Characterization of the length polymorphism in the A+T-rich region of the Drosophila obscura group species

Summary In the twelve Drosophila obscura group species studied, belonging to the affinis, obscura, and pseudoobscura subgroups, the mitochondrial DNA length ranges from 15.8 to 17.2 kb. This length polymorphism is mainly due to insertions/deletions in the variable region of the A+T-rich region. In addition, one species (D. tristis) possess a tandem duplication of a 470-bp fragment that contains the replication origin.The same duplication has occurred at least twice in the Drosophila evolutionary history due to the fact that the repetition is analogous to repetitions found in the four species of the D. melanogaster complex.By comparing the nucleotide sequence of the conserved region in D. ambigua, D. obscura, D. yakuba, D. teissieri, and D. virilis, we show the presence of a secondary structure, likely implied in the replication origin, which could favor the generation of this kind of duplications.Finally, we propose that the high A and T content in the variable region of the A + T-rich region favors the formation of less-stable secondary structures, which could explain the generation of minor insertion/deletions found in this region.Offprint requests to: A. Latorre     

Evolution of thedec-1 eggshell locus inDrosophila. II. Intraspecific DNA sequence analysis reveals length mutations in a repetitive region inD. melanogaster

Summary Thedec-1 eggshell gene inDrosophila melanogaster encodes follicle cell proteins required for proper eggshell assembly. As shown by Southern and Northern analyses thedec-1 gene occurs in four alleles (Fcl-4) among wild-type strains. Its second exon has a distinct feature in the form of 12 repeats with 78–91 nucleotides; the first five show nearly 100% homology. DNA sequence comparison of the repeated region of the alleles revealed that the length polymorphisms are caused by changes in the numbers of the first five repeats. The results suggest that the alleles have been generated by unequal intragenic crossing-over and/or slippage during DNA replication and that the allelic length variants have arisen independently. The possiblilty that the most common allele,FC1, has a selective advantage over the other alleles is discussed.     

环境因子对荒漠沙蜥种群密度影响的研究

本文研究人类改造荒漠的活动,植被,潜在的可利用的食物资源,竞争种的密度,土壤理化性质等坏境因子对荒漠沙蜥种群密度的影响。结果说明：人类的活动对沙蜥种群密度没有显著影响;决定沙蜥种群密度的主导因子是潜在的可利用的食物资源,植被,土壤含水量,竞争种的密度。这些因子的任何改变都能改变沙蜥的种群密度,均具有调节种群的作用。     

Discrimination of folding types of globular proteins based on average distance maps constructed from their sequences

It has been shown that probable portions which form contacts in a protein can be predicted by means of an average distance map (ADM) as well as regular structures (-helices and -turns) defined as short-range compact regions (Kikuchiet al., 1988a,c). In this paper, we analyze the occurrence of those portions and short-range compact regions on ADMs for various proteins regarding their folding types. We have found out that each folding type of proteins shows characteristic distribution of such parts on ADMS. We also discuss the possibility of the prediction of folding types of proteins by ADMs.     

Metabarcoding reveals seasonal and spatial patterns of arthropod community assemblages in two contrasting habitats: Desert and oasis of the Baja California Peninsula,Mexico

Aim

Desert springs or oases are the only permanent mesic environments in highly water-limited arid regions. Oases have immense cultural, evolutionary and ecological importance for people and a high number of endemic and relic species. Nevertheless, they are also highly vulnerable ecosystems, with invasive species, overexploitation and climate change being the primary threats. We used the arthropod communities' spatiotemporal diversity and distribution patterns as a proxy to understand biodiversity dynamics in two geographically close but ecologically contrasting and highly threatened ecosystems: deserts and oases.

Location

Baja California Peninsula, Mexico.

Methods

Arthropod communities at five oases and surrounding desert scrub areas were sampled in two seasons. Using DNA metabarcoding and traditional taxonomic surveys, we tried to identify what biotic and abiotic characteristics of the habitat are important drivers of arthropod diversity and how these characteristics can change across spatial and temporal scales.

