Mostrando recursos 1 - 20 de 23

  1. Genetic analyses favour an ancient and natural origin of elephants on Borneo

    Sharma, Reeta; Goossens, Benoit; Heller, Rasmus; Rasteiro, Rita; Othman, Nurzhafarina; Bruford, Michael W.; Chikhi, Lounès
    This deposit is composed by the main article plus the supplementary materials of the publication.

  2. The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection.

    Lopez, Saioa; Thomas, Mark G; van Dorp, Lucy; Ansari-Pour, Naser; Stewart, Sarah; Jones, Abigail L; Jelinek, Erik; Chikhi, Lounes; Parfitt, Tudor; Bradman, Neil; Weale, Michael E; Hellenthal, Garrett
    The deposited article version is a "Pre-print version" provided by Biorxiv posted online on April 18, 2017 - 12:26, and it contains attached the supplementary materials within the pdf.

  3. Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant

    Sharma, Reeta; Goossens, Benoit; Kun-Rodrigues, Célia; Teixeira, Tatiana; Othman, Nurzhafarina; Boone, Jason Q.; Jue, Nathaniel K.; Obergfell, Craig; O'Neill, Rachel J.; Chikhi, Lounès
    High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic information are currently under way. Recent sequencing technologies provide new opportunities for gathering genomic data in natural populations, laying the empirical foundation for future research in the field of conservation and population genomics. Here we present the case study of the Bornean elephant, which is the most endangered subspecies of Asian elephant and exhibits very low genetic diversity. We used two different sequencing platforms, the Roche...

  4. Signature of a Pre-Human Population Decline in the Critically Endangered Reunion Island Endemic Forest Bird Coracina newtoni

    Salmona, Jordi; Salamolard, Marc; Fouillot, Damien; Ghestemme, Thomas; Larose, Jerry; Centon, Jean-François; Sousa, Vitor; Dawson, Deborah A.; Thebaud, Christophe; Chikhi, Lounès
    The exceptional biodiversity of Reunion Island is threatened by anthropogenic landscape changes that took place during the 350 years of human colonization. During this period the human population size increased dramatically from 250 to 800,000. The arrival of humans together with the development of agriculture, invasive species such as rats and cats, and deforestation has lead to the extinction of more than half of the original vertebrate species of the island. For the remaining species, significant work is being carried out to identify threats and conservation status, but little genetic work has been carried on some of the most endangered...

  5. Effective Population Size Dynamics and the Demographic Collapse of Bornean Orang-Utans

    Sharma, Reeta; Arora, Natasha; Goossens, Benoit; Nater, Alexander; Morf, Nadja; Salmona, Jordi; Bruford, Michael W.; Van Schaik, Carel P.; Krützen, Michael; Chikhi, Lounès
    Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric...

  6. Reassessing the Evolutionary History of the 17q21 Inversion Polymorphism

    Alves, Joao M.; Lima, Ana C.; Pais, Isa A.; Amir, Nadir; Celestino, Ricardo; Piras, Giovanna; Monne, Maria; Comas, David; Heutink, Peter; Chikhi, Lounès; Amorim, António; Lopes, Alexandra M.
    A polymorphic inversion that lies on chromosome 17q21 comprises two major haplotype families (H1 and H2) that not only differ in orientation but also in copy-number. Although the processes driving the spread of the inversion-associated lineage (H2) in humans remain unclear, a selective advantage has been proposed for one of its subtypes. Here, we genotyped a large panel of individuals from previously overlooked populations using a custom array with a unique panel of H2-specific single nucleotide polymorphisms and found a patchy distribution of H2 haplotypes in Africa, with North Africans displaying a higher frequency of inverted subtypes, when compared with...

