Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids

Steele, P. Roxanne; Guisinger-Bellian, Mary; Linder, C. Randal; Jansen, Robert K.

doi:10.1016/j.ympev.2008.05.017

Cited by 31 publications

(23 citation statements)

References 45 publications

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“…To estimate the size of introgressed linkage blocks, low-copy nuclear markers are required. The primer design and cloning required to confirm a single amplified product is time-consuming (Mcfadden and Hutchinson, 2004;Steele et al, 2008). Typically, conserved orthologous markers for amplifying nuclear genes are limited to well-studied families (for example, Asteraceae; Chapman et al, 2007).…”

Section: Problems Of the Current Methodologiesmentioning

confidence: 99%

Next-generation hybridization and introgression

2011

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Hybridization has a major role in evolution-from the introgression of important phenotypic traits between species, to the creation of new species through hybrid speciation. Molecular studies of hybridization aim to understand the class of hybrids and the frequency of introgression, detect the signature of ancient hybridization, and understand the behaviour of introgressed loci in their new genomic background. This often involves a large investment in the design and application of molecular markers, leading to a compromise between the depth and breadth of genomic data. New techniques designed to assay a large sub-section of the genome, in association with next-generation sequencing (NGS) technologies, will allow genome-wide hybridization and introgression studies in organisms with no prior sequence data. These detailed genotypic data will unite the breadth of sampling of loci characteristic of population genetics with the depth of sequence information associated with molecular phylogenetics. In this review, we assess the theoretical and methodological constraints that limit our understanding of natural hybridization, and promote the use of NGS for detecting hybridization and introgression between non-model organisms. We also make recommendations for the ways in which emerging techniques, such as pooled barcoded amplicon sequencing and restriction site-associated DNA tags, should be used to overcome current limitations, and enhance our understanding of this evolutionary significant process. Heredity (2012) 108, 179-189; doi:10.1038/hdy.2011.68; published online 7 September 2011Keywords: next-generation sequencing; hybridization; introgression; reticulate evolution; single-nucleotide polymorphisms (SNPs); restriction site-associated DNA (RAD) tags INTRODUCTION Hybridization, the crossbreeding between individuals of different species, and introgression, the transfer of genes between species mediated primarily by backcrossing, have been the focus of evolutionary studies over many decades (see Anderson, 1949;Arnold, 1992;Rieseberg and Carney, 1998). Hybridization is potentially a creative evolutionary process, allowing genetic novelties to accumulate faster than through mutation alone (Anderson and Hubricht, 1938;Martinsen et al., 2001). This may increase allelic variation at selectively neutral loci, and transfer adaptively important genetic variation, which may increase the fitness of the introgressed lineage (Choler et al., 2004;Martin et al., 2006;Castric et al., 2008;Kim et al., 2008). Moreover, hybridization can have a role in speciation. Hybridization in association with whole-genome duplication (polyploidy) is considered a likely route to speciation, particularly in plants ( Hegarty and Hiscock, 2008). The difference in ploidy levels between the polyploid hybrid and diploid progenitors acts as a strong reproductive barrier (Soltis et al., 2004), although there are examples of introgression across ploidy levels (for example, Senecio; Chapman and Abbott, 2010). Hybrid speciation can also occur without a change i...

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Section: Problems Of the Current Methodologiesmentioning

confidence: 99%

Next-generation hybridization and introgression

2011

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“…The use of multiple data sources is therefore of great benefit in the analysis of species complexes. However, despite many efforts to this end, there are few nuclear markers available that provide genetic resolution at low taxonomic levels (Malhotra et al, 2010;Steele et al, 2008;Willows-Munro et al, 2005). Despite the fact that molecular approaches to taxonomy have dominated the literature in recent years, combined analyses of genetic and morphological datasets remain a highly informative (Bailey et al, 2010;Bart et al, 2010;Sanders et al, 2004Sanders et al, , 2006.…”

Section: The Ovophis Complex Of Asian Pitvipersmentioning

confidence: 99%

Phylogenetic structure and species boundaries in the mountain pitviper Ovophis monticola (Serpentes: Viperidae: Crotalinae) in Asia

Malhotra

Dawson

Guo

et al. 2011

Molecular Phylogenetics and Evolution

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“…Low-copy nuclear genes have a number of advantages over chloroplast markers: they are unlinked [26], possess increased sequence variation [27], and are bi-parentally inherited [23], [25], [28]. Unlinked nuclear genes allow for multiple, independent datasets and, therefore, independent estimates of phylogenetic relationships.…”

Section: Introductionmentioning

confidence: 99%

“…Unlinked nuclear genes allow for multiple, independent datasets and, therefore, independent estimates of phylogenetic relationships. In contrast, the chloroplast and mitochondrial genomes provide single markers due to gene linkage [26], [29]. Furthermore, the higher rate of sequence evolution of low-copy nuclear genes [23], [25] may allow for greater phylogenetic resolution in clades containing slowly evolving or recently diverged taxa.…”

Section: Introductionmentioning

confidence: 99%

Phylogeny of Campanuloideae (Campanulaceae) with Emphasis on the Utility of Nuclear Pentatricopeptide Repeat (PPR) Genes

et al. 2014

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BackgroundThe Campanuloideae (Campanulaceae) are a highly diverse clade of angiosperms found mostly in the Northern Hemisphere, with the highest diversity in temperate areas of the Old World. Chloroplast markers have greatly improved our understanding of this clade but many relationships remain unclear primarily due to low levels of molecular evolution and recent and rapid divergence. Furthermore, focusing solely on maternally inherited markers such as those from the chloroplast genome may obscure processes such as hybridization. In this study we explore the phylogenetic utility of two low-copy nuclear loci from the pentatricopeptide repeat gene family (PPR). Rapidly evolving nuclear loci may provide increased phylogenetic resolution in clades containing recently diverged or closely related taxa. We present results based on both chloroplast and low-copy nuclear loci and discuss the utility of such markers to resolve evolutionary relationships and infer hybridization events within the Campanuloideae clade.ResultsThe inclusion of low-copy nuclear genes into the analyses provides increased phylogenetic resolution in two species-rich clades containing recently diverged taxa. We also obtain support for the placement of two early diverging lineages (Jasione and Musschia-Gadellia clades) that have previously been unresolved. Furthermore, phylogenetic analyses of PPR loci revealed potential hybridization events for a number of taxa (e.g., Campanula pelviformis and Legousia species). These loci offer greater overall topological support than obtained with plastid DNA alone.ConclusionThis study represents the first inclusion of low-copy nuclear genes for phylogenetic reconstruction in Campanuloideae. The two PPR loci were easy to sequence, required no cloning, and the sequence alignments were straightforward across the entire Campanuloideae clade. Although potentially complicated by incomplete lineage sorting, these markers proved useful for understanding the processes of reticulate evolution and resolving relationships at a wide range of phylogenetic levels. Our results stress the importance of including multiple, independent loci in phylogenetic analyses.

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Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids

Cited by 31 publications

References 45 publications

Next-generation hybridization and introgression

Next-generation hybridization and introgression

Phylogenetic structure and species boundaries in the mountain pitviper Ovophis monticola (Serpentes: Viperidae: Crotalinae) in Asia

Phylogeny of Campanuloideae (Campanulaceae) with Emphasis on the Utility of Nuclear Pentatricopeptide Repeat (PPR) Genes

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