基于叶绿体基因序列rbcL-accD研究莛子藨的分子遗传多样性和谱系地理结构

莛子藨是莛子藨属的一种多年生草本植物,主要分布在青藏高原东北部及邻近高山地区和日本,为东亚特有种。本文基于叶绿体DNA基因间隔区rbcL-accD序列,对莛子藨物种水平的序列特征、分子遗传多样性和谱系地理结构进行研究。分析结果发现该区域莛子藨种群的遗传变异主要来自于居群间（72.28%）,优势单倍型（H2）广泛分布,特有单倍型分散在多个居群。居群间遗传分化系数N_STST,没有检测到显著谱系地理结构,而且居群间基因流较低（N_m=0.096）,青藏高原及其邻近地区特殊地形和生态环境造成的地理隔离或者生境异质化可能是现有单倍型分布格局形成的原因。种群动态历史分析显示莛子藨经历过不显著的种群选择或者扩张事件,综合分析推测莛子藨居群应该是在间冰期或者冰期后从不同避难所扩散形成现在的分布格局,具体避难所还需进一步深入研究才能确认。     

Phylogeographic evidence for two mesic refugia in a biodiversity hotspot

Phylogeographic studies of flora in species-rich south-western Australia point to complex evolutionary histories, reflecting patterns of persistence and resilience to climatic changes during the Pleistocene. We asked whether coastal areas of the mid-west and south, as well as granite outcrops and inland ranges, have acted as major refugia within this region during Pleistocene climatic fluctuations by analysing phylogeographic patterns in the shrub Calothamnus quadrifidus R.Br. (Myrtaceae). We determined variation in chloroplast DNA data for 41 populations across the geographic range. Relationships and major clades were resolved using parsimony and Bayesian analyses. We tested for demographic and spatial expansion of the major clades and estimated clade divergence dates using an uncorrelated, lognormal relaxed clock based on two conservative chloroplast mutation rates. Two distinct phylogeographic clades were identified showing divergence during the Pleistocene, consistent with other phylogeographic studies of south-west Australian flora, emphasising the impact of climatic oscillations in driving divergence in this landscape. The southern clade was more diverse, having higher haplotype diversity and greater genetic structure, while the northern clade showed evidence of fluctuation in population size. Regions of high haplotype diversity with adjacent areas of low diversity observed in each clade indicated the locations of two coastal refugia: one on the south coast and another along the mid-west coast. This is the first evidence for major Pleistocene refugia using chloroplast genetic data in a common, widespread species from this region.     

Pleistocene refugia and polytopic replacement of diploids by tetraploids in the Patagonian and Subantarctic plant Hypochaeris incana (Asteraceae, Cichorieae)

We report the phylogeographic pattern of the Patagonian and Subantarctic plant Hypochaeris incana endemic to southeastern South America. We applied amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) analysis to 28 and 32 populations, respectively, throughout its distributional range and assessed ploidy levels using flow cytometry. While cpDNA data suggest repeated or simultaneous parallel colonization of Patagonia and Tierra del Fuego by several haplotypes and/or hybridization, AFLPs reveal three clusters corresponding to geographic regions. The central and northern Patagonian clusters (∼38–51° S), which are closer to the outgroup, contain mainly tetraploid, isolated and highly differentiated populations with low genetic diversity. To the contrary, the southern Patagonian and Fuegian cluster (∼51–55° S) contains mainly diploid populations with high genetic diversity and connected by high levels of gene flow. The data suggest that H. incana originated at the diploid level in central or northern Patagonia, from where it migrated south. All three areas, northern, central and southern, have similar levels of rare and private AFLP bands, suggesting that all three served as refugia for H. incana during glacial times. In southern Patagonia and Tierra del Fuego, the species seems to have expanded its populational system in postglacial times, when the climate became warmer and more humid. In central and northern Patagonia, the populations seem to have become restricted to favourable sites with increasing temperature and decreasing moisture and there was a parallel replacement of diploids by tetraploids in local populations.     

