Noninvasive population genetics: a review of sample source, diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates

Noninvasive population genetics has found many applications in ecology and conservation biology. However, the technical difficulties inherent to the analysis of low quantities of DNA generally tend to limit the efficiency of this approach. The nature of samples and loci used in noninvasive population genetics are important factors that may help increasing the potential success of case studies. Here we reviewed the effects of the source of DNA (hair vs. faeces), the diet of focal species, the length of mitochondrial DNA fragments, and the length and repeat motif of nuclear microsatellite loci on genotyping success (amplification success and rate of allelic dropout). Locus-specific effects appeared to have the greatest impact, amplification success decreasing with both mitochondrial and microsatellite fragments' length, while error rates increase with amplicons' length. Dinucleotides showed best amplification success and lower error rates compared to longer repeat units. Genotyping success did not differ between hair- versus faeces-extracted DNA, and success in faeces-based analyses was not consistently influenced by the diet of focal species. While the great remaining variability among studies implies that other unidentified parameters are acting, results show that the careful choice of genetic markers may allow optimizing the success of noninvasive approache

Quelques aspects de la socioécologie de la vigogne Lama vicugna

A population sample of vicunas has been studied during 1979-1980 in the Pampa Galeras National Reserve in Southern Peru. Since 1965 the populations of this species which were previously on the verge to extinction, have increased sharply following effective measures of protection and good pasture conditions favoured by a succession of wet years. The social structure of the population studied includes groups of bachelor males roaming over extensive ranges, and harems settled on smaller territories and defended by an adult male. The observations were mainly focused on two family groups: - the Canllapampa Valley harem, composed of one male, one adult female and her young, one 2-year old female and one yearling female; - the Llamaiso Valley group, composed of one male and one adult female with her young. Since 1974, there has been a severe drought in the Reserve, causing changes in the social organisation and the social structure of the whole population, as well as in the pattern of range use. Therefore, our 1979-1980 observations are compared to those of Franklin, carried out in 1971, during a typical rainy year. Since that time annual censuses have shown that the population has increased regularly until 1978 and that its demographic structure changed, through an increase in the nomber of bachelors. Whereas the size of reproductive territorial groups, as well as the surface area of their territories, decreased during that period, the mean reproduction rate changed from 74% in 1971, to only 33% in 1979 due to numerous miscarriages. Our 1979-1980 observations indicate that the males on Canllapampa became aggressive towards juvenile females during the dry season (from May through November 1979) before expelling them. Moreover the one adult female studied suckled her young until February, whereas weaning occured between September and December in 1971. This indicates a tendency to breed only once every second year. All the year round, vicunas presently spend an average of 89% of their time grazing, without any significant seasonal variation. During the dry season vicunas may temporarily leave the male territories and cover great distances to graze on other pastures. All these changes which have occured after several dry years seem to indicate that the vicuna population is presently facing very harsh living conditions on very poor pastures. Indeed, the population began to decrease in numbers during 197

Is diet flexibility an adaptive life trait for relictual and peri-urban populations of the endangered primate Macaca Sylvanus?

International audienceHabitat loss, fragmentation and urban expansion may drive some species to marginal habitats while others succeed in exploiting urban areas. Species that show dietary flexibility are more able to take advantage of human activities to supplement their diet with anthropogenically abundant and accessible resources. The Barbary macaque (Macaca sylvanus) is an endangered species due to the loss of its habitat, and human pressure. The population of Gouraya National Park (Algeria) lives in a relictual habitat that constitutes about 0.6%of the species range. In addition, this population is a unique case where urban expansion favours contact zones between Barbary macaque habitats and a big city (Bejaia). We quantified the dietary composition of Gouraya macaques over an annual cycle with the objective to understand how diet flexibility of this species may help it adapt to a relictual habitat or cope with urban expansion.We recorded the phenology of plant species every month. This study shows that Gouraya macaques, compared to those living in other forest types of the distribution area, are under lower seasonal constraints. They consume a greater amount of fruit and seeds that are available throughout much of the year, and a lesser amount of costly to find and extract subterranean foods. Therefore the Gouraya relictual habitat appears as a favourable environment compared to other major habitats of that species. This study also shows that colonizing peri-urban zones increases the availability and species richness of diet resourcesfor Barbary macaques as they consume more human foods and exotic plants than in farther sites. Adult males eat more human foods than adult females and immatures do. The exploitation of high-energy anthropogenic food could favour macaque population growth and expansion towards the city center associated with human/macaque conflicts. We recommend applying management actions to restore macaques back to their natural habitat

How Ebola Impacts Genetics of Western Lowland Gorilla Populations

12 pagesInternational audienceBackground: Emerging infectious diseases in wildlife are major threats for both human health and biodiversity conservation. Infectious diseases can have serious consequences for the genetic diversity of populations, which could enhance the species' extinction probability. The Ebola epizootic in western and central Africa induced more than 90% mortality in Western lowland gorilla population. Although mortality rates are very high, the impacts of Ebola on genetic diversity of Western lowland gorilla have never been assessed. Methodology/Principal Findings: We carried out long term studies of three populations of Western lowland gorilla in the Republic of the Congo (Odzala-Kokoua National Park, Lossi gorilla sanctuary both affected by Ebola and Lossi's periphery not affected). Using 17 microsatellite loci, we compared genetic diversity and structure of the populations and estimate their effective size before and after Ebola outbreaks. Despite the effective size decline in both populations, we did not detect loss in genetic diversity after the epizootic. We revealed temporal changes in allele frequencies in the smallest population. Conclusions/Significance: Immigration and short time elapsed since outbreaks could explain the conservation of genetic diversity after the demographic crash. Temporal changes in allele frequencies could not be explained by genetic drift or random sampling. Immigration from genetically differentiated populations and a non random mortality induced by Ebola, i.e., selective pressure and cost of sociality, are alternative hypotheses. Understanding the influence of Ebola on gorilla genetic dynamics is of paramount importance for human health, primate evolution and conservation biology

