Impact of Geography and Climate on the Genetic Differentiation of the Subtropical Pine Pinus yunnanensis

Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species’ range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.     

Livestock Diversification: an Adaptive Strategy to Climate and Rangeland Ecosystem Changes in Southern Ethiopia

Pastoral cattle production in southern Ethiopia is becoming increasingly vulnerable to impacts of climate variability and rangeland resource degradation, giving rise to livestock diversification. Using a household (n?=?242) survey among herders, the relative functions, adaptability and vulnerability of four livestock species and factors influencing livestock diversification were analyzed. The stated major drivers of livestock diversification were recurrent droughts, bush encroachment, increased vulnerability of cattle and growing demand for adaptive species. Different livestock species are kept to fulfill various livelihood priorities with subsistence objectives outweighing production goals of the herders. Adaptability and vulnerability analyses of the livestock species showed camels and cattle to be the most and least adaptable species, respectively. Livestock species diversification varied significantly with family size and per capita holding of cattle, implicating the influence of labor and economic factors on adoptions. Multispecies herding emerged as the dominant local adaptation strategy, likely because it enhances resilience of households to climate and rangeland ecosystem changes by broadening the set of existing strategies.     

Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing

Phylogenetic relationships among Chinese species of Morella (Myricaceae) are unresolved. Here, we use restriction site-associated DNA sequencing (RAD-seq) to identify candidate loci that will help in determining phylogenetic relationships among Morella rubra, M. adenophora, M. nana and M. esculenta. Three methods for inferring phylogeny, maximum parsimony (MP), maximum likelihood (ML) and Bayesian concordance, were applied to data sets including as many as 4253 RAD loci with 8360 parsimony informative variable sites. All three methods significantly favored the topology of (((M. rubra, M. adenophora), M. nana), M. esculenta). Two species from North America (M. cerifera and M. pensylvanica) were placed as sister to the four Chinese species. According to BEAST analysis, we deduced speciation of M. rubra to be at about the Miocene-Pliocene boundary (5.28 Ma). Intraspecific divergence in M. rubra occurred in the late Pliocene (3.39 Ma). From pooled data, we assembled 29378, 21902 and 23552 de novo contigs with an average length of 229, 234 and 234 bp for M. rubra, M. nana and M. esculenta respectively. The contigs were used to investigate functional classification of RAD tags in a BLASTX search. Additionally, we identified 3808 unlinked SNP sites across the four populations of M. rubra and discovered genes associated with fruit ripening and senescence, fruit quality and disease/defense metabolism based on KEGG database.     

Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties

1. Download : Download high-res image (186KB)
2. Download : Download full-size image

     

The Double Helix: Applying an Ethic of Care to the Duty to Warn Genetic Relatives of Genetic Information

Genetic testing reveals information about a patient's health status and predictions about the patient's future wellness, while also potentially disclosing health information relevant to other family members. With the increasing availability and affordability of genetic testing and the integration of genetics into mainstream medicine, the importance of clarifying the scope of confidentiality and the rules regarding disclosure of genetic findings to genetic relatives is prime. The United Nations International Declaration on Human Genetic Data urges an appreciation for principles of equality, justice, solidarity and responsibility in the context of genetic testing, including a commitment to honoring the privacy and security of the person tested. Considering this global mandate and recent professional statements in the context of a legal amendment to patient privacy policies in Australia, a fresh scrutiny of the legal history of a physician's duty to warn is warranted. This article inquiries whether there may be anything ethically or socially amiss with a potential future recommendation for health professionals or patients to universally disclose particular cancer predisposition genetic diagnosis to genetic family members. While much of the discussion remains applicable to all genetic diagnosis, the article focuses on the practice of disclosure within the context of BRCA1/2 diagnosis. An ‘ethic of care’ interpretation of legal tradition and current practice will serve to reconcile law and medical policy on the issue of physician disclosure of genetic results to family members without patient consent.     

