Low genetic diversity and significant population structuring in the relict Amentotaxus argotaenia complex (Taxaceae) based on ISSR fingerprinting

Amentotaxus, a genus of the Taxaceae, represents an ancient lineage that has long existed in Eurasia. All Amentotaxus species experienced frequent population expansion and contraction over periodical glaciations in Tertiary and Quaternary. Among them, Amentotaxus argotaenia complex consists of three morphologically alike species, A. argotaenia, Amentotaxus yunnanensis, and Amentotaxus formosana. This complex is distributed in the subtropical region of mainland China and Taiwan where many Pleistocene refugia have been documented. In this study, genetic diversity and population structuring within and between species were investigated based on the inter-simple sequence repeats (ISSR) fingerprinting. Mean genetic diversity within populations was estimated in three ways: (1) the percentage of polymorphic loci out of all loci (P) (2) Neis unbiased expected heterozygosity (He), and (3) Shannons index of phenotypic diversity. For a total of 310 individuals of 15 populations sampled from the three species, low levels of ISSR genetic variation within populations were detected, with P=4.66–16.58%, He=0.0176–0.0645 and Hpop=0.0263–0.0939, agreeing with their seriously threatened status. AMOVA analyses revealed that the differences between species only accounted for 27.38% of the total variation, whereas differences among populations and within populations were 57.70 and 14.92%, respectively, indicating substantial isolation between the patch-like populations. A neighbor-joining tree identified a close affinity between A. yunnanensis and A. formosana. Genetic drift due to small population size, plus limited current gene flow, resulted in significant genetic structuring. Low levels of intrapopulational genetic variation and considerable interpopulational divergence were also attributable to demographic bottlenecks during and/or after the Pleistocene glaciations.     

Population genetic structure of Ceriops tagal (Rhizophoraceae) in Thailand and China

Knowledge of the amount and patterns of genetic variation within and among populations of mangrove trees is essential for devising optimum genetic management strategies for their conservation and sustainable utilization. Ceriops tagal is a widespread viviparous mangrove. Genetic diversity in the species was examined with inter-simple sequence repeat (ISSR). Nine natural populations were collected from Thailand and China. The estimates of genetic variation were extremely low (H_T = 0.0179 ± 0.005, H_S = 0.0084 ± 0.001), and only 47% of the total gene diversity was maintained within populations (G_ST = 0.529). The eastern coastal populations of Thailand were more similar to populations from China than to populations from the western coastline of Thailand. A high level of Nei's genetic identity exists between populations of C. tagal (I = 0.989), suggesting their common ancestry. The low levels of genetic diversity in the species may result from a series of genetic bottlenecks during several glacial epochs.     

Patterns of Genetic Variation in Swertia przewalskii, an Endangered Endemic Species of the Qinghai-Tibet Plateau

Swertia przewalskii Pissjauk. (Gentianaceae) is a critically endangered and endemic plant of the Qinghai-Tibet Plateau in China. RAPD and ISSR analyses were carried out on a total of 63 individuals to assess the extent of genetic variation in the remaining three populations. Percentage of polymorphic bands was 94% (156 bands) for RAPD and 96% (222 bands) for ISSR. A pairwise distance measure calculated from the RAPD and ISSR data was used as input for analysis of molecular variance (AMOVA). AMOVA indicated that a high proportion of the total genetic variation (52% for RAPD and 56% for ISSR) was found among populations; pairwise Φ _ST comparisons showed that the three populations examined were significantly different (p < 0.001). Significant genetic differentiation was found based on different measures (AMOVA and Hickory θ_B) in S. przewalskii (0.52 on RAPD and 0.56 on ISSR; 0.46 on RAPD and 0.45 on ISSR). The differentiation of the populations corresponded to low average gene flow (0.28 based on RAPD and 0.31 based on ISSR), whereas genetic distance-based clustering and coalescent-based assignment analyses revealed significant genetic isolation among populations. Our results indicate that genetic diversity is independent of population size. We conclude that although sexual reproduction and gene flow between populations of S. przewalskii are very limited, they have preserved high levels of genetic diversity. The main factors responsible for the high level of difference among populations are the isolation and recent fragmentation under human disturbance.     