Phylogeography of an alpine aquatic herb Ranunculus bungei (Ranunculaceae) on the Qinghai–Tibet Plateau

Many phylogeographic studies of terrestrial plant species on the Qinghai–Tibet Plateau (QTP) have been carried out to elucidate the range shifts in response to climatic oscillations in the Quaternary. However, patterns of range shifts for aquatic plants following the climate change on the QTP are poorly understood. Here, we studied the historical range shifts of the aquatic herb Ranunculus bungei Steud. on the QTP using four chloroplast (cpDNA) non-coding spacers. We revealed low within-population genetic diversity (H_S = 0.052) and high interpopulation genetic differentiation (G_ST = 0.914; N_ST = 0.954). But the high population differentiation was not coupled with a distinct phylogeographic structure (N_ST > G_ST, P > 0.05). Phylogenetic analyses revealed two main cpDNA haplotype lineages and the split between these two lineages can be dated back to the late Tertiary (3.84–11.90 Ma). Two independent range expansions within the two intraspecific lineages at approximately 0.15–0.46 and 0.17–0.50 Ma were revealed. Our results suggested that R. bungei survived the Last Glacial Maximum and/or previous glacial periods on the QTP. Colonization or recolonization during the repeated range expansions may have replaced the early haplotypes and the pre-existing genetic structure and could explain the non-significant phylogeographical structure.     

Potential refugium on the Qinghai–Tibet Plateau revealed by the chloroplast DNA phylogeography of the alpine species Metagentiana striata (Gentianaceae)

Metagentiana striata is an alpine annual herbaceous plant endemic to the east of the Qinghai–Tibet (Q–T) Plateau and adjacent areas. The phylogeography of M. striata was studied by sequencing the chloroplast DNA (cpDNA) trn S– trn G intergenic spacer. Ten haplotypes were identified from an investigation of 232 individuals of M. striata from 14 populations covering the entire geographical range of this species. The level of differentiation amongst populations was very high ( G _ST = 0.746; N _ST = 0.774) and a significant phylogeographical structure was observed ( P  < 0.05). An analysis of molecular variance found a high variation amongst populations (76%), with F _ST = 0.762 (highly significant, P  < 0.001), indicating that little gene flow occurred amongst the different regions; this was explained by the isolation of populations by high mountains along the Q–T Plateau and adjacent areas ( N _m = 0.156). Only one ancestral haplotype (A) was common and widespread throughout the distributional range of M. striata. The populations of the Hengduan Mountains region of the south-eastern Q–T Plateau showed high diversity and uniqueness of haplotypes. It is suggested that this region was the potential refugium of M. striata during the Quaternary glaciation, and that interglacial and postglacial range expansion occurred from this refugium. This scenario was in good agreement with the results of nested clade analysis, which inferred that the current spatial distribution of cpDNA haplotypes and populations resulted from range expansion, together with past allopatric fragmentation events.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 125–140.     

基于叶绿体DNA trnT-trnF序列研究祁连圆柏的谱系地理学

由于青藏高原的地貌效应,第四纪冰期气候的反复变化应对现今该地区生物的地理分布及其居群遗传结构产生重大影响。本文对这一地区特有分布物种祁连圆柏Juniperus przewalskii Kom.整个分布区内20居群392个个体的trnT-trnF序列变化进行了研究;共发现3种单倍型(haplotype),构成两种地理区域:高原台面上的居群主要固定Hap A,而Hap A、Hap B和Hap C在高原边缘居群均有分布。所有居群总的遗传多样性HT = 0.511,GST= 0.847。在低海拔的高原边缘,Hap A、Hap B和Hap C高频率固定在不同的居群中,表明可能存在多个不同的避难所,居群反复缩小和扩张的瓶颈效应造成了遗传多样性的丢失。而边缘的一个居群含有两种相似单倍型频率则可能是冰期后迁移融合而成或者该居群在冰期经受的瓶颈作用更弱。高原台面东部间断分布的居群只固定Hap A,表明它们可能经历了冰期后共同的回迁过程和由此产生的奠基者效应。我们的研究结果表明祁连圆柏在冰期可能存在多个避难所,瓶颈效应和奠基者效应造成了这些居群现在的遗传多样性分布式样。     

