Biology subjects

Ramos, T.

Publications and source records attributed to Ramos, T..

4 recordsLinked to original sources

bioRxiv2021

Landscape dynamics promoted the evolution of mega-diversity in South American freshwater fishes

Landscape dynamics and river network rearrangements are widely thought to shape the diversity of Neotropical freshwater fishes, the most species-rich continental vertebrate fauna on Earth. Yet the effects of hydrogeographic changes on fish dispersal and diversification remain poorly understood. Here we integrate an unprecedented occurrence dataset of 4,967 South American freshwater fish species with a species-dense phylogeny to track the evolutionary processes associated with hydrogeographic events over 100 Ma. Net lineage diversification was heterogeneous through time, across space, and among clades. Three abrupt shifts in diversification rates occurred during the Paleogene (between 63 and 23 Ma) in association with major landscape evolution events, and net diversification accelerated from the Miocene to the Recent (c. 20 - 0 Ma). The Western Amazon exhibited the highest rates of in situ diversification and was also the most important source of species dispersing to other regions. All regional biotic interchanges were associated with documented hydrogeographic events and the formation of biogeographic corridors, including Early Miocene (c. 20 Ma) uplift of the Serra do Mar, and Late Miocene (c. 10 Ma) uplift of the Northern Andes and formation of the modern transcontinental Amazon River. Reciprocal mass dispersal of fishes between the Western and Eastern Amazon coincided with this phase of Andean uplift. The Western Amazon has the highest contemporary levels of species richness and phylogenetic endemism. Our results support the hypothesis that landscape dynamics were constrained by the history of drainage basin connections, strongly affecting the assembly and diversification of basin-wide fish faunas. Significance StatementDespite progress in mapping geographic distributions and genealogical relationships, scientists have few clear answers about the origins of South American freshwater fishes, the most diverse vertebrate fauna on Earth. Here we used the most complete dataset of geographic distributions and evolutionary relationships of South American fishes to track how the geological history of river dynamics influenced the origin, extinction, and interchange of species over the past 100 Ma. We found abrupt increases of species origination between 66 and 23 Ma, coinciding with repeated uplifts of the Andes. The Western Amazon region served as source of freshwater fishes to other regions, as a place where species tended to persist over longer historical periods, and where species originations occurred with higher frequency.

ecology↗

bioRxiv2021

Bsh coordinates neuronal fate specification with synaptic connectivity

How our brain generates diverse neuron types that assemble into precise neural circuits remains unclear. Using Drosophila lamina neuron types (L1-L5), we show that the primary homeodomain transcription factor (HDTF) Brain-specific homeobox (Bsh) is initiated in progenitors and maintained in L4/L5 neurons to adulthood. Bsh activates secondary HDTFs Ap (L4) and Pdm3 (L5) and specifies L4/L5 neuronal fates while repressing the HDTF Zfh1 to prevent ectopic L1/L3 fates (control: L1-L5; Bsh-knockdown: L1-L3), thereby generating lamina neuronal diversity for normal visual sensitivity. Subsequently, in L4 neurons, Bsh and Ap function in a feed-forward loop to activate the synapse recognition molecule DIP-{beta}, thereby bridging neuronal fate decision to synaptic connectivity. Expression of a Bsh:Dam, specifically in L4, reveals Bsh binding to the DIP-{beta} locus and additional candidate L4 functional identity genes. We propose that HDTFs function hierarchically to coordinate neuronal molecular identity, circuit formation, and function. Hierarchical HDTFs may represent a conserved mechanism for linking neuronal diversity to circuit assembly and function.

developmental biology↗

bioRxiv2020

RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction

Non-coding RNAs (ncRNAs) are important players in the cellular regulation of organisms from different kingdoms. One of the key steps in ncRNAs research is the ability to distinguish coding/non-coding sequences. We applied 7 machine learning algorithms (Naive Bayes, SVM, KNN, Random Forest, XGBoost, ANN and DL) through 15 model organisms from different evolutionary branches. Then, we created a stand-alone and web server tool (RNAmining) to distinguish coding and noncoding sequences, selecting the algorithm with the best performance (XGBoost). Firstly, we used coding/non-coding sequences downloaded from Ensembl (April 14th, 2020). Then, coding/non-coding sequences were balanced, had their tri-nucleotides counts analysed and we performed a normalization by the sequence length. Thus, in total we built 180 models. All the machine learning algorithms tests were performed using 10-folds cross-validation and we selected the algorithm with the best results (XGBoost) to implement at RNAmining. Best F1-scores ranged from 97.56% to 99.57% depending on the organism. Moreover, we produced a benchmarking with other tools already in literature (CPAT, CPC2, RNAcon and Transdecoder) and our results outperformed them, opening opportunities for the development of RNAmining, which is freely available at https://rnamining.integrativebioinformatics.me/.

bioinformatics↗

bioRxiv2020

A bacterial tragedy of the commons that masks the actual frequency of mutants

The frequency of mutants in a population is central to the understanding of evolution. Mutant frequency is usually assessed by plating a bacterial culture on selective medium in which only specific rare mutants can grow, assuming that all mutant cells present on the plate are able to form colonies. Here we show an exception to this rule. Wild-type Escherichia coli cells are unable to grow with glycerol-2-phosphate (G2P) as a carbon source. In contrast, PHO-constitutive mutants can hydrolyse G2P to glycerol and form colonies on plates having G2P as their sole carbon source. However, the frequency of PHO-constitutive colonies on the selective plate is exceptionally low. Here we show that such mutations occur at a relatively high rate, but the growth of the existing mutants is inhibited due to a competition with the surrounding wild-type cells for the limited amounts of glycerol produced by the mutants. This scenario in which neither the wild-type nor the majority of the mutants are able to grow constitutes an unavoidable case of the tragedy of the commons. Evidence shows that the few mutants that do form colonies derive from micro-clusters of mutants on the selective plate. In addition, a mathematical model describes the fate of the wild-type and mutant populations on the selective plate.

genetics↗