Assessing genetic diversity of Elymus sibiricus (Poaceae: Triticeae) populations from Qinghai-Tibet Plateau by ISSR markers

Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population structure in eight populations of Elymus sibiricus L. from the southeast of Qinghai-Tibet Plateau of China. Of the 100 primers screened, 13 produced highly reproducible ISSR bands. Using these primers, 193 discernible DNA fragments were generated with 149 (77.2%) being polymorphic, indicating considerable genetic variation at the species level. In contrast, there were relatively low levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 44.04 to 54.92%. The mean gene diversity (H_E) was estimated to be 0.181 within populations (range 0.164–0.200), and 0.274 at the species level. A high level of genetic differentiation among populations was detected based on Nei's genetic diversity analysis (33.1%), Shannon's index analysis (34.5%), Bayesian method (33.2%) and AMOVA analysis (42.5%). No significant statistical differences (analysis of molecular variance [AMOVA], P = 0.08) in ISSR variation were found between the sample collection regions. However, among populations (42.5% of the variance) and within populations (57.5% of the variance), there were significant differences (P < 0.001). Populations shared high levels of genetic identity. This pattern of genetic variation was different from that for most of inbreeding Triticeae species reported. In addition, a geographical pattern of population differentiation, where the populations from south and north of sampling sites were clearly separated from each other, was revealed by both the cluster and principal coordinates analyses. Generally, the result of this study indicates that E. sibiricus contains high molecular variation in its populations. The implications of these results for the conservation of the species are discussed.     

Genetic differentiation between eastern populations and recent introductions of potato psyllid (Bactericera cockerelli) into western North America

Although tomato psyllid, Bactericera cockerelli (Sulc) (Homoptera, Psyllidae), annually causes significant losses in potato and tomato crops in eastern Mexico and the central United States, infestations in western North America have been historically rare. However, substantial populations appeared in 2001 in western North America and caused losses in tomato production exceeding 80%; losses in 2004 reached 50%. To determine if these new outbreaks were the result of a simple range expansion or the evolution of a new B. cockerelli biotype, inter simple sequence repeat (ISSR) markers, as well as mitochondrial gene cytochrome oxidase I (COI), internal transcribed spacer 2 (ITS2), and wsp sequence data were used to characterize populations of the psyllid. Western populations from Baja, Mexico, Orange County, and Ventura County were compared with populations from central USA (Colorado and Nebraska) and eastern Mexico (Coahuila). Based on ISSR markers, the psyllid populations clustered into two groups, with one group including populations from western North America and the other group including populations from central USA and eastern Mexico. For COI comparisons, there was one base‐pair difference found in the 544 bp‐long COI fragments, but the populations again segregated along the same geographic lines. Two strains of Wolbachia were identified, the maximal differences between wsp clones from all populations was 5 bp for strain Bac1 and 23 bp for strain Bac2 out of a 555‐bp fragment. The ISSR data, therefore, were consistent in indicating the development of a new psyllid biotype that has adapted to western North America rather than a simple range expansion, but the other genetic data sets were less conclusive.     

Variability of Wing Size and Shape in Three Populations of a Recent Brazilian Invader, Zaprionus indianus (Diptera: Drosophilidae), from Different Habitats

Zaprionus indianus (Diptera: Drosophilidae) is an African species that was introduced in Brazil near the end of the 1990’s decade. To evaluate the adaptive potential of morphological traits in natural populations of this recently introduced species, we have investigated wing size and shape variation at Rio de Janeiro populations only two years after the first record of Z. indianus in Brazil. Significant genetic differences among populations from three distinct ecological habitats were detected. The heritability and evolvability estimates show that, even with the population bottleneck that should have occurred during the invasion event, an appreciable amount of additive genetic variation for wing size and shape was retained. Our results also indicated a greater influence of environmental variation on wing size than on wing shape. The importance of quantitative genetic variability and plasticity in the successful establishment and dispersal of Z. indianus in the Brazilian territory is then discussed.     

