Cristina V. Ariani

Assembly of the Genome of the Disease Vector Aedes aegypti onto a Genetic Linkage Map Allows Mapping of Genes Affecting Disease Transmission

The mosquito Aedes aegypti transmits some of the most important human arboviruses, including dengue, yellow fever and chikungunya viruses. It has a large genome containing many repetitive sequences, which has resulted in the genome being poorly assembled — there are 4,758 scaffolds, few of which have been assigned to a chromosome. To allow the mapping of genes affecting disease transmission, we have improved the genome assembly by scoring a large number of SNPs in recombinant progeny from a cross between two strains of Ae. aegypti, and used these to generate a genetic map. This revealed a high rate of misassemblies in the current genome, where, for example, sequences from different chromosomes were found on the same scaffold. Once these were corrected, we were able to assign 60% of the genome sequence to chromosomes and approximately order the scaffolds along the chromosome. We found that there are very large regions of suppressed recombination around the centromeres, which can extend to as much as 47% of the chromosome. To illustrate the utility of this new genome assembly, we mapped a gene that makes Ae. aegypti resistant to the human parasite Brugia malayi, and generated a list of candidate genes that could be affecting the trait.

Herpetofauna of an Atlantic rainforest area (Morro São João) in Rio de Janeiro State, Brazil

We studied the herpetofaunal community from the Atlantic forest of Morro São João, in Rio de Janeiro State, Brazil, and present data on species composition, richness, relative abundance and densities. We combined three sampling methods: plot sampling, visual encounter surveys and pit-fall traps. We recorded sixteen species of amphibians and nine of reptiles. The estimated densities (based on results of plot sampling) were 4.5 ind/100 m2 for amphibians and 0.8 ind/100 m2 for lizards, and the overall density (amphibians and lizards) was 5.3 ind/100 m2. For amphibians, Eleutherodactylus and Scinax were the most speciose genera with three species each, and Eleutherodactylus binotatus was the most abundant species (mean density of 3.0 frogs/100 m2). The reptile community of Morro São João was dominated by species of the families Gekkonidae and Gymnophtalmidae (Lacertilia) and Colubridae (Serpentes). The gymnophtalmid lizard Leposoma scincoides was the most abundant reptile species (mean density of 0.3 ind/100 m2). We compare densities obtained in our study data with those of other studied rainforest sites in various tropical regions of the world.

Feeding Ecology of Thoropa miliaris (Anura, Cycloramphidae) in Four Areas of Atlantic Rain Forest, Southeastern Brazil

Abstract We analyzed the feeding ecology of four Thoropa miliaris (Anura, Cycloramphidae) populations from the Atlantic Rain Forest in Brazil. The diet was composed mostly of invertebrates, especially ants, beetles, grasshoppers, caterpillars, and spiders. Plant consumption was considered incidental because of its low frequency. Ants were the most frequent (range 70–100%) and numerous (range 54.9–63.8%) dietary items. In terms of volume, ants were the principal item at two localities (26.1% and 47.6%), being also important items for the other two areas (19.3% and 21.9%). Grasshoppers (20.1%) and beetles (22.8%) had the largest volume for two populations. There was a significant relationship of prey size and volume with frog jaw width in three of the four areas. Only in one area was this relationship not found, probably because of the high frequency with which small ants and termites were ingested. Many of the dominant prey taxa of T. miliaris were similar to those of other rain-forest frogs.

