Revision and analysis of the chromosome variability in the speciose genus Akodon (Rodentia, Sigmodontinae), including new data from Argentina.

Rodentia has a high species number and chromosomal variability. The South American genus Akodon is one of the most speciose muroids, with more than 40 species included in several species groups. Here, we characterize cytogenetically specimens of Akodon from central-western Argentina. Subsequently, we reviewed and analyzed the cytogenetic data for this genus, build a phylogeny and mapped chromosome changes to interpret its evolution. Specimens of A. dolores from central-western Argentina have 2n=42-44/FNa=44 (46, 48) due to a Robertsonian rearrangement. Our data expand the distribution range known for this polymorphism and confirm its geographic structure. Other specimens had 2n=40/FNa=40, representing populations of A. oenos, A. polopi, and A. spegazzinii. All karyotypes have a low amount of heterochromatin, concentrated in centromeres and sex chromosomes, as in other rodents. The complement with 2n=40/FNa=40 is the most frequent in Akodon and is shared by most species in some groups. Chromosome numbers are very diverse. The FNa shows less variability; FNa=42 was recovered as ancestral, excluding A. mimus, which was connected at the base of the Akodon tree and has FNa=44. This indicates a complex chromosome evolution in Akodon, and suggests that reductions and increases in the 2n and FNa evolved independently in some lineages.

Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships.

Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history.

DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina.

Rodents are an important component of South America fauna. Their high diversity has motivated researchers to continually review their taxonomy, genetic diversity, species limits, and phylogenetic relationships. Here, we applied DNA-barcodes for assessing the taxonomic and genetic diversity in the two major lineages of South American rodents: caviomorphs and sigmodontines. We analysed 335 COI barcodes in 34 morphologically determined species from 39 localities along central Andes and arid lands of Argentina. Neighbour-joining and maximum likelihood reconstruction provided clear separation between species. The Barcode Index number and Bayesian Poisson tree processes were used to confirm concordance between sequence clusters and species designations by taxonomy. We found deep divergence within the Phyllotis xanthopygus species complex, with distances up to 13.0% between geographically separated lineages. Minor divergences (3.30% and 2.52%) were found within Abrothrix hirta, and Tympanoctomys barrerae, respectively, with differentiation in their genetic lineages. Also, we documented geographically separated clusters for Akodon spegazzinii and A. oenos with up to 2.3% divergence, but clustering methods failed to distinguish them as different species. Sequence results show a clear barcode gap with a mean intraspecific divergence (0.56%) versus a minimum nearest-neighbour distance averaging (10.1%). Distances between congeneric species varied from 4.1 to 14%, with the exception of two related forms within Euneomys and the sister species Akodon spegazzinii and A. oenos. This study constitutes a substantial contribution to the global barcode reference library. It provides insights into the complex phylogeographic patterns and speciation scenarios in rodents, while highlighting areas that require in-depth taxonomic and integrative research.

Assessment of the quality of the vital registration system for under-5 mortality in Yucatan, Mexico.

INTRODUCTION: Vital registration is an important element in health information systems which can inform policy and strengthen health systems. Mexico has a well-functioning vital registration system; however, there is still room for improvement, especially for deaths of children under 5. This study assesses the quality of the vital registration system in capturing deaths and evaluates the quality of cause of death certification in under-5 deaths in Yucatan, Mexico. METHODS: We collected information on under-5 deaths that occurred in 2015 and 2016 in Yucatan, Mexico. We calculated the Vital Statistics Performance Index (VSPI) to have a general assessment of the vital registration performance. We examined the agreement between vital registration records and medical records at the individual and population levels using the chance-corrected concordance (CCC) and cause-specific mortality fraction (CSMF) accuracy as quality metrics. RESULTS: We identified 966 records from the vital registry for all under-5 deaths, and 390 were linked to medical records of deaths occurring at public hospitals. The Yucatan vital registration system captured 94.8% of the expected under-5 deaths, with an overall VSPI score of 87.2%. Concordance between underlying cause of death listed in the vital registry and the cause determined by the medical record review varied substantially across causes, with a mean overall chance-corrected concordance across causes of 6.9% for neonates and 46.9% for children. Children had the highest concordance for digestive diseases, and neonates had the highest concordance for meningitis/sepsis. At the population level, the CSMF accuracy for identifying the underlying cause listed was 35.3% for neonates and 67.7% for children. CONCLUSIONS: Although the vital registration system has overall good performance, there are still problems in information about causes of death for children under 5 that are related mostly to certification of the causes of death. The accuracy of information can vary substantially across age groups and causes, with causes reported for neonates being generally less reliable than those for older children. Results highlight the need to implement strategies to improve the certification of causes of death in this population.

Evolution of the Largest Mammalian Genome.

The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrerae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared with the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects-including during the evolution of hypersaline dietary tolerance in T. barrerae.

Geographic Variation in Cranial Morphology of the Southern Mountain Cavy, Microcavia australis (Rodentia, Caviidae): Taxonomic Implications, with the Description of a New Species.

Pablo Teta, Ricardo A. Ojeda, Sergio O. Lucero, and Guillermo D'Elía (2017) We analyzed the geographic variation in cranial morphology of the Southern Mountain Cavy, Microcavia australis, throughout of its distributional range. Our analysis allows us to recognize three geographically allopatric morphotypes. These morphotypes differ in the general size and shape of the skull and discrete morphological traits of the zygomatic arch, palate and mesopterygoid fossa. Based on these results, we restrict the name australis to populations distributed in southern Argentina and west-central Andes and the name maenas to the morphotype of northwestern and central Argentina. The third morphotype occurs in the Dry Chaco ecoregion and is described here as a new species.

Karyotypic variation in the Andean rodent Phyllotisxanthopygus (Waterhouse, 1837) (Rodentia, Cricetidae, Sigmodontinae).

Phyllotisxanthopygus (Waterhouse, 1837) is an Andean rodent endemic to South America. Despite its wide geographical distribution in Argentina, few individuals have been studied on the cytogenetic level and only through conventional staining. In this work, chromosome characterization of Argentine samples of this species was performed using solid staining, C-banding and base-specific fluorochromes. Twenty two specimens were analyzed, collected in the provinces of Jujuy, Catamarca, and the north and south of Mendoza. All studied specimens showed 2n=38, having mostly the bi-armed autosomes, metacentric or submetacentric. Fundamental Number varied between 70 and 72. These changes were due to the presence of chromosome heteromorphisms in individuals from southern Mendoza and Jujuy. C-banding revealed pericentromeric blocks of constitutive heterochromatin in most chromosomes. Acrocentric chromosomes involved in heteromorphisms showed high variation in the amount of heterochromatin within and among populations. Additionally, banding with fluorochromes (DAPI and chromomycin A3) revealed homologous localization of AT and GC rich regions among chromosomes of the different populations analyzed. Comparisons among heteromorphic pairs suggested, however, that the variation might be the result of complex chromosome rearrangements, involving possibly amplifications and/or deletions of heterochromatic segments. These results are in accordance with molecular studies that indicate genetic variability within and among the populations of this taxon.