Integrative taxonomy and molecular phylogeny of genus Aplysina (Demospongiae: Verongida) from Mexican Pacific

José Antonio Cruz-Barraza (2012, [Artículo])

Integrative taxonomy provides a major approximation to species delimitation based on integration of different perspectives (e.g. morphology, biochemistry and DNA sequences). The aim of this study was to assess the relationships and boundaries among Eastern Pacific Aplysina species using morphological, biochemical and molecular data. For this, a collection of sponges of the genus Aplysina from the Mexican Pacific was studied on the basis of their morphological, chemical (chitin composition), and molecular markers (mitochondrial COI and nuclear ribosomal rDNA: ITS1-5.8-ITS2). Three morphological species were identified, two of which are new to science. A. clathrata sp. nov. is a yellow to yellow-reddish or -brownish sponge, characterized by external clathrate-like morphology; A. revillagigedi sp. nov. is a lemon yellow to green, cushion-shaped sometimes lobate sponge, characterized by conspicuous oscules, which are slightly elevated and usually linearly distributed on rims; and A. gerardogreeni a known species distributed along the Mexican Pacific coast. Chitin was identified as the main structural component within skeletons of the three species using FTIR, confirming that it is shared among Verongida sponges. Morphological differences were confirmed by DNA sequences from nuclear ITS1-5.8-ITS2. Mitochondrial COI sequences showed extremely low but diagnostic variability for Aplysina revillagigedi sp. nov., thus our results corroborate that COI has limited power for DNA-barcoding of sponges and should be complemented with other markers (e.g. rDNA). Phylogenetic analyses of Aplysina sequences from the Eastern Pacific and Caribbean, resolved two allopatric and reciprocally monophyletic groups for each region. Eastern Pacific species were grouped in general accordance with the taxonomic hypothesis based on morphological characters. An identification key of Eastern Pacific Aplysina species is presented. Our results constitute one of the first approximations to integrative taxonomy, phylogeny and evolutionary biogeography of Eastern Pacific marine sponges; an approach that will significantly contribute to our better understanding of their diversity and evolutionary history. © 2012 Cruz et al.

chitin, genomic DNA, mitochondrial DNA, molecular marker, ribosome DNA, allopatry, Aplysina clatharata, Aplysina gerardogreeni, Aplysina revillagigedi, article, DNA barcoding, DNA sequence, genetic polymorphism, genetic variability, infrared spectros CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Interaction between plants growing together from germination to 2 years: A test of competition and phylogenetic closeness for Northeastern Mexico

Interacción entre plantas coexistiendo desde la germinación hasta los 2 años: un experimento de competencia y cercanía filogenética en el noreste de México

ENRIQUE JURADO YBARRA Joel David Flores Rivas Jonathan Marroquín MARISELA PANDO MORENO DAVID ALBERTO RODRIGUEZ TRAPERO Humberto González Rodríguez José Alejandro Selvera Mancha Juan Ángel López Carmona (2022, [Artículo])

"Competition and facilitation are important factors affecting seedling survival. These factors probably affect plant distribution and abundance. Interactions between species relate to phylogeny, in that closely related species are likely to compete more for resources and facilitation is expected between more distantly related species. We tested for Tamaulipan thornscrub plants, grown with close and distant relatives if they differed in survival, length and weight of shoots and roots, assuming that closely related species would compete more than distant ones. We also explored whether seed mass was associated with plant size from 1-24 months after germination. We grew plants from Tamaulipan thornscrub, with a sibling or with one individual from other species from 1-24 months. Seedling survival was similar for all species when their seedlings grew alone or under competition, at 1, 6 and 12 months. At 24 months seedling survival of Vachellia farnesiana was lower when grown with Havardia pallens. There was no evidence of stronger competition or facilitation for phylogenetically closer species. Seedling size correlated with seed mass one month after germination but not after 6 months. Maximum and mean adult plant height did not correlate with seed mass or with plant height in our trials. We found no evidence of phylogeny explaining nearest neighbors in competition during germination for Tamaulipan thornscrub."

