cpDNA Data Research Articles

Less Pollen-Mediated Gene Flow for More Signatures of Glacial Lineages: Congruent Evidence from Balsam Fir cpDNA and mtDNA for Multiple Refugia in Eastern and Central North America

The phylogeographic structure and postglacial history of balsam fir (Abies balsamea), a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) markers. Genetic structure among 107 populations (mtDNA data) and 75 populations (cpDNA data) was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only), but also for cpDNA (dispersed by seeds and pollen), indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.

Molecular phylogeny revealed distinct origin of the Y and St genome in Elymus longearistatus (Triticeae: Poaceae)

Cytogenetic data has indicated the presence of St and Y genome in Elymus longearistatus (Boiss.) Tzvelev. However, a random amplified polymorphic DNA (RAPD) based sequence tagged site (STS) study suggested one accession of Pseudoroegneria spicata (Pursh) Á Löve (St genome) as a potential Y genome donor candidate in tetraploid E. longearistatus. To examine the origin of Y genome in and the phylogeny of tetraploid E. longearistatus, sequences of cpDNA (RPS16 and TrnD/T intergenic spacer) and single copy nuclear genes (EF-G and HTL) from eight accessions of E. longearistatus, six StY genomic Elymus species and 62 accessions of diploid in Triticeae were analyzed. The cpDNA data suggested that P. stipifolia (St) is the most likely maternal donor of these six Iranian accessions of E. longearistatus, although P. strigosa could not be excluded. Two nuclear gene data convincingly showed that tetraploid E. longearistatus contains two distinct genomes, St and Y genome. The phylogenetic analyses from both the EF-G and HTL rejected the previous suggestion that accession PI232134 of Pseudoroegneria spicata (Pursh) Á Löve (St genome) was potential Y genome donor to E. longearistatus. Phylogenetic analyses revealed a separation of the Y genome sequences in Iranian accessions of E. longearistatus from the sequences in the Pakistan accession, indicating that geographic isolation might influence the evolution of the Y genome in E. longearistatus.

Molecular and morphological data reveal hybrid origin of wild Prunus yedoensis (Rosaceae) from Jeju Island, Korea: implications for the origin of the flowering cherry.

The subgenus Cerasus of the genus Prunus includes several popular ornamental flowering cherries. Of the hundreds of cultivars, P. ×yedoensis ('Somei-yoshino') is the most popular and familiar cultivar in Korea and Japan and is considered to be of hybrid origin. However, the hybrid origin of P. ×yedoensis and its relationship to wild P. yedoensis, naturally occurring on Jeju Island, Korea, are highly controversial. We extensively sampled wild P. yedoensis, cultivated P. ×yedoensis, and numerous individuals from other species belonging to subgenus Cerasus on Jeju Island. Samples from 71 accessions, representing 13 species and one cultivar (P. ×yedoensis), were sequenced for nrDNA ITS/ETS (952 characters) and seven noncoding cpDNA regions (5421 characters) and subjected to maximum parsimony and maximum likelihood analysis. Additive polymorphisms in the ITS/ETS regions were confirmed by cloning amplicons from representative species. The nuclear (ITS/ETS and G3pdh) and cpDNA data, along with several morphological characteristics, provide the first convincing evidence for the hybrid origin of wild P. yedoensis. The maternal parent was determined to be P. spachiana f. ascendens, while the paternal parent was unresolved from the taxonomically complex P. serrulata/P. sargentii clade. The presence of two kinds of ribotypes was confirmed by cloning, and the possible origin of cultivated P. ×yedoensis from wild populations on Jeju Island was also suggested. Bidirectional and multiple hybridization events were responsible for the origin of wild P. yedoensis. Extensive gene flow was documented in this study, suggesting an important role of reticulate evolution in subgenus Cerasus.

