High Genetic Diversity and Population Differentiation in the Critically Endangered Plant Species Trailliaedoxa gracilis (Rubiaceae)

Trailliaedoxa gracilis W. W. Smith et Forrest (Rubiaceae), a Chinese endemic monotypic genus belonging to the Alberteae (Rubiaceae), exhibits a narrow distribution in the dry valleys of the Jinsha River and Red River drainage area in southwestern China. The few sites at which T. gracilis occurs are fragmented and isolated, and several are highly vulnerable to human disturbance. As T. gracilis is a protected plant with a second-degree national priority, the genetic diversity and structure of the populations of this species should be investigated to determine the most suitable conservation strategy. In this study, two chloroplast regions and one nuclear region were used to investigate the genetic diversity, genetic structure, and demographic history of T. gracilis. We observed a high total genetic diversity (H _T?=?0.952 and 0.966) and low average within-population diversity (H _S?=?0.07 and 0.489) based on cpDNA and nDNA analyses. Thus, a strong genetic structure (F _ST?=?0.98049 and 0.59731) was detected. A phylogeographic structure was detected by nuclear DNA analysis (N _ST?>?G _ST, P?<?0.05); however, the chloroplast data did not show a significant phylogeographic structure (N _ST?<?G _ST, P?>?0.05). The Bayesian skyline plot and isolation with migration analysis were used to estimate the demographic history of T. gracilis. The results indicated that a marked bottleneck effect occurred during the glacial-interglacial of the Pleistocene. Among the extant populations of T. gracilis, the population found in ChunJiang, LuQuan, and YuXi showed the highest haplotype diversity based on cpDNA sequences and should be given priority for protection. According to the nDNA analysis, every population presented a high level of diversity and a high content of private haplotypes. Therefore, every population should be protected.

     

Contemporary habitat loss reduces genetic diversity in an ecologically specialized butterfly

Aim This study investigated the influence of contemporary habitat loss on the genetic diversity and structure of animal species using a common, but ecologically specialized, butterfly, Theclinesthes albocincta (Lepidoptera: Lycaenidae), as a model. Location South Australia. Methods We used amplified fragment length polymorphism (AFLP) and allozyme datasets to investigate the genetic structure and genetic diversity among populations of T. albocincta in a fragmented landscape and compared this diversity and structure with that of populations in two nearby landscapes that have more continuous distributions of butterflies and their habitat. Butterflies were sampled from 15 sites and genotyped, first using 363 informative AFLP bands and then using 17 polymorphic allozyme loci (n = 248 and 254, respectively). We complemented these analyses with phylogeographic information based on mitochondrial DNA (mtDNA) haplotype information derived from a previous study in the same landscapes. Results Both datasets indicated a relatively high level of genetic structuring across the sampling range (AFLP, F_ST = 0.34; allozyme, F_ST = 0.13): structure was greatest among populations in the fragmented landscape (AFLP, F_ST = 0.15; allozyme, F_ST = 0.13). Populations in the fragmented landscape also had significantly lower genetic diversity than populations in the other two landscapes: there were no detectable differences in genetic diversity between the two continuous landscapes. There was also evidence (r² = 0.33) of an isolation by distance effect across the sampled range of the species. Main conclusions The multiple lines of evidence, presented within a phylogeographic context, support the hypothesis that contemporary habitat fragmentation has been a major driver of genetic erosion and differentiation in this species. Theclinesthes albocincta populations in the fragmented landscape are thus likely to be at greater risk of extinction because of reduced genetic diversity, their isolation from conspecific subpopulations in other landscapes, and other extrinsic forces acting on their small population sizes. Our study provides compelling evidence that habitat loss and fragmentation have significant rapid impacts on the genetic diversity and structure of butterfly populations, especially specialist species with particular habitat preferences and poor dispersal abilities.     

