High molecular and phenotypic diversity in the Merodon avidus complex (Diptera,Syrphidae): cryptic speciation in a diverse insect taxon

This paper examines molecular and phenotypic variability in the widely spread European hoverfly species complex Merodon avidus. Herein, based on the mitochondrial DNA (mtDNA) sequences of the cytochrome c oxidase subunit I (COI) and morphometric wing parameters, M. avidus is shown to comprise a complex of cryptic species, and one variety is redefined as a valid species: M. bicolor Gil Collado, 1930 (as var. of spinipes). The species M. bicolor, M. avidus A, and M. avidus B were clearly delimited based on their wing size. A total of 29 M. avidus and M. bicolor individuals presented 20 mtDNA haplotypes, four of which were shared by M. avidus A and M. avidus B, three were confined to M. bicolor, seven to M. avidus A, and six to M. avidus B. Sequence divergences between lineages occurring in the Balkan and in Spain ranged from 4.93 to 6.0 (uncorrected p in %) whereas divergences between M. avidus A and M. avidus B were 0.26 to 1.56. Divergence among morphologically identified individuals of M. avidus A and M. avidus B species ranged from 0.13 to 1.58, and from 0.13 to 0.52, respectively. The phenotypic substructuring and observed genetic uniqueness of populations in spatially and temporally fragmented M. avidus taxa were used to identify genetic units. The early split of two allopatric lineages, Spanish M. bicolor and Balkan M. avidus, was followed by diversification in each lineage. Present‐day morphological uniformity masks much of the genetic complexity of lineages within the M. avidus complex. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 819–833.     

Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks

Background  

DNA recognition by proteins is one of the most important processes in living systems. Therefore, understanding the recognition process in general, and identifying mutual recognition sites in proteins and DNA in particular, carries great significance. The sequence and structural dependence of DNA-binding sites in proteins has led to the development of successful machine learning methods for their prediction. However, all existing machine learning methods predict DNA-binding sites, irrespective of their target sequence and hence, none of them is helpful in identifying specific protein-DNA contacts. In this work, we formulate the problem of predicting specific DNA-binding sites in terms of contacts between the residue environments of proteins and the identity of a mononucleotide or a dinucleotide step in DNA. The aim of this work is to take a protein sequence or structural features as inputs and predict for each amino acid residue if it binds to DNA at locations identified by one of the four possible mononucleotides or one of the 10 unique dinucleotide steps. Contact predictions are made at various levels of resolution viz. in terms of side chain, backbone and major or minor groove atoms of DNA.     

Parkin‐independent mitophagy requires Drp1 and maintains the integrity of mammalian heart and brain

Mitochondrial dynamics and mitophagy have been linked to cardiovascular and neurodegenerative diseases. Here, we demonstrate that the mitochondrial division dynamin Drp1 and the Parkinson's disease‐associated E3 ubiquitin ligase parkin synergistically maintain the integrity of mitochondrial structure and function in mouse heart and brain. Mice lacking cardiac Drp1 exhibited lethal heart defects. In Drp1KO cardiomyocytes, mitochondria increased their connectivity, accumulated ubiquitinated proteins, and decreased their respiration. In contrast to the current views of the role of parkin in ubiquitination of mitochondrial proteins, mitochondrial ubiquitination was independent of parkin in Drp1KO hearts, and simultaneous loss of Drp1 and parkin worsened cardiac defects. Drp1 and parkin also play synergistic roles in neuronal mitochondrial homeostasis and survival. Mitochondrial degradation was further decreased by combination of Drp1 and parkin deficiency, compared with their single loss. Thus, the physiological importance of parkin in mitochondrial homeostasis is revealed in the absence of mitochondrial division in mammals.     

Nestling growth and mortality of Pied Flycatchers Ficedula hypoleuca in relation to weather and breeding effort

The growth pattern and mortality of young Pied Flycatchers Ficedula hypoleuca were studied to focus on the mechanisms and constraints behind the widely studied optimization of clutch size. The clutch sizes were modified, and the growth and survival of chicks from different clutch sizes were monitored along with the prevailing weather during the nestling period to detect the effect of weather on reproductive success. The weather conditions during the feeding period of the nestlings varied within a season as well as between breeding seasons. The prevailing weather markedly affected both the growth rate and the survival of chicks, yet, the effects of weather on growth were not greater in enlarged clutches. The impact of adverse weather was more pronounced in the later phases of nesting, when the food demand of a brood was highest. Brood reduction and total nest losses were more likely during extensive rainfall during the nestling phase and also in the enlarged clutches. Thus, weather is a very important determinant of reproductive success in this species. Weather conditions during the breeding season are unpredictable, however, and therefore brood reduction through sibling competition is a mechanism whereby brood size can be adjusted to the level the parents can rear under the prevailing conditions.     

Impact of invasive apple snails in Hong Kong on wetland macrophytes,nutrients, phytoplankton and filamentous algae

1. Grazing by invasive species can affect many aspects of an aquatic system, but most studies have focused on the direct effects on plants. We conducted mesocosm and laboratory experiments to examine the impact of the invasive apple snail Pomacea canaliculata on macrophytes, filamentous algae, nutrients and phytoplankton. 2. In a freshwater pond, we confined 500 g of Myriophyllum aquaticum or Eichhornia crassipes with 0, 2, 4 or 8 apple snails in 1 m × 1 m × 1 m enclosures for approximately 1 month. Apple snails grazed heavily on both species of macrophytes, with higher overall weight losses at higher snail densities. The damage patterns differed between the two macrophytes. In M. aquaticum, both leaves and stems suffered from substantial herbivory, whereas in E. crassipes, only the roots suffered significant weight reduction. 3. In addition to grazing on macrophytes, apple snails appeared to have controlled the growth of filamentous algae, as these did not develop in the snail treatments. The ability of P. canaliculata to control filamentous algae was supported by a laboratory experiment where the consumption was as high as 0.25 g g⁻¹ snail DW d⁻¹. Because of a lack of native herbivorous snails in the pond, the growth of filamentous algae (mainly Spirogyra sp.) reached 80.3 g m⁻², forming a spongy pond scum in the no‐apple snail control. Together with previous reports that apple snails could eat the juveniles and eggs of other freshwater snails, our results indicated that P. canaliculata could have out‐competed native herbivorous snails from the pond by predation on their juveniles or eggs. Alternatively, P. canaliculata might have out‐competed them by monopolisation of food resources. 4. Nitrogen and phosphorous concentrations remained low throughout both experiments and were not correlated with apple snail density. The treatment effects on chlorophyll a (Chl a) and phytoplankton composition varied in the two experiments. In the M. aquaticum experiment, with increasing snail density, Chl a increased, and the phytoplankton community became dominated by Cryptophyceae. In the E. crassipes experiment, Chl a level was independent of snail density, but with increasing snail density, the phytoplankton community became co‐dominated by Cryptophyceae, Chlorophyceae and Bacillariophyceae. 5. Given the multiple effects of P. canaliculata on wetland biodiversity and function, management strategies should be developed to prevent its further spread. In invaded wetlands, strategies should be developed to eradicate the apple snail and re‐introduce native snails which can control the development of filamentous algae.