Results

Over 6200 individuals representing 23 orders were collected. In oasis samples, the community composition fluctuated more in space (i.e. among sites) than in time (i.e. seasons). Thus, seasonal changes did not affect oasis community diversity and composition, but the dissimilarity among sites increased with geographic distance. Moreover, anthropic activities negatively correlated with arthropod diversity in oases. On the other hand, the season, geography (e.g. latitude) and biotic characteristics of the habitat (e.g. sampled scrub species) significantly affected the diversity and composition of the desert arthropod communities.

Main Conclusions

Neutral dynamics (e.g. historical climatic events, dispersal limitation and spatial component) and human impact significantly influenced the biodiversity patterns of each oasis. In contrast, the habitat's seasonal variation and biotic characteristics were the most important variables influencing the diversity of the desert communities. Baja California oases harbour distinct invertebrate communities; therefore, each oasis should be conserved individually to preserve these unique assemblages.     

Two centuries of spatial and temporal dynamics of freshwater fish introductions

Aim

Investigating major freshwater fish flows (translocations) between biogeographic regions and their temporal dynamics and also quantifying spatial patterns and temporal changes in the array of introduced species, and the emergence and distance between major donor and recipient regions.

Location

Global.

Time Period

1800–2020.

Major Taxa Studied

Freshwater fishes.

Methods

We analysed a global dataset on freshwater fish introductions (4241 events of 688 species). Freshwater fish flows were investigated with flow diagrams and χ² tests, while PERMANOVA (permutational multivariate analysis of variance) was used to test the association between species and regions and temporal shifts. Cluster analysis revealed major recipient areas and composition of the introduced species. Finally, changes in distances between donor and recipient sites were tested with PERMANOVA.

Results

The number of introductions between biogeographic regions mirrored the European and North American dominance before World War II (WWII) and the trends in recreational fishing, biocontrol programmes and food production, especially in the Sino-Oriental region, which has a long tradition of aquaculture and fishkeeping. Over the years, the origins and composition of introduced species changed uniquely in each biogeographic region, although the most introduced species are common to every region. Salmonids and other cold-water species were frequently introduced before the 1950s, whereas tropical ornamental and aquaculture species currently prevail. Distances between donor and recipient sites did not vary over the time. After WWII, the Sino-Oriental region consolidated its dominance and the Ethiopian and Neotropical regions emerged as new global donor and recipient regions.

Main Conclusions

Global policy should focus on tropical ornamental and aquaculture species, which could benefit from global warming, especially in the Sino-Oriental region, because it currently dominates freshwater fish species flows, and the Ethiopian and Neotropical regions, because they recently emerged as important global donor and recipient regions of freshwater fish introductions.     

荒漠草原生态恢复与重建：人工植被推动下水分介导的系统响应、生态阈值与互馈作用

荒漠草原(生态区)横贯我国西北地区东部,生态地位十分重要。近二十年来,通过封育禁牧、退耕还林(草),植被覆盖显著改善,但是生态系统质量和稳定性依然不高。由于长期将荒漠草原单纯视作草原的一部分,对其生态系统过渡性、脆弱性和复杂性本质特征认识不足,造成了荒漠草原生态学研究与区域生态建设实践之间不同程度的脱节。在分析荒漠草原生态区未来在我国生态安全格局中突出的但是被一定程度上忽视的地位的基础上,进一步归纳了荒漠草原生态系统的一般特征,指出了生态恢复与重建研究中存在的主要问题。进而以人工植被引入荒漠草原生态工程为案例,分析了人工植被驱动荒漠草原生态恢复与重建的过程与机制,归纳了“植被-水文-土壤”互馈作用驱动生态系统层级响应模式,并展望了今后的发展趋势与研究方向。     

Population structure of mud flounder Paralichthys orbignyanus from the south-western Atlantic Ocean

