Biology subjects

Hrbek, T.

Publications and source records attributed to Hrbek, T..

11 recordsLinked to original sources

bioRxiv2026

Historical biogeography and population genetic structure of the giant gilded catfish (Brachyplatystoma rousseauxii): expanding Humboldtian connectivity routes between the Orinoco and Amazon River basins

Understanding the evolutionary history of species within a geographic context is key to historical biogeography, as it reveals how geological and climatic changes shaped biodiversity. This is especially important in ecologically significant regions like the Amazon and Orinoco basins. Together, they host the worlds greatest freshwater fish diversity ([~]3,500 species), sharing a common but not yet fully understood evolutionary history. The gilded catfish (Brachyplatystoma rousseauxii), an ancient species widely distributed as a metapopulation in Neotropics, is an important model for studying past connectivity, divergence, and historical processes shaping fish diversity between these basins. This study analyzed the genetic structure, connectivity routes, and demographic history of B. rousseauxii using nuclear (microsatellite and ddRADseq) and mitochondrial DNA. Population structure analyses and coalescent models indicate that B. rousseauxii populations from the Orinoco and Amazon basins are genetically distinct, with no evidence of current gene flow. However, our results support the occurrence of a possible secondary contact event after the divergence, with the Boa Vista population retaining the genetic signal of this process. The ancestral population split occurred at the Rupununi Portal around 2.54 Ma (ddRAD) or 1.31 Ma (mtDNA). Then, the species colonized the Branco and Orinoco Rivers [~]1.90 Ma (ddRAD) or 0.6 Ma (mtDNA), rapidly expanding in the Orinoco (>1.3 or >0.29 Ma), while colonization of the Amazon from the Branco River was more recent ([≤]1.0 or [≤]0.15 Ma). Population expansion signal was detected in the Orinoco ([~]0.20 Ma), whereas the Amazon remained stable. Our findings suggest that the rise of the Vaupes Arch in the Late Miocene does not explain the observed genetic divergence. Likewise, the Casiquiare Canal and Japura-Guaviare headwaters are not connectivity routes between basins. Instead, the Rupununi Portal, including the recent capture of the Branco River by the Negro River, was the last point of connection and played a key role in shaping B. rousseauxiis distribution. These findings provide insights into Neotropical fish biogeography and the historical configuration of the Orinoco and Amazon basins.

evolutionary biology↗

bioRxiv2025

Assessing fish diversity in the Amazon: The impact of primers and reference libraries in eDNA surveys

Selecting primers for DNA amplification poses a challenge in environmental DNA (eDNA) studies, particularly in biodiverse tropical ecosystems. Researchers must balance taxonomic coverage, primer specificity, and study feasibility when choosing between a single primer pair and multiple primer pairs. Empirical tests comparing these strategies are essential for improving eDNA protocols, enhancing the detection of aquatic biodiversity, and supporting conservation and environmental monitoring efforts. This study aimed to evaluate how different approaches affect the specificity and efficiency of detecting fish species in eDNA samples from the Teles Pires River basin. We (1) synthesized modified versions of primers commonly used in ichthyofaunal surveys; (2) compared the results generated by these modified primers with the standard primer versions; and (3) evaluated the species detection using two reference sequence databases: a global taxonomic database (GenBank) and a locally constructed taxonomic database containing samples of fish species previously collected in situ. The 12S-V5_mod primers detected the most fish species across the databases (67, 104, and 130 in the Midori2, Local, and joint databases, respectively), followed by the MiFish_mod primers, which detected 47, 101, and 114 species. Finally, the MiFish primers detected 39, 73, and 78 species. The 12S-V5_mod primers also had lower taxonomic specificity of fish species and amplified a broader range of vertebrate taxa than the MiFish_mod primers. The modified primers outperformed the MiFish primers, and detectability nearly doubled when the Local reference database was used. These results speak to the critical need for constructing reference databases of regional biodiversity, and the need to incorporate multiple primer pairs in eDNA studies.

genetics↗

bioRxiv2025

First Comprehensive Examination of the Molecular Phylogenetics of Saki Monkeys, Genus Pithecia Desmarest, 1804, Reveals an Unexpectedly Low Taxonomic Diversity

Saki monkeys (Pithecia) are found exclusively in the Amazon, ranging from the Guiana Shield in the east to the Andean foothills in the west. The taxonomy of this genus is complex due to indeterminate type localities, numerous synonyms, sexual dichromatism and considerable geographical diversity in coat colour patterns. Previous assessments have indicated two to four species and a variable few subspecies based on morphological analyses of museum specimens. Just two species have been consistently recognised--Pithecia pithecia and Pithecia monachus. This study presents the first comprehensive molecular phylogeny of the genus, using mitochondrial cytochrome b sequences from 137 individuals across their range and a ddRADseq genomic analysis on 34 individuals. The phylogenetic results revealed three main clades: (1) Guiana Shield sakis, (2) Sedimentary Basin and Brazilian Shield sakis, and (3) a basal P. albicans south of the Rio Solimoes. The ddRADseq data further clarified species boundaries and relationships, identifying six distinct species: P. chrysocephala and P. pithecia sensu Hershkovitz (1987) on the Guiana Shield; P. albicans in central Amazonia south of the Rio Solimoes; P. monachus in western Amazonia; P. irrorata between the rios Purus, Tapajos, and Juruena; and P. vanzolinii in a limited area east of the Rio Jurua.

zoology↗

bioRxiv2025

The genomic landscape of spider monkeys and northern muriquis from a conservation perspective

BackgroundMost populations of spider monkeys (Ateles) and muriquis (Brachyteles), two Neotropical primate genera, are under severe anthropogenic threats. Yet, taxon-wide population-level studies leveraging their degree of endangerment linked to their genetic diversity patterns and demographic history are lacking. To properly address this, there is a need to expand from morphological and genetic marker-based studies. ResultsWe generated high-coverage genome sequencing for 58 individuals sampled across 8 Atelidae species, in the first population-wide study of all extant spider monkey species, in the wild and captivity, alongside northern muriquis (Brachyteles hypoxanthus). Additionally, we present a high-contiguity reference genome for Ateles hybridus. Here, we observe the overall levels of genetic diversity and genetic load of the analyzed populations do not align to their IUCN endangerment category. Moreover, we show that in the wild, genetic load is overall higher compared to the captive populations analyzed. Then, we depict two main trans and cis-Andean sister clades in Ateles, and further structure and dynamics outlined by the Madeira River in the latter clade. Lastly, we find that genes in highly divergent regions between Ateles and B. hypoxanthus are involved in central nervous system development and photorreception. ConclusionsOur study shows i) the lack of concordance between the genetic diversity levels and extinction risk of these populations, suggestive of recent and strong external drivers; ii) increased genetic load in the wild in contrast to effective captive management, indicating mostly past demographic events; iii) structure and dynamics in spider monkeys that agrees with common biogeographical patterns and iv) genetic divergence between Ateles and Brachyteles potentially linked to distinct environmental light levels.

genomics↗

bioRxiv2023

Whole genome approach to the structure and dynamics of Cacajao wild populations

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into bald and black uakaris, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of uakari populations. Beyond increasing their representation, with this work we explored the effects of the Amazon rainforests dynamism on platyrrhine species.

evolutionary biology↗

bioRxiv2023

The impact of Quaternary Amazonian river dynamics on patterns and process of diversification in uakari monkeys (genus Cacajao)

AimWestern Amazonia is a region that underwent several landscape changes during the Quaternary. While Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of the Amazonia biota. Here we test how river rearrangements in western Amazonia influenced the evolutionary history of uakari monkeys, a primate group most associated with seasonally flooded forests in western Amazonia. LocationWestern Amazonia TaxonThe uakari monkey (genus Cacajao) MethodsWe performed a continuous phylogeographic analysis using 77 cytochrome b sequences and used digital elevation models to identify the role of landscape and riverscape characteristics in the geographic distribution of Cacajao. Finally, we used genome-wide SNPs variation (ddRADseq) to investigate population structure, gene flow and demographic history in three Cacajao species that were impacted by river rearrangements. ResultsOur continuous phylogeographical reconstruction points that the ancestral Cacajao lineage occupied the flooded forests of the Solimoes River at [~]1.7 Mya, and descendant lineages dispersed throughout western Amazonia more recently. We identified gene flow among both black and bald-headed uakari populations, even across rivers considered barriers (e.g., the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure in Cacajao. The demographic analysis indicates that C. calvus, C. amuna, and C. rubicundus went through a population decline in the last 70 Kya and have a low effective population size. Main conclusionOur results support that the river rearrangements have shaped the geographic distribution and divergence of recently diverged Cacajao lineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated some Cacajao populations in floodplain areas. Our study also suggests that these events led to the recent population decline in species with a restricted geographic distribution.

evolutionary biology↗

bioRxiv2023

Genomics resolves historical uncertainties on phylogenetics and accommodates the systematics of marmosets and Goeldi's monkey (Primates: Platyrrhini)

Marmosets, with a total of 24 species classified into four genera (Callithrix, Cebuella, Mico and Callibella), are the smallest of the anthropoids and one of the most diverse and widespread groups of primates in South America. In contrast, the Goeldis monkey (Callimico goeldii) is represented by a single species of black, small, fungi-eating primates, endemic to west Amazonia. The phylogenetic relationships of marmoset genera and the phylogenetic position of Goeldis monkey, and consequently their systematics, remain uncertain and subject to debate because earlier studies revealed incongruent conclusions. Here we tackle this issue by first reviewing the systematics and the history of phylogenetic studies of marmosets and Goeldis monkey. We then explore their phylogenetic relationships by reconstructing a time-calibrated phylogeny using a genome-wide sampling of all lineages of marmosets, tamarins, Goeldis monkey, lion tamarins, capuchins, and squirrel monkeys. Our results clearly demonstrate that historical disagreements on phylogenetics and systematics of marmosets are due to incomplete lineage sorting, low phylogenetic signal of morphological and ecological characters, and low sampling at the DNA level. We show that Goeldis monkey is a sister lineage to marmosets and suggest that past incongruencies between studies on its phylogenetics and systematics are due to homoplasy of morphological characters traditionally used to infer primate relationships. Accordingly, we accommodate a genus-level classification for marmosets based on a fully-resolved phylogeny and multiple biological traits, redefine the genus Mico, update the definitions of Callibella, Callithrix, and Cebuella, and sediment the family-level classification of Goeldis monkey.

zoology↗

bioRxiv2023

A dataset of new occurrence records of primates from the arc of deforestation, Brazil

The arc of deforestation, located between the southern Amazonia and the northern Cerrado of Brazil, is a top deforestation frontier worldwide. The high deforestation rates in this region are caused by human activities and threatens a rich diversity of primates that are still poorly-known and therefore investments into taxonomy and distribution research are urgent to support science-driven conservation of primates of this region. Here we present a dataset of 192 new occurrence records for 22 species of primates of the genera Alouatta, Aotus, Ateles, Cebus, Chiropotes, Lagothrix, Leontocebus, Pithecia, Plecturocebus, Saimiri, and Sapajus, collected during 10 field expeditions carried out across the arc of deforestation between 2015-2018. Based on these occurrence records we extend the ranges of Saimiri collinsi, Sapajus apella, and Alouatta puruensis, identify a potential hybridization zone between A. puruensis and Alouatta discolor, and redefine the range of Plecturocebus moloch. Moreover, this dataset is a useful source of information otherwise scarce for further researches on species distributions and habitat use patterns, on the effect of environmental variables on such patterns, for estimating population sizes, evaluating habitat suitability, for predicting effects of climate change, habitat loss and fragmentation on populations, and for assessing species extinction risks. The ranges of primates endemic to the arc of deforestation, with a few exceptions, are fragile hypotheses, which hampers the establishment of effective conservation efforts for species increasingly threatened on a global deforestation frontier.

