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1.
Qiang Fan Sufang Chen Renchao Zhou Xu Xiang Wenbo Liao Suhua Shi 《Conservation Genetics》2011,12(3):753-760
Understanding the amount and distribution of genetic diversity in natural populations can inform the conservation strategy
for the species in question. In this study, genetic variation at eight nuclear microsatellite loci was used to investigate
genetic diversity and population structure of wild litchi (Litchi chinensis Sonn. subsp. chinensis). Totally 215 individuals were sampled, representing nine populations of wild litchi. All eight loci were polymorphic, with
a total of 51 alleles. The expected heterozygosity in the nine populations ranged from 0.367 to 0.638 with an average value
of 0.526. Inbreeding within wild litchi populations was indicated by a strong heterozygote defect. Significant bottleneck
events were detected in the populations from Yunnan and Vietnam, which could be responsible for lower levels of genetic diversity
in these populations. Measures of genetic differentiation (F
ST = 0.269) indicated strong differentiation among wild litchi populations. Significant correlation was found between genetic
differentiation and geographical distance (r = 0.655, P = 0.002), indicating a strong isolation by distance in these populations. Bayesian clustering suggested genetic separation
among three regional groups, namely, the western group, the central group and the eastern group. Some conservation strategies
for wild litchi populations were also proposed based on our results. 相似文献
2.
Cupressus chenggiana S. Y. Hu (Cupressaceae) is an endemic and endangered conifer species in southwest China. In order to study the population
genetics and design the effective conservation methods, we aimed to develop microsatellite primers for this species in the
present study. We developed eight new microsatellite loci for this species through biotin capture method. Polymorphism of
each locus was further assessed in 18 individuals from three geographically distant populations. The number of alleles per
locus ranged from 6 to 11 with an average of 8.13. The observed and expected heterozygosities ranged from 0.219 to 0.296 and
from 0.374 to 0.470, with averages of 0.254 and 0.417, respectively. We further found that three of nine microsatellite loci
developed previously for another congeneric species showed polymorphic banding patters. We performed primer-crossing tests
of these loci in the other two congeneric species which are closely related to C. chenggiana (C. gigantea and C. duclouxiana). These microsatellite markers would be effective for analyzing genetic diversity and population genetic structure of this
species and its morphological differentiation with the close relatives. 相似文献
3.
Commiphora wightii is a medicinally important endangered species endemic to the Thar Desert of Rajasthan, India and adjoining areas of Pakistan.
The populations of this species are declining sharply because of its extensive use as a natural herb. Random amplified polymorphic
DNA analysis was conducted to find the genetic variation among 7 populations of C. wightii. Of the 100 random primers screened, 44 primers yielded 220 loci. Statistical analysis indicated low genetic diversity (H
pop = 0.0958; I = 0.1498; mean polymorphic loci = 14.28%), and high genetic differentiation among the populations (G
ST = 0.3990; AMOVA Φ
ST of 0.3390; Bayesian θ
(II) = 0.3002). The low genetic diversity may be due to geographic isolation and restricted gene flow (N
m = 0.7533) between the fragmented populations. Unsustainable utilization of the plant has fragmented the population continuum
which served the purpose of genetic exchange between populations. Mantel’s test was performed which revealed a highly significant
positive correlation between genetic and geographic distance (r
2 = 0.614, P = 0.023) among the populations studied. Low variation can also be attributed to poor seed setting and the slow growth pattern
of the species, which is also an apomict. In UPGMA dendrogram the Commiphora wightii samples were divided into two major and one minor cluster. These findings can serve as a guide to preserving the genetic
resources of this medicinal plant species. 相似文献
4.