  7. STR-based genetic structure of the Berber population of Bejaia (Northern Algeria) and its relationships to various ethnic groups

    Amir, Nadir; Sahnoune, Mohamed; Chikhi, Lounes; Atmani, Djebbar
    Patterns of genetic variation in human populations have been described for decades. However, North Africa has received little attention and Algeria, in particular, is poorly studied, Here we genotyped a Berber-speaking population from Algeria using 15 short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA from the commercially available AmpF/STR Identifiler kit. Altogether 150 unrelated North Algerian individuals were sampled across 10 administrative regions or towns from the Bejaia Wilaya (administrative district). We found that all of the STR loci met Hardy-Weinberg equilibrium expectations, after Bonferroni correction and...

  8. Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey

    Ottoni, Claudio; Rasteiro, Rita; Willet, Rinse; Claeys, Johan; Talloen, Peter; Van de Vijver, Katrien; Chikhi, Lounès; Poblome, Jeroen; Decorte, Ronny
    More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in...

  9. Genomics and the challenging translation into conservation practice

    Shafer, Aaron B.A.; Wolf, Jochen B.W.; Alves, Paulo C.; Bergström, Linnea; Bruford, Michael W.; Brännström, Ioana; Colling, Guy; Dalén, Love; De Meester, Luc; Ekblom, Robert; Fawcett, Katie D.; Fior, Simone; Hajibabaei, Mehrdad; Hill, Jason A.; Hoezel, A. Rus; Höglund, Jacob; Jensen, Evelyn L.; Krause, Johannes; Kristensen, Torsten N.; Krützen, Michael; McKay, John K.; Norman, Anita J.; Ogden, Rob; Österling, E. Martin; Ouborg, N. Joop; Piccolo, John; Popović, Danijela; Primmer, Craig R.; Reed, Floyd A.; Roumet, Marie; Salmona, Jordi; Schenekar, Tamara; Schwartz, Michael K.; Segelbacher, Gernot; Senn, Helen; Thaulow, Jens; Valtonen, Mia; Veale, Andrew; Vergeer, Philippine; Vijay, Nagarjun; Vilà, Carles; Weissensteiner, Matthias; Wennerström, Lovisa; Wheat, Christopher W.; Zieliński, Piotr
    The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods...

  10. The Araguaia River as an Important Biogeographical Divide for Didelphid Marsupials in Central Brazil

    Rocha, Rita Gomes; Ferreira, Eduardo; Loss, Ana Carolina; Heller, Rasmus; Fonseca, Carlos; Costa, Leonora Pires
    The riverine barrier model suggests that rivers play a significant role in separating widespread organisms into isolated populations. In this study, we used a comparative approach to investigate the phylogeography of 6 didelphid marsupial species in central Brazil. Specifically, we evaluate the role of the mid-Araguaia River in differentiating populations and estimate divergence time among lineages to assess the timing of differentiation of these species, using mitochondrial DNA sequence data. The 6 didelphid marsupials revealed different intraspecific genetic patterns and structure. The 3 larger and more generalist species, Didelphis albiventris, Didelphis marsupialis, and Philander opossum, showed connectivity across the Araguaia...

  11. Genetic diversity of serotype A foot-and-mouth disease viruses in Kenya from 1964 to 2013; implications for control strategies in eastern Africa

    Wekesa, Sabenzia N.; Sangula, Abraham K.; Belsham, Graham J.; Muwanika, Vincent B.; Heller, Rasmus; Balinda, Sheila N.; Masembe, Charles; Siegismund, Hans R.
    Serotype A is the most genetically and antigenically diverse of the foot-and-mouth disease virus (FMDV) serotypes. Records of its occurrence in Kenya date back to 1952 and the antigenic diversity of the outbreak viruses in this region is reflected by the current use of two different vaccine strains (K5/1980 and K35/1980) and previous use of two other strains (K18/66 and K179/71). This study aimed at enhancing the understanding of the patterns of genetic variation of serotype A FMDV in Kenya. The complete VP1 coding region sequences of 38 field isolates, identified as serotype A FMDV, collected between 1964 and 2013...