Phylogenetic relationships, possible ancient hybridization, and biogeographic history of Abies (Pinaceae) based on data from nuclear, plastid, and mitochondrial genomes

Abies, the second largest genus of Pinaceae, consists of approximately 48 species occurring in the north temperate region. Previous molecular phylogenetic studies improved our understanding of relationships within the genus, but were limited by relying on only DNA sequence data from single genome and low taxonomic sampling. Here we use DNA data from three genomes (sequences of internal transcribed spacer of nrITS, three chloroplast DNA intergenic spacers, and two mitochondrial intergenic spacers) from 42 species to elucidate species relationships and construct the biogeographic history of Abies. We further estimated the divergence times of intercontinental disjunction using a relaxed molecular clock calibrated with three macro-fossils. Our phylogenetic analyses recovered six robust clades largely consistent with previous classifications of sections. A sister relationship between the eastern Asian and Europe–Mediterranean clades was highly supported. The monophyly of section Balsamea, disjunct in Far East and western North America, is supported by the nrITS data but not by the cpDNA data. Discordance on placement of section Balsamea between the paternally inherited cpDNA and maternally inherited mtDNA trees was also observed. The data suggested that ancient hybridization was likely involved in the origin of sect. Balsamea. Results from biogeographic analyses and divergence time estimation suggested an origin and early diversification of Abies in an area of high latitude around the Pacific during the Eocene. The present disjunction in eastern Asia and Europe–Mediterranean area of Abies was likely the result of southward migration and isolation by the Turgai Strait in the Late Eocene. An ‘out-of-America’ migration, for the origin of an eastern Asian and western North American disjunct species pairs in section Amabilis was supported. The results suggested a western North American origin of the section with subsequent dispersal across the Bering Land Bridge (BLB) to Japan during the Middle Miocene.

Phylogenetic analyses and chromosome counts reveal multiple cryptic species in Bupleurum commelynoideum (Apiaceae)

AbstractBupleurum commelynoideum H. Boissieu is a perennial herb occurring throughout the Hengduan Mountains region. This species was found to have more than one chromosome number in our previous chromosomal study. For a better understanding of its intraspecific genetic differentiation and interspecific relationships with other Bupleurum members, phylogenetic relationships among 15 populations of B. commelynoideum and 22 other Bupleurum members were investigated using the nuclear ribosomal DNA internal transcribed spacer (ITS) region and three chloroplast DNA (cpDNA) fragments (trnL‐F, rps16, and rpl32‐trnL). Both phylogenetic analyses of the ITS region and combined cpDNA data indicated that B. commelynoideum has more than one geographically delimited lineage. Among them, accessions from Shangri‐La and other regions were considered as different cryptic species according to the unified species concept. Our analyses also revealed that a complex pattern of reticulate relationship exists in B. commelynoideum and its allied species. The chromosome numbers of four populations of B. commelynoideum and a closely related species B. rockii H. Wolff are reported. The results showed that the chromosome number of B. commelynoideum has abundant variations in both chromosome ploidy (2x; 4x; 6x) and basic chromosome number (x = 5; x = 6). Population DXS (x = 6), which has the different basic chromosome number, should represent a different kind of cryptic speciation in B. commelynoideum. The karyological evidence, together with the molecular data, indicated that the existence of at least three cryptic species in B. commelynoideum. This kind of genetic differentiation without morphological divergence might be caused by stabilizing selection imposed by the extreme environmental conditions of the alpine area.

Towards a better understanding of the Taraxacum evolution (Compositae–Cichorieae) on the basis of nrDNA of sexually reproducing species