Plastid DNA variation in highly fragmented populations of <Emphasis Type="Italic">Microbiota decussata</Emphasis> Kom. (Cupressaceae), an endemic to Sikhote Alin Mountains

Microbiota decussata Kom. (Cupressaceae) is a subalpine species endemic to the Sikhote Alin Mountains with populations scattered throughout the range. We used sequence data for four noncoding regions of chloroplast DNA to characterize the genetic diversity in populations sampled from different parts of M. decussata natural range. No variation was observed in the trnT–trnF region, whereas the trnH–psbA, trnS–trnfM, and trnS–trnG regions showed polymorphisms. At the species level, we found a low nucleotide diversity (π = 0.0009) and high haplotype diversity (h = 0.981) as well as high differentiation (Φ_ST = 0.420). N _ST and G _ST values suggested the existence of a phylogeographic structure in M. decussata. The observed patterns of diversity could be explained in part by ecological features of the species and its long-term persistence throughout the range with population expansion, successive fragmentation and isolation.     

Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine (Perisoreus canadensis)

An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, Φ_ST, SAMOVA, F_ST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.     

Strong Genetic Differentiation of Primula sikkimensis in the East Himalaya–Hengduan Mountains

The East Himalaya-Hengduan Mountains region is the center of diversity of the genus Primula, and P. sikkimensis is one of the most common members of the genus in the region. In this study, the genetic diversity and structure of P. sikkimensis populations in China were assessed using inter-simple sequence repeat (ISSR) and chloroplast microsatellite markers. The 254 individuals analyzed represented 13 populations. High levels of genetic diversity were revealed by ISSR markers. At the species level, the expected heterozygosity and Shannon’s index were 0.4032 and 0.5576, respectively. AMOVA analysis showed that 50.3% of the total genetic diversity was partitioned among populations. Three pairs of chloroplast microsatellite primers tested yielded a total of 12 size variants and 15 chloroplast haplotypes. Strong cpDNA genetic differentiation (G _ST = 0.697) and evidence for phylogeographic structure were detected (N _ST = 0.788, significantly higher than G _ST). Estimated rates of pollen-mediated gene flow are approximately 27% greater than estimated rates of seed-mediated gene flow in P. sikkimensis. Both seed and pollen dispersal, however, are limited, and gene flow among populations appears to be hindered by the patchiness of the species’ habitats and their geographic isolation. These features may have played important roles in shaping the genetic structure of P. sikkimensis. A minimum-spanning tree of chloroplast DNA haplotypes was constructed, and possible glacial refugia of P. sikkimensis were identified.     

Population structure and colonization of Bactrocera dorsalis (Diptera: Tephritidae) in China,inferred from mtDNA COI sequences

The oriental fruit fly, Bactrocera dorsalis, is a serious pest of fruits and vegetables in South‐east Asia, and, because of quarantine restrictions, impedes international trade and economic development in the region. Revealing genetic variation in oriental fruit fly populations will provide a better understanding of the colonization process and facilitate the quarantine and management of this species. The genetic structure in 15 populations of oriental fruit fly from southern China, Laos and Myanmar in South‐east Asia was examined with a 640‐bp sequence of the mitochondrial cytochrome oxidase subunit I (COI) gene. The highest levels of genetic diversity were found in Laos and Myanmar. Low to medium levels of genetic differentiation (F_ST ≤ 0.134) were observed among populations. Pooled populations from mainland China differed from those in Laos and Myanmar (F_ST = 0.024). Genetic structure across the region did not follow the isolation‐by‐distance model. The high genetic diversity observed in Laos and Myanmar supports the South‐east Asian origin of B. dorsalis. High genetic diversity and significant differentiation between some populations within mainland China indicate B. dorsalis populations have been established in the region for an extended period of time. High levels of genetic diversity observed among the five populations from Hainan Island and similarity between the Island and Chinese mainland populations indicate that B. dorsalis was introduced to Hainan from the mainland and has been on the island for many years. High genetic diversity in the recently established population in Shanghai (Pudong) suggests multiple introductions or a larger number of founders.     

