Phylogenetic relationships in Lupinus (Fabaceae: Papilionoideae) based on internal transcribed spacer sequences (ITS) of nuclear ribosomal DNA

Abstract

Internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA from 44 taxa of the genus Lupinus and five outgroup taxa were used for phylogenetic analysis. Lupinus appears as a strongly supported monophyletic genus, which is unambiguously part of the Genisteae. The lupines are distributed into five main clades in general accordance with their geographical origin. In the Old World, almost all the recognized taxonomic units are well resolved. The ITS data reveal an unexpectedly close relationship between the diverse sections Angustifoli and Lutei. The ITS results suggest a geographical division between the western New World lupines and the eastern ones. They also indicate the presence of some moderately to strongly supported groups of taxa, such as the Microcarpi-Pusilli group, the L. spariflorus-L. arizonicus group, the L. mexicanus-L. elegans group in the western New World, and the notable L. multiflorus-L. paraguariensis group in the eastern New World. The latter group strongly suggests that the eastern South American compound- and simple-leaved perennial lupines derive from a common ancestor. However, apart from some exceptions, relationships within the genus still remain largely unresolved based on ITS data. The lack of resolution at the base of the genus is suggestive of a rapid initial radiation of the lupines subsequent to the dispersal of their common ancestor. Relative rate tests demonstrate the presence of rate heterogeneity of ITS sequences within Lupinus. In many pairwise comparisons between taxa, substitution rate inequalities are correlated with the habit (annual, perennial), suggesting some role for the generation time effects in the evolutionary history of lupines.

Island radiation on a continental scale: Exceptional rates of plant diversification after uplift of the Andes

“…One hundred forty-eight accessions representing 98 species covering previously recognized Lupinus clades (24), the geographic range, and eight outgroup species representing five genera from tribe Genisteae were sampled. To test the monophyly of the Andean species, 53 accessions representing 36 species were sampled spanning the range of life forms (Fig.…”

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

“…The vast range of morphological variation (from tiny herbs to large trees) and ecological adaptation (from coastal sand dunes to montane forests) pose challenges for resolving phylogenetic relationships using taxonomic methods (Drummond et al, 2012). Comparisons of nuclear and chloroplast DNA sequences (Ainouche and Bayer, 1999;Wink and Mohamed, 2003;Ainouche et al, 2004;Ree et al, 2004;Drummond and Hamilton, 2007;Drummond, 2008;Eastwood et al, 2008b;Drummond et al, 2012) have made some progress toward resolving Lupinus phylogeny, but ambiguities still remain. Current efforts are underway to sample large gene sets obtained by whole transcriptome sequencing across New World Lupinus (C. Hughes, G. Atchison, D. Filatov, personal communication), which should definitively answer these remaining questions.…”

“…Chromosome numbers range from 2n = 32 to 2n = 52, and nuclear DNA contents range from 2C = 0.97 pg to 2C = 2.44 pg (Naganowska et al, 2003), although rare autopolyploids have been observed with 2n = 100 and 2n = 104 chromosomes (Ainouche and Bayer, 1999). The most strongly supported clade within the Old World lupins is the rough-seeded type, with four less well-defined smooth-seeded sections recognized (Ainouche and Bayer, 1999). Three smooth-seeded Old World species have been used regularly in agriculture: L. albus, as long ago as 2,000 BC; and L. angustifolius and L. luteus by the 19th century (Gladstone, 1970).…”

“…Old World lupins comprise 13 annual species and include rough-seeded and smooth-seeded types distributed around the Mediterranean region and North Africa (Mahé et al, 2011). Chromosome numbers range from 2n = 32 to 2n = 52, and nuclear DNA contents range from 2C = 0.97 pg to 2C = 2.44 pg (Naganowska et al, 2003), although rare autopolyploids have been observed with 2n = 100 and 2n = 104 chromosomes (Ainouche and Bayer, 1999). The most strongly supported clade within the Old World lupins is the rough-seeded type, with four less well-defined smooth-seeded sections recognized (Ainouche and Bayer, 1999).…”

“…The Genisteae tribe is currently considered to include 618 species in 25 genera (Cardoso et al, 2013), and its diversity is centered in the Mediterranean region and in the Canary Islands (Cristofolini, 1997; Cristofolini and Chiapella, 1984). Lupinus is the largest Genisteae genus, comprising 267 species, and appears to be monophyletic in origin (Ainouche and Bayer, 1999;Drummond et al, 2012). Chromosome numbers range between 2n = 24 to 2n = 52, and there are multiple lines of evidence showing that at least one polyploidy event has taken place since the divergence of Genisteae from other Papilionoid legumes (Wolko and Weeden, 1989;Gupta et al, 1996;Naganowska et al, 2003;Nelson et al, 2006;Parra-Gonzalez et al, 2012;Yang et al, 2013b;Kroc et al, 2014).…”