The diet of Macaca sylvanus in various Algerian habitats. I. The diet in deciduous oak forest

Annuellement, ce Singe consacre 89 % de son temps passé en alimentation à se nourrir de végétaux. Il est principalement granivore-folivore (60 %) ; les lichens et les proies animales occupent une place importante dans son régime (14 et 10, 5 %). Son régime alimentaire subit d'importantes variations en cours d'année : principalement carnivore au printemps au moment de la pullulation des chenilles de Géométrides prédatrices de jeunes feuilles de chênes, le Magot est granivore en été et en automne, consommant surtout des glands et « folivore » en hiver lorsqu'il s'alimente de feuilles de Dactylis glomerata et de lichens. Quelle que soit la période de l'année, on note des différences du régime alimentaire entre les classes d'âge, les jeunes consommant trois fois plus de lichens et deux fois plus de proies animales que les adultes, tout en étant moins folivores. Les subadultes ont un régime intermédiaire entre ces deux classes. Bien que comportant un grand nombre d'espèces, le régime alimentaire du Magot apparaît peu diversifié ; en effet, sur les 73 espèces végétales, les 3 espèces de lichens, les divers champignons et les 6 catégories de proies animales consommées annuellement, seulement 4 espèces végétales (Dactylis glomerata, Quercus faginea, Q. afares et Cytisus triflorus), les lichens et une espèce animale (chenilles de Géométrides) composent 73 % de l'alimentation. En outre, seulement 2 espèces sur les 8 à 27 consommées chaque mois contribuent à plus de la moitié du régime mensuel. La moitié (50,5 %) de la nourriture du Magot (chenilles, lichens, glands) provient de la strate arborescente, 12,4 % de la strate arbustive et 37,1 % de la strate herbacée. Communément considéré comme un Singe terrestre, le Magot passe néanmoins 44 % de son temps de recherche alimentaire dans les arbres. Les variations des taux d'arboricolisme et de terrestrialité s'ajustent donc sur les modifications des taux de consommation des différents aliments. On remarque également que les jeunes passent deux fois plus de temps à s'alimenter dans les arbres que les adultes, les subadultes occupant une position intermédiaire.The composition of the diet of a troop of Barbary macaques Macaca sylvanus was studied in Algeria, from February 1 9 8 3 to October 1 984, in a deciduous oak forest (Quercus faginea and Q. afares). Eighty nine percent of the feeding time was devoted annually to feeding on plant material. The troop observed had a basically granivorous and folivorous diet (60%), lichens and animal prey contributing to 1 4 and 1 0. 5 percent of the diet respectively. Great seasonal variations were observed: Barbary macaques were mainly carnivorous in spring, feeding on Geometrid moth caterpillars teeming on oak trees leaves; in summer and autumn they essentially ate acorns, before turning to leaves of Dactylis glomerata and lichens in winter time. Differences in the diet of the three age classes were apparent throughout the year. Young monkeys (0. 5 to 3 year old) ate three times as many lichens and twice as many animal prey than adults. Adults (> 4 year old) were more folivorous, while the diet of sub-adults stood in-between. Seventy three plant species, three kinds of lichens, some mushrooms and six kinds of prey were identified in the macaques'diet. However, 74% of the food items were contributed by four plant species only (Dactylis glomerata, Quercus faginea, Q. afares and Cytisus triflorus) , three l ichens and the caterpillars. Furthermore, 2 species out of the 8 to 27 consumed e ach month contributed to more than half of the monthly diet

Quelques aspects de la socioécologie de la Vigogne Lama vicugna

A population sample of vicunas has been studied during 1979-1980 in the Pampa Galeras National Reserve in Southern Peru. Since 1965 the populations of this species which were previously on the verge to extinction, have increased sharply following effective measures of protection and good pasture conditions favoured by a succession of wet years. The social structure of the population studied includes groups of bachelor males roaming over extensive ranges, and harems settled on smaller territories and defended by an adult male. The observations were mainly focused on two family groups : — the Canllapampa Valley harem, composed of one male, one adult female and her young, one 2-year old female and one yearling female ; — the Llamaiso Valley group, composed of one male and one adult female with her young. Since 1974, there has been a severe drought in the Reserve, causing changes in the social organisation and the social structure of the whole population, as well as in the pattern of range use. Therefore, our 1979-1980 observations are compared to those of Franklin, carried out in 1971, during a typical rainy year. Since that time annual censuses have shown that the population has increased regularly until 1978 and that its demographic structure changed, through an increase in the nomber of bachelors. Whereas the size of reproductive territorial groups, as well as the surface area of their territories, decreased during that period, the mean reproduction rate changed from 74 % in 1971, to only 33 % in 1979 due to numerous miscarriages. Our 1979-1980 observations indicate that the males on Canllapampa became aggressive towards juvenile females during the dry season (from May through November 1979) before expelling them. Moreover the one adult female studied suckled her young until February, whereas weaning occured between September and December in 1971. This indicates a tendency to breed only once every second year. All the year round, vicunas presently spend an average of 89 % of their time grazing, without any significant seasonal variation. During the dry season vicunas may temporarily leave the male territories and cover great distances to graze on other pastures. All these changes which have occured after several dry years seem to indicate that the vicuna population is presently facing very harsh living conditions on very poor pastures. Indeed, the population began to decrease in numbers during 1979.Ménard Nelly. Quelques aspects de la socioécologie de la Vigogne Lama vicugna. In: Revue d'Écologie (La Terre et La Vie), tome 36, n°1, 1982. pp. 15-35

Group fission

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