Comparative genomics uncovers the evolutionary history, demography, and molecular adaptations of South American canids.

The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary history remain unknown. Here, we analyzed 31 whole genomes encompassing all extant SA canid species to assess phylogenetic relationships, interspecific hybridization, historical demography, current genetic diversity, and the molecular bases of adaptations in the bush dog and maned wolf. We found that SA canids originated from a single ancestor that colonized South America 3.9 to 3.5 Mya, followed by diversification east of the Andes and then a single colonization event and radiation of Lycalopex species west of the Andes. We detected extensive historical gene flow between recently diverged lineages and observed distinct patterns of genomic diversity and demographic history in SA canids, likely induced by past climatic cycles compounded by human-induced population declines. Genome-wide scans of selection showed that disparate limb proportions in the bush dog and maned wolf may derive from mutations in genes regulating chondrocyte proliferation and enlargement. Further, frugivory in the maned wolf may have been enabled by variants in genes associated with energy intake from short-chain fatty acids. In contrast, unique genetic variants detected in the bush dog may underlie interdigital webbing and dental adaptations for hypercarnivory. Our analyses shed light on the evolution of a unique carnivoran radiation and how it was shaped by South American topography and climate change.

Phylogeographic analyses of an endemic Neotropical fox (Lycalopex vetulus) reveal evidence of hybridization with a different canid species (L. gymnocercus).

The hoary fox (Lycalopex vetulus) is the only species of the Canidae (Mammalia: Carnivora) endemic to Brazil, and so far has been the target of few genetic studies. Using microsatellites and mtDNA markers, we investigated its present genetic diversity and population structure. We also tested the hypothesis that this species currently hybridizes with the pampas fox (L. gymnocercus), as suggested by previous mtDNA data from two individuals. We collected tissue and blood samples from animals representing most of the two species' distributions in Brazil (n = 87), including their recently discovered geographic contact zone in São Paulo state. We observed that the hoary fox exhibits high levels of genetic diversity and low levels of population structure. We identified six individuals from São Paulo state with clear evidence of hybridization based on introgressed pampas fox mitochondrial DNA and/or admixed microsatellite genotypes (three individuals bore both types of evidence). These results demonstrate the existence of admixed individuals between hoary and pampas foxes in southeastern Brazil, representing the first identified case of interspecies admixture between native South American canids. We discuss our findings in the context of the evolutionary history of these foxes and address potential conservation implications of this interspecies hybridization process.

Spatial distribution and seasonality of Biomphalaria spp. in São Luís (Maranhão, Brazil).

Two of the three vector species of Schistosoma mansoni Sambon, 1907 in Brazil occur in the state of Maranhão: Biomphalaria glabrata (Say, 1818) and Biomphalaria straminea (Dunker, 1848). For the implementation of effective measures to combat schistosomiasis, it is necessary to identify the spatial and seasonal dynamics of these snails. Therefore, this work brought together information from malacological survey carried out in São Luís (Maranhão, Brazil) to identify the spatial and seasonal distribution patterns of Biomphalaria spp. snails. We used data from malacological surveys of the Municipal Health Secretary of São Luís, conducted between 2006 and 2013 in 23 neighborhoods. We also used data from the mollusk surveys that we conducted for 2 years (2012-2014) in four of these neighborhoods. During the 8-year period (2006-2013), 15,990 specimens of Biomphalaria spp. were collected. There was a positive association between precipitation and the abundance of mollusks of the genus Biomphalaria. During 2012-2014, a total of 2487 snail specimens were obtained (B. glabrata: 1046 specimens; B. straminea: 1426 specimens). There was a positive correlation between precipitation and B. straminea abundance. High density of human occupation and high precipitation are two factors that affect the distribution and density of Biomphalaria spp.

Changes in Glutathione S-Transferase Activity and Parental Care Patterns in a Catfish (Pisces, Ariidae) as a Biomarker of Anthropogenic Impact in a Brazilian Harbor.