Tamarix chinensis, with its important ecological significance, is a vital dominant plant in the Yellow River Delta of China. To understand
its genetic structure and population dynamics, five populations of T. chinensis, consisting of 140 individuals, were analyzed in this study using inter simple sequence repeat markers. Seventy-eight polymerase
chain reaction fragments were scored, of which 62 were polymorphic. The mean percentage of polymorphic loci (P), the mean Nei’s gene diversity (h), and the mean Shannon’s information index (I) were 79.5%, 0.239, and 0.363, respectively. These indexes indicated that a moderate level of genetic diversity existed in
T. chinensis populations of the Yellow River Delta. Both analysis of molecular variance (AMOVA) (Φ
st = 0.169) and Popgene (G
st = 0.159) analyses revealed the low level of genetic differences among the five populations of T. chinensis. The results implied that relatively frequent gene flow existed among populations. However, slightly uneven genetic diversity
was also found among populations. Unweighted pair group method with arithmetic mean and principal component analysis showed
that populations with similar soil salinity had a close relationship, rather than populations with closer geographical distance.
A significant negative correlation between genetic diversity and soil salinity of the five populations (r = −0.958, p < 0.01) showed that soil salinity played an important role in shaping the population genetic structure of T. chinensis in the Yellow River Delta, China. 相似文献
5.
Rauquírio Marinho da Costa Luci Cajueiro Carneiro Pereira Felipe Fernández 《Hydrobiologia》2008,605(1):55-63
Coenagrionid damselflies are in general decline in the British Isles. Numerous factors have been implicated in the loss of
these species including recent speculation that hybridisation between congeners may result in species decline. Here we use
a panel of 12 microsatellite loci to examine levels of genetic divergence and the likely occurrence of hybridisation in five
populations of Coenagrion puella and C. pulchellum using samples from four sites in south-east England. Coenagrion puella and C. pulchellum were highly genetically divergent, and there was no evidence of hybridisation between any of the populations examined, even
where C. puella and C. pulchellum were sympatric. There was some suggestion that C. pulchellum was less genetically diverse than C. puella, though this may have been a result of ascertainment bias associated with cross-species application of microsatellite markers.
We conclude that there is no evidence that hybridisation between C. puella/pulchellum could be responsible for the on-going demographic decline in C. pulchellum. Nevertheless, further genetic studies such as this one are likely to provide estimates of diversity, population structure
and dispersal capacity that will be invaluable in future conservation management strategies for coenagrionid damselflies.
Handling editor: S. Wellekens 相似文献
6.
The razor clam (Sinonovacula constricta) is an important aquacultured bivalve in China. The natural populations of this species are decreasing quickly. To facilitate
studies on genetic diversity and population structure of wild populations, microsatellites were isolated from a CA enriched
genomic library. Eight microsatellite loci were polymorphic in 30 individuals from Chongming in Shanghai, China. The number
of alleles per polymorphic locus varied from 6 to 13 and the values of observed heterozygosity and expected heterozygosity
ranged from 0.350 to 1.000 and from 0.602 to 0.902, respectively. These microsatellites are being used in studying population
differentiation and genetic diversity for effective conservation and management genetic resources of S. constricta. 相似文献
7.
Genetic variation and clonal diversity of nine populations of Bromus ircutensis Kom. from the Otingdag sandy land were investigated using Inter Simple Sequence Repeat (ISSR) markers. A total of 102 bands were amplified by using 11 ISSR primers chosen for the study. Among those 99% were polymorphic indicating high level of genetic variation at the species
level with a mean genetic diversity (H) of 0.292 and Shannon information index (I) of 0.450. Percentage of polymorphic loci (PPL) of nine populations was 76.48% on average, which provides more evidence of considerable genetic variation at the population
level. AMOVA analysis revealed that total genetic variation was higher within populations (87.06%) than between populations (12.94%),
which is mainly the result of the extensive gene flow (Nm = 1.682) among B. ircutensis populations. UPGMA cluster analysis divided the nine populations into two groups. There was significant or moderate negative correlations between
genetic diversity parameters (PPL, H, I) and longitude or latitude. Mantel test also showed a significant correlation between geographical distance and genetic distance
(r = 0.681, p = 0.002). Our findings indicated that distribution of B. ircutensis populations was influenced by geographical and ecological factors. Clonal diversity was also high with 108 individuals identified
by 11 ISSR primers being all of different genets. Our results provide a molecular basis for sustainable management and conservation
of B. ircutensis in the study area. 相似文献
8.
