Order within a mosaic distribution of mitochondrial c-type cytochrome biogenesis systems?

Mitochondrial cytochromes c and c(1) are present in all eukaryotes that use oxygen as the terminal electron acceptor in the respiratory chain. Maturation of c-type cytochromes requires covalent attachment of the heme cofactor to the protein, and there are at least five distinct biogenesis systems that catalyze this post-translational modification in different organisms and organelles. In this study, we use biochemical data, comparative genomic and structural bioinformatics investigations to provide a holistic view of mitochondrial c-type cytochrome biogenesis and its evolution. There are three pathways for mitochondrial c-type cytochrome maturation, only one of which is present in prokaryotes. We analyze the evolutionary distribution of these biogenesis systems, which include the Ccm system (System I) and the enzyme heme lyase (System III). We conclude that heme lyase evolved once and, in many lineages, replaced the multicomponent Ccm system (present in the proto-mitochondrial endosymbiont), probably as a consequence of lateral gene transfer. We find no evidence of a System III precursor in prokaryotes, and argue that System III is incompatible with multi-heme cytochromes common to bacteria, but absent from eukaryotes. The evolution of the eukaryotic-specific protein heme lyase is strikingly unusual, given that this protein provides a function (thioether bond formation) that is also ubiquitous in prokaryotes. The absence of any known c-type cytochrome biogenesis system from the sequenced genomes of various trypanosome species indicates the presence of a third distinct mitochondrial pathway. Interestingly, this system attaches heme to mitochondrial cytochromes c that contain only one cysteine residue, rather than the usual two, within the heme-binding motif. The isolation of single-cysteine-containing mitochondrial cytochromes c from free-living kinetoplastids, Euglena and the marine flagellate Diplonema papillatum suggests that this unique form of heme attachment is restricted to, but conserved throughout, the protist phylum Euglenozoa.     

Spatial mosaic and interfacial dynamics in a Müllerian mimicry system

Uncovering why spatial mosaics of mimetic morphs are maintained in a Müllerian mimicry system has been a challenging issue in evolutionary biology. In this article, we analyze the reaction diffusion system that describes two-species Müllerian mimicry in one- and two-dimensional habitats. Due to positive frequency-dependent selection, a local population first approaches the state where one of the comimicking patterns predominates, which is followed by slow movement of boundaries where different patterns meet. We then analyze the interfacial dynamics of the boundaries to find whether a stable cline is maintained and to obtain the wave speed if the cline is unstable. The results are: (1) In a spatially uniform habitat the morph with greater base fitness spreads both in one and two species system. (2) The strength of cross-species interaction determines whether the mimetic morph clines of model and mimic species coalesce into the same geographical region or pass through each other. The joint wave speed of clines decreases by increasing the number of comimicking species in the mimicry ring. (3) In spatial heterogeneous habitats, stable clines can be maintained due to the balance between the base fitness gradient and the biased gene flow by negative curvature of boundary. This allows the persistence of a spatial mosaic even if one of the morphs is in every place advantageous over the other. A balanced cline is also maintained if there is a gradient in the population density. (4) A new advantageous morph occurring at a local region is doomed to go to extinction in a finite time if the "radius" of initial distribution is below a threshold. Possible applications to the heliconiine butterfly mimicry ring, heterozygous disadvantage systems of chromosomal rearrangement and hybrid zone, the third phase of Wright's Shifting Balance theory, and cytoplasmic incompatibility are discussed.     

Impatiens parviflora DC. — a natural host of cabbage black ringspot and cucumber mosaic viruses

Identification trials were carried out to determine a virus-like disease ofImpatiene parviflora DC. Two forms of foliar symptoms were observed:

1. a)
   Chiorotie and necrotic areas sometimes fallen out, leaving the leaves “shot holed”;     
   
   

Mapping a forest mosaic – A comparison of vegetation and bird distributions using geographic boundary analysis

Many areas of ecological inquiry require the ability to detect and characterize change in ecological variables across both space and time. The purpose of this study was to investigate ways in which geographic boundary analysis techniques could be used to characterize the pattern of change over space in plant distributions in a forested wetland mosaic. With vegetation maps created using spatially constrained clustering and difference boundary delineation, we examined similarities between the identified boundaries in plant distributions and the occurrence of six species of songbirds. We found that vegetation boundaries were significantly cohesive, suggesting one or more crisp vegetation transition zones exist in the study site. Smaller, less cohesive boundary areas also provided important information about patterns of treefall gaps and dense patches of understory within the study area. Boundaries for songbird abundance were not cohesive, and bird and vegetation difference boundaries did not show significant overlap. However, bird boundaries did overlap significantly with vegetation cluster boundaries. Vegetation clusters delineated using constrained clustering techniques have the potential to be very useful for stratifying bird abundance data collected in different sections of the study site, which could be used to improve the efficiency of monitoring efforts for rare bird species.     