Catfish have been used as a model system for studying biochemical mechanisms of biotransformation. The main goal of this study was to identify alterations in hepatic glutathione S-transferase (GST) activity and changes in the parental care pattern of a mouth-brooding catfish, Sciades herzbergii, as a biomarker of anthropogenic impact in a port area on the northeastern coast of Brazil. The fish were sampled from a natural reserve (A1 = reference site) and from an industrialized port area (A2 = impacted site). Two analyses were carried out: hepatic GST activity and mouth-brooding behavior of males. Catfish collected from the A1 site displayed all stages of gonadal maturation, and some of the adult males were mouth brooding 12-30 embryos. Not all gonadal maturation stages of the catfish were represented at the A2 site, and no mouth-brooding males were observed. GST activity in the liver of S. herzbergii was significantly higher in fish from the impacted site compared with fish from the reference site. Values for the enzymatic activity increased progressively in fish sampled from the reserve area as they became more reproductively mature (immature ≤ maturing ≤ mature ≤ spent). However, the greatest values for GST activity (2.84 ± 0.31 µmol min-1 mg protein-1) among fish sampled from the impacted area were found in (immature) juveniles. These data suggest that changes in hepatic GST activity and mouth-brooding behavior of S. herzbergii can be used as biomarkers of anthropogenic impact.

Molecular assessment of the phylogeny and biogeography of a recently diversified endemic group of South American canids (Mammalia: Carnivora: Canidae).

To investigate the evolution and biogeography of an endemic group of South American foxes, we examined mitochondrial DNA control region sequences for 118 individuals belonging to all six extant species of the genus Lycalopex. Phylogenetic and molecular dating analyses supported the inference that this genus has undergone a very recent and rapid radiation, stemming from a common ancestor that lived ca. 1 million years ago. The Brazilian endemic L. vetulus was supported as the most basal species in this genus, whereas the most internal group is comprised by the recently diverged (ca. 350,000 years ago) Andean/Patagonian species L. griseus and L. culpaeus. We discuss the inferred phylogenetic relationships and divergence times in the context of the current geographic distributions of these species, and the likely effects of Pleistocene climatic changes on the biogeography of this group. Furthermore, a remarkable finding was the identification of multiple individuals classified as L. gymnocercus bearing mtDNA haplotypes clearly belonging to L. griseus, sampled in regions where the latter is not known to occur. At a minimum, this result implies the need to clarify the present-day geographic distribution of each of these fox species, while it may also indicate an ongoing hybridization process between them. Future testing of this hypothesis with in-depth analyses of these populations is thus a priority for understanding the history, evolutionary dynamics and present-day composition of this endemic Neotropical genus.

Community Perceptions on Schistosomiasis in Northeast Brazil.

Schistosomiasis is a serious public health issue in the world infecting more than 200 million people. In Maranhão state, Brazil, the disease has a high prevalence in the Baixada Maranhense microregion, where the socioeconomic conditions, high prevalence of freshwater snails, elevated incidence of human infection, and large rodent populations make the area highly conducive to the life cycle and persistence of schistosomiasis. The objective of this study was to record the perception of residents and health/public education professionals regarding this parasitosis and also understand their knowledge of the relationship between schistosomiasis and the environment. We conducted 53 interviews addressing the socioeconomic, behavioral, and environmental issues surrounding schistosomiasis. It was recorded that the population believed the environment is the main cause of the disease and the fisherman may be stigmatized by their chance of having the disease. Health/public educational professionals in the region indicated that there were no regular educational campaigns, which contributed to the high rates of reinfection and the difficulties in preventing and controlling the spread of the disease. These data clearly demonstrate the need for interdisciplinary work that engages the community in gathering and disseminating knowledge and developing solutions to minimize the occurrence of this major health issue in the region.

Analysis of the supply chain and conservation status of sharks (Elasmobranchii: Superorder Selachimorpha) based on fisher knowledge.