S. J. Välilä K. E. Knott E. P. Ieshko A. E. Veselov J. K. Taskinen 《Biology Bulletin》2017,44(1):92-98
The freshwater pearl mussel Margaritifera margaritifera L. is one of the most endangered freshwater mussels in the world. Effective conservation of threatened species requires not only ecological, but also genetic information from the target species and populations. Since low genetic diversity can reduce the ability of a species to adapt to environmental changes, maintaining genetic diversity has been identified as one of the key elements in successful conservation programs. We examined genetic variation of the freshwater pearl mussel from the River Vuokkijoki, Karelia, Russia. We sequenced a fragment of the cytochrome c oxidase subunit I gene (COI) from 22 individuals and compared the data to 32 previously published COI sequences available in GenBank. We identified 10 different COI haplotypes in the sequenced samples, three of which had not been previously reported. Our results show that the River Vuokkijoki has high genetic diversity and suggest that the colonization of this northern freshwater pearl mussel population might have occurred from multiple and even distant refugia. Therefore, the freshwater pearl mussel population of the River Vuokkijoki is valuable for the conservation of the whole species. 相似文献
9.
Castilleja levisecta (Scrophulariaceae), the golden paintbrush, is an insect-pollinated herbaceaous perennial found in the Pacific Northwest. Currently restricted to two island populations off British Columbia and nine populations (eight on islands) in Washington, C. levisecta is a rare species threatened with extinction. Allozymes were used to describe genetic diversity and structure in these eleven populations. Despite its threatened status and small geographic range, exceptionally high levels of genetic diversity are maintained within C. levisecta. All sixteen of the loci resolved were polymorphic within the species (Ps=100%), while the mean percentage of loci polymorphic within populations (Pp) was 65.7%. The mean number of alleles per polymorphic locus (APs) was 2.94 within the species and averaged 2.38 within populations (APp). Genetic diversity (Hes) was 0.285 for the species, whereas mean population genetic diversity (Hep) was 0.213. Smaller populations had, on average, fewer observed alleles and less genetic diversity. A significant negative correlation (r = –0.72) was found between genetic identity and geographic distance, indicating reduced gene flow between distant populations. The most geographically isolated population was one of the larger populations, one of the most genetically diverse and the most genetically divergent. A wide range of pairwise population genetic identities (I = 0.771 – 0.992) was found, indicating considerable genetic divergence between some populations. Overall, 19% of the total genetic diversity was distributed among populations. Results of this survey indicate that genetic augmentation of existing populations is unnecessary. The high allelic diversity found for the species and within its populations holds promise for conservation and restoration efforts to save this rare and threatened plant species. 相似文献
10.
We report on the isolation and characterization of eight microsatellite markers from repetitive DNA enriched libraries for
Cryptocarya chinensis from lower subtropical China. These are the first microsatellite loci reported for Cryptocarya species. The number of alleles ranged from three to nine. Observed and expected heterozygosities ranged from 0.0518 to 0.9910
and 0.5241 to 0.7935 for polymorphic loci, respectively. These markers will allow analyses of the baseline genetic variability
and population structure of C. chinensis to enrich our scientific understanding of forest fragmentation on genetic health of this species and provide strategies for
effective conservation and management in this area. 相似文献
11.