Persistence of a vegetation mosaic in a peripheral region: could turbulent medieval history disrupt Holocene continuity of extremely species-rich grasslands?

Fluctuations in intensity of human impact and corresponding vegetation changes have been reported from different parts of Europe for the period from the beginning of the 1st millennium ad to the high Middle Ages. In the Bílé Karpaty mountains (White Carpathians), a region well-known for its biologically valuable ancient grasslands, an extensive spread of woodland could have occurred in the Migration period (4th–6th century) and especially in the Confinium period (11th–12th century), when settling of this border region was legally prohibited. However, Holocene continuity of non-woodland vegetation was suggested as an explanation for the unique species richness of the local grasslands. If this explanation is true, then the turbulent times in medieval history could not have led to complete re-establishment of woodland. To test this idea palaeoecologically, we analysed four new profiles from wetland deposits for pollen, macrofossils and abiotic proxies, and re-dated some old profiles from the area. The results show the continual presence of human impact indicators since the Migration period in the southwest of the Bílé Karpaty, where these unique grasslands occur. Agricultural activities were indicated by pollen of crops, ruderals, weeds and grassland taxa and by macrofossils of fen-grassland plants. Grazing and burning seem to have been the main disturbances during the older period, while mowing of meadows by scythe became more important since the 17th century. Fossil records differed among the sites as a consequence of differences in altitude and disturbance regimes, but converged gradually with time. Despite intensification of human activities, the landscape remained mosaic-like. Indicators of undisturbed woodlands have been detected only in the northeast. Continuous yet perhaps never too intensive disturbances might therefore have maintained the ancient grassland species pool in the long term.     

Food habits of three carnivores in a mosaic landscape of São Paulo state,Brazil

São Paulo is the most developed state in Brazil, but despite intense land use changes, some mammal species still inhabit remnant fragments of native vegetation of the state. We used fecal analyses to investigate prey diversity, trophic niche breadth, and trophic niche overlap of pumas, ocelots, and maned wolves in protected and non-protected areas in São Paulo state. During 18 months, we inspected more than 10,000 km of roads and trails and collected 233 fecal samples. Maned wolves showed generalist food habit, ocelots were predominantly carnivores, and pumas were strict carnivores. The European hare, an exotic species which had not yet been reported in the study area, was identified in the feces of a puma. Trophic niche breadth was the lowest for maned wolves (BA?=?0.339) and the highest for pumas (BA?=?0.723). Trophic niche overlap was high between maned wolves and ocelots (O_jk?=?0.765) and between pumas and ocelots (O_jk?=?0.639). Significantly different diets of maned wolves and ocelots were observed between dry and rainy seasons. Our findings indicate that these three species may adapt their diets to the disturbed landscapes. This is the second study characterizing food habits of ocelots in Cerrado areas but the first considering a large number of samples.     

Effects of the cucumber mosaic virus 2a protein on aphid–plant interactions in Arabidopsis thaliana

The cucumber mosaic virus (CMV) 2a RNA-dependent RNA polymerase protein has an additional function in Arabidopsis thaliana, which is to stimulate feeding deterrence (antixenosis) against aphids. Antixenosis is thought to increase the probability that aphids, after acquiring CMV particles from brief probes of an infected plant's epidermal cells, will be discouraged from settling and instead will spread inoculum to neighbouring plants. The amino acid sequences of 2a proteins encoded by a CMV strain that induces antixenosis in A. thaliana (Fny-CMV) and one that does not (LS-CMV) were compared to identify residues that might determine the triggering of antixenosis. These data were used to design reassortant viruses comprising Fny-CMV RNAs 1 and 3, and recombinant CMV RNA 2 molecules encoding chimeric 2a proteins containing sequences derived from LS-CMV and Fny-CMV. Antixenosis induction was detected by measuring the mean relative growth rate and fecundity of aphids (Myzus persicae) confined on infected and on mock-inoculated plants. An amino acid sequence determining antixenosis induction by CMV was found to reside between 2a protein residues 200 and 300. Subsequent mutant analysis delineated this to residue 237. We conjecture that the Fny-CMV 2a protein valine-237 plays some role in 2a protein-induced antixenosis.     

