Mitochondrial DNA phylogeny of the family cichlidae: monophyly and fast molecular evolution of the neotropical assemblage

Abstract. A mitochondrial DNA (mtDNA) phylogeny of cichlid fish is presented for the most taxonomically inclusive data set compiled to date (64 taxa). 16S rDNA data establish with confidence relationships among major lineages of cichlids, with a general pattern congruent with previous morphological studies and less inclusive molecular phylogenies based on nuclear genes. Cichlids from Madagascar and India are the most basal groups of the family Cichlidae and sister to African–Neotropical cichlids. The cichlid phylogeny suggests drift-vicariance events, consistent with the fragmentation of Gondwana, to explain current biogeographic distributions. Important phylogenetic findings include the placement of the controversial genus Heterochromis basal among African cichlids, the South American genus Retroculus as th

Phylogeny of the Serrasalmidae (Characiformes) based on mitochondrial DNA sequences

Abstract Previous studies based on DNA sequences of mitochondrial (mt) rRNA genes showed three main groups within the subfamily Serrasalminae: (1) a "pacu" clade of herbivores (Colossoma, Mylossoma, Piaractus); (2) the "Myleus" clade (Myleus, Mylesinus, Tometes, Ossubtus); and (3) the "piranha" clade (Serrasalmus, Pygocentrus, Pygopristis, Pristobrycon, Catoprion, Metynnis). The genus Acnodon was placed as the sister taxon of clade (2+3). However, poor resolution within each clade was obtained due to low levels of variation among rRNA gene sequences. Complete sequences of the hypervariable mtDNA control region for a total of 45 taxa, and additional sequences of 12S and 16S rRNA from a total of 74 taxa representing all genera in the family are now presented to address intragroup relationships. Control region sequences of several serrasalmid species exhibit tandem repeats of short motifs (12 to 33 bp) in the 3' end of this region, accounting for substantial length variation. Bayesian inference and maximum parsimony analyses of these sequences identify the same groupings as before and provide further evidence to support the following observations: (a) Serrasalmus gouldingi and species of Pristobrycon (non-striolatus) form a monophyletic group that is the sister group to other species of Serrasalmus and Pygocentrus; (b) Catoprion, Pygopristis, and Pristobrycon striolatus form a well supported clade, sister to the group described above; (c) some taxa assigned to the genus Myloplus (M. asterias, M tiete, M ternetzi, and M rubripinnis) form a well supported group whereas other Myloplus species remain with uncertain affinities (d) Mylesinus, Tometes and Myleus setiger form a monophyletic group

Automatic Generators for a Family of Matrix Multiplication Routines with Apache TVM

We explore the utilization of the Apache TVM open source framework to automatically generate a family of algorithms that follow the approach taken by popular linear algebra libraries, such as GotoBLAS2, BLIS and OpenBLAS, in order to obtain high-performance blocked formulations of the general matrix multiplication (GEMM). % In addition, we fully automatize the generation process, by also leveraging the Apache TVM framework to derive a complete variety of the processor-specific micro-kernels for GEMM. This is in contrast with the convention in high performance libraries, which hand-encode a single micro-kernel per architecture using Assembly code. % In global, the combination of our TVM-generated blocked algorithms and micro-kernels for GEMM 1)~improves portability, maintainability and, globally, streamlines the software life cycle; 2)~provides high flexibility to easily tailor and optimize the solution to different data types, processor architectures, and matrix operand shapes, yielding performance on a par (or even superior for specific matrix shapes) with that of hand-tuned libraries; and 3)~features a small memory footprint.Comment: 35 pages, 22 figures. Submitted to ACM TOM

Semiconductor Porous Hydrogen-Bonded Organic Frameworks Based on Tetrathiafulvalene Derivatives

Herein, we report on the use of tetrathiavulvalene-tetrabenzoic acid, H4TTFTB, to engender semiconductivity in porous hydrogen-bonded organic frameworks (HOFs). By tuning the synthetic conditions, three different polymorphs have been obtained, denoted MUV-20a, MUV-20b, and MUV-21, all of them presenting open structures (22, 15, and 27%, respectively) and suitable TTF stacking for efficient orbital overlap. Whereas MUV-21 collapses during the activation process, MUV-20a and MUV-20b offer high stability evacuation, with a CO2 sorption capacity of 1.91 and 1.71 mmol g-1, respectively, at 10 °C and 6 bar. Interestingly, both MUV-20a and MUV-20b present a zwitterionic character with a positively charged TTF core and a negatively charged carboxylate group. First-principles calculations predict the emergence of remarkable charge transport by means of a through-space hopping mechanism fostered by an efficient TTF π-π stacking and the spontaneous formation of persistent charge carriers in the form of radical TTF¿+ units. Transport measurements confirm the efficient charge transport in zwitterionic MUV-20a and MUV-20b with no need for postsynthetic treatment (e.g., electrochemical oxidation or doping), demonstrating the semiconductor nature of these HOFs with record experimental conductivities of 6.07 × 10-7 (MUV-20a) and 1.35 × 10-6 S cm-1 (MUV-20b)

Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling

<p>Abstract</p> <p>Background</p> <p>With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity.</p> <p>Results</p> <p>In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered <it>incertae sedis </it>in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses.</p> <p>Conclusion</p> <p>A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance across the Neotropics and portions of Africa.</p

Estrategias para la búsqueda de bacterias degradadoras de atrazina en la laguna salada de Pétrola (SE Albacete)

El humedal salino de Pétrola, situado en un ambiente semiárido en el sureste de la provincia de Albacete (España), constituye la zona de descarga de una cuenca endorreica de alrededor de 42 km2. La laguna está sometida a múltiples entradas de contaminación derivadas de actuaciones antrópicas, originando que las condiciones biológicas y físico-químicas de partida de la masa de agua hayan sido gravemente modificadas. La elevada salinidad del sistema (123.000 μS/cm, noviembre 2010) da lugar a un ambiente extremo que propicia condiciones exclusivas capaces de albergar ciertos procesos redox mediados por extremófilos adaptados. Estos microorganismos pueden ejercer un papel fundamental en la atenuación de la contaminación de origen urbano y agrícola existente. Entre las entradas de contaminantes destacan el nitrato, y la atrazina, un herbicida usado ampliamente en las prácticas agrícolas, y sus metabolitos desetilatrazina y deisopropilatrazina. Las concentraciones de atrazina y sus productos de transformación pueden superan los 100 ng/L. Por ello, el objetivo de este trabajo es la búsqueda de microrganismos extremófilos implicados en la atenuación de contaminantes en la laguna de Pétrola, con especial atención en aquellos que puedan estar biodegradar la atrazina. El primer enfoque para la detección de microorganismos extremófilos, que puedan participar en procesos de biorremediación, ha consistido en un análisis metagenómico. Para ello, se recogieron sedimentos de la laguna en 7 puntos cuyas aguas presentan diferentes características físico-químicas. Se extrajo el ADN genómico bacteriano del sedimento y se sometió al análisis metagenómico mediante secuenciación del gen 16S rRNA, lo que permitió caracterizar las poblaciones bacterianas presentes en la laguna. Como resultado, se ha detectado una gran diversidad de microorganismos extremófilos. Entre ellos, destaca el grupo relacionado con procesos de desnitrificación fototrófica y nitrato-sulfato-reducción. Dentro de este grupo, se ha buscado la presencia de microorganismos relacionados con procesos de degradación de contaminantes, aunque, debido al gran número de datos generados, los resultados todavía se encuentran en proceso de análisis. El segundo enfoque ha consistido en la búsqueda de bacterias degradadoras de atrazina, mediante la amplificación por PCR con cebadores diseñados para la amplificación de los genes involucrados en la ruta de degradación de este contaminante organoclorado (Figura). En este punto, se ha conseguido la amplificación de fragmentos, con un patrón diferente en los distintos sedimentos evaluados, lo cual da idea de los diferentes procesos que se están produciendo en puntos de la laguna sometidos a distintas condiciones ambientales. Los resultados ofrecen información acerca de la presencia de microorganismos extremófilos que pueden participar en procesos de atenuación de contaminantes. Se vislumbra la formación de un complejo sistema simbiótico de degradación en cadena que debe seguir estudiándose en mayor profundidad en futuros trabajos orientados a la biorremediación

The ERK5/NF-κB signaling pathway targets endometrial cancer proliferation and survival

Endometrial cancer (EC) is the most common type of gynecologic cancer in women of developed countries. Despite surgery combined with chemo-/radiotherapy regimens, overall survival of patients with high-risk EC tumors is poor, indicating a need for novel therapies. The MEK5-ERK5 pathway is activated in response to growth factors and to different stressors, including oxidative stress and cytokines. Previous evidence supports a role for the MEK5-ERK5 pathway in the pathology of several cancers. We investigated the role of ERK5 in EC. In silico analysis of the PanCancer Atlas dataset showed altera- tions in components of the MEK5-ERK5 pathway in 48% of EC patients. Here, we show that ERK5 inhibition or silencing decreased EGF-induced EC cell proliferation, and that genetic deletion of MEK5 resulted in EC impaired proliferation and reduced tumor growth capacity in nude mice. Pharmacologic inhibition or ERK5 silencing impaired NF-kB pathway in EC cells and xenografts. Furthermore, we found a positive correlation between ERK5 and p65/RELA protein levels in human EC tumor samples. Mechanistically, genetic or pharmacologic impairment of ERK5 resulted in downregulation of NEMO/ IKKγ expression, leading to impaired p65/RELA activity and to apoptosis in EC cells and xenografts, which was rescued by NEMO/IKKγ overexpression. Notably, ERK5 inhibition, MEK5 deletion or NF-kB inhibition sensitized EC cells to standard EC chemotherapy (paclitaxel/carboplatin) toxicity, whereas ERK5 inhibition synergized with paclitaxel to reduce tumor xenograft growth in mice. Together, our results suggest that the ERK5-NEMO-NF-κB pathway mediates EC cell prolifera- tion and survival. We propose the ERK5/NF-κB axis as new target for EC treatment.The online version contains supplementary material available at 10.1007/s00018-022-04541-

