Choosing and Using Introns in Molecular Phylogenetics

Creer, Simon

doi:10.1177/117693430700300011

Cited by 40 publications

(29 citation statements)

References 128 publications

(177 reference statements)

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“…Cam-3; Table 2), which can be due to either amplification of the paralogous intron in several genes of the family (e.g. Creer, 2007;Friedberg and Rhoads, 2002), or perhaps non-specific amplification within a single gene (i.e. several introns of the same gene might have been amplified).…”

Section: Resultsmentioning

confidence: 98%

“…Last, an undesirable property of microsatellites is allele-size homoplasy (Ellegren, 2004;Garza and Freimer, 1996), which is unlikely to occur with EPIC markers when mutations that affect allele size are caused by indels (Creer, 2007). We screened for size polymorphism a number of primer pairs that are known to amplify EPICs in teleost fishes.…”

Section: Introductionmentioning

confidence: 99%

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Population genetic structure of blue-spotted maskray Neotrygon kuhlii and two other Indo-West Pacific stingray species (Myliobatiformes: Dasyatidae), inferred from size-polymorphic intron markers

Borsa

Arlyza

Laporte

et al. 2012

Journal of Experimental Marine Biology and Ecology

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a b s t r a c tExon-primed, intron crossing DNA markers (EPICs) were screened for Mendelian-like allele size polymorphisms in three stingray species (Himantura gerrardi, Neotrygon kuhlii and Taeniura lymna) from the central Indo-West Pacific, where they are commercially exploited. Four to 7 size-polymorphic intron loci were selected in a species, and were subsequently tested as genetic markers of stock structure. Sharp genetic differentiation was observed between populations within each species across the Indo-Malay-Papua archipelago (Weir and Cockerham'sθ-values reaching 0.153-0.557 over a few thousand kilometers). A trend of increasing genetic differentiation with increasing geographic distance was apparent in N. kuhlii, in which populations distant by 3000 km were differentiated by an estimatedθ~0.375. This value was an order of magnitude higher than usually reported in coastal benthic teleost fishes and indicates strong sub-population structure. This is likely, at least partly, a consequence of the sedentary benthic habits of N. kuhlii at all life stages. Because replenishment of overexploited populations of N. kuhlii and two other stingray species from the central Indo-West Pacific is unlikely at ecological timescales, management should be planned at the local geographic scale.

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Section: Resultsmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Population genetic structure of blue-spotted maskray Neotrygon kuhlii and two other Indo-West Pacific stingray species (Myliobatiformes: Dasyatidae), inferred from size-polymorphic intron markers

Borsa

Arlyza

Laporte

et al. 2012

Journal of Experimental Marine Biology and Ecology

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“…Theoretically, exon-primed intron crossing (EPIC) sequence loci represent an excellent nDNA marker for use in phylogeography [8]–[10], [14]. Intron sequences, while not obviously functional, are not junk DNA [15] and affect a number of eukaryotic gene expression pathways [16]–[18].…”

Section: Introductionmentioning

confidence: 99%

Next-Generation Phylogeography: A Targeted Approach for Multilocus Sequencing of Non-Model Organisms

2012

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The field of phylogeography has long since realized the need and utility of incorporating nuclear DNA (nDNA) sequences into analyses. However, the use of nDNA sequence data, at the population level, has been hindered by technical laboratory difficulty, sequencing costs, and problematic analytical methods dealing with genotypic sequence data, especially in non-model organisms. Here, we present a method utilizing the 454 GS-FLX Titanium pyrosequencing platform with the capacity to simultaneously sequence two species of sea star (Meridiastra calcar and Parvulastra exigua) at five different nDNA loci across 16 different populations of 20 individuals each per species. We compare results from 3 populations with traditional Sanger sequencing based methods, and demonstrate that this next-generation sequencing platform is more time and cost effective and more sensitive to rare variants than Sanger based sequencing. A crucial advantage is that the high coverage of clonally amplified sequences simplifies haplotype determination, even in highly polymorphic species. This targeted next-generation approach can greatly increase the use of nDNA sequence loci in phylogeographic and population genetic studies by mitigating many of the time, cost, and analytical issues associated with highly polymorphic, diploid sequence markers.

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“…EPIC, having both the exon and intron fragments, could help in examining genetic variation at the intraspecific and interspecific level simultaneously, which could be particularly helpful when studying a species complex [29, 30, 32]. …”

Section: Introductionmentioning

confidence: 99%

Exon-intron structure and sequence variation of the calreticulin gene among Rhipicephalus sanguineus group ticks

et al. 2016

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BackgroundCalreticulin proteins (CRTs) are important components of tick saliva, which is involved in the blood meal success, pathogen transmission and host allergic responses. The characterization of the genes encoding for salivary proteins, such as CRTs, is pivotal to understand the mechanisms of tick-host interaction during blood meal and to develop tick control strategies based on their inhibition. In hard ticks, crt genes were shown to have only one intron with conserved position among species. In this study we investigated the exon-intron structure and variation of the crt gene in Rhipicephalus spp. ticks in order to assess the crt exon-intron structure and the potential utility of crt gene as a molecular marker.MethodsWe sequenced the exon-intron region of crt gene in ticks belonging to so-called tropical and temperate lineages of Rhipicephalus sanguineus (sensu lato), Rhipicephalus sp. I, Rhipicephalus sp. III, Rhipicephalus sp. IV, R. guilhoni, R. muhsamae and R. turanicus. Genetic divergence and phylogenetic relationships between the sequences obtained were estimated.ResultsAll individuals belonging to the tropical lineage of R. sanguineus (s.l.), R. guilhoni, R. muhsamae, R. turanicus, Rhipicephalus sp. III and Rhipicephalus sp. IV analysed showed crt intron-present alleles. However, both crt intron-present and intron-absent alleles were found in Rhipicephalus sp. I and the temperate lineage of R. sanguineus (s.l.), showing the occurrence of an intraspecific intron presence-absence polymorphism. Phylogenetic relationships among the crt intron-present sequences showed distinct lineages for all taxa, with the tropical and temperate lineages of R. sanguineus (s.l.) being more closely related to each other.ConclusionsWe expanded previous studies about the characterization of crt gene in hard ticks. Our results highlighted a previously overlooked variation in the crt structure among Rhipicephalus spp., and among hard ticks in general. Notably, the intron presence/absence polymorphism observed herein can be a candidate study-system to investigate the early stages of intron gain/loss before fixation at species level and some debated questions about intron evolution. Finally, the sequence variation observed supports the suitability of the crt gene for molecular recognition of Rhipicephalus spp. and for phylogenetic studies in association with other markers.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-016-1909-3) contains supplementary material, which is available to authorized users.

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Choosing and Using Introns in Molecular Phylogenetics

Cited by 40 publications

References 128 publications

Population genetic structure of blue-spotted maskray Neotrygon kuhlii and two other Indo-West Pacific stingray species (Myliobatiformes: Dasyatidae), inferred from size-polymorphic intron markers

Population genetic structure of blue-spotted maskray Neotrygon kuhlii and two other Indo-West Pacific stingray species (Myliobatiformes: Dasyatidae), inferred from size-polymorphic intron markers

Next-Generation Phylogeography: A Targeted Approach for Multilocus Sequencing of Non-Model Organisms

Exon-intron structure and sequence variation of the calreticulin gene among Rhipicephalus sanguineus group ticks

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