Mosaic formation by developmental loss of a chromosomal fragment in a “mottled striped” mosaic strain of the silkworm,Bombyx mori

A separable chromosomal fragment of about 2.5 Mb, which carries the larval body marking gene striped (p ^S), is present in a recessive background in the kind of genetic mosaic called mottled striped in the silkworm, Bombyx mori. The somatic loss of this chromosomal fragment during cell division gives rise to white patches (variegated pigmentation) in the dorsal black stripes of the fifth instar larva. Each larger white patch in the black p ^S stripe represents the clonal expansion of an epidermal cell that lost the fragment carrying p ^S during an early developmental stage. To gain information on the developmental history of the larval epidermal cells, we have analysed a variety of mosaic individuals showing extreme mottling patterns. Based on several common features observed in mosaic patterns, we constructed a schematic model for migration of epidermal cells, which implies that several polyclonal founding cells on each lateral side of a segment move and expand toward the dorsal mid-line. To determine the timing of loss of the fragment in half-stripe mosaics, which are completely lacking the mottled black stripe on one half of the larval body, we examined several tissues from either body side for the chromosomal fragment. Pulsed field gel electrophoresis (PFGE) and restriction fragment length polymorphism (RFLP) analysis showed that testes and silk glands from each side of the half-stripe mosaics (two and five individuals, respectively) contained the chromosomal fragment carrying the p ^S allele, independent of the epidermal phenotypes of the respective body half. This result suggests that loss of the chromosomal fragment leading to external half-stripe mosaics might occur, not at an early stage of development such as the first nuclear division, but rather after the progenies of epidermis and internal tissues examined here diverged from each other developmentally.     

A mosaic of opportunities? Spatio-temporal patterns of bat diversity and activity in a strongly humanized Mediterranean wetland

The Baixo Vouga Lagunar (BVL) landscape, in the Portuguese central-west coast, harbours a mosaic of wetland habitat types, interspersed by intensive and extensive agricultural fields, pastures, production forests and urban areas. In this study, we aimed to determine the species composition and the structure of the bat assemblages of the different habitats that constitute this heterogeneous landscape and to investigate seasonal changes in the patterns of bat diversity and activity across habitats. We acoustically sampled bats across 24 sampling sites representative of the eight main habitat types that shape the landscape—Bocage, forests, maize fields, marshlands, reed beds, rice fields, sea rushes and urban settlements. We compared bat richness, diversity and evenness across habitat types and seasons. We analysed habitat-specific and season-specific overall bat activity, and because habitat selection by bats is known to reflect morphological characters, foraging strategies and echolocation call structures, we also analysed the activity of individual species and of eco-morphological guilds. From 1,544 bat-passes recorded, we identified 12 species. Pipistrellus pygmaeus, Pipistrellus pipistrellus and Eptesicus serotinus/Eptesicus isabellinus were the most frequently recorded. Species composition and activity were similar across habitats, whilst exhibiting strong seasonal dynamics within habitats. Our results suggest that the mosaicism of the landscape provides several opportunities for bats, enabling them to explore different resources in distinct habitat patches. However, it may also reflect a forced exploitation of less optimal habitats and resources by bats, due to the scarcity of opportunities provided by fragmented landscapes.     

The mosaic diversity of field layer vegetation in the natural and exploited forests of Białowieża

The main focus of the study was to find out whether and how the forestry management in the Biaowiea Forest has influenced the mosaic diversity of field layer vegetation and habitat heterogeneity in the temperate hard wood forest (Tilio-Carpinetum). Five belt-transects represent natural and semi-natural old-growths in Biaowiea National Park (BNP), the commercial forest (CF), and secondary stands in the CF. Along the transects, distinct patches of field layer vegetation were identified and delimited, and their species composition was assessed. Along central lines of the transects the environmental data was collected from sample points established at regular intervals: soil pH and the distances to the 4 closest trees, their species, and dbh (diameter at the breast height=135 cm). The group of patches (on average 50 per transect) was subjected to the dichotomous classification in order to identify a number of characteristic types of microphytocoenoses – synusiae. Beta-diversity of the vegetation was expressed with the Simpson diversity index calculated on the basis of areas occupied by synusiae. The most structurally diversified were the transects representing natural old-growths in the BNP. A calculation of similarity coefficients between the transects on the basis of their mosaic composition displayed sharper differences between old-growth and secondary communities in summer than those found in spring. Forestry management has seriously modified the tree species composition in two studied stands, through planting oak or initiating succession. This resulted, both in plantation and pioneer stand, in loss of the main components of natural old-growths: hornbeam (Carpinus betulus), Norway spruce (Picea abies), lime (Tilia cordata) and maple (Acer platanoides). Significantly a wider range of soil pH values in natural old-growths coincided with a higher diversity of herbaceous mosaics comparing to secondary stands. The elimination of spruce (the species being most commonly blown down, projecting an acid canopy shadow) in two studied areas, elimination of dead wood, and destruction of humus layers through ploughing, could contribute to a reduction of specific microenvironments. A lower mosaic diversity of secondary stands coinciding with the unification of environmental conditions along the transects may indicate that forestry management can lead to the disappearance of a highly structural character in natural forest communities.Nomenclature: Flora europaea; Sokoowski (1993).     

