Phylogenetic relationships of diploid and polyploid species inLudwigiasect.Isnardia(Onagraceae) based on chloroplast and nuclear DNAs

Abstract

Ludwigia, a genus with rampant interspecific hybridization, is an ideal model for examining the impact of gene introgression and polyploidization on species diversification. We examined the evolution of the Ludwigia sect. Isnardia, which is a polyploid complex (x = 8) of five species distributed in North America. The phylogeny of L. sect. Isnardia was reconstructed based on sequences of cpDNA atpB­rbcL intergenic spacer and nrITS (internal transcribed spacer). Most L. sect. Isnardia species are polyphyletic at both loci, indicating possible recurrent hybridization, based on maximum likelihood trees rooted at L. sect. Microcarpium. A minimum spanning network was also constructed to examine genealogical relationships among haplotypes. In the cpDNA network, haplotypes of tetraploid L. spathulata are nested at the most interior nodes, suggesting a parental genome origin of an extinct diploid or an unsampled extant diploid with a DD cytotype. Allopolyploid L. arcuata contributed its cpDNA to hexaploid L. repens and L. brevipes. ITS haplotypes of diploid L. palustris were clustered with L. spathulata, suggesting L. palustris as the paternal genome donor. Ludwigia brevipes may have arisen via bi3directional hybridization between L. palustris and L. arcuata followed by polyploidy. Genetic and phylogenetic analyses using molecular markers with different inheritance modes provided sufficient insights into the reticulate evolution of the species of L. sect. Isnardia. Interspecific hybridization and polyploidy play a key role in the species evolution in L. sect. Isnardia.

Multi‐locus phylogeny of Ludwigia (Onagraceae): Insights on infra‐ generic relationships and the current classification of the genus

“…Based on his study of floral anatomy, Eyde (1981) was the first to propose that Ludwigia formed a distinct evolutionary lineage sister to the rest of the family, and his hypothesis has been confirmed by subsequent research (Raven, 1988;Hoch & al., 1993), including molecular studies (Bult & Zimmer, 1993;Conti & al., 1993Conti & al., , 1996Levin & al., 2003Levin & al., , 2004Berry & al., 2004;Berger & al., 2016). However, these and other molecular studies (e.g., Hung & al., 2009;Armitage & al., 2013;Ghahramanzadeh & al., 2013) were generally limited in scope, and the present study presents the first comprehensive phylog eny of the genus Ludwigia. Raven (1963) presented the first synopsis of the entire genus Ludwigia, recognizing 17 sections, 11 of them new, and nine from the Old World.…”

Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)

“…In total, three noncoding regions of cpDNA, i.e., trnE-trnT, trnT-trnL spacers, and trnL intron (Baumel et al, 2002;Taberlet et al, 2007;Melotto-Passarin et al, 2008), nad intron of mtDNA (Soria-Hernanz et al, 2008), and fourteen regions of nuclear DNA (thirteen genes and one nrDNA spacer) were amplified and sequenced. Genes AGAMOUS (AG), gamma carbonic anhydrase (CA), chalcone isomerase (CHI), chalcone synthase (CHS), CONSTANS-LIKE 2 (CO2), cryptochrome 2 gene R (Cry2), dihydroflavonol 4-reductase (Dfr), ethylene forming enzyme (EFE), flavanone-3-hydroxylase (F3h), ferulic acid 5-hydroxylase (Fah), LEAFY, PISTILLATA (PIS), Feregulated transporter-like protein (ZIP) and nuclear ribosomal internal spacers (nrITS) (El-Assal et al, 2001;Olsen et al, 2004;Ramos-Onsins et al, 2004;Masuzaki et al, 2006;Flowers et al, 2009;Hung et al, 2009). The annotated A. thaliana genome from The Arabidopsis Information Resource database [TAIR; (Rhee et al, 2003)] was used to design primers to amplify the targeted regions.…”

“…Over the past decades, botanists generated numerous phylogenetic hypotheses based on molecular data with organelle noncoding spacers or nuclear DNA introns (Slowinski and Page, 1999;Savolainen et al, 2000;Chiang et al, 2006;Hung et al, 2009). Besides, multilocus analyses that assess the genetic divergence within and between sister species also provide genealogical information for inferring the phylogeography (Stadler et al, 2005;Wright and Gaut, 2005;Zhu et al, 2007;Zou et al, 2008;Wang et al, 2010).…”

Predicting Plastid Marker Variation: Can Complete Plastid Genomes from Closely Related Species Help?

“…In plant systematics, NCPs have become one of the most commonly used tools in elucidating species relationships, especially so in groups with complex evolutionary histories involving hybridisation, polyploidy and/or introgression, where plastid gene trees are used as baseline data for resolving true species trees due to their uniparental inheritance [11]–[13].…”