A Newly Isolated Family of Short Interspersed Repetitive Elements (Sines) in Coregonid Fishes (Whitefish) with Sequences That Are Almost Identical to Those of the Smai Family of Repeats: Possible Evidence for the Horizontal Transfer of Sines

The SmaI family of repeats is present only in the chum salmon and the pink salmon, and it is not present in five other species in the same genus or in other species in closely related genera. In the present study, we showed that another short interspersed repetitive elements (SINEs) family, which is almost identical to the SmaI family, is present in all fishes in the subfamily Coregoninae, being regarded as the most primitive salmonids. This new family of SINEs was designated the SmaI-cor family (SmaI family of repeats in coregonids). The consensus sequence of the SmaI-cor family was found to be 98.6% homologous to that of the SmaI family. Accordingly, it is difficult to explain the high degree of homology between these two families of SINEs by any mechanism other than the horizontal transfer of SINEs. The estimates of the rate of neutral mutation of nuclear genes, comparing chum salmon and European whitefish, confirmed this possibility. Our results strongly suggest that a member(s) of the SmaI-cor family might have been transferred horizontally from one coregonid species to a common ancestor of chum and pink salmon or to these two species independently, to allow subsequent amplification of the SmaI family in their respective genomes.     

BoS: A Large and Diverse Family of Short Interspersed Elements (SINEs) in Brassica oleracea

Short interspersed elements (SINEs) are nonautonomous non-LTR retrotransposons that populate eukaryotic genomes. Numerous SINE families have been identified in animals, whereas only a few have been described in plants. Here we describe a new family of SINEs, named BoS, that is widespread in Brassicaceae and present at ∼2000 copies in Brassica oleracea. In addition to sharing a modular structure and target site preference with previously described SINEs, BoS elements have several unusual features. First, the head regions of BoS RNAs can adopt a distinct hairpin-like secondary structure. Second, with 15 distinct subfamilies, BoS represents one of the most diverse SINE families described to date. Third, several of the subfamilies have a mosaic structure that has arisen through the exchange of sequences between existing subfamilies, possibly during retrotransposition. Analysis of BoS subfamilies indicate that they were active during various time periods through the evolution of Brassicaceae and that active elements may still reside in some Brassica species. As such, BoS elements may be a valuable tool as phylogenetic makers for resolving outstanding issues in the evolution of species in the Brassicaceae family.     

短散在元件的筛选方法及其在鲸类和爬行类系统发育与进化研究中的应用

短散在元件(short interspersed repetitive elements,SINEs)是广泛分布于真核生物基因组中的一种反转录转座子。近年来越来越多的研究表明SINEs对基因组的结构、功能和进化起着重要作用,是研究物种系统发育和种群生物学的一个良好分子标记。本文简单介绍了SINEs的特征、基本结构、分离和鉴定,以及近年来SINEs标记在系统发育与进化研究中的应用。     

Retroposition of the AFC Family of SINEs (Short Interspersed Repetitive Elements) Before and During the Adaptive Radiation of Cichlid Fishes in Lake Malawi and Related Inferences About Phylogeny

Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation. To clarify the phylogenetic relationships among these fish, we examined the presence and absence of SINEs (short interspersed repetitive elements) at orthologous loci. We identified six loci at which a SINE sequence had apparently been specifically inserted by retroposition in the common ancestor of all the investigated species of endemic cichlids in Lake Malawi. At another locus, unique sharing of a SINE sequence was evident among all the investigated species of endemic non-Mbuna cichlids with the exception of Rhamphochromis sp. The relationships were in good agreement with those deduced in previous studies with various different markers, demonstrating that the SINE method is useful for the elucidation of phylogenetic relationships among cichlids in Lake Malawi. We also characterized a locus that exhibited transspecies polymorphism with respect to the presence or absence of the SINE sequence among non-Mbuna species. This result suggests that incomplete lineage sorting and/or interspecific hybridization might have occurred or be occurring among the species in this group, which might potentially cause misinterpretation of phylogenetic data, in particular when a single-locus marker, such as a sequence in the mitochondrial DNA, is used for analysis. Received: 15 December 2000 / Accepted: 30 January 2001     

Erratum to: Composition of Peripheral Blood Leukocytes of Pink Salmon Oncorhynchus gorbuscha and Chum Salmon O. keta (Salmonidae) during the Marine Life Period

Journal of Ichthyology - An Erratum to this paper has been published: https://doi.org/10.1134/S0032945222330025     

