Microsatellites and kinship

Queller, David C.; Strassmann, Joan E.; Hughes, Colin

doi:10.1016/0169-5347(93)90256-o

Cited by 681 publications

(412 citation statements)

References 39 publications

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“…Lexer et al, 1999). Microsatellites are codominant markers that usually display high levels of allelic diversity, which make them particularly useful to population genetic studies (Queller et al, 1993;Jarne & Lagoda, 1996). Drawback of microsatellites is that sequence information is needed for marker development.…”

Section: Introductionmentioning

confidence: 99%

Variation in effective pollination rates in relation to the spatial and temporal distribution of pollen release in rejuvenated perennial ryegrass

2006

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SummaryGenebank accessions stored as seed populations require periodic rejuvenation in order to maintain sufficient numbers of viable seeds. During rejuvenation the genetic composition of accessions may be altered for a variety of reasons, of which variation in pollination rates between plants is the least understood. In the present study, a paternity exclusion analysis was performed on a rejuvenated accession of perennial ryegrass. In addition, flowering data of the 49 parental plants were collected during the flowering season. The aim of the study was to determine how accurate variation in pollination rates between plants can be predicted from data on the spatial and temporal distribution of pollen release. The parental population and a total of 551 offspring from 12 progeny arrays were genotyped by means of molecular analysis. Using 25 microsatellites, paternity was identified for 81.9% of the offspring, while remaining ambiguities were resolved by AFLP analysis, except in four cases. Within the total sample 9 cases of contamination were observed. Mating within the study population was clearly non-random, as 61.9% of the identified pollen donors were located within 1 m distance from the mother plant. Observed pollination rates were very well described by an inverse quadratic function of inter-plant distance between potential mating pairs. Incorporation of the recorded flowering data in the calculation of expected pollination rates improved the goodness of fit with observed values by only 0.77%. Suggestions to reduce the variance in paternal contributions were presented. However, contamination was considered more threatening to the genetic integrity of perennial ryegrass germplasm than variation in pollination rates between plants, and indicated the need for improved measures to avoid gene flow from other germplasm.

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Section: Introductionmentioning

confidence: 99%

Variation in effective pollination rates in relation to the spatial and temporal distribution of pollen release in rejuvenated perennial ryegrass

2006

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“…Therefore, development of microsatellite markers would be an important contribution. The use of molecular technology has become increasingly important in conservation biology (Queller et al, 1993;Hillis et al, 1996;Haig, 1998). The development of molecular markers within the mitochondrial DNA (mtDNA), and nuclear microsatellites have provided the potential for determining evolutionary relationships among individuals (Avise, 1992;Moritz, 1995;Georges and Adams, 1996), and are also useful to measure levels of gene flow and population structure (Hurwood and Hughes, 1998;Waters and Wallis, 2000).…”

Section: Descriptionmentioning

confidence: 99%

“…Samples can be obtained from skin biopsies, individual hairs and scat. DNA can also be amplified from dried or preserved museum specimens (Queller et al, 1993;Mitton, 1994;Taylor et al, 1994;Moritz, 1994b). Most importantly, the analysis of genetic structure does not require tracking the fate of individuals, or even capturing individuals more than once (Steinberg and Jordan, 1998).…”

Section: Descriptionmentioning

confidence: 99%

Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species

Choupina¹,

Martins

2014

Braz. J. Biol.

