Restriction fragment length polymorphism and allozyme linkage map of Cuphea lanceolata

Summary Cuphea lanceolata Ait. has had a significant role in the domestication of Cuphea and is a useful experimental organism for investigating how medium-chain lipids are synthesized in developing seeds. To expand the genetics of this species, a linkage map of the C. lanceolata genome was constructed using five allozyme and 32 restriction-fragment-length-polymorphism (RFLP) marker loci. These loci were assigned to six linkage groups that correspond to the six chromosomes of this species. Map length is 288 cM. Levels of polymorphism were estimated for three inbred lines of C. lanceolata and an inbred line of C. viscosissima using 84 random genomic clones and two restriction enzymes, EcoRI and HindIII. Of the probes 29% detected RFLPs between C. lanceolata and C. viscosissima lines. Crosses between these species can be exploited to expand the map.     

On birth and death in the sea

We present the first comparative study of the stage-specific patterns of mortality of Calanus and Pseudocalanus, two widely distributed genera that are representative of a relatively large-bodied, broadcast spawning calanoid copepod and a relatively small-bodied, egg-brooding calanoid. The study site is Georges Bank, a continental shelf locality in the Northwestern Atlantic with retentive circulation that renders it suitable for studies of population dynamics. Based on extensive mortality estimates from 30 cruises, we find that co-occurring Calanus finmarchicus and Pseudocalanus spp. have markedly different patterns of stage-specific mortality, the former bimodal and the latter relatively uniform with respect to developmental stage. Neither taxon exhibits a monotonic decline in mortality with developmental stage, nor are rates of mortality predictable in a useful manner by copepod body size or by ambient temperature. Young stages of the broadcast-spawning C. finmarchicus show conditional density-dependence of mortality rates, i.e. mortality rates are independent of population density when adult females are low in abundance but positively related to population density at high female abundances. This density-dependence, which is probably attributable to egg cannibalism, introduces a quadratic mortality term into population dynamic models. The egg-brooding Pseudocalanus spp., in contrast, show no evidence of density-dependent mortality. The two taxa illustrate a life history trade-off: the broadcast-spawning Calanus exhibits birth rates that are greatly elevated with respect to those of Pseudocalanus, but there is a compensatory cost in very low survivorship of the freely spawned eggs. Both the high fecundity, high mortality life history of Calanus and the low fecundity, low mortality life history of Pseudocalanus appear to have approximately equal fitness in this study site.     

A genetic comparison of two species of clam shrimp in the genus Eulimnadia: An electrophoretic approach

Herein we report the first genetic comparison among species in the genus Eulimnadia. Multilocus genotypic patterns (using six allozyme loci) were compared for a total of 2277 clam shrimp from nine populations from Arizona and New Mexico. Seven of these populations were morphologically typed as Eulimnadia texana Packard and two were typed as Eulimnadia diversa Mattox. All populations were hermaphrodite-biased, and highly inbred (inbreeding coefficients ranging from 0.33 to 0.98). Genetic distances showed the two species to be within the range described for other arthropods. One of the two E. diversa populations appeared to be a hybrid between E. texana and E. diversa, showing electrophoretic patterns similar to both species, although morphologically, they were typed as E. diversa. A phenogram (generated using coancestry distances and a neighbor joining algorithm) placed this hybrid population half-way between these two species, and a breakdown of individuals within this hybrid population (based on allozyme scores) indicated individuals very similar to the second E. diversa population, and two groups of apparent hybrid individuals. Therefore, the distinction between these two species is questionable due to their apparent hybridization in this area of Arizona. Genetic population structuring was noted among the seven E. texana pools. Estimated migration rates were less than one migrant per generation. Even in the geographically close pools in New Mexico, which were separated by only hundreds of meters, significant sub-structuring was noted, and estimates of migration rate were less than two migrants per generation.     

