The SARS-CoV-2 virus infection led to millions of deaths during the COVID-19 pandemic. Hundreds of workers from several other Brazilian cities, as well as from other countries, arrive daily in Macaé ...to work in the oil supply chain, making this city a putative hotspot for the introduction of new viral lineages. In this study, we performed a genomic survey of SARS-CoV-2 samples from Macaé during the first outbreak of COVID-19, combined with clinical data and a molecular integrative analysis. First, phylogenomic analyses showed a high occurrence of viral introduction events and the establishment of local transmissions in Macaé, including the ingression and spread of the B.1.1.28 lineage in the municipality from June to August 2020. Second, SARS-CoV-2 mutations were identified in patients with distinct levels of COVID-19 severity. Third, molecular interactions of the mutated spike protein from three B.1.1.33 local samples and human ACE2 showed higher interactions than that of the wild-type spike protein from the ancestral virus. Altogether, these results elucidate the SARS-CoV-2 genomic profile in a strategic Brazilian city and further explore the functional aspects of SARS-CoV-2 with a characterization of emerging viral mutations associated with clinical data and the potential targets for drug development against SARS-CoV-2.
The taxonomy of common dolphins (Delphinus sp.) has always been controversial, with over twenty described species since the original description of the type species of the genus (Delphinus delphis ...Linnaeus, 1758). Two species and four subspecies are currently accepted, but recent molecular data have challenged this view. In this study we investigated the molecular taxonomy of common dolphins through analyses of cytochrome b sequences of 297 individuals from most of their distribution. We included 37 novel sequences from the Southwestern Atlantic Ocean, a region where the short- and long-beaked morphotypes occur in sympatry, but which had not been well sampled before. Skulls of individuals from the Southwestern Atlantic were measured to test the validity of the rostral index as a diagnostic character and confirmed the presence of the two morphotypes in our genetic sample. Our genetic results show that all common dolphins in the Atlantic Ocean belong to a single species, Delphinus delphis. According to genetic data, the species Delphinus capensis is invalid. Long-beaked common dolphins from the Northeastern Pacific Ocean may constitute a different species. Our conclusions prompt the need for revision of currently accepted common dolphin species and subspecies and of Delphinus delphis distribution.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Triatoma dimidiata is among the main vectors of Chagas disease in Latin America. However, and despite important advances, there is no consensus about the taxonomic status of phenotypically divergent ...T. dimidiata populations, which in most recent papers are regarded as subspecies.
A total of 126 cyt b sequences (621 bp long) were produced for specimens from across the species range. Forty-seven selected specimens representing the main cyt b clades observed (after a preliminary phylogenetic analysis) were also sequenced for an ND4 fragment (554 bp long) and concatenated with their respective cyt b sequences to produce a combined data set totalling 1175 bp/individual. Bayesian and Maximum-Likelihood phylogenetic analyses of both data sets (cyt b, and cyt b+ND4) disclosed four strongly divergent (all pairwise Kimura 2-parameter distances >0.08), monophyletic groups: Group I occurs from Southern Mexico through Central America into Colombia, with Ecuadorian specimens resembling Nicaraguan material; Group II includes samples from Western-Southwestern Mexico; Group III comprises specimens from the Yucatán peninsula; and Group IV consists of sylvatic samples from Belize. The closely-related, yet formally recognized species T. hegneri from the island of Cozumel falls within the divergence range of the T. dimidiata populations studied.
We propose that Groups I-IV, as well as T. hegneri, should be regarded as separate species. In the Petén of Guatemala, representatives of Groups I, II, and III occur in sympatry; the absence of haplotypes with intermediate genetic distances, as shown by multimodal mismatch distribution plots, clearly indicates that reproductive barriers actively promote within-group cohesion. Some sylvatic specimens from Belize belong to a different species - likely the basal lineage of the T. dimidiata complex, originated ~8.25 Mya. The evidence presented here strongly supports the proposition that T. dimidiata is a complex of five cryptic species (Groups I-IV plus T. hegneri) that play different roles as vectors of Chagas disease in the region.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Rhodnius montenegrensis (Triatominae), a potential vector of Chagas disease, was described after R. robustus-like bugs from southwestern Amazonia. Mitochondrial cytb sequence near-identity with ...sympatric R. robustus (genotype II) raised doubts about the taxonomic status of R. montenegrensis, but comparative studies have reported fairly clear morphological and genetic differences between R. montenegrensis and laboratory stocks identified as R. robustus. Here, we use a transcriptome-based approach to investigate this apparent paradox.
