行政院國家科學委員會補助專題研究計畫成果報告
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※ 烏心石舅的演化與冰河歷史的相關研究 ※
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計畫類別：□個別型計畫 □整合型計畫 計畫編號： NSC89-2311-B-006-008
執行期間： 89 年 8 月 1 日至 90 年 7 月 31 日 計畫主持人：蔣鎮宇
共同主持人：
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□赴國外出差或研習心得報告一份
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□國際合作研究計畫國外研究報告書一份
執行單位：國立成功大學生物學系
中 華 民 國 九十 年 十 月三十 日
行政院國家科學委員會專題研究計畫成果報告 國科會專題研究計畫成果報告撰寫格式說明
Pr epar ation of NSC Pr oject Repor ts 計畫編號：NSC89-2311-B-006-008 執行期限：89 年 8 月 1 日至 90 年 7 月 31 日 主持人：蔣鎮宇
共同主持人：
計畫參與人員：
執行機構及單位名稱：國立成功大學生物學系 一、中文摘要
本 研 究 藉 由 葉 綠 體 DNA atpB-rbcL intergenic spacer 及粒線體重建台灣特有屬 烏 心 石 舅 之 地 理 親 緣 歷 史 , 因 lineage sorting 效應各族群之 monophyly 並未顯 現, 相對地, 二胞器 DNA 之分子親緣亦不 一致, 此遺傳變異分布型式主要受冰河歷 史影響
關鍵詞：親緣地理、烏心石舅、葉綠體 DNA、粒線體 DNA、族群遺傳結構 Abstr act
Phylogegraphic pattern of Magnolia
kachirachirai, an endemic species with two remaining populations in Taiwan, was investigated based on genetic variability and phylogeny of the atpB-rbcL noncoding spacer of cpDNA and the rDNA ITS of mtDNA was investigated. High levels of genetic variation at both organelle loci, due to frequent intramolecular recombination, and low levels of genetic differentiation were detected in the relict gymnosperm. The apportionment of genetic variation within and between populations agreed with a migrant-pool model, which describes a migratory pattern with colonists recruited from a random sample of earlier existing populations. Phylogenies obtained from cp- and mtDNA were discordant according to neighbor-joining analyses. A total of four chlorotypes (clades I-IV) and five mitotypes (clades A-E) were identified based on minimum spanning networks of each locus.
Significant linkage disequilibrium in mitotype-chlorotype associations excluded the possibility of the recurrent homoplasious mutations as the major force causing
phylogenetic inconsistency. The most
abundant chlorotype I was associated with all mitotypes and the most abundant mitotype C with all chlorotypes; no combinations of rare mitotypes with rare chlorotypes were found.
According to nested clade analyses, such nonrandom associations may be ascribed to relative ages among alleles associated with the geological history that the species evolved through. Nested in networks as interior nodes coupled with wide geographic distribution, the most dominant cytotypes of CI and EI may represent ancestral haplotypes of Magnolia kachirachirai with a possible long existence prior to the Pleistocene glacial maximum. In contrast, rare chlorotypes and mitotypes with restricted and patchy
distribution may have relatively recent origins. Newly evolved genetic elements of mtDNA, with a low frequency, were likely to be associated with the dominant chlorotype, and vice versa, resulting in the nonrandom mitotype-chlorotype associations. Paraphyly of CI and EI cytotypes, leading to the low level of genetic differentiation between populations, indicated a short period for isolation, which allowed low possibilities of the attainment of coalescence at polymorphic ancestral alleles.
Keywor ds: phylogeography、Magnolia kachirachirai 、chloroplast DNA、glaciation 、population genetic structure
二、緣由與目的
In this study, we investigated the
apportionment and levels of genetic variation among populations of Magnolia
kachirachirai, a genus endemic to Taiwan.
Molecular markers of the atpB-rbcL
intergenic spacer of cpDNA and the internal transcribed spacer (ITS) of ribosomal DNA of the mitochondrial genome were used to estimate the phylogeographic pattern of Magnolia kachirachirai. Although
chloroplasts are paternally inherited in a few gymnosperms (Rebound & Zeyl 1994), according to experimental pollination, maternal inheritance of atpB-rbcL spacer of Magnolia kachirachirai was determined.
Phylogenetic contradiction between nuclear and organelle genomes due to different inheritance modes have been
frequently encountered (Moore 1995). On the contrary, as being maternally inherited, both chloroplasts and mitochondrias were thought to remain associated and behave as if they are completely linked (Schnabel & Asmussen 1989). Consistent phylogenetic patterns of cpDNA and mtDNA are thus expected (cf.
Dumolin-Lapégue et al. 1998). Despite the phylogenetic consistency occurred frequently in plants [e.g., Brassica (Nugent & Palmer 1988), and cocoa (Laurent et al. 1993)], exceptions were also met (e.g., rice, Ishii et al. 1993; coffee, Berthou et al. 1983; and oaks, Dumolin- Lapégue et al. 1998).
