鸮形目4种鸟类线粒体调控区全序列的测定与比较研究

利用Long-PCR和Primer Walking的方法对鸮形目的短耳鸮、长耳鸮、纵纹腹小鸮、灰林鸮4种鸟类的线粒体调控区进行了全序列测定。结果表明：短耳鸮的调控区跃度为3290bp;长耳鸮为2848bp;纵纹腹小鸮为2444bp;灰林鸮为1771bp。短耳鸮的调控区长度是4种鸮中最大的,并且是目前已知最大的鸟类线粒体调控区。这4种鸮类调控区的基本结构和其他鸟类相似,按照碱基变化速率的不同可以分为3个区：碱基变化速率较快的外围区域Ⅰ、Ⅲ和保守的中间区域Ⅱ。这4种鸟类调控区的3’端均存在大量的串联重复序列,短耳鸮为126bp单元重复7次和78bp单元重复14次;长耳鸮为127bp单元重复8次和78bp单几重复6次;纵纹腹小鸮有3个重复单元,分别为89bp单元重复3次、77bp单元重复4次和71bp单元重复6次;灰林鸮仅有1个单元的串联重复为78bp重复5次。调控区中串联重复序列可能是由链的滑动错配产生,另外这些重复序列都能形成热力学稳定的多重茎环二级结构,而且在重复序列中还发现一些保守基序,这说明重复序列可能具有一定的生理功能,影响调控区的调重控功能从而影响线粒体基因组的复制和转录。     

Origin and evolution of homologous repeated sequences in the mitochondrial DNA control region of shrews

The complete mitochondrial DNA (mtDNA) control region was amplified and directly sequenced in two species of shrew, Crocidura russula and Sorex araneus (Insectivora, Mammalia). The general organization is similar to that found in other mammals: a central conserved region surrounded by two more variable domains. However, we have found in shrews the simultaneous presence of arrays of tandem repeats in potential locations where repeats tend to occur separately in other mammalian species. These locations correspond to regions which are associated with a possible interruption of the replication processes, either at the end of the three-stranded D-loop structure or toward the end of the heavy-strand replication. In the left domain the repeated sequences (R1 repeats) are 78 bp long, whereas in the right domain the repeats are 12 bp long in C. russula and 14 bp long in S. araneus (R2 repeats). Variation in the copy number of these repeated sequences results in mtDNA control region length differences. Southern blot analysis indicates that level of heteroplasmy (more than one mtDNA form within an individual) differs between species. A comparative study of the R2 repeats in 12 additional species representing three shrew subfamilies provides useful indications for the understanding of the origin and the evolution of these homologous tandemly repeated sequences. An asymmetry in the distribution of variants within the arrays, as well as the constant occurrence of shorter repeated sequences flanking only one side of the R2 arrays, could be related to asymmetry in the replication of each strand of the mtDNA molecule. The pattern of sequence and length variation within and between species, together with the capability of the arrays to form stable secondary structures, suggests that the dominant mechanism involved in the evolution of these arrays in unidirectional replication slippage.      

Environmental factors affecting the densities of owls in Polish farmland during 1980–2005

During the last decades, farmland habitats in central European countries have changed significantly, seriously affecting populations of many farmland bird species. We compiled available published data on densities of three owl species, Athene noctua, Asio otus and Strix aluco collected in the Polish farmland. All results of censuses based on the playback method conducted between 1980–2005 were included in the analysis. The proportions of grassland, fields, built-up land and forest at each studied plot were estimated and used as predictors in additive models. Proportions of main land use types, extracted with the principal component analysis, explained much of the variation found in owl densities, although some of the relationships were nonlinear. In general, owl densities were found to be affected positively by a high percentage of grasslands and built-up land, and negatively by the amount of fields and forests. Little owl densities showed a significant negative trend over the study period. It seems that high prey availability is an important factor accounting for the positive relationship between grassland proportion and owl density. The significant decrease in grassland areas and increase in forest coverage that were recently recorded in Poland may thus negatively affect populations of the three owl species studied here.     