The mud flounder Paralichthys orbignyanus (Pleuronectiformes, Paralichthyidae) inhabits shallow waters of low salinities and mud bottoms in the temperate marine coastal regions of the Bonaerensean Ecoregion of the Argentinean Biogeographic Province in the south-western Atlantic Ocean. Specimens of P. orbignyanus were collected from Lagoa dos Patos (LDP) (southern Brazil), Mar Chiquita (MCH) and Marisol (MAR) both located in Buenos Aires (Argentina), and San Antonio Oeste (SAO) in the San Matías Gulf, Rio Negro (Argentina). A fragment of the mitochondrial DNA of the Control Region and seven microsatellite loci were characterized. In the Control Region, P. orbignyanus showed high variability, low nucleotide diversity, mild population expansion and a coalescence time of 35,000 years before the present. Flounders provided evidence of a genetic structure between the sampling sites LDP, MCH, MAR vs. SAO. On the other hand, P. orbignyanus displayed a lower to moderate contemporary genetic structure among all samples except between LDP and MCH. With no evidence of isolation by distance, this analysis supports a model of limited gene flow that is likely to be associated with a consistent larvae retention in all sampling sites. In addition, the present connectivity is ascribed to a lower migration process from SAO in the San Matías Gulf congruent with the prevailing littoral drift.     

Responses of the desert green algae,Chlorella sp. to drought stress

Desert algae are important components of the desert soil crust and play an essential role in desert soil ecosystem development. Owing to their special habitat, desert algae are often exposed to harsh environments, among which drought represents the most common stress. Green algae are considered to have drought tolerance potential; however, only a few studies have investigated this. In this study, we selected the green alga Chlorella sp., which was isolated from desert soil, and studied its physiological response to polyethylene glycol (PEG) 6000-induced drought stress. The results showed that drought stress can affect the photosynthetic efficiency of Chlorella sp., reduce its water retention ability, and destroy its ultrastructure. However, Chlorella sp. can cope with drought stress through a series of physiological regulatory strategies. Protective strategies include quick recovery of photosynthetic efficiency and increased chlorophyll content. In addition, induced synthesis of soluble proteins, lipids, and extracellular polysaccharide (EPS), and accumulation of osmotic regulatory substances, such as sucrose and trehalose, also contribute to improving drought tolerance in Chlorella sp. This study provides insights into the physiological responses of Chlorella sp. to drought stress, which may be valuable for understanding the underlying drought adaptation mechanisms of desert green algae.     

Nucleotide Sequence Assessment of Four ORFs of Citrus Tristeza Virus: Evidence of Recombination

Citrus Tristeza Virus (CTV), usually occurs in nature as a mixture of genotypes. Six naturally infected citrus (Citrus sinensis) trees grafted on sour orange rootstock were collected from three citrus growing governorates in Egypt (Sharqia, Qalyubia and Garbia). In this study, RT-PCR, Single-Strand Conformation Polymorphism (SSCP) and nucleotide sequence analysis were used for four independent CTV genomic regions (p65, p18, p20, and p23) to detect and assess the sequence and genetic variabilities among CTV Egyptian isolates. RTPCR products (650 bp) for the CTV p23 gene obtained from the selected isolates were used for the SSCP analysis and DNA sequencing. SSCP patterns of p23 gene for individual isolates yielded different complex haplotype patterns. Nucleotide sequence analysis of p23 region amplified from six isolates under study revealed that p23 shared high nucleotide identity 98.7% with T36 isolate from USA, Florida. Phylogenetic analysis of p23 gene indicated a close evolutionary relationship between all examined isolates and Qaha isolate (T36 isolate group), suggesting that they may have originated from closely related ancestors. Nucleotide sequence analysis of the three genes located on CTV 3′-coterminal overhang, p18, p20 and p65, amplified from isolate A3, Sharqia governorate, revealed that the p18, p65, and p20 genes were related to the T3-KB isolate from South Africa with 99%–100% sequence homology. Phylogenetic relationship analysis for p65, p18 and p20 ORFs clustered the current A3 isolate with T3 genotype group. The recombination analysis identified three of six isolates from Sharqia, and Garbia as potential recombinant for p23 gene. The isolates T36 and T3 were identified as major donors for recombination events in isolate A3. Our results concluded that p23 ORF likely to be as a hotspot region for recombination and originated through recombination event. The current study indicated that recombination is an important factor for the origin of CTV strains in Egypt.