Genetic diversity and structure of Cordyceps sinensis populations from extensive geographical regions in China as revealed by inter-simple sequence repeat markers

Cordyceps sinensis is one of the most valuable medicinal caterpillar fungi native to China. However, its productivity is extremely limited and the species is becoming endangered. The genetic diversity of eighteen C. sinensis populations across its major distributing regions in China was evaluated by inter-simple sequence repeat (ISSR) markers. A total of 141 markers were produced in 180 individuals from the 18 populations, of which 99.3% were polymorphic. The low average of Shannon (0.104) and Nei index (0.07) of the 18 populations indicates that there are little genetic variations within populations. For all 18 populations, estimates of total gene diversity (H_T), gene diversity within populations (H_S), coefficient of genetic differentiation (G_ST), and gene flow (Nm) were 0.170, 0.071, 0.583, and 0.357, respectively. This pattern suggests that the genetic diversity of C. sinensis is low and most of the ISSR variations are found among populations with little gene exchange. The 18 populations are divided into five groups based on the genetic distance and the grouping pattern matches with the geographic distribution along the latitudinal gradient. The five groups show obvious difference in the G_ST and Nm values. Therefore, the genetic diversification of C. sinensis populations may be determined by geographic isolation and the combined effects of life history characters and the interaction with host insect species. The information illustrated by this study is useful for selecting in situ conservation sites of C. sinensis.     

Molecular phylogeography of Fagus engleriana (Fagaceae) in subtropical China: limited admixture among multiple refugia

Beech is one of the most important trees in the temperate and subtropical forests of the Northern Hemisphere. Despite Chinese beeches have the particularity that only grow in subtropical areas, they have received few phylogeographic research. In this study, we sampled 25 populations of the northernmost-distributed Chinese beech, Fagus engleriana, and detected six haplotypes across 350 individuals by using sequences of two chloroplast intergenic spacers. The chloroplast genetic diversity was relatively low (h _T?=?0.659), with most genetic variance residing among populations (G _ST?=?0.831, N _ST?=?0.855, G _ST??N _ST). SAMOVA analysis indicated that populations clustered into six groups with little admixture among them (most groups were characterized by a unique hapotype). Pairwise difference among haplotypes and Fu??s Fs statistic indicated that populations of F. engleriana have not experienced recent sudden expansions. Both the phylogeographic and demographic patterns found in this study suggest that F. engleriana remained fragmented in multiple refugia throughout the Pleistocene climatic changes, and experienced limited both glacial and interglacial/postglacial expansion. The results of this study imply that long-term isolation among multiple refugia, coupled with little admixture among populations of different refugia provided numerous opportunities for population divergence and allopatric speciation, which might be a driving factor for the exceptionally broad temperate species diversity in southern China.     

The phylogeography of Fagus hayatae (Fagaceae): genetic isolation among populations

The beech species Fagus hayatae is an important relict tree species in subtropical China, whose biogeographical patterns may reflect floral responses to climate change in this region during the Quaternary. Previous studies have revealed phylogeography for three of the four Fagus species in China, but study on F. hayatae, the most sparsely distributed of these species, is still lacking. Here, molecular methods based on eight simple sequence repeat (SSR) loci of nuclear DNA (nDNA) and three chloroplast DNA (cpDNA) sequences were applied for analyses of genetic diversity and structure in 375 samples from 14 F. hayatae populations across its whole range. Both nDNA and cpDNA indicated a high level of genetic diversity in this species. Significant fixation indexes and departures from the Hardy–Weinberg equilibrium, with a genetic differentiation parameter of R_st of 0.233, were detected in nDNA SSR loci among populations, especially those on Taiwan Island, indicating strong geographic partitioning. The populations were classified into two clusters, without a prominent signal of isolation‐by‐distance. For the 15 haplotypes detected in the cpDNA sequence fragments, there was a high genetic differentiation parameter (G_st = 0.712) among populations. A high G_st of 0.829 was also detected outside but not within the Sichuan Basin. Consistent with other Fagus species in China, no recent population expansion was detected from tests of neutrality and mismatch distribution analysis. Overall, genetic isolation with limited gene flow was prominent for this species and significant phylogeographic structures existed across its range except for those inside the Sichuan Basin. Our study suggested long‐term geographic isolation in F. hayatae with limited population admixture and the existence of multiple refugia in the mountainous regions of the Sichuan Basin and southeast China during the Quaternary. These results may provide useful information critical for the conservation of F. hayatae and other Chinese beech species.     