Population structure and spatial pattern of predominant tree species in a pine–oak mosaic mixed forest in the Qinling Mountains,China

This study investigated a typical pine-oak mosaic mixed forest in the Qinling Mountains, China. In the sample plot, the population structure and spatial distribution of the stems were analyzed for the predominant species, to identify the mechanisms of species coexistence and successional trends of the forest. The population structures of all species were bimodally distributed, with young trees (DBH <1 cm) more abundant than older trees. The population structures of Quercus aliena var. acuteserrata was bimodal and rather continuous. However, Pinus tabuliformis and Pinus armandii were discontinuously bimodal, with distinct size deficiencies. Q. aliena var. acuteserrata trees were clumped throughout the plot, although those of P. tabuliformis and P. armandii were clumped at small scales. Notable negative spatial associations between Q. aliena var. acuteserrata and P. tabuliformis were found at almost scales. P. armandii and Q. aliena var. acuteserrata were negatively spatially associated at small scales but positively associated at large scales. Our findings suggest that interspecific competition gradually develops among the predominant tree species. The dynamics of the pine-oak mosaic mixed forest formed a mosaic distribution of uniformly mixed types, with the slow infiltration of Q. aliena var. acuteserrata populations that would eventually establish a pure stand.     

Spatial mosaic formation through frequency-dependent selection in Müllerian mimicry complexes

Although contemporary models of Müllerian mimicry have considered the movement of interfacial boundaries between two distinct mimetic forms, and even the possibility of polymorphisms in two patch systems, no model has considered how multiple forms of Müllerian mimics might evolve and be maintained over large geographical areas. A spatially explicit individual-based model for the evolution of Müllerian mimicry is presented, in which two unpalatable species are distributed over discrete cells within a regular lattice. Populations in each cell are capable of genetic drift and experience localized dispersal as well as frequency-dependent selection by predators. When each unpalatable prey species was introduced into a random cell and allowed to spread, then mimicry evolved throughout the system in the form of a spatial mosaic of phenotypes, separated by narrow "hybrid zones". The primary mechanism generating phenotypic diversity was the occasional establishment of new mutant forms in unoccupied cells and their subsequent maintenance (and spread) through frequency-dependent selection. The mean number of discrete clusters of the same morph that formed in the lattice was higher the higher the intensity of predation, and higher the lower the dispersal rate of unpalatable prey. Under certain conditions the hybrid zones moved, in a direction dependent on the curvature of their interfacial boundaries. However, the mimetic mosaics were highly stable when the intensity of predation was high and the rate of prey dispersal was low. Overall, this model highlights how a stable mosaic of different mimetic forms can evolve from a range of starting conditions through a combination of chance effects and localized frequency-dependent selection.     

A fragile X case with an amplification/deletion mosaic pattern

Fragile X syndrome is the most common cause of hereditary mental retardation. The FMR1 gene, which is involved in fragile X syndrome, contains a polymorphic CGG repeat, which expands in affected patients. Expanding triplet repeats have been shown to be a new type of mutation, termed "dynamic mutation", responsible for more than 12 genetic diseases. These mutations occur as multiple steps rather than as a single event. The first step leads to an unstable allele that then becomes increasingly unstable generally achieving further increases in copy or occasionally contraction. In this report, we describe a fragile X boy with both a hypermethylated full mutation and a deletion of 905 bp encompassing the CGG repeat. The upstream breakpoint is 438 bp 5' to the CGG repeat and the downstream breakpoint is 420 bp 3' of the triplet repeats. The deletion includes the ATG starting codon for translation of the FMR1 gene. This was confirmed by using FMRP immunocytochemistry both on blood smears and hair roots. The deleted region is flanked by a ccgg direct repeat next to the breakpoints; this may have had a critical role in the formation of a secondary DNA structure leading to the deletion.     