Distribution of <Emphasis Type="Italic">Calanus</Emphasis> populations in a glaciated fjord in the Arctic (Hornsund,Spitsbergen)—the interplay between biological and physical factors

The distribution and diversity of copepods of the genus Calanus were investigated in Hornsund Fjord (on the southwest coast of Spitsbergen) in summer 2001. The Bhattacharya method was used to sort individuals by species based on their prosome length. The established prosome length boundary values for the Calanus copepodid stages coincided with those defined for the Calanus species from Kongsfjorden (on the northwest coast of Spitsbergen). The predominant species in the main and inner fjord basins was Calanus glacialis, whereas Calanus finmarchicus was the prevailing species outside Hornsund. Younger copepodid stages (CI–CIII) of both species concentrated in the surface water layers (0–50∼70 m), while older copepodids (CIV–CVI females) that were ready for wintering stayed in deep layers (50∼70 m to bottom). Calanus hyperboreus was present in low numbers, predominantly as CIV, and in Hornsund deep water layers. The distribution and diversity of Calanus species complied with the notion that the marine fauna in Hornsund is of a more Arctic character than in Kongsfjorden, a fjord 260 km to the north on the west coast of Spitsbergen.     

Organization of repeated sequences in species of the genus Avena

Summary Four repetitive sequences from Avena murphyi have been isolated and their genome organization studied in different species of the genus Avena. A tandem sequence array was found for the Avena species that contain the C genome. Three other dispersed sequences present in the A and C genomes were arranged in a genomespecific manner. The fact that no major differences in the hybridization patterns were found between species with the same basic genome is consistent with the current taxonomy of Avena species.     

Relationships and Hybridization among Smilax china and Its Affinities: Evidence from Allozyme Data

Smilax china L. is a widespread species in China with different ploidy levels. It is morphologically similar to S. davidiana, S. trinervula, and S. glauco-china. In this study, the chromosome number and the variation in allozyme patterns of eight enzyme systems with 25 alleles in 11 populations of S. china and three affinitive species were investigated. The allozyme data, together with morphological and cytological data, suggest that S. glauco-china is not closely related to the other taxa investigated. The diploid species S. davidiana and S. trinervula are involved as ancestor species and share great introgressions with S. china. In S. china, populations from Guilin and Guiyang are allotetraploid; their diploid progenitors probably are diploid populations of S. china and S. trinervula. The results suggest this species arose from multiple origins.     

Analysis of F ST outliers at allozyme loci in Pacific salmon: implications for natural selection

Natural selection has been invoked to explain the observed geographic distribution of allozyme allele frequencies for a number of teleost species. The effects of selection on allozyme loci in three species of Pacific salmon were tested. A simulation-based approach to estimate the null distribution of population differentiation (F _ST) and test for F _ST outliers was used. This approach showed that a majority of allozyme loci conform to neutral expectations predicted by the simulation model, with relatively few F _ST outliers found. No consistent F _ST outlier loci were found across species. Analysis of population sub-groups based on geography and genetic identity reduced the number of outlier loci for some species, indicating that large geographic groups may include genetically divergent populations and/or that there is geographic heterogeneity in selection pressure upon allozyme loci. Two outlier allozyme loci found in this analysis, lactate dehydrogenase-B and malic enzyme, have been shown to be influenced by selection in other teleost species. This approach is also useful in identifying allozyme loci (or other genetic markers) that meet assumptions for population genetic study.     

Comparison of allozyme,RFLP, and RAPD markers for revealing genetic variation within and between trembling aspen and bigtooth aspen