Distribution and polymorphism of Mariner-like elements in the Bambusoideae subfamily

Picea omorika (Pan?.) Purk. is a relict from the Arcto-Tertiary flora with its entire current natural range confined to an area of only 10,000 km² within the Balkans, a region well known as a Quaternary refugium. We have amplified the second intron of the mitochondrial NADH dehydrogenase subunit1 gene in 200 trees originating from ten natural populations to assess the phylogeographic structure and history of this conifer. Five haplotypes harbouring different numbers of 34-bp minisatellites were detected, revealing haplotypic richness of 3.007 and gene diversities H _S = 0.075 and H _T = 0.225. More interestingly, despite the very small distribution range of P. omorika and its dispersal by wind, non-random distribution of haplotypes was observed, resulting in an unexpectedly high estimate of population differentiation (G _ST = 0.668), and 56.8% of molecular variation assigned to variation among populations. Those findings suggest substantial isolation of populations and their partitioning into two gene pools characterized by different history and levels of genetic diversity, and very limited seed flow in this species (Nm = 0.25). They support the hypothesised early arrival of P. omorika in the Balkan region, and residence within this refugium during several ice ages at least. We demonstrate that the assessment of genetic diversity and structuring are not straightforward in species confined to refugial regions, and that past microvicariance might bias formal phylogeographic (G _ST = N _ST = 0.668) and isolation-by-distance analysis (r = 0.028, P > 0.05).     

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     

Spatial Patterns of Haplotype Variation in the Epiphytic Bromeliad Catopsis nutans

Identifying factors governing the origin, distribution, and maintenance of Neotropical plant diversity is an enduring challenge. To explore the complex and dynamic historical processes that shaped contemporary genetic patterns for a Central American plant species, we investigated the spatial distribution of chloroplast haplotypes of a geographically and environmentally widespread epiphytic bromeliad with wind‐dispersed seeds, Catopsis nutans, in Costa Rica. We hypothesized that genetic discontinuities occur between northwestern and southwestern Pacific slope populations, resembling patterns reported for other plant taxa in the region. Using non‐coding chloroplast DNA from 469 individuals and 23 populations, we assessed the influences of geographic and environmental distance as well as historical climatic variation on the genetic structure of populations spanning >1200 m in elevation. Catopsis nutans revealed seven haplotypes with low within‐population diversity (mean haplotype richness = 1.2) and moderate genetic structure (F_ST = 0.699). Pairwise F_ST was significantly correlated with both geographic and environmental distance. The frequency of dominant haplotypes was significantly correlated with elevation. A cluster of nine Pacific lowland populations exhibited a distinct haplotype profile and contained five of the seven haplotypes, suggesting historical isolation and limited seed‐mediated gene flow with other populations. Paleodistribution models indicated lowland and upland habitats in this region were contiguous through past climatic oscillations. Based on our paleodistribution analysis and comparable prior phylogeographic studies, the genetic signature of recent climatic oscillations are likely superimposed upon the distribution of anciently divergent lineages. Our study highlights the unique phylogeographic history of a Neotropical plant species spanning an elevation gradient.     

