Postglacial population growth of Cunninghamia konishii (Cupressaceae) inferred from phylogeographical and mismatch analysis of chloroplast DNA variation

Phylogeographical and mismatch analysis of chloroplast DNA (cpDNA) variation were used to infer the temporal dynamics of distributional and demographic history of Taiwan fir (Cunninghamia konishii). We examined 64 and 52 trees from 17 populations of C. konishii and 14 provenances of C. lanceolata, respectively, by sequencing three intergenic spacers and one intron using cpDNA universal primers. Of the aligned 1888 base pairs (bp) sequence, 30 varied among 28 haplotypes, which consisted of three transitions, 14 transversions and 13 indels. One ancestral haplotype was found in 86 individuals across the surveyed range of both species, C. konishii and C. lanceolata, which was distributed in all populations and provenances. The 28 haplotypes also included 15 C. konishii specific and 12 C. lanceolata-specific haplotypes. Ancestral haplotype was found fixed in five populations of C. konishii and five provenances of C. lanceolata. Other haplotypes occurred mainly as singletons. The levels of population differentiation studied are relatively low in both Cunninghamia species. The nucleotide diversity (theta) of chloroplast DNA sequences within C. konishii was slightly higher than that of C. lanceolata. Excess in singletons as well as star-like phylogeny of haplotypes suggested no clearcut migration patterns of C. konishii after glacial maximum. One probable demographic history of C. konishii is the postglacial population growth of C. konishii after a glacial bottleneck event. This inference is supported by the combined results of fossil pollen record, low nucleotide diversity, significant Tajima's d-value, phylogeographical analysis and unimodal mismatch distribution. Similarities and discrepancies between our results and those of Lu et al. (2001) are discussed.     

Genetic diversity and biogeography of Cunninghamia konishii (Cupressaceae), an island species in Taiwan: a comparison with Cunninghamia lanceolata, a mainland species in China

Luanta-fir (Cunninghamia konishii), an endemic to Taiwan, is an outcrossing, long-lived conifer. Populations of C. konishii are generally fragmented due to a once high intensity of timber exploitation. C. konishii and Cunninghamia lanceolata are two sibling taxa constituting derivative-progenitor species relationship. The amount of genetic variations within and between 11 and 10 populations of C. konishii and C. lanceolata, respectively, were assessed using amplified fragment length polymorphism (AFLP) markers in this report. Three AFLP primer pairs generated a total of 357 and 226 markers for C. konishii and C. lanceolata samples, of which 56.1 and 65.3% are polymorphic, respectively. Analysis of molecular variance indicates a 4.78% variation between C. konishii and C. lanceolata. A relatively high value of genetic variation (24.60%) was apportioned between the populations of C. konishii. In contrast, a lower divergence value (12.21%) between populations was found for C. lanceolata. The population with the highest genetic diversity was found in Nantou County, which concurred with the results of many other tree species investigated in Taiwan. The estimates of the number of migrants between populations (Nm), obtained from population pair-wise PhiST, suggest that gene flow in C. konishii is efficient in some adjacent populations but is restricted in the rest. Individual UPGMA tree, generated based on AFLP markers, suggests six evolutionary lineages for C. konishii. All evolutionary lineages of C. konishii were derived from C. lanceolata. In conclusion, the migration patterns of Cunninghamia from mainland China may have been established following multiple sources, migrant-pools, long-distance dispersal events, and via different directions.     

Phylogeography of Sylvirana latouchii (Anura, Ranidae) in Taiwan

Biogeographic studies are important for understanding the natural history of faunas. To comprehend the geographical patterns of genetic variation in anurans in Taiwan, we investigated the genetic structure of Sylvirana latouchii (Anura, Ranidae) from 31 populations by using mitochondrial DNA (mtDNA) cytochrome b sequences. A neighbor-joining tree of 38 haplotypes revealed three major divergences in Taiwanese S. latouchii: the northern, western, and eastern-and-southern clades. Each clade was restricted to a single geographical district and showed obvious differentiation. The patterns of geographical divergence in this species reflect common historical events experienced by other native animals distributed in Taiwan. The order of divergence times between clades was inferred using a molecular clock test. The population relationship of S. latouchii between Taiwan and mainland China is discussed. Further study employing more populations of S. latouchii from mainland China is necessary to clarify the original geographical patterns and migratory history of this species.     