  12. The scaling of genetic diversity in a changing and fragmented world

    Arenas, M.; Mona, S.; Trochet, A.; Sramkova Hanulova, A.; Currat, M.; Ray, N.; Chikhi, L.; Rasteiro, R.; Schmeller, D.S.; Excoffier, L.
    Most species do not live in a constant environment over space or time. Their environment is often heterogeneous with a huge variability in resource availability and exposure to pathogens or predators, which may affect the local densities of the species. Moreover, the habitat might be fragmented, preventing free and isotropic migrations between local sub-populations (demes) of a species, making some demes more isolated than others. For example, during the last ice age populations of many species migrated towards refuge areas from which re-colonization originated when conditions improved. However, populations that could not move fast enough or could not adapt to...

  13. The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data

    Paz-Vinas, I.; Quéméré, E.; Chikhi, L.; Loot, G.; Blanchet, S.
    Population structure can significantly affect genetic-based demographic inferences, generating spurious bottleneck-like signals. Previous studies have typically assumed island or stepping-stone models, which are characterized by symmetric gene flow. However, many organisms are characterized by asymmetric gene flow. Here, we combined simulated and empirical data to test whether asymmetric gene flow affects the inference of past demographic changes. Through the analysis of simulated genetic data with three methods (i.e. bottleneck, M-ratio and msvar), we demonstrated that asymmetric gene flow biases past demographic changes. Most biases were towards spurious signals of expansion, albeit their strength depended on values of effective population size...

  14. Noninvasive molecular sexing: An evaluation and validation of the SRY- and amelogenin-based method in three new lemur species

    Vanpé, Cécile; Salmona, Jordi; Pais, Isa; Kun-Rodrigues, Célia; Pichon, Claire; Meyler, Samuel Viana; Rabarivola, Clément; Lewis, Rebecca J.; Ibouroi, Mohamed Thani; Chikhi, Lounès
    Many lemur species are arboreal, elusive, and/or nocturnal and are consequently difficult to approach, observe and catch. In addition, most of them are endangered. For these reasons, non-invasive sampling is especially useful in primates including lemurs. A key issue in conservation and ecological studies is to identify the sex of the sampled individuals to investigate sex-biased dispersal, parentage, social organization and population sex ratio. Several molecular tests of sex are available in apes and monkeys, but only a handful of them work in the lemuriform clade. Among these tests, the coamplification of the SRY gene with the amelogenin X gene...

  15. Is Diagnosability an Indicator of Speciation? Response to "Why One Century of Phenetics Is Enough"

    Heller, R.; Frandsen, P.; Lorenzen, E. D.; Siegismund, H. R.
    Recently (Heller et al. 2013; H&A), we commented on a revision of the bovid taxonomy, which proposes a doubling in the number of recognized species (Groves and Grubb 2011; G&G). The subsequent response by Cotterill et al. (2014; C&A) contains a number of misunderstandings and leaves much of the critique voiced in our paper unanswered, focusing instead on species ontologies and taxonomic history. C&A argue strongly against phenetics, morphospecies, and taxonomic conservatism, ascribing us views that we do not hold and hence confusing the substance of our disagreement. These misconceptions oblige us to clarify our views on certain key issues...

  16. Are There Really Twice as Many Bovid Species as We Thought?

    Heller, R.; Frandsen, P.; Lorenzen, E. D.; Siegismund, H. R.
    A major reappraisal of the taxonomy of ungulates (hoofed mammals) was presented in 2011 (Groves and Grubb 2011; G&G henceforth). The reappraisal presents a drastic revision of the taxonomic diversity of the group. It nearly doubles the number of bovid species—a group comprising cattle, bison, buffalo, goats, sheep, and antelopes—currently recognized (IUCN 2012), raising the number of species from 143 to 279. In our opinion, this represents taxonomic inflation; ecotypes or subspecies have been raised to the level of full species based not on new data, but solely on a change in the species concept used (Isaac et al. 2004)....