Strong genetic differentiation of the East-Himalayan <Emphasis Type="Italic">Megacodon stylophorus</Emphasis> (Gentianaceae) detected by Inter-Simple Sequence Repeats (ISSR)

Megacodon stylophorus (Clarke) Smith is a perennial alpine herb endemic to the species-rich eastern Himalayan region. Its populations are locally scattered as isolated patches throughout this region. Genetic variation within and among six populations of this species was assessed using ISSR fingerprinting with 13 primers. High levels of genetic diversity exist within species (P = 69.83%, H_T = 0.1949 and H_sp = 0.3047), while the within-population diversity is low (P = 11.21%, H_E = 0.0532 and H_pop = 0.0792). Extraordinarily high levels of genetic differentiation were detected among populations based on various statistics, including Neis genetic diversity analysis (72.7%), Shannons diversity index (74.01%) and AMOVA (80.70%). That is, populations shared low levels of genetic identity (I = 0.8203 ± 0.0430). This genetic structure was probably due to severe genetic drift of the small-sized patchy populations resulting from postglacial habitat fragmentations. The observed genetic structure of the populations implies that as many populations as possible should be considered for any in situ and ex situ conservation practice on this species.     

Phylogeography of the endangered tideland snail Batillaria zonalis in the Japanese and Ryukyu Islands

The phylogeography of the endangered tideland snail Batillaria zonalis in the Japanese and Ryukyu Islands was analyzed on the basis of nucleotide sequences of a mitochondrial gene for cytochrome oxidase c subunit I (COI). Extremely low genetic diversity was found in populations at both the northern and southern boundaries of the geographic distribution of this species in Japan, i.e., Sendai Bay and Iriomotejima Island, respectively, which might be attributed to the population bottleneck due to historical environmental variations and/or the recent foundation of populations in the marginal part of the inhabitable range. Most populations contained unique rare haplotypes, and significant genetic differentiation on the whole was shown, while no clear geographic genetic structure was detected between the Japanese and Ryukyu Islands or over the distribution area of B. zonalis in Japan, with the exception of significant genetic divergences in Ago Bay in the central part of Honshu and the southern part of Okinawajima Island.     

Genetic diversity and geographic differentiation of disjunct Atlantic and Amazonian populations of <Emphasis Type="Italic">Psychotria ipecacuanha</Emphasis> (Rubiaceae)

Ipecac (Psychotria ipecacuanha) is a perennial, medicinal herb that grows in the understory of semi-deciduous tropical forests in the Neotropics. Ipecacs present a widely disjunct distribution, with two of its three ranges occurring in Brazil. The Amazonian populations are at least 1600 km from the nearest Atlantic populations. This work used ISSR markers to compare the genetic diversity and structure of populations from the two Brazilian ranges. Lower genetic diversity in Amazon populations (P = 60.11%, Hs = 0.18) and higher genetic diversity in Atlantic populations (P = 73.94%, Hs = 0.20) were detected. Differentiation between ranges were high (θ ^B = 0.6838, G_ST-B = 0.6665). AMOVA revealed that 65.3% of the total molecular variance can be attributed to regional differences between the two ranges. Principal coordinate analyses and cluster analyses organized ipecacs at either individual or population level into two exclusive groups that correspond each to one of the two disjunct ranges, without exception. The results do not support a scenario that postulates human-mediated, long-distance dispersal events as a plausible origin for the distribution of the Brazilian ipecacs, but indicate geographic isolation as a long-standing barrier to genetic exchange and connectivity among populations from different ranges. Conservation implications are discussed.     