承德光秃山不同海拔油松居群遗传多样性

为了解光秃山不同海拔下天然油松居群之间的遗传差异及探求遗传多样性与土壤因子的关联,为油松种源筛选和管理提供参考,本研究运用ISSR技术,对位于河北承德辽河源光秃山4个不同海拔油松天然居群共118个植株个体的遗传多样性进行分析。13个引物共扩增出177条清晰的条带,种群多态位点百分比(PPL)为60.2775%,Nei’s基因多样性指数(h)为0.2171,Shannon信息指数(I)为0.3222;不同种群遗传变异水平随海拔差异呈规律性变化,表现为沿海拔升高而呈低-高-低的分布规律,其中1354～1274 m范围的遗传多样性水平最高;在物种水平上油松具有较高的遗传多样性(PPL=98.33%,h=0.38142,I=0.5550),种群间的遗传分化系数Gst=0.6562。利用AMOVA软件对遗传变异的等级剖分结果表明,种群间有显著的遗传分化,约2/5的遗传变异存在种群间,种群内占3/5。Pearson相关分析表明,油松居群内遗传多样性与海拔、土壤养分(有机质、速效磷、速效钾含量)之间存在显著或一定的相关关系。Mantel检验结果显示,油松居群遗传距离与海拔差距、土壤养分因子的分异存在一定相关性。以上结果表明不同海拔区域的生态因子、低基因流等对油松居群间的遗传分化影响较大。     

Global Genetic Differentiation in a Cosmopolitan Pest of Stored Beans: Effects of Geography,Host-Plant Usage and Anthropogenic Factors

Genetic differentiation can be promoted allopatrically by geographic isolation of populations due to limited dispersal ability and diversification over time or sympatrically through, for example, host-race formation. In crop pests, the trading of crops across the world can lead to intermixing of genetically distinct pest populations. However, our understanding of the importance of allopatric and sympatric genetic differentiation in the face of anthropogenic genetic intermixing is limited. Here, we examined global sequence variation in two mitochondrial and one nuclear genes in the seed beetle Callosobruchus maculatus that uses different legumes as hosts. We analyzed 180 samples from 42 populations of this stored bean pest from tropical and subtropical continents and archipelagos: Africa, the Middle East, South and Southeast Asia, Oceania and South America. For the mitochondrial genes, there was weak but significant genetic differentiation across continents/archipelagos. Further, we found pronounced differentiation among subregions within continents/archipelagos both globally and within Africa but not within Asia. We suggest that multiple introductions into Asia and subsequent intermixing within Asia have generated this pattern. The isolation by distance hypothesis was supported globally (with or without continents controlled) but not when host species was restricted to cowpeas Vigna unguiculata, the ancestral host of C. maculatus. We also document significant among-host differentiation both globally and within Asia, but not within Africa. We failed to reject a scenario of a constant population size in the recent past combined with selective neutrality for the mitochondrial genes. We conclude that mitochondrial DNA differentiation is primarily due to geographic isolation within Africa and to multiple invasions by different alleles, followed by host shifts, within Asia. The weak inter-continental differentiation is most likely due to frequent inter-continental gene flow mediated by human crop trade.     

植物开花时间: 自然变异与遗传分化

开花时间是植物的重要生活史性状。对模式植物的研究表明: 从感受内外环境信号开始到最终分化形成功能性花器官的过程涉及复杂的信号转导途径和调控网络; 开花时间受多种因子的调控, 而FT基因作为整合途径成分起到非常关键的作用。植物的花期变异在物种、群体和个体水平上具有复杂的自然变异模式, 且不同植物的花期变异随全球环境变化而具有不同的变异趋势。植物个体之间通过传粉进行的基因交流需要功能性开花时间的一致或重叠, 而花期变异会导致群体之间或群体内部亚群体之间的基因流障碍和遗传分化, 并可能导致邻域或同域的物种形成。该文分析了植物花期变异与群体遗传分化的关系, 认为决定开花时间的基因在物种分化中可能起到关键的作用, 而对开花时间自然变异模式的研究对于揭示晚近分化快速辐射物种的进化模式具有重要意义。     