The mitochondrial DNA control region comparison studies of four hinged turtles and its phylogentic significance of the genusCuora sensu lato (Testudinata: Geoemydidae)

The complete sequences of the mitochondrial DNA (mtDNA) control region (CR) ofCistoclemmys flavomarginata, Cistoclemmys galbinifrons, Cuora aurocapitata andCyclemys atripons were amplified by long-polymerase chain reaction (Long-PCR). The lengths were 1207 bp, 1722 bp, 1379 bp and 980 bp, respectively. Combining with the CR sequence ofPyxidea mouhotii (DQ659152), we compared the CR structure, and identified three functional domains (TAS, CD and CSB) in which the conservation sequences (TAS, CSB-F, CSB-1, CSB-2 and CSB-3) were also successfully identified according to their homology to those of other turtles. These 5 turtles have the identical CSB-2 and CSB-3 sequences, and 4 of them have the same CSB-1 sequence while there is one base transversion (T → A) inCy. atripons. We analyzed the variable number of tandem repeat (VNTR) sequences or microsatellites at the 3′ end of CR. The motifs of tandem repeats (7 types) are made up of 2–8 nucleotides, and the copy numbers are from 4 to 48. All of the 5 turtles exceptCy. atripons have the “TATTATAT” repeats and are ended by TA. The results of CR structure analysis displayed that theCuora, Cistoclemmys, andPyxidea have many similarities, but differ fromCyclemys. WithIndotestudo elongate (DQ080043) andIndotestudo forstenii (DQ080044) as outgroups, using the CR sequences (1123bp) excluded the microsatellites at the 3′ end of CR, we constructed the molecular phylogenetic trees using the MP, ML and BI methods. The results showed that there was a strong support to the monophyly of theCuora group consisting ofCuora,Cistoclemmys andPyxidea, which has a close relationship withMauremys andChinemys but far fromCyclemys, which are consistent with the analysis of the CR structure of the 5 turtles.     

Freie porphyrine in federn

Zusammenfassung In den Daunenfedern der EulenAthene noctua undStrix aluco findet sich als vorherrschendes Porphyrin Koproporphyrin III. Papierchromatographisch lassen sich daneben in Spuren noch regelmäßig Porphyrine mit 3 und 2 Carboxylgruppen nachweisen.In den Daunen der TrappeOtis tarda findet sich Koproporphyrin III neben Spuren von Porphyrin mit 3 und 2 Carboxylgruppen. Es gelang, den Koproporphyrin-III-ester in Form seines Kupferkomplexsalzes als kristallisierte Substanz zu fassen.Die Methoden, die zum Nachweis der Substanzen dienen, werden ausführlich beschrieben.

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Summary In the downs of the owlsAthene noctua andStrix aluco coproporphyrin III as well traces of 3- and 2- carboxyl porphyrins were demonstrated by means of paper chromatography.In the downs of the bustardOtis tarda coproporphyrin III was demonstrated together with traces of 3 and 2 carboxyl porphyrin. Coproporphyrin III copper complex was prepared in crystalline condition fromOtis tarda downs.The methods — preparation, identification, chromatography, analysis — are described in detail.

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Aus dem Englischen ins Deutsche übertragen und mit Anmerkungen versehen vonO. Völker, Gießen.     

Die Gro?gefieder-Mauser des Steinkauzes(Athene noctua)

Zusammenfassung Zwei im Jahre 1959 geschlüpfte Steinkäuze (Athene noctua) dienten zur Untersuchung des zeitlichen Verlaufs ihrer ersten, 1960 einsetzenden Großgefieder-Mauser.98 Tage () bzw. 99 Tage () nach der ersten Schwungfeder fiel die letzte Schwungfeder aus. Die Flügelmauser setzte beim am 13. Juni, beim am 8. Juni ein. Ihr Verlauf geht aus den Diagrammen 1 und 2 hervor.Die 12 Armschwingen wurden wie beiStrix aluco von drei Foci aus erneuert, nämlich von A 12 bis A 8 descendent, von A 1 bis A 4 ascendent und von A 5 bis A 7 gleichfalls ascendent. — Die vier Federn des Daumenfittichs fielen in descendenter Reihenfolge, die 6 Steuerfeder-Paare beim nahezu synchron (binnen 4 Tagen), etwa zugleich mit dem Ausfall von H 3.

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Summary The sequence and chronology of the first moult of flight-feathers has been studied in two captive specimens of the Little Owl,Athene noctua. The result is shown in the diagrams 1 and 2. InStrix aluco, the sequence (diagr. 3) agrees in principle with that followed byAthene noctua.