The genus Taraxacum is characterized by prevailing complex multiple hybridity, frequent polyploidy and widespread agamospermous reproduction, which makes the phylogenetic analysis difficult. On the basis of the previous analysis of the variation of nrDNA in Taraxacum taxa with different ploidy levels and modes of reproduction, to mitigate consequences of the reticulate complexity of the genus, a phylogenetic study of 52 samples of sexually reproducing dandelions of 26 sections (and another 13 agamospermous representatives of other sections known to include sexuals) was carried out. Both sexual and agamospermous samples were analysed using maximum parsimony and neighbour network. Exclusively sexual dandelions were analysed using the same approaches. In spite of the general agreement among various types of analyses, there is a limited overall congruence between results of nrDNA analyses and the established taxonomic system of the genus Taraxacum. The analyses shed light on the relationships among the most primitive groups. A stable clade is formed by representatives of the sections Primigenia, Orientalia, Sonchidium, Piesis and T. cylleneum. Another case of stable relationships is that of the members of the sect. Dioszegia. Relationships between the sects. Erythrosperma and Erythrocarpa were supported, and the relatedness of the members of sect. Australasica was confirmed. Rather unexpectedly, the agamospermous samples of the sect. Oligantha (T. minutilobum) are shown to be closely related with the sect. Macrocornuta. The latter section is generally considered to be close to sect. Ceratoidea (T. koksaghyz) on morphological grounds but this presumption is not corroborated by the results of nrDNA analyses. Analyses of 72 samples of sexual dandelions were also performed using the trnL–trnF region of the chloroplast DNA. The maximum parsimony analysis of this region reveals intraspecific variation in a number of ancestral diploid sexual species, all present in the two main branches of the cladogram. This phenomenon is attributed to the ancient gene flow and possibly to the persistence of ancestral cpDNA polymorphism. The strict consensus cpDNA tree information content and interpretability is quite low. The maximum parsimony analysis of combined nrDNA and cpDNA data sets was also performed with expectably low interpretability of the results.

Molecular data and ecological niche modeling reveal population dynamics of widespread shrub Forsythia suspensa (Oleaceae) in China's warm-temperate zone in response to climate change during the Pleistocene.

BackgroundDespite its high number of endemic deciduous broad-leaved species in China’s warm-temperate zone, far less attention has been paid to phylogeographic studies in this region. In this work, the phylogeographic history of Forsythia suspensa endemic to China’s warm-temperate zone was investigated to explore the effect of climate change during the Pleistocene on the distribution of this deciduous broad-leaved species in China.ResultsThe cpDNA data revealed seven phylogeographical groups corresponding to geographical regions. By contrast, the nrDNA data supported the samples clustered into three groups, which was inconsistent with separate geographical regions supported by cpDNA data. Ecological niche modeling showed that the climatically suitable area during the cold period was larger than that during the warm period.ConclusionsBoth molecular data and ecological niche modeling indicated that F. suspensa expanded to nearby low-elevation plains in the glacial periods, and retreated to mountaintops during interglacial warmer stages. This study thus supported that F. suspensa persisted in situ during the glacial of the Pleistocene with enlarged distribution area, contrary to the hypothesis of long distance southward migration or large-scale range contraction.

Phylogenetic Analysis of the Far Eastern Salix (Salicaceae) Based on Sequence Data from Chloroplast DNA Regions and ITS of Nuclear Ribosomal DNA

In order to further elucidate the relationships in the Salix genus, phylogenetic ana lysis was conducted based on comparison of the nucleotide sequences of the chlo roplast DNA regions (petG–trnP, petN–psbM, psaA–ycf3, psbM–trnD, rpoB– trnC, trnC–petN, trnD–trnT, trnS–psbZ, rbcL, matK) and the ITS region (ITS1–5.8S rRNA–ITS2) of nuclear ribosomal DNA of 86 Salix species from three sub­ genera: Salix, Chamaetia, Vetrix, 27 sections and Chosenia arbutifolia. The previous ly recognized genera Chosenia and Toisusu merged with Salix. The divergence of spe­ cies in the Salix genus (according to ITS and cpDNA data) was very low. In most spe cies from Chamaetia and Vetrix subgenera, the sequences differed by several sub­stitutions­or­were­ identical.­Molecular­differences­were­ identified­mainly­ in­ spe cies belonging to the subgenus Salix in its previous broad meaning. ITS­phy­ lo­geny­generally­agrees­with­the­most-recent­infrageneric­classification­of ­Salix: the isolation of subgenera Pleuradenia, Chosenia, Salix (for exception sect. Triand­ rae), Longifoliae has been well supported, but the isolation of subgenera Protitea and Chamaetia is not supported. Relationships between the subgenera Chamaetia and Vetrix remain unresolved. High similarity of the plastid and nuclear genomes re vealed in the majority of Salix species included in the analysis may indicate that they have relatively recently diverged from a common ancestor or there is a result of lineage sorting through hybridization. K e y w o r d s chloroplast DNA, ITS, phylogenetic analysis, Salicaceae, Salix

Molecular data and ecological niche modelling reveal the phylogeographic pattern ofCotinus coggygria(Anacardiaceae) in China's warm‐temperate zone

