Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals

An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed clement (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR clement is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.

Evolutionary implications of avian infectious Bronchitis Virus (AIBV) analysis

For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus (AIBV) antigenic domain o

Evidence of gene conversion in the evolutionary process of the codon 41/42 (-CTTT) mutation causing beta-thalassemia in southern China

The 4-bp deletion (-CTTT) at codon 41/42 (CD41/42) of the human beta-globin gene represents one of the most common beta-thalassemia mutations in East Asia and Southeast Asia, which is historically afflicted with endemic malaria, thus hypothetically evolvi

Tracing the Origins of Hakka and Chaoshanese by Mitochondrial DNA Analysis

Hakka and Chaoshanese are two unique Han populations residing in southern China but with northern Han (NH) cultural traditions and linguistic influences. Although most of historical records indicate that both populations migrated from northern China in the last two thousand years, no consensus on their origins has been reached so far. To shed more light on the origins of Hakka and Chaoshanese, mitochondrial DNAs (mtDNAs) of 170 Hakka from Meizhou and 102 Chaoshanese from Chaoshan area, Guangdong Province, were analyzed. Our results show that some southern Chinese predominant haplogroups, e.g. B, F, and M7, have relatively high frequencies in both populations. Although median network analyses show that Hakka/Chaoshanese share some haplotypes with NH, interpopulation comparison reveals that both populations show closer affinity with southern Han (SH) populations than with NH. In consideration of previous results from nuclear gene (including Y chromosome) research, it is likely that matrilineal landscapes of both Hakka and Chaoshanese have largely been shaped by the local people during their migration southward and/or later colonization in southern China, and factors such as cultural assimilation, patrilocality, and even sex-bias in the immigrants might have played important roles during the process. Am J Phys Anthropol 141:124-130, 2010. (C) 2009 Wiley-Liss, Inc.

Reconstructing the evolutionary history of China: A caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modem data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (similar to 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modem populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

Evolutionary characteristics of exons expressed at different abundance levels in mammals

With comparative genomics approaches, we evaluated the evolutionary characteristics of conservation of exons which are expressed abundantly, moderately or lowly in mammals. Using non-coding regions and pseudogenes as controls, sequence identity, phastCons

Community Based Fisheries Management (CBFM) in Sunamganj district of Bangladesh: the nature of cooperation and conflicts

There are altogether 411 haors comprising an area of about 8000 square kilometer, covering 25% of entire region dispersed in the districts of Sunamgonj, Sylhet, Moulvibazar, Hobigonj, Netrokona and Kishoreganj. Sunamganj district is particularly known as a district of haors and baors where a large number of people depend on fishing for their livelihood. Some people are basically fishermen and fish all the year round. Community Based Fisheries Management (CBFM) project has been initiated in this area to develop fishery sector as well as for the development of the inland fishermen of haor area. Healthy cooperation among the beneficiaries of the project is very much present and some NGOs are found working actively there to help the fishermen for the sound implementation of the project. But the influentials of different villages around create troubles and conflicts intentionally in the project area because of which fishermen cannot fish smoothly and the implementation of the project is getting hampered. Therefore, a kind of consensus needs to be reached among the inhabitants of the haor area and a powerful association of the fishermen should be established so that fishing may be undertaken in the beel without having any troubles and conflicts. In this article the conflicts and cooperation that are in existence in the implementation process of CBFM project in the haor areas of Sunamgonj district have been discussed. Some suggestions have been offered in the paper to overcome the existing conflicts impeding the smooth implementation of CBFM project in the fishery sector of haor area under Sunamganj district.

Evolutionary status of Entamoeba

In addition to its medical importance as parasitic pathogen, Entamoeba has aroused people's interest in its evolutionary status for a long time. Lacking mitochondrion and other intracellular organelles common to typical eukaryotes, Entamoeba and several other amitochondrial protozoans have been recognized as ancient pre-mitochondriate eukaryotes and named "archezoa", the most primitive extant eukaryotes. It was suggested that they might be living fossils that remained in a primitive stage of evolution before acquisition of organelles, lying close to the transition between prokaryotes and eukaryotes. However, recent studies revealed that Entamoeba contained an organelle, "crypton" or "mitosome", which was regarded as specialized or reductive mitochondrion. Relative molecular phylogenetic analyses also indicated the existence or the probable existence of mitochondrion in Entamoeba. Our phylogenetic analysis based on DNA topoisomerase II strongly suggested its divergence after some mitchondriate eukaryotes. Here, all these recent researches are reviewed and the evolutionary status of Entamoeba is discussed.

Intergroup interactions in Tibetan macaques at Mt. Emei, China

Data on intergroup-interactions (I-I) were collected in 5 seasonally provisioned groups (A, B, D, D-1, and E) of Tibetan macaques (Macaca Thibetana) at Mt. Emei in three 70-day periods between 1991 April-June (P1), September-November (P2), December-1992 February (P3). The I-I were categorized as forewarning made by high-ranking males (including Branch Shaking and/or Loud Calls), long-distance interactions in space (specified by changes in their foraging movements), and close encounters (with Affinitive Behavior, Male's Herding Female, Sexual Interaction, Severe Conflict, Adult Male-male Conflict, Opportunistic Advance and Retreat, etc. performed by different age-sex classes). From periods Fl to P3, the I-I rate decreased with reduction in population density as a positive correlate of food clumpedness or the number of potential feeders along a pedestrian trail. On the other hand, from the birth season (BS, represented by P1 and P3) to the mating season (MS, represented by P2) the dominance relation between groups, which produced a winner and a loser in the encounters, became obscure; the proportion of close encounters in the I-I increased; the asymmetry (local groups over intruders) of forewarning signals disappeared; the rate of branch shaking decreased; and sometimes intergroup cohesion appeared. Considering that sexual interactions also occurred between the encountering groups, above changes in intergroup behaviors may be explained with a model of the way in which the competition for food (exclusion) and the sexual attractiveness between opposite sexes were in a dynamic equilibrium among the groups, with the former outweighing the latter in the BS, and conversely in the MS. Females made 93% of severe conflicts, which occurred in 18% of close encounters. Groups fissioned in the recent past shared the same home range, and showed the highest hostility to each other by females. In conspicuous contrast with females' great interest in intergroup food/range competition, adult male-male conflicts that were normally without body contact occurred in 66% bf close encounters; high-ranking male herding of females, which is typical in baboons, appeared in 83% of close encounters, and showed no changes with season and sexual weight-dimorphism; peripheral juvenile and subadult males were the main performers of the affinitive behaviors, opportunistic advance and retreat, and guarding at the border. In brief, all males appeared to "sit on the fence" at the border, likely holding out hope of gaining the favor of females both within and outside the group. Thus, females and males attempted to maximize reproductive values in different ways, just as expected by Darwin-Trivers' theory of sexual selection. In addition, group fission was observed in the largest and highest-ranking group for two times (both in the MS) when its size increased to a certain level, and the mother group kept their dominant position in size and rank among the groups that might encounter, suggesting that fission takes a way of discarding the "superfluous part" in order to balance the cost of competition for food and mates within a group, and the benefit of cooperation to access the resources for animals in the mother group. (C) 1997 Wiley-Liss, Inc.

SuperJunction IGBTS: An evolutionary step of silicon power devices with high impact potential

15 years ago the vertical SuperJunction (SJ) concept conceived for SJ power MOSFETs was the last, major breakthrough in the field of silicon power devices. Today, the SuperJunction MOSFET technologies have reached a mature stage characterized by gradual performance improvements. SuperJunction Insulated Gate Bipolar Transistors (SJ IGBTs) could interrupt this stagnation holding promise to revitalize voltage classes from 600 up to 1200 V. Such SJ IGBTs surpass by a very significant margin their SJ MOSFET counterparts both in terms of power handling capability, on-state and turn-off losses, all at the same time. On the higher end of the voltage class, SJ IGBTs would top the performance of 1.2 kV IGBTs by a similar margin. © 2012 IEEE.

Evolutionary Conservation of Dazl Genomic Organization and its Continuous and Dynamic Distribution Throughout Germline Development in Gynogenetic Gibel Carp

To investigate germline development and germ cell specification, we identified a Dazl homolog (CagDazl) from gynogenetic gibel carp (Carassius auratus gibelio). Its cDNA sequence and BAC clone sequence analyses revealed the genomic organization conservation and conserved synteny of the Dazl family members and their neighborhood genes among vertebrates, especially in fish. Moreover, a polyclonal antibody specific to CagDazl was produced and used to examine its expression and distribution throughout germline development at protein level. Firstly, ovary-specific expression pattern of CagDazl was confirmed in adult tissues by RT-PCR and Western blot. In addition, in situ hybridization and immunofluorescence localization demonstrated its specific expression in germ cells, and both its transcript and protein were localized to germ plasm. Then, co-localization of CagDazl and mitochondrial cloud was found, confirming that CagDazl transcript and its protein are germ plasm component and move via METRO pathway during oogenesis. Furthermore, the CagDazl is abundant and continuous throughout germline development and germ cell specification including primordial germ cell (PGC) formation, oogonium differentiation, oocyte development, and embryogenesis, and the dynamic distribution occurs at different development stages. The data suggest that maternal CagDazl might play an important role in gibel carp PGC formation. Therefore, CagDazl is a useful and specific marker for tracing germ plasm and germ cell development in the gynogenetic gibel carp. In addition, in comparison with previous studies in sexual reproduction species, the continuous and dynamic distribution of CagDazl protein in the germ plasm throughout the life cycle seems to have significant implication in sex evolution of vertebrates. J. Exp. Zool. (Mol. Deu. Euol.) 312B:855-871, 2009. (C) 2009 Wiley-Liss, Inc.

Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes

We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus-Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color vision genes had unequal evolutionary rates, which may lead to a related function divergence. Divergence of LWS-1 was strongly influenced by positive selection causing an accelerated rate of substitution in the proportion of pocket-forming residues. The SWS2 pigment experienced divergent selection between lineages, and no positively selected site was found. A duplicate copy of LWS-1 of some cyprinine species had become a pseudogene, but all SWS2 sequences remained intact in the regions examined in the cyprinid fishes examined in this study. The pseudogenization events did not occur randomly in the two copies of LWS-1 within Sinocyclocheilus species. Some cave species of Sinocyclocheilus with numerous morphological specializations that seem to be highly adapted for caves, retain both intact copies of color vision genes in their genome. We found some novel amino acid substitutions at key sites, which might represent interesting target sites for future mutagenesis experiments. Our data add to the increasing evidence that duplicate genes experience lower selective constraints and in some cases positive selection following gene duplication. Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes.

Phylogenetic relationships of Danio within the order cypriniformes: A framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.