Biology subjects

Neme, R.

Publications and source records attributed to Neme, R..

6 recordsLinked to original sources

bioRxiv2025

Taxonomic Diversity of Ants (Formicidae) in Forest Fragments of Tropical Dry Forest in Atlantico, Colombia

This study provides the first taxonomic diversity analysis of ants in the department of Atlantico, Colombia, documenting 6.75% of the countrys known ant species, 29.5% of its genera, and 63.3% of its subfamilies. We report the first record of Leptogenys volcanica in the Colombian Caribbean and expand the known distribution of 19 species within Atlantico. Our results show marked differences in species composition among forest fragments. El Morro exhibited the highest taxonomic distinctness (TD), supporting a community composed of more distantly related species. In contrast, Uninorte, an isolated urban fragment, had the lowest TD value, suggesting a more taxonomically clustered community and potentially acting as a diversity sink. Nesting values indicate that El Morro functions as a biodiversity reservoir, while the species composition of Los Charcones appears shaped by past land-use changes. The dominance of Myrmicinae and Formicinae aligns with patterns observed in other tropical dry forests. Although fragmentation was not directly assessed, patterns of alpha, beta, and taxonomic distinctness suggest that isolation and land use may influence community composition. El Morro emerges as a key fragment for regional conservation. Enhancing habitat connectivity could help mitigate biodiversity loss in these fragmented landscapes. This study provides a critical baseline for future research on ant ecology and conservation in the Caribbean region of Colombia.

ecology↗

bioRxiv2024

Unprecedented sighting of coral populations and associated fauna in the High Sedimentation Waters of Puerto Velero, Atlantico, Colombia

The marine coastal zone of Atlantico, Colombia, faces significant anthropogenic impact due to sediment and organic matter from the Magdalena River. This study reports the presence of two distinct coral patches in Puerto Velero, Atlantico, an area previously considered unfavorable for coral growth. Located at depths of 1-6 meters, these patches harbor a variety of marine species, extending the known distribution of 15 species in the Colombian Caribbean. Despite high sedimentation rates, the larger coral colonies show resilience, surviving mass mortality events and diseases. These findings highlight the adaptive capacity of corals in adverse conditions, emphasizing the importance of systematic monitoring and conservation efforts to understand their response to environmental changes and support marine biodiversity in the Colombian Caribbean.

ecology↗

bioRxiv2022

SDRAP for annotating scrambled or rearranged genomes

DNA rearrangements are important in various contexts, such as in vertebrate immunity, and cancer genome instability. The single-celled eukaryote Oxytricha trifallax undergoes massive and reproducible genome rearrangement during post-zygotic development, making it a compelling model organism to study DNA rearrangements. To date, computational tools for the extraction and analysis of rearrangement annotations lack transparency and rely on assumptions that may not hold for all analyzed data, leading to irreproducibility of results and loss of information through data filtering or misrepresentation. An implementation of a procedure for the annotation and analysis of DNA rearrangement as a web application is discussed and tested. The resulting annotations provide an improvement over previous annotations in the following manner. (a) SDRAP achieves more complete precursor-product mappings than previous software (b) the software allows for full transparency of all parameters used during the annotation and therefore facilitates reproducible results, and (c) this parameter transparency makes SDRAP suitable for comparison of genomic data from different sources, including cancer genomes. This work introduces a theoretical framework and software to systematically extract and analyze annotations from pairs of genome assemblies corresponding to precursor and product rearrangement data. The software makes no assumptions about the structure of the rearrangements, and permits the user to select parameters to suit the data.

bioinformatics↗

bioRxiv2022

Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes.

Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax, Tetrahymena thermophila and Paramecium tetraurelia, but only the Oxytricha lineage has a massively scrambled genome whose assembly requires hundreds of thousands of precise DNA joining events. Here we study the emergence of genome complexity by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage. We sequenced, assembled and annotated the germline and somatic genomes of Euplotes woodruffi and the germline genome of Tetmemena sp., and compared their genome rearrangement features to that of the model ciliate Oxytricha trifallax. The germline genome of Tetmemena is as massively scrambled and interrupted as Oxytrichas: 13.6% of its gene loci rearrange via translocations and/or inversions. This study revealed that the earlier-diverged spirotrich, E. woodruffi, also has a scrambled genome, but approximately half as many loci (7.3%) are scrambled, supporting its position as a possible evolutionary intermediate in this lineage, in the process of accumulating complex genome rearrangements. Scrambled loci are more often associated with local duplications, supporting a simple model for the origin of scrambled genes via DNA duplication and decay.

evolutionary biology↗

bioRxiv2020

Transcribed germline-limited coding sequences in Oxytricha trifallax

The germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein coding sequences whose gene expression is terminated by DNA elimination.

genomics↗

bioRxiv2017

Russian Doll Genes and Complex Chromosome Rearrangements in Oytricha trifallax

Ciliates have two different types of nuclei per cell, with one acting as a somatic, transcriptionally active nucleus (macronucleus; abbr. MAC) and another serving as a germline nucleus (micronucleus; abbr. MIC). Furthermore, Oxytricha trifallax undergoes extensive genome rearrangements during sexual conjugation and post-zygotic development of daughter cells. These rearrangements are necessary because the precursor MIC loci are often both fragmented and scrambled, with respect to the corresponding MAC loci. Such genome architectures are remarkably tolerant of encrypted MIC loci, because RNA-guided processes during MAC development reorganize the gene fragments in the correct order to resemble the parental MAC sequence. Here, we describe the germline organization of several nested and highly scrambled genes in Oxytricha trifallax. These include cases with multiple layers of nesting, plus highly interleaved or tangled precursor loci that appear to deviate from previously described patterns. We present mathematical methods to measure the degree of nesting between precursor MIC loci, and revisit a method for a mathematical description of scrambling. After applying these methods to the chromosome rearrangement maps of O. trifallax we describe cases of nested arrangements with up to five layers of embedded genes, as well as the most scrambled loci in O. trifallax.

genomics↗