The phylogeography of common and widespread species helps to elucidate the history of local flora and vegetation. In this study, we selected Cotinus coggygria, a species widely distributed in China's warm-temperate zone. One chloroplast DNA (cpDNA) region and ecological niche modelling were used to examine the phylogeographic pattern of C.coggygria. The cpDNA data revealed two phylogeographic groups (Southern and Northern) corresponding to the geographic regions. Divergence time analyses revealed that divergence of the two groups occurred at approximately 147,000years before the present (BP), which coincided with the formation of the downstream area of the Yellow River, indicating that the Yellow River was a weak phylogeographic divide for C.coggygria. The molecular data and ecological niche modelling also indicated that C.coggyria did not experience population expansion after glaciations. This study thus supports the fact that Pleistocene glacial cycles only slightly affected C. coggygria, which survived in situ and occupied multiple localised glacial refugia during glaciations. This finding is contrary to the hypothesis of large-scale range habitat contraction and retreat into a few main refugia.

Molecular phylogeny of Cotoneaster (Rosaceae) inferred from nuclear ITS and multiple chloroplast sequences

Cotoneaster Medik. (Rosaceae, Maloideae) is distributed in Europe, North Africa, and temperate areas of Asia except Japan. Members of the genus exhibit considerable morphological variation. The infrageneric classification is also obscured by polyploidy, hybridization, and apomixis. In this study, phylogenetic analyses were conducted to test infrageneric classifications of this genus using DNA sequence data from the nuclear ITS (nrITS) region and three chloroplast intergenic spacer regions. Maximum parsimony and Bayesian inference analyses of both datasets agreed with the two sections/subgenera of Koehne’s classification system, and suggested that four subsections (Microphylli, Chaenopetalum, Adpressi, and Cotoneaster) and the series of Koehne’s classification system were non-monophyletic. The incongruence length difference test indicated that the nrITS and cpDNA datasets were significantly incongruent (P = 0.001), and the placement of 14 species was discordant in phylogenetic trees derived from the two datasets. Within Cotoneaster, hybridization was indicated to be an important factor contributing to the incongruence between the nrITS and cpDNA data. By mapping nine morphological characters onto the combined nrITS–cpDNA phylogenetic tree, we inferred that a deciduous habit, glabrous fruit, white anthers, erect and light pink petals, and white filaments are plesiomorphic character states in Cotoneaster.

Evolution of rbcL among Lathyrus and Kupicha's classification.

Phylogenetic relationships in the Lathyrus genus were examined using cpDNA data, particularly data attributed to the "barcode" rbcL gene to construct a possible evolutionary scenario. Plant barcoding can be used to differentiate between species within a genus and to conserve DNA within the same species. We assessed the phylogeny of 29 species of Lathyrus using maximum parsimony, maximum likelihood and unweighted pair-group method and arithmetic mean. The classifications did not agree with current morphological and basic Lathyrus classification. Lathyrus belinensis is a new species that was not described by Kupicha; according to rbcL analysis, the species belongs in the Lathyrus genus. Additionally, the genus Lathyrus has undergone a rapid population expansion as indicated by neutral selection indices.

Genetic structure of Ipomoea imperati (Convolvulaceae) in the Mediterranean region and implications for its conservation

In this paper, we studied the relationships of the only surviving Italian population of Ipomoea imperati (Convolvulaceae), a pantropical sandy coastal species, in Sicily and other populations in the Mediterranean region. Herbarium samples which are representative of extinct populations growing in Campania (Italy) were also investigated together with populations from various Atlantic and Mediterranean localities. Chloroplast DNA microsatellites (cp-SSR) and nuclear ribosomal Internal Transcribed Spacer (ITS) sequences were jointly employed, in order to detect relationships among populations. Our aims were several-fold: (1) to clarify if the species is autochthonous in the Mediterranean basin or a post-Columbian introduction; (2) to investigate phylogeographic patterns in the species and (3) to establish the possible role of dispersal in explaining the patterns observed. Chloroplast microsatellite variation indicates that extinct Italian mainland populations of I. imperati from Campania are not closely related to the extant Sicilian one, as they do not share haplotypes. Chloroplast DNA microsatellite variation is largely between populations, and the within populations component accounts for only approximately 10%. CpDNA data is consistent with a single Mediterranean entry point hypothesis or with the notion that some populations display plesiomorphic variability. ITS data is congruent with the possibility that the presence of I. imperati in the Mediterranean is the result of transatlantic dispersal. The population from Sicily and extinct populations from Campania share an ITS type. A Bayesian analysis employing clock calibration data on an expanded ITS dataset with appropriate outgroups indicates that dates of transoceanic distribution are probably earlier than historical times.