"La competencia y la facilitación son factores importantes que afectan la supervivencia de las plántulas y probablemente afectan la distribución y abundancia de las plantas. Las interacciones entre especies se relacionan con la filogenia, es probable que las especies estrechamente relacionadas compitan más por recursos y que en las menos emparentadas ocurra facilitación. Se investigó si plantas de matorral tamaulipeco creciendo junto a parientes cercanos y lejanos diferían en supervivencia, longitud y peso de tallos y raíces, asumiendo que las especies estrechamente relacionadas competirían más que las lejanas. También se exploró si el peso de semillas se asoció con el tamaño de la planta entre 1 y 24 meses de edad. Se pusieron a crecer plantas de matorral tamaulipeco, con un hermano o con un individuo de otras especies, de 1-24 meses. La supervivencia de plántulas fue similar para todas las especies cuando éstas crecieron solas o en competencia, a los 1, 6 y 12 meses. A los 24 meses, la supervivencia de plántulas de Vachellia farnesiana fue menor cuando creció con Havardia pallens. No hubo evidencia de una competencia o facilitación fuerte para especies filogenéticamente más cercanas. El tamaño de la plántula se correlacionó con el peso de la semilla únicamente al mes de germinadas. La altura máxima y promedio de la planta adulta no se correlacionó con el peso de semillas o con la altura de la planta. La filogenia no explicó la competencia con los vecinos más cercanos durante la germinación de especies del matorral tamaulipeco."

Phylogeny Seed mass Seedling Shoot/root ratio Tamaulipan thornscrub BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) BIOLOGÍA VEGETAL (BOTÁNICA)

Characterization of Mediterranean durum wheat for resistance to Pyrenophora tritici-repentis

marwa laribi Khaled Sassi Sarrah Ben M'barek (2022, [Artículo])

Tan Spot Durum Wheat Phenotypic Diversity CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA SPOTS HARD WHEAT LANDRACES PHENOTYPIC VARIATION PLANT HEIGHT DISEASE RESISTANCE

Dormitator latifrons (Richardson, 1844) a Pacific fat sleeper, but skinny in research: a scientometric study

MARTIN ALONSO ARECHIGA PALOMERA KAREN NOEMI NIEVES RODRIGUEZ OLIMPIA CHONG CARRILLO Héctor Gerardo Nolasco Soria Emyr Saúl Peña Marín Carlos Alfonso Alvarez_González DAVID JULIAN PALMA CANCINO RAFAEL MARTINEZ GARCIA DANIEL BADILLO ZAPATA FERNANDO VEGA VILLASANTE (2022, [Artículo])

"In order to provide information on the current knowledge about the native fish Dormitator latifrons and identify the gaps that must be filled to achieve correct resource management, a scientometric study was carried out using different scientific databases. A total of 103 publications were registered between the years 1972 and 2021. Results indicate that the species has been addressed since 2001 with less than one publication per year, with 2008 being the year with the highest number of publications (10). The main topics addressed were ecology, physiology, and parasitology of fish. The available knowledge generated about the species is concentrated in 68 journals, with Mexico as the most productive country, followed by USA and Ecuador, and the most productive research centers about this fish were Mexico’s Instituto Politécnico Nacional and Universidad de Guadalajara. A total of 285 authors were detected contributing knowledge to the species, with Violante-González in the top with ten publications. The co-authorship co-occurrence maps suggest there is no solid collaborative relationship between the scientific community and that the information generated is insufficient for conserving and exploiting this fish. It is essential to increase the study of thematic areas that allow their comprehensive management in the medium term; topics like reproduction in captivity, aquaculture, and nutrition must be addressed in the future to assure a sustainable use of this resource."