     

Recombination and Evolution of Duplicate Control Regions in the Mitochondrial Genome of the Asian Big-Headed Turtle,Platysternon megacephalum

Complete mitochondrial (mt) genome sequences with duplicate control regions (CRs) have been detected in various animal species. In Testudines, duplicate mtCRs have been reported in the mtDNA of the Asian big-headed turtle, Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with MEGA 4.1 using the complete duplicate CR sequences revealed that within turtle subspecies, genetic distances between orthologous copies from different individuals were 0.63% for CR1 and 1.2% for CR2app:addword:respectively, and the average distance between paralogous copies of CR1 and CR2 was 4.8%. Phylogenetic relationships were reconstructed from the CR sequences, excluding the variable number of tandem repeats (VNTRs) at the 3′ end using three methods: neighbor-joining, maximum likelihood algorithm, and Bayesian inference. These data show that any two CRs within individuals were more genetically distant from orthologous genes in different individuals within the same subspecies. This suggests independent evolution of the two mtCRs within each P. megacephalum subspecies. Reconstruction of separate phylogenetic trees using different CR components (TAS, CD, CSB, and VNTRs) suggested the role of recombination in the evolution of duplicate CRs. Consequently, recombination events were detected using RDP software with break points at ≈290 bp and ≈1,080 bp. Based on these results, we hypothesize that duplicate CRs in P. megacephalum originated from heterological ancestral recombination of mtDNA. Subsequent recombination could have resulted in homogenization during independent evolutionary events, thus maintaining the functions of duplicate CRs in the mtDNA of P. megacephalum.     

不同产地中华鳖的线粒体控制区序列分析及结构比较

采用PCR特异引物,扩增了两产地中华鳖（Pelodiscus sinensis）个体的mtDNA控制区（CR）及其邻近片段,测序获得了长度分别为1830bp和1630bp的序列。结合GenBank中已发表的韩国产中华鳖mtDNA的CR区序列,比较了3个产地中华鳖的CR区结构。分析显示：中华鳖不同产地mtDNA CR区DNA中的A＋T含量分别为60.5%、63.6%和64.8%,它们的5′、3′末端以及CSB1-CSB2之间均存在丰富的可变数目串联重复序列（variable numbers oftandem repeats,VNTR）。基于mtDNA CR区序列和结构分析,显示中华鳖不同产地的野生个体中存在丰富的遗传多样性。     

The decline of Common Kestrels Falco tinnunculus in a forested area of northern England: the role of predation by Northern Goshawks Accipiter gentilis

We have previously documented the decline of the Common Kestrel Falco tinnunculus over a 23‐year period in a large coniferous forest in northern England. Kestrels fed predominantly on Field Voles Microtus agrestis, which were most abundant in young plantations (1–11 years old). Over the 23 years, voles remained abundant in the study area, but their numbers fluctuated cyclically. Here we consider whether the decline of Kestrels was linked to predation by Northern Goshawk Accipiter gentilis. Goshawks first bred in the study area in 1973 and increased until 1989, after which numbers stabilized. We use a number of approaches to explore the role of Goshawk predation, all of which are correlative, but independent. First, there was a significant negative relationship between Kestrel and Goshawk numbers after controlling for a decline in vole habitat. Short‐eared Owls Asio flammeus, which also hunt by day, declined over the same period as Kestrels. Second, numbers of Tawny Owl Strix aluco and Long‐eared Owl Asio otus did not decline as Goshawk numbers increased. These two species are also vole‐dependent, but active by night, and less vulnerable to Goshawk attack. Third, six species of raptor comprised 4.5% of 5445 Goshawk prey items during the breeding season, but more Kestrels were killed than the combined total of all other raptors. Goshawks not only killed many adult Kestrels in early spring, prior to breeding, when it would have most impact on population levels, but there was also a temporal trend for predation on Kestrels to be inversely density‐dependent. Finally, we estimated that Goshawks removed more Kestrels than were recorded each spring in the study area. We interpreted this as indicating that immigrant Kestrels were being removed continually, mostly before they could breed. We conclude that the decline of Kestrels (and possibly Short‐eared Owls) was mainly due to predation by Goshawks. This study provides some of the strongest evidence yet of the role of predation in the hierarchical structuring of raptor communities.     

Mitochondrial telomeres: surprising diversity of repeated telomeric DNA sequences among six species of Tetrahymena

The DNA sequences at the ends of the linear mtDNA of 6 species of Tetrahymena encompassing 13 strains were determined. All the strains have variable numbers of a tandemly repeated DNA sequence, 31 bp to 53 bp in size, at their mtDNA termini. Based upon the size and nucleotide sequence of the terminal repeats, the telomeres can be separated into four classes. T. pigmentosa, hyperangularis, and hegewischi have different telomeric repeats on the two ends of their mtDNAs. The only conserved feature of the mtDNA termini is the presence of tandem repeats. The function of the repeats might be to promote unequal crossing over during recombination, thereby overcoming the problem of telomere replication for these linear DNAs.     