Population genetic structure and larval dispersal potential of spottedtail goby Synechogobius ommaturus in the north‐west Pacific

Larval dispersal may have an important effect on genetic structure of benthic fishes. To examine the population genetic structure of spottedtail goby Synechogobius ommaturus, a 478 base pair (bp) fragment of the hypervariable portion of the mtDNA control region was sequenced and used to interpret life‐history characteristics and larval dispersal strategy. Individuals (n = 186) from 10 locations on the coasts of China and Korea were analysed and 44 haplotypes were obtained. The levels of haplotype and nucleotide diversity were higher in East China Sea populations than in other populations. Both the phylogenetic tree and the minimum spanning tree showed that no significant genealogical structures corresponding to sampling locations existed. AMOVA and pair‐wise F_ST revealed significant genetic differentiation between populations from Korea and China. A significant isolation by distance pattern was observed in this species (r = 0·53, P < 0·001). Both mismatch distribution analysis and neutrality tests showed S. ommaturus to have experienced a recent population expansion. These results suggest that the Pleistocene ice ages had a major effect on the phylogeographic pattern of S. ommaturus, that larvae might avoid offshore dispersal and that dispersal of larvae may maintain a migration–drift equilibrium.     

The effects of Quaternary glaciations in Patagonia as evidenced by chloroplast DNA phylogeography of Southern beech Nothofagus obliqua

Climatic oscillations during the Quaternary strongly affected the distribution of warm-temperate tree species, which experienced local restrictions into ice-free areas and posterior expansions. To evaluate the impact of these range movements on the genetic structure of populations, we performed a phylogeographical analysis of the species Nothofagus obliqua with chloroplast DNA markers. A total of 27 populations covering the whole natural distribution range were analyzed using polymerase chain reaction-restriction fragment length polymorphism. Diversity (h _T, h _S), allelic richness (r _g), and differentiation among populations for unordered (G _ST) and ordered alleles (N _ST) were calculated. The relationships among haplotypes were evaluated by the construction of a minimum spanning network. The spatial distribution of the genetic variation was analyzed through a Mantel test and with a nested analysis of molecular variance to differentiate between geographic regions. The screening of 11 non-coding regions allowed the identification of 14 haplotypes. A high genetic differentiation was detected (N _ST = 0.875 and G _ST = 0.824) with the existence of phylogeographic structure (p < 0.05). The distribution of the genetic variation was partially explained by the topography of the region when the populations were divided longitudinally into Coastal Mountains, Central Valley, and Andes Mountains (ϕ _RT = 0.093, p = 0.001). In agreement with pollen records, our results support the hypothesis of Coastal refuges since the region harbors high diversity together with older and private haplotypes. Long-lasting persistence of some Coastal populations without contribution to re-colonization is proposed. Additional refuges are also postulated along the Andes and Longitudinal Valley. Survival in multiple glacial refuges is discussed together with the possible migratory routes.     

High genetic diversity and significant population structure in Cedrus brevifolia Henry, a narrow endemic Mediterranean tree from Cyprus

Endemic island plant species with a narrow distribution are often, but not always, linked to low genetic variation within populations and a lack of differentiation among populations. Cedrus brevifolia is a narrow endemic island tree species of Cyprus. Its range is restricted to a single forest, divided into five neighbouring sites. This study, using biparentally inherited nuclear microsatellites and paternally inherited plastid (chloroplast) microsatellites, assessed the genetic variation of C. brevifolia within its sole population and the level of genetic differentiation among formed sites. The results from both markers showed high diversity (nuclear H _T?=?0.70; plastid H _T?=?0.93), strongly suggesting that the species did not experience severe bottleneck events or extensive genetic drift. Besides, the maintenance of a high genetic diversity in C. brevifolia may suggest that it originates from a widespread congener species. Significant genetic differentiation at nuclear (G _ST?=?0.052) and plastid (G _ST?=?0.119) markers was found among the formed sites. Remarkably, the relatively high genetic differentiation found at plastid markers was comparable to values observed in two widespread congener cedar species. The genetic differentiation probably occurred due to fragmentation of a previously uniform population. This would lead to the shaping of different genetic groups (Bayesian analysis) and to significant population substructure. Furthermore, significant values observed for both isolation by distance and large-scale spatial genetic structure could indicate ineffective gene flow among sites and the early geographical isolation of the more isolated sites from the core population.     

