High Levels Of Population Differentiation Research Articles

Genetic survey extension of the threatened Iberian Arnica montana L. revealed the presence of divergent plastid lineages and highly structured populations in northern Spain

Iberian populations of Arnica montana L. (Asteraceae) represent a valuable resource both for conservation and pharmaceutical industry. Previous genetic analyses pointed out the presence of different genetic groups, but a wide region is still genetically unexplored. In order to fill this scientific gap, the present study analysed a wider sampling area along the northern Iberian Peninsula. Nuclear (i.e. microsatellite loci) and plastid DNA (cpDNA) molecular markers were used to assess the levels of genetic diversity and the population structure in 16 locations, eight analysed for the first time in the present study and eight representative of the different genetic groups previously identified. The two divergent cpDNA groups previously described were found, but their distribution was extended and refined. Thus, one of the groups (suggested as ancestral) was predominantly distributed in adjacent zones of the Cantabrian coasts while the other (more related to Central-European populations) was predominant in inner Cantabrian regions and Pyrenees. Genetic diversity with microsatellite loci (He = 0.280) was in accordance with the figures previously described, with a high level of population differentiation (FST > 0.500) identifying the presence of up to five population genetic units. Genetic and geographical distances were not related (no isolation-by-distance pattern identified), suggesting an important effect of genetic drift. Finally, due to the conservation and evolutionary interest of the populations analysed, different management actions useful for the maintenance of wild A. montana resources are provided.

Population and conservation genetics using RAD sequencing in four endemic conifers from South America

The emblematic conifer flora of Chile has experienced wide-scale habitat loss and fragmentation. Coupled with the complex topography of the region, this leads to a prediction of high levels of genetic drift and isolation resulting in strong population differentiation, and the potential for negative genetic consequences. To address the degree to which these predictions are realised, we conducted a comparative population genetic survey in four endemic conifers from South America, each of conservation concern and with a restricted distribution area. Between seven and ten populations per species were sampled, covering their entire natural distribution in Chile. We used restriction site-associated DNA markers (RAD-seq), with de novo assembly and optimisation, to accommodate the large and complex genome of conifers. The main finding was low levels of genetic structure in all four conifer species (FST = 0.017–0.062). This pattern was strikingly consistent across all four species. These results are likely due to the extreme longevity of individuals restricting divergence due to genetic drift. Thus, despite the currently highly fragmented ranges of these conifer species, we did not detect evidence for high levels of population differentiation and genetic isolation. This suggests some resilience to negative genetic impacts of habitat fragmentation, and the longevity of the individual trees may provide considerable buffering capacity. We recommend follow-up studies focusing on genotyping the seedling generation, to assess whether there is any evidence for the early warning of genetic isolation and/or elevated inbreeding in the currently established cohorts.

Deep sequencing of 1320 genes reveals the landscape of protein-truncating variants and their contribution to psoriasis in 19,973 Chinese individuals.

Protein-truncating variants (PTVs) have important impacts on phenotype diversity and disease. However, their population genetics characteristics in more globally diverse populations are not well defined. Here, we describe patterns of PTVs in 1320 genes sequenced in 10,539 healthy controls and 9434 patients with psoriasis, all of Han Chinese ancestry. We identify 8720 PTVs, of which 77% are novel, and estimate 88% of all PTVs are deleterious and subject to purifying selection. Furthermore, we show that individuals with psoriasis have a significantly higher burden of PTVs compared to controls (P = 0.02). Finally, we identified 18 PTVs in 14 genes with unusually high levels of population differentiation, consistent with the action of local adaptation. Our study provides insights into patterns and consequences of PTVs.

Patterns of allele frequency differences among domestic cat breeds assessed by a 63K SNP array.