Dormitator latifrons, native fish, amphidromous, worldwide database, regional database, cooccurrence map CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS PECES Y FAUNA SILVESTRE DINÁMICA DE LAS POBLACIONES DINÁMICA DE LAS POBLACIONES

Freshwater exchanges and surface salinity in the Colombian basin, Caribbean Sea

Emilio Beier (2017, [Artículo])

Despite the heavy regional rainfall and considerable discharge of many rivers into the Colombian Basin, there have been few detailed studies about the dilution of Caribbean Surface Water and the variability of salinity in the southwestern Caribbean. An analysis of the precipitation, evaporation and runoff in relation to the climate variability demonstrates that although the salt balance in the Colombian Basin overall is in equilibrium, the area south of 12N is an important dilution sub-basin. In the southwest of the basin, in the region of the Panama-Colombia Gyre, Caribbean Sea Water is diluted by precipitation and runoff year round, while in the northeast, off La Guajira, its salinity increases from December to May by upwelling. At the interannual scale, continental runoff is related to El Niño Southern Oscillation, and precipitation and evaporation south of 12°N are related to the Caribbean Low Level Jet. During El Niño years the maximum salinification occurs in the dry season (December-February) while in La Niña years the maximum dilution (or freshening), reaching La Guajira Coastal Zone, occurs in the wet season (September-November). © 2017 Beier et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

sea water, fresh water, Article, Caribbean, dilution, dry season, El Nino, environmental parameters, evaporation, freshwater exchange, geographic distribution, molecular weight, oscillation, precipitation, river basin, salinity, seasonal variation, s CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Chapter 9. Genome-informed discovery of genes and framework of functional genes in wheat

awais rasheed Rudi Appels (2024, [Capítulo de libro])

Wheat Genomics KASP Markers Gene Discovery Functional Markers Gene Networks CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA WHEAT GENOMICS SINGLE NUCLEOTIDE POLYMORPHISMS FUNCTIONAL GENOMICS

Whole-genome comparison between reference sequences and oyster Vibrio vulnificus C-genotype strains

CARLOS ABRAHAM GUERRERO RUIZ (2019, [Artículo])

Whole-genome sequences of Vibrio vulnificus clinical genotype (C-genotype) from the CICESE Culture Collection, isolated from oysters, were compared with reference sequences of CMCP6 and YJ016 V. vulnificus C-genotype strains of clinical origin. The RAST web server estimated the whole genome to be ~4.8 Mb in CICESE strain 316 and ~4.7 Mb in CICESE strain 325. No plasmids were detected in the CICESE strains. Based on a phylogenetic tree that was constructed with the whole-genome results, we observed high similarity between the reference sequences and oyster C-genotype isolates and a sharp contrast with environmental genotype (E-genotype) reference sequences, indicating that the differences between the C- and E-genotypes do not necessarily correspond to their isolation origin. The CICESE strains share 3488 genes (63.2%) with the YJ016 strain and 3500 genes (63.9%) with the CMCP6 strain. A total of 237 pathogenicity associated genes were selected from reference clinical strains, where—92 genes were from CMCP6, 126 genes from YJ016, and 19 from MO6-24/ O; the presence or absence of these genes was recorded for the CICESE strains. Of the 92 genes that were selected for CMCP6, 67 were present in both CICESE strains, as were as 86 of the 126 YJ016 genes and 13 of the 19 MO6-24/O genes. The detection of elements that are related to virulence in CICESE strains—such as the RTX gene cluster, vvhA and vvpE, the type IV pili cluster, the XII genomic island, and the viuB genes, suggests that environmental isolates with the C-genotype, have significant potential for infection. © 2019 Guerrero et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Article, bacterial gene, bacterial strain, bacterial virulence, comparative study, controlled study, gene cluster, gene identification, genomic island, genotype, nonhuman, phylogenetic tree, sequence analysis, strain identification, Vibrio vulnificus BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA

Un gen para ti, un gen para mí: flujo genético entre parientes silvestres y plantas domesticadas

Mauricio Heredia Pech MARIANA CHAVEZ PESQUEIRA (2023, [Artículo])

El flujo genético se refiere al movimiento de genes entre individuos o poblaciones. En ocasiones puede darse también entre especies cercanamente emparentadas, como en el caso de las plantas domesticadas y sus parientes silvestres. Los parientes silvestres son de gran importancia para la seguridad alimentaria debido a su gran diversidad genética, que los convierte en una reserva natural de genes. Las consecuencias del flujo genético silvestre-domesticado dependerán de la intensidad y dirección en la que se muevan los genes, siendo la preocupación principal el riesgo que puede existir para el mantenimiento de la diversidad genética de los parientes silvestres.

