Genetic variation and population differentiation of Michelia formosana (Magnoliaceae) based on cpDNA variation and RAPD fingerprints: relevance to post-Pleistocene recolonization

Abstract

We used sequence variation of the atpB- rbcL intergenic spacer of cpDNA and nested clade analysis to assess the phylogeographic pattern of Michelia formosana, a species restricted to Taiwan and the Ryukyus. In total, 31 haplotypes were identified and clustered into four major chlorotypes. Genetic composition of nearly all populations was heterogeneous and paraphyletic phylogenetically. Although the apportionment of cpDNA variation hardly revealed a geographic pattern due to the coancestry of dominant sequences, some chlorotypes were restrictedly distributed. According to the patterns of clade dispersion and displacement, a reconstructed minimum spanning network revealed that historical events of past fragmentation and range expansion, associated with glaciation, may have shaped the phylogeographic patterns of M. formosana. Four possible refugia were identified: the Iriomote and Ishigaki Islands (the southern Ryukyus), Wulai (northern Taiwan), and Nanjen (southern Taiwan), on the basis of the interior positions of their haplotypes in the network and the high level of nucleotide diversity. Given insufficient time for coalescence at the cpDNA locus since the late Pleistocene recolonization, lineage sorting led to low levels of genetic differentiation among populations. In contrast, hierarchical examination of the random amplified polymorphic DNA (RAPD) data scored from six populations across three geographical regions, using an analysis of molecular variance (AMOVA), indicated high genetic differentiation both among populations (Phi(ST) = 0.471) and among regions (Phi(CT) = 0.368). An unweighted pair group method with arithmetic mean (UPGMA) tree of the RAPD fingerprints revealed that populations of two offshore islands of eastern Taiwan ( M. formosana var. kotoensis) were clustered with geographically remote populations of the Ryukyus instead of those in southern Taiwan, suggesting some historical division due to geographic barriers of the central mountain range. In contrast to the paraphyly of the nearly neutral cpDNA alleles, differentiated RAPDs may have experienced diversifying selection.

Population genetic structure and phylogeographical pattern of a relict tree fern, Alsophila spinulosa (Cyatheaceae), inferred from cpDNA atpB?rbcL intergenic spacers

“…Moreover, as a noncoding region, the atpB-rbcL spacer of cpDNA has relatively few functional constraints, mutations to some extent would have been retained within each lineage (Chiang and Schaal 1999). The same evolutionary feature of cpDNA spacers was previously reported in many tree species, such as oak, Fagus, and Michelia formosana (Demesure et al 1996;Petit et al 1997;Lu et al 2002).…”

“…Sequence length varied from 724 bp to 731 bp, with a consensus length of 739 bp; 68 sites (9.2%) were variable. Nucleotides A and T were shown to be common in the chloroplast sequence, with contents between 63.17% and 63.95%, which is consistent with the nucleotide composition of most noncoding regions and pseudogenes (Li 1997;Lu et al 2002). In total, 19 haplotypes of cpDNA atpB-rbcL spacers were identified in A. spinulosa.…”

“…Phylogeographical studies can also shed light on formation, distribution, and expansion of populations during geological processes (Hewitt 1996;Larena et al 2002). Recently, cpDNA noncoding spacers have been frequently applied to survey population genetic variation and phylogeography of plants Huang et al 2001;Chiang et al 2001;Trewick et al 2002;Lu et al 2002;Hwang et al 2003). Their uniparental inheritance and nearly neutral, fast evolution are well suited to reconstruct intraspecific phylogeographical patterns (Ferris et al 1998).…”

Genetic variation of Ginkgo biloba L. (Ginkgoaceae) based on cpDNA PCR-RFLPs: inference of glacial refugia

“…In contrast to intense investigations on plants of Europe and northern America (Hewitt, 2000;Shen et al, 2002), understanding of the effects of past climatic events on population structure and phylogeny of species in Asia is relatively limited (Szmidt and Wang, 1993;Wang and Szmidt, 1994;Szmidt et al, 1996;Chen et al, 1997;Tomaru et al, 1997;Lin, 2001;Huang et al, 2002;Lu et al, 2002;Okaura and Harada, 2002;Aoki et al, 2004). The Eurasian ice sheets covered millions of square kilometers of the continent in the late Pleistocene period (Svendsen et al, 1999).…”

A SCAR marker for the analysis of chloroplast DNA from different cultivars of Cornus officinalis

“…A 25-μL reaction system was chosen to optimize the RAPD reaction conditions based on previous work (Comes and Abbott et al, 2000;Esselman et al, 2000;Bautista et al, 2001;Lu et al, 2002;Collins et al, 2003;Uzonur et al, 2012;Xin et al, 2014).…”