Increasing fishing effort has caused declines in shark populations worldwide. Understanding biological and ecological characteristics of sharks is essential to effectively implement management measures, but to fully understand drivers of fishing pressure social factors must be considered through multidisciplinary and integrated approaches. The present study aimed to use fisher and trader knowledge to describe the shark catch and product supply chain in Northeastern Brazil, and evaluate perceptions regarding the regional conservation status of shark species. Non-systematic observations and structured individual interviews were conducted with experienced fishers and traders. The demand and economic value of shark fins has reportedly decreased over the last 10 years while the shark meat trade has increased slightly, including a small increase in the average price per kilogram of meat. Several threatened shark species were reportedly often captured off shore and traded at local markets. This reported and observed harvest breaches current Brazilian environmental laws. Fishing communities are aware of population declines of several shark species, but rarely take action to avoid capture of sharks. The continuing capture of sharks is mainly due to a lack of knowledge of environmental laws, lack of enforcement by responsible authorities, and difficulties encountered by fishers in finding alternative income streams. National and regional conservation measures are immediately required to reduce overfishing on shark populations in Northeastern Brazil. Social and economic improvements for poor fishing communities must also be implemented to achieve sustainable fisheries.

DNA-based identification reveals illegal trade of threatened shark species in a global elasmobranch conservation hotspot.

Here, we report trading of endangered shark species in a world hotspot for elasmobranch conservation in Brazil. Data on shark fisheries are scarce in Brazil, although the northern and northeastern regions have the highest indices of shark bycatch. Harvest is made primarily with processed carcasses lacking head and fins, which hampers reliable species identification and law enforcement on illegal catches. We used partial sequences of two mitochondrial genes (COI and/or NADH2) to identify 17 shark species from 427 samples being harvested and marketed on the northern coast of Brazil. Nine species (53%) are listed under some extinction threat category according to Brazilian law and international authorities (IUCN - International Union for Conservation of Nature; CITES - Convention on International Trade of Endangered Species of Wild Fauna and Flora). The number increases to 13 (76%) if we also consider the Near Threatened category. Hammerhead sharks are under threat worldwide, and composed 18.7% of samples, with Sphyrna mokarran being the fourth most common species among samples. As illegal trade of threatened shark species is a worldwide conservation problem, molecular identification of processed meat or specimens lacking diagnostic body parts is a highly effective tool for species identification and law enforcement.

Evaluation of environmental quality of two estuaries in Ilha do Maranhão, Brazil, using histological and genotoxic biomarkers in Centropomus undecimalis (Pisces, Centropomidae).

Estuaries are subjected to continual environmental impacts from activities in the catchment areas. This research assessed the quality of two estuarine habitats located in Ilha do Maranhão, Brazil, through histological and genotoxic biomarkers in Centropomus undecimalis, comparing the data obtained to metal, physical, and chemical concentrations of water samples. The gill histological alterations were analyzed by the histological alteration index and genotoxic lesions in erythrocytes were detected by the Micronucleus Test. The analysis of metals revealed that all water samples contained at least two elements with concentrations higher than that allowed by the current Brazilian law. For gill histological analysis, snook of both areas assessed exhibited moderate lesions, indicating that the local fish are affected by environmental stress. Micronucleus analysis of snook showed that the Bacanga river basin is the most affected. In addition to assessing the health of commercial fish populations, the information about the biomarkers used for the species can serve to contribute to the preparation and/or application of health assessment models and implementation of environmental recovery policies for coastal aquatic environments.

Genotoxic and hematological parameters in Colossoma macropomum (Pisces, Serrasalmidae) as biomarkers for environmental impact assessment in a protected area in northeastern Brazil.