Zhou HF Zheng XM Wei RX Second G Vaughan DA Ge S 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2008,117(7):1181-1189
The cross compatible wild relatives of crops have furnished valuable genes for crop improvement. Understanding the genetics
of these wild species may enhance their further use in breeding. In this study, sequence variation of the nuclear Lhs1 gene was used to investigate the population genetic structure and gene flow of Oryza rufipogon and O. nivara, two wild species most closely related to O. sativa. The two species diverge markedly in life history and mating system, with O. rufipogon being perennial and outcrossing and O. nivara being annual and predominantly inbreeding. Based on sequence data from 105 plants representing 11 wild populations covering
the entire geographic range of these wild species, we detected significantly higher nucleotide variation in O. rufipogon than in O. nivara at both the population and species levels. At the population level the diversity in O. rufipogon (Hd = 0.712; θ
sil = 0.0017) is 2–3 folds higher than that in O. nivara (Hd = 0.306; θ
sil = 0.0005). AMOVA partitioning indicated that genetic differentiation among O. nivara populations (78.2%) was much higher than that among O. rufipogon populations (52.3%). The different level of genetic diversity and contrasting population genetic structure between O. rufipogon and O. nivara might be explained by their distinct life histories and mating systems. Our simulation using IM models demonstrated significant
gene flow from O. nivara to O. rufipogon, indicating a directional introgression from the annual and selfing species into the perennial and outcrossing species. The
ongoing introgression has played an important role in shaping current patterns of genetic diversity of these two wild species.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
12.
Serene Hargreaves Nigel Maxted Ryoko Hirano Michael Abberton Leif Skøt Brian V. Ford-Lloyd 《Conservation Genetics》2010,11(4):1317-1326
Island populations are often thought to be more susceptible to the loss of genetic diversity as a consequence of limited population
size and genetic drift, greater susceptibility to detrimental stochastic events and low levels of immigration. However the
geographic isolation of islands may create refuges for native crop species whose genetic diversity is threatened from the
genetic erosion occurring in mainland areas as a result of crop-wild gene flow and genetic swamping. Many UK islands remain
uncharacterised in terms of plant genetic diversity. In this study we compared the genetic diversity of mainland populations
and landraces of Trifolium repens with wild populations collected from the islands surrounding the UK, including the island of Hirta in the St Kildan archipelago.
Individuals from St Kilda represent a unique conservation resource, with populations both highly differentiated from UK mainland
populations and genetically distinct from cultivated varieties, whilst able to retain diversity through limited human influence
on the islands. In contrast, there is relative genetic similarity of wild UK populations to cultivated forms highlighted in
mainland populations, but with geographic barriers preventing complete homogenisation of the mainland UK genepool. We underline
the need for conservation priorities to include common species that are threatened by gene flow from cultivation, and draw
attention to the potential of islands to preserve natural levels of genetic diversity. 相似文献
13.
Conservation of 16 nuclear microsatellite loci, originally developed for Quercus macrocarpa (section Albae), Q. petraea, Q. robur (section Robur), and Q. myrsinifolia, (subgenus Cyclobalanopsis) was tested in a Q. infectoria ssp. veneris population from Cyprus. All loci could be amplified successfully and displayed allele size and diversity patterns that match
those of oak species belonging to the section Robur. At least in one case, limited amplification and high levels of homozygosity support the occurrence of “null alleles” caused
by a possible mutation in the highly conserved primer areas, thus hindering PCR. The sampled population exhibited high levels
of diversity despite the very limited distribution of this species in Cyprus and extended population fragmentation. Allele
sizes of Q. infectoria at locus QpZAG9 partially match those of Q. alnifolia and Q. coccifera from neighboring populations. However, sequencing showed homoplasy, excluding a case of interspecific introgression with
the latter, phylogenetically remote species. Q. infectoria ssp. veneris sequences at this locus were concordant to those of other species of section Robur, while sequences of Quercus alnifolia and Quercus coccifera were almost identical to Q. cerris. 相似文献
14.
