Conservation of wild animals by assisted reproduction and molecular marker technology (original) (raw)
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Comparison of genetic diversity indices of heterologous and species-specific microsatellite loci within a species may provide a panel of appropriate markers for genetic studies, but few studies have carried out such comparisons. We examined and compared the genetic characteristics of tiger-specific and heterologous loci in eight captive Bengal tigers. The mean polymorphic information content (PIC) value of the tiger-specific microsatellite loci (n = 15) was 0.447, and the number of alleles was from 2 to 4 per locus. In comparison, the heterologous microsatellite loci (n = 15) had a mean PIC value of 0.539, and the number of alleles per locus was three to five. Our findings indicate that the heterologous markers have a higher frequency (n = 11) of polymorphic microsatellite loci and number of alleles per locus compared with tiger-specific loci. We pooled the highly polymorphic (PIC > 0.5) tiger-specific loci (n = 5) and heterologous microsatellite loci (n = 11) except one and noted a higher mean observed heterozygosity and PIC values of 0.668 and 0.575, respectively, compared with the heterologous and tiger-specific loci taken alone. Using a locus selection criterion of PIC > 0.5, we recommend a combined panel of 16 highly polymorphic loci for genetic studies of the wild population of the Bengal tigers and suggest that either a combination of tiger-specific and heterologous microsatellite primers or heterologous primers be used in genetic studies related to the ecology, biology, socio-biology and behavior of Bengal tigers as >13 loci are needed in such studies.
SpringerPlus, 2014
In India, six landscapes and source populations that are important for long-term conservation of Bengal tigers (Panthera tigris tigris) have been identified. Except for a few studies, nothing is known regarding the genetic structure and extent of gene flow among most of the tiger populations across India as the majority of them are small, fragmented and isolated. Thus, individual-based relationships are required to understand the species ecology and biology for planning effective conservation and genetics-based individual identification has been widely used. But this needs screening and describing characteristics of microsatellite loci from DNA from good-quality sources so that the required number of loci can be selected and the genotyping error rate minimized. In the studies so far conducted on the Bengal tiger, a very small number of loci (n = 35) have been tested with high-quality source of DNA, and information on locus-specific characteristics is lacking. The use of such characteristics has been strongly recommended in the literature to minimize the error rate and by the International Society for Forensic Genetics (ISFG) for forensic purposes. Therefore, we describe for the first time locus-specific genetic and genotyping profile characteristics, crucial for population genetic studies, using high-quality source of DNA of the Bengal tiger. We screened 39 heterologous microsatellite loci (Sumatran tiger, domestic cat, Asiatic lion and snow leopard) in captive individuals (n = 8), of which 21 loci are being reported for the first time in the Bengal tiger, providing an additional choice for selection. The mean relatedness coefficient (R = −0.143) indicates that the selected tigers were unrelated. Thirty-four loci were polymorphic, with the number of alleles ranging from 2 to 7 per locus, and the remaining five loci were monomorphic. Based on the PIC values (> 0.500), and other characteristics, we suggest that 16 loci (3 to 7 alleles) be used for genetic and forensic study purposes. The probabilities of matching genotypes of unrelated individuals (3.692 × 10 -19 ) and siblings (4.003 × 10 -6 ) are within the values needed for undertaking studies in population genetics, relatedness, sociobiology and forensics.
The Central African journal of medicine
Comparison of genetic diversity indices of heterologous and species-specific microsatellite loci within a species may provide a panel of appropriate markers for genetic studies, but few studies have carried out such comparisons. We examined and compared the genetic characteristics of tiger-specific and heterologous loci in eight captive Bengal tigers. The mean polymorphic information content (PIC) value of the tiger-specific microsatellite loci (n = 15) was 0.447, and the number of alleles was from 2 to 4 per locus. In comparison, the heterologous microsatellite loci (n = 15) had a mean PIC value of 0.539, and the number of alleles per locus was three to five. Our findings indicate that the heterologous markers have a higher frequency (n = 11) of polymorphic microsatellite loci and number of alleles per locus compared with tiger-specific loci. We pooled the highly polymorphic (PIC > 0.5) tiger-specific loci (n = 5) and heterologous microsatellite loci (n = 11) except one and note...
International Journal of Biodiversity and Conservation, 2013
Population size estimation is a prerequisite for assessment of conservation status of a species in its natural habitat. With a global scenario of vanishing local population of tigers in many parts of its range distribution, estimation of the minimum number of individuals is vital for prioritizing conservation attention to specific areas with long term possibility of survival of the species. In the present study, DNA based techniques were used to identify species, individuals and sex from 72 faecal samples collected from Buxa Tiger Reserve of West Bengal. Present study confirms the presence of 15 individual tigers with 3 male, 9 female and 3 with unknown sex identity. Genetic capture recapture estimate based on single session sampling using CAPWIRE yields population size of 25 (95% CI 19 to 31) following the even capture probability model. Results obtained from the present study indicate possible movement of tigers from contiguous forest patches of Bhutan to the north and Manas Tiger Reserve on the east of Buxa. The present study shows that noninvasive genetics can be an effective tool in monitoring elusive species such as tiger, especially in areas of low population density.