Anurofauna of an Atlantic Rainforest fragment and its surroundings in Northern Rio de Janeiro State, Brazil

We carried out a study on the anurofaunal community from an Atlantic Forest fragment (Monte Verde mountains) and the surrounding area in Cambuci municipality, Rio de Janeiro State, Brazil, which constitutes one of the largest fragments remaining in the largely deforested landscape of the northern portion of the State. We combined three sampling methods: plot sampling, transects and pit-fall traps. We recorded twenty species of amphibians, of which only eleven were found within the forest fragment (and five of these also occurred in the surrounding matrix). Two of the species recorded in the present study (Crossodactylus sp. and Ischnocnema cf. parva) may represent undescribed taxa. Our records expand the distribution range of one species (Scinax trapicheiroi) to the north, and fill a geographic distribution gap for another one (Ischnocnema oea). The estimated overall density of frogs living in the leaf litter of the fragment (based on results of plot sampling) was 3.1 individuals/100 m², with Haddadus binotatus being the most abundant species (2.4 individuals/100 m²). Comparisons of our data with those of other studies suggest that anuran communities in forest fragments ca. 1,000 ha or smaller may be severely limited in their richness, and often include a large proportion of species tolerant to open areas, such as many hylids. Our results show the importance of increasing knowledge about the anurofaunal community of the northern portion of the State of Rio de Janeiro and preserve the forest remnants that still exist in the region.

Evolutionary history and identification of conservation units in the giant otter, Pteronura brasiliensis

The giant otter, Pteronura brasiliensis, occupies a range including the major drainage basins of South America, yet the degree of structure that exists within and among populations inhabiting these drainages is unknown. We sequenced portions of the mitochondrial DNA (mtDNA) cytochrome b (612bp) and control region (383 bp) genes in order to determine patterns of genetic variation within the species. We found high levels of mtDNA haplotype diversity (h = 0.93 overall) and support for subdivision into four distinct groups of populations, representing important centers of genetic diversity and useful units for prioritizing conservation within the giant otter. We tested these results against the predictions of three hypotheses of Amazonian diversification (Pleistocene Refugia, Paleogeography, and Hydrogeology). While the phylogeographic pattern conformed to the predictions of the Refugia Hypothesis, molecular dating using a relaxed clock revealed the phylogroups diverged from one another between 1.69 and 0.84 Ma, ruling out the influence of Late Pleistocene glacial refugia. However, the role of Plio-Pleistocene climate change could not be rejected. While the molecular dating also makes the influence of geological arches according to the Paleogeography Hypothesis extremely unlikely, the recent Pliocene formation of the Fitzcarrald Arch and its effect of subsequently altering drainage pattern could not be rejected. The data presented here support the interactions of both climatic and hydrological changes resulting from geological activity in the Plio-Pleistocene, in shaping the phylogeographic structure of the giant otter.

Density and richness of leaf litter frogs (Amphibia: Anura) of an Atlantic Rainforest area in the Serra dos Órgãos, Rio de Janeiro State, Brazil

Data on species composition, richness, and density are presented for the leaf litter frog assemblage of an area of Atlantic Rainforest at the Serra dos Orgaos mountain range, in the state of Rio de Janeiro, southeastern Brazil. Three sampling methods were used: plot sampling, visual encounter surveys, and pitfall traps. The local assemblage of leaf litter frogs was composed of 16 species, with the direct-developing species, Euparkerella brasiliensis (Parker, 1926), being the most abundant. The estimated density of the local leaf litter frog assemblage based on plot sampling was 17.1 ind/100 m2 and the estimated overall leaf litter frog mass was 684.2 g/ha. The estimated density of leaf litter frogs at the present study is the highest currently reported for Atlantic Rainforest areas, which reinforces the idea of higher densities of leaf litter frogs in the Neotropical Region compared to the Old World tropics.

The endemic and threatened lizard Liolaemus lutzae (Squamata: Liolaemidae): current geographic distribution and areas of occurrence with estimated population densities.

Liolaemus lutzae Mertens, 1938 is a critically endangered lizard endemic to the restinga habitat of the state of Rio de Janeiro. We surveyed 25 restinga habitats in order to locate remaining populations, evaluate the status of the species, and determine the nature of local habitat degradation. We found remnant populations of L. lutzae in 18 restinga habitats of six municipalities. The conservation status of each population varied between areas: the population of Grumari, in Rio de Janeiro municipality, is the most preserved and the population of Praia do Forte, in Cabo Frio, is the most disturbed. No L. lutzae were found in Niteroi municipality. The most destructive type of habitat degradation identified was the removal of beach vegetation associated with the construction of coastal roads and/or sidewalks, destruction of the vegetation due to trampling, vehicle traffic and garbage dumping. Our data revealed that generally, beach habitats under a larger number of impact sources were those with smaller population sizes of L. lutzae. We consider that the most effective conservation measure for L. lutzae is the strict protection of its habitat, with restoration of the original beach vegetation. Finally, we recommend vegetation recovery to be followed by a program of reintroduction of the species in localities where it has been eradicated.

