Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus)

Abstract

Botanists have long recognised interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterised and the complex genomic signals resulting from the combination of vertical and horizontal gene transmission may confound phylogenetic inference and obscure our ability to accurately infer the deep evolutionary history of oaks.Using anchored enrichment, we obtained a phylogenomic dataset consisting of hundreds of single-copy nuclear loci. Concatenation, species-tree and network analyses were carried out in an attempt to uncover the genomic signal of ancient introgression and infer the divergent phylogenetic topology for the white oak clade. Locus and site-level likelihood comparisons were then conducted to further explore the introgressed signal within our dataset.Historical, intersectional gene flow is suggested to have occurred between an ancestor of the Eurasian Roburoid lineage and Quercus pontica and North American Dumosae and Prinoideae lineages.Despite extensive time past, our approach proved successful in detecting the genomic signature of ancient introgression. Our results, however, highlight the importance of sampling and the use of a plurality of analytical tools and methods to sufficiently explore genomic datasets, uncover this signal, and accurately infer evolutionary history.

Genomic landscape of the global oak phylogeny

“…,” contrasted with “white oaks s.str. ” for just section Quercus ) was observed to be at odds with previous close studies (Crowl et al ., In review; McVay et al ., 2017b,a; Hipp et al ., 2018) that have shown the topology of the white oaks s.l. to be sensitive to taxon and locus sampling.…”

“…We utilized neighbor-net (Bryant & Moulton, 2004) to visualize overall patterns of molecular genetic diversity. Likelihood-based methods (e.g., Solís-Lemus & Ané, 2016; Solís-Lemus et al ., 2017; Wen et al ., 2018; Zhang et al ., 2018) that we have utilized on smaller oak datasets (Crowl et al ., In review; Eaton et al ., 2015; Hauser et al ., 2017; McVay et al ., 2017b,a) proved computationally intractable for the current dataset. Consequently, we utilized a splits network inferred with SPLITSTREE v. 14.3 (Huson & Bryant, 2006) based on the maximum-likelihood (GTR+gamma) pairwise distance matrix estimated in RAxML and the same datasets utilized for the singletons tree.…”

“…Oaks ( Quercus L., Fagaceae) are no exception (Hipp, 2018), and in fact the genus is rife with case-studies in localized gene flow (e.g. Hardin, 1975; Whittemore & Schaal, 1991; McVay et al ., 2017a; Kim et al ., 2018), and ancient introgression (Crowl et al ., In review; McVay et al ., 2017b; Kim et al ., 2018). Oaks have in fact been held up as a paradigmatic syngameon (Hardin, 1975; Van Valen, 1976; Dodd & Afzal-Rafii, 2004; Cannon & Scher, 2017; Boecklen, 2017), a system of interbreeding species in which incomplete reproductive isolation may facilitate adaptive gene flow and species migration (Petit et al ., 2003; Dodd & Afzal-Rafii, 2004).…”

Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

“…In this paper we have explored several common sources of disproportionate influence, however, with greater data dissection researchers continue to discover more (e.g., varying signal across chromosomes (Crowl et al 2019;Li et al 2019), or the influence of taxon sampling Shen et al 2018) and individual sites (Shen et al 2017)). One approach to handling these is to avoid incorporating likelihood score as is done in some coalescent-based summary methods.…”

A snapshot of progenitor-derivative speciation in action inIberodes(Boraginaceae)

“…The advent of inexpensive phylogenomic approaches in the last decade have made the genetic side of testing recent speciation scenarios tractable (Mc Cormack et al , 2013; Mc Vay et al , 2017a). High Throughput Sequencing (HTS) approaches help to analyze loci sampled from the entire genome in reconstructing species trees (Fernández-Mazuecos et al , 2018) and speciation in the face of gene flow (Leroy et al , 2017; Folk et al , 2018; Crowl et al , 2019). In particular, restriction-site associated DNA (RAD-seq) is considerably contributing to our understanding of recent evolutionary processes, being especially helpful for non-model organisms since a reference genome is not needed for accurate phylogenetic inference (e.g.…”