Despite the considerable morbidity and mortality of Yellow fever virus (YFV) infections in Brazil... more Despite the considerable morbidity and mortality of Yellow fever virus (YFV) infections in Brazil, as well as its widespread presence in non-human primate host, our understanding of disease outbreaks is hampered by limited viral genomic data. Determining the timing and spatial corridors of YFV spread, as well as the geographic hotspots that link the endemic north of the country with epidemic extra-Amazonian regions, are central to predicting and preventing future outbreak events and epidemics. Here, we tracked the recent spread of the virus by integrating genome sequences of new YFV infections sampled from infected non-human primates and humans with both epidemiological and vector data. Through a combination of phylogenetic and epidemiological models we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticatedAedes aegyptiwas able to capture the seasonality of reported human infections. Spat...
The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered p... more The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address...
Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully r... more Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have been introduced into the southeastern Brazilian Atlantic Forest by the pet trade. There, these species hybridize with each other and endangered, native congeners. We aimed here to reconstruct a robust Callithrix phylogeny and divergence time estimates, and identify the biogeographic origins of autochthonous and allochthonous Callithrix mitogenome lineages. We sequenced 49 mitogenomes from four species (C. aurita, C. geoffroyi, C. jacchus, C. penicillata) and anthropogenic hybrids (C. aurita x Callithrix sp., C. penicillata x C. jacchus, Callithrix sp. x Callithrix sp., C. penicillata x C. geoffroyi) via Sanger and whole genome sequencing. We combined these data with previously published Callithrix mitogenomes to analyze five Callithrix species in total.ResultsWe report the co...
Zoonotic pathogens that cause leprosy (Mycobacterium leprae) and tuberculosis (Mycobacterium tube... more Zoonotic pathogens that cause leprosy (Mycobacterium leprae) and tuberculosis (Mycobacterium tuberculosis complex, MTBC) continue to impact modern human populations. Therefore, methods able to survey mycobacterial infection in potential animal hosts are necessary for proper evaluation of human exposure threats. Here we tested for mycobacterialspecific single-and multi-copy loci using qPCR. In a trial study in which armadillos were artificially infected with M. leprae, these techniques were specific and sensitive to pathogen detection, while more traditional ELISAs were only specific. These assays were then employed in a case study to detect M. leprae as well as MTBC in wild marmosets. All marmosets were negative for M. leprae DNA, but 14 were positive for the mycobacterial rpoB gene assay. Targeted capture and sequencing of rpoB and other MTBC genes validated the presence of mycobacterial DNA in these samples and revealed that qPCR is useful for identifying mycobacterial-infected animal hosts.
Animal hybridization is well documented, but evolutionary outcomes and conservation priorities of... more Animal hybridization is well documented, but evolutionary outcomes and conservation priorities often differ for natural and anthropogenic hybrids. Among primates, an order with many endangered species, the two contexts can be hard to disentangle from one another, which carries important conservation implications. Callithrix marmosets give us a unique glimpse of genetic hybridization effects under distinct natural and human-induced contexts. Here, we use a 44 autosomal microsatellite marker panel to examine genome-wide admixture levels and introgression at a natural C. jacchus and C. penicillata species border along the São Francisco River in NE Brazil and in an area of Rio de Janeiro state where humans introduced these species exotically. Additionally, we describe for the first time autosomal genetic diversity in wild C. penicillata and expand previous C. jacchus genetic data. We characterize admixture within the natural zone as bimodal where hybrid ancestry is biased toward one parental species or the other. We also show evidence that São Francisco River islands are gateways for bidirectional gene flow across the species border. In the anthropogenic zone, marmosets essentially form a hybrid swarm with intermediate levels of admixture, likely from the absence of strong physical barriers to interspecific breeding. Our data show that while hybridization can occur naturally, the presence of physical, even if leaky, barriers to hybridization is important for maintaining species genetic integrity. Thus, we suggest further study of hybridization under different contexts to set well informed conservation guidelines for hybrid populations that often fit somewhere between "natural" and "man-made."
