor
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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.
    PLoS ONE 04/2013; 8(4). DOI:10.1371/journal.pone.0060174 · 3.53 Impact Factor
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    06/2012; 4(6):2637-2643. DOI:10.11609/JoTT.o2993.2637-43
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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.
    The Journal of heredity 08/2011; 102 Suppl 1:S87-90. DOI:10.1093/jhered/esr047 · 1.97 Impact Factor
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    Biology and Conservation of Wild Felids, Edited by D.W. Macdonald, A.J. Loveridge, 01/2010: pages 83-106; Oxford University Press., ISBN: 9780199234448
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    A. Kitchener, N. Yamaguchi
    Tigers of the World 2nd Edition, Edited by R. Tilson, P.J. Nyhus, 01/2010: pages 53-84; Elsevier., ISBN: 9780815515708
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    Biology and Conservation of Wild Felids, Edited by D.W. Macdonald, A.J. Loveridge, 01/2010: pages 471-491; Oxford University Press., ISBN: 9780199234448
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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.
    European Journal of Wildlife Research 01/2010; 56(1):21-31. DOI:10.1007/s10344-009-0280-5 · 1.21 Impact Factor
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    Biology and Conservation of Wild Felids, Edited by D.W. Macdonald, A.J. Loveridge, 01/2010: pages 59-82; Oxford University Press., ISBN: 9780199234448
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    ABSTRACT: Intraspecific encephalization of the lion and the tiger is investigated for the first time using a very large sample. Using cranial volume as a measure of brain size, the tiger has a larger brain relative to greatest length of skull than the lion, the leopard and the jaguar. The Asian lion has a relatively much smaller brain compared with those of sub-Saharan lions, between which there are few differences. The Balinese and Javan tigers had relatively larger brains compared with those of Malayan and Sumatran tigers, even although these four putative subspecies occupy adjacent ranges in south-eastern Asia. Differences in brain size do not appear to correlate with any known differences in behaviour and ecology and, therefore, may reflect only chance differences in intrageneric and intraspecific phylogeny. However, captive-bred big cats generally have a reduced brain size compared with that of wild animals, so that an animal's life history and living conditions may affect brain size and, hence, functional or environmental explanations should be considered when linking brain size differences to intraspecific phylogenies. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 85–93.
    Biological Journal of the Linnean Society 08/2009; 98(1):85 - 93. DOI:10.1111/j.1095-8312.2009.01249.x · 2.54 Impact Factor
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    ABSTRACT: In order to conserve mammalian top predators in human-dominated landscapes, large scale habitat requirements and food habits of the Japanese weasel (Mustela itatsi) were studied using 237 faecal samples, from a 901 km2 area in the vicinity of Mito City, Ibaraki Prefecture, Japan between 1999 and 2001. Findings show a significant difference in the faeces distribution among the nine biotope types surveyed, with a marked preference for rice fields and conifer plantations, coupled with an avoidance of farming and urban areas. In terms of weasel diet, mammals occured most frequently in relative volume and single occupancy in faeces and most often observed in conifer plantations along river banks. Second, Orthoptera insects, crustaceans, fruits, Coleoptera insects and fish were also found both in high frequency and relative volume, most often in rice fields and riparian habitats along river banks. Third, a high frequency of occurrence among combinations of (1) mammals with Coleoptera insects and (2) crustaceans with Orthoptera insects suggests the necessity of interaction among habitats. Artificial items were rare. These patterns provide evidence that weasels require diverse landscapes and further suggest weasels do not use urban areas because of their predatory preference for fresh animal food. This has implications for weasel conservation strategies.
    Mammal Study 07/2009; DOI:10.3106/041.034.0205 · 0.43 Impact Factor

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