GENETIC DIVERSITY AMONG COMMON LEOPARDS INHABITING AZAD JAMMU AND KASHMIR, PAKISTAN
The common leopard (Pantherapardus) is one of the highly threatened species of big cats in Pakistan. Azad Jammu and Kashmir (AJK) is among the main distribution areas of these leopards but due to poaching, habitat fragmentation and other anthropogenic activities, there is a rapid decline of the population in the state. We carried out the study to analyze the genetic diversity of common leopard in Azad Jammu and Kashmir (AJK).We used skin samples that were collected from the killed leopards by farmers and local hunters from six different localities of AJK. We used phenol chloroform triton modified method to extract the DNA and used four SSR markers (FCA043, FCA026, FCA075 and FCA090) to analyze genetic diversity by using PCR-based simple sequence repeat (SSR) analysis. We also calculated Allelic frequencies, Nei’s genetic diversities index(within and among populations) and Shannon information index with POPGENE 32 program which showed that highest genetic distance (0.4275) was established between the Kotli (Pop-6) and Hattian (Pop-3) populations, and lowest between Hattian (Pop-3) and Neelum (Pop-2) populations (0.0393) of common leopard. Mean gene flow (Nm) was found to be 0.8030 which showed low level of gene flow between different populations and higher level genetic differentiation between populations supported our hypothesis of habitat fragmentation.
Molecular Genetic Approaches in Wildlife Conservation
Genetic Diversity - Recent Advances and Applications [Working Title]
Wildlife conservation is of major biological importance due to the survivability of organisms in an ecosystem and population stability. The primary concern of the management and genetics of populations is inbreeding. The small population size can play a diminishing role in genetic variability and increasing inbreeding in animal populations. Inbreeding depression can be due to major factors such as rare, deleterious, recessive alleles which can be repressed under heterozygous conditions. The decreasing effect in heterozygosity can be significant upon severe bottleneck effect. The genetic variations between populations could be assessed using molecular techniques. Mitochondrial DNA variations for determining the founder’s effect can be widely applicable in the management of wild populations. The maternal lineages in a captive population can signify the variations in the population as well as the number of males contributing to the gene pool of the various population. Molecular markers...
BMC genetics, 2006
Bengal tiger Panthera tigris tigris the National Animal of India, is an endangered species. Estimating populations for such species is the main objective for designing conservation measures and for evaluating those that are already in place. Due to the tiger's cryptic and secretive behaviour, it is not possible to enumerate and monitor its populations through direct observations; instead indirect methods have always been used for studying tigers in the wild. DNA methods based on non-invasive sampling have not been attempted so far for tiger population studies in India. We describe here a pilot study using DNA extracted from faecal samples of tigers for the purpose of population estimation. In this study, PCR primers were developed based on tiger-specific variations in the mitochondrial cytochrome b for reliably identifying tiger faecal samples from those of sympatric carnivores. Microsatellite markers were developed for the identification of individual tigers with a sibling Prob...
Twenty polymorphic microsatellite markers in the Asiatic lion (Panthera leo persica
The Asiatic lion (Panthera leo persica) is driven to a single habitat in Gir forests in India for its survival. In order to devise adequate conservation and management strategies for this critically endangered species, it is important to characterize its genetic diversity and understand its population structure. Here we report twenty microsatellite loci, in addition to seven reported earlier, from the genome of a pure Asiatic lion. The microsatellite loci described here will provide potentially useful markers for the assessment of genetic variability in the only existing wild population of the Asiatic lions and other big cat species.
PeerJ
Background The Hindu Kush and Karakoram mountain ranges in Pakistan’s northern areas are a natural habitat of the snow leopard (Panthera uncia syn. Uncia uncia) but the ecological studies on this animal are scarce since it is human shy by nature and lives in difficult mountainous tracts. The pilot study is conducted to exploit the genetic diversity and population structure of the snow leopard in this selected natural habitat of the member of the wildcat family in Pakistan. Method About 50 putative scat samples of snow leopard from five localities of Gilgit-Baltistan (Pakistan) along with a control sample of zoo maintained male snow leopard were collected for comparison. Significant quality and quantity of genomic DNA was extracted from scat samples using combined Zhang–phenol–chloroform method and successful amplification of cytochrome c oxidase I gene (190 bp) using mini-barcode primers, seven simple sequence repeats (SSR) markers and Y-linked AMELY gene (200 bp) was done. Results ...
The use of molecular markers in conservation programmes of live animals
Genetics Selection Evolution, 1998
Monte Carlo simulation has been carried out to study the benefits of using molecular markers in a conservation programme to minimize the homozygosity by descent in the overall genome. Selection of the breeding individuals was either at random or based on two alternative criteria: overall heterozygosity of the markers or frequency-dependent selection. Even molecular information was available for all the 1 900 simulated loci, a conventional tactic such as restriction in the variance of the family size is the most important strategy for maintaining genetic variability. In this context: a) frequency-dependent selection seems to be a more efficient criterion than selection for heterozygosity; and b) the value of marker information increases as the selection intensity increases. Results from more realistic cases (1, 2, 3, 4, 6 or 10 markers per chromosome and 2, 4, 6 or 10 alleles per marker) confirm the above conclusions. This is an expensive strategy with respect to the number of candidates and the number of markers required in order to obtain substantial benefits, the usefulness of a marker being related to the number of alleles. The minimum coancestry mating system was also compared with random mating and it is concluded that it is advantageous at least for many generations. © Inra/Elsevier, Paris molecular markers / conservation genetics / frequency-dependent selection / minimum coancestry mating * Correspondence and reprints E-mail: toroCinia.es Résumé-Utilisation de marqueurs moléculaires dans les programmes de conservation des animaux. Des simulations Monte Carlo ont été effectuées pour étudier l'intérêt de l'utilisation des marqueurs moléculaires dans un programme de conservation avec N S (= 4, 8 ou 16) mâles et N d = 3 N,, femelles, choisis parmi 3 N d candidats de chaque sexe. Le génome a été simulé avec 1 900 locus distribués sur 19 chromosomes d'une longueur de 100 cM chacun. L'objectif était de minimiser le taux d'homozygotie chez la descendance pour l'ensemble du génome, le choix des