Ecological Requirements for Abundance and Dispersion of Brazilian Yellow Fever Vectors in Tropical Areas.

In the Americas, wild yellow fever (WYF) is an infectious disease that is highly lethal for some non-human primate species and non-vaccinated people. Specifically, in the Brazilian Atlantic Forest, Haemagogus leucocelaenus and Haemagogus janthinomys mosquitoes act as the major vectors. Despite transmission risk being related to vector densities, little is known about how landscape structure affects vector abundance and movement. To fill these gaps, we used vector abundance data and a model-selection approach to assess how landscape structure affects vector abundance, aiming to identify connecting elements for virus dispersion in the state of São Paulo, Brazil. Our findings show that Hg. leucocelaenus and Hg. janthinomys abundances, in highly degraded and fragmented landscapes, are mainly affected by increases in forest cover at scales of 2.0 and 2.5 km, respectively. Fragmented landscapes provide ecological corridors for vector dispersion, which, along with high vector abundance, promotes the creation of risk areas for WYF virus spread, especially along the border with Minas Gerais state, the upper edges of the Serra do Mar, in the Serra da Cantareira, and in areas of the metropolitan regions of São Paulo and Campinas.

Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes.

The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs from desired species inside a group of organisms. The procedure is divided two main steps, (1) ortholog detection and (2) creation of a matrix with the median amino acid distance measures of all pairwise orthologous sequences. We tested this approach within three different group of organisms: Kinetoplastida protozoa, hematophagous Diptera vectors and Primates. Our approach was robust and efficacious to reconstruct the phylogenetic relationships for the three groups. Moreover, novel branch topologies could be achieved, providing insights about some phylogenetic relationships between some taxa.

Anthropogenic river fragmentation reduces long-term viability of the migratory fish Salminus brasiliensis (Characiformes: Bryconidae) populations

Life-history, geographical barriers, and damming can shape the genetic diversity of freshwater migratory fish, which are particularly vulnerable to anthropogenic impacts. We investigated the genetic diversity of Salminus brasiliensis, a long-distance migratory species that is recognized as an important provider of ecosystem services. We implemented microsatellite analyses to assess genetic diversity and simulate future scenarios for evaluating the long-term viability of dammed and non-dammed populations from the Uruguay River. High levels of genetic diversity were detected for all sampled populations. However, effective population sizes were lower in the uppermost river stretches, where the landscape is highly fragmented. Population structure analysis indicated two spatial genetic populations. It is suggested that this genetic structure preserves populations partially isolated by an ancient natural barrier, instead of being a result of the presence of dams. The simulated genetic scenarios indicated that genetic variability of S. brasiliensis populations from upstream dams could collapse over the years, mainly due to the reduction in the number of alleles. Therefore, besides helping to better understand issues related to the influence of dams on the genetic diversity of migratory fish, our results are especially relevant for driving local fishery policies and management actions for the species conservation.'

História de vida, barreiras geográficas e barramento dos rios podem moldar a diversidade genética de grandes peixes migratórios de água doce, que são particularmente vulneráveis a impactos antrópicos. Nós investigamos a diversidade genética de Salminus brasiliensis, uma espécie migratória de longa distância que é reconhecida como um importante provedor de serviços ecossistêmicos. Realizamos análises de microssatélites para avaliar a diversidade genética e simular cenários futuros, possibilitando estimar a viabilidade em longo prazo de populações situadas em regiões com e sem represas do rio Uruguai. Altos níveis de diversidade genética foram detectados para todas as populações amostradas. Contudo, os tamanhos populacionais efetivos foram menores nos trechos superiores do rio, onde a paisagem é altamente fragmentada. A análise da estrutura populacional indicou duas populações genéticas espaciais. Sugere-se que esta estrutura genética preserva populações parcialmente isoladas por uma antiga barreira natural, ao invés de ser resultado da presença de barragens. Os cenários genéticos simulados indicaram que a variabilidade genética das populações de S. brasiliensis situadas a montante das barragens entraria em colapso ao longo dos anos, principalmente como resultado da redução do número de alelos. Portanto, além de ajudar a entender melhor questões relacionadas à influência de barragens na diversidade genética de peixes migradores, nossos resultados são especialmente relevantes para a condução de políticas pesqueiras locais e ações de manejo para a conservação das espécies.(AU)

Studbook and molecular analyses for the endangered black-lion-tamarin; an integrative approach for assessing genetic diversity and driving management in captivity.

Breeding strategies based on molecular markers have been adopted by ex-situ conservation programs to assess alternative parameters for the genetic diversity estimates. In this work we evaluated molecular and studbook data for captive populations of black-lion-tamarin (BLT), an endangered primate endemic to Brazil's Atlantic Forest. Pedigree analyses were performed using BLT studbook information collected from 1973 to 2018. We analyzed the whole captive population since its foundation; the current captive population (CCP); and all extant BLTs in the Brazilian captive population (BCP), separately. Microsatellite analyses were implemented on the BCP individuals from the eighth generation (BCP-F8) only to avoid generation overlap. The expected heterozygosity for BCP-F8, using molecular, data was 0.45, and the initial expected heterozygosity was 0.69. Kinship parameters showed high genetic relationships in both pedigree and molecular analyses. The genealogy-based endogamy evidenced a high inbreeding coefficient, while the molecular analyses suggested a non-inbreeding signature. The Mate Suitability Index showed detrimental values for the majority of potential pairs in the CCP. Nevertheless, some individuals evidenced high individual heterozygosity and allele representation, demonstrating good potential to be used as breeders. Thus, we propose the use of molecular data as a complementary parameter to evaluate mating-pairs and to aid management decision-making.