CONSERVACION DISPERSION DIVERSIDAD GENETICA FUERZA EVOLUTIVA SELECCION ARTIFICIAL BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) ECOLOGÍA VEGETAL ECOLOGÍA VEGETAL

Cell carbon content and biomass assessments of dinoflagellates and diatoms in the oceanic ecosystem of the Southern Gulf of Mexico

LORENA PATRICIA LINACRE ROJAS (2021, [Objeto de congreso])

This study assessed the cell carbon content and biomass for genera of dinoflagellates and diatoms in the oceanic ecosystem of the Southern Gulf of Mexico. Carbon content estimates were based on biovolume calculations derived from linear dimension measurements of individual cells and the approximate geometric body shape of each genus. Then, biomass assessments were performed for both groups in two gulf regions (Perdido and Coatzacoalcos) using these carbon content factors and cell abundances. After four seasonal cruises, 11,817 cells of dinoflagellates and 3,412 cells of diatoms were analyzed. Diverse body shapes and cell sizes were observed among 46 dinoflagellate genera and 37 diatom genera. Nano-cells of dinoflagellates (68% <20 μm) and micro-cells of diatoms (77% 20–200 μm, mostly 50–75 μm) were predominant. According to this cell-size structure, on average, diatoms contained 40% more carbon per cell than dinoflagellates. Contrasting carbon content estimates were observed within the genera of both microalgae. Large carbon averages (>10,000 pg C cell-1) were attributed to Gonyaulacal and some occasional genera of dinoflagellates (e.g., Pyrocystis and Noctiluca) and centric diatoms. In contrast, values up to 3 orders of magnitude lower were found for Peridinial and Gymnodinial dinoflagellates and pennate diatoms. Based on these carbon content estimates, which can be considered representative for most of this oceanic ecosystem, seasonal and regional differences were found in the biomass assessments conducted for these functional groups. Overall, dinoflagellates (mostly low-carbon Gymnodinales) had larger depth-integrated biomass than diatoms (mainly rich-carbon centric forms) within the euphotic zone. An exception to it was the late-summer cruise at the Coatzacoalcos region when a surface bloom of centric diatoms was observed in stations influenced by river runoff. This work contributes useful reference information for future ecological studies and models for understanding the biogeochemical functioning of this open-ocean ecosystem. © 2021 Linacre et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Carbon, biomass, Oceanic ecosystem, Southern Gulf of Mexico, Mexico CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Regional analysis of the wage discrimination in the indigenous workers in Mexico

Christian De la Luz-Tovar SIBYL ITALIA PINEDA SALAZAR (2023, [Artículo, Artículo])

The objective of this research is to estimate and decompose the wage gap between indigenous and non-indigenous workers by region in Mexico, to examine whether there are regional differences in the existing wage inequality that a priori affects the indigenous population and whether these differences can be attributed to the job profile of this group or by systematic labor discrimination against them. Using the data from the 2018 National Household Expenditure Revenue Survey (ENIGH-N) and the Oaxaca-Blinder decomposition, it was found that indigenous workers face a wage gap in all regions of the county. But, this gap is more pronounced in the center and south regions, where, on average, the associated component with labor discrimination has a percentage greater than 56. In contrast, in the north-central and northern regions of Mexico, the residual component is on average less than 33%, which suggests that the wage gap is explained by differences in productivity between groups.                         

Labor economics Ethnicity wage gap Indigenous population Regions Oaxaca-Blinder decomposition Economía laboral Brecha salarial étnica Población indígena Regiones Descomposición de Oaxaca-Blinder CIENCIAS SOCIALES CIENCIAS SOCIALES