Ecology and Natural History of the Easternmost Native Lizard Species in South America, Trachylepis atlantica (Scincidae), from the Fernando de Noronha Archipelago, Brazil

Abstract We studied the ecology of Trachylepis atlantica, the easternmost native lizard species in South America, endemic to the Fernando de Noronha archipelago, approximately 350 km off the northeastern coast of Brazil. Activity of this species extended from dawn to dusk, with a peak from 1200–1400 h. Mean body temperature of active T. atlantica was 32.2 ± 2.9°C and was significantly related to both air and substrate temperatures. Trachylepis atlantica used most types of available substrates in the area but was found most frequently (72.5% of observations) on rocks and normally used perches up to 80 cm high. There was sexual dimorphism in body size, with males larger than females. Trachylepis atlantica had an omnivorous diet, with plant material comprising 77% of the volume ingested and being present in 67% of stomachs with food. Formicidae and insect larvae were the main animal items in the diet. Mean prey volume (6.9 ± 5.3 mm3) was small compared to other related species. This, coupled with the high plant consumption, suggests that local availability of suitable prey may be limited, as expected for small islands in general.

Genetic diversity and population structure in the endangered giant otter, Pteronura brasiliensis

We assessed levels of genetic diversity and investigated patterns of population structure in three remnant populations of the endangered giant otter, Pteronura brasiliensis, using microsatellite loci. All populations displayed moderate to low levels of heterozygosity and allelic richness (HO 0.56–0.57, AR 4.00–5.15) and effective population sizes were low (NE 10.8–54) although only the Iténez population exhibited the signature of a genetic bottleneck. Population structure analyses revealed a pattern in which the populations of the Upper Amazon, Orinoco and Essequibo drainages comprised partially differentiated segments of a northern South American metapopulation, whereas the population of the Iténez appeared isolated. The observed patterns are congruent with previous mitochondrial DNA analysis which suggested the Iténez and northern South American groups constitute two evolutionary significant units. The results presented here should be considered in planning future policies aiming to manage the recovery of the giant otter across its range.

Exome and transcriptome sequencing of Aedes aegypti identifies a locus that confers resistance to Brugia malayi and alters the immune response.

Many mosquito species are naturally polymorphic for their abilities to transmit parasites, a feature which is of great interest for controlling vector-borne disease. Aedes aegypti, the primary vector of dengue and yellow fever and a laboratory model for studying lymphatic filariasis, is genetically variable for its capacity to harbor the filarial nematode Brugia malayi. The genome of Ae. aegypti is large and repetitive, making genome resequencing difficult and expensive. We designed exome captures to target protein-coding regions of the genome, and used association mapping in a wild Kenyan population to identify a single, dominant, sex-linked locus underlying resistance. This falls in a region of the genome where a resistance locus was previously mapped in a line established in 1936, suggesting that this polymorphism has been maintained in the wild for the at least 80 years. We then crossed resistant and susceptible mosquitoes to place both alleles of the gene into a common genetic background, and used RNA-seq to measure the effect of this locus on gene expression. We found evidence for Toll, IMD, and JAK-STAT pathway activity in response to early stages of B. malayi infection when the parasites are beginning to die in the resistant genotype. We also found that resistant mosquitoes express anti-microbial peptides at the time of parasite-killing, and that this expression is suppressed in susceptible mosquitoes. Together, we have found that a single resistance locus leads to a higher immune response in resistant mosquitoes, and we identify genes in this region that may be responsible for this trait.