Phylogeographical Patterns of an Alpine Plant, Rhodiola dumulosa (Crassulaceae), Inferred from Chloroplast DNA Sequences

The phylogeographical patterns of Rhodiola dumulosa, an alpine plant species restrictedly growing in the crevices of rock piles, were investigated based on 4 fragments of the chloroplast genome. To cover the full distribution of R. dumulosa in China, 19 populations from 3 major disjunct distribution areas (northern, central, and northwestern China) were sampled. A total of 5881bp (after alignment) of chloroplast DNA (cpDNA) from 100 individuals were sequenced. The combined cpDNA data set yielded 36 haplotypes. The total genetic diversity of R. dumulosa was remarkably high (H(T) = 0.981). The interpopulation genetic differentiation was significantly large (F(ST) = 0.8537, P < 0.001), possibly due to the long-term isolation of the natural populations. N(ST) was significantly larger than G(ST) (P < 0.001), indicating the presence of phylogeographical structure among the R. dumulosa populations. We propose 2 migration steps to explain the current distribution of R. dumulosa in China. First, this species migrated from refugia in the Qinghai-Tibetan Plateau to northern areas via the intervening highlands when temperatures increased; second, the highland populations migrated toward the mountaintops when temperatures increased further because R. dumulosa is adapted to cold environments. During the second migration step, the common ancestral haplotypes may have been gradually lost.

Phylogenetic analysis of PISTILLATA sequences in Neillia (Rosaceae)

Putative PISTILLATA genes were generated in nine species of Neillia, to examine the phylogenetic relationships among the species, and to test the hypothesis of hybrid origin within the genus. The PI genes determined in Neillia have two introns in the I-box region, which is consistent with PI genes in other Rosaceae. Phylogenetic analyses of the I-box region, including the introns, indicated that the species formerly classified in Stephanandra were nested within Neillia, supporting the taxonomic merger of the two genera. The PI data do not have a sufficiently strong signal to reject the hypothesis that Stephanandra is a hybrid in origin. The PI data, in conjunction with nuclear LEAFY, ribosomal DNA, and chloroplast DNA data, suggest that N. affinis might have been derived from hybridization between N. thibetica and N. gracilis. The phylogenetic position of N. affinis in the N. thibetica clade is supported by the PI and rDNA data, whereas N. affinis is also supported as a sister to N. gracilis in the LEAFY and cpDNA data. The pattern of phylogenetic placements of N. affinis in two different clades in two different sets of data suggests that the genome of the species might be comprised of a combination of the putative parental species.

Phylogenetic relationships among Orostachys subsection Orostachys species (Crassulaceae) based on nuclear and chloroplast DNA data

AbstractNuclear ribosomal ITS and four cpDNA intergenic spacer sequences were used to assess how the patterns of molecular differentiation are related to taxonomic boundaries and geographic distribution in polymorphic and taxonomically complex Orostachys subsection Orostachys (Crassulaceae). Two major cpDNA lineages were identified in a set of Orostachys populations, lineage A, comprising 13 closely related haplotypes found in 11 populations of monocarpic O. malacophylla var. malacophylla, O. maximowiczii, and O. gorovoii and lineage B that included 9 out of 10 divergent haplotypes found in five populations of O. paradoxa, distinct in perennial stoloniferous habit. Our data suggest that the current concepts of O. malacophylla var. malacophylla, O. maximowiczii, and O. gorovoii are incompatible with the differentiation at the cpDNA level. Neither of these taxa could be allied to a particular haplotype or haplotype clade. The pattern of relationships between 7 ITS ribotypes found in 17 populations supported neither the morphology‐based taxonomic subdivision in the subsection Orostachys nor grouping according to geographical origin of the populations or lineages recovered with cpDNA data. A high level of similarity of ITS rDNA sequences between the subsection members suggests their relatively recent and rapid divergence from a common ancestor.