Evolutionary forces, such as lineage sorting effect (Hoelzer et al. 1998), and frequent recurrent mutations (Desplanque et al. 2000), can result in systematic inconsistency and thus lead to wide variance of Fst values among loci and a loose correlation between Fst and Nm as well (cf. Bossart & Prowell 1998; Whitlock & McCauley 1999).
Difficulties in interpreting phylogeography and population structure will be thus
inevitably encountered. In other words, when discrepant estimates obtained from two or more loci, these estimates are not necessarily indicatives of recurrent gene flow. Explicit analysis of associations between alleles of different loci coupled with nested clade analysis (cf. Chiang 2000; Schaal & Olsen 2000) will be required to clarify historical and recurrent events.
In this study, we are interested in looking into the genetic variability of chloroplast and mitochondrial loci and the phylogenetic consistency between organelle
lineages in Magnolia kachirachirai. Usually genetic variation of relict and endangered species tends to become depauperate because of their small effective population size (e.g., Saxifraga cernua, Bauert et al., 1998). The objectives of the present study are to investigate the followings: 1) Are populations of Magnolia kachirachirai genetically differentiated due to limited ongoing gene flow? 2) Should the lineage of cpDNA locus be consistent with that of mtDNA locus or should alleles of the
physically unlinked loci associate randomly?
3) What evolutionary agents will cause the lineage discordance? And 4) How is the apportionment of genetic variation associated with geological events?
三、研究方法
Two populations of Magnolia kachirachirai were surveyed. In total, 102 individuals were sampled randomly. Young and healthy leaves were collected in the field, rinsed with tap water and dried in the silica gel. All samples were stored at -70°C until they were
processed.
DNA extr action, pr imer design, and PCR Leaf tissue or embryo of the above materials was ground to powder in liquid nitrogen and stored in a -70℃ freezer.
Genomic DNA was extracted from the powdered tissue following CTAB procedures (Murray & Thompson 1980). The noncoding spacer between rbcL and atpB genes of the cpDNA and the rDNA internal transcribed spacer of mtDNA were amplified and sequenced. PCR amplification was carried out in a volume of 100 µl reaction using 10 ng of template DNA, 10 µl of 10X reaction buffer, 10 µl MgCl2 (25 mM), 10 µl dNTP mix (8 mM), 10 pmole of each primer, 10 µl of 10% NP-40, and 2 U of Taq polymerase (Promega, Madison, USA). The reaction was programmed on a MJ Thermal Cycler (PTC 100) as one cycle of denaturation at 95°C for 4 min, 30 cycles of 45s denaturation at 92°C, 1 min 15s annealing at 52°C, and 1 min 30s extension at 72°C, followed by 10 min extension at 72°C. Template DNA was denatured with reaction buffer, MgCl2,
NP-40 and ddH2O for 4 mins (first cycle), and cooled on ice immediately. A pair of universal primers for cpDNA atpB-rbcL spacer (Chiang et al. 1998) or mtDNA rITS (Chao et al. 1984), dNTP and Taq
polymerase were added to the above ice-cold mix. Reaction was restarted at the first annealing at 52°C.
T-A cloning and nucleotide sequencing PCR products were purified by
electrophoresis in 1.0 % agarose gel using 1 X TAE buffer. The gel was stained with ethidium bromide and the desired DNA band was cut and eluted using agarose gel
purification (QIAGEN). Purified DNAs were ligated to a pGEM-T easy vector (Promega).
Plasmid DNAs were selected randomly with five clones and purified using plasmid mini kit (QIAGEN). Purified plasmid DNAs were sequenced in both directions by standard methods of the Taq dye deoxy terminator cycle sequencing kit (Perkin Elmer) on an Applied Biosystems Model 377A automated sequencer (Applied Biosystems). Primers for sequence determination were T7-promoter and SP6-promoter located on p-GEM-T easy Vector termination site.
Sequence alignments and phylogenetic analyses
Nucleotide sequences were registered to the EMBL with bulk accession numbers of ds 38139.dat for rDNA ITS of mtDNA and ds 38133.dat for atpB-rbcL noncoding spacer of cpDNA. Nucleotide sequences were aligned with the program Genetics Computer Group (GCG) Wisconsin Package (Version 10.0, Madison, Wisconsin) and later adjusted visually.
Neighbor-joining (NJ) analysis, calculating Kimura's (1980) two-parameter distance, was performed using software Treecon for Windows (version 1.3 b, Van de Peer & De-Wachter 1997).
Indels were treated as the fifth character.
Confidence of the clades reconstructed was tested by bootstrapping (Felsenstein 1985) with 1,000 replicates using unweighted characters.
The nodes with bootstrap values greater than 0.70, as a rule of thumb, are significantly
supported with ≥ 95% probability (Hillis & Bull 1993). The number of mutations between DNA genotypes in a pairwise comparisons, which were calculated using MEGA (Kumar et al. 1993),
was used to construct a minimum spanning network with the aid of the MINSPNET (Excoffier & Smouse 1994).
