Evolution of the pili nut genus (Canarium L., Burseraceae) and its cultivated species

Abstract

Seeds from species of Canarium L. (Burseraceae) have been recommended as a potential nut crop for global trade that, if adopted, would be the first 'new' nut commodity since the introduction of the Macadamia nut in the early 20th century. The present study addresses several knowledge gaps about the evolutionary biology of Canarium species in order to explore their phylogeny and cultivation history in greater detail. The phylogeny of select Canarium species (16 spp.) from the three taxonomic sections of the genus was reconstructed using DNA sequence data from seven regions and included cultivated species C. album (Lour.) Raeusch., C. decumanum Gaertn., C. harveyi Seem., C. indicum L., C. ovatum Engl., C. tramdenum C.D. Dai et Yakovlev, and C. vulgare Leenh.. Sequence data from the nuclear genome (rDNA external transcribed spacer (ETS), the third intron of nitrate reductase (NIA-i3)) and the chloroplast genome (rbcL, rps16 intron, psbA-trnH spacer, trnL intron and trnL-F spacer) were analyzed using parsimony and Bayesian inference. Results indicate that Canarium comprises at least two distantly related evolutionary lineages within its tribe, desirable fruit characteristics of cultivated and wild-harvested edible species have evolved multiple times, and autopolyploidization rather than allopolyploidization may have been associated with speciation in Canarium sensu stricto. The markers ETS, NIA-i3, rps16 intron, and psbAtrnH spacer will provide the most informative variation for future expanded studies of Canarium phylogeny, although detailed morphological study and taxonomic revision of the genus will be necessary as well.

Phylogeny of Acronychia (Rutaceae) and First Insights into Its Historical Biogeography and the Evolution of Fruit Characters

“…The amplification program used for ETS, ITS, psbA-trnH and trnL-trnF consisted of 5 minutes of initial denaturation at 95°C; 36 cycles of 1 minute denaturation at 95°C, 40 seconds of annealing at 53–54°C, an elongation of 40 seconds to 1 minute (depending on the length of the target sequence) at 72°C; and a final elongation for 5 minutes. A touchdown PCR program was used for the amplification of NIAi3 [34]. …”

Molecular phylogenetic analysis of Hawaiian Rutaceae (Melicope,PlatydesmaandZanthoxylum) and their different colonization patterns

“…For the Melicope / Platydesma data set, four nuclear markers [ITS, external transcribed spacer (ETS), AT103 and NIAi3 ] and two plastid markers ( trnL–trnF and psbA–trnH ) were amplified by the polymerase chain reaction (PCR) using a standard protocol (see Appelhans et al ., ) with primer annealing temperatures of 51–55 °C for all markers except NIAi3. Amplification of NIAi3 followed a touchdown protocol (Weeks, ). Universal primers were used for amplification: ITS (ITS2, ITS3, ITS4, ITS5a; White et al ., ; Stanford, Harden & Parks, ); ETS (Bur1, 18S‐IGS; Baldwin & Markos, ; Becerra, ); AT103 (At103 forward, At103 reverse; Li et al ., ); NIAi3 (NIA3F, NIA3R; Howarth & Baum, ); trnL–trnF (c, d, e, f; Taberlet et al ., ); and psbA–trnH (psbA, trnH; Sang, Crawford & Stuessy, ).…”

Diversification in species complexes: Tests of species origin and delimitation in the Bursera simaruba clade of tropical trees (Burseraceae)

“…Differences between the sequences are comparable to those found between alleles in Scaevola (Howarth and Baum, 2005), which, together with the absence of stop codons, would suggest that the versions are alleles rather than pseudogenes. At the same time, duplications of NIAi3 have been found in the tribe Canarieae within Burseraceae (Weeks, 2009), and in other families (Hamman-Khalifa et al, 2007;Yi et al, 2008), although the sequences found in B. simaruba did not correspond to those in Canarieae. Whether they represent alleles or paralogues with potential associated lineage sorting, in the genus these sequences seem to be restricted to B. simaruba (J.A.…”