新疆地区番茄潜叶蛾遗传多样性的ISSR分析

[目的]番茄潜叶蛾已成为世界性番茄的重要害虫,对番茄产业的发展造成了严重的威胁,研究其遗传多样性有利于揭示不同地理种群的遗传变异结构。[方法]采用ISSR分子标记技术分析了20个地理种群番茄潜叶蛾的遗传多样性和遗传结构特征。[结果]15条引物扩增出137条ISSR条带,其中多态性条带占96.35%,所有个体显示了各自独特的ISSR图谱。ISSR的标记遗传多样性结果表明,20个番茄潜叶蛾地理种群遗传距离大小范围为0.0065~0.1623,遗传一致度范围为0.8502~0.9935。种群变异来源分析表明,25.36%的遗传变异来自种群间,74.64%的变异来源于种群内部。UPGMA系统发育分析结果表明,各地理种群的聚类与地理位置无较强的关联性。[结论]番茄潜叶蛾尚处在入侵早期阶段,且具备频繁入侵和多点的特征。防控上要注意加强检疫,阻绝多点入侵来源。     

Genetic diversity and structure of the invasive tree Miconia calvescens in Pacific islands

Aim This study investigates the amount and distribution of genetic variation within and among populations of the highly invasive tree, Miconia calvescens (Melastomataceae; hereafter miconia), in tropical island habitats that are differently impacted (distribution and spread) by this weed. Location Invasive populations were included from northern and southern Pacific islands including the Hawaiian Islands (Hawaii, Kauai and Maui), Marquesas Islands (Nuku Hiva), Society Islands (Tahiti, Tahaa, Moorea, Raiatea) and New Caledonia. Methods We used 9 codominant microsatellite and 77 highly variable dominant intersimple sequence repeat markers (ISSRs) to characterize and compare genetic diversity among and within invasive miconia populations. For the codominant microsatellite data we calculated standard population genetic estimates (heterozygosity, number of alleles, inbreeding coefficients, etc.) and described population genetic structure using AMOVA, Mantel tests (to test for isolation by distance), unweighted pair‐group method with arithmetic averages (UPGMA) cluster analysis and principal components analysis (PCA). We also tested for the presence of a population bottleneck and used a Bayesian analysis of population structure in combination with individual assignment tests. For the dominant ISSR data we used AMOVA, PCA, upgma and a Bayesian approach to investigate population genetic structure. Results Both markers types showed little to no genetic differentiation among miconia populations from northern and southern Pacific hemispheres (AMOVA: microsatellite, 3%; ISSR, 0%). Bayesian and frequency‐based analysis also failed to support geographical genetic structure, confirming considerable low genetic differentiation throughout the Pacific. Molecular data furthermore showed that highly successful miconia populations throughout the Pacific are currently undergoing severe bottlenecks and high levels of inbreeding (f = 0.91, ISSR; F_IS = 0.27, microsatellite). Main conclusions The lack of population genetic structure is indicative of similar geographical sources for both hemispheres and small founding populations. Differences in invasive spread and distribution among Pacific islands are most likely the result of differences in introduction dates to different islands and their accompanying lag phases. Miconia has been introduced to relatively few tropical islands in the Pacific, and the accidental introduction of a few or even a single seed into favourable habitats could lead to high invasive success.     

Detection of Low Genetic Variation in a Critically Endangered Chinese Pine, Pinus squamata, Using RAPD and ISSR Markers

With only 32 individuals in the northeastern corner of Yunnan Province, China, Pinus squamata is one of the most endangered conifers in the world. Using two classes of molecular markers, RAPD and ISSR, its very low genetic variation was revealed. Shannon's index of phenotypic diversity (I) was 0.030, the mean effective number of alleles per locus (A_e) was 1.032, the percentage of polymorphic loci (P) was 6.45, and the expected heterozygosity (H_e) was 0.019 at the species level based on RAPD markers. The results of ISSR were consistent with those detected by RAPD but somewhat higher (I = 0.048, A_e = 1.042, P = 12.3, H_e = 0.029). The genetic variation of the subpopulation on the southwest-facing slope was much higher than that of the subpopulation on the northeast-facing slope, which may be attributed to the more diverse environment on the southwest-facing slope. The genetic differentiation between the two subpopulations was very low. The between-subpopulation variabilities, Φ_ST, calculated from RAPD and ISSR data were 0.011 and 0.024. Because of the lack of fossil records and geological historical data, it was difficult to explain the extremely low genetic diversity of the species. We postulate that this ancient pine might have experienced strong bottlenecks during its long evolutionary history, which caused the loss of genetic variation. Genetic drift and inbreeding in post-bottlenecked small populations may be the major forces that contribute to low genetic diversity. Human activities such as logging may have accelerated the loss of genetic diversity in P. squamata.     