The soil seed bank represents the potential plant population since it is the source for population replacement. The genetic
structure of a Stipa kryiovii (Roshev.) plant population and its soil seed bank was investigated in the Xilinguole Steppe of Inner Mongolia using random
amplified polymorphic DNA (RAPD) analyses. The population was sampled at two sites that were in close proximity to each other
(0.5 km apart). Thirty plants and 18 seed bank samples were taken from each site to determine the genetic diversity between
sites and between sources (plant or seed). The material was analyzed using 13 primers to produce 92 loci. Eighty-six were
multi-loci, of which 23 loci (26.74%) of allele frequencies showed significant differences (P ≤ 0.05). The genetic similarity between two seed bank sites was 0.9843 while the genetic similarity between two plant sites
was 0.9619. Their similarities were all greater than that between the seed bank and plant populations. An analysis of their
genetic structure showed that 87.86% of total variation was derived by two-loci. Genetic structures between plant and soil
seed bank populations in S. krylovii were different due to the variance of mean gametic disequilibria and mean gene diversity. AMOVA results showed that the majority
of variance (88.62%) occurred within sites, 12.75% was from between-groups. Further research is needed to investigate the
selective function in maintaining the genetic diversity of Stipa krylovii plant populations. 相似文献
15.
The majority of research in genetic diversity yields recommendations rather than actual conservation achievements. We assessed
the efficacy of actual in situ and ex situ efforts to conserve Parashorea chinensis (Dipterocarpaceae) against the background of the geographic pattern of genetic variation of this species. Samples from seven
natural populations, including three in a nature reserve, and one ex situ conservation population were studied. Across the
natural populations, 47.8% of RAPD loci were polymorphic; only 20.8% on average varied at the population level. Mean population
genetic diversity was 0.787 within natural populations and 1.410 for the whole species. Significant genetic differentiation
among regions and isolation by distance were present on larger scales (among regions). AMOVA revealed that the majority of
the among-population variation occurred among regions rather than among populations within regions. Regression analysis, Mantel
test, principal coordinates analysis, and cluster analysis consistently demonstrated increasing genetic isolation with increasing
geographic distance. Genetic differentiation within the region was quite low compared to that among regions. Multilocus spatial
autocorrelation analysis of these three populations revealed random distribution of genetic variation in two populations,
but genetic clustering was detected in the third population. The ex situ conserved population contained a medium level of
genetic variation compared with the seven natural populations; it contained 77.1% of the total genetic variation of this species
and 91% of the moderate to high frequency RAPD fragments (f > 0.05). Exclusive bands were detected in natural populations,
but none were found in the ex situ conserved population. The populations protected in the nature reserve contained most of
the genetic variation of the whole species, with 81.4% of the total genetic variation and 95.7% of the fragments with moderate
to high frequency (f > 0.05) of this species conserved. The results show that the ex situ conserved population does not contain
enough genetic variation to meet the need of release in the future, and that more extensive ex situ sampling in natural populations
TY, NP, HK, and MG is needed. The in situ conserved population contains representative genetic variation to maintain long-term
survival and evolutionary processes of P. chinensis. 相似文献
16.
Most of our current understanding of comparative population structure has been come from studies of parasite–host systems,
whereas the genetic comparison of gallnut-aphids and their host-plants remain poorly documented. Here, we examined the population
genetic structure of the Chinese sumac aphid Schlechtendalia chinensis and its unique primary host-plant Rhus chinensis in a mountainous province in western China using inter-simple sequence repeat (ISSR) markers. Despite being sampled from
a mountainous geographic range, analysis of molecular variance (AMOVA) showed that the majority of genetic variation occurred
among individuals within populations of both the aphid and its host. The aphid populations were found to be structured similarly
to their primary host populations (F
ST values were 0.239 for the aphid and 0.209 for its host), suggesting that there are similar patterns of gene flow between
the populations of the aphid and between populations of its host-plant. The genetic distances (F
ST/1 − F
ST) between the aphid populations and between its host-plant populations were uncorrelated, indicating that sites with genetically
similar host-plant populations may not always have genetically similar aphid populations. The lack of relationships between
genetic and geographical distance matrices suggested that isolation by distance (IBD) played a negligible role at this level.
This may be mainly attributed to the founder effect, genetic drift and the relative small spatial scale between populations.