Geographic clines in wing morphology relate to colonization history in New World but not Old World populations of yellow dung flies

Geographic clines offer insights about putative targets and agents of natural selection as well as tempo and mode of adaptation. However, demographic processes can lead to clines that are indistinguishable from adaptive divergence. Using the widespread yellow dung fly Scathophaga stercoraria (Diptera: Scathophagidae), we examine quantitative genetic differentiation (Q_ST) of wing shape across North America, Europe, and Japan, and compare this differentiation with that of ten microsatellites (F_ST). Morphometric analyses of 28 populations reared at three temperatures revealed significant thermal plasticity, sexual dimorphism, and geographic differentiation in wing shape. In North America morphological differentiation followed the decline in microsatellite variability along the presumed route of recent colonization from the southeast to the northwest. Across Europe, where S. stercoraria presumably existed for much longer time and where no molecular pattern of isolation by distance was evident, clinal variation was less pronounced despite significant morphological differentiation (Q_ST>F_ST). Shape vector comparisons further indicate that thermal plasticity (hot‐to‐cold) does not mirror patterns of latitudinal divergence (south‐to‐north), as might have been expected under a scenario with temperature as the major agent of selection. Our findings illustrate the importance of detailed phylogeographic information when interpreting geographic clines of dispersal traits in an adaptive evolutionary framework.     

西南地区6种魔芋属植物基于cpDNA序列的遗传多样性研究

研究野生作物资源的遗传变异及分化机制对种质资源的收集与改良具有重要意义。魔芋是我国西南地区的特色经济作物,但由于受到人为活动干扰,野生种群不断衰退。为评估西南地区魔芋属(Amorphophallus)野生群体的遗传多样性,探究代表性物种的系统发育地位,该研究利用3个叶绿体DNA(cpDNA)片段,分析了魔芋6个物种的遗传多样性,重建了种间系统发育关系。结果表明:(1)西南地区野生魔芋群体的遗传多样性普遍较低,虽然单倍型多样性(H_d)均值为0.428,但近一半群体只有1个单倍型,6个物种整体水平上的单倍型多样性在0.704到0.983之间。(2)在6个物种间检测到高水平的遗传分化,遗传分化系数(F_ST)值在0.481到0.967之间。(3)系统发育分析表明,选取的27个魔芋种主要聚成3个分支:非洲分支、东南亚分支和东亚大陆分支。疣柄魔芋(A. paeoniifolius)隶属于东南亚分支,而东亚大陆分支A包含花魔芋(A. konjac)和西盟魔芋(A. krausei),东亚大陆分支B由东亚魔芋(A. kiusianus)、滇魔芋(A. yunnanensis)和东京魔芋(A. tonkinensis)构成。生境隔离与人为干扰造成了西南地区野生魔芋群体较低的遗传多样性,魔芋属东亚大陆分支的分化可能与早期的快速扩张和生态适应有关。该研究为西南地区魔芋资源的合理保护、可持续利用和杂交育种提供了参考资料。     

Phylogeography of <Emphasis Type="Italic">Ceriops tagal</Emphasis> (Rhizophoraceae) in Southeast Asia: the land barrier of the Malay Peninsula has caused population differentiation between the Indian Ocean and South China Sea