Intraspecific and Interspecific Variation of the Mitochondrial Gene of Cytochrome Oxidase I in Ladybirds (Coleoptera: Coccinellidae)

Intergeneric, interspecific, and intraspecific genetic variation of the 310-bp 3-end region of the mitochondrial gene of cytochrome oxidase I (COI) has been assessed in ladybirds (Coleoptera: Coccinnellidae). The phylogenetic distances between eight species of ladybirds have been determined. Mitochondrial DNA (mtDNA) nucleotide sequences have been compared in Adalia bipunctata L. differing in the elytron and pronotum colors that have been sampled from several geographically remote populations. The taxonomic statuses of two morphs from the genus Adalia, A. bipunctata bipunctata and A. bipunctata fasciatopunctata, have been identified.     

PCR Detection of DNAs of Animal Origin in Feed by Primers Based on Sequences of Short and Long Interspersed Repetitive Elements

PCR primers for the detection of materials derived from ruminants, pigs, and chickens were newly designed on the basis of sequences of the Art2 short interspersed repetitive element (SINE), PRE-1 SINE, and CR1 long interspersed repetitive element (LINE), respectively. These primers amplified the SINE or LINE from total DNA extracted from the target animals and from test feed containing commercial meat and bone meal (MBM). With the primers, detection of Art2, PRE-1, or CR1 in test feed at concentrations of 0.01% MBM or less was possible. This method was suitable for the detection of microcontamination of feed by animal materials.     

Genetic Population Structure of Chum Salmon in the Pacific Rim Inferred from Mitochondrial DNA Sequence Variation

We examined the genetic population structure of chum salmon, Oncorhynchus keta, in the Pacific Rim using mitochondrial (mt) DNA analysis. Nucleotide sequence analysis of about 500 bp in the variable portion of the 5′ end of the mtDNA control region revealed 20 variable nucleotide sites, which defined 30 haplotypes of three genealogical clades (A, B, and C), in more than 2,100 individuals of 48 populations from Japan (16), Korea (1), Russia (10), and North America (21 from Alaska, British Columbia, and Washington). The observed haplotypes were mostly associated with geographic regions, in that clade A and C haplotypes characterized Asian populations and clade B haplotypes distinguished North American populations. The haplotype diversity was highest in the Japanese populations, suggesting a greater genetic variation in the populations of Japan than those of Russia and North America. The analysis of molecular variance and contingency χ² tests demonstrated strong structuring among the three geographic groups of populations and weak to moderate structuring within Japanese and North American populations. These results suggest that the observed geographic pattern might be influenced primarily by historic expansions or colonizations and secondarily by low or restricted gene flow between local groups within regions. In addition to the analysis of population structure, mtDNA data may be useful for constructing a baseline for stock identification of mixed populations of high seas chum salmon.     

珙桐群落种内与种间竞争研究

采用Hegyi的单木竞争指数模型对卧龙自然保护区的珙桐群落种内与种间竞争强度进行定量分析,并讨论了不同竞争强度下珙桐的形态变化。结果表明：珙桐受到的竞争强度随着林木径级的增大而逐渐减小,珙桐种内竞争较之与其伴生树种间的竞争剧烈;在群体水平上,珙桐种内与种间竞争强度顺序为：珙桐种内〉汶川钓樟〉野核桃〉灯台树〉光叶珙桐〉白楠〉总状山矾〉五裂槭〉稠李〉蛮青冈;竞争强度和对象木胸径的关系服从幂函数关系（CI=AD^-B）,当珙桐的胸径达到30cm以上时,竞争强度变化很小,所得的模型能很好的预测珙桐种内与种间的竞争强度;不同竞争强度下,珙桐主干各层的逐级分枝率（R1：2）、分枝角度、平均枝长和当年生枝条长都有一定的差异,其中下层的分枝角度、平均枝长和当年生枝条长对邻体竞争表现出极强的可塑性。说明珙桐通过自身形态变化,提高了对资源的利用能力,增强了对不同生境的适应性。     

Intraspecific and Interspecific Competition in Davidia involucrata (Davidiaceae) Community

