Biology subjects

Dergam, J. A.

Publications and source records attributed to Dergam, J. A..

6 recordsLinked to original sources

bioRxiv2025

Genomic Insights into Derived Dwarfism and Exudivory in a Genus (Callithrix) of the World's Smallest Anthropoid Monkeys

The primate Callitrichidae family represents the smallest anthropoid primates, which are known to possess dietary specializations for eating viscous plant exudates (exudivory), and as callitrichids Callithrix marmosets push these biological traits to extremes. Using low-coverage whole genome sequencing of Callithrix species, we investigated Callithrix evolutionary history, species genetic diversity, and the genomic basis of derived small body size and exudivory. Our phylogenetic species tree shows that Callithrix likely originated in southeastern Brazil and migrated northward to the semi-arid regions of central and northeastern Brazil. We show that there is greater genetic similarity between smaller and more exudivorous Callithrix species relative to larger and less exudivorous species, and that the genus likely experienced extensive past reticulation. Based on these results, we argue that the Callithrix migration from the Atlantic Forest biome to the relatively more extreme environments of Cerrado/Caatinga biomes progressively reduced body size and increased exudivory specialization in Callithrix marmosets. We also identified species-specific candidate genes under putative positive selection for traits that include body growth, bone development, reproduction, fat metabolism, insulin signaling, and liporegulation. In conclusion, we increased genomic resources for understudied Callithrix species, while providing the most comprehensive overview of marmoset genomic diversity to-date, and identify several candidate genes under positive selection for traits related to small body size and exudivory. Future studies should sample wild marmosets more widely and perform higher-coverage genomic sequencing to better understand how specific genomic variants may impact the evolution of key Callithrix biological traits.

evolutionary biology↗

bioRxiv2021

Genomic Skimming and Nanopore Sequencing Uncover Cryptic Hybridization in One of World's Most Threatened Primates

The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the worlds 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 deficiencies in genomic data for endangered, non-model species such as C. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies of C. aurita and other marmosets.

evolutionary biology↗

bioRxiv2020

Chromosomal Radiation: a model to explain karyotypic diversity in cryptic species

Hypostominae is a subfamily of Loricariidae with great variation in color characters and external morphology. The genus Hypostomus presents the largest number of species ever karyotyped, with Hypostomus ancistroides characterized as a group of cryptic species. In the 15 natural populations of H. ancistroides studied, there are 15 different karyomorphs, with variations in diploid number, sex chromosome systems, and markers, such as C-banding and location of ribosomal cistrons. The objective of this work was to present molecular and chromosomal data of four new populations of Hypostomus ancistroides and to discuss the observed evolutionary trends for this group of a cryptic complex of species. We analyzed specimens from four sampling points in the Tiete, Mogi-Guacu, and Grande river basins, all in the state of Sao Paulo, southeastern Brazil. We performed techniques such as the detection of constitutive heterochromatin and ribosomal sites (5S and 18S), in addition to phylogenetic analyses. All specimens presented 2n=68 chromosomes without supernumerary elements or sex-related heteromorphisms. However, each population has a different karyotype with unique characteristics. The different karyomorphs are a consequence of the presence of Robertsonian rearrangements, such as centric fissions and pericentric inversions, which play an important role in the evolution of Hypostominae. Although variable in relation to the location of constitutive heterochromatin, we observed the presence of banding C in some chromosomes of all karyomorphs, which may indicate the existence of some homology. Another conservative feature is the presence of two pairs of subtelocentric or acrocentric chromosomes carrying 18S rDNA cistrons in the terminal region of the chromosomes. However, we observed the discontinuity of cytogenetic and phylogenetic data, with the formation of different groups (Araras + Indaiatuba and Botucatu + Terra Roxa in cytogenetics, in contrast to Araras + Terra Roxa and Botucatu and Indaiatuba in the phylogeny), suggesting that several derived karyomorphs may be produced from a pluripotent karyomorph as a result of the intrinsic plasticity of the species karyotype. Thus, each new arrangement would be independent in the forms analyzed, as they do not seem to be lineages from the same direct ancestor. Given the above, we believe that the genus Hypostomus continues to be one of the most diverse among the Siluriformes, however, we began to understand a little more about the karyotypic diversity of the group by associating different approaches, such as phylogenetic analyses.