Glacial history of the alpine herb Rumex Nivalis (Polygonaceae): a comparison of common phylogeographic methods with nested clade analysis

The glacial history of the alpine herb Rumex nivalis was investigated using amplified fragment length polymorphisms (AFLPs) and restriction fragment length polymorphisms with polymerase chain reaction (PCR-RFLPs) of cpDNA. Both traditional statistical methods widely applied in phylogeographic research and nested clade analysis were used. The AFLPs indicated little geographic structure probably due to the wind-pollinated reproductive system of the dioecious R. nivalis. Because cpDNA haplotypes exhibited distinct distributional patterns, correlation between AFLPs and PCR-RFLPs was low. The results of common statistical methods and of nested clade analysis were largely congruent. Both supported in situ survival of one group of common haplotypes in the Central Alps. For another group of common haplotypes, classical phylogeographic analyses gave strong evidence for survival in peripheral refugia at the northern alpine border, whereas this conclusion was not as clearly supported in the nested clade analysis. Nested clade analysis provided several detailed insights on past and ongoing populational demographic processes. Thus, it is a valuable tool in the phylogeographical analysis of haplotype data, but it should preferably be combined with other statistical analyses. In situations with low genetic variation in cpDNA, classical phylogeographic analytical tools on nuclear DNA will still be the methods of choice.     

Intraspecific differentiation of Allium wallichii (Amaryllidaceae) inferred from chloroplast DNA and internal transcribed spacer fragments

In the present study, we used two chloroplast DNA (cpDNA) fragments (trnL-F and rps16) and the nuclear ribosomal internal transcribed spacer (ITS) sequence data to examine intraspecific differentiation and phylogeographical history of Allium wallichii. Based on wide scale sampling (28 populations and 174 individuals) across the entire distribution range of this species, 33 cpDNA haplotypes and 25 ITS ribotypes were detected in our investigation. These cpDNA haplotypes were divided into three major lineages, which was further supported by the ITS phylogenetic results. High haplotype/ribotype diversity and population differentiation, together with most of the haplotypes/ribotypes being exclusive to single populations, implied restricted gene flow among populations and significant geographical isolation. Nearly all populations with high haplotype/ribotype diversity were found in the Hengduan Mountain Region (HMR), whereas the populations of the Himalayas and Nanling Mountains showed a lower level, suggesting the HMR might serve as a potential divergence center for A. wallichii. The main lineages of A. wallichii diverged from each other between Mid–Late Pliocene and Early Quaternary based on two sets of molecular markers, indicating that the Quaternary climatic fluctuation could not have contributed greatly to the divergence of the main lineages of A. wallichii. Instead, the intricate topography and heterogeneous habitats resulting from the drastic uplift of the Qinghai–Tibet Plateau from the Late Pliocene could be responsible for the intraspecific differentiation of A. wallichii. The present study further highlights the importance of geographic isolation and habitat heterogeneity in shaping and maintaining high species diversity within the HMR.     

Population genomic evidence for multiple Pliocene refugia in a montane‐restricted harvestman (Arachnida,Opiliones, Sclerobunus robustus) from the southwestern United States

The integration of ecological niche modelling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis‐based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of nonrefugial populations are corroborated with empirical data. In this study, we focus on a montane‐restricted cryophilic harvestman, Sclerobunus robustus, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double‐digest RAD‐seq data and conducted population‐level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid‐latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades of S. robustus. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades pre‐dates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model‐based coalescent approaches, we find support for postdivergence migration between clades from separate refugia.     

Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation

The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-steppe with sparse forests scattered within it. To obtain a better understanding of the phylogeography of one constituent species of the forests in this region, we examined chloroplast trnT-trnF and trnS-trnG sequence variation within Juniperus przewalskii, a key endemic tree species. Sequence data were obtained from 392 trees in 20 populations covering the entire distribution range of the species. Six cpDNA haplotypes were identified. Significant population subdivision was detected (G(ST) = 0.772, N(ST) = 0.834), suggesting low levels of recurrent gene flow among populations and significant phylogeographic structure (N(ST) > G(ST), P < 0.05). Eight of the nine disjunct populations surveyed on the high-elevation northeast plateau were fixed for a single haplotype (A), while the remaining, more westerly population, contained the same haplotype at high frequency together with two low frequency haplotypes (C and F). In contrast, most populations that occurred at lower altitudes at the plateau edge were fixed or nearly fixed for one of two haplotypes, A or E. However, two plateau edge populations had haplotype compositions different from the rest. In one, four haplotypes (A, B, D and E) were present at approximately equivalent frequencies, which might reflect a larger refugium in the area of this population during the last glacial period. Phylogenetic analysis indicated that the most widely distributed haplotype A is not ancestral to other haplotypes. The contrasting phylogeographic structures of the haplotype-rich plateau edge area and the almost haplotype-uniform plateau platform region indicate that the plateau platform was recolonized by J. przewalskii during the most recent postglacial period. This is supported by the findings of a nested clade analysis, which inferred that postglacial range expansion from the plateau edge followed by recent fragmentation is largely responsible for the present-day spatial distribution of cpDNA haplotypes within the species.     

Genetic diversity pattern of Stipa purpurea populations in the hinterland of Qinghai–Tibet Plateau

Stipa purpurea is among constructive endemic species in alpine meadow and steppe on the Qinghai–Tibet Plateau. To reveal the genetic diversity of this species and its relationship with geographic distribution pattern, we sampled eight populations across a northward transect with an increasing aridity gradient in the hinterland of Qinghai–Tibet Plateau. Their genetic diversity was quantified using eight intersimple sequence repeat (ISSR) primers. We found that S. purpurea had relatively low genetic diversity ( H _e = 0.135) but significant genetic differentiation among populations ( G _st = 0.391), indicating relatively more genetic diversity retained within populations. A Mantel test revealed a significant relationship between genetic and geographic distance in the S. purpurea populations. The genetic diversity tended to decrease with increasing latitude and longitude, while no significant relationship was found between genetic diversity and altitude, suggesting the possible influences of humidity and temperature on genetic diversity of alpine plant. We propose conservation measures for this plant on the plateau.     

Phylogeography of the Qinghai–Tibet Plateau endemic alpine herb Pomatosace filicula (Primulaceae)

In order to trace the response of alpine plants on the Qinghai–Tibet Plateau (QTP) to the Quaternary climate oscillations, the phylogeographic history of Pomatosace filicula Maxim. was investigated in the present study. Based on sequence variations of two maternally inherited plastid markers, matK and trnH-psbA, and the biparentally inherited nuclear ribosomal internal transcribed spacer (nrITS), we estimated the population genetic structure, lineage divergence timescale, and population dynamics of P. filicula. Seven plastid haplotypes and two nrITS genotypes were identified across the range-wide sampling of 200 individuals from 24 populations. Although AMOVA revealed a high level of differentiation among populations (F_ST = 0.560), no significant phylogeographic structure was detected (N_ST = 0.503, G_ST = 0.518, P > 0.05). Molecular dating suggested that the divergences between major plastid lineages and nrITS genotypes occurred during the early and middle Pleistocene, and the middle Pleistocene, respectively. This species most likely survived at multiple unglaciated sites on the QTP during the Last Glacial Maximum, with most of these sites located above 4000 m a.s.l. The species probably experienced range expansion at its distribution fringe, but demographic tests did not suggest significant population size changes. We proposed that pronounced effective gene flow (N_em = 0.393) and short generation time may have obscured the phylogeographic and demographic patterns of this species. Our findings will shed new light on the Quaternary evolutionary history of the alpine flora of the QTP.     