Population genetic analysis of the cpDNA and mtDNA sequence var iation
Levels of inter- and intra-population genetic diversity were quantified by indices of haplotype diversity (h) (Nei & Tajima 1983) and estimates of nucleotide divergence (dij) (Jukes & Cantor 1969) using DnaSP (Version 3.0, Rozas & Rozas 1999). Patterns of geographical subdivision and gene flow were estimated also hierarchically with the aid of DnaSP. Gene flow within and among regions (populations) was approximated as Nm, the number of female migrants per generation between populations, and was estimated using the expression FST = 1/ (1 + 2 Nm) where N is the female elective
population size and m is the female migration rate (Slatkin 1993).
Genetic recombination among organelle sequences was detected using partial
likelihood assessed through optimization (PLATO) (Grassly & Holmes 1997), a program developed for detecting gene regions that do not fit with a “global”
phylogenetic topology based on Monte Carol simulations. Using maximum-likelihood phylogeny, the likelihood for each site of a sequence can be calculated independently.
四、結果與討論
Nucleotide and haplotype diversity:
At both loci, no within-individual variation was detected. The rITS region of mtDNA in Magnolia kachirachirai was amplified and sequenced with the length varying from 482 bp to 536 bp. The mtDNA sequences were aligned with a consensus length of 538 bp. A+T (56.4%) was rich in the DNA fragment, which agreed with the nucleotide composition of most noncoding regions (cf. Li 1997). Length of the
atpB-rbcL spacer of cpDNA varied from 762 bp to 830 bp. A+T (63.6%) was also rich in this noncoding spacer. 97 haplotypes and 55 haplotypes were determined in cpDNA and mtDNA, respectively.
Association between cpDNA and mtDNA lineages and population differentiation:
A neighbor-joining (NJ) tree was
recovered based on the nucleotide sequence variation of the atpB-rbcL noncoding spacer of cpDNA. In order to unravel the phylogeny of the haplotypes in Magnolia kachirachirai, a minimum spanning network was
constructed by linking the sequences in a hierarchical manner (cf. Chiang & Schaal 1999) based on the mutational changes between haplotypes. After linking the affined haplotypes, a higher clade was grouped.
Closely related clades were linked further to each other and formed a network (Fig. 3).
According to NJ tree and the network, four major clades (chlorotypes) were identified in this cpDNA gene tree (Fig. 2): Clade I of 92 sequences, Clade II, Clade III, and Clade IV.
Most clades were significantly supported with bootstrap values more than 0.70. Closer relationship between Clades I and IV as well as between Clades II and III was suggested.
A NJ tree and a spanning network were recovered based on the nucleotide variation of the ribosomal ITS region of mitochondrial DNA (Figs. 4 & 5). Three major clades (mitotypes) were identified: Clade A
(bootstrap value = 100%), Clade B (bootstrap value = 100%), and Clade C (bootstrap value
= 100%). According to the links suggested by MIN-SP-NET analysis, two additional types were identified, i.e., D and E (Fig. 5). The mitotype C was nested in the network as an interior node, which happened to be most dominant in number (89.21%) over other mitotypes (A, 2.94%; B, 1.96%; D, 1.96%;
and E, 3.92%). 70 substitutions and a 53 bp deletion characterized the mitotype D; while 18 substitutions characterized the mitotype E.
Likewise, 66 substitutions and a 44 bp deletion distinguished mitotype A from B.
Within the mitotype C, all sequences were linked to a most dominant haplotype (n = 12), which was nested in the group as the most interior node. All mitotypes were restricted to the larger populations, except for types C and E.
Low consistency was found between NJ trees of cpDNA and mtDNA. Two of the major clades, A and B (Fig. 4), identified in the mtDNA tree did not correspond to any clade of the cpDNA tree (Fig. 2). The topology of the haplotypes within the most
dominant type C of the mtDNA was not congruent with the dominant clade I of the cpDNA either. Individuals of the same cpDNA haplotype usually had different mtDNA sequences.
Associations between cpDNA and mtDNA haplotypes were nonrandom (χ2 = 12.36, p = 0.00044). Eight cpDNA-mtDNA cytotypes were observed. The most abundant chlorotype I was associated with all
mitotypes and the most abundant mitotype C with all chlorotypes; no combinations of rare mitotypes with rare chlorotypes were found.
Spatially most cytotypes had a patchy
structure, as found in European oaks (Petit et al. 1997), except for the types CI and EI, which scattered in both populations. The cytotype CI (81.4%) was predominant over all others (AI, 2.9 %; BI 2.0 %; DI, 2.0 %; EI, 3.9 %; CII, 2.0%; CIII 2.9%; and CIV 2.9%) (Fig. 1). Apparently, according to minimum spanning networks and cytotype associations, lineage of cpDNA was disassociated with that of mtDNA.
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