Tertiary Origin and Pleistocene Diversification of Dragon Blood Tree (Dracaena cambodiana-Asparagaceae) Populations in the Asian Tropical Forests

BackgroundThe origin of extraordinarily rich biodiversity in tropical forests is often attributed to evolution under stable climatic conditions over a long period or to climatic fluctuations during the recent Quaternary period. Here, we test these two hypotheses using Dracaena cambodiana, a plant species distributed in paleotropical forests.MethodsWe analyzed nucleotide sequence data of two chloroplast DNA (cpDNA: atpB-rbcL and trnD-trnT) regions and genotype data of six nuclear microsatellites from 15 populations (140 and 363 individuals, respectively) distributed in Indochina Peninsular and Hainan Island to infer the patterns of genetic diversity and phylogeographic structure. The population bottleneck and genetic drift were estimated based upon nuclear microsatellites data using the software programs BOTTLENECK and 2MOD. The lineage divergence times and past population dynamics based on cpDNA data were estimated using coalescent-based isolation-with-migration (IMa) and BEAST software programs.ResultsA significant phylogeographic structure (N ST = 0.876, G ST = 0.796, F ST-SSR = 0.329, R ST = 0.449; N ST>G ST, R ST>F ST-SSR, P<0.05) and genetic differentiation among populations were detected. Bottleneck analyses and Bayesian skyline plot suggested recent population reduction. The cpDNA haplotype network revealed the ancestral populations from the southern Indochina region expanded to northward. The most recent ancestor divergence time of D. cambodiana dated back to the Tertiary era and rapid diversification of terminal lineages corresponded to the Quaternary period.ConclusionsThe results indicated that the present distribution of genetic diversity in D. cambodiana was an outcome of Tertiary dispersal and rapid divergence during the Quaternary period under limited gene flow influenced by the uplift of Himalayan-Tibetan Plateau and Quaternary climatic fluctuations respectively. Evolutionary processes, such as extinction-recolonization during the Pleistocene may have contributed to the fast diversification in D. cambodiana.

Quaternary Divergence and Holocene Secondary Contact via the Northwest Passage in the CircumpolarLathyrus japonicus(Leguminosae)

We used the geographic distribution of genetic diversity in the beach pea, Lathyrus japonicus (Leguminosae) to reconstruct the location of a Pleistocene refugium and Holocene range expansion. DNA sequence data for the chloroplast ndhF-trnH spacer from a global sample of 22 populations in Asia, North America, and Europe were used to assess broad-scale, circumpolar patterns. The cpDNA data revealed five haplotypes including two largely allopatric, widespread haplotypes (one Pacific, the other Atlantic and inland in the Great Lakes). Three geographically restricted haplotypes were also recovered: one each in New Jersey, Lake Champlain, and the Pacific Northwest. The distribution of isozyme variation at 14 loci for 38 populations of beach peas from the Atlantic and Pacific coasts of North America, Lake Champlain, and the Great Lakes was used to reconstruct a North American history. One subset of allozymes was found on the Atlantic Coast and in the Great Lakes; a second subset was widespread from northwestern North America to Newfoundland. There was a nested pattern to the localization of allozymes along the Atlantic Coast; Cape Cod had the greatest number of allozymes. Pacific and Atlantic isozymes and cpDNA haplotypes occurred together along the coast of Newfoundland and adjacent Labrador. The pattern of genetic variation as assessed from isozymes and cpDNA allow the inferences that: 1) an early divergence yielded Atlantic and Pacific lineages and 2) the Atlantic lineage occupied a Wisconsinan refugium on the now-submerged coast of northeastern North America. Our evidence is consistent with there being Holocene secondary contact between the Atlantic and Pacific lineages in the area where they now overlap. We also suggest that an early post-glacial vicariance event is implicated in the history of the Lake Champlain populations.