Genome-wide RAD sequencing data suggest predominant role of vicariance in Sino-Japanese disjunction of the monotypic genus Conandron (Gesneriaceae)

Disjunct distribution is a key issue in biogeography and ecology, but it is often difficult to determine the relative roles of dispersal vs. vicariance in disjunctions. We studied the phylogeographic pattern of the monotypic Conandron ramondioides (Gesneriaceae), which shows Sino-Japanese disjunctions, with ddRAD sequencing based on a comprehensive sampling of 11 populations from mainland China, Taiwan Island, and Japan. We found a very high degree of genetic differentiation among these three regions, with very limited gene flow and a clear Isolation by Distance pattern. Mainland China and Japan clades diverged first from a widespread ancestral population in the middle Miocene, followed by a later divergence between mainland China and Taiwan Island clades in the early Pliocene. Three current groups have survived in various glacial refugia during the Last Glacial Maximum, and experienced contraction and/or bottlenecks since their divergence during Quaternary glacial cycles, with strong niche divergence between mainland China + Japan and Taiwan Island ranges. Thus, we verified a predominant role of vicariance in the current disjunction of the monotypic genus Conandron. The sharp phylogenetic separation, ecological niche divergence among these three groups, and the great number of private alleles in all populations sampled indicated a considerable time of independent evolution, and suggests the need for a taxonomic survey to detect potentially overlooked taxa.     

中国穗状狐尾藻遗传多样性的初步分析

利用叶绿体DNA三个片段(trnK-matK、trnL-trnF、rpl32-trnL)对中国大陆广布的水生植物穗状狐尾藻(Myriophyllum spicatum L.)的遗传多样性进行了初步分析,以探讨其自然居群的遗传结构及具有广泛分布格局的可能机制。AMOVA分析显示,穗状狐尾藻8个居群间的遗传变异为84.97%,而居群内的遗传变异为15.03%,居群遗传分化系数(Fst)为0.85,表明穗状狐尾藻具有较高的遗传多样性(Hd=0.83)且主要存在于居群间,奠基者效应可能导致了最初的遗传差异,而隔离障碍(Nm=0.09)又进一步导致了居群间的遗传分化。基于17个单倍型构建的系统发育树和网络关系图均显示,单倍型H5和H6在居群中的分布范围最广且出现频率最高,表明H5和H6可能为最古老的祖先单倍型。Mantel检验表明居群间的遗传距离与地理距离之间不存在显著的相关性,失配分布检测结果显示穗状狐尾藻在历史上曾发生过扩张事件,而Tajima’s、FuLi’s D*和F*检测发现,该物种不存在明显的谱系地理格局,这可能与穗状狐尾藻种子的长距离扩散有关。     

基于cpDNA非编码序列的北沙柳遗传多样性分析

为揭示北沙柳(Salix psammophila)的遗传多样性、遗传结构及分化特征,利用叶绿体非编码区序列(trnL-trnF和trnD-trnT)对分布于毛乌素沙地和库布齐沙漠的16个北沙柳居群(339个个体)进行了遗传研究,为北沙柳种子资源库遗传管理、遗传改良、遗传育种及品种选育提供理论依据。结果表明:(1)经trnL-trnF和trnD-trnT片段联合比对获得了1811 bp序列,共有12个核苷酸变异位点(8个简约信息位点,4个变异位点),得到16个单倍型。(2)单倍型多样性指数(Hd)为0.737,核苷酸多样性指数(π)为0.00107;且单倍型H3的分布在所有居群中位于单倍型网络图中心,其余单倍型随机分布于各个居群。(3)AMOVA分析表明,北沙柳cpDNA的变异主要来源于居群内(91.16%),居群间遗传分化程度中等(FST=0.08837),各居群间的基因交流非常频繁(Nm=2.58);遗传分化系数NST(0.085)显著大于GST(0.056,0.01相似文献   

Distinct Phylogeographic Structures of Wild Radish (Raphanus sativus L. var. raphanistroides Makino) in Japan

