Multi-modal deep learning improves grain yield prediction in wheat breeding by fusing genomics and phenomics

Xu Wang Sandesh Kumar Shrestha Philomin Juliana Suchismita Mondal Francisco Pinto Govindan Velu Leonardo Abdiel Crespo Herrera JULIO HUERTA_ESPINO Ravi Singh Jesse Poland (2023, [Artículo])

New Crop Varieties Plant Breeding Programs Yield Prediction CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA LEARNING GRAIN YIELDS WHEAT BREEDING FOOD SECURITY

INFLUENCIA DE CONDICIONES AMBIENTALES SOBRE LA DISTRIBUCIÓN, ABUNDANCIA Y DESARROLLO DE LARVAS DE Totoaba macdonaldi (Gilbert, 1890), EN EL ALTO GOLFO DE CALIFORNIA

Marcelo Vidal Curiel Bernal (2023, [Tesis de doctorado])

"La presente tesis aborda una investigación sobre la biología, ecología y crecimiento de la Totoaba macdonaldi en el alto golfo de California. La totoaba, una especie endémica a esta región se encuentra actualmente en peligro de extinción debido a una serie de amenazas como: cambios en su ecosistema reproductivo y de crianza, pesca, incidental de juveniles e ilegal de adultos. Aunque en los últimos 30 años la población dio signos de recuperación, existen indicios de que tanto la población adulta como las abundancias de larvas presentan una tendencia decreciente. Lo que resalta la importancia de estudiar cómo la variabilidad ambiental incide en la distribución y abundancia de larvas de totoaba y subsecuentemente en el stock recluta de la especie. El estudio comienza con un análisis de la variabilidad del crecimiento individual en etapas juveniles y adultas de la totoaba. Para este propósito, se utiliza la varianza observada como elemento clave para parametrizar modelos de crecimiento individual. Los resultados indican que este enfoque proporciona estimaciones sólidas de los parámetros de crecimiento. A continuación, se investiga el crecimiento de las larvas de totoaba en condiciones de cultivo. Los datos revelan que un modelo sigmoideo describe mejor el crecimiento y se identifican dos puntos de inflexión en el crecimiento de las larvas. Estos hallazgos tienen importantes implicaciones para la cría y el cultivo de la totoaba para efectos de repoblación. Por último, se analiza la ecología y el transporte de las larvas de totoaba en el alto golfo de California. Se identifica una ventana óptima para el desove de la totoaba en términos de temperatura y concentración de clorofila, y se sugiere que las condiciones ambientales y la distribución de los adultos pueden influir en las abundancias de larvas en diferentes años. Además, se destaca la importancia del frente permanente al sur del alto golfo de California como una posible zona de acumulación de larvas como factor que contribuye al endemismo en la región. En conjunto, esta tesis representa un enfoque multidisciplinario para comprender los aspectos clave de la biología, ecología y crecimiento de la totoaba en el alto golfo de California. Los resultados proporcionan información valiosa para la conservación de esta especie amenazada y destacan la importancia de un enfoque integral en la gestión de los recursos marinos en esta región única."

"The following thesis addresses a research on the biology, ecology, and growth of Totoaba macdonaldi in the upper gulf of California. The totoaba, a fish species endemic to this region, is currently endangered due to a series of threats such as: changes in its reproductive and breeding ecosystem, juvenile bycatch, and illegal fishing. Although over the last 30 years, the population has shown signs of recovery, there are indications that both the adult population and larval abundances are on a declining trend. This underscores the importance of studying how environmental variability affects the distribution and abundance of totoaba larvae and subsequently the recruitment stock of the species. The study begins with an analysis of growth in juvenile and adult stages of the totoaba. For this purpose, observed variance is used to parameterize individual growth models. Results indicate that this approach provides robust estimates of growth parameters. Next, the growth of cultivated totoaba larvae is investigated. The data reveal that a sigmoid model better describes the growth in the early life stages of the totoaba, and two inflection points in larval growth are identified. These findings have important implications for the breeding and cultivation of the totoaba for restocking purposes. Finally, the ecology and transport of totoaba larvae in the upper gulf of California are analyzed. An optimal window for totoaba spawning in terms of temperature and chlorophyll concentration is identified, and it is suggested that environmental conditions and the distribution of adults may influence larval abundances in different years. Additionally, the importance of the permanent front to the south of the upper gulf of California is highlighted as a possible larval accumulation zone and a contributing factor to endemism in the region. Overall, this thesis represents a multidisciplinary approach to understanding key aspects of the biology, ecology, and growth of the totoaba in the upper gulf of California. The results provide valuable information for the conservation of this threatened species and underscore the importance of a comprehensive approach in the management of marine resources in this unique region."