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Freshwater mussel species are in global decline. Anthropogenic changes of river channels and the decrease of autochthonous fish population, the natural hosts of mussels larval stages (glochidia), are the main causes. Therefore, the conservation of mussel species depends not only on habitat conservation, but also on the availability of the fish host. In Portugal, information concerning most of the mussel species is remarkably scarce. One of the most known species, Unio pictorum is also in decline however, in the basins of the rivers Tua and Sabor (Northeast of Portugal), there is some indication of relatively large populations. The aforementioned rivers can be extremely important for this species conservation not only in Portugal, but also in the remaining Iberian Peninsula. Thus, it is important to obtain data concerning Unio pictorum bioecology (distribution, habitat requirements, population structure, genetic variability, reproductive cycle and recruitment rates), as well as the genetic variability and structure of the population. Concomitantly, information concerning fish population structure, the importance of the different fish species as "glochidia" hosts and their appropriate density to allow effective mussel recruitment, will also be assessed. The achieved data is crucial to obtain information to develop effective management measures in order to promote the conservation of this bivalve species, the conservation of autochthonous fish populations, and consequently the integrity of the river habitats.Keywords: molecular markers, freshwater mussel, mtDNA, PCR.Marcadores moleculares para estudo da diversidade genética, fluxo génico e estrutura genética de populações de espécies de mexilhões de água doce ResumoAs espécies de mexilhões de água doce estão em declínio global. Mudanças antropogénicas do canal dos rios e diminuição das populações de peixes autóctones, os hospedeiros naturais do mexilhão nos estágios larvais (glochidia), são as principais causas. Portanto, a conservação de espécies de mexilhão depende não só da conservação dos habitats, mas também da disponibilidade do hospedeiro peixe. Em Portugal, a informação relativa à maioria das espécies de mexilhão é extremamente escassa. Uma das espécies mais conhecidas, Unio pictorum também está em declínio, no entanto, nas bacias dos rios Tua e Sabor (Nordeste de Portugal), existe indicação de populações relativamente grandes. Os rios acima mencionados podem ser extremamente importantes para a conservação das espécies, não só em Portugal, mas também na restante Península Ibérica. Assim, é importante obter dados relativos à bioecologia do Unio pictorum (distribuição, requisitos de habitat, estrutura populacional, variabilidade genética, ciclo reprodutivo e as taxas de recrutamento), bem como a variabilidade e estrutura genética da população. Concomitantemente, informações sobre a estrutura da população de peixes, a importância das diferentes espécies de peixes como hospedeiros e sua densidade adequada para permitir o recrutamento eficaz do mexilhão,...

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“…Microsatellites are especially useful for studying population demographics and reproductive patterns because they are neutral and co-dominant markers, and the inference of genotypes at each locus is straightforward. More importantly, microsatellites are preferred because of high numbers of alleles and heterozygosities, providing the highest resolution for identifying related individuals (Queller et al 1993). Because of these advantages and their widespread use, we focus our development of sibling relationship (sibship) reconstruction methods to unlinked, multi-allelic, codominantly inherited markers such as microsatellites.…”

Section: Microsatellite Datamentioning

confidence: 99%

New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers

Chaovalitwongse

Chou

Berger-Wolf

et al. 2010

INFORMS Journal on Computing

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W ith improved tools for collecting genetic data from natural and experimental populations, new opportunities arise to study fundamental biological processes, including behavior, mating systems, adaptive trait evolution, and dispersal patterns. Full use of the newly available genetic data often depends upon reconstructing genealogical relationships of individual organisms, such as sibling reconstruction. This paper presents a new optimization framework for sibling reconstruction from single generation microsatellite genetic data. Our framework is based on assumptions of parsimony and combinatorial concepts of Mendel's inheritance rules. Here, we develop a novel optimization model for sibling reconstruction as a large-scale mixed-integer program (MIP), shown to be a generalization of the set covering problem. We propose a new heuristic approach to efficiently solve this large-scale optimization problem. We test our approach on real biological data as presented in other studies as well as simulated data, and compare our results with other state-of-the-art sibling reconstruction methods. The empirical results show that our approaches are very efficient and outperform other methods while providing the most accurate solutions for two benchmark data sets. The results suggest that our framework can be used as an analytical and computational tool for biologists to better study ecological and evolutionary processes involving knowledge of familial relationships in a wide variety of biological systems.

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Microsatellites and kinship

Cited by 681 publications

References 39 publications

Variation in effective pollination rates in relation to the spatial and temporal distribution of pollen release in rejuvenated perennial ryegrass

Variation in effective pollination rates in relation to the spatial and temporal distribution of pollen release in rejuvenated perennial ryegrass

Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species

New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers

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