Historical and recent genetic bottlenecks in European grayling, Thymallus thymallus

Sharp declines in population size, known as genetic bottlenecks, increase the level of inbreeding and reduce genetic diversity threatening population sustainability in both short- and long-term. We evaluated the presence, severity and approximate time of bottlenecks in 34 European grayling (Thymallus thymallus) populations covering the majority of the species distribution using microsatellite markers. We identified footprints of population decline in all grayling populations using the M ratio test. In contrast to earlier simulation studies assuming isolated populations, forward simulations allowing low levels of migration demonstrated that bottleneck footprints measured using the M ratio can persist within small populations much longer (up to thousands of generations) than previously anticipated. Using a coalescence approach, the beginning of population reduction was dated back to 1,000–10,000 years ago which suggests that the extremely low M ratio in European grayling is most likely caused by the last glaciation and subsequent post-glacial recolonization processes. In contrast to the M ratio, two alternative methods for bottleneck detection identified more recent bottlenecks in six populations and thus, from a conservation perspective, these populations warrant future monitoring. Based on a single time-point analysis using approximate Bayesian computation methodology, all grayling populations exhibited very small effective population sizes with the majority of N _e estimates below 50. Taken together, our results demonstrate the predominate role of genetic drift in European grayling populations in the short term but also emphasize the importance of gene flow counteracting the effects of genetic drift and loss of variation over longer evolutionary timescales.     

Molecular phylogeography of the microturbellarian Monocelis lineata (Platyhelminthes: Proseriata) in the North‐East Atlantic

Monocelis lineata is a complex of cryptic species (three in the Mediterranean and one in the Atlantic) widespread in midlittoral habitats. Throughout the range, populations with or without an ocular pigmented shield are found. We investigated the genetic structure of the North‐East Atlantic populations with the aim of shedding light on their phylogeography and reconstructing possible patterns of recolonization after the Würmian glaciation. Fourteen samples were investigated using cytochrome c oxidase subunit I (COI) and 13 by inter‐simple sequence repeats (ISSRs). COI did not exhibit a clear pattern of decreased genetic diversity along a latitudinal gradient. Populations from Ferrol (Spain), Doolin (Ireland), and Helsingør (Denmark) showed a higher genetic variability, whereas a reduction in the number of haplotypes was found at the northernmost edge of the distribution and in northern Ireland and Scotland. Two genetically differentiated areas (southern Europe and south‐western Ireland versus northern Atlantic) were revealed by ISSR data. The results obtained provided evidence of three refugia (Iberian Peninsula, south‐western Ireland, and North Sea), and the occurrence of secondary contacts that shaped the genetic variability of some of the populations examined. Two different recolonization pathways of north‐western Europe during the post‐Würmian glaciations have been detected. Furthermore, ISSR analysis provided evidence of genetic divergence among populations with and without pigmented eyespot, suggesting the action of ecological differentiation. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 117–135.     