Variabilidad ambiental, crecimiento, dispersión, rutas larvarias Environmental variability, growth, dispersion, larval routes CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS PECES Y FAUNA SILVESTRE PROPAGACIÓN Y ORDENACIÓN PROPAGACIÓN Y ORDENACIÓN

Variación fenotípica de caracteres vegetativos y reproductivos de Hesperoyucca whipplei (Asparagaceae) en Baja California, México

Phenotypic variation of vegetative and reproductive traits of Hesperoyucca whipplei (Asparagaceae) in Baja California, Mexico

Melissa Michelle Alvarez Mexia (2024, [Tesis de maestría])

La variación fenotípica hereditaria de diferentes órganos de las plantas se ha relacionado con adaptaciones para tolerar el ambiente abiótico y mantener relaciones ecológicas. Específicamente se ha planteado que los órganos vegetativos de las plantas están bajo selección por disponibilidad de agua o luz, mientras que la variación de rasgos florales en especies con polinización zoocórica está fuertemente influenciada por sus polinizadores. Esto sugiere que la fortaleza de la covariación fenotípica entre órganos vegetativos y florales puede ser diferente dependiendo del estrés ambiental considerado. Según la hipótesis de Berg, las plantas con sistemas de polinización especializados desvinculan la morfología floral de la variación fenotípica en los caracteres vegetativos debido a la presión selectiva del polinizador. Se probó esto en la yuca de chaparral, Hesperoyucca whipplei, ya que se distribuye en diferentes ambientes a lo largo de la península de Baja California, y es polinizada únicamente por la polilla Tegeticula maculata. Esperamos que la heterogeneidad ambiental afecte principalmente a los niveles de variación fenotípica de los órganos vegetativos de las poblaciones de H. whipplei, causando cambios en la morfología entre poblaciones. Sin embargo, dada la polinización obligada, esperamos que la variación de los rasgos florales sea menor que la variación de sus rasgos vegetativos. Para probarlo, se tomaron datos morfométricos vegetativos y reproductivos de 202 individuos en 16 localidades. Los resultados mostraron amplia variación fenotípica en los caracteres vegetativos y reproductivos no florales y una menor variación fenotípica en los caracteres florales, especialmente el pistilo, con el cual interactúa directamente el polinizador. La temperatura y precipitación influyeron significativamente en la variación de la altura total de la planta y sobre los pétalos y pistilo en las flores. Se detectó una asociación entre los caracteres vegetativos y los reproductivos no florales, mientras que no se encontró una relación con los caracteres florales. A partir de esto se identificaron dos módulos fenotípicos altamente integrados, uno vegetativo y uno floral, lo que respalda la hipótesis de Berg y sugiere que experimentan presiones de selección diferentes. Nuestros hallazgos resaltan como la variación fenotípica en poblaciones de plantas es modulada por condiciones ambientales e interacciones ecológicas.

Hereditary phenotypic variation of different plant organs has been related to adaptations that allow them to tolerate the abiotic environment and maintain ecological relationships with other organisms. Specifically, it has been proposed that the vegetative organs of the plants are under selection due to the availability of water or sunlight, while the variation of floral traits in species with zoochoric pollination is strongly influenced by their pollinators. This suggests that the strength of the phenotypic co-variation between vegetative and floral organs may be different depending on the environmental stress considered. According to Berg's hypothesis, plants with specialized pollination systems dissociate floral morphology from phenotypic variation in vegetative traits due to selective pressure from the pollinator. The chaparral yuca, Hesperoyucca whipplei, is a good model to test this, since it is distributed in different environments along the Baja California peninsula, and this plant is pollinated only by the Tegeticula maculata moth. We expect that environmental heterogeneity primarily affects the levels of phenotypic variation of the vegetative organs of H. whipplei populations, causing changes in morphology between populations. However, given the obligatory pollination by the moth, we expect that the variation in the floral traits will be lesser than the variation in their vegetative traits. To test this, vegetative and reproductive morphometric data were taken from 202 individuals in 16 locations. The results showed wide phenotypic variation in vegetative and non-floral reproductive traits and lower phenotypic variation in floral traits, especially the pistil, which directly interacts with the pollinator. Temperature and precipitation significantly influenced the variation of the total height of the plant and on the petals and pistil in the flowers. An association was detected between vegetative and non-floral reproductive characters, while no relationship was found with floral characters. From this, two highly integrated phenotypic modules, one vegetative and one floral, were identified, which supports Berg's hypothesis and suggests that they experience different selection pressures. Our findings highlight how phenotypic variation in plant populations is modulated by environmental conditions and ecological interactions.

Baja California, Hesperoyucca whipplei, hipótesis de Berg, variación fenotípica Baja California, Berg’s hypothesis, Hesperoyucca whipplei, phenotypic variation BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) ECOLOGÍA VEGETAL ECOLOGÍA VEGETAL

Variaciones en un transecto profundo frente a la costa de Nayarit, México

Emilio Palacios Hernández Luis Brito Castillo LAURA ELENA CARRILLO BIBRIEZCA CARLOS EDUARDO CABRERA RAMOS JORGE MANUEL MONTES ARECHIGA (2022, [Artículo])

"Six oceanographic cruises in a NE-SW transect were made nearshore of southern Sinaloa and Nayarit from March 2006 through May 2008, where no in situ hydrographic data are available. Applying the Thermodynamic Equation of Seawater 2010 (TEOS-10) to the observations, the hydrography and geostrophic currents of the region were characterized. Results indicate that surface variability (0-50 m) emerged mainly from seasonal atmospheric forcing. A relative salinity maximum was present during all cruises below this surface layer, which is attributed to a water mass intrusion of Subtropical Subsurface Water that could be associated with the Mexican Coastal Current. Another water mass intrusion is from the California Current. Samples from the 2007-2008 La Niña produced an uncommon circulation, where water flowing from the Gulf of California along the coast of Sinaloa was observed, opposite to what is commonly known as a mean circulation. This uncommon circulation matches the generation of anticyclonic eddies around the Islas Marias archipelago."

Gulf of California, Mexican Coastal Current, Nayarit Coast, seasonal variation, La Niña CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA DESCRIPTIVA OCEANOGRAFÍA DESCRIPTIVA

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

Biodiversity conservation in an anthropized landscape: Trees, not patch size drive, bird community composition in a low-input agroecosystem

ERIC MELLINK BIJTEL (2017, [Artículo])

One of the most typical agro-ecosystems in the Llanos de Ojuelos, a semi-arid region of central Mexico, is that of fruit-production orchards of nopales (prickly pear cacti). This perennial habitat with complex vertical structure provides refuge and food for at least 112 species of birds throughout the year. Nopal orchards vary in their internal structure, size and shrub/ tree composition, yet these factors have unknown effects on the animals that use them. To further understand the conservation potential of this agro-ecosystem, we evaluated the effects of patch-size and the presence of trees on bird community composition, as well as several habitat variables, through an information-theoretical modelling approach. Community composition was obtained through a year of census transects in 12 orchards. The presence of trees in the orchards was the major driver of bird communities followed by seasonality; bird communities are independent of patch size, except for small orchard patches that benefit black-chin sparrows, which are considered a sensitive species. At least 55 species of six trophic guilds (insectivores, granivores, carnivores, nectivores, omnivores, and frugivores) used the orchards. Orchards provide adequate habitat and food resources for several sensitive species of resident and migratory sparrows. The attributes that make orchards important for birds: trees, shrubs, herb seeds, and open patches can be managed to maintain native biodiversity in highly anthropized regions with an urgent need to find convergence between production and biological conservation. © 2017 Mellink 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.

agroecosystem, carnivore, chin, conservation biology, driver, frugivore, granivore, habitat, human, insectivore, landscape, nonhuman, omnivore, orchard, resident, seasonal variation, shrub, sparrow, theoretical model, agriculture, animal, biodiversit CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

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

Genetic analysis of Vibrio parahaemolyticus O3:K6 strains that have been isolated in Mexico since 1998

CARLOS ABRAHAM GUERRERO RUIZ (2017, [Artículo])

Vibrio parahaemolyticus is an important human pathogen that has been isolated worldwide from clinical cases, most of which have been associated with seafood consumption. Environmental and clinical toxigenic strains of V. parahaemolyticus that were isolated in Mexico from 1998 to 2012, including those from the only outbreak that has been reported in this country, were characterized genetically to assess the presence of the O3:K6 pandemic clone, and their genetic relationship to strains that are related to the pandemic clonal complex (CC3). Pathogenic tdh+ and tdh+/trh+ strains were analyzed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Also, the entire genome of a Mexican O3:K6 strain was sequenced. Most of the strains were tdh/ORF8-positive and corresponded to the O3:K6 serotype. By PFGE and MLST, there was very close genetic relationship between ORF8/O3:K6 strains, and very high genetic diversities from non-pandemic strains. The genetic relationship is very close among O3:K6 strains that were isolated in Mexico and sequences that were available for strains in the CC3, based on the PubMLST database. The whole-genome sequence of CICESE-170 strain had high similarity with that of the reference RIMD 2210633 strain, and harbored 7 pathogenicity islands, including the 4 that denote O3:K6 pandemic strains. These results indicate that pandemic strains that have been isolated in Mexico show very close genetic relationship among them and with those isolated worldwide. © 2017 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 strain, biofouling, controlled study, Crassostrea, food intake, gene sequence, genetic analysis, genetic variability, Japan, Mexican, Mexico, molecular phylogeny, nonhuman, pandemic, pathogenicity island, sea food, serotyping, toxi BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA