Population genomics of wild and laboratory zebrafish (Danio rerio)

Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large‐scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST‐based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among‐clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall F_ST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low F_ST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.     

The evolution of waving displays in fiddler crabs (Uca spp., Crustacea: Ocypodidae)

Male fiddler crabs are commonly recognized by the presence of a single massive claw used in a variety of contexts, including territorial defence, agonistic interactions, and courtship behaviour. The most common behavioural context involving these enlarged chelipeds is their use in waving displays, which are remarkably diverse among species. Although the waving display is one of the most obvious behavioural features of male fiddler crabs, little is known about their main evolutionary trends during the diversification of the genus. The present study employed phylogenetic comparative methods to investigate the evolution of waving behaviour in a sample of 19 species of Uca from Central and North America. Digital recordings were used to quantify the temporal dynamics of waving behaviour in each species. Multivariate ordination methods were used to assess whether different elements of the display showed distinct evolutionary dynamics, particularly with respect to body size and the environment where species are most commonly found. Most of the interspecific variation in displays involves differences in the overall waving velocity, with no correspondence to their local environments, nor their body size. Interestingly, despite the strong concentration of variance in the first two ordination axes, there was no statistically significant evidence for phylogenetic signals in their respective scores. These results suggest that the overall structure of waving displays is evolutionarily labile, at the same time as being concentrated in a few particular axes of variation, possibly indicating evolution along lines of least resistance. The approach employed in the present study highlights the utility of phylogenetic comparative methods for elucidating the evolution of complex behavioural characteristics, such as the waving display in male fiddler crabs. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 307–315.     

Leaf breakdown in an Atlantic Rain Forest stream

The hypothesis of this study was that colonizers in decaying leaf litter prefer native species (Erythrina verna) to exotic ones (Eucalyptus camaldulensis and Protium heptaphyllum). Therefore, native species are expected to show higher breakdown rates, increased biomass, richness and density of invertebrate species, and increased biomass of decomposer fungi. Breakdown of leaf litter from these three species was assessed in an Atlantic Rain Forest stream. Four samples were collected during a period of 90 days and washed on a sieve to separate the invertebrates. Then, a series of leaf disks were cut to determine ash‐free dry mass and fungal biomass, and the remaining material was oven‐dried to determine the dry weight. Eucalyptus camaldulensis and E. verna showed higher breakdown rates than P. heptaphyllum, due to differences in leaf physical and chemical characteristics. The harder detritus (P. heptaphyllum) broke down more slowly than detritus with high concentrations of labile compounds (E. camaldulensis). The density of the invertebrates associated with detritus increased with time. There were no differences in density, taxonomic richness or biomass of invertebrates among the leaf types, which indicated that the invertebrates did not distinguish between exotic and native detritus. Fungal colonization varied among samples; E. camaldulensis showed the lowest ergosterol concentrations, mainly due to a high concentration of total phenolics. The detritus with the highest hardness value was colonized most slowly by fungi. These results showed that leaf breakdown in Atlantic Rain Forest streams could be affected either by changes in riparian vegetation, or by becoming more savanna‐like process due to climate change.     

Ecotone delimitation: Epigean–hypogean transition in cave ecosystems

Abstract The ecotone zone between epigean and hypogean environments has been delimited for two limestone caves using a new method proposed herein. The richness and the diversity of the ecotone, epigean and hypogean environments and their similarities have also been determined. The ecotones were delimited using a similarity matrix between the inner and outer sectors of each cave. The ecotone of Dona Rita's cave was estimated to be 12 m long and the ecotone of Retiro's cave 16 m. The richness (S) of arthropods in Dona Rita's cave was higher in the ecotone (S = 131), intermediate in the epigean environment (S = 75) and lower in the hypogean system (S = 45). The invertebrate diversity (H′) was lower in the hypogean environment (H′ = 2.89) and not statistically different between the epigean environment and the ecotone (H′ = 3.56 and H′ = 3.76, respectively). The richness in Retiro's cave was higher in the ecotone (S = 86), intermediate in the epigean environment (S = 39) and lower in the hypogean system (S = 12). The invertebrate diversity was lower in the hypogean environment (H′ = 0.48), intermediate in the ecotone (H′ = 3.02) and higher in the epigean region (H′ = 3.29). Species migration patterns, differential environmental barriers and determination of accidental versus trogloxenes/troglophylous species are topics that are primarily approached by establishing ecotone zones in caves. The aim of the present paper is to establish the delimitation of theses zones.     

Carrion flies of forensic interest: a study of seasonal community composition and succession in Lisbon,Portugal

Information on Diptera community, seasonality and successional patterns in every geographical region is fundamental for the use of flies as forensic indicators of time of death. In order to obtain these data from the Lisbon area (Portugal), experiments were conducted during the four seasons of the year, using piglet carcasses as animal models. Five stages were recognized during the decomposition process. The stages, besides visually defined, could be separated taking into account the occurrence and abundance of the specific groups of Diptera collected. In general, the bloated stage recorded higher abundance and species‐richness values. Seventy‐one species were identified, belonging to 39 families, in a total of 20 144 adult Diptera collected. Autumn yielded the highest values of species richness, whereas winter had the lowest. In all seasons of the year, Calliphoridae was the dominant family; Muscidae and Fanniidae were very abundant as well. Calliphora vicina Robineau‐Desvoidy, Calliphora vomitoria (Linnaeus), Chrysomya albiceps (Wiedemann), Lucilia ampullacea Villeneuve, Lucilia caesar (Linnaeus), Lucilia sericata (Meigen) (Calliphoridae), Hydrotaea ignava (Harris), Muscina prolapsa (Harris), Synthesiomyia nudiseta (van der Wulp) (Muscidae), Piophila megastigmata McAlpine, Stearibia nigriceps (Meigen) (Piophilidae) and Nemopoda nitidula (Fallén) (Sepsidae) were revealed to be very important members of the Diptera community collected. The necrophagous behaviour, demonstrated by their immatures, using carrion as a food source makes them useful forensic indicator species. Also of relevance is the presence of Chrysomya megacephala (Fabricius), S. nudiseta and P. megastigmata, foreign species established in the local carrion communities. This study also marks the first record of S. nudiseta in Portugal.     

Spatial distribution of chitinases and β-1,3-glucanase transcripts in bean arbuscular mycorrhizal roots under low and high soil phosphate conditions

Arbuscular mycorrhizal (AM) fungi extensively colonize the root cortex under low-soil-phosphate (P) conditions, whereas infection is limited under high-P conditions. Fungal growth under both P conditions might be influenced by plant defence-related gene expression. In this study, we used in situ hybridization methods to compare the cellular localization of three defence-related mRNAs in non-infected bean roots and in relation to fungal infection units. In non-infected and infected roots, mRNAs encoding acidic and basic endochitinases were generally most abundant in the vascular cylinder. High-P-grown mycorrhizal roots showed localized accumulation of the acidic endochitinase mRNA in cortical cells containing arbuscules and in their immediate vicinity (one to five cell layers). The pattern of accumulation of the basic endochitinase mRNA was not affected by P or AM fungal infection. At the low P concentration, the β-1,3-glucanase mRNA accumulated predominantly in the vascular cylinder of non-infected roots. Suppression of β-1,3-glucanase mRNA accumulation in these tissues was observed in non-infected roots at the high-P and in mycorrhizal roots at both P concentrations. The observed suppression extends at least several mm from fungal infection units, characterizing a systemic effect. Beta-1,3-glucanase mRNA accumulated also around a number of cortical cells containing arbuscules only at the low P concentration. The localized accumulations of the endochitinase and β-1,3-glucanase mRNAs suggest that the encoded proteins might be involved in the control of intraradical fungal growth.     

Insecticide resistance,associated mechanisms and fitness aspects in two Brazilian Stegomyia aegypti (= Aedes aegypti) populations