Coastal plants with simple linear distribution ranges along coastlines provide a suitable system for improving our understanding of patterns of intra-specific distributional history and genetic variation. Due to the combination of high seed longevity and high dispersibility of seeds via seawater, we hypothesized that wild radish would poorly represent phylogeographic structure at the local scale. On the other hand, we also hypothesized that wild radish populations might be geographically differentiated, as has been exhibited by their considerable phenotypic variations along the islands of Japan. We conducted nuclear DNA microsatellite loci and chloroplast DNA haplotype analyses for 486 samples and 144 samples, respectively, from 18 populations to investigate the phylogeographic structure of wild radish in Japan. Cluster analysis supported the existence of differential genetic structures between the Ryukyu Islands and mainland Japan populations. A significant strong pattern of isolation by distance and significant evidence of a recent bottleneck were detected. The chloroplast marker analysis resulted in the generation of eight haplotypes, of which two haplotypes (A and B) were broadly distributed in most wild radish populations. High levels of variation in microsatellite loci were identified, whereas cpDNA displayed low levels of genetic diversity within populations. Our results indicate that the Kuroshio Current would have contributed to the sculpting of the phylogeographic structure by shaping genetic gaps between isolated populations. In addition, the Tokara Strait would have created a geographic barrier between the Ryukyu Islands and mainland Japan. Finally, extant habitat disturbances (coastal erosion), migration patterns (linear expansion), and geographic characteristics (small islands and sea currents) have influenced the expansion and historical population dynamics of wild radish. Our study is the first to record the robust phylogeographic structure in wild radish between the Ryukyu Islands and mainland Japan, and might provide new insight into the genetic differentiation of coastal plants across islands.     

Allopatric divergence and regional range expansion of Juniperus sabina in China

In this study, we aimed to study the phylogeographic pattern of Juniperus sabina, a shrub species commonly occurring in the northern, northwestern and western China. We sequenced three chloroplast DNA fragments (trnL-trnF, trnS-trnG, and trriD-trriT) for 137 individuals from 16 populations of this species. Five chloroplast DNA chlorotypes (A, B, C, D, and E) were identified and they showed no overlapping distribution. The population subdivision is very high (GST = 0.926, NST= 0.980), suggesting a distinct phylogeographic structure (NST > GST, P < 0.05). Phylogenetic analyses of the five chlorotypes were clustered into three clades, consistent with their respective distributions in three separate regions: northern Xinjiang, western Xinjiang, and northern-northwestern China. However, within each region, the interpopulation differentiation is extremely low. These results as well as statistical tests suggested distinct allopatric differentiations between regional populations and independent glacial refugia for postglacial recolonization. The deserts that developed during the late Quaternary might have acted as effective barriers to promote genetic differentiation among these regions. However, the low diversity dominated by the single chlorotype within each fragmented region suggested that all current populations were derived from a common regional range expansion.     

Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan

Nucleotide sequences of 3' end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5' end of the 12S rRNA of mitochondrial DNA (mtDNA) were used to assess the genetic and phylogeographic structure of Acrossocheilus paradoxus populations, a Cyprinidae fish of Taiwan. A hierarchical examination of populations in 12 major streams from three geographical regions using an analysis of molecular variance (AMOVA) indicates high genetic differentiation both among populations (PhiST = 0.511, P < 0.001) and among regions (PhiCT = 0.368, P < 0.001). Limited migration largely contributed to the genetic differentiation. High nucleotide diversity (1.13%) and haplotype diversity (0.80%) were detected among populations. The degree of genetic differentiation was correlated with geographical distance between populations, a result consistent with the one-dimensional stepping stone models. A neighbour-joining tree recovered by (DAMBE) supports the pattern of isolation by distance and reveals a closer relationship between populations of the central and southern regions. A minimum spanning network based on nucleotide substitutions reflected migration routes from populations of the central region to the northern and southern regions, respectively. Postglacial colonization and expansion can explain the phylogeographical pattern. Single and ancient migration events may have allowed the northern region to attain the monophyly of mtDNA alleles. In contrast, most populations within geographical regions are either paraphyletic or polyphyletic due to the relatively shorter time period for coalescence. Both low haplotype number and genetic variability suggest a bottleneck event in the Chingmei population of northern Taiwan. Based on coalescence theory, the monophyly of the Tungkang population of the southern region may be associated with a founder event.     

Source populations of Quercus glauca in the last glacial age in Taiwan revealed by nuclear microsatellite markers

In this work, we attempted to study genetic differentiation between populations of Quercus glauca in Taiwan using nuclear microsatellite markers to infer the potential refugium in the last glaciation stage. Four microsatellite loci for 20 individuals each in 10 populations of Taiwan were analyzed. We found that Q. glauca has relatively high within-population diversity (H(E) = 0.741) and low population differentiation (F(ST) = 0.042) but shows isolation by distance. The most divergent populations, according to the average F(ST) for individual populations in comparison with every other population, were found in populations Cy, Sa, and Hy in southern Taiwan and Pa in north-central Taiwan. Moreover, populations Cy, Sa, and Pa were recognized as being the source populations for gene recolonization after the last glaciation stage. In addition, the three sites of Wu, Ym, and Cy exhibited the highest gene diversities that coincided with populations with the highest chloroplast DNA variations. This may have resulted from an admixture of colonization routes. In conclusion, observations of the most divergent populations and source populations suggest that southern and probably north-central Taiwan may have potentially been refugia for Q. glauca in the last glaciation. This agrees with the possible refugium in southern Taiwan revealed by a previous study using chloroplast DNA markers.     

