Primers for EPIC amplification of intron sequences for fish and other vertebrate population genetic studies

Atarhouch, Touriya; Rami, M.; Cattaneo-Berrebi, G.; Ibáñez, Carla; Augros, Stéphane; Boissin, Émilie; Dakkak, A.; Berrebi, Patrick

doi:10.2144/03354bm02

Cited by 35 publications

(9 citation statements)

References 7 publications

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“…A part of nuclear DNA containing 2nd intron of actin gene (336 bp) was amplified using primers Act-2-R and Act-2-F designed by Touriya et al (2003) and another part containing 1st intron of RPS7 gene (900 total bp) using primers S7RPEX2R and S7RPEX1F (Chow and Hazama 1998). In addition, an approximately 1,225 bp long portion of mtDNA containing entire gene for cytochrome b was amplified for fish from Felchowsee using primers GluF and ThrR (Machordom and Doadrio 2001).…”

Section: Data Acquisitionmentioning

confidence: 99%

Lack of reproductive isolation between the Western and Eastern phylogroups of the tench

Lajbner

Kohlmann

Linhart

et al. 2009

Rev Fish Biol Fisheries

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The Eurasian range of the tench distribution is subdivided into deeply divergent Western and Eastern phylogroups evidenced by nuclear and mitochondrial DNA sequence markers. A broad zone of overlap exists in central and western Europe, suggesting post-glacial contact with limited hybridisation. We conducted a population genetic test of this indication that the two phylogroups may represent distinct species. We analysed variation at introns of nuclear genes, microsatellites, allozymes and mitochondrial DNA in populations from two postglacial lakes within the contact zone in Germany. The test is based on the expectation that in the presence of strong barriers to reproduction, a hybrid population will show genome-wide associations among alleles and genotypes from each phylogroup even after hundreds of generations of interbreeding. In contrast to this expectation, no consistent significant deviations from linkage and Hardy-Weinberg equilibria were found. Samples from both lakes did show significant disequilibria but they were limited to individual loci and were not concordant between populations, and were not robust to the method used. The single consistent association can be attributed to physical linkage between two microsatellite loci. Thus, results of our study support the hypothesis of free interbreeding between the two phylogroups of tench. Therefore, although the phylogroups may be considered as separate phylogenetic species, the present data suggest that they are a single species under the biological species concept.

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Section: Data Acquisitionmentioning

confidence: 99%

Lack of reproductive isolation between the Western and Eastern phylogroups of the tench

Lajbner

Kohlmann

Linhart

et al. 2009

Rev Fish Biol Fisheries

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“…Although truly universally applicable primers do not exist, a number of putatively broad, and taxon-specific EPIC primers are now available for potential use in animals (Slade et al 1993; Palumbi and Baker, 1994; Friesen et al 1997, 1999; Prychitko and Moore, 1997; Hassan et al 2002; Jarman et al 2002; Touriya et al 2003; Sota and Vogler, 2003; Aitken et al 2004) and vascular and non-vascular plants, (Shaw et al 2005; Ishikawa et al 2002). Thus, one approach that can be utilized to locate a suitable selection of markers, is to assay the performance of numerous primers from existing studies (Creer et al 2005), or primers that have worked well in related taxa.…”

Section: Locus Selection and Primer Designmentioning

confidence: 99%

Choosing and Using Introns in Molecular Phylogenetics

Creer

2007

Evol Bioinform Online

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Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently discussed in empirical studies that utilize intron data. This review outlines expedient approaches for locus selection, overcoming paralogy problems, recombination detection methods and the identification and incorporation of LVHs in molecular systematics. A range of parsimony and Bayesian analytical approaches are also described in order to highlight the methods that can currently be employed to align sequences and treat indels in subsequent analyses. By covering the main points associated with the generation and analysis of intron data, this review aims to provide a comprehensive introduction to using introns (or any non-coding nuclear data partition) in contemporary phylogenetics.

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“…[16,17]; Aurelle et al ., submitted). Only vertebrates benefit from a relatively consistent set of EPIC loci [18,19]. Several reasons for such biases can be invoked.…”

Section: Introductionmentioning

confidence: 99%

An efficient method to find potentially universal population genetic markers, applied to metazoans

et al. 2010

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BackgroundDespite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families.ResultsIn order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals.ConclusionsOur new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa.

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Primers for EPIC amplification of intron sequences for fish and other vertebrate population genetic studies

Cited by 35 publications

References 7 publications

Lack of reproductive isolation between the Western and Eastern phylogroups of the tench

Lack of reproductive isolation between the Western and Eastern phylogroups of the tench

Choosing and Using Introns in Molecular Phylogenetics

An efficient method to find potentially universal population genetic markers, applied to metazoans

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