Genetic Variation and De Novo Mutations in the Parthenogenetic Caucasian Rock Lizard Darevskia unisexualis

Badaeva, T. N.; Malysheva, D. N.; Korchagin, V. I.; Ryskov, A. P.

doi:10.1371/journal.pone.0002730

Cited by 24 publications

(23 citation statements)

References 32 publications

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“…This method is also applicable to parthenogenetic organisms, such as Daphnia (Hebert and Ward, 1972;Lynch et al, 1989), aphids (Wilson et al, 2003;Kanbe andAkimoto, 2009), certain lizards (Cuellar, 1981;Cuellar, 1984;Badaeva et al, 2008) and selffertilizing hermaphrodites, such as Caenorhabditis elegans (Keightley and Caballero, 1997;Morran et al, 2010). The only difference here is that such organisms can produce clutches of multiple offspring.…”

Section: Resultsmentioning

confidence: 99%

SAPling: a Scan-Add-Print barcoding database system to label and track asexual organisms

Thomas

Schötz

2011

Journal of Experimental Biology

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SUMMARYWe have developed a 'Scan-Add-Print' database system, SAPling, to track and monitor asexually reproducing organisms. Using barcodes to uniquely identify each animal, we can record information on the life of the individual in a computerized database containing its entire family tree. SAPling has enabled us to carry out large-scale population dynamics experiments with thousands of planarians and keep track of each individual. The database stores information such as family connections, birth date, division date and generation. We show that SAPling can be easily adapted to other asexually reproducing organisms and has a strong potential for use in large-scale and/or long-term population and senescence studies as well as studies of clonal diversity. The software is platform-independent, designed for reliability and ease of use, and provided open source from our webpage to allow project-specific customization.Supplementary material available online at

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Section: Resultsmentioning

confidence: 99%

SAPling: a Scan-Add-Print barcoding database system to label and track asexual organisms

Thomas

Schötz

2011

Journal of Experimental Biology

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“…This assignment could be in conflict with the p-variable and h-variable values, because their associated path/cycle constraints were not included in the ILP instance. We will try to fix the problem by re-evaluating the free µ-variables using the determined pvariables and h-variables and Equation (3). For any free µ-variable in conflict, we change its value to 1 (which incurs a new mutation).…”

Section: Phasing Missing Allele Imputation and Mutation Detectionmentioning

confidence: 99%

“…In particular, a de novo mutation is a mutation that is present for the first time in a family member as a result of a mutation in a germ cell (egg or sperm) of one of the parents or in the fertilized egg itself. It has been found that the detection and analysis of mutations in a pedigree could provide a good alternative for some genetic variation research [3,5,14]. In fact, Ellegren [5] has stated that "To reveal the mutational contribution to overall genetic variability, the most straightforward and conclusive way is the direct detection of mutation events in pedigree genotyping."…”

Section: Introductionmentioning

confidence: 99%

Efficient Inference of Haplotypes from Genotypes on a Pedigree with Mutations and Missing Alleles (Extented Abstract)

Wang

Jiang

2009

Combinatorial Pattern Matching

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Abstract. Driven by the international HapMap project, the haplotype inference problem has become an important topic in the computational biology community. In this paper, we study how to efficiently infer haplotypes from genotypes of related individuals as given by a pedigree. Our assumption is that the input pedigree data may contain de novo mutations and missing alleles but is free of genotyping errors and recombinants, which is usually true for tightly linked markers. We formulate the problem as a combinatorial optimization problem, called the minimum mutation haplotype configuration (MMHC) problem, where we seek haplotypes consistent with the given genotypes that incur no recombinants and require the minimum number of mutations. This extends the well studied zero-recombinant haplotype configuration (ZRHC) problem. Although ZRHC is polynomial-time solvable, MMHC is NP-hard. We construct an integer linear program (ILP) for MMHC using the system of linear equations over the field F (2) that has been developed recently to solve ZRHC. Since the number of constraints in the ILP is large (exponentially large in the general case), we present an incremental approach for solving the ILP where we gradually add the constraints to a standard ILP solver until a feasible haplotype configuration is found. Our preliminary experiments on simulated data demonstrate that the method is very efficient on large pedigrees and can infer haplotypes very accurately as well as recover most of the mutations and missing alleles correctly.

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“…Polymorphic loci characterized by rather low variability were also iden tified. However, exactly characterization of the poly morphic loci provided new information on molecular nature of their variation [9,10]. Identification of new highly variable loci in the genomes of unisexual verte brate species is very important for gaining insight into mechanisms of the appearance of genetic and clonal diversity in these species and evaluating the level of this diversity.…”

Section: Introductionmentioning

confidence: 99%

Molecular nature of allelic polymorphism of highly variable microsatellite locus Du161(arm) in unisexual lizard Darevskia armeniaca (lacertidae)

et al. 2012

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In the genome of unisexual (parthenogenetic) lizard Darevskia armeniaca, highly variable locus Du161 (arm) was discovered. Analysis of allelic polymorphism was carried out using locus specific PCR of the lizard DNA specimens from 13 isolated Armenian populations (N = 138). In the sample examined, a total of 12 Du161(arm) alleles were identified, and their differences at the level of primary DNA structure were determined. Sequence analysis of the Du161(arm) alleles showed that their microsatellite clusters contained repeats of one type (GATA repeats). Allelic Du161(arm) variants differed in the number of GATA monomers in microsatellite, point mutations of transition and transversion types, located at fixed distances from micro satellite cluster, and by single nucleotide insertions, as well as by longer insertions located within and outside of the microsatellite cluster. Moreover, point mutations formed different combinations (haplotypes), typical of certain alleles. These combinations can be used for the analysis of the origin and inheritance of these alleles in D. armeniaca, as well as for investigation of their interspecific variation in the representatives of the genus Darevskia.

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Genetic Variation and De Novo Mutations in the Parthenogenetic Caucasian Rock Lizard Darevskia unisexualis

Cited by 24 publications

References 32 publications

SAPling: a Scan-Add-Print barcoding database system to label and track asexual organisms

SAPling: a Scan-Add-Print barcoding database system to label and track asexual organisms

Efficient Inference of Haplotypes from Genotypes on a Pedigree with Mutations and Missing Alleles (Extented Abstract)

Molecular nature of allelic polymorphism of highly variable microsatellite locus Du161(arm) in unisexual lizard Darevskia armeniaca (lacertidae)

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