Reticulate evolution and incomplete lineage sorting among the ponderosa pines

Willyard, Ann; Cronn, Richard; Liston, Aaron

doi:10.1016/j.ympev.2009.02.011

Cited by 120 publications

(124 citation statements)

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“…Wolbachia infections can lead to divergent mitochondrial lineages within insect species (Smith et al 2012;Whitworth et al 2007), but this bacterial endoparasite has not yet been found in Chironomidae. Although other endosymbionts might cause similar patterns, we are not aware of such documentation in Chironomidae and regard incomplete lineage sorting (Ballard & Whitlock 2004;Heckman et al 2007;Willyard et al 2009) a better explanation for the observed differences in DNA barcodes.…”

Section: Dna Barcodes and Morphospeciesmentioning

confidence: 86%

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

Stur

Ekrem

2018

Insect Syst. Evol.

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For over a decade, DNA barcoding has proven an effective modern tool in taxonomy, evolutionary biology and biodiversity research. Many new species have been discovered and described with DNA barcodes as part of their diagnostic features. Using DNA barcodes, we uncovered a number of potential species within the Tanytarsus curticornis and Tanytarsus heusdensis species complexes (Diptera: Chironomidae) and detected morphological differences a posteriori that support the description of new species. Unusually large intraspecific divergence in COI p-distance (up to 10%) was observed for two species complexes. In total, eight species new to science are described and figured: T. adustus sp. n., T. heberti sp. n., T. madeiraensis sp. n., T. pseudoheusdensis sp. n., T. songi sp. n., T. thomasi sp. n., T. tongmuensis sp. n. and T. wangi sp. n.. Tanytarsus reei and T. tamaoctavus are redescribed, and T. tusimatneous is listed as a new junior synonym of T. tamaduodecimus. The diagnostic characters of the remaining species of the complexes are discussed. Keys to males and pupae are given.

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Section: Dna Barcodes and Morphospeciesmentioning

confidence: 86%

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

Stur

Ekrem

2018

Insect Syst. Evol.

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“…Where alternate genealogies are supported for tightly linked genes, this can be used to infer the introgression of chromosome blocks (Hobolth et al, 2007). Interpreting phylogenetic reconstructions of formerly hybridizing taxa is challenging (Willyard et al, 2009) as reticulation may obscure the pattern of bifurcation, and the sequence evolution of these species will more closely fit a net-like rather than a tree-like pattern over time. Therefore, the aim of these studies is to identify non-recombinant sections of DNA for phylogenetic comparisons between species, and homoploid hybrids have successfully been detected using phylogenetic reconstructions incorporating intragenic recombination (for example, in tobacco plants, Kelly et al, 2010;soft corals, Mcfadden and Hutchinson, 2004).…”

Section: Phylogenetic Approachmentioning

confidence: 99%

“…The greatest theoretical challenge posed by genetic introgression studies is proving that the observed pattern of shared alleles between species is the product of recent introgression, as opposed to noncontemporary process such as ancient introgression or the incomplete lineage sorting of genes after speciation (deep coalescence; Pollard et al, 2006;Willyard et al, 2009), as shown in Figure 1. The genetic signature of incomplete lineage sorting is the same as ancient introgression soon after speciation, so we treat these together, and contrast this with recent introgression (introgression here).…”

Section: Proving Introgression As Opposed To Incomplete Lineage Sortingmentioning

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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“…While the exclusive use of organellar genes to construct species trees is misleading in the case of chloroplast capture, their uniparental inheritance can be helpful in conjunction with nuclear genes to infer the direction, as well as the relative timing, of introgression, (e.g. Bossu and Near, 2009;Dunbar-Co et al, 2008;Howarth and Baum, 2005;Lindqvist et al, 2003;Willyard et al, 2009). …”

Section: Reticulate Evolutionmentioning

confidence: 99%