Wild sunflower diversity in Argentina revealed by ISSR and SSR markers: an approach for conservation and breeding programmes

Wild sunflower Helianthus annuus originates from North America and has naturalised in Argentina where it is considered invasive. The present study attempts to assess the genetic diversity using two different molecular marker systems to study the wild genetic patterns and to provide data applicable to conservation and breeding uses. Ten natural populations sampled throughout the wild range and six inbred lines were studied using inter‐simple sequence repeat (ISSR) and simple sequence repeats (SSR) markers. A total of 64 ISSR bands and 29 SSR alleles were produced from 106 wild and cultivated plants. We found 9 ISSR private bands and 21 SSR private alleles in wild accessions, but no private bands/alleles were found in cultivated sunflowers. Molecular variability in wild populations was approximately 60% higher than in inbred lines. Local wild sunflowers kept considerable diversity levels in comparison with populations in the centre of origin (approximately 70%) and therefore they might possess a potential for adaptive evolutionary change. Analysis of molecular variance (AMOVA) indicated population structure with nearly 20% of genetic variability attributable to between‐population differentiation. Principal coordinate analyses (PCO) grouped wild populations from different geographic locations, and a Mantel test showed low congruence between genetic distance (GD) and geographic distances (GGD); hence, molecular data could not rule out multiple wild introduction events. Low correlations were found between ISSR and SSR GD at individual and population levels; thus, divergent evolutionary groups were not evident in local wild sunflowers. Several genetic diversity criteria were utilised to assign conservation value and certain wild populations emerged as interesting sites for more extensive sampling.     

The genetic consequences of a demographic bottleneck in an introduced biological control insect

Population bottlenecks may result in the loss of genetic diversity, with potentially negative consequences for species of interest in conservation biology, including rare species, invasive species and biological control agents. We examined mtDNA sequence data and four variable microsatellite loci (SSRs) in the melaleuca psyllid Boreioglycaspis melaleucae, which was introduced from Australia to Florida as a biological control agent of the invasive plant Melaleuca quinquenervia. We sampled psyllids in the native and introduced ranges as well as individuals stored from the original founding population. There was a clear loss of mtDNA haplotype diversity, as well as a loss of rare microsatellite alleles, in the introduced range. However, there was little genetic differentiation between the home and introduced ranges, and no evidence for a genetic bottleneck based on an analysis of heterozygosity with the microsatellite markers. Overall, the data showed that the demographic bottleneck had a limited effect on the genetics of populations in the new range.     

Population genetic structure of <Emphasis Type="Italic">Sargassum thunbergii</Emphasis> (Fucales,Phaeophyta) detected by RAPD and ISSR markers

Genetic variation of four populations of Sargassum thunbergii (Mert.) O. Kuntze and one outgroup of S. fusiforme (Harv.) Setchell from Shandong peninsula of China was studied with random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. A total of 28 RAPD primers and 19 ISSR primers were amplified, showing 174 loci and 125 loci, respectively. Calculation of genetic diversity with different indicators (P%, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon’s information index) revealed low or moderate levels of genetic variations within each S. thunbergii population. High genetic differentiations were determined with pairwise Nei’s unbiased genetic distance (D) and fixation index (F _ST ) between the populations. The Mantel test showed that two types of matrices of D and F _ST were highly correlated, whether from RAPD or ISSR data, r = 0.9310 (P  = 0.008) and 0.9313 (P = 0.009) respectively. Analysis of molecular variance (AMOVA) was used to apportion the variations between and within the S. thunbergii populations. It indicated that the variations among populations were higher than those within populations, being 57.57% versus 42.43% by RAPD and 59.52% versus 40.08% by ISSR, respectively. Furthermore, the Mantel test suggested that the genetic differentiations between the four populations were related to the geographical distances (r > 0.5), i.e., they conformed to the IBD (isolation by distance) model, as expected from UPGMA (unweighted pair group method with arithmetic averages) cluster analysis. As a whole, the high genetic structuring between the four S. thunbergii populations along distant locations was clearly indicated in the RAPD and ISSR analyses (r > 0.8) in our study.     