Circumpolar phylogeography of Juncus biglumis (Juncaceae) inferred from AFLP fingerprints, cpDNA sequences, nuclear DNA content and chromosome numbers

We explored the circumpolar phylogeographic history of the arctic-alpine Juncus biglumis using amplified fragment length polymorphisms (AFLPs), sequences of cpDNA, relative nuclear DNA content and chromosome numbers. The analyses of the AFLP and cpDNA data gave congruent results and revealed three distinct clades. One of them, represented by a single population from the Taymyr peninsula in northern Siberia, had approximately fourfold larger genome size than the other samples and produced an AFLP pattern that was too aberrant to be analysed together with the rest of the data set. The two other clades represented different ploidy levels (2n = 60 and 120) as judged from chromosome counts of selected populations but differed only in c. 6% relative DNA content. Based on the AFLP and partly also on the cpDNA data, each of the two main clades was further subdivided into two well-supported subgroups. Three of the subgroups were widespread and exhibited largely overlapping distribution patterns. The fourth subgroup seems to be absent from the North Atlantic region and from western Siberia. We suggest that the four subgroups diverged during isolation in different glacial refugia during the Quaternary. Interestingly, individuals of both main clades were encountered in geographically close populations in eastern Greenland and even within a single population from Svalbard, indicating that both areas were colonised at least twice. The different genome sizes and ploidy levels strongly suggest that the three main clades represent distinct gene pools and act as cryptic species.     

Origin of Ostryopsis intermedia (Betulaceae) in the southeast Qinghai–Tibet Plateau through hybrid speciation

It remains unknown how Ostryopsis intermedia B. Tian & J. Q. Liu (Betulaceae) originated in the SE Qinghai–Tibet Plateau (QTP). We examined sequence variations of two maternally inherited chloroplast (cp) DNA fragments and amplified fragment length polymorphisms (AFLP) of 32 populations for this species and two congeners, O. davidiana Decne. and O. nobilis Balf. f. W. W. Sm., distributed in northern China and the SE QTP. Each of the two distinct cpDNA haplotype groups was fixed by O. davidiana or O. intermedia, respectively, whereas both were found in O. nobilis. All analyses of AFLP suggested that O. intermedia is more closely related to O. davidiana than to O. nobilis and Bayesian clustering analysis (K = 2) further suggested that the genomic composition of O. intermedia showed a slightly mosaic origin from the other two species, although mostly from O. davidiana. Analyses of AFLP indicated the highest nuclear genetic diversity for O. davidiana and lowest forO. intermedia. The origin of O. intermedia through hybrid speciation due to southward migration of O. davidiana and the following hybridization with O. nobilis may provide the most reasonable explanation for the inconsistency between phylogenetic relationships of three species and degrees of genetic diversity from cpDNA sequences or AFLP datasets. Ostryopsis intermedia may represent one more diploid hybrid species found in the QTP, although further strong tests are needed based on additional data.     

Phylogeography of a marsh herb Sagittaria trifolia (Alismataceae) in China inferred from cpDNA atpB-rbcL intergenic spacers

Sagittaria trifolia L. is a perennial, erect herb that is confined to ponds, rice fields, ditches, and freshwater wetlands. Using chloroplast DNA (cpDNA) atpB-rbcL intergenic spacer sequences, we studied the phylogeographic pattern and demographic history of S. trifolia with 108 samples from 42 populations representing the entire geographic range in China. Twenty-seven haplotypes were characterized and two of them were widely distributed in the populations. In the minimum-spanning network, all tip haplotypes were unique to a particular population, while the interior nodes represented widespread haplotypes. Nested clade analysis (NCA) of cpDNA haplotypes indicated that long distance dispersal characterized the post-glacial recolonization of S. trifolia in China. No specific refugia areas were suggested because genetic differentiation was low among the sampled regions and among populations within regions although a large number of the haplotypes were unique to a single population. The present data support that the unique haplotypes in individual population most likely represent recent mutational derivatives after long distance dispersal rather than the relics in refugia. These results for S. trifolia represent the first phylogeographic analysis of a widespread marsh herb in China and support the importance of long distance dispersal events in the post-glacial migrations of plants.     

Chloroplast DNA phylogeography of Cunninghamia konishii (Cupressaceae), an endemic conifer of Taiwan.