Cats are ubiquitous companion animals that have been keenly associated with humans for thousands of years and only recently have been intentionally bred for aesthetically appealing coat looks and body forms. The intense selection on single gene phenotypes and the various breeding histories of cat breeds have left different marks on the genomes. Using a previously published 63K Feline SNP array dataset of twenty-six cat breeds, this study utilized a genetic differentiation-based method (di) to empirically identify candidate regions under selection. Defined as three or more overlapping (500Kb) windows of high levels of population differentiation, we identified a total of 205 candidate regions under selection across cat breeds with an average of 6 candidate regions per breed and an average size of 1.5 Mb per candidate region. Using the combined size of candidate regions of each breed, we conservatively estimate that a minimum of ~ 0.1–0.7% of the autosomal genome is potentially under selection in cats. As positive controls and tests of our methodology, we explored the candidate regions of known breed-defining genes (e.g., FGF5 for longhaired breeds) and we were able to detect the genes within candidate regions, each in its corresponding breed. For breed specific exploration of candidate regions under selection, eleven representative candidate regions were found to encompass potential candidate genes for several phenotypes such as brachycephaly of Persian (DLX6, DLX5, DLX2), curled ears of American Curl (MCRIP2, PBX1), and body-form of Siamese and Oriental (ADGRD1), which encourages further molecular investigations. The current assessment of the candidate regions under selection is empiric and detailed analyses are needed to rigorously disentangle effects of demography and population structure from artificial selection.

Strong Sexual Selection Does Not Induce Population Differentiation in a Fish Species with High Dispersal Potential: The Curious Case of the Worm Pipefish Nerophis lumbriciformis (Teleostei: Syngnathidae).

High levels of population differentiation are a common demographic pattern in syngnathids, even at small geographical scales. This is probably the end result of the common life history traits observed within the family, involving limited dispersal capabilities and strong habitat dependency. The worm pipefish, Nerophis lumbriciformis, which displays all these characteristics, also presents an additional variable potentially able to promote population differentiation: high sexual selection intensity, especially at the extremes of its distribution. Nevertheless, an early life pelagic stage, which presumably allows for admixture, could prevent population structuring. Here, we assessed the phylogeography of N. lumbriciformis through the amplification of the cytochrome b, 12S, and 16S rDNA mitochondrial markers as well as the rhodopsin nuclear marker, performed upon 119 individuals. We observed a genetically homogeneous population with indications of extensive gene flow. We tentatively attribute this finding to the dispersal potential of the species' pelagic larvae, supported by marine currents acting as major dispersal vectors. We also detected a signal of expansion towards the poles, consistent with the current climate change scenario. Despite the marked latitudinal differences in the phenotype of reproducing worm pipefish, the absence of clear population structuring suggests that phenotypic plasticity can have a significant role in the expression of sexual selection-related traits.

Orostachys spinosa (Crassulaceae) origin and diversification: East Asia or South Siberian Mountains? Chloroplast DNA data

Limited data are available on genetic structures of the herbaceous plant species populations inhabiting mountainous areas of Siberia and Northeastern Asian (Russian Far East). Although this area was not directly impacted by the extensive ice-sheets during the Quaternary, it experienced significant climatic fluctuations that influenced rich local flora. Orostachys spinosa (Crassulaceae) lacks any adaptations for long-distance dispersal, yet the species is characterized by an unusually wide range spanning from the Urals to the coast of the Pacific Ocean. We studied O. spinosa phylogeography and genetic diversity across its range sampling 203 individuals from 21 natural populations. Using sequences from three chloroplast DNA non-coding regions, we revealed 82 haplotypes and observed high level of population differentiation indicating presence of the phylogeographic structure (GST = 0.501 and NST = 0.822 (p < 0.01)). In concordance with the previous phylogenetic analyses based on ITS rDNA data, parsimony network revealed two distinct cpDNA haplotype lineages deferring in their structure and characteristics of genetic diversity. The split between these haplotype groups can be dated to the Pliocene (ca. 3.6 Mya). According to our estimates diversification in the Western group of populations took place ca. 1 Mya earlier than in the Eastern group (3.1 Mya and 2.26 Mya, respectively). Apart from the generally accepted notion about East Asian origin of O. spinosa, our results indicated that the species could have originated in mountains of Southern Siberia (Altai). This region was colonized independently from O. thyrsiflora which has a largely overlapping distribution in this area.

Living at the edge: population differentiation in endangered Arnica montana from NW Iberian Peninsula

Arnica montana (Asteraceae) is a herbaceous species with high interest for pharmaceutical industry due its anti-inflammatory properties. However, commercial collection in wild, habitat loss, abandonment of land, reforestation and the ongoing climate change threaten the conservation of the species throughout its natural distribution. Galicia (north-western Spain) is one of the main flower suppliers, but no legislation on A. montana exploitation is currently applied. In order to assess the genetic status and population structure in this region, 27 locations were genotyped for 14 microsatellite loci and sequenced for 2 plastid DNA (cpDNA) markers. The relationship of environmental, biochemical and morphological variables with genetic differentiation was also evaluated. Two different cpDNA groups previously described were found. One of them was widely distributed while the other was restricted to heathlands of the O Courel Mountains. The percentage of clonality was low (< 10%). Genetic diversity based on microsatellites (He = 0.245) was lower than in Central European populations, with high levels of population differentiation (FST = 0.441), suggesting strong effects of genetic drift. Bayesian clustering methods revealed the presence of four genetically distinct population units, one of them corresponding to the O Courel Mountains group described by cpDNA analysis. Environmental and biochemical factors were related to genetic differentiation, suggesting local adaptation. Necessary conservation measures include the overdue implementation of the Habitats Directive by the Galician Regional Administration, establishing sustainable harvesting regimes, and aim to conserve genetic variation in these endangered populations at the southern range edge.

Genetic differentiation in mountain-dwelling clam shrimp, Paralimnadia (Crustacea : Branchiopoda : Spinicaudata), in eastern Australia

The majority of Australian Spinicaudata Linder, 1945 inhabit the (semi)arid deserts of Australia’s lowlands. However, several closely related species of Paralimnadia Sars, 1896 inhabit small temporary habitats throughout the Great Dividing Range in eastern Australia. By combining analyses of mitochondrial cytochrome c oxidase subunit I (COI) with double-digest restriction-site associated DNA (ddRAD) data, we studied the species diversity and genetic diversity of this group of mountain-dwelling branchiopods. Levels of genetic differentiation in COI are relatively low between putative species (mostly between 1.5 and 6.7%), complicating COI-based species delimitation. Depending on the applied threshold, three to six species are inferred in the studied area, with most putative species being geographically restricted. Particularly notable are the high levels of population differentiation indicated by ddRAD analyses between nearby populations within putative species. This suggests that gene flow is limited, even between populations separated only by a few kilometres. This may lead to fast population differentiation, which in turn might drive speciation. Our data suggest that the species diversity of Paralimnadia in the Great Dividing Range is much higher than currently appreciated.

Population Pharmacogenomics for Precision Public Health in Colombia.

While genomic approaches to precision medicine hold great promise, they remain prohibitively expensive for developing countries. The precision public health paradigm, whereby healthcare decisions are made at the level of populations as opposed to individuals, provides one way for the genomics revolution to directly impact health outcomes in the developing world. Genomic approaches to precision public health require a deep understanding of local population genomics, which is still missing for many developing countries. We are investigating the population genomics of genetic variants that mediate drug response in an effort to inform healthcare decisions in Colombia. Our work focuses on two neighboring populations with distinct ancestry profiles: Antioquia and Chocó. Antioquia has primarily European genetic ancestry followed by Native American and African components, whereas Chocó shows mainly African ancestry with lower levels of Native American and European admixture. We performed a survey of the global distribution of pharmacogenomic variants followed by a more focused study of pharmacogenomic allele frequency differences between the two Colombian populations. Worldwide, we found pharmacogenomic variants to have both unusually high minor allele frequencies and high levels of population differentiation. A number of these pharmacogenomic variants also show anomalous effect allele frequencies within and between the two Colombian populations, and these differences were found to be associated with their distinct genetic ancestry profiles. For example, the C allele of the single nucleotide polymorphism (SNP) rs4149056 [Solute Carrier Organic Anion Transporter Family Member 1B1 (SLCO1B1)∗5], which is associated with an increased risk of toxicity to a commonly prescribed statin, is found at relatively high frequency in Antioquia and is associated with European ancestry. In addition to pharmacogenomic alleles related to increased toxicity risk, we also have evidence that alleles related to dosage and metabolism have large frequency differences between the two populations, which are associated with their specific ancestries. Using these findings, we have developed and validated an inexpensive allele-specific PCR assay to test for the presence of such population-enriched pharmacogenomic SNPs in Colombia. These results serve as an example of how population-centered approaches to pharmacogenomics can help to realize the promise of precision medicine in resource-limited settings.

Comparative phylogeography of parasitic Laelaps mites contribute new insights into the specialist-generalist variation hypothesis (SGVH)

BackgroundThe specialist-generalist variation hypothesis (SGVH) in parasites suggests that, due to patchiness in habitat (host availability), specialist species will show more subdivided population structure when compared to generalist species. In addition, since specialist species are more prone to local stochastic extinction events with their hosts, they will show lower levels of intraspecific genetic diversity when compared to more generalist.ResultsTo test the wider applicability of the SGVH we compared 337 cytochrome oxidase I mitochondrial DNA and 268 nuclear tropomyosin DNA sequenced fragments derived from two co-distributed Laelaps mite species and compared the data to 294 COI mtDNA sequences derived from the respective hosts Rhabdomys dilectus, R. bechuanae, Mastomys coucha and M. natalensis. In support of the SGVH, the generalist L. muricola was characterized by a high mtDNA haplotypic diversity of 0.97 (±0.00) and a low level of population differentiation (mtDNA Fst = 0.56, p < 0.05; nuDNA Fst = 0.33, P < 0.05) while the specialist L. giganteus was overall characterized by a lower haplotypic diversity of 0.77 (±0.03) and comparatively higher levels of population differentiation (mtDNA Fst = 0.87, P < 0.05; nuDNA Fst = 0.48, P < 0.05). When the two specialist L. giganteus lineages, which occur on two different Rhabdomys species, are respectively compared to the generalist parasite, L. muricola, the SGVH is not fully supported. One of the specialist L. giganteus species occurring on R. dilectus shows similar low levels of population differentiation (mtDNA Fst = 0.53, P < 0.05; nuDNA Fst = 0.12, P < 0.05) than that found for the generalist L. muricola. This finding can be correlated to differences in host dispersal: R. bechuanae populations are characterized by a differentiated mtDNA Fst of 0.79 (P < 0.05) while R. dilectus populations are less structured with a mtDNA Fst = 0.18 (P < 0.05).ConclusionsThese findings suggest that in ectoparasites, host specificity and the vagility of the host are both important drivers for parasite dispersal. It is proposed that the SGHV hypothesis should also incorporate reference to host dispersal since in our case only the specialist species who occur on less mobile hosts showed more subdivided population structure when compared to generalist species.

Gene copy number variation in natural populations of Plasmodium falciparum in Eastern Africa

BackgroundGene copy number variants (CNVs), which consist of deletions and amplifications of single or sets of contiguous genes, contribute to the great diversity in the Plasmodium falciparum genome. In vitro studies in the laboratory have revealed their important role in parasite fitness phenotypes such as red cell invasion, transmissibility and cytoadherence. Studies of natural parasite populations indicate that CNVs are also common in the field and thus may facilitate adaptation of the parasite to its local environment.ResultsIn a survey of 183 fresh field isolates from three populations in Eastern Africa with different malaria transmission intensities, we identified 94 CNV loci using microarrays. All CNVs had low population frequencies (minor allele frequency < 5%) but each parasite isolate carried an average of 8 CNVs. Nine CNVs showed high levels of population differentiation (FST > 0.3) and nine exhibited significant clines in population frequency across a gradient in transmission intensity. The clearest example of this was a large deletion on chromosome 9 previously reported only in laboratory-adapted isolates. This deletion was present in 33% of isolates from a population with low and highly seasonal malaria transmission, and in < 9% of isolates from populations with higher transmission. Subsets of CNVs were strongly correlated in their population frequencies, implying co-selection.ConclusionsThese results support the hypothesis that CNVs are the target of selection in natural populations of P. falciparum. Their environment-specific patterns observed here imply an important role for them in conferring adaptability to the parasite thus enabling it to persist in its highly diverse ecological environment.

Searching for signals of recent natural selection in genes of the innate immune response - ancient DNA study

The last decade has seen sharp progress in the field of human evolutionary genetics and a great amount of genetic evidence of natural selection has been provided so far. Since host-pathogen co-evolution is difficult to trace due to the polygenic nature of human susceptibility to microbial diseases, of particular interest is any signal of natural selection in response to the strong selective pressure exerted by pathogens. Analysis of ancient DNA allows for the direct insight into changes of a gene pool content over time and enables monitoring allele frequency fluctuations. Among pathogenic agents, mycobacteria are proved to have remained in an intimate, long-lasting relation with humans, reflected by the current high level of host resistance. Therefore, we aimed to investigate the prevalence of several polymorphisms within innate immune response genes related to susceptibility to mycobacterial diseases (in SLC11A1, MBL2, TLR2, P2RX7, IL10, TNFA) in time series data from North and East Poland (1st–18th century AD, n = 207). The comparison of allele frequencies over time revealed a predominant role of genetic drift in shaping past gene pool of small, probably isolated groups, which was explained by the high level of population differentiation and limited gene flow. However, the trajectory of frequency fluctuations of two SNPs suggested the possibility of their non-neutral evolution and the results of applied forward simulations further strengthened the hypothesis of natural selection acting on those loci. However, we observed an unusual excess of homozygosity in the profile of several SNPs, which pinpoints to the necessity of further research on temporally and spatially diverse samples to support our inference on non-stochastic evolution, ideally employing pathway-based approaches. Nevertheless, our study confirms that time series data could help to decipher very recent human adaptation to life-threatening pathogens and assisting demographic events.

Demographic history of the Magellanic Penguin (Spheniscus magellanicus) on the Pacific and Atlantic coasts of South America

Spatial subdivision, local extinction and recolonization influence the genetic variation of natural populations. Different levels of population structure can be identified in nature, from panmictic populations, in which high gene flow homogenizes diversity across localities, to metapopulations, where combinations of moderate to high levels of population differentiation and source-sink population dynamics are expected. Gene flow, dispersal and recolonization can be affected by changes in ecological conditions such as climate and resource distribution. Evaluating demographic history is crucial for understanding current population dynamics. We assessed a mitchondrial DNA (mtDNA) control region and microsatellite data for 210 Magellanic Penguins (Spheniscus magellanicus) from 13 breeding colonies on the coastlines of Chile and Argentina, covering a great portion of the species’ distribution. We found high levels of genetic diversity and detected two genetic-geographic regions, Pacific and Atlantic, probably due to interruption of the connection between the oceans during the Last Glacial Maximum (LGM), when several parts of the Magellanic Channel were connected to the continent. The Atlantic ocean colonies showed a slight differentiation between the northern and southern colonies, and the Falkand/Malvinas one seems to be a mix of northern, southern and Pacific colonies. Magellanic Penguins showed intense gene flown among colonies, and exhibited low levels of genetic differentiation in each region. Furthermore, our findings indicate that the Magellanic Penguin experienced a population expansion around 17,500 years ago, which is in agreement with the timing of a decreased sea level and the exposure of the continental shelf along the coast of Argentina and the Falkland/Malvinas Islands at the end of the LGM. Thus, our results suggest that climate changes that affect the sea level in South America can play important roles in the migration of Magellanic Penguins.

Plastid DNA variation of the endemic species Oxytropis glandulosa Turcz. (Fabaceae)

Oxytropis glandulosa Turcz. (Fabaceae) is a rare perennial plant endemic to Buryatia (Russia). We sequenced three intergenic spacers (the psbA−trnH, trnL−trnF, and trnS−trnG) of chloroplast DNA (cpDNA) in specimens of four populations from two geographic regions (Barguzin and Yeravna depressions) within this species range. The levels of haplotype and nucleotide diversity varied in the range of 0.133−0.911 and 0.0002−0.0059, respectively. The highest values of these parameters are characteristic of populations located in the Barguzin depression. Variable sites detected within the intergenic spacers allowed the identification of eleven haplotypes; nine of them were found in the populations from the Barguzin depression and only two haplotypes were found in the populations from the Yeravna depression. No common haplotypes for all four populations were found. A high level of population differentiation (ΦST = 0.758, P < 0.0001) and the absence of evidence for isolation by distance were also found in O. glandulosa. Genealogical and phylogenetic analyses and Bayesian analysis of the genetic structure showed a clear division of the studied populations of O. glandulosa into three major lineages.

High levels of population differentiation in two New Caledonian Scaevola species (Goodeniaceae) and its implications for conservation prioritisation and restoration

Population genetic structure was studied in two Scaevola (Goodeniaceae) species across their ranges in New Caledonia. Scaevola montana is locally common and distributed primarily on ultramafic substrates, and is used for ecological restoration of mining sites. Scaevola coccinea is a narrow endemic restricted to ultramafic soils in a single valley, where intensive mining activity occurs. We compared levels of diversity and differentiation in the two species using nuclear microsatellites, so as to understand the spatial scale at which populations become isolated. We also measured environmental distances among sites as a crude proxy to estimate where adaptive differentiation may occur. Populations of S. montana were sampled over a total distance of ~500 km. In contrast, the total range of S. coccinea is 12 × 6 km. Greater allelic diversity and gene diversity was detected within populations of S. montana than S. coccinea. Both species show high levels of population differentiation (S. montana FʹST = 0.437; S. coccinea FʹST = 0.54). The marked population structure in S. coccinea despite the close proximity of the sampled populations is associated with its pollination by territorial birds and no observed seed-dispersal agents, compared with the greater vagility of insect pollination and bird dispersal of S. montana. In S. coccinea, given the high levels of differentiation, we highlight the importance of each individual population for the conservation of intra-specific biodiversity in this species. In S. montana, we used a combination of the genetic data and environmental characteristics of each of the sample sites to outline general guidelines on seed sources for restoration programs.