ABSTRACTHybridization is continually documented in primates, but effects of natural and anthropog... more ABSTRACTHybridization is continually documented in primates, but effects of natural and anthropogenic hybridization on biodiversity are still unclear and differentiating between these contexts remains challenging in regards to primate evolution and conservation. Here, we examine hybridization effects on the mitochondrial DNA (mtDNA) control region of Callithrix marmosets, which provide a unique glimpse into interspecific mating under distinct anthropogenic and natural conditions. DNA was sampled from 40 marmosets along a 50‐km transect from a previously uncharacterized hybrid zone in NE Brazil between the ranges of Callithrix jacchus and Callithrix penicillata. DNA was also collected from 46 marmosets along a 30‐km transect in a hybrid zone in Rio de Janeiro state, Brazil, where exotic marmosets appeared in the 1980s. Combining Callithrix DNA sampled inside and outside of these hybrid zones, phylogenetic and network analyses show C. jacchus and C. penicillata being parental species ...
This study investigated rickettsial infection in Amblyomma auricularium ticks from the state of P... more This study investigated rickettsial infection in Amblyomma auricularium ticks from the state of Pernambuco, northeastern Brazil. An engorged female of A. auricularium collected from a skunk (Conepatus semistriatus) was sent alive to the laboratory, where the female was found through molecular analysis to be infected by Rickettsia amblyommii. This engorged female oviposited, and its offspring was reared through three consecutive generations, always using tick-naïve rabbits to feed the ticks. PCR performed on five egg pools, 10 larvae, 10 nymphs, and 10 adults of each of the three generations always yielded rickettsial DNA, indicating maintenance of rickettsial infection in the ticks by transstadial and transovarial passages. DNA sequences of random PCR products from eggs, larvae, nymphs, and adults were identified as R. amblyommii. All infested rabbits seroconverted to R. amblyommii antigens at the 21 st day after infestation, indicating that larvae, nymphs, and adults transmitted R. amblyommii through parasitism. However, no infested rabbit presented fever or any clinical alteration during the experimental period. Rickettsiae were successfully isolated from the two A. auricularium females, and the isolates were established in Vero cell culture. Molecular characterization of the isolates confirmed R. amblyommii by sequencing partial gltA, ompA, and ompB genes. From another sample of 15 A. auricularium adult ticks collected from two armadillos (Euphractus sexcinctus), eight (53.3%) were infected by R. amblyommii. This study reports R. amblyommii infecting the tick A. auricularium for the first time. This is also the first report of rickettsia infecting ticks in the northeastern region of Brazil.
ABSTRACTMammalian captive dietary specialists like folivores are prone to gastrointestinal distre... more ABSTRACTMammalian captive dietary specialists like folivores are prone to gastrointestinal distress and primate dietary specialists suffer the greatest gut microbiome diversity losses in captivity compared to the wild. Marmosets represent another group of dietary specialists, exudivores that eat plant exudates, but whose microbiome remains relatively less studied. The common occurrence of gastrointestinal distress in captive marmosets prompted us to study the Callithrix gut microbiome composition and predictive function through bacterial 16S ribosomal RNA V4 region sequencing. We sampled 59 wild and non-wild Callithrix across four species and their hybrids. Host environment had a stronger effect on the gut microbiome than host taxon. Wild Callithrix gut microbiomes were enriched for Bifidobacterium, which process host-indigestible carbohydrates. Captive marmoset guts were enriched for Enterobacteriaceae, a family containing pathogenic bacteria. While gut microbiome function was simi...
Coffee is one of the most valuable agricultural commodities and ranks second on international tra... more Coffee is one of the most valuable agricultural commodities and ranks second on international trade exchanges. The genus Coffea belongs to the Rubiaceae family which includes other important plants. The genus contains about 100 species but commercial production is based only on two species, Coffea arabica and Coffea canephora that represent about 70 % and 30 % of the total coffee market, respectively. The Brazilian Coffee Genome Project was designed with the objective of making modern genomics resources available to the coffee scientific community, working on different aspects of the coffee production chain. We have single-pass sequenced a total of 214,964 randomly picked clones from 37 cDNA libraries of C. arabica, C. canephora and C. racemosa, representing specific stages of cells and plant development that after trimming resulted in 130,792, 12,381 and 10,566 sequences for each species, respectively. The ESTs clustered into 17,982 clusters and 32,155 singletons. Blast analysis of...
Despite the considerable morbidity and mortality of Yellow fever virus (YFV) infections in Brazil... more Despite the considerable morbidity and mortality of Yellow fever virus (YFV) infections in Brazil, as well as its widespread presence in non-human primate host, our understanding of disease outbreaks is hampered by limited viral genomic data. Determining the timing and spatial corridors of YFV spread, as well as the geographic hotspots that link the endemic north of the country with epidemic extra-Amazonian regions, are central to predicting and preventing future outbreak events and epidemics. Here, we tracked the recent spread of the virus by integrating genome sequences of new YFV infections sampled from infected non-human primates and humans with both epidemiological and vector data. Through a combination of phylogenetic and epidemiological models we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticatedAedes aegyptiwas able to capture the seasonality of reported human infections. Spat...
The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered p... more The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address...
Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully r... more Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have been introduced into the southeastern Brazilian Atlantic Forest by the pet trade. There, these species hybridize with each other and endangered, native congeners. We aimed here to reconstruct a robust Callithrix phylogeny and divergence time estimates, and identify the biogeographic origins of autochthonous and allochthonous Callithrix mitogenome lineages. We sequenced 49 mitogenomes from four species (C. aurita, C. geoffroyi, C. jacchus, C. penicillata) and anthropogenic hybrids (C. aurita x Callithrix sp., C. penicillata x C. jacchus, Callithrix sp. x Callithrix sp., C. penicillata x C. geoffroyi) via Sanger and whole genome sequencing. We combined these data with previously published Callithrix mitogenomes to analyze five Callithrix species in total.ResultsWe report the co...
Zoonotic pathogens that cause leprosy (Mycobacterium leprae) and tuberculosis (Mycobacterium tube... more Zoonotic pathogens that cause leprosy (Mycobacterium leprae) and tuberculosis (Mycobacterium tuberculosis complex, MTBC) continue to impact modern human populations. Therefore, methods able to survey mycobacterial infection in potential animal hosts are necessary for proper evaluation of human exposure threats. Here we tested for mycobacterialspecific single-and multi-copy loci using qPCR. In a trial study in which armadillos were artificially infected with M. leprae, these techniques were specific and sensitive to pathogen detection, while more traditional ELISAs were only specific. These assays were then employed in a case study to detect M. leprae as well as MTBC in wild marmosets. All marmosets were negative for M. leprae DNA, but 14 were positive for the mycobacterial rpoB gene assay. Targeted capture and sequencing of rpoB and other MTBC genes validated the presence of mycobacterial DNA in these samples and revealed that qPCR is useful for identifying mycobacterial-infected animal hosts.
Animal hybridization is well documented, but evolutionary outcomes and conservation priorities of... more Animal hybridization is well documented, but evolutionary outcomes and conservation priorities often differ for natural and anthropogenic hybrids. Among primates, an order with many endangered species, the two contexts can be hard to disentangle from one another, which carries important conservation implications. Callithrix marmosets give us a unique glimpse of genetic hybridization effects under distinct natural and human-induced contexts. Here, we use a 44 autosomal microsatellite marker panel to examine genome-wide admixture levels and introgression at a natural C. jacchus and C. penicillata species border along the São Francisco River in NE Brazil and in an area of Rio de Janeiro state where humans introduced these species exotically. Additionally, we describe for the first time autosomal genetic diversity in wild C. penicillata and expand previous C. jacchus genetic data. We characterize admixture within the natural zone as bimodal where hybrid ancestry is biased toward one parental species or the other. We also show evidence that São Francisco River islands are gateways for bidirectional gene flow across the species border. In the anthropogenic zone, marmosets essentially form a hybrid swarm with intermediate levels of admixture, likely from the absence of strong physical barriers to interspecific breeding. Our data show that while hybridization can occur naturally, the presence of physical, even if leaky, barriers to hybridization is important for maintaining species genetic integrity. Thus, we suggest further study of hybridization under different contexts to set well informed conservation guidelines for hybrid populations that often fit somewhere between "natural" and "man-made."
ABSTRACTHybridization is continually documented in primates, but effects of natural and anthropog... more ABSTRACTHybridization is continually documented in primates, but effects of natural and anthropogenic hybridization on biodiversity are still unclear and differentiating between these contexts remains challenging in regards to primate evolution and conservation. Here, we examine hybridization effects on the mitochondrial DNA (mtDNA) control region of Callithrix marmosets, which provide a unique glimpse into interspecific mating under distinct anthropogenic and natural conditions. DNA was sampled from 40 marmosets along a 50‐km transect from a previously uncharacterized hybrid zone in NE Brazil between the ranges of Callithrix jacchus and Callithrix penicillata. DNA was also collected from 46 marmosets along a 30‐km transect in a hybrid zone in Rio de Janeiro state, Brazil, where exotic marmosets appeared in the 1980s. Combining Callithrix DNA sampled inside and outside of these hybrid zones, phylogenetic and network analyses show C. jacchus and C. penicillata being parental species ...
This study investigated rickettsial infection in Amblyomma auricularium ticks from the state of P... more This study investigated rickettsial infection in Amblyomma auricularium ticks from the state of Pernambuco, northeastern Brazil. An engorged female of A. auricularium collected from a skunk (Conepatus semistriatus) was sent alive to the laboratory, where the female was found through molecular analysis to be infected by Rickettsia amblyommii. This engorged female oviposited, and its offspring was reared through three consecutive generations, always using tick-naïve rabbits to feed the ticks. PCR performed on five egg pools, 10 larvae, 10 nymphs, and 10 adults of each of the three generations always yielded rickettsial DNA, indicating maintenance of rickettsial infection in the ticks by transstadial and transovarial passages. DNA sequences of random PCR products from eggs, larvae, nymphs, and adults were identified as R. amblyommii. All infested rabbits seroconverted to R. amblyommii antigens at the 21 st day after infestation, indicating that larvae, nymphs, and adults transmitted R. amblyommii through parasitism. However, no infested rabbit presented fever or any clinical alteration during the experimental period. Rickettsiae were successfully isolated from the two A. auricularium females, and the isolates were established in Vero cell culture. Molecular characterization of the isolates confirmed R. amblyommii by sequencing partial gltA, ompA, and ompB genes. From another sample of 15 A. auricularium adult ticks collected from two armadillos (Euphractus sexcinctus), eight (53.3%) were infected by R. amblyommii. This study reports R. amblyommii infecting the tick A. auricularium for the first time. This is also the first report of rickettsia infecting ticks in the northeastern region of Brazil.
ABSTRACTMammalian captive dietary specialists like folivores are prone to gastrointestinal distre... more ABSTRACTMammalian captive dietary specialists like folivores are prone to gastrointestinal distress and primate dietary specialists suffer the greatest gut microbiome diversity losses in captivity compared to the wild. Marmosets represent another group of dietary specialists, exudivores that eat plant exudates, but whose microbiome remains relatively less studied. The common occurrence of gastrointestinal distress in captive marmosets prompted us to study the Callithrix gut microbiome composition and predictive function through bacterial 16S ribosomal RNA V4 region sequencing. We sampled 59 wild and non-wild Callithrix across four species and their hybrids. Host environment had a stronger effect on the gut microbiome than host taxon. Wild Callithrix gut microbiomes were enriched for Bifidobacterium, which process host-indigestible carbohydrates. Captive marmoset guts were enriched for Enterobacteriaceae, a family containing pathogenic bacteria. While gut microbiome function was simi...
Coffee is one of the most valuable agricultural commodities and ranks second on international tra... more Coffee is one of the most valuable agricultural commodities and ranks second on international trade exchanges. The genus Coffea belongs to the Rubiaceae family which includes other important plants. The genus contains about 100 species but commercial production is based only on two species, Coffea arabica and Coffea canephora that represent about 70 % and 30 % of the total coffee market, respectively. The Brazilian Coffee Genome Project was designed with the objective of making modern genomics resources available to the coffee scientific community, working on different aspects of the coffee production chain. We have single-pass sequenced a total of 214,964 randomly picked clones from 37 cDNA libraries of C. arabica, C. canephora and C. racemosa, representing specific stages of cells and plant development that after trimming resulted in 130,792, 12,381 and 10,566 sequences for each species, respectively. The ESTs clustered into 17,982 clusters and 32,155 singletons. Blast analysis of...
Uploads
Papers by Luiz Pereira