植物开花时间：自然变异与遗传分化

开花时间是植物的重要生活史性状。对模式植物的研究表明： 从感受内外环境信号开始到最终分化形成功能性花器官的过程涉及复杂的信号转导途径和调控网络; 开花时间受多种因子的调控, 而FT基因作为整合途径成分起到非常关键的作用。植物的花期变异在物种、群体和个体水平上具有复杂的自然变异模式, 且不同植物的花期变异随全球环境变化而具有不同的变异趋势。植物个体之间通过传粉进行的基因交流需要功能性开花时间的一致或重叠, 而花期变异会导致群体之间或群体内部亚群体之间的基因流障碍和遗传分化, 并可能导致邻域或同域的物种形成。该文分析了植物花期变异与群体遗传分化的关系, 认为决定开花时间的基因在物种分化中可能起到关键的作用, 而对开花时间自然变异模式的研究对于揭示晚近分化快速辐射物种的进化模式具有重要意义。     

The Contributions of Wobbling and Superwobbling to the Reading of the Genetic Code

Reduced bacterial genomes and most genomes of cell organelles (chloroplasts and mitochondria) do not encode the full set of 32 tRNA species required to read all triplets of the genetic code according to the conventional wobble rules. Superwobbling, in which a single tRNA species that contains a uridine in the wobble position of the anticodon reads an entire four-fold degenerate codon box, has been suggested as a possible mechanism for how tRNA sets can be reduced. However, the general feasibility of superwobbling and its efficiency in the various codon boxes have remained unknown. Here we report a complete experimental assessment of the decoding rules in a typical prokaryotic genetic system, the plastid genome. By constructing a large set of transplastomic knock-out mutants for pairs of isoaccepting tRNA species, we show that superwobbling occurs in all codon boxes where it is theoretically possible. Phenotypic characterization of the transplastomic mutant plants revealed that the efficiency of superwobbling varies in a codon box-dependent manner, but—contrary to previous suggestions—it is independent of the number of hydrogen bonds engaged in codon-anticodon interaction. Finally, our data provide experimental evidence of the minimum tRNA set comprising 25 tRNA species, a number lower than previously suggested. Our results demonstrate that all triplets with pyrimidines in third codon position are dually decoded: by a tRNA species utilizing standard base pairing or wobbling and by a second tRNA species employing superwobbling. This has important implications for the interpretation of the genetic code and will aid the construction of synthetic genomes with a minimum-size translational apparatus.     

Paleo-Balkan and Slavic Contributions to the Genetic Pool of Moldavians: Insights from the Y Chromosome

Moldova has a rich historical and cultural heritage, which may be reflected in the current genetic makeup of its population. To date, no comprehensive studies exist about the population genetic structure of modern Moldavians. To bridge this gap with respect to paternal lineages, we analyzed 37 binary and 17 multiallelic (STRs) polymorphisms on the non-recombining portion of the Y chromosome in 125 Moldavian males. In addition, 53 Ukrainians from eastern Moldova and 54 Romanians from the neighboring eastern Romania were typed using the same set of markers. In Moldavians, 19 Y chromosome haplogroups were identified, the most common being I-M423 (20.8%), R-M17* (17.6%), R-M458 (12.8%), E-v13 (8.8%), R-M269* and R-M412* (both 7.2%). In Romanians, 14 haplogroups were found including I-M423 (40.7%), R-M17* (16.7%), R-M405 (7.4%), E-v13 and R-M412* (both 5.6%). In Ukrainians, 13 haplogroups were identified including R-M17 (34.0%), I-M423 (20.8%), R-M269* (9.4%), N-M178, R-M458 and R-M73 (each 5.7%). Our results show that a significant majority of the Moldavian paternal gene pool belongs to eastern/central European and Balkan/eastern Mediterranean Y lineages. Phylogenetic and AMOVA analyses based on Y-STR loci also revealed that Moldavians are close to both eastern/central European and Balkan-Carpathian populations. The data correlate well with historical accounts and geographical location of the region and thus allow to hypothesize that extant Moldavian paternal genetic lineages arose from extensive recent admixture between genetically autochthonous populations of the Balkan-Carpathian zone and neighboring Slavic groups.     