Repetitive sequences in Eurasian lynx (Lynx lynx L.) mitochondrial DNA control region

Mitochondrial DNA (mtDNA) control region (CR) of numerous species is known to include up to five different repetitive sequences (RS1-RS5) that are found at various locations, involving motifs of different length and extensive length heteroplasmy. Two repetitive sequences (RS2 and RS3) on opposite sides of mtDNA central conserved region have been described in domestic cat (Felis catus) and some other felid species. However, the presence of repetitive sequence RS3 has not been detected in Eurasian lynx (Lynx lynx) yet. We analyzed mtDNA CR of 35 Eurasian lynx (L. lynx L.) samples to characterize repetitive sequences and to compare them with those found in other felid species. We confirmed the presence of 80 base pairs (bp) repetitive sequence (RS2) at the 5' end of the Eurasian lynx mtDNA CR L strand and for the first time we described RS3 repetitive sequence at its 3' end, consisting of an array of tandem repeats five to ten bp long. We found that felid species share similar RS3 repetitive pattern and fundamental repeat motif TACAC.     

Palindromic repeated sequences (PRSs) in the mitochondrial genome of rice: evidence for their insertion after divergence of the genus Oryza from the other Gramineae

We have identified a family of small repeated sequences (from 60 to 66 bp in length) in the mitochondrial genome of rice (Oryza sativa cv. Nipponbare). There are at least ten copies of these sequences and they are distributed throughout the mitochondrial genome. Each is potentially capable of forming a stem-and-loop structure and we have designated them PRSs (palindromic repeated sequences). Their features are reminiscent of the small dispersed repeats in the mitochondrial DNA (mtDNA) of some lower eukaryotes, such as Saccharomyces cerevisiae, Neurospora crassa and Chlamydomonas reinhardtii. Some of the PRSs of rice mtDNA are located in the intron of the gene for ribosomal protein S3 (rps3) and in the flanking sequence of the gene for chloroplast-like tRNA^Asn (trnN). An analysis of PCR-amplified fragments of these regions from the DNA of some Gramineae suggests that the PRSs were inserted into these regions of the Oryza mtDNA after the divergence of Oryza from the other Gramineae.     

Sequence variation and evolution of the mitochondrial DNA control region in the musk shrew, Suncus murinus

The complete mitochondrial DNA (mtDNA) control region was cloned and sequenced in the musk shrew, Suncus murinus, Insectivora. The general aspect was similar to that found in other mammals. We have found in two locations of this region the presence of arrays of tandem repeats like those in other shrew species. One array was located in the left domain containing the termination-associated sequences (TAS) and the length of a copy was 77 bp. The other repeats were situated upstream from the recognition site for the end of H-strand replication in the right domain and were 20 bp long. The left halves of the control region containing the former repeats were sequenced and compared in several laboratory lines and wild animals from different localities, variations in copy number of repeated sequences were found both among individuals and within an individual. A comparative study of repeated sequences provides useful indication for the origin and evolution of tandem repeated sequences. Strand slippage and mispairing during replication of mtDNA with concerted manner is currently regarded as a dominant theory to account molecular mechanism for tandemly repeated sequences, and the pattern of sequence and length variation in our study supports this theory. Our results, however, suggest that the evolution of the repeated sequences containing the TAS in the musk shrew might go through the process of two steps; at the first step one complete repeated and several incomplete repeated sequences had reproduced in common ancestor of the shrew, and the second stage step-up of complete repeated sequences occurred with concerted evolution after differentiation into continental and insular groups.     

鳄龟科和平胸龟科线粒体控制区序列分析和结构比较

本文参照龟类近缘种的线粒体DNA(mitochondrial DNA,mtDNA)控制区(control region,CR)及邻接序列,设计了二对特异引物,采用PCR和测序技术,获得了大鳄龟(Macroclemys temminckii)、小鳄龟(Chelydra serpentina)和平胸龟(Platysternon megacephalum)mtDNA CR区序列,其长度分别为1062bp、1124bp和1119bp;A T的含量分别为68.93%、69.34%和69.44%。序列分析显示,三种龟CR区3'末端均存在丰富的微卫星序列,其中大鳄龟和小鳄龟各有一段2bp的TA序列分别重复20和15次;小鳄龟另有一段5bp的TATAT序列重复13次;平胸龟则是一段10bp的AGTATGTTAT序列重复4次和一段17bp的GTTGTTATATAACATAT序列重复13次。本文还结合GenBank中已发表的其他6种龟鳖类动物的控制区序列,探讨了龟鳖类动物微卫星序列的类型及分布,结果表明:9种龟鳖类动物都存在丰富的微卫星序列,且微卫星所在位置及序列存在很大差异。     