We retrieved publicly-available transcriptome sequence-reads from R. montenegrensis and from the R. robustus stocks used as the taxonomic benchmark in comparative studies. We (i) aligned transcriptome sequence-reads to mitochondrial (cytb) and nuclear (ITS2, D2-28S and AmpG) query sequences (47 overall) from members of the R. prolixus-R. robustus cryptic-species complex and related taxa; (ii) computed breadth- and depth-coverage for the 259 consensus sequences generated by these alignments; and, for each locus, (iii) appraised query sequences and full-breadth-coverage consensus sequences in terms of nucleotide-sequence polymorphism and phylogenetic relations. We found evidence confirming that R. montenegrensis and R. robustus genotype II are genetically indistinguishable and, hence, implying that they are, in all likelihood, the same species. Furthermore, we found compelling genetic evidence that the benchmark 'R. robustus' stocks used in R. montenegrensis description and in later transcriptome-based comparisons are in fact R. prolixus, although likely mixed to some degree with R. robustus (probably genotype II, a.k.a. R. montenegrensis).
We illustrate how public-domain genetic/transcriptomic data can help address challenging issues in disease-vector systematics. In our case-study, taxonomic confusion apparently stemmed from the misinterpretation of sequence-data analyses and misidentification of taxonomic-benchmark stocks. More generally, and together with previous reports of mixed and/or misidentified Rhodnius spp. laboratory colonies, our results call into question the conclusions of many studies (on morphology, genetics, physiology, behavior, bionomics or interactions with microorganisms including trypanosomes) based on non-genotyped 'R. prolixus' or 'R. robustus' stocks. Correct species identification is a prerequisite for investigating the factors that underlie the physiological, behavioral or ecological differences between primary domestic vectors of Chagas disease, such as R. prolixus, and their sylvatic, medically less-relevant relatives such as R. robustus (s.l.) including R. montenegrensis.
The franciscana (
Pontoporia blainvillei
) is the most threatened small cetacean in the South Atlantic. In this study we report the development of 13 microsatellite markers for franciscanas through ...next-generation sequencing, and the characterization of those loci in 38 samples from the species’ northernmost population (Espírito Santo, Brazil). Besides providing diversity indices for the new, specific loci, we also report on the transferability of heterologous loci which had not been screened in franciscanas before, and review all loci used in previous studies. Expected heterozygosity in the new loci ranged between 0.107 and 0.595, and all but one were in Hardy Weinberg Equilibrium. These are the first microsatellite loci isolated from franciscanas, and they are an important addition to heterologous markers that were available previously.
In this chapter, we review and update current knowledge about the evolution, systematics, and biogeography of the Triatominae (Hemiptera: Reduviidae)-true bugs that feed primarily on vertebrate ...blood. In the Americas, triatomines are the vectors of Trypanosoma cruzi, the etiological agent of Chagas disease. Despite declining incidence and prevalence, Chagas disease is still a major public health concern in Latin America. Triatomines occur also in the Old World, where vector-borne T. cruzi transmission has not been recorded. Triatomines evolved from predatory reduviid bugs, most likely in the New World, and diversified extensively across the Americas (including the Caribbean) and in parts of Asia and Oceania. Here, we first discuss our current understanding of how, how many times, and when the blood-feeding habit might have evolved among the Reduviidae. Then we present a summary of recent advances in the systematics of this diverse group of insects, with an emphasis on the contribution of molecular tools to the clarification of taxonomic controversies. Finally, and in the light of both up-to-date phylogenetic hypotheses and a thorough review of distribution records, we propose a global synthesis of the biogeography of the Triatominae. Over 130 triatomine species contribute to maintaining T. cruzi transmission among mammals (sometimes including humans) in almost every terrestrial ecoregion of the Americas. This means that Chagas disease will never be eradicated and underscores the fact that effective disease prevention will perforce require stronger, long-term vector control-surveillance systems.
