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Life Sciences	100%

Selected Abstracts

Phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum: contrasting results from mitochondrial and microsatellite data

MOLECULAR ECOLOGY, Issue 2 2009
JON FLANDERS
Abstract Phylogeographical studies are typically based on haplotype data, occasionally on nuclear markers such as microsatellites, but rarely combine both. This is unfortunate because the use of markers with contrasting modes of inheritance and rates of evolution might provide a more accurate and comprehensive understanding of a species' history. Here we present a detailed study of the phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum, using 1098 bp of the mitochondrial ND2 gene from 45 localities from across its Palaearctic range to infer population history. In addition, we re-analysed a large microsatellite data set available for this species and compared the results of both markers to infer population relationships and the historical processes influencing them. We show that mtDNA, the most popular marker in phylogeography studies, yielded a misleading result, and would have led us to conclude erroneously that a single expansion had taken place in Europe. Only by combining the mitochondrial and microsatellite data sets are we able to reconstruct the species' history and show two colonization events in Europe, one before the Last Glacial Maximum (LGM) and one after it. Combining markers also revealed the importance of Asia Minor as an ancient refugium for this species and a source population for the expansion of the greater horseshoe bat into Europe before the LGM. [source]

Estimation of P -value of MAX test with double triangle diagram for 2 × 3 SNP case-control tables

GENETIC EPIDEMIOLOGY, Issue 6 2010
Katsura Hirosawa
Abstract Single nucle otide polymorphisms (SNPs) are the most popular markers in genetic epidemiology. Multiple tests have been applied to evaluate genetic effect of SNPs, such as Pearson's test with two degrees of freedom, three tests with one degree of freedom (,2 tests for dominant and recessive modes and Cockran-Armitage trend test for additive mode) as well as MAX3 test and MAX test, which are combination of four tests mentioned earlier. Because MAX test is a combination of Pearson's test of two degrees of freedom and two tests of one degree of freedom, the probability density function (pdf) of MAX statistics does not match pdf of ,2 distribution of either one or two degrees of freedom. In order to calculate P -value of MAX test, we introduced a new diagram, Double Triangle Diagram, which was an extension of de Finetti diagram in population genetics which characterized all of the tests for 2 × 3 tables. In the diagram the contour lines of MAX statistics were consisted of elliptic curves and two tangent lines to the ellipses in the space. We normalized the ellipses into regular circles and expressed P -value of MAX test in an integral form. Although a part of the integral was not analytically solvable, it was calculable with arbitrary accuracy by dividing the area under pdf into finite rectangles. We confirmed that P -values from our method took uniform distribution from 0 to 1 in three example marginal count sets and concluded that our method was appropriate to give P -value of MAX test for 2 × 3 tables. Genet. Epidemiol. 34:543,551, 2010. © 2010 Wiley-Liss, Inc. [source]

Chloroplast microsatellites reveal colonization and metapopulation dynamics in the Canary Island pine

MOLECULAR ECOLOGY, Issue 10 2006
MIGUEL NAVASCUÉS
Abstract Chloroplast microsatellites are becoming increasingly popular markers for population genetic studies in plants, but there has been little focus on their potential for demographic inference. In this work the utility of chloroplast microsatellites for the study of population expansions was explored. First, we investigated the power of mismatch distribution analysis and the FS test with coalescent simulations of different demographic scenarios. We then applied these methods to empirical data obtained for the Canary Island pine (Pinus canariensis). The results of the simulations showed that chloroplast microsatellites are sensitive to sudden population growth. The power of the FS test and accuracy of demographic parameter estimates, such as the time of expansion, were reduced proportionally to the level of homoplasy within the data. The analysis of Canary Island pine chloroplast microsatellite data indicated population expansions for almost all sample localities. Demographic expansions at the island level can be explained by the colonization of the archipelago by the pine, while population expansions of different ages in different localities within an island could be the result of local extinctions and recolonization dynamics. Comparable mitochondrial DNA sequence data from a parasite of P. canariensis, the weevil Brachyderes rugatus, supports this scenario, suggesting a key role for volcanism in the evolution of pine forest communities in the Canary Islands. [source]

A standard panel of microsatellites for Asian seabass (Lates calcarifer)

ANIMAL GENETICS, Issue 2 2010
Z. Y. Zhu
Summary Microsatellites are the most popular markers for parentage assignment and population genetic studies. To meet the demand for international comparability for genetic studies of Asian seabass, a standard panel of 28 microsatellites has been selected and characterized using the DNA of 24 individuals from Thailand, Malaysia, Indonesia and Australia. The average allele number of these markers was 10.82 ± 0.71 (range: 6,19), and the expected heterozygosity averaged 0.76 ± 0.02 (range: 0.63,1.00). All microsatellites showed Mendelian inheritance. In addition, eight standard size controls have been developed by cloning a set of microsatellite alleles into a pGEM-T vector to calibrate allele sizes determined by different laboratories, and are available upon request. Seven multiplex PCRs, each amplifying 3,5 markers, were optimized to accurately and rapidly genotype microsatellites. Parentage assignment using 10 microsatellites in two crosses (10 × 10 and 20 × 20) demonstrated a high power of these markers for revealing parent-sibling connections. This standard set of microsatellites will standardize genetic diversity studies of Asian seabass, and the multiplex PCR sets will facilitate parentage assignment. [source]