We examined genetic variation in allozyme loci, nuclear DNA restriction fragment length polymorphisms (RFLPs), and random amplified polymorphic DNAs (RAPDs) in 130 trembling aspen (Populus tremuloides) and 105 bigtooth aspen (P. grandidentata) trees. In trembling aspen 10 out of 13 allozyme loci assayed (77%) were polymorphic (P), with 2.8 alleles per locus (A) and an expected heterozygosity (H_e) of 0.25. In contrast, bigtooth aspen had a much lower allozyme genetic variability (P=29%; A=1.4; H_e=0.08). The two species could be distinguished by mutually exclusive alleles at Idh-1, and bigtooth aspen has what appears to be a duplicate 6PG locus not present in trembling aspen. We used 138 random aspen genomic probes to reveal RFLPs in HindIII digests of aspen DNA. The majority of the probes were from sequences of low copy number. RFLP results were consistent with those of the allozyme analyses, with trembling aspen displaying higher genetic variation than bigtooth aspen (P=71%, A=2.7, and H_e=0.25 for trembling aspen; P=65%, A=1.8, and H_e=0.13 for bigtooth aspen). The two species could be distinguished by RFLPs revealed by 21 probes (15% of total probes assayed). RAPD patterns in both species were studied using four arbitrary decamer primers that revealed a total of 61 different amplified DNA fragments in trembling aspen and 56 in bigtooth aspen. Assuming a Hardy-Weinberg equilibrium, estimates of P=100%, A=2, and H_e=0.30 in trembling aspen and P=88%, A=1.9, and H_e=0.31 in bigtooth aspen were obtained from the RAPD data. Five amplified DNA fragments were species diagnostic. All individuals within both species, except for 2 that likely belong to the same clone, could be distinguished by comparing their RAPD patterns. These results indicate that (1) RFLPs and allozymes reveal comparable patterns of genetic variation in the two species, (2) trembling aspen is more genetically variable than bigtooth aspen at both the allozyme and DNA levels, (3) one can generate more polymorphic and species-specific loci with DNA markers than with allozymes in aspen, and (4) RAPDs provide a very powerful tool for fingerprinting aspen individuals.     

Codon usage and base composition inRickettsia prowazekii

Codon usage and base composition in sequences from the A + T-rich genome ofRickettsia prowazekii, a member of the alpha Proteobacteria, have been investigated. Synonymous codon usage patterns are roughly similar among genes, even though the data set includes genes expected to be expressed at very different levels, indicating that translational selection has been ineffective in this species. However, multivariate statistical analysis differentiates genes according to their G + C contents at the first two codon positions. To study this variation, we have compared the amino acid composition patterns of 21R. prowazekii proteins with that of a homologous set of proteins fromEscherichia coli. The analysis shows that individual genes have been affected by biased mutation rates to very different extents: genes encoding proteins highly conserved among other species being the least affected. Overall, protein coding and intergenic spacer regions have G + C content values of 32.5% and 21.4%, respectively. Extrapolation from these values suggests thatR. prowazekii has around 800 genes and that 60–70% of the genome may be coding. Correspondence to: S.G.E. Andersson     

Inter‐ and intraspecific variation in body‐ and genome size in calanoid copepods from temperate and arctic waters

The tendency of ectotherms to get larger in the cold (Bergmann clines) has potentially great implications for individual performance and food web dynamics. The mechanistic drivers of this trend are not well understood, however. One fundamental question is to which extent variation in body size is attributed to variation in cell size, which again is related to genome size. In this study, we analyzed body and genome size in four species of marine calanoid copepods, Calanus finmarchicus, C. glacialis, C. hyperboreus and Paraeuchaeta norvegica, with populations from both south Norwegian fjords and the High Arctic. The Calanus species showed typical interspecific Bergmann clines, and we assessed whether they also displayed similar intraspecific variations—and if correlation between genome size and body size differed between species. There were considerable inter‐ as well as intraspecific variations in body size and genome size, with the northernmost populations having the largest values of both variables within each species. Positive intraspecific relationships suggest a functional link between body and genome size, although its adaptiveness has not been settled. Impact of additional drivers like phylogeny or specific adaptations, however, was suggested by striking divergences in body size – genome size ratios among species. Thus, C. glacialis and C. hyperboreus, had fairly similar genome size despite very different body size, while P. norvegica, of similar body size as C. hyperboreus, had the largest genome sizes ever recorded from copepods. The inter‐ and intraspecific latitudinal body size clines suggest that climate change may have major impact on body size composition of keystone species in marine planktonic food webs.     