青藏高原濒危植物唐古特大黄的遗传多样性

PDF HTML阅读 XML下载 导出引用 引用提醒 青藏高原濒危植物唐古特大黄的遗传多样性 DOI: 10.5846/stxb201608091635 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金项目（31000104） Genetic diversity of an endangered species, Rheum tanguticum (Polygonaceae), on the Qinghai-Tibetan Plateau Author: Affiliation: Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:唐古特大黄（Rheum tanguticum）是中国传统的中藏药材，近几年由于生境的严重破坏，已濒临灭绝，并被列入濒危植物名单。为了探索唐古特大黄物种濒危的原因并保护其野生资源，本研究采集了9个居群87个个体的唐古特大黄样本，基于该物种的叶绿体基因trnS-G序列对其进行了遗传多样性研究。结果表明，唐古特大黄物种具有较高的遗传多样性水平（Ht=0.694），其中95.97%的遗传分化来自于居群间（GST=0.960），4.03%的遗传分化来自于居群内（Hs=0.028）。AMOVA分析也显示唐古特大黄居群间基因流较小（Nm=0.01），存在较高的遗传分化（FST=0.9631）。唐古特大黄较高的遗传多样性水平可能与该物种较长的进化史和生活史有关，居群间较高的遗传分化可能与高山地区特殊的地理环境和人类活动有关。根据研究结果，建议对唐古特大黄所有野生居群进行就地保护，同时收集种质资源开展异地繁殖工作，以保护物种的遗传多样性，维持其进化潜力。 Abstract:Rheum tanguticum (Polygonaceae), an endangered traditional Chinese and Tibetan medicines, is distributed in the Tibetan Plateau. To investigate endangered reasons and protect the wild resources, we collected 87 individuals fromnine populations of R. tanguticum, and estimated the genetic diversity of this speciesbased on the cpDNAtrnS-G region.The results showed that there was high genetic diversity within this species. The length of the total trnS-G region of the 87 individuals ranged from 944 to 954bp, and covered 965 nucleotide positions after being aligned. Variations were detected in 23 nucleotides, including 13 nucleotide substitutions and 10 indel sites. On the basis of these nucleotide mutations, a total of four nucleotide haplotypes (H1-H4) were identified. The development of a parsimony network showed that the four haplotypes made up a shallow star genetic tree. Haplotypes H1, H2, and H4 were located at the tips of the network, representing recent haplotypes.Haplotype H3 and three missing haplotypes were in the center of the star network.Moreover,since haplotype H3 had the highest frequency, it was identified as an ancestral haplotype.The total diversity (Ht) among the individuals collected was 0.694, indicating a high genetic diversity. In addition, a high level of population differentiation was observed (GST=0.960), as determined by PERMUT analysis, showing 95.97% genetic differentiation between populations, whereas the remainder of the total genetic variation (4.03%) was attributed to within-population diversity (Hs=0.028). AMOVA analysis (FST=0.9631) also indicated that the genetic diversity among populations was greater than that within populations. The value for gene flow was fairly low (Nm=0.01), indicating a limited gene flow between populations, which is consistent with the findings of PERMUT and AMOVA analysis.The NJ tree of populations based on genetic distance revealed three supported groups. However, populations with close geographic distance did not cluster together, indicating that there was no direct relationship between the geographic distances and genetic distances of the nine populations, which was confirmed by the Mantel test(r=0.2461, p=0.2060). The high genetic diversity of the examined populations is probably associated with the long evolutionary history and life history of R.tanguticum.The large genetic differentiation between populations might be related tothe alpine geographical environment and human activity. Therefore, we suggest that more wild populations with high genetic diversity should be protected by an in-situ conservation program at sites distant from human activity. We also recommend the collection and conservation of seeds from populations with rich genetic diversity for the ex-situ conservation of genetic stocks and their propagation. These conservation measures will certainly provide the basic resources required to increase the number of populations of this species and extend its range of distribution. 参考文献 相似文献 引证文献

Lack of direct evidence for natural selection at the candidate thrifty gene locus, PPARGC1A.

BackgroundThe gene PPARGC1A, in particular the Gly482Ser variant (rs8192678), had been proposed to be subject to natural selection, particularly in recent progenitors of extant Polynesian populations. Reasons include high levels of population differentiation and increased frequencies of the derived type 2 diabetes (T2D) risk 482Ser allele, and association with body mass index (BMI) in a small Tongan population. However, no direct statistical tests for selection have been applied.MethodsUsing a range of Polynesian populations (Tongan, Māori, Samoan) we re-examined evidence for association between Gly482Ser with T2D and BMI as well as gout. Using also Asian, European, and African 1000 Genome Project samples a range of statistical tests for selection (F ST, integrated haplotype score (iHS), cross population extended haplotype homozygosity (XP-EHH), Tajima’s D and Fay and Wu’s H) were conducted on the PPARGC1A locus.ResultsNo statistically significant evidence for association between Gly482Ser and any of BMI, T2D or gout was found. Population differentiation (F ST) was smallest between Asian and Pacific populations (New Zealand Māori ≤ 0.35, Samoan ≤ 0.20). When compared to European (New Zealand Māori ≤ 0.40, Samoan ≤ 0.25) or African populations (New Zealand Māori ≤ 0.80, Samoan ≤ 0.66) this differentiation was larger. We did not find any strong evidence for departure from neutral evolution at this locus when applying any of the other statistical tests for selection. However, using the same analytical methods, we found evidence for selection in specific populations at previously identified loci, indicating that lack of selection was the most likely explanation for the lack of evidence of selection in PPARGC1A.ConclusionWe conclude that there is no compelling evidence for selection at this locus, and that this gene should not be considered a candidate thrifty gene locus in Pacific populations. High levels of population differentiation at this locus and the reported absence of the derived 482Ser allele in some Melanesian populations, can alternatively be explained by multiple out-of-Africa migrations by ancestral progenitors, and subsequent genetic drift during colonisation of Polynesia. Intermediate 482Ser allele frequencies in extant Western Polynesian populations could therefore be due to recent admixture with Melanesian progenitors.Electronic supplementary materialThe online version of this article (doi:10.1186/s12881-016-0341-z) contains supplementary material, which is available to authorized users.