Phylogeography of the fanged dicroglossine frog, Limnonectes fujianensis (Anura, Ranidae), in Taiwan

A phylogenetic analysis of Taiwanese fanged dicroglossine frog, Limnonectes fujianensis (Anura, Ranidae), was conducted to examine its genetic diversification using sequence data from a portion of the mitochondrial DNA (mtDNA) cytochrome b sequences. We collected genetic data from 200 individuals at 23 localities in Taiwan and three localities in China. A neighbor-joining tree of 39 haplotypes revealed two clades in Taiwan and a clade in China, each showing restricted geographical distribution. The pattern of geographical divergence suggests a single invasion into Taiwan. Divergence times between clades were inferred using molecular clock tests. The population relationship of L. fujianensis between Taiwan and mainland China, and the phylogenetic relationships with its congeners, e.g., L. bannaensis, L. fragilis and L. kuhlii, were obtained and discussed.     

Molecular phylogeny of diploid Hordeum species and incongruence between chloroplast and nuclear datasets

The phylogeny of diploid Hordeum species has been studied using both chloroplast and nuclear gene sequences. However, the studies of different nuclear datasets of Hordeum species often arrived at similar conclusions, whereas the studies of different chloroplast DNA data generally resulted in inconsistent conclusions. Although the monophyly of the genus is well supported by both morphological and molecular data, the intrageneric phylogeny is still a matter of controversy. To better understand the evolutionary history of Hordeum species, two chloroplast gene loci (trnD-trnT intergenic spacer and rps16 gene) and one nuclear marker (thioreoxin-like gene (HTL)) were used to explore the phylogeny of Hordeum species. Two obviously different types of trnD-trnT sequences were observed, with an approximately 210 base pair difference between these two types: one for American species, another for Eurasian species. The trnD-trnT data generally separated the diploid Hordeum species into Eurasian and American clades, with the exception of Hordeum marinum subsp. gussoneanum. The rps16 data also grouped most American species together and suggested that Hordeum flexuosum has a different plastid type from the remaining American species. The nuclear gene HTL data clearly divided Hordeum species into two clades: the Xu+H genome clade and the Xa+I genome clade. Within clades, H genome species were well separated from the Xu species, and the I genome species were well separated from the Xa genome species. The incongruence between chloroplast and nuclear datasets was found and discussed.     

Phylogeography of Chrysanthemum indicum L. (Compositae) in China based on trnL-F sequences

Using chloroplast DNA (cpDNA) trnL-F sequences, we studied the phylogeographic pattern and demographic history of Chrysanthemum indicum with 81 individuals from 27 populations representing the partial geographic range in China. Fifteen haplotypes were identified based on nucleotide variation. Relatively high levels of haplotype diversity (Hd = 0.783) and low levels of nucleotide diversity (Pi = 0.00521) were detected in C. indicum. An analysis of molecular variance (AMOVA) indicated that most of the genetic variation (59.9%, P < 0.001) was partitioned within populations. Genetic differentiation among populations was high (F_ST = 0.35), suggesting that there is little gene flow among populations. Nested clade analysis showed that 15 haplotypes formed twelve 1-step clades, five 2-step clades and two 3-step clades, with four clades showing significant geographical association. We concluded that contiguous range expansion and restricted gene flow/dispersal but with some long distance dispersal seemed to have shaped the present-day distribution of the haplotypes of C. indicum in China.     

Phylogeography of the widespread plant Ailanthus altissima (Simaroubaceae) in China indicated by three chloroplast DNA regions

Ailanthus altissima (Mill.) Swingle, a temperate tree species, has a wide distribution in China. To infer its refugia and patterns of migration during past climatic changes in China, genetic variations among different populations were studied. Gene sequences of three chloroplast DNA spacer regions, psbA-trnH, trnL-trnF, andtrnD-trnT, were obtained from 440 individuals of 44 populations. The distribution of haplotype and the relationships among them were investigated by haplotype network. In addition, the genetic diversity of the sampled regions was inferred, and the biogeographic history was also reconstructed. Twelve haplotypes were identified, among which, five were unique. The phylogenetic analysis and geographical distribution of haplotypes indicate that multiple glacial refugia existed in mainland China during the Quaternary oscillations. Due to the combined effects of contiguous range expansion and allopatric fragmentation, significant genetic structure was not found in this study. Based on biogeographic and demographic analysis, three main dispersal routes were identified for the major haplotypes, whereas others were more likely localized demographic expansion.     