Seed dispersal mechanisms and the vegetation of forest islands in a West African forest-savanna mosaic (Comoé National Park,Ivory Coast)

The transition zone between forest and savanna is typically characterized by a dynamic patchwork of forest and savanna. We studied the woody plant species composition of 49 forest islands, 18 savanna, and 3 gallery forest plots in the Comoé National Park (Ivory Coast), West Africa's largest savanna reserve. TWINSPAN makes a clear distinction in vegetational composition between these three major habitat types but, nevertheless, more than 50% of the 292 species occur in at least 2 of them. The gallery forest is dominated by Cynometra megalophylla (Caesalpiniaceae), a genus known to dominate humid forests in other afrotropical regions. Ordination reveals four distinct categories of forest islands, (1) humid forests comparable to the gallery forest in their species composition, (2) dry disturbed and (3) dry undisturbed forests and (4) forests formerly inhabited by humans. Disturbed forests harbor more savanna species but also a distinct group of disturbance-tolerant forest species. Compared to other forest species, in this latter group we found an exceptionally high fraction of animal dispersed species (80% vs. 58%), while wind dispersed species or species lacking long distance seed dispersal mechanisms were correspondingly rare. This pattern occurs in spite of the fact that the frequency of wind dispersed species in general increases from dense humid forests to open dry forests and savanna. Species lacking long distance dispersal mechanisms are most abundant among those specialized on humid forests. These observations suggest that the species composition of forest islands is to some extent determined by the seed dispersal abilities of the different species.     

Composition and diversity of bird communities in Swedish farmland–forest mosaic landscapes

CapsuleThe amount of forest (at local and landscape scales) and occurrence of residual habitats at the local scale are shown to be the major factors influencing bird community composition in farmland–forest landscapes in central Sweden.

Aims To investigate the importance of local habitat and landscape structure for breeding birds in farmland–forest landscapes in central Sweden.

Methods Breeding birds were censused at 292 points. A detailed habitat mapping was made within 300 m of the points. Within a 300–600 m radius only two major habitats (forests and arable fields) were identified.

Results Cluster analyses of bird communities identified three site types that also differed in habitat composition: (i) partially forested sites in forested landscapes; (ii) heterogeneous sites with residual habitats in mosaic landscapes; and (iii) field-dominated farmland sites in open landscapes. A total of 19 of 25 farmland bird species (restricted to farmland or using both farmland and forest) had the highest abundance in farmland sites with mosaics of forest and farmland, while only six farmland species had the highest abundance in field-dominated sites. The bird community changed from being dominated by farmland species to being dominated by forest species (common in forest landscapes without farmland) at small proportions (10–20%) of forest at the local scale. A major difference in habitat composition between heterogeneous and field-dominated sites was the occurrence of different residual habitats (e.g. shrubby areas and seminatural grasslands). These habitats seemed to influence bird community composition more than land-use, despite covering <10% of the area. Seminatural grasslands were important for bird community composition and species-richness, but grazing seemed to be less important. Among different land-use types, cereal crops were the least preferred fields. Set-asides with tall vegetation and short rotation coppices were positively associated with species-richness of farmland birds.

Conclusion In general, the composition of the landscape was important for bird community composition, although amount and distribution of forests, occurrence of residual habitats and land-use of fields at the local scale had the strongest influence on bird community composition. The possible implications of these patterns for managing farmland–forest landscapes are discussed.     

What shapes cerambycid beetle communities in a tropical forest mosaic? Assessing the effects of host tree identity,forest structure,and vertical stratification

Due to anthropogenic activities, tropical rain forests face many challenges in sustaining biodiversity and maintaining global climates. This study explores how forest successional stage, tree composition, and stratum affect communities of saproxylic cerambycid beetles—concealed feeders that play important roles in forest nutrient cycling. Forty trees in five families (Fabaceae, Lecythidaceae, Malvaceae, Moraceae, and Sapotaceae) were sampled in a mosaic of old‐growth and secondary forest on the Osa Peninsula, Costa Rica. Bait branches yielded 3549 cerambycid individuals in 49 species. Species richness was almost identical in old‐growth and secondary forest, and both yielded specialists, but abundance was higher in old‐growth forest. Overall community structure was most strongly influenced by host plant species; within most plant families it was also impacted by forest successional status. Moraceae was the exception, presumably because the focal tree species was abundant in both old‐growth and secondary forest. Several host and old‐growth specialist species reached high densities within patches of old‐growth forest, but seldom colonized apparently suitable trees within secondary forest. This suggests that even small areas of old‐growth forest can act as refuges, but that secondary forest may act as a barrier to dispersal. The vulnerability of specialized saproxylic insects to land use change will be linked to the ability of their preferred hosts to disperse to and persist in successional habitats; rearing studies may provide the most accurate method to monitor community changes over time.