Isozyme evidence regarding the origins of three allopolyploid species ofPolytrichastrum (Polytrichaceae, Bryophyta)

Electrophoretic data show thatPolytrichastrum pallidisetum, P. ohioense, andP. sexangulare are allopolyploids. They display fixed, heterozygous banding patterns at five to six of the 11 enzyme loci that we screened. In total, we sampled 304 populations representing three genera (Polytrichastrum, Polytrichum, andPogonatum) and 18 species in our examination of the allopolyploids and their putative haploid progenitors. There were no extant species that fit perfectly as a progenitor of any allopolyploid. BothP. pallidisetum andP. ohioense appear to have originated as intergeneric hybrids between one progenitor with aPolytrichastrum-type genome and another with aPolytrichum-type genome. The extant haploid species with the most similar genomes to the putative progenitors ofP. pallidisetum werePolytrichastrum appalachianum andPolytrichum commune, whereas forPolytrichastrum ohioense the species werePolytrichastrum formosum (orP. longisetum) andPolytrichum commune. Polytrichastrum sexangulare was genetically more similar to species ofPogonatum, as was one taxon that appears to be one of its progenitors,P. sexangulare var.vulcanicum ( =Polytrichum/Pogonatum sphaerothecium). The other progenitor also must have possessed alleles that are common in species ofPogonatum. The Polytrichaceae are a relatively ancient group of mosses, and the hybridizations that gave rise to these allopolyploids may have occurred long ago. It is likely that the genomes of the original progenitors have changed over time or that those progenitors are now extinct.     

Repeated DNA sequences inTriticum (Poaceae): Chromosomal mapping and its bearing on the evolution of B and G genomes

The somatic chromosomes ofTriticum turgicum var.durum cv. Langdon andT. dicoccoides (AABB tetraploids),T. timopheevii, andT. araraticum (AAGG tetraploids) were assayed for distribution patterns of a highly repeated 120bp DNA sequence by in situ hybridization. The repeated sequence appears to be an ancient sequence shared withSecale andAegilops. The distribution patterns of the chromosomes were compared to the patterns of the A and B genome chromosomes ofT. aestivum cv. Chinese Spring (AABBDD hexaploid).T. turgidum andT. dicoccoides were observed to have identical in situ hybridization patterns. In both species, nine chromosomes with a total of 21 sites of hybridization were observed. The pattern, with few exceptions, was identical to that of Chinese Spring.T. araraticum andT. timopheevii were observed to have different patterns. InT. araraticum, six chromosomes with 21 total hybridization sites are present while inT. timopheevii nine chromosomes with 19 total sites exist. Major differences in hybridization patterns were observed between the B and G genomes. The divergence of the tetraploid wheats in this study appears to have resulted in changes in location, not in amount, of the ancient repeated sequence.     

Patterns of allozyme variation in Nordic Pilosella

Patterns of allozyme variation have been investigated in 101 clones representing most of the morphological variation (and taxa) found in the amphi-apomictic genus Pilosella Hill. in the Nordic countries. Levels of variation were very high, both within narrowly defined taxa and within the whole data-set, but the correlation between a morphology-based taxonomy and patterns of allozyme variation was very weak. Almost all enzyme bands were found in more than one taxon and the differences between broadly defined species in terms of the frequency of bands were generally small. Cluster analyses did not perfectly recover any taxon but there were some tendencies for samples of some broadly defined taxa (e.g. P. officinarum s. l., and P. cymosa ssp. cymosa) to cluster together. It is concluded that there is considerable gene-flow among virtually all Nordic morpho-types of Pilosella and this is considered an argument for applying a very broad species concept in this genus.Financial support for the present study has been recieved from Stiftelsen Harald E. Johanssons minnesfond at the Royal Swedish Academy of Sciences.     

Genetic relationships in the genus Cicer L. as revealed by polyacrylamide gel electrophoresis of seed storage proteins

Summary Total seed storage protein of the cultivated chickpea, C. arietinum L., and eight other wild annual Cicer species (all 2n = 16) was separated and compared by sodium dodecyl sulphate polyacrylamide gel electrophoresis. The seed-protein profile was a conservative and species-specific trait. Relative interspecific similarities of protein patterns were estimated using Jaccard's similarity index, and a cluster analysis was performed. The resultant dendrogram generally agreed with the limited data already available on interspecific relationships in Cicer based on morphological characteristics, crossability, genome pairing in hybrids, karyotypes and isozyme analysis. The difference between the profiles of C. judaicum and C. pinnatifidum supported the idea that they are indeed two separate species. The closest relative of C. arietinum was C. reticulatum, followed by C. echinospermum and other species, while C. cuneatum was the farthest relative. In general, C. cuneatum was also genetically the farthest removed from any other species. The suggestion that C. reticulatum is the wild progenitor of the cultivated chickpea was therefore further supported.     