  17. The value of the spineless monkey orange tree (Strychnos madagascariensis) for conservation of northern sportive lemurs (Lepilemur milanoii and L. ankaranensis)

    Salmona, J; Banks, M; Ralantoharijaona, TN; Rasolondraibe, E; Zaranaina, R; Rakotonanahary, A; Wohlhauser, S; Sewall, BJ; Chikhi, L
    Tree hollows provide shelters for a large number of forest-dependent vertebrate species worldwide. In Madagascar, where high historical and ongoing rates of deforestation and forest degradation are responsible for a major environmental crisis, reduced availability of tree hollows may lead to declines in hollow-dwelling species such as sportive lemurs, one of the most species-rich groups of lemurs. The identification of native tree species used by hollow-dwelling lemurs may facilitate targeted management interventions to maintain or improve habitat quality for these lemurs. During an extensive survey of sportive lemurs in northern Madagascar, we identified one tree species, Strychnos madagascariensis (Loganiaceae), the spineless...

  18. Conservation Status and Abundance of the Crowned Sifaka (Propithecus coronatus)

    Salmona, Jordi; Rasolondraibe, Emmanuel; Jan, Fabien; Besolo, Aubin; Rakotoarisoa, Heriniaina; Meyler, Sam Viana; Wohlhauser, Sébastien; Rabarivola, Clément; Chikhi, Lounès
    The crowned sifaka (Propithecus coronatus) is Endangered. It has a large but highly fragmented distribution; its known range extends from the Betsiboka River in the north of Madagascar, to the Mahavavy River in the north-west, and down to the Tsiribihina River in the south-west. The species lives in forest habitats that are highly and increasingly fragmented and are continuously suffering perturbations and destruction. In order to carry out effective conservation measures targeting P. coronatus, its conservation status needs to be updated so that measures can be taken before anthropogenic or natural environmental changes lead to the extirpation of the species...

  19. Estimation des densités et tailles de population du Microcèbe Roux du Nord de (Microcebus tavaratra) dans la région Loky-Manambato (Daraina)

    Salmona, J.; Rakotonanahary, A.; Thani, I.M.; Zaranaina, R.; Ralantoharijaona, T.; Jan, F.; Rasolondraibe, E.; Barnavon, M.; Beck, A.; Wholhauser, S.; Ranirison, P.; Zaonarivelo, J.R.; Rabarivola, C.; Chikhi, L.
    La région Loky-Manambato dans le Nord de Madagascar, est connue pour abriter le propithèque à couronne dorée (Propithecus tattersalli), un lémurien emblématique et endémique de la région. Néanmoins cette région composée d’une dizaine de fragments forestiers de taille moyenne et encore relativement peu étudiés, abrite aussi le microcèbe roux du nord (Microcebus tavaratra). Malgré la gestion des forêts de cette région par l’ONG Fanamby depuis 2005, aucune étude n’avait encore été menée dans chacun des fragments forestiers de la région pour déterminer la présence et quantifier la taille des populations de microcèbes de chacun d’entre eux. Lors de notre étude...

  20. Daraina sportive lemur (Lepilemur milanoii) density and population size estimates in most of its distribution range: the Loky-Manambato region.

    Salmona, J.; Ralantoharijaona, T.; Thani, I.M.; Rakotonanahary, A.; Zaranaina, R.; Jan, F.; Rasolondraibe, E.; Barnavon, M.; Beck, A.; Wholhauser, S.; Ranirison, P.; Zaonarivelo, J.R.; Rabarivola, C.; Chikhi, L.
    The population of the Daraina sportive lemur (Lepilemur milanoii) is believed to be mostly confined to the Loky-Manambato region (Louis et al., 2006). Very little is known about L. milanoii and it is classified as “Data Deficient” by the IUCN (IUCN, 2013; Schwitzer et al., 2013). Despite the management of the area by the NGO Fanamby since 2005, no study had been conducted to determine the presence and the abundance of L. milanoii in the main forest fragments of the region. During the 2011 dry season we surveyed the ten main forest fragments of the Loky-Manambato region and estimated L....

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