In this study, we investigated the genetic structure and phylogeographic pattern of the genus Cunninghamia, a member of the Cupressaceae restricted to mainland China and Taiwan, based on sequences of the trnD-trnT noncoding spacer of the chloroplast DNA. Maternal inheritance of chloroplasts was determined experimentally. No paternal leakage was detected. Both parsimony and neighbor-joining analyses revealed the polyphyly of Cunninghamia konishii, populations of which were nested in clades of C. lanceolata from mainland China. The nucleotide diversity of chloroplast DNA sequences within C. konishii (0.0118) was higher than that between species (0.0104), which agrees with a previous allozyme investigation. Based on mutational differences between sequences, a minimum spanning network consisting of five clades was constructed. Significant genetic differentiation (phiST = 0.130, P < 0.001) was detected between the clades based on AMOVA analyses. We infer several possible refugia in the Yunnan, Zhejiang, and Guangdong provinces of south China, all located in the minimum network as interior nodes. We also infer possible migration routes of Cunninghamia populations. The phylogeographic pattern shown in the reconstructed network suggests that the present-day Cunninghamia populations in Taiwan were derived from six different sources in continental Asia via long-distance seed dispersal. A migrant-pool model explains the heterogeneous composition of the organelle DNA in Taiwan's populations and the low differentiation between populations of Taiwan and China (phiCT = 0.012, P = 0.454). In contrast with the genetic heterogeneity within geographic populations, many local populations have attained coalescence at the trnD-trnT alleles, which has led to significant differentiation at the population level.     

Genetic diversity, structure, and demographic change in tanoak, Lithocarpus densiflorus (Fagaceae), the most susceptible species to sudden oak death in California

Knowledge of population genetic structure of tanoak (Lithocarpus densiflorus) is of interest to pathologists seeking natural variation in resistance to sudden oak death disease, to resource managers who need indications of conservation priorities in this species now threatened by the introduced pathogen (Phytophthora ramorum), and to biologists with interests in demographic processes that have shaped plant populations. We investigated population genetic structure using nuclear and chloroplast DNA (cpDNA) and inferred the effects of past population demographic processes and contemporary gene flow. Our cpDNA results revealed a strong pattern of differentiation of four regional groups (coastal California, southern Oregon, Klamath mountains, and Sierra Nevada). The chloroplast haplotype phylogeny suggests relatively deep divergence of Sierra Nevada and Klamath populations from those of coastal California and southern Oregon. A widespread coastal California haplotype may have resulted from multiple refugial sites during the Last Glacial Maximum or from rapid recolonization from few refugia. Analysis of nuclear microsatellites suggests two major groups: (1) central coastal California and (2) Sierra Nevada/Klamath/southern Oregon and an area of admixture in north coastal California. The low level of nuclear differentiation is likely to be due to pollen gene flow among populations during postglacial range expansion.     

Population genetic structure in European populations of Spiranthes romanzoffiana set in the context of other genetic studies on orchids

Spiranthes romanzoffiana Cham. is restricted in Europe to the British Isles, where it is recognised as a conservation priority species due to frequent extirpation of populations along with no evidence of seed set; vegetative reproduction has been invoked as the sole means of perpetuation and dispersal. To investigate the reproductive ecology of this species, 17 populations have been sampled for chloroplast microsatellites and amplified fragment length polymorphisms (AFLPs). These markers revealed a previously unsuspected genetic-geographic split in the species, which correlates with differences in patterns of within-population variation. Northern populations were fixed for one chloroplast haplotype but showed high levels of AFLP genotypic diversity consistent with sexual reproduction (proportion of genotypes distinguishable, PD = 0.98). More southerly populations showed fixed differences from the northern populations in their chloroplast haplotype and for 10 AFLP markers. They harboured only 12 unique multilocus genotypes among 113 individuals from six populations (PD = 0.11). These genotypes differed mostly by single bands, and none by more than 4/138 loci, with identical multilocus genotypes occurring in widely separated populations. This uniformity in southern populations is consistent with agamospermous or autogamous reproduction, and/or an extreme population bottleneck. Finally, the observed patterns of population differentiation in S. romanzoffiana are compared with other studies of orchids, revealing a wide range of values that belie recent contrasting published generalisations that claim that orchids show either higher, or lower, levels of population differentiation than other plant families.     