Genetic variation at allozyme and RAPD markers in Pinus longaeva (Pinaceae) of the White Mountains, California

We compared genetic diversity estimated from allozymes and from random amplified polymorphic DNA (RAPDs) in a sample of 210 Great Basin bristlecone pines (Pinus longaeva Bailey) from three groves in the White Mountains, California, USA. The White Mountains are the most westerly extension of bristlecone pine and home to the oldest known living trees. We assayed two forks of each tree to determine whether they originated from multiple seed caches of the Clark's nutcracker. Despite the limited and fragmented distribution of bristlecone pine, its level of genetic diversity was comparable to that of other pines, but lower than that reported for eastern populations of Great Basin bristlecone pine. Twenty-six of 36 allozymes were polymorphic (p(95) = 38.9%; p = 63.0%), with observed heterozygosity (H(o)) of 0.122 and expected heterozygosity (H(e)) of 0.134. The proportion of the total variation among populations (G(ST)) was only 0.011. The high proportion of trees with multiple stems was not due to germination in seed caches; only six of 210 forked trees had multiple allozyme genotypes. Of the 42 RAPD loci scored, 27 were monomorphic. Genetic diversity for RAPDs was nearly the same as that for allozymes (p(95) = 34.1%, H(e) = 0.130). However, the estimates of diversity and differentiation were much higher (H(e) = 0.321, G(ST) = 0.039) after excluding monomorphic loci.     

Genetic structure of Pinus henryi and Pinus tabuliformis: Natural landscapes as significant barriers to gene flow among populations

Mountains as natural barriers often have important effects on intraspecific genetic structure through restraining gene flow and enhancing differentiation among populations. While the Qinling and Daba mountains are considered significant geographic barriers, dividing China into temperate and subtropical regions, little is known about how this barrier influences the genetic patterns of sister species represented in distinct habitats. In this study, we analyzed genetic differentiation and the geographic boundary between Pinus henryi and Pinus tabuliformis using chloroplast microsatellite markers. Our data show high levels of among-population differentiation, consistent with the effects of historical demographic bottlenecks, local adaptation and climate effects. Three main geographic boundaries coinciding with mountain systems indicate natural landscapes, such as large rivers, and habitat loss caused by anthropogenic deforestation, are significant barriers to genetic exchange among populations. The divergence between populations in the eastern and western Qinling Mountains populations may possibly be ascribed to fragmentation driven by climate change. The genetic boundary of P. henryi and P. tabuliformis generally coincides with the previous morphological dividing line based on the unweighted pair group method using arithmetic averages and on spatial analysis of molecular variance.     

Colonisation and Diversification of the Zenaida Dove (Zenaida aurita) in the Antilles: Phylogeography,Contemporary Gene Flow and Morphological Divergence

Caribbean avifaunal biogeography has been mainly studied based on mitochondrial DNA. Here, we investigated both past and recent island differentiation and micro-evolutionary changes in the Zenaida Dove (Zenaida aurita) based on combined information from one mitochondrial (Cytochrome c Oxydase subunit I, COI) and 13 microsatellite markers and four morphological characters. This Caribbean endemic and abundant species has a large distribution, and two subspecies are supposed to occur: Z. a. zenaida in the Greater Antilles (GA) and Z. a. aurita in the Lesser Antilles (LA). Doves were sampled on two GA islands (Puerto Rico and the British Virgin Islands) and six LA islands (Saint Barthélemy, Guadeloupe, Les Saintes, Martinique, Saint Lucia and Barbados). Eleven COI haplotypes were observed that could be assembled in two distinct lineages, with six specific to GA, four to LA, the remaining one occurring in all islands. However, the level of divergence between those two lineages was too moderate to fully corroborate the existence of two subspecies. Colonisation of the studied islands appeared to be a recent process. However, both phenotypic and microsatellite data suggest that differentiation is already under way between all of them, partly associated with the existence of limited gene flow. No isolation by distance was observed. Differentiation for morphological traits was more pronounced than for neutral markers. These results suggest that despite recent colonisation, genetic drift and/or restricted gene flow are promoting differentiation for neutral markers. Variation in selective pressures between islands may explain the observed phenotypic differentiation.     

近20年亚欧大陆植被指数(NDVI)对大尺度气候变化的敏感性(英文)

The influence of climate change on the terrestrial vegetation health (condition) is one of themost significant problems of global change study. The vegetation activity plays a key role in the globalcarbon cycle. The authors investigated the relationship of the advanced very high resolution radiometer-normalized difference vegetation index (AVHRR-NDVI) with the large-scale climate variations on the inter-annual time scale during the period 1982-2000 for the growing seasons (April to October). A singular valuedecomposition analysis was applied to the NDV! and surface air temperature data in the time-domain todetect the most predominant modes coupling them. The first paired-modes explain 60.9%, 39.5% and 24.6%of the squared covariance between NDV! and temperature in spring (April and May), summer (June andAugust), and autumn (September to October), respectively, which implies that there is the highest NDVIsensitivity to temperature in spring and the lowest in autumn. The spatial centers, as revealed by themaximum or minimum vector values corresponding to the leading singular values, indicate the highsensitive regions. Only considering the mode 1, the sensitive center for spring is located in westernSiberia and the neighbor eastern Europe with a sensitivity of about 0.308 0 NDVI/℃. For summer, thereare no predominantly sensitive centers, and on average for the relatively high center over 100^o-120^o E by 45^o-60^o N, the (110^o-140^o E,55^o-65^oN)sitivity is 0.248 0 NDVI/℃. For autumn, the center is located over the high latitudes ofeastern Asia (110^o-140^o E, 55^o-65^o N), and the sensitivity is 0.087 5 NDVI/℃. The coherent patters asrevealed by the singular decomposition analysis remain the same when coarser resolution NDVI data wereused, suggesting a robust and stable climate/vegetation relationship.     

近20年亚欧大陆植被指数(NDVI)对大尺度气候变化的敏感性

利用1982～2000年4～10月的AVHRR-NDVI数据,分析了大尺度的气候(温度)变化对欧亚大陆植被状况的影响.分析方法为奇异值分解,从温度和NDVI的年际变化中检测出二者最重要和最密切的大尺度空间相关特征.用每个奇异值的平方占总的协方差平方和的比例(解释率),可以度量每对模态的重要性.春季(4和5月)、夏季和秋季(9和10月)的解释率分别是60.9%、39.5%和24.6%,这说明整体上春季植被状况对温度的敏感性高于夏季和秋季.奇异值分解的显著模态中心是二者关系最密切的地区,也就是NDVI对温度最敏感的地区,春季为西西伯利亚和东欧东北部,敏感性为 0.308 0 NDVI/℃;夏季没有特别突出的敏感中心,选择与计算春季相同格点数的高值中心,其敏感性为 0.248 0 NDVI/℃;秋季敏感中心在亚洲东部高纬度地区,相同格点大小范围(110°～140° E,55°～65°N)平均敏感性为 0.087 5 NDVI/℃.这种大尺度的NDVI-气温的关系及其敏感性非常稳定,并不随使用的NDVI的空间分辨率的改变而改变.     

nter-annual Changes in Eurasian Continent NDVI and Its ensitivity to the Large-scale Climate Variations in the Last 20 Years

The influence of climate change on the terrestrial vegetation health (condition) is one of the most significant problems of global change study. The vegetation activity plays a key role in the global carbon cycle. The authors investigated the relationship of the advanced very high resolution radiometer-normalized difference vegetation index (AVHRR-NDVI) with the large-scale climate variations on the inter-annual time scale during the period 1982-2000 for the growing seasons (April-October). A singular value decomposition analysis was applied to the NDVI and surface air temperature data in the time-domain to detect the most predominant modes coupling them. The first paired-modes explain 60.9%, 39.5% and 24.6% of the squared covariance between NDVI and temperature in spring (April-May), summer (June-August), and autumn (September-October), respectively, which implies that there is the highest NDVI sensitivity to temperature in spring and the lowest in autumn. The spatial centers, as revealed by the maximum or minimum vector values corresponding to the leading singular values, indicate the high sensitive regions. Only considering the mode 1, the sensitive center for spring is located in western Siberia and the neighbor eastern Europe with a sensitivity of about 0.308 0 NDVI/℃. For summer, there are no predominantly sensitive centers, and on average for the relatively high center over 1000-1200 E by 450-600 N, the sensitivity is 0.248 0 NDVI/℃. For autumn, the center is located over the high latitudes of eastern Asia (1100-1400 E, 550-650 N), and the sensitivity is 0.087 5 NDVI/℃. The coherent patters as revealed by the singular decomposition analysis remain the same when coarser resolution NDVI data were used, suggesting a robust and stable climate/vegetation relationship.