Genetic diversity and population structure of common walnut (Juglans regia) in China based on EST-SSRs and the nuclear gene phenylalanine ammonia-lyase (PAL)

Common walnut (Juglans regia L.) is an economically important temperate tree species valued for both its nut and wood. We investigated the genetic diversity and population structure of J. regia germplasm from 13 locations in China using 10 markers derived from expressed sequences (EST-SSR) and sequence polymorphisms within the phenylalanine ammonia-lyase (PAL) gene. Analysis of the population genetic structure based on EST-SSRs showed distinct populations in northern versus southern China that were not reflected in the spatial distribution of PAL haplotypes. High levels of population differentiation were probably the result of reproductive isolation and in southern China, hybridization with Juglans sigillata. The results indicate the possible presence of distinct evolutionary lineages of J. regia in the Qinling and Daba Mountains of China and in Yunnan province that may require ecological management if they are to be retained as in situ resources.

Phylogeny and biogeography of Arabian populations of the Persian Horned Viper Pseudocerastes persicus (Duméril, Bibron & Duméril, 1854)

The Persian Horned Viper (Pseudocerastes persicus) is distributed from northeast Iraq through the Iranian Plateau to western Pakistan with isolated populations in the Hajar Mountains of south-eastern Arabia. Like the other members of the genus Pseudocerastes, P. persicus is a sit-and-wait ambush feeder with low vagility, a characteristic that often results in high levels of population differentiation. In order to clarify the level of genetic variability, phylogenetic relationships, and biogeography of the Arabian populations of P. persicus we sequenced 597 base pairs of the mitochondrial cytochrome b of four individuals from the Hajar Mountains in south-eastern Arabia and inferred their phylogenetic relationships including 10 samples of P. persicus from Iran and Pakistan, four P. urarachnoides and one P. fieldi downloaded from GenBank. The four Arabian samples are genetically very similar in the gene fragment analysed and are phylogenetically very closely related to populations of P. persicus from coastal south Iran. Biogeographically, it appears that colonisation of the Hajar Mountains by P. persicus took place from Iran very recently, most probably during the last glaciation, when most of the Persian Gulf was above sea level and did not represent a barrier for dispersal.

Population genetic structure of Rhizoctonia solani AG 3-PT from potatoes in South Africa

Rhizoctonia solani AG 3-PT is an important potato pathogen causing significant yield and quality losses in potato production. However, little is known about the levels of genetic diversity and structure of this pathogen in South Africa. A total of 114 R. solani AG 3-PT isolates collected from four geographic regions were analysed for genetic diversity and structure using eight microsatellite loci. Microsatellite analysis found high intra-population genetic diversity, population differentiation and evidence of recombination. A total of 78 multilocus genotypes were identified with few shared among populations. Low levels of clonality (13–39 %) and high levels of population differentiation were observed among populations. Most of the loci were in Hardy–Weinberg equilibrium and all four populations showed evidence of a mixed reproductive mode of both clonality and recombination. The PCoA clustering method revealed genetically distinct geographic populations of R. solani AG 3-PT in South Africa. This study showed that populations of R. solani AG 3-PT in South Africa are genetically differentiated and disease management strategies should be applied accordingly. This is the first study of the population genetics of R. solani AG 3-PT in South Africa and results may help to develop knowledge-based disease management strategies.