Davidia involucrata was a rare valuable and endangered plant in China. In order to study neighborhood competition effects, the intraspecific and interspecific competion intensity in Davidia involucrata community in Wolong Nature Reserve was analyzed quantitatively by using Hegyi individual tree competition index model. And the morphological characteristics of Davidia involucrata were investigated under different neighborhood competition intensity . The results showed that the competition intensity in Davidia involucrata decreased gradually with the increasing of forest tree diameter class and the intraspecific competition in Davidia involucrata was more intensive than interspecific competition. The order of the intraspecific and interspecific competition intensity at the community level was: intraspecific > Lindira pulcherrima > Juglanscathayensis> Cornus controversa > Davidia involucrata var. vilmoriniana > Phoebe neurantha >Symplocos botryantha Franch>Acer oliverianum > Prunus branchypoda > Cyclobalanopsis oxyodon . The relationship between competition intensity and individual growth of objective tree closely followed the following equation: CI = AD^{- B} . The change in competition intensity is very small when the diameter of the objective tree reaches 30 cm . The model can stimulate and predict the intraspecific and interspecific competition efficiently. The morphology of Davidia involucrata , such as stepwise bifurcation ratio 1∶2, branching angle, average branch and current-year branch lenghth of the main stem in different strata , was modified under differentcompetition intensity. The plasticity of substrate branching angle , substrate average branch length and substrate currentyearbranch length was very obvious in response to different neighborhood competion intensity. That suggests Davidia involucrata can improve its capacity to explore the resource and adapt to different habitats through morphological changes .     

PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation

High-throughput parallel sequencing is a powerful tool for the quantification of microbial diversity through the amplification of nuclear ribosomal gene regions. Recent work has extended this approach to the quantification of diversity within otherwise difficult-to-study metazoan groups. However, nuclear ribosomal genes present both analytical challenges and practical limitations that are a consequence of the mutational properties of nuclear ribosomal genes. Here we exploit useful properties of protein-coding genes for cross-species amplification and denoising of 454 flowgrams. We first use experimental mixtures of species from the class Collembola to amplify and pyrosequence the 5′ region of the COI barcode, and we implement a new algorithm called PyroClean for the denoising of Roche GS FLX pyrosequences. Using parameter values from the analysis of experimental mixtures, we then analyse two communities sampled from field sites on the island of Tenerife. Cross-species amplification success of target mitochondrial sequences in experimental species mixtures is high; however, there is little relationship between template DNA concentrations and pyrosequencing read abundance. Homopolymer error correction and filtering against a consensus reference sequence reduced the volume of unique sequences to approximately 5% of the original unique raw reads. Filtering of remaining non-target sequences attributed to PCR error, sequencing error, or numts further reduced unique sequence volume to 0.8% of the original raw reads. PyroClean reduces or eliminates the need for an additional, time-consuming step to cluster reads into Operational Taxonomic Units, which facilitates the detection of intraspecific DNA sequence variation. PyroCleaned sequence data from field sites in Tenerife demonstrate the utility of our approach for quantifying evolutionary diversity and its spatial structure. Comparison of our sequence data to public databases reveals that we are able to successfully recover both interspecific and intraspecific sequence diversity.     

Inheritance of Alpha-Glycerophosphate Dehydrogenase in the Pink Salmon, ONCORHYNCHUS GORBUSCHA (Walbaum)

Genetic crosses of alpha-glycerophosphate dehydrogenase (alpha-GPDH) phenotypes in the pink salmon, Oncorhynchus gorbuscha (Walbaum), reveal that this enzyme is encoded by a single locus with two codominant alleles (Slow and Fast). The significance of single gene control of alpha-GPDH is discussed in relation to the purported tetraploid nature of the salmonids.     

Density-dependence in the survival and reproduction of Bald Eagles: Linkages to Chum Salmon

During the late 20th Century, due to decreases in both contamination and persecution, bald eagle (Haliaeetus leucocephalus) populations increased dramatically. Currently, mechanisms regulating eagle populations are not well understood. To examine potential regulating processes in the Pacific Northwest, where eagles are no longer primarily regulated by contaminants or direct persecution, we examined bald eagle reproductive success, breeding populations, winter populations, mortality, and salmon stream use. Wintering and breeding eagle populations in south-coastal British Columbia (BC) quadrupled between the early 1980s and the late 1990s, and have since stabilized. Density-dependent declines in reproduction occurred during 1986–2009, but not through changes in site quality. Mid-winter survival was crucial as most mortality occurred then, and models showed that density-dependent reductions in population growth rates were partially due to reduced survival. Wintering eagles in British Columbia fed heavily on chum salmon (Oncorhynchus keta) runs, and then switched to birds in late winter, when mortality was highest. Eagles tended to arrive after the peak in salmon availability at streams in BC as part of a migration associated with salmon streams from Alaska to northern Washington. Eagles were most abundant in southern BC during cold Alaskan winters and in years of high chum salmon availability. We suggest that eagle populations in the Pacific Northwest are currently partially limited by density on the breeding grounds and partially by adult mortality in late winter, likely due to reduced late winter salmon stocks forcing eagles to exploit more marginal prey supplies. Larger eagle populations have affected some local prey populations. © 2011 The Wildlife Society.     