evolutionary biology↗

bioRxiv2020

Mitogenomic Phylogeny of Callithrix with Special Focus on Human Transferred Taxa

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 complete sequence and organization of the C. aurita mitogenome. Phylogenetic analyses showed that C. aurita was the first to diverge within Callithrix 3.54 million years ago (Ma), while C. jacchus and C. penicillata lineages diverged most recently 0.5 Ma as sister clades. MtDNA clades of C. aurita, C. geoffroyi, and C. penicillata show intraspecific geographic structure, but C. penicillata clades appear polyphyletic. Hybrids, which were identified by phenotype, possessed mainly C. penicillata or C. jacchus mtDNA haplotypes. The biogeographic origins of mtDNA haplotypes from hybrid and allochthonous Callithrix were broadly distributed across natural Callithrix ranges. Our phylogenetic results also evidence introgression of C. jacchus mtDNA into C. aurita. ConclusionOur robust Callithrix mitogenome phylogeny shows C. aurita lineages as basal and C. jacchus lineages among the most recent within Callithrix. We provide the first evidence that parental mtDNA lineages of anthropogenic hybrid and allochthonous marmosets are broadly distributed inside and outside of the Atlantic Forest. We also show evidence of cryptic hybridization between allochthonous Callithrix and autochthonous C. aurita. Our results encouragingly show that further development of genomic resources will allow to more clearly elucidate Callithrix evolutionary relationships and understand the dynamics of Callithrix anthropogenic introductions into the Brazilian Atlantic Forest.

genomics↗

bioRxiv2020

Impacts of the Samarco tailing dam collapse on metals and arsenic concentration in freshwater fish muscle from Doce River, southeastern Brazil

On November 2015, Samarco tailings dam in Mariana MG, Brazil, collapsed, releasing 62 million tons of tailings that advanced through 668 km of the Doce River and adjacent floodplain. Although being the worst environmental disaster in Brazil, little is known about consequences to aquatic biota. Here we evaluate the effects of the tailings mudflow on metal and arsenic concentration in fish and how concentration correlates with water and fish characteristics. We quantified semitotal amounts of Ag, Al, As, Cd, Cr, Cu, Fe, Hg, Mn, Ni, Pb and Zn in fish muscle tissue using ICP-MS in 255 individuals (34 species) sampled in unaffected and affected along the Doce River basin. Arsenic and Hg were higher in fish from affected sites, likely due to turbulent mixing of previously sedimented material by the giant tailings wave. Silver and Zn concentrations were higher in unaffected sites. Arsenic concentration in Geophagus brasiliensis decreased with increasing fish weight. Copper and Zn decreased with increasing fish weight considering the whole assembly of fish. The tailings mudflow increased water conductivity and conductivity increased Al concentration in fish, so we expected a larger Al concentration in fishes from affected sites. However, the observed Al concentration in fishes from affected sites was lower than expected by water conductivity. Thus, the tailings mudflow reduced Al uptake or accumulation in fishes. Mercury decreased with increasing water conductivity in both unaffected and affected sites considering all species and in G. brasiliensis alone. Despite the relatively low concentration range of metals and As found in fish, fishes from sites affected by the iron ore tailings mudflow showed higher As and Hg concentration, compared to fishes from unaffected sites. The higher As and Hg in affected sites require further detailed monitoring to ensure safeguards of human health by fishing activity along the Doce River.

ecology↗

bioRxiv2019

The Effects of Host Taxon, Hybridization, and Environment on the Gut Microbiome of Callithrix Marmosets

Mammalian 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 similar across marmosets, Enterobacteriaceae seem to carry out most functional activities in captive host guts. More diverse bacterial taxa seem to perform gut functions in wild marmosets, with Bifidobacterium being important for carbohydrate metabolism. Non-wild marmosets showed gut microbiome composition aspects seen in human gastrointestinal diseases. Thus, captivity may perturb the exudivore gut microbiome, which raises implications for captive exudivore welfare and calls for husbandry modifications.

microbiology↗