红锥叶绿体基因组特征及系统发育分析

为确定红锥(Castanopsis hystrix)叶绿体基因组的结构组成情况,判定其在锥属中的进化位置及与同锥属叶绿体基因组的区别,为锥属物种鉴定、遗传多样性分析和资源保护提供相关依据。使用Illumina HiSeq 2500测序平台对红锥叶绿体基因组进行测序,通过生物信息学分析方法进行序列组装、注释和特征分析,并利用R、Python、MISA、CodonW和MEGA 6等生物信息学软件对其基因组结构和数目、密码子偏好性、序列重复、简单重复序列(simple sequence repeat,SSR)位点和系统发育进行分析。结果表明红锥叶绿体基因组大小为153754 bp,呈现四分体结构;共拥有130个基因,包含85个编码基因、37个tRNA基因和8个rRNA基因;通过密码子偏好性分析,平均有效密码子数为55.5,说明其密码子随机性强、偏好性低;通过SSR及长重复片段分析,检测到45个重复序列及111个SSR位点;与近缘种比较,发现其叶绿体基因组序列高度保守,尤其蛋白质编码序列相似度极高;此外,系统发育分析发现红锥与海南锥聚为一支,关系密切。本研究得到了红锥的叶绿体基因组基本情况与系统发育位置,为红锥的物种辨别、天然种群遗传多样性与功能基因组学提供前期研究铺垫。     

秦巴山区三种人参属药用植物叶绿体基因组特征分析

为明确珠子参、羽叶三七和秀丽假人参3种药用植物叶绿体基因组特征与系统发育关系,该文以秦巴山区3种人参属药用植物为研究对象,运用生物信息学技术,分析其叶绿体基因组特征及密码子使用偏好性,并探讨三者之间的亲缘关系。结果表明:(1)3种人参属药用植物的叶绿体基因组为典型的四分体结构,序列全长为 156 071～156 104 bp,总 GC 含量为 38.10%,基因组大小相似度较高。(2)均注释到 133 个基因,包括 88 个蛋白编码基因、37 个tRNA基因和 8 个 rRNA 基因。(3)3种人参属药用植物叶绿体密码子使用偏好性相似,密码子第 3 位碱基以 A/U 结尾为主,密码子使用模式在受到突变影响的同时,主要受到自然选择的影响。(4)系统发育结果显示,3种人参属药用植物的亲缘关系较近,并且秀丽假人参同羽叶三七亲缘关系更近。综上认为,秀丽假人参与珠子参基源植物之间存在近缘关系,这项发现对于珠子参中药材的资源开发利用和分子鉴定,以及进一步研究人参属物种的分类、系统发育和进化机制提供了重要依据。     

A profile of Drosophila species' enzymes assayed by electrophoresis. I. Number of alleles,heterozygosities, and linkage disequilibrium in glucose-metabolizing systems and some other enzymes

Seven isolated large populations of Drosophila belonging to five different species were examined by starch gel electrophoresis for allozyme variation. Six to eleven enzyme loci in the glucose-metabolizing system (group I) and six to eight enzyme loci (group II) which were not directly involved in the above-mentioned system were assayed. The parameters estimated were the average number of alleles per locus, allele frequencies, proportions of polymorphic loci, and average heterozygosity per population for group I and group II loci. The major finding is that genetic variability measured by allozyme variations is much higher for group II than for group I enzymes in terms of every parameter in all the populations. This is consistent with the earlier findings in D. ananassae by Gillespie and Kojima (1968). Linkage disequilibrium, a measure of genome integration, was computed between an enzyme locus and an inversion segment of the same chromosome. The preliminary analysis of this aspect of the study indicates that no substantial linkage disequilibrium builds up between the chromosomal segments unless the pair of segments is less than 10 centimorgan units apart.This study was supported by USPHS Grant GM-15769 and Atomic Energy Commission Contract AT-(40-1)-3681.NIH Trainee supported by Grant 5 TO 1 GM 00337.