We isolated and characterized the first polymorphic microsatellite for the Brazilian and Hooded slipper lobsters species (
Scyllarides
brasiliensis
and
S
.
deceptor
). Thirteen polymorphic loci (2–31 ...alleles/locus, H
o
= 0.056–0.975, H
e
= 0.155–0.958), were characterized in
S
.
brasiliensis
(N = 40). Twelve polymorphic loci (3–22 alleles/locus, H
o
= 0.333–0.900, H
e
= 0.337–0.940), were characterized in
S
.
deceptor
(N = 30) from different localities on the Brazilian coast. These loci were also tested in four scyllarid lobsters,
Scyllarides aequinoctialis
,
S
.
delfosi
,
Scyllarus depressus
and
Parribacus antarcticus
.
Aim
The disjunct distributions of freshwater organisms along coastal drainages are usually explained by palaeodrainages formed during sea‐level retreats that connected currently isolated basins, or ...by river capture from tectonic adjustments between adjoining watersheds. We evaluate the relative importance of these events on the genetic variation of freshwater fishes inhabiting the Serra do Mar in eastern Brazil, a region with steep mountains and pronounced bays.
Location
Coastal river drainages in southeastern Brazil.
Taxon
Catfishes of the Trichomycterus alternatus group.
Methods
We tested the effects of palaeolandscape connections (GIS‐reconstructed palaeodrainages and putative river captures) on the genetic structure (mitochondrial and nuclear markers) of T. alternatus from 15 drainages using phylogenetic reconstructions, lineage delimitation methods and analyses of molecular variance.
Results
Trichomycterus alternatus is monophyletic and comprised of three main lineages: two restricted to the basin at its northernmost distribution and another broadly distributed to the south. In the latter, seven major cytb clades were geographically compatible with the eight palaeodrainages, with three incongruences matching river captures previously described for the Guanabara Bay (GB). Shared haplotypes among isolated rivers flowing into GB provide the first molecular evidence of the ‘Rio de Janeiro’ palaeoriver.
Main conclusions
Dispersal via palaeorivers is an important process, but it is not enough to recover the most recent dispersive events. Therefore, integrating both palaeo‐riverine configuration (GIS‐based) and localized river captures (geological studies) is crucial to reveal the role of past geological and climatic events on the distribution of freshwater organisms. Taken together, these two factors significantly explained a high portion T. alternatus genetic structure along coastal drainages, revealing a palaeolandscape scenario that may have been used by other freshwater Atlantic Forest taxa.
The identification of native mangrove oyster species of the genus Crassostrea in Brazil is a recurring issue for specialists. Studies have recognized the presence of two species in the littoral zone: ...C. rhizophorae and C. gasar. However, other names may be used, such as C. mangle for C. rhizophorae and C. brasiliana or C. tulipa for C.gasar. As in most oyster taxonomic studies, their identification requires genetic evaluation for the precise determination of taxa. Moreover, previous revisions have proposed some morphological traits by which each species could be precisely identified, leading to a series of debates about the best model for species identity. The aim of this study was to apply an integrative taxonomic approach to native Crassostrea mangrove oyster species on the Brazilian coast to assert the correct species names, delimitations, and concise descriptions. Molecular tracing of cultivated specimens, along with wild specimens of Crassostrea collected from the Brazilian coast, was used to confirm the morphological identity of the taxa. The wild specimens were tentatively identified as either C. gasar or C. rhizophorae based on previous morphological revisions. PCR-RFLP and DNA analyses of the mitochondrial 16S gene mitochondrial rDNA from wild specimens were used to confirm taxa and re-evaluate morphological boundaries and descriptions of the species. We confirmed two patterns in the RFLP and sequence analyses: C. gasar and C. rhizophorae. Conchological and anatomical evaluations of 1006 identified Crassostrea specimens confirmed the inherent polymorphism between the native species, preventing reliable identification of the species by morphology alone. A clear exception, however, is found for specimens whose shell height is greater than 110 mm with internal view of white-colored valves and without an umbonal cavity, fitting the description of C. paraibanensis, which belongs to C. gasar. C. brasiliana and C. mangle are synonyms of C. gasar and C. rhizophorae, respectively. C. tulipa represents a species disconnected from any described mangrove oyster species from Atlantic seas. Conchological and anatomical descriptions of both species were improved to include the variability encountered.
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