In Brazil, insecticide resistance in Stegomyia aegypti (= Aedes aegypti) (Diptera: Culicidae) populations to pyrethroids and to the organophosphate (OP) temephos is disseminated. Currently, insect growth regulators (IGRs) and the OP malathion are employed against larvae and adults, respectively. Bioassays with mosquitoes from two northeast municipalities, Crato and Aracaju, revealed, in both populations, susceptibility to IGRs and malathion (RR₉₅ ≤ 2.0), confirming the effectiveness of these compounds. By contrast, temephos and deltamethrin (pyrethroid) resistance levels were high (RR₉₅ > 10), which is consistent with the use of intense chemical control. In Crato, RR₉₅ values were > 50 for both compounds. Knock‐down‐resistant (kdr) mutants in the voltage‐gated sodium channel, the pyrethroid target site, were found in 43 and 32%, respectively, of Aracaju and Crato mosquitoes. Biochemical assays revealed higher metabolic resistance activity (esterases, mixed function oxidases and glutathione‐S‐transferases) at Aracaju. With respect to fitness aspects, mating effectiveness was equivalently impaired in both populations, but Aracaju mosquitoes showed more damaging effects in terms of longer larval development, decreased bloodmeal acceptance, reduced engorgement and lower numbers of eggs laid per female. Compared with mosquitoes in Crato, Aracaju mosquitoes exhibited lower OP and pyrethroid RR₉₅, increased activity of detoxifying enzymes and greater effect on fitness. The potential relationship between insecticide resistance mechanisms and mosquito viability is discussed.     

Leaf Ecology of Pre-reproductive Ontogenetic Stages of the Palm TreeEuterpe edulisMart. (Arecaceae)

We studied leaves of 208 seedlings (S), infants (I) and juveniles(J) ofEuterpe edulis,randomly selected from plants in 1 ha ofswampy forest in SE Brazil. Each new leaf began extending afterthe complete development of the preceding leaf. The sequencesteps of leaf growth were emergence, linear growth while closed,opening of segments and logarithmic growth of the petiole. Averageleaf production rate (2.21 leaves per plant year^-1) did notvary among ontogenetic stages, conforming to a plastochronicrhythm. Average linear growth rate of the closed leaf was directlyrelated to average area of the open lamina. Herbivores attacked33.0% of all leaves giving rise to up to 10% loss of area andincluded damping-off-inducing suckers (7.1%), ordinary suckers(9.8%), chewers (5.4%), miners (2.7%) and multiple attacks (8.0%).These attacks varied among stages (S=22.4%, I=38.1%, J=33.3%),as did leaf mortality rates (S=26.5%, I=14.3% and J=0.0%). Unknownfactors were the main cause of leaf mortality (S=14.3%, I=7.1%).Not losing a leaf while a seedling and attaining a minimum leafarea in the infant stage were critical events for survival.Plants gained leaf area by not losing leaves while a seedling,by producing larger leaves with greater growth rates, and byaccumulating leaves with longer lifespans. The petiole can simulatean energetically cheaper branch, delimit a vital space aroundthe stem, favourably position the leaf lamina and substituteprovisionally for stem growth in height.Copyright 1999 Annalsof Botany Company Arecaceae,Euterpe edulis, herbivory, leaf ecology, leaf growth, leaf production, semideciduous forest, southeastern Brazil.     

Diversity and specificity of host‐natural enemy interactions in an urban‐rural interface

1. Urbanisation and agricultural intensification cause the replacement of natural ecosystems but might also create novel habitats in urban and rural ecosystems promoting some insect communities by providing food and nesting resources. 2. This study investigated how host–natural enemy communities change in urban and rural landscapes and their transitional zone, the urban–rural interface, by using trap nests for cavity‐nesting Hymenoptera in gardens and rapeseed fields that were either isolated or paired in the urban–rural interface. 3. Host dynamics were important for natural enemy occurrence, species richness and parasitism rates, and landscape effects were evident for natural enemy variables except for the richness of bee natural enemies. The number of parasitised brood cells was at its highest in the urban–rural interface, but the highest parasitism rates of bees were observed in isolated gardens. Parasitism rates of bees were negatively affected by host abundance, while parasitism rates of wasps were positively affected. 4. Higher specialisation and lower connectivity of host–natural enemy interactions were found in paired habitats than in isolated habitats. This indicates that paired habitats comprise more specific natural enemies and vulnerable interactions, while isolated habitats comprise more generalist natural enemies, and thus interactions appear more stable. 5. These results confirm that host dynamics play an essential role in the abundance and richness of natural enemies and drive parasitism. However, high habitat heterogeneity found in the urban–rural interface can also have an effect on host–natural enemy communities. This highlights that the provisioning of resources in the urban–rural interface can benefit insect communities in these areas.