The genetic structure of mangrove species is greatly affected by their geographic history. Nine natural populations of Ceriops tagal were collected from Borneo, the Malay Peninsula, and India for this phylogeographic study. Completely different haplotype compositions on the east versus west coasts of the Malay Peninsula were revealed using the atpB-rbcL and trnL-trnF spacers of chloroplast DNA. The average haplotype diversity (Hd) of the total population was 0.549, nucleotide diversity (θ) was 0.030, and nucleotide difference (π) was 0.0074. The cladogram constructed by the index of population differentiation (G _ST) clearly separated the South China Sea populations from the Indian Ocean populations. In the analysis of the minimum spanning network, the Indian Ocean haplotypes were all derived from South China Sea haplotypes, suggesting a dispersal route of C. tagal from Southeast Asia to South Asia. The Sunda Land river system and surface currents might be accountable for the gene flow directions in the South China Sea and Bay of Bengal, respectively. The historical geography not only affected the present genotype distribution but also the evolution of C. tagal. These processes result in the genetic differentiation and the differentiated populations that should be considered as Management Units (MUs) for conservation measurements instead of random forestation, which might lead to gene mixing and reduction of genetic variability of mangrove species. According to this phylogeographic study, populations in Borneo, and east and west Malay Peninsula that have unique genotypes should be considered as distinct MUs, and any activities resulting in gene mixing with each other ought to be prevented.     

Genetic diversity and population structure of Taxus cuspidata in the Changbai Mountains assessed by chloroplast DNA sequences and microsatellite markers

Taxus cuspidata, a tree species with high economic value because of its anticancer properties, is experiencing severe reduction in populations across its range in China. We examined one chloroplast DNA (cpDNA) region (petA-psbE) and 9 nuclear simple sequence repeats (SSRs) loci variations among seven populations in the Changbai Mountains of China to investigate the levels of genetic diversity and population structure. A moderate level of haplotype diversity (H_T = 0.625), low nuclear microsatellite diversity (H_E = 0.261 ± 0.028), significant genetic differences (F_ST = 0.065) and substantial gene flow (Nm = 2.806) were observed. Most of the total genetic variation was partitioned within the population (87.8% and 94.0% for cpDNA and SSRs, respectively). Our haplotype identification permutation tests revealed that G_ST > N_ST, indicating an absence of phylogeographic structure in T. cuspidata. Neither STRUCTURE nor UPGMA analyses showed any geographic pattern in T. cuspidata populations. By comparatively analyzing the genetic diversity and survival situation of T. cuspidata, our results provide a theoretical foundation for the resource protection, utilization cultivation and breeding of this valuable plant.     

Genetic variation and effective population size in isolated populations of coastal cutthroat trout

Following glacial recession in southeast Alaska, waterfalls created by isostatic rebound have isolated numerous replicate populations of coastal cutthroat trout (Oncorhynchus clarkii clarkii) in short coastal streams. These replicate isolated populations offer an unusual opportunity to examine factors associated with the maintenance of genetic diversity. We used eight microsatellites to examine genetic variation within and differentiation among 12 population pairs sampled from above and below these natural migration barriers. Geological evidence indicated that the above-barrier populations have been isolated for 8,000–12,500 years. Genetic differentiation among below-barrier populations (F _ST = 0.10, 95% C.I. 0.08–0.12) was similar to a previous study of more southern populations of this species. Above-barrier populations were highly differentiated from adjacent below-barrier populations (mean pairwise F _ST = 0.28; SD 0.18) and multiple lines of evidence were consistent with asymmetric downstream gene flow that varied among streams. Each above-barrier population had reduced within-population genetic variation when compared to the adjacent below-barrier population. Within-population genetic diversity was significantly correlated with the amount of available habitat in above-barrier sites. Increased genetic differentiation of above-barrier populations with lower genetic diversity suggests that genetic drift has been the primary cause of genetic divergence. Long-term estimates of N _e based on loss of heterozygosity over the time since isolation were large (3,170; range 1,077–7,606) and established an upper limit for N _e if drift were the only evolutionary process responsible for loss of genetic diversity. However, it is likely that a combination of mutation, selection, and gene flow have also contributed to the genetic diversity of above-barrier populations. Contemporary above-barrier N _e estimates were much smaller than long-term N _e estimates, not correlated with within-population genetic diversity, and not consistent with the amount of genetic variation retained, given the approximate 10,000-year period of isolation. The populations isolated by waterfalls in this study that occur in larger stream networks have retained substantial genetic variation, which suggests that the amount of habitat in headwater streams is an important consideration for maintaining the evolutionary potential of isolated populations.