Bottlenecks and rescue effects in a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis)

Mammal species characterized by highly fluctuating populations often maintain genetic diversity in response to frequent demographic bottlenecks, suggesting the ameliorating influence of life history and behavioral factors. Immigration in particular is expected to promote genetic recovery and is hypothesized to be the most likely process maintaining genetic diversity in fluctuating mammal populations. Most demographic bottlenecks have been inferred retrospectively, and direct analysis of a natural population before, during, and after a bottleneck is rare. Using a continuous 10-year dataset detailing the complete demographic and genetic history of a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis), we analyzed the genetic consequences of a 4-year demographic bottleneck that reduced the population to seven adult squirrels, and we evaluated the potential “rescue effect” of immigration. Analysis of six microsatellite loci revealed that, while a decline in allelic richness was observed during the bottleneck, there was no observed excess of heterozygosity, a characteristic bottleneck signature, and no evidence for heterozygote deficiency during the recovery phase. In addition, we found no evidence for inbreeding depression during or after the bottleneck. By identifying immigrants and analyzing their demographic and genetic contributions, we found that immigration promoted demographic recovery and countered the genetic effects of the bottleneck, especially the loss of allelic richness. Within 3 years both population size and genetic variation had recovered to pre-bottleneck levels, supporting the role of immigration in maintaining genetic variation during bottleneck events in fluctuating populations. Our analyses revealed considerable variation among analytical techniques in their ability to detect genetic bottlenecks, suggesting that caution is warranted when evaluating bottleneck events based on one technique.     

Genetic structure analysis of natural <Emphasis Type="Italic">Sargassum muticum</Emphasis> (Fucales,Phaeophyta) populations using RAPD and ISSR markers

Sargassum muticum is important in maintaining the structure and function of littoral ecosystems, and is used in aquaculture and alginate production, however, little is known about its population genetic attributes. In this study, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to investigate the genetic structure of four populations of S. muticum and one outgroup of S. fusiforme (Harv.) Setchell from Shandong peninsula of China. The selected 24 RAPD primers and 19 ISSR primers amplified 164 loci and 122 loci, respectively. Estimates of genetic diversity with different indicators (P%, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon’s information index) revealed low or moderate level of genetic variations within each S. muticum population, and a high level of genetic differentiations were determined with pairwise unbiased genetic distance (D) and fixation index (F _ST ) among the populations. The Mantel test showed that two types of matrices of D and F _ST were highly correlated whether from RAPD (r = 0.9706, P = 0.009) or ISSR data (r = 0.9161, P = 0.009). Analysis of molecular variance (AMOVA) was conducted to apportion the variations among and within the S. muticum populations. It indicated that variations among populations were higher than those within populations, being 55.82% verse 44.18% by RAPD and 55.21% verse 44.79% by ISSR, respectively. Furthermore, the Mantel test suggested that genetic differentiations among populations were related to the geographical distances (r > 0.6), namely, conformed to the IBD (isolation by distance) model, as expected from UPGMA (unweighted pair group method with arithmetic averages) cluster analysis. On the whole, the high genetic structuring among the four S. muticum populations along the distant locations was clearly indicated in RAPD and ISSR analyses (r > 0.9, P < 0.05) in our study.     

Genetic diversity and maternal origin of Northeast African and South American donkey populations

To investigate the mtDNA variation and origin of maternal lineages in South American donkeys and to reassess the domestication of donkeys in northeast Africa, we analyzed sequences (489 bp of the D‐loop) from 323 domestic donkeys sampled from Peru, Brazil, Ethiopia and Egypt. Altogether, the 323 sequences displayed 53 different haplotypes (45 in Ethiopia, 14 in Egypt, eight in Peru and six in Brazil). Among the four populations, Egyptian donkeys possessed the highest haplotype diversity (0.910 ± 0.032), followed by Brazilian donkeys (0.879 ± 0.060). The Clade I haplotypes dominated in Peruvian donkeys (65%), whereas Clade II haplotypes dominated in Brazilian donkeys (67%). Estimates of F_ST values showed a high genetic differentiation between Peruvian and Brazilian donkey populations (F_ST = 0.4066), which could be explained by the complex introduction history of South American donkeys. Phylogeographic analysis indicates that northeast Africa could be the most probable domestication center for Clade I donkeys. Analysis of molecular variance confirmed a weak genetic structure in domestic donkey populations among four continents (Europe, Asia, Africa and South America).