Genotoxic and hematological parameters in tambaqui (Colossoma macropomum), a native freshwater fish, were used as biomarkers to assess exposure to environmental stressors within the Maracanã Protected Area of Maranhão State, Brazil. Fish were sampled at two sites-Serena Lagoon (control) and Ambude River-on four occasions (dry and rainy season), and biometric data (length and weight) recorded and blood collected from all fish for analysis. Erythrocyte indices-mean corpuscular volume, mean corpuscular hemoglobin, and mean corpuscular hemoglobin concentration-were calculated. Blood samples were stained with Giemsa and acridine orange, and microscopically examined for micronuclei and morphological nuclear abnormalities. Micronuclei were observed in fish from both sites, although the frequency was significantly higher in fish from the Ambude River and morphological nuclear abnormalities were only observed in fish from the Ambude River. More morphological nuclear abnormalities and a larger number of micronuclei were observed in erythrocytes stained with acridine orange compared with those stained with Giemsa. On average, erythrocyte indices were lower in fish from the Ambude River than from the Serena Lagoon. The results confirm that genotoxic and hematological parameters in C. macropomum can be used as indicators of environmental health and could be valuable tools for monitoring environmental conditions within protected areas.

A histopathological and biometric comparison between catfish (Pisces, Ariidae) from a harbor and a protected area, Brazil.

BACKGROUND: Histopathological lesions and biometric variations in catfish species are statistically associated with chemical contaminant exposure. A histopathological and biometric database for the catfish Sciades herzbergii and Bagre bagre from São Luís Island (Port Area) and Caranguejos Island (Reference Area) is presented. Branchial and hepatic lesions were classified into three reaction patterns: 1) circulatory or inflammatory disturbances; 2) regressive changes; 3) progressive changes. This paper summarizes research efforts aimed at characterizing the biomonitoring potential of catfish from two islands in Brazil, which exhibit great habitat diversity and different levels of human intervention. RESULTS: The weights and lengths of the catfish caught at the Port Area were smaller than those from the Reference Area. No histopathological lesions were observed in S. herzbergii examined at the reference site (Caranguejos Island). In contrast, 90% of S. herzbergii from sites located in the Port Area (São Luís Island) had one or more types of branchial and hepatic lesions. One or more of the five lesions were observed on 16 B. bagre from São Luís Island and Caranguejos Island. CONCLUSION: The utility of histopathological lesions and biometric data as sensitive indicators of the health of wild catfish populations has been demonstrated. Sciades herzbergii proved to be a better species for biomonitoring because it was more sensitive to the impacted site (Port Area) compared with the region relatively free of contaminants (Reference Area).

Cross-amplification and characterization of 13 tetranucleotide microsatellites in multiple species of Neotropical canids.

We tested 47 tetranucleotide microsatellite loci developed for the domestic dog in four species of Neotropical canids, aiming to produce a standardized set that could be successfully used even in noninvasive samples across this group. We identified 13 suitable loci, nine of which constitute a standardized set for all species. Considering only the ideal panel of nine loci, the mean expected heterozygosity (averaged across species) per locus ranged from 0.58 to 0.92 (overall mean 0.76), and the maximum probability of identity value was 1.3 × 10(-9) . This set of loci has a great potential for application in evolutionary, ecological and conservation studies.

Phylogeography and population history of the crab-eating fox (Cerdocyon thous).

The crab-eating fox is a medium-sized Neotropical canid with generalist habits and a broad distribution in South America. We have investigated its genetic diversity, population structure and demographic history across most of its geographic range by analysing 512 base pairs (bp) of the mitochondrial DNA (mtDNA) control region, 615 bp of the mtDNA cytochrome b gene and 1573 total nucleotides from three different nuclear fragments. MtDNA data revealed a strong phylogeographic partition between northeastern Brazil and other portions of the species' distribution, with complete separation between southern and northern components of the Atlantic Forest. We estimated that the two groups diverged from each other c. 400,000-600,000 years ago, and have had contrasting population histories. A recent demographic expansion was inferred for the southern group, while northern populations seem to have had a longer history of large population size. Nuclear sequence data did not support this north-south pattern of subdivision, likely due at least in part to secondary male-mediated historical gene flow, inferred from multilocus coalescent-based analyses. We have compared the inferred phylogeographic patterns to those observed for other Neotropical vertebrates, and report evidence for a major north-south demographic discontinuity that seems to have marked the history of the Atlantic Forest biota.