Phylogeography of North American herbaceous Smilax (Smilacaceae): Combined AFLP and cpDNA data support a northern refugium in the Driftless Area

The genetic structure of North American herbaceous Smilax, a clade of closely related understory herbs that has a wide and disjunct distribution, was investigated to test the hypothesis of whether a northern refugium in the upper Midwest may have existed for these plants during the last glaciation. We analyzed 33 populations sampled from California and throughout the eastern United States using AFLP and chloroplast DNA sequence data. Individuals of S. jamesii from northern California formed a clade sister to the eastern North American species, and they likely diverged from each other during the Pleistocene. Among the eastern species, two lineages were found on opposite sides of the Appalachian Mountains. The populations near the "Driftless Area" contained most of the chlorotypes found in the Midwest, including a unique one endemic to this area, and the AFLP data indicated that one population from this area has the highest frequency-down-weighted-marker value. This study, and others that have focused on mammals, amphibians, and woody plants, provides further evidence for the debate over whether the upper Midwest's "Driftless Area" may have hosted a biologically diverse northern glacial refugium. Herbaceous species of Smilax from eastern North American exhibit an Appalachian discontinuity. They appear to have persisted in multiple refugia both east and west of the Appalachians, with several populations persisting in situ through the Last Glacial Maximum (LGM). We suggest that they experienced localized expansion after the LGM, possibly followed by subsequent contact between the Midwest and the East Coastal lineages.

엽록체 DNA 염기서열에 근거한 물여뀌 종집단(마디풀과)의 분류학적 연구

The Polygonum amphibium complex (Poygonaceae) is a highly polymorphic taxon that can grow in aquatic environments as well as in moist terrestrial habitats. Aquatic and terrestrial plants of the P. amphibium complex vary significantly in morphology and exhibit very complicated patterns of morphological variation, resulting in the description of numerous infra-specific taxa. Principal components analysis of 107 individuals of the P. amphibium complex from Asia and North America using 11 morphological characters showed that the aquatic plants can be discerned from the terrestrial plants by leaf size, shape, and petiole length. In contrast, both aquatic and terrestrial plants collected from the same population or locality shared identical sequences in the matK, psbA-trnH IGS, rbcL-accD IGS and trnL-trnF regions of the chloroplast DNA (cpDNA), suggesting that aquatic and terrestrial forms of the P. amphibium complex are not genetically diverged; morphological differ- ences between the two forms are probably due to the differences in environmental conditions of the habitats. In addition, results from the morphological analysis and the maximum parsimony analysis of the cpDNA data set revealed that the plants from Asia including Korea, Japan, China, Mongolia and Russia Far East are diverged from those in North America and Europe, suggesting that the Asian populations should be recognized as a dis- tinct variety, P. amphibium var. amurense Korsh.

我国特有植物青檀遗传结构的ISSR分析

青檀是我国特有的第三纪残遗植物,是宣纸纤维来源的重要原材料,现已被列入国家Ⅲ级保护植物。采用简单序列重复区间扩增多态性(ISSR)标记技术,对采自27个地理种群的628个青檀个体的遗传多样性和遗传结构进行了检测。8对引物共得到66个清晰的扩增位点,其中多态性位点63个,多态性位点百分率为95.45%。分析结果表明,青檀在物种水平上具有很高的遗传多样性(PPB=95.45%、<em>Ao</em>=1.9545、<em>Ae</em>=1.5729、<em>He</em>=0.3335、<em>I</em>=0.4980、<em>Hb=</em>0.3437)。在种群水平上的遗传多样性(PPB=69.98%、<em>Ao</em>=1.6998、<em>Ae</em>=1.4449、<em>He</em>=0.2561、<em>I</em>=0.3793、<em>Hb=</em>0.2656)和种群间遗传分化水平(<em>Gst</em>=0.23,<em>Ф_ST</em>=0.25)均处于中等水平。华北地区(30°-42°N)和华南地区(22°-30° N)青檀的遗传多样性和遗传结构的差异并不显著。古老的起源历史、较广的分布范围、异交的繁育系统、风媒种子、长命的生活史以及华南和华北地形和植被的差异可能是导致青檀目前遗传格局的主要原因。结合叶绿体序列(cpDNA)序列的遗传结构特征对青檀的保护策略进行了探讨。