Genetic variation and phylogenetic relationship between three serow species of the genus Capricornis based on the complete mitochondrial DNA control region sequences

The molecular evidence of phylogenetic status regarding the Formosan serow (Capricornis swinhoei) is not robust and little is known about the genetic diversity of the Sumatran serow (Capricornis sumatraensis), which partly is due to the hardness in sample collection. Here we determined the sequences of the complete mitochondrial DNA control region (1,014 bp) of 19 Sumatran-serow individuals. Nine new haplotypes were defined based on 78 variable sites. Combined analysis with other 32 haplotypes downloaded from the public database, including 1 Sumatran-serow, 11 Formosan-serow and 20 Japanese-serow (Capricornis crispus) haplotypes, a relatively high level of nucleotide diversity was first observed in Sumatran serow (π = 0.0249). By comparative analysis with structural consensus sequences from other mammals, we have identified central, left and right domains and depicted the putative functional structure, including extend termination associated sequences and conserve sequence blocks, in mtDNA control region. The alignment of mtDNA control region revealed that both Sumatran and Japanese serow have two tandem repeats (TRs), but three TRs in Formosan serow. Phylogenetic analyses revealed that the Formosan serow is distinct species with the Japanese serow, but a sister group with the Sumatran serow. The divergence time estimated among three serow species revealed that Pleistocene climate changes and the uplift of Qinghai-Tibetan plateau might play an important role in the genetic differentiation of the serows. These results mainly provide the convinced evidence on the genetic relationship between three serow species.     

Organization and evolutionary progress of a dispersed repetitive family of sequences in widely separated rodent genomes

The genomes of Mus musculus and other rodent species share a long conserved family of sequences that are dispersed and abundant (approx. 20,000 copies), and that have several novel features of organization and evolution. EcoR1 restriction of M. musculus DNA reveals a prominent 1350 bp² set of sequences. Two nonhomologous sequences of 850 and 500 bp, representing almost the total population of the 1350 bp repeats, were used to examine the detailed organization of the dispersed family and its surrounding sequences using a combination of restriction analysis and “Southern” hybridization. The 1350 bp sequence is contained within a longer repeating unit of approximately 3 kb that is dispersed amongst a wide variety of non-homologous and seemingly non-repetitive sequences. At some sites within the 3 kb repeat, considerable sequence heterogeneity has been found between members of the family, such that the family can be divided into largely non-overlapping subsets (or “segments”) according to the positioning of HinIII sites. Underlying the segmental organization there is a low background overlap of each segment with every other. Some but not all members of the family and its variants have been located on the X-chromosome in a Chinese hamster, M. musculus, X chromosome cell line: suggesting a wide genomic dispersion of the family. Homologous repeated sequences to the M. musculus 1350 bp repeat have been identified in species of Mus and Apodemus, with strikingly similar features of organization and dispersion. In M. spretus a 1350 bp sequence is contained within a dispersed repeat of at least 2·9 kb. However, the majority of M. spretus repeats contain an additional restriction site not present in the equivalent M. musculus array, suggesting a mechanism of widespread substitution or “conversion” of one variant by another in each genome. Apodemus sylvaticus possesses two dispersed and homologous families of 1350 bp and 1850 bp repetition, respectively, which contain sequences that have diverged from M. musculus to differing extents. A. mystacinus possesses only one family of dispersed and homologous repeats of 1850 bp. The majority of members within each Apodemus homologous family also contain characteristic variant restriction-site arrangements. The mechanisms underlying the spread of such variants within each array; the generation of segmental patterns; and the evolutionary conservation of this mouse interspersed family (MIF-1) are discussed in relation to the present knowledge of the organization and activity of other dispersed sequence families.     

The telomeres of the linear mitochondrial DNA of tetrahymena thermophila consist of 53 bp tandem repeats

We have cloned and sequenced the telomeric DNA of the linear mitochondrial DNA (mtDNA) of T. thermophila BVII. The mtDNA telomeres consist of a 53 bp sequence tandemly repeated from 4 to 30 times, with most molecules having 15 ± 4 repetitions. The previously recognized terminal heterogeneity of the mtDNA is completely accounted for by the variability in the number of repeats. The 53 bp repeat does not resemble known telomeric DNA in sequence, repeat size, or number of repetitions. The termini occur at heterogeneous positions within the 53 bp repeat. The junction of the telomeric repeat with the internal DNA is at a different position within the telomeric repeat on each end of the mtDNA. We propose a model for the maintenance of the mtDNA ends involving unequal homologous recombination.