Next-Generation Sequencing of the Complete Mitochondrial Genome of the Endangered Species Black Lion Tamarin Leontopithecus chrysopygus (Primates) and Mitogenomic Phylogeny Focusing on the Callitrichidae Family.

We describe the complete mitochondrial genome sequence of the Black Lion Tamarin, an endangered primate species endemic to the Atlantic Rainforest of Brazil. We assembled the Leontopithecus chrysopygus mitogenome, through analysis of 523M base pairs (bp) of short reads produced by next-generation sequencing (NGS) on the Illumina Platform, and investigated the presence of nuclear mitochondrial pseudogenes and heteroplasmic sites. Additionally, we conducted phylogenetic analyses using all complete mitogenomes available for primates until June 2017. The single circular mitogenome of BLT showed organization and arrangement that are typical for other vertebrate species, with a total of 16618 bp, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region (D-loop region). Our full phylogenetic tree is based on the most comprehensive mitogenomic dataset for Callitrichidae species to date, adding new data for the Leontopithecus genus, and discussing previous studies performed on primates. Moreover, the mitochondrial genome reported here consists of a robust mitogenome with 3000X coverage, which certainly will be useful for further phylogenetic and evolutionary analyses of Callitrichidae and higher taxa.

Genetic variation in a closed line of the white shrimp Litopenaeus vannamei (Penaeidae)

The culture of the marine shrimp Litopenaeus vannamei has recently boosted the Brazilian shrimp industry. However, it is well known that selection methods based solely on phenotypic characteristics, a reduced number of breeders and the practice of inbreeding may promote a significant raise in the genetic similarity of the captive populations, leading to greater disease susceptibility and impairing both the growth and final size of the shrimps. We used four microsatellite loci to investigate genetic variation in three generations (F5, F6 and F7) of a closed and reared L. vannamei lineage. Although an accentuated heterozygosis deficit was detected, we also observed that the captive propagation of this lineage did not lead to a significant loss of genetic variability over the three generations studied. One possible reason for this is that the breeding conditions of this lineage were good enough to prevent any significant loss of genetic variability. However, three generations may have been insufficient to produce detectable changes in genetic frequencies in the loci studied. Alternatively, the microsatellite loci may have been non-neutral (biased) and related to the conditions in which the shrimps were kept, resulting in a similar allele pool in respect to these four microsatellites over the three generations studied. Any generalizations regarding microsatellite variation in closed shrimp lines may thus be incomplete and should be carefully analyzed.

In silico analysis of polymorphic microsatellites in penaeid shrimp and construction of a free-access database

We performed an in silico analysis of all microsatellites so far described for penaeid shrimp and for which the polymorphic behavior has previously been analyzed. The objective of the study was to evaluate the structural characteristics of these microsatellites and identifying patterns which allow the characterization of the nature of these sequences in the penaeid genome. All data were compiled in a free-access database specially constructed for this study. Three hundred non-mononucleotide polymorphic microsatellite loci described for 12 shrimp species belonging to the family Penaeidae were analyzed and simple and compound microsatellites with di-, tri-, tetra-, penta- and hexanucleotide motifs were found. Dinucleotides and trinucleotides were the most frequent motifs among both the simple and the compound microsatellites. Although a certain bias related to different microsatellite isolation methodology could not be discarded, it is possible that part of this microsatellite abundance reflects some degree of conservation of microsatellite motifs among the different species. There was a pronounced motif variability within and between species, indicating high differentiation dynamism of these repetitions in this animal group. This study not only sheds light on the structure of the microsatellites present in the penaeid shrimp genome but also resulted in the free-access Penaeid Shrimp Microsatellite Database (available at http://www.shrimp.ufscar.br) which may be very useful for optimizing the use of these microsatellites.

Fluorescent amplified fragment length polymorphism (fAFLP) analyses and genetic diversity in Litopenaeus vannamei (Penaeidae)

The Pacific white shrimp, Litopenaeus vannamei (Penaeidae), represents about 95 percent of all Brazilian shrimp production. The Brazilian L. vannamei foundation broodstock was made up of specimens collected from different American Pacific sites, but little information was collected on the genetic structure of the broodstock. We used the fluorescence amplified fragment length polymorphism (fAFLP) method to study the genetic diversity of L. vannamei broodstock lines 03CMF1 and 03CBF1 originally produced by breeder-shrimps imported mainly from Panama and Ecuador, although wild individuals from other localities may also have been used in producing these two lines. Our results showed a total of 93 polymorphic bands ranging from 50 to 500 bp, the mean Nei's genetic diversity calculated for the total sample was 13.4 percent and identity and genetic distance analyses indicated high genetic homogeneity within and between both the broodstock lineages studied which suggests that they had similar genetic structure. These results may represent an important tool for the appropriate management of L. vannamei broodstocks.

PCR-based VNTR core sequence analysis for inferring genetic diversity in the shrimp Litopenaeus vannamei

The genetic variation in two farmed strains (F3-Panama and F17-Venezuela) of the shrimp Litopenaeus vannamei was examined based on DNA multiloci analyses. Eighteen adults of each strain were analyzed by PCR using a set of VNTR core sequence primers. Genetic similarity, mean allele frequency, mean heterozygosity and the frequency of polymorphic loci were determined for both strains. A dendrogram of genetic similarity was produced by UPGMA clustering. The results for three primers (INS, M13, YN73) revealed different levels of genetic variation within the strains. The higher genetic similarity seen within strain F17 was apparently related to inbreeding, although a bottleneck effect could not be discarded. The low level of genetic variability of this strain could account for the reduced adaptive advantage of these animals and their inability to adjust to breeding conditions in Brazil