zoology↗

bioRxiv2023

A global catalog of whole-genome diversity from 233 primate species

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology, and is urgent given severe threats these species are facing. Here, we present high coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human-specific. This study will open a wide range of research avenues for future primate genomic research. One-Sentence SummaryThe whole genome sequences of 233 primate species provide insight into the determinants of genetic diversity, phylogenomics, and human uniqueness.

genomics↗

bioRxiv2022

Landscape configurations determining the genetic structure of the Yellow-Spotted Amazon River Turtle (Podocnemis unifilis) in Brazilian Amazonia

ContextWaterfalls and rapids of Amazon basin have been suggested as causing the speciation and genetic structure of many freshwater species, including turtles. The species behavior affects the way waterfalls and rapids limit gene flow. The Yellow-spotted River Turtle (Podocnemis unifilis), a widely distributed and endangered Amazonian turtle, does not show the habit to migrate long distances for breeding or eating, but has a complex geographic pattern of genetic variation. ObjectivesHere, we investigate isolation by distance and by resistance of P. unifilis. We analyzed if the species ecological niche and waterfalls explain the genetic distance in Brazilian Amazonia. MethodsWe evaluated the P. unifilis spatial distribution of genetic variability and diversity using the control region of mitochondrial DNA. We tested the hypotheses of isolation either by distance and resistance through an integrative approach using genetic, geographic, and ecological data. We created a resistance matrix using species niche modeling. We compared the explanation power of geographical distance (both linear and in-water distance) and resistance distance on genetic distance ({Phi}ST fixation index) using multiple regressions and Mantel tests. ResultsWe found a high genetic diversity and pattern of genetic structure proved to be geographically complex. The population structure followed some watersheds but also showed structuring within different rivers. We found that landscape resistance better explains genetic distance than linear and in-water distance. ConclusionsThe resistance of the landscape influences the displacement of individuals by aquatic, vegetational, biological, and geomorphological variables, and efforts to species conservation need to be applied throughout its distribution considering landscape genetics.

molecular biology↗

bioRxiv2021

Using ddRAD-seq phylogeography to test for genetic effects of headwater river capture in suckermouth armored catfish (Loricariidae: Hypostomus) from the central Brazilian Shield

River capture is a geological process of potentially great importance in shaping the genetic diversity, distributions, and community composition of freshwater taxa. Using phylogeographic analyses of ddRAD-seq data from suckermouth armored catfish (Hypostomus sp. 2) populations, we tested for predicted genetic effects of headwater river capture events in central Brazil, previously supported by geological and community ecological data. We analyzed 227 ddRAD tags (3829 SNP loci) across 42 samples. Molecular results strongly supported six Hypostomus genetic clusters/lineages, with the deepest divergence [~]1.25 million years ago in the early Pleistocene between a clade from the Upper Parana and Upper Sao Francisco river basins versus all other lineages. Consistent with the Parana Capture Hypothesis, several lines of evidence supported mid-Pleistocene colonization and vicariant isolation of Hypostomus populations from an ancestral Upper Parana population, including: (1) significant phylogeographic structure, with predicted phylogenetic patterns, (2) higher Parana lineage diversity, (3) ancestral geographic locations reconstructed in the Parana basin, and (4) non-random interdrainage dispersal and vicariance events, indicating river captures primarily into the Tocantins and Upper Sao Francisco basins c. [~]220,000-145,500 years ago. Phylogeographic inference was complicated by lack of lineage monophyly across loci and lineages distributed in multiple basins, the latter of which lent support to the non-mutually exclusive Frequent Interdrainage Dispersal Hypothesis. However, species tree and demographic modeling results suggested these were artefacts of incomplete sorting of alleles in large ancestral populations over a geologically recent timeframe of divergence. Qualitative and quantitative sensitivity analyses demonstrated that our downstream genetic results were robust to effects of varying ddRAD-seq assembly parameters, which heavily influenced the number of output loci. We predict that codistributed freshwater taxa in Central Brazil may not exhibit phylogeographic patterns similar to Hypostomus sp. 2 due to complex patterns of superimposed river capture events, or if smaller ancestral population sizes have allowed more complete lineage sorting in other taxa.

evolutionary biology↗