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genomescale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.Fil: Hughes, Lily C.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Ortí, Guillermo. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Huang, Yu. Beijing Genomics Institute; China. Chinese Academy of Sciences; República de ChinaFil: Sun, Ying. China National Genebank; China. Beijing Genomics Institute; ChinaFil: Baldwin, Carole C.. National Museum of Natural History; Estados UnidosFil: Thompson, Andrew W.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Arcila, Dahiana. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Betancur, Ricardo. National Museum of Natural History; Estados Unidos. Universidad de Puerto Rico, Recinto de Rio Piedras; Puerto RicoFil: Li, Chenhong. Shanghai Ocean University; ChinaFil: Becker, Leandro Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Bellora, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Zhao, Xiaomeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; ChinaFil: Li, Xiaofeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; ChinaFil: Wang, Min. Beijing Genomics Institute; ChinaFil: Fang, Chao. Chinese Academy of Sciences; República de ChinaFil: Xie, Bing. Bgi-shenzhen; ChinaFil: Zhoui, Zhuocheng. China Fisheries Association; ChinaFil: Huang, Hai. Hainan Tropical Ocean University; ChinaFil: Chen, Songlin. Yellow Sea Fisheries Research Institute Chinese Academy Of Fishery Science; ChinaFil: Venkatesh, Byrappa. A-star, Institute Of Molecular And Cell Biology;Fil: Shi, Qiong. Chinese Academy of Sciences; República de Chin

Optimal Data Partitioning and a Test Case for Ray-Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci

Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative partitioning schemes, based on Bayesian and maximum likelihood (ML) criteria, is shown here to produce an optimal number of partitions. We tested this method using sequence data of 10 nuclear genes collected from 52 ray-finned fish (Actinopterygii) and four tetrapods. The concatenated sequences included 7995 nucleotide sites maximally split into 30 partitions defined a priori based on gene and codon position. Our results show that a model based on only 10 partitions defined by cluster analysis performed better than partitioning by both gene and codon position. Alternative data partitioning schemes also are shown to affect the topologies resulting from phylogenetic analysis, especially when Bayesian methods are used, suggesting that overpartitioning may be of major concern. The phylogenetic relationships among the major clades of ray-finned fish were assessed using the best data-partitioning schemes under ML and Bayesian methods. Some significant results include the monophyly of “Holostei” (Amia and Lepisosteus), the sister-group relationships between (1) esociforms and salmoniforms and (2) osmeriforms and stomiiforms, the polyphyly of Perciformes, and a close relationship of cichlids and atherinomorphs

Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data

Rivers and lake systems in the southern cone of South America have been widely influenced by historic glaciations events, carrying important implications on the evolution of aquatic organisms including prompting transitions between marine and freshwater habitats and by triggering hybridization among incipient species via waterway connectivity and stream capture events. Silverside fishes (Odontesthes) in the region comprise a radiation of 19 marine and freshwater species that have been hypothesized on the basis of morphological or mitochondrial DNA data to have either transitioned repeatedly into continental waters from the sea or colonized marine habitats following freshwater diversification. New ddRAD data presented here provide a robust framework to investigate biogeographic history and habitat transitions in Odontesthes. We show that Odontesthes silversides originally diversified in the Pacific but independently colonized the Atlantic three times, producing three independent marine-to-freshwater transitions. Our results also indicate recent introgression of marine mitochondrial haplotypes into two freshwater clades, with more recurring instances of hybridization among Atlantic- vs. Pacific-slope species. In Pacific freshwater drainages, hybridization with a marine species appears to be geographically isolated and may be related to glaciation events. Substantial structural differences of estuarine gradients between these two geographic areas may have influenced the frequency, intensity, and evolutionary effects of hybridization events.Laboratorio de Sistemática y Biología EvolutivaFacultad de Ciencias Naturales y Muse