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

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.     

Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex

Species whose geographical distribution encompasses both mainland and island populations provide an ideal system for examining isolation and genetic divergence. In this study, paternally transmitted chloroplast DNA (cpDNA) and maternally transmitted mitochondrial DNA (mtDNA) were used to estimate population structure and phylogeography of Pinus luchuensis, a species found in eastern China (ssp. hwangshanensis), Taiwan (ssp. taiwanensis), and the Ryukyu Archipelago (ssp. luchuensis). Gene genealogies of both mtDNA and cpDNA reveal two major lineages. Molecular dating indicates that these lineages diverged before the colonization of P. luchuensis subspecies in Taiwan and the Ryukyu Archipelago. Both mtDNA and cpDNA show a lack of correspondence between molecular phylogeny and subspecies designation. Phylogeographical analysis suggests that paraphyly of the subspecies is the result of recent divergence rather than secondary contacts. In spite of the short divergence history of P. luchuensis on islands, the island populations show the same degree of genetic divergence as mainland populations. Low levels of genetic diversity in the mainland ssp. hwangshanensis suggest demographic bottlenecks. In contrast, the high heterogeneity of genetic composition for island populations is likely to be associated with a history of multiple colonization from the mainland. The spatial apportionment of organelle DNA polymorphisms is consistent with a pattern of stepwise colonization on island populations.     

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

 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 (Φ_ST = 0.471) and among regions (Φ_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. Received: July 2, 2001 / Accepted: February 20, 2002     

Montane refugia isolation and plateau population expansion: Phylogeography of Sino-Himalayan endemic Spenceria ramalana (Rosaceae)

Climate oscillations and landscape heterogeneity make the historical population processes of organisms of the Qinghai–Tibet Plateau quite complex. We used chloroplast DNA sequences and amplified fragment length polymorphism (AFLPs) to study the phylogeography and genetic variation of the Qinghai–Tibet Plateau endemic Spenceria ramalana Trimen. The parsimony network contains two star-like evolutionary units, nested into two nested clades, coinciding with geographic population groups indicated by samova software. The central group shows genetic homogeneity, indicating a bottleneck or founder effect of population dynamics. Margin groups contribute more haplotype diversity (C_T), indicating potential refugia. Several expansion events during several interglacial periods were detected. The latest expansion of the eastern population contributed to the modern population structure of the central area. Four AFLP clusters were detected. Higher C_T, a relict pattern of haplotype distribution and DW values of marginal populations, confirmed the location of potential montane refugia. Relict distribution pattern, nested clade phylogeographic analysis conclusions, and restricted gene flow detected by AFLPs indicated an isolation pattern of the populations of montane areas. Heterogeneity of landscape of the western and southern montane areas could be the main barrier for gene flow. Moisture conditions and ecotype transformation might help to build the phylogeographic pattern of this species. Neither chloroplast DNA markers nor AFLP was able to differentiate the two varieties of this species.     

Identifying main evolutionary mechanisms shaping genetic variation of Leuciscus cephalus L. 1758 (Cyprinidae) in western Greece: discordance between methods.

Numerous methods can be used in intraspecific phylogeographic studies to infer the evolutionary mechanisms that shaped observed genetic variation in populations. However, these methods are scarcely used jointly, and the evolutionary outcomes they could propose are not fully compared. In this study, using a chub (Leuciscus cephalus; Cyprinidae) mitochondrial DNA data set (13 populations in Western Greece, 14 haplotypes), we compare three distinct 'historical' methods that could possibly infer relative importance of basic evolutionary mechanisms (isolation vs migration) shaping genetic variation: the nested clade analysis, the psi-test and the 'mismatch distributions'. Taking together, interpretations of these analyses allow to draw a picture of the evolutionary history of chub in Western Greece based on isolation and genetic drift for higher clades. However, results issued each method can differ for low differentiated clades. We discuss such differences and suggest that methods should be used jointly in phylogeographic studies for a better evaluation of the evolutionary mechanisms that shaped genetic variation.     

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.