Intraspecific Variation and Interspecific Differences in the Bacterial and Fungal Assemblages of Blue Tit (Cyanistes caeruleus) and Great Tit (Parus major) Nests

Although interest in the relationship between birds and microorganisms is increasing, few studies have compared nest microbial assemblages in wild passerines to determine variation within and between species. Culturing microorganisms from blue tit (Cyanistes caeruleus) and great tit (Parus major) nests from the same study site demonstrated diverse microbial communities with 32 bacterial and 13 fungal species being isolated. Dominant bacteria were Pseudomonas fluorescens, Pseudomonas putida, and Staphylococcus hyicus. Also common in the nests were the keratinolytic bacteria Pseudomonas stutzeri and Bacillus subtilis. Dominant fungi were Cladosporium herbarum and Epicoccum purpurascens. Aspergillus flavous, Microsporum gallinae, and Candida albicans (causative agents of avian aspergillosis, favus, and candidiasis, respectively) were present in 30%, 25%, and 10% of nests, respectively. Although there were no differences in nest mass or materials, bacterial (but not fungal) loads were significantly higher in blue tit nests. Microbial species also differed interspecifically. As regards potential pathogens, the prevalence of Enterobacter cloacae was higher in blue tit nests, while Pseudomonas aeruginosa—present in 30% of blue tit nests—was absent from great tit nests. The allergenic fungus Cladosporium cladosporioides was both more prevalent and abundant in great tit nests. Using discriminant function analysis (DFA), nests were classified to avian species with 100% accuracy using the complete microbial community. Partial DFA models were created using a reduced number of variables and compared using Akaike’s information criterion on the basis of model fit and parsimony. The best models classified unknown nests with 72.5–95% accuracy using a small subset of microbes (n = 1–8), which always included Pseudomonas agarici. This suggests that despite substantial intraspecific variation in nest microflora, there are significant interspecific differences—both in terms of individual microbes and the overall microbial community—even when host species are closely related, ecologically similar, sympatric, and construct very similar nests.     

Characterization of a Novel Class of Interspersed LTR Elements in Primate Genomes: Structure, Genomic Distribution, and Evolution

Retrovirus-like sequences and their solitary (solo) long terminal repeats (LTRs) are common repetitive elements in eukaryotic genomes. We reported previously that the tandemly arrayed genes encoding U2 snRNA (the RNU2 locus) in humans and apes contain a solo LTR (U2-LTR) which was presumably generated by homologous recombination between the two LTRs of an ancestral provirus that is retained in the orthologous baboon RNU2 locus. We have now sequenced the orthologous U2-LTRs in human, chimpanzee, gorilla, orangutan, and baboon and examined numerous homologs of the U2-LTR that are dispersed throughout the human genome. Although these U2-LTR homologs have been collectively referred to as LTR13 in the literature, they do not display sequence similarity to any known retroviral LTRs; however, the structure of LTR13 closely resembles that of other retroviral LTRs with a putative promoter, polyadenylation signal, and a tandemly repeated 53-bp enhancer-like element. Genomic blotting indicates that LTR13 is primate-specific; based on sequence analysis, we estimate there are about 2,500 LTR13 elements in the human genome. Comparison of the primate U2-LTR sequences suggests that the homologous recombination event that gave rise to the solo U2-LTR occurred soon after insertion of the ancestral provirus into the ancestral U2 tandem array. Phylogenetic analysis of the LTR13 family confirms that it is diverse, but the orthologous U2-LTRs form a coherent group in which chimpanzee is closest to the humans; orangutan is a clear outgroup of human, chimpanzee, and gorilla; and baboon is a distant relative of human, chimpanzee, gorilla, and orangutan. We compare the LTR13 family with other known LTRs and consider whether these LTRs might play a role in concerted evolution of the primate RNU2 locus. Received: 29 September 1997 / Accepted: 16 January 1998     

Patterns of Downstream Migration of Pink Salmon Oncorhynchus gorbuscha in the Malaya Khusi River (Sakhalin Oblast)

Journal of Ichthyology - Patterns of downstream migration of juvenile pink salmon Oncorhynchus gorbuscha in the Malaya Khusi River (northeast of Sakhalin island) are revealed as a result of...