药食同源植物薤白的谱系地理学研究

对我国14个地区的药食同源植物薤白（Allium macrostemon）的叶绿体基因片段（psbA-trnH、rps16和trnL-F）与核基因片段（ITS）进行测序分析,揭示薤白的遗传变异分布式样、单倍型地理分布格局,并推断其在第四纪冰期的避难所。结果表明：薤白叶绿体基因（cpDNA）遗传多样性低于核基因（nrDNA）遗传多样性（cpDNA：H_T=0.868;nrDNA：H_T=0.890）。cpDNA和nrDNA的分子变异分析（AMOVA）结果显示：薤白遗传变异主要发生在居群间（cpDNA：92.84%;nrDNA：98.40%）,存在遗传分化（cpDNA：N_st=0.918,G_st=0.866,F_st=0.928;nrDNA：N_st=0.984,G_st=0.855,F_st=0.984）,且N_st均大于G_st,表明该物种具有明显的谱系地理结构。在薤白居群中,共检测到11个叶绿体单倍型和14个nrDNA基因型;单倍型网络图及地理分布图表明,叶绿体单倍型H3、核DNA基因型H1频率最高,位于网络结构图的中心位置,可能为古老单倍型。此外,冰期避难所假说认为遗传多样性高、拥有古老单倍型和较多特有单倍型的区域可能是该物种的冰期避难所,因此推测薤白在第四纪冰期时可能在大盘山、天水和通化地区存在多个冰期避难所。这些分析可为类似草本植物的进化提供参考,丰富对东亚草本植物分子系统与生物地理学的认识。     

Quaternary range dynamics of ecologically divergent species (Edraianthus serpyllifolius and E. tenuifolius,Campanulaceae) within the Balkan refugium

Aim We investigated Quaternary range dynamics of two closely related but ecologically divergent species (cold‐tolerant Edraianthus serpyllifolius and thermophilic Edraianthus tenuifolius) with overlapping distribution ranges endemic to the western Balkan Peninsula, an important yet understudied Pleistocene refugium. Our aims were: to test predictions of the ‘refugia‐within‐refugia’ model of strong genetic subdivisions due to population isolation in separate refugia; to explore whether two ecologically divergent species reacted differently to Pleistocene climatic fluctuations; and to test predictions of the displacement refugia model of stronger differentiation among populations in the thermophilic E. tenuifolius compared with the cold‐tolerant E. serpyllifolius. Location The western Balkan Peninsula. Methods We gathered amplified fragment‐length polymorphism (AFLP) data and plastid DNA sequences from two to five individuals from 10 populations of E. serpyllifolius and 22 populations of E. tenuifolius, spanning their entire respective distribution areas. AFLP data were analysed using a Bayesian clustering approach and a distance‐based network approach. Plastid sequences were used to depict relationships among haplotypes in a statistical parsimony network, and to obtain age estimates in a Bayesian framework. Results In E. serpyllifolius, both AFLP and plastid sequence data showed clear geographic structure. Western populations showed high AFLP diversity and a high number of rare fragments. In E. tenuifolius, both markers congruently identified a major phylogeographic split along the lower Neretva valley in central Dalmatia. The most distinct and earliest diverging chloroplast DNA (cpDNA) haplotypes were found further south in the south‐easternmost populations. North‐western populations, identified as a separate cluster by Bayesian clustering, were characterized by low genetic diversity and a low number of rare AFLP markers. Main conclusions Clear evidence for multiple Pleistocene refugia is found not only in the high‐elevation E. serpyllifolius, but also in the lowland E. tenuifolius, despite the lack of obvious dispersal barriers, in line with the refugia‐within‐refugia model. Genealogical relationships and genetic diversity patterns support the hypothesis that cold‐adapted E. serpyllifolius responded to climatic oscillations mostly by elevational range shifts, whereas thermophilic E. tenuifolius did so mainly by latitudinal range shifts, with different phases (and probably extents) of range expansion. In contrast to the displacement refugia hypothesis, the two elevationally differentiated species do not differ in their genetic diversity.