Zhumei Ren and Bin Zhu contributed equally to this work. 相似文献
17.
In order to establish a strategy for conservation, the distribution of genetic diversity in four natural populations of Ocotea catharinensis in the Brazilian Atlantic rain forest was investigated using 18 allozyme loci. Estimates of the average number of alleles
per loci (2.2), percentage of polymorphic loci (83.3%) and expected genetic diversity (0.427) in adult individuals were high;
suggesting that all populations have genetic potential for conservation. The inbreeding within populations ([^(f)] = - 0.0 1 1 \hat{f} = - 0.0 1 1 ) and the total inbreeding ([^(F)] = 0. 1 3 3 \hat{F} = 0. 1 3 3 ) suggest population structure, since a high level of divergence among populations (
[^(q)]\textP = 0. 1 4 3 \hat{\theta }_{\text{P}} = 0. 1 4 3 ) was also detected. Significant values of spatial genetic structure were found inside the four populations. This study demonstrates
that the realized gene flow among the remaining populations of O. catharinensis is not sufficient to stop population divergence due to genetic drift and local selection, which threatens the future viability
of this species. 相似文献
18.
Dong-Yuan Zhang Na Chen Yan-Zhuo Yang Qian Zhang Jian-Quan Liu 《Conservation Genetics》2008,9(2):475-477
Rhubarb is an important Traditional Chinese Medicine. However, the wild resource has been declining. In order to design appropriate
conservation methods for the official species across their natural distributions, it is important to characterize their genetic
diversity. Here, we describe the development of 10 new microsatellite loci for AC/TG/CCA in Rheum tanguticum. The microsatellites were enriched using the combined biotin capture method. The polymorphism of each locus was further assessed
in 12 individuals from four geographically distinct populations of this species. The number of alleles ranged from three to
seven and the expected heterozygosity ranged from 0.53 to 0.73. All markers have been checked in the other three species in
the genus and two of them together comprise the official medicinal rhubarb resource with R. tanguticum. These microsatellite markers could provide a useful tool for genetic and conservation studies of the rhubarb species. 相似文献
19.
Schisandra sphenanthera (Schisandraceae) is a traditional Chinese medicinal plant. In this study, nine polymorphic microsatellite loci were developed
and characterized for the species. A genomic DNA enrichment protocol was used to isolate microsatellite loci and polymorphism
was explored using 36 individuals sampled from a natural population. The observed number of alleles ranged from 2 to 10 with
an average of 5.2. Expected and observed heterozygosity ranged from 0.30 to 0.82 and 0.33 to 0.97, respectively. These microsatellites
have been directly applied to both population and conservation genetic studies of S. sphenanthera. 相似文献
20.
Allozyme variation was investigated in two local populations of Bulbophyllum drymoglossum and three populations Sarcanthus scolopendrifolius, two rare and endangered lithophytes and epiphytes from South Korea. Genetic diversity was extremely low within populations
(mean H
e = 0.011 for B. drymoglossum; 0.002 for S. scolopendrifolius). Among the putative screened 21 loci, we found only one polymorphic locus for each species. Only one polymorphic locus,
detected just one population of each species, revealed significantly high degree of population differentiation between and
among populations (F
ST = 0.253 for B. drymoglossum and F
ST = 0.899 for S. scolopendrifolius). These results suggest that genetic drift (consequence of a very small effective population size), coupled with a limited
gene flow would play a major role in shaping population genetics of these species in South Korea. The current status of both
species (small population sizes, spatially isolated populations, and highly localized habitats) in addition to the extremely
low levels of genetic diversity and reckless collection of endangered orchids by plant sellers, significantly threaten the
long-term survival of these species in Korea. Conservation of the two species requires both in situ strategies, by introducing of genets to increase effective population sizes by minimizing adverse effects (e.g., outbreeding
depression and genetic swamping by non-